Transcriptional Approach for Decoding the Mechanism of rpoC Compensatory Mutations for the Fitness Cost in Rifampicin-Resistant Mycobacterium tuberculosis

Multidrug-resistant tuberculosis (TB), defined as TB resistant to the two first-line drugs, isoniazid and rifampin, is a serious challenge to global TB eradication efforts. Although mutations in rpoA or rpoC have been proposed to compensate for this fitness cost due to rpoB mutation in rifampicin-resistant Mycobacterium tuberculosis mutants, whether the compensatory effect exists and the underlying mechanisms of compensation remain unclear. Here, we used RNA sequencing to investigate the global transcriptional profiles of 6 rifampin-resistant clinical isolates with either single mutation in rpoB or dual mutations in rpoB/rpoC, as well as 3 rifampin-susceptible clinical isolates, trying to prove the potential compensatory effect of rpoC by transcriptomic alteration. In rifampinfree conditions, rpoC mutation was associated with M. tuberculosis upregulation of ribosomal protein-coding genes, dysregulation of growth-related essential genes and balancing the expression of arginine and glutamate synthesis-associated genes. Upon rifampin exposure of M. tuberculosis isolates, rpoC mutations were associated with the upregulation of the oxidative phosphorylation machinery, which was inhibited in the rpoB single mutants, as well as stabilization of the expression of rifampin-regulated essential genes and balancing the expression of genes involved in metabolism of sulfur-containing amino acids. Taken together, our data suggest that rpoC mutation may compensate for the fitness defect of rifampicin-resistant M. tuberculosis by altering gene expression in response to rifampin exposure.

耐多药结核病（TB），定义为对两种一线药物异烟肼和利福平耐药的结核病，是全球根除结核病工作面临的一项严峻挑战。尽管有人提出rpoA或rpoC的突变可弥补利福平耐药结核分枝杆菌突变体中因rpoB突变而产生的适应性代价，但这种补偿作用是否存在以及潜在的补偿机制仍不清楚。在此，我们利用RNA测序研究了6株具有rpoB单突变或rpoB/rpoC双突变的利福平耐药临床分离株以及3株利福平敏感临床分离株的全局转录谱，试图通过转录组改变来证明rpoC的潜在补偿作用。在无利福平的条件下，rpoC突变与结核分枝杆菌核糖体蛋白编码基因的上调、生长相关必需基因的失调以及精氨酸和谷氨酸合成相关基因表达的平衡有关。在结核分枝杆菌分离株暴露于利福平后，rpoC突变与氧化磷酸化机制的上调有关，而该机制在rpoB单突变体中受到抑制，同时与利福平调节的必需基因表达的稳定以及含硫氨基酸代谢相关基因表达的平衡有关。综上所述，我们的数据表明，rpoC突变可能通过改变基因表达以应对利福平暴露来弥补利福平耐药结核分枝杆菌的适应性缺陷。