Chen Xin, Ma Anjun, McDermaid Adam, Zhang Hanyuan, Liu Chao, Cao Huansheng, Ma Qin
Center for Applied Mathematics, Tianjin University, Tianjin 300072, China.
Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57006, USA.
Genes (Basel). 2018 May 30;9(6):278. doi: 10.3390/genes9060278.
Regulons, which serve as co-regulated gene groups contributing to the transcriptional regulation of microbial genomes, have the potential to aid in understanding of underlying regulatory mechanisms. In this study, we designed a novel computational pipeline, regulon identification based on comparative genomics and transcriptomics analysis (RECTA), for regulon prediction related to the gene regulatory network under certain conditions. To demonstrate the effectiveness of this tool, we implemented RECTA on MG1363 data to elucidate acid-response regulons. A total of 51 regulons were identified, 14 of which have computational-verified significance. Among these 14 regulons, five of them were computationally predicted to be connected with acid stress response. Validated by literature, 33 genes in MG1363 were found to have orthologous genes which were associated with six regulons. An acid response related regulatory network was constructed, involving two trans-membrane proteins, eight regulons (, , , , NHP6A, , regulons #8 and #39), nine functional modules, and 33 genes with orthologous genes known to be associated with acid stress. The predicted response pathways could serve as promising candidates for better acid tolerance engineering in . Our RECTA pipeline provides an effective way to construct a reliable gene regulatory network through regulon elucidation, and has strong application power and can be effectively applied to other bacterial genomes where the elucidation of the transcriptional regulation network is needed.
调控子作为共同调控的基因群组，有助于微生物基因组的转录调控，具有辅助理解潜在调控机制的潜力。在本研究中，我们设计了一种新颖的计算流程，即基于比较基因组学和转录组学分析的调控子识别（RECTA），用于预测特定条件下与基因调控网络相关的调控子。为了证明该工具的有效性，我们在MG1363数据上实施RECTA以阐明酸应答调控子。总共识别出51个调控子，其中14个具有经计算验证的意义。在这14个调控子中，有5个经计算预测与酸应激反应相关。经文献验证，发现MG1363中的33个基因具有与6个调控子相关的直系同源基因。构建了一个酸应答相关的调控网络，涉及两个跨膜蛋白、8个调控子（、、、、NHP6A、、调控子#8和#39）、9个功能模块以及33个具有已知与酸应激相关的直系同源基因的基因。预测的应答途径可作为在中进行更好的耐酸工程的有前景的候选途径。我们的RECTA流程提供了一种通过阐明调控子来构建可靠基因调控网络的有效方法，具有强大的应用能力，可有效应用于其他需要阐明转录调控网络的细菌基因组。
