Fishery Resource and Environmental Management Division, Biotechnology Laboratory, ICAR- Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India.
Parasitology and Microbiology Research Laboratory, Department of Zoology, University of Burdwan, Burdwan, West Bengal, India.
PLoS One. 2020 Feb 10;15(2):e0228199. doi: 10.1371/journal.pone.0228199. eCollection 2020.
In the present study, we identified salt stress tolerant genes from the marine bacterium Staphylococcus sp. strain P-TSB-70 through transcriptome sequencing. In favour of whole-genome transcriptome profiling of Staphylococcus sp. strain P-TSB-70 (GenBank Accn. No. KP117091) which tolerated upto 20% NaCl stress, the strain was cultured in the laboratory condition with 20% NaCl stress. Transcriptome analyses were performed by SOLiD4.0 sequencing technology from which 10280 and 9612 transcripts for control and treated, respectively, were obtained. The coverage per base (CPB) statistics were analyzed for both the samples. Gene ontology (GO) analysis has been categorized at varied graph levels based on three primary ontology studies viz. cellular components, biological processes, and molecular functions. The KEGG analysis of the assembled transcripts using KAAS showed presumed components of metabolic pathways which perhaps implicated in diverse metabolic pathways responsible for salt tolerance viz. glycolysis/gluconeogenesis, oxidative phosphorylation, glutathione metabolism, etc. further involving in salt tolerance. Overall, 90 salt stress tolerant genes were identified as of 186 salt-related transcripts. Several genes have been found executing normally in the TCA cycle pathway, integral membrane proteins, generation of the osmoprotectants, enzymatic pathway associated with salt tolerance. Recognized genes fit diverse groups of salt stress genes viz. abc transporter, betaine, sodium antiporter, sodium symporter, trehalose, ectoine, and choline, that belong to different families of genes involved in the pathway of salt stress. The control sample of the bacterium showed elevated high proportion of transcript contigs (29%) while upto 20% salt stress treated sample of the bacterium showed a higher percentage of transcript contigs (31.28%). A total of 1,288 and 1,133 transcript contigs were measured entirely as novel transcript contigs in both control and treated samples, respectively. The structure and function of 10 significant salt stress tolerant genes of Staphylococcus sp. have been analyzed in this study. The information acquired in the present study possibly used to recognize and clone the salt stress tolerant genes and support in developing the salt stress-tolerant plant varieties to expand the agricultural productivity in the saline system.
在本研究中，我们通过转录组测序从海洋细菌葡萄球菌属菌株 P-TSB-70 中鉴定出耐盐基因。为了对耐高达 20%NaCl 胁迫的葡萄球菌属菌株 P-TSB-70（GenBank Accn. No. KP117091）进行全基因组转录组谱分析，我们在实验室条件下用 20%NaCl 胁迫培养该菌株。使用 SOLiD4.0 测序技术进行转录组分析，分别获得了对照和处理组的 10280 和 9612 个转录本。对两个样本的每个碱基的覆盖度（CPB）统计进行了分析。GO 分析根据三个主要本体研究（即细胞成分、生物过程和分子功能）在不同的图形级别进行分类。使用 KAAS 对组装的转录本进行 KEGG 分析显示，代谢途径的假定组成部分可能参与了不同的代谢途径，这些代谢途径负责耐盐性，例如糖酵解/糖异生、氧化磷酸化、谷胱甘肽代谢等，进一步涉及耐盐性。总体而言，从 186 个与盐相关的转录本中鉴定出 90 个耐盐基因。一些基因在 TCA 循环途径、完整的膜蛋白、渗透保护剂的产生、与盐耐受性相关的酶途径中正常表达。已识别的基因适合于不同的盐胁迫基因组，例如 ABC 转运体、甜菜碱、钠离子反向转运体、钠离子同向转运体、海藻糖、ectoine 和胆碱，这些基因属于参与盐胁迫途径的不同基因家族。细菌的对照样本显示出较高比例的转录本（29%），而在 20%盐胁迫处理的细菌样本中，转录本的比例更高（31.28%）。在对照和处理样本中，分别有 1288 个和 1133 个转录本被完全测量为全新的转录本。本研究分析了葡萄球菌属 10 个重要耐盐基因的结构和功能。本研究获得的信息可能用于识别和克隆耐盐基因，并支持开发耐盐植物品种，以扩大在盐系统中的农业生产力。
