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UniProt release 2015_07

Published June 24, 2015

Headline

Coding-non-coding RNAs: a game of hide-and-seek

It is well-established that microRNAs (miRNAs) are small eukaryotic non-coding RNA molecules that repress the expression of their target genes. miRNAs are transcribed by RNA polymerase II as large primary transcripts (pri-miRNA), that share the same characteristics as all other RNA polymerase II-transcribed RNAs, such as the presence of a 5’-cap and a 3’-poly(A) tail. pri-miRNAs are processed to smaller pre-miRNAs, which in turn are cleaved to produce mature miRNAs. In animals, this final maturation step occurs in the cytoplasm, while in plants it takes place in the nucleus. Cytosolic mature miRNAs guide the RNA-induced silencing complex (RISC) in repressing target genes through either cleavage or translational repression of their mRNAs.

A recent article published in Nature revealed that plant pri-miRNAs may not be as non-coding as previously assumed. Some do actually encode small regulatory peptides, called miPEPs, which enhance the accumulation of their corresponding mature miRNAs. This has been shown for Medicago truncatula pri-miR171b and Arabidopsis thaliana pri-miR165a which encode miPEP171b and miPEP165a, respectively. These two 20- and 18-amino acid-long peptides have been shown to be translated in vivo and to promote the transcription of their pri-miRNAs, resulting in the accumulation of mature miR171b and miR165a. This increase leads to the reduction of lateral root development in the case of miR171b and stimulation of main root growth for miR165a. The same effects were observed when synthetic peptides were applied to plants, suggesting that miPEPs might have agronomical applications.

Five other pri-miRNAs were experimentally shown to encode active miPEPs, suggesting that the presence of such small regulatory peptides may be widespread in plants. Computer analysis of the 5’-end of 50 pri-miRNAs in Arabidopsis thaliana revealed that all of them contained at least one ORF, which, if translated, could give rise to 3- to 59-amino acid-long peptides of unknown biological activity. No common signature was found among them, possibly due to the specificity of each putative miPEP for its own pri-miRNA.

Arabidopsis thaliana miPEP165a, miPEP160b, miPEP164a and miPEP319a and Medicago truncatula miPEP171b peptides have been manually annotated and are integrated into UniProtKB/Swiss-Prot as of this release. The sequences of the other 2 Medicago truncatula functionally characterized peptides, miPEP169d and miPEP171e, are unfortunately not available.

UniProtKB news

Cross-references to ESTHER

Cross-references have been added to ESTHER, a database of the Alpha/Beta-hydrolase fold superfamily of proteins.

ESTHER is available at http://bioweb.ensam.inra.fr/ESTHER/general?what=index.

The format of the explicit links is:

Resource abbreviation ESTHER
Resource identifier Gene locus.
Optional information 1 Family name.

Example: P0C064

Show all entries having a cross-reference to ESTHER.

Text format

Example: P0C064

DR   ESTHER; bacbr-grsb; Thioesterase.

XML format

Example: P0C064

<dbReference type="ESTHER" id="bacbr-grsb">
  <property type="family name" value="Thioesterase"/>
</dbReference>

Cross-references to Genevisible

Cross-references have been added to Genevisible, a search portal to normalized and curated expression data from GENEVESTIGATOR.

Genevisible is available at http://genevisible.com/search.

The format of the explicit links is:

Resource abbreviation Genevisible
Resource identifier Gene identifier.
Optional information 1 Organism code.

Example: P31946

Show all entries having a cross-reference to Genevisible.

Text format

Example: P31946

DR   Genevisible; P31946; HS.

XML format

Example: P31946

<dbReference type="Genevisible" id="P31946">
  <property type="organism ID" value="HS"/>
</dbReference>

Removal of the cross-references to Genevestigator

Cross-references to Genevestigator have been removed.

Change of the cross-references to PomBase

Cross-references to PomBase may now optionally indicate a gene designation in order to align them with the format of other model organism databases.

Text format

Example: Q9P3A7

DR   PomBase; SPAC1565.08; cdc48.

Example: O60058

DR   PomBase; SPBC56F2.07c; -.

XML format

Example: Q9P3A7

<dbReference type="PomBase" id="SPAC1565.08">
  <property type="gene designation" value="cdc48"/>
</dbReference>

Example: O60058

<dbReference type="PomBase" id="SPBC56F2.07c"/>

This change did not affect the XSD, but may nevertheless require code changes.

Changes to the controlled vocabulary of human diseases

New diseases:

Modified diseases:

Deleted disease:

  • Hypogonadism LHB-related

Changes to keywords

New keywords: