mRNA Degradation Rates Are Coupled to Metabolic Status in Mycobacteria

Abstract

17The success of Mycobacterium tuberculosis (Mtb) as a human pathogen is due in part to its 18 ability to survive stress conditions, such as hypoxia or nutrient deprivation, by entering non-19 growing states. In these low-metabolic states, Mtb can tolerate antibiotics and develop 20 genetically encoded antibiotic resistance, making its metabolic adaptation to stress crucial for 21 survival. Numerous bacteria, including Mtb, have been shown to reduce their rates of mRNA 22 degradation under growth limitation and stress. While the existence of this response appears to 23 be conserved across species, the underlying bacterial mRNA stabilization mechanisms remains 24 65 for other bacteria under stress conditions that slow or halt growth, including carbon deprivation, 66 stationary phase, and temperature shock (4-13). However, the mechanisms responsible for global 67 regulation of mRNA stability in prokaryotes have yet to be elucidated. 68 In better studied bacteria such as E. coli and B. subtilis, the major ribonucleases (RNases) 69 involved in mRNA processing and decay are RNase E and RNase Y, respectively. A 70 conventional model for RNA decay in E. coli start with an endonucleolytic cleavage event 71 usually carried by RNase E in AU-rich regions, particularly in mRNA substrates that possess a 5' 72 monophosphate (14-16). The resulting 5' monophosphorylated fragments are rapidly cleaved by 73 RNase E, resulting in shorter fragments that can be fully degraded by exonucleases such as 74 PNPase, RNase II, and RNase R (17, 18). mRNA degradation seems to be coordinated by 75 formation of a complex known as the degradosome. In E. coli, RNase E serves as the scaffold for 76 this multiprotein complex that comprises RNA helicases, the glycolytic enzyme enolase, and 77 PNPase (19-23). Other organisms that encode RNase E form similar degradosomes (24, 25). In 78 organisms where RNase E is not present, RNase Y and/or RNase J seem to assume the scaffold 79 function (26-28). Mycobacteria encode RNase E, but efforts to define the mycobacterial 80 degradosome have produced inconsistent results (29, 30). It is unclear if degradosome 81 reorganization or dissolution contribute to the global regulation of mRNA degradation under 82 stress conditions in any bacteria. Interestingly, the importance of degradosome formation in E. 83 coli varies depending on the carbon sources provided, suggesting specific links between RNase E 84 degradosomes and metabolic capabilities (31). Furthermore, the chaperones DnaK and CsdA can 85 become degradosome components in E. coli under certain stresses (20, 32, 33). 86Global transcript stabilization in stressed bacteria could plausibly result from reduced RNase 87 abundance, reduced RNase activity, and/or reduced accessibility of transcripts to degradation 88 proteins. In E. coli it has been shown that multiple stressors can upregulate RNase R, possibly as 89 a way to overcome ribosome misassembly (34, 35), and that RNase III levels decrease under 90 cold-shock and stationary phase (36). Surprisin...