Bergum Olaug Elisabeth Torheim, Singleton Amanda Holstad, Røst Lisa Marie, Bodein Antoine, Scott-Boyer Marie-Pier, Rye Morten Beck, Droit Arnaud, Bruheim Per, Otterlei Marit
Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
Front Microbiol. 2024 Mar 26;15:1373344. doi: 10.3389/fmicb.2024.1373344. eCollection 2024.
The DNA damage inducible SOS response in bacteria serves to increase survival of the species at the cost of mutagenesis. The SOS response first initiates error-free repair followed by error-prone repair. Here, we have employed a multi-omics approach to elucidate the temporal coordination of the SOS response. was grown in batch cultivation in bioreactors to ensure highly controlled conditions, and a low dose of the antibiotic ciprofloxacin was used to activate the SOS response while avoiding extensive cell death. Our results show that expression of genes involved in error-free and error-prone repair were both induced shortly after DNA damage, thus, challenging the established perception that the expression of error-prone repair genes is delayed. By combining transcriptomics and a sub-proteomics approach termed signalomics, we found that the temporal segregation of error-free and error-prone repair is primarily regulated after transcription, supporting the current literature. Furthermore, the heterology index (i.e., the binding affinity of LexA to the SOS box) was correlated to the maximum increase in gene expression and not to the time of induction of SOS genes. Finally, quantification of metabolites revealed increasing pyrimidine pools as a late feature of the SOS response. Our results elucidate how the SOS response is coordinated, showing a rapid transcriptional response and temporal regulation of mutagenesis on the protein and metabolite levels.
细菌中的DNA损伤诱导型SOS反应有助于以诱变作用为代价提高物种的存活率。SOS反应首先启动无差错修复，随后是易错修复。在这里，我们采用了多组学方法来阐明SOS反应的时间协调性。在生物反应器中进行分批培养以确保高度可控的条件，并使用低剂量的抗生素环丙沙星来激活SOS反应，同时避免大量细胞死亡。我们的结果表明，参与无差错修复和易错修复的基因表达在DNA损伤后不久均被诱导，因此，挑战了易错修复基因表达延迟的既定观念。通过结合转录组学和一种称为信号组学的亚蛋白质组学方法，我们发现无差错修复和易错修复的时间分离主要在转录后受到调控，这与当前文献一致。此外，异源指数（即LexA与SOS框的结合亲和力）与基因表达的最大增加相关，而与SOS基因的诱导时间无关。最后，代谢物定量显示嘧啶池增加是SOS反应的晚期特征。我们的结果阐明了SOS反应是如何协调的，显示了快速的转录反应以及在蛋白质和代谢物水平上对诱变作用的时间调控。
