Escherichia coli K-12: a cooperatively developed annotation snapshot—2005

By M. Riley, Takashi Abe, Martha B. Arnaud, M. Berlyn, Frederick R. Blattner, R. Chaudhuri, J. Glasner, T. Horiuchi, I. Keseler, T. Kosuge and 9 more. Nucleic Acids Research, 2006

631 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/fb73922c5322701b4be5a82adbc5e67504b6970c

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

Citations in the corpus

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection (2006, methodology): “Our ORF deletions include 3912 genes annotated in both E. coli K-12 MG1655 and W3110 and 73 previously annotated genes (Supplementary Table 4).”
Genome Majority Vote Improves Gene Predictions (2011, positive): “coli map, which has benefited from a rigorous community annotation effort [11]; 2) Genbank gene maps have as much as twice as many inconsistencies as Prodigal gene maps; and 3) we have directly measured the impact of GMV on the accuracy of Prodigal gene maps.”
Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths (2009, methodology): “coli K-12 MG1655 orthologous gene annotations [96] if any, or to similarity results obtained using the MicroScope analysis pipeline described in [95].”
Hfq Modulates the σE-Mediated Envelope Stress Response and the σ32-Mediated Cytoplasmic Stress Response in Escherichia coli (2006, background): “g Expected number of gene products in each category based on the total number of gene products for the entire genome (38).”
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information (2007, methodology): “The E. coli genome annotation (Riley et al, 2006) was used as a citation source for biochemical characterization studies and a framework upon which translated metabolic proteins, and subsequently reactions, were assigned to form gene to protein to reaction (GPR) assignments.”
Escherichia coli Physiology in Luria-Bertani Broth (2007, neutral): “which has been sequenced and annotated (2, 10), was chosen”
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads (2016, methodology): “3) generated using Sanger-based capillary sequencing at the University of Wisconsin in 1997[31].”
EcoCyc: fusing model organism databases with systems biology (2012, background): “coli strain K-12 MG1655 was chosen for genome sequencing because it had undergone comparatively minimal genetic manipulation since its isolation; the completed sequence was published in 1997 (27) and updated in 2006 (28,29).”
Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction (2013, neutral): “…functions of 1541 unique proteincoding open reading frames (ORFs) and 109 RNA genes; it thus accounts for B35% of the 4420 protein-coding ORFs, B65% of the functionally well-annotated ORFs (Riley et al, 2006), and 53.7% of the non-coding RNA genes identified in E. coli K-12 (Keseler et al, 2013).”
Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures (2017, background): “We note that the Eco and Mtb genomes have very different GC contents [ Eco , 50.8% GC 32 ; Mtb , 65.6% (ref.”
A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011 (2011, background): “coli K-12 MG1655 genes, many of which are predicted to have metabolic functions”