Genome-scale analysis reveals a role for NdgR in the thiol oxidative stress response in Streptomyces coelicolor

BMC Genomics
Ji-Nu KimByung-Gee Kim

Abstract

NdgR is an IclR-type transcription factor that regulates leucine biosynthesis and other metabolic pathways in Streptomyces coelicolor. Recent study revealed that NdgR is one of the regulatory targets of SigR, an oxidative stress response sigma factor, suggesting that the NdgR plays an important physiological role in response to environmental stresses. Although the regulatory functions of NdgR were partly characterized, determination of its regulon is required for better understanding of the transcriptional regulatory network related with the oxidative stress response. We determined genome-wide binding loci of NdgR by using chromatin immunoprecipitation coupled with sequencing (ChIP-seq) and explored its physiological roles. The ChIP-seq profiles revealed 19 direct binding loci with a 15-bp imperfect palindromic motif, including 34 genes in their transcription units. Most genes in branched-chain amino acid and cysteine biosynthesis pathways were involved in the NdgR regulon. We proved that ndgR is induced by SigR under the thiol oxidation, and that an ndgR mutant strain is sensitive to the thiol oxidizing agent, diamide. Through the expression test of NdgR and the target genes for NdgR under diamide treatment, regulatory motifs ...Continue Reading

References

Jan 1, 1982·Journal of Bacteriology·S R Maloy, W D Nunn
Jul 1, 1996·Journal of Bacteriology·B PanD C LaPorte
Mar 27, 1998·Journal of Bacteriology·U GerischerL N Ornston
Nov 25, 1998·Proceedings of the National Academy of Sciences of the United States of America·K NomuraS Tsuyumu
Jun 23, 2001·Protein Science : a Publication of the Protein Society·L J DonaldH W Duckworth
Feb 28, 2002·The EMBO Journal·Maria A SchumacherRichard G Brennan
Mar 6, 2002·The Journal of Biological Chemistry·Rong-Guang ZhangAlexei Savchenko
Oct 8, 2003·Proceedings of the National Academy of Sciences of the United States of America·S Mangan, U Alon
Nov 5, 2003·Nature Structural Biology·M Elizabeth StroupeElizabeth D Getzoff
Jul 12, 2005·FEMS Microbiology Letters·Nirpjit S DosanjhYossef Av-Gay
Oct 6, 2005·BMC Microbiology·Alexander V SeliverstovVassily A Lyubetsky
Feb 14, 2006·FEMS Microbiology Reviews·Antonio J Molina-HenaresJuan L Ramos
Apr 1, 2008·Journal of Bacteriology·Yasuo OhnishiSueharu Horinouchi
Jun 19, 2012·Biochemical and Biophysical Research Communications·Ji-Nu KimByung-Gee Kim
Aug 14, 2012·Cellular and Molecular Life Sciences : CMLS·Toshihiro Obata, Alisdair R Fernie
Sep 1, 2012·Nature Protocols·Jianxing FengXiaole Shirley Liu

❮ Previous
Next ❯

Citations

Jun 21, 2015·Biochimica Et Biophysica Acta·Alba Romero-RodríguezSergio Sánchez
Mar 24, 2018·The Journal of Biological Chemistry·Julien HerrouSean Crosson
Dec 19, 2016·F1000Research·Keith F Chater
Oct 30, 2015·The Journal of Biological Chemistry·Deepti JainDeepak T Nair
Jul 22, 2017·Bioprocess and Biosystems Engineering·Bo-Rahm LeeYung-Hun Yang
Aug 12, 2020·Journal of Industrial Microbiology & Biotechnology·Yongjae LeeByung-Kwan Cho
Jan 4, 2017·World Journal of Microbiology & Biotechnology·Shenghu ZhouJingwen Zhou

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE59010

Methods Mentioned

BETA
immunoprecipitation
ChIP-seq
electrophoretic mobility shift assay
ChIP-chip
ChIP
PCR

Software Mentioned

FIMO
MEME
MACS
CLC Genomics Workbench
FFL
I1

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.