Purification of the polyenzymes responsible for tyrocidine synthesis and their dissociation into subunits

Engineering enzymatic assembly lines to produce new antibiotics

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Many clinical antibiotics are natural products produced by thiotemplate-based assembly line biosynthetic pathways.

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Assembly line pathways provide an opportunity for rational bioengineering to modify complex natural product structures.

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New, rule-based mix and match strategies facilitate the engineering of non-ribosomal peptide assembly line synthetases.

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Evolutionary guided approaches highlight new avenues for polyketide synthase assembly line reprogramming.

Numerous important therapeutic agents, including widely-used antibiotics, anti-cancer drugs, immunosuppressants, agrochemicals and other valuable compounds, are produced by microorganisms. Many of these are biosynthesised by modular enzymatic assembly line polyketide synthases, non-ribosomal peptide synthetases, and hybrids thereof. To alter the backbone structure of these valuable but difficult to modify compounds, the respective enzymatic machineries can be engineered to create even more valuable molecules with improved properties and/or to bypass resistance mechanisms. In the past, many attempts to achieve assembly line pathway engineering failed or led to enzymes with compromised activity. Recently our understanding of assembly line structural biology, including an appreciation of the conformational changes that occur during the catalytic cycle, have improved hugely. This has proven to be a driving force for new approaches and several recent examples have demonstrated the production of new-to-nature molecules, including anti-infectives. We discuss the developments of the last few years and highlight selected, illuminating examples of assembly line engineering.

Nonribosomal peptide synthetases involved in the production of medically relevant natural products

Natural products biosynthesized wholly or in part by nonribosomal peptide synthetases (NRPSs) are some of the most important drugs currently used clinically for the treatment of a variety of diseases. Since the initial research into NRPSs in the early 1960s, we have gained considerable insights into the mechanism by which these enzymes assemble these natural products. This review will present a brief history of how the basic mechanistic steps of NRPSs were initially deciphered and how this information has led us to understand how nature modified these systems to generate the enormous structural diversity seen in nonribosomal peptides. This review will also briefly discuss how drug development and discovery are being influenced by what we have learned from nature about nonribosomal peptide biosynthesis.

Whole cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and in situ structure analysis of streptocidins, a family of tyrocidine-like cyclic peptides

Streptocidins, a family of tyrocidine-like cyclic decapeptides, are an ideal demonstration object for the detection and in situ structure analysis of natural compounds directly in microbial cells using whole cell matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry (MALDI-TOFMS), an emerging technique that can be used for rapid sensitive metabolic profiling of microorganisms. Five main members of the streptocidin family (A-E) were detected in Brevibacillus cells picked from agar plates and identified by in situ structure analysis with post-source decay MALDI-TOFMS. This efficient modern method allows the precise detection of metabolites within minutes without the need to isolate and purify the target compounds. The generated mass spectra are of similar quality to those obtained for the purified peptides. In addition, surface extracts were prepared by treating Brevibacillus cells with 70% acetonitrile in the presence of 0.1% trifluoroacetic acid and fractionated by high-resolution reversed-phase high-performance liquid chromatography (HPLC). In this way ten minor streptocidins were detected demonstrating the full biosynthetic variety of streptocidin production on the cellular level. The streptocidins differ from the well-known tyrocidines essentially in position 3 of the decapeptide chain by replacement of the aromatic amino acid (F/W) found in tyrocidines by L-leucine or L-valine.

Characterization of a unique glycosylated anchor endopeptidase that cleaves the LPXTG sequence motif of cell surface proteins of Gram-positive bacteria

The precursors of most surface proteins on Gram-positive bacteria have a C-terminal hydrophobic domain and charged tail, preceded by a conserved LPXTG motif that signals the anchoring process. This motif is the substrate for an enzyme, termed sortase, which has transpeptidation activity resulting in the cleavage of the LPXTG sequence and ultimate attachment of the protein to the peptidoglycan. While screening a group A streptococcal membrane extract for cleavage activity of the LPXTG motif, we identified an enzyme (which we term "LPXTGase") that differs significantly from sortase but also cleaves this motif. The enzyme is heavily glycosylated, which is required for its activity. Amino acid composition and sequence analysis revealed that LPXTGase differs from other enzymes, in that the molecule, which is about 14 kDa in size, has no aromatic amino acids, is rich in alanine, and is 30% composed of uncommon amino acids, suggesting a nonribosomal construction. A similar enzyme found in the membrane extract of Staphylococcus aureus, indicates that this unusual molecule may be common among Gram-positive bacteria. Whereas peptide antibiotics have been reported from bacillus species that also contain unusual amino acids and are synthesized non-ribosomally on amino acid-activating polyenzyme templates, this would be the first reported enzyme that may be similarly synthesized.

The tyrocidine biosynthesis operon of Bacillus brevis: complete nucleotide sequence and biochemical characterization of functional internal adenylation domains

The cyclic decapeptide antibiotic tyrocidine is produced by Bacillus brevis ATCC 8185 on an enzyme complex comprising three peptide synthetases, TycA, TycB, and TycC (tyrocidine synthetases 1, 2, and 3), via the nonribosomal pathway. However, previous molecular characterization of the tyrocidine synthetase-encoding operon was restricted to tycA, the gene that encodes the first one-module-bearing peptide synthetase. Here, we report the cloning and sequencing of the entire tyrocidine biosynthesis operon (39.5 kb) containing the tycA, tycB, and tycC genes. As deduced from the sequence data, TycB (404,562 Da) consists of three modules, including an epimerization domain, whereas TycC (723,577 Da) is composed of six modules and harbors a putative thioesterase domain at its C-terminal end. Each module incorporates one amino acid into the peptide product and can be further subdivided into domains responsible for substrate adenylation, thiolation, condensation, and epimerization (optional). We defined, cloned, and expressed in Escherichia coli five internal adenylation domains of TycB and TycC. Soluble His6-tagged proteins, ranging from 536 to 559 amino acids, were affinity purified and found to be active by amino acid-dependent ATP-PPi exchange assay. The detected amino acid specificities of the investigated domains manifested the colinear arrangement of the peptide product with the respective module in the corresponding peptide synthetases and explain the production of the four known naturally occurring tyrocidine variants. The Km values of the investigated adenylation domains for their amino acid substrates were found to be comparable to those published for undissected wild-type enzymes. These findings strongly support the functional integrities of single domains within multifunctional peptide synthetases. Directly downstream of the 3' end of the tycC gene, and probably transcribed in the tyrocidine operon, two tandem ABC transporters, which may be involved in conferring resistance against tyrocidine, and a putative thioesterase were found.

ATP binding in peptide synthetases: determination of contact sites of the adenine moiety by photoaffinity labeling of tyrocidine synthetase 1 with 2-azidoadenosine triphosphate

Characterization of the nucleotide binding domain in peptide synthetases was approached by photoaffinity labeling of tyrocidine synthetase 1 (TY1) with 2-azidoadenosine triphosphate (2-azido-ATP). Exposure of TY1 in the presence of photolabel to irradiation with ultraviolet light resulted in a time-dependent covalent modification of the enzyme with a concomitant loss of catalytic activity. Inactivation was not observed if incubation was performed in the absence of either light or the nucleotide analogue. Specificity of labeling was indicated by the ability of 2-azido-ATP to serve as a substrate in the amino acid activation reaction. The modified protein was subjected to tryptic digestion, and the fragments labeled by the nucleotide analogue were purified by reverse-phase high-performance liquid chromatography. Sequence analysis identified three tryptic peptides corresponding to residues G373-K384, W405-R416, and L483-K494, derived from the N-terminal half of the TY1 sequence. As this region shows similarity to strongly conserved regions in other peptide synthetases and acyl-CoA synthetases, it is considered to be the region catalyzing aminoacyl adenylate formation. The identified sequences appear to define components of the nucleotide binding domain found in close proximity to the adenine ring in ATP. Conservation of primary structure and homology to other carboxyl-activating enzymes of this superfamily, including peptide synthetases, insect luciferases, and acyl-CoA synthetases, is discussed.

Analysis of core sequences in the D-Phe activating domain of the multifunctional peptide synthetase TycA by site-directed mutagenesis

The D-phenylalanine-activating enzyme tyrocidine synthetase I (TycA) from Bacillus brevis ATCC 8185 was overexpressed in Escherichia coli, purified to homogeneity, and assayed for ATP-PPi exchange and covalent binding of phenylalanine by the thiotemplate mechanism. Amino acid exchanges in four different cores of TycA created by site-directed mutagenesis revealed the amino acid residues involved in aminoacyladenylate formation and in covalent thioester formation. Mutations in the putative ATP-binding site SGTTGKPKG caused a decreased phenylalanine-dependent ATP-PPi exchange activity to 10% of the wild-type level for a Lys-186-to-Arg substitution and an almost complete loss of activity (< 1%) for a Lys-186-to-Thr exchange. Alteration of Asp-401 to Asn in the ATPase motif TGDL of TycA decreased the phenylalanine-dependent ATP-PPi exchange activity to 75% of wild type, while an Asp-401-to-Ser mutation decreased the activity to 10% of the wild-type level. Replacement of Ser-562 in the putative thioester-binding motif LGGDSI to Ala or Gly caused a reduction in trichloroacetic acid-precipitable TycA-[14C]phenylalanine complex to one-third of the wild-type level. However, no cleavable [14C]phenylalanine could be detected after treatment with performic acid, indicating that the resulting mutant was unable to form thioester with phenylalanine. In E. coli, TycA was labeled with beta-[3H]alanine, a precursor of 4'-phosphopantetheine, indicating that TycA is modified with a beta-alanine-containing cofactor.

Cyclosporin synthetase is a 1.4 MDa multienzyme polypeptide. Re-evaluation of the molecular mass of various peptide synthetases

The earlier determined molecular mass of 0.8 MDa for the multifunctional polypeptide, cyclosporin synthetase, was re-evaluated by SDS-PAGE and CsCl density gradient centrifugation. In SDS-PAGE, new molecular mass values as standards were available from sequencing data. In the CsCl density gradient extremely low protein concentrations, such as 10-50 nM could be analysed due to the fluorescence detection system of the analytical ultracentrifuge. Both methods yielded approximately the same value of about 1.4 MDa. Using this molecular mass of cyclosporin synthetase as a reference the molecular masses of various related enzymes could be re-evaluated in SDS-PAGE. The sedimentation coefficient of 26.3 S for cyclosporin synthetase indicates an oblate overall shape of the enzyme.

[Molecular biology and regulatory mechanisms of antibiotic production in Bacillus]

Several species of the genus Bacillus produce linear and cyclic peptide antibiotics nonribosomally through multienzyme complexes by the so-called thiotemplate mechanism. Molecular genetic studies have shown that some peptide antibiotic biosynthesis genes are organized in operons and that they are expressed postexponentially under conditions that also activate the process of endospore formation in Bacillus. Furthermore, DNA-sequence analysis of some multifunctional peptide synthetase genes revealed that they contain a highly conserved and repeated domain structure. The same domain was also found to be conserved within a superfamily of peptide synthetases and adenylate-forming enzymes of diverse origins. Based on sequence homology and functional similarity I conclude that those enzymes bearing domain(s) represent a family of superenzymes which may have a common evolutionary origin.

Origin of genetically encoded protein synthesis: a model based on selection for RNA peptidation

The difficulty in explaining the origin of genetic coding centres on the need to identify selective advantages that could account for the synthesis of peptidyl-tRNA, the essential intermediate in genetically programmed translation. It is resolved by a recognition of the functional advantages derivable from the post-transcriptional addition of peptide cofactors to RNA apo-catalysts. This enables the formulation of a theory for the origin of the genetic encoding of protein synthesis by RNA.

Nonribosomal biosynthesis of peptide antibiotics

Peptide antibiotics are known to contain non-protein amino acids, D-amino acids, hydroxy acids, and other unusual constituents. In addition they may be modified by N-methylation and cyclization reactions. Their biosynthetic origin has been connected in many cases to an enzymatic system referred to as the 'thiotemplate multienzymic mechanism'. This mechanism includes the activation of the constituent residues as adenylates on the enzymic template, the acylation of specific template thiol groups, epimerization or N-methylation at this thioester stage, and polymerization in the sequence directed by the multienzymic structure with the aid of 4'-phosphopantetheine as a cofactor, including possible cyclization or terminal modification reactions. The reaction sequences leading to gramicidin S, tyrocidine, cyclosporine, bacitracin, polymyxin, actinomycin, enniatin, beauvericin, delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine and linear gramicidin are discussed. The structures of the multienzymes, their genetic organization, the biological functions of these peptides and results on related systems are discussed.

Molecular biology of antibiotic production in Bacillus

Several species of the genus Bacillus produce peptide antibiotics which are synthesized either through a ribosomal or non-ribosomal mechanism. The antibiotics gramicidin, tyrocidine, and bacitracin are synthesized nonribosomally by the multienzyme thiotemplate mechanism. Surfactin and mycobacillin are also synthesized nonribosomally but by a mechanism that, apparently, is distinct from that of the multienzyme thiotemplate. Other antibiotics such as subtilin are gene encoded and are ribosomally synthesized. Molecular genetic and DNA sequence analysis have shown that biosynthesis genes for some antibiotics are clustered into polycistronic transcription units and are under the control of global regulatory systems that govern the expression of genes that are induced when Bacillus cells enter stationary phase of growth. Future experiments involving the molecular dissection of peptide antibiotic biosynthesis genes in Bacillus will be attempted in hopes of further examining the mechanism and regulation of antibiotic production.

Role of ATP and enzyme-bound nascent peptides in the control of elongation for mycobacillin synthesis

The enzyme fraction A, a constituent of the three-fraction (A, B and C) enzyme complex mycobacillin synthetase, elongated tri- and tetra-peptides, under enzyme-bound conditions, to tetra- and penta-peptides respectively in the presence of the 'next' amino acid (in the mycobacillin sequence). The enzyme fraction B synthesized hexapeptide from free pentapeptide and the next amino acid, but synthesized heptapeptide from hexapeptide only under enzyme-bound conditions in the presence of the next amino acid. Similarly, the enzyme fraction C synthesized decapeptide from free nonapeptide in the presence of the next amino acid, but undecapeptide only from enzyme-bound decapeptide in the presence of the next amino acid during the elongation process. The Km values for the initiating reactions for each of the three enzyme fractions were 6-7-fold lower than those for the succeeding reactions catalysed by each of the enzyme fractions. The specificity of the initiation and elongation is discussed in the light of these findings.

Purification of the constituent enzyme fractions of mycobacillin synthetase

The final purification of the three-fraction enzyme complex mycobacillin synthetase was done by hydroxyapatite column chromatography and sucrose-density-gradient centrifugation; each of the fractions obtained migrates as a single component in SDS/polyacrylamide-gel electrophoresis and gel electrofocusing. The Mr of the enzyme fractions A, B and C by gel filtration is 260 000, 190 000 and 105 000, and that by SDS/polyacrylamide-gel electrophoresis is 252 000, 198 000 and 108 000 respectively. None of the enzyme fractions appears to possess subunit structure.

Functional characterization of constituent enzyme fractions of mycobacillin synthetase

The enzyme fraction A, a constituent enzyme of the three-fraction enzyme mycobacillin synthetase, independently and sequentially activated five amino acids starting from L-proline, producing the pentapeptide Pro(Asp1,Glu1,Tyr1)Asp. The fractions B and C were unable to function independently. However, the fraction B synthesized the nonapeptide Pro(Asp3,Glu1,Tyr2,Ser1)Leu, sequentially activating the pentapeptide and next four amino acids, whereas the fraction C synthesized mycobacillin by the sequential activation of the nonapeptide and the remaining four amino acids. The pH optima of the above enzymes are almost identical (pH 7.8), but their Km values are a little different.

Isolation and properties of Bacillus brevis mutants unable to produce tyrocidine

Mutants of Bacillus brevis ATCC 10068 were isolated which produced less than 1/100 of the amount of tyrocidine produced by the parent strain. These mutants produced spores at the same frequency and which were as resistant to heating at 80 degrees C for up to 3 h as were those produced by the parent strain. A partially purified tyrocidine synthetase from strain ATCC 10068 catalyzed [32P]PPi-ATP exchange reactions dependent on added tyrocidine-constituent amino acids. These activities were separated into three groups (I, II, and III) by fractionation on an Ultrogel AcA34 column. Each group was similar to one of the three components (heavy, intermediate, and light, respectively) found previously for strain ATCC 8185 except that glutamate-dependent activity was not detected in the group I activities and some amino acyl-tRNA synthetase activities were associated with the group III activities. Some of the mutants were shown to have defective tyrocidine synthetase enzymes. Mutant BH30 was defective in two of the group II amino acid-dependent [32P]PPi-ATP exchange reactions, mutant BH16 was defective in one of the group I and one of the group II reactions, and mutant BH34 had alterations to activities in all of the groups. It is unlikely that any of these mutants could synthesise tyrocidine. We conclude that tyrocidine is not involved in either the sporulation process or the resistance of spores of B. brevis ATCC 10068 to heating at 80 degrees C for up to 3 h.

Gramicidin S-synthetase. Preparation of the multienzymic complex with a high specific activity

A new purification procedure for the multienzyme of gramicidin S-synthetase has been developed. In vitro proteolysis with partial inactivation is suppressed by protease inhibitors EDTA, phenylmethylsulfonylfluoride, and fast preparation methods during initial separation steps. Activity has only been assayed by the total reaction of gramicidin S-synthetase, not by partial reactions of amino acid activation. The assay has been improved by evaluation of inhibitory concentrations of buffers, salts, and the product gramicidin S. It has been demonstrated that the rate of peptide synthesis in extracts containing both enzymes of gramicidin S-synthetase depends on protein concentration in a second order function. The multienzyme or heavy enzyme has been purified about 1400-fold to a specific activity of 24 nM/min per mg of protein, and the relation of this activity to the calculated in vivo activity is discussed.

Biosynthesis of thyrotropin releasing factor: effect of RNase treatment

In the present study the role of RNA in the vitro biosynthesis of thyrotropin releasing factor (TRF) was investigated. The biosynthesis of TRF was assessed by measuring the ability of a 1000 g supernatant fraction of newt brain origin to incorporate (3H)proline into (3H)TRF. It was found that measurable amounts of (3H)TRF are synthesized by newt brain homogenates, that preincubation of these homogenates with protease-free RNase completely abolishes (3H)TRF synthesis, while preincubation of homogenates with inactivated RNase allows for (3H)TRF synthesis to proceed. These studies suggest that the presence of intact RNA is mandatory for TRF biosynthesis by newt brain homogenates.

Citrate lyase from Streptococcus diacetilactis. Association with its acetylating enzyme

Citrate lyase (EC 4.1.3.6) was purified 38-fold from cell-free extracts of Streptococcus diacetilactis. The enzyme was homogeneous in analytical ultracentrifugation and polyacrylamide gel electrophoresis. The final enzyme preparation contained acetate: HS-citrate lyase ligase--an acetylating enzyme which converts inactive HS-citrate lyase into enzymatically active acetyl-S-citrate lyase. This enzyme activity was purified 25-fold over the crude extract and seemed to be associated with citrate lyase. Partially purified citrate lyase from Leuconostoc citrovorum contained also its acetylating enzyme. Purified citrate lyases from Klebsiella aerogenes and Rhodopseudomonas gelatinosa were devoid of acetylating enzyme activity. The HS-form of citrate lyase from S. diacetilactis was completely acetylated and hence activated by incubation with ATP and acetate for 25 min at 25 degrees C. The enzyme did not acetylate the HS-lyases from R. gelatinosa and K. aerogenes. In contrast to the citrate lyases from R. gelatinosa and K. aerogenes the enzymes from S. diacetilactis and L. citrovorum showed only a very weak reaction inactivation. It is assumed that this is due to the association of the acetylating enzymes with these lyases.

Isolation of a peptidyl-pantetheine-protein from tyrocidine-synthesizing polyenzymes

The polyenzyme complex responsible for the synthesis of tyrocidine in Bacillus brevis (ATCC 8185) was found to contain 4'-phosphopantetheine, which appeared to be connected with the production of growing peptide chains. Confirmation of this assumption has now been obtained by purifying from bacterial lysates a polyenzyme-dissociation product; this was labeled with [(14)C]pantothenic acid and peptide chains containing tritiated amino acids, and had a molecular weight of 17,000. To obtain these results, organisms were grown udner conditions favorable for incorporation of radioactive pantothenic acid into tyrocidine-synthesizing enzymes. A crude lysate of the [(14)C]pantothenic acid-labeled organisms was preincubated with the tritiated amino acids to form enzyme-bound growing peptide chains. The doubly labeled fragments were purified from the polyenzyme-dissociation products produced by prolonged lysis. In a second set of experiments, the three enzymes responsible for tyrocidine synthesis, including the two polyenzymes containing pantetheine, were purified and incubated with radioactive amino acids and ATP to form polyenzyme-bound peptide chains. Thereupon, a Triton X-100 extract of the 20,000 x g fraction of crude homogenate was added to dissociate the purified polyenzymes. The dissociation products were purified and yielded, on dodecyl sulfate gel electrophoresis, peptidyl-marked products ranging in molecular weight from 90,000 to 17,000, the latter being most abundant. Electrophoresis of analogous preparations after preincubation with higher concentrations of dodecyl sulfate and dithiothreitol at 100 degrees yielded a single product of 17,000 molecular weight, indicating that the larger molecular weight fractions were aggregates thereof.