Characterization of the GATC regulatory network in E. coli

Riva, Alessandra; Delorme, Marie-Odile; Chevalier, Tony; Guilhot, Nicolas; Hénaut, Corinne; Hénaut, Alain
January 2004
BMC Genomics;2004, Vol. 5, p1
Academic Journal
Background: The tetranucleotide GATC is methylated in Escherichia. coli by the DNA methyltransferase (Dam) and is known to be implicated in numerous cellular processes. Mutants lacking Dam are characterized by a pleiotropic phenotype. The existence of a GATC regulated network, thought to be involved in cold and oxygen shift, had been proposed and its existence has recently been confirmed. The aim of this article is to describe the components of the GATC regulated network of E. coli in detail and propose a role of this network in the light of an evolutionary advantage for the organism. Results: We have classified the genes of the GATC network according to the EcoCyc functional classes. Comparisons with all of E. coli's genes and the genes involved in the SOS and stress response show that the GATC network forms a group apart. The functional classes that characterize the network are the Energy metabolism (in particular respiration), Fatty acid/Phospholipid metabolism and Nucleotide metabolism. Conclusions: The network is thought to come into play when the cell undergoes coldshock and is likely to enter stationary phase. The respiration is almost completely under GATC control and according to our hypothesis it will be blocked at the moment of coldshock; this might give the cell a selective advantage as it increases its chances for survival when entering stationary phase under coldshock. We predict the accumulation of formate and possibly succinate, which might increase the cell's resistance, in this case to antimicrobial agents, when entering stationary phase.


Related Articles

  • Global Transcriptional and Phenotypic Analyses of Escherichia coli O157:H7 Strain Xuzhou21 and Its pO157_Sal Cured Mutant Zhao, Hongqing; Chen, Chen; Xiong, Yanwen; Xu, Xuefang; Lan, Ruiting; Wang, Haiyin; Yao, Xinyue; Bai, Xiangning; Liu, Xuetong; Meng, Qiong; Zhang, Xiaoai; Sun, Hui; Zhao, Ailan; Bai, Xuemei; Cheng, Yuli; Chen, Qiang; Ye, Changyun; Xu, Jianguo // PLoS ONE;May2013, Vol. 8 Issue 5, p1 

    Escherichia coli O157:H7 is an important food-borne pathogen that can cause hemorrhagic colitis and hemolytic-uremic syndrome in humans. pO157_Sal, a novel conjugative plasmid is present in a Chinese O157:H7 outbreak strain Xuzhou21. Here we investigated the phenotypic and transcriptional...

  • Identification of Escherichia coli ygaQ and rpmG as novel mitomycin C resistance factors implicated in DNA repair. Bolt, Edward L.; Jenkins, Tabitha; Russo, Valeria Moreira; Ahmed, Sharlene; Cavey, James; Cass, Simon D. // Bioscience Reports;Feb2016, Vol. 36 Issue 1, p1 

    Using the ASKA (A Complete Set of Escherichia coli K-12 ORF Archive) library for genome-wide screening of E. coli proteins we identified that expression of ygaQ and rpmG promotes mitomycin C resistance (MMCR). YgaQ mediated MMCR was independent of homologous recombination involving RecA or...

  • Tuning the Expression Level of a Gene Located on a Bacterial Chromosome. Katashkina, J. L.; Skorokhodova, A. Yu.; Zimenkov, D. V.; Gulevich, A. Yu.; Minaeva, N. I.; Doroshenko, V. G.; Biryukova, I. V.; Mashko, S. V. // Molecular Biology;Sep2005, Vol. 39 Issue 5, p719 

    A new method of constructing a set of bacterial cell clones varying in the strength of a promoter upstream of the gene of interest was developed with the use of Escherichia coli MG1655 and lacZ as a reporter. The gist of it lies in constructing a set of DNA fragments with tac-like promoters by...

  • Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12. Anton, Brian P.; Mongodin, Emmanuel F.; Agrawal, Sonia; Fomenkov, Alexey; Byrd, Devon R.; Roberts, Richard J.; Raleigh, Elisabeth A. // PLoS ONE;May2015, Vol. 10 Issue 5, p1 

    We report the complete sequence of ER2796, a laboratory strain of Escherichia coli K-12 that is completely defective in DNA methylation. Because of its lack of any native methylation, it is extremely useful as a host into which heterologous DNA methyltransferase genes can be cloned and the...

  • The HU Regulon Is Composed of Genes Responding to Anaerobiosis, Acid Stress, High Osmolarity and SOS Induction. Oberto, Jacques; Nabti, Sabrina; Jooste, Valérie; Hervé Mignot; Rouviere-Yaniv, Josette // PLoS ONE;2009, Vol. 4 Issue 2, p1 

    Background: The Escherichia coli heterodimeric HU protein is a small DNA-bending protein associated with the bacterial nucleoid. It can introduce negative supercoils into closed circular DNA in the presence of topoisomerase I. Cells lacking HU grow very poorly and display many phenotypes....

  • Revisiting operons: an analysis of the landscape of transcriptional units in E. coli. Xizeng Mao; Qin Ma; Bingqiang Liu; Xin Chen; Hanyuan Zhang; Ying Xu // BMC Bioinformatics;11/4/2015, Vol. 16, p1 

    Background: Bacterial operons are considerably more complex than what were thought. At least their components are dynamically rather than statically defined as previously assumed. Here we present a computational study of the landscape of the transcriptional units (TUs) of E. coli K12, revealed...

  • The RpoS-Mediated Regulation of Isocitrate Dehydrogenase Gene Expression in Escherichia coli. II Lae Jung; Sung Keun Kim; In Gyu Kim // Current Microbiology;Jan2006, Vol. 52 Issue 1, p21 

    The Escherichia coli NADP+-dependent isocitrate dehydrogenase (IDH; EC, encoded by an icd gene, is a tricarboxylic acid (TCA) cycle enzyme responsible for the oxidative decarboxylation of isocitrate to α-ketoglutarate. In order to examine how the icd gene expression is regulated, an...

  • Life on track for a new genetic code. Jabr, Ferris // New Scientist;7/23/2011, Vol. 211 Issue 2822, p8 

    The article discusses an experiment by Farren Isaacs of Yale University in which the genome of Escherichia coli (E. coli) bacteria was changed by replacing the stop codon TAG with the codon TAA. Bacteria were zapped with electricity in order to introduce foreign DNA through their cell membranes,...

  • Knock-in/Knock-out (KIKO) vectors for rapid integration of large DNA sequences, including whole metabolic pathways, onto the Escherichia coli chromosome at well-characterised loci. Sabri, Suriana; Steen, Jennifer A.; Bongers, Mareike; Nielsen, Lars K.; Vickers, Claudia E. // Microbial Cell Factories;2013, Vol. 12 Issue 1, p1 

    Background: Metabolic engineering projects often require integration of multiple genes in order to control the desired phenotype. However, this often requires iterative rounds of engineering because many current insertion approaches are limited by the size of the DNA that can be transferred onto...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics