Table_4_The transcriptional regulator CtrA controls gene expression in Alphaproteobacteria phages: Evidence for a lytic deferment pathway.CSV

Pilitropic and flagellotropic phages adsorb to bacterial pili and flagella. These phages have long been used to investigate multiple aspects of bacterial physiology, such as the cell cycle control in the Caulobacterales. Targeting cellular appendages for adsorption effectively constrains the population of infectable hosts, suggesting that phages may have developed strategies to maximize their infective yield. Brevundimonas phage vB_BsubS-Delta is a recently characterized pilitropic phage infecting the Alphaproteobacterium Brevundimonas subvibrioides. Like other Caulobacterales, B. subvibrioides divides asymmetrically and its cell cycle is governed by multiple transcriptional regulators, including the master regulator CtrA. Genomic characterization of phage vB_BsubS-Delta identified the presence of a large intergenic region with an unusually high density of putative CtrA-binding sites. A systematic analysis of the positional distribution of predicted CtrA-binding sites in complete phage genomes reveals that the highly skewed distribution of CtrA-binding sites observed in vB_BsubS-Delta is an unequivocal genomic signature that extends to other pilli- and flagellotropic phages infecting the Alphaproteobacteria. Moreover, putative CtrA-binding sites in these phage genomes localize preferentially to promoter regions and have higher scores than those detected in other phage genomes. Phylogenetic and comparative genomics analyses show that this genomic signature has evolved independently in several phage lineages, suggesting that it provides an adaptive advantage to pili/flagellotropic phages infecting the Alphaproteobacteria. Experimental results demonstrate that CtrA binds to predicted CtrA-binding sites in promoter regions and that it regulates transcription of phage genes in unrelated Alphaproteobacteria-infecting phages. We propose that this focused distribution of CtrA-binding sites reflects a fundamental new aspect of phage infection, which we term lytic deferment. Under this novel paradigm, pili- and flagellotropic phages exploit the CtrA transduction pathway to monitor the host cell cycle state and synchronize lysis with the presence of infectable cells.

嗜菌毛噬菌体（pilitropic phage）与嗜鞭毛噬菌体（flagellotropic phage）可靶向吸附于细菌菌毛与鞭毛之上。长期以来，这类噬菌体被用于研究细菌生理学的诸多维度，例如柄杆菌目（Caulobacterales）的细胞周期调控机制。通过靶向细胞附属结构完成吸附的策略，会有效限定可感染宿主的种群规模，这提示噬菌体或已演化出最大化感染效能的策略。新近被鉴定的嗜菌毛噬菌体——短单胞菌属（Brevundimonas）噬菌体vB_BsubS-Delta，可感染α-变形菌纲（Alphaproteobacteria）的Brevundimonas subvibrioides。与其他柄杆菌目物种类似，B. subvibrioides以不对称方式进行细胞分裂，其细胞周期受多种转录调控因子管控，其中包括核心调控因子CtrA。对噬菌体vB_BsubS-Delta的基因组表征分析显示，其基因组中存在一段大型基因间区，该区域的推定CtrA结合位点密度异乎寻常地高。针对完整噬菌体基因组中预测所得CtrA结合位点的位置分布开展系统性分析后发现，vB_BsubS-Delta中观测到的CtrA结合位点高度偏态分布，是一类明确的基因组特征，该特征同样存在于其他感染α-变形菌纲的菌毛靶向与鞭毛靶向噬菌体中。此外，此类噬菌体基因组中的推定CtrA结合位点，优先定位于启动子区域，且其结合评分高于其他噬菌体基因组中检测到的结合位点。系统发育与比较基因组学分析表明，这类基因组特征在多个噬菌体谱系中独立演化，这提示该特征可为感染α-变形菌纲的菌毛/鞭毛靶向噬菌体带来适应性优势。实验结果证实，CtrA可结合启动子区域内的预测CtrA结合位点，并调控不同类别的感染α-变形菌纲噬菌体的基因转录。我们提出，CtrA结合位点的这种集中分布，反映了噬菌体感染过程中一项此前未被认知的核心新机制，我们将其命名为裂解延迟（lytic deferment）。在这一新的范式框架下，菌毛靶向与鞭毛靶向噬菌体可利用CtrA信号转导通路，感知宿主细胞周期状态，并将噬菌体裂解与可感染宿主细胞的存在同步化。