Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India.
Department of Biophysics, University of Delhi South Campus, India.
J Proteomics. 2019 May 30;200:102-110. doi: 10.1016/j.jprot.2019.04.003. Epub 2019 Apr 3.
The emergence of carbapenem resistance has become a major problem worldwide. This has made treatment of K. pneumoniae infections a difficult task. In this study, we have explored the whole proteome of the carbapenem-resistant Klebsiella pneumonia clinical isolate (NDM-4) under the meropenem stress. Proteomics (LC-MS/MS) and bioinformatics approaches were employed to uncover the novel mystery of the resistance over the existing mechanisms. Gene ontology, KEGG and STRING were used for functional annotation, pathway enrichment and protein-protein interaction (PPI) network respectively. LC-MS/MS analysis revealed that 52 proteins were overexpressed (≥10 log folds) under meropenem stress. These proteins belong to four major groups namely protein translational machinery complex, DNA/RNA modifying enzymes or proteins, proteins involved in carbapenems cleavage, modifications & transport and energy metabolism & intermediary metabolism-related proteins. Among the total 52 proteins 38 {matched to Klebsiella pneumonia subsp. pneumoniae (strain ATCC 700721/MGH 78578)} were used for functional annotation, pathways enrichment and protein-protein interaction. These were significantly enriched in the "intracellular" (14 of 38), "cytoplasm" (12 of 38) and "ribosome" (10 of 38). We suggest that these 52 over expressed proteins and their interactive proteins cumulatively contributed in survival of bacteria and meropenem resistance through various mechanisms or enriched pathways. These proteins targets and their pathways might be used for development of novel therapeutics against the resistance; therefore, the situation of the emergence of "bad-bugs" could be controlled.
碳青霉烯类耐药的出现已成为全球范围内的一个主要问题。这使得治疗肺炎克雷伯菌感染成为一项艰巨的任务。在这项研究中，我们在美罗培南应激下探索了碳青霉烯类耐药肺炎克雷伯菌临床分离株（NDM-4）的全蛋白质组。采用蛋白质组学（LC-MS/MS）和生物信息学方法来揭示现有机制之外的新型耐药机制。GO、KEGG 和 STRING 分别用于功能注释、通路富集和蛋白质-蛋白质相互作用（PPI）网络。LC-MS/MS 分析显示，在美罗培南应激下有 52 种蛋白质过度表达（≥10 log 倍）。这些蛋白质属于四个主要组，即蛋白质翻译机制复合物、DNA/RNA 修饰酶或蛋白质、参与碳青霉烯类药物切割、修饰和运输的蛋白质以及与能量代谢和中间代谢相关的蛋白质。在总共 52 种蛋白质中，有 38 种{与肺炎克雷伯亚种肺炎克雷伯菌（菌株 ATCC 700721/MGH 78578）匹配}用于功能注释、通路富集和蛋白质-蛋白质相互作用。这些蛋白质在“细胞内”（38 个中的 14 个）、“细胞质”（38 个中的 12 个）和“核糖体”（38 个中的 10 个）中显著富集。我们认为，这些过度表达的 52 种蛋白质及其相互作用蛋白通过各种机制或富集的途径共同促进了细菌的存活和对美罗培南的耐药性。这些蛋白质的靶点及其途径可能被用于开发针对耐药性的新型治疗方法；因此，可以控制“坏细菌”的出现情况。
