转录组分析揭示盐酸克林霉素胁迫下嗜根考克氏菌DC2201的响应机制

Transcriptome analysis reveals the response mechanism of Kocuria rhizophila DC2201 to clindamycin hydrochloride

摘要:

【目的】 研究0.5倍最低抑菌浓度(minimal inhibitory concentration, MIC)的盐酸克林霉素胁迫下，嗜根考克氏菌DC2201的差异表达基因(differentially expressed genes, DEGs)，揭示盐酸克林霉素胁迫下嗜根考克氏菌(Kocuria rhizophila) DC2201的响应机制。【方法】 以LB液体培养基培养的嗜根考克氏菌DC2201细胞为对照，采用Illumina Hiseq测序平台进行RNA-seq双端测序，分析0.5 MIC的盐酸克林霉素胁迫下嗜根考克氏菌的基因表达情况，并采用实时荧光定量PCR方法验证。【结果】 从盐酸克林霉素胁迫下的嗜根考克氏菌中共筛选到1 202个显著DEGs，其中显著上调表达基因604个，显著下调表达基因598个。经基因本体论(gene ontology, GO)注释，筛选到分子功能(molecular function, MF)、细胞组分(cellular component, CC)和生物学过程(biological process, BP) 3个一级分类指标，35个二级分类指标共1 041个显著DEGs。经京都基因与基因组百科全书(kyoto encyclopedia of genes and genomes, KEGG)注释，筛选到与DNA修复途径相关的显著DEGs 16个，与核糖体合成途径相关的显著DEGs 43个，与ATP结合盒(ATP-binding cassette, ABC)转运蛋白相关的显著DEGs 28个，与戊糖磷酸途径、糖酵解、三羧酸(tricarboxylic acid, TCA)循环、淀粉与蔗糖、丙酮酸、丁酸等碳水化合物代谢相关的显著DEGs 77个，与肽聚糖合成相关的显著DEGs 5个。【结论】 盐酸克林霉素胁迫下，嗜根考克氏菌DC2201的响应机制是一个全局性反应机制，细菌通过增强多重耐药性(multidrug resistance, MDR)家族的主要促进者超家族(major facilitator superfamily, MFS)转运体的表达来增加对盐酸克林霉素的外排，通过增强DNA修复和RNA代谢途径，以保证基因组的稳定性和RNA的正常功能，通过增强核糖体合成途径来弥补盐酸克林霉素与自身50S核糖体结合后导致的蛋白质合成障碍，以提高蛋白质合成效率。与此同时，减少碳水化合物的吸收和转运，抑制自身的能量代谢途径，以减缓自身的生长速率而降低对能量的需求，相应地，细胞壁的稳定性也受到影响。

Abstract:

[Objective] To mine the differentially expressed genes (DEGs) of Kocuria rhizophila DC2201 exposed to clindamycin hydrochloride at 0.5 minimum inhibitory concentration (MIC) and reveal the response mechanism of Kocuria rhizophila DC2201 to clindamycin hydrochloride. [Methods] With the Kocuria rhizophila DC2201 cells cultured in LB liquid medium as the control, Illumina HiSeq platform was used for paired-end sequencing to determine the gene expression of Kocuria rhizophila DC2201 cells exposed to clindamycin hydrochloride at 0.5 MIC. Real-time fluorescence quantitative PCR was then conducted for validation. [Results] A total of 1 202 significantly DEGs were screened out from Kocuria rhizophila DC2201 under the stress of clindamycin hydrochloride, including 604 significantly up-regulated genes and 598 significantly down-regulated genes. After gene ontology (GO) annotation, 1 041 significantly DEGs were annotated into 35 GO terms of molecular function (MF), cell composition (CC), and biological process (BP). The Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis predicted 16 significantly DEGs related to DNA repair, 43 significantly DEGs related to ribosomal synthesis, 28 DEGs associated with ATP-binding cassette (ABC) transporters, 77 significantly DEGs associated with the pentose phosphate pathway, glycolysis, tricarboxylic acid (TCA) cycle, starch and sucrose, pyruvate, butyrate and other carbohydrate metabolisms, and 5 significantly DEGs related to peptidoglycan synthesis. [Conclusion] Kocuria rhizophila DC2201 exposed to clindamycin hydrochloride adopts a global response mechanism. It increases the efflux of clindamycin hydrochloride by up-regulating the gene expression of major facilitator superfamily (MFS) transporters in the multidrug resistance (MDR) family. By enhancing DNA repair and RNA metabolism pathways, the strain ensures the genomic stability and normal RNA function. In addition, it enhances the ribosome synthesis pathway to compensate for the protein synthesis barrier caused by the binding of clindamycin hydrochloride with the 50S ribosome. Furthermore, the strain reduces the absorption and transportation of carbohydrates to restrain the energy metabolisms pathways, thus slowing down the growth and reducing the energy demand. Correspondingly, the cell wall stability of Kocuria rhizophila DC2201 is also affected.