slrP

id: Q8ZQQ2
gene_symbol: slrP
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:99287
  label: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
description: >-
  SlrP (Salmonella leucine-rich repeat protein) is a type III secretion system (T3SS)
  effector protein in Salmonella enterica serovar Typhimurium. It belongs to the
  LRR-containing bacterial E3 ubiquitin ligase family (IpaH-like) and contains an
  N-terminal leucine-rich repeat domain that mediates target recognition and a C-terminal
  NEL (novel E3 ligase) domain with E3 ubiquitin ligase catalytic activity (Cys-546 is
  the catalytic residue). SlrP is secreted via both SPI-1 and SPI-2 T3SS into host cells,
  where it ubiquitinates host thioredoxin (TXN) in the cytosol, leading to decreased
  TXN activity and increased host cell death (PMID:19690162). It also targets the ER
  lumenal chaperone ERdj3 (DNAJB11), interfering with ERdj3's binding to denatured
  substrates (PMID:20335166). SlrP is a virulence factor, not a chaperone.
existing_annotations:
- term:
    id: GO:0004842
    label: ubiquitin-protein transferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      Combined IEA annotation for ubiquitin-protein transferase activity based on
      ARBA and InterPro (NEL domain). SlrP has E3 ubiquitin ligase activity
      demonstrated experimentally (PMID:19690162).
    action: ACCEPT
    reason: >-
      Correct. SlrP is an E3 ubiquitin ligase demonstrated to ubiquitinate both
      ubiquitin and host thioredoxin (PMID:19690162). Consistent with IDA evidence.
- term:
    id: GO:0005576
    label: extracellular region
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      IEA annotation for extracellular region from UniProt subcellular location
      mapping. SlrP is secreted via T3SS into the host cell, so it passes through
      the extracellular space during delivery.
    action: ACCEPT
    reason: >-
      Acceptable. SlrP is secreted via T3SS. UniProt annotates it as "Secreted"
      based on ISS evidence. The protein is translocated into host cells via the
      secretion apparatus.
- term:
    id: GO:0016567
    label: protein ubiquitination
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      Combined IEA annotation for protein ubiquitination based on ARBA and InterPro
      (NEL domain). SlrP ubiquitinates host thioredoxin (PMID:19690162).
    action: ACCEPT
    reason: >-
      Correct. SlrP mediates ubiquitination of host thioredoxin and ubiquitin itself
      in vitro (PMID:19690162). Consistent with IDA evidence.
- term:
    id: GO:0016740
    label: transferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      IEA annotation for transferase activity from UniProt keyword mapping. This is
      a broad parent of ubiquitin-protein transferase activity.
    action: ACCEPT
    reason: >-
      Correct but very broad. The more specific terms GO:0004842 and GO:0061630 are
      also annotated. Acceptable as a broad IEA.
- term:
    id: GO:0030430
    label: host cell cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      IEA annotation for host cell cytoplasm from UniProt subcellular location mapping.
      SlrP is translocated into the host cell cytoplasm via T3SS (PMID:20335166).
    action: ACCEPT
    reason: >-
      Correct. SlrP is delivered into the host cell cytoplasm where it targets
      thioredoxin for ubiquitination. Consistent with IDA evidence (PMID:20335166).
- term:
    id: GO:0061630
    label: ubiquitin protein ligase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000003
  review:
    summary: >-
      IEA annotation for ubiquitin protein ligase activity from EC mapping (EC 2.3.2.27).
      SlrP is annotated as E3 ubiquitin-protein ligase in UniProt with EC 2.3.2.27.
    action: ACCEPT
    reason: >-
      Correct and more specific than GO:0004842 for describing the E3 ligase function.
      SlrP functions as an E3 ubiquitin ligase (PMID:19690162).
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:20335166
  review:
    summary: >-
      IPI annotation for protein binding showing interaction with ERdj3 (DNAJB11,
      Q9UBS4). SlrP binds ERdj3 via its leucine-rich repeat domain and interferes
      with ERdj3's chaperone function (PMID:20335166).
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding (GO:0005515) is uninformative. The interaction with ERdj3 is
      real but the generic term does not convey the functional significance. The
      interaction is part of SlrP's virulence mechanism targeting the host ER
      chaperone ERdj3 for functional disruption.
- term:
    id: GO:0044165
    label: host cell endoplasmic reticulum
  evidence_type: IDA
  original_reference_id: PMID:20335166
  review:
    summary: >-
      IDA annotation for host cell ER localization. Confocal microscopy and
      subcellular fractionation showed that SlrP is partially located in the ER
      of transfected HeLa cells (PMID:20335166).
    action: ACCEPT
    reason: >-
      Direct experimental evidence from confocal microscopy and subcellular
      fractionation (PMID:20335166). SlrP localizes to the host ER where it
      targets ERdj3.
    supported_by:
      - reference_id: PMID:20335166
        supporting_text: "Confocal microscopy and subcellular fractionation demonstrated that, in transfected HeLa cells, SlrP was partially located in the endoplasmic reticulum."
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IPI
  original_reference_id: PMID:20335166
  review:
    summary: >-
      IPI annotation for unfolded protein binding based on interaction with ERdj3
      (Q9UBS4). However, SlrP does not bind unfolded proteins itself. Rather, SlrP
      binds the chaperone ERdj3 and interferes with ERdj3's ability to bind denatured
      substrates (PMID:20335166). The "unfolded protein binding" annotation appears to
      be a misannotation -- SlrP disrupts chaperone function, it does not itself bind
      unfolded proteins in a chaperone-like manner.
    action: REMOVE
    reason: >-
      This annotation is incorrect. SlrP does not bind unfolded proteins. The paper
      (PMID:20335166) shows that SlrP binds ERdj3 (a chaperone) and interferes with
      ERdj3's binding to a denatured substrate. The IPI with/from column shows Q9UBS4
      (ERdj3/DNAJB11), which is a folded chaperone protein, not an unfolded protein.
      The annotation confuses SlrP's interaction with a chaperone with binding to
      unfolded proteins. SlrP is a virulence factor/E3 ubiquitin ligase that targets
      specific host proteins (thioredoxin, ERdj3) for functional disruption, not a
      protein that binds unfolded substrates.
    supported_by:
      - reference_id: PMID:20335166
        supporting_text: "The presence of SlrP interfered with the binding of ERdj3 to a denatured substrate."
- term:
    id: GO:0030430
    label: host cell cytoplasm
  evidence_type: IDA
  original_reference_id: PMID:20335166
  review:
    summary: >-
      IDA annotation for host cell cytoplasm from Bernal-Bayard et al. (2010).
      Consistent with IEA annotation and the known T3SS-mediated delivery of SlrP
      into host cells.
    action: ACCEPT
    reason: >-
      Correct. Direct experimental evidence for host cell cytoplasm localization.
      SlrP targets thioredoxin in the cytosol and ERdj3 in the ER (PMID:20335166).
- term:
    id: GO:0032091
    label: negative regulation of protein binding
  evidence_type: IDA
  original_reference_id: PMID:20335166
  review:
    summary: >-
      IDA annotation for negative regulation of protein binding. SlrP interferes
      with ERdj3's ability to bind denatured substrates (PMID:20335166). This
      captures SlrP's virulence mechanism of disrupting host chaperone function.
    action: ACCEPT
    reason: >-
      This accurately describes the functional consequence of SlrP-ERdj3 interaction:
      SlrP negatively regulates ERdj3's protein binding (chaperone) activity. This is
      a documented virulence mechanism (PMID:20335166).
    supported_by:
      - reference_id: PMID:20335166
        supporting_text: "The presence of SlrP interfered with the binding of ERdj3 to a denatured substrate."
- term:
    id: GO:0004842
    label: ubiquitin-protein transferase activity
  evidence_type: IDA
  original_reference_id: PMID:19690162
  review:
    summary: >-
      IDA annotation for ubiquitin-protein transferase activity from Bernal-Bayard
      and Ramos-Morales (2009). SlrP mediates ubiquitination of ubiquitin and host
      thioredoxin in vitro. Cys-546 to Ala mutation abolishes this activity
      (PMID:19690162).
    action: ACCEPT
    reason: >-
      Core molecular function of SlrP. Directly demonstrated by in vitro
      ubiquitination assays with Cys-546 mutant as negative control (PMID:19690162).
    supported_by:
      - reference_id: PMID:19690162
        supporting_text: "In vitro, SlrP was able to mediate ubiquitination of ubiquitin and thioredoxin."
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19690162
  review:
    summary: >-
      IPI annotation for protein binding showing interaction with host thioredoxin
      (TXN, P10599). SlrP binds thioredoxin as its ubiquitination substrate
      (PMID:19690162).
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding (GO:0005515) is uninformative. The interaction with thioredoxin
      is real but the generic term does not capture the functional significance -- SlrP
      binds TXN as an E3 ubiquitin ligase substrate. The ubiquitin ligase activity
      annotations already capture this function more informatively.
- term:
    id: GO:0016567
    label: protein ubiquitination
  evidence_type: IDA
  original_reference_id: PMID:19690162
  review:
    summary: >-
      IDA annotation for protein ubiquitination from Bernal-Bayard and Ramos-Morales
      (2009). SlrP ubiquitinates host thioredoxin (PMID:19690162).
    action: ACCEPT
    reason: >-
      Core biological process of SlrP. Directly demonstrated by ubiquitination
      assays (PMID:19690162). Consistent with IEA annotation.
    supported_by:
      - reference_id: PMID:19690162
        supporting_text: "In vitro, SlrP was able to mediate ubiquitination of ubiquitin and thioredoxin."
- term:
    id: GO:0030254
    label: protein secretion by the type III secretion system
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: >-
      ISS annotation for T3SS-mediated secretion based on manual transfer from
      ortholog. SlrP is translocated via both SPI-1 and SPI-2 T3SS into host cells.
    action: ACCEPT
    reason: >-
      Correct. SlrP is a well-characterized T3SS effector secreted via both SPI-1
      and SPI-2 systems. This is fundamental to its delivery mechanism.
references:
- id: GO_REF:0000003
  title: Gene Ontology annotation based on Enzyme Commission mapping
  findings: []
- id: GO_REF:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
    by curator judgment of sequence similarity
  findings: []
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:19690162
  title: Salmonella type III secretion effector SlrP is an E3 ubiquitin ligase for
    mammalian thioredoxin.
  findings:
  - statement: SlrP is an E3 ubiquitin ligase that ubiquitinates host thioredoxin and ubiquitin
    supporting_text: "In vitro, SlrP was able to mediate ubiquitination of ubiquitin and thioredoxin."
  - statement: Cys-546 is essential for E3 ligase catalytic activity
    supporting_text: "A Cys residue conserved in other effectors of the same family that also possess E3 ubiquitin ligase activity was essential for this catalytic function."
  - statement: SlrP expression decreases thioredoxin activity and increases host cell death
    supporting_text: "Stable expression of SlrP in HeLa cells resulted in a significant decrease of thioredoxin activity and in an increase of cell death."
- id: PMID:20335166
  title: The Salmonella type III secretion effector, salmonella leucine-rich repeat
    protein (SlrP), targets the human chaperone ERdj3.
  findings:
  - statement: ERdj3 (DNAJB11) identified as a second host target of SlrP
    supporting_text: "Here, we identified ERdj3, an endoplasmic reticulum lumenal chaperone of the Hsp40/DnaJ family, as a new target for SlrP."
  - statement: SlrP partially localizes to the host ER in transfected HeLa cells
    supporting_text: "Confocal microscopy and subcellular fractionation demonstrated that, in transfected HeLa cells, SlrP was partially located in the endoplasmic reticulum."
  - statement: SlrP interferes with ERdj3 binding to denatured substrates
    supporting_text: "The presence of SlrP interfered with the binding of ERdj3 to a denatured substrate."
  - statement: SlrP modulates two independent targets -- thioredoxin in cytosol and ERdj3 in ER
    supporting_text: "these data suggest that the role of SlrP in the interaction between Salmonella and the host cell is exerted through the modulation of the function of two independent targets: thioredoxin in the cytosol, and ERdj3 in the endoplasmic reticulum."
core_functions:
- description: >-
    E3 ubiquitin-protein ligase that is translocated into host cells via the type III
    secretion system, where it ubiquitinates host thioredoxin leading to decreased
    thioredoxin activity and increased host cell death.
  molecular_function:
    id: GO:0061630
    label: ubiquitin protein ligase activity
  directly_involved_in:
  - id: GO:0016567
    label: protein ubiquitination
  - id: GO:0030254
    label: protein secretion by the type III secretion system
  locations:
  - id: GO:0030430
    label: host cell cytoplasm
  - id: GO:0044165
    label: host cell endoplasmic reticulum