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UniProt release 2014_01

Published January 22, 2014

Headline

Mouse attacks!

In the arid lands of Arizona lives a fierce predator whose howls pierce the desert night, terrifying its prey. This predator is… a mouse, Onychomys torridus, also called the grasshopper mouse. It may sound like a tale looming straight from the imagination of Tim Burton or Monthy Python, but this mouse really exists. It is carnivorous and it regularly howls just before a kill, although the emitted sound is more a sustained whistle than the actual howl of a wolf. Its prey is no less astonishing, including crickets, other rodents, tarantulas and bark scorpions (Centruroides sculpturatus).

Bark scorpions are not easy prey. They are venomous and inflict intensely painful, sometimes lethal stings. Surprisingly grasshopper mice do not seem to be seriously bothered by that, and it takes little time before the scorpion is captured, killed and eaten. How can O. torridus ignore the venom, while common house mice are sensitive to it? Overall, grasshopper mice do feel pain normally, but when they are injected with scorpion venom or with a physiological saline solution in their hind paws, they are much more irritated by the control saline solution than by the venom. In grasshopper mice, bark scorpion venom acts as an analgesic.

Venom from Buthidae scorpions initiates acute pain in sensitive mammals, such as house mice, rats and humans, by activating the voltage-gated sodium channel Nav1.7/SCN9A, but has no effect on the Nav1.8/SCN10A sodium channel. Recent experiments by Rowe et al. on freshly isolated O. torridus sensory neurons showed that, in this species, the venom strongly inhibits Nav1.8/SCN10A Na+ currents. These Na+ currents are necessary for action potential sustained firing and propagation. By inhibiting Nav1.8/SCN10A, the scorpion venom blocks pain transmission to the central nervous system, and hence induces analgesia. The diametrically opposed response of rodents towards scorpion venom seems to be due to only 2 residues within the Nav1.8/SCN10A sequence. In O. torridus, a glutamate residue is found at position 859 (E-859) and a glutamine residue at position 862 (Q-862), while in species known to be sensitive to the venom, these positions are reversed: Q-859 and E-862. Site-directed mutagenesis of these 2 residues in the O. torridus sequence (Q859E/E862Q) abolished venom sensitivity. Conversely, mutation of the glutamine position in Mus musculus (Q861E) conferred inhibition by C. sculpturatus venom.

Pain sensitivity is essential for survival, since it helps avoid damaging situations. Hence any change in pain perception has to be finely tuned in order not to be deleterious. O. torridus has evolved a brilliant strategy allowing it to exploit an abundant food resource in its environment, i.e. bark scorpions, while keeping intact its ability to feel the necessary pain.

Persistent pain can turn into a nightmare and improving our understanding of pain signaling may be a tremendous help in the discovery of new analgesic drugs. Nav1.7/SCN9A is already under close investigation as a potential target for pain prevention. The new and very exciting study by Rowe et al. shows that the Nav1.8/SCN10A channel also plays a crucial key role in the transmission of pain signals and may be an interesting target for analgesic development.

As of this release, the fully annotated O. torridus Nav1.8/SCN10A protein is available in UniProtKB/Swiss-Prot.

UniProtKB news

Removal of the cross-references to IPI

Cross-references to IPI have been removed.

IPI has closed in 2011. The last release is archived at ftp://ftp.ebi.ac.uk/pub/databases/IPI.

The Ensembl and Ensembl Genomes projects offer access to genomic data from vertebrate and non-vertebrate species respectively.

Complete proteome data is available from UniProtKB.

An archive of the last mapping table between UniProtKB and IPI is archived at ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/.

Documents and RSS feeds for UniProt Forthcoming changes and News

We have replaced the documents sp_soon.htm (“UniProt Knowledgebase – Forthcoming changes”) and xml_soon.htm (“UniProt Knowledgebase – Forthcoming changes in XML”) by a searchable section Forthcoming changes on our website to announce planned changes for all UniProt data sets and file formats in one place and to provide a common RSS feed. The same information can also be downloaded from our FTP site.

Changes that have been implemented are described in our “News archive”, which can be searched in the News section of our website, followed via an RSS feed and downloaded from the FTP site. These news include the historical contents of sp_news.htm (“What’s new?”), but not that of xml_news.htm (“What’s new in XML?”). The latter file was renamed to xml_news_prior_2014_01.html to archive the XML changes that were implemented before 2014. This file will no longer be updated.

We have generated symbolic links on the FTP site for the files that have been replaced to give everyone time to update their FTP download procedures to the new files’ locations:

New version of DASty

Our DAS web client DASty has been redesigned. DASty provides a visual representation of the compilation of protein annotations from different third-party sources. This allows users to get a global overview of all protein annotation available for their protein of interest, from UniProt as well as other sources. The “Third-party data” link that is available on each UniProtKB entry now leads to this new version of DASty. Any bookmarks should be updated accordingly. For instance, the “Third-party data” link for UniProt accession P05067 now links to http://www.ebi.ac.uk/dasty/client/index.html?q=P05067

Changes to the controlled vocabulary of human diseases

New diseases:

Modified diseases:

Changes to the controlled vocabulary for PTMs

Modified terms for the feature key ‘Cross-link’ (‘CROSSLNK’ in the flat file):

  • 1-(tryptophan-3-yl)-tryptophan (Trp-Trp) (interchain) -> 1-(tryptophan-3-yl)-tryptophan (Trp-Trp) (interchain with W-...)
  • 5’-tyrosyl-5’-aminotyrosine (Tyr-Tyr) (interchain) -> 5’-tyrosyl-5’-aminotyrosine (Tyr-Tyr) (interchain with Y-...)
  • Glycyl threonine ester (Gly-Thr) (interchain with G-...) -> Glycyl threonine ester (Gly-Thr) (interchain with T-...)

Changes to keywords

New keywords:

Modified keywords:

Deleted keyword:

  • Phage maturation