Revisiting the y-ome of Escherichia coli

• Published in: Nucleic acids research 2024-11, Vol.52 (20), p.12201-12207
• Main Authors: Moore, Lisa R, Caspi, Ron, Boyd, Dana, Berkmen, Mehmet, Mackie, Amanda, Paley, Suzanne, Karp, Peter D
• Format: Article
• Language: English
• Subjects: Data Resources and Analyses; Databases, Genetic; Escherichia coli - genetics; Escherichia coli K12 - genetics; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Genes, Bacterial; Genome, Bacterial; Molecular Sequence Annotation
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkae857

The model organism Escherichia coli K-12 has one of the most extensively annotated genomes in terms of functional characterization, yet a significant number of genes, ∼35%, are still considered poorly characterized. Initially genes without known functional understanding were given 'y' gene names. However, due to inconsistency in changing 'y' names to non-'y' names over the years, gene name alone does not provide sufficient information as to the characterization level of genes. Attempts to characterize y-ome genes, i.e. those that lack experimental evidence for function, are ongoing, and recent categorization based on the level of experimental evidence has helped clarify those genes that are well characterized versus uncharacterized. EcoCyc, the most comprehensive, curated genome database for E. coli K-12 substr. MG1655, has updated this approach by expanding the categories to include Partially characterized genes using a set of computational rules that includes keywords, experimental evidence codes and Gene Ontology terms. Approximately half of the previously categorized y-ome genes are now categorized as Partially characterized, leaving 15.5% (738) as Uncharacterized genes in EcoCyc. This new categorization scheme is searchable in the EcoCyc database, will be updated as new experimental evidence is curated and provides important information for research decisions.