Genome-wide mapping of TnrA-binding sites provides new insights into the TnrA regulon in Bacillus subtilis

MicrobiologyOpen
Nicolas MirouzeSandrine Auger

Abstract

Under nitrogen limitation conditions, Bacillus subtilis induces a sophisticated network of adaptation responses. More precisely, the B. subtilis TnrA regulator represses or activates directly or indirectly the expression of a hundred genes in response to nitrogen availability. The global TnrA regulon have already been identified among which some directly TnrA-regulated genes have been characterized. However, a genome-wide mapping of in vivo TnrA-binding sites was still needed to clearly define the set of genes directly regulated by TnrA. Using chromatin immunoprecipitation coupled with hybridization to DNA tiling arrays (ChIP-on-chip), we now provide in vivo evidence that TnrA reproducibly binds to 42 regions on the chromosome. Further analysis with real-time in vivo transcriptional profiling, combined with results from previous reports, allowed us to define the TnrA primary regulon. We identified 35 promoter regions fulfilling three criteria necessary to be part of this primary regulon: (i) TnrA binding in ChIP-on-chip experiments and/or in previous in vitro studies; (ii) the presence of a TnrA box; (iii) TnrA-dependent expression regulation. In addition, the TnrA primary regulon delimitation allowed us to improve the TnrA box...Continue Reading

References

Nov 5, 1989·Journal of Molecular Biology·H J SchreierA L Sonenshein
Feb 1, 1980·Journal of Bacteriology·D R Dean, A I Aronson
Apr 1, 1996·Journal of Bacteriology·S W Brown, A L Sonenshein
Aug 20, 1996·Proceedings of the National Academy of Sciences of the United States of America·L V WrayS H Fisher
Dec 30, 1999·Journal of Bacteriology·P J Pomposiello, B Demple
May 2, 2001·Genes & Development·M Ratnayake-LecamwasamA L Sonenshein
Mar 27, 2002·Journal of Bacteriology·Susan H Fisher, Lewis V Wray
Oct 11, 2002·Journal of Bacteriology·Jaclyn L BrandenburgSusan H Fisher
Jun 26, 2003·Molecular Microbiology·Ken-ichi YoshidaYasutaro Fujita
Jul 16, 2004·Journal of Proteome Research·Mahel ZeghoufJack F Greenblatt
Dec 20, 2005·Biochemical and Biophysical Research Communications·Yunho LeeWoojun Park
Jul 18, 2006·Nucleic Acids Research·Timothy L BaileyWilfred W Li
Nov 15, 2006·The Journal of Biological Chemistry·Soojin Jang, James A Imlay
May 27, 2008·Journal of Bacteriology·Ayako YasumuraTeruo Tanaka
Apr 14, 2009·Nature Methods·Daniel G GibsonHamilton O Smith
Aug 18, 2009·Molecular Microbiology·Simon RasmussenHanne Jarmer
Jun 28, 2011·Journal of Molecular Biology·Boris R Belitsky, Abraham L Sonenshein
Oct 4, 2011·Applied and Environmental Microbiology·Thi-Huyen DoKeitarou Kimura
Mar 19, 2013·Journal of Bacteriology·Semen A LeynDmitry A Rodionov

❮ Previous
Next ❯

Citations

May 15, 2015·Molecular Microbiology·Boris R BelitskyAbraham L Sonenshein
Dec 5, 2015·The Journal of Biological Chemistry·Ksenia HaufKarl Forchhammer
Nov 19, 2015·Molecular Systems Biology·Mario L Arrieta-OrtizPatrick Eichenberger
Aug 25, 2017·BMC Research Notes·Paola RandazzoSandrine Auger
Jul 22, 2020·Journal of Bacteriology·Rajesh BiswasBoris R Belitsky
May 10, 2018·Scientific Reports·Tal HassanovIlana Kolodkin-Gal
May 3, 2020·FEMS Microbiology Ecology·Marina Spona-FriedlMartin Elsner
May 28, 2019·Frontiers in Molecular Biosciences·Björn RichtsFabian M Commichau
Feb 6, 2020·Frontiers in Microbiology·Alejandra AlvaradoChristine Josenhans
Jul 30, 2021·Microbiological Research·Abhinav Nair, Saurabh Jyoti Sarma

❮ Previous
Next ❯

Methods Mentioned

BETA
immunoprecipitation
PCR
Immnunoprecipitation

Software Mentioned

MEME
MEME ( Em for

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.