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The manifold roles of microbial ribosomal peptide–based natural products in physiology and ecology

  • Yanyan Li
    Correspondence
    To whom correspondence may be addressed. Tel.: 33-140-795-791
    Affiliations
    Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM, UMR 7245 CNRS-MNHN), National Museum of Natural History (MNHN), CNRS, CP 54, 57 rue Cuvier 75005, Paris, France
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  • Sylvie Rebuffat
    Correspondence
    To whom correspondence may be addressed. Tel.: 33-140-793-118
    Affiliations
    Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM, UMR 7245 CNRS-MNHN), National Museum of Natural History (MNHN), CNRS, CP 54, 57 rue Cuvier 75005, Paris, France
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Open AccessPublished:November 29, 2019DOI:https://doi.org/10.1074/jbc.REV119.006545
      The ribosomally synthesized and posttranslationally modified peptides (RiPPs), also called ribosomal peptide natural products (RPNPs), form a growing superfamily of natural products that are produced by many different organisms and particularly by bacteria. They are derived from precursor polypeptides whose modification by various dedicated enzymes helps to establish a vast array of chemical motifs. RiPPs have attracted much interest as a source of potential therapeutic agents, and in particular as alternatives to conventional antibiotics to address the bacterial resistance crisis. However, their ecological roles in nature are poorly understood and explored. The present review describes major RiPP actors in competition within microbial communities, the main ecological and physiological functions currently evidenced for RiPPs, and the microbial ecosystems that are the sites for these functions. We envision that the study of RiPPs may lead to discoveries of new biological functions and highlight that a better knowledge of how bacterial RiPPs mediate inter-/intraspecies and interkingdom interactions will hold promise for devising alternative strategies in antibiotic development.

      Introduction

      Microorganisms have a remarkable social life. They generally live in complex polymicrobial communities and diverse environments where interactions between individuals shape the composition of populations and communities as well as their functions (
      • Hibbing M.E.
      • Fuqua C.
      • Parsek M.R.
      • Peterson S.B.
      Bacterial competition: surviving and thriving in the microbial jungle.
      ,
      • Inglis R.F.
      • Brown S.P.
      • Buckling A.
      Spite versus cheats: competition among social strategies shapes virulence in Pseudomonas aeruginosa.
      ,
      • Inglis R.F.
      • West S.
      • Buckling A.
      An experimental study of strong reciprocity in bacteria.
      ). Microbial communities colonize niches at all levels of the biosphere, from soils and oceans to living organisms. Indeed, it is now firmly established that all organisms are living in tight association with microorganisms, forming the so-called holobionts that are found in all environments, marine or terrestrial, and all organisms from plants to vertebrates, including humans (
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      What is the hologenome concept of evolution?.
      ,
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      • Zilber-Rosenberg I.
      The hologenome concept of evolution after 10 years.
      ). However, deciphering the mechanisms and interplays between the molecules and macromolecules from the host and microorganisms that make up the holobiont is still in its infancy.
      Social interactions are widespread in microorganisms and play a major role in bacterial evolution and virulence. Either they are antagonistic, leading to the elimination of competitors, or they are cooperative or synergistic, which permits bacteria from obtaining benefits that could not be acquired by a single individual (
      • Inglis R.F.
      • Brown S.P.
      • Buckling A.
      Spite versus cheats: competition among social strategies shapes virulence in Pseudomonas aeruginosa.
      ). These interactions lead to various behaviors, such as communication, toxin secretion, and acquisition of nutrients or metals that are essential for growth and development, such as iron for all bacteria (
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      Chemistry and biology of siderophores.
      ,
      • McRose D.L.
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      Multiple siderophores: bug or feature?.
      ) or copper for methanotrophic bacteria (
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      • Rosenzweig A.C.
      Methanobactins: from genome to function.
      ). Adverse molecules, such as antimicrobials, have been considered for many years as weapons used by bacteria to inhibit or kill competitors in a given niche. But more recently, alternative hypotheses consider that antimicrobial compounds would act also as signaling molecules able to coordinate cooperative social interactions between bacteria (
      • Hibbing M.E.
      • Fuqua C.
      • Parsek M.R.
      • Peterson S.B.
      Bacterial competition: surviving and thriving in the microbial jungle.
      ,
      • Cornforth D.M.
      • Foster K.R.
      Competition sensing: the social side of bacterial stress responses.
      ). Moreover, the production of antimicrobials would be influenced by social and competitive interactions between competing bacteria (
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      • Smakman F.
      • Grimbergen A.J.
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      Socially mediated induction and suppression of antibiosis during bacterial coexistence.
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      Antibiotics and the art of bacterial war.
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      ). Whereas the traditional model of bacterial life is that of cells swimming in a liquid environment, bacteria also commonly live in complex communities associated with various surfaces, either natural or human-engineered ones, which are called biofilms (
      • Hall-Stoodley L.
      • Costerton J.W.
      • Stoodley P.
      Bacterial biofilms: from the natural environment to infectious diseases.
      ). Biofilms result from the coordinated action of several bacterial strains working together to acquire benefits. They often occur as a response to ecological competition from other strains and toxic stresses (
      • Oliveira N.M.
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      • Xavier J.
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      • Foster K.R.
      Biofilm formation as a response to ecological competition.
      ,
      • Sharma D.
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      • Khan A.U.
      Antibiotics versus biofilm: an emerging battleground in microbial communities.
      ). Antimicrobial compounds and communication or signaling molecules are involved in these processes through the so-called quorum-sensing (QS)
      The abbreviations used are: QS
      quorum sensing
      NP
      natural product
      NRPS
      nonribosomal peptide synthetase
      PKS
      polyketide synthase
      RiPP
      ribosomally synthesized and posttranslationally modified peptide
      RPNP
      ribosomal peptide natural product
      TOMM
      thiazole/oxazole-modified microcin
      AMP
      antimicrobial peptide
      BGC
      biosynthetic gene cluster
      LAP
      linear azol(in)e-containing peptide
      SKF
      sporulation killing factor
      EcN
      E. coli Nissle 1917
      GI
      gastrointestinal
      MccE492
      microcin E492
      AIP
      autoinducing peptide
      TCS
      two-component system
      SHP
      small hydrophobic peptide
      PQQ
      pyrroloquinoline quinone.
      mechanism (
      • Sharma D.
      • Misba L.
      • Khan A.U.
      Antibiotics versus biofilm: an emerging battleground in microbial communities.
      ). Currently, the ecological aspects of microbial research take particular importance both in environmental domains and in the field of bacterial pathogenesis (
      • Korgaonkar A.
      • Trivedi U.
      • Rumbaugh K.P.
      • Whiteley M.
      Community surveillance enhances Pseudomonas aeruginosa virulence during polymicrobial infection.
      ), pointing to an acute need for understanding the underlying mechanisms.
      Bacteria can produce a broad range of metabolites that, among other functions, can mediate bacterial interactions and display antimicrobial activity. A large number of these natural products (NPs) originate from large multifunctional enzymatic complexes, nonribosomal peptide synthetases (NRPSs), polyketide synthases (PKSs), or hybrid PKS/NRPS systems (
      • Fischbach M.A.
      • Walsh C.T.
      Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: logic, machinery, and mechanisms.
      ,
      • Marahiel M.A.
      A structural model for multimodular NRPS assembly lines.
      ). Another broad and diverse class of natural products consists of the superfamily of ribosomally derived molecules, the so-called ribosomally synthesized and posttranslationally modified peptides (RiPPs) (
      • Arnison P.G.
      • Bibb M.J.
      • Bierbaum G.
      • Bowers A.A.
      • Bugni T.S.
      • Bulaj G.
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      • Dawson M.
      • Dittmann E.
      • Donadio S.
      • et al.
      Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature.
      ), also termed ribosomal peptide natural products (RPNPs). Their biosynthesis starts with ribosomally synthesized linear peptides that are subject to enzymatic modifications. The peptide precursor is composed of a core peptide that is preceded by an N-terminal leader region, often involved in recognition events (
      • Burkhart B.J.
      • Hudson G.A.
      • Dunbar K.L.
      • Mitchell D.A.
      A prevalent peptide-binding domain guides ribosomal natural product biosynthesis.
      ). In rare cases, the core peptide is followed by a C-terminal extension (i.e. a follower peptide). The core peptide is decorated with posttranslational modifications set up by dedicated enzymes (Fig. 1). The posttranslational modifications involved in RiPP biosynthesis are diverse, including for example dehydration, cyclodehydration, cyclization, glycosylation, and phosphorylation, resulting in a vast array of structures (
      • Arnison P.G.
      • Bibb M.J.
      • Bierbaum G.
      • Bowers A.A.
      • Bugni T.S.
      • Bulaj G.
      • Camarero J.A.
      • Campopiano D.J.
      • Challis G.L.
      • Clardy J.
      • Cotter P.D.
      • Craik D.J.
      • Dawson M.
      • Dittmann E.
      • Donadio S.
      • et al.
      Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature.
      ).
      Figure thumbnail gr1
      Figure 1General biosynthetic pathway leading to RiPP production, from the gene cluster to the mature active compound. The ribosomally synthesized precursor can be only cleaved by a protease (green) and exported by an ABC transporter (brown) as an unmodified peptide. For RiPP biosynthesis, the core peptide is fused to a leader peptide (gray) that contributes to the action of the posttranslational modification enzymes (blue). Cleavage of the leader and export of the RiPP are both generally ensured by a peptidase-containing ATP-binding transporter (PCAT) that accomplishes the two functions.
      RiPPs are essentially produced by bacteria, but many eukaryotic cells, such as fungi, plants, or marine organisms, are also producers of such compounds (
      • Luo S.
      • Dong S.H.
      Recent advances in the discovery and biosynthetic study of eukaryotic RiPP natural products.
      ). They are classified according to their structural features that rely on the types of posttranslational modifications. Among the most extensively studied classes, we can cite lanthipeptides and lantibiotics, thiopeptides, lasso peptides, cyanobactins, and thiazole/oxazole-modified microcins (TOMMs) (
      • Arnison P.G.
      • Bibb M.J.
      • Bierbaum G.
      • Bowers A.A.
      • Bugni T.S.
      • Bulaj G.
      • Camarero J.A.
      • Campopiano D.J.
      • Challis G.L.
      • Clardy J.
      • Cotter P.D.
      • Craik D.J.
      • Dawson M.
      • Dittmann E.
      • Donadio S.
      • et al.
      Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature.
      ). RiPPs are considered promising molecules to be developed for applications in environmental, medical, veterinary, and food industrial domains. They constitute a fast-expanding area of research due to increased genome-mining efforts and to the huge interest raised by their structures, biological properties, biosynthesis pathways, and posttranslational modification enzymes (for reviews, see Refs.
      • Arnison P.G.
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      • Bulaj G.
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      • Craik D.J.
      • Dawson M.
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      Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature.
      and
      • Hetrick K.J.
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      RiPP antibiotics: biosynthesis and engineering potential.
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      YcaO-dependent posttranslational amide activation: biosynthesis, structure, and function.
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      • Repka L.M.
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      Mechanistic understanding of lanthipeptide biosynthetic enzymes.
      ,
      • Gu W.
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      The biochemistry and structural biology of cyanobactin pathways: enabling combinatorial biosynthesis.
      ,
      • Sikandar A.
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      The role of protein–protein interactions in the biosynthesis of ribosomally synthesized and post-translationally modified peptides.
      ). Metagenome analyses of various holobionts offer great promise for discovering novel RiPPs. The high abundance of RiPPs in the human microbiome has been reported based on genome-mining, metabolomics, and computational MS approaches (
      • Liu L.
      • Hao T.
      • Xie Z.
      • Horsman G.P.
      • Chen Y.
      Genome mining unveils widespread natural product biosynthetic capacity in human oral microbe Streptococcus mutans.
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      • Donia M.S.
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      A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics.
      ,
      • Balty C.
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      • Fradale L.
      • Brewee C.
      • Boulay M.
      • Kubiak X.
      • Benjdia A.
      • Berteau O.
      Ruminococcin C, an anti-clostridial sactipeptide produced by a prominent member of the human microbiota Ruminococcus gnavus.
      ,
      • Chiumento S.
      • Roblin C.
      • Kieffer-Jaquinod S.
      • Tachon S.
      • Leprètre C.
      • Basset C.
      • Aditiyarini D.
      • Olleik H.
      • Nicoletti C.
      • Bornet O.
      • Iranzo O.
      • Maresca M.
      • Hardré R.
      • Fons M.
      • Giardina T.
      • et al.
      Ruminococcin C, a promising antibiotic produced by a human gut symbiont.
      ,
      • Huo L.
      • Zhao X.
      • Acedo J.Z.
      • Estrada P.
      • Nair S.K.
      • Van der Donk W.A.
      Characterization of a dehydratase and methyltransferase in the biosynthesis of a ribosomally-synthesized and post-translationally modified peptide in Lachnospiraceae.
      ,
      • Aleti G.
      • Baker J.L.
      • Tang X.
      • Alvarez R.
      • Dinis M.
      • Tran N.C.
      • Melnik A.V.
      • Zhong C.
      • Ernst M.
      • Dorrestein P.C.
      • Edlund A.
      Identification of the bacterial biosynthetic gene clusters of the oral microbiome illuminates the unexplored social language of bacteria during health and disease.
      ). The development of novel and efficient software tools will allow expansion of the repertoire of RiPPs from diverse microbiomes, including those with unknown posttranslational modifications (
      • Cao L.
      • Gurevich A.
      • Alexander K.L.
      • Naman C.B.
      • Leão T.
      • Glukhov E.
      • Luzzatto-Knaan T.
      • Vargas F.
      • Quinn R.
      • Bouslimani A.
      • Nothias L.F.
      • Singh N.K.
      • Sanders J.G.
      • Benitez R.A.S.
      • Thompson L.R.
      • et al.
      MetaMiner: a scalable peptidogenomics approach for discovery of ribosomal peptide natural products with blind modifications from microbial communities.
      ).
      Despite the significant interest in RiPPs from an anthropocentric point of view, very little is known about the ecological roles of RiPPs in nature. Given that peptides mediate many biological processes across all domains of life, it is conceivable that RiPPs would play diverse roles in the social behavior and physiology of microorganisms. A number of RiPPs have been shown in vivo and/or in vitro to be involved in competition, communication, and various physiological functions such as biofilm formation and morphological development. The scope of this review will cover different classes of bacterial RiPPs and summarize current knowledge of their natural functions, particularly in the context of interactions within microbial communities and with their hosts.

      RiPPs as actors of niche competitions

      An overview of antibacterial RiPP families involved in competition

      One obvious function for RiPPs is related to that of antimicrobial peptides (AMPs), which act as chemical weapons for defense and competition. Antibacterial RiPPs are posttranslationally modified bacteriocins or microcins produced by Gram-positive and Gram-negative bacteria (
      • Duquesne S.
      • Destoumieux-Garzón D.
      • Peduzzi J.
      • Rebuffat S.
      Microcins, gene-encoded antibacterial peptides from enterobacteria.
      ,
      • Drider D.
      • Rebuffat S.
      Prokaryotic Antimicrobial Peptides: From Genes to Applications.
      ). Their biosynthetic gene clusters (BGCs) share common features. They encompass genes that encode at least one precursor peptide, one or several posttranslational modification enzymes, self-immunity proteins, and transporters that ensure the export of the RiPP and can be involved in immunity of the producer to the toxic RiPP in certain cases. The archetypes for each family of antibacterial RiPPs are described briefly below with regard to their structures (Fig. 2), biosynthesis pathways, and modes of action (Table 1). The roles in niche competition played by a number of such peptides have been evidenced. However for others, in particular the nucleotide peptide microcin C, there is not yet available information on their ecological roles in microbial communities, although it can be envisioned that they should fulfill similar functions.
      Figure thumbnail gr2
      Figure 2Representative structures of different classes of RiPPs cited in this review. Unmodified amino acids are circled. In the microcin J25 structure, the residues forming the macrolactam linkage and entrapping the tail within the ring by steric hindrance are highlighted in green and red, respectively.
      Table 1Selected microbial RiPPs covering different chemical classes cited in this review for which an ecological function has been described
      RiPP classRiPP nameProducing strains (examples)Ecological roleMode of antibacterial action (when applicable)References
      Circular bacteriocinEnterocin AS-48/Bac-21E. faecalis AS-48, OG1RFInterference competitionPore-forming activity
      • Grande Burgos M.J.
      • Pulido R.P.
      • Del Carmen López Aguayo M.
      • Gálvez A.
      • Lucas R.
      The cyclic antibacterial peptide enterocin AS-48: isolation, mode of action, and possible food applications.
      Cyclic peptideAIPS. aureus, S. hominisQuorum-sensing signal
      The terms of autoinducing peptide and quorum-sensing signal are distinguished, the former describing peptides that only autoinduce their own production and the latter relating to peptides that also regulate transcription of other genes in addition to autoinduction.
      • Williams M.R.
      • Costa S.K.
      • Zaramela L.S.
      • Khalil S.
      • Todd D.A.
      • Winter H.L.
      • Sanford J.A.
      • O'Neill A.M.
      • Liggins M.C.
      • Nakatsuji T.
      • Cech N.B.
      • Cheung A.L.
      • Zengler K.
      • Horswill A.R.
      • Gallo R.L.
      Quorum sensing between bacterial species on the skin protects against epidermal injury in atopic dermatitis.
      ,
      • Gless B.H.
      • Bojer M.S.
      • Peng P.
      • Baldry M.
      • Ingmer H.
      • Olsen C.A.
      Identification of autoinducing thiodepsipeptides from staphylococci enabled by native chemical ligation.
      ,
      • Paharik A.E.
      • Parlet C.P.
      • Chung N.
      • Todd D.A.
      • Rodriguez E.I.
      • Van Dyke M.J.
      • Cech N.B.
      • Horswill A.R.
      Coagulase-negative Staphylococcal strain prevents Staphylococcus aureus colonization and skin infection by blocking quorum sensing.
      Cyclic peptideStreptideS. thermophilusQuorum-sensing response
      Other physiological functions have not been identified.
      • Ibrahim M.
      • Guillot A.
      • Wessner F.
      • Algaron F.
      • Besset C.
      • Courtin P.
      • Gardan R.
      • Monnet V.
      Control of the transcription of a short gene encoding a cyclic peptide in Streptococcus thermophilus: a new quorum-sensing system?.
      • Schramma K.R.
      • Bushin L.B.
      • Seyedsayamdost M.R.
      Structure and biosynthesis of a macrocyclic peptide containing an unprecedented lysine-to-tryptophan crosslink.
      • Fleuchot B.
      • Guillot A.
      • Mézange C.
      • Besset C.
      • Chambellon E.
      • Monnet V.
      • Gardan R.
      Rgg-associated SHP signaling peptides mediate cross-talk in streptococci.
      Lanthipeptide (lantibiotic)Nisin
      Also an antibacterial peptide, but its function in niche competition has not yet been demonstrated.
      L. lactisAutoinducing peptide
      The terms of autoinducing peptide and quorum-sensing signal are distinguished, the former describing peptides that only autoinduce their own production and the latter relating to peptides that also regulate transcription of other genes in addition to autoinduction.
      Pore-forming activity; Blocking of peptidoglycan synthesis (binding to lipid II)
      • Lubelski J.
      • Rink R.
      • Khusainov R.
      • Moll G.N.
      • Kuipers O.P.
      Biosynthesis, immunity, regulation, mode of action and engineering of the model lantibiotic nisin.
      • Asaduzzaman S.M.
      • Sonomoto K.
      Lantibiotics: diverse activities and unique modes of action.
      ,
      • Knerr P.J.
      • van der Donk W.A.
      Discovery, biosynthesis, and engineering of lantipeptides.
      • Ortega M.A.
      • van der Donk W.A.
      New insights into the biosynthetic logic of ribosomally synthesized and post-translationally modified peptide natural products.
      ,
      • Islam M.R.
      • Nagao J.
      • Zendo T.
      • Sonomoto K.
      Antimicrobial mechanism of lantibiotics.
      Lanthipeptide (two-peptide lantibiotic)Sh-lantibiotics-α/βS. hominis A9Interference competitionUnknown
      • Nakatsuji T.
      • Chen T.H.
      • Narala S.
      • Chun K.A.
      • Two A.M.
      • Yun T.
      • Shafiq F.
      • Kotol P.F.
      • Bouslimani A.
      • Melnik A.V.
      • Latif H.
      • Kim J.N.
      • Lockhart A.
      • Artis K.
      • David G.
      • et al.
      Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis.
      LanthipeptideSapB/SapTS. coelicolor, S. tendaeMorphological development in Streptomyces
      • Kodani S.
      • Hudson M.E.
      • Durrant M.C.
      • Buttner M.J.
      • Nodwell J.R.
      • Willey J.M.
      The SapB morphogen is a lantibiotic-like peptide derived from the product of the developmental gene ramS in Streptomyces coelicolor.
      ,
      • Kodani S.
      • Lodato M.A.
      • Durrant M.C.
      • Picart F.
      • Willey J.M.
      SapT, a lanthionine-containing peptide involved in aerial hyphae formation in the streptomycetes.
      Lanthipeptide (lantibiotic)Planosporicin
      Also an antibacterial peptide, but its function in niche competition has not yet been demonstrated.
      Planomonospora albaAutoinducing peptide
      The terms of autoinducing peptide and quorum-sensing signal are distinguished, the former describing peptides that only autoinduce their own production and the latter relating to peptides that also regulate transcription of other genes in addition to autoinduction.
      Blocking of peptidoglycan biosynthesis (binding to lipid II)
      • Sherwood E.J.
      • Bibb M.J.
      The antibiotic planosporicin coordinates its own production in the actinomycete Planomonospora alba.
      ,
      • Castiglione F.
      • Cavaletti L.
      • Losi D.
      • Lazzarini A.
      • Carrano L.
      • Feroggio M.
      • Ciciliato I.
      • Corti E.
      • Candiani G.
      • Marinelli F.
      • Selva E.
      A novel lantibiotic acting on bacterial cell wall synthesis produced by the uncommon Actinomycete Planomonospora sp.
      Lanthipeptide (lantibiotic)UnnamedS. pneumoniaeQuorum-sensing response; niche competitionUnknown
      • Hoover S.E.
      • Perez A.J.
      • Tsui H.C.
      • Sinha D.
      • Smiley D.L.
      • DiMarchi R.D.
      • Winkler M.E.
      • Lazazzera B.A.
      A new quorum-sensing system (TprA/PhrA) for Streptococcus pneumoniae D39 that regulates a lantibiotic biosynthesis gene cluster.
      Lanthipeptide (two-peptide lantibiotics)CytolysinE. faecalisAutoinducing peptide
      The terms of autoinducing peptide and quorum-sensing signal are distinguished, the former describing peptides that only autoinduce their own production and the latter relating to peptides that also regulate transcription of other genes in addition to autoinduction.
      ; virulence factor
      Pore-forming activity
      • Van Tyne D.
      • Martin M.J.
      • Gilmore M.S.
      Structure, function, and biology of the Enterococcus faecalis cytolysin.
      Lanthipeptide (two-peptide lantibiotics)Lacticin 3147 (LtnA1/LtnA2)L. lactisInterference competitionPore-forming activity (LtnA1/LtnA2/lipid II synergy)
      • Rea M.C.
      • Clayton E.
      • O'Connor P.M.
      • Shanahan F.
      • Kiely B.
      • Ross R.P.
      • Hill C.
      Antimicrobial activity of lacticin 3,147 against clinical Clostridium difficile strains.
      ,
      • Gardiner G.E.
      • Rea M.C.
      • O'Riordan B.
      • O'Connor P.
      • Morgan S.M.
      • Lawlor P.G.
      • Lynch P.B.
      • Cronin M.
      • Ross R.P.
      • Hill C.
      Fate of the two-component lantibiotic lacticin 3147 in the gastrointestinal tract.
      Lasso peptideMicrocin J25E. coli AY25Interference competitionBlocking of transcription (binding to RNA polymerase)
      • Salomón R.A.
      • Farías R.N.
      Microcin 25, a novel antimicrobial peptide produced by Escherichia coli.
      ,
      • Kuznedelov K.
      • Semenova E.
      • Knappe T.A.
      • Mukhamedyarov D.
      • Srivastava A.
      • Chatterjee S.
      • Ebright R.H.
      • Marahiel M.A.
      • Severinov K.
      The antibacterial threaded-lasso peptide capistruin inhibits bacterial RNA polymerase.
      MethanobactinMethanobactinMethylosinus trichosporiumMetallophore
      • Kenney G.E.
      • Rosenzweig A.C.
      Methanobactins: maintaining copper homeostasis in methanotrophs and beyond.
      Modified short peptideComXB. subtilisQuorum-sensing signal
      The terms of autoinducing peptide and quorum-sensing signal are distinguished, the former describing peptides that only autoinduce their own production and the latter relating to peptides that also regulate transcription of other genes in addition to autoinduction.
      • Okada M.
      • Sato I.
      • Cho S.J.
      • Iwata H.
      • Nishio T.
      • Dubnau D.
      • Sakagami Y.
      Structure of the Bacillus subtilis quorum-sensing peptide pheromone ComX.
      Modified small peptideRaxXX. oryzae pv. oryzaeHost-bacteria interaction
      • Luu D.D.
      • Joe A.
      • Chen Y.
      • Parys K.
      • Bahar O.
      • Pruitt R.
      • Chan L.J.G.
      • Petzold C.J.
      • Long K.
      • Adamchak C.
      • Stewart V.
      • Belkhadir Y.
      • Ronald P.C.
      Biosynthesis and secretion of the microbial sulfated peptide RaxX and binding to the rice XA21 immune receptor.
      Peptide-derived small moleculePyrroloquinoline quinoneK. pneumoniaeRedox enzyme cofactor
      • Klinman J.P.
      • Bonnot F.
      Intrigues and intricacies of the biosynthetic pathways for the enzymatic quinocofactors: PQQ, TTQ, CTQ, TPQ, and LTQ.
      Peptide-derived small moleculeMycofactocinM. tuberculosisRedox enzyme cofactor
      • Ayikpoe R.
      • Govindarajan V.
      • Latham J.A.
      Occurrence, function, and biosynthesis of mycofactocin.
      ,
      • Ayikpoe R.S.
      • Latham J.A.
      MftD catalyzes the formation of a biologically active redox center in the biosynthesis of the ribosomally synthesized and post-translationally modified redox cofactor mycofactocin.
      SactipeptideSporulation killing factorB. subtilis 168Cannibalism
      • Liu W.T.
      • Yang Y.L.
      • Xu Y.
      • Lamsa A.
      • Haste N.M.
      • Yang J.Y.
      • Ng J.
      • Gonzalez D.
      • Ellermeier C.D.
      • Straight P.D.
      • Pevzner P.A.
      • Pogliano J.
      • Nizet V.
      • Pogliano K.
      • Dorrestein P.C.
      Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis.
      Sactipeptide (sactibiotic)Ruminococcin CR. gnavus E1Interference competitionPerturbation of nucleic acid synthesis
      • Balty C.
      • Guillot A.
      • Fradale L.
      • Brewee C.
      • Boulay M.
      • Kubiak X.
      • Benjdia A.
      • Berteau O.
      Ruminococcin C, an anti-clostridial sactipeptide produced by a prominent member of the human microbiota Ruminococcus gnavus.
      ,
      • Chiumento S.
      • Roblin C.
      • Kieffer-Jaquinod S.
      • Tachon S.
      • Leprètre C.
      • Basset C.
      • Aditiyarini D.
      • Olleik H.
      • Nicoletti C.
      • Bornet O.
      • Iranzo O.
      • Maresca M.
      • Hardré R.
      • Fons M.
      • Giardina T.
      • et al.
      Ruminococcin C, a promising antibiotic produced by a human gut symbiont.
      ,
      • Crost E.H.
      • Ajandouz E.H.
      • Villard C.
      • Geraert P.A.
      • Puigserver A.
      • Fons M.
      Ruminococcin C, a new anti-Clostridium perfringens bacteriocin produced in the gut by the commensal bacterium Ruminococcus gnavus E1.
      Sactipeptide (two-peptide sactibiotic)Thuricin CD (Trnα/Trnβ)B. thuringiensis DPC 6431Interference competitionPore-forming activity
      • Mathur H.
      • Fallico V.
      • O'Connor P.M.
      • Rea M.C.
      • Cotter P.D.
      • Hill C.
      • Ross R.P.
      Insights into the mode of action of the sactibiotic thuricin CD.
      Siderophore peptideMicrocin E492/E492mK. pneumoniae RYC492 E. coli VCS257 with pJAM229 plasmidInterference competition; exploitative competition (iron)Pore-forming activity; Perturbation of mannose transport
      • de Lorenzo V.
      • Pugsley A.P.
      Microcin E492, a low-molecular-weight peptide antibiotic which causes depolarization of the Escherichia coli cytoplasmic membrane.
      • Lagos R.
      • Wilkens M.
      • Vergara C.
      • Cecchi X.
      • Monasterio O.
      Microcin E492 forms ion channels in phospholipid bilayer membrane.
      ,
      • Bieler S.
      • Silva F.
      • Soto C.
      • Belin D.
      Bactericidal activity of both secreted and nonsecreted microcin E492 requires the mannose permease.
      • Thomas X.
      • Destoumieux-Garzón D.
      • Peduzzi J.
      • Afonso C.
      • Blond A.
      • Birlirakis N.
      • Goulard C.
      • Dubost L.
      • Thai R.
      • Tabet J.C.
      • Rebuffat S.
      Siderophore peptide, a new type of post-translationally modified antibacterial peptide with potent activity.
      Siderophore peptideMicrocin H47 Microcin ME. coli H47, Nissle 1917, CA46, CA58Interference competition; exploitative competition (iron)Perturbation of ATP synthesis
      • Vassiliadis G.
      • Destoumieux-Garzón D.
      • Lombard C.
      • Rebuffat S.
      • Peduzzi J.
      Isolation and characterization of two members of the siderophore-microcin family, microcins M and H47.
      ,
      • Patzer S.I.
      • Baquero M.R.
      • Bravo D.
      • Moreno F.
      • Hantke K.
      The colicin G, H and X determinants encode microcins M and H47, which might utilize the catecholate siderophore receptors FepA, Cir, Fiu and IroN.
      ThiopeptideLactocillinL. gasseriInterference competitionUnknown
      • Donia M.S.
      • Cimermancic P.
      • Schulze C.J.
      • Wieland Brown L.C.
      • Martin J.
      • Mitreva M.
      • Clardy J.
      • Linington R.G.
      • Fischbach M.A.
      A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics.
      ThiopeptideThiocillin
      Also an antibacterial peptide, but its function in niche competition has not yet been demonstrated.
      B. cereusStimulation of biofilm formation in BacillusInhibition of ribosomal protein synthesis (binding to EF-Tu)
      • Bleich R.
      • Watrous J.D.
      • Dorrestein P.C.
      • Bowers A.A.
      • Shank E.A.
      Thiopeptide antibiotics stimulate biofilm formation in Bacillus subtilis.
      ThiopeptideThiostrepton
      Also an antibacterial peptide, but its function in niche competition has not yet been demonstrated.
      S. laurentiiMorphological development in StreptomycesInhibition of ribosomal protein synthesis (binding to EF-Tu)
      • Wang H.
      • Zhao G.
      • Ding X.
      Morphology engineering of Streptomyces coelicolor M145 by sub-inhibitory concentrations of antibiotics.
      TOMM/LAPGoadsporin
      Also an antibacterial peptide, but its function in niche competition has not yet been demonstrated.
      Streptomyces sp.Morphological development in StreptomycesUnknown
      • Onaka H.
      • Tabata H.
      • Igarashi Y.
      • Sato Y.
      • Furumai T.
      Goadsporin, a chemical substance which promotes secondary metabolism and morphogenesis in streptomycetes. I. Purification and characterization.
      TOMM/LAPListeriolysin SL. monocytogenesInterference competition (virulence factor)Unknown
      • Cotter P.D.
      • Draper L.A.
      • Lawton E.M.
      • Daly K.M.
      • Groeger D.S.
      • Casey P.G.
      • Ross R.P.
      • Hill C.
      Listeriolysin S, a novel peptide haemolysin associated with a subset of lineage I Listeria monocytogenes.
      • Quereda J.J.
      • Meza-Torres J.
      • Cossart P.
      • Pizarro-Cerdá J.
      Listeriolysin S: a bacteriocin from epidemic Listeria monocytogenes strains that targets the gut microbiota.
      • Quereda J.J.
      • Dussurget O.
      • Nahori M.A.
      • Ghozlane A.
      • Volant S.
      • Dillies M.A.
      • Regnault B.
      • Kennedy S.
      • Mondot S.
      • Villoing B.
      • Cossart P.
      • Pizarro-Cerda J.
      Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection.
      ,
      • Quereda J.J.
      • Nahori M.A.
      • Meza-Torres J.
      • Sachse M.
      • Titos-Jiménez P.
      • Gomez-Laguna J.
      • Dussurget O.
      • Cossart P.
      • Pizarro-Cerdá J.
      Listeriolysin S is a streptolysin S-like virulence factor that targets exclusively pokaryotic cells in vivo.
      TOMM/LAPStreptolysin SS. pyogenesVirulence factor (cytotoxin)
      • Molloy E.M.
      • Cotter P.D.
      • Hill C.
      • Mitchell D.A.
      • Ross R.P.
      Streptolysin S-like virulence factors: the continuing sagA.
      a The terms of autoinducing peptide and quorum-sensing signal are distinguished, the former describing peptides that only autoinduce their own production and the latter relating to peptides that also regulate transcription of other genes in addition to autoinduction.
      b Other physiological functions have not been identified.
      c Also an antibacterial peptide, but its function in niche competition has not yet been demonstrated.

      Nucleotide peptides

      The nucleotide peptide microcin C (Fig. 2) is synthesized by several strains of Escherichia coli as a leaderless precursor heptapeptide that has to undergo a two-step maturation in both the producer and the target bacterium for acquiring activity (for a review, see Ref.
      • Severinov K.
      • Nair S.K.
      Microcin C: biosynthesis and mechanisms of bacterial resistance.
      ). First, posttranslational modifications of the precursor happen in the producing bacterium, leading to a formylated heptapeptide linked to a nucleotide moiety, which remains inactive. Second, after export outside of the producer, a double proteolytic cleavage occurs in the susceptible bacteria, providing the toxic entity, which is a nonhydrolyzable aspartyl-adenylate. This mimic of aspartyl adenylate is an inhibitor of aspartyl-tRNA synthetase, which therefore blocks protein synthesis at the translation step (
      • Metlitskaya A.
      • Kazakov T.
      • Kommer A.
      • Pavlova O.
      • Praetorius-Ibba M.
      • Ibba M.
      • Krasheninnikov I.
      • Kolb V.
      • Khmel I.
      • Severinov K.
      Aspartyl-tRNA synthetase is the target of peptide nucleotide antibiotic Microcin C.
      ).

      Siderophore peptides

      Siderophore peptides are exemplified by microcins E492, M, and H47 (
      • Azpiroz M.F.
      • Laviña M.
      Involvement of enterobactin synthesis pathway in production of microcin H47.
      ,
      • Vassiliadis G.
      • Destoumieux-Garzón D.
      • Lombard C.
      • Rebuffat S.
      • Peduzzi J.
      Isolation and characterization of two members of the siderophore-microcin family, microcins M and H47.
      ) (Fig. 2) (Table 1). Microcin E492 (MccE492) was initially characterized in Klebsiella pneumoniae RYC492 as an unmodified ribosomally synthesized peptide with a potent antibacterial activity directed essentially against Escherichia and Salmonella (
      • de Lorenzo V.
      Isolation and characterization of microcin E492 from Klebsiella pneumoniae.
      ). This activity is associated with a pore-forming property (
      • de Lorenzo V.
      • Pugsley A.P.
      Microcin E492, a low-molecular-weight peptide antibiotic which causes depolarization of the Escherichia coli cytoplasmic membrane.
      ,
      • Lagos R.
      • Wilkens M.
      • Vergara C.
      • Cecchi X.
      • Monasterio O.
      Microcin E492 forms ion channels in phospholipid bilayer membrane.
      ) and with interaction with the inner membrane components ManYZ of the mannose permease complex involved in mannose uptake (
      • Bieler S.
      • Silva F.
      • Soto C.
      • Belin D.
      Bactericidal activity of both secreted and nonsecreted microcin E492 requires the mannose permease.
      ). According to the growth conditions, this microcin is biosynthesized as the initially characterized unmodified form MccE492 (
      • de Lorenzo V.
      • Pugsley A.P.
      Microcin E492, a low-molecular-weight peptide antibiotic which causes depolarization of the Escherichia coli cytoplasmic membrane.
      ) or as a posttranslationally modified form (MccE492m) that carries a linear catechol-type siderophore at the C terminus (
      • Thomas X.
      • Destoumieux-Garzón D.
      • Peduzzi J.
      • Afonso C.
      • Blond A.
      • Birlirakis N.
      • Goulard C.
      • Dubost L.
      • Thai R.
      • Tabet J.C.
      • Rebuffat S.
      Siderophore peptide, a new type of post-translationally modified antibacterial peptide with potent activity.
      ). The siderophore-microcin has a much higher antibacterial activity than the unmodified counterpart, which is reflected by an enlarged spectrum of activity, including Klebsiella and Enterobacter species. Actually, it has been shown that the unmodified microcin is an incompletely processed form and that the final mature compound (i.e. the siderophore microcin) is an RiPP (
      • Vassiliadis G.
      • Peduzzi J.
      • Zirah S.
      • Thomas X.
      • Rebuffat S.
      • Destoumieux-Garzón D.
      Insight into siderophore-carrying peptide biosynthesis: enterobactin is a precursor for microcin E492 posttranslational modification.
      ). The MccE492/MccE492m biosynthesis requires four enzymes (MceC, MceD, MceI, and MceJ) that work with two precursors: the peptide precursor MceA and enterobactin, a catechol siderophore, which itself results from an NRPS pathway. Enterobactin is glucosylated and linearized by a C-glucosyl transferase (MceC) and an enterobactin esterase (MceD), successively, before an ester linkage is established between glucosylated enterobactin and the C-terminal serine of the peptide precursor. The resulting modified MceA is then processed at the membrane, and the mature modified peptide is exported after cleavage of the leader peptide (
      • Vassiliadis G.
      • Peduzzi J.
      • Zirah S.
      • Thomas X.
      • Rebuffat S.
      • Destoumieux-Garzón D.
      Insight into siderophore-carrying peptide biosynthesis: enterobactin is a precursor for microcin E492 posttranslational modification.
      ,
      • Nolan E.M.
      • Fischbach M.A.
      • Koglin A.
      • Walsh C.T.
      Biosynthetic tailoring of microcin E492m: post-translational modification affords an antibacterial siderophore-peptide conjugate.
      ).

      Lasso peptides

      Lasso peptides are produced by Enterobacteriaceae (Proteobacteria), Actinobacteria, and a few Firmicutes. They are characterized by a [1]rotaxane knotted structure, which has been named after the shape adopted by the lasso of a cowboy (for reviews, see Refs.
      • Hegemann J.D.
      • Zimmermann M.
      • Xie X.
      • Marahiel M.A.
      Lasso peptides: an intriguing class of bacterial natural products.
      ,
      • Maksimov M.O.
      • Pan S.J.
      • James Link A.
      Lasso peptides: structure, function, biosynthesis, and engineering.
      ,
      • Li Y.
      • Zirah S.
      • Rebuffat S.
      Lasso Peptides: Bacterial Strategies to Make and Maintain Bioactive Entangled Scaffolds.
      ,
      • Cheung-Lee W.L.
      • Link A.J.
      Genome mining for lasso peptides: past, present, and future.
      ,
      • Tan S.
      • Moore G.
      • Nodwell J.
      Put a bow on it: knotted antibiotics take center stage.
      ). The lasso topology is composed of a macrocycle closed by an isopeptide bond linkage from an Asp or Glu side chain to the N terminus of the core peptide. The resulting C-terminal tail is threaded through the ring and maintained in this entropically disfavored situation by bulky residues that firmly straddle the tail into the ring or, by disulfide bonds, or by an association of both means. Microcin J25 is the most intensively studied lasso peptide (Fig. 2 and Table 1). It remained for more than 10 years the archetype of this RiPP family. It is produced by E. coli AY25 (
      • Salomón R.A.
      • Farías R.N.
      Microcin 25, a novel antimicrobial peptide produced by Escherichia coli.
      ) and deserved attention over the years due to its potent narrow-spectrum antibacterial activity, essentially directed against Salmonella and Escherichia. Its lasso structure was determined in the 2000s (
      • Bayro M.J.
      • Mukhopadhyay J.
      • Swapna G.V.
      • Huang J.Y.
      • Ma L.C.
      • Sineva E.
      • Dawson P.E.
      • Montelione G.T.
      • Ebright R.H.
      Structure of antibacterial peptide microcin J25: a 21-residue lariat protoknot.
      ,
      • Rosengren K.J.
      • Clark R.J.
      • Daly N.L.
      • Göransson U.
      • Jones A.
      • Craik D.J.
      Microcin J25 has a threaded sidechain-to-backbone ring structure and not a head-to-tail cyclized backbone.
      ,
      • Wilson K.A.
      • Kalkum M.
      • Ottesen J.
      • Yuzenkova J.
      • Chait B.T.
      • Landick R.
      • Muir T.
      • Severinov K.
      • Darst S.A.
      Structure of microcin J25, a peptide inhibitor of bacterial RNA polymerase, is a lassoed tail.
      ,
      • Rebuffat S.
      • Blond A.
      • Destoumieux-Garzon D.
      • Goulard C.
      • Peduzzi J.
      Microcin J25, from the macrocyclic to the lasso structure: implications for biosynthetic, evolutionary and biotechnological perspectives.
      ). Microcin J25 biosynthesis requires only four genes assembled on a plasmid (mcjABCD). It was shown that the lasso topology can be reconstituted in vitro from the precursor McjA in the presence of the two enzymes McjB and McjC and ATP only (
      • Duquesne S.
      • Destoumieux-Garzón D.
      • Zirah S.
      • Goulard C.
      • Peduzzi J.
      • Rebuffat S.
      Two enzymes catalyze the maturation of a lasso peptide in Escherichia coli.
      ). McjC and McjB act as a lasso cyclase homologous to an asparagine synthetase and a leader peptidase, respectively, which presumably form a complex (lasso synthetase) (
      • Yan K.P.
      • Li Y.
      • Zirah S.
      • Goulard C.
      • Knappe T.A.
      • Marahiel M.A.
      • Rebuffat S.
      Dissecting the maturation steps of the lasso peptide microcin J25 in vitro.
      ). The mature lassoed microcin is then exported outside the producing cells by the ATP-binding cassette (ABC) exporter McjD, which ensures secretion of the toxic peptide into the environment. This both provides self-immunity to the producer and allows it to compete with other bacteria in the same niche thanks to the microcin (
      • Choudhury H.G.
      • Tong Z.
      • Mathavan I.
      • Li Y.
      • Iwata S.
      • Zirah S.
      • Rebuffat S.
      • van Veen H.W.
      • Beis K.
      Structure of an antibacterial peptide ATP-binding cassette transporter in a novel outward occluded state.
      ,
      • Bountra K.
      • Hagelueken G.
      • Choudhury H.G.
      • Corradi V.
      • El Omari K.
      • Wagner A.
      • Mathavan I.
      • Zirah S.
      • Yuan Wahlgren W.
      • Tieleman D.P.
      • Schiemann O.
      • Rebuffat S.
      • Beis K.
      Structural basis for antibacterial peptide self-immunity by the bacterial ABC transporter McjD.
      ). Microcin J25 enters susceptible bacteria by hijacking the outer-membrane siderophore receptor FhuA/TonB-ExbB-ExbD–dependent pathway and the inner-membrane SbmA transporter to cross the double membrane of Gram-negative bacteria (for reviews, see Refs.
      • Drider D.
      • Rebuffat S.
      Prokaryotic Antimicrobial Peptides: From Genes to Applications.
      and
      • Li Y.
      • Zirah S.
      • Rebuffat S.
      Lasso Peptides: Bacterial Strategies to Make and Maintain Bioactive Entangled Scaffolds.
      ) and subsequently inhibits gene transcription by inhibiting the RNA polymerase. Although many newly identified lasso peptides do not show significant antibacterial activities against tested strains, some of them are found to inhibit a range of bacterial RNA polymerases (
      • Metelev M.
      • Arseniev A.
      • Bushin L.B.
      • Kuznedelov K.
      • Artamonova T.O.
      • Kondratenko R.
      • Khodorkovskii M.
      • Seyedsayamdost M.R.
      • Severinov K.
      Acinetodin and klebsidin, RNA polymerase targeting lasso peptides produced by human isolates of Acinetobacter gyllenbergii Klebsiella pneumoniae.
      ,
      • Kuznedelov K.
      • Semenova E.
      • Knappe T.A.
      • Mukhamedyarov D.
      • Srivastava A.
      • Chatterjee S.
      • Ebright R.H.
      • Marahiel M.A.
      • Severinov K.
      The antibacterial threaded-lasso peptide capistruin inhibits bacterial RNA polymerase.
      ,
      • Cheung-Lee W.L.
      • Parry M.E.
      • Jaramillo Cartagena A.
      • Darst S.A.
      • Link A.J.
      Discovery and structure of the antimicrobial lasso peptide citrocin.
      ), indicating that the entry of the sensitive cells is the key determinant of the activity of lasso peptides.

      Circular bacteriocins

      Circular bacteriocins are characterized by a head-to-tail cyclization, which is actually the only posttranslational modification undergone by the ribosomal precursor. The BGCs of circular bacteriocins encode a membrane protein, which is hypothesized to ensure the N to C terminus cyclization and possibly the protease activity. About 14 circular bacteriocins have been characterized to date (
      • Perez R.H.
      • Zendo T.
      • Sonomoto K.
      Circular and leaderless bacteriocins: biosynthesis, mode of action, applications, and prospects.
      ), among which is enterocin AS-48 (Fig. 2 and Table 1), the representative of the group, which has been characterized in Enterococcus faecalis strains from both food and clinical origins (
      • Grande Burgos M.J.
      • Pulido R.P.
      • Del Carmen López Aguayo M.
      • Gálvez A.
      • Lucas R.
      The cyclic antibacterial peptide enterocin AS-48: isolation, mode of action, and possible food applications.
      ). Circular bacteriocins share a common, highly compact three-dimensional structural fold, which typically consists of an arrangement of 4–5 α-helices, packed into a helical bundle or a saposin-like fold (
      • Perez R.H.
      • Zendo T.
      • Sonomoto K.
      Circular and leaderless bacteriocins: biosynthesis, mode of action, applications, and prospects.
      ,
      • Towle K.M.
      • Vederas J.C.
      Structural features of many circular and leaderless bacteriocins are similar to those in saposins and saposin-like peptides.
      ). Circular bacteriocins have been proposed to kill bacteria by interaction with the bacterial cell membrane, causing its permeabilization and leading to leakage of ions, dissipation of membrane potential, and cell death. The dimerization process of enterocin AS-48 at physiological pH was proposed to play a role in the mechanism of action. However, although it has been established for many circular bacteriocins that they did not require a receptor for antimicrobial activity, the maltose ABC transporter complex has been shown to be important for activity in the case of garvicin ML, leading to the hypothesis of a dual concentration-dependent mode of action, with membrane activity operating at higher concentrations than perturbation of maltose transport (
      • Gabrielsen C.
      • Brede D.A.
      • Hernández P.E.
      • Nes I.F.
      • Diep D.B.
      The maltose ABC transporter in Lactococcus lactis facilitates high-level sensitivity to the circular bacteriocin garvicin ML.
      ).

      TOMMs-linear azol(in)e-containing peptides (LAPs)

      LAPs exhibit various combinations of thiazole and oxazole or methyl-oxazole heterocycles. Although the term microcin is usually restricted to AMPs produced by Gram-negative bacteria, LAPs are also called thiazole/oxazole-modified microcins (TOMMs) (
      • Molloy E.M.
      • Cotter P.D.
      • Hill C.
      • Mitchell D.A.
      • Ross R.P.
      Streptolysin S-like virulence factors: the continuing sagA.
      ) even when they are produced by Gram-positive bacteria. This nomenclature was adopted by homology to microcin B17 produced by E. coli (Fig. 2), the prototypic molecule endowed with such modifications (
      • Yorgey P.
      • Lee J.
      • Kördel J.
      • Vivas E.
      • Warner P.
      • Jebaratnam D.
      • Kolter R.
      Posttranslational modifications in microcin B17 define an additional class of DNA gyrase inhibitor.
      ) and the first RiPP to have its biosynthesis reconstituted in vitro (
      • Li Y.M.
      • Milne J.C.
      • Madison L.L.
      • Kolter R.
      • Walsh C.T.
      From peptide precursors to oxazole and thiazole-containing peptide antibiotics: microcin B17 synthase.
      ). The thiazole/oxazole rings of microcin B17 are made from Cys and Ser/Thr residues by a three-component B17 synthetase that catalyzes dehydration and cyclization to form azolines, which are subsequently oxidized to azoles (
      • Collin F.
      • Maxwell A.
      The microbial toxin microcin B17: prospects for the development of new antibacterial agents.
      ). Peptides from the TOMM family include several toxins from pathogenic bacteria (streptolysin S from Streptococcus pyogenes and other Streptococcus species, listeriolysin S from Listeria monocytogenes (Table 1), clostridiolysin S from Clostridium botulinum and Clostridium sporogenes, and stapholysin S from Staphylococcus aureus RF122, whose structures all remain elusive) and other TOMMs from nonpathogenic bacterial species (
      • Molloy E.M.
      • Cotter P.D.
      • Hill C.
      • Mitchell D.A.
      • Ross R.P.
      Streptolysin S-like virulence factors: the continuing sagA.
      ,
      • Collin F.
      • Maxwell A.
      The microbial toxin microcin B17: prospects for the development of new antibacterial agents.
      ). Those have been shown to exert different biological activities among which are antibacterial properties (microcin B17 from E. coli, klebsazolicin from Klebsiella pneumoniae, goadsporin from soil Streptomyces sp. (Table 1), plantazolicin from the saprophyte Bacillus amyloliquefaciens FZB42 (
      • Molohon K.J.
      • Blair P.M.
      • Park S.
      • Doroghazi J.R.
      • Maxson T.
      • Hershfield J.R.
      • Flatt K.M.
      • Schroeder N.E.
      • Ha T.
      • Mitchell D.A.
      Plantazolicin is an ultranarrow-spectrum antibiotic that targets the Bacillus anthracis membrane.
      ), or trifolitoxin and phazolicin from the legume symbionts Rhizobium leguminosarum bv. trifolii T24 (
      • Triplett E.W.
      • Barta T.M.
      Trifolitoxin production and nodulation are necessary for the expression of superior nodulation competitiveness by Rhizobium leguminosarum bv. trifolii strain T24 on clover.
      ) and Rhizobium sp. Pop5, respectively (
      • Travin D.Y.
      • Watson Z.L.
      • Metelev M.
      • Ward F.R.
      • Osterman I.A.
      • Khven I.M.
      • Khabibullina N.F.
      • Serebryakova M.
      • Mergaert P.
      • Polikanov Y.S.
      • Cate J.H.D.
      • Severinov K.
      Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition.
      )). It has been firmly established that microcin B17 blocks DNA gyrase (
      • Collin F.
      • Maxwell A.
      The microbial toxin microcin B17: prospects for the development of new antibacterial agents.
      ,
      • Pierrat O.A.
      • Maxwell A.
      The action of the bacterial toxin microcin B17: insight into the cleavage-religation reaction of DNA gyrase.
      ) and that phazolicin and klebsazolicin inhibit the ribosome (
      • Travin D.Y.
      • Watson Z.L.
      • Metelev M.
      • Ward F.R.
      • Osterman I.A.
      • Khven I.M.
      • Khabibullina N.F.
      • Serebryakova M.
      • Mergaert P.
      • Polikanov Y.S.
      • Cate J.H.D.
      • Severinov K.
      Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition.
      ), but the modes of action of other TOMM peptides remain largely unknown.

      Thiopeptides

      Thiopeptides are macrocyclic peptides containing a characteristic six-membered nitrogen-containing ring, oxazole/thiazol(in)e moieties, and/or dehydroamino acids (Fig. 2). They are produced by and show potent activity against Gram-positive pathogens, such as methicillin-resistant S. aureus and Clostridium difficile (
      • Bagley M.C.
      • Dale J.W.
      • Merritt E.A.
      • Xiong X.
      Thiopeptide antibiotics.
      ). Their mode of action consists of inhibition of protein synthesis, interfering either with the 50S ribosomal subunit (
      • Reusser F.
      Mode of action of berninamycin: an inhibitor of protein biosynthesis.
      ) or the elongation factor Tu (
      • Heffron S.E.
      • Jurnak F.
      Structure of an EF-Tu complex with a thiazolyl peptide antibiotic determined at 2.35 Å resolution: atomic basis for GE2270A inhibition of EF-Tu.
      ). Biosynthesis of the oxazole/thiazole motifs is similar to that of TOMMs. The central nitrogen-containing ring is synthesized by a dedicated enzyme catalyzing a [4 + 2]-cycloaddition reaction. Thorough genome mining studies have revealed that the human microbiome harbors abundant thiopeptide BGCs (
      • Donia M.S.
      • Cimermancic P.
      • Schulze C.J.
      • Wieland Brown L.C.
      • Martin J.
      • Mitreva M.
      • Clardy J.
      • Linington R.G.
      • Fischbach M.A.
      A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics.
      ) and that Actinobacteria or Bacilli species are the dominant producers of thiopeptides (
      • Schwalen C.J.
      • Hudson G.A.
      • Kille B.
      • Mitchell D.A.
      Bioinformatic expansion and discovery of thiopeptide antibiotics.
      ), raising the questions of their ecological roles in the related complex ecosystems (e.g. soil environment and human microbiota).

      Lanthipeptides and lantibiotics

      Lanthipeptides, including those that have antimicrobial properties, called lantibiotics, are produced by and active against Gram-positive bacteria. They are generally inactive against Enterobacteriaceae and other Gram-negative bacteria. The major producers are lactic acid bacteria (e.g. Lactococcus and Streptococcus) and certain Staphylococcus strains. Lanthipeptides are characterized by the presence of the unusual residues lanthionine and 3-methyllanthionine (for reviews, see Refs.
      • Lubelski J.
      • Rink R.
      • Khusainov R.
      • Moll G.N.
      • Kuipers O.P.
      Biosynthesis, immunity, regulation, mode of action and engineering of the model lantibiotic nisin.
      ,
      • Asaduzzaman S.M.
      • Sonomoto K.
      Lantibiotics: diverse activities and unique modes of action.
      ,
      • Knerr P.J.
      • van der Donk W.A.
      Discovery, biosynthesis, and engineering of lantipeptides.
      ,
      • Ortega M.A.
      • van der Donk W.A.
      New insights into the biosynthetic logic of ribosomally synthesized and post-translationally modified peptide natural products.
      ). These residues result from dehydration of serine and threonine in the core peptide to give dehydroamino acids that cyclize with cysteines via the formation of thioether linkages between β-carbons. Nisin, produced by Lactococcus lactis, is the first studied lantibiotic (Fig. 2 and Table 1). It has been used as a food preservative (Nisaplin® and Niprosin®) in more than 80 countries for over 50 years. Its mechanism of action involves binding to and sequestration of lipid II, the essential peptidoglycan precursor for cell wall biosynthesis. This interaction both blocks peptidoglycan biosynthesis and causes the formation of lipid II–nisin heteromolecular pores in the membrane bilayer, leading to leakage of ions and essential metabolites. Other lantibiotics called “two-peptide lantibiotics” (or two-component lantibiotics) are produced as two distinct peptide entities, which function in a synergistic fashion to give optimal activity, whereas separately they are not active or are weakly active (
      • Lawton E.M.
      • Ross R.P.
      • Hill C.
      • Cotter P.D.
      Two-peptide lantibiotics: a medical perspective.
      ). Each component of two-peptide lantibiotics fulfills one of the two roles involved in the mechanism of action of nisin (i.e. binding to lipid II and pore formation) (
      • Islam M.R.
      • Nagao J.
      • Zendo T.
      • Sonomoto K.
      Antimicrobial mechanism of lantibiotics.
      ). They are exemplified by lacticin 3147 (consisting of peptides LtnA1/LtnA2) (Table 1) produced by L. lactis and haloduracin (peptides Halα/Halβ) from Bacillus halodurans, the most studied of the group (
      • Li Y.
      • Zirah S.
      • Rebuffat S.
      Lasso Peptides: Bacterial Strategies to Make and Maintain Bioactive Entangled Scaffolds.
      ). The structure and mechanism of action of lacticin 3147 have been completely deciphered, showing the specific role of each of the two peptide components LtnA1 and LtnA2 in the synergistic mechanism (
      • Wiedemann I.
      • Böttiger T.
      • Bonelli R.R.
      • Wiese A.
      • Hagge S.O.
      • Gutsmann T.
      • Seydel U.
      • Deegan L.
      • Hill C.
      • Ross P.
      • Sahl H.-G.
      The mode of action of the lantibiotic lacticin 3147—a complex mechanism involving specific interaction of two peptides and the cell wall precursor lipid II.
      ,
      • Bakhtiary A.
      • Cochrane S.A.
      • Mercier P.
      • McKay R.T.
      • Miskolzie M.
      • Sit C.S.
      • Vederas J.C.
      Insights into the mechanism of action of the two-peptide lantibiotic lacticin 3147.
      ). LtnA2 can form pores in membrane bilayers without the help of LtnA1 or lipid II. LtnA1 cannot form pores in membrane bilayers but has the ability to bind lipid II with its C terminus. The synergistic mechanism of action of the two lacticin 3147 components appears flexible, as lipid II binding enhances the membrane activity, which, however, can happen, although to a lesser extent, independently of lipid II.

      Sactipeptides and sactibiotics

      Similar to lanthipeptides and lantibiotics, the term sactipeptides includes the subclass of antimicrobial sactibiotics (
      • Flühe L.
      • Marahiel M.A.
      Radical S-adenosylmethionine enzyme catalyzed thioether bond formation in sactipeptide biosynthesis.
      ,
      • Mathur H.
      • Rea M.C.
      • Cotter P.D.
      • Hill C.
      • Ross R.P.
      The sactibiotic subclass of bacteriocins: an update.
      ). They are characterized by an intramolecular sulfur to α-carbon linkage between a cysteine and another residue (Fig. 2) and, as such, are distinguished from lanthipeptides/lantibiotics (thioether linkages between β-carbons) and from sactipeptide-like peptides that contain sulfur to β- or γ-carbon linkages (
      • Hudson G.A.
      • Burkhart B.J.
      • DiCaprio A.J.
      • Schwalen C.J.
      • Kille B.
      • Pogorelov T.V.
      • Mitchell D.A.
      Bioinformatic mapping of radical S-adenosylmethionine-dependent ribosomally synthesized and post-translationally modified peptides identifies new Cα, Cβ, and Cγ-linked thioether-containing peptides.
      ). The sactionine motif is established by a radical-based mechanism ensured by a radical SAM enzyme called sactisynthase. Only few sactipeptides have been characterized to date. They are produced mainly by the Bacillus genus (subtilosin A from B. subtilis 168, the first reported sactipeptide, the sporulation-killing factor (SKF) from B. subtilis 168 (Fig. 2) (Table 1), thurincin H from Bacillus thuringiensis SF361, the two-peptide thuricin CD from the human fecal isolate B. thuringiensis DPC 6431, and huazacin or thuricin Z from B. thuringiensis serovar Huazhongensis) (
      • Hudson G.A.
      • Mitchell D.A.
      RiPP antibiotics: biosynthesis and engineering potential.
      ,
      • Balty C.
      • Guillot A.
      • Fradale L.
      • Brewee C.
      • Boulay M.
      • Kubiak X.
      • Benjdia A.
      • Berteau O.
      Ruminococcin C, an anti-clostridial sactipeptide produced by a prominent member of the human microbiota Ruminococcus gnavus.
      ,
      • Hudson G.A.
      • Burkhart B.J.
      • DiCaprio A.J.
      • Schwalen C.J.
      • Kille B.
      • Pogorelov T.V.
      • Mitchell D.A.
      Bioinformatic mapping of radical S-adenosylmethionine-dependent ribosomally synthesized and post-translationally modified peptides identifies new Cα, Cβ, and Cγ-linked thioether-containing peptides.
      ,
      • Mo T.
      • Ji X.
      • Yuan W.
      • Mandalapu D.
      • Wang F.
      • Zhong Y.
      • Li F.
      • Chen Q.
      • Ding W.
      • Deng Z.
      • Yu S.
      • Zhang Q.
      Thuricin Z, a narrow-spectrum sactibiotic that targets cell membrane.
      ). They have been found recently in Ruminococcus (ruminococcins from Ruminococcus gnavus isolated from the human microbiota) (
      • Balty C.
      • Guillot A.
      • Fradale L.
      • Brewee C.
      • Boulay M.
      • Kubiak X.
      • Benjdia A.
      • Berteau O.
      Ruminococcin C, an anti-clostridial sactipeptide produced by a prominent member of the human microbiota Ruminococcus gnavus.
      ,
      • Chiumento S.
      • Roblin C.
      • Kieffer-Jaquinod S.
      • Tachon S.
      • Leprètre C.
      • Basset C.
      • Aditiyarini D.
      • Olleik H.
      • Nicoletti C.
      • Bornet O.
      • Iranzo O.
      • Maresca M.
      • Hardré R.
      • Fons M.
      • Giardina T.
      • et al.
      Ruminococcin C, a promising antibiotic produced by a human gut symbiont.
      ) and presumably in Staphylococcus (hyicin from Staphylococcus hyicus 4244). The structure of ruminococcin C was recently established, showing that this sactipeptide is stabilized by four thioether bonds that generate a double hairpin fold (
      • Balty C.
      • Guillot A.
      • Fradale L.
      • Brewee C.
      • Boulay M.
      • Kubiak X.
      • Benjdia A.
      • Berteau O.
      Ruminococcin C, an anti-clostridial sactipeptide produced by a prominent member of the human microbiota Ruminococcus gnavus.
      ,
      • Chiumento S.
      • Roblin C.
      • Kieffer-Jaquinod S.
      • Tachon S.
      • Leprètre C.
      • Basset C.
      • Aditiyarini D.
      • Olleik H.
      • Nicoletti C.
      • Bornet O.
      • Iranzo O.
      • Maresca M.
      • Hardré R.
      • Fons M.
      • Giardina T.
      • et al.
      Ruminococcin C, a promising antibiotic produced by a human gut symbiont.
      ).

      RiPP-mediated competition mechanisms

      Competition has long been recognized as a major regulatory process in populations and community dynamics, which structures the ecological systems. It involves one organism decreasing the survival, development, or reproduction of others. Competition is categorized into two major modes identified in ecosystems, including microbial communities either hosted in holobionts or living in open environments: (i) exploitative competition, which is an indirect process and occurs via resource consumption when organisms compete for common nutrients and one organism depletes its surroundings of nutrients, and (ii) interference competition or direct competition, which happens when one individual directly attacks another, generally by the secretion of harmful molecules (
      • Cornforth D.M.
      • Foster K.R.
      Competition sensing: the social side of bacterial stress responses.
      ,
      • Stubbendieck R.M.
      • Straight P.D.
      Multifaceted interfaces of bacterial competition.
      ,
      • Raffatellu M.
      Learning from bacterial competition in the host to develop antimicrobials.
      ). The battle for iron is a typical example of exploitative competition (
      • Wilson B.R.
      • Bogdan A.R.
      • Miyazawa M.
      • Hashimoto K.
      • Tsuji Y.
      Siderophores in iron metabolism: from mechanism to therapy potential.
      ), whereas the production of antimicrobial molecules and toxins (bacteriocins, microcins, and other NPs) exemplifies interference competition. In some cases, interference competition can be driven through an indirect action of a metabolite that triggers at sublevel concentration the production of an antibiotic molecule. This process, which involves a cross-talk between antibiotic biosynthesis pathways, is exemplified by jadomycin B, an angucyclin antibiotic produced by Streptomyces venezuaelae, which at subinhibitory concentration regulates the production of prodigiosin (an NRPS-derived antibiotic) by Streptomyces coelicolor and concomitantly its morphological development (
      • Wang W.
      • Ji J.
      • Li X.
      • Wang J.
      • Li S.
      • Pan G.
      • Fan K.
      • Yang K.
      Angucyclines as signals modulate the behaviors of Streptomyces coelicolor.
      ).
      It has been proposed that bacteria have evolved to detect and respond to ecological competition by modifying regulatory networks and drive responses to defend them and counterattack. This physiological response that detects harms caused by other cells but not from abiotic stresses has been called competition sensing (
      • Cornforth D.M.
      • Foster K.R.
      Competition sensing: the social side of bacterial stress responses.
      ). Engagement in interference and exploitative mechanisms of competition contributes to colonization resistance, the process by which in healthy conditions and in the absence of harmful molecules, microbiota can efficiently inhibit colonization and overgrowth by invading nonindigenous microorganisms, including pathogens (
      • Buffie C.G.
      • Pamer E.G.
      Microbiota-mediated colonization resistance against intestinal pathogens.
      ,
      • Lawley T.D.
      • Walker A.W.
      Intestinal colonization resistance.
      ).
      Among the different roles played (or supposed to be played) by RiPPs in nature, their involvement in microbial competition is the most documented one. The gut microbiota is probably the most extensively studied and the better known natural microbial ecosystem due to its extremely high importance for human health (
      • Thursby E.
      • Juge N.
      Introduction to the human gut microbiota.
      ). Indeed, perturbation of its equilibrium (dysbiosis) is correlated to many diseases. Therefore, it has been analyzed from both a strict microbiological and a biochemical aspect to gain a better understanding of the interplay between molecules from the microorganisms and the host. Moreover, the therapeutic potential of the molecules secreted by the gut microbiota has increased in the context of bacterial resistance and its implications for human, animal, and environmental health (
      • Donia M.S.
      • Fischbach M.A.
      Small molecules from the human microbiota.
      ). Currently, other mammal-associated microbiota are increasingly being studied, and among them, skin microbiota is pretty well-documented (
      • Schommer N.N.
      • Gallo R.L.
      Structure and function of the human skin microbiome.
      ,
      • Yamazaki Y.
      • Nakamura Y.
      • Núñez G.
      Role of the microbiota in skin immunity and atopic dermatitis.
      ). In this context, it has been evidenced both in vivo and in vitro that certain RiPPs are actors in microbiota and particularly in the gut microbiota. To describe these aspects, we selected several classes of RiPPs produced by Gram-negative and Gram-positive bacteria, including modified microcins and bacteriocins, which illustrate different contexts in the field.

      Interference competition driven by RPNPs in Gram-negative bacteria

      The siderophore peptides microcins M and H47 use two complementary strategies to serve as efficient actors in colonization of the gut and competition. They are produced by E. coli Nissle 1917 (also called Mutaflor and abbreviated as EcN), a probiotic strain originally isolated in 1917 by the army surgeon Alfred Nissle from the feces of a soldier who resisted a severe outbreak of shigellosis during the First World War (
      • Nissle A.
      Die antagonistische Behandlung chronischer Darmstörungen mit Colibakterien.
      ). Today it is one of the most investigated bacterial strains, but despite its commercialization and numerous applications, the mechanisms underlining its positive properties to regulate intestinal disorders of infectious or inflammatory origin remain still obscure (
      • Jacobi C.A.
      • Malfertheiner P.
      Escherichia coli Nissle 1917 (Mutaflor): new insights into an old probiotic bacterium.
      ). Microcins M and H47 initially identified in EcN (
      • Patzer S.I.
      • Baquero M.R.
      • Bravo D.
      • Moreno F.
      • Hantke K.
      The colicin G, H and X determinants encode microcins M and H47, which might utilize the catecholate siderophore receptors FepA, Cir, Fiu and IroN.
      ) have been shown further to be siderophore peptides (
      • Vassiliadis G.
      • Destoumieux-Garzón D.
      • Lombard C.
      • Rebuffat S.
      • Peduzzi J.
      Isolation and characterization of two members of the siderophore-microcin family, microcins M and H47.
      ). Although the potent bacterial inhibitory properties of microcins in vitro were known for a long time (
      • Baquero F.
      • Moreno F.
      The microcins.
      ), their action and interplay with competitors in vivo remained elusive (
      • Altenhoefer A.
      • Oswald S.
      • Sonnenborn U.
      • Enders C.
      • Schulze J.
      • Hacker J.
      • Oelschlaeger T.A.
      The probiotic Escherichia coli strain Nissle 1917 interferes with invasion of human intestinal epithelial cells by different enteroinvasive bacterial pathogens.
      ). However, microcins M and H47 were recently demonstrated for the first time to mediate competition among Enterobacteriaceae exclusively in the inflamed gut, which represents highly competitive conditions for resources, and particularly for iron (
      • Sassone-Corsi M.
      • Nuccio S.P.
      • Liu H.
      • Hernandez D.
      • Vu C.T.
      • Takahashi A.A.
      • Edwards R.A.
      • Raffatellu M.
      Microcins mediate competition among Enterobacteriaceae in the inflamed gut.
      ). Indeed, in such conditions, EcN colonizes the inflamed gut, where it uses its microcins for niche competition against related Enterobacteriaceae, without modifying substantially the gut microbiota. Furthermore, in these conditions, EcN microcins impair the growth of enterobacterial pathogens, such as Salmonella enterica subsp. enterica serovar Typhimurium or adherent invasive E. coli. Moreover, in a recent study, evidence that the posttranslational modification of EcN microcins with a siderophore is required for antibacterial activity in vivo has been obtained (
      • Massip C.
      • Branchu P.
      • Bossuet-Greif N.
      • Chagneau C.V.
      • Gaillard D.
      • Martin P.
      • Boury M.
      • Sécher T.
      • Dubois D.
      • Nougayrède J.-P.
      • Oswald E.
      Deciphering the interplay between the genotoxic and probiotic activities of Escherichia coli Nissle 1917.
      ). This study also shows that the biosynthesis pathway of siderophore microcins tightly depends on that of the genotoxin colibactin (
      • Xue M.
      • Kim C.S.
      • Healy A.R.
      • Wernke K.M.
      • Wang Z.
      • Frischling M.C.
      • Shine E.E.
      • Wang W.
      • Herzon S.B.
      • Crawford J.M.
      Structure elucidation of colibactin and its DNA cross-links.
      ), which is also produced by EcN and is correlated with the frequency and severity of colorectal cancer in humans (
      • Nougayrède J.P.
      • Homburg S.
      • Taieb F.
      • Boury M.
      • Brzuszkiewicz E.
      • Gottschalk G.
      • Buchrieser C.
      • Hacker J.
      • Dobrindt U.
      • Oswald E.
      Escherichia coli induces DNA double-strand breaks in eukaryotic cells.
      ), making the use of this commercialized probiotic problematic.
      Taken altogether, these studies show on one side that siderophore microcins M and H47 efficiently act in microbial competition through both exploitative competition (i.e. in the present case, competition for iron) and interference competition (contact-dependent killing) (
      • Raffatellu M.
      Learning from bacterial competition in the host to develop antimicrobials.
      ) (Fig. 3A), because they both trap catechol siderophores to anchor them at the peptide C terminus and hijack siderophore receptors for import. On the other side, they highlight the versatility of the biosynthetic assembly lines to produce both virulence factors and competition molecules and the consequential fine margin between pathogenicity and probiotic activity for a given strain.
      Figure thumbnail gr3
      Figure 3Schematic of the main strategies of Gram-negative (A) and -positive (B) bacteria for colonization resistance and competition involving RPNPs. 1, interference competition using RPNPs as contact-dependent killer molecules (several examples from both Gram-negative and -positive bacteria, among which are the lasso peptide microcin J25 and the two-peptide sactibiotic thuricin CD, respectively); 2, exploitative competition exemplified by the battle for iron involving competition between siderophores and siderophore-modified peptides for the same high affinity receptors (MccE492m from K. pneumoniae RYC 492 and MccH47 from E. coli Nissle 1917); 3, reservoir of killing RPNPs using functional amyloids for delivering killers (MccE492 from K. pneumoniae RYC 492); 4, synergy between RPNPs and host AMPs (Sh-lantibiotic-α and Sh-lantibiotic-β from S. hominis A9, each synergizing with the host cathelicidin LL-37); 5, quorum-sensing interference (an autoinducing RPNP from S. hominis A9 acts as a disruptor of quorum sensing that inhibits the secretion of the virulence factor PSMα in S. aureus; 6, cooperation between host and RPNP producing bacterium in the gut for the final processing step leading to mature RPNP acting by interference competition (ruminococcin C from R. gnavus E1); 7, manipulation of commensals by the pathogen to occupy the niche and increase virulence (the pathogenic strain L. monocytogenes F2365 produces listeriolysin S, a TOMM virulence factor, which targets commensal bacteria occupying the same niche and devoid of self-immunity to the toxin, to increase nutrient level and favor invasion).
      Microcin J25 initially produced by a newborn infant fecal isolate of E. coli AY25 has been known for about 25 years for exerting a potent and narrow-spectrum antibacterial activity directed essentially against Escherichia, Salmonella, and Shigella at concentrations in the nanomolar to micromolar range (
      • Salomón R.A.
      • Farías R.N.
      Microcin 25, a novel antimicrobial peptide produced by Escherichia coli.
      ). The activity of microcin J25 in complex matrices and in vivo in a mouse model of Salmonella infection was evidenced (
      • Lopez F.E.
      • Vincent P.A.
      • Zenoff A.M.
      • Salomón R.A.
      • Farías R.N.
      Efficacy of microcin J25 in biomatrices and in a mouse model of Salmonella infection.
      ). Competitive exclusion of Salmonella in poultry under field conditions has been applied since the 1990s in several countries, using diverse preparations, including complex consortia of bacterial strains (
      • Stavric S.
      • D'Aoust J.Y.
      Undefined and defined bacterial preparations for the competitive exclusion of Salmonella in poultry: a review.
      ). But it was not until recent years that evidence of the involvement of microcin J25 in these properties was obtained. In that way, the ability of microcin J25 to compete the pathogen Salmonella in the human or animal gut conditions, as well as its stability in the different GI tract compartments, were examined using gut simulators. The degradome of microcin J25 was examined in both dynamic (TIM1 dynamic simulator) and static models of digestion, using antibacterial assays, LC-MS/MS, and molecular networking analysis (
      • Naimi S.
      • Zirah S.
      • Hammami R.
      • Fernandez B.
      • Rebuffat S.
      • Fliss I.
      Fate and biological activity of the antimicrobial lasso peptide microcin J25 under gastrointestinal tract conditions.
      ). The stability and activity are quite good in the stomach acidic conditions, but the lassoed microcin partly degrades in the compartment mimicking the duodenum conditions, in particular upon the action of elastase, one of the main enzymes in this GI compartment, showing that protection of the microcin will be required for further applications. Our current work indicates that microcin J25 has a potent antagonistic activity against the pathogen Salmonella enterica subsp. enterica serovar Newport without strong perturbation of the microbiota composition in an in vitro model of colon.
      S. Rebuffat and I. Fliss, unpublished results.
      The efficacy of microcin J25 in the GI tract was also evaluated in vivo as a strategy to control the negative effects of postweaning stress in pig husbandry (
      • Yu H.T.
      • Ding X.L.
      • Li N.
      • Zhang X.Y.
      • Zeng X.F.
      • Wang S.
      • Liu H.B.
      • Wang Y.M.
      • Jia H.M.
      • Qiao S.Y.
      Dietary supplemented antimicrobial peptide microcin J25 improves the growth performance, apparent total tract digestibility, fecal microbiota, and intestinal barrier function of weaned pigs.
      ). Microcin J25 used as a feed additive was shown to reduce inflammation, attenuate diarrhea, and improve growth performance for weaned pigs, which are particularly susceptible to pathogen infections. Otherwise, the EcN strain was engineered to express and secrete microcin J25 (strain E. coli Nissle(J25)) (
      • Forkus B.
      • Ritter S.
      • Vlysidis M.
      • Geldart K.
      • Kaznessis Y.N.
      Antimicrobial probiotics reduce Salmonella enterica in turkey gastrointestinal tracts.
      ). When administered to turkeys challenged with pathogenic Salmonella, the engineered probiotic E. coli Nissle(J25) significantly reduced the S. enterica Enteritidis counts in turkey caeca compared with nonengineered EcN, indicating that the lassoed microcin is responsible for this competitive effect. Therefore, rigorous scientific bases obtained thanks to the numerous studies on the structure, mechanisms of antibacterial properties, and activity in gut (both in in vitro models and in vivo) of microcin J25 testify to the role of the lasso peptide as a competition molecule in the gut microbial community (Fig. 3A). These data also support the possibility of translation of the ecological properties of an RiPP to society via potential applications to the animal feed industry.

      Functional amyloids as reservoirs of toxic compounds and modulators of antibacterial activity

      Siderophore microcins develop another strategy to exert their dominance in microbial communities by using their ability to form or not form functional amyloids (depending on the environmental conditions), which serve as reservoirs of toxic compounds. Amyloid aggregates have been studied initially as associated with misfolded proteins involved in cytotoxicity and pathologies, including prion diseases, diabetes type II, or Alzheimer's and Parkinson's diseases (
      • Eisenberg D.S.
      • Sawaya M.R.
      Structural studies of amyloid proteins at the molecular level.
      ,
      • Chiti F.
      • Dobson C.M.
      Protein misfolding, amyloid formation, and human disease: a summary of progress over the last decade.
      ). However, in the last 2 decades, it has been shown that amyloids have critical functions in all domains of life and that their production can be beneficial for the organism (
      • Pham C.L.
      • Kwan A.H.
      • Sunde M.
      Functional amyloid: widespread in Nature, diverse in purpose.
      ). Particularly in the bacterial world, the amyloid state represents a functional structure, which can ensure important functions in bacterial fitness and social behavior (
      • Cámara-Almirón J.
      • Caro-Astorga J.
      • de Vicente A.
      • Romero D.
      Beyond the expected: the structural and functional diversity of bacterial amyloids.
      ,
      • Shanmugam N.
      • Baker M.O.D.G.
      • Ball S.R.
      • Steain M.
      • Pham C.L.L.
      • Sunde M.
      Microbial functional amyloids serve diverse purposes for structure, adhesion and defence.
      ). Functional amyloids take part in virulence, cytotoxicity, adhesion to surfaces, biofilm formation as well as protein/peptide reservoirs, and their role continues to expand.
      Posttranslational modification was shown to play a particular role in both the formation and function of amyloids, which ensures a subtle role in microbial competition. Indeed, microcin E492 (MccE492) has the capacity to form amyloid fibrils in vitro and in vivo in the extracellular space, and this property was correlated with a loss of antibacterial activity of the peptide (
      • Bieler S.
      • Estrada L.
      • Lagos R.
      • Baeza M.
      • Castilla J.
      • Soto C.
      Amyloid formation modulates the biological activity of a bacterial protein.
      ,
      • Marcoleta A.
      • Marín M.
      • Mercado G.
      • Valpuesta J.M.
      • Monasterio O.
      • Lagos R.
      Microcin E492 amyloid formation is retarded by posttranslational modification.
      ). Similar to the extracellular toxin inactivation process, intracellular amyloid accumulation does not have a toxic effect (
      • Aguilera P.
      • Marcoleta A.
      • Lobos-Ruiz P.
      • Arranz R.
      • Valpuesta J.M.
      • Monasterio O.
      • Lagos R.
      Identification of key amino acid residues modulating intracellular and in vitro microcin E492 amyloid formation.
      ). Indeed, amyloid fiber nucleation by the MccE492m modified form of the microcin appears less efficient than by the unmodified peptide, although both forms can be incorporated into preformed fibers (
      • Marcoleta A.
      • Marín M.
      • Mercado G.
      • Valpuesta J.M.
      • Monasterio O.
      • Lagos R.
      Microcin E492 amyloid formation is retarded by posttranslational modification.
      ). It was shown that in vitro amyloid formation by MccE492 is a dynamic and reversible process and that amyloids could represent a reservoir of toxic molecules (
      • Shahnawaz M.
      • Soto C.
      Microcin amyloid fibrils A are reservoir of toxic oligomeric species.
      ,
      • Shahnawaz M.
      • Park K.W.
      • Mukherjee A.
      • Diaz-Espinoza R.
      • Soto C.
      Prion-like characteristics of the bacterial protein Microcin E492.
      ). Although such a process has not been shown in vivo, it can be envisaged that the toxic or antibacterial compounds would be stocked when the concentration reaches a high level and released when required upon modification of the environmental conditions (Fig. 3A). Furthermore, bacteria generally use dedicated immunity proteins or ABC transporters encoded in the bacteriocin gene cluster to inactivate or expel the toxin they produce and make them resistant. Thus, amyloidogenesis would be a strategy used by bacteria to modulate the release of potent weapons against niche-occupying competitors and simultaneously contribute to self-immunity.

      Interference competition driven by RPNPs in Gram-positive bacteria

      Enterococci are Gram-positive bacteria belonging to the commensal gut microbiota, but they are also opportunistic pathogens that can be responsible for significant diseases in immune-compromised people. An E. faecalis strain, OG1RF, harboring the sex pheromone–responsive conjugative plasmid pPD1 (
      • Tomita H.
      • Fujimoto S.
      • Tanimoto K.
      • Ike Y.
      Cloning and genetic organization of the bacteriocin 31 determinant encoded on the Enterococcus faecalis pheromone-responsive conjugative plasmid pYI17.
      ) has been shown to replace indigenous enterococci and outcompete E. faecalis strains lacking the pPD1 plasmid in a model of colonization of the mouse gut with E. faecalis (
      • Kommineni S.
      • Bretl D.J.
      • Lam V.
      • Chakraborty R.
      • Hayward M.
      • Simpson P.
      • Cao Y.
      • Bousounis P.
      • Kristich C.J.
      • Salzman N.H.
      Bacteriocin production augments niche competition by enterococci in the mammalian gastrointestinal tract.
      ,
      • Kommineni S.
      • Kristich C.J.
      • Salzman N.H.
      Harnessing bacteriocin biology as targeted therapy in the GI tract.
      ). This model allowed the establishment of long-term colonization of the gut by a marked strain without the need for antibiotics by delivering the strain in drinking water, therefore modeling commensal colonization. The plasmid pPD1 encodes bacteriocin 21 (Bac-21), which is actually identical (
      • Tomita H.
      • Fujimoto S.
      • Tanimoto K.
      • Ike Y.
      Cloning and genetic organization of the bacteriocin 31 determinant encoded on the Enterococcus faecalis pheromone-responsive conjugative plasmid pYI17.
      ) to the well-characterized 70-amino acid circular bacteriocin AS-48. In this mammalian GI tract model, Bac-21 was shown to provide colonization advantage in the highly competitive environment of the gut to outcompete indigenous enterococci and drive the competition between closely related bacterial species. Moreover, pPD1 is actively transferred to other E. faecalis strains by conjugation in the GI tract, showing that this strategy can be used to enhance the number of Bac-21 producers in the niche and eliminate more efficiently and rapidly the susceptible population. Thus, the circular bacteriocin Bac-21/enterocin AS-48 serves as a killing factor that facilitates competition between the E. faecalis producer and other enterococci that are not able to synthesize this RiPP (Fig. 3B). Therefore, the production of circular bacteriocin by commensal bacteria, such as E. faecalis, drives niche competition in the GI tract by the interference competition strategy boosted by a conjugation transfer strategy of the encoding plasmid to enhance the level of production of the killer molecule.
      Thuricin CD is a two-component sactibiotic produced by B. thuringiensis DPC 6431 isolated from a human fecal isolate (
      • Rea M.C.
      • Sit C.S.
      • Clayton E.
      • O'Connor P.M.
      • Whittal R.M.
      • Zheng J.
      • Vederas J.C.
      • Ross R.P.
      • Hill C.
      Thuricin CD, a posttranslationally modified bacteriocin with a narrow spectrum of activity against Clostridium difficile.
      ) (Table 1). The two distinct 30-amino acid sactipeptides, Trn-α and Trn-β, forming thuricin CD act synergistically (optimal 1:2 ratio) to kill the pathogens Clostridium difficile, the causative agent of hospital-acquired infections, and L. monocytogenes at nanomolar concentrations. But they have a moderate impact on most other genera, indicating a very restricted spectrum of activity. In an in vitro distal colon model, thuricin CD killed highly efficiently a wide range of clinical C. difficile isolates while having a low impact on other genera and in particular on gastrointestinal commensal strains, such as Lactobacillus casei and Bacillus lactis, known to contribute to microbiota health. Thuricin CD is thus significantly stable in the gut conditions, where it can selectively outcompete a pathogen by interference competition (Fig. 3B) without perturbing the commensal microbiota.
      Recently, ruminococcin C purified from caecal contents of rats associated with the human symbiont R. gnavus E1 has been shown to kill pathogenic Clostridia and Gram-positive multidrug-resistant bacteria without showing toxicity to eukaryotic cells (
      • Chiumento S.
      • Roblin C.
      • Kieffer-Jaquinod S.
      • Tachon S.
      • Leprètre C.
      • Basset C.
      • Aditiyarini D.
      • Olleik H.
      • Nicoletti C.
      • Bornet O.
      • Iranzo O.
      • Maresca M.
      • Hardré R.
      • Fons M.
      • Giardina T.
      • et al.
      Ruminococcin C, a promising antibiotic produced by a human gut symbiont.
      ). It was proposed to inhibit nucleic acid synthesis in a way similar to that of the commercial antibiotic metronidazole. Moreover, ruminococcin C maturation from the inactive precursor into its active form was shown to involve two successive steps. The first one occurs in the R. gnavus producer thanks to a specific zinc-metallopeptidase, whereas the second one is ensured by the human pancreatic trypsin (Fig. 3B). This is the first description in RiPPs of a two-step maturation process involving enzymes from both the symbiont and the host, which affords an example of the tight cooperation between host and associated bacteria for the production of a competition molecule identified as a RiPP.
      By contrast, the broad-spectrum two-peptide lantibiotic lacticin 3147 produced by the WT strain L. lactis DPC 3147, which requires the synergistic action of its two components LtnA1 and LtnA2 (Table), inhibits beneficial commensal Gram-positive bacteria as well as the pathogen C. difficile in an anaerobic fecal-based fermentation protocol (
      • Rea M.C.
      • Clayton E.
      • O'Connor P.M.
      • Shanahan F.
      • Kiely B.
      • Ross R.P.
      • Hill C.
      Antimicrobial activity of lacticin 3,147 against clinical Clostridium difficile strains.
      ). Moreover, it is not stable, both in vivo in pig and in vitro and ex vivo in conditions simulating the mammalian GI tract (
      • Gardiner G.E.
      • Rea M.C.
      • O'Riordan B.
      • O'Connor P.
      • Morgan S.M.
      • Lawlor P.G.
      • Lynch P.B.
      • Cronin M.
      • Ross R.P.
      • Hill C.
      Fate of the two-component lantibiotic lacticin 3147 in the gastrointestinal tract.
      ). Degradation of the two peptide components LtnA1 and LtnA2 and concomitant significant loss of antibacterial activity were shown to be mainly due to the α-chymotrypsin activity in in vitro experiments, with the LtnA1 peptide being more susceptible to digestion than LtnA2. This two-peptide lantibiotic, while having a good activity against C. difficile in vitro, thus appears to be a poor competitor in the intestinal context. This series of examples points to the necessity of examining the antibacterial properties of a given RiPP in its ecological context.
      If the gut microbiota is the most largely studied ecological niche in terms of bacterial competition or communication mediated by diverse natural compounds, the skin microbiota is also the site for such complex interactions. The ability of two lantibiotics produced by Staphylococcus hominis A9 to compete S. aureus, a pathogen closely related to the commensal producer, has been evidenced in the context of atopic dermatitis, where the commensal bacterial community is deficient (
      • Nakatsuji T.
      • Chen T.H.
      • Narala S.
      • Chun K.A.
      • Two A.M.
      • Yun T.
      • Shafiq F.
      • Kotol P.F.
      • Bouslimani A.
      • Melnik A.V.
      • Latif H.
      • Kim J.N.
      • Lockhart A.
      • Artis K.
      • David G.
      • et al.
      Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis.
      ). This led to the isolation and characterization of two lantibiotics termed Sh-lantibiotic-α and Sh-lantibiotic-β (Table 1) that were shown to participate in the host defense. Furthermore, they potentiate LL-37, a human AMP of the cathelicidin family, which protects the skin from infections by invasive bacteria (
      • Nizet V.
      • Ohtake T.
      • Lauth X.
      • Trowbridge J.
      • Rudisill J.
      • Dorschner R.A.
      • Pestonjamasp V.
      • Piraino J.
      • Huttner K.
      • Gallo R.L.
      Innate antimicrobial peptide protects the skin from invasive bacterial infection.
      ). Thus, it is shown that a synergy between a commensal bacterial RiPP and a host AMP leads to an improved protection of the host (Fig. 3B). Moreover, a second competition strategy was identified in S. hominis. A small peptide was isolated and identified as a branched-cyclic nonapeptide (Fig. 2) close to other Staphylococcus autoinducing peptides (AIPs) involved in the QS mechanism (
      • Williams M.R.
      • Costa S.K.
      • Zaramela L.S.
      • Khalil S.
      • Todd D.A.
      • Winter H.L.
      • Sanford J.A.
      • O'Neill A.M.
      • Liggins M.C.
      • Nakatsuji T.
      • Cech N.B.
      • Cheung A.L.
      • Zengler K.
      • Horswill A.R.
      • Gallo R.L.
      Quorum sensing between bacterial species on the skin protects against epidermal injury in atopic dermatitis.
      ) (also see “Functions in communication and QS”). It was shown to inhibit the S. aureus system regulating the secretion of a virulence factor (phenol-soluble modulin α (PSMα)) that promotes inflammation in mice hosts (Fig. 3B). Therefore, a complex array of interactions using RiPPs as communication and competition molecules is established between commensals and pathogens. It includes synergistic effects between RiPPs and AMPs and the production of an AIP by commensals (Fig. 3B). This highlights the importance of a complex and well-balanced chemical dialog in maintaining a healthy symbiosis system.
      Another example of competition in the skin microbiota is illustrated by the interaction between Propionibacterium acnes and Staphylococcus epidermidis. A group of P. acnes strains isolated from both healthy and acne-affected skin exhibited higher antibacterial activity toward S. epidermidis. Comparative genomics showed that they differ in other groups of P. acnes strains by harboring a genomic island encoding a thiopeptide BGC, which is likely to be responsible for the anti-S. epidermidis activity. This study highlights a likely role of mediating interspecies interactions in the microbiota played by thiopeptides (
      • Christensen G.J.
      • Scholz C.F.
      • Enghild J.
      • Rohde H.
      • Kilian M.
      • Thürmer A.
      • Brzuszkiewicz E.
      • Lomholt H.B.
      • Brüggemann H.
      Antagonism between Staphylococcus epidermidis Propionibacterium acnes and its genomic basis.
      ). In further support of this assumption, thiopeptide BGCs have been identified as the dominant RiPP clusters in genomes and metagenomes of the human microbiota (
      • Donia M.S.
      • Cimermancic P.
      • Schulze C.J.
      • Wieland Brown L.C.
      • Martin J.
      • Mitreva M.
      • Clardy J.
      • Linington R.G.
      • Fischbach M.A.
      A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics.
      ,
      • Aleti G.
      • Baker J.L.
      • Tang X.
      • Alvarez R.
      • Dinis M.
      • Tran N.C.
      • Melnik A.V.
      • Zhong C.
      • Ernst M.
      • Dorrestein P.C.
      • Edlund A.
      Identification of the bacterial biosynthetic gene clusters of the oral microbiome illuminates the unexplored social language of bacteria during health and disease.
      ). A thiopeptide lactocillin has been identified from a vaginal isolate of Lactobacillus gasseri (Fig. 2 and Table 1). It shows activity to Gram-positive pathogens, including S. aureus, E. faecalis, Gardnerella vaginalis, and Corynebacterium aurimucosum, implicating its role in protecting the vaginal microbiota against invading pathogens. Remarkably, it has no activities against vaginal commensal bacteria, which was hypothesized to be related to an evolved resistance by the related microbiota to a compound produced by their community (
      • Donia M.S.
      • Cimermancic P.
      • Schulze C.J.
      • Wieland Brown L.C.
      • Martin J.
      • Mitreva M.
      • Clardy J.
      • Linington R.G.
      • Fischbach M.A.
      A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics.
      ).
      Listeriolysin S is the first bacteriocin to be reported from the Gram-positive genus Listeria (
      • Cotter P.D.
      • Draper L.A.
      • Lawton E.M.
      • Daly K.M.
      • Groeger D.S.
      • Casey P.G.
      • Ross R.P.
      • Hill C.
      Listeriolysin S, a novel peptide haemolysin associated with a subset of lineage I Listeria monocytogenes.
      ) (Table 1). It belongs to the TOMM family of RiPPs that contain thiazole and oxazole rings as posttranslational modifications. Contrary to most microcins and bacteriocins that act as competitors due to their antimicrobial properties, listeriolysin S is a virulence factor produced by epidemic strains of the food-borne pathogen Listeria, L. monocytogenes F2365, responsible for listeriosis outbreaks. Indeed, with the cytotoxin streptolysin S from S. pyogenes, listeriolysin S belongs to a class of TOMM virulence peptides from pathogens (
      • Molloy E.M.
      • Cotter P.D.
      • Hill C.
      • Mitchell D.A.
      • Ross R.P.
      Streptolysin S-like virulence factors: the continuing sagA.
      ). Listeriolysin S has been shown to manipulate the host microbiota, targeting selectively direct competitors, L. lactis, S. aureus, and L. monocytogenes, lacking the listeriolysin S operon (which confers self-immunity), to provide a more favorable niche for the pathogenic Listeria strains in a mouse oral infection model (
      • Quereda J.J.
      • Meza-Torres J.
      • Cossart P.
      • Pizarro-Cerdá J.
      Listeriolysin S: a bacteriocin from epidemic Listeria monocytogenes strains that targets the gut microbiota.
      ). Moreover, listeriolysin S does not contribute to injuries caused to host tissues by L. monocytogenes infection or to virulence in host organs, but it is specifically produced in the gastrointestinal tract and targets exclusively bacteria in the gut, leading to altered gut microbiota (
      • Quereda J.J.
      • Meza-Torres J.
      • Cossart P.
      • Pizarro-Cerdá J.
      Listeriolysin S: a bacteriocin from epidemic Listeria monocytogenes strains that targets the gut microbiota.
      ,
      • Quereda J.J.
      • Dussurget O.
      • Nahori M.A.
      • Ghozlane A.
      • Volant S.
      • Dillies M.A.
      • Regnault B.
      • Kennedy S.
      • Mondot S.
      • Villoing B.
      • Cossart P.
      • Pizarro-Cerda J.
      Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection.
      ). The listeriolysin S TOMM can thus act as a virulence factor that only and selectively targets bacterial cells in vivo without detrimental effects on the host cells (Fig. 3B). Importantly, the dehydratase/dehydrogenase LlsB, which is encoded in the TOMM operon and is putatively involved in establishment of the lysteriolysin S posttranslational modification, was shown to be required for the mice gut colonization, whereas lysteriolysin S itself is not. LlsB thus plays an additional role for virulence, which is hypothesized as participating in the posttranslational modification of another molecule. This shows here again the subtle and essential roles played by posttranslational modifications in the competition strategies of bacteria.

      Functions in communication and QS

      Microorganisms are now widely appreciated for their ability to communicate and coordinate social traits. To do so, they employ a QS strategy, which involves the production, diffusion, and perception of an extracellular signaling molecule that regulates subsequently gene expression at the community level (
      • Papenfort K.
      • Bassler B.L.
      Quorum sensing signal-response systems in Gram-negative bacteria.
      ). QS allows the microorganisms to alter behavior collectively in response to changes in the biotic or abiotic environment, thus granting them an adaptive advantage (
      • Mukherjee S.
      • Bassler B.L.
      Bacterial quorum sensing in complex and dynamically changing environments.
      ). Autoinduction of the production of signaling molecules is a hallmark of QS. In contrast to Gram-negative bacteria that use frequently small molecules, such as homoserine lactones, as autoinducers, Gram-positive bacteria employ commonly ribosomal peptide–mediated QS mechanisms (
      • Sturme M.H.J.
      • Kleerebezem M.
      • Nakayama J.
      • Akkermans A.D.L.
      • Vaughan E.E.
      • de Vos W.M.
      Cell to cell communication by autoinducing peptides in Gram-positive bacteria.
      ,
      • Thoendel M.
      • Horswill A.R.
      Biosynthesis of peptide signals in Gram-positive bacteria.
      ). For the focus of this review, we only include examples of QS-related peptides with post-translational modifications, although many of them are linear, resulting from the peptidase cleavage from a precursor. The involvement of RiPPs in QS can be categorized into three types. (i) the RiPP itself is a QS signaling molecule, termed peptide pheromone, and the process regulates other physiological aspects; (ii) the RiPP is an AIP, but it only controls its own production; and (iii) the RiPP biosynthesis is tightly regulated by QS that relies on other signals.

      RiPPs as QS signals

      The most prominent example is the AIPs, derived from the agrABCD system, which controls the production of virulence factors and biofilm formation in several pathogens, including S. aureus, L. monocytogenes, and Clostridium species (
      • Lyon G.J.
      • Novick R.P.
      Peptide signaling in Staphylococcus aureus and other Gram-positive bacteria.
      ,
      • Martin M.J.
      • Clare S.
      • Goulding D.
      • Faulds-Pain A.
      • Barquist L.
      • Browne H.P.
      • Pettit L.
      • Dougan G.
      • Lawley T.D.
      • Wren B.W.
      The agr locus regulates virulence and colonization genes in Clostridium difficile 027.
      ,
      • Yu Q.
      • Lepp D.
      • Mehdizadeh Gohari I.
      • Wu T.
      • Zhou H.
      • Yin X.
      • Yu H.
      • Prescott J.F.
      • Nie S.P.
      • Xie M.Y.
      • Gong J.
      The Agr-Like quorum sensing system is required for pathogenesis of necrotic enteritis caused by Clostridium perfringens in poultry.
      ,
      • Cooksley C.M.
      • Davis I.J.
      • Winzer K.
      • Chan W.C.
      • Peck M.W.
      • Minton N.P.
      Regulation of neurotoxin production and sporulation by a putative agrBD signaling system in proteolytic Clostridium botulinum.
      ,
      • Zetzmann M.
      • Sánchez-Kopper A.
      • Waidmann M.S.
      • Blombach B.
      • Riedel C.U.
      Identification of the agr peptide of Listeria monocytogenes.
      ) (Table 1). These are short peptides (7–12 amino acids) with a C-terminal five-member thiolactone ring (Fig. 2). Except for the conserved Cys required for thiolactone formation, amino acid composition in AIPs is highly variable, with a high frequency of hydrophobic residues (
      • Rémy B.
      • Mion S.
      • Plener L.
      • Elias M.
      • Chabrière E.
      • Daudé D.
      Interference in bacterial quorum sensing: a biopharmaceutical perspective.
      ,
      • Gless B.H.
      • Bojer M.S.
      • Peng P.
      • Baldry M.
      • Ingmer H.
      • Olsen C.A.
      Identification of autoinducing thiodepsipeptides from staphylococci enabled by native chemical ligation.
      ). AIP maturation and regulation have been extensively studied in S. aureus. AIP is made from the precursor AgrD by a membrane-bound endopeptidase AgrB. Matured in and released to the extracellular environment, AIP binds to the sensor histidine kinase AgrC. This induces signal transduction via phospho-relay to the response regulator, AgrA, which in turn activates the expression of the agrABCD operon and an effector RNA gene that elicits QS responses. AgrC and AgrA form a canonical two-component system (TCS), as frequently seen in peptide-related QS mechanisms. AIPs activate their cognate AgrC receptor and can modulate the activity of AgrC receptors from other related species (
      • Gless B.H.
      • Bojer M.S.
      • Peng P.
      • Baldry M.
      • Ingmer H.
      • Olsen C.A.
      Identification of autoinducing thiodepsipeptides from staphylococci enabled by native chemical ligation.
      ,
      • Canovas J.
      • Baldry M.
      • Bojer M.S.
      • Andersen P.S.
      • Gless B.H.
      • Grzeskowiak P.K.
      • Stegger M.
      • Damborg P.
      • Olsen C.A.
      • Ingmer H.
      Cross-talk between Staphylococcus aureus and other Staphylococcal species via the agr quorum sensing system.
      ). Thus, it can be envisioned that AIP-mediated interspecies cross-talks play a role in maintaining homeostasis of related microbiota in a complex environment. Indeed, as mentioned above, it has been evidenced that commensal, non-S. aureus staphylococcal strains in the human skin microbiota can block the agr QS system of S. aureus by secreting different AIPs, hence preventing its damage to the skin (
      • Williams M.R.
      • Costa S.K.
      • Zaramela L.S.
      • Khalil S.
      • Todd D.A.
      • Winter H.L.
      • Sanford J.A.
      • O'Neill A.M.
      • Liggins M.C.
      • Nakatsuji T.
      • Cech N.B.
      • Cheung A.L.
      • Zengler K.
      • Horswill A.R.
      • Gallo R.L.
      Quorum sensing between bacterial species on the skin protects against epidermal injury in atopic dermatitis.
      ,
      • Paharik A.E.
      • Parlet C.P.
      • Chung N.
      • Todd D.A.
      • Rodriguez E.I.
      • Van Dyke M.J.
      • Cech N.B.
      • Horswill A.R.
      Coagulase-negative Staphylococcal strain prevents Staphylococcus aureus colonization and skin infection by blocking quorum sensing.
      ). Such a phenomenon has implications for the development of therapeutic strategies using AIP variants (
      • Canovas J.
      • Baldry M.
      • Bojer M.S.
      • Andersen P.S.
      • Gless B.H.
      • Grzeskowiak P.K.
      • Stegger M.
      • Damborg P.
      • Olsen C.A.
      • Ingmer H.
      Cross-talk between Staphylococcus aureus and other Staphylococcal species via the agr quorum sensing system.
      ,
      • Gless B.H.
      • Peng P.
      • Pedersen K.D.
      • Gotfredsen C.H.
      • Ingmer H.
      • Olsen C.A.
      Structure–activity relationship study based on autoinducing peptide (AIP) from dog pathogen S. schleiferi.
      ,
      • Yang T.
      • Tal-Gan Y.
      • Paharik A.E.
      • Horswill A.R.
      • Blackwell H.E.
      Structure–function analyses of a Staphylococcus epidermidis autoinducing peptide reveals motifs critical for AgrC-type receptor modulation.
      ). Similarly, E. faecalis harbors a cyclic peptide-based fsrABCD QS system that regulates virulence. It differs from the agr system in the autoinducer, termed gelatinase biosynthesis-activating pheromone, that contains a 9-residue lactone ring at the C terminus.
      ComX pheromones derived from the comQXPA system of B. subtilis regulate genetic competence, surfactin production, and biofilm formation (Table 1). They are short peptides (4–13 amino acids) with a conserved, modified Trp residue that is formed upon isoprenylation and cyclization (
      • Esmaeilishirazifard E.
      • De Vizio D.
      • Moschos S.A.
      • Keshavarz T.
      Genomic and molecular characterization of a novel quorum sensing molecule in Bacillus licheniformis.
      ,
      • Okada M.
      • Sato I.
      • Cho S.J.
      • Iwata H.
      • Nishio T.
      • Dubnau D.
      • Sakagami Y.
      Structure of the Bacillus subtilis quorum-sensing peptide pheromone ComX.
      ) (Fig. 2). Regulation by ComX via a dedicated TCS (ComP/A) parallels that of the agr system. Great variation in terms of amino acid sequence and the nature of the isoprenyl modification on ComX has been observed among Bacillus strains, both contributing to their activation specificity of the TCS (
      • Ansaldi M.
      • Marolt D.
      • Stebe T.
      • Mandic-Mulec I.
      • Dubnau D.
      Specific activation of the Bacillus quorum-sensing systems by isoprenylated pheromone variants.
      ,
      • Okada M.
      • Sugita T.
      • Abe I.
      Posttranslational isoprenylation of tryptophan in bacteria.
      ,
      • Ansaldi M.
      • Dubnau D.
      Diversifying selection at the Bacillus quorum-sensing locus and determinants of modification specificity during synthesis of the ComX pheromone.
      ). Although some QS interferences were detected among Bacillus strains isolated from the same location, the lack of consistency in the interference pattern suggested that ComX diversification is driven by gain-of-function, such as genetic competence upon TCS activation, instead of competition advantages (
      • Ansaldi M.
      • Marolt D.
      • Stebe T.
      • Mandic-Mulec I.
      • Dubnau D.
      Specific activation of the Bacillus quorum-sensing systems by isoprenylated pheromone variants.
      ). This is in contrast with AIPs in staphylococcal species.

      RiPP autoinducer that only autoregulates its own biosynthesis

      This phenomenon is frequently observed for lantibiotic production, including nisin, subtilin, mersacidin (
      • Schmitz S.
      • Hoffmann A.
      • Szekat C.
      • Rudd B.
      • Bierbaum G.
      The lantibiotic mersacidin is an autoinducing peptide.
      ,
      • Kleerebezem M.
      Quorum sensing control of lantibiotic production; nisin and subtilin autoregulate their own biosynthesis.
      ), cytolysin (
      • Haas W.
      • Shepard B.D.
      • Gilmore M.S.
      Two-component regulator of Enterococcus faecalis cytolysin responds to quorum-sensing autoinduction.
      ), microbisporicin (
      • Foulston L.C.
      • Bibb M.J.
      Microbisporicin gene cluster reveals unusual features of lantibiotic biosynthesis in actinomycetes.
      ,
      • Fernández-Martínez L.T.
      • Gomez-Escribano J.P.
      • Bibb M.J.
      A relA-dependent regulatory cascade for auto-induction of microbisporicin production in Microbispora corallina.
      ), and planosporicin (
      • Sherwood E.J.
      • Bibb M.J.
      The antibiotic planosporicin coordinates its own production in the actinomycete Planomonospora alba.
      ), although the regulation mechanisms differ. In this case, a trigger signal is required to initiate the RiPP production. Autoinduction of cytolysin, a two-peptide lantibiotic and a virulence factor associated with hemolysis of E. faecalis, is remarkably triggered by the presence of eukaryotic cells (
      • Coburn P.S.
      • Pillar C.M.
      • Jett B.D.
      • Haas W.
      • Gilmore M.S.
      Enterococcus faecalis senses target cells and in response expresses cytolysin.
      ,
      • Van Tyne D.
      • Martin M.J.
      • Gilmore M.S.
      Structure, function, and biology of the Enterococcus faecalis cytolysin.
      ). As for microbisporicin and planosporicin produced by Actinobacteria, their initial autoinduction is induced by nutrient limitation. It is suggested that this would allow the coordination of antibiotic production across all mycelium cells to achieve an ecologically effective concentration (
      • Fernández-Martínez L.T.
      • Gomez-Escribano J.P.
      • Bibb M.J.
      A relA-dependent regulatory cascade for auto-induction of microbisporicin production in Microbispora corallina.
      ). However, the advantages of autoinduction of antibacterial peptides in niche competition remain to be firmly demonstrated.

      RiPPs regulated by QS

      QS-controlled production of RiPPs, in particular modified bacteriocins, has been observed and intensively studied in streptococci. Placing antibacterial synthesis under QS regulation would allow these bacteria to fine-adjust interaction with the host and other species according to environmental and cell population conditions. For example, the human pathogen Streptococcus pneumoniae produces a lantibiotic as a QS response triggered by the presence of galactose via an internalized pheromone-based QS system (
      • Hoover S.E.
      • Perez A.J.
      • Tsui H.C.
      • Sinha D.
      • Smiley D.L.
      • DiMarchi R.D.
      • Winkler M.E.
      • Lazazzera B.A.
      A new quorum-sensing system (TprA/PhrA) for Streptococcus pneumoniae D39 that regulates a lantibiotic biosynthesis gene cluster.
      ) (Table 1). As galactose is a major sugar of the human nasopharynx, lantibiotic production at high cell density thus would be a strategy to gain competition advantages for S. pneumoniae during colonization of this niche. Moreover, as seen in S. pneumoniae and Streptococcus mutans, bacteriocin production is tightly regulated by the QS system involved in the regulation of competence (
      • van der Ploeg J.R.
      Regulation of bacteriocin production in Streptococcus mutans by the quorum-sensing system required for development of genetic competence.
      ,
      • Wang C.Y.
      • Patel N.
      • Wholey W.Y.
      • Dawid S.
      ABC transporter content diversity in Streptococcus pneumoniae impacts competence regulation and bacteriocin production.
      ). This would provide new DNA materials from the lysis of competitors to be taken up by the pathogen and to stimulate biofilm formation, which has been demonstrated to confer an adaptive advantage in S. pneumoniae when grown on the mucosal surface (
      • Wholey W.Y.
      • Kochan T.J.
      • Storck D.N.
      • Dawid S.
      Coordinated bacteriocin expression and competence in Streptococcus pneumoniae contributes to genetic adaptation through neighbor predation.
      ). This phenomenon has also been shown to have a huge impact on the outcome of mixed-species biofilms, using dual-biofilm formed by S. mutans and Candida albicans as a model (
      • Sztajer H.
      • Szafranski S.P.
      • Tomasch J.
      • Reck M.
      • Nimtz M.
      • Rohde M.
      • Wagner-Döbler I.
      Cross-feeding and interkingdom communication in dual-species biofilms of Streptococcus mutans Candida albicans.
      ).
      As another example, Streptococcus thermophilus produces a short cyclic peptide, named streptide, having a C–C linkage between a Lys and a Trp residue (Fig. 2 and Table 1). The cyclization is introduced on the precursor peptide by a radical SAM enzyme. Streptide biosynthesis is under the control of a QS system involving a small hydrophobic peptide (SHP) as signaling molecule and a transcriptional regulator (i.e. SHP/Rgg system) (
      • Ibrahim M.
      • Guillot A.
      • Wessner F.
      • Algaron F.
      • Besset C.
      • Courtin P.
      • Gardan R.
      • Monnet V.
      Control of the transcription of a short gene encoding a cyclic peptide in Streptococcus thermophilus: a new quorum-sensing system?.
      ,
      • Schramma K.R.
      • Bushin L.B.
      • Seyedsayamdost M.R.
      Structure and biosynthesis of a macrocyclic peptide containing an unprecedented lysine-to-tryptophan crosslink.
      ,
      • Fleuchot B.
      • Guillot A.
      • Mézange C.
      • Besset C.
      • Chambellon E.
      • Monnet V.
      • Gardan R.
      Rgg-associated SHP signaling peptides mediate cross-talk in streptococci.
      ). Genome-mining efforts identified a large panel of streptide-like biosynthetic systems in streptococci, all likely within the context of QS control (
      • Bushin L.B.
      • Clark K.A.
      • Pelczer I.
      • Seyedsayamdost M.R.
      Charting an unexplored streptococcal biosynthetic landscape reveals a unique peptide cyclization motif.
      ). Biochemical characterization of these radical SAM enzymes led to the discovery of novel cyclization motifs such as β-thioether and α-ether linkages (
      • Caruso A.
      • Bushin L.B.
      • Clark K.A.
      • Martinie R.J.
      • Seyedsayamdost M.R.
      Radical approach to enzymatic β-thioether bond formation.
      ,
      • Clark K.A.
      • Bushin L.B.
      • Seyedsayamdost M.R.
      Aliphatic ether bond formation expands the scope of radical SAM enzymes in natural product biosynthesis.
      ). Such unprecedented chemical diversity would reflect functional divergence. However, the roles of streptide-like molecules remain elusive.

      Host-bacteria interaction

      Few studies exist in probing the roles of microbial RiPPs in host-bacteria interaction. Recently, it was discovered that the plant pathogen Xanthomonas oryzae pv. oryzae utilizes a tyrosine-sulfonated small peptide (RaxX) as a mimic of plant peptide hormones to activate the immune receptor XA21 in rice, triggering immune responses (Table 1). RaxX thus functions as an immunogen and has a role in the virulence (
      • Luu D.D.
      • Joe A.
      • Chen Y.
      • Parys K.
      • Bahar O.
      • Pruitt R.
      • Chan L.J.G.
      • Petzold C.J.
      • Long K.
      • Adamchak C.
      • Stewart V.
      • Belkhadir Y.
      • Ronald P.C.
      Biosynthesis and secretion of the microbial sulfated peptide RaxX and binding to the rice XA21 immune receptor.
      ). Although RaxX resembles phosphorylated peptides that are commonly involved in the regulation of various biological processes, the mode of biosynthesis of RaxX that requires pathway-encoded modification enzymes and a precursor peptide parallels the canonical RiPP pathways. RaxX apparently belongs to a large family of bacterial and plant RiPPs with a sulfated tyrosine, suggesting that such plant-bacteria interaction is prevalent in nature. Interestingly, sulfonation can potentially occur on other RiPPs, such as lasso peptides, as their BGCs from proteobacteria frequently encode sulfotransferases (
      • Hegemann J.D.
      • Zimmermann M.
      • Zhu S.
      • Klug D.
      • Marahiel M.A.
      Lasso peptides from proteobacteria: genome mining employing heterologous expression and mass spectrometry.
      ). Sulfonated molecules are rather unusual in prokaryotes; however, known examples are frequently involved in the communication between eukaryotic hosts and bacterial symbionts or pathogens. Those include the factor Nod from the nitrogen-fixing rhizobium Sinorhizobium meliloti (
      • Gibson K.E.
      • Kobayashi H.
      • Walker G.C.
      Molecular determinants of a symbiotic chronic infection.
      ) and sulfolipid-1 from Mycobacterium tuberculosis (
      • Gilmore S.A.
      • Schelle M.W.
      • Holsclaw C.M.
      • Leigh C.D.
      • Jain M.
      • Cox J.S.
      • Leary J.A.
      • Bertozzi C.R.
      Sulfolipid-1 biosynthesis restricts Mycobacterium tuberculosis growth in human macrophages.
      ). It thus remains a promising direction to study sulfonated RiPPs in host-bacteria interaction. In addition, there are several remarkable RiPPs isolated from animal symbionts, such as polytheonamides produced by a sponge symbiont (
      • Freeman M.F.
      • Gurgui C.
      • Helf M.J.
      • Morinaka B.I.
      • Uria A.R.
      • Oldham N.J.
      • Sahl H.-G.
      • Matsunaga S.
      • Piel J.
      Metagenome mining reveals polytheonamides as posttranslationally modified ribosomal peptides.
      ,
      • Wilson M.C.
      • Mori T.
      • Rückert C.
      • Uria A.R.
      • Helf M.J.
      • Takada K.
      • Gernert C.
      • Steffens U.A.E.
      • Heycke N.
      • Schmitt S.
      • Rinke C.
      • Helfrich E.J.N.
      • Brachmann A.O.
      • Gurgui C.
      • Wakimoto T.
      • et al.
      An environmental bacterial taxon with a large and distinct metabolic repertoire.
      ) and cyanobactins by the Prochloron cyanobacteria symbionts of tunicates (
      • Lin Z.
      • Torres J.P.
      • Tianero M.D.
      • Kwan J.C.
      • Schmidt E.W.
      Origin of chemical diversity in prochloron-tunicate symbiosis.
      ). It would be very interesting to decipher whether these peptides play a role in the symbiosis.

      Effects on microbial physiology

      Biofilm formation and morphological development

      Being unicellular organisms, many bacteria have evolved to adopt multicellular lifestyles, manifested by, for example, the formation of biofilms, fruiting bodies, or morphological differentiation (
      • Claessen D.
      • Rozen D.E.
      • Kuipers O.P.
      • Søgaard-Andersen L.
      • van Wezel G.P.
      Bacterial solutions to multicellularity: a tale of biofilms, filaments and fruiting bodies.
      ). It is now largely appreciated that some natural antibiotics function as signaling molecules at subinhibitory concentrations in these processes, playing a role in modulating the physiology of the producing bacteria or the interacting ones (
      • Romero D.
      • Traxler M.F.
      • López D.
      • Kolter R.
      Antibiotics as signal molecules.
      ,
      • López D.
      • Fischbach M.A.
      • Chu F.
      • Losick R.
      • Kolter R.
      Structurally diverse natural products that cause potassium leakage trigger multicellularity in Bacillus subtilis.
      ). Consistent with this view, a thiopeptide produced by Bacillus cereus, thiocillin, was identified to stimulate biofilm formation in B. subtilis using a coculture approach (Table 1). Other Bacillus strains with thiopeptide BGCs in the genome produced the same effect (
      • Bleich R.
      • Watrous J.D.
      • Dorrestein P.C.
      • Bowers A.A.
      • Shank E.A.
      Thiopeptide antibiotics stimulate biofilm formation in Bacillus subtilis.
      ,
      • Townsley L.
      • Shank E.A.
      Natural-product antibiotics: cues for modulating bacterial biofilm formation.
      ). Similarly, another thiopeptide, thiostrepton, was found to stimulate the biofilm formation in Pseudomonas aeruginosa at a concentration that does not inhibit the pathogen's growth (
      • Ranieri M.R.M.
      • Chan D.C.K.
      • Yaeger L.N.
      • Rudolph M.
      • Karabelas-Pittman S.
      • Abdo H.
      • Chee J.
      • Harvey H.
      • Nguyen U.
      • Burrows L.L.
      Thiostrepton hijacks pyoverdine receptors to inhibit growth of Pseudomonas aeruginosa.
      ) (Table 1). Although the molecular mechanisms underlying the biofilm induction effect remain unknown, these studies highlight a role of thiopeptides in modulating bacterial physiology. Given the dominant prevalence of thiopeptide BGCs in metagenomes of the human microbiota, future studies should focus on the function of these molecules in microbial competition and interaction (
      • Donia M.S.
      • Cimermancic P.
      • Schulze C.J.
      • Wieland Brown L.C.
      • Martin J.
      • Mitreva M.
      • Clardy J.
      • Linington R.G.
      • Fischbach M.A.
      A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics.
      ,
      • Aleti G.
      • Baker J.L.
      • Tang X.
      • Alvarez R.
      • Dinis M.
      • Tran N.C.
      • Melnik A.V.
      • Zhong C.
      • Ernst M.
      • Dorrestein P.C.
      • Edlund A.
      Identification of the bacterial biosynthetic gene clusters of the oral microbiome illuminates the unexplored social language of bacteria during health and disease.
      ).
      The Streptomyces genus is extensively studied for its extraordinary specialized metabolism. This is intimately linked to its complex life cycle encompassing vegetative mycelia, aerial hyphae, and spores. Some RiPPs are identified to mediate the morphological development in Streptomyces. The lanthipeptides SapB and SapT from S. coelicolor and Streptomyces tendae, respectively, are required for the emergence of aerial hyphae from vegetative cells (
      • Kodani S.
      • Hudson M.E.
      • Durrant M.C.
      • Buttner M.J.
      • Nodwell J.R.
      • Willey J.M.
      The SapB morphogen is a lantibiotic-like peptide derived from the product of the developmental gene ramS in Streptomyces coelicolor.
      ,
      • Kodani S.
      • Lodato M.A.
      • Durrant M.C.
      • Picart F.
      • Willey J.M.
      SapT, a lanthionine-containing peptide involved in aerial hyphae formation in the streptomycetes.
      ) (Table 1). They function as surfactants by reducing the surface tension for aerial growth (
      • Willey J.M.
      • Willems A.
      • Kodani S.
      • Nodwell J.R.
      Morphogenetic surfactants and their role in the formation of aerial hyphae in Streptomyces coelicolor.
      ). This developmental stage can be interfered with by the surfactants produced by other bacteria, adding a new strategy of interspecies interaction. It has been shown that the lipopeptide surfactin produced by B. subtilis inhibits Streptomyces aerial development, whereas it is required for its own aerial structure formation toward spore genesis (
      • Straight P.D.
      • Willey J.M.
      • Kolter R.
      Interactions between Streptomyces coelicolor Bacillus subtilis: role of surfactants in raising aerial structures.
      ,
      • Gaskell A.A.
      • Giovinazzo J.A.
      • Fonte V.
      • Willey J.M.
      Multi-tier regulation of the streptomycete morphogenetic peptide SapB.
      ). Furthermore, the TOMM peptide goadsporin produced by Streptomyces sp. induces spore formation and/or pigment production in other Streptomyces species (
      • Onaka H.
      • Tabata H.
      • Igarashi Y.
      • Sato Y.
      • Furumai T.
      Goadsporin, a chemical substance which promotes secondary metabolism and morphogenesis in streptomycetes. I. Purification and characterization.
      ) (Table 1). Hence, goadsporin has been used as an elicitor at subinhibitory concentration for triggering specialized metabolite production in Streptomyces. Similarly, thiostrepton produced by Streptomyces laurentii was identified to stimulate pellet formation accompanied by a decrease in pigment synthesis in S. coelicolor (
      • Wang H.
      • Zhao G.
      • Ding X.
      Morphology engineering of Streptomyces coelicolor M145 by sub-inhibitory concentrations of antibiotics.
      ).

      Cannibalism

      Microbial antimicrobial peptides are commonly considered as part of the chemical weapons for the microorganisms to eliminate competitors from other species. On the other side, they can be used against a distinct subpopulation of the same species, in analogy to cannibalism, for the benefit of the whole community. In filamentous fungi, this function is hypothesized to be fulfilled by Cys-rich antifungal peptides (
      • Meyer V.
      • Jung S.
      Antifungal peptides of the AFP family revisited: are these cannibal toxins?.
      ). In B. subtilis, under nutrient limitation conditions, cells produce a disulfide-containing sactipeptide, termed sporulation killing factor (SKF) (
      • Liu W.T.
      • Yang Y.L.
      • Xu Y.
      • Lamsa A.
      • Haste N.M.
      • Yang J.Y.
      • Ng J.
      • Gonzalez D.
      • Ellermeier C.D.
      • Straight P.D.
      • Pevzner P.A.
      • Pogliano J.
      • Nizet V.
      • Pogliano K.
      • Dorrestein P.C.
      Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis.
      ) (Fig. 2 and Table 1), and a sporulation-delaying protein to lyse nonsporulation sibling cells (
      • Allenby N.E.
      • Watts C.A.
      • Homuth G.
      • Prágai Z.
      • Wipat A.
      • Ward A.C.
      • Harwood C.R.
      Phosphate starvation induces the sporulation killing factor of Bacillus subtilis.
      ). This allows the release of nutrients to sustain the growth of sporulating cells, hence delaying the time- and energy-consuming process of sporulation. The ecological significance of such cannibalism in B. subtilis would be to avoid the growth disadvantage when the nutrients become available again. It is more difficult to resume growth from spores compared with vegetative cells (
      • González-Pastor J.E.
      Cannibalism: a social behavior in sporulating Bacillus subtilis.
      ). Moreover, the cannibalism has been shown to stimulate biofilm formation via the increased extracellular matrix production in B. subtilis, and both processes were triggered by the NRPS-derived lipopeptide surfactin (
      • López D.
      • Vlamakis H.
      • Losick R.
      • Kolter R.
      Cannibalism enhances biofilm development in Bacillus subtilis.
      ). Interestingly