Pfeifer Eugen, Hünnefeld Max, Popa Ovidiu, Polen Tino, Kohlheyer Dietrich, Baumgart Meike, Frunzke Julia
Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany.
Quantitative and Theoretical Biology, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany.
Nucleic Acids Res. 2016 Dec 1;44(21):10117-10131. doi: 10.1093/nar/gkw692. Epub 2016 Aug 4.
DNA of viral origin represents a ubiquitous element of bacterial genomes. Its integration into host regulatory circuits is a pivotal driver of microbial evolution but requires the stringent regulation of phage gene activity. In this study, we describe the nucleoid-associated protein CgpS, which represents an essential protein functioning as a xenogeneic silencer in the Gram-positive Corynebacterium glutamicum CgpS is encoded by the cryptic prophage CGP3 of the C. glutamicum strain ATCC 13032 and was first identified by DNA affinity chromatography using an early phage promoter of CGP3. Genome-wide profiling of CgpS binding using chromatin affinity purification and sequencing (ChAP-Seq) revealed its association with AT-rich DNA elements, including the entire CGP3 prophage region (187 kbp), as well as several other elements acquired by horizontal gene transfer. Countersilencing of CgpS resulted in a significantly increased induction frequency of the CGP3 prophage. In contrast, a strain lacking the CGP3 prophage was not affected and displayed stable growth. In a bioinformatics approach, cgpS orthologs were identified primarily in actinobacterial genomes as well as several phage and prophage genomes. Sequence analysis of 618 orthologous proteins revealed a strong conservation of the secondary structure, supporting an ancient function of these xenogeneic silencers in phage-host interaction.
病毒来源的DNA是细菌基因组中普遍存在的元素。它整合到宿主调控回路中是微生物进化的关键驱动力，但需要严格调控噬菌体基因活性。在本研究中，我们描述了类核相关蛋白CgpS，它是革兰氏阳性谷氨酸棒杆菌中一种作为异源沉默子发挥作用的必需蛋白。CgpS由谷氨酸棒杆菌菌株ATCC 13032的隐蔽前噬菌体CGP3编码，最初是通过使用CGP3的早期噬菌体启动子进行DNA亲和色谱法鉴定的。使用染色质亲和纯化和测序（ChAP-Seq）对CgpS结合进行全基因组分析，揭示了它与富含AT的DNA元件相关联，包括整个CGP3前噬菌体区域（187 kbp），以及通过水平基因转移获得的其他几个元件。CgpS的反沉默导致CGP3前噬菌体的诱导频率显著增加。相比之下，缺乏CGP3前噬菌体的菌株不受影响且生长稳定。在一种生物信息学方法中，主要在放线菌基因组以及几个噬菌体和前噬菌体基因组中鉴定出了cgpS直系同源物。对618个直系同源蛋白的序列分析揭示了二级结构的高度保守性，支持了这些异源沉默子在噬菌体-宿主相互作用中的古老功能。
