Cloning and characterization of a new hetero-gene cluster of nonribosomal peptide synthetase and polyketide synthase from the cyanobacterium Microcystis aeruginosa K-139

ABSTRACTCyanobacteria are a rich source of natural products with interesting pharmaceutical properties. Here, we report the identification, sequencing, annotation, and biochemical analysis of the nostophycin (npn) biosynthetic gene cluster. Thenpngene cluster spans 45.1 kb and consists of three open reading frames encoding a polyketide synthase, a mixed polyketide nonribosomal peptide synthetase, and a nonribosomal peptide synthetase. The genetic architecture and catalytic domain organization of the proteins are colinear in arrangement, with the putative order of the biosynthetic assembly of the cyclic heptapeptide. NpnB contains an embedded monooxygenase domain linking nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) catalytic domains and predicted here to hydroxylate the nostophycin during assembly. Expression of the adenylation domains and subsequent substrate specificity assays support the involvement of this cluster in nostophycin biosynthesis. Biochemical analyses suggest that the loading substrate of NpnA is likely to be a phenylpropanoic acid necessitating deletion of a carbon atom to explain the biosynthesis of nostophycin. Biosyntheses of nostophycin and microcystin resemble each other, but the phylogenetic analyses suggest that they are distantly related to one another.

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Characterization of the Saframycin A Gene Cluster from Streptomyces lavendulae NRRL 11002 Revealing a Nonribosomal Peptide Synthetase System for Assembling the Unusual Tetrapeptidyl Skeleton in an Iterative Manner

Journal of Bacteriology ◽

10.1128/jb.00826-07 ◽

2007 ◽

Vol 190 (1) ◽

pp. 251-263 ◽

Cited By ~ 76

Author(s):

Lei Li ◽

Wei Deng ◽

Jie Song ◽

Wei Ding ◽

Qun-Fei Zhao ◽

...

Keyword(s):

Gene Cluster ◽

Biosynthetic Gene Cluster ◽

Nonribosomal Peptide Synthetase ◽

Combinatorial Biosynthesis ◽

Common Mechanism ◽

Nonribosomal Peptide ◽

Streptomyces Lavendulae ◽

Peptide Synthetase

ABSTRACT Saframycin A (SFM-A), produced by Streptomyces lavendulae NRRL 11002, belongs to the tetrahydroisoquinoline family of antibiotics, and its core is structurally similar to the core of ecteinascidin 743, which is a highly potent antitumor drug isolated from a marine tunicate. In this study, the biosynthetic gene cluster for SFM-A was cloned and localized to a 62-kb contiguous DNA region. Sequence analysis revealed 30 genes that constitute the SFM-A gene cluster, encoding an unusual nonribosomal peptide synthetase (NRPS) system and tailoring enzymes and regulatory and resistance proteins. The results of substrate prediction and in vitro characterization of the adenylation specificities of this NRPS system support the hypothesis that the last module acts in an iterative manner to form a tetrapeptidyl intermediate and that the colinearity rule does not apply. Although this mechanism is different from those proposed for the SFM-A analogs SFM-Mx1 and safracin B (SAC-B), based on the high similarity of these systems, it is likely they share a common mechanism of biosynthesis as we describe here. Construction of the biosynthetic pathway of SFM-Y3, an aminated SFM-A, was achieved in the SAC-B producer (Pseudomonas fluorescens). These findings not only shed new insight on tetrahydroisoquinoline biosynthesis but also demonstrate the feasibility of engineering microorganisms to generate structurally more complex and biologically more active analogs by combinatorial biosynthesis.

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Characterization of a Gene Cluster Responsible for the Biosynthesis of Anticancer Agent FK228 in Chromobacterium violaceum No. 968

Applied and Environmental Microbiology ◽

10.1128/aem.01751-06 ◽

2007 ◽

Vol 73 (11) ◽

pp. 3460-3469 ◽

Cited By ~ 38

Author(s):

Yi-Qiang Cheng ◽

Min Yang ◽

Andrea M. Matter

Keyword(s):

Gene Cluster ◽

Genomic Dna ◽

Polyketide Synthase ◽

Anticancer Agent ◽

Biosynthetic Gene Cluster ◽

Nonribosomal Peptide Synthetase ◽

Biosynthetic Gene ◽

Biosynthetic Genes ◽

Nonribosomal Peptide ◽

Peptide Synthetase

ABSTRACT A gene cluster responsible for the biosynthesis of anticancer agent FK228 has been identified, cloned, and partially characterized in Chromobacterium violaceum no. 968. First, a genome-scanning approach was applied to identify three distinctive C. violaceum no. 968 genomic DNA clones that code for portions of nonribosomal peptide synthetase and polyketide synthase. Next, a gene replacement system developed originally for Pseudomonas aeruginosa was adapted to inactivate the genomic DNA-associated candidate natural product biosynthetic genes in vivo with high efficiency. Inactivation of a nonribosomal peptide synthetase-encoding gene completely abolished FK228 production in mutant strains. Subsequently, the entire FK228 biosynthetic gene cluster was cloned and sequenced. This gene cluster is predicted to encompass a 36.4-kb DNA region that includes 14 genes. The products of nine biosynthetic genes are proposed to constitute an unusual hybrid nonribosomal peptide synthetase-polyketide synthase-nonribosomal peptide synthetase assembly line including accessory activities for the biosynthesis of FK228. In particular, a putative flavin adenine dinucleotide-dependent pyridine nucleotide-disulfide oxidoreductase is proposed to catalyze disulfide bond formation between two sulfhydryl groups of cysteine residues as the final step in FK228 biosynthesis. Acquisition of the FK228 biosynthetic gene cluster and acclimation of an efficient genetic system should enable genetic engineering of the FK228 biosynthetic pathway in C. violaceum no. 968 for the generation of structural analogs as anticancer drug candidates.

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Characterization of the Ketosynthase and Acyl Carrier Protein Domains at the LnmI Nonribosomal Peptide Synthetase–Polyketide Synthase Interface for Leinamycin Biosynthesis

Organic Letters ◽

10.1021/acs.orglett.6b02033 ◽

2016 ◽

Vol 18 (17) ◽

pp. 4288-4291 ◽

Cited By ~ 9

Author(s):

Yong Huang ◽

Gong-Li Tang ◽

Guohui Pan ◽

Chin-Yuan Chang ◽

Ben Shen

Keyword(s):

Polyketide Synthase ◽

Acyl Carrier Protein ◽

Protein Domains ◽

Nonribosomal Peptide Synthetase ◽

Carrier Protein ◽

Nonribosomal Peptide ◽

Peptide Synthetase

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Draft Genome Sequence of Saccharomonospora sp. Strain LRS4.154, a Moderately Halophilic Actinobacterium with the Biotechnologically Relevant Polyketide Synthase and Nonribosomal Peptide Synthetase Systems

Genome Announcements ◽

10.1128/genomea.00392-17 ◽

2017 ◽

Vol 5 (21) ◽

Author(s):

Scarlett Alonso-Carmona ◽

Blanca Vera-Gargallo ◽

Rafael R. de la Haba ◽

Antonio Ventosa ◽

Horacio Sandoval-Trujillo ◽

...

Keyword(s):

Genome Sequence ◽

Polyketide Synthase ◽

Draft Genome ◽

Nonribosomal Peptide Synthetase ◽

Open Reading Frames ◽

Draft Genome Sequence ◽

Nonribosomal Peptide ◽

Moderately Halophilic ◽

Peptide Synthetase ◽

Reading Frames

ABSTRACT The draft genome sequence of Saccharomonospora sp. strain LRS4.154, a moderately halophilic actinobacterium, has been determined. The genome has 4,860,108 bp, a G+C content of 71.0%, and 4,525 open reading frames (ORFs). The clusters of PKS and NRPS genes, responsible for the biosynthesis of a large number of biomolecules, were identified in the genome.

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Polyketide Synthase and Nonribosomal Peptide Synthetase Gene Clusters in Type Strains of the Genus Phytohabitans

Life ◽

10.3390/life10110257 ◽

2020 ◽

Vol 10 (11) ◽

pp. 257

Author(s):

Hisayuki Komaki ◽

Tomohiko Tamura

Keyword(s):

Secondary Metabolites ◽

Polyketide Synthase ◽

Gene Clusters ◽

Nonribosomal Peptide Synthetase ◽

Nrps Gene ◽

Nonribosomal Peptide ◽

Rare Actinomycetes ◽

Whole Genomes ◽

Peptide Synthetase ◽

Established Genus

(1) Background: Phytohabitans is a recently established genus belonging to rare actinomycetes. It has been unclear if its members have the capacity to synthesize diverse secondary metabolites. Polyketide and nonribosomal peptide compounds are major secondary metabolites in actinomycetes and expected as a potential source for novel pharmaceuticals. (2) Methods: Whole genomes of Phytohabitans flavus NBRC 107702T, Phytohabitans rumicis NBRC 108638T, Phytohabitans houttuyneae NBRC 108639T, and Phytohabitans suffuscus NBRC 105367T were sequenced by PacBio. Polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters were bioinformatically analyzed in the genome sequences. (3) Results: These four strains harbored 10, 14, 18 and 14 PKS and NRPS gene clusters, respectively. Most of the gene clusters were annotated to synthesis unknown chemistries. (4) Conclusions: Members of the genus Phytohabitans are a possible source for novel and diverse polyketides and nonribosomal peptides.

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