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UniProt release 2019_07

Published July 31, 2019

Headline

The enemy of my enemy is my friend

When prey encounters predator, escape is often the best form of defense. Unfortunately this is not an option for plants, who instead have evolved a range of chemical defenses to deter herbivores, such as insects and other arthropods. These chemical defenses include compounds that are toxic to herbivores (direct defense) as well as compounds that attract herbivore predators (indirect defense).

Indirect defense has been extensively studied in maize. Upon foliar damage by lepidopteran larvae, maize releases a complex volatile terpenoid mixture, which attracts parasitic wasps, like Cotesia marginiventris or Cotesia sesamiae. These wasps deposit eggs in the lepidopteran larvae, which leads to an understandable loss of appetite by the lepidopterans, and eventually their death, when the wasp finally emerges from its host. These volatile terpenoids can also ‘prime’ neighboring plants, causing them to increase the transcription of defense-related genes and respond faster and more vigorously to subsequent herbivore attacks.

The volatile terpenoid mixture produced by maize under lepidopteran attack includes one sesquiterpene of special interest, which is (E)-beta-caryophyllene. This same sesquiterpene is also produced by roots upon damage by root-feeding pests, such as western corn rootworm (Diabrotica virgifera virgifera). Here it attracts entomopathogenic nematodes, which also live parasitically inside the infected lepidopterans. (E)-beta-caryophyllene is produced by the (E)-beta-caryophyllene synthase encoded by TPS23, which catalyzes the cyclization of farnesyl diphosphate to (E)-beta-caryophyllene. As expected for a gene involved in plant defense, TPS23 gene expression is tightly regulated. Herbivore-induced leaf damage causes increased expression in leaves, but not in roots, while attack by root-feeding pests increases expression in roots, but not in the shoots. TPS23 transcript levels correlate with the production of (E)-beta-caryophyllene and high-level expressing maize lines are more resistant to herbivores than low-level expressing ones.

(E)-beta-caryophyllene is just one of a host of chemical deterrents that plants deploy against herbivores and other pests: the UniProt plant annotation program aims to capture knowledge of the relevant biochemical pathways using Rhea and ChEBI, as well as many other aspects of plant biology too. Find out more about maize TPS23 in the latest updated version of UniProtKB/Swiss-Prot.

UniProtKB news

Cross-references to ChEBI in the ptmlist.txt document file

The ptmlist.txt document, which is available by FTP and on the website, describes post-translational modifications (PTMs) annotated in the UniProt knowledgebase. This release sees the addition of optional cross-references from ptmlist.txt to ChEBI (Chemical Entities of Biological Interest), a freely available dictionary of molecular entities focused on small chemical compounds and derivatives, including modified residues.

Example:

ID   (3R)-3-hydroxyarginine
AC   PTM-0476
FT   MOD_RES
..
KW   Hydroxylation.
DR   ChEBI; CHEBI:78294.

This new mapping to ChEBI will facilitate the integration of data on PTMs with knowledge of enzymatic reactions described in UniProt using the Rhea knowledgebase of biochemical reactions (itself built on ChEBI). The following query allows users to find enzymes in UniProtKB that are capable of creating the modified (3R)-3-hydroxyarginine residue (PTM-0476, CHEBI:78294):

annotation:(type:"catalytic activity" chebi:"(3R)-3-hydroxy-L-arginine residue [78294]")

We have currently mapped over 120 of the most common PTMs in UniProtKB to ChEBI and will continue to add new cross-references to ChEBI in forthcoming releases. This mapping of PTMs to ChEBI is part of our ongoing work on the standardization of knowledge of small molecule chemistry in UniProtKB that now covers enzyme cofactors and reactions as well as PTMs, and that will eventually extend to all small molecule protein interactions. We welcome your feedback on these current and future developments.

Retirement of UniProt decoy databases

Based on usage statistics, we decided to retire the UniProt decoy databases from our FTP site. If you wish to generate decoy databases from UniProt FASTA databases, you can use this software.

Please contact us if you have questions about this change.

Cross-references to NIAGADS

Cross-references have been added to the NIAGADS Alzheimer’s GenomicsDB. NIAGADS is a searchable annotation resource that provides access to publicly available NIAGADS summary statistics datasets for Alzheimer’s Disease (AD) and related neuropathologies.

NIAGADS is available at https://www.niagads.org/genomics/.

The format of the explicit links is:

Resource abbreviationNIAGADS
Resource identifierResource identifier

Example: E9PDY4

Show all entries having a cross-reference to NIAGADS.

Text format

Example: E9PDY4

DR   NIAGADS; ENSG00000203710; -.

XML format

Example: E9PDY4

<dbReference type="NIAGADS" id="ENSG00000203710"/>

RDF format

Example: E9PDY4

uniprot:E9PDY4
  rdfs:seeAlso <http://purl.uniprot.org/niagads/ENSG00000203710> .
<http://purl.uniprot.org/niagads/ENSG00000203710>
  rdf:type up:Resource ;
  up:database <http://purl.uniprot.org/database/NIAGADS> .

Cross-references to CPTAC

Cross-references have been added to the CPTAC Assay Portal. CPTAC serves as a centralized public repository of “fit-for-purpose” multiplexed quantitative mass spectrometry-based proteomic targeted assays.
CPTAC is available at https://assays.cancer.gov/.

The format of the explicit links is:

Resource abbreviationCPTAC
Resource identifierResource identifier

Example: P04083

Show all entries having a cross-reference to CPTAC.

Text format

Example: P04083

DR  CPTAC; CPTAC-311; -.

XML format

Example: P04083

<dbReference type="CPTAC" id="CPTAC-311"/>

RDF format

Example: P04083

uniprot:P04083
  rdfs:seeAlso <http://purl.uniprot.org/cptac/CPTAC-311> .
<http://purl.uniprot.org/cptac/CPTAC-311>
  rdf:type up:Resource ;
  up:database <http://purl.uniprot.org/database/CPTAC> .

Removal of the cross-references to H-InvDB

Cross-references to H-InvDB have been removed.

Changes to the controlled vocabulary of human diseases

New diseases:

Modified diseases:

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