Update on the Keio collection of Escherichia coli single-gene deletion mutants

The Keio collection (Baba et al, 2006) has been established as a set of single‐gene deletion mutants of Escherichia coli K‐12. These mutants have a precisely designed deletion from the second codon from the seventh to the last codon of each predicted ORF. Further information is available at http://sal.cs.purdue.edu:8097/GB7/index.jsp or http://ecoli.naist.jp/. The distribution is now being handled by the National Institute of Genetics of Japan (http://www.shigen.nig.ac.jp/ecoli/pec/index.jsp). To date more than 4 million samples have been distributed worldwide. As we described earlier (Baba et al, 2006), gene amplification during construction is likely to have led to a small number of mutants with genetic duplications

GlgS, previously described as a glycogen synthesis control protein, negatively regulates motility and biofilm formation in Escherichia coli

Escherichia coli glycogen metabolism involves regulation of the glgBXCAP operon expression and allosteric control of GlgC-mediated catalysis of ATP and glucose-1-phosphate (G1P) to ADP-glucose linked to glycogen biosynthesis. E. coli glycogen metabolism is also affected by glgS. Though the precise function of the protein it encodes is unknown, its deficiency causes both reduced glycogen content and enhanced levels of the GlgC negative allosteric regulator AMP. Transcriptomic analyses carried out in this work revealed that, compared with their isogenic BW25113 wild type strain, glgS null (DglgS) mutants have increased expression of operons involved in the synthesis of type 1 fimbriae adhesins, flagella, and nucleotides. In concordance, ÄglgS cells were hyperflagellated and hyperfimbriated, and displayed elevated swarming motility; these phenotypes were all reverted by ectopic glgS expression. Also, DglgS cells accumulated high colanic acid content, and displayed increased ability to form biofilms on polysterene surfaces. F-driven conjugation based large-scale interaction studies of glgS with all the nonessential genes of E. coli showed that deletion of purine biosynthesis genes complement the glycogen-deficient, high motility and high biofilm content phenotypes of DglgS cells. Overall, these data indicate that glycogen deficiency in ÄglgS cells can be ascribed to high flagellar propulsion, and high exopolysaccharide and purine nucleotides biosynthetic activites competing with GlgC for the same ATP and G1P pools. Supporting this proposal, glycogen-less DglgC cells displayed an elevated swarming motility, and accumulated high levels of colanic acid and biofilm. Furthermore, glgC over-expression reverted the glycogen-deficient, high swarming motility, high colanic acid and high biofilm content phenotypes of DglgS cells. Because GlgS emerges now as a major determinant of E. coli surface composition, and because its effect on glycogen metabolism appears to be only indirect, we propose to rename it as ScoR for Surface Composition Regulator.Fil: Rahimpour, Mehdi. Consejo Superior de Investigaciones Cientificas. Instituto de Agrobiotecnología; EspañaFil: Montero, Manuel. Consejo Superior de Investigaciones Cientificas. Instituto de Agrobiotecnología; EspañaFil: Almagro, Goizeder. Consejo Superior de Investigaciones Cientificas. Instituto de Agrobiotecnología; EspañaFil: Viale, Alejandro Miguel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Instituto de Biología Molecular y Celular de Rosario; Argentina. Consejo Superior de Investigaciones Cientificas. Instituto de Agrobiotecnología; EspañaFil: Sevilla, Angel. Universidad de Murcia. Facultad de Química. Departamento de Bioquímica y Biología Molecular e Inmunología; EspañaFil: Cánovas, Manuel. Universidad de Murcia. Facultad de Química. Departamento de Bioquímica y Biología Molecular e Inmunología; EspañaFil: Muñoz, Francisco J.. Consejo Superior de Investigaciones Cientificas. Instituto de Agrobiotecnología; EspañaFil: Baroja Fernandez, Edurne. Consejo Superior de Investigaciones Cientificas. Instituto de Agrobiotecnología; EspañaFil: Bahaji, Abdellatif. Consejo Superior de Investigaciones Cientificas. Instituto de Agrobiotecnología; EspañaFil: Eydallin, Gustavo. Consejo Superior de Investigaciones Cientificas. Instituto de Agrobiotecnología; EspañaFil: Dose, Hitomi. Nara Institute of Science and Technology. Graduate School of Biological Sciences; JapónFil: Takeuchi, Rikiya. Nara Institute of Science and Technology. Graduate School of Biological Sciences; JapónFil: Mori, Hirotada. Nara Institute of Science and Technology. Graduate School of Biological Sciences; JapónFil: Pozueta Romero, Javier. Consejo Superior de Investigaciones Cientificas. Instituto de Agrobiotecnología; Españ

Extensive impact of non-antibiotic drugs on human gut bacteria

Supplementary data files for a study to quantify the impact of drugs on human gut commensals

GenoBase: comprehensive resource database of Escherichia coli K-12

Comprehensive experimental resources, such as ORFeome clone libraries and deletion mutant collections, are fundamental tools for elucidation of gene function. Data sets by omics analysis using these resources provide key information for functional analysis, modeling and simulation both in individual and systematic approaches. With the long-term goal of complete understanding of a cell, we have over the past decade created a variety of clone and mutant sets for functional genomics studies of Escherichia coli K-12. We have made these experimental resources freely available to the academic community worldwide. Accordingly, these resources have now been used in numerous investigations of a multitude of cell processes. Quality control is extremely important for evaluating results generated by these resources. Because the annotation has been changed since 2005, which we originally used for the construction, we have updated these genomic resources accordingly. Here, we describe GenoBase (http://ecoli.naist.jp/GB/), which contains key information about comprehensive experimental resources of E. coli K-12, their quality control and several omics data sets generated using these resources