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Originally published In Press as doi:10.1074/jbc.M411026200 on November 29, 2004

J. Biol. Chem., Vol. 280, Issue 6, 4339-4349, February 11, 2005
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Functional Cross-talk between Fatty Acid Synthesis and Nonribosomal Peptide Synthesis in Quinoxaline Antibiotic-producing Streptomycetes*

Gernot Schmoock, Frank Pfennig{ddagger}, Julien Jewiarz, Wilhelm Schlumbohm, Werner Laubinger, Florian Schauwecker, and Ullrich Keller§

From the Institut für Chemie, Arbeitsgruppe Biochemie und Molekularbiologie, Technische Universität Berlin, Franklinstrasse 29, D-10587 Berlin-Charlottenburg, Germany

Received for publication, September 24, 2004 , and in revised form, November 24, 2004.


   ABSTRACT
TOP
 ABSTRACT
INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Quinoxaline antibiotics are chromopeptide lactones embracing the two families of triostins and quinomycins, each having characteristic sulfur-containing cross-bridges. Interest in these compounds stems from their antineoplastic activities and their specific binding to DNA via bifunctional intercalation of the twin chromophores represented by quinoxaline-2-carboxylic acid (QA). Enzymatic analysis of triostin A-producing Streptomyces triostinicus and quinomycin A-producing Streptomyces echinatus revealed four nonribosomal peptide synthetase modules for the assembly of the quinoxalinoyl tetrapeptide backbone of the quinoxaline antibiotics. The modules were contained in three protein fractions, referred to as triostin synthetases (TrsII, III, and IV). TrsII is a 245-kDa bimodular nonribosomal peptide synthetase activating as thioesters for both serine and alanine, the first two amino acids of the quinoxalinoyl tetrapeptide chain. TrsIII, represented by a protein of 250 kDa, activates cysteine as a thioester. TrsIV, an unstable protein of apparent Mr about 280,000, was identified by its ability to activate and N-methylate valine, the last amino acid. QA, the chromophore, was shown to be recruited by a free-standing adenylation domain, TrsI, in conjunction with a QA-binding protein, AcpPSE. Cloning of the gene for the QA-binding protein revealed that it is the fatty acyl carrier protein, AcpPSE, of the fatty acid synthase of S. echinatus and S. triostinicus. Analysis of the acylation reaction of AcpPSE by TrsI along with other A-domains and the aroyl carrier protein AcmACP from actinomycin biosynthesis revealed a specific requirement for AcpPSE in the activation and also in the condensation of QA with serine in the initiation step of QA tetrapeptide assembly on TrsII. These data show for the first time a functional interaction between nonribosomal peptide synthesis and fatty acid synthesis.


   INTRODUCTION
TOP
 ABSTRACT
 INTRODUCTION
MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
The family of quinoxaline antibiotics embraces two structurally similar series of compounds, the triostins and quinomycins, produced by various Streptomyces strains (1). They consist of octadepsipeptide rings to which are attached two quinoxaline-2-carboxylic acid (QA)1 residues in amide linkages (Fig. 1). The triostins and quinomycins differ in their cross-bridges, represented by either a disulfide or a thioacetal structure, respectively. These are contributed from the thiol groups of the two cysteines present in the octadepsipeptide rings (2) (Fig. 1). The various members of each group differ by amino acid substitutions in the peptide chains (3, 4). Other compounds with similarity to the quinoxaline antibiotics are the luzopeptins and sandramycin, which are cyclodecadepsipeptides carrying 3-hydroxyquinoline residues as side groups (5, 6).



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  		FIG. 1.
Structures of triostin A and quinomycin A (echinomycin). The amino acids in the peptide chains are: D-Ser (D-serine), Ala (alanine), MeCys (N-Methyl-L-cysteine), MeVal (N-Methyl-L-valine).

 
The quinoxaline antibiotics specifically bind to DNA as bis-intercalators via their twin chromophores (7, 8). Like actinomycin, another intercalating agent from streptomycetes, quinoxaline antibiotics inhibit transcription (9). More recent findings indicate that quinomycin A (known as echinomycin) also selectively inhibits DNA synthesis (10). Furthermore, the quinoxaline antibiotics, as well as luzopeptin and sandramycin, have antineoplastic activities (11).

In contrast to the wealth of information on the mechanisms of action of the bis-intercalating chromopeptides, only little is known on their biosynthesis. In the case of the quinoxaline antibiotics, in vivo studies of quinomycin A (echinomycin) formation in Streptomyces echinatus have shown that QA is derived from tryptophan and that the amino acids of the peptide rings stem from the free cellular pool (12). Importantly, the demonstration of the conversion of triostins into quinomycins by reduction and rearrangement of the triostin cross-bridge with subsequent S-methylation showed that triostins are the immediate precursors of quinomycins. Accordingly, it was shown that triostin-producing streptomycete strains lack the converting enzyme activity, whereas quinomycin producers possess it (13).

Triostin synthetase I (TrsI), a 58-kDa protein present in triostin A-producing S. triostinicus and in echinomycin-producing S. echinatus, activates QA as the adenylate (14). It can also activate a number of structural analogues of QA such as quinoline-2-carboxylic acid, thieno[3,2b]pyridine-5-carboxylic acid (TPA), and 3-hydroxyquinoline-2-carboxylic acid. These compounds were readily incorporated into triostins or quinomycins when fed to cultures of S. echinatus instead of the endogenous QA to give new compounds (15). These findings suggested that TrsI is involved in the assembly of the quinoxalinoyl peptides, but this assembly remained enigmatic.

In several chromopeptide biosynthesis systems, adenylating enzymes (i.e. free-standing A-domains) have been described that activate aryl carboxylic acids as adenylates with subsequent transfer to specific binding proteins that contain ArCP (aroyl carrier protein) domains (16, 17). These ArCP domains are always fused to other proteins such as isochorismate lyase in the case of several aryl capped siderophore peptide syntheses, e.g. EntB in Escherichia coli, or to a nonribosomal peptide synthetase (NRPS) such as HMWP2 from Yersinia pestis (18, 19). The ArCP-thioester interacts with the next downstream module in the biosynthetic sequence by condensation with the tethered amino acid, resulting in an aroyl amino acid that can undergo elongation cycles until the peptide product is completed. The ArCP domains of siderophore synthetases resemble the peptidyl carrier protein (PCP) or acyl carrier protein (ACP) domains of the modular NRPS or polyketide synthases of type I (17). In the case of synthesis of the chromopeptide actinomycin, the binding protein for the 4-methyl-3-hydroxyanthranilic acid starter unit (4-MHA) was found to be a small free-standing ArCP domain, AcmACP, with significant similarity to fatty acyl carrier proteins of type II fatty acid synthase and polyketide synthases (20). AcmACP is loaded by the adenylating enzyme actinomycin synthetase I (ACMSI), and transfers the 4-MHA to the bimodular NRPS actinomycin synthetase II on which 4-MHA is condensed with threonine, the first amino acid of the actinomycin peptide chain. 4-MHA threonine is later elongated in four further cycles to the 4-MHA pentapeptide lactone end product (21) (Fig. 2).



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  		FIG. 2.
NRPS assembly line of the actinomycin half-molecule (4-MHA pentapeptide lactone). The assembly line comprises six modules including the "truncated" initiation module consisting of the stand-alone A-domain ACMSI and the stand-alone AcmACP. The symbols denote condensation domains (C), adenylation domains (A), peptidyl carrier protein domains (PCP), epimerization domain (E), methylation domains (M), thioesterase domain (Te). The amino acids in 4-MHA pentapeptide lactone chain are: Thr (L-threonine), D-Val (D-valine), Pro (L-proline), Sar (sarcosine, N-methyl-glycine), MeVal (N-methyl-L-valine).

 
Comparing the QA tetrapeptide chains of quinoxaline antibiotics with the chains of other chromopeptide lactones such as 4-MHA pentapeptide lactone (Fig. 2), enzymatic assembly of QA tetrapeptide should have basic steps in common with other streptomycete biosynthesis systems. We show the enzymatic characterization of the triostin NRPS assembly system that surprisingly uses the acyl carrier protein of fatty acid synthase, AcpPSE, as the QA-binding ArCP domain, indicating a functional link between fatty acid synthesis and nonribosomal peptide synthesis.


   MATERIALS AND METHODS
TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
RESULTS
 DISCUSSION
 REFERENCES
 
Chemicals and Radiochemicals—L-[U-14C]Serine (155 Ci/mol), L-[U-14C]alanine (162 Ci/mol), L-[methyl-14C]methionine (56.7 Ci/mol), p-[ring-U-14C]toluic acid (56 Ci/mol), and L-[35S]cysteine (>1000 Ci/mmol) were purchased from Amersham Biosciences. L-[U-14C]Valine (260 Ci/mol) was from ICN Pharmaceuticals (ICN Radiochemicals, Zoetermeer, The Netherlands). [Benzene ring-14C(U)]QA (28.8 Ci/mol) and tetrasodium [32P]pyrophosphate (2.9 Ci/mmol) were from PerkinElmer Life Sciences. Quinoxalinoyl-2-chloride, pyrazine-2-carboxylic acid, quinoline-3-carboxylic acid, and echinomycin were obtained from Sigma. Quinoline-2-carboxylic acid was from Janssen (Beerse, Belgium). Thieno[3,2-b]-pyridine-5-carboxylic acid was kindly provided by Dr. S. Gronowitz (University of Lund, Sweden).

Strains and Cultures—S. echinatus A8331 was kindly provided by Drs. J. Nüesch and K. Scheibli (Basel). Streptomyces triostinicus ATCC21043 and Streptomyces chrysomallus ATCC11523 were obtained from the American Type Culture Collection (Manassus VA). Streptomyces griseoviridus DSM40229was from the Deutsche Sammlung für Mikroorganismen (Braunschweig, Germany). Maintenance, preparation of inocula for liquid culture of S. echinatus, and S. triostinicus, as well as growth in liquid cultures were carried out essentially as described previously, except that S. echinatus liquid cultures were incubated for up to 38 h depending on the maximum rate of [methyl-14C]methionine incorporation into echinomycin during short term incorporation experiments (14). Streptomyces lividans TK64 and Streptomyces coelicolor M145 were obtained from the John Innes strain collection (Norwich, United Kingdom). E. coli strains for cloning were DH5{alpha} and JM109, and the strain for expression was M15 (Qiagen, Hilden, Germany). They were maintained and grown according to standard protocols.

Plasmids, DNA Manipulations, Cloning, and Sequencing Procedures—Techniques for DNA isolation, manipulation, and transformation were as described (22, 23). The plasmids used for subcloning fragments were pTZ18U (Amersham Biosciences), pSP72 (Promega), or pSL1180 (Amersham Biosciences). Expression plasmids for E. coli were pQE30, pQE32, and pQE70 (Qiagen). Plasmid pIJ702 (24) was used as replicon for gene expressions in S. lividans TK64 as described in Ref. 25.

Analytical Methods—SDS-PAGE was performed according to Refs. 26 and 27. Protein determinations were carried out according to Ref. 28. Amino-terminal microsequencing of proteins was performed on an Applied Bioscience (ABI) Procise Microsequencer. DNA sequencing was performed on a ABI capillary electrophoresis sequencing system (3100 Genetic Analyzer). Amino acid and peptidyl thioester intermediates bound to protein were released either by performic acid treatment or saponification with 0.1 M NaOH and subsequent acidification and solvent extraction with ethyl acetate (EtOAc). Labeled compounds on thin layer chromatography (TLC) plates were detected by radioscanning with a Bertolt Radioscanning System or by autoradiography using Kodak Bio-Max x-ray film. Amino acid or peptidyl intermediates were analyzed by TLC. Reference material on plates was either visualized by spraying with ninhydrin (amino acids) or by UV detection (aroyl peptides). Amino acid hydrolysis was performed with 6 M HCl under reduced pressure for 22 h at 110 °C. Autofluorography or autoradiography of SDS-PAGE gels for visualization of labeled protein bands was as described (20). Radioactive determinations of filters or of liquid samples were achieved by liquid scintillation counting using a Wallac scintillation system. Echinomycin production in cultures was monitored by short term incorporation tests as described (14). Echinomycin or triostin extracted from cultures was identified by TLC along with authentic standards using solvent system I. Amino acids were chromatographed on silica gel plates using solvent system II. Quinoxalinoyl peptides were chromatographed on silica gel plates using solvent system III. Determination of optical configurations was done by TLC on chiral plates using solvent system IV.

Matrix-assisted Laser Desorption Ionization (MALDI)-TOF Spectrometry—Protein samples were analyzed with a Voyager-DE PRO (Applied Biosystems). The MALDI-TOF MS system was operated in the linear mode. Samples were further purified with ZipTipC18 and dissolved in a 50% solution of acetonitril, 0.1% trifluoroacetic acid containing sinapinic acid (5 mg ml–1) and dried on a sample plate. A nitrogen laser operating at 337 nm and a 3-ns pulse rate was used. The accelerating voltage was set at 25 kV, and a delay of 350 ns was used to accelerate ions into the flight tube of the mass spectrometer. The mass scale (m/z 5000–20000) was calibrated with a mixture of peptides, and 80 laser shots were used to obtain each spectrum.

Buffers and Solvent Systems—Solvent systems were: I (EtOAc, MeOH, H2O (100:5:5, by volume)), II (BuOH, AcOH, H2O (4:1:1, by volume)), III (2-propanol, di-n-butylether, AcOH, H2O (4:3:3:2, by volume)), and IV (acetone, MeOH, H2O (10:2:2, by volume)). Buffer for nickel affinity chromatography was NTA (15% glycerol (w/v), 50 mM KPO4 (pH 8.0), 300 mM NaCl, 1 mM benzamidine, and 1 mM phenylmethylsulfonyl fluoride) and buffer NTA-W (buffer NTA with 50 mM KPO4 (pH 6.0)). Buffer A was 15% glycerol (w/v), 150 mM Tris-HCl (pH 8.0), 30 mM MgCl2, 1 mM EDTA, 4 mM dithioerythritol, 1 mM benzamidine, 1 mM phenylmethylsulfonyl fluoride. Buffer B was 15% glycerol (w/v), 100 mM Tris-HCl (pH 8.0), 1 mM EDTA, 4 mM dithioerythritol, 1 mM benzamidine, 1 mM phenylmethylsulfonyl fluoride. Buffer C was buffer B with 2 mM EDTA and without phenylmethylsulfonyl fluoride and benzamidine. Buffer D was buffer C with 50 mM Tris-HCl (pH 8.0). Buffer E was buffer C with 100 mM Tris-HCl (pH 7.2). Buffer F was buffer E with 10% glycerol (w/v).

Cloning of trsA, trsB, and trsC from S. triostinicus—A probe suitable for screening the gene trsA encoding TrsI in a plasmid gene bank of S. triostinicus DNA in E. coli was obtained by PCR using forward primer FTRIO1 derived from a part of the known amino-terminal sequence of TrsI (5'-ATGCSGACGGCTTCGTCCCSTGGGTCGACCACCT-3') and reverse primer F2RC derived from the conserved A3 motif of the A-domains ACMSI (20), SnbA (29), and EntE (30) (5'-GGAATTCCCTTSGGCTTGCCGGTGGTGCC-3'). The template was chromosomal DNA from S. triostinicus. A 580-bp fragment was cloned in E. coli via SalI and EcoRI restriction sites using SalI/EcoRI-cleaved pTZ18U. Sequencing revealed that the fragment encoded an amino acid sequence that comprised the complete sequenced amino terminus of TrsI and showed high sequence similarity to ACMSI, SnbA, and EntE (31). The 580-bp gene fragment was 32P-labeled by using a Random Primers DNA Labeling System (Invitrogen, Eggenstein, Germany) and used as a probe to localize the complete trsA gene by hybridization analysis of various restriction blots of chromosomal DNA of S. triostinicus.

A 6.1-kb BamHI fragment apparently comprising the complete trsA and its flanking regions was cloned by isolating BamHI-digested S. triostinicus total DNA size fractionated on agarose gels to about 6 kb, followed by fractionation and ligation of the mixture to BamHI-cleaved pTZ18U. After introduction by transformation into E. coli DH5{alpha}, 8000 colonies were subjected to screening with the labeled probe. Two hybridizing colonies were found to contain the 6.1-kb BamHI band in the plasmid, which was named pTR1. To facilitate sequencing ~1/3 of the insert of pTR1 was removed by KpnI digestion with subsequent religation to yield pTR1sub5. Sequencing the 4-kb BamHI-KpnI insert contained in pTR1sub5 revealed the trsA gene flanked by the two genes trsB and trsC, to the 5'- and 3'-end, respectively (GenBankTM accession number AY825941 [GenBank] ).

Expression of trsA in S. lividans TK64 —To express TrsI as a carboxyl-terminal His6 fusion protein from the mel promoter of pIJ702, forward primer FTRS1 (5'-AAAGGAACGCCGCATGCTCGACGGTTTCGTCCCCCTG-3') and reverse primer RTRS1 (5'-CGTAGATCTTCAGTGGTGGTGGTGGTGGTGAGGCATCCGCGCCGTCACGGCACG-3') were used for PCR amplification with 200 ng of chromosomal DNA as template. The 1.6-kb fragment was digested with SphI and BglII and ligated to BglII/SphI-cleaved pSP72. From the plasmid obtained (pTRSA1) the fragment was excised with BglII and SphI and ligated to BglII/SphI-cleaved pIJ702 and introduced by transformation into S. coelicolor M145 or S. lividans TK64, to yield pTRSA2. For expression of TrsI from pTRSA2, S. lividans TK64 harboring pTRSA2 was grown for 3 days in 300-ml Erlenmeyer flasks containing 100 ml of YEME medium with 50 µg ml–1 thiostrepton equipped with steel springs as baffles.

Expression of trsA in E. coli—Expression of trsA in E. coli was as amino- and carboxyl-terminal His6 fusion proteins. The trsA gene was amplified by PCR using pTR1sub5 as template with forward primer FTRS1 (5'-AAAGGAACGCCGCATGCTCGACGGTTTCGTCCCCTG-3') and reverse primer GS230201 (5'-GGCAAGCTTTCAAGATCTAGGCATCCGCGCCGTCACGGCACGCTC-3'). The resulting 1.56-kb PCR fragment was digested with SphI and HindIII and ligated to SphI/HindIII-cleaved pQE32 to yield pTRSN1. Alternatively, the same PCR fragment was digested with SphI and BglII and ligated into SphI/BglII-cleaved pQE70, producing pTRSC1. pTRSN1 and pTRSC1 were introduced by transformation into E. coli strain M15, respectively. Cultures of M15/pTRSN1 and M15/pTRSC1 (1.6 liters of 2x YT medium, 100 µg ml–1 ampicillin, 25 µgml–1 kanamycin) were grown at 37 °C to an A600 of 0.7 and then induced with 0.5 mM isopropyl 1-thio-{beta}-D-galactopyranoside (final concentration). Cultivation was continued for 18 h at 29 °C and cells finally harvested.

Isolation of QA-binding Protein from S. echinatus—All operations were carried out at 2–4 °C. Mycelium of S. echinatus (12.5 g wet weight) was suspended in a 3.5-fold volume of buffer C (w/v). After passage through a French press (Aminco) at 10,000 p.s.i., MgCl2 was added at 15 mM (final concentration) and solid DNase (Type I, grade 2, Sigma, 50 µg ml–1 final concentration) were added. After stirring for 1 h on ice the suspension was centrifuged for 30 min in a Sorvall centrifuge at 25,000 x g. The supernatant (83 ml) was applied to a Q-Sepharose (fast flow) column (4 x 5 cm) and, after washing, a 200-ml 0–0.5 M NaCl gradient was applied. 5-ml fractions were collected. QA binding activity eluted between 0.3 and 0.4 M NaCl. Active fractions were pooled and diluted to 0.1 M NaCl concentration by adding 3 volumes of buffer D. The solution was then applied onto an anion exchange column (Resource Q, 6 ml) and proteins were eluted with 1 M NaCl. Fractions of 0.5 ml were collected and those with the highest protein concentrations were combined (final volume 3.1 ml). This pool was applied to a Superdex 75 column (Amersham Biosciences) previously equilibrated with buffer D, and 2-ml fractions were collected at a flow rate of 0.5 ml min–1. Active fractions were combined and subjected to anion exchange chromatography on a Mono Q (HR/5R) column, eluting with a 0–0.5 M NaCl gradient in buffer E. Fractions of 0.75 ml were collected (flow rate 0.5 ml min–1, gradient rate 5 mM min–1 NaCl). Activity eluted between 0.2 and 0.3 M NaCl. Further purification of the QA-binding protein was achieved by chromatography on a high-resolution anion exchange chromatography system (Smart Chromatography System, Amersham Biosciences) using a Mono Q PC 1.6/5 column. For this purpose, the enzyme pool from the Mono Q (HR/5R) step was diluted with 100 mM Tris-HCl, 2 mM EDTA, 4 mM dithioerythritol to 10% glycerol final concentration, to obtain the same salt concentration as in buffer F. After application to the Mono Q PC 1.6/5 column, the enzyme was eluted with a 0–0.35 M NaCl gradient in buffer F and 100-µl fractions were collected. The activity resided in one single fraction at 185 mM NaCl. SDS-gel electrophoresis revealed the presence of two bands representing sizes of about 10 and 28 kDa.

Determination of the Amino-terminal Sequence of the Quinoxaline-2-Carboxylic Acid-binding Protein—The fraction containing the quinoxaline-2-carboxylic acid-binding protein (about 200 pmol) was incubated for 30 min at 28 °C with 2 picokatal TrsI and about 0.25 µCi of [14C]QA in the presence of 20 mM MgCl2 and 10 mM ATP. After this, the sample was subjected to preparative SDS-gel electrophoresis and subsequently blotted to a polyvinylidene difluoride membrane. Autoradiography of the blot showed that the radioactivity stemming from QA exclusively resided in the 10-kDa band. The band was cut out and subjected to microsequencing.

Cloning of the Gene of Quinoxaline-2-Carboxylic Acid-binding Protein from S. echinatus and Expression in E. coli—Based on the aminoterminal sequence of the QA-binding protein (G/A)ATQEEIVAGLAEIVNEIAAPIVEDDQ(Q/L)(L/D), the oligonucleotide QANTERM (5'-GCCACCCAGGAGGAGATCGTCGCCGGC-3') was synthesized. After 5' labeling with [32P]phosphate, the labeled oligo was used for Southern hybridizations with various restriction blots of S. echinatus DNA. In each restriction lane, two bands with different intensities were present. In the case of the BglII/PstI double digestion, these bands were of 3.6 and 1.8 kb. BglII/PstI-digested DNA was eluted from the respective size ranges of parallel gels and each DNA mixture was ligated to BamHI/PstI-cleaved pTZ18U (pM2PB). Transformation of E. coli DH5{alpha} and colony hybridization yielded clones for each fragment. In the case of the 1.8-kb fragment (with lower hybridization signal), sequence analysis did not reveal a sequence coding for a protein with similarity to an ACP or PCP domain, whereas sequence analysis of the 3.6-kb fragment (stronger hybridizing fragment contained in pM2PB) showed an open reading frame that comprised the previously determined amino-terminal sequence of the QA-binding protein. Furthermore, the sequence displayed nearly total identity with the amino termini of the acyl carrier proteins of fatty acid synthases from streptomycetes. The gene was named acpPSE. It was flanked by genes encoding putative 3-oxoacyl-ACP synthase III and 3-oxoacyl-ACP synthase II, respectively (deposited under GenBankTM accession number AY825942 [GenBank] ).

The acpPSE gene encoding the QA-binding protein was engineered with suitable restriction ends for insertion into expression plasmid pQE32 to express it as an amino-terminal His6 fusion protein. To this end the gene was amplified using forward primer FECH1 (5'-AGCGCCTGGCATGCTCGCCACTCA-3') and reverse primer RECH1 (5'-AGCCTGGATCCTACGGGATGGCTCA-3') with pM2PB as template. The resultant approximate 300-bp PCR product was digested with BamHI and SphI and ligated to SphI/BamHI-cleaved pTZ18U. Transformation of DH5{alpha} yielded pEACPN1. From pEACPN1, the engineered acpPSE was excised as a SphI/KpnI fragment and ligated to SphI/KpnI-cleaved pQE32. The resultant plasmid was designated pEACPN2. For expression of acpPSE, pEACPN2 was introduced by transformation into E. coli strain M15. A culture of M15/pEACPN2 (1.6 liters of 2x YT medium, 100 µg ml–1 ampicillin, 25 µg ml–1 kanamycin) was grown at 37 °C and expression was induced with 0.1 mM isopropyl 1-thio-{beta}-D-galactopyranoside (final concentration) at an A600 of 0.7 and the cells were allowed to grow for an additional 42 h at 26 °C.

Expression of acpPSE in S. lividans TK64 —To express acpPSE in S. lividans TK64 under the control of the mel promoter of pIJ702, acpPSE was engineered by PCR using forward primer GER240401A (5'-ACTCGCATGCACCACCACCACCACCACATGGCCGCCACTCAGGAAGAGATCGT-3') and reverse primer RECH1 (5'-AGCCTGGATCCTACGGGATGGCTCA-3'). The resultant 300-bp PCR band was eluted from the gel and, after digestion with SphI and BamHI, ligated to SphI/BamHI-cleaved pSP72. Transformation of E. coli DH5{alpha} gave pEACPN12. The acpPSE gene was excised from pEACPN12 by cleavage with SphI and BglII and ligated to SphI/BglII-cleaved pIJ702 (pEACPN13). pEACN13 was introduced into S. lividans TK64 and the transformants were grown for 3 days in YEME medium under the same conditions as above for pTRSA1.

Cloning and Heterologous Expression of sfp—The phosphopantetheine transferase gene sfp from Bacillus subtilis ATCC6633 was amplified and cloned into pUC19 (accession number X63158 [GenBank] ; Ref. 32). The resulting plasmid served as template for PCR with primers FSFP1 (5'-GGAGGATCTGGATCCAAGATTTACGGAA-3') and RSFP1 (5'-GCTCGGTACCCGTCGACCCCATTTATAA-3'). The 696-bp amplicon was digested with BamHI and KpnI and ligated into BamHI/KpnI-cleaved pTZ18 (pSFP1). The insert from this plasmid was removed as a BamHI/SalI fragment and cloned into BamHI/SalI-cleaved expression vector pQE30. The resulting plasmid was named pSFP30 and was used for expression of an NH2-terminal His6-tagged protein. Expression was achieved after transformation of E. coli M15 and a culture of M15/pSFP30 was grown at 37 °C and 200 rpm up to an A600 of 0.6. Induction with 0.2 mM isopropyl 1-thio-{beta}-D-galactopyranoside was followed by further incubation for 18 h at 30 °C (1.2 liters of 2x YT medium, 100 µg ml–1 ampicillin, 25 µg ml–1 kanamycin).

Purification of Recombinant TrsI from E. coli M15 Carrying pTRSN1—All operations were carried out at 0–4 °C. 16 g of cell paste were suspended in 48 ml of cold buffer NTA and passed through a French press (Aminco) at 10,000 p.s.i.. After adding MgCl2 to give 20 mM final concentration and adding solid DNase (type I, Sigma) to give 20 µg ml–1 final concentration, the homogenate was stirred for 45 min on ice. The suspension was centrifuged for 30 min at 25,000 x g. The supernatant was applied onto a Ni-NTA-agarose column (1.3-ml gel volume) equilibrated previously with NTA buffer. After washing with NTA-W buffer, the bound protein was eluted with increasing concentrations of imidazole in NTA buffer (containing 10, 50, and 250 mM imidazole). Fractions containing QA-activating activity were pooled (3 ml) and gel-filtered on a Superdex 75 (Amersham Biosciences) column previously equilibrated with buffer B. Fractions of 2 ml were collected and those containing the enzyme were pooled. Pooled enzyme was applied onto a {omega}-aminohexyl-Sepharose (Sigma) column (4.7 x 1 cm). After washing with buffer B, the bound protein was eluted with a 75-ml 0–0.4 M NaCl gradient (2 ml fractions). After concentration of the pooled fractions with Centricon30 microconcentrators to a protein concentration of about 1 mg ml–1 protein concentration, the enzyme was frozen at –80 °C.

Purification of His6AcpPSE from E. coli M15 Carrying pEACPN2— 11.3 g of cell paste of E. coli suspended in 45 ml of cold buffer NTA (with 4 mM dithioerythritol) was passed through a French press (Aminco) at 10,000 p.s.i. After addition of MgCl2 to a 20 mM final concentration and DNase treatment with DNase I (Sigma) (20 µg ml–1), the homogenate was stirred for 45 min on ice. The suspension was centrifuged for 30 min at 25,000 x g. To reduce the dithioerythritol concentration for the subsequent step, the supernatant was diluted with 4 volumes of buffer NTA and applied onto a Ni-NTA-agarose column (1.8 ml volume) equilibrated previously with buffer NTA. After washing with NTA-W buffer (see above), protein was eluted with increasing concentrations of imidazole in NTA buffer (containing 10, 50, and 250 mM imidazole). Fractions were analyzed by SDS-PAGE and those containing recombinant His6AcpPSE were pooled and gel filtered on a Superdex 75 column (Amersham Biosciences) equilibrated with buffer B. Fractions of 2 ml were collected and the fractions with QA-binding activity were pooled.

Purification of Triostin Synthetases from S. echinatus—30 g of freshly harvested mycelium of S. echinatus was suspended in 75 ml of buffer A. The suspension was passed twice through a French press (Aminco) at a cell pressure of 8,000 p.s.i. MgCl2 (20 mM final concentration) and DNase I (Sigma, 20 µg ml–1 final concentration) were added. The suspension was stirred on ice for 30 min. The homogenate was centrifuged for 30 min at 25,000 x g. Saturated ammonium sulfate was added to the supernatant to give 60% saturation. After leaving on ice for 3 h, the precipitate was collected by centrifugation (30 min, 25,000 x g). The pellet was taken up in a minute volume of buffer B and applied onto a Ultrogel AcA34 gel filtration column (48 x 2 cm) that had been equilibrated previously with buffer B. Fractions of 6.0 ml were collected. Fractions catalyzing covalent binding to protein as thioester of either L-serine and L-alanine (triostin synthetase II) or cysteine (triostin synthetase III) or valine (triostin synthetase IV) were pooled. The various fractions were separately subjected to anion exchange chromatography, respectively, on a ResourceQ column (6 ml, Amersham Biosciences) using buffer B. After washing, enzymes were eluted with a 60-ml 0–400 mM NaCl gradient in buffer B (fraction size 2 ml). Fractions catalyzing serine/alanine thioester or valine thioester formation were pooled for analysis of thioester formation or (in the case of TrsII) for testing quinoxalinoyl peptide formation in conjunction with TrsI and AcpPSE.

Purification of Recombinant Sfp from E. coli M15 Carrying pSFP30— 6.3 g of cell paste was suspended in 19 ml of buffer NTA and passed through a French press (Aminco) at 10,000 p.s.i., followed by digestion with DNase I (Sigma) (20 µg ml–1 final concentration and 15 mM MgCl2) for 30 min on ice with gentle stirring. This suspension was centrifuged (30 min, 25,000 x g) and the supernatant (20 ml) was applied onto a Ni-NTA-agarose column (3 ml resin) equilibrated prior with buffer NTA. After standard wash steps as described above for the purification of recombinant TrsI, the His6 fusion protein was eluted with 50 mM imidazole in NTA buffer. Finally a gel filtration step on the AcA54 column (Ultrogel) previously equilibrated with buffer B yielded a homogeneous 29-kDa protein.

Purification of Other Enzymes Used in this Work—ACMSI was obtained by expression of acmA in S. lividans as described previously (20). AcmACP was obtained by expression of acmD in E. coli (20). Because most of the protein was in the apo-form, conversion into the holo-form had to be performed. This was achieved by incubation of His6AcmACP, which had been expressed in E. coli, with the 4'-phosphopantetheine transferase Sfp and CoA. After purification by gel filtration on Superdex 75, checking for intactness by MALDI-TOF mass spectrometry revealed the exclusive presence of the holo-form of protein (10641.5, theoretical value 10640.9). The hydroxypicolinic acid activating enzyme from S. griseoviridus (mikamycin synthetase I, MkmsI) and actinomycin synthetase II (ACMSII) from S. chrysomallus were prepared as described previously (33, 47).

Chemical Synthesis of Quinoxalinoyl-L-serine and Quinoxalinoyl-D-serine—To L-serine or D-serine (26.3 mg, 0.25 mmol) dissolved in 0.5 ml of 2 M NaOH was added quinoxalinoyl-2-chloride (48.2 mg, 0.25 mmol dissolved in 0.6 ml of diethyl ether) under vigorous mixing at 0 °C. After 2 min, solid KHCO3 (60 mg, 0.6 mmol) was added gradually during a 10-min period. After stirring for an additional 2 h at room temperature, 0.5 ml of 2 M HCl was added and the mixture was applied on a reversed-phase column (SuperPac Pep-S, Amersham Biosciences). Chromatography was performed at a flow rate of 1.0 ml min–1 with solvent A (0.1% trifluoric acid) and solvent B (acetonitril with 0.1% trifluoric acid) with the following gradient profiles: 0 min, 0% B; 25 min, 25% B; 40 min, 100% B. Fractions of 1.0 ml were collected and quinoxalinoyl L- or D-serine were identified by their different migration behavior compared with QA. Mass spectrometric analysis gave peaks for the [M–H]+ ions with m/z = 262 as expected for quinoxalinoyl serine (261), confirming the identity of the compounds (courtesy of Dr. Fred Rosche, Probiodrug AG, Halle, Germany).

Enzyme Assays—In the case of NRPS, 1 unit is defined as the amount of enzyme that binds 1 nmol of serine (TrsII) or threonine (ACMSII) during 30 min of incubation at 30 °C. Specific activity in the ATP-pyrophosphate exchange reaction is determined as nanokatal mg–1 protein. 1 katal is the amount of enzyme catalyzing the incorporation of 1 mol of [32P]pyrophosphate into ATP per second. The ATP-pyrophosphate exchange reaction dependent on the aromatic carboxylic acids was carried out as described previously (14, 20). For routine measurements of enzyme thioester formation, the standard filter binding assay was used as described previously (20). The latter assay was also used for characterization of the kinetic behavior of ArCPs such as AcpPSE and AcmACP as substrates toward adenylating enzymes TrsI, ACMSI, and MkmsI. The assays contained 150 µM [14C]QA, [14C]p-toluic acid, or [14C]picolinic acid, 10 mM ATP, 20 mM MgCl2, purified recombinant TrsI (30 nM) or ACMSI (7.5 nM), and the respective ArCPs at concentrations varying from 1.5 to 12 µM for AcpPSE and 0.25 to 4 µM for AcmACP. To calculate Kcat/Km, initial velocities were determined by recording time curves of ArCP loading for each concentration of ArCP. At different times, the reactions were stopped by the addition of trichloroacetic acid, proteins were collected by suction filtration on ME25 membrane filters (Schleicher & Schuell) and counted. Alternatively, precipitated protein was centrifuged, washed several times with trichloroacetic acid and ethanol, finally dissolved in 0.1 M NaOH, and counted. For testing aroyl peptide formations, TrsI (3–5 picokatal) and TrsII (0.05–0.1 units) were incubated with 0.5 µCi of [14C]L-serine, 2 mM QA or thieno[3,2-b]pyridine-5-carboxylic acid, 10 mM ATP, 20 mM MgCl2, and AcpPSE (0.4–0.8 µM) in a total volume of 250 µl. In parallel experiments, TrsII was replaced by ACMSII (0.05–0.15 units). After incubation at 30 °C for 30 min the reaction was stopped by trichloroacetic acid precipitation. Isolation and identification of quinoxalinoyl peptide was as described above.

Data Processing—Multiple alignments and sequence analyses were performed using the Clustal W package (34).


   RESULTS
TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
DISCUSSION
 REFERENCES
 
Isolation and Identification of Triostin Synthetases (TRSs)— To isolate NRPS activities involved in quinoxalinoyl peptide assembly, protein fractions from S. echinatus or S. triostinicus were tested for protein-thioester formation with the amino acids serine, alanine, cysteine, and valine. These amino acids occur in the peptide chains of triostin A or echinomycin. Fractionated concentration by ammonium sulfate precipitation of broken cell extracts of the streptomycetes and subsequent gel filtration on Ultrogel AcA34 revealed covalent binding of alanine and serine in the fractionation range of Mr 280,000–230,000. Valine activation was found in a broad range of Mr 320,000 and 100,000 with two maxima at Mr 280,000 and 130,000 as determined from the calibration curve of the Ultrogel AcA34 columns (results not shown). The Mr 280,000 maximum did not reproducibly appear in preparations, whereas the smaller Mr 130,000 species did. This indicated that the smaller enzyme might have arisen from the larger by proteolysis. Anion exchange chromatography of protein taken from the fractionation range 300,000–200,000 of the Ultrogel AcA34 column is shown in Fig. 3 (panel A). There was a peak of serine activation that coincided with alanine activation (the latter not shown). Valine activation was represented by an enzyme peak eluting at higher salt strength. This showed that the serine/alanine activating enzyme is distinct from the one activating valine.



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  		FIG. 3.
Separation and characterization of serine/alanine and valine activating NRPS subunits TrsII and TrsIV of S. echinatus by anion exchange chromatography. A, anion exchange chromatography of the high Mr fraction of gel filtration fractionation of S. echinatus on ResourceQ. Shown are the serine binding activity (•) and valine binding activity ({blacksquare}) of the triostin synthetases II and IV (TrsII and IV). Dotted line, protein. The serine binding activity was concomitantly associated with alanine binding activity (not shown here), which indicated that the protein harbors both modules for the first two amino acids of the quinoxalinoyl tetrapeptide chain. B, analysis of the serine- and alanine-thioester complex: lane a, addition of formic acid to serine-thioester; b, addition of performic acid to serine-thioester; c, addition of formic acid to alanine-thioester; d, addition of performic acid to alanine-thioester. 100 µl of (•) peak fraction was incubated with 1 µCi of 14C-labeled alanine or serine in the presence of MgATP for 30 min at 30 °C. Enzyme thioester was precipitated with trichloroacetic acid and after washing was subjected to analysis. C, analysis of the valine-thioester complex: lane a, formic acid to valine-thioester; b, performic acid to valinethioester; c, performic acid to valine-thioester formed in the additional presence of S-adenosyl-L-methionine. 100 µl of enzyme fraction of the ({blacksquare}) peak fraction were incubated with 1 µCi of [14C]valine, MgATP for 30 min at 30 °C with and without 1 mM S-adenosyl-L-methionine.

 
Analysis of the covalent linkage of amino acid to protein is shown in Fig. 3. Serine or alanine (panel B) were released from the activating protein by treatment with performic acid but not with formic acid, proving the nature of the thioester bond. Similarly, valine was split from valine-binding enzyme only with performic acid (Fig. 3, panel C). In addition, incubation of enzyme with valine in the additional presence of S-adenosyl-L-methionine resulted in the exclusive detection of N-methyl-L-valine instead of valine, indicating the ability of enzyme to methylate its thioester-bound substrate (Fig. 3, panel C, lane c). This clearly indicated the presence of a M-domain (methylating domain) in the valine module, in full agreement with the presence of N-methylvaline in the fourth position of the peptide chain of triostin A or echinomycin. The enzymes were found to be present in both S. echinatus and S. triostinicus. Because in S. echinatus the amounts of these enzyme as measured by titration with serine or valine were about 2–3-fold higher than in S. triostinicus, for all of the further analyses of quinoxaline antibiotics NRPS, S. echinatus was chosen as the source of enzyme.

Detection of activity catalyzing cysteine-protein thioester in S. echinatus protein fractions was hampered by the nonspecific binding of [35S]cysteine to proteins, presumably via disulfide bonds (not shown). Applying fractions from Ultrogel AcA34 gel filtrations of S. echinatus protein extracts incubated with [35S]cysteine and ATP onto SDS-PAGE gels with subsequent autoradiography and inspection of the various lanes for ATP-dependent radiolabeled bands revealed a 250-kDa protein that bound [35S]cysteine in an ATP-dependent manner (Fig. 4). The protein resided in the fractionation Mr range of 230,000–300,000 of the Ultrogel AcA34 gel filtration column. In aging protein preparations the 250-kDa band gradually converted into a 120-kDa band, indicating proteolysis. Nevertheless, still in this case the native activity still resided in the Mr 230,000–280,000 fractionation range of the column, suggesting that the proteolytic fragment still held together with other fragments of the protein or protein complex. The identification of the cysteine binding activity prompted a similar analysis for the serine, alanine, and valine activating proteins. Fig. 4 shows, in fact, that [14C]serine and [14C]alanine both labeled the same 245-kDa band. This indicated that the protein is bimodular. It was designated triostin synthetase II (TrsII). Inspection of the valine peak from the gel filtrations did not show the expected band of more than 200 kDa. Instead, the enzyme showed labeled bands of 110 and 80 kDa, which were unreproducible in their abundance (not shown). This enzyme was difficult to handle because of its susceptibility to proteolysis, which could not be inhibited. The cysteine activating activity was designated triostin synthetase III (TrsIII) and the valine-activating protein was designated triostin synthetase IV. Whether TrsIII and -IV are proteolytic fragments of a larger enzyme could not be determined. TrsII, with a size of 245 kDa, is in the same size range as its counterpart, ACMSII, from the biosynthesis of actinomycin, which has a molecular mass of 280 kDa (25) and therefore was regarded as an intact species. TrsII never changed its size in other separation steps and always stayed as a 245-kDa band that could be labeled with [14C]serine and [14C]alanine.



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  		FIG. 4.
Size determinations of serine/alanine and cysteine activating NRPS subunits TrsII and TrsIII of S. echinatus. Shown are autoradiographs of SDS-PAGE separations of loading reactions involving TrsII or TrsIII with [14C]serine, [14C]alanine, and [35S]cysteine, respectively. The fractions used for these loading reactions were from Ultrogel AcA34 gel filtrations using a column calibrated with ferritin (450 kDa), catalase (250 kDa), and aldolase (154 kDa). The indicated Ve/Vo ratios of the NRPS represent the peak maxima of binding activities for serine/valine or cysteine. The left inset shows the labeled band of TrsII after incubation with [14C]serine or [14C]alanine. The right inset shows the ATP-dependent labeling of the band representing TrsIII with [35S]cysteine. Sizes of the denatured bands are 245 and 250 kDa, respectively. The incubations were carried out as described in the legend to Fig. 3 except that the reaction was stopped by the addition of acetone and the precipitate after dissolution in buffer B with 2% SDS was applied to SDS-PAGE gels. The 350-kDa marker in the marker lanes is enniatin synthetase.

 
Molecular Cloning of the trsA Gene of TrsI—TrsI was purified to homogeneity from S. triostinicus according to an earlier purification procedure (14). Microsequencing revealed the following sequence: MLDGFVPWPDHLADEYRRRGIWLG (Gen-BankTM accession number P80436 [GenBank] ). Based on this sequence and the highly conserved signature sequence A3 of A-domains (35) taken from the A-domains of SnbA (29), EntE (30), and ACMS I (20), primers were synthesized for PCR using total DNA from S. triostinicus as template (see "Materials and Methods"). Using the resultant 580-bp amplicon as a probe, the complete trsA gene of TrsI could be located and finally cloned on a 6.1-kb BamHI fragment of S. triostinicus DNA. Sequence analysis of 4 kb (subclone pTR1sub5) of the fragment revealed an open reading frame of 1587 bp that was designated trsA. TrsA is a typical streptomycete gene of 71.5% G + CwithaG + C of 90.7% in the third positions of codons. It encodes a protein of 528 amino acids with a calculated molecular mass of 58.6 kDa, which fits the previously determined molecular mass of 52 kDa (14). The protein sequence of TrsI is highly similar to that of SnbA (47%) from S. pristinaespiralis (29), DhbE (47%) from B. subtilis (36), YbtE (43%) from Y. pestis (37), EntE (36%) from E. coli (30), and ACMSI (20%) from S. chrysomallus (20). Like TrsI, all of these enzymes are stand-alone A-domains and are involved in the initiation of various aryl peptide syntheses such as pristinamycin I (29), enterobactin (30), yersiniabactin (37), or actinomycin (20). Alignment of the putative substrate determining amino acid residues in the substrate-binding pocket of TrsI with those of various other A-domain activating aromatic carboxylic acids (38, 39) (Fig. 5) revealed the highest similarity of the binding pocket of TrsI with the active site of SnbA, which adenylates hydroxypicolinic acid (29).



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  		FIG. 5.
Substrate specificity determining residues in the active site adenylate binding pocket of TrsI. Alignment of amino acid residues in positions of the substrate binding pockets of various aromatic carboxylic acid activating enzymes (A-domains). The residues were extracted from A-domain sequences according to Refs. 38 and 39 on the basis of the crystal structure of gramicidin S synthetase 1 A-domain complexed with phenylalanine-adenylate. The following are shown in the figure: TrsI, this work, SnbA (29), EntE (30), YbtE (37), ACMSI (20).

 
Sequence analysis of the flanking regions of trsA revealed 5' to trsA an open reading frame of 1206 bp designated trsB. It encodes a protein of 401 amino acids with a calculated molecular mass of 44.6 kDa. It has high similarity to cytochrome P450 monooxygenases, in particular to NovI from Streptomyces spheroides (39% identity) (40). 3' to trsA but in the opposite direction an open reading frame designated trsC of 747 nucleotides was localized. TrsC had a lower G + C content of 65.3% (85.5% G + C in the third codon position). The deduced amino acid sequence comprises 248 amino acids and the calculated molecular mass is 27.9 kDa. TrsC has high similarity to various tryptophan-2,3-dioxygenases that catalyze the conversion of tryptophan to formylkynurenine. Most probably, this gene, like trsB, is involved in the synthesis of QA that has been reported to be derived from tryptophan (12).

Expression of trsA—To further characterize the trsA gene product, its gene was expressed as a His6 fusion protein in E. coli M15 or S. lividans TK64. Cloning in pQE32 or pQE70 with subsequent expression in E. coli afforded both the amino-terminal and carboxyl-terminal His6-tagged versions of the protein in active form (as tested by the QA-dependent ATP-pyrophosphate exchange). By contrast, in S. lividans expression gave active protein, also, but with loss of the carboxyl-terminal His6 tag. The amino-terminal His6 fusion from E. coli was used throughout this study. Purification to homogeneity of the protein from E. coli M15 harboring pTRSN1 was achieved by Ni-NTA affinity chromatography, Superdex 75 gel filtration, and chromatography on {omega}-aminohexyl-Sepharose (Fig. 6). The purification from the eluate of the Ni-NTA column was 4.87-fold with an overall yield of 78% (1.4 mg liter–1 culture). The specific activity of the homogeneous enzyme was 7.8 nanokatal mg–1 protein, which drastically contrasts the specific activity of the same enzyme obtained from S. triostinicus, which was determined to be 1.1 nanokatal mg–1. This can be explained, at least in part, by the fact that purification of enzyme from the streptomycete requires seven purification steps compared with two with the His6-tagged protein, suggesting that during purification from the streptomycete a considerable portion of enzyme might have been inactivated. Like wild type enzyme, the recombinant enzyme adenylated all of the structural analogues of QA with the same relative activity compared with QA (14).



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  		FIG. 6.
Purification of amino terminal His6-tagged triostin synthetase I. Shown are SDS-PAGE separations of individual purification steps. Lane M, Mr markers; 1, crude extract; 2, Ni-NTA affinity chromatography; 3, Superdex 75 gel filtration; 4, {omega}-aminohexyl-Sepharose anion exchange chromatography.

 
Isolation of QA-binding Protein—Next we set out to identify the binding protein for QA. First, TrsII was incubated with TrsI and [14C]QA, and covalent binding of QA to protein was measured. No binding was seen and it was concluded that the QA-binding domain was located neither on TrsI or TrsII but on a separate protein in S. echinatus (or S. triostinicus). Therefore, protein extracts of S. echinatus were analyzed for the presence of the QA-binding protein by chromatography of S. echinatus broken cell extracts on anion exchange columns (Q-Sepharose) and testing fractions with TrsI in the presence of [14C]QA and ATP. Such separations showed [14C]QA binding activity in the eluent range of 0.3 to 0.4 M NaCl using the usual filter-binding test. Further fractionation of the binding activity was achieved by gel filtration and repeated anion exchange chromatography steps, revealing an about 10-kDa protein that, after loading with [14C]QA, could be visualized on SDS gels by autoradiography (not shown). Remarkably, the binding protein was obtained in appreciable yields exceeding TrsII from S. echiantus by more than 10-fold on a molar basis. Microsequencing of the 10-kDa protein from blots revealed the sequence (G/A)-ATQEEIVAGLAEIVNEIAAPIVEDDQQ(L)L(D). Comparison of that sequence with protein sequences in the data base surprisingly showed nearly complete identity with the amino-terminal amino acid sequence of the fatty acid synthase (FAS) acyl carrier protein from S. coelicolor (AcpP, SCO2389 (41)), the FAS acyl carrier protein from Streptomyces avermitilis (BAC73498 [GenBank] (42)), and the FAS acyl carrier protein from Streptomyces glaucescens (43).

The gene of the QA-binding protein was cloned by screening various restriction blots of chromosomal DNA of S. echinatus with an oligonucleotide probe derived from part of the amino-terminal sequence of the binding protein. Sequencing of the hybridizing 3.6-kb BglII/PstI fragment revealed in its middle an open reading frame of 249 bp encoding a protein of 8.91 kDa. The gene had a G + C content of 62.3%, which increases to 90.4% in the third codon positions. The derived amino acid sequence perfectly fitted the determined amino-terminal sequence of the QA-binding protein, confirming the correctness of the cloned sequence. Alignment of the protein sequence with known sequences in the data base revealed that as had already been obvious from the amino-terminal sequence, the protein was nearly identical over its whole length with FAS acyl carrier proteins from S. coelicolor (98% identity), S. glaucescens (98% identity), and S. avermitilis (96% identity). This suggested that this gene encodes the fatty acyl carrier protein of FAS in S. echinatus, which of course clearly explained why the protein was much more abundant in S. echinatus than the peptide synthetase TrsII.

Further proof for the identity of the binding protein with FAS ACP came from analysis of its flanking regions. The gene 5'-flanking to the acyl carrier protein gene was found to be identical to the gene coding for 3-oxoacyl-[acyl carrier protein] synthase III (FabH, SCO2388) of S. coelicolor. The gene 3' to the acyl carrier protein was identical with the gene encoding 3-oxoacyl-[acyl carrier protein] synthase II (FabF, SCO2390) of S. coelicolor. In S coelicolor, these two genes directly flank the acyl carrier protein gene (AcpP, SCO2389) as in S. echinatus with the same orientations (Fig. 7). The same positioning is present in S. avermitilis (42) and S. glaucescens (43). Therefore, we conclude that the QA-binding protein is the ACP of fatty acid synthase of S. echinatus. The gene and protein were designated acpPSE and AcpPSE, respectively. Testing the ACPs of FAS of other streptomycetes not producing quinoxaline antibiotics such as S. coelicolor M145, S. lividans TK64, S. griseoviridus DSM40229 or S. chrysomallus ATCC11523 in cell extracts from these strains supplemented with purified TrsI revealed in all cases QA binding in comparable specific activities as in S. echinatus (not shown). Binding of QA was not observed in these extracts when TrsI was not added, which leaves no doubt that Streptomyces FAS ACP is a specific substrate of TrsI. Repeated attempts using different experimental approaches to find other QA-binding proteins besides AcpPSE in S. echinatus or S. triostinicus always ended in the isolation of the same protein, AcpPSE. Moreover, hybridization analysis of S. echinatus DNA revealed that the gene acpPSE was present in one single copy.



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  		FIG. 7.
Fatty acid synthase genes in various streptomycete genomes and location of acpPSE on the chromosome of S. echinatus.

 
Expression of acpPSE of S. echinatus in E. coli and Characterization of the Gene Product—For expression of acpPSE of S. echinatus as the amino-terminal His6 fusion protein, the expression plasmid pEACPN2 (using vector pQE32) was constructed. Expression in E. coli strain M15 gave protein in high yield, which was purified from extracts of broken cells by Ni-NTA affinity chromatography with subsequent gel filtration on Superdex 75 (Fig. 8). MALDI-TOF mass spectrometry of the purified protein revealed a single mass peak of 10,872 Da, which exactly fitted the calculated holo-form of the protein (not shown). By contrast, expression of the S. echinatus acpPSE in S. lividans under the control of the mel promoter of pIJ702 always resulted in the appearance of a mixture of apo- and holo-form including the acetylated holo-form, which made use of the protein expressed in S. lividans inadvisable (not shown). The yield of the holo-protein from E. coli was about 1 mg liter–1 culture.



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  		FIG. 8.
Loading of recombinant AcpPSE with [14C]QA. Purified amino-terminal His6 fusion of AcpPSE on a 12.5% SDS-polyacrylamide gel (lane 1). Incubation of protein with TrsI, [14C]QA, and MgATP with subsequent SDS-PAGE and autoradiography reveals exclusive labeling of the monomer (lane 1'), whereas the AcpPSE dimer (moving as a about 28-kDa band) is not labeled. M denotes the markers and M' the location of that lane on the autoradiogram.

 
Comparison of AcpPSE with AcmACP—The recombinant AcpPSE, which under non-reducing conditions was accompanied by the disulfide form, could be loaded efficiently with [14C]QA in the presence of ATP (Fig. 8). The finding that TrsI loads AcpPSE with QA raised the question how specific this acyl carrier protein of fatty acid synthase is as substrate for A-domains. To compare the TrsI/AcpPSE pair with an "authentic" truncated initiation module such as ACMSI/AcmACP from actinomycin biosynthesis (20), AcpPSE was tested as binding protein for both ACMSI and TrsI and compared with AcmACP. Moreover, as an additional A-domain, the 3-hydroxypicolinic acid adenylating enzyme MkmsI from etamycin-producing S. griseoviridus was tested (33, 44). Fig. 9 shows time courses of loading reactions involving ACMSI, AcmACP, and AcpPSE on the one hand and TrsI, AcpPSE, and AcmACP on the other. It can be seen that TrsI strictly loaded only its cognate AcpPSE, whereas ACMSI did so for AcmACP. Replacing TrsI or ACMSI by MkmsI, the 3-hydroxypicolinic acid activating enzyme from etamycin-producing S. griseoviridus, did not show any loading of AcpPSE or AcmACP with the model substrate [14C]picolinic acid of MkmsI, indicating mutual exclusion of the carrier proteins versus the different A-domains from the streptomycetes (not shown). Kinetic analysis of the pairs TrsI/AcpPSE and ACMSI/AcmACP by measuring initial velocities at varying ACP concentrations resulted in typical velocity versus substrate curves, which allowed determination (Fig. 8, left and right panels), kcat/Km of 12.3 µM–1 min–1 for the acylation of AcpPSE by TrsI (QA) and 3.5 µM–1 min–1 for acylation of AcmACP by ACMSI (p-toluic acid). These values fit the values determined for the EntB/EntE pair from enterobactin synthesis (18) or the VibB/VibE pair from vibriobactin synthesis (45) and shows that AcpPSE behaves as a specific partner of TrsI.



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  		FIG. 9.
Kinetic analysis of the initiation modules TrsI/AcpPSE and ACMSI/AcmACP. Time courses of loading of AcpPSE ({blacksquare}) and AcmACP (•) by TrsI with [14C]QA is shown in the inset of panel A. Time courses of loading AcmACP (•) and AcpPSE ({blacksquare}) by ACMSI with [14C]p-toluic acid is shown in the inset of panel B. Velocity-substrate curves for TrsI/AcpPSE (panel A ({blacksquare})) and ACMSI/AcmACP (panel B (•)) were obtained by measuring initial velocities of carrier protein loading reactions at various carrier protein concentrations with fixed total concentration [Et] of the A-domain present. Values for kcat/Km derived from initial velocities were 13.5 and 3.5 µM–1 min–1 for TrsI/AcpPSE and ACMSI/AcmACP, respectively. Concentrations of adenylating enzymes were 30 (TrsI) and 7.5 nM (ACMSI). Note that the substrate p-toluic acid is not the natural substrate for ACMSI. With natural substrate, higher kcat/Km values are expected based on the results of total cell-free synthesis studies.2

 
AcpPSE Mediates Transfer of Quinoxaline-2-Carboxylic Acid to Triostin Synthetase II with Formation of Quinoxalinoyl D-serine—To demonstrate transfer of QA from AcpPSE to serine bound to the serine module of TrsII, partially purified TrsII was reacted with [14C]serine, in the presence of non-labeled QA, AcpPSE, TrsII, and ATP. The enzyme-bound reaction products formed were isolated by treatment of protein with NaOH and extracted with EtOAc. Fig. 10 shows the autoradiogram of a TLC separation of reaction products formed under these conditions. There was clear formation of an EtOAc-extractable radioactive compound bound to the enzyme, when all ingredients including QA were present. No formation was observed when AcpPSE, QA, or TrsI were missing from the reactions. Co-chromatography of authentic quinoxalinoyl L- or D-serine in a number of solvent systems revealed that the radioactive compound had the same Rf value as quinoxalinoyl L- or D-serine. Acid hydrolysis of the radioactive compound yielded back radioactive serine. When the same experiments were performed with TPA, a radioactive compound was formed with coordinately higher Rf value, suggesting that this was the TPA-serine analogue of quinoxalinoyl serine (Fig. 10). These findings strongly suggest that loaded AcpPSE is the specific substrate for TrsII in the initiation of QA tetrapeptide assembly. By contrast, when ACMSII was incubated with AcpPSE, TrsI, QA, and threonine no formation of quinoxalinoyl threonine was observed, indicating strict specificity of AcpPSE for TrsII. Determination of the optical configuration of the serine moiety in the enzymatically formed radioactive quinoxalinoyl serine after acid hydrolysis of the compound showed that more than two-thirds of the serine was in the D-configuration, consistent with the fact that the serine in the quinoxaline antibiotics has the D-configuration (Fig. 10). The formation of a mixture of quinoxalinoyl D-serine and quinoxalinoyl L-serine on the surface of the enzyme is obviously the result of reaction under non-turnover conditions. In other epimerizing NRPS systems, enzymes such as gramidicin synthetase I bound substrates (D- and L-phenylalanine in the ratio of 7:3) (46) or actinomycin synthetase II (threonyl-L-valine and threonyl-D-valine in the ratio of 1:1) (47), mixtures of enantiomers also exist in non-turnover conditions. In conclusion, these data clearly identify AcpPSE as a fully functional component of the quinoxaline antibiotics producing NRPS system and clearly identify TrsI and TrsII as its partners in the initiation process of quinoxaline antibiotics assembly.



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  		FIG. 10.
Synthesis of quinoxalinoyl-D-serine catalyzed by TrsI and TrsII in conjunction with AcpPSE. The various lanes show autoradiographs of TLC separations of reaction products formed in the presence of TrsI (15 nM), TrsII (0.05 units), and AcpPSE (0.6 µM) bound as thioester to TrsII. The incubations were with 0.5 µCi of [14C]L-serine, 2mM QA or TPA, 10 mM ATP, and 20 mM MgCl2 in a total volume of 250 µl (buffer B). After incubation, protein was precipitated by addition of 7% (w/v) trichloroacetic acid. Washing of the precipitate was with 7% trichloroacetic acid and finally with ethanol. Reaction products were released from protein by saponification with NaOH. After acidification, product was extracted with ethyl acetate and subjected to TLC. Panel A, formation of quinoxalinoyl serine (compound denoted a) dependent on the presence of the indicated components. Panel B shows formation of thieno[3,2-b]pyridine-5-carboxyloyl serine (denoted b) with TPA replacing QA. Panel C shows the separation on a chiral plate of an acid hydrolysate of the enzymatically formed radioactive quinoxalinoyl serine (a), which yields back [14C]serine. The major portion of the serine has the D-configuration. Solvent systems were III (panels A and B) and IV (panel C).

 

   DISCUSSION
TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
REFERENCES
 
Chromopeptide lactones are heterodetic cyclopeptides in which aromatic or heteroaromatic carboxylic acids are attached via amide bonds to the free amino groups of peptide lactone rings (48). The biosynthesis of such compounds proceeds by the enzymatic assembly of aroyl peptide chains on a multifunctional NRPS with final cyclization or cyclodimerization (16, 44). A specific feature of these NRPS systems is that recruitment of the aromatic carboxylic acids is by free-standing A-domains. These enzymes transfer the aromatic carboxylic acid, after its activation as adenylate to a binding or carrier protein that reacts with the first NRPS module in the biosynthetic sequence, condensing the aroyl residue with the first amino acid.

The QA tetrapeptide chains of the quinoxaline antibiotics from their structures resemble the aroyl peptide chains of other chromopeptide lactones from streptomycetes such as the actinomycins or the mikamycin B II group of antibiotics, which points to similar organizations of the catalytic domains of their assembly systems (21, 29). In fact, TrsI from S. triostinicus and S. echinatus, which activate QA as adenylate, is similar in size and sequence to its counterparts in the syntheses of actinomycin (ACMSI), pristinamycin I (SnbA), and etamycin (MkmsI) (33, 44). It also has significant similarity to the various aryl carboxylic acid activating A-domains from the biosynthetic systems for the bacterial catechol/hydroxyphenyl-capped siderophore peptides such as enterobactin (EntE), yersiniabactin (YbtE), or vibriobactin (VibE) (17). Analysis of the specificity determining amino acid residues in the putative substrate-binding pocket of TrsI derived by comparison with the binding pocket structure of gramicidin synthetase I (Fig. 5) indicated the highest similarity with the binding pocket of SnbA, which activates 3-hydroxypicolinic acid, the chromophore of pristinamycin I (29). Although TrsI does not activate 3-hydroxypicolinic acid, the similarity agrees with the finding that it prefers quinoline-derived carboxylic acids as substrates where the ring nitrogen (like in 3-hydroxypicolinic acid) is proximal to the carboxyl group (14). Both TrsI and MkmsI (the SnbA orthologue) from etamycin-producing S. griseoviridus, albeit weakly, activate the compound pyrazine-2-carboxylic acid, which may indirectly confirm the similarity seen in the substrate binding pockets of TrsI and SnbA.2

All of the free-standing A-domains that activate aromatic carboxylic acids in the biosynthesis of the various catechol- or hydroxyphenyl-capped peptide siderophores acylate specific carrier proteins (ArCPs) (17). These are similar to the PCP domains of NRPS and are fused to isochorismate lyase, an enzyme involved in the synthesis of the aromatic carboxylic acid 2,3-dihdroxybenzoic acid used as starter residue in these syntheses. In other cases, such as in the synthesis systems of yersiniabactin or pyochelin, the carrier domain is fused amino-terminal to the NRPS lying downstream in the biosynthetic sequence, HMWP2 or PchE, respectively (17, 19, 37). By contrast, in the case of quinoxaline antibiotic biosynthesis described here, a stand-alone ArCP domain has been identified as the binding protein for QA. This protein, AcpPSE, was identified as the fatty acyl ACP of S. echinatus by comparison of its sequence to those of FAS ACPs of S. coelicolor, S. avermitilis, or S. glaucescens. Further confirmation came from the analysis of the 5'- and 3'-flanking regions of acpPSE, which contain genes encoding putative 3-oxoacyl-ACP synthase III and 3-oxoacyl-ACP synthase II enzymes, both components of the fatty acid synthase complex. Analysis of AcpPSE using the A-domains TrsI, ACMSI, and MkmsI showed exclusive acylation by TrsI with QA (Fig. 8), suggesting intimate functional linkage between the two proteins. The kcat/Km values obtained from the loading reactions were for the pairs TrsI/AcpPSE and ACMS I/AcmACP between 5 and 15 µM–1 min–1 and therefore comparable with data obtained with the pairs EntE/EntB (18) or VibE/VibB (45), which were interpreted as the result of specific protein-protein interactions. Clearly, these values were several orders higher than those obtained when measuring acylation of coenzyme A or pantetheine with aryl carboxylic acids, which may possibly be nonenzymatic trapping of acyladenylate by these highly reactive sulfhydryl compounds (45, 49).

A further contribution to proving the involvement of AcpPSE in triostin synthesis was the identification of the NRPS modules for QA tetrapeptide assembly (Fig. 11). The data show that the triostin assembly line is analogous to those for actinomycin (Fig. 2) and pristinamycin I, indicating an evolutionary relationship in the synthetic strategies for formation of these compounds although quite different in their final structures. TrsII, as the enzyme carrying the first two modules (Fig. 4), has its counterparts in ACMSII of actinomycin or SnbC of pristinamycin I biosynthesis (14, 29). Like these, TrsII activates the first two amino acids of the peptide chain and condenses QA to the first amino acid in the initiation step by interacting in trans with the ArCP domain. Also the modules in the distal part of the assembly line, TrsIII and IV, albeit their analysis is still hampered by their instability, are strongly reminiscent of ACMSIII or SnbDE. Similar to the latter, TrsIII and TrsIV activate and most likely methylate the two carboxyl-terminal amino acids, cysteine and valine, of the QA peptide chain (as exemplified in the case of valine, Fig. 3), and cyclodimerize the QA peptide chain to the final product triostin A (Fig. 11). TrsII was an important tool to demonstrate involvement of AcpPSE in quinoxalinoyl tetrapeptide assembly by showing specificity of AcpPSE also in the condensation reaction with TrsII. Thus, AcpPSE exclusively reacted with TrsII in the formation of quinoxalinoyl L-serine (with subsequent epimerization to quinoxalinoyl D-serine) but not with ACMSII to form quinoxalinoyl L-threonine, giving strong evidence for active and highly specific participation of AcpPSE in quinoxaline antibiotic synthesis.



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  		FIG. 11.
Model of NRPS assembly line of quinoxaline antibiotics. The depicted assembly line is based on the identification of TrsII, III, and IV, together with the characterization of AcpPSE as QA carrier protein shown here and the analogy to the actinomycin assembly system (Fig. 2). D-Ser (D-serine), Ala (alanine), MeCys (N-methyl-L-cysteine), and MeVal (N-methyl-L-valine) are shown. The proposed module organization is based on the structure of the quinoxalinoyl tetrapeptide chain considering colinearity of modules and amino acid sequence of the peptide product.

 
The observed strict mutual exclusion as substrates of AcpPSE and AcmACP by TrsI and ACMSI is surprising in the light of previous findings that PCP domains in NRPS systems can be portable (50). Apparently, the portability of PCP domains in modules may be due to the high sequence similarity among PCP domains in NRPS modules and their positive charges at neutral pH that contrasts the negative charges of stand-alone ACP domains of fatty acid synthases or polyketide synthases of type II. The negative charges may facilitate protein-protein interaction with positively charged partners (16, 51). In fact, the free-standing A-domains of chromopeptide synthesis systems have pI values around 6–7, which could facilitate their interaction with acidic ACPs. By contrast, the A-domains in modules have slightly acidic pI values of 5–6.

Previous reports show that the amino acid residues conferring specificity of the recognition of the ArCP of vibriobactin synthesis, VibB, by the A-domain VibE and the amide synthase VibH could be mapped to the 4'-phosphopantetheine binding site of the ArCP (45). ACPs are four-helix bundle proteins (52) from which helix 2, directly lying carboxyl-terminal to the 4'-phosphopantetheine binding site, is critical for recognition of ACPs by phosphopantetheine transferases in the post-translational modification of the protein with 4'-phosphopantetheine cofactor (53, 54). Helix 2 has also been assigned a critical role in recognition of ACP by acyl-ACP synthetase in the acylation with fatty acids (55) and in the recognition by ketoacyl synthase III in the elongation cycles of fatty acid synthases (56). AcpPSE has an acidic helix 2, whereas in AcmACP, the free standing ArCP domain of actinomycin synthesis, that helix is less acidic because of the presence of a histidine missing in the AcpPSE sequence (Fig. 12). This, besides other features in the structures, may possibly explain the different behavior of the two carrier protein versus TrsI and ACMSI, respectively. AcmACP also in respect of its total pI (4.1) stands between AcpPSE (3.9) and the ArCP domains (5 to 9) of the aryl-capped siderophore NRPS systems, which appear to belong to the family of PCP domains of modular NRPS. These conclusions also agree with our observation that expression of acpPSE in E. coli resulted exclusively in the holo-protein, whereas expression of acmD (encoding AcmACP) resulted in only 10% holo-form, indicating that AcpS as the principal 4'-phosphopantetheine transferase in growing E. coli modifies AcmACP poorly. Whether these differences also reflect the role of helix 2 in the recognition of AcpPSE and AcmACP as substrates by their cognate A-domains remains to be seen.



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  		FIG. 12.
Alignment of putative protein recognition regions in sequences of ACPs from fatty acid synthases and ArCPs and PCP domains of several NRPS systems. The following are shown: AcpP, P02901 [GenBank] (E. coli); ACP, BAC73498 [GenBank] (S. coelicolor); AcpP, CAB62721 [GenBank] (S. avermitilis); AcpPSE, this work (S. echinatus); AcmACP, AAD30112 [GenBank] (S. chrysomallus); VibB, AAG00563 [GenBank] (V. cholerae); ACMSII(2), AAC38442 [GenBank] (PCP domain in module 2 of the peptide synthetase ASCMSII, S. chrysomallus), ACMSII(1), AAC38442 [GenBank] (PCP domain in module 1 of ACMSII).

 
Previous reports indicate that components of the fatty acid synthase complex could play a role as active participants in the processes catalyzed by polyketide synthases of type II. Thus, malonyl transferase has been shown to catalyze actinorhodin formation in S. coelicolor (57) or tetracenomycin synthesis in S. glaucescens (58). Remarkably, FAS ACP has as yet not been reported to functionally replace the corresponding ACPs in polyketide-type systems. Attempts to functionally replace the ACP of the actinorhodin polyketide synthases system in S. coelicolor A(3)2 by FAS ACPs (such as from Saccharopolyspora erythreae or from S. coelicolor A(3)2 itself) gave only traces of polyketide materials when expression of the FAS ACP genes was in cis to the other genes of the polyketide synthases gene cluster (59, 60). When expressed in trans, neither FAS ACP could complement mutants that has lost the actinorhodin ACP (60). The involvement of AcpPSE in the process of quinoxaline antibiotics assembly therefore is the first example of a FAS ACP playing a principal role in the assembly line of a secondary metabolite as well as in fatty acid synthesis. Interestingly, we noted that the amount of AcpPSE in extracts of the producer strain S. echinatus is in about 10-fold excess over TrsII, which indicates that most of the FAS ACP is involved in fatty acid synthesis and that only part of it participates in antibiotic synthesis. This raises questions in respect of physiology and regulation and how FAS ACP is distributed between the two biosynthetic systems. Possibly, a minor fraction of total AcpPSE has to be shuttled to a specific compartment or be distributed in an equilibrium reaction between the two multienzyme systems. It will be interesting to see whether the role of AcpPSE shown here in nonribosomal peptide synthesis is a unique example of interaction between primary metabolism and nonribosomal peptide synthesis or whether other chromopeptide biosynthesis systems also recruit FAS ACP as binding protein. Such investigations could lead in the future to more precisely assigning the lineage of the aromatic carboxylic acid carrier proteins to their modular companion PCP domains or to the free fatty acyl carrier proteins of type II systems of fatty acid synthase.


   FOOTNOTES
 
* This work was supported by Technical University Berlin Grant 42511/08 and Forschungsschwerpunkt SPP1152 of the Deutsche Forschungsgemeinschaft project Ke 452/11-3. 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 nucleotide sequence(s) reported in this paper has been submitted to the GenBankTM/EBI Data Bank with accession number(s) AY825941 [GenBank] . Back

{ddagger} Present address: Technische Universität Dresden, Institut für Zoologie, Mommsenstr. 13, D-01062 Dresden, Germany. Back

§ To whom correspondence should be addressed. Tel.: 49-303-142-5653; Fax: 49-303-142-4783; E-mail: ullrich.keller{at}tu-berlin.de.

1 The abbreviations used are: QA, quinoxaline-2-carboxylic acid; 4-MHA, 4-methyl-3-hydroxyanthranilic acid; TPA, thieno[3,2-b]pyridine-5-carboxylic acid; NRPS, nonribosomal peptide synthetase; FAS, fatty acid synthase; Trs, triostin synthetase; ACMS, actinomycin synthetase; Mkms, mikamycin synthetase; acm, actinomycin; trs, triostin; ACP, acyl carrier protein; ArCP, aroyl carrier protein; PCP, peptidyl carrier protein; A-domain, adenylation domain; C-domain, condensation domain; M-domain, methylation domain; E-domain, epimerization domain; MALDI-TOF, matrix-assisted laser desorption ionization time-of-flight. Back

2 U. Keller and W. Schlumbohm, unpublished data. Back


   ACKNOWLEDGMENTS
 
We thank David Hopwood for valuable discussions and critical reading of the manuscript. We also thank Sandor Biro for helpful comments. Thanks also to Ariane Zwintscher and Nicolas Grammel (ActinoDrug GmbH, Hennigsdorf, Germany) for MALDI-TOF measurements of ACPs and Fred Rosche (Probiodrug AG, Halle, Germany) for ESI measurements.



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