Global Analysis of Photosynthesis Transcriptional Regulatory Networks

Photosynthesis is a crucial biological process that depends on the interplay of many components. This work analyzed the gene targets for 4 transcription factors: FnrL, PrrA, CrpK and MppG (RSP_2888), which are known or predicted to control photosynthesis in Rhodobacter sphaeroides. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identified 52 operons under direct control of FnrL, illustrating its regulatory role in photosynthesis, iron homeostasis, nitrogen metabolism and regulation of sRNA synthesis. Using global gene expression analysis combined with ChIP-seq, we mapped the regulons of PrrA, CrpK and MppG. PrrA regulates ∼34 operons encoding mainly photosynthesis and electron transport functions, while CrpK, a previously uncharacterized Crp-family protein, regulates genes involved in photosynthesis and maintenance of iron homeostasis. Furthermore, CrpK and FnrL share similar DNA binding determinants, possibly explaining our observation of the ability of CrpK to partially compensate for the growth defects of a ΔFnrL mutant. We show that the Rrf2 family protein, MppG, plays an important role in photopigment biosynthesis, as part of an incoherent feed-forward loop with PrrA. Our results reveal a previously unrealized, high degree of combinatorial regulation of photosynthetic genes and significant cross-talk between their transcriptional regulators, while illustrating previously unidentified links between photosynthesis and the maintenance of iron homeostasis.

光合作用是依赖多种组分相互作用的关键生物学过程。本研究针对4种已知或被预测可调控球形红杆菌（Rhodobacter sphaeroides）光合作用的转录因子——FnrL、PrrA、CrpK与MppG（RSP_2888）——分析了其基因靶标。采用染色质免疫共沉淀结合高通量测序（ChIP-seq）技术，鉴定出52个受FnrL直接调控的操纵子，阐明了其在光合作用、铁稳态、氮代谢以及小RNA（small RNA，sRNA）合成调控中的调控作用。结合全基因组基因表达分析与ChIP-seq，我们绘制了PrrA、CrpK与MppG的调控子图谱。PrrA调控约34个操纵子，其编码产物主要参与光合作用与电子传递过程；而此前未被表征的Crp家族蛋白CrpK，则调控参与光合作用与铁稳态维持的基因。此外，CrpK与FnrL具有相似的DNA结合特征，这或可解释本研究中观察到的CrpK可部分补偿ΔFnrL突变体生长缺陷的现象。我们证实，Rrf2家族蛋白MppG作为与PrrA构成的不一致前馈环的组成部分，在光色素生物合成中发挥重要作用。本研究结果揭示了此前未被认知的光合基因高度组合式调控模式，以及其转录调控因子间广泛的交叉对话，同时阐明了光合作用与铁稳态维持之间此前未被发现的关联。