Pathak Ashish, Chauhan Ashvini, Blom Jochen, Indest Karl J, Jung Carina M, Stothard Paul, Bera Gopal, Green Stefan J, Ogram Andrew
School of the Environment, Florida A&M University, Tallahassee, Florida, United States of America.
Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany.
PLoS One. 2016 Aug 17;11(8):e0161032. doi: 10.1371/journal.pone.0161032. eCollection 2016.
The genome of Rhodococcus opacus strain M213, isolated from a fuel-oil contaminated soil, was sequenced and annotated which revealed a genome size of 9,194,165 bp encoding 8680 putative genes and a G+C content of 66.72%. Among the protein coding genes, 71.77% were annotated as clusters of orthologous groups of proteins (COGs); 55% of the COGs were present as paralog clusters. Pulsed field gel electrophoresis (PFGE) analysis of M213 revealed the presence of three different sized replicons- a circular chromosome and two megaplasmids (pNUO1 and pNUO2) estimated to be of 750Kb 350Kb in size, respectively. Conversely, using an alternative approach of optical mapping, the plasmid replicons appeared as a circular ~1.2 Mb megaplasmid and a linear, ~0.7 Mb megaplasmid. Genome-wide comparative analysis of M213 with a cohort of sequenced Rhodococcus species revealed low syntenic affiliation with other R. opacus species including strains B4 and PD630. Conversely, a closer affiliation of M213, at the functional (COG) level, was observed with the catabolically versatile R. jostii strain RHA1 and other Rhodococcii such as R. wratislaviensis strain IFP 2016, R. imtechensis strain RKJ300, Rhodococcus sp. strain JVH1, and Rhodococcus sp. strain DK17, respectively. An in-depth, genome-wide comparison between these functional relatives revealed 971 unique genes in M213 representing 11% of its total genome; many associating with catabolic functions. Of major interest was the identification of as many as 154 genomic islands (GEIs), many with duplicated catabolic genes, in particular for PAHs; a trait that was confirmed by PCR-based identification of naphthalene dioxygenase (NDO) as a representative gene, across PFGE-resolved replicons of strain M213. Interestingly, several plasmid/GEI-encoded genes, that likely participate in degrading naphthalene (NAP) via a peculiar pathway, were also identified in strain M213 using a combination of bioinformatics, metabolic analysis and gene expression measurements of selected catabolic genes by RT-PCR. Taken together, this study provides a comprehensive understanding of the genome plasticity and ecological competitiveness of strain M213 likely facilitated by horizontal gene transfer (HGT), bacteriophage attacks and genomic reshuffling- aspects that continue to be understudied and thus poorly understood, in particular for the soil-borne Rhodococcii.
从受燃油污染的土壤中分离出的食油红球菌菌株M213的基因组进行了测序和注释，结果显示其基因组大小为9,194,165 bp，编码8680个推定基因，G+C含量为66.72%。在蛋白质编码基因中，71.77%被注释为直系同源蛋白簇（COG）；55%的COG以旁系同源簇的形式存在。对M213进行脉冲场凝胶电泳（PFGE）分析，发现存在三种不同大小的复制子——一条环状染色体和两个大质粒（pNUO1和pNUO2），估计大小分别为750Kb和350Kb。相反，使用光学图谱的另一种方法，质粒复制子呈现为一个环状的1.2 Mb大质粒和一个线性的0.7 Mb大质粒。对M213与一组已测序的红球菌物种进行全基因组比较分析，发现与其他食油红球菌物种（包括菌株B4和PD630）的共线性关联较低。相反，在功能（COG）水平上，观察到M213与代谢功能多样的约氏红球菌菌株RHA1以及其他红球菌（如弗罗茨瓦夫红球菌菌株IFP 2016、英特肯红球菌菌株RKJ300、红球菌属菌株JVH1和红球菌属菌株DK17）的亲缘关系更近。对这些功能相关菌株进行深入的全基因组比较，发现M213中有971个独特基因，占其总基因组的11%；许多基因与分解代谢功能相关。最令人感兴趣的是鉴定出多达154个基因组岛（GEI），其中许多含有重复的分解代谢基因，特别是针对多环芳烃的基因；通过基于PCR的萘双加氧酶（NDO）鉴定作为代表性基因，在菌株M213的PFGE分离的复制子中证实了这一特征。有趣的是，还使用生物信息学、代谢分析和通过RT-PCR对选定分解代谢基因进行基因表达测量的组合方法，在菌株M213中鉴定出几个可能通过特殊途径参与降解萘（NAP）的质粒/GEI编码基因。综上所述，本研究全面了解了菌株M213的基因组可塑性和生态竞争力，这可能是由水平基因转移（HGT）、噬菌体攻击和基因组重排所促进的——这些方面仍在研究中，因此了解甚少，特别是对于土壤中的红球菌而言。
