E. coli K-12 sequence and annotations

Update released June 10, 2004: The Escherichia coli K-12 strain MG1655 sequence and annotations have been updated; see this announcement for further information. In addition, an Excel spreadsheet is available which summarizes the MG1655 update in terms of nucleotide sequence corrections and the consequent protein sequence changes.

Contribute to annotation updates!

A wealth of new information has become available recently for the annotation of Escherichia coli K-12 strain MG1655. Annotation of the genome is an ongoing task that benefits from the work of all end-users of the sequence. To this end, we have adopted the ASAP relational database as the venue for maintaining and updating the annotations, as well as enabling community input towards that goal. Please note that while you are invited to become a registered annotator and contribute to the information within ASAP, there is no requirement to register in order to view the current MG1655 annotations -- simply log on as a guest. Furthermore, the "Add a note for the curator" function allows even guest users to suggest additional annotation updates and corrections. Finally, we are working with other groups to correlate and reconcile the various lists and databases containing E. coli genomic information (see, for example, the sites listed at the E. coli Database Portal).

Some annotations have already been updated within ASAP, including a number of revised gene boundaries, gene names and known or predicted gene products. In addition, several new genes have been added to the annotations, and perhaps inevitably, several previously annotated genes have been deaccessioned. Some of these changes have been previously reported as personal communications (see Serres, et al. 2001). While you are directed to ASAP for the current annotations, we will provide summary information on this page from time to time; updated December 8, 2003.

   The following genes have been added to the annotations (also see RNA genes, below):

   These previously annotated genes have been deaccessioned:

RNA genes, including small regulatory RNAs

Although over 85% of the genome consists of protein-encoding genes, other genes encode RNAs that function without being translated into proteins. These "RNA genes" are often referred to as noncoding or non-coding RNAs (ncRNA); other designations include small RNA (sRNA), non-messenger RNA (nmRNA), small non-messenger RNA (snmRNA), functional RNA (fRNA), and the generic miscellaneous RNA (misc_RNA) used in GenBank. The best-known RNA genes encode transfer RNAs (tRNA) and ribosomal RNAs (rRNA), but since the late 1990s many new noncoding RNAs have been found to play significant roles in the cell.

New annotations of RNA genes

In addition to 22 rRNAs and 86 tRNAs, a handful of misc_RNAs were already annotated in our GenBank entry. In consultation with Susan Gottesman, Gisela Storz, and Karen Wassarman, we have begun an effort to add a number of other RNA genes to the annotations – initially in ASAP and eventually in GenBank as well. The following table lists these RNA genes, including their assigned b-numbers; it includes those previously annotated; updated October 30, 2003.

A note on nomenclature: b-numbers, y-names, and all that

Beginning with our publication of the complete genome sequence (Blattner, et al. 1997) we have assigned each gene (protein- or RNA-encoding) a unique numeric identifier beginning with a "b" -- the so-called b-numbers or Blattner numbers. These designations remain constant through further updates, gene identifications, etc. It has come to our attention that others have assigned b-numbers without consulting us; for example, yaeP (b4406) has been designated B0189.1 in Swiss-Prot, and b4502 in the RefSeq version of the genome sequence. In general, we will not track those designations, just as we do not invent our own GenBank accession numbers, etc.

The provisional y-names for uncharacterized ORFs are based on a systematic nomenclature described by Kenn Rudd (Rudd 1998). Briefly, the first three letters of a "y" name are based on the map position of an ORF at the time the name was assigned, in a manner analogous to the "z" naming system for transposon insertions. As with b-numbers, the y-names are not reused if an ORF is given a new gene name or if an ORF becomes defunct. According to the original scheme, once a function was established for an E. coli gene the provisional y-name would be abandoned and a new gene name chosen. Since the y-names are used in the literature, ASAP retains them as synonyms when a gene is renamed.

The standard genetic nomenclature for E. coli is that of Demerec et al. 1966, as subsequently amended through use, and as described in Instructions to Authors for the Journal of Bacteriology. In order to avoid chaos, we tend to defer to the E. coli Genetic Stock Center (CGSC) database at Yale University as the final authority on gene names.

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