scholarly journals Biosynthesis of Akaeolide and Lorneic Acids and Annotation of Type I Polyketide Synthase Gene Clusters in the Genome of Streptomyces sp. NPS554

Marine Drugs ◽  
2015 ◽  
Vol 13 (1) ◽  
pp. 581-596 ◽  
Author(s):  
Tao Zhou ◽  
Hisayuki Komaki ◽  
Natsuko Ichikawa ◽  
Akira Hosoyama ◽  
Seizo Sato ◽  
...  
Keyword(s):  
Polyketide Synthase ◽  
Gene Clusters ◽  
Type I ◽  
Streptomyces Sp ◽  
Polyketide Synthase Gene

scholarly journals Identification of polyketide synthase gene clusters in a phage P1-derived artificial chromosome library of a Philippine strain of Streptomyces sp. PCS3-D2

2019 ◽  
pp. 56-63
Author(s):  
Aileen Bayot Custodio ◽  
Edwin Plata Alcantara
Keyword(s):  
Gene Cluster ◽  
Polyketide Synthase ◽  
Genetic Manipulation ◽  
Gene Clusters ◽  
Artificial Chromosome ◽  
Restriction Enzyme Digestion ◽  
Type I ◽  
Putative Gene ◽  
Streptomyces Sp ◽  
Type Iii

A phage P1-derived artificial chromosome (PAC) library was constructed from genomic DNA of Streptomyces sp. PCS3-D2. Polymerase chain reaction (PCR) screening of the PAC library revealed two clones, PAC16D and P222O, which were positively identified to harbor polyketide synthase (PKS) Type I and PKS Type III gene clusters, respectively. Restriction enzyme digestion showed that PAC16D and PAC222O contained a 130 kb and a 140 kb insert, respectively. Results of sequencing and bioinformatics analyses revealed that PAC16D comprised of a full-length PKS type I bafilomycin gene cluster while PAC222O harbored truncated siderophore and putative gene clusters as well as a complete PKS III biosynthetic gene cluster. The PKS III gene cluster had three genes similar to alkyl resorcinol biosynthetic genes, however majority of the novel gene cluster had little similarity to known PKS Type III gene clusters. The successful cloning and identification of these gene clusters from Streptomyces sp. PCS3-D2 serve as the jump off point to further genetic manipulation in order to produce the insecticidal natural product in a heterologous host.

scholarly journals In Silico Analysis of PKS and NRPS Gene Clusters in Arisostatin- and Kosinostatin-Producers and Description of Micromonospora okii sp. nov.

Antibiotics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1447
Author(s):  
Hisayuki Komaki ◽  
Natsuko Ichikawa ◽  
Akira Hosoyama ◽  
Moriyuki Hamada ◽  
Yasuhiro Igarashi
Keyword(s):  
Gene Cluster ◽  
Polyketide Synthase ◽  
Sequence Similarity ◽  
In Silico Analysis ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Rrna Gene ◽  
Type I ◽  
Phenotypic Differences ◽  
Polyketide Synthase Gene

Micromonospora sp. TP-A0316 and Micromonospora sp. TP-A0468 are producers of arisostatin and kosinostatin, respectively. Micromonospora sp. TP-A0316 showed a 16S rRNA gene sequence similarity of 100% to Micromonosporaoryzae CP2R9-1T whereas Micromonospora sp. TP-A0468 showed a 99.3% similarity to Micromonospora haikouensis 232617T. A phylogenetic analysis based on gyrB sequences suggested that Micromonospora sp. TP-A0316 is closely related to Micromonospora oryzae whereas Micromonospora TP-A0468 is an independent genomospecies. As Micromonospora sp. TP-A0468 showed some phenotypic differences to its closely related species, it was classified as a novel species, for which the name Micromonospora okii sp. nov. is proposed. The type strain is TP-A0468T (= NBRC 110461T). Micromonospora sp. TP-A0316 and M. okii TP-A0468T were both found to harbor 15 gene clusters for secondary metabolites such as polyketides and nonribosomal peptides in their genomes. Arisostatin-biosynthetic gene cluster (BGC) of Micromonospora sp. TP-A0316 closely resembled tetrocarcin A-BGC of Micromonospora chalcea NRRL 11289. A large type-I polyketide synthase gene cluster was present in each genome of Micromonospora sp. TP-A0316 and M. okii TP-A0468T. It was an ortholog of quinolidomicin-BGC of M. chalcea AK-AN57 and widely distributed in the genus Micromonospora.

scholarly journals Microfluidic automated plasmid library enrichment for biosynthetic gene cluster discovery

2020 ◽  
Vol 48 (8) ◽  
pp. e48-e48 ◽  
Author(s):  
Peng Xu ◽  
Cyrus Modavi ◽  
Benjamin Demaree ◽  
Frederick Twigg ◽  
Benjamin Liang ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Polyketide Synthase ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Bioactive Molecules ◽  
Type I ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Plasmid Library ◽  
Polyketide Synthase Gene

Abstract Microbial biosynthetic gene clusters are a valuable source of bioactive molecules. However, because they typically represent a small fraction of genomic material in most metagenomic samples, it remains challenging to deeply sequence them. We present an approach to isolate and sequence gene clusters in metagenomic samples using microfluidic automated plasmid library enrichment. Our approach provides deep coverage of the target gene cluster, facilitating reassembly. We demonstrate the approach by isolating and sequencing type I polyketide synthase gene clusters from an Antarctic soil metagenome. Our method promotes the discovery of functional-related genes and biosynthetic pathways.

scholarly journals Metagenomic Analysis Reveals Diverse Polyketide Synthase Gene Clusters in Microorganisms Associated with the Marine Sponge Discodermia dissoluta

2005 ◽  
Vol 71 (8) ◽  
pp. 4840-4849 ◽  
Author(s):  
Andreas Schirmer ◽  
Rishali Gadkari ◽  
Christopher D. Reeves ◽  
Fadia Ibrahim ◽  
Edward F. DeLong ◽  
...  
Keyword(s):  
Marine Sponge ◽  
Polyketide Synthase ◽  
Pcr Amplification ◽  
Gene Clusters ◽  
Type I ◽  
Metagenomic Libraries ◽  
Dna Libraries ◽  
Peptide Synthetase ◽  
Sponge Associated Bacteria ◽  
Polyketide Synthase Gene

ABSTRACT Sponge-associated bacteria are thought to produce many novel bioactive compounds, including polyketides. PCR amplification of ketosynthase domains of type I modular polyketide synthases (PKS) from the microbial community of the marine sponge Discodermia dissoluta revealed great diversity and a novel group of sponge-specific PKS ketosynthase domains. Metagenomic libraries totaling more than four gigabases of bacterial genomes associated with this sponge were screened for type I modular PKS gene clusters. More than 90% of the clones in total sponge DNA libraries represented bacterial DNA inserts, and 0.7% harbored PKS genes. The majority of the PKS hybridizing clones carried small PKS clusters of one to three modules, although some clones encoded large multimodular PKSs (more than five modules). The most abundant large modular PKS appeared to be encoded by a bacterial symbiont that made up <1% of the sponge community. Sequencing of this PKS revealed 14 modules that, if expressed and active, is predicted to produce a multimethyl-branched fatty acid reminiscent of mycobacterial lipid components. Metagenomic libraries made from fractions enriched for unicellular or filamentous bacteria differed significantly, with the latter containing numerous nonribosomal peptide synthetase (NRPS) and mixed NRPS-PKS gene clusters. The filamentous bacterial community of D. dissoluta consists mainly of Entotheonella spp., an unculturable sponge-specific taxon previously implicated in the biosynthesis of bioactive peptides.

scholarly journals Draft Genome Sequence of an Anthracimycin Producer, Streptomyces sp. TP-A0875

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Hisayuki Komaki ◽  
Natsuko Ichikawa ◽  
Akira Hosoyama ◽  
Nobuyuki Fujita ◽  
Enjuro Harunari ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Genome Sequence ◽  
Polyketide Synthase ◽  
Draft Genome ◽  
Gene Clusters ◽  
Draft Genome Sequence ◽  
Type I ◽  
Type Ii ◽  
Streptomyces Sp ◽  
Peptide Synthetase

Here, we report the draft genome sequence of an anthracimycin producer, Streptomyces sp. TP-A0875. The genome contains at least two type I polyketide synthase (PKS) gene clusters, two type II PKS gene clusters, and three nonribosomal peptide synthetase gene clusters. The gene cluster for anthracimycin biosynthesis was identified based on the PKS domain organization.

scholarly journals The Fusarium verticillioides FUM Gene Cluster Encodes a Zn(II)2Cys6 Protein That Affects FUM Gene Expression and Fumonisin Production

2007 ◽  
Vol 6 (7) ◽  
pp. 1210-1218 ◽  
Author(s):  
Daren W. Brown ◽  
Robert A. E. Butchko ◽  
Mark Busman ◽  
Robert H. Proctor
Keyword(s):  
Gene Cluster ◽  
Polyketide Synthase ◽  
Fusarium Verticillioides ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Regulatory Proteins ◽  
Wild Type ◽  
Polyketide Synthase Gene ◽  
Splice Forms ◽  
Self Protection

ABSTRACT Fumonisins are mycotoxins produced by some Fusarium species and can contaminate maize or maize products. Ingestion of fumonisins is associated with diseases, including cancer and neural tube defects, in humans and animals. In fungi, genes involved in the synthesis of mycotoxins and other secondary metabolites are often located adjacent to each other in gene clusters. Such genes can encode structural enzymes, regulatory proteins, and/or proteins that provide self-protection. The fumonisin biosynthetic gene cluster includes 16 genes, none of which appear to play a role in regulation. In this study, we identified a previously undescribed gene (FUM21) located adjacent to the fumonisin polyketide synthase gene, FUM1. The presence of a Zn(II)2Cys6 DNA-binding domain in the predicted protein suggested that FUM21 was involved in transcriptional regulation. FUM21 deletion (Δfum21) mutants produce little to no fumonisin in cracked maize cultures but some FUM1 and FUM8 transcripts in a liquid GYAM medium. Complementation of a Δfum21 mutant with a wild-type copy of the gene restored fumonisin production. Analysis of FUM21 cDNAs identified four alternative splice forms (ASFs), and microarray analysis indicated the ASFs were differentially expressed. Based on these data, we present a model for how FUM21 ASFs may regulate fumonisin biosynthesis.

scholarly journals Streptomyces sp. Strain MUSC 125 from Mangrove Soil in Malaysia with Anti-MRSA, Anti-Biofilm and Antioxidant Activities

Molecules ◽  
2020 ◽  
Vol 25 (15) ◽  
pp. 3545
Author(s):  
Hefa Mangzira Kemung ◽  
Loh Teng-Hern Tan ◽  
Kok-Gan Chan ◽  
Hooi-Leng Ser ◽  
Jodi Woan-Fei Law ◽  
...  
Keyword(s):  
Polyketide Synthase ◽  
Methanolic Extract ◽  
Antioxidant Activities ◽  
Pcr Amplification ◽  
Gene Clusters ◽  
Bacterial Strains ◽  
Phenotypic Analysis ◽  
Streptomyces Sp ◽  
Mangrove Soil ◽  
Promising Source

There is an urgent need to search for new antibiotics to counter the growing number of antibiotic-resistant bacterial strains, one of which is methicillin-resistant Staphylococcus aureus (MRSA). Herein, we report a Streptomyces sp. strain MUSC 125 from mangrove soil in Malaysia which was identified using 16S rRNA phylogenetic and phenotypic analysis. The methanolic extract of strain MUSC 125 showed anti-MRSA, anti-biofilm and antioxidant activities. Strain MUSC 125 was further screened for the presence of secondary metabolite biosynthetic genes. Our results indicated that both polyketide synthase (pks) gene clusters, pksI and pksII, were detected in strain MUSC 125 by PCR amplification. In addition, gas chromatography-mass spectroscopy (GC-MS) detected the presence of different chemicals in the methanolic extract. Based on the GC-MS analysis, eight known compounds were detected suggesting their contribution towards the anti-MRSA and anti-biofilm activities observed. Overall, the study bolsters the potential of strain MUSC 125 as a promising source of anti-MRSA and antibiofilm compounds and warrants further investigation.

scholarly journals Genome-based survey of nonribosomal peptide synthetase and polyketide synthase gene clusters in type strains of the genus Microtetraspora

2016 ◽  
Vol 69 (9) ◽  
pp. 712-718 ◽  
Author(s):  
Hisayuki Komaki ◽  
Natsuko Ichikawa ◽  
Tomohiko Tamura ◽  
Akio Oguchi ◽  
Moriyuki Hamada ◽  
...  
Keyword(s):  
Polyketide Synthase ◽  
Gene Clusters ◽  
Nonribosomal Peptide Synthetase ◽  
Nonribosomal Peptide ◽  
Peptide Synthetase ◽  
Polyketide Synthase Gene ◽  
Type Strains
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