Gene Ontology Newsletter

Issue No. 10

August 2008

Genes of the Quarter: Excision-Repair Proteins

Graph showing excision-repair annotations

Part of the annotation graph for ERCC4, showing the distribution of annotations by species

In order to maintain the integrity of DNA, various repair mechanisms exist in cells to repair damage caused by endogenous and exogenous factors. One such mechanism is nucleotide excision repair (NER). This versatile repair mechanism senses and responds to lesions and distortions in DNA, such as UV-induced dimers and bulky chemical adducts. When this mechanism fails, genetic disorders develop; in humans, these include xeroderma pigmentosum and Cockayne syndrome, both characterized by photosensitivity and neurological dysfunction.

A conserved set of seven NER proteins has been annotated in nine species (H. sapiens, M. musculus, R. norvegicus, C. elegans, S. pombe, D. discoideum, D. melanogaster, and S. cerevisiae). All proteins in the set are associated with the biological process term nucleotide-excision repair or one of its child terms. Each protein has a specific activity within the repair process, and this is reflected in the GO molecular function annotations: ERCC3 and ERCC2 are helicases that open the denaturation bubble of the DNA lesion, and are annotated to 3'-5' DNA helicase activity and 5'-3' DNA helicase activity respectively; ERCC5 and the heterodimer ERCC4/ERCC1 cut the damaged strand around the lesion, and are both annotated to endodeoxyribonuclease activity. Cellular component annotations are to nucleotide-excision repair complex or holo TFIIH complex, a general transcription factor complex involved in DNA repair. These annotations are very similar across the nine species curated, which suggests a highly conserved mechanism of DNA repair that may have arisen early in evolution.

Annotations and the full version of the ERCC4 graphic, as well as those for other genes, can be accessed on the GO website; see the Reference Genome graphs, or download GO annotations.

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Resource List: ID Mapping

Translating between different gene and protein identifiers can be a problem when looking at annotations from different databases. There are a number of web-based resources available to help.

Draghici et al. compare the performance of some of these tools in a 2006 paper, which is available as a PDF.

Mappings files between UniProtKB and RefSeq accessions for equivalent proteins are available from the NCBI FTP site.

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Announcements

Dual Taxon Annotations Now in the GO Association Files

For several years, GO has had the ability to capture the taxon IDs of both the organism encoding the annotated gene product, and another organism with which the gene product interacts. This is needed to fully annotate gene products involved in symbiotic (including pathogenic) interactions. Gene association files containing dual taxon information are now available in the repository; see the annotation files for P. syringae, M. grisea and Oomycetes. For more information on dual taxon annotations, please go to the GO annotation documentation.

Process-Function Relationships

The introduction of relationships between the biological process and molecular function ontologies has been delayed until 9 February 2009. More information can be found on the GO wiki.

JCVI Eukaryotic Genome Annotation and Analysis Course

The JCVI Eukaryotic Genome Annotation and Analysis Course will be offered October 1–3, 2008 at the JCVI Rockville, Maryland, USA campus. The course is suitable for postdocs, academics and industry scientists planning to annotate new genomic sequences, as well as anyone interested in understanding how annotations in public databases are derived. More information can be found on the course website. There is also a complementary class on prokaryote annotation.

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Upcoming Events

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Please contact the Gene Ontology Consortium with any comments or suggestions. Frequently asked questions will appear as tutorials or tips in upcoming newsletters.

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