Superhelical destabilization in regulatory regions of stress response genes.

PLoS Computational Biology
Huiquan Wang, C J Benham

Abstract

Stress-induced DNA duplex destabilization (SIDD) analysis exploits the known structural and energetic properties of DNA to predict sites that are susceptible to strand separation under negative superhelical stress. When this approach was used to calculate the SIDD profile of the entire Escherichia coli K12 genome, it was found that strongly destabilized sites occur preferentially in intergenic regions that are either known or inferred to contain promoters, but rarely occur in coding regions. Here, we investigate whether the genes grouped in different functional categories have characteristic SIDD properties in their upstream flanks. We report that strong SIDD sites in the E. coli K12 genome are statistically significantly overrepresented in the upstream regions of genes encoding transcriptional regulators. In particular, the upstream regions of genes that directly respond to physiological and environmental stimuli are more destabilized than are those regions of genes that are not involved in these responses. Moreover, if a pathway is controlled by a transcriptional regulator whose gene has a destabilized 5' flank, then the genes (operons) in that pathway also usually contain strongly destabilized SIDD sites in their 5' flanks. ...Continue Reading

References

Aug 1, 1979·Proceedings of the National Academy of Sciences of the United States of America·C J Benham
Feb 1, 1992·Molecular Microbiology·K Drlica
Jun 5, 1992·Journal of Molecular Biology·C J Benham
Feb 24, 1989·Cell·G J Pruss, K Drlica
Oct 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·L F Liu, J C Wang
Dec 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·D KowalskiM J Eddy
Jan 1, 1984·Journal of Cell Science. Supplement·J C Wang
Jan 1, 1993·Annual Review of Microbiology·M A Schell
Apr 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·C J Benham
Apr 28, 1997·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·T Mizuno
Oct 24, 1997·Science·R L TatusovD J Lipman
Feb 12, 1998·Journal of Molecular Biology·C BenhamJ Bode
Jun 6, 1998·The Journal of Biological Chemistry·K Y RheeG W Hatfield
Mar 13, 1999·The Journal of Biological Chemistry·S D SheridanG W Hatfield
May 14, 1999·Current Opinion in Microbiology·X Dai, L B Rothman-Denes
Dec 10, 1999·Proceedings of the National Academy of Sciences of the United States of America·K Y RheeG W Hatfield
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Sep 14, 2000·Proceedings of the National Academy of Sciences of the United States of America·B P LeblancD J Clark
Aug 2, 2001·Archives of Microbiology·J R van der PloegT Leisinger
Oct 10, 2002·FEBS Letters·Remus Thei Dame, Nora Goosen
Nov 14, 2002·Annual Review of Genetics·G Wesley Hatfield, Craig J Benham
May 20, 2003·The Journal of Biological Chemistry·Kirsty SalmonRobert P Gunsalus
Aug 14, 2003·Trends in Microbiology·Jetta J E Bijlsma, Eduardo A Groisman
Dec 19, 2003·Nucleic Acids Research·Margrethe H SerresMonica Riley
Sep 7, 2004·The Journal of Biological Chemistry·Concetta C Dirusso, Paul N Black

❮ Previous
Next ❯

Citations

Oct 17, 2014·Proceedings of the National Academy of Sciences of the United States of America·Yue DingLaura Finzi
Sep 8, 2009·Journal of Bacteriology·Aldert ZomerDouwe van Sinderen
Oct 13, 2009·Nucleic Acids Research·David G DineenDesmond G Higgins
Jul 15, 2015·Plant Signaling & Behavior·Karl J Niklas, Ulrich Kutschera
Jan 1, 2009·Standards in Genomic Sciences·Peter F HallinDavid W Ussery
Mar 3, 2009·Journal of Molecular Biology·Aristeidis GiannakopoulosAglaia Athanassiadou
Sep 5, 2014·PLoS Computational Biology·Sam Meyer, Guillaume Beslon
May 10, 2012·PLoS Computational Biology·Dina Zhabinskaya, Craig J Benham
Jun 23, 2011·PloS One·Cheryl L SershenCraig J Benham
Jul 26, 2008·Annual Review of Genetics·Carla J Davidson, Michael G Surette
Feb 2, 2011·PLoS Computational Biology·Dina Zhabinskaya, Craig J Benham
Jan 30, 2016·PLoS Computational Biology·Iman Farasat, Howard M Salis
Jan 20, 2017·Microbiology·Zhongge ZhangMilton H Saier
Nov 9, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Daniel JostRalf Everaers
Feb 29, 2020·The Journal of Biological Chemistry·Frederic Chedin, Craig J Benham
Mar 10, 2019·Proceedings of the National Academy of Sciences of the United States of America·Robert StolzFrederic Chedin

❮ Previous
Next ❯

Methods Mentioned

BETA
environmental stresses
environmental stress

Software Mentioned

GenProtEC

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.