tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence

Abstract

Microbial pathogens adapt to the stress of infection by regulating transcription, translation and protein modification. We report that changes in gene expression in hypoxia-induced non-replicating persistence in mycobacteria—which models tuberculous granulomas—are partly determined by a mechanism of tRNA reprogramming and codon-biased translation. Mycobacterium bovis BCG responded to each stage of hypoxia and aerobic resuscitation by uniquely reprogramming 40 modified ribonucleosides in tRNA, which correlate with selective translation of mRNAs from families of codon-biased persistence genes. For example, early hypoxia increases wobble cmo5U in tRNAThr(UGU), which parallels translation of transcripts enriched in its cognate codon, ACG, including the DosR master regulator of hypoxic bacteriostasis. Codon re-engineering of dosR exaggerates hypoxia-induced changes in codon-biased DosR translation, with altered dosR expression revealing unanticipated effects on bacterial survival during hypoxia. These results reveal a coordinated system of tRNA modifications and translation of codon-biased transcripts that enhance expression of stress response proteins in mycobacteria.

Factors That Shape Eukaryotic tRNAomes: Processing, Modification and Anticodon–Codon Use

“…As detailed in the next section, this type of secondary code information was first described for yeast, and was followed by additional examples involving separate wobble modifications and cognate groups of mRNAs. This was recently extended to Bacteria, in the Mycobacterium tuberculosis surrogate, Mycobacterium bovis during hypoxia-induced non-replicating persistence [107]. …”

“…During hypoxia-induced persistence, a phenomenon that occurs during tuberculosis granulomas formation, cmo 5 U modification of tRNA Thr UGU increases to aid translation of mRNAs enriched with the cognate codon [107]. …”

“…Multiple collective examples from yeast and bacteria [93,107,115,116,117] provide compelling cohesive evidence to suggest that the redundancy component of the genetic code is widely used as a means of secondary information involving wobble-dependent, coordinated translation of functionally-related mRNAs [18,118,119,120]. This system comprises one type of secondary information in the redundancy component of the code [16,18,19].…”

Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions

“…The discovery of new roles for tRNA in cellular processes is greatly facilitated by the development of systems-levels approaches for assessing tRNA modification fluctuations in response to various stress and growth conditions, which was first utilized in yeast [41]. A more recent application of the systems-level approach by the same group revealed that a similar phenomenon occurs in Mycobacterium bovis BCG, which reprograms 40 modified nucleosides in response to hypoxia, consequently affecting translation of various genes involved in bacterial persistence [151]. A detailed investigation was conducted to understand the nearly 8-fold increase in cmo 5 U observed upon exposure to hypoxia, but this experiment also revealed a significant change in thionucleosides that has yet to be explored.…”

Systems proteomics approaches to study bacterial pathogens: application to Mycobacterium tuberculosis

“…However, some regulatory mechanisms are not apparent from transcriptional results. For instance, the vaccine strain of Mtb, BCG, modifies 40 ribonucleosides in tRNA in response to hypoxia which results in the selective translation of mRNAs from families of codon-biased persistence genes [23]. Although Mtb exposed to nitric oxide stress respond rapidly at the transcriptome level, it takes some time of these changes to be revealed on protein level, a behavior that has been linked to protein degradation rather than proteins synthesis [24].…”