Hosseinkhan Nazanin, Mousavian Zaynab, Masoudi-Nejad Ali
Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
Department of Computer Science, School of Mathematics, Statistics, and Computer Science, University of Tehran, Tehran, Iran; Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
Gene. 2018 Jan 10;639:1-10. doi: 10.1016/j.gene.2017.10.005. Epub 2017 Oct 4.
Pseudomonas aeruginosa and Staphylococcus aureus are two evolutionary distant bacterial species that are frequently isolated from persistent infections such as chronic infectious wounds and severe lung infections in cystic fibrosis patients. To the best of our knowledge no comprehensive genome scale co-expression study has been already conducted on these two species and in most cases only the expression of very few genes has been the subject of investigation. In this study, in order to investigate the level of expressional conservation between these two species, using heterogeneous gene expression datasets the weighted gene co-expression network analysis (WGCNA) approach was applied to study both single and cross species genome scale co-expression patterns of these two species. Single species co-expression network analysis revealed that in P. aeruginosa, genes involved in quorum sensing (QS), iron uptake, nitrate respiration and type III secretion systems and in S. aureus, genes associated with the regulation of carbon metabolism, fatty acid-phospholipids metabolism and proteolysis represent considerable co-expression across a variety of experimental conditions. Moreover, the comparison of gene co-expression networks between P. aeruginosa and S. aureus was led to the identification of four co-expressed gene modules in both species totally consisting of 318 genes. Several genes related to two component signal transduction systems, small colony variants (SCVs) morphotype and protein complexes were found in the detected modules. We believe that targeting the key players among the identified co-expressed orthologous genes will be a potential intervention strategy to control refractory co-infections caused by these two bacterial species.
铜绿假单胞菌和金黄色葡萄球菌是两种在进化上亲缘关系较远的细菌物种，它们经常从持续性感染中分离出来，如慢性感染伤口以及囊性纤维化患者的严重肺部感染。据我们所知，尚未对这两个物种进行全面的全基因组规模共表达研究，在大多数情况下，只有极少数基因的表达受到研究。在本研究中，为了探究这两个物种之间的表达保守程度，我们使用异质基因表达数据集，应用加权基因共表达网络分析（WGCNA）方法来研究这两个物种的单物种和跨物种全基因组规模共表达模式。单物种共表达网络分析表明，在铜绿假单胞菌中，参与群体感应（QS）、铁摄取、硝酸盐呼吸和III型分泌系统的基因，以及在金黄色葡萄球菌中，与碳代谢调节、脂肪酸 - 磷脂代谢和蛋白水解相关的基因，在各种实验条件下都呈现出显著的共表达。此外，对铜绿假单胞菌和金黄色葡萄球菌之间的基因共表达网络进行比较，发现两个物种中共有四个共表达基因模块，总共包含318个基因。在检测到的模块中发现了几个与双组分信号转导系统、小菌落变体（SCV）形态型和蛋白质复合物相关的基因。我们认为，针对已鉴定的共表达直系同源基因中的关键参与者，将是控制由这两种细菌物种引起的难治性混合感染的潜在干预策略。
