Data_Sheet_1_The impact of PrsA over-expression on the Bacillus subtilis transcriptome during fed-batch fermentation of alpha-amylase production.zip

The production of the alpha-amylase (AMY) enzyme in Bacillus subtilis at a high rate leads to the accumulation of unfolded AMY, which causes secretion stress. The over-expression of the PrsA chaperone aids enzyme folding and reduces stress. To identify affected pathways and potential mechanisms involved in the reduced growth, we analyzed the transcriptomic differences during fed-batch fermentation between a PrsA over-expressing strain and control in a time-series RNA-seq experiment. We observe transcription in 542 unannotated regions, of which 234 had significant changes in expression levels between the samples. Moreover, 1,791 protein-coding sequences, 80 non-coding genes, and 20 riboswitches overlapping UTR regions of coding genes had significant changes in expression. We identified putatively regulated biological processes via gene-set over-representation analysis of the differentially expressed genes; overall, the analysis suggests that the PrsA over-expression affects ATP biosynthesis activity, amino acid metabolism, and cell wall stability. The investigation of the protein interaction network points to a potential impact on cell motility signaling. We discuss the impact of these highlighted mechanisms for reducing secretion stress or detrimental aspects of PrsA over-expression during AMY production.

巴氏芽孢杆菌中α-淀粉酶（AMY）酶的大规模生产导致未折叠的AMY累积，进而引起分泌压力。通过过表达prsA伴侣蛋白，有助于酶的折叠并减轻压力。为识别受影响的途径和参与生长减慢的潜在机制，我们在时间序列RNA测序实验中分析了prsA过表达菌株与对照菌株在补料分批发酵过程中的转录组差异。我们观察到542个未注释区域存在转录，其中234个区域在样本间表达水平发生显著变化。此外，1,791个蛋白质编码序列、80个非编码基因以及20个与编码基因UTR区域重叠的核糖开关在表达上发生了显著变化。通过差异表达基因的基因集富集分析，我们确定了可能受调控的生物学过程；总体而言，分析表明prsA过表达影响了三磷酸腺苷（ATP）的生物合成活性、氨基酸代谢和细胞壁稳定性。对蛋白质相互作用网络的探究指向了对细胞运动信号传导的潜在影响。我们讨论了这些突出机制对降低分泌压力或amy生产过程中prsA过表达的有害影响。