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* This work was supported in part by Howard Hughes Medical Institute Grant 55000309 and Ludwig Institute for Cancer Research Grant CRDF RBO-1268. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. The on-line version of this article (available at http://www.jbc.org) contains an additional table.
Using comparative analysis of genes, operons, and regulatory elements, we describe the cobalamin (vitamin B12) biosynthetic pathway in available prokaryotic genomes. Here we found a highly conserved RNA secondary structure, the regulatory B12 element, which is widely distributed in the upstream regions of cobalamin biosynthetic/transport genes in eubacteria. In addition, the binding signal (CBL-box) for a hypothetical B12 regulator was identified in some archaea. A search for B12 elements and CBL-boxes and positional analysis identified a large number of new candidate B12-regulated genes in various prokaryotes. Among newly assigned functions associated with the cobalamin biosynthesis, there are several new types of cobalt transporters, ChlI and ChlD subunits of the CobN-dependent cobaltochelatase complex, cobalt reductase BluB, adenosyltransferase PduO, several new proteins linked to the lower ligand assembly pathway, l-threonine kinase PduX, and a large number of other hypothetical proteins. Most missing genes detected within the cobalamin biosynthetic pathways of various bacteria were identified as nonorthologous substitutes. The variable parts of the cobalamin metabolism appear to be the cobalt transport and insertion, the CobG/CbiG- and CobF/CbiD-catalyzed reactions, and the lower ligand synthesis pathway. The most interesting result of analysis of B12 elements is that B12-independent isozymes of the methionine synthase and ribonucleotide reductase are regulated by B12 elements in bacteria that have both B12-dependent and B12-independent isozymes. Moreover, B12 regulons of various bacteria are thought to include enzymes from known B12-dependent or alternative pathways.
along with chlorophyll, heme, siroheme, and coenzyme F430, constitute a class of the most structurally complex cofactors synthesized by bacteria. The distinctive feature of these cofactors is their tetrapyrrole-derived framework with a centrally chelated metal ion (cobalt, magnesium, iron, or nickel). Methylcobalamin and Ado-CBL, two derivatives of vitamin B12 (cyanocobalamin) with different upper axial ligands, are essential cofactors for several important enzymes that catalyze a variety of transmethylation and rearrangement reactions. Among the most prominent vitamin B12-dependent enzymes in bacteria and archaea are the methionine synthase isozyme MetH from enteric bacteria; the ribonucleotide reductase isozyme NrdJ from deeply rooted eubacteria and archaea; diol dehydratases and ethanolamine ammonia lyase from enteric bacteria involved in anaerobic glycerol, 1,2-propanediol, and ethanolamine fermentation; glutamate and methylmalonyl-CoA mutases from clostridia and streptomycetes; and various CBL-dependent methyltransferases from methane-producing archaea (
Most prokaryotic organisms as well as animals (including humans) and protists have enzymes that require CBL as cofactor, whereas plants and fungi are thought not to use it. Among the CBL-utilizing organisms, only some bacterial and archaeal species are able to synthesize CBL de novo (
). To our knowledge, there are two distinct routes of the CBL biosynthesis in bacteria (Fig. 1): the well studied oxygen-dependent (aerobic) pathway studied in Pseudomonas denitrificans and the oxygen-independent (anaerobic) pathway that was partially resolved in Salmonella typhimurium, Bacillus megaterium and Propionibacterium shermanii (
) and can be divided into two major parts. The first part, the corrin ring synthesis, is different in the anaerobic and aerobic pathways; the former starts with the insertion of cobalt into precorrin-2, whereas in the latter, this chelation reaction occurs only after the corrin ring synthesis. The second part of the Ado-CBL pathway is common for both anaerobic and aerobic routes and involves adenosylation of CR, attachment of the aminopropanol arm, and assembly of the nucleotide loop that bridges the lower ligand dimethylbenzimidazole and CR (
). The corresponding CBL genes from S. typhimurium and P. denitrificans have different traditional names, mainly using prefixes cbi and cob, respectively (Fig. 1). For example, S. typhimurium has two separate genes, cbiE and cbiT, that encode precorrin methyltransferase and decarboxylase, respectively, whereas in P. denitrificans these functions are encoded by one gene, cobL. For consistency, we use the S. typhimurium names whenever possible. In particular, we assign gene names to experimentally uncharacterized genes using analysis of orthology.
The anaerobic and aerobic pathways contain several pathway-specific enzymes. First, the cobalt insertion is performed by the ATP-dependent aerobic cobalt chelatase of P. denitrificans, which consists of CobN, CobS, and CobT subunits, and two distinct, ATP-independent, single subunit cobalt chelatases, CbiK from S. typhimurium and CbiX from B. megaterium, which are associated with the anaerobic pathway (
). Second, since the majority of the intermediates of the anaerobic, but not aerobic, pathway have the cobalt ion inserted into the macrocycle, the pathways could use enzymes with different substrate specificities. CobG from P. denitrificans requires molecular oxygen to oxidize precorrin 3A and is specific for the aerobic pathway (
). The respective CR oxidation of anaerobic route is probably mediated via the complexed cobalt ion, which can assume different valence states. In summary, CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans.
In most bacteria, cobalt and other heavy metal ions are mainly accumulated by the fast and unspecific CorA transport system (
). An additional cobalt transporter, a part of the cobalt-dependent nitrile hydratase gene cluster, was identified in Rhodococcus rhodochrous and, together with some nickel-specific transporters, belongs to the HoxN family of chemiosmotic transporters (
). Vitamin B12, cobinamide, and other corrinoids are actively transported in enteric bacteria using the TonB-dependent outer membrane receptor BtuB in the complex with the ABC transport system BtuFCD (
). The evolutionarily conserved B12-box, a cis-acting translational enhancer element, contains a stem-loop structure that would mask the ribosome binding site as well as several additional RNA structural elements. This element is found in the 5′-untranslated regions of the CBL operons and is absolutely required for their regulation, which is conferred mainly at the translational level (
). Recently, it was shown that the btuB mRNA leader sequence can directly bind an effector molecule, Ado-CBL, and consequently undergo conformational changes in the secondary and tertiary structure of the RNA and that the likely mechanism of regulation involves formation of two alternative RNA structures (
Combination of the comparative analysis of gene regulation, positional clustering of genes, and phylogenetic profiling, when applied to a metabolic pathway in a variety of bacterial species, is a powerful approach to the search of missing genes within the pathway as well as identification of specific metabolite transport genes (
). Here we use this combined comparative approach for the analysis of the CBL biosynthetic pathway in prokaryotes. The expression of genes involved in the CBL biosynthesis and vitamin B12 transport in eubacteria was predicted to be regulated mainly by a conserved RNA regulatory element, the B12 element. In four archaeal genomes, a new DNA-type regulatory signal was observed upstream of the CBL-related genes. After reconstruction of the B12 regulon and the CBL pathway in most bacterial and archaeal genomes, we identified several new enzymes and transporters related to the CBL biosynthesis. In particular, numerous new cobalt transporters and chelatases, as well as new CR methyltransferases, were found. Furthermore, the vitamin B12 transporters are widely distributed in bacteria and archaea and mostly B12-regulated. Finally, the B12 element was predicted to regulate B12-independent methionine synthase and ribonucleotide reductase isozymes in bacteria that also have corresponding B12-dependent isozymes.
Complete and partial sequences of bacterial genomes were downloaded from GenBank™ (
). Gene identifiers from the ERGO data base and GenBank™ are used throughout. The amino acid sequences of uncharacterized genes predicted here to be involved in the CBL metabolism have been collected in one FASTA file that is available upon request.
Procedings of the Third International Conference on “Complex Systems: Control and Modeling Problems,” Samara, Russia, September 4–9, 2001. The Institute of Control of Complex Systems,
Samara, Russia2001: 623-625
) was used to search for conserved RNA regulatory elements. The input RNA pattern included both the RNA secondary structure and the sequence consensus motifs. The RNA secondary structure was described as a set of the following parameters: the number of helices, the length of each helix, the loop lengths, and description of the topology of helix pairs. The initial RNA pattern of the B12 element was constructed using a training set of upstream regions of the btuB orthologs from proteobacteria. Each genome was scanned with the B12 element pattern, resulting in detection of approximately 200 B12 elements.
A protein similarity search was done using the Smith-Waterman algorithm implemented in the GenomeExplorer program (
) and, if necessary, confirmed by construction of phylogenetic trees. Note that the fact of gene absence used in phylogenetic profiling is reliable only for complete genomes. The phylogenetic trees were created by the maximum likelihood method implemented in PHYLIP (
Conserved Structure of the B12 Element—Previously, we have described two highly conserved RNA elements, RFN and THI, involved in the regulation of the riboflavin and thiamin biosynthetic genes in bacteria (
). Vitamin B12-dependent regulation of the btuB and cbiA genes in enterobacteria requires their upstream regions and occurs via a post-transcriptional mechanism involving formation of alternative RNA structures. Several recent studies describe possible secondary structures of the E. coli btuB and S. typhimurium cbiA 5′-untranslated leader sequences, but the proposed structures have a limited number of conserved elements (
). Similarly to the RFN and THI elements, the B12 element has a set of unique stem-loops closed by a single base stem and highly conserved sequence regions, including the previously known B12-box (Fig. 2). In addition to seven conserved stem-loops, the B12 element has three additional facultative stem-loops and one internal variable structure. Since direct binding of Ado-CBL to the btuB mRNA leader was recently shown (
), it is interesting that all internal loops of the B12 element are highly conserved on the sequence level and, therefore, may be involved in Ado-CBL binding. By analogy to the model of regulation for riboflavin and thiamin regulons (
B12 Regulon: Identification of Genes and Regulatory Elements—Initially, orthologs of the cobalamin biosynthetic and transport genes (“CBL genes” below) in all available prokaryotic genomes were identified by similarity search (Table I). For further analysis, positional clusters (including possible operons) of the CBL genes are also described in Table I. The multifunctional gene cysG of E. coli, which encodes URO′III methyltransferase (CysGA) and precorrin-2 oxidase/ferrochelatase (CysGB) activities and is partially shared by the CBL and siroheme biosynthesis, was considered only if it was co-localized with other CBL genes.
Table ICobalamin biosynthesis and transport genes and B12-elements in bacteria
Then we scanned nearly 100 genomic sequences using the RNA-PATTERN program and the pattern of a novel, B12-specific RNA element (
) and found approximately 200 B12 elements unevenly distributed in 66 eubacterial genomes (Table I). All genomes with B12 elements, except Bacillus cereus, contain CBL biosynthesis and/or transport genes. Most obligate pathogenic bacteria (see below) as well as Aquifex aeolicus have neither CBL genes nor B12 elements. Staphylococcus aureus, Corynebacterium glutamicum, Bordetella pertussis, Magnetococcus, and all archaeal genomes lack B12 elements but have CBL genes. The detailed phylogenetic and positional analysis of the CBL genes and the B12 elements is given below.
In attempt to analyze potential cobalamin regulons in archaea, a large phylogenetic group without B12 elements, we collected upstream regions of all CBL genes and applied the signal detection procedure to each archaeal genome (
). The same strongest signal, a 15-bp palindrome with consensus 5′-TGGATAantTATCCA-3′, was observed in candidate cobalamin regulons in three Pyrococcus genomes (Table I). To find new members of the regulon, the derived profile (named CBL-box) was used to scan the genomes. The cobalamin regulon in the pyrococci appears to include all CBL biosynthesis and transport genes except btuR. In addition, conserved CBL-boxes were identified upstream of the P. horikoshii genes PH0021, PH1306, PH0275, PH1928, and PH0272 and their orthologs in two other pyrococci. These genes are predicted to encode anaerobic ribonucleotide reductase NrdDG, two subunits of methylmalonyl-CoA mutase MutB, succinyl-CoA synthase SucS, and methylmalonyl-CoA epimerase MmcE, respectively. All of these genes are unrelated to the CBL biosynthesis or transport, but their co-regulation with the CBL genes seems to be rational because of their direct or indirect association with B12-dependent enzymes (see below). The same CBL-specific profiles were obtained for two other archaea, Aeropyrum pernix and Sulfolobus solfataricus, but not for the remaining archaeal species. The predicted CBL regulon of A. pernix again contains the B12 transport system and methylmalonyl-CoA mutase. Among all archaea in this study, only pyrococci and A. pernix are likely to be unable to synthesize CBL de novo but may uptake and transform CBL precursors to Ado-CBL. The CBL regulon of S. solfataricus includes, in addition to the cobT and btuFCD genes, the cbiGECHDTLF genes for the de novo CBL synthesis and predicted cobalt transporter hoxN.
To select bacterial species that potentially require coenzyme B12 for their metabolism, we carried out a similarity search for all known B12-dependent enzymes in prokaryotic genomes. As a result, Chlamydia spp., Rickettsiae spp., Neisseria spp., Streptococcaceae, Mycoplasmataceae, Pasteurellaceae, ϵ-proteobacteria, Borellia burgdorferi, Treponema pallidum, and Xylella fastidiosa (obligate pathogenic bacteria) as well as A. aeolicus were found to have no B12-dependent enzymes (Supplementary Table VI). This finding is in agreement with the absence of the CBL biosynthetic and transport genes as well as with the absence of B12 elements in these microorganisms. However, two other bacteria without any known B12-dependent enzyme, Bacillus subtilis and S. aureus, were predicted to have the B12 transport system BtuFCD. Interestingly, btuFCD-pduO is the only B12 element-regulated operon in B. subtilis. This shows that other, currently unknown, B12-dependent enzymes may be present in these bacteria.
Vitamin B12 Transporters—Nearly one-fourth of the B12-utilizing bacteria appear to have no complete pathway for the CBL biosynthesis and, therefore, should actively transport vitamin B12 or some precursor from the external medium. The only known transport system for vitamin B12 is the ABC transporter BtuFCD of enteric bacteria, which consists of periplasmic substrate-binding protein BtuF, two transmembrane subunits BtuC, and two peripheral ATP-binding subunits BtuD. In Gram-negative bacteria, the translocation of vitamin B12 across the outer membrane involves B12-specific receptor BtuB and the periplasmic energy-coupling proteins TonB, ExbB, and ExbD, which are shared between various TonB-dependent receptors. Thus, the B12-specific components of the transporters are BtuBFCD and BtuFCD in Gram-negative and Gram-positive bacteria, respectively. The corresponding components of ABC transporters involved in the uptake of ferric siderophores, heme, and vitamin B12 are similar and belong to the same families (
). Therefore, a similarity search is not sufficient to dissect the B12 and ferric transporters in species distant from enteric bacteria.
We combined a similarity search with identification of highly specific regulatory B12 elements and with positional analysis of genes. The phylogenetic trees for the protein families formed by various components of the B12 and ferric transporters revealed B12-specific subfamilies within each family (data not shown). The predicted transporters for vitamin B12 were found to be widely distributed in prokaryotes; among B12-utilizing bacteria with complete genomes, they were not found only in four cyanobacterial and three archaeal species, in Mycobacterium spp., and in Bacillus cereus (Supplementary Table VI). In most cases, components of B12 transporters are encoded by clusters of co-localized genes that are regulated by the B12 element (Table I). Interestingly, the regulatory B12 element was found upstream of the exbBD-tonB operon from Rhodobacter capsulatus encoding common components of the TonB-dependent receptors for ferric siderophores and vitamin B12.
Various variants of incomplete B12 transport systems were revealed in some bacteria. The btuFCD genes were absent in Nitrosomonas europaea and Xanthomonas axonopodis, and the btuCD genes were absent in B. pertussis, Methylobacillus flagellatus, Azotobacter vinelandii, Listeria monocytogenes, and Leptospira interrogans. The btuB gene of N. europaea, M. flagellatus, A. vinelandii, and X. axonopodis is located within the btuB-btuM-btuR cluster, which is a single fused gene in the latter bacterium. The hypothetical protein BtuM is not similar to any known protein and has five predicted transmembrane segments, indicating that, in these bacteria, BtuM may be a new type of transmembrane component of the B12 transporter, substituting the BtuC and BtuD proteins. The btuB-btuN cluster, one more example of the conserved positional linkage between BtuB and another hypothetical transmembrane protein (BtuN has four predicted TMSs), was found in BtuCD-deficient B. pertussis, M. flagellatus, and X. axonopodis. Similarly to BtuM, BtuN may be involved in the BtuCD-independent transport of vitamin B12. The BtuFC system of S. aureus is another example of an incomplete transporter that does not include a specific ATPase, suggesting that it can share the ATPase component with some other ABC transport system.
Cobalt Transporters—The cbiMNQO locus encoding an ATP-dependent transport system for cobalt was identified in the CBL-producing microorganisms from different taxonomic groups including enterobacteria, ϵ- and δ-proteobacteria, the Bacillus/Clostridium group, cyanobacteria, actinobacteria, chloroflexi, and archaea (Table II). In most cases, the cbiMNQO genes were found either within large CBL operons or as separate operons and were preceded by regulatory B12 elements. However, among 56 CBL-producing bacteria in this study, only 24 possess this high affinity cobalt transport system. This indicates the existence of other cobalt-specific transporters required for the CBL biosynthesis. Analysis of possible operon structures and regulatory B12 elements allowed us to identify new candidate cobalt transporters (Table II).
Table IIDifferences in the predicted cobalt transporters required for cobalamin synthesis in prokaryotes
We assign cobalt specificity to seven uncharacterized transporters from the HoxN family in various proteobacteria and archaea. Notably, most characterized members of this family are specific for nickel ions, but only one HoxN-type transporter was known as a cobalt transporter associated with Co2+-depedent nitrile hydratase (
). Genes for the predicted HoxN-type transporters of cobalt are B12-regulated and co-localized with CBL-biosynthetic genes in eubacteria. Predicted co-regulation of the hoxN gene with CBL genes in S. solfataricus argues for the cobalt specificity of archaeal HoxN transporters as well (Table I and see above).
Two other B12-regulated genes, cbtA and cbtC, detected in various α-proteobacteria and pseudomonades (one per genome), possibly encode cobalt transporters with five predicted TMSs. These genes are not similar to any known protein and have only B12-regulated homologs, the majority of which are positionally linked to CBL genes. In addition, cbtA is always co-localized (or fused in P. aeruginosa) with a short gene, cbtB, which encodes one TMS followed by a histidine-rich motif probably involved in metal binding. In result, α-proteobacteria are predicted to possess at least four different types of cobalt transporters (CbiMNQO, HoxN, CbtAB, and CbtC).
In three cyanobacterial species that do not have the CbiMNQO transporter, the only member of the B12 regulon is the hypothetical transmembrane protein HupE with a histidine-rich metal-binding motif at its N terminus (TrEMBL accession number P73671). Other proteins from the HupE family are required for activities of Ni2+-dependent hydrogenases and ureases and thought to be involved in nickel transport (
). Analysis of B12 elements allows us to assign cobalt specificity to HupE-type transporters in cyanobacteria.
A candidate cobalt transporter of Porphyromonas gingivalis and Bacteroides fragilis, encoded by the B12-regulated gene cbtD, contains 10 predicted TMSs and a ligand-binding TrkA-like domain between TMS V and VI. In mycobacteria, the B12-regulated gene cbtG encodes a predicted cobalt transporter with seven TMSs. In two other actinobacteria, Thermobifida fusca and Rhodococcus str., we identified one more candidate cobalt transporter, encoded by the B12-regulated gene cbtE, which has six possible TMSs and a histidine-rich loop between transmembrane segments I and II.
A new member of the B12 regulon in Treponema denticola, CbtF, has a predicted signal peptide cleavage site on its N terminus. In Brucella melitensis, cbtF lies in one locus with Ni2+-dependent urease immediately upstream of the cbiMQO genes and is thought to be involved in the nickel transport. In addition, Rhodobacter capsulatus and F. nucleatum have a single cbtF gene, which is B12-regulated in the former genome. In view of the existence of mixed cobalt/nickel families of transporters (see above), CbtF, in conjunction with systems homologous to CbiMQO, could be involved in cobalt transport.
Cobalt Chelatases—Insertion of cobalt ions into CR at early and late stages of the CBL biosynthesis is mediated by different cobalt chelatases, termed here as “early” and “late.” There are at least two distinct early chelatases, CbiK and CbiX, and one late chelatase composed of CobN, CobS, and CobT subunits. In contrast to the CobN component of the late chelatase, which is widely distributed in bacteria, the CobS and CobT components were found only in α-proteobacteria and Burkholderia pseudomallei, where the cobST cluster is always separated from other CBL genes and never has an upstream B12 element. Thus, the CobST components of cobalt chelatase are missing in actinobacteria and pseudomonades. Nevertheless, genes similar to the Mg-chelatase subunits, namely chlID, were found in clusters with various CBL genes, most often with cobN. Notably, similar to CobNST, ATP-dependent Mg-chelatase involved in the bacteriochlorophyll biosynthesis consists of three subunits, ChlH, ChlI, and ChlD, and ChlH is a close homolog of CobN (
). The hypothesis that ChlI and ChlD are the missing components of the late cobalt chelatase was proved by phylogenetic analysis. Indeed, proteins associated with the chlorophyll and CBL biosynthesis form separate branches on the phylogenetic trees for both CobN/ChlH and ChlI families (data not shown). Based on these facts, we suggest that, in contrast to α-proteobacteria, the late cobaltochelatase complex of actinobacteria, pseudomonads, and β-proteobacteria consists of the CobN, ChlI, and ChlD subunits (Table III).
Table IIIDifferences in the cobalamin biosynthetic pathways of prokaryotes
CBL gene clusters of proteobacteria possessing late cobalt chelatase contain the hypothetical gene cobW. This gene is always located immediately upstream of the cobN chelatase component (Table I). Interestingly, the N-terminal part of CobW has a P-loop nucleotide-binding motif and is similar to the urease/hydrogenase accessory proteins UreG and HypB, which are involved in the GTP-dependent incorporation of Ni2+ into the metallocenters of target enzymes. In addition, the variable loop between the conserved N- and C-terminal domains of CobW contains a histidine-rich motif possibly involved in metal binding. Finally, cobW is co-localized with predicted cobalt transporters in some genomes. We suggest that CobW is required for the cobalt chelation during CBL biosynthesis and it is possible that the histidine-rich region of CobW is used to store the cobalt ions within of the cell prior to their delivery to the chelatase complex.
Another predicted member of the B12 regulon, the cfrX gene, was found within the conserved gene cluster cfrX-cobW-cobN in all CBL-producing α-proteobacteria except Sinorhizobium meliloti and B. melitensis. CfrX is weakly similar to various ferredoxin proteins including the CBL-related ferredoxin CbiW of B. megaterium (
) and could act as an oxidoreductant during cobalt insertion.
Cobalt Reductases—Reduction of the cobalt ion of corrinoids is the least studied stage the CBL biosynthesis. It is a prerequisite for further corrinoid adenosylation. Although the NADH-dependent flavoprotein with cobalt reductase activity was purified in P. denitrificans, the gene encoding this activity has not been identified (
). Using a similarity search, the fldA gene was found in enterobacteria, Pasteurellaceae, ϵ-proteobacteria, and cyanobacteria as well as in the Bacillus/Clostridium and CFB groups of bacteria. Since FldA was found in some CBL pathway-deficient bacteria, its function is unlikely to be restricted to the B12 synthesis. It is consistent with experimental facts that the FldA protein, shared by several metabolic pathways, is an essential enzyme in E. coli (
). Nevertheless, FldA was not found in bacteria with the aerobic CBL biosynthetic pathway.
In this work, a candidate cobalt reductase associated with the CBL biosynthesis was identified in most bacteria with the aerobic CBL pathway (α-proteobacteria, burkholderia, pseudomonads, and actinobacteria), as well as in several other species (Table I). The corresponding gene, bluB, was previously described in R. capsulatus as a gene of unknown function essential for the CBL synthesis (
). We found that bluB orthologs are predominantly regulated by B12 elements and often co-localized with various CBL genes. The BluB proteins are similar to various FMN-dependent reductases from the nitroreductase family, including oxygen-insensitive NADH nitroreductase and NADH-flavin oxidoreductase, that catalyze the electron transfer from NADH to various electron acceptors. The bluB and fldA genes never co-occur in CBL-producing proteobacteria. The majority of these bacteria have only bluB, whereas it is not present in the fldA-containing group of enterobacteria. Thus, we propose that BluB functions in cobalt reduction for the CBL biosynthesis. Moreover, bluB was also found in three proteobacteria with incomplete CBL pathways, M. flagellatus, A. vinelandii, and Ralstonia eutropha. The CBL pathways in these bacteria include all genes for the conversion of cobyrinic acid to Ado-CBL and are possibly involved in the assimilation of exogenous corrinoids. We believe that predicted cobalt reductase BluB, which presumably acts on cob(II)yrinic acid a,c-diamide, is necessary for these incomplete pathways as well.
ATP:Corrinoid Adenosyltransferases—The active form of coenzyme B12, Ado-CBL, can be obtained either by de novo synthesis or by assimilation of exogenous corrinoids. Both routes require ATP:corrinoid adenosyltransferase encoded by the btuR gene. BtuR adenosylates either CBL or an intermediate prior to CBL. The search for btuR in bacterial genomes showed that this widely distributed gene is usually co-localized with other CBL genes and sometimes is B12-regulated (Table I). However, among nearly 80 B12-utilizing species, BtuR was not found in 18 genomes. It is known that, besides BtuR, enterobacteria possess two other CBL adenosyltransferases, PduO and EutT, which are associated with the CBL-dependent 1,3-propanediol dehydratase and ethanolamine ammonia lyase encoded by the pdu and eut gene clusters, respectively (
). Strikingly, the BtuR, PduO, and EutT adenosyltransferases show no sequence similarity. Homologs of the eutT gene were found only within eut gene clusters, strongly suggesting that its only function is in the ethanolamine utilization. In contrast, pduO appears to be widely distributed in prokaryotes and, in particular, in most BtuR-deficient bacteria, where it would fill the gaps in the CBL pathways (Supplementary Table VI). The pduO genes may reside within the pdu and CBL gene clusters or be single genes. Notably, the phylogenetic tree of the PduO family contains distinct branches corresponding to the CBL- and PDU-associated genes and to the single genes (data not shown).
In summary, adenosyltransferases were found in all B12-utilizing prokaryotes except two clostridia and three methanogenic archaea. However, the latter have only one B12-dependent enzyme, a methyl-CBL-dependent methyltransferase, and thus do not require the adenosylated form of CBL. Interestingly, pduO from Archaeoglobus fulgidus and btuR from Geobacter metallireducens appear in one putative operon with B12-dependent methylmalonyl-CoA mutase. Overall, it seems that particular types of adenosyltransferases are specialized for particular B12-dependent enzymes or for the de novo CBL biosynthesis.
Nucleotide Loop Assembly Pathway—The pathways for the lower ligand synthesis of CBL (also known as the nucleotide loop assembly) are thought to vary between bacterial groups (
). Some bacterial genomes have neither cobT nor cobC genes required for the synthesis of α-ribazole from dimethylbenzimidazole or have only one of these genes. In contrast, two other genes of the nucleotide loop assembly pathway, cobU and cobS, are conserved in all CBL-synthesizing bacteria with the exception of cobU in archaea (see below).
Three Gram-positive bacteria, L. monocytogenes, Clostridium botulinum, and Thermoanaerobacter tengcongensis, lack the cobT gene but have all other genes for nucleotide loop assembly, including cobC. Instead, the CBL gene clusters of these bacteria contain two hypothetical genes, named cblT and cblS, which are not similar to any known protein. However, these two genes were found in several other Gram-positive bacteria simultaneously with cobT. The cblTS operon of Clostridium perfringes and single cblS genes of D. halfniense and Heliobacillus mobilis are preceded by regulatory B12 elements. In addition, the B12-regulated CBL operon of B. stearothermophilus contains the cblTS genes. The hypothetical protein CblT has five predicted transmembrane segments. These facts allow us to propose a possible role of new CblT and CblS proteins in uptake of dimethylbenzimidazole and its subsequent transformation into α-ribazole-5P, respectively.
A case of nonorthologous displacement of the CBL genes was previously found in archaea, where the bacterial-type nucleotidyltransferase CobU is replaced by a new nucleotidyltransferase named CobY (
). Here we extend this analysis using 13 instead of 6 complete archaeal genomes. All of these genomes appear to lack the cobU gene and possess the cobY gene, thus confirming the nonorthologous displacement. The only exception is Pyrobaculum aerophilum, which lacks both nucleotidyltransferases. In 9 of 12 archaeal species, cobY is positionally linked to other CBL genes.
Here we identified one more case of nonorthologous gene displacement of CBL genes in archaea. The cobC gene encoding α-ribazole-5P phosphatase was found in only two archaea, S. solfataricus and Thermoplasma. In all other archaea, except A. fulgidus and Halobacterium sp., the hypothetical gene cobZ (PF0294 in P. furiousus) was found within the CBL gene clusters, being most often linked with cobS. CobZ is weakly similar to bacterial phosphatidylglycerophosphatases but not to CobC. Thus, we predict that CobZ is the missing α-ribazole-5P phosphatase replacing CobC. In Halobacterium sp., the CBL locus contains the hypothetical gene HSL01294, another predicted nonorthologous displacement of CobC, which is weakly similar to the phosphoglycolate phosphatases from proteobacteria but has no orthologs in other archaea.
Among CBL-synthesizing α-proteobacteria, only four rhizobacteria, Mesorhizobium loti, S. meliloti, B. melitensis, and A. tumefaciens, lack the cobC gene. Instead, we have found a pair of genes, named cblXY, which is clustered with the cobT and cobS genes. Similarly, all CBL-synthesizing actinobacteria lack the cobC gene but have a new hypothetical gene, named cblZ, which is mainly clustered with cobT, cobS, and cobU genes. The hypothetical proteins CblX, CblY, and CblZ are not similar to any known protein; nevertheless, the CblX, containing a zinc ribbon motif, comprises a small metal-binding protein of about 60 amino acids. Thus, we propose that cblXY and cblZ are nonorthologous replacements of the cobC gene in rhizobacteria and actinobacteria, respectively.
Other New Members of the B12 Regulon Related to the CBL Biosynthesis—The 1,2-propanediol utilization operon pdu of S. typhimurium includes the pduX gene of unknown function (
). Here we found that some Gram-positive bacteria, namely three clostridia, L. monocytogenes, D. halfniense, and H. mobilis, contain the pduX genes located within the CBL gene clusters, usually adjacent to the cobD gene (Table I). Most of these clusters are predicted to be B12-regulated. In addition, the single pduX gene preceded by a B12 element was found in S. coelicolor. Finally, Y. enterocolitica has two copies of pduX, and one of them is co-localized with the cobD gene. The PduX protein belongs to the GHMP kinase family and is weakly similar to galactokinase, l-homoserine kinase, and mevalonate kinase. Since the CBL biosynthesis requires l-threonine-3P as a substrate for the CobD aminotransferase, and the positional analysis shoes that PduX is probably CBL-related, we propose the l-threonine kinase function to PduX.
The phylogenetic tree of CobN-related proteins has three main branches (data not shown). The first two branches comprise the B12-regulated cobalt chelatases CobN involved in the CBL synthesis and the magnesium chelatases ChlH required for the bacteriochlorophyll biosynthesis. The third branch, named here BtuS, includes hypothetical proteins of unknown function from diverse bacterial and archaeal genomes. In all cases, the btuS genes are clustered with a new gene, named btuT, which encodes a hypothetical transporter with four predicted TMSs. In addition, the btuST clusters of P. aeruginosa, R. palustris, and N. europaea are co-localized with hypothetical outer membrane receptor genes encoding proteins homologous to the vitamin B12 receptor BtuB. Moreover, in P. gingivalis and B. fragilis, the btuST genes form a candidate operon with the iron-induced hemoglobin transport genes hmuYR (
). In archaea, the btuST genes are linked to the btuW gene encoding a hypothetical transporter with seven predicted TMSs. These observations allow us to propose that the hypothetical transporter BtuT, chelatase BtuS, and homologs of the BtuB/HmuR receptors (or BtuW in archaea) are involved in the transport and salvage of various metalloporphyrines rather than in the CBL biosynthesis.
The first gene of the B. megaterium cbi operon, cbiW, encodes a hypothetical ferredoxin and could be involved in the CBL biosynthesis, possibly acting as oxidoreductant during the ring contraction process under anaerobic conditions (
). Homologs of cbiW are widely distributed in prokaryotes, but only some of them are clustered with CBL genes and regulated by B12 elements. The cbiW genes are co-localized with cobalt transporters and CBL biosynthetic genes in Ralstonia solanacearum and B. stearothermophilus and with B12 transport systems in Chloroflexus aurantiacus and Anabaena sp. In L. interrogans and Halobacterium sp., CbiW and the cobalt chelatase CbiX are encoded by a single fused gene. Thus, the B12-related ferredoxins CbiW occur only in bacteria with anaerobic CBL pathways (see below).
M. tuberculosis, in contrast to most actinobacteria, lacks the cobF gene, but the CBL cluster of this bacterium contains another gene, named metZ, which is not similar to cobF but is similar to various methyltransferases. We predict that metZ is the possible nonorthologous gene displacement of cobF.
The CBL gene cluster of R. solanacearum, a bacterium without an ortholog of the bifunctional methyltransferase/decarboxylase Cbi(ET), contains a distant homolog of the CbiE methyltransferases from archaea. This exemplifies a possible xenologous gene displacement, whereby CbiE is displaced by a horizontally transferred homolog from another lineage. However, the CbiT-associated activity is still missing in this bacterium.
Differences in Prokaryotic Cobalamin Biosynthetic Pathways—Identification of known CBL genes and new B12-regulated genes allows us to reconstruct and compare the CBL pathways in various organisms. In addition to cobalt transporters and chelatases (see above), the enzymatic step of ring contraction during the CR biosynthesis is highly variable in bacteria (Table III). This reaction is mediated by the CobG or CbiG proteins and determines the aerobic or anaerobic type of the CBL pathway, respectively, since CobG, in contrast to CbiG, is an oxygen-dependent enzyme (
). Although B. melitensis, B. pseudomallei, Anbaena sp., and Pseudomonas species have both CobG and fused CbiG-CbiH proteins, the CbiG domains in these bacteria contain a large deletion and, therefore, may be nonfunctional. In contrast to other α-proteobacteria, R. capsulatus and R. palustris, lacking the CobG mono-oxygenase, have another enzyme, ORF663, involved in the ring contraction during CBL biosynthesis (
Analyzing genomes of 56 CBL-producing bacteria, we detected a correlation between the time of cobalt insertion and the oxygen dependence of the CBL pathway. The CobG monooxygenases were found only in bacteria with the ATP-dependent CobN-CobST/ChlDI cobaltochelatase complexes corresponding to the late cobalt insertion. With the exception of several archaeal genomes, where we could not detect cobaltochelatase genes, the CbiG proteins co-occur with ATP-independent CbiK/CbiX chelatases corresponding to the early cobalt insertion. In addition, C. aurantiacus and T. volcanicum are predicted to have early cobalt chelatases of another type, which are similar to the ferrochelatase CysGB. The remaining question is the function of the additional cobN-chlID chelatases in the genomes of R. solanacearum, S. coelicolor, C. aurantiacus, C. tepidum, T. denticola, and Halobacterium sp., where they co-occur with cobalt chelatases cbiK/cbiX and cbiG and are co-localized with CBL genes (Table III).
In contrast to CobG, the exact biochemical role of CbiG in the CBL biosynthesis is unknown (
). Identification of a pair of genes from one genome that appear to be fused into a single gene within another genome represents strong evidence that the functions implemented by these genes may be closely related (
). In an attempt to identify the CbiG-catalyzed reaction in the CBL pathway, we summarized all CbiG-related protein fusion events. The CbiG-CbiH fusion proteins appear in Pseudomonas species, B. melitensis, B. pseudomallei, S. coelicolor, and cyanobacteria, whereas the CbiG-CbiF fusions were found in the CFB group of bacteria. Thus, we place CbiG between CbiH and CbiF on the pathway of CBL biosynthesis (Fig. 1).
B12-regulated Genes Not Involved in the CBL Biosynthesis and Transport—Analysis of the regulatory B12 elements in bacterial genomes allowed us to detect B12-regulated genes that are not involved in the CBL biosynthesis. An unexpected result was that most of these genes appear to belong to B12-dependent metabolic pathways (Table IV).
Table IVPredicted B12-element-mediated regulation of bacterial genes, which are not involved in the CBL biosynthesis and transport
First, in some α-proteobacteria, actinobacteria, and Bacillus species, as well as in B. fragilis and T. elongatus, B12 elements were found upstream of the metE gene encoding the B12-independent methionine synthase. On the other hand, genes encoding the NrdDG and NrdAB ribonucleotide reductases are preceded by B12 elements in three α-proteobacteria, two Bacillus species, the CFB and Thermus/Deinococcus groups, M. flagellatus, S. coelicolor, C. difficile, and D. halfniense. To our knowledge, there are only two B12-dependent enzymes, methionine synthase MetH and ribonucleotide reductase isozyme NrdJ, that are known to have B12-independent isozymes, MetE and NrdAB/NrdDG, respectively (
). To put these scattered observations into a more general context, we scanned bacterial genomes for the presence of both B12-dependent and -independent isozymes and found that the B12-independent isozymes are regulated by B12 elements in most bacteria that have both isozymes. Although arhaeal genomes lack regulatory B12 elements, in three Pyrococcus genomes with both NrdJ (B12-dependent) and NrdDG (B12-independent) isozymes, the nrdDG genes are predicted to be co-regulated with CBL biosynthetic genes via conserved CBL-boxes (see above). Thus, we propose that when vitamin B12 is present in the cell, expression of B12-independent isozymes is inhibited, and only relatively more efficient B12-dependent isozymes are used.
The rocG gene, encoding a catabolic glutamate dehydrogenase, has an upstream B12 element in T. denticola. Further, this bacterium has an ortholog of the B12-dependent glutamate mutase MutSL, which is known to catalyze the first step of the B12-dependent pathway of glutamate catabolism (
). Moreover, MutSL is the only B12-dependent enzyme found in T. denticola. These findings allow us to propose that, first, T. denticola has two alternative pathways of glutamate utilization, and second, an excess of vitamin B12, repressing expression the rocG gene, would inhibit the B12-independent glutamate pathway in this bacterium.
The predicted B12 regulon in Pyrococcus species includes the mutB, sucS, and mmcE genes, which are thought to be involved in the B12-dependent succinate-propionate fermentation pathway. In B. fragilis, a B12 element precedes the pccCAB operon encoding propionyl-CoA carboxylase, an enzyme from the same B12-dependent pathway. In P. gingivalis, a hypothetical B12 element-regulated operon, named butD-butA-4hbD-sucD, encodes enzymes of the B12-independent pathway of succinate fermentation, namely 4-hydroxybutanoyl-CoA dehydratase, 4-hydroxybutyrate coenzyme A transferase, NAD-dependent 4-hydroxybutyrate dehydrogenase, and succinate-semialdehyde dehydrogenase.
As demonstrated above, several genes for B12-dependent and alternative pathways are often members of the vitamin B12 regulons both in eubacteria and archaea. This raises the possibility of identifying previously unknown B12-dependent enzymes based on analysis of regulatory B12 elements. In this vein, we identified a new member of the B12 regulon in B. halodurans, hypothetical acyl-CoA hydrolase AchX, which belongs to the thioesterase superfamily. This family includes 4-hydroxybenzoyl-CoA thioesterase, which catalyzes the final step in the catabolism of 4-hydroxybenzoate in Pseudomonas CBS-3 (
), and various cytosolic long-chain acyl-CoA thioester hydrolases. The achX gene was found in one B12-regulated operon with B12-independent ribonucleotide reductase nrdBA in Deinococcus radiodurans. The candidate achX-metR operon of A. tumefaciens is also preceded by a B12 element. Another new member of the B12 regulon, named the ardX-frdX operon, was found in three α-proteobacteria, S. meliloti, M. loti, and R. capsulatus. The hypothetical ArdX and FrdX proteins are highly similar to the alpha and ferredoxin-like subunits of various bacterial ring-hydroxylating dioxygenases. However, ArdX-FrdX and AchX orthologs from several other bacteria have no upstream B12 elements. The only possible explanation of observed B12 element-dependent regulation of the hypothetical achX and ardX-frdX genes is that they could encode B12-independent analogs of yet unidentified B12-dependent enzymes.
The biosynthesis of coenzyme B12 (Ado-CBL) is a metabolic pathway widely distributed in bacteria and archaea, but it is not found in eukaryotes. In addition, many prokaryotes have active transport systems for vitamin B12 and related compounds. Identification of the B12-specific regulatory elements allows us to identify new genes related to the CBL biosynthesis. As a result, we reconstructed and compared the CBL biosynthesis pathways in various organisms. The most variable parts of the CBL pathway are the CobG/CbiG-mediated reaction of the corrin ring synthesis and cobalt chelation that could occur at either early or late stage of the pathway. The CobG and CbiG proteins determine the aerobic or anaerobic types of the CBL pathway. The type of a cobalt chelatase corresponds to the time of cobalt insertion and seems to be correlated with oxygen dependence of the CBL pathway (Table III). Furthermore, we observed two major corrinoid adenosyltransferases and nine different cobalt transport systems in various prokaryotes (Table II).
Identification of all known B12-dependent enzymes in prokaryotic genomes allowed us to select bacterial species requiring coenzyme B12 for their metabolism. Not surprisingly, all of these genomes are capable of either de novo synthesis or transport of this vitamin or both. The only exception is the complete genome of B. cereus, which has neither CBL biosynthetic nor known transport genes but has B12-dependent methionine synthase metH. On the other hand, there are bacteria (e.g. B. subtilis and S. aureus) that possess a vitamin B12 transporter but lack any known B12-dependent enzyme. This indicates that previously unknown B12-dependent enzymes may exist in these bacteria.
The metabolic reconstruction techniques reveal a large number of missing genes in the CBL biosynthetic pathways of various bacteria. Simultaneous analysis of gene clusters on the chromosome, protein fusion events, phylogenetic profiles, and regulatory B12 elements allowed us to make functional assignment for several new genes related to the CBL biosynthesis (Table V). About half of them encode various transporters, whereas the remaining ones are enzymes involved in the CBL synthesis. In particular, we tentatively identified eight additional cobalt transporters, two vitamin B12 transporters, one 5,6-dimethylbenzimidazole transporter, and two possible transporters for various metalloporphyrines. Among new enzymes, we ascribed cobalt reductase function to BluB, cobalt chelatase function to ChlDI, and l-threonine kinase function to PduX as well as the involvement of the CobW, CfrX, and CbiW proteins in oxidation-reduction processes during the corrin ring synthesis. In addition, most functions corresponding to missing genes in several genomes were assigned to nonorthologous genes. Most remarkably, we identified the nonorthologous gene displacements for the cobC gene in archaea, α-proteobacteria, and actinobacteria. However, among complete genomes, still missing functions in the CBL pathway are CbiA in C. perfringes, CobD in Shewanella oneidensis and L. interrogans, CobU and CbiP in P. aerophilum, CobC in C. tepidum, and CbiJ in L. interrogans and in almost all archaeal genomes.
Using the global analysis of the B12 elements in available bacterial genomes, we have found that this conserved RNA regulatory element is widely distributed in eubacteria and regulates most CBL genes. The B12 elements do not occur in archaea, but we identified candidate B12-regulatory operator sites in several archaeal genomes. Among all bacterial genes related to the CBL biosynthesis, only cobalt transporter genes, both known and predicted, are always B12-regulated. The only exceptions are the cbiMNQO operon in two cyanobacteria, Anabaena sp. and T. elongatus, and the cbtF gene in F. nucleatum. Most vitamin B12 transport systems as well as cobalt chelatases are also regulated by B12 elements.
In this work, we for the first time demonstrated that B12 elements regulate not only genes related to the CBL biosynthesis and transport but also several genes from B12-dependent pathways. It appears that in most cases, the B12-independent isozymes of methionine synthase and ribonucleotide reductase are regulated by B12 elements in the genomes possessing both B12-dependent and B12-independent isozymes. Although the repression of B12-independent enzymes by the excess of coenzyme B12 looks rational, this regulatory strategy was not previously known. This finding, together with identification of other B12 element-regulated enzymes not related to the CBL biosynthesis and mostly hypothetical, opens an intriguing possibility to reveal new B12-dependent pathways. In particular, the ardX-frdX gene pair, existing in most α-proteobacteria, has an upstream B12 element in three bacterial species. Therefore, we predict the existence of a novel, alternative to ArdX-FrdX, B12-dependent enzyme in these three α-proteobacteria.
From the practical standpoint, this work once again demonstrates the power of comparative genomics for functional annotation of genomes, especially when experimental data are limited. In particular, analysis of regulatory elements is a powerful tool for prediction of missing transport genes, as demonstrated here and in our analyses of other vitamin regulons (
Procedings of the Third International Conference on “Complex Systems: Control and Modeling Problems,” Samara, Russia, September 4–9, 2001. The Institute of Control of Complex Systems,
Samara, Russia2001: 623-625