Zinc depletion induces ribosome hibernation in mycobacteria

Abstract

SignificanceMycobacteria as well as other bacteria remodel their ribosomes in response to zinc depletion by replacing zinc-binding ribosomal proteins with zinc-free paralogues, releasing zinc for other metabolic processes. In this study, we show that the remodeled ribosome acquires a structurally stable but functionally inactive and aminoglycoside-resistant state in zinc-starved Mycobacterium smegmatis. Conversely, M. smegmatis cells that are growth arrested in zinc-rich conditions have unstable ribosomes and reduced survival. We further provide evidence for ribosome remodeling in Mycobacterium tuberculosis in host tissues, suggesting that ribosome hibernation occurs during TB infections. Our findings could offer insights into mechanisms of persistence and antibiotic tolerance of mycobacterial infections.

Stress response as implemented by hibernating ribosomes: a structural overview

“…Alternatively, one cannot exclude the possibility that in the cell, HPF long is a monomer and upon binding to the ribosome, dimerization occurs via homodimerization of the HPF long -CTD. The presence of HPF long does not necessarily result in ribosome dimer formation, as demonstrated by the structures of ribosomes from Mycobacterium smegmatis [37,38] (which is frequently used as a model of Mycobacterium tuberculosis) and the spinach chloro-ribosome [35], in complex with HPF long . Both organisms carry HPF long ; but ribosomal dimers have not been reported in these species.…”

“…2A). The presence of HPF long does not necessarily result in ribosome dimer formation, as demonstrated by the structures of ribosomes from Mycobacterium smegmatis [37,38] (which is frequently used as a model of Mycobacterium tuberculosis) and the spinach chloro-ribosome [35], in complex with HPF long . Alternatively, one cannot exclude the possibility that in the cell, HPF long is a monomer and upon binding to the ribosome, dimerization occurs via homodimerization of the HPF long -CTD.…”

Selective translation by alternative bacterial ribosomes

“…2A). Both strains were similarly regulated by zinc (27, 33) (Fig. S2), suggesting they had comparable physiology.…”

“…Mycobacteria encode for several alternative C- ribosomal proteins, four of which are conserved throughout the genus and are encoded within one operon (27, 33) (Fig. 1A).…”

“…In mycobacteria, the conserved alternative C- ribosomal subunits are coded in a single operon regulated by a zinc uptake regulator (zur), which represses expression in the presence of zinc ions (29), and has led to the suggestion that the function for C-/C+ ribosomal subunit paralogues is to allow for dynamic storage of zinc (30–32). Furthermore, although these alternative mycobacterial ribosomal proteins (AltRPs) have recently been demonstrated to incorporate into assembled ribosomes, it has been suggested that they form non-translating hibernating ribosome complexes due to exclusive association of a hibernation factor with alternative ribosomes (33). Here, we demonstrate convincingly using a fully reconstituted mycobacterial translation system that ribosomes containing the alternative subunit RpsR2 (AltRpsR) actively translate.…”