title: Transcriptome and proteome analyses of adaptive responses to methyl methanesulfonate in Escherichia coli K-12 and ada mutant strains.
abstract: BACKGROUND
  The Ada-dependent adaptive response system in Escherichia coli is important for increasing resistance to alkylation damage. However, the global transcriptional and translational changes during this response have not been reported. Here we present time-dependent global gene and protein expression profiles following treatment with methyl methanesulfonate (MMS) in E. coli W3110 and its ada mutant strains.
  
  
  RESULTS
  Transcriptome profiling showed that 1138 and 2177 genes were differentially expressed in response to MMS treatment in the wild-type and mutant strains, respectively. A total of 81 protein spots representing 76 nonredundant proteins differentially expressed were identified using 2-DE and LC-MS/MS. In the wild-type strain, many genes were differentially expressed upon long-exposure to MMS, due to both adaptive responses and stationary phase responses. In the ada mutant strain, the genes involved in DNA replication, recombination, modification and repair were up-regulated 0.5 h after MMS treatment, indicating its connection to the SOS and other DNA repair systems. Interestingly, expression of the genes involved in flagellar biosynthesis, chemotaxis, and two-component regulatory systems related to drug or antibiotic resistance, was found to be controlled by Ada.
  
  
  CONCLUSIONS
  These results show in detail the regulatory components and pathways controlling adaptive response and how the related genes including the Ada regulon are expressed with this response.
authors.affiliation: Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical & Biomolecular Engineering (BK21 Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology and Institute for the BioCentury, KAIST, Daejeon, Republic of Korea. swcry@kaist.ac.kr
authors.forename: Jong Hwan
authors.initials: JH
authors.lastname: Baek
authors.forename: Mee-Jung
authors.initials: MJ
authors.lastname: Han
authors.forename: Sang Yup
authors.initials: SY
authors.lastname: Lee
authors.forename: Jong-Shin
authors.initials: JS
authors.lastname: Yoo
mesh_terms: D004260:DNA Repair; D004269:DNA, Bacterial / Q000235:genetics; D015180:Electrophoresis, Gel, Two-Dimensional; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D008741:Methyl Methanesulfonate / Q000494:pharmacology*; D020411:Oligonucleotide Array Sequence Analysis; D020543:Proteome / Q000378:metabolism*; D018085:Regulon; D053719:Tandem Mass Spectrometry
chemical_list: D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D020543:Proteome; D008741:Methyl Methanesulfonate