Bioinformatic and Functional Analysis of the pSID Siderophore Biosynthesis Plasmid of Rhodococcus pyridinivorans 5Ap

IF 16.4 1区化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Accounts of Chemical Research Pub Date : 2024-07-26 DOI:10.1134/s0026261724604603

M. I. Mandryk, A. A. Vysotskaya, Yu. V. Yahorava, D. U. Surzhyk, A. Yu. Larchenka, S. L. Vasylenko

{"title":"Bioinformatic and Functional Analysis of the pSID Siderophore Biosynthesis Plasmid of Rhodococcus pyridinivorans 5Ap","authors":"M. I. Mandryk, A. A. Vysotskaya, Yu. V. Yahorava, D. U. Surzhyk, A. Yu. Larchenka, S. L. Vasylenko","doi":"10.1134/s0026261724604603","DOIUrl":null,"url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">\nAbstract—</h3>Complete genome sequencing of R. pyridinivorans strain 5Ap revealed the pSID plasmid (CP063453.1) 250 428 bp in size. The gene responsible for replication of this plasmid is, most probably, dnaB. The genes which may be involved in the replication (dnaB, ssb) and plasmid separation after replication (parA) showed the highest similarity to the determinants located on large (224‒343 kb) plasmids of rhodococci: unnamed1 of R. pyridinivorans YF3, unnamed1 of R. rhodochrous LH-B3, pRJH1 of R. pyridinivorans YC-JH2, pRDE01 of Rhodococcus sp. RDE2, and pRho-VOC14-C342 of R. opacus VOC-14. The pSID plasmid was found to contain two loci responsible for the synthesis of secondary metabolites, one of them determining the synthesis of a polyketide compound (similar sequences have been revealed on plasmids of other rhodococci) and the other one probably determines the synthesis of a siderophore: the genes for biosynthesis of this compound (sid1–5) exhibited the highest similarity (not exceeding 75%) with the sequences from Streptomyces vilmorinianum YP1 (CP040244.1), S. ficellus NRRL 8067 (CP034279.1), Streptomyces sp. NBC00162 (CP102509.1), and some other streptomycetes, while showing no similarity to the known siderophore biosynthesis genes of rhodococci. The locus of the pSID plasmid responsible for the siderophore synthesis had a unique organization, since transcription of the sid5 (iucC) gene occurs in the opposite direction, while in other bacteria it belongs to an operon and is located at one of its termini. Inactivation of the sid1 gene was found to result in decreased antagonistic activity of R. pyridinivorans 5Ap against plant-pathogenic bacteria P. carotovorum 2.18, lower resistance to iron and cadmium ions and arsenate, as well as in emergence of phytotoxic properties against radish, while wild-type bacteria exhibit plant growth-promoting activity.","PeriodicalId":1,"journal":{"name":"Accounts of Chemical Research","volume":null,"pages":null},"PeriodicalIF":16.4000,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Accounts of Chemical Research","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1134/s0026261724604603","RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}

引用次数: 0

Abstract—

Complete genome sequencing of R. pyridinivorans strain 5Ap revealed the pSID plasmid (CP063453.1) 250 428 bp in size. The gene responsible for replication of this plasmid is, most probably, dnaB. The genes which may be involved in the replication (dnaB, ssb) and plasmid separation after replication (parA) showed the highest similarity to the determinants located on large (224‒343 kb) plasmids of rhodococci: unnamed1 of R. pyridinivorans YF3, unnamed1 of R. rhodochrous LH-B3, pRJH1 of R. pyridinivorans YC-JH2, pRDE01 of Rhodococcus sp. RDE2, and pRho-VOC14-C342 of R. opacus VOC-14. The pSID plasmid was found to contain two loci responsible for the synthesis of secondary metabolites, one of them determining the synthesis of a polyketide compound (similar sequences have been revealed on plasmids of other rhodococci) and the other one probably determines the synthesis of a siderophore: the genes for biosynthesis of this compound (sid1–5) exhibited the highest similarity (not exceeding 75%) with the sequences from Streptomyces vilmorinianum YP1 (CP040244.1), S. ficellus NRRL 8067 (CP034279.1), Streptomyces sp. NBC00162 (CP102509.1), and some other streptomycetes, while showing no similarity to the known siderophore biosynthesis genes of rhodococci. The locus of the pSID plasmid responsible for the siderophore synthesis had a unique organization, since transcription of the sid5 (iucC) gene occurs in the opposite direction, while in other bacteria it belongs to an operon and is located at one of its termini. Inactivation of the sid1 gene was found to result in decreased antagonistic activity of R. pyridinivorans 5Ap against plant-pathogenic bacteria P. carotovorum 2.18, lower resistance to iron and cadmium ions and arsenate, as well as in emergence of phytotoxic properties against radish, while wild-type bacteria exhibit plant growth-promoting activity.

Abstract Image

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

Rhodococcus pyridinivorans 5Ap 的 pSID 苷元合成质粒的生物信息学和功能分析

摘要--对R. pyridinivorans菌株5Ap进行的全基因组测序发现，pSID质粒（CP063453.1）大小为250 428 bp。负责复制该质粒的基因很可能是 dnaB。可能参与复制的基因（dnaB、ssb）和复制后质粒分离的基因（parA）与位于大质粒（224-343 kb）上的根球菌决定基因相似度最高：R.pyridinivorans YF 的 unnamed1、R.Pyridinivorans YF 的 unnamed2、R.Pyridinivorans YF 的 unnamed3。Pyridinivorans YF3 的 unnamed1、R. rhodochrous LH-B3 的 unnamed1、R. pyridinivorans YC-JH2 的 pRJH1、Rhodococcus sp.发现 pSID 质粒含有两个负责合成次生代谢物的基因座，其中一个决定了一种多酮化合物的合成（在其他根瘤菌的质粒上也发现了类似的序列），另一个可能决定了一种苷元的合成：这种化合物的生物合成基因（sid1-5）与 vilmorinianum 链霉菌 YP1（CP040244.1）、S. ficellus NRRL 8067（CP034279.1）、Streptomyces sp.负责合成苷元的 pSID 质粒基因座具有独特的组织结构，因为 sid5（iucC）基因的转录发生在相反的方向上，而在其他细菌中，它属于一个操作子，位于其末端之一。研究发现，sid1 基因的失活会导致 R. pyridinivorans 5Ap 对植物病原菌 P. carotovorum 2.18 的拮抗活性降低，对铁、镉离子和砷酸盐的抗性降低，并对萝卜产生植物毒性，而野生型细菌则表现出促进植物生长的活性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文去求助

来源期刊

Accounts of Chemical Research 化学-化学综合

CiteScore

31.40

自引率

1.10%

发文量

312

审稿时长

2 months

期刊介绍： Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance. Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.

期刊最新文献

Management of Cholesteatoma: Hearing Rehabilitation. Congenital Cholesteatoma. Evaluation of Cholesteatoma. Management of Cholesteatoma: Extension Beyond Middle Ear/Mastoid. Recidivism and Recurrence.