Transcriptional and Physiological Changes during Mycobacterium tuberculosis Reactivation from Non-replicating Persistence

Abstract

Mycobacterium tuberculosis can persist for years in the hostile environment of the host in a non-replicating or slowly replicating state. While active disease predominantly results from reactivation of a latent infection, the molecular mechanisms of M. tuberculosis reactivation are still poorly understood. We characterized the physiology and global transcriptomic profiles of M. tuberculosis during reactivation from hypoxia-induced non-replicating persistence. We found that M. tuberculosis reactivation upon reaeration was associated with a lag phase, in which the recovery of cellular physiological and metabolic functions preceded the resumption of cell replication. Enrichment analysis of the transcriptomic dynamics revealed changes to many metabolic pathways and transcription regulons/subnetworks that orchestrated the metabolic and physiological transformation in preparation for cell division. In particular, we found that M. tuberculosis reaeration lag phase is associated with down-regulation of persistence-associated regulons/subnetworks, including DosR, MprA, SigH, SigE, and ClgR, as well as metabolic pathways including those involved in the uptake of lipids and their catabolism. More importantly, we identified a number of up-regulated transcription regulons and metabolic pathways, including those involved in metal transport and remobilization, second messenger-mediated responses, DNA repair and recombination, and synthesis of major cell wall components. We also found that inactivation of the major alternative sigma factors SigE or SigH disrupted exit from persistence, underscoring the importance of the global transcriptional reprogramming during M. tuberculosis reactivation. Our observations suggest that M. tuberculosis lag phase is associated with a global gene expression reprogramming that defines the initiation of a reactivation process.

The hydrolase LpqI primes mycobacterial peptidoglycan recycling

“…The O 2 dependence of this growth is intriguing as Nglycolylation is also an O 2 -dependent activity, suggesting significant alterations to PG metabolism in hypoxic vs. aerobically growing mycobacteria 44 . Consistent with this observation, expression of lpqI is upregulated 2-fold during re-aeration after re-activation from non-replicating persistence in the Wayne hypoxia model 45 .…”

AbmR (Rv1265) is a novel transcription factor of Mycobacterium tuberculosis that regulates host cell association and expression of the non‐coding small RNA Mcr11

“…The EMSA super-shift pattern observed with AbmR may reflect binding of DNA by AbmR oligomers. However, AbmR oligomerized in the absence of added DNA ligand, suggesting that oligomerization is not occurring on DNA as it does with EthR repressor complexes in Mtb (Engohang-Ndong et al, 2003). This conclusion is further supported by the observation that point replacement of amino acids critical for the optimal DNA-binding activity of AbmR did not adversely affect the oligomerization of AbmR.…”

“…Bacterial adaptation to the hypoxic environment of a mature granuloma is critical for the persistence of Mtb in non-human primates (Majumdar et al, 2012;Mehra et al, 2015). Mtb's adaptation to host conditions during infection requires gene regulation, so elucidating the gene regulatory networks used by Mtb to sense and respond to host-associated environments may facilitate the design of targeted therapeutics (Shi et al, 2005;Garton et al, 2008;Galagan et al, 2013;Gautam et al, 2015;Banerjee et al, 2016;Du et al, 2016;Flentie et al, 2016;Iona et al, 2016;Sharp et al, 2016).…”

Revisiting the expression signature ofpks15/1unveils regulatory patterns controlling phenolphtiocerol and phenolglycolipid production in pathogenic mycobacteria

“…Comparing results obtained when cells were grown in hypoxia with the first 4 days after reaeration (51), it was possible to verify that lppX, pks1, pks15, fadD22, Rv2949c and fadD29 were extremely significantly down-regulated in hypoxia, with some of the higher log 2 fold change values verified across all assays. Also, lppX and pks1 were found to be down-regulated with extremely significant differences from the first to the third and fourth days (Figure 6).…”