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    VPS9A Vacuolar sorting protein 9 (VPS9) domain-containing protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 821514, updated on 18-Sep-2024

    Summary

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    Official Symbol
    VPS9A
    Official Full Name
    Vacuolar sorting protein 9 (VPS9) domain-containing protein
    Primary source
    TAIR:AT3G19770
    Locus tag
    AT3G19770
    See related
    Araport:AT3G19770
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    ARABIDOPSIS THALIANA VACUOLAR PROTEIN SORTING 9A; ATVPS9A; MMB12.26; VPS9
    Summary
    Guanine nucleotide exchange factor VPS9a. Can activate all Rab5 members to GTP-bound forms in vitro. Required for embryogenesis. Regulates the localization of ARA7 and ARA6. Involved in postembryonic root development.
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    Genomic context

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    See VPS9A in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    5
    Sequence:
    Chromosome: 3; NC_003074.8 (6866717..6869501)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene P-loop containing nucleoside triphosphate hydrolases superfamily protein Neighboring gene eukaryotic initiation factor 4A-III Neighboring gene uncharacterized protein Neighboring gene ncRNA Neighboring gene uncharacterized protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003074.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. VPS9a Activates the Rab5 GTPase ARA7 to Confer Distinct Pre- and Postinvasive Plant Innate Immunity. Nielsen ME, et al. Plant Cell, 2017 Aug. PMID 28808134, Free PMC Article
    2. Functional analyses of the plant-specific C-terminal region of VPS9a: the activating factor for RAB5 in Arabidopsis thaliana. Sunada M, et al. J Plant Res, 2016 Jan. PMID 26493488
    3. RAB5 activation is required for multiple steps in Arabidopsis thaliana root development. Inoue T, et al. Plant Cell Physiol, 2013 Oct. PMID 23893024
    4. GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5·Vps9 system. Uejima T, et al. J Biol Chem, 2010 Nov 19. PMID 20833725, Free PMC Article
    5. VPS9a, the common activator for two distinct types of Rab5 GTPases, is essential for the development of Arabidopsis thaliana. Goh T, et al. Plant Cell, 2007 Nov. PMID 18055610, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Here, the authors identified an effector molecule of the plant-unique RAB5 in Arabidopsis thaliana, ARA6, which thex designated PLANT-UNIQUE RAB5 EFFECTOR 2 (PUF2).The authors showed that ARA6 negatively regulates canonical RAB5-mediated vacuolar transport by titrating PUF2 and VPS9a.
      Title: Integration of two RAB5 groups during endosomal transport in plants.
    2. endosome-associated VPS9a, the conserved guanine-nucleotide exchange factor activating Rab5 GTPases, is required for both pre- and postinvasive immunity against a nonadapted powdery mildew fungus.
      Title: VPS9a Activates the Rab5 GTPase ARA7 to Confer Distinct Pre- and Postinvasive Plant Innate Immunity.
    3. This study investigated the function of the C-terminal region (CTR) by generating truncated versions of VPS9a and found that it was specifically responsible for ARA6 regulation. The CTR was required for oligomerization and correct localization of VPS9a.
      Title: Functional analyses of the plant-specific C-terminal region of VPS9a: the activating factor for RAB5 in Arabidopsis thaliana.
    4. Data indicate that VPS9a is practically the sole guanine nucleotide exchange factor (GEF) for RAB5s (ARA6) in vegetative developmental stages.
      Title: RAB5 activation is required for multiple steps in Arabidopsis thaliana root development.
    5. Both types of Rab5 members, ARA7 and RHA1 in Arabidopsis, are activated by a single Rab5 GEF, VPS9a. The activity of VPS9a is essential for various plant functions, such as cytokinesis, embryogenesis, and organ development. [VPS9a]
      Title: VPS9a, the common activator for two distinct types of Rab5 GTPases, is essential for the development of Arabidopsis thaliana.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_001035651.2
    NM_112867.5

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables guanyl-nucleotide exchange factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within cell plate assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within cell wall biogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within embryo development ending in seed dormancy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within late endosome to vacuole transport IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within post-embryonic root development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    Vacuolar sorting protein 9 (VPS9) domain-containing protein
    NP_001030728.1
    • VPS9A; FUNCTIONS IN: Rho guanyl-nucleotide exchange factor activity; INVOLVED IN: cell plate assembly, transport, cell wall biogenesis, post-embryonic root development, embryo development; LOCATED IN: cytosol, nucleus, membrane; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Vacuolar sorting protein 9, subgroup (InterPro:IPR013995), Vacuolar sorting protein 9 (InterPro:IPR003123); BEST Arabidopsis thaliana protein match is: Vacuolar sorting protein 9 (VPS9) domain (TAIR:AT5G09320.1); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink).
    NP_566645.1
    • VPS9A; FUNCTIONS IN: Rho guanyl-nucleotide exchange factor activity; INVOLVED IN: cell plate assembly, transport, cell wall biogenesis, post-embryonic root development, embryo development; LOCATED IN: cytosol, nucleus, membrane; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Vacuolar sorting protein 9, subgroup (InterPro:IPR013995), Vacuolar sorting protein 9 (InterPro:IPR003123); BEST Arabidopsis thaliana protein match is: Vacuolar sorting protein 9 (VPS9) domain (TAIR:AT5G09320.1); Has 1001 Blast hits to 992 proteins in 208 species: Archae - 0; Bacteria - 4; Metazoa - 518; Fungi - 219; Plants - 81; Viruses - 0; Other Eukaryotes - 179 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_003074.8 Reference assembly

      Range
      6866717..6869501
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_112867.5 → NP_566645.1  Vacuolar sorting protein 9 (VPS9) domain-containing protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_566645.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9LT31
      UniProtKB/TrEMBL
      A0A178VEC6, A0A5S9XE66, A0A654FE53
      Conserved Domains (2) summary
      pfam02204
      Location:136 → 241
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      pfam18151
      Location:27 → 91
      DUF5601; Domain of unknown function (DUF5601)

    2. NM_001035651.2 → NP_001030728.1  Vacuolar sorting protein 9 (VPS9) domain-containing protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001030728.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      F4JCD2
      Conserved Domains (1) summary
      pfam02204
      Location:3 → 105
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9LT31.1

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