A Comprehensive Genome Mining Analysis of Biosynthetic Gene Clusters in Pseudomonas sp. SXM-1

Levent Çavaş; Yagmur Bilgin; İbrahim Kırkız

Makale detayları

A Comprehensive Genome Mining Analysis of Biosynthetic Gene Clusters in Pseudomonas sp. SXM-1

Yazarlar:

Levent Çavaş | Yagmur Bilgin | İbrahim Kırkız

Yayıncı:

Ordu University

Ana Başlıklar:

Fisheries Technologies

Dergi:

Turkish Journal of Maritime and Marine Sciences Vol.11 Issue 2, pp.82-94

Belge Tipi:

Makale

Yayın Tarihi:

1/2025

Belge Dili:

İngilizce

Document ID (Org No.):

2001349259

pISSN:

2564-7016

Anahtar kelimeler:

Özet:

 Very resistant pathogenic microorganisms have been reported to current antibiotics in the last decade. Therefore, there is a great need to understand not only resistance metabolism but also secondary metabolites of pathogenic microorganisms. Genome mining tools have so far been improved to understand secondary metabolites from biosynthetic gene clusters. Microorganisms whose genomes and secondary metabolites are predicted by these tools are widely used in the pharmaceutical and industrial studies. Pseudomonas spp. are widely used in recombinant DNA technology to produce commercial products. Bioinformatics-based in silico tools significantly contribute to the discovery of new bioactive compounds for pharmacy and medicine. This study aims to conduct a comprehensive gene cluster analysis of the Pseudomonas sp. SXM-1 strain isolated from the coastal seawater of Xiamen Bay using antiSMASH 7.0.1. The accession number of Pseudomonas sp. SXM-1 strain was retrieved from NCBI. 14 regions were found, including non-ribosomal peptides metallophores NRP-metallophore, nonribosomal peptide-synthetase NRPS, NRPS-like, ribosomally synthesized and post-translationally modified peptide-like RiPP-like, betalactone, nonribosomal peptide-synthetase NRPS, ectoine and N-acetylglutaminylglutamine amide NAGGN. Analysis of all 14 regions revealed secondary metabolites with potential applications in diverse fields. Microbiologists are strongly advised to conduct wet-lab experiments to validate the secondary metabolites discussed in this study.

 Very resistant pathogenic microorganisms have been reported to current antibiotics in the last decade. Therefore, there is a great need to understand not only resistance metabolism but also secondary metabolites of pathogenic microorganisms. Genome mining tools have so far been improved to understand secondary metabolites from biosynthetic gene clusters. Microorganisms whose genomes and secondary metabolites are predicted by these tools are widely used in the pharmaceutical and industrial studies. Pseudomonas spp. are widely used in recombinant DNA technology to produce commercial products. Bioinformatics-based in silico tools significantly contribute to the discovery of new bioactive compounds for pharmacy and medicine. This study aims to conduct a comprehensive gene cluster analysis of the Pseudomonas sp. SXM-1 strain isolated from the coastal seawater of Xiamen Bay using antiSMASH 7.0.1. The accession number of Pseudomonas sp. SXM-1 strain was retrieved from NCBI. 14 regions were found, including non-ribosomal peptides metallophores NRP-metallophore, nonribosomal peptide-synthetase NRPS, NRPS-like, ribosomally synthesized and post-translationally modified peptide-like RiPP-like, betalactone, nonribosomal peptide-synthetase NRPS, ectoine and N-acetylglutaminylglutamine amide NAGGN. Analysis of all 14 regions revealed secondary metabolites with potential applications in diverse fields. Microbiologists are strongly advised to conduct wet-lab experiments to validate the secondary metabolites discussed in this study.

 Very resistant pathogenic microorganisms have been reported to current antibiotics in the last decade. Therefore, there is a great need to understand not only resistance metabolism but also secondary metabolites of pathogenic microorganisms. Genome mining tools have so far been improved to understand secondary metabolites from biosynthetic gene clusters. Microorganisms whose genomes and secondary metabolites are predicted by these tools are widely used in the pharmaceutical and industrial studies. Pseudomonas spp. are widely used in recombinant DNA technology to produce commercial products. Bioinformatics-based in silico tools significantly contribute to the discovery of new bioactive compounds for pharmacy and medicine. This study aims to conduct a comprehensive gene cluster analysis of the Pseudomonas sp. SXM-1 strain isolated from the coastal seawater of Xiamen Bay using antiSMASH 7.0.1. The accession number of Pseudomonas sp. SXM-1 strain was retrieved from NCBI. 14 regions were found, including non-ribosomal peptides metallophores NRP-metallophore, nonribosomal peptide-synthetase NRPS, NRPS-like, ribosomally synthesized and post-translationally modified peptide-like RiPP-like, betalactone, nonribosomal peptide-synthetase NRPS, ectoine and N-acetylglutaminylglutamine amide NAGGN. Analysis of all 14 regions revealed secondary metabolites with potential applications in diverse fields. Microbiologists are strongly advised to conduct wet-lab experiments to validate the secondary metabolites discussed in this study.

 Son on yılda mevcut antibiyotiklere karşı çok dirençli patojen mikroorganizmaların olduğu rapor edilmiştir. Bu nedenle patojenik mikroorganizmaların sadece direnç metabolizmasını değil aynı zamanda sekonder metabolitlerini de anlamaya büyük ihtiyaç vardır. Günümüze kadar biyosentetik gen kümelerindeki sekonder metabolitleri ortaya çıkarmaya yönelik genom madenciliği araçları geliştirilmiştir. Bu araçları kullanarak genomları ve sekonder metabolitleri tahmin edilen mikroorganizmalar, farmasötik ve endüstriyel çalışmalarda yaygın olarak kullanılmaktadır. Pseudomonas spp. ticari ürünler üretmek için rekombinant DNA teknolojisinde yaygın olarak kullanılmaktadır. Biyoenformatik tabanlı in silico araçları, eczacılık ve tıp için yeni biyoaktif bileşiklerin keşfedilmesine önemli ölçüde katkıda bulunmaktadır. Bu çalışma, AntiSMASH 7.0.1 kullanılarak Xiamen Körfezinin deniz suyundan izole edilen Pseudomonas sp. SXM-1 suşunun kapsamlı bir gen kümesi analizini yapmayı amaçlamaktadır. Pseudomonas sp.nin erişim numarası NCBIdan alınmıştır. Ribozomal olmayan peptitler metaloforlar NRP-metalofor, ribozomal olmayan peptit sentetaz NRPS, NRPS benzeri, ribozomal olarak sentezlenmiş ve translasyon sonrası modifiye edilmiş peptit benzeri RiPP benzeri, betalakton, ribozomal olmayan peptit sentetaz NRPS, ektoin ve N-asetilglutaminilglutamin amid NAGGN dahil olmak üzere 14 bölge bulunmuştur. 14 bölgenin genom analizi, farklı alanlarda potansiyel uygulamalara sahip sekonder metabolitleri ortaya çıkarmıştır. Mikrobiyologlara bu çalışmada tartışılan sekonder metabolitleri doğrulamak için laboratuvar deneyleri yapmaları şiddetle tavsiye edilir.

Makale detayları

A Comprehensive Genome Mining Analysis of Biosynthetic Gene Clusters in Pseudomonas sp. SXM-1

Yazarlar:

Levent Çavaş | Yagmur Bilgin | İbrahim Kırkız

Yayıncı:

Ordu University

Ana Başlıklar:

Fisheries Technologies

Dergi:

Turkish Journal of Maritime and Marine Sciences Vol.11 Issue 2, pp.82-94

Belge Tipi:

Makale

Yayın Tarihi:

1/2025

Belge Dili:

İngilizce

Document ID (Org No.):

2001349259

pISSN:

2564-7016

antiSMASH

biosynthetic gene clusters

genome

Pseudomonas sp. SXM-1antiSMASH

biyosentetik gen kümeleri

genom

Pseudomonas sp. SXM-1

Sayı

Makale detayları

Yazarlar: Levent Çavaş | Yagmur Bilgin | İbrahim Kırkız

Yayıncı: Ordu University

Ana Başlıklar: Fisheries Technologies

Dergi: Turkish Journal of Maritime and Marine Sciences Vol.11 Issue 2, pp.82-94

Belge Tipi: Makale

Yayın Tarihi: 1/2025

Belge Dili: İngilizce

Document ID (Org No.): 2001349259

pISSN: 2564-7016

Sayı

Yazarlar:

Levent Çavaş | Yagmur Bilgin | İbrahim Kırkız

Yayıncı:

Ordu University

Ana Başlıklar:

Fisheries Technologies

Dergi:

Turkish Journal of Maritime and Marine Sciences Vol.11 Issue 2, pp.82-94

Belge Tipi:

Makale

Yayın Tarihi:

1/2025

Belge Dili:

İngilizce

Document ID (Org No.):

2001349259

pISSN:

2564-7016