Pseudomonas sp’deki Biyosentetik Gen Kümelerinin Detaylı Genom Madenciliği Analizi

Year 2025, In Press Articles, 1 - 13

Levent Çavaş , Yagmur Bilgin , İbrahim Kırkız

https://doi.org/10.52998/trjmms.1557940

Abstract

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 seconder 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 Körfezi'nin deniz suyundan izole edilen Pseudomonas sp. SXM-1 suşunun kapsamlı bir gen kümesi analizini yapmayı amaçlamaktadır. Pseudomonas sp.'nin erişim numarası NCBI'dan 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.

Keywords

antiSMASH, biyosentetik gen kümeleri, genom, Pseudomonas sp. SXM-1

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

Abstract

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 predicted for their genomes and secondary metabolites using these tools are widely employed in 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.

Keywords

antiSMASH, biosynthetic gene clusters, genome, Pseudomonas sp. SXM-1

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