Department of Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany.
Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
BMC Genomics. 2017 Nov 3;18(1):846. doi: 10.1186/s12864-017-4235-z.
The plant growth promoting rhizobacterium Paenibacillus riograndensis SBR5 is a promising candidate to serve as crop inoculant. Despite its potential in providing environmental and economic benefits, the species P. riograndensis is poorly characterized. Here, we performed for the first time a detailed transcriptome analysis of P. riograndensis SBR5 using RNA-seq technology.
RNA was isolated from P. riograndensis SBR5 cultivated under 15 different growth conditions and combined together in order to analyze an RNA pool representing a large set of expressed genes. The resultant total RNA was used to generate 2 different libraries, one enriched in 5'-ends of the primary transcripts and the other representing the whole transcriptome. Both libraries were sequenced and analyzed to identify the conserved sequences of ribosome biding sites and translation start motifs, and to elucidate operon structures present in the transcriptome of P. riograndensis. Sequence analysis of the library enriched in 5'-ends of the primary transcripts was used to identify 1082 transcription start sites (TSS) belonging to novel transcripts and allowed us to determine a promoter consensus sequence and regulatory sequences in 5' untranslated regions including riboswitches. A putative thiamine pyrophosphate dependent riboswitch upstream of the thiamine biosynthesis gene thiC was characterized by translational fusion to a fluorescent reporter gene and shown to function in P. riograndensis SBR5.
Our RNA-seq analysis provides insight into the P. riograndensis SBR5 transcriptome at the systems level and will be a valuable basis for differential RNA-seq analysis of this bacterium.
植物促生根际细菌解淀粉芽孢杆菌 SBR5 是一种很有前途的作物接种剂候选物。尽管它具有提供环境和经济效益的潜力，但该种解淀粉芽孢杆菌的特征描述较差。在这里，我们首次使用 RNA-seq 技术对解淀粉芽孢杆菌 SBR5 进行了详细的转录组分析。
从在 15 种不同生长条件下培养的解淀粉芽孢杆菌 SBR5 中分离 RNA，并将其组合在一起，以分析代表大量表达基因的 RNA 池。所得总 RNA 用于生成 2 个不同的文库，一个文库富含初级转录物的 5'端，另一个文库代表整个转录组。对这两个文库进行测序和分析，以鉴定核糖体结合位点和翻译起始基序的保守序列，并阐明解淀粉芽孢杆菌转录组中的操纵子结构。对富含初级转录物 5'端的文库进行序列分析，确定了 1082 个属于新转录本的转录起始位点 (TSS)，并确定了启动子保守序列和包括核糖开关在内的 5'非翻译区的调控序列。通过与荧光报告基因的翻译融合，对硫胺素生物合成基因 thiC 上游的假定硫胺素焦磷酸依赖性核糖开关进行了表征，并证明其在解淀粉芽孢杆菌 SBR5 中起作用。
我们的 RNA-seq 分析提供了对解淀粉芽孢杆菌 SBR5 转录组的系统水平的深入了解，并将成为该细菌差异 RNA-seq 分析的有价值基础。
