De Lemos, D. | bioRxiv Science

bioRxiv2024

Competence induction of homologous recombination genes protects pneumococcal cells from genotoxic stress.

Homologous recombination (HR) is a universally conserved mechanism of DNA strand exchange between homologous sequences, driven in bacteria by the universal recombinase RecA. HR is key for the maintenance of bacterial genomes via replication fork restart and DNA repair, as well as for their plasticity via the widespread mechanism of natural transformation. Transformation involves the capture and internalisation of exogenous DNA in the form of single strands (ssDNA), followed by chromosomal integration via HR. In the human pathogen Streptococcus pneumoniae, transformation occurs during a transient, stress-induced physiological state called competence. RecA and its partner DNA branch migration translocase RadA both cooperate in HR during transformation and in some recombinational DNA repair pathways of genome maintenance. Both recA and radA genes are basally expressed and transcriptionally induced during competence. In this study, we explored the importance of competence induction of recA and radA expression in transformation and genome maintenance processes. We confirmed that competence induction of recA was important for optimal transformation, but found this was not the case for radA. In contrast, the competence induction of both genes was required for optimal tolerance faced with transient exposure to the lethal genotoxic agent methyl methanesulfonate (MMS). However, this was not the case for another DNA-damaging agent, norfloxacin. These results show that competence induction of HR effectors is important for the increased tolerance to genotoxic stress provided to competent pneumococcal cells. This reinforces the finding that pneumococcal competence is a stress-sensing mechanism, transiently increasing the expression of some genes not to optimise transformation but to improve survival faced with specific lethal stresses. ImportanceHomologous recombination (HR) is a mechanism of DNA strand exchange important for both the maintenance and plasticity of bacterial genomes. Bacterial HR is driven by the recombinase RecA along with many accessory partner proteins, which define multiple dedicated pathways crucial to genome biology. Thus, a main mechanism of genome plasticity in bacteria is natural genetic transformation, which involves uptake and chromosomal integration of exogenous DNA via HR. In the human pathogen Streptococcus pneumoniae, transformation occurs during a transient, stress-induced physiological state called competence. RecA and the helicase RadA are key for both genome maintenance and transformation, and both are over-produced during competence. Here, we explore the importance of this over-production for transformation and genome maintenance, quantified by tolerance to genotoxic stress. While over-production of RecA was important for both processes, over-production of RadA was required only for genotoxic stress tolerance. This highlights the importance of competence as a stress-responsive mechanism, with induction of HR genes important for genotoxic stress tolerance.

microbiology↗

bioRxiv2023

Pneumococcal competence, a populational health sensor driving multilevel heterogeneity in response to antibiotics.

Competence for natural transformation is a central driver of genetic diversity in bacteria. In the human pathogen Streptococcus pneumoniae, competence exhibits a populational character mediated by the stress-induced ComABCDE quorum-sensing (QS) system. Here, we explore how this cell-to-cell communication mechanism proceeds and the functional properties acquired by competent cells grown under lethal stress. We show that populational competence development depends on self-induced cells stochastically emerging in response to stresses, including antibiotics. Competence is demonstrated to propagate through the population from a low threshold density of self-induced cells, defining a biphasic Self-Induction and Propagation (SI&P) QS mechanism. We also reveal that a competent population displays either increased sensitivity or improved tolerance to lethal doses of antibiotics, dependent in the latter case on the competence-induced ComM division inhibitor. Remarkably, these surviving competent cells also display an altered transformation potential. Thus, the unveiled SI&P QS mechanism shapes pneumococcal competence as a health sensor of the clonal population, promoting a bet-hedging strategy that both responds to and drives cells towards heterogeneity.

microbiology↗

bioRxiv2020

The alternative sigma factor σX mediates competence shut-off at the cell pole in Streptococcus pneumoniae.

Bacterial competence for genetic transformation is a well-known species-specific differentiation program driving genome plasticity, antibiotic resistance and virulence in many pathogens. How competence regulation is spatiotemporally integrated in the cell is ill-defined. Here, we unraveled the localization dynamics of the key regulators that master the two intertwined transcription waves controlling competence in Streptococcus pneumoniae. The first wave relies on a stress-inducible phosphorelay system, made up of the ComD and ComE proteins, and the second is directed by an alternative sigma factor, {sigma}X, which includes in its regulon the DprA protein that turns off competence through interaction with phosphorylated ComE. Remarkably, we found that ComD, {sigma}X and DprA stably co-localize at a single cell pole over the competence period. In contrast, ComE assembles into dynamic patches in the cell periphery, colocalizing temporarily with DprA and ComD at the pole. Furthermore, we provide evidence that {sigma}X directly conveys DprA polar anchoring. Through this protein targeting function, {sigma}X is shown to be actively involved in the timely shut-off of the competence cycle, hence preserving cell fitness. Altogether, this study unveils an unprecedented role for a bacterial transcription {sigma} factor in spatially coordinating the negative feedback loop of its own genetic circuit.

microbiology↗