Biology subjects

Yahr, T. L.

Publications and source records attributed to Yahr, T. L..

4 recordsLinked to original sources

bioRxiv2026

Mining the Pseudomonas aeruginosa genome for regulators of type III secretion system gene expression using FT-Tn-seq

The Pseudomonas aeruginosa type III secretion system (T3SS) is an important virulence determinant used to mute and/or impair host immune defenses. Traditional transposon mutagenesis screens have been instrumental in identifying genes required for T3SS gene expression but our understanding of how those genes orchestrate regulatory control remains incomplete. A comprehensive inventory of the genes involved in the control of T3SS gene expression would help define regulatory mechanisms and provide additional targets for anti-virulence therapeutics. Here, we designed a fluorescently tagged transposon mutagenesis screen (FT-Tn-seq) and identified over 70 new genes important for T3SS gene expression. A role for 31 of those genes was validated using a secondary screen. Several candidate genes were selected for further studies. We demonstrate that deletion of shaC, which encodes a sodium-proton antiporter subunit, results in a significant defect in T3SS gene expression. That defect results from a combined effect on exsA transcription and ExsA translation. Deletion of wspF, a cyclic-di-GMP phosphodiesterase, results in a significant reduction of T3SS expression in strain PAK, but not in PA103. The effect on the T3SS is likely due to elevated levels of c-di-GMP in PAK. Finally, we identified a new sRNA (ivy) that participates in the control of the T3SS. Expression of ivy inhibits T3SS gene expression and requires the RNA-chaperone Hfq for inhibitory activity. Findings from this study will open new research avenues to better understand regulation of T3SS gene expression in P. aeruginosa and develop T3SS-specific therapeutic interventions.

microbiology↗

bioRxiv2024

Thermodynamic modeling of Csr/Rsm- RNA interactions capture novel, direct binding interactions across the Pseudomonas aeruginosa transcriptome

BackgroundPseudomonas aeruginosa (PA) is a ubiquitous, Gram-negative, bacteria that can attribute its survivability to numerous sensing and signaling pathways; conferring fitness due to speed of response. Post-transcriptional regulation is an energy efficient approach to quickly shift gene expression in response to the environment. The conserved post-transcriptional regulator RsmA is involved in regulating translation of genes involved in pathways that contribute to virulence, metabolism, and antibiotic resistance. Prior high-throughput approaches to map the full regulatory landscape of RsmA have estimated a target pool of approximately 500 genes; however, these approaches have been limited to a narrow range of growth phase, strain, and media conditions. Computational modeling presents a condition-independent approach to generating predictions for binding between the RsmA protein and highest affinity mRNAs. In this study, we draft a two-state thermodynamic model to predict the likelihood of RsmA binding to the 5 UTR sequence of genes present in the PA genome. ResultsOur modeling approach predicts 1043 direct RsmA-mRNA binding interactions, including 457 novel mRNA targets. We then perform GO term enrichment tests on our predictions that reveal significant enrichment for DNA binding transcriptional regulators. In addition, quorum sensing, biofilm formation, and two-component signaling pathways were represented in KEGG enrichment analysis. We confirm binding predictions using in vitro binding assays, and regulatory effects using in vivo translational reporters. These reveal RsmA binding and regulation of a broader number of genes not previously reported. An important new observation of this work is the direct regulation of several novel mRNA targets encoding for factors involved in Quorum Sensing and the Type IV Secretion system, such as rsaL and mvaT. ConclusionsOur study demonstrates the utility of thermodynamic modeling for predicting interactions independent of complex and environmentally-sensitive systems, specifically for profiling the post-transcriptional regulator RsmA. Our experimental validation of RsmA binding to novel targets both supports our model and expands upon the pool of characterized target genes in PA. Overall, our findings demonstrate that a modeling approach can differentiate direct from indirect binding interactions and predict specific sites of binding for this global regulatory protein, thus broadening our understanding of the role of RsmA regulation in this relevant pathogen.

bioinformatics↗

bioRxiv2022

Pseudomonas aeruginosa can diversify after host cell invasion to establish multiple intracellular niches

Within epithelial cells, Pseudomonas aeruginosa depends on its type three secretion system (T3SS) to escape vacuoles and replicate rapidly in the cytosol. Previously, it was assumed that intracellular subpopulations remaining T3SS-negative (and therefore in vacuoles) were destined for degradation in lysosomes, supported by data showing vacuole acidification. Here, we report in both corneal and bronchial human epithelial cells that vacuole associated-bacteria can persist, sometimes in the same cells as cytosolic bacteria. Using a combination of phase-contrast, confocal, and correlative light and electron microscopy, we also found they can demonstrate biofilm-associated markers: cdrA and cyclic-di-GMP (c-di-GMP). Vacuolar-associated bacteria, but not cytosolic counterparts, tolerated the cell-permeable antibiotic ofloxacin. Surprisingly, use of mutants showed that both persistence in vacuoles and ofloxacin tolerance were independent of the biofilm-associated protein CdrA or exopolysaccharides (Psl, Pel, alginate). A T3SS mutant ({Delta}exsA) unable to escape vacuoles phenocopied vacuolar-associated sub-populations in wild-type PAO1-infected cells, results revealing that epithelial cell death depended upon bacterial viability. Intra-vital confocal imaging of infected mouse corneas confirmed that P. aeruginosa formed similar intracellular sub-populations within epithelial cells in vivo. Together, these results show that P. aeruginosa differs from other pathogens by diversifying intracellularly into vacuolar and cytosolic sub-populations that both contribute to pathogenesis. Their different gene expression and behavior (e.g., rapid replication versus slow replication/persistence) suggest cooperation favoring both short- and long-term interests and another potential pathway to treatment failure. How this intracellular diversification relates to previously described "acute versus chronic" virulence gene-expression phenotypes of P. aeruginosa remains to be determined. ImportancePseudomonas aeruginosa can cause sight- and life-threatening opportunistic infections, and its evolving antibiotic resistance is a growing concern. Most P. aeruginosa strains can invade host cells, presenting a challenge to therapies that do not penetrate host cell membranes. Previously, we showed that the P. aeruginosa type III secretion system (T3SS) plays a pivotal role in survival within epithelial cells, allowing escape from vacuoles, rapid replication in the cytoplasm, and suppression of host cell death. Here, we report the discovery of a novel T3SS-negative sub-population of intracellular P. aeruginosa within epithelial cells that persist in vacuoles rather than the cytoplasm, and that tolerate a cell-permeable antibiotic (ofloxacin) that is able to kill cytosolic bacteria. Classical biofilm-associated markers, although demonstrated by this sub-population, are not required for vacuolar persistence or antibiotic tolerance. These findings advance our understanding of how P. aeruginosa hijacks host cells, showing it diversifies into multiple populations with T3SS-negative members enabling persistence whilst rapid replication is accomplished by more vulnerable T3SS-positive siblings. Intracellular P. aeruginosa persisting and tolerating antibiotics independently of the T3SS or biofilm-associated factors could present additional challenges to development of more effective therapeutics.

microbiology↗

bioRxiv2018

RsmV a small non-coding regulatory RNA in Pseudomonas aeruginosa that sequesters RsmA and RsmF from target mRNAs

The Gram-negative opportunistic pathogen Pseudomonas aeruginosa has distinct genetic programs that favor either acute or chronic virulence gene expression. Acute virulence is associated with twitching and swimming motility, expression of a type III secretion system (T3SS), and the absence of alginate, Psl, or Pel polysaccharide production. Traits associated with chronic infection include growth as a biofilm, reduced motility, and expression of a type VI secretion system (T6SS). The Rsm post-transcriptional regulatory system plays an important role in the inverse control of phenotypes associated with acute and chronic virulence. RsmA and RsmF are RNA-binding proteins that interact with target mRNAs to control gene expression at the post-transcriptional level. Previous work found that RsmA activity is controlled by at least three small, non-coding regulatory RNAs (RsmW, RsmY, and RsmZ). In this study, we took an in-silico approach to identify additional sRNAs that might function in the sequestration of RsmA and/or RsmF and identified RsmV, a 192 nt transcript with four predicted RsmA/RsmF consensus binding sites. RsmV is capable of sequestering RsmA and RsmF in vivo to activate translation of tssA1, a component of the T6SS, and to inhibit T3SS gene expression. Each of the predicted RsmA/RsmF consensus binding sites contribute to RsmV activity. Electrophoretic mobility shifts assays show that RsmF binds RsmV with >10-fold higher affinity than RsmY and RsmZ. Gene expression studies revealed that the temporal expression pattern of RsmV differs from RsmW, RsmY, and RsmZ. These findings suggest that each sRNA may play distinct roles in controlling RsmA and RsmF activity.\n\nIMPORTANCEThe role of RsmF in post-transcriptional control of gene expression remains enigmatic. While numerous rsmA-dependent phenotypes are more pronounced in an rsmAF double mutant, deletion of rsmF alone has only modest effects. Understanding mechanisms that control RsmF activity will provide insight into additional roles for RsmF. In the current study we identify RsmV as an sRNA that controls RsmA and RsmF activity, and show that RsmV, RsmW, RsmY, and RsmZ are differentially expressed during growth.

microbiology↗