scholarly journals OmpA, a Common Virulence Factor, Is Under RNA Thermometer Control in Yersinia pseudotuberculosis

2021 ◽  
Vol 12 ◽  
Author(s):  
Daniel Scheller ◽  
Christian Twittenhoff ◽  
Franziska Becker ◽  
Marcel Holler ◽  
Franz Narberhaus
Keyword(s):  
Virulence Factor ◽  
Rna Structure ◽  
Yersinia Pseudotuberculosis ◽  
Translational Repression ◽  
Gene Fusions ◽  
Closed Conformation ◽  
Reverse Transcription Pcr ◽  
Structure Probing ◽  
Rna Thermometer ◽  
Increasing Temperature

The outer membrane protein OmpA is a virulence factor in many mammalian pathogens. In previous global RNA structure probing studies, we found evidence for a temperature-modulated RNA structure in the 5'-untranslated region (5'-UTR) of the Yersinia pseudotuberculosis ompA transcript suggesting that opening of the structure at host-body temperature might relieve translational repression. Here, we support this hypothesis by quantitative reverse transcription PCR, translational reporter gene fusions, enzymatic RNA structure probing, and toeprinting assays. While ompA transcript levels decreased at 37°C compared to 25°C, translation of the transcript increased with increasing temperature. Biochemical experiments show that this is due to melting of the RNA structure, which permits ribosome binding to the 5'-UTR. A point mutation that locks the RNA structure in a closed conformation prevents translation by impairing ribosome access. Our findings add another common virulence factor to the growing list of pathogen-associated genes that are under RNA thermometer control.

scholarly journals FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

2010 ◽  
Vol 7 (12) ◽  
pp. 995-1001 ◽  
Author(s):  
Jason G Underwood ◽  
Andrew V Uzilov ◽  
Sol Katzman ◽  
Courtney S Onodera ◽  
Jacob E Mainzer ◽  
...  
Keyword(s):  
High Throughput ◽  
Rna Structure ◽  
High Throughput Sequencing ◽  
Structure Probing

scholarly journals Effects of Antibiotics on Quorum Sensing in Pseudomonas aeruginosa

2008 ◽  
Vol 52 (10) ◽  
pp. 3648-3663 ◽  
Author(s):  
Mette E. Skindersoe ◽  
Morten Alhede ◽  
Richard Phipps ◽  
Liang Yang ◽  
Peter O. Jensen ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Quorum Sensing ◽  
Virulence Factor ◽  
Dna Microarrays ◽  
Underlying Mechanism ◽  
Homoserine Lactone ◽  
Reverse Transcription Pcr ◽  
Animal Infection ◽  
Beneficial Action ◽  
Severe Infections

ABSTRACT During infection, Pseudomonas aeruginosa employs bacterial communication (quorum sensing [QS]) to coordinate the expression of tissue-damaging factors. QS-controlled gene expression plays a pivotal role in the virulence of P. aeruginosa, and QS-deficient mutants cause less severe infections in animal infection models. Treatment of cystic fibrosis (CF) patients chronically infected with P. aeruginosa with the macrolide antibiotic azithromycin (AZM) has been demonstrated to improve the clinical outcome. Several studies indicate that AZM may accomplish its beneficial action in CF patients by impeding QS, thereby reducing the pathogenicity of P. aeruginosa. This led us to investigate whether QS inhibition is a common feature of antibiotics. We present the results of a screening of 12 antibiotics for their QS-inhibitory activities using a previously described QS inhibitor selector 1 strain. Three of the antibiotics tested, AZM, ceftazidime (CFT), and ciprofloxacin (CPR), were very active in the assay and were further examined for their effects on QS-regulated virulence factor production in P. aeruginosa. The effects of the three antibiotics administered at subinhibitory concentrations were investigated by use of DNA microarrays. Consistent results from the virulence factor assays, reverse transcription-PCR, and the DNA microarrays support the finding that AZM, CFT, and CPR decrease the expression of a range of QS-regulated virulence factors. The data suggest that the underlying mechanism may be mediated by changes in membrane permeability, thereby influencing the flux of N-3-oxo-dodecanoyl-l-homoserine lactone.

scholarly journals Molecular Characterization of a Flagellar Export Locus of Helicobacter pylori

1999 ◽  
Vol 67 (5) ◽  
pp. 2060-2070 ◽  
Author(s):  
Steffen Porwollik ◽  
Brian Noonan ◽  
Paul W. O’Toole
Keyword(s):  
Helicobacter Pylori ◽  
Virulence Factor ◽  
Housekeeping Genes ◽  
Reading Frame ◽  
Reverse Transcription Pcr ◽  
Mutant Strains ◽  
H Pylori ◽  
Export Protein ◽  
Successful Colonization

ABSTRACT Motility of Helicobacter species has been shown to be essential for successful colonization of the host. We have investigated the organization of a flagellar export locus in Helicobacter pylori. A 7-kb fragment of the H. pylori CCUG 17874 genome was cloned and sequenced, revealing an operon comprising an open reading frame of unknown function (ORF03), essential housekeeping genes (ileS and murB), flagellar export genes (fliI and fliQ), and a homolog to a gene implicated in virulence factor transport in other pathogens (virB11). A promoter for this operon, showing similarity to the Escherichia coli ς70 consensus, was identified by primer extension. Cotranscription of the genes in the operon was demonstrated by reverse transcription-PCR, and transcription of virB11, fliI, fliQ, andmurB was detected in human or mouse biopsies obtained from infected hosts. The genetic organization of this locus was conserved in a panel of H. pylori clinical isolates. EngineeredfliI and fliQ mutant strains were completely aflagellate and nonmotile, whereas a virB11 mutant still produced flagella. The fliI and fliQ mutant strains produced reduced levels of flagellin and the hook protein FlgE. Production of OMP4, a member of the outer membrane protein family identified in H. pylori 26695, was reduced in both thevirB11 mutant and the fliI mutant, suggesting related functions of the virulence factor export protein (VirB11) and the flagellar export component (FliI).

scholarly journals An ultra low-input method for global RNA structure probing uncovers Regnase-1-mediated regulation in macrophages

2021 ◽  
Author(s):  
Meiling Piao ◽  
Pan Li ◽  
Xiaomin Zeng ◽  
Xi-Wen Wang ◽  
Lan Kang ◽  
...  
Keyword(s):  
Rna Structure ◽  
Low Input ◽  
Input Method ◽  
Structure Probing

scholarly journals Physical and Functional Analysis of Viral RNA Genomes by SHAPE

2019 ◽  
Vol 6 (1) ◽  
pp. 93-117 ◽  
Author(s):  
Mark A. Boerneke ◽  
Jeffrey E. Ehrhardt ◽  
Kevin M. Weeks
Keyword(s):  
Rna Structure ◽  
Rna Viruses ◽  
Genome Structure ◽  
Regulatory Elements ◽  
Viral Rna ◽  
Host Immune Responses ◽  
Linear Sequence ◽  
Structure Probing ◽  
Shape Structure ◽  
Shape Selective

RNA viruses encode the information required to usurp cellular metabolism and gene regulation and to enable their own replication in two ways: in the linear sequence of their RNA genomes and in higher-order structures that form when the genomic RNA strand folds back on itself. Application of high-resolution SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) structure probing to viral RNA genomes has identified numerous new regulatory elements, defined new principles by which viral RNAs interact with the cellular host and evade host immune responses, and revealed relationships between virus evolution and RNA structure. This review summarizes our current understanding of genome structure-function interrelationships for RNA viruses, as informed by SHAPE structure probing, and outlines opportunities for future studies.

scholarly journals mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis inArabidopsis thaliana

2020 ◽  
Vol 117 (35) ◽  
pp. 21785-21795 ◽  
Author(s):  
Susheel Sagar Bhat ◽  
Dawid Bielewicz ◽  
Tomasz Gulanicz ◽  
Zsuzsanna Bodi ◽  
Xiang Yu ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Structure ◽  
Methylation Status ◽  
Mirna Biogenesis ◽  
Stem Loop ◽  
Structure Probing ◽  
Plant Transcriptome ◽  
Loop Regions

InArabidopsis thaliana, the METTL3 homolog, mRNA adenosine methylase (MTA) introducesN6-methyladenosine (m6A) into various coding and noncoding RNAs of the plant transcriptome. Here, we show that an MTA-deficient mutant (mta) has decreased levels of microRNAs (miRNAs) but accumulates primary miRNA transcripts (pri-miRNAs). Moreover, pri-miRNAs are methylated by MTA, and RNA structure probing analysis reveals a decrease in secondary structure within stem–loop regions of these transcripts inmtamutant plants. We demonstrate interaction between MTA and both RNA Polymerase II and TOUGH (TGH), a plant protein needed for early steps of miRNA biogenesis. Both MTA and TGH are necessary for efficient colocalization of the Microprocessor components Dicer-like 1 (DCL1) and Hyponastic Leaves 1 (HYL1) with RNA Polymerase II. We propose that secondary structure of miRNA precursors induced by their MTA-dependent m6A methylation status, together with direct interactions between MTA and TGH, influence the recruitment of Microprocessor to plant pri-miRNAs. Therefore, the lack of MTA inmtamutant plants disturbs pri-miRNA processing and leads to the decrease in miRNA accumulation. Furthermore, our findings reveal that reduced miR393b levels likely contributes to the impaired auxin response phenotypes ofmtamutant plants.

scholarly journals Robust statistical modeling improves sensitivity of high-throughput RNA structure probing experiments

2016 ◽  
Vol 14 (1) ◽  
pp. 83-89 ◽  
Author(s):  
Alina Selega ◽  
Christel Sirocchi ◽  
Ira Iosub ◽  
Sander Granneman ◽  
Guido Sanguinetti
Keyword(s):  
Statistical Modeling ◽  
High Throughput ◽  
Rna Structure ◽  
Structure Probing

scholarly journals Decreased translation of Dio3 mRNA is associated with drug-induced hepatotoxicity

2013 ◽  
Vol 453 (1) ◽  
pp. 71-82 ◽  
Author(s):  
Kate M. Dudek ◽  
Laura Suter ◽  
Veerle M. Darras ◽  
Emma L. Marczylo ◽  
Timothy W. Gant
Keyword(s):  
Mrna Translation ◽  
Northern Blotting ◽  
Translational Repression ◽  
Global Changes ◽  
Drug Induced ◽  
Iodothyronine Deiodinase ◽  
Reverse Transcription Pcr ◽  
Pituitary Thyroid Axis ◽  
Canonical Pathways ◽  
Transcriptional Gene Regulation

Recent work has demonstrated the importance of post-transcriptional gene regulation in toxic responses. In the present study, we used two rat models to investigate mRNA translation in the liver following xenobiotic-induced toxicity. By combining polysome profiling with genomic methodologies, we were able to assess global changes in hepatic mRNA translation. Dio3 (iodothyronine deiodinase type III) was identified as a gene that exhibited specific translational repression and had a functional role in a number of relevant canonical pathways. Western blot analysis indicated that this repression led to reduced D3 (the protein expressed by Dio3) levels, enhanced over time and with increased dose. Using Northern blotting techniques and qRT-PCR (quantitative reverse transcription–PCR), we confirmed further that there was no reduction in Dio3 mRNA, suggesting that translational repression of Dio3 is an important determinant of the reduced D3 protein expression following liver damage. Finally, we show that drug-induced hepatotoxicity appears to cause localized disruptions in thyroid hormone levels in the liver and plasma. We suggest that this leads to reduced translation of Dio3 mRNA, which results in decreased D3 production. It may therefore be possible that this is an important mechanism by which the liver can, upon early signs of damage, act rapidly to maintain its own energy equilibrium, thereby avoiding global disruption of the hypothalamic–pituitary–thyroid axis.

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