Abstract
Phenotypically agnostic screens for positive selection in pathogen populations provide a means of pinpointing genes and regulatory regions involved in adaptation to the local environment or host population. We screened a large (n = 2506) collection of Vietnamese Mycobacterium tuberculosis (Mtb) isolates, finding targets of selection to be lineage-specific, and encompass diverse functions, including dormancy (Rv0080), zinc homeostasis (zur), and virulence (ESX-1 structure). Extending our screen to the wider Mtb complex (MTBC) phylogeny demonstrated Rv0080 to display an extraordinarily dynamic evolutionary history, acquiring premature stop codons or putative functional mutations on branches upstream of 8 of the 10 human-adapted lineages, and undergoing positive selection in the remaining 2. Lineage 1, which is one of two such lineages retaining the ancestral Rv0080 sequence, displays a rate of selection for this gene (dN/dS=9.37) exceeding any other in the Mtb genome, save a transcription factor linked to its expression (Rv0042c; dN/dS=11.02). Deletion of Rv0080’s M. smegmatis orthologue confers a survival advantage in hypoxic conditions, as does the evolution of nonsense or missense mutations on an ancestral Rv0080 background. We show the dormancy survival regulon experienced recurrent episodes of reductive evolution across the MTBC phylogeny, illuminating a novel mechanism via which it adapted to human populations.
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Data availability
All data analysed in this manuscript were drawn from previously published studies and are publicly available. All relevant sources from which data were obtained are referenced in the text.
Code availability
Code for performing the Rosetta DDG prediction is available on GitHub (https://github.com/jlingford/ddg_rosetta).
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Acknowledgements
The authors acknowledge support from the National Health and Medical Research Council, Australia APP1172853 (S.J.D.), the US National Institutes of Health U19AI162583 (S.J.D.), and the Australian Research Council DE250101214 (M.S.).
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M.S. and S.J.D. conceived the initial genomic study, with J.P.L., C.G., C.A.M., J.S.C. and M.B.M. playing conceptual roles in the structural and functional analyses that followed. M.S. completed the genomic and bioinformatic analyses, under the supervision of S.J.D., and with contributions from D.E. and K.E.H. relating to the use of SNPPar software. J.P.L. completed the protein structure prediction analysis for Rv0080/Fsq under the supervision of C.G., and C.A.M. completed the protein structure prediction of zur, with contributions from S.L.N. and M.J.M. Mycobacterial functional experiments were completed by C.Y.C. W.J.J. R.M.M. C.D.R. and L.K.H. under the supervision of M.B.M., J.S.C., and G.M.C. Whole genome sequencing data from Vietnamese patients was generated and contributed by P.V.K.T., K.E.H., N.T.T.T., M.C. and S.J.D. Assistance with bioinformatic or statistical aspects of this analysis was provided by E.P.T., A.C.B., X.C., N.S.B. and T.R.H. The initial draft of this manuscript was prepared by M.S., with relevant sections contributed by J.P.L, C.A.M and M.B.M. The final draft of the manuscript was edited and approved by all authors.
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Silcocks, M., Lingford, J.P., Cheung, CY. et al. Dormancy regulon reduction was pivotal to the evolution of Mycobacterium tuberculosis. Nat Commun (2026). https://doi.org/10.1038/s41467-026-71566-x
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DOI: https://doi.org/10.1038/s41467-026-71566-x
