Functional determinants of transcription factors in Escherichia coli: protein families and binding sites

Trends in Genetics : TIG
M Madan Babu, Sarah A Teichmann

Abstract

DNA-binding transcription factors regulate the expression of genes near to where they bind. These factors can be activators or repressors of transcription, or both. Thus, a fundamental question is what determines whether a transcription factor acts as an activator or a repressor? Previous research into this question found that a protein's regulatory function is determined by one or more of the following factors: protein-protein contacts, position of the DNA-binding domain in the protein primary sequence, altered DNA structure, and the position of its binding site on the DNA relative to the transcription start site. Although there are many aspects specific to different transcription factors, in this work we demonstrate that, in general, in the prokaryote Escherichia coli, a transcription factor's protein family is not indicative of its regulatory function, but the position of its binding site on the DNA is.

References

Oct 26, 1990·Science·R B Lobell, R F Schleif
Feb 3, 1999·Bioinformatics·K KarplusR Hughey
Mar 6, 1999·Current Opinion in Microbiology·B Müller-Hill
Mar 6, 1999·Current Opinion in Microbiology·V A Rhodius, Stephen J W Busby
May 14, 1999·Current Opinion in Microbiology·X Dai, L B Rothman-Denes
Nov 11, 1999·Nucleic Acids Research·L Aravind, E V Koonin
Mar 29, 2000·Nucleic Acids Research·Ernesto Pérez-Rueda, Julio Collado-Vides
Jan 11, 2000·Nucleic Acids Research·Heladia SalgadoJulio Collado-Vides
Dec 26, 2001·Nucleic Acids Research·Alex BatemanErik L L Sonnhammer
Apr 23, 2002·Nature Genetics·Shai S Shen-OrrUri Alon

Citations

May 12, 2011·Archives of Microbiology·Shamlan M S Reshamwala, Santosh B Noronha
May 8, 2007·Applied Microbiology and Biotechnology·M VeselýM Pátek
Jun 19, 2008·Applied Microbiology and Biotechnology·Lei ChenWeihong Jiang
Feb 3, 2005·Nature Reviews. Microbiology·Ildefonso Cases, Víctor de Lorenzo
Feb 13, 2003·Nucleic Acids Research·M Madan Babu, Sarah A Teichmann
Jul 16, 2010·Nucleic Acids Research·Sarath Chandra Janga, Bruno Contreras-Moreira
Oct 24, 2006·Journal of Bacteriology·P Scott Hefty, Richard S Stephens
Nov 17, 2009·Journal of Bacteriology·Kevin P O'RourkeGrace A Spatafora
Sep 2, 2009·Microbiology and Molecular Biology Reviews : MMBR·Sacha A F T van HijumOscar P Kuipers
Jan 9, 2010·BMC Genomics·Jasmin SchröderAndreas Tauch
Dec 5, 2006·PLoS Computational Biology·Rutger HermsenPieter Rein ten Wolde
Mar 29, 2008·PLoS Computational Biology·Jason ErnstZiv Bar-Joseph
May 1, 2008·PloS One·Ali Kinkhabwala, Călin C Guet
Oct 27, 2015·Applied Microbiology and Biotechnology·Koichi Toyoda, Masayuki Inui
Nov 13, 2007·Research in Microbiology·Sarath Chandra Janga, Julio Collado-Vides
Jun 14, 2005·Molecular Microbiology·Sylvie ElsenEric Giraud
Nov 12, 2010·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Tae-Min Kim, Peter J Park
Jun 15, 2004·Current Opinion in Structural Biology·M Madan BabuSarah A Teichmann
Oct 23, 2015·BioMed Research International·Md Altaf-Ul-AminShigehiko Kanaya
Jan 13, 2015·Molecular Oral Microbiology·M VujanacD Ajdic
Dec 17, 2008·FEMS Microbiology Reviews·Enrique BallezaJulio Collado-Vides
Sep 25, 2016·Microbiology·David C Grainger
Sep 7, 2017·Proceedings of the National Academy of Sciences of the United States of America·Xin FangBernhard O Palsson
Oct 1, 2004·Molecular Carcinogenesis·Mark D GustavsonLynn M Matrisian
Sep 19, 2009·Molecular BioSystems·Ernesto Pérez-RuedaAgustino Martínez-Antonio
May 23, 2019·Journal of the Royal Society, Interface·Renana Sabi, Tamir Tuller
Jan 8, 2017·BMC Systems Biology·Patricia AquinoJames E Galagan
Oct 27, 2020·Nucleic Acids Research·Adam B Zaborowski, Dirk Walther
Nov 17, 2020·Frontiers in Microbiology·San-Chi Chang, Chia-Yin Lee

Related Concepts

DNA Helix Destabilizing Proteins
Alkalescens-Dispar Group
Protein Conformation
Repressor Molecules
Transcription Factor
Gene Activation
Trans-Activators
Gene Expression Regulation, Bacterial
Tertiary Protein Structure

Related Feeds

CZI Human Cell Atlas Seed Network

The aim of the Human Cell Atlas (HCA) is to build reference maps of all human cells in order to enhance our understanding of health and disease. The Seed Networks for the HCA project aims to bring together collaborators with different areas of expertise in order to facilitate the development of the HCA. Find the latest research from members of the HCA Seed Networks here.