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UniProt release 2012_11

Published November 28, 2012

Headline

RALF, a growing family of plant peptide hormones

The first plant peptide hormone to be identified was systemin. Systemin regulates systemic wound signaling during herbivore and pathogen attacks. Since its discovery in 1991, several other polypeptide signals have been reported in plants, including phytosulfokines and CLAVATA3 and CLAVATA3-related proteins.

In 2001, Pearce et al. used a cell suspension culture assay to identify polypeptide hormones in plant extracts that cause alkalinization of the medium. In addition to systemins, the authors isolated a 5-kDa polypeptide from tobacco leaves that induced rapid alkalinization of the culture medium and the concomitant activation of an intracellular mitogen-activated protein kinase. The peptide has been called RALF for Rapid ALkalinization Factor. The 49-amino acid long active peptide is produced by processing of a 115 amino acid long preprotein. Genes encoding RALF preproproteins are expressed in various tissues and organs in many different plant species. In Arabidopsis thaliana, the RALF family consists of 36 members. As in tobacco, they are produced by the processing of precursors containing signal peptides and, for some of them, the cleavage of an additional propeptide is required. The presence of disulfide bonds contributes to their stabilization after secretion. One member of the family, RALF1, has been shown to induce an intracellular Ca(2+) increase, likely caused by both Ca(2+) influx across the plasma membrane and release of Ca(2+) from intracellular stores. This mechanism could be common to other RALFs.

Further studies are needed for a better understanding of RALF functions, but as of this release, all Arabidopsis thaliana RALF family members have been manually annotated with all available information.

UniProtKB news

Cross-references to ChEMBL

Cross-references have been added to ChEMBL, a database of bioactive drug-like small molecules.

ChEMBL is available at https://www.ebi.ac.uk/chembldb

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

Resource abbreviation ChEMBL
Resource identifier ChEMBL identifier
Example P69332:
DR   ChEMBL; CHEMBL4259; -.

Show all the entries having a cross-reference to ChEMBL.

Cross-references to PaxDb

Cross-references have been added to PaxDb (Protein Abundance Across Organisms), a comprehensive absolute protein abundance database, which contains whole genome protein abundance information across organisms.

PaxDb is available at http://pax-db.org

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

Resource abbreviation PaxDb
Resource identifier UniProtKB accession number
Example P85829:
DR   PaxDb; P85829; -.

Show all the entries having a cross-reference to PaxDb.

Removal of the cross-reference to ECO2DBASE

Cross-references to ECO2DBASE have been removed.

Removal of the cross-reference to TIGR

Cross-references to TIGR have been removed.

New format of the documentation files yeast.txt, yeast chromosome files, pombe.txt and calbican.txt

UniProtKB provides documentation files for some key species. These files list the relevant UniProtKB/Swiss-Prot entries with information like the primary accession number and entry name, gene designations, protein length, cross-references to organism-specific databases and whether a 3D structure is available or not.

We have slightly changed the file format so that all information from one protein is now found on a single line, which should make it easier to parse these files.

The following files are affected by this change:

Yeast
Yeast chromosome I
Yeast chromosome II
Yeast chromosome III
Yeast chromosome IV
Yeast chromosome V
Yeast chromosome VI
Yeast chromosome VII
Yeast chromosome VIII
Yeast chromosome IX
Yeast chromosome X
Yeast chromosome XI
Yeast chromosome XII
Yeast chromosome XIII
Yeast chromosome XIV
Yeast chromosome XV
Yeast chromosome XVI
Candida albicans
Schizosaccharomyces pombe