Computer analysis of regulatory signals in bacterial genomes. Fnr binding sites

被引：4

作者：

Gerasimova, AV ^{[1
]}

Rodionov, DA ^{[1
]}

Mironov, AA ^{[1
]}

Gelfand, AS ^{[1
]}

机构：

[1] State Res Ctr Biotechnol GosNIIGenet, Moscow 113545, Russia

来源：

MOLECULAR BIOLOGY | 2001年 / 35卷 / 06期

基金：

俄罗斯基础研究基金会;

关键词：

Fnr; computer analysis; aerobic/anaerobic regulation; Escherichia coli;

D O I：

10.1023/A:1013286202014

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Comparative approach to computer analysis of regulatory signals allows one to predict new signals in bacterial genomes with high accuracy. A prediction is reliable whenever candidate signals are consistently observed in several related genomes. We applied comparative approach to the analysis of the Fnr regulon of gamma-proteobacteria. Responding to changes in the aerobic/anaerobic state of the medium, the transcriptional factor Fnr regulates expression of many genes. We predicted Fnr binding sites in 12 genes regulated by Fnr, and identified 17 new operons as potential members of the Fnr regulon of Escherichia coli. In addition, we described the Fnr regulon of other gamma-proteobacteria.

引用

页码：853 / 861

页数：9

共 50 条

[31] DNA Motifs and Transcription Factor Binding Sites Analysis of Regulatory Regions of MicroRNAs Relating to Psoriasis Disease
Wang, Lina
Jing, Yuxiao
Du, Jianqiang
Wu, Xiaoming
Guo, Jiaqi
Zheng, Yan
PROCEEDINGS OF THE 2015 INTERNATIONAL CONFERENCE ON COMPUTER SCIENCE AND ENGINEERING TECHNOLOGY (CSET2015), MEDICAL SCIENCE AND BIOLOGICAL ENGINEERING (MSBE2015), 2016, : 322 - 325
[32] Network analysis of adhesion/growth-regulatory galectins and their binding sites in adult chicken retina and choroid
Manning, Joachim C.
Caballero, Gabriel Garcia
Knospe, Clemens
Kaltner, Herbert
Gabius, Hans-Joachim
JOURNAL OF ANATOMY, 2017, 231 (01) : 23 - 37
[33] Characterization of binding sites of metal ions at bacterial cell surface by REE distribution patterns and EXAFS analysis
Takhashi, Y.
Yamamoto, M.
Ozaki, T.
Fortin, D.
GEOCHIMICA ET COSMOCHIMICA ACTA, 2008, 72 (12) : A926 - A926
[34] Computer-based analysis of completely sequenced bacterial genomes reveals a link between nucleotide bias and amino acid composition
Singer, GAC
Hickey, DA
HIGH PERFORMANCE COMPUTING SYSTEMS AND APPLICATIONS, 2000, 541 : 171 - 180
[35] Analysis of secretion signals and type III chaperone binding sites of two Pseudomonas syringae type III effectors
Ge, Z.
Guo, M.
Alfano, J.
PHYTOPATHOLOGY, 2005, 95 (06) : S34 - S34
[36] Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites
Hemberg, Martin
Gray, Jesse M.
Cloonan, Nicole
Kuersten, Scott
Grimmond, Sean
Greenberg, Michael E.
Kreiman, Gabriel
NUCLEIC ACIDS RESEARCH, 2012, 40 (16) : 7858 - 7869
[37] Functional analysis of repressor binding sites in the iab-2 regulatory region of the abdominal-A homeotic gene
Shimell, MJ
Peterson, AJ
Burr, J
Simon, JA
O'Connor, MB
DEVELOPMENTAL BIOLOGY, 2000, 218 (01) : 38 - 52
[38] Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data
Chung, Dongjun
Kuan, Pei Fen
Li, Bo
Sanalkumar, Rajendran
Liang, Kun
Bresnick, Emery H.
Dewey, Colin
Keles, Suenduez
PLOS COMPUTATIONAL BIOLOGY, 2011, 7 (07)
[39] Evolutionary analysis of endogenous intronic retroviruses in primates reveals an enrichment in transcription binding sites associated with key regulatory processes
Calero-Layana, Melissa
Lopez-Cruz, Carmen
Ocana, Agustin
Tejera, Eduardo
Armijos-Jaramillo, Vinicio
PEERJ, 2022, 10
[40] DNA-BINDING SITE-SPECIFICITY OF THE NEUROSPORA GLOBAL NITROGEN REGULATORY PROTEIN NIT2 - ANALYSIS WITH MUTATED BINDING-SITES
CHIANG, TY
RAI, R
COOPER, TG
MARZLUF, GA
MOLECULAR & GENERAL GENETICS, 1994, 245 (04): : 512 - 516

← 1 2 3 4 5 →