Global effects of deletion of the sdh genes, encoding succinate dehydrogenase, and of cobalt on protein abundance in stationary phase Salmonella enterica serovar Typhimurium.

A common strategy that bacteria utilize to increase their survival under stressful conditions in their natural environments, including antibiotic treatment, is the entry into quiescence, a state of reversible cell growth arrest that offers protection against many environmental insults. Understanding quiescence is an important fundamental question, with relevance in the medical and environmental fields. Little is known about the molecular and physiological determinants that orchestrate survival during this temporary arrest of proliferation, or those that allow a rapid transition back to the proliferating state when conditions again become favorable. In the wide host-range pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) and other Gram-negative bacteria, this temporary arrest of proliferation induces the expression of the alternative sigma subunit of RNA polymerase, σS/RpoS, which remodels global gene expression to reshape the cell physiology and ensure survival under starvation and various stress conditions (i.e., the general stress response). One important aspect of persistence is the phenotypic differentiation of quiescent populations into sub-population(s) of "persisters" that survive in the presence of lethal concentrations of antibiotics. This phenomenon is worsening the worldwide antibiotic crisis, by causing therapy failure and chronic infections and potentially favoring the development of antibiotic resistance. Understanding mechanisms governing bacterial persisters is thus an important topic and a key issue for drug developments. However, despites many studies, the physiological and molecular mechanisms controlling the formation of persisters are poorly understood and controversial.

We have recently discovered an unexpected functional interaction between σS and succinate dehydrogenase (Sdh) in the formation of persisters. Succinate dehydrogenase (Sdh), a membrane bound complex that connects the TCA cycle and respiratory chain, is one major target down regulated by σS (Levi-Meyrueis et al. 2014, 2015, Lago et al. 2017). Stationary-phase Salmonella grown in LB rich medium form persisters with a higher frequency than actively growing bacteria, after transfer to fresh LB medium in the presence of lethal concentrations of ampicillin and ciprofloxacin, but not significant effect of the ΔrpoS mutation on this phenomenon was observed. Surprisingly however, the ΔrpoS mutation suppressed the defect in persister formation of a Δsdh mutant. It is very likely that the ΔrpoS mutation compensates for a metabolic perturbation provoked by the Δsdh mutation, and key for persister formation.

To get further insights into the synthetic rescue process involved in persisters formation, we used a mass spectrometry-based proteomics approach to compare the proteome of the wild-type, ΔrpoS, Δsdh and ΔsdhΔrpoS strains grown to late stationary phase in nutrient-rich LB medium. Cells were also grown in LB supplemented with cobalt to pinpoint major changes induced by cobalt on the Salmonella proteome. Indeed, the synthetic rescue process involved in persisters formation in the presence of ampicillin was abolished when the inoculum has been grown in the presence of a non-lethal dose of cobalt (100 μM).

Accession number.The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD043726.

See also:

NOREL, F., & MONTEIL, V. (2023). Unraveling a synthetic rescue process involved in persisters formation [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10277562

Phégnon, L., Uttenweiler-Joseph, S., & Létisse, F. (2024). Key physiological and metabolic characteristics for the differentiation of quiescent Salmonella's cells into persisters [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10885905

This work was supported by the French National Research Agency (ANR-19-CE44-0005-01, PERIOMET project).

References

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Levi-Meyrueis C, Monteil V, Sismeiro O, Dillies M-A, Kolb A, Monot M et al. Repressor activity of the RpoS/sigmaS-dependent RNA polymerase requires DNA binding. Nucleic Acids Res 2015 43, 1456–1468.

Lago M, Monteil V, Douche T, Guglielmini J, Criscuolo A, Maufrais C, et al. Proteome remodelling by the stress sigma factor RpoS/sigma(S) in Salmonella: identification of small proteins and evidence for post-transcriptional regulation. Scientific reports. 2017;7(1):2127.