RNA Modifications in Pathogenic Bacteria: Impact on Host Adaptation and Virulence

Antoine, Laura; Bahena-Ceron, Roberto; Bunwaree, Heemee Devi; Gobry, Martin; Loegler, Victor; Romby, Pascale; Marzi, Stefano

doi:10.3390/genes12081125

Cited by 19 publications

(14 citation statements)

References 232 publications

(247 reference statements)

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“…Many of these genes mentioned above have been demonstrated to be important bacterial pathogenicity-related factors and could serve as potential targets for future mitigation strategies [36][37][38]. Besides the genes mentioned above, the high abundance of specific L. mesenteroides rRNA genes indicate the role of these genes during early bacterial pathogenesis [39] when rapid multiplication is one of the key events.…”

Section: Global Gene Expressionmentioning

confidence: 99%

Cell-Wall-Degrading Enzymes-Related Genes Originating from Rhizoctonia solani Increase Sugar Beet Root Damage in the Presence of Leuconostoc mesenteroides

Majumdar

Strausbaugh

Galewski

et al. 2022

IJMS

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Sugar beet crown and root rot caused by Rhizoctonia solani is a major yield constraint. Root rot is highly increased when R. solani and Leuconostoc mesenteroides co-infect roots. We hypothesized that the absence of plant cell-wall-degrading enzymes in L. mesenteroides and their supply by R. solani during close contact, causes increased damage. In planta root inoculation with or without cell-wall-degrading enzymes showed greater rot when L. mesenteroides was combined with cellulase (22 mm rot), polygalacturonase (47 mm), and pectin lyase (57 mm) versus these enzymes (0–26 mm), R. solani (20 mm), and L. mesenteroides (13 mm) individually. Carbohydrate analysis revealed increased simpler carbohydrates (namely glucose + galactose, and fructose) in the infected roots versus mock control, possibly due to the degradation of complex cell wall carbohydrates. Expression of R. solani cellulase, polygalacturonase, and pectin lyase genes during root infection corroborated well with the enzyme data. Global mRNAseq analysis identified candidate genes and highly co-expressed gene modules in all three organisms that might be critical in host plant defense and pathogenesis. Targeting R. solani cell-wall-degrading enzymes in the future could be an effective strategy to mitigate root damage during its interaction with L. mesenteroides.

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Section: Global Gene Expressionmentioning

confidence: 99%

Cell-Wall-Degrading Enzymes-Related Genes Originating from Rhizoctonia solani Increase Sugar Beet Root Damage in the Presence of Leuconostoc mesenteroides

Majumdar

Strausbaugh

Galewski

et al. 2022

IJMS

View full text Add to dashboard Cite

show abstract

“…Moreover, their roles during adaptation to environmental stresses and to infection have started to be acknowledged. Recent examples of tRNA modifications regulating host-pathogen interactions include the regulation of immune responses, antibiotic resistance, expression of virulence genes, and bacterial persistence ( Antoine et al, 2021 ). The most modified region of tRNA is the anticodon stem loop (ASL).…”

Section: Discussionmentioning

confidence: 99%

Skin-to-blood pH shift triggers metabolome and proteome global remodelling in Staphylococcus epidermidis

et al. 2022

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Staphylococcus epidermidis is one of the most common bacteria of the human skin microbiota. Despite its role as a commensal, S. epidermidis has emerged as an opportunistic pathogen, associated with 80% of medical devices related infections. Moreover, these bacteria are extremely difficult to treat due to their ability to form biofilms and accumulate resistance to almost all classes of antimicrobials. Thus new preventive and therapeutic strategies are urgently needed. However, the molecular mechanisms associated with S. epidermidis colonisation and disease are still poorly understood. A deeper understanding of the metabolic and cellular processes associated with response to environmental factors characteristic of SE ecological niches in health and disease might provide new clues on colonisation and disease processes. Here we studied the impact of pH conditions, mimicking the skin pH (5.5) and blood pH (7.4), in a S. epidermidis commensal strain by means of next-generation proteomics and 1H NMR-based metabolomics. Moreover, we evaluated the metabolic changes occurring during a sudden pH change, simulating the skin barrier break produced by a catheter. We found that exposure of S. epidermidis to skin pH induced oxidative phosphorylation and biosynthesis of peptidoglycan, lipoteichoic acids and betaine. In contrast, at blood pH, the bacterial assimilation of monosaccharides and its oxidation by glycolysis and fermentation was promoted. Additionally, several proteins related to virulence and immune evasion, namely extracellular proteases and membrane iron transporters were more abundant at blood pH. In the situation of an abrupt skin-to-blood pH shift we observed the decrease in the osmolyte betaine and changes in the levels of several metabolites and proteins involved in cellular redoxl homeostasis. Our results suggest that at the skin pH S. epidermidis cells are metabolically more active and adhesion is promoted, while at blood pH, metabolism is tuned down and cells have a more virulent profile. pH increase during commensal-to-pathogen conversion appears to be a critical environmental signal to the remodelling of the S. epidermidis metabolism toward a more pathogenic state. Targeting S. epidermidis proteins induced by pH 7.4 and promoting the acidification of the medical device surface or surrounding environment might be new strategies to treat and prevent S. epidermidis infections.

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“…Non-coding RNAs (ncRNAs) are often decorated with post-transcriptional modifications that render them difficult to amplify using reverse transcriptase 27,28 . In particular, tRNA derivatives formed by cleavage and base-specific modifications are interesting because they serve functions beyond their canonical role in translation 29,30 , with implications for pathogenesis 31,32 and bacterial physiology 33,34 . Quantifying microbiome tRNA abundances often requires mass spectrometry or tailored protocols to remove these modifications prior to sequencing 35,36 .…”

Section: Concurrent Transcription and Cleavage Also Occurs At Trna Locimentioning

confidence: 99%

Run-on sequencing reveals nascent transcriptomics of the human microbiome

Vill

Rice

Vlaminck

et al. 2022

Preprint

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Precise regulation of transcription initiation and elongation enables bacteria to control cellular responses to environmental stimuli. RNAseq is the most common tool for measuring the transcriptional output of bacteria, comprising predominantly mature transcripts. To gain further insight into transcriptional dynamics, it is necessary to discriminate actively transcribed loci from those represented in the total RNA pool. One solution is to capture RNA polymerase (RNAP) in the act of transcription, but current methods are restricted to culturable and genetically tractable organisms. Here, we apply precision run-on sequencing (PRO-seq) to profile nascent transcription, a method amenable to diverse species. We find that PRO-seq is well-suited to profile small, structured, or post-transcriptionally modified RNAs, which are often excluded from RNAseq libraries. When PRO-seq is applied to the human microbiome, we identify taxon-specific RNAP pause motifs. We also uncover concurrent transcription and cleavage of guide RNAs and tRNA fragments at active CRISPR and tRNA loci. We demonstrate the specific utility of PRO-seq as a tool for exploring transcriptional dynamics in diverse microbial communities.

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RNA Modifications in Pathogenic Bacteria: Impact on Host Adaptation and Virulence

Cited by 19 publications

References 232 publications

Cell-Wall-Degrading Enzymes-Related Genes Originating from Rhizoctonia solani Increase Sugar Beet Root Damage in the Presence of Leuconostoc mesenteroides

Cell-Wall-Degrading Enzymes-Related Genes Originating from Rhizoctonia solani Increase Sugar Beet Root Damage in the Presence of Leuconostoc mesenteroides

Skin-to-blood pH shift triggers metabolome and proteome global remodelling in Staphylococcus epidermidis

Run-on sequencing reveals nascent transcriptomics of the human microbiome

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