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1.
Biochem Biophys Res Commun ; 579: 175-180, 2021 11 19.
Article in English | MEDLINE | ID: mdl-34607171

ABSTRACT

Embryonic stem cells (ESCs) maintain a pluripotent state and genome integrity in long-term culture. A rare population of ESCs showing 2-cell embryo-specific gene expression is believed to play critical roles in sustainable pluripotency and genome stability. However, the molecular mechanism controlling this transition to a 2-cell embryo-like (2CL) state remains unclear. We carried out screening to search for the factors involved in 2CL state induction and found a ribosomal RNA processing factor, Pum3 to be a candidate. Increased 2CL state population accompanied with an accumulation of pre-ribosomal RNA and activated p53 in the Pum3-KO ESC. Furthermore, the increase of 2CL state cells in the Pum3-KO ESCs was completely abrogated by the deletion of p53. The DNA damage induced by the Ultraviolet light (UV) irradiation and Zeocin promoted the transition to a 2CL state in a p53-dependent manner. Thus, our study provides new insights into a 2CL state transition mechanism through stress-dependent p53 activation of ESCs.


Subject(s)
Bleomycin/biosynthesis , Mouse Embryonic Stem Cells/metabolism , Ribosomes/metabolism , Stress, Physiological , Tumor Suppressor Protein p53/metabolism , Animals , Apoptosis , Cell Differentiation , DNA Damage , Gene Deletion , Haploidy , Mice , Mice, Knockout , Mutagenesis , RNA/chemistry , RNA/metabolism , RNA-Binding Proteins , Ultraviolet Rays
2.
Microb Cell Fact ; 19(1): 32, 2020 Feb 13.
Article in English | MEDLINE | ID: mdl-32054531

ABSTRACT

BACKGROUND: Bleomycin is a broad-spectrum glycopeptide antitumor antibiotic produced by Streptomyces verticillus. Clinically, the mixture of bleomycin A2 and bleomycin B2 is widely used in combination with other drugs for the treatment of various cancers. As a secondary metabolite, the biosynthesis of bleomycin is precisely controlled by the complex extra-/intracellular regulation mechanisms, it is imperative to investigate the global metabolic and regulatory system involved in bleomycin biosynthesis for increasing bleomycin production. RESULTS: N-acetylglucosamine (GlcNAc), the vital signaling molecule controlling the onset of development and antibiotic synthesis in Streptomyces, was found to increase the yields of bleomycins significantly in chemically defined medium. To mine the gene information relevant to GlcNAc metabolism, the DNA sequences of dasR-dasA-dasBCD-nagB and nagKA in S. verticillus were determined by chromosome walking. From the results of Real time fluorescence quantitative PCR (RT-qPCR) and electrophoretic mobility shift assays (EMSAs), the repression of the expression of nagB and nagKA by the global regulator DasR was released under induction with GlcNAc. The relief of blmT expression repression by BlmR was the main reason for increased bleomycin production. DasR, however, could not directly affect the expression of the pathway-specific repressor BlmR in the bleomycins gene cluster. With at the beginning of bleomycin synthesis, the supply of the specific precursor GDP-mannose played the key role in bleomycin production. Genetic engineering of the GDP-mannose synthesis pathway indicated that phosphomannose isomerase (ManA) and phosphomannomutase (ManB) were key enzymes for bleomycins synthesis. Here, the blmT, manA and manB co-expression strain OBlmT/ManAB was constructed. Based on GlcNAc regulation and assisted metabolic profiling analysis, the yields of bleomycin A2 and B2 were ultimately increased to 61.79 and 36.9 mg/L, respectively. CONCLUSIONS: Under GlcNAc induction, the elevated production of bleomycins was mainly associated with the alleviation of the inhibition of BlmT, so blmT and specific precursor synthesis pathways were genetically engineered for bleomycins production improvement. Combination with subsequent metabolomics analysis not only effectively increased the bleomycin yield, but also extended the utilization of chitin-derived substrates in microbial-based antibiotic production.


Subject(s)
Acetylglucosamine/metabolism , Bleomycin/biosynthesis , Guanosine Diphosphate Mannose/metabolism , Streptomyces/metabolism , Bacterial Proteins/metabolism , Gene Expression Regulation, Bacterial , Metabolic Networks and Pathways , Metabolomics/methods , Secondary Metabolism
3.
Appl Microbiol Biotechnol ; 103(16): 6629-6644, 2019 Aug.
Article in English | MEDLINE | ID: mdl-31187208

ABSTRACT

Bleomycin, a broad-spectrum antibiotic, has been widely used for various tumor treatments. However, its poor fermentation yield is not satisfactory for industrial production. Here, the ArsR/SmtB family regulator BlmR was characterized as a repressor of bleomycin production. As an autoregulator, BlmR was found to bind to a 12-2-12 imperfect palindrome sequence in its own promoter, and deletion of blmR led to a 34% increase of bleomycin B2 production compared with the wild-type strain. Using reverse transcription and quantitative PCR (RT-qPCR), blmT, which encoded a putative transporter, was identified as the target gene regulated by BlmR. Therefore, high-production strain was constructed by blmT overexpression in a blmR deletion strain, and the bleomycin B2 titer reached to 80 mg/L, which was 1.9-fold higher than the wild-type strain. Moreover, electrophoretic mobility shift assay (EMSA) showed neither metal-binding motifs nor redox switches in BlmR. In order to elucidate the regulatory mechanism, a model of BlmR was constructed by homology modeling and protein-protein docking. The BlmR-DNA complex was generated by protein-DNA docking with the assistance of site-directed mutagenesis and molecular dynamic (MD) simulation, which directly revealed several key amino acid residues needed for the maintenance and stabilization of the interface between BlmR and target DNA. The interface information could provide the configuration reference and seek the potential effectors that could interact with BlmR, thereby extending the regulation role of ArsR/SmtB family members on the improvement of antibiotic production.


Subject(s)
Antibiotics, Antineoplastic/biosynthesis , Biosynthetic Pathways/genetics , Bleomycin/biosynthesis , Gene Expression Regulation, Bacterial , Repressor Proteins/metabolism , Streptomyces/genetics , Streptomyces/metabolism , DNA, Bacterial/metabolism , Gene Deletion , Gene Expression , Gene Expression Profiling , Molecular Docking Simulation , Promoter Regions, Genetic , Protein Binding , Repressor Proteins/deficiency , Repressor Proteins/genetics
4.
Appl Microbiol Biotechnol ; 102(4): 1651-1661, 2018 Feb.
Article in English | MEDLINE | ID: mdl-29279956

ABSTRACT

The bleomycins (BLMs) are important clinical drugs extensively used in combination chemotherapy for the treatment of various cancers. Dose-dependent lung toxicity and the development of drug resistance have restricted their wide applications. 6'-Deoxy-BLM Z, a recently engineered BLM analogue with improved antitumor activity, has the potential to be developed into the next-generation BLM anticancer drug. However, its low titer in the recombinant strain Streptomyces flavoviridis SB9026 has hampered current efforts, which require sufficient compound, to pursue preclinical studies and subsequent clinical development. Here, we report the strain improvement by combined UV mutagenesis and ribosome engineering, as well as the fermentation optimization, for enhanced 6'-deoxy-BLM production. A high producer, named S. flavoviridis G-4F12, was successfully isolated, producing 6'-deoxy-BLM at above 70 mg/L under the optimized fermentation conditions, representing a sevenfold increase in comparison with that of the original producer. These findings demonstrated the effectiveness of combined empirical breeding methods in strain improvement and set the stage for sustainable production of 6'-deoxy-BLM via pilot-scale microbial fermentation.


Subject(s)
Antibiotics, Antineoplastic/biosynthesis , Bleomycin/biosynthesis , Metabolic Engineering/methods , Mutagenesis , Ribosomes/metabolism , Streptomyces/metabolism , Ultraviolet Rays , Bleomycin/analogs & derivatives , Fermentation , Ribosomes/genetics , Streptomyces/genetics , Streptomyces/isolation & purification , Streptomyces/radiation effects
5.
Org Lett ; 19(6): 1386-1389, 2017 03 17.
Article in English | MEDLINE | ID: mdl-28256838

ABSTRACT

Streptomyces mobaraensis DSM40847 has been identified by genome mining and confirmed to be a new bleomycin (BLM) producer. Manipulation of BLM biosynthesis in S. mobaraensis has been demonstrated, as exemplified by the engineered production of 6'-deoxy-BLM A2, providing a biotechnology platform for BLM biosynthesis and engineering. Comparison of DNA cleavage efficiency and kinetics among 6'-deoxy-BLM A2 and selected analogues supports the wisdom of altering the disaccharide moiety to fine-tune BLM activity.


Subject(s)
Bleomycin/biosynthesis , Genome, Bacterial , Streptomyces/metabolism , Biosynthetic Pathways , Computer Simulation , DNA/chemistry , DNA Cleavage , Databases, Genetic , Disaccharides/chemistry , Molecular Structure , Streptomyces/genetics
6.
PLoS One ; 8(9): e76021, 2013.
Article in English | MEDLINE | ID: mdl-24069455

ABSTRACT

Although numerous marine bacteria are known to produce antibiotics via hybrid NRPS-PKS gene clusters, none have been previously described in an Alteromonas species. In this study, we describe in detail a novel hybrid NRPS-PKS cluster identified in the plasmid of the Alteromonasmacleodii strain AltDE1 and analyze its relatedness to other similar gene clusters in a sequence-based characterization. This is a mobile cluster, flanked by transposase-like genes, that has even been found inserted into the chromosome of some Alteromonasmacleodii strains. The cluster contains separate genes for NRPS and PKS activity. The sole PKS gene appears to carry a novel acyltransferase domain, quite divergent from those currently characterized. The predicted specificities of the adenylation domains of the NRPS genes suggest that the final compound has a backbone very similar to bleomycin related compounds. However, the lack of genes involved in sugar biosynthesis indicates that the final product is not a glycopeptide. Even in the absence of these genes, the presence of the cluster appears to confer complete or partial resistance to phleomycin, which may be attributed to a bleomycin-resistance-like protein identified within the cluster. This also suggests that the compound still shares significant structural similarity to bleomycin. Moreover, transcriptomic evidence indicates that the NRPS-PKS cluster is expressed. Such sequence-based approaches will be crucial to fully explore and analyze the diversity and potential of secondary metabolite production, especially from increasingly important sources like marine microbes.


Subject(s)
Alteromonas/genetics , Alteromonas/metabolism , Antibiotics, Antineoplastic/biosynthesis , Bleomycin/biosynthesis , Multigene Family , Peptide Synthases/genetics , Polyketide Synthases/genetics , Alteromonas/classification , Amino Acids/chemistry , Antibiotics, Antineoplastic/pharmacology , Bleomycin/pharmacology , Drug Resistance, Bacterial/genetics , Gene Expression Regulation, Bacterial , Gene Order , Peptide Synthases/chemistry , Peptide Synthases/metabolism , Phylogeny , Polyketide Synthases/chemistry , Polyketide Synthases/metabolism , Protein Interaction Domains and Motifs
7.
Stem Cells Dev ; 22(19): 2678-90, 2013 Oct 01.
Article in English | MEDLINE | ID: mdl-23656529

ABSTRACT

Epigenetic regulation is implicated in embryonic development and the control of gene expression in a cell-specific manner. However, little is known about the role of histone methylation changes on human cardiac differentiation and maturation. Using human embryonic stem cells (hESCs) and their derived ventricular (V) cardiomyocytes (CMs) as a model, we examined trimethylation of histone H3 lysine 4 (H3K4me3) and lysine 27 (H3K27me3) on promoters of genes associated with cardiac electrophysiology, contraction, and Ca(2+) handling. To avoid ambiguities due to heterogeneous chamber-specific types, hESC-derived ventricular cardiomyocytes (VCMs) were selected by dual zeocin-GFP expression under the transcriptional control of the MLC2v promoter and confirmed electrophysiologically by its signature action potential phenotype. High levels of H3K4me3 are present on pluripotency genes in hESCs with an absence of H3K27me3. Human ESC-VCMS, relative to hESCs, were characterized by a profound loss of H3K27me3 and an enrichment of H3K4me3 marks on cardiac-specific genes, including MYH6, MYH7, MYL2, cTNT, and ANF. Gene transcripts encoding key voltage-gated ion channels and Ca(2+)-handling proteins in hESC-VCMs were significantly increased, which could be attributed to a distinct pattern of differential H3K4me3 and H3K27me3 profiles. Treatment of hESC-VCMs with the histone deacetylase inhibitor valproic acid increased H3K4me3 on gene promoters, induced hypertrophic growth (as gauged by cell volume and capacitance), and augmented cardiac gene expression, but it did not affect electrophysiological properties of these cells. Hence, cardiac differentiation of hESCs involves a dynamic shift in histone methylation, which differentially affects VCM gene expression and function. We conclude that the epigenetic state of hESC-VCMs is dynamic and primed to promote growth and developmental maturation, but that proper environmental stimuli with chromatin remodeling will be required to synergistically trigger global CM maturation to a more adult-like phenotype.


Subject(s)
Chromatin/metabolism , Embryonic Stem Cells/metabolism , Heart Ventricles/metabolism , Histones/metabolism , Myocytes, Cardiac/metabolism , Atrial Natriuretic Factor/genetics , Bleomycin/biosynthesis , Cardiac Myosins/genetics , Cell Differentiation , Cell Line , Cell Proliferation , DNA Methylation , Electrophysiological Phenomena , Embryonic Stem Cells/cytology , Epigenesis, Genetic , Gene Expression , Gene Expression Regulation , Green Fluorescent Proteins/genetics , Heart Ventricles/embryology , Histone Deacetylase Inhibitors/pharmacology , Histone Deacetylases/metabolism , Humans , Ion Channels/genetics , Ion Transport/genetics , Myocardial Contraction/genetics , Myosin Heavy Chains/genetics , Myosin Light Chains/genetics , Patch-Clamp Techniques , Phenotype , Promoter Regions, Genetic , Valproic Acid/pharmacology
8.
Appl Microbiol Biotechnol ; 86(5): 1345-53, 2010 May.
Article in English | MEDLINE | ID: mdl-20049429

ABSTRACT

Tallysomycin (TLM) H-1, a novel TLM analog, is the major product isolated from Streptoalloteichus hindustanus SB8005, a genetically engineered strain from S. hindustanus E465-94 ATCC 31158. Based on the structural comparison and experimental assays, TLM H-1 represents a novel bleomycin (BLM) analog displaying DNA cleavage activity similar to its parent compounds TLM and BLM, both representatives of the glycopeptide anticancer antibiotics. The low titer of TLM H-1 in the engineered SB8005 strain has greatly limited its further study. In this paper, fermentation optimization for TLM H-1 production in the SB8005 strain is described; single-factor optimization and response surface methodology proved invaluable. The results indicated that three variables including distiller's grains and solubles, copper sulfate, and maltose out of eight parameters could significantly influence the TLM H-1 production. With systematic comparison and evaluation, the final optimized fermentation medium was determined. The optimized yield of TLM H-1 in the bench-top fermentor was 249.9 mg/L, which is 26.8 times higher than reported using the original medium, and 12.9-fold higher than that of the parent compound TLM produced by the wild-type strain. This work provides important parameters for TLM H-1 production by fermentation and should facilitate further mechanistic studies and clinical developments of TLM H-1 as an anticancer agent.


Subject(s)
Actinomycetales/enzymology , Antibiotics, Antineoplastic/biosynthesis , Bleomycin/analogs & derivatives , Actinomycetales/genetics , Amino Acids/metabolism , Antibiotics, Antineoplastic/chemistry , Bleomycin/biosynthesis , Carbon/metabolism , Culture Media/metabolism , Fermentation , Nitrogen/metabolism , Phosphates/metabolism , Salts/metabolism
9.
J Biol Chem ; 284(13): 8256-64, 2009 Mar 27.
Article in English | MEDLINE | ID: mdl-19189972

ABSTRACT

Tallysomycins (TLMs) belong to the bleomycin family of anticancer antibiotics. TLMs differ from bleomycins primarily by the presence of a 4-amino-4,6-dideoxy-l-talose sugar attached to C-41 as part of a glycosylcarbinolamide. We previously proposed, on the basis of bioinformatics analysis of the tlm biosynthetic gene cluster from Streptoalloteichus hindustanus E465-94 ATCC 31158, that the tlmK gene is responsible for the attachment of this sugar moiety. We now report that inactivation of tlmK in S. hindustanus abolished TLM A and TLM B production, the resultant DeltatlmK mutant instead accumulated five new metabolites, and introduction of a functional copy of tlmK to the DeltatlmK mutant restored TLM A and TLM B production. Two major metabolites, TLM K-1 and TLM K-2, together with three minor metabolites, TLM K-3, TLM K-4, and TLM K-5, were isolated from the DeltatlmK mutant, and their structures were elucidated. These findings provide experimental evidence supporting the previous functional assignment of tlmK to encode a glycosyltransferase and unveil two carbinolamide pseudoaglycones as key intermediates in the TLM biosynthetic pathway. TlmK stabilizes the carbinolamide intermediates by glycosylating their hemiaminal hydroxyl groups, thereby protecting them from hydrolysis during TLM biosynthesis. In the absence of TlmK, the carbinolamide intermediates fragment to produce an amide TLM K-1 and aldehyde intermediates, which undergo further oxidative fragmentation to afford carboxylic acids TLM K-2, TLM K-3, TLM K-4, and TLM K-5.


Subject(s)
Actinomycetales/enzymology , Antibiotics, Antineoplastic/biosynthesis , Bacterial Proteins/metabolism , Bleomycin/analogs & derivatives , Genes, Bacterial/physiology , Glucosyltransferases/metabolism , Multigene Family/physiology , Actinomycetales/genetics , Bacterial Proteins/genetics , Bleomycin/biosynthesis , Gene Deletion , Glucosyltransferases/genetics
10.
J Biol Chem ; 283(42): 28236-45, 2008 Oct 17.
Article in English | MEDLINE | ID: mdl-18697737

ABSTRACT

Bleomycin (BLM), an important clinically used antitumor compound, and its analogs are challenging to prepare by chemical synthesis. Genetic engineering of the biosynthetic pathway in the producer strain would provide an efficient and convenient method of generating new derivatives of this complex molecule in vivo. However, the BLM producing Streptomyces verticillus ATCC15003 has been refractory to all means of introducing plasmid DNA into its cells for nearly two decades. Several years after cloning and identification of the bleomycin biosynthetic gene cluster, this study demonstrates, for the first time, genetic accessibility of this pharmaceutically relevant producer strain by intergeneric Escherichia coli-Streptomyces conjugation. Gene replacement and in-frame deletion mutants were created by lambdaRED-mediated PCR targeting mutagenesis, and the secondary metabolite profile of the resultant mutants confirmed the identity of the BLM biosynthetic gene cluster and established its boundaries. Ultimately, the in-frame blmD deletion mutant strain S. verticillus SB5 resulted in the production of a bleomycin intermediate. The structure of this compound, decarbamoyl-BLM, was elucidated, and its DNA cleavage activity was compared with the parent compounds.


Subject(s)
Bleomycin/biosynthesis , Multigene Family , Streptomyces/metabolism , DNA/metabolism , Disaccharides/chemistry , Escherichia coli/metabolism , Gene Deletion , Genetic Engineering , Models, Biological , Models, Chemical , Models, Genetic , Mutation , Plasmids/metabolism , Recombination, Genetic , Sequence Analysis, DNA
11.
Mol Pharm ; 5(2): 191-211, 2008.
Article in English | MEDLINE | ID: mdl-18217713

ABSTRACT

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.


Subject(s)
Biological Products/biosynthesis , Peptide Biosynthesis, Nucleic Acid-Independent , Peptide Synthases/physiology , Anti-Bacterial Agents/biosynthesis , Bleomycin/biosynthesis , Capreomycin/biosynthesis , Catalytic Domain , Cyclosporine/metabolism , Glycopeptides/biosynthesis , Peptide Synthases/chemistry , Quinoxalines/metabolism , beta-Lactams/metabolism
12.
Mol Biosyst ; 3(1): 60-74, 2007 Jan.
Article in English | MEDLINE | ID: mdl-17216057

ABSTRACT

The tallysomycins (TLMs) belong to the bleomycin (BLM) family of antitumor antibiotics. The BLM biosynthetic gene cluster has been cloned and characterized previously from Streptomyces verticillus ATCC 15003, but engineering BLM biosynthesis for novel analogs has been hampered by the lack of a genetic system for S. verticillus. We now report the cloning and sequencing of the TLM biosynthetic gene cluster from Streptoalloteichus hindustanus E465-94 ATCC 31158 and the development of a genetic system for S. hindustanus, demonstrating the feasibility to manipulate TLM biosynthesis in S. hindustanus by gene inactivation and mutant complementation. Sequence analysis of the cloned 80.2 kb region revealed 40 open reading frames (ORFs), 30 of which were assigned to the TLM biosynthetic gene cluster. The TLM gene cluster consists of nonribosomal peptide synthetase (NRPS) genes encoding nine NRPS modules, a polyketide synthase (PKS) gene encoding one PKS module, genes encoding seven enzymes for deoxysugar biosynthesis and attachment, as well as genes encoding other biosynthesis, resistance, and regulatory proteins. The involvement of the cloned gene cluster in TLM biosynthesis was confirmed by inactivating the tlmE glycosyltransferase gene to generate a TLM non-producing mutant and by restoring TLM production to the DeltatlmE::ermE mutant strain upon expressing a functional copy of tlmE. The TLM gene cluster is highly homologous to the BLM cluster, with 25 of the 30 ORFs identified within the two clusters exhibiting striking similarities. The structural similarities and differences between TLM and BLM were reflected remarkably well by the genes and their organization in their respective biosynthetic gene clusters.


Subject(s)
Antibiotics, Antineoplastic/biosynthesis , Bleomycin/analogs & derivatives , Bleomycin/biosynthesis , Streptomyces/genetics , Amino Acid Sequence , Antibiotics, Antineoplastic/chemistry , Bleomycin/chemistry , Carbohydrates/biosynthesis , Cloning, Molecular , Electroporation , Escherichia coli/genetics , Molecular Sequence Data , Polyketide Synthases/genetics , Sequence Analysis, DNA , Sequence Homology, Amino Acid , Spores, Bacterial/genetics , Streptomyces/metabolism , Substrate Specificity
14.
Nat Chem Biol ; 1(3): 122-4, 2005 Aug.
Article in English | MEDLINE | ID: mdl-16408011

ABSTRACT

Chemical biologists studying natural-product pathways encoded in genomes have unearthed new chemistry and insights into the evolution of biologically active metabolites.


Subject(s)
Biochemistry/trends , Drug Design , Bacterial Proteins/genetics , Bleomycin/biosynthesis , Bleomycin/chemical synthesis , Computational Biology/trends , Ivermectin/analogs & derivatives , Ivermectin/chemical synthesis , Lovastatin/biosynthesis , Lovastatin/chemical synthesis , Mass Spectrometry/trends , Molecular Structure , Proteomics/trends
15.
Biochemistry ; 42(32): 9722-30, 2003 Aug 19.
Article in English | MEDLINE | ID: mdl-12911314

ABSTRACT

The natural products epothilone and bleomycin are assembled by hybrid polyketide/nonribosomal peptide synthetases. Of note in these assembly lines is the conversion of internal cysteine residues into thiazolines and their subsequent oxidation to heteroaromatic thiazole rings. We have excised the EpoB oxidase domain, EpoB-Ox, proposed to be responsible for thiazoline to thiazole oxidation in epothilone biosynthesis, and expressed it in soluble form in Escherichia coli. The purified domain is an FMN-containing flavoprotein that demonstrates thiazoline to thiazole oxidase activity when incubated with thioester substrate mimics. Kinetic parameters were determined for both thiazoline and oxazoline substrates, with k(cat) values ranging between 48.8 and 0.55 min(-1). While the physiological electron acceptor is not yet known, molecular oxygen is needed in these in vitro assays to mediate reoxidation of reduced FMN. Additionally, the oxidase domain-containing BlmIII from the bleomycin assembly line was heterologously expressed and purified. BlmIII is also an FMN-containing protein with activity similar to EpoB-Ox. This work marks the first direct characterization of nonribosomal peptide synthetase oxidase domain activity and will lead to further exploration of these flavoproteins.


Subject(s)
Bleomycin/biosynthesis , Epothilones/biosynthesis , Oxidoreductases/metabolism , Peptide Chain Elongation, Translational , Thiazoles/metabolism , Escherichia coli/metabolism , Escherichia coli Proteins/chemistry , Esters/chemistry , Esters/metabolism , Flavin Mononucleotide/chemistry , Flavin Mononucleotide/metabolism , Kinetics , Oxidation-Reduction , Oxidoreductases/chemistry , Protein Structure, Tertiary , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Stereoisomerism , Sulfhydryl Compounds/chemistry , Sulfhydryl Compounds/metabolism , Thiazoles/chemistry
16.
Biochemistry ; 42(32): 9731-40, 2003 Aug 19.
Article in English | MEDLINE | ID: mdl-12911315

ABSTRACT

Cloning and sequence analysis of the bleomycin (BLM) biosynthetic gene cluster predicted that the two nonribosomal peptide synthetases (NRPSs), BlmIV and BlmIII, are responsible for the biosynthesis of the BLM bithiazole moiety. BlmIV is a seven domain (C(2)-A(2)-PCP(2)-Cy(1)-A(1)-PCP(1)-Cy(0)) NRPS, and BlmIII is a three domain (A(0)-PCP(0)-Ox) NRPS. The three domains of Cy(1)-A(1)-PCP(1) residing on the BlmIV subunit, the four domains of Cy(0) residing on the BlmIV subunit, and A(0)-PCP(0)-Ox residing on the BlmIII subunit constitute the two thiazole-forming NRPS-1 and NRPS-0 modules, respectively. BlmIII-A(0) was predicted to be nonfunctional, raising the question of how the NRPS-0 module activates and loads the Cys substrate to its cognate BlmIII-PCP(0). The NRPS-0 module consists of domains residing on two different subunits, requiring precise protein-protein interaction. Here, we report the production of the BlmIV and BlmIII NRPSs as an excised domain(s), module, or intact subunit form and biochemical characterizations of the resultant enzymes in vitro for their roles in BLM bithiazole biosynthesis. Our results (a) confirm that BlmIII-A(0) is a naturally occurring nonfunctional mutant, (b) demonstrate that BlmIV-A(1) activates Cys and catalyzes both in cis aminoacylation of BlmIV-PCP(1) (for NRPS-1) and in trans aminoacylation of BlmIII-PCP(0) (for NRPS-0), and (c) reveal that the C-terminus of the BlmIV subunit, characterized by the unprecedented AGHDDD(G) and PGHDDG repeats, is absolutely required for in trans aminoacylation of BlmIII-PCP(0). These findings underscore the flexibility and versatility of NRPSs in both structure and mechanism for natural product biosynthesis and provide an outstanding opportunity to study the molecular recognition and protein-protein interaction mechanism in NRPS assembly line enzymology.


Subject(s)
Bleomycin/analogs & derivatives , Peptide Synthases/metabolism , Thiazoles/chemistry , Thiazoles/metabolism , Acylation , Amino Acid Motifs , Amino Acid Sequence , Bleomycin/biosynthesis , Cloning, Molecular , Consensus Sequence , Cysteine/metabolism , Escherichia coli Proteins/metabolism , Molecular Sequence Data , Peptide Synthases/chemistry , Peptide Synthases/genetics , Protein Structure, Tertiary , Protein Subunits/chemistry , Protein Subunits/genetics , Protein Subunits/metabolism , Recombinant Proteins/metabolism , Repetitive Sequences, Amino Acid , Stereoisomerism
17.
J Nat Prod ; 65(3): 422-31, 2002 Mar.
Article in English | MEDLINE | ID: mdl-11908996

ABSTRACT

Bleomycin (BLM) biosynthesis has been studied as a model for hybrid peptide-polyketide natural product biosynthesis. Cloning, sequencing, and biochemical characterization of the blm biosynthetic gene cluster from Streptomyces verticillus ATCC15003 revealed that (1) the BLM hybrid peptide-polyketide aglycon is assembled by the BLM megasynthetase that consists of both nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) modules; (2) BlmIX/BlmVIII/BlmVII constitute a natural hybrid NRPS/PKS/NRPS system, serving as a model for both hybrid NRPS/PKS and PKS/NRPS systems; (3) the catalytic sites appear to be conserved in both hybrid NRPS/PKS and nonhybrid NRPS or PKS systems, with the exception of the KS domains in the hybrid NRPS/PKS systems that are unique; (4) specific interpolypeptide linkers may play a critical role in intermodular communication to facilitate the transfer of the growing intermediates between the interacting NRPS and/or PKS modules; (5) post-translational modification of the BLM megasynthetase has been accomplished by a single PPTase with broad carrier protein specificity; and (6) BlmIV/BlmIII-templated assembly of the BLM bithiazole moiety requires intriguing protein juxtaposition and modular recognition. These results lay the foundation to investigate the molecular basis for intermodular communication between NRPS and PKS in hybrid peptide-polyketide natural product biosynthesis and set the stage for engineering novel BLM analogues by genetic manipulation of genes governing BLM biosynthesis.


Subject(s)
Antibiotics, Antineoplastic/biosynthesis , Biological Factors/biosynthesis , Bleomycin/biosynthesis , Multienzyme Complexes/metabolism , Peptide Synthases/metabolism , Streptomyces , Biotechnology/methods , Catalysis , Genes, Bacterial , Models, Chemical , Molecular Structure , Multienzyme Complexes/genetics , Multigene Family , Streptomyces/enzymology , Streptomyces/genetics , Streptomyces/metabolism , Substrate Specificity
18.
J Biol Chem ; 277(3): 2311-20, 2002 Jan 18.
Article in English | MEDLINE | ID: mdl-11706014

ABSTRACT

Bleomycin (Bm) in the culture broth of Streptomyces verticillus is complexed with Cu(2+) (Cu(II)). In the present study, we determined the x-ray crystal structures of the Cu(II)-bound and the metal-free types of Bm at a high resolution of 1.6 and 1.8 A, respectively, which are complexed with a Bm resistance determinant from Bm-producing S. verticillus, designated BLMA. In the current model of Cu(II).Bm complexed with BLMA, two Cu(II).Bm molecules bind to the BLMA dimer. The electron density map shows that the copper ion is clearly defined in the metal-binding domain of the Bm molecule. The metal ion is penta-coordinated by a tetragonal monopyramidal cage of nitrogens and binds to the primary amine of the beta-aminoalanine moiety of Bm. The binding experiment between Bm and BLMA showed that each of the two Bm-binding pockets has a different dissociation constant (K(d)(1) and K(d)(2)). The K(d)(1) value of 630 nm for the first Bm binding is larger than the K(d)(2) value of 120 nm, indicating that the first Bm binding gives rise to a cooperative binding of the second Bm to the other pocket.


Subject(s)
Acetyltransferases/chemistry , Bacterial Proteins , Bleomycin/chemistry , Copper/chemistry , Streptomyces/metabolism , Bleomycin/biosynthesis , Bleomycin/metabolism , Crystallography, X-Ray , Culture Media , Models, Molecular , Molecular Structure , Protein Binding
19.
Chem Biol ; 8(7): 725-38, 2001 Jul.
Article in English | MEDLINE | ID: mdl-11451672

ABSTRACT

BACKGROUND: Phosphopantetheinyl transferases (PPTases) catalyze the posttranslational modification of carrier proteins by the covalent attachment of the 4'-phosphopantetheine (P-pant) moiety of coenzyme A to a conserved serine residue, a reaction absolutely required for the biosynthesis of natural products including fatty acids, polyketides, and nonribosomal peptides. PPTases have been classified according to their carrier protein specificity. In organisms containing multiple P-pant-requiring pathways, each pathway has been suggested to have its own PPTase activity. However, sequence analysis of the bleomycin biosynthetic gene cluster in Streptomyces verticillus ATCC15003 failed to reveal an associated PPTase gene. RESULTS: A general approach for cloning PPTase genes by PCR was developed and applied to the cloning of the svp gene from S. verticillus. The svp gene is mapped to an independent locus not clustered with any of the known NRPS or PKS clusters. The Svp protein was overproduced in Escherichia coli, purified to homogeneity, and shown to be a monomer in solution. Svp is a PPTase capable of modifying both type I and type II acyl carrier proteins (ACPs) and peptidyl carrier proteins (PCPs) from either S. verticillus or other Streptomyces species. As compared to Sfp, the only 'promiscuous' PPTase known previously, Svp displays a similar catalytic efficiency (k(cat)/K(m)) for the BlmI PCP but a 346-fold increase in catalytic efficiency for the TcmM ACP. CONCLUSIONS: PPTases have recently been re-classified on a structural basis into two subfamilies: ACPS-type and Sfp-type. The development of a PCR method for cloning Sfp-type PPTases from actinomycetes, the recognition of the Sfp-type PPTases to be associated with secondary metabolism with a relaxed carrier protein specificity, and the availability of Svp, in addition to Sfp, should facilitate future endeavors in engineered biosynthesis of peptide, polyketide, and, in particular, hybrid peptide-polyketide natural products.


Subject(s)
Cloning, Molecular , Streptomyces/enzymology , Transferases (Other Substituted Phosphate Groups)/genetics , Amino Acid Sequence , Antineoplastic Agents , Bleomycin/biosynthesis , Carrier Proteins/genetics , Carrier Proteins/isolation & purification , Carrier Proteins/metabolism , Kinetics , Molecular Sequence Data , Multigene Family , Polymerase Chain Reaction , Sequence Alignment , Transferases (Other Substituted Phosphate Groups)/metabolism
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