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.

[1]  Michael K. Gilson,et al.  ASAP, a systematic annotation package for community analysis of genomes , 2003, Nucleic Acids Res..

[2]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[3]  B. Bochner.  Innovations: New technologies to assess genotype–phenotype relationships , 2003, Nature Reviews Genetics.

[4]  J. Roth,et al.  Spontaneous tandem genetic duplications in Salmonella typhimurium arise by unequal recombination between rRNA (rrn) cistrons. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[5]  K. Isono,et al.  Construction of a contiguous 874-kb sequence of the Escherichia coli -K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features. , 1997, DNA research : an international journal for rapid publication of reports on genes and genomes.

[6]  Yukako Tohsato,et al.  Phenotype profiling of single gene deletion mutants of E. coli using Biolog technology. , 2008, Genome informatics. International Conference on Genome Informatics.

[7]  B. Wanner,et al.  Phenotype MicroArray Analysis of Escherichia coli K-12 Mutants with Deletions of All Two-Component Systems , 2003, Journal of bacteriology.

[8]  T. Hübschmann,et al.  Advanced tool for characterization of microbial cultures by combining cytomics and proteomics , 2010, Applied Microbiology and Biotechnology.

[9]  K. Isono,et al.  The physical map of the whole E. coli chromosome: Application of a new strategy for rapid analysis and sorting of a large genomic library , 1987, Cell.

[10]  J R Roth,et al.  Tandem duplications of the histidine operon observed following generalized transduction in Salmonella typhimurium. , 1976, Journal of molecular biology.

[11]  R..  Tandem Genetic Duplications in Salmonella typhimurium : Amplification of the Histidine Operon , 2003 .

[12]  J R Roth,et al.  Tandem chromosomal duplications in Salmonella typhimurium: fusion of histidine genes to novel promoters. , 1978, Journal of molecular biology.

[13]  K. Isono,et al.  A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map. , 1996, DNA research : an international journal for rapid publication of reports on genes and genomes.

[14]  H. Mori,et al.  Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-4.1 min (110,917-193,643 bp) region. , 1994, Nucleic acids research.

[15]  Yukako Tohsato,et al.  Environmental dependency of gene knockouts on phenotype microarray analysis in Escherichia coli. , 2010, Journal of bioinformatics and computational biology.

[16]  Masaru Tomita,et al.  Update on the Keio collection of Escherichia coli single-gene deletion mutants , 2009, Molecular systems biology.

[17]  Takeyuki Tamura,et al.  Colony-live — a high-throughput method for measuring microbial colony growth kinetics— reveals diverse growth effects of gene knockouts in Escherichia coli , 2014, BMC Microbiology.

[18]  K. Isono,et al.  A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map. , 1996, DNA research : an international journal for rapid publication of reports on genes and genomes.

[19]  Peter Uetz,et al.  The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology , 2010, BMC Genomics.

[20]  H. Mori,et al.  Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection , 2006, Molecular systems biology.

[21]  Kay Nieselt,et al.  Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli , 2014, Journal of bacteriology.

[22]  Andrew Emili,et al.  eSGA: E. coli Synthetic Genetic Array analysis , 2008 .

[23]  Monica Riley,et al.  Escherichia coli K-12: a cooperatively developed annotation snapshot—2005 , 2006, Nucleic acids research.

[24]  P Berg,et al.  Transduction of Merodiploidy: Induced Duplication of Recipient Genes , 1969, Journal of bacteriology.

[25]  Jindan Zhou,et al.  EcoGene 3.0 , 2012, Nucleic Acids Res..

[26]  Koji Hayashi,et al.  Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110 , 2006, Molecular systems biology.

[27]  Sean R. Collins,et al.  A tool-kit for high-throughput, quantitative analyses of genetic interactions in E. coli , 2008, Nature Methods.

[28]  Peter D. Karp,et al.  EcoCyc: fusing model organism databases with systems biology , 2012, Nucleic Acids Res..

[29]  L. Chao,et al.  The Coupon Collector and the Suppressor Mutation , 2005, Genetics.

[30]  S. Brenner,et al.  An Unstable Intermediate Carrying Information from Genes to Ribosomes for Protein Synthesis , 1961, Nature.

[31]  B. Bochner,et al.  Phenotype microarrays for high-throughput phenotypic testing and assay of gene function. , 2001, Genome research.

[32]  Barry L. Wanner,et al.  Unprecedented High-Resolution View of Bacterial Operon Architecture Revealed by RNA Sequencing , 2014, mBio.

[33]  N. W. Davis,et al.  The complete genome sequence of Escherichia coli K-12. , 1997, Science.

[34]  J R Roth,et al.  Tandem genetic duplications in phage and bacteria. , 1977, Annual review of microbiology.

[35]  P Berg,et al.  Instability of a missense suppressor resulting from a duplication of genetic material. , 1969, Journal of molecular biology.

[36]  Pierluigi Mauri,et al.  Dissecting Escherichia coli Outer Membrane Biogenesis Using Differential Proteomics , 2014, PloS one.

[37]  Ronald W. Davis,et al.  Functional profiling of the Saccharomyces cerevisiae genome , 2002, Nature.

[38]  Kenneth E. Rudd,et al.  Linkage Map of Escherichia coli K-12, Edition 10: The Physical Map , 1998, Microbiology and Molecular Biology Reviews.

[39]  P. Uetz,et al.  The binary protein-protein interaction landscape of Escherichia coli , 2014, Nature Biotechnology.

[40]  Peili Zhang,et al.  Using Chado to store genome annotation data. , 2006, Current protocols in bioinformatics.

[41]  S. Kanaya,et al.  Large-scale identification of protein-protein interaction of Escherichia coli K-12. , 2006, Genome research.

[42]  Anushya Muruganujan,et al.  PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools , 2013, Nucleic Acids Res..

[43]  Aaron E. Darling,et al.  ASAP: a resource for annotating, curating, comparing, and disseminating genomic data , 2005, Nucleic Acids Res..

[44]  H. Mori,et al.  Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. , 2006, DNA research : an international journal for rapid publication of reports on genes and genomes.

[45]  B. Wanner,et al.  One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[46]  Yukiko Yamazaki,et al.  Profiling of Escherichia coli Chromosome database. , 2008, Methods in molecular biology.

[47]  Chris Mungall,et al.  A Chado case study: an ontology-based modular schema for representing genome-associated biological information , 2007, ISMB/ECCB.

[48]  Nobuyuki Fujita,et al.  Systematic sequencing of the Escherichia coli genome: analysis of the 0- 2.4 min region , 1992, Nucleic Acids Res..

[49]  J R Roth,et al.  Gene duplication in bacteria: alteration of gene dosage by sister-chromosome exchanges. , 1979, Cold Spring Harbor symposia on quantitative biology.

[50]  H. Mori,et al.  Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism , 2009, Molecular systems biology.