Department of Biochemistry, University of Calcutta, West Bengal 700019, India.
Department of Medical Zoology, Kyung Hee University, School of Medicine, Seoul 02447, Republic of Korea.
FEMS Microbiol Ecol. 2019 Nov 1;95(11). doi: 10.1093/femsec/fiz165.
Bradyrhizobium is a biologically important bacterial genus. Different Bradyrhizobium strains exhibit distinct niche selection like free living, root nodular and stem nodular. The present in-silico study was undertaken to identify the role of bacterial secretome in the phylogenetic niche conservation (PNC) of Bradyrhizobium sp. Analysis was carried out with the publicly available 19 complete genome assembly and annotation reports. A protocol was developed to screen the secretome related genes using three different database, viz. genome, proteome and gene ortholog. This resulted into 139 orthologs that include type secretion systems (T1SS-T6SS) along with flagella (Flg), type IV pili (T4P) and tight adherence (Tad) systems. Multivariate analysis using bacterial secretome was undertaken to find out the role of these secretion systems in PNC. In free living strains, T3SS, T4SS and T6SS were completely absent. Whereas, in the stem nodulating strains, T3SS and T6SS were absent, but T4SS was found to be present. On the other hand, the T3SS was found to be present only in the root-nodulating strains. The present investigation clearly demonstrated a pattern of PNC based on the distribution of secretion system components. To the best of our knowledge, this is the first report on PNC of Bradyrhizobium using the multivariate analysis of secretome.
慢生根瘤菌是一种具有重要生物学意义的细菌属。不同的慢生根瘤菌菌株表现出不同的生态位选择，如自由生活、根瘤和茎瘤。本研究采用生物信息学方法，对慢生根瘤菌的系统发育生态位保守性（PNC）与细菌分泌系统的关系进行了分析。分析采用了 19 株已公开的全基因组序列和注释报告。我们开发了一种使用三个不同数据库（基因组、蛋白质组和基因直系同源物）筛选分泌相关基因的方案。结果共鉴定到 139 个直系同源物，包括 1 型分泌系统（T1SS-T6SS）、鞭毛（Flg）、4 型菌毛（T4P）和紧密附着（Tad）系统。利用细菌分泌组进行了多元分析，以确定这些分泌系统在 PNC 中的作用。在自由生活菌株中，完全不存在 T3SS、T4SS 和 T6SS。而在茎瘤菌株中，T3SS 和 T6SS 不存在，但 T4SS 存在。另一方面，仅在根瘤菌株中发现了 T3SS。本研究清楚地表明，基于分泌系统组件的分布，存在着 PNC 模式。据我们所知，这是首次利用分泌组的多元分析来研究慢生根瘤菌的 PNC。
