Biology subjects

Baharoglu, Z.

Publications and source records attributed to Baharoglu, Z..

11 recordsLinked to original sources

bioRxiv2025

The tRNA epitranscriptomic landscape and RNA modification enzymes in Vibrio cholerae

Transfer RNAs (tRNAs) are central to protein synthesis, ensuring precise decoding of the genetic code by delivering aminoacids to the ribosome. Among all RNA species, tRNAs are the most heavily and diversely modified, with modifications playing critical roles in stability, folding, and function. Here, we present a comprehensive, isodecoder-level map of tRNA modifications in the human pathogen Vibrio cholerae. This map was generated by chemical-based sequencing methods, comparing wild-type and deletion strains. By assigning specific tRNA modifications to their cognate enzymes, we defined a comprehensive modification landscape in Vibrio cholerae and confirmed species-specific features, such as the presence of a functional TrmK enzyme, largely restricted to Gram-positive bacteria. Additionally, we detected a modification at U55 that occurs independently of TruB. To assess the biological significance of these modifications, we evaluated fitness under both standard conditions and subinhibitory antibiotic stress, and examined how modifications in the anticodon stem-loop region influence codon decoding efficiency and accuracy. Based on a comparative analysis of E. coli and V. cholerae, we discuss how species-specific differences in tRNA isodecoder gene repertoires may influence the functional impact and biological importance of tRNA modifications. This work provides the first experimentally validated, genome-wide map of tRNA modifications in V. cholerae, serving as a reference for future research into RNA modifications, translation regulation, and pathogen biology. Author summaryThis study charts the first genome-wide map of transfer RNA (tRNA) modifications in the cholera pathogen, Vibrio cholerae, revealing how chemical marks on tRNAs shape translation and stress responses. Using complementary chemical sequencing methods and a panel of targeted gene deletions, we assigned specific modifications to their enzymes across individual tRNA isodecoders. This integrative approach validates conserved features (e.g., {Psi}55 and T54), and specific ones, such as an active TrmK that installs m{superscript 1}A22 despite being considered largely restricted to Gram-positive bacteria, and uncovers enzyme interplay among dihydrouridine synthases. By testing mutant strains in standard and sub-inhibitory antibiotic conditions, we show that several modifications are dispensable for basal growth but become critical under proteotoxic stress, influencing fitness and translation accuracy, including stop-codon readthrough. Codon-specific reporter assays further demonstrate that modifications at wobble position 34 and at position 37 modulate decoding of distinct codon families, linking epitranscriptomic changes to gene expression programs. Comparative analysis with Escherichia coli suggests that species-specific tRNA isodecoder repertoires tune the functional impact of modifications. Our map provides an additional reference for studying RNA modification biology in pathogens and how it contributes to stress adaptation and virulence.

microbiology↗

bioRxiv2024

Fine-tuning of a CRISPRi screen in the seventh pandemic Vibrio cholerae

Vibrio cholerae O1 El Tor, the etiological agent responsible for the last cholera pandemic, has become a well-established model organism for which some genetic tools exist. While CRISPRi has been applied in V. cholerae, improvements were necessary to upscale it and enable pooled screening by high-throughput sequencing in this bacterium. In this study, we introduce a pooled genome wide CRISPRi library construction specifically optimized for this V. cholerae strain, characterized by minimal cytotoxicity and streamlined experimental setup. This library allows the depletion of 3, 674 (98.9%) annotated genes from the V. cholerae genome. To confirm its effectiveness, we screened for essential genes during exponential growth in rich medium and identified 368 genes for which guides were significantly depleted from the library (log2FC < - 2). Remarkably, 82% of these genes had previously been described as hypothetical essential genes in V. cholerae or in a closely related bacterium, V. natriegens. We thus validated the robustness and accuracy of our CRISPRi-based approach for assessing gene fitness in a given condition. Our findings highlight the efficacy of the developed CRISPRi platform as a powerful tool for high-throughput functional genomics studies of V. cholerae. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=72 SRC="FIGDIR/small/601881v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@bab54aorg.highwire.dtl.DTLVardef@1d412c6org.highwire.dtl.DTLVardef@1cba6borg.highwire.dtl.DTLVardef@12d11d_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2023

Uridine as a potentiator of aminoglycosides through activation of carbohydrate transporters

Aminoglycosides (AGs) are broad-spectrum antibiotics effective against Gram-negative bacteria. AG uptake depends on membrane potential, but the precise mechanisms are incompletely understood. We report here a new mechanism of active AG uptake in Gram-negative bacteria. In E. coli, overexpression of various carbohydrate transporters increases susceptibility to AGs. Conversely, deletion of a single transporter has little impact. We propose a new uptake model where AGs act as substrates for redundant carbohydrate transporters. This mechanism appears to be shared among Gram-negative ESKAPE pathogens. We screened for molecules that induce transporters expression and identified uridine. When uridine is co-administered with AGs under conditions mimicking urinary tract infections, the efficacy of AG therapies is significantly improved against E. coli, including resistant strains, due to enhanced bacterial uptake. Based on previous knowledge on the use of uridine in humans, we propose that uridine can be a potentiating adjuvant to AG treatment of infectious diseases in the hospital.

microbiology↗

bioRxiv2023

Identification of the active mechanism of aminoglycoside entry in V. cholerae through characterization of sRNA ctrR, regulating carbohydrate utilization and transport.

The possible active entry of aminoglycosides in bacterial cells has been debated since the development of this antibiotic family. Here we report the identification of their active transport mechanism in Vibrio species. We combined genome-wide transcriptional analysis and fitness screens to identify alterations driven by treatment of V. cholerae with sub-minimum inhibitory concentrations (sub-MIC) of the aminoglycoside tobramycin. RNA-seq data showed downregulation of the small non-coding RNA ncRNA586 during such treatment, while Tn-seq revealed that inactivation of this sRNA was associated with improved fitness in the presence of tobramycin. This sRNA is located near sugar transport genes and previous work on a homologous region in Vibrio tasmaniensis suggested that this sRNA stabilizes gene transcripts for carbohydrate transport and utilization, as well as phage receptors. The role for ncRNA586, hereafter named ctrR, in the transport of both carbohydrates and aminoglycosides, was further investigated. Flow cytometry on cells treated with a fluorescent aminoglycoside confirmed the role of ctrR and of carbohydrate transporters in differential aminoglycoside entry. Despite sequence diversity, ctrR showed functional conservation across the Vibrionales. This system in directly modulated by carbon sources, suggesting regulation by carbon catabolite repression, a widely conserved mechanism in Gram-negative bacteria, priming future research on aminoglycoside uptake by sugar transporters in other bacterial species.

microbiology↗

bioRxiv2023

RavA-ViaA links Vibrio cholerae Cpx and Zra2 envelope stress to antibiotic response

RavA-ViaA were reported to play a role in aminoglycoside sensitivity but the mechanisms remain elusive. Here, we performed competition and survival experiments to confirm that deletion of ravA-viaA increases tolerance of the Gram-negative pathogen Vibrio cholerae to low and high aminoglycoside concentrations, during aerobic growth. Using high throughput strategies in this species, we identify Cpx and Zra2 two-component systems as new partners of RavA-ViaA. We show that the aminoglycoside tolerance of{Delta} ravvia requires the presence of these membrane stress sensing two-component systems. We propose that deletion of the RavA-ViaA function facilitates the response aminoglycosides because of a pre-activated state of Cpx and Zra2 membrane stress response systems. We also find an impact of these genes on polymyxin B sensitivity and vancomycin resistance, and we show that simultaneous inactivation of ravvia function together with envelope stress response systems leads to outer membrane permeabilization. Vancomycin is mostly used for Gram-positive because of its low efficiency for crossing the Gram-negative outer membrane. Targeting of the ravA-viaA operon for inactivation could be a future strategy to allow uptake of vancomycin into multidrug resistant Gram-negative bacteria.

microbiology↗

bioRxiv2023

Measuring single-cell susceptibility to antibiotics within monoclonal bacterial populations

Given the emergence of antimicrobial drug resistance, it is critical to understand the heterogeneity of response to an antibiotic within a population of cells. Since the drug can exert a selection pressure that leads to the emergence of resistant phenotypes. To date, neither bulk nor single-cell methods are able to link the heterogeneity of single-cell susceptibility to the population-scale response to antibiotics. Here we present a platform that measures the ability of individual E. coli cells to form small colonies at different ciprofloxacin concentrations, by using anchored microfluidic drops and an image and data analysis pipelines. The microfluidic results are benchmarked against classical microbiology measurements of antibiotic susceptibility, showing an agreement between the pooled microfluidic chip and replated bulk measurements. Further, the experimental likelihood of a single cell to form a colony is used to provide a probabilistic antibiotic susceptibility curve. In addition to the probabilistic viewpoint, the microfluidic format enables the characterization of morphological features over time for a large number of individual cells. This pipeline can be used to compare the response of different bacterial strains to antibiotics with different action mechanisms.

bioengineering↗

bioRxiv2022

Queuosine modification of tRNA-Tyrosine elicits translational reprogramming and enhances growth of Vibrio cholerae with aminoglycosides.

Tgt is the enzyme modifying the guanine (G) in tRNAs with GUN anticodon to queuosine (Q). tgt is required for optimal growth of Vibrio cholerae in the presence of sub-lethal aminoglycoside concentrations. We further explored here the role of the Q34 in the efficiency of codon decoding upon tobramycin exposure. We characterized its impact on the overall bacterial proteome, and elucidated the molecular mechanisms underlying the effects of Q34 modification in antibiotic translational stress response. Using molecular reporters, we showed that Q34 impacts the efficiency of decoding at tyrosine TAT and TAC codons. Proteomics analyses revealed that the anti-SoxR factor RsxA is better translated in the absence of tgt. RsxA displays a codon bias towards tyrosine TAT and overabundance of RsxA leads to decreased expression of genes belonging to SoxR oxidative stress regulon. We also identified conditions that regulate tgt expression. We propose that regulation of Q34 modification in response to environmental cues leads to translational reprogramming of transcripts bearing a biased tyrosine codon usage. In silico analysis further identified candidate genes which could be subject to such translational regulation, among which DNA repair factors. Such transcripts, fitting the definition of modification tunable transcripts, are central in the bacterial response to antibiotics.

microbiology↗

bioRxiv2022

Non-essential tRNA and rRNA modifications impact the bacterial response to sub-MIC antibiotic stress

Antimicrobial resistance (AMR) develops as a major problem in infectious diseases treatment. While antibiotic resistance mechanisms are usually studied using lethal antibiotic doses, lower doses allowing bacterial growth are now considered as factors influencing the development and selection of resistance. Based on high throughput transposon insertion sequencing (TN-seq) in V. cholerae, we have undertaken the phenotypic characterization of 23 transfer RNA (tRNA) and ribosomal RNA (rRNA) modifications deletion mutants, for which growth is globally not affected in the absence of stress. We uncover a specific involvement of different RNA modification genes in the response to aminoglycosides (tobramycin (TOB), gentamicin (GEN)), fluoroquinolones (ciprofloxacin (CIP)), {beta}-lactams (carbenicillin (CRB)), chloramphenicol (CM) and trimethoprim (TRM). Our results identify t/rRNA modification genes, not previously associated to any antibiotic resistance phenotype, as important factors affecting the bacterial response to sub-MIC antibiotics from different families. This suggests differential translation and codon decoding as critical factors involved in the bacterial response to stress.

microbiology↗

bioRxiv2021

Deficiency in cytosine DNA methylation leads to high chaperonin expression and tolerance to aminoglycosides in Vibrio cholerae

Antibiotic resistance has become a major global issue. Understanding the molecular mechanisms underlying microbial adaptation to antibiotics is of keen importance to fight Antimicrobial Resistance (AMR). Aminoglycosides are a class of antibiotics that target the small subunit of the bacterial ribosome, disrupting translational fidelity and increasing the levels of misfolded proteins in the cell. In this work, we investigated the role of VchM, a DNA methyltransferase, in the response of the human pathogen Vibrio cholerae to aminoglycosides. VchM is a V. cholerae specific orphan m5C DNA methyltransferase that generates cytosine methylation at 5'-RCCGGY-3' motifs. We show that deletion of vchM, although causing a growth defect in absence of stress, allows V. cholerae cells to cope with aminoglycoside stress at both sub-lethal and lethal concentrations of these antibiotics. Through transcriptomic and genetic approaches, we show that groESL-2 (a specific set of chaperonin-encoding genes located on the second chromosome of V. cholerae), are upregulated in cells lacking vchM and are needed for the tolerance of vchM mutant to lethal aminoglycoside treatment, likely by fighting aminoglycoside-induced misfolded proteins. Interestingly, preventing VchM methylation of the four RCCGGY sites located in groESL-2 region, leads to a higher expression of these genes in WT cells, showing that VchM modulates the expression of these chaperonins in V. cholerae directly through DNA methylation. AUTHOR SUMMARYBacteria are organisms with a remarkable ability to adapt to several stress conditions, including to the presence of antibiotics. The molecular mechanisms underlying such adaptation lead, very often, to phenomena like antimicrobial tolerance and resistance, responsible for the frequent failure of antibiotic treatment. The study of these molecular mechanisms is thus an important tool to understand development of antimicrobial resistance in bacteria. In this work, we show that abrogating cytosine DNA methylation in Vibrio cholerae increases its tolerance to aminoglycosides, a class of antibiotics that cause protein misfolding. DNA methylation is known to affect gene expression and regulate several cellular processes in bacteria. Here we provide evidence that DNA methylation also has a more direct role in controlling antibiotic susceptibility in bacteria. Consequently, the study of bacterial DNA methyltransferases and DNA methylation should not be overlooked when addressing the problem of antimicrobial tolerance/resistance.

microbiology↗

bioRxiv2021

A qnr-plasmid allows aminoglycosides to induce SOS in Escherichia coli

The plasmid-mediated quinolone resistance (PMQR) genes have been shown to promote high-level bacterial resistance to fluoroquinolone antibiotics, potentially leading to clinical treatment failures. In Escherichia coli, sub-inhibitory concentrations (sub-MIC) of the widely used fluoroquinolones are known to induce the SOS response. Interestingly, the expression of several PMQR qnr genes is controlled by the SOS master regulator. During the characterization of a small qnrD-plasmid carried in E. coli, we observed that the aminoglycosides become able to induce the SOS response in this species, thus leading to the transcription of qnrD. We found that induction of the SOS response is due to nitric oxide (NO) accumulation in presence of sub-MIC of aminoglycosides. We demonstrated that the NO accumulation is driven by two plasmid genes, ORF3 and ORF4, whose products act at two levels. ORF3 encode a FAD-binding oxidoreductase which helps NO synthesis, while ORF4 code for an FNR-type transcription factor, related to an O2-responsive regulator of hmp expression, able to repress the Hmp-mediated NO detoxification pathway of E. coli. Thus, this discovery, that other major classes of antibiotics may induce the SOS response could have worthwhile implications for antibiotic stewardship efforts in preventing the emergence of resistance.

microbiology↗

bioRxiv2020

Sleeping ribosomes: bacterial signaling triggers RaiA mediated persistence to aminoglycosides.

Indole is a small molecule derived from tryptophan degradation and proposed to be involved in bacterial signaling. We find that indole secretion is induced by sublethal tobramycin concentrations and increases persistence to aminoglycosides in V. cholerae. Indole transcriptomics showed strongly increased expression of raiA, a ribosome associated factor. Deletion of raiA abolishes the appearance of indole dependent persisters to aminoglycosides, while its overexpression leads to 100-fold increase of persisters, and a reduction in lag phase, evocative of increased active 70S ribosome content, which was confirmed by sucrose gradient analysis. We propose that, under stress conditions, inactive 70S ribosomes are associated with RaiA to be stored and rapidly reactivated when growth conditions become favorable again, in a mechanism different than ribosome hibernation. Our results point to an active process of persistent cell formation, through ribosome protection during translational stress and relief upon antibiotic removal. Translation is a universal process, and these results could help elucidate a mechanism of persistence formation in a controlled, thus inducible way.

microbiology↗