Orsi Renato H, Chaturongakul Soraya, Oliver Haley F, Ponnala Lalit, Gaballa Ahmed, Wiedmann Martin
Department of Food Science, Cornell University, Ithaca, NY 14853, USA.
Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
Pathogens. 2021 Apr 1;10(4):411. doi: 10.3390/pathogens10040411.
can regulate and fine-tune gene expression, to adapt to diverse stress conditions encountered during foodborne transmission. To further understand the contributions of alternative sigma (σ) factors to the regulation of gene expression, RNA-Seq was performed on strain 10403S and five isogenic mutants (four strains bearing in-frame null mutations in three out of four alternative σ factor genes, ΔCHL, ΔBHL, ΔBCL, and ΔBCH, and one strain bearing null mutations in all four genes, ΔBCHL), grown to stationary phase. Our data showed that 184, 35, 34, and 20 genes were positively regulated by σ, σ, σ, and σ (posterior probability > 0.9 and Fold Change (FC) > 5.0), respectively. Moreover, σ-dependent genes showed the highest FC (based on comparisons between the ΔCHL and the ΔBCHL strain), with 44 genes showing an FC > 100; only four σ-dependent, and no σ- or σ-dependent genes showed FC >100. While σ-regulated genes identified in this study are involved in stress-associated functions and metabolic pathways, σ appears to largely regulate genes involved in a few specific metabolic pathways, including positive regulation of operons encoding phosphoenolpyruvate (PEP)-dependent phosphotransferase systems (PTSs). Overall, our data show that (i) σ and σ directly and indirectly regulate genes involved in several energy metabolism-related functions; (ii) alternative σ factors are involved in complex regulatory networks and appear to have epistatic effects in stationary phase cells; and (iii) σ regulates multiple stress response pathways, while σ and σ positively regulate a smaller number of specific pathways.
可以调节和微调基因表达，以适应食源传播过程中遇到的各种应激条件。为了进一步了解替代σ因子对基因表达调控的贡献，对处于稳定期的10403S菌株和五个同基因突变体（四个菌株在四个替代σ因子基因中的三个基因中带有框内无效突变，即ΔCHL、ΔBHL、ΔBCL和ΔBCH，以及一个在所有四个基因中都带有无效突变的菌株ΔBCHL）进行了RNA测序。我们的数据表明，分别有184、35、34和20个基因受到σ、σ、σ和σ的正向调控（后验概率>0.9且变化倍数（FC）>5.0）。此外，σ依赖基因显示出最高的FC（基于ΔCHL和ΔBCHL菌株之间的比较），有44个基因的FC>100；只有四个σ依赖基因，没有σ或σ依赖基因的FC>100。虽然本研究中鉴定的σ调控基因参与应激相关功能和代谢途径，但σ似乎主要调控参与少数特定代谢途径的基因，包括对编码磷酸烯醇丙酮酸（PEP）依赖性磷酸转移酶系统（PTSs）的操纵子的正向调控。总体而言，我们的数据表明：（i）σ和σ直接和间接调控参与多种能量代谢相关功能的基因；（ii）替代σ因子参与复杂的调控网络，并且在稳定期细胞中似乎具有上位效应；（iii）σ调控多种应激反应途径，而σ和σ正向调控较少数量的特定途径。
