Bidnenko Vladimir, Nicolas Pierre, Grylak-Mielnicka Aleksandra, Delumeau Olivier, Auger Sandrine, Aucouturier Anne, Guerin Cyprien, Repoila Francis, Bardowski Jacek, Aymerich Stéphane, Bidnenko Elena
Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France.
PLoS Genet. 2017 Jul 19;13(7):e1006909. doi: 10.1371/journal.pgen.1006909. eCollection 2017 Jul.
In eukaryotes, RNA species originating from pervasive transcription are regulators of various cellular processes, from the expression of individual genes to the control of cellular development and oncogenesis. In prokaryotes, the function of pervasive transcription and its output on cell physiology is still unknown. Most bacteria possess termination factor Rho, which represses pervasive, mostly antisense, transcription. Here, we investigate the biological significance of Rho-controlled transcription in the Gram-positive model bacterium Bacillus subtilis. Rho inactivation strongly affected gene expression in B. subtilis, as assessed by transcriptome and proteome analysis of a rho-null mutant during exponential growth in rich medium. Subsequent physiological analyses demonstrated that a considerable part of Rho-controlled transcription is connected to balanced regulation of three mutually exclusive differentiation programs: cell motility, biofilm formation, and sporulation. In the absence of Rho, several up-regulated sense and antisense transcripts affect key structural and regulatory elements of these differentiation programs, thereby suppressing motility and biofilm formation and stimulating sporulation. We dissected how Rho is involved in the activity of the cell fate decision-making network, centered on the master regulator Spo0A. We also revealed a novel regulatory mechanism of Spo0A activation through Rho-dependent intragenic transcription termination of the protein kinase kinB gene. Altogether, our findings indicate that distinct Rho-controlled transcripts are functional and constitute a previously unknown built-in module for the control of cell differentiation in B. subtilis. In a broader context, our results highlight the recruitment of the termination factor Rho, for which the conserved biological role is probably to repress pervasive transcription, in highly integrated, bacterium-specific, regulatory networks.
在真核生物中，源自广泛转录的RNA种类是各种细胞过程的调节因子，从单个基因的表达到细胞发育和肿瘤发生的控制。在原核生物中，广泛转录的功能及其对细胞生理的影响仍然未知。大多数细菌都拥有终止因子Rho，它抑制广泛的、主要是反义的转录。在这里，我们研究了革兰氏阳性模式细菌枯草芽孢杆菌中Rho控制的转录的生物学意义。通过对富培养基中指数生长期间的rho缺失突变体进行转录组和蛋白质组分析评估，Rho失活强烈影响枯草芽孢杆菌中的基因表达。随后的生理分析表明，Rho控制的转录的相当一部分与三种相互排斥的分化程序的平衡调节有关：细胞运动性、生物膜形成和孢子形成。在没有Rho的情况下，几种上调的正义和反义转录本会影响这些分化程序的关键结构和调节元件，从而抑制运动性和生物膜形成并刺激孢子形成。我们剖析了Rho如何参与以主调节因子Spo0A为中心的细胞命运决策网络的活动。我们还揭示了一种通过蛋白激酶kinB基因的Rho依赖性基因内转录终止激活Spo0A的新调节机制。总之，我们的研究结果表明，不同的Rho控制的转录本具有功能，并构成了枯草芽孢杆菌中一种以前未知的用于控制细胞分化的内置模块。在更广泛的背景下，我们的结果突出了终止因子Rho在高度整合的、细菌特异性的调节网络中的作用，其保守的生物学作用可能是抑制广泛转录。
