The Helicobacter pylori Heat-Shock Repressor HspR: Definition of Its Direct Regulon and Characterization of the Cooperative DNA-Binding Mechanism on Its Own Promoter

Frontiers in Microbiology
Simona PepeDavide Roncarati

Abstract

The ability of pathogens to perceive environmental conditions and modulate gene expression accordingly is a crucial feature for bacterial survival. In this respect, the heat-shock response, a universal cellular response, allows cells to adapt to hostile environmental conditions and to survive during stress. In the major human pathogen Helicobacter pylori the expression of chaperone-encoding operons is under control of two auto-regulated transcriptional repressors, HrcA and HspR, with the latter acting as the master regulator of the regulatory circuit. To further characterize the HspR regulon in H. pylori, we used global transcriptome analysis (RNA-sequencing) in combination with Chromatin Immunoprecipitation coupled with deep sequencing (ChIP-sequencing) of HspR genomic binding sites. Intriguingly, these analyses showed that HspR is involved in the regulation of different crucial cellular functions through a limited number of genomic binding sites. Moreover, we further characterized HspR-DNA interactions through hydroxyl-radical footprinting assays. This analysis in combination with a nucleotide sequence alignment of HspR binding sites, revealed a peculiar pattern of DNA protection and highlighted sequence conservation with the...Continue Reading

References

May 11, 1992·Gastroenterology·D G EvansD Y Graham
Jan 1, 1990·Methods in Enzymology·F W StudierJ W Dubendorff
Jun 5, 1983·Journal of Molecular Biology·D Hanahan
Oct 24, 1997·Science·R L TatusovD J Lipman
Dec 10, 1998·Microbiology·David G MarshallCyril J Smyth
Feb 23, 1999·Molecular Microbiology·C GrandvaletP Mazodier
Jul 5, 2001·International Journal of Medical Microbiology : IJMM·V ScarlatoD Beier
Nov 8, 2002·Molecular Microbiology·Isabel DelanyVincenzo Scarlato
May 6, 2004·Journal of Bacteriology·Gunther SpohnVincenzo Scarlato
Feb 22, 2005·Molecular Microbiology·Amy K SchmidMary E Lidstrom
Nov 23, 2005·Proceedings of the National Academy of Sciences of the United States of America·David C GraingerStephen J W Busby
Jun 22, 2006·Journal of Bacteriology·Alberto DanielliVincenzo Scarlato
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Oct 24, 2009·Microbiology·Christopher W HolmesPeter A Lund
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Jun 29, 2010·FEMS Microbiology Reviews·Alberto Danielli, Vincenzo Scarlato
Jun 15, 2011·Nucleic Acids Research·Cécile MullerHilde De Reuse
Sep 17, 2011·Alimentary Pharmacology & Therapeutics·J P Gisbert, X Calvet
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Jul 10, 2012·Applied and Environmental Microbiology·Andrea VanniniAlberto Danielli
May 9, 2013·Nature Reviews. Microbiology·Nina R SalamaAnne Müller
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Sep 9, 2015·Frontiers in Microbiology·Simone PelliciariAlberto Danielli
Oct 8, 2015·IUBMB Life·Priyanka Parijat, Janendra K Batra
Feb 13, 2016·Cellular and Molecular Life Sciences : CMLS·Andrea VanniniAlberto Danielli
Apr 24, 2016·Biomedical Journal·Cheng-Yen KaoJiunn-Jong Wu
Aug 26, 2016·Nature Communications·Davide RoncaratiAlberto Danielli
Apr 13, 2017·FEMS Microbiology Reviews·Davide Roncarati, Vincenzo Scarlato

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Citations

Feb 20, 2020·Microorganisms·Simona PepeDavide Roncarati
Jun 9, 2018·International Journal of Molecular Sciences·Davide Roncarati, Vincenzo Scarlato
Oct 17, 2019·Microorganisms·Davide RoncaratiVincenzo Scarlato

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Datasets Mentioned

BETA
PRJNA421261

Methods Mentioned

BETA
footprinting
FCS
PCR
RNA-seq
Immunoprecipitation
ChIP-seq
footprintings

Software Mentioned

BEDTools
R package DESeq2
SAMtools
Bowtie 2
Homer
ENCODE

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