|Publications on this gene:|
Nucleic Acids Res 2006 ; 1(34):1-9.
Escherichia coli K-12: a cooperatively developed annotation snapshot--2005.
Riley M ,Abe T ,Arnaud MB ,Berlyn MK ,Blattner FR ,Chaudhuri RR ,Glasner JD ,Horiuchi T ,Keseler IM ,Kosuge T ,Mori H ,Perna NT ,Plunkett G 3rd,Rudd KE ,Serres MH ,Thomas GH ,Thomson NR ,Wishart D ,Wanner BL ,
Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA. firstname.lastname@example.org
The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an organism entails identification of genes, the boundaries of genes in terms of precise start and end sites, and description of the gene products. Known and predicted functions were assigned to each gene product on the basis of experimental evidence or sequence analysis. Since both kinds of evidence are constantly expanding, no annotation is complete at any moment in time. This is a snapshot analysis based on the most recent genome sequences of two E.coli K-12 bacteria. An accurate and up-to-date description of E.coli K-12 genes is of particular importance to the scientific community because experimentally determined properties of its gene products provide fundamental information for annotation of innumerable genes of other organisms. Availability of the complete genome sequence of two K-12 strains allows comparison of their genotypes and mutant status of alleles.
Publication Type: Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.;
Science 2005 May 27; 5726(308):1321-3.
Global topology analysis of the Escherichia coli inner membrane proteome.
Daley DO ,Rapp M ,Granseth E ,Melén K ,Drew D ,von Heijne G ,
Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
The protein complement of cellular membranes is notoriously resistant to standard proteomic analysis and structural studies. As a result, membrane proteomes remain ill-defined. Here, we report a global topology analysis of the Escherichia coli inner membrane proteome. Using C-terminal tagging with the alkaline phosphatase and green fluorescent protein, we established the periplasmic or cytoplasmic locations of the C termini for 601 inner membrane proteins. By constraining a topology prediction algorithm with this data, we derived high-quality topology models for the 601 proteins, providing a firm foundation for future functional studies of this and other membrane proteomes. We also estimated the overexpression potential for 397 green fluorescent protein fusions; the results suggest that a large fraction of all inner membrane proteins can be produced in sufficient quantities for biochemical and structural work.
Publication Type: Research Support, Non-U.S. Gov't;
Appl Environ Microbiol 2005 Jan ; 1(71):451-9.
Phenotypic screening of Escherichia coli K-12 Tn5 insertion libraries, using whole-genome oligonucleotide microarrays.
Winterberg KM ,Luecke J ,Bruegl AS ,Reznikoff WS ,
Department of Biochemistry, University of Wisconsin--Madison, 433 Babcock Dr., Madison, WI 53706-1544, USA.
Complete genome sequences in combination with global screening methods allow parallel analysis of multiple mutant loci to determine the requirement for specific genes in different environments. In this paper we describe a high-definition microarray approach for investigating the growth effects of Tn5 insertions in Escherichia coli K-12. Libraries of insertion mutants generated by a unique Tn5 mutagenesis system were grown competitively in defined media. Biotin-labeled runoff RNA transcripts were generated in vitro from transposon insertions in each population of mutants. These transcripts were then hybridized to custom-designed oligonucleotide microarrays to detect the presence of each mutant in the population. By using this approach, the signal associated with 25 auxotrophic insertions in a 50-mutant pool was not detectable following nine generations of growth in glucose M9 minimal medium. It was found that individual insertion sites could be mapped to within 50 bp of their genomic locations, and 340 dispensable regions in the E. coli chromosome were identified. Tn5 insertions were detected in 15 genes for which no previous insertions have been reported. Other applications of this method are discussed.
Publication Type: Evaluation Studies; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, U.S. Gov't, P.H.S.;
J Bacteriol 2002 Nov ; 22(184):6225-34.
Escherichia coli gene expression responsive to levels of the response regulator EvgA.
Masuda N ,Church GM ,
Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
To investigate the function of the EvgA response regulator, we compared the genome-wide transcription profile of EvgA-overexpressing and EvgA-lacking Escherichia coli strains by oligonucleotide microarrays. The microarray measurements allowed the identification of at least 37 EvgA-activated genes, including acid resistance-related genes gadABC and hdeAB, efflux pump genes yhiUV and emrK, and 21 genes with unknown function. EvgA overexpression conferred acid resistance to exponentially growing cells. This acid resistance was abolished by deletion of ydeP, ydeO, or yhiE, which was induced by EvgA overexpression. These results suggest that ydeP, ydeO, and yhiE are novel genes related to acid resistance and that EvgA regulates several acid resistance genes. Furthermore, the deletion of yhiE completely abolished acid resistance in stationary-phase cells, suggesting that YhiE plays a critical role in stationary-phase acid resistance. The multidrug resistance in an acrB deletion mutant caused by EvgA overexpression was completely abolished by deletion of yhiUV, while the emrKY deletion had no effect on the increase in resistance by EvgA overexpression. In addition, EvgA overexpression did not confer resistance in a tolC-deficient strain. These results suggest that YhiUV induced by EvgA overexpression is functionally associated with TolC and contributes to multidrug resistance.
Publication Type: Comparative Study; Research Support, U.S. Gov't, Non-P.H.S.;