Characterization of the GATC regulatory network in E. coli.
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.
Riva
Alessandra
A
Laboratoire Génome et Informatique, UMR 8116, CNRS, Université d'Evry Val d'Essonne, Tour Evry 2, 523 Place des Terrasses, 91034 Evry, France. gucki@genopole.cnrs.fr
Delorme
Marie-Odile
MO
Chevalier
Tony
T
Guilhot
Nicolas
N
Hénaut
Corinne
C
Hénaut
Alain
A
D005075:Biological Evolution; D003080:Cold Temperature; D004734:Energy Metabolism / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics / Q000502:physiology*; D029968:Escherichia coli Proteins / Q000502:physiology*; D005227:Fatty Acids / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D016685:Mitomycin / Q000494:pharmacology; D009711:Nucleotides / Q000378:metabolism; D010641:Phenotype; D010743:Phospholipids / Q000378:metabolism; D012475:Salmonella / Q000235:genetics; D012641:Selection, Genetic; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000502:physiology*; D013045:Species Specificity; D013386:Succinates / Q000378:metabolism
D029968:Escherichia coli Proteins; D005227:Fatty Acids; D009711:Nucleotides; D010743:Phospholipids; D013386:Succinates; D016685:Mitomycin; C058693:Dam methyltransferase; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific); C499294:dam protein, E coli