Identification of a Napsamycin Biosynthesis Gene Cluster by Genome Mining

ChemBioChem ◽  
2010 ◽  
Vol 12 (3) ◽  
pp. 477-487 ◽  
Author(s):  
Leonard Kaysser ◽  
Xiaoyu Tang ◽  
Emmanuel Wemakor ◽  
Katharina Sedding ◽  
Susanne Hennig ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Genome Mining ◽  
Biosynthesis Gene Cluster ◽  
Biosynthesis Gene

scholarly journals A Pseudoalteromonas clade with remarkable biosynthetic potential

2021 ◽  
Author(s):  
Rocky Chau ◽  
Leanne A. Pearson ◽  
Jesse Cain ◽  
John A. Kalaitzis ◽  
Brett A. Neilan
Keyword(s):  
Natural Products ◽  
Gene Cluster ◽  
Genome Mining ◽  
Gene Clusters ◽  
Average Density ◽  
Biologically Active ◽  
Biosynthesis Gene Cluster ◽  
Diverse Range ◽  
Siderophore Biosynthesis ◽  
Biosynthesis Gene

Pseudoalteromonas species produce a diverse range of biologically active compounds, including those biosynthesized by non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). Here we report the biochemical and genomic analysis of Pseudoalteromonas sp. HM-SA03, isolated from the blue-ringed octopus, Hapalochalaena sp. Genome mining for secondary metabolite pathways revealed seven putative NRPS/PKS biosynthesis gene clusters, including those for the biosynthesis of alterochromides, pseudoalterobactins, alteramides and four hitherto novel compounds. Among these was a novel siderophore biosynthesis gene cluster with unprecedented architecture (NRPS-PKS-NRPS-PKS-NRPS-PKS-NRPS). Alterochromide production in HM-SA03 was also confirmed by liquid chromatography-mass spectrometry. An investigation of the biosynthetic potential of 42 publicly available Pseudoalteromonas genomes indicated that some of these gene clusters are distributed throughout the genus. Through phylogenetic analysis, a particular subset of strains formed a clade with extraordinary biosynthetic potential, with an average density of ten biosynthesis gene clusters per genome. In contrast, the majority of Pseudoalteromonas strains outside this clade contained an average of three clusters encoding complex biosynthesis. These results highlight the under-explored potential of Pseudoalteromonas as a source of new natural products. Importance This study demonstrates that the Pseudoalteromonas strain, HM-SA03, isolated from the venomous blue-ringed octopus, Hapalochalaena sp., is a biosynthetically talented organism, capable of producing alterochromides and potentially six other specialized metabolites. We have identified a pseudoalterobactin biosynthesis gene cluster and proposed a pathway for the production of the associated siderophore. A novel siderophore biosynthesis gene cluster with unprecedented architecture was also identified in the HM-SA03 genome. Finally, we have demonstrated that HM-SA03 belongs to a phylogenetic clade of strains with extraordinary biosynthetic potential. While our results do not support a role of HM-SA03 in Hapalochalaena sp. venom (tetrodotoxin) production, they emphasize the untapped potential of Pseudoalteromonas as a source of novel natural products.

scholarly journals Overproduction of Ristomycin A by Activation of a Silent Gene Cluster in Amycolatopsis japonicum MG417-CF17

2014 ◽  
Vol 58 (10) ◽  
pp. 6185-6196 ◽  
Author(s):  
Marius Spohn ◽  
Norbert Kirchner ◽  
Andreas Kulik ◽  
Angelika Jochim ◽  
Felix Wolf ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Gene Cluster ◽  
High Performance ◽  
Pathogenic Bacteria ◽  
Genome Mining ◽  
Gene Clusters ◽  
Von Willebrand Disease ◽  
Biosynthesis Gene Cluster ◽  
Content Type ◽  
Bioinformatic Tools

ABSTRACTThe emergence of antibiotic-resistant pathogenic bacteria within the last decades is one reason for the urgent need for new antibacterial agents. A strategy to discover new anti-infective compounds is the evaluation of the genetic capacity of secondary metabolite producers and the activation of cryptic gene clusters (genome mining). One genus known for its potential to synthesize medically important products isAmycolatopsis. However,Amycolatopsis japonicumdoes not produce an antibiotic under standard laboratory conditions. In contrast to mostAmycolatopsisstrains,A. japonicumis genetically tractable with different methods. In order to activate a possible silent glycopeptide cluster, we introduced a gene encoding the transcriptional activator of balhimycin biosynthesis, thebbrgene fromAmycolatopsis balhimycina(bbrAba), intoA. japonicum. This resulted in the production of an antibiotically active compound. Following whole-genome sequencing ofA. japonicum, 29 cryptic gene clusters were identified by genome mining. One of these gene clusters is a putative glycopeptide biosynthesis gene cluster. Using bioinformatic tools, ristomycin (syn. ristocetin), a type III glycopeptide, which has antibacterial activity and which is used for the diagnosis of von Willebrand disease and Bernard-Soulier syndrome, was deduced as a possible product of the gene cluster. Chemical analyses by high-performance liquid chromatography and mass spectrometry (HPLC-MS), tandem mass spectrometry (MS/MS), and nuclear magnetic resonance (NMR) spectroscopy confirmed thein silicoprediction that the recombinantA. japonicum/pRM4-bbrAbasynthesizes ristomycin A.

An alginate-like exopolysaccharide biosynthesis gene cluster involved in biofilm aerial structure formation by Pseudomonas alkylphenolia

2014 ◽  
Vol 98 (9) ◽  
pp. 4137-4148 ◽  
Author(s):  
Kyoung Lee ◽  
Eun Jin Lim ◽  
Keun Soo Kim ◽  
Shir-Ly Huang ◽  
Yaligara Veeranagouda ◽  
...  
Keyword(s):  
Structure Formation ◽  
Gene Cluster ◽  
Biosynthesis Gene Cluster ◽  
Biosynthesis Gene ◽  
Exopolysaccharide Biosynthesis

Response of microcystin biosynthesis and its biosynthesis gene cluster transcription in Microcystis aeruginosa on electrochemical oxidation

2018 ◽  
Vol 40 (27) ◽  
pp. 3593-3601 ◽  
Author(s):  
Yu Gao ◽  
Kazuya Shimizu ◽  
Chie Amano ◽  
Xin Wang ◽  
Thanh Luu Pham ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Electrochemical Oxidation ◽  
Microcystis Aeruginosa ◽  
Biosynthesis Gene Cluster ◽  
Biosynthesis Gene

scholarly journals Characterization of the Biosynthesis Gene Cluster for the Pyrrole Polyether Antibiotic Calcimycin (A23187) inStreptomyces chartreusisNRRL 3882

2010 ◽  
Vol 55 (3) ◽  
pp. 974-982 ◽  
Author(s):  
Qiulin Wu ◽  
Jingdan Liang ◽  
Shuangjun Lin ◽  
Xiufen Zhou ◽  
Linquan Bai ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Mutational Analysis ◽  
Divalent Cations ◽  
Biological Effects ◽  
Biosynthetic Gene Cluster ◽  
Type I ◽  
Biosynthesis Gene Cluster ◽  
Biosynthesis Gene ◽  
Hydroxyanthranilic Acid

ABSTRACTThe pyrrole polyether antibiotic calcimycin (A23187) is a rare ionophore that is specific for divalent cations. It is widely used as a biochemical and pharmacological tool because of its multiple, unique biological effects. Here we report on the cloning, sequencing, and mutational analysis of the 64-kb biosynthetic gene cluster fromStreptomyces chartreusisNRRL 3882. Gene replacements confirmed the identity of the gene cluster, andin silicoanalysis of the DNA sequence revealed 27 potential genes, including 3 genes for the biosynthesis of the α-ketopyrrole moiety, 5 genes that encode modular type I polyketide synthases for the biosynthesis of the spiroketal ring, 4 genes for the biosynthesis of 3-hydroxyanthranilic acid, anN-methyltransferase tailoring gene, a resistance gene, a type II thioesterase gene, 3 regulatory genes, 4 genes with other functions, and 5 genes of unknown function. We propose a pathway for the biosynthesis of calcimycin and assign the genes to the biosynthesis steps. Our findings set the stage for producing much desired calcimycin derivatives using genetic modification instead of chemical synthesis.

scholarly journals Enhancement of the Diversity of Polyoxins by a Thymine-7-Hydroxylase Homolog outside the Polyoxin Biosynthesis Gene Cluster

2010 ◽  
Vol 76 (21) ◽  
pp. 7343-7347 ◽  
Author(s):  
Changming Zhao ◽  
Tingting Huang ◽  
Wenqing Chen ◽  
Zixin Deng
Keyword(s):  
Gene Cluster ◽  
Carbon Skeleton ◽  
Open Reading Frame ◽  
Streptomyces Avermitilis ◽  
Biosynthesis Gene Cluster ◽  
Reading Frame ◽  
Biosynthesis Gene ◽  
Pyrimidine Moiety

ABSTRACT Polyoxins consist of 14 structurally variable components which differentiate at three branch sites of the carbon skeleton. Open reading frame (ORF) SAV_4805 of Streptomyces avermitilis, showing similarity to thymine-7-hydroxylase, was proved to enhance the diversity of polyoxins at the C-5 site of the 1-(5′-amino-5′-deoxy-β-d-allofuranuronosyl) pyrimidine moiety.

scholarly journals Characterization of the Amicetin Biosynthesis Gene Cluster from Streptomyces vinaceusdrappus NRRL 2363 Implicates Two Alternative Strategies for Amide Bond Formation

2012 ◽  
Vol 78 (7) ◽  
pp. 2393-2401 ◽  
Author(s):  
Gaiyun Zhang ◽  
Haibo Zhang ◽  
Sumei Li ◽  
Ji Xiao ◽  
Guangtao Zhang ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Acyl Carrier Protein ◽  
Bond Formation ◽  
Antiviral Agent ◽  
Amide Bond ◽  
Biosynthesis Gene Cluster ◽  
Alternative Strategies ◽  
Content Type ◽  
Amide Bond Formation ◽  
Biosynthesis Gene

ABSTRACTAmicetin, an antibacterial and antiviral agent, belongs to a group of disaccharide nucleoside antibiotics featuring an α-(1→4)-glycoside bond in the disaccharide moiety. In this study, the amicetin biosynthesis gene cluster was cloned fromStreptomyces vinaceusdrappusNRRL 2363 and localized on a 37-kb contiguous DNA region. Heterologous expression of the amicetin biosynthesis gene cluster inStreptomyces lividansTK64 resulted in the production of amicetin and its analogues, thereby confirming the identity of theamigene cluster.In silicosequence analysis revealed that 21 genes were putatively involved in amicetin biosynthesis, including 3 for regulation and transportation, 10 for disaccharide biosynthesis, and 8 for the formation of the amicetin skeleton by the linkage of cytosine,p-aminobenzoic acid (PABA), and the terminal (+)-α-methylserine moieties. The inactivation of the benzoate coenzyme A (benzoate-CoA) ligase geneamiLand theN-acetyltransferase geneamiFled to two mutants that accumulated the same two compounds, cytosamine and 4-acetamido-3-hydroxybenzoic acid. These data indicated that AmiF functioned as an amide synthethase to link cytosine and PABA. The inactivation ofamiR, encoding an acyl-CoA-acyl carrier protein transacylase, resulted in the production of plicacetin and norplicacetin, indicating AmiR to be responsible for attachment of the terminal methylserine moiety to form another amide bond. These findings implicated two alternative strategies for amide bond formation in amicetin biosynthesis.

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