van der Meulen Sjoerd B, de Jong Anne, Kok Jan
Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands.
Top Institute Food and NutritionWageningen, Netherlands.
Front Microbiol. 2017 Sep 14;8:1704. doi: 10.3389/fmicb.2017.01704. eCollection 2017.
Bacteria can deploy various mechanisms to combat environmental stresses. Many genes have previously been identified in that are involved in sensing the stressors and those that are involved in regulating and mounting a defense against the stressful conditions. However, the expression of small regulatory RNAs (sRNAs) during industrially relevant stress conditions has not been assessed yet in , while sRNAs have been shown to be involved in many stress responses in other bacteria. We have previously reported the presence of hundreds of putative regulatory RNAs in , and have used high-throughput RNA sequencing (RNA-seq) in this study to assess their expression under six different stress conditions. The uniformly designed experimental set-up enabled a highly reliable comparison between the different stress responses and revealed that many sRNAs are differentially expressed under the conditions applied. The primary stress responses of NCDO712 was benchmarked to earlier work and, for the first time, the differential expression was assessed of transfer RNAs (tRNAs) and the genes from the six recently sequenced plasmids of NCDO712. Although, we only applied stresses for 5 min, the majority of the well-known specific stress-induced genes are already differentially expressed. We find that most tRNAs decrease after all stresses applied, except for a small number, which are increased upon cold stress. Starvation was shown to induce the highest differential response, both in terms of number and expression level of genes. Our data pinpoints many novel stress-related uncharacterized genes and sRNAs, which calls for further assessment of their molecular and cellular function. These insights furthermore could impact the way parameters are designed for bacterial culture production and milk fermentation, as we find that very short stress conditions already greatly alter gene expression.
细菌可采用多种机制来应对环境压力。此前已在[细菌名称]中鉴定出许多参与感知应激源以及调控和抵御应激条件的基因。然而，在[细菌名称]中，尚未评估与工业相关应激条件下小调节RNA（sRNA）的表达情况，而在其他细菌中，sRNA已被证明参与多种应激反应。我们之前报道过[细菌名称]中存在数百种假定的调节RNA，并且在本研究中使用高通量RNA测序（RNA-seq）来评估它们在六种不同应激条件下的表达。统一设计的实验设置使得能够在不同应激反应之间进行高度可靠的比较，并揭示出许多sRNA在应用的条件下差异表达。将[细菌名称]NCDO712的主要应激反应与早期工作进行了基准对比，并且首次评估了转移RNA（tRNA）以及来自NCDO712六个最近测序质粒的基因的差异表达。尽管我们仅施加应激5分钟，但大多数著名的特定应激诱导基因已经差异表达。我们发现，除了少数在冷应激时增加的tRNA外，所有应激处理后大多数tRNA都会减少。饥饿被证明在基因数量和表达水平方面都会诱导最高的差异反应。我们的数据确定了许多与应激相关的新的未表征基因和sRNA，这需要进一步评估它们的分子和细胞功能。此外，这些见解可能会影响细菌培养生产和牛奶发酵参数的设计方式，因为我们发现非常短的应激条件已经极大地改变了基因表达。
