Lobel Lior, Herskovits Anat A
The Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
PLoS Genet. 2016 Feb 19;12(2):e1005870. doi: 10.1371/journal.pgen.1005870. eCollection 2016 Feb.
Bacteria sense and respond to many environmental cues, rewiring their regulatory network to facilitate adaptation to new conditions/niches. Global transcription factors that co-regulate multiple pathways simultaneously are essential to this regulatory rewiring. CodY is one such global regulator, controlling expression of both metabolic and virulence genes in Gram-positive bacteria. Branch chained amino acids (BCAAs) serve as a ligand for CodY and modulate its activity. Classically, CodY was considered to function primarily as a repressor under rich growth conditions. However, our previous studies of the bacterial pathogen Listeria monocytogenes revealed that CodY is active also when the bacteria are starved for BCAAs. Under these conditions, CodY loses the ability to repress genes (e.g., metabolic genes) and functions as a direct activator of the master virulence regulator gene, prfA. This observation raised the possibility that CodY possesses multiple functions that allow it to coordinate gene expression across a wide spectrum of metabolic growth conditions, and thus better adapt bacteria to the mammalian niche. To gain a deeper understanding of CodY's regulatory repertoire and identify direct target genes, we performed a genome wide analysis of the CodY regulon and DNA binding under both rich and minimal growth conditions, using RNA-Seq and ChIP-Seq techniques. We demonstrate here that CodY is indeed active (i.e., binds DNA) under both conditions, serving as a repressor and activator of different genes. Further, we identified new genes and pathways that are directly regulated by CodY (e.g., sigB, arg, his, actA, glpF, gadG, gdhA, poxB, glnR and fla genes), integrating metabolism, stress responses, motility and virulence in L. monocytogenes. This study establishes CodY as a multifaceted factor regulating L. monocytogenes physiology in a highly versatile manner.
细菌能够感知并响应多种环境信号，重新调整其调控网络以促进对新环境/生态位的适应。同时共同调控多条途径的全局转录因子对于这种调控重编程至关重要。CodY就是这样一种全局调节因子，它控制革兰氏阳性菌中代谢基因和毒力基因的表达。支链氨基酸（BCAAs）作为CodY的配体并调节其活性。传统上，CodY被认为在丰富的生长条件下主要作为一种阻遏物发挥作用。然而，我们之前对细菌病原体单核细胞增生李斯特菌的研究表明，当细菌缺乏BCAAs时，CodY也具有活性。在这些条件下，CodY失去了抑制基因（如代谢基因）的能力，并作为主要毒力调节基因prfA的直接激活因子发挥作用。这一观察结果提出了一种可能性，即CodY具有多种功能，使其能够在广泛的代谢生长条件下协调基因表达，从而使细菌更好地适应哺乳动物生态位。为了更深入地了解CodY的调控范围并鉴定直接靶基因，我们使用RNA测序和染色质免疫沉淀测序技术，在丰富和基本生长条件下对CodY调控子和DNA结合进行了全基因组分析。我们在此证明，CodY在这两种条件下确实都具有活性（即结合DNA），作为不同基因的阻遏物和激活因子。此外，我们鉴定了由CodY直接调控的新基因和途径（如sigB、arg、his、actA、glpF、gadG、gdhA、poxB、glnR和fla基因），整合了单核细胞增生李斯特菌中的代谢、应激反应、运动性和毒力。这项研究确定CodY是一个以高度通用的方式调节单核细胞增生李斯特菌生理学的多面因子。
