XRE Transcription Factors in Caulobacter and φCbK Modulate Adhesion and Phage Viability [ChIP-seq]

During infection, transcriptional changes in both the phage and its host bacterium influence the outcome of infection. The xenobiotic response element (XRE) family of transcription factors (TFs), which are commonly encoded by bacteria and phages, regulate diverse aspects of bacterial cell physiology and can impact phage infection dynamics. Through a pangenome analysis of Caulobacter species isolated from soil and aquatic ecosystems, we uncovered an apparent radiation of an XRE TF gene cluster, several of which have established functions in the regulation of holdfast adhesin development and biofilm formation in C. crescentus. We further discovered related XRE TFs across the class Alphaproteobacteria and its phages, including the φCbK Caulophage, suggesting that members of this gene cluster impact host-phage interactions. Here we show that that a closely related group of XRE proteins, encoded by both C. crescentus and φCbK, can interact to form heteromeric associations and control the transcription of a common gene set, influencing processes such as adhesin development and the progression of φCbK infection. The φCbK XRE paralog, tgrL, is highly expressed at the earliest stages of infection and can directly repress transcription of hfiA, a potent adhesion factor, and gafYZ, a transcriptional activator of prophage-like gene transfer agents (GTAs) encoded on the C. crescentus chromosome. A group of C. crescentus XRE proteins also directly repress gafYZ transcription, revealing a functionally redundant set of host regulators that may protect against spurious production of GTA particles and inadvertent cell lysis. Deleting host XRE transcription factors reduced φCbK burst size, while overexpressing these genes or φCbK tgrL rescued this burst defect. We conclude that a large XRE TF gene cluster, shared by C. crescentus and φCbK, plays an important role in adhesion regulation under phage-free conditions, and influences host-phage dynamics during infection. Chromatin Immunoprecipitation sequencing (ChIP-seq) for 3xFLAG-tagged XRE transcription factors in Caulobacter crescentus CB15

在噬菌体感染过程中，噬菌体与其宿主细菌的转录组变化均会影响感染结局。异源反应元件（xenobiotic response element, XRE）家族转录因子（transcription factors, TFs）广泛编码于细菌和噬菌体基因组中，可调控细菌细胞生理的多个方面，并能影响噬菌体感染动态。我们通过对分离自土壤与水生生态系统的柄杆菌属（Caulobacter）物种开展泛基因组分析（pangenome analysis），发现了一类明显扩增的XRE转录因子基因簇；其中多个基因已在新月柄杆菌（Caulobacter crescentus）中被证实可调控固着素黏附素发育与生物膜形成。我们进一步在α-变形菌纲（Alphaproteobacteria）及其噬菌体（包括φCbK柄杆菌噬菌体）中发现了相关的XRE转录因子，提示该基因簇成员可影响宿主-噬菌体互作。本研究显示，由新月柄杆菌与φCbK编码的一组紧密同源的XRE蛋白可相互结合形成异源多聚体复合物，并调控一套共同基因集的转录，进而影响黏附素发育与φCbK感染进程等生命过程。φCbK的XRE旁系同源基因tgrL在感染早期即被高度表达，可直接抑制黏附因子hfiA的转录，同时也可直接抑制新月柄杆菌染色体上编码的前噬菌体样基因转移剂（gene transfer agents, GTAs）转录激活因子gafYZ的转录。一组新月柄杆菌的XRE蛋白同样可直接抑制gafYZ的转录，这揭示了一组功能冗余的宿主调控因子，其可能用于防止基因转移剂颗粒的异常产生与意外细胞裂解。敲除宿主XRE转录因子会降低φCbK的裂解量（burst size），而过表达这些宿主基因或φCbK的tgrL则可挽救该裂解量缺陷表型。综上，新月柄杆菌与φCbK共有的一类大型XRE转录因子基因簇，在无噬菌体感染的条件下可调控黏附相关生理过程，并在感染期间影响宿主-噬菌体互作动态。本研究针对新月柄杆菌CB15中经3xFLAG标签标记的XRE转录因子开展了染色质免疫共沉淀测序（Chromatin Immunoprecipitation sequencing, ChIP-seq）。