scholarly journals Genome Mining and Metabolic Profiling Uncover Polycyclic Tetramate Macrolactams from Streptomyces koyangensis SCSIO 5802

Marine Drugs ◽  
2021 ◽  
Vol 19 (8) ◽  
pp. 440
Author(s):  
Wenjuan Ding ◽  
Jiajia Tu ◽  
Huaran Zhang ◽  
Xiaoyi Wei ◽  
Jianhua Ju ◽  
...  
Keyword(s):  
Natural Products ◽  
Gene Cluster ◽  
Metabolic Profiling ◽  
Biosynthetic Pathway ◽  
Genome Mining ◽  
Biosynthetic Gene Cluster ◽  
Open Reading Frames ◽  
Bioactive Metabolites ◽  
Bioinformatics Analyses ◽  
Reading Frames

We have previously shown deep-sea-derived Streptomyces koyangensis SCSIO 5802 to produce two types of active secondary metabolites, abyssomicins and candicidins. Here, we report the complete genome sequence of S. koyangensis SCSIO 5802 employing bioinformatics to highlight its potential to produce at least 21 categories of natural products. In order to mine novel natural products, the production of two polycyclic tetramate macrolactams (PTMs), the known 10-epi-HSAF (1) and a new compound, koyanamide A (2), was stimulated via inactivation of the abyssomicin and candicidin biosynthetic machineries. Detailed bioinformatics analyses revealed a PKS/NRPS gene cluster, containing 6 open reading frames (ORFs) and spanning ~16 kb of contiguous genomic DNA, as the putative PTM biosynthetic gene cluster (BGC) (termed herein sko). We furthermore demonstrate, via gene disruption experiments, that the sko cluster encodes the biosynthesis of 10-epi-HSAF and koyanamide A. Finally, we propose a plausible biosynthetic pathway to 10-epi-HSAF and koyanamide A. In total, this study demonstrates an effective approach to cryptic BGC activation enabling the discovery of new bioactive metabolites; genome mining and metabolic profiling methods play key roles in this strategy.

scholarly journals Biosynthesis of the β-Methylarginine Residue of Peptidyl Nucleoside Arginomycin in Streptomyces arginensis NRRL 15941

2014 ◽  
Vol 80 (16) ◽  
pp. 5021-5027 ◽  
Author(s):  
Jun Feng ◽  
Jun Wu ◽  
Jie Gao ◽  
Zhigui Xia ◽  
Zixin Deng ◽  
...  
Keyword(s):  
Amino Acid ◽  
Biosynthetic Pathway ◽  
Biosynthetic Gene Cluster ◽  
Open Reading Frames ◽  
Enzymatic Conversion ◽  
Content Type ◽  
Gram Positive Bacteria ◽  
Adenosyl Methionine ◽  
Bacteria And Fungi ◽  
Reading Frames

ABSTRACTThe peptidyl nucleoside arginomycin is active against Gram-positive bacteria and fungi but displays much lower toxicity to mice than its analog blasticidin S. It features a rare amino acid, β-methylarginine, which is attached to the deoxyhexose moiety via a 4′-aminoacyl bond. We here report cloning of the complete biosynthetic gene cluster for arginomycin fromStreptomyces arginensisNRRL 15941. Among the 14 putative essential open reading frames,argM, encoding an aspartate aminotransferase (AAT), and adjacentargN, encoding anS-adenosyl methionine (SAM)-dependent methyltransferase, are coupled to catalyze arginine and yield β-methylarginine inEscherichia coli. Purified ArgM can transfer the α-amino group ofl-arginine to α-ketoglutaric acid to give glutamate and thereby convertsl-arginine to 5-guanidino-2-oxopentanoic acid, which is methylated at the C-3 position by ArgN to form 5-guanidino-3-methyl-2-oxopentanoic acid. Iteratively, ArgM specifically catalyzes transamination from the donorl-aspartate to the resulting 5-guanidino-3-methyl-2-oxopentanoic acid, generating β-methylarginine. The complete and concise biosynthetic pathway for the rare and bioactive amino acid revealed by this study may pave the way for the production of β-methylarginine either by enzymatic conversion or by engineered living cells.

scholarly journals Biosynthesis of Sibiromycin, a Potent Antitumor Antibiotic

2009 ◽  
Vol 75 (9) ◽  
pp. 2869-2878 ◽  
Author(s):  
Wei Li ◽  
Ankush Khullar ◽  
ShenChieh Chou ◽  
Ashley Sacramo ◽  
Barbara Gerratana
Keyword(s):  
Gene Cluster ◽  
Biosynthetic Pathway ◽  
Gene Replacement ◽  
Open Reading Frames ◽  
Hydroxyl Group ◽  
Antitumor Antibiotic ◽  
Resistance Proteins ◽  
Peptide Synthetase ◽  
Antitumor Properties ◽  
Reading Frames

ABSTRACT Pyrrolobenzodiazepines, a class of natural products produced by actinomycetes, are sequence selective DNA alkylating compounds with significant antitumor properties. Among the pyrrolo[1,4]benzodiazepines (PBDs) sibiromycin, one of two identified glycosylated PBDs, displays the highest affinity for DNA and the most potent antitumor properties. Despite the promising antitumor properties clinical trials of sibiromycin were precluded by the cardiotoxicity effect in animals attributed to the presence of the C-9 hydroxyl group. As a first step toward the development of sibiromycin analogs, we have cloned and localized the sibiromycin gene cluster to a 32.7-kb contiguous DNA region. Cluster boundaries tentatively assigned by comparative genomics were verified by gene replacement experiments. The sibiromycin gene cluster consisting of 26 open reading frames reveals a “modular” strategy in which the synthesis of the anthranilic and dihydropyrrole moieties is completed before assembly by the nonribosomal peptide synthetase enzymes. In addition, the gene cluster identified includes open reading frames encoding enzymes involved in sibirosamine biosynthesis, as well as regulatory and resistance proteins. Gene replacement and chemical complementation studies are reported to support the proposed biosynthetic pathway.

scholarly journals GIP2, a Putative Transcription Factor That Regulates the Aurofusarin Biosynthetic Gene Cluster in Gibberella zeae

2006 ◽  
Vol 72 (2) ◽  
pp. 1645-1652 ◽  
Author(s):  
Jung-Eun Kim ◽  
Jianming Jin ◽  
Hun Kim ◽  
Jin-Cheol Kim ◽  
Sung-Hwan Yun ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Biosynthetic Gene Cluster ◽  
Gibberella Zeae ◽  
Open Reading Frames ◽  
Biosynthetic Gene ◽  
Targeted Gene Deletion ◽  
Binuclear Cluster ◽  
Putative Transcription Factor ◽  
Type Strains ◽  
Reading Frames

ABSTRACT Gibberella zeae (anamorph: Fusarium graminearum) is an important pathogen of maize, wheat, and rice. Colonies of G. zeae produce yellow-to-tan mycelia with the white-to-carmine red margins. In this study, we focused on nine putative open reading frames (ORFs) closely linked to PKS12 and GIP1, which are required for aurofusarin biosynthesis in G. zeae. Among them is an ORF designated GIP2 (for Gibberella zeae pigment gene 2), which encodes a putative protein of 398 amino acids that carries a Zn(II)2Cys6 binuclear cluster DNA-binding domain commonly found in transcription factors of yeasts and filamentous fungi. Targeted gene deletion and complementation analyses confirmed that GIP2 is required for aurofusarin biosynthesis. Expression of GIP2 in carrot medium correlated with aurofusarin production by G. zeae and was restricted to vegetative mycelia. Inactivation of the 10 contiguous genes in the ΔGIP2 strain delineates an aurofusarin biosynthetic gene cluster. Overexpression of GIP2 in both the ΔGIP2 and the wild-type strains increases aurofusarin production and reduces mycelial growth. Thus, GIP2 is a putative positive regulator of the aurofusarin biosynthetic gene cluster, and aurofusarin production is negatively correlated with vegetative growth by G. zeae.

scholarly journals Identification of the Novobiocin Biosynthetic Gene Cluster of Streptomyces spheroides NCIB 11891

2000 ◽  
Vol 44 (5) ◽  
pp. 1214-1222 ◽  
Author(s):  
Marion Steffensky ◽  
Agnes Mühlenweg ◽  
Zhao-Xin Wang ◽  
Shu-Ming Li ◽  
Lutz Heide
Keyword(s):  
Heterologous Expression ◽  
Gene Cluster ◽  
Biosynthetic Gene Cluster ◽  
Streptomyces Lividans ◽  
Open Reading Frames ◽  
Biosynthetic Gene ◽  
Insertional Inactivation ◽  
Key Enzyme ◽  
Novobiocin Resistance ◽  
Reading Frames

ABSTRACT The novobiocin biosynthetic gene cluster from Streptomyces spheroides NCIB 11891 was cloned by using homologous deoxynucleoside diphosphate (dNDP)-glucose 4,6-dehydratase gene fragments as probes. Double-stranded sequencing of 25.6 kb revealed the presence of 23 putative open reading frames (ORFs), including the gene for novobiocin resistance, gyrB r, and at least 11 further ORFs to which a possible role in novobiocin biosynthesis could be assigned. An insertional inactivation experiment with a dNDP-glucose 4,6-dehydratase fragment resulted in abolishment of novobiocin production, since biosynthesis of the deoxysugar moiety of novobiocin was blocked. Heterologous expression of a key enzyme of novobiocin biosynthesis, i.e., novobiocic acid synthetase, inStreptomyces lividans TK24 further confirmed the involvement of the analyzed genes in the biosynthesis of the antibiotic.

scholarly journals Analysis of Genes Involved in Biosynthesis of Coronafacic Acid, the Polyketide Component of the Phytotoxin Coronatine

1998 ◽  
Vol 180 (13) ◽  
pp. 3330-3338 ◽  
Author(s):  
Vidhya Rangaswamy ◽  
Robin Mitchell ◽  
Matthias Ullrich ◽  
Carol Bender
Keyword(s):  
Gene Cluster ◽  
Pseudomonas Syringae ◽  
Biosynthetic Gene Cluster ◽  
Open Reading Frames ◽  
Plant Pathogenic Bacterium ◽  
Biosynthetic Gene ◽  
Future Studies ◽  
Coronafacic Acid ◽  
Single Transcript ◽  
Reading Frames

ABSTRACT Coronafacic acid (CFA) is the polyketide component of coronatine (COR), a phytotoxin produced by the plant-pathogenic bacteriumPseudomonas syringae. The genes involved in CFA biosynthesis are encoded by a single transcript which encompasses 19 kb of the COR gene cluster. In the present study, the nucleotide sequence was determined for a 4-kb region located at the 3′ end of the CFA biosynthetic gene cluster. Three open reading frames were identified and designated cfa8, cfa9, andtnp1; the predicted translation products of these genes showed relatedness to oxidoreductases, thioesterases, and transposases, respectively. The translational products of cfa8 andcfa9 were overproduced in Escherichia coliBL21; however, tnp1 was not translated in these experiments. Mutagenesis and complementation analysis indicated thatcfa8 is required for the production of CFA and COR. Analysis of a cfa9 mutant indicated that this gene is dispensable for CFA and COR production but may increase the release of enzyme-bound products from the COR pathway; tnp1, however, had no obvious function in CFA or COR biosynthesis. A genetic strategy was used to produce CFA in a P. syringae strain which lacks the COR gene cluster; this approach will be useful in future studies designed to investigate biosynthetic products of the CFA gene cluster.

scholarly journals Identification and Analysis of the Biosynthetic Gene Cluster Encoding the Thiopeptide Antibiotic Cyclothiazomycin in Streptomyces hygroscopicus 10-22

2010 ◽  
Vol 76 (7) ◽  
pp. 2335-2344 ◽  
Author(s):  
Jiang Wang ◽  
Yi Yu ◽  
Kexuan Tang ◽  
Wen Liu ◽  
Xinyi He ◽  
...  
Keyword(s):  
Heterologous Expression ◽  
Gene Cluster ◽  
Posttranslational Modifications ◽  
Biosynthetic Gene Cluster ◽  
Open Reading Frames ◽  
Streptomyces Hygroscopicus ◽  
Biosynthetic Gene ◽  
Thiopeptide Antibiotics ◽  
Reading Frames ◽  
Macrocyclic Structure

ABSTRACT Thiopeptide antibiotics are an important class of natural products resulting from posttranslational modifications of ribosomally synthesized peptides. Cyclothiazomycin is a typical thiopeptide antibiotic that has a unique bridged macrocyclic structure derived from an 18-amino-acid structural peptide. Here we reported cloning, sequencing, and heterologous expression of the cyclothiazomycin biosynthetic gene cluster from Streptomyces hygroscopicus 10-22. Remarkably, successful heterologous expression of a 22.7-kb gene cluster in Streptomyces lividans 1326 suggested that there is a minimum set of 15 open reading frames that includes all of the functional genes required for cyclothiazomycin production. Six genes of these genes, cltBCDEFG flanking the structural gene cltA, were predicted to encode the enzymes required for the main framework of cyclothiazomycin, and two enzymes encoded by a putative operon, cltMN, were hypothesized to participate in the tailoring step to generate the tertiary thioether, leading to the final cyclization of the bridged macrocyclic structure. This rigorous bioinformatics analysis based on heterologous expression of cyclothiazomycin resulted in an ideal biosynthetic model for us to understand the biosynthesis of thiopeptides.

scholarly journals Biosynthetic Gene Cluster for the Polyenoyltetramic Acid α-Lipomycin

2006 ◽  
Vol 50 (6) ◽  
pp. 2113-2121 ◽  
Author(s):  
C. Bihlmaier ◽  
E. Welle ◽  
C. Hofmann ◽  
K. Welzel ◽  
A. Vente ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Polyketide Synthase ◽  
Biosynthetic Gene Cluster ◽  
Open Reading Frames ◽  
Biosynthetic Gene ◽  
Peptide Synthetases ◽  
Insight Into ◽  
Reading Frames ◽  
Module System

ABSTRACT The gram-positive bacterium Streptomyces aureofaciens Tü117 produces the acyclic polyene antibiotic α-lipomycin. The entire biosynthetic gene cluster (lip gene cluster) was cloned and characterized. DNA sequence analysis of a 74-kb region revealed the presence of 28 complete open reading frames (ORFs), 22 of them belonging to the biosynthetic gene cluster. Central to the cluster is a polyketide synthase locus that encodes an eight-module system comprised of four multifunctional proteins. In addition, one ORF shows homology to those for nonribosomal peptide synthetases, indicating that α-lipomycin belongs to the classification of hybrid peptide-polyketide natural products. Furthermore, the lip cluster includes genes responsible for the formation and attachment of d-digitoxose as well as ORFs that resemble those for putative regulatory and export functions. We generated biosynthetic mutants by insertional gene inactivation. By analysis of culture extracts of these mutants, we could prove that, indeed, the genes involved in the biosynthesis of lipomycin had been cloned, and additionally we gained insight into an unusual biosynthesis pathway.

scholarly journals Molecular Cloning, Sequence Analysis, and Heterologous Expression of the Phosphinothricin Tripeptide Biosynthetic Gene Cluster from Streptomyces viridochromogenes DSM 40736

2005 ◽  
Vol 49 (1) ◽  
pp. 230-240 ◽  
Author(s):  
Joshua A. V. Blodgett ◽  
Jun Kai Zhang ◽  
William W. Metcalf
Keyword(s):  
Sequence Analysis ◽  
Heterologous Expression ◽  
Gene Cluster ◽  
Genomic Dna ◽  
Biosynthetic Gene Cluster ◽  
Fosmid Library ◽  
Open Reading Frames ◽  
Biosynthetic Gene ◽  
Heterologous Host ◽  
Reading Frames

ABSTRACT A fosmid library from genomic DNA of Streptomyces viridochromogenes DSM 40736 was constructed and screened for the presence of genes known to be involved in the biosynthesis of phosphinothricin tripeptide (PTT). Eight positives were identified, one of which was able to confer PTT biosynthetic capability upon Streptomyces lividans after integration of the fosmid into the chromosome of this heterologous host. Sequence analysis of the 40,241-bp fosmid insert revealed 29 complete open reading frames (ORFs). Deletion analysis demonstrated that a minimum set of 24 ORFs were required for PTT production in the heterologous host. Sequence analysis revealed that most of these PTT genes have been previously identified in either S. viridochromogenes or S. hygroscopicus (or both), although only 11 out of 24 of these ORFs have experimentally defined functions. Three previously unknown genes within the cluster were identified and are likely to have roles in the stepwise production of phosphonoformate from phosphonoacetaldehyde. This is the first report detailing the entire PTT gene cluster from any producing streptomycete.

scholarly journals A Single Biosynthetic Gene Cluster Is Responsible for the Production of Bagremycin Antibiotics and Ferroverdin Iron Chelators

mBio ◽  
2019 ◽  
Vol 10 (4) ◽  
Author(s):  
Loïc Martinet ◽  
Aymeric Naômé ◽  
Benoit Deflandre ◽  
Marta Maciejewska ◽  
Déborah Tellatin ◽  
...  
Keyword(s):  
Natural Product ◽  
Gene Cluster ◽  
Biosynthetic Pathway ◽  
Genome Mining ◽  
Gene Clusters ◽  
Bioactive Molecules ◽  
Bioactive Metabolites ◽  
Biosynthetic Gene ◽  
Single Family ◽  
Biosynthetic Gene Clusters

ABSTRACT Biosynthetic gene clusters (BGCs) are organized groups of genes involved in the production of specialized metabolites. Typically, one BGC is responsible for the production of one or several similar compounds with bioactivities that usually only vary in terms of strength and/or specificity. Here we show that the previously described ferroverdins and bagremycins, which are families of metabolites with different bioactivities, are produced from the same BGC, whereby the fate of the biosynthetic pathway depends on iron availability. Under conditions of iron depletion, the monomeric bagremycins are formed, representing amino-aromatic antibiotics resulting from the condensation of 3-amino-4-hydroxybenzoic acid with p-vinylphenol. Conversely, when iron is abundantly available, the biosynthetic pathway additionally produces a molecule based on p-vinylphenyl-3-nitroso-4-hydroxybenzoate, which complexes iron to form the trimeric ferroverdins that have anticholesterol activity. Thus, our work shows a unique exception to the concept that BGCs should only produce a single family of molecules with one type of bioactivity and that in fact different bioactive molecules may be produced depending on the environmental conditions. IMPORTANCE Access to whole-genome sequences has exposed the general incidence of the so-called cryptic biosynthetic gene clusters (BGCs), thereby renewing their interest for natural product discovery. As a consequence, genome mining is the often first approach implemented to assess the potential of a microorganism for producing novel bioactive metabolites. By revealing a new level of complexity of natural product biosynthesis, we further illustrate the difficulty of estimation of the panel of molecules associated with a BGC based on genomic information alone. Indeed, we found that the same gene cluster is responsible for the production of compounds which differ in terms of structure and bioactivity. The production of these different compounds responds to different environmental triggers, which suggests that multiplication of culture conditions is essential for revealing the entire panel of molecules made by a single BGC.

scholarly journals Biosynthetic Gene Cluster of Simocyclinone, a Natural Multihybrid Antibiotic

2002 ◽  
Vol 46 (5) ◽  
pp. 1174-1182 ◽  
Author(s):  
A. Trefzer ◽  
S. Pelzer ◽  
J. Schimana ◽  
S. Stockert ◽  
C. Bihlmaier ◽  
...  
Keyword(s):  
Gene Cluster ◽  
High Performance ◽  
Biosynthetic Gene Cluster ◽  
Open Reading Frames ◽  
Primary Metabolites ◽  
Streptomyces Antibioticus ◽  
Mutant Strains ◽  
In The Wild ◽  
Simocyclinone D8 ◽  
Reading Frames

ABSTRACT The entire simocyclinone biosynthetic cluster (sim gene cluster) from the producer Streptomyces antibioticus Tü6040 was identified on six overlapping cosmids (1N1, 5J10, 2L16, 2P6, 4G22, and 1K3). In total, 80.7 kb of DNA from these cosmids was sequenced, and the analysis revealed 49 complete open reading frames (ORFs). These ORFs include genes responsible for the formation and attachment of four different moieties originating from at least three different pools of primary metabolites. Also in the sim gene cluster, four ORFs were detected that resemble putative regulatory and export functions. Based on the putative function of the gene products, a model for simocyclinone D8 biosynthesis was proposed. Biosynthetic mutants were generated by insertional gene inactivation experiments, and culture extracts of these mutants were analyzed by high-performance liquid chromatography. Production of simocyclinone D8 was clearly detectable in the wild-type strain but was not detectable in the mutant strains. This indicated that indeed the sim gene cluster had been cloned.

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