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UniProt release 2018_06

Published June 20, 2018

Headline

Neuronal express mRNA delivery service

In mammals, the activity-regulated cytoskeleton-associated protein ARC is a key regulator of synaptic plasticity, being involved in many aspects of synapse formation, maturation, and plasticity, as well as in learning and memory. ARC expression is known to be induced by synaptic activity and its mRNA accumulates at sites of local synaptic activity where it is locally translated.

ARC originates from the Ty3/Gypsy retrotransposon family and it has retained some retroviral features. Its protein architecture is remarkably similar to that of the capsid domain of human immunodeficiency virus (HIV) GAG protein. GAG proteins are essential for viral infection. They can self-assemble to form capsids and encapsulate genomic RNA via direct sequence-specific interactions. At first glance, these properties do not seem crucial for eukaryotic proteins, but two recent studies unravel a quite unexpected means of neuronal communication, that is reminiscent of viral infection.

The intriguing observation was that ARC protein and mRNA are not only present at synapses, but also enriched in extracellular vesicles (EVs) released by neurons. These EVs are endocytosed by target cells, where ARC mRNA is postsynaptically translated, as has been described both at the Drosophila neuromuscular junction (NMJ), between motor neurons and muscles, and in rat hippocampal neurons. How is this achieved? Presynaptic ARC proteins bind the 3'-UTR of ARC mRNA, oligomerize and form capsid-like structures, in which the mRNA is packaged. These eukaryotic ‘capsids’ are then released by neurons in EVs and they mediate ARC mRNA transfer into postsynaptic target cells. In flies, ARC knockdown in motor neurons results in a decrease in ARC mRNA and protein in muscles, and leads to impaired expansion of the NMJ, synaptic bouton maturation, and activity-dependent synaptic bouton formation. This phenotype is not rescued by the expression of an ARC construct in muscle alone, nor if the neuronal ARC mRNA construct is missing its 3'-UTR. Overall, these data suggest that it is not just the presence of ARC in presynaptic terminals, but the actual transfer to the postsynaptic region that is required for ARC function.

This exciting piece of information has been transferred to UniProtKB/Swiss-Prot rat and Drosophila ARC entries by means of the classical pathway of expert curation and, as of this release, the updated records are publicly available.

International protein nomenclature guidelines

The European Bioinformatics Institute (EMBL-EBI), the National Center for Biotechnology Information (NCBI), the Protein Information Resource (PIR) and the Swiss Institute for Bioinformatics (SIB) have worked together to produce a shared set of protein naming guidelines. These guidelines are intended for use by anyone who wants to name a protein and aim to promote consistent nomenclature which is indispensable for communication, literature searching and data retrieval. They replace the previous UniProt protein naming guidelines and are available on the UniProt website as part of this release.

UniProtKB news

Cross-references to ComplexPortal

Cross-references have been added to ComplexPortal, a manually curated resource of macromolecular complexes.

ComplexPortal is available at https://www.ebi.ac.uk/complexportal/.

The format of the explicit links is:

Resource abbreviationComplexPortal
Resource identifierResource identifier
Optional information 1Complex name

Example: Q8IY92

Show all entries having a cross-reference to ComplexPortal.

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

h4#a. Text format

Example: Q8IY92

DR   ComplexPortal; CPX-484; SLX4-TERF2 complex.

h4#a. XML format

Example: Q8IY92

<dbReference type="ComplexPortal" id="CPX-484">
  <property type="entry name" value="SLX4-TERF2 complex"/>
</dbReference>

h4#a. RDF format

Example: Q8IY92

uniprot:Q8IY92
  rdfs:seeAlso <http://purl.uniprot.org/complexportal/CPX-484> .
<http://purl.uniprot.org/complexportal/CPX-484>
  rdf:type up:Resource ;
  up:database <http://purl.uniprot.org/database/ComplexPortal> ;
  rdfs:comment "SLX4-TERF2 complex" .

Cross-references to ProteomicsDB

Cross-references have been added to the ProteomicsDB, a human proteome resource.

ProteomicsDB is available at https://www.proteomicsdb.org/.

The format of the explicit links is:

Resource abbreviationProteomicsDB
Resource identifierResource identifier

Example: P41182

Show all entries having a cross-reference to ProteomicsDB.

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

h4#b. Text format

Example: P41182

DR   ProteomicsDB; 55413; -.
DR   ProteomicsDB; 55414; -. [P41182-2]

h4#b. XML format

Example: P41182

<dbReference type="ProteomicsDB" id="55413"/>
<dbReference type="ProteomicsDB" id="55414">
   <molecule id="P41182-2"/>
</dbReference>

h4#b. RDF format

Example: P41182

uniprot:P41182
  rdfs:seeAlso <http://purl.uniprot.org/proteomicsdb/55413> ;
  rdfs:seeAlso <http://purl.uniprot.org/proteomicsdb/55414> .
<http://purl.uniprot.org/proteomicsdb/55413> rdf:type up:Resource ;
  up:database <http://purl.uniprot.org/database/ProteomicsDB> .
<http://purl.uniprot.org/proteomicsdb/55414> rdf:type up:Resource ;
  up:database <http://purl.uniprot.org/database/ProteomicsDB> ;
  rdfs:seeAlso isoform:P41182-2 .

Cross-references to MoonDB

Cross-references have been added to MoonDB, a database of extreme multifunctional and moonlighting proteins.

MoonDB is available at http://moondb.hb.univ-amu.fr.

The format of the explicit links is:

Resource abbreviationMoonDB
Resource identifierUniProtKB accession number
Optional information 1Entry type (“Curated” or “Predicted”)

Example: Q13492

Show all entries having a cross-reference to MoonDB.

h4#c. Text format

Example: Q13492

DR   MoonDB; Q13492; Curated.

h4#c. XML format

Example: Q13492

<dbReference type="MoonDB" id="Q13492">
  <property type="type" value="Curated"/>
</dbReference>

h4#c. RDF format

Example: Q13492

uniprot:Q13492
  rdfs:seeAlso <http://purl.uniprot.org/moondb/Q13492> .
<http://purl.uniprot.org/moondb/Q13492>
  rdf:type up:Resource ;
  up:database <http://purl.uniprot.org/database/MoonDB> ;
  rdfs:comment "Curated" .

Changes to the controlled vocabulary of human diseases

New diseases:

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