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UniProt release 2015_10

Published October 14, 2015

Headline

The smell of the sea in UniProtKB

Memories left by a walk on the seashore bring into play all our senses, of which smell is not the least. This characteristic ‘smell of the sea’ is carried by a little molecule, dimethylsulfide (DMS), which is an enzymatic cleavage product of dimethylsulfoniopropionate (DMSP).

DMSP is one of the most abundant organic molecules in the world, with a billion tons made and turned over every year. It is produced by marine macroalgae, as well as by single-cell phytoplankton species, such as diatoms, dinoflagellates and haptophytes, and occurs at high concentrations in their cytoplasm. The physiological function of DMSP is not yet fully established. It is thought to function as an osmolyte. It has also been proposed to serve as a cryoprotectant in polar algae. DMSP enzymatic cleavage products, DMS and acrylate, are quite effective at scavenging free radicals and other reactive oxygen species. Hence they may serve as an antioxidant system.

In healthy growing phytoplankton, DMSP freely diffuses in the cytoplasm, and only minute quantities are released. This amount is sufficient to attract zooplankton which start feeding on algae. Organisms grazed upon or infected by viruses as well as stressed or senescent cells release greater amount of DMSP, which is taken up by bacterioplankton, metabolized into DMS and used as a source of carbon and sulfur. DMS is not only used by seawater microorganisms, it is also volatile and a small fraction of it is released into the atmosphere where it creates an olfactory landscape providing seabirds with orientation cues to potential food supplies. In the atmosphere, DMS is oxidized to sulfuric acid and becomes an important source of sulfate aerosols. These act as condensation nuclei, causing water molecules to coalesce and cloud to form. The cycle is closed when rain brings back the sulfur-containing particles into the ocean. Interestingly, phytoplankton appear to convert DMSP into DMS very rapidly when they are stressed by UV radiation. The local increase in volatile DMS increases cloud formation, hence decreasing direct sun light exposure and relieving stress. Through this mechanism, plankton may shape local weather for their own benefit.

DMS release by seaweed was described in 1935 and DMSP was identified as its precursor almost 70 years ago, but the enzyme catalyzing the reaction remained elusive until last June. Using classical biochemical approaches, as well as genomic and proteomic analyses, Alcombri et al. identified ALMA1 from the chloroplastic membrane fraction of the coccolithophore alga Emiliania huxleyi, an abundant bloom-forming marine phytoplankton. This enzyme is a redox-sensitive homotetramer, that belongs to the aspartate/glutamate racemase superfamily and catalyzes DMSP cleavage into DMS and acrylate. Phylogenetic studies show the presence of numerous ALMA1 homologs in major, globally distributed phytoplankton taxa and in other marine organisms. This major discovery paves the way for future investigations on the physiological role of DMS and may allow quantification of the relative biogeochemical contribution of algae and bacteria to global DMS production.

If you want to take a deep, though virtual breath of sea smell, you can visit ALMA1 entries that are available to you as of this release.

UniProtKB news

Cross-references to WBParaSite

Cross-references have been added to WBParaSite, an open access resource providing access to the genome sequences, genome browsers, semi-automatic annotation and comparative genomics analysis of parasitic worms (helminths). WormBase ParaSite is closely integrated with and complementary to the main WormBase resource, the central focus of which is the model nematode Caenorhabditis elegans and its close relatives.

WBParaSite is available at http://parasite.wormbase.org.

The format of the explicit links is:

Resource abbreviation WBParaSite
Resource identifier Transcript identifier
Optional information 1 Protein identifier
Optional information 2 Gene identifier

Cross-references to WBParaSite may be isoform-specific. The general format of isoform-specific cross-references was described in release 2014_03.

Example: A8PGQ3

Show all entries having a cross-reference to WBParaSite.

Text format

Example: A8PGQ3

DR   WBParaSite; Bm6838; Bm6838; WBGene00227099.

XML format

Example: A8PGQ3

<dbReference type="WBParaSite" id="Bm6838">
  <property type="protein sequence ID" value="Bm6838"/>
  <property type="gene ID" value="WBGene00227099"/>
</dbReference>

RDF format

Example: A8PGQ3

uniprot:A8PGQ3
  rdfs:seeAlso <http://purl.uniprot.org/wbparasite/Bm6838> .
<http://purl.uniprot.org/wbparasite/Bm6838>
  rdf:type up:Transcript_Resource ;
  up:database <http://purl.uniprot.org/database/WBParaSite> ;
  up:translatedTo <http://purl.uniprot.org/wbparasite/Bm6838> ;
  up:transcribedFrom <http://purl.uniprot.org/wbparasite/WBGene00227099> .

Removal of the cross-references to CYGD

Cross-references to CYGD have been removed.

Changes to the controlled vocabulary of human diseases

New diseases:

Modified diseases:

UniParc news

UniParc cross-reference types changes

UniParc and UniProtKB entries both contain cross-references to external databases. For consistency reasons we have adjusted the names of these databases in UniParc to the ones in UniProtKB. In particular we have changed the following types of cross-references in UniParc:

Old type New type
ENSEMBL Ensembl
FLYBASE FlyBase
H_INV H-InvDB
REFSEQ RefSeq
TAIR_ARABIDOPSIS TAIR
WORMBASE WormBase
WormBase ParaSite WBParaSite

Example:

Previous XML:

<dbReference type="WormBase ParaSite" id="A_03330" version_i="1" active="Y" created="2014-09-12" last="2015-07-09">
  <property type="NCBI_taxonomy_id" value="6185"/>
</dbReference>

New XML:

<dbReference type="WBParaSite" id="A_03330" version_i="1" active="Y" created="2014-09-12" last="2015-07-09">
  <property type="NCBI_taxonomy_id" value="6185"/>
</dbReference>