Gene transfer agents promote survival and DNA repair during stationary phase for Caulobacter crescentus (RNA-Seq). Gene transfer agents promote survival and DNA repair during stationary phase for Caulobacter crescentus (RNA-Seq)

Gene transfer agents (GTAs) are prophage-like entities found in many bacterial genomes that cannot propagate themselves and instead package ~5-15 kbp fragments of the host genome that can be subsequently transferred to related recipient cells. Although suggested to facilitate horizontal gene transfer in the wild, no clear physiological role for GTAs has been elucidated. Here, we demonstrate that the a-proteobacterium Caulobacter crescentus produces bona fide GTAs. The production of Caulobacter GTAs is tightly regulated by a novel transcription factor, RogA, that represses gafYZ, which are direct activators of GTA gene transcription. Cells lacking rogA or expressing gafYZ produce GTAs harboring an ~8.3 kbp fragment of the genome that can, after cell lysis, promote transfer of DNA into recipient cells. Notably, we find that GTAs promote the survival of Caulobacter in stationary phase and following DNA damage by providing recipient cells a template for homologous recombination-based repair. This function may be broadly conserved in other GTA-producing organisms and explain the prevalence of this unusual horizontal gene transfer mechanism. Overall design: RNA-seq was performed on stationary-phase Caulobacter crescentus samples, including WT NA1000 cells or cells with a deletion in rogA, as well as cells expressing gafYZ (or an empty vector) in inducing and non-inducing conditions.

基因转移因子（Gene Transfer Agents, GTAs）是一类存在于众多细菌基因组中的类原噬菌体实体，其无法自主增殖，而是包装宿主基因组中约5~15千碱基对的片段，这些片段可随后被转移至相关受体细胞。尽管有研究推测GTAs可在自然环境中促进水平基因转移，但目前尚未阐明其确切的生理功能。本研究证实，α-变形菌门的新月柄杆菌（Caulobacter crescentus）可产生真正具有功能的GTAs。新月柄杆菌GTAs的生成受到一种新型转录因子RogA的严格调控，该因子可抑制GTA基因转录的直接激活因子gafYZ的表达。缺失rogA或过表达gafYZ的细胞所产生的GTAs会携带约8.3千碱基对的基因组片段，这些片段可在细胞裂解后促进DNA向受体细胞的转移。值得注意的是，本研究发现GTAs可通过为受体细胞提供基于同源重组修复的模板，提升新月柄杆菌在稳定期以及DNA损伤后的存活率。这一功能可能在其他产GTAs的生物体中广泛保守，并可解释这一特殊水平基因转移机制的普遍性。整体实验设计：本研究对处于稳定期的新月柄杆菌样本开展了RNA测序（RNA-seq），样本涵盖野生型（Wild Type, WT）NA1000细胞、缺失rogA的细胞，以及在诱导与非诱导条件下过表达gafYZ（或空载载体）的细胞。