Acid stress pushes TB bacteria into persistent, protein-changing states

Tuberculosis bacteria face many hostile conditions inside the human immune system, including the acidification of the phagosome that engulfs them. One survival strategy of Mycobacterium tuberculosis is to produce a subpopulation of viable but non-replicating (VBNR) cells, often called persisters, which tolerate antibiotics and can lead to treatment failure or disease recurrence. In work led by Nastassja L. Kriel, researchers set out to learn how acid stress influences this behavior in a clinical isolate named M. tuberculosis S169, which has an increased propensity to form VBNR cells. To do this, they used an in vitro acid stress model to nudge cultures into either an actively replicating state (pH 6.5) or a VBNR-enriched state (pH 4.5). They then compared the cellular proteome and the proteins found in the culture filtrate to see which bacterial proteins changed under acidic conditions. The goal was to identify proteins and secretion patterns linked to persister formation in a real clinical strain rather than a long-used laboratory reference.

The team applied mass spectrometry-based proteomics to comprehensively measure proteins inside cells and in culture filtrates from the two conditions. They also used a protein aggregation capture culture filtrate proteomic approach that allowed them to profile secreted proteins while using less bacterial culture material. In the acid-stressed, VBNR-enriched M. tuberculosis S169, several known acid stress response proteins were more abundant, including the methyltransferase Rv1405c and the acid stress response two-component regulatory protein TcrX. By contrast, components of the dormancy response regulon were less abundant in the low-pH cultures. The culture filtrates from low-pH cultures contained fewer proteins overall than those from actively replicating cultures, but they did include proteins previously implicated in persistence, such as the toxin-antitoxin proteins VapC51 and VapB10 and the chorismate mutase Rv1885c, along with several uncharacterized proteins. The authors also note differences between this clinical isolate and published data from M. tuberculosis H37Rv.

These findings point to a specific acid-triggered protein response in a clinical M. tuberculosis isolate that is not simply a general dormancy program. The increased abundance of particular stress proteins like Rv1405c and TcrX, and the presence of persistence-associated proteins such as VapC51, VapB10 and Rv1885c in culture filtrates, suggest that acid stress can reshape both internal bacterial physiology and what the bacterium secretes into its environment. Because secreted proteins can influence the host immune response and because persister cells tolerate antibiotics, the observed changes could help explain how VBNR subpopulations survive during infection and after treatment. The differences from the reference strain M. tuberculosis H37Rv underscore the value of studying clinical isolates to get a more representative picture of tuberculosis stress responses and to identify targets for interventions aimed at eradicating persister cells.