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首页> 外文期刊>BMC Genomics >RNA-Seq analysis of the multipartite genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock
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RNA-Seq analysis of the multipartite genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock

机译：根瘤菌CE3多部分基因组的RNA-Seq分析显示在热和盐水冲击下不同的复制子贡献

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Background Regulation of transcription is essential for any organism and Rhizobium etli (a multi-replicon, nitrogen-fixing symbiotic bacterium) is no exception. This bacterium is commonly found in the rhizosphere (free-living) or inside of root-nodules of the common bean (Phaseolus vulgaris) in a symbiotic relationship. Abiotic stresses, such as high soil temperatures and salinity, compromise the genetic stability of R. etli and therefore its symbiotic interaction with P. vulgaris. However, it is still unclear which genes are up- or down-regulated to cope with these stress conditions. The aim of this study was to identify the genes and non-coding RNAs (ncRNAs) that are differentially expressed under heat and saline shock, as well as the promoter regions of the up-regulated loci. Results Analysing the heat and saline shock responses of R. etli CE3 through RNA-Seq, we identified 756 and 392 differentially expressed genes, respectively, and 106 were up-regulated under both conditions. Notably, the set of genes over-expressed under either condition was preferentially encoded on plasmids, although this observation was more significant for the heat shock response. In contrast, during either saline shock or heat shock, the down-regulated genes were principally chromosomally encoded. Our functional analysis shows that genes encoding chaperone proteins were up-regulated during the heat shock response, whereas genes involved in the metabolism of compatible solutes were up-regulated following saline shock. Furthermore, we identified thirteen and nine ncRNAs that were differentially expressed under heat and saline shock, respectively, as well as eleven ncRNAs that had not been previously identified. Finally, using an in silico analysis, we studied the promoter motifs in all of the non-coding regions associated with the genes and ncRNAs up-regulated under both conditions. Conclusions Our data suggest that the replicon contribution is different for different stress responses and that the heat shock response is more complex than the saline shock response. In general, this work exemplifies how strategies that not only consider differentially regulated genes but also regulatory elements of the stress response provide a more comprehensive view of bacterial gene regulation.
机译：背景技术转录调节对于任何生物都是必不可少的，而根瘤菌（一种多复制子，固氮共生细菌）也不例外。该细菌通常以共生关系存在于普通豆（菜豆）的根际（自由活动）或根瘤内。非生物胁迫（例如高土壤温度和盐分）损害了R. etli的遗传稳定性，并因此损害了其与寻常型P. pulgaris的共生相互作用。然而，尚不清楚哪些基因被上调或下调以应付这些压力条件。这项研究的目的是鉴定在热和盐水冲击下差异表达的基因和非编码RNA（ncRNA），以及上调基因座的启动子区域。结果通过RNA-Seq分析R. etli CE3的热休克反应和生理盐水休克反应，我们分别鉴定了756个和392个差异表达的基因，并且在两种条件下均上调了106个。值得注意的是，在任一条件下均过表达的基因组优先编码在质粒上，尽管这种观察对于热休克反应更为重要。相反，在盐水冲击或热冲击期间，下调的基因主要是染色体编码的。我们的功能分析表明，在热激反应过程中，编码伴侣蛋白的基因被上调，而在盐水激荡后，参与相容性溶质代谢的基因被上调。此外，我们分别鉴定了在热和盐水冲击下差异表达的13个和9个ncRNA，以及之前未鉴定的11个ncRNA。最后，使用计算机分析，我们研究了在两种条件下与上调的基因和ncRNA相关的所有非编码区的启动子基序。结论我们的数据表明，对于不同的应激反应，复制子的贡献是不同的，并且热休克反应比盐水休克反应更为复杂。总的来说，这项工作例证了不仅考虑差异调节基因而且考虑应激反应调节因素的策略如何提供更全面的细菌基因调节观点。

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