UniProt release 2011_01

Headline

An old-timer, but still trendy: 10’000 entries for Arabidopsis thaliana in UniProtKB/Swiss-Prot

Arabidopsis thaliana belongs to the Brassicaceae family that includes the well-known dietary staples cauliflower, broccoli, cabbage, turnip, radish, canola and mustard. The split between the Arabidopsis group and the other crops of the genus Brassica has been estimated at around 43 million years ago. A. thaliana has been widely studied since the 1980s, when the development of T-DNA mediated transformation made the generation of mutants and their study relatively easy. Since then, A. thaliana has been become the model of choice for the study of many biological processes of flowering plants, as well as those specific to the Brassica species.

Its utility as a model organism was further boosted by the completion of the whole genome sequence, which revealed a relatively small genome with a low level of duplication compared to other flowering plants, and by the inception of a number of complementary efforts to sequence the transcriptome.

In 2001, the Swiss-Prot group created the Plant Proteome Annotation Program (PPAP) whose main focus is the annotation of proteins and protein families of A. thaliana and rice. One decade on, we have now annotated over 10’000 A. thaliana entries in UniProtKB/Swiss-Prot. This corresponds to around 36% of the A. thaliana proteome according to version 10 Arabidopsis thaliana genome annotation from The Arabidopsis Information Resource (TAIR), which estimates at 27’416 the number of protein-coding genes in this organism. According to the Multinational Arabidopsis Steering Committee (MASC) report 2010, at least one third of these genes still have no known function, so the work of experimentally characterizing and of annotating each gene is far from finished.

All manually annotated A.thaliana entries can be retrieved from UniProtKB/Swiss-Prot using the organism name “Arabidopsis thaliana” (or the taxonomy identifier 3702), with the restriction: “reviewed:yes”.

UniProtKB news

Cross-references to Allergome

Cross-references have been added to Allergome, a platform for allergen knowledge.

Allergome is available at http://www.allergome.org/.

The format of the explicit link in the flat file is:

DR   Allergome; 2; Aca s 13.
DR   Allergome; 3051; Aca s 13.0101.

Changes to keywords

• Jasmonic acid signaling pathway

• Envelope protein -> Viral envelope protein

• Core protein
• Fiber protein
• Fusion protein
• Hexon protein
• Hexon-associated protein
• Phage recognition

Changes in the controlled vocabulary for PTMs

• N,N-dimethylleucine