UniProt release 15.3

Rotavirus: a serial killer in UniProtKB/Swiss-Prot

Rotaviruses can infect humans, as well as other vertebrates. They cause severe diarrheal disease and dehydration of infants in both developed and developing countries. An estimated 0.6-0.8 million children aged 5 and under die from rotavirus-induced severe dehydrating diarrhea each year. Although mortality due to rotavirus infection is much higher in developing than in developed countries, infection frequency is remarkably similar. In temperate climates, rotavirus disease is seasonal, peaking in winter. Rotavirus gastroenteritis is transmitted by the fecal-oral route and characterized by watery stools, vomiting and fever. Commercially available vaccines are effective in preventing infection.

The virus infects the mature enterocytes of the small intestine and induces structural changes in the intestinal epithelium, secretion of a viral enterotoxin by infected cells, impaired absorption, cellular and tight junction damage and stimulation of intestinal motility, leading to watery diarrhea.

Rotaviruses have a segmented double-stranded RNA genome (dsRNA) protected by a three- layered capsid resistant to the acidic pH of the stomach. The genome is composed of 11 segments coding for about 12 proteins. One of its features is that its dsRNA genome is never completely uncoated during replication. Only the outermost layer is lost following entry into the host cell. Replication of the viral genome thus occurs within a protective shell to avoid detection and degradation by the host cell.

Seven different species of rotavirus have been described: A, B, C, D, E, F and G. Humans are primarily infected by species A, but also by species B and C. All seven species cause disease in other vertebrates. As of this release, sequences representative of all currently known rotavirus A, B, and C species have been annotated in UniProtKB/Swiss-Prot. This represents 480 entries, from 100 distinct strains, 40 of which are of human origin.

In addition to manually annotated sequences and functional information, we paid special attention to viral taxonomy. We decided to follow the recent recommendations for genome-based classification, in addition to the older antigenic classification system. This allows us to better reflect the frequent rearrangements (segment exchanges) that occur between strains. As a result, a detailed taxonomy is provided for each DNA segment/protein (see for instance Q3ZK61).

For more detailed information on rotaviruses, see the ViralZone portal.

UniProtKB News

Cross-references to PMAP-CutDB

Cross-references have been added to the CutDB - Proteolytic event database. PMAP-CutDB is one of the first systematic efforts to build an easily accessible collection of documented proteolytic events for natural proteins in vivo or in vitro. A CutDB entry is defined by a unique combination of these three attributes: protease, protein substrate and cleavage site.

PMAP-CutDB is available at http://www.proteolysis.org/.

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

P02760:
DR   PMAP-CutDB; P02760; -.

Q02383:
DR   PMAP-CutDB; Q02383; -.

Removal of the ec2dtosp.txt document file.

The document ec2dtosp.txt, which listed the Escherichia coli Gene- protein database (ECO2DBASE) entries cross-referenced in UniProtKB/Swiss-Prot, has been removed.

Changes concerning keywords

New keyword:

• Diamond-Blackfan anemia