A haloarchaeal VapBC toxin-antitoxin system: regulatory mechanism and role in establishing population heterogeneity to facilitate survival of subpopulations under stress conditions
The results demonstrate that a VapBC system of the haloarchaeon Natrinema gari J7-2 is regulated at multiple levels and mediates the establishment of population heterogeneity, thereby facilitating the survival of the strain J7-2 population as a whole in diverse and changing environments.
Abstract
ABSTRACT Toxin-antitoxin (TA) systems are ubiquitously distributed in bacteria and archaea and have been implicated in various functions such as plasmid maintenance, phage defense, biofilm formation, stress response, and persistence, but their regulatory mechanisms and roles in haloarchaea are largely unknown. In this study, we found that four of the eight putative VapBC TA systems of Natrinema gari J7-2 are functional in strain J7-2 and Haloferax volcanii. Among them, the NgVapBC1 system is composed of the antitoxin NgVapB1 and the toxin NgVapC1, and the two proteins could form a NgVapBC1 complex. The NgVapBC1 system could be transcriptionally autoregulated, wherein a pseudo-palindromic sequence in the vapBC1 operon promoter acts as a negative cis-regulatory element, and the NgVapBC1 complex is a stronger repressor than NgVapB1. The qRT-PCR and in vivo toxicity analyses showed that strain J7-2 maintains a high vapB1/vapC1 mRNA ratio through truncation of the vapBC1 operon transcript within the toxin-coding region for preventing the synthesis of excess toxin NgVapC1 to release toxicity abnormally. Mutational analyses showed that differential start codon usage by vapB1 and vapC1 and a −4 nt overlap of their stop and start codons contribute to maintaining a higher vapB1/vapC1 mRNA ratio, and the −4 nt overlap-mediated translational coupling of vapB1 and vapC1 would enable both post-transcriptional and translational regulation of the NgVapBC1 system. The phenotypic comparison of strain J7-2 and its ΔvapBC1 mutant revealed that the NgVapBC1 system contributes to population heterogeneity of decline-phase rather than exponential-phase strain J7-2 and facilitates the survival of subpopulations under stress conditions. IMPORTANCE Although TA systems are regarded as versatile modulators of prokaryotic cell fate, their bona fide physiological roles remain elusive. Moreover, so far, there is no report on the regulatory mechanism and function of haloarchaeal VapBCs, which constitute the major group of TA systems in haloarchaea. Our results demonstrate that a VapBC system of the haloarchaeon Natrinema gari J7-2 is regulated at multiple levels and mediates the establishment of population heterogeneity, thereby facilitating the survival of the strain J7-2 population as a whole in diverse and changing environments. This study provides the first experimental evidence of the regulatory mechanism of the biological role of the VapBC system in conferring fitness advantages to haloarchaea. Although TA systems are regarded as versatile modulators of prokaryotic cell fate, their bona fide physiological roles remain elusive. Moreover, so far, there is no report on the regulatory mechanism and function of haloarchaeal VapBCs, which constitute the major group of TA systems in haloarchaea. Our results demonstrate that a VapBC system of the haloarchaeon Natrinema gari J7-2 is regulated at multiple levels and mediates the establishment of population heterogeneity, thereby facilitating the survival of the strain J7-2 population as a whole in diverse and changing environments. This study provides the first experimental evidence of the regulatory mechanism of the biological role of the VapBC system in conferring fitness advantages to haloarchaea.
The Type VI secretion system (T6SS) is a key nanoweapon in Gram-negative bacteria that mediates microbial competition and pathogenesis via toxic effector delivery. Three functionally distinct T6SS clusters (H1-H3) are known in Pseudomonas aeruginosa, yet the broader evolutionary diversity and regulatory networks of T6SS in this pathogen remain poorly defined. Here, we identify Sfa4, a transcriptional regulator linked to a fourth T6SS (H4-T6SS) in clinical isolate LYSZa7. Sfa4 directly binds amrZ and H4-T6SS cluster to activate their transcription. AmrZ, in turn, directly regulates all four T6SS clusters. We further show that c-di-GMP receptor FleQ directly binds the promoters of all four T6SS clusters, revealing a direct regulatory link between c-di-GMP signaling and T6SS transcription. This regulation, together with Sfa4-mediated elevation of intracellular c-di-GMP levels, coordinately enhances H4-T6SS activity, biofilm formation, and virulence in A549 alveolar epithelial cells and Galleria mellonella models. Phylogenetic analysis shows Sfa4 homologs are present in Gram-negative bacteria, implying a potential T6SS-regulatory function. Collectively, our findings shed light on regulatory cascades and provide a mechanistic basis for understanding how clinically acquired T6SS clusters may be integrated into existing virulence networks.
Yizhou Zhang, T. Ye, Jie Deng et al.· International Journal of Bio...· 0 citations
YgeP plays a central role in APEC pathogenesis by balancing two infection strategies: motility-mediated dissemination and colonization, and biofilm-mediated attachment and tolerance, and negatively regulates key virulence traits during the early stages of infection.
Weiyang Su, Zhe Li, Siqi Feng et al.· Veterinary Microbiology· 0 citations
This study provides novel and unexpected insights into the involvement of a LuxR homolog in regulating a QS system in Gram-positive bacteria and demonstrates that functional GBL-based QS systems are conserved and active in R. erythropolis.
Héloïse Bizière-Maco, Nathan Jordier, J. F. Barbosa-de-Bessa et al.· Frontiers in Microbiology· 0 citations
It is demonstrated that MrFTRP1 exerts a dual-regulatory functioning as a positive regulator of conidiation and pathogenesis but a negative regulator of environmental stress tolerance, which expands the understanding of the regulatory diversity within the C6 TF family and identifies him as a promising target for the genetic improvement of mycoinsecticides.
Chentian Jiang, Hao Wu, You-Gui Tong et al.· Journal of Invertebrate Path...· 0 citations
Pseudomonas sp. MUP55, isolated from rainfall water in Western Australia, was characterized by polyphasic taxonomy and functional assays. Whole-genome and 16S rRNA phylogeny placed Pseudomonas sp. MUP55 in the Pseudomonas fluorescens species group. Massetolide A/D was identified as the leading candidate bioactive compound(s), consistent with its biosynthetic gene cluster, GNPS library matching, and loss of activity in regulatory mutants. The strain showed broad-spectrum antimicrobial activity against bacterial (Escherichia coli and Xanthomonas campestris) and fungal (Fusarium oxysporum and Rhizoctonia solani) plant pathogens. GacA regulates Massetolide production: a P58L mutation abolished synthesis and reduced biocontrol efficacy. Metabolomic and transcriptomic analysis of a ΔpvfC mutant revealed that the pvf cluster regulates specialized metabolism while also contributing to secreted growth-inhibitory activity. The pvf cluster differentially regulates dual siderophore systems and uncouples the co-regulated small RNAs rsmY and rsmZ in the Gac/Rsm cascade. Deletion of pvfC partially reduced the growth-inhibitory activity of Pseudomonas sp. MUP55 supernatants against bacterial pathogens, indicating that pvfC also influences secreted antimicrobial activity beyond its global regulatory role. These findings establish Pseudomonas sp. MUP55 as a taxonomically novel, mechanistically characterized biocontrol agent with potential for sustainable agriculture.
Hussain Alattas, Samuele Sala, Joseph Boctor et al.· International Journal of Mol...· 0 citations
ABSTRACT Group A Streptococcus (GAS) is a human-restricted pathogen whose global incidence has surged in the post-COVID era. The ability of GAS to shift from a colonizing to invasive phenotype depends on coordinated virulence gene regulation in response to host-derived signals. However, the mechanisms by which individual stress-sensing systems interact to reshape the virulence gene regulatory landscape remain incompletely understood. Here, we define the regulatory programs of two conserved transcriptional regulator paralogs, SpxA1 and SpxA2, using an integrated multi-omic approach combining RNA-seq, data-independent acquisition proteomics, NanoString-based transcriptional profiling across multiple host-relevant stress conditions, and chromatin immunoprecipitation with exonuclease treatment (ChIP-exo). RNA-seq revealed functionally distinct regulons with SpxA1 governing oxidative stress defense and SpxA2 coordinating virulence-associated gene expression linked to the CovRS two-component regulatory system. Proteomic analysis established SpxA2 as a ClpXP protease substrate in GAS and identified reciprocal paralog accumulation upon loss of either SpxA1 or SpxA2, consistent with compensatory transcriptional upregulation. NanoString profiling under bacitracin and human neutrophil peptide-1 challenge identified four gene modules with distinct stoichiometry-dependent and condition-dependent regulatory logic, revealing that the SpxA1/SpxA2 ratio rather than the activity of either paralog alone determines which transcriptional programs are engaged. ChIP-exo demonstrated that SpxA2 directly modulates CovR-DNA binding occupancy in a CovR-binding motif-dependent manner, simultaneously antagonizing CovR dimer binding at an extended (25 bp) CovR motif and facilitating CovR monomer binding at the canonical ATTARA motif. These findings establish the LiaFSR-SpxA2-CovRS axis as a cross-regulatory circuit through which GAS cell envelope stress sensing is directly transduced into coordinated virulence gene regulatory changes. IMPORTANCE Group A Streptococcus (GAS) causes millions of infections annually, including a recent global surge in invasive disease. To survive in the human host, GAS must rapidly reprogram virulence gene expression in response to host-derived stresses. This study characterizes two conserved transcriptional regulators, SpxA1 and SpxA2, that govern this response through interaction with RNA polymerase to indirectly influence the DNA-binding activity of downstream transcription factors. We show that SpxA2, activated by a cell envelope stress-sensing system responding to human antimicrobial peptides, reshapes the binding of the master virulence regulator CovR in a promoter-specific manner, coupling cell envelope stress sensing to virulence gene regulation. The stoichiometric balance between SpxA1 and SpxA2 functions as a regulatory rheostat calibrating overall virulence gene regulatory tone, providing a framework for understanding how RNA polymerase-interacting regulators coordinate stress responses and virulence gene control across Gram-positive bacterial pathogens. Group A Streptococcus (GAS) causes millions of infections annually, including a recent global surge in invasive disease. To survive in the human host, GAS must rapidly reprogram virulence gene expression in response to host-derived stresses. This study characterizes two conserved transcriptional regulators, SpxA1 and SpxA2, that govern this response through interaction with RNA polymerase to indirectly influence the DNA-binding activity of downstream transcription factors. We show that SpxA2, activated by a cell envelope stress-sensing system responding to human antimicrobial peptides, reshapes the binding of the master virulence regulator CovR in a promoter-specific manner, coupling cell envelope stress sensing to virulence gene regulation. The stoichiometric balance between SpxA1 and SpxA2 functions as a regulatory rheostat calibrating overall virulence gene regulatory tone, providing a framework for understanding how RNA polymerase-interacting regulators coordinate stress responses and virulence gene control across Gram-positive bacterial pathogens.
Gretchen A. Morrison, L. Vega, Misú Sanson Iglesias et al.· bioRxiv· 0 citations
