Published online 5 January 2006
Survey and Summary |
Escherichia coli K-12: a cooperatively developed annotation snapshot—2005
Josephine Bay Paul Center, Marine Biological Laboratory Woods Hole, MA 02543, USA 1Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems Yata 1111, Mishima, Shizuoka 411-8540, Japan 2Department of Genetics, Candida Genome Database Stanford University School of Medicine Stanford, CA 94305-5120, USA 3Department of Molecular, Cellular and Developmental Biology, Yale University New Haven, CT 06520-8103, USA 4Genome Center of Wisconsin 425 Henry Mall University of Wisconsin Madison, WI 53706, USA 5Division of Immunity and Infection, University of Birmingham Edgbaston, Birmingham B15 2TT, UK 6National Institute for Basic Biology Nishigonaka 38, Myodaiji, Okazaki 444-8585 Aichi, Japan 7SRI International 333 Ravenswood Avenue, Menlo Park, CA 94025-3493, USA 8Graduate School of Biological Sciences, Nara Institute of Science and Technology Ikoma, Nara 630-0101, Japan 9The Institute of Advanced Biosciences, Keio University Tsuruoka, Yamagata 997-0017, Japan 10Department of Biochemistry and Molecular Biology, The University of Miami Miller School of Medicine Miami, FL 33140, USA 11Department of Biology, University of York PO Box 373, York YO10 5YW, UK 12The Wellcome Trust Sanger Institute Genome Campus, Hinxton, Cambridge CB10 1SA, UK 13Department of Computing Science and Biological Sciences, 2-21 Athabasca Hall University of Alberta Edmonton, Alberta, Canada T6G 2E8 14Department of Biological Sciences, Purdue University 915 W. State Street, West Lafayette, IN 47907-2054, USA
*To whom correspondence should be addressed. Tel: +1 508 269 7388; Fax: +1 508 457 4727; Email: mriley{at}mbl.edu
Received November 5, 2005. Revised December 5, 2005. Accepted December 5, 2005.
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.
Correspondence may also be addressed to Barry L. Wanner. Tel: +1 765 494 8034; Fax: +1 765 494 0876; Email: blwanner{at}purdue.edu
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  N. E. Lewis, B.-K. Cho, E. M. Knight, and B. O. Palsson Gene Expression Profiling and the Use of Genome-Scale In Silico Models of Escherichia coli for Analysis: Providing Context for Content J. Bacteriol., June 1, 2009; 191(11): 3437 - 3444. [Full Text] [PDF]
|
|
|
|
 |
|
 C. Simon, J. Herath, S. Rockstroh, and R. Daniel Rapid Identification of Genes Encoding DNA Polymerases by Function-Based Screening of Metagenomic Libraries Derived from Glacial Ice Appl. Envir. Microbiol., May 1, 2009; 75(9): 2964 - 2968. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Niwa, B.-W. Ying, K. Saito, W. Jin, S. Takada, T. Ueda, and H. Taguchi Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins PNAS, March 17, 2009; 106(11): 4201 - 4206. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Didelot, A. Darling, and D. Falush Inferring genomic flux in bacteria Genome Res., February 1, 2009; 19(2): 306 - 317. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. S. P. Horler, A. Butcher, N. Papangelopoulos, P. D. Ashton, and G. H. Thomas EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations Bioinformatics, January 15, 2009; 25(2): 163 - 166. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Rasko, M. J. Rosovitz, G. S. A. Myers, E. F. Mongodin, W. F. Fricke, P. Gajer, J. Crabtree, M. Sebaihia, N. R. Thomson, R. Chaudhuri, et al. The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates J. Bacteriol., October 15, 2008; 190(20): 6881 - 6893. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Mizoguchi, Y. Sawano, J.-i. Kato, and H. Mori Superpositioning of Deletions Promotes Growth of Escherichia coli with a Reduced Genome DNA Res, October 1, 2008; 15(5): 277 - 284. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Guisbert, T. Yura, V. A. Rhodius, and C. A. Gross Convergence of Molecular, Modeling, and Systems Approaches for an Understanding of the Escherichia coli Heat Shock Response Microbiol. Mol. Biol. Rev., September 1, 2008; 72(3): 545 - 554. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Umezawa, T. Shimada, A. Kori, K. Yamada, and A. Ishihama The Uncharacterized Transcription Factor YdhM Is the Regulator of the nemA Gene, Encoding N-Ethylmaleimide Reductase J. Bacteriol., September 1, 2008; 190(17): 5890 - 5897. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. C. Sleight, C. Orlic, D. Schneider, and R. E. Lenski Genetic Basis of Evolutionary Adaptation by Escherichia coli to Stressful Cycles of Freezing, Thawing and Growth Genetics, September 1, 2008; 180(1): 431 - 443. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Kazuta, J. Adachi, T. Matsuura, N. Ono, H. Mori, and T. Yomo Comprehensive Analysis of the Effects of Escherichia coli ORFs on Protein Translation Reaction Mol. Cell. Proteomics, August 1, 2008; 7(8): 1530 - 1540. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Menda, R. M. Buels, I. Tecle, and L. A. Mueller A Community-Based Annotation Framework for Linking Solanaceae Genomes with Phenomes Plant Physiology, August 1, 2008; 147(4): 1788 - 1799. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Montgomerie, J. A. Cruz, S. Shrivastava, D. Arndt, M. Berjanskii, and D. S. Wishart PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation Nucleic Acids Res., July 1, 2008; 36(suppl_2): W202 - W209. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. E. Martinez-Guerrero, R. Ciria, C. Abreu-Goodger, G. Moreno-Hagelsieb, and E. Merino GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways Nucleic Acids Res., July 1, 2008; 36(suppl_2): W176 - W180. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Kim and S. B. Levy Increased Fitness of Pseudomonas fluorescens Pf0-1 Leucine Auxotrophs in Soil Appl. Envir. Microbiol., June 15, 2008; 74(12): 3644 - 3651. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Durfee, R. Nelson, S. Baldwin, G. Plunkett III, V. Burland, B. Mau, J. F. Petrosino, X. Qin, D. M. Muzny, M. Ayele, et al. The Complete Genome Sequence of Escherichia coli DH10B: Insights into the Biology of a Laboratory Workhorse J. Bacteriol., April 1, 2008; 190(7): 2597 - 2606. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Krzeslak, G. Gerritse, R. van Merkerk, R. H. Cool, and W. J. Quax Lipase Expression in Pseudomonas alcaligenes Is Under the Control of a Two-Component Regulatory System Appl. Envir. Microbiol., March 1, 2008; 74(5): 1402 - 1411. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Berlanda Scorza, F. Doro, M. J. Rodriguez-Ortega, M. Stella, S. Liberatori, A. R. Taddei, L. Serino, D. Gomes Moriel, B. Nesta, M. R. Fontana, et al. Proteomics Characterization of Outer Membrane Vesicles from the Extraintestinal Pathogenic Escherichia coli {Delta}tolR IHE3034 Mutant Mol. Cell. Proteomics, March 1, 2008; 7(3): 473 - 485. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Severi, A. Muller, J. R. Potts, A. Leech, D. Williamson, K. S. Wilson, and G. H. Thomas Sialic Acid Mutarotation Is Catalyzed by the Escherichia coli {beta}-Propeller Protein YjhT J. Biol. Chem., February 22, 2008; 283(8): 4841 - 4849. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Durfee, A.-M. Hansen, H. Zhi, F. R. Blattner, and D. J. Jin Transcription Profiling of the Stringent Response in Escherichia coli J. Bacteriol., February 1, 2008; 190(3): 1084 - 1096. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Le Gac, M. D. Brazas, M. Bertrand, J. G. Tyerman, C. C. Spencer, R. E. W. Hancock, and M. Doebeli Metabolic Changes Associated With Adaptive Diversification in Escherichia coli Genetics, February 1, 2008; 178(2): 1049 - 1060. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Su, J. M. Peregrin-Alvarez, G. Butland, S. Phanse, V. Fong, A. Emili, and J. Parkinson Bacteriome.org an integrated protein interaction database for E. coli Nucleic Acids Res., January 11, 2008; 36(suppl_1): D632 - D636. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Noivirt-Brik, R. Unger, and A. Horovitz Low folding propensity and high translation efficiency distinguish in vivo substrates of GroEL from other Escherichia coli proteins Bioinformatics, December 15, 2007; 23(24): 3276 - 3279. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Yan, Z. Guan, and C. R. H. Raetz An Undecaprenyl Phosphate-Aminoarabinose Flippase Required for Polymyxin Resistance in Escherichia coli J. Biol. Chem., December 7, 2007; 282(49): 36077 - 36089. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. D. Karp, I. M. Keseler, A. Shearer, M. Latendresse, M. Krummenacker, S. M. Paley, I. Paulsen, J. Collado-Vides, S. Gama-Castro, M. Peralta-Gil, et al. Multidimensional annotation of the Escherichia coli K-12 genome Nucleic Acids Res., December 3, 2007; 35(22): 7577 - 7590. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. C. M. Fogg, S. M. Gossage, D. L. Smith, J. R. Saunders, A. J. McCarthy, and H. E. Allison Identification of multiple integration sites for Stx-phage {Phi}24B in the Escherichia coli genome, description of a novel integrase and evidence for a functional anti-repressor Microbiology, December 1, 2007; 153(12): 4098 - 4110. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Sezonov, D. Joseleau-Petit, and R. D'Ari Escherichia coli Physiology in Luria-Bertani Broth J. Bacteriol., December 1, 2007; 189(23): 8746 - 8749. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Eguchi, J. Itou, M. Yamane, R. Demizu, F. Yamato, A. Okada, H. Mori, A. Kato, and R. Utsumi B1500, a small membrane protein, connects the two-component systems EvgS/EvgA and PhoQ/PhoP in Escherichia coli PNAS, November 20, 2007; 104(47): 18712 - 18717. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Weiss The Deoxycytidine Pathway for Thymidylate Synthesis in Escherichia coli J. Bacteriol., November 1, 2007; 189(21): 7922 - 7926. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. D. King-Lyons, K. F. Smith, and T. D. Connell Expression of hurP, a Gene Encoding a Prospective Site 2 Protease, Is Essential for Heme-Dependent Induction of bhuR in Bordetella bronchiseptica J. Bacteriol., September 1, 2007; 189(17): 6266 - 6275. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. D. Magnuson Hypothetical Functions of Toxin-Antitoxin Systems J. Bacteriol., September 1, 2007; 189(17): 6089 - 6092. [Full Text] [PDF]
|
|
|
|
|
|
H. Ogasawara, Y. Ishida, K. Yamada, K. Yamamoto, and A. Ishihama PdhR (Pyruvate Dehydrogenase Complex Regulator) Controls the Respiratory Electron Transport System in Escherichia coli J. Bacteriol., August 1, 2007; 189(15): 5534 - 5541. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Ogasawara, A. Hasegawa, E. Kanda, T. Miki, K. Yamamoto, and A. Ishihama Genomic SELEX Search for Target Promoters under the Control of the PhoQP-RstBA Signal Relay Cascade J. Bacteriol., July 1, 2007; 189(13): 4791 - 4799. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Q. Feng, S. E. Hawes, J. E. Stern, A. Dem, P. S. Sow, B. Dembele, P. Toure, P. Sova, P. W. Laird, and N. B. Kiviat Promoter Hypermethylation of Tumor Suppressor Genes in Urine from Patients with Cervical Neoplasia Cancer Epidemiol. Biomarkers Prev., June 1, 2007; 16(6): 1178 - 1184. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-Y. Ou, X. He, E. M. Harrison, B. R. Kulasekara, A. B. Thani, A. Kadioglu, S. Lory, J. C. D. Hinton, M. R. Barer, Z. Deng, et al. MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands Nucleic Acids Res., May 30, 2007; (2007) gkm380v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Reig, C. del Rio, F. Casagrande, M. Ratera, J. L. Gelpi, D. Torrents, P. J. F. Henderson, H. Xie, S. A. Baldwin, A. Zorzano, et al. Functional and Structural Characterization of the First Prokaryotic Member of the L-Amino Acid Transporter (LAT) Family: A MODEL FOR APC TRANSPORTERS J. Biol. Chem., May 4, 2007; 282(18): 13270 - 13281. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Guisbert, V. A. Rhodius, N. Ahuja, E. Witkin, and C. A. Gross Hfq Modulates the {sigma}E-Mediated Envelope Stress Response and the {sigma}32-Mediated Cytoplasmic Stress Response in Escherichia coli J. Bacteriol., March 1, 2007; 189(5): 1963 - 1973. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Weiss YjjG, a dUMP Phosphatase, Is Critical for Thymine Utilization by Escherichia coli K-12 J. Bacteriol., March 1, 2007; 189(5): 2186 - 2189. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Sugawara, T. Abe, T. Gojobori, and Y. Tateno DDBJ working on evaluation and classification of bacterial genes in INSDC Nucleic Acids Res., January 12, 2007; 35(suppl_1): D13 - D15. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. R. Joyce, J. L. Reed, A. White, R. Edwards, A. Osterman, T. Baba, H. Mori, S. A. Lesely, B. O. Palsson, and S. Agarwalla Experimental and Computational Assessment of Conditionally Essential Genes in Escherichia coli J. Bacteriol., December 1, 2006; 188(23): 8259 - 8271. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. L. Reed, T. R. Patel, K. H. Chen, A. R. Joyce, M. K. Applebee, C. D. Herring, O. T. Bui, E. M. Knight, S. S. Fong, and B. O. Palsson Systems approach to refining genome annotation PNAS, November 14, 2006; 103(46): 17480 - 17484. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. G. Elsik, K. C. Worley, L. Zhang, N. V. Milshina, H. Jiang, J. T. Reese, K. L. Childs, A. Venkatraman, C. M. Dickens, G. M. Weinstock, et al. Community annotation: Procedures, protocols, and supporting tools Genome Res., November 1, 2006; 16(11): 1329 - 1333. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Schlicht, C. Berens, J. Daam, and W. Hillen Random Insertion of a TetR-Inducing Peptide Tag into Escherichia coli Proteins Allows Analysis of Protein Levels by Induction of Reporter Gene Expression Appl. Envir. Microbiol., August 1, 2006; 72(8): 5637 - 5642. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Gough Genomic scale sub-family assignment of protein domains Nucleic Acids Res., July 28, 2006; 34(13): 3625 - 3633. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Posfai, G. Plunkett III, T. Feher, D. Frisch, G. M. Keil, K. Umenhoffer, V. Kolisnychenko, B. Stahl, S. S. Sharma, M. de Arruda, et al. Emergent Properties of Reduced-Genome Escherichia coli Science, May 19, 2006; 312(5776): 1044 - 1046. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Arifuzzaman, M. Maeda, A. Itoh, K. Nishikata, C. Takita, R. Saito, T. Ara, K. Nakahigashi, H.-C. Huang, A. Hirai, et al. Large-scale identification of protein-protein interaction of Escherichia coli K-12 Genome Res., May 1, 2006; 16(5): 686 - 691. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Kosuge, T. Abe, T. Okido, N. Tanaka, M. Hirahata, Y. Maruyama, J. Mashima, A. Tomiki, M. Kurokawa, R. Himeno, et al. Exploration and Grading of Possible Genes from 183 Bacterial Strains by a Common Protocol to Identification of New Genes: Gene Trek in Prokaryote Space (GTPS) DNA Res, January 1, 2006; 13(6): 245 - 254. [Abstract] [Full Text] [PDF]
|
|