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UniProt release 2019_09

Published October 16, 2019

Headline

Biological weapons in the struggle for life

The apoplast, the extracellular space between plant cells, is a battleground between plants and attacking microorganisms. The battle often starts with the secretion of carbohydrate-degrading enzymes by the invader and a counter-attack by the plant with dedicated enzyme inhibitors. This happens for instance when Phytophthora sojae invades soybean. During very early infection stages (20 minutes to 2 hours), the oomycete expresses and secretes high levels of a xyloglucanase enzyme, called XEG1. XEG1 degrades the plant cell wall polymers and not only permits pathogen invasion, but also provides it with nutrients. XEG1 expression declines rapidly from 3 hours onwards.

Like other plants, soybean monitors the apoplastic environment through pattern recognition receptors and recognizes XEG1 as a PAMP (pathogen-associated molecular pattern). This recognition triggers defense responses, which include the secretion of GIP1, a xyloglucanase inhibitor. Efficient XEG1 inhibition by GIP1 increases soybean resistance towards P. sojae. This could be the end of the story, but P. sojae has another trick up its sleeve.

When Ma et al. studied GIP1 binding to XEG1 paralogs, they retrieved only one protein, called XLP1, in addition to XEG1. Like XEG1, XLP1 is targeted to the apoplast. It also shows a similar expression time course to XEG1, i.e. high levels during very early infection stages, followed by a rapid decline, suggesting a role in virulence. Unlike XEG1, however, XLP1 does not show any xyloglucanase activity. It is 52 residues shorter and is missing one of the residues critical for xyloglucanase activity. XLP1 contributes to P. sojae infectivity, but only in the presence of active XEG1. Thus XLP1 acts as a decoy to disrupt plant defenses. It interacts with GIP1 with a five-fold higher affinity than that of XEG1 and hence neutralizes the GIP1 inhibitor. In this setting, XEG1 can pursue plant cell wall digestion without any hindrance.

The 3 belligerent proteins have been annotated in UniProtKB/Swiss-Prot and are publicly available.

UniProtKB news

Change of annotation topic 'Sequence caution'

The annotation topic Sequence caution reports differences between the protein sequence shown in a UniProtKB entry and other available protein sequences derived from the same gene. It indicates the likely cause for the differences, and when that cause is a frameshift or erroneous termination, the amino acid sequence position(s) of these errors were listed when possible. Since it is nowadays easy to align two protein sequences for comparison, we no longer curate error positions and removed the field where this information was stored.

Text format

We removed the optional Positions field.

Example: P14332

Previous format:

CC   -!- SEQUENCE CAUTION: Sequence=CAA34633.1; Type=Frameshift; Positions=226, 249; Evidence={ECO:0000305};

New format:

CC   -!- SEQUENCE CAUTION: Sequence=CAA34633.1; Type=Frameshift; Evidence={ECO:0000305};

XML format

This change did not affect the UniProtKB XSD.

Example: P14332

Previous format:

<comment type="sequence caution" evidence="3">
  <conflict type="frameshift">
    <sequence resource="EMBL-CDS" id="CAA34633" version="1"/>
  </conflict>
  <location>
    <position position="226"/>
  </location>
  <location>
    <position position="249"/>
  </location>
</comment>

New format:

<comment type="sequence caution" evidence="3">
  <conflict type="frameshift">
    <sequence resource="EMBL-CDS" id="CAA34633" version="1"/>
  </conflict>
</comment>

RDF format

This change required an adaptation of the hierarchy of Annotation classes in the UniProt RDF schema ontology: The Sequence_Caution_Annotation class is no longer an rdfs:subClassOf of the Sequence_Annotation class, but a direct rdfs:subClassOf of the Annotation class.

Example: P14332

Previous format:

uniprot:P14332
  up:annotation <P14332#SIP7159608509D280BB> .

<P14332#SIPBBAF3CC29FCD3715>
  rdf:type up:Frameshift_Annotation ;
  up:conflictingSequence <P14332#SIPD8B2EDFEB46FA203> ;
  up:range range:22572098403906094tt226tt226 ,
           range:22572098403906094tt249tt249 .
range:22572098403906094tt226tt226
  rdf:type faldo:Region ;
  faldo:begin position:22572098403906094tt226 ;
  faldo:end position:22572098403906094tt226 .
position:22572098403906094tt226
  rdf:type faldo:Position , faldo:ExactPosition ;
  faldo:position 226 ;
  faldo:reference isoform:P14332-1 .
range:22572098403906094tt249tt249
  rdf:type faldo:Region ;
  faldo:begin position:22572098403906094tt249 ;
  faldo:end position:22572098403906094tt249 .
position:22572098403906094tt249
  rdf:type faldo:Position , faldo:ExactPosition ;
  faldo:position 249 ;
  faldo:reference isoform:P14332-1 .

New format:

uniprot:P14332
  up:annotation <P14332#SIP7159608509D280BB> .

<P14332#SIPBBAF3CC29FCD3715>
  rdf:type up:Frameshift_Annotation ;
  up:conflictingSequence <P14332#SIPD8B2EDFEB46FA203> .

Cross-references to PlantReactome

Cross-references have been added to PlantReactome, a curated resource of core pathways and reactions in plant biology.

PlantReactome is available at https://plantreactome.gramene.org

The format of the explicit links is:

Resource abbreviationPlantReactome
Resource identifierResource identifier
Optional information Pathway name

Example: P0C128

Show all entries having a cross-reference to PlantReactome.

Text format

Example: P0C128

DR   PlantReactome; R-OSA-5608118; Auxin signalling.

XML format

Example: P0C128

<dbReference type="PlantReactome" id="R-OSA-5608118">
  <property type="pathway name" value="Auxin signalling"/>
</dbReference>

RDF format

Example: P0C128

uniprot:P0C128
  rdfs:seeAlso <http://purl.uniprot.org/plantreactome/R-OSA-5608118> .
<http://purl.uniprot.org/plantreactome/R-OSA-5608118>
  rdf:type up:Resource ;
  up:database <http://purl.uniprot.org/database/PlantReactome> ;
  rdfs:comment "Auxin signalling" .

Change of the cross-references to Reactome

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

Example: P00167

Changes to the controlled vocabulary of human diseases

New diseases:

Modified diseases:

Deleted diseases

  • Mental retardation, X-linked 17

Changes to the controlled vocabulary for PTMs

New terms for the feature key ‘Cross-link’ (‘CROSSLNK’ in the flat file):

  • N5-[4-(S-L-cysteinyl)-5-methyl-1H-imidazol-2-yl]-L-ornithine (Arg-Cys) (interchain with C-...)
  • N5-[4-(S-L-cysteinyl)-5-methyl-1H-imidazol-2-yl]-L-ornithine (Cys-Arg) (interchain with R-...)

New term for the feature key ‘Glycosylation’ (‘CARBOHYD’ in the flat file):

  • N-linked (Glc) (glycation) arginine

New terms for the feature key ‘Modified residue’ (‘MOD_RES’ in the flat file):

  • S-(2-succinyl)cysteine
  • N6-carbamoyllysine
  • S-(2,3-dicarboxypropyl)cysteine
  • S-cGMP-cysteine

Changes in subcellular location controlled vocabulary

New subcellular locations:

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