scholarly journals Characterization of a Novel Riboswitch-Regulated Lysine Transporter in Aggregatibacter actinomycetemcomitans

2010 ◽  
Vol 192 (23) ◽  
pp. 6240-6250 ◽  
Author(s):  
Peter Jorth ◽  
Marvin Whiteley
Keyword(s):  
Oral Cavity ◽  
Experimental Approach ◽  
Bacterial Species ◽  
Opportunistic Pathogen ◽  
Aggregatibacter Actinomycetemcomitans ◽  
Host Immune System ◽  
Biofilm Growth ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas

ABSTRACT Aggregatibacter actinomycetemcomitans is an opportunistic pathogen that resides primarily in the mammalian oral cavity. In this environment, A. actinomycetemcomitans faces numerous host- and microbe-derived stresses, including intense competition for nutrients and exposure to the host immune system. While it is clear that A. actinomycetemcomitans responds to precise cues that allow it to adapt and proliferate in the presence of these stresses, little is currently known about the regulatory mechanisms that underlie these responses. Many bacteria use noncoding regulatory RNAs (ncRNAs) to rapidly alter gene expression in response to environmental stresses. Although no ncRNAs have been reported in A. actinomycetemcomitans, we propose that they are likely important for colonization and persistence in the oral cavity. Using a bioinformatic and experimental approach, we identified three putative metabolite-sensing riboswitches and nine small regulatory RNAs (sRNAs) in A. actinomycetemcomitans during planktonic and biofilm growth. Molecular characterization of one of the riboswitches revealed that it is a lysine riboswitch and that its target gene, lysT, encodes a novel lysine-specific transporter. Finally, we demonstrated that lysT and the lysT lysine riboswitch are conserved in over 40 bacterial species, including the phylogenetically related pathogen Haemophilus influenzae.

scholarly journals TheprrF-Encoded Small Regulatory RNAs Are Required for Iron Homeostasis and Virulence of Pseudomonas aeruginosa

2014 ◽  
Vol 83 (3) ◽  
pp. 863-875 ◽  
Author(s):  
Alexandria A. Reinhart ◽  
Daniel A. Powell ◽  
Angela T. Nguyen ◽  
Maura O'Neill ◽  
Louise Djapgne ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Iron Homeostasis ◽  
Opportunistic Pathogen ◽  
Wild Type ◽  
Content Type ◽  
Genes Encoding ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Heme Regulation ◽  
Heme Binding Protein

Pseudomonas aeruginosais an opportunistic pathogen that requires iron to cause infection, but it also must regulate the uptake of iron to avoid iron toxicity. The iron-responsive PrrF1 and PrrF2 small regulatory RNAs (sRNAs) are part ofP. aeruginosa'siron regulatory network and affect the expression of at least 50 genes encoding iron-containing proteins. The genes encoding the PrrF1 and PrrF2 sRNAs are encoded in tandem inP. aeruginosa, allowing for the expression of a distinct, heme-responsive sRNA named PrrH that appears to regulate genes involved in heme metabolism. Using a combination of growth, mass spectrometry, and gene expression analysis, we showed that the ΔprrF1,2mutant, which lacks expression of the PrrF and PrrH sRNAs, is defective for both iron and heme homeostasis. We also identifiedphuS, encoding a heme binding protein involved in heme acquisition, andvreR, encoding a previously identified regulator ofP. aeruginosavirulence genes, as novel targets ofprrF-mediated heme regulation. Finally, we showed that theprrFlocus encoding the PrrF and PrrH sRNAs is required forP. aeruginosavirulence in a murine model of acute lung infection. Moreover, we showed that inoculation with a ΔprrF1,2deletion mutant protects against future challenge with wild-typeP. aeruginosa. Combined, these data demonstrate that theprrF-encoded sRNAs are critical regulators ofP. aeruginosavirulence.

scholarly journals The Mycobacterium tuberculosis sRNA F6 Modifies Expression of Essential Chaperonins, GroEL2 and GroES

2021 ◽  
Author(s):  
Joanna Houghton ◽  
Angela Rodgers ◽  
Graham Rose ◽  
Alexandre D’Halluin ◽  
Terry Kipkorir ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mycobacterium Tuberculosis ◽  
Differential Gene Expression ◽  
Control Of Gene Expression ◽  
Content Type ◽  
Infection Models ◽  
Small Regulatory Rnas ◽  
Differential Gene ◽  
Regulatory Rnas

Control of gene expression via small regulatory RNAs (sRNAs) is poorly understood in one of the most successful pathogens, Mycobacterium tuberculosis . Here, we present an in-depth characterization of the sRNA F6, including its expression in different infection models and the differential gene expression observed upon deletion of the sRNA.

scholarly journals Cis- and Trans-Encoded Small Regulatory RNAs in Bacillus subtilis

2021 ◽  
Vol 9 (9) ◽  
pp. 1865
Author(s):  
Sabine Brantl ◽  
Peter Müller
Keyword(s):  
Potential Role ◽  
Bacterial Species ◽  
Model Organism ◽  
Physiological Role ◽  
Base Pairing ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Rna Chaperones ◽  
Cis And Trans

Small regulatory RNAs (sRNAs) that act by base-pairing are the most abundant posttranscriptional regulators in all three kingdoms of life. Over the past 20 years, a variety of approaches have been employed to discover chromosome-encoded sRNAs in a multitude of bacterial species. However, although largely improved bioinformatics tools are available to predict potential targets of base-pairing sRNAs, it is still challenging to confirm these targets experimentally and to elucidate the mechanisms as well as the physiological role of their sRNA-mediated regulation. Here, we provide an overview of currently known cis- and trans-encoded sRNAs from B. subtilis with known targets and defined regulatory mechanisms and on the potential role of RNA chaperones that are or might be required to facilitate sRNA regulation in this important Gram-positive model organism.

scholarly journals sRNARFTarget: A fast machine-learning-based approach for transcriptome-wide sRNA Target Prediction

2021 ◽  
Author(s):  
Kratika Naskulwar ◽  
Lourdes Peña-Castillo
Keyword(s):  
Machine Learning ◽  
Bacterial Species ◽  
Prediction Method ◽  
Target Prediction ◽  
Accurate Method ◽  
Adaptive Responses ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Species Specific ◽  
Bacterial Transcriptome

AbstractBacterial small regulatory RNAs (sRNAs) are key regulators of gene expression in many processes related to adaptive responses. A multitude of sRNAs have been identified in many bacterial species; however, their function has yet to be elucidated. A key step to understand sRNAs function is to identify the mRNAs these sRNAs bind to. There are several computational methods for sRNA target prediction, and the most accurate one is CopraRNA which is based on comparative-genomics. However, species-specific sRNAs are quite common and CopraRNA cannot be used for these sRNAs. The most commonly used transcriptome-wide sRNA target prediction method and second-most-accurate method is IntaRNA. However, IntaRNA can take hours to run on a bacterial transcriptome. Here we present sRNARFTarget, a machine-learning-based method for transcriptome-wide sRNA target prediction applicable to any sRNA. We comparatively assessed the performance of sRNARFTarget, CopraRNA and IntaRNA in three bacterial species. Our results show that sRNARFTarget outperforms IntaRNA in terms of accuracy, ranking of true interacting pairs, and running time. However, CopraRNA substantially outperforms the other two programs in terms of accuracy. Thus, we suggest using CopraRNA when homolog sequences of the sRNA are available, and sRNARFTarget for transcriptome-wide prediction or for species-specific sRNAs. sRNARFTarget is available at https://github.com/BioinformaticsLabAtMUN/sRNARFTarget.

scholarly journals Transcriptional Response of Mucoid Pseudomonas aeruginosa to Human Respiratory Mucus

mBio ◽  
2012 ◽  
Vol 3 (6) ◽  
Author(s):  
V. Cattoir ◽  
G. Narasimhan ◽  
D. Skurnik ◽  
H. Aschard ◽  
D. Roux ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Opportunistic Pathogen ◽  
Secretion System ◽  
Type Vi Secretion System ◽  
Transcript Levels ◽  
Content Type ◽  
Type Vi Secretion ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas

ABSTRACTAdaptation of bacterial pathogens to a host can lead to the selection and accumulation of specific mutations in their genomes with profound effects on the overall physiology and virulence of the organisms. The opportunistic pathogenPseudomonas aeruginosais capable of colonizing the respiratory tract of individuals with cystic fibrosis (CF), where it undergoes evolution to optimize survival as a persistent chronic human colonizer. The transcriptome of a host-adapted, alginate-overproducing isolate from a CF patient was determined following growth of the bacteria in the presence of human respiratory mucus. This stable mucoid strain responded to a number of regulatory inputs from the mucus, resulting in an unexpected repression of alginate production. Mucus in the medium also induced the production of catalases and additional peroxide-detoxifying enzymes and caused reorganization of pathways of energy generation. A specific antibacterial type VI secretion system was also induced in mucus-grown cells. Finally, a group of small regulatory RNAs was identified and a fraction of these were mucus regulated. This report provides a snapshot of responses in a pathogen adapted to a human host through assimilation of regulatory signals from tissues, optimizing its long-term survival potential.IMPORTANCEThe basis for chronic colonization of patients with cystic fibrosis (CF) by the opportunistic pathogenPseudomonas aeruginosacontinues to represent a challenging problem for basic scientists and clinicians. In this study, the host-adapted, alginate-overproducingPseudomonas aeruginosa2192 strain was used to assess the changes in its transcript levels following growth in respiratory CF mucus. Several significant and unexpected discoveries were made: (i) although the alginate overproduction in strain 2192 was caused by a stable mutation, a mucus-derived signal caused reduction in the transcript levels of alginate biosynthetic genes; (ii) mucus activated the expression of the type VI secretion system, a mechanism for killing of other bacteria in a mixed population; (iii) expression of a number of genes involved in respiration was altered; and (iv) several small regulatory RNAs were identified, some being mucus regulated. This work highlights the strong influence of the host environment in shaping bacterial survival strategies.

scholarly journals First characterization of methanogens in oral cavity in Malian patients with oral cavity pathologies

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Elisabeth Sogodogo ◽  
Ogobara Doumbo ◽  
Gérard Aboudharam ◽  
Bourema Kouriba ◽  
Ousseynou Diawara ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Fluorescent In Situ Hybridization ◽  
Bacterial Species ◽  
Chain Reaction ◽  
New Knowledge ◽  
Columbia Agar ◽  
Collection Period ◽  
Polymerase Chain

Abstract Background The oral cavity of humans is inhabited by several hundreds of bacterial species and other microorganisms such as fungi and archaeal methanogens. Regarding methanogens, data have been obtained from oral cavity samples collected in Europe, America and Asia. There is no study published on the presence of methanogens in the oral cavity in persons living in Africa. The objective of our study was to bring new knowledge on the distribution of oral methanogens in persons living in Mali, Africa. Methods A total of 31 patients were included in the study during a 15-day collection period in September. Bacterial investigations consisted in culturing the bacteria in 5% sheep blood–enriched Columbia agar and PolyViteX agar plates. For archaeal research, we used various methods including culture, molecular biology and fluorescent in situ hybridization (FISH). Results Eight of 31 (26%) oral samples collected in eight patients consulting for stomatology diseases tested positive in polymerase chain-reaction (PCR)-based assays for methanogens including five cases of Methanobrevibacter oralis and one case each of Methanobrevibacter smithii, Methanobrevibacter massiliense and co-infection Methanobrevibacter oralis and Methanobrevibacter massiliense. Conclusions In this pilot study, we are reporting here the first characterization of methanogens in the oral cavity in eight patients in Mali. These methanogen species have already been documented in oral specimens collected from individuals in Europe, Asia, North America and Brazil.

scholarly journals The Core Proteome of Biofilm-Grown Clinical Pseudomonas aeruginosa Isolates

Cells ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 1129 ◽  
Author(s):  
Jelena Erdmann ◽  
Janne G. Thöming ◽  
Sarah Pohl ◽  
Andreas Pich ◽  
Christof Lenz ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Bacterial Species ◽  
Protein Profile ◽  
Opportunistic Pathogen ◽  
Growth Conditions ◽  
Protein Quantification ◽  
Clinical Isolates ◽  
Biofilm Growth ◽  
Regulatory Pathways ◽  
Data Independent Acquisition

Comparative genomics has greatly facilitated the identification of shared as well as unique features among individual cells or tissues, and thus offers the potential to find disease markers. While proteomics is recognized for its potential to generate quantitative maps of protein expression, comparative proteomics in bacteria has been largely restricted to the comparison of single cell lines or mutant strains. In this study, we used a data independent acquisition (DIA) technique, which enables global protein quantification of large sample cohorts, to record the proteome profiles of overall 27 whole genome sequenced and transcriptionally profiled clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. Analysis of the proteome profiles across the 27 clinical isolates grown under planktonic and biofilm growth conditions led to the identification of a core biofilm-associated protein profile. Furthermore, we found that protein-to-mRNA ratios between different P. aeruginosa strains are well correlated, indicating conserved patterns of post-transcriptional regulation. Uncovering core regulatory pathways, which drive biofilm formation and associated antibiotic tolerance in bacterial pathogens, promise to give clues to interactions between bacterial species and their environment and could provide useful targets for new clinical interventions to combat biofilm-associated infections.

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