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    Pdss2 prenyl (solanesyl) diphosphate synthase, subunit 2 [ Mus musculus (house mouse) ]

    Gene ID: 71365, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Pdss2provided by MGI
    Official Full Name
    prenyl (solanesyl) diphosphate synthase, subunit 2provided by MGI
    Primary source
    MGI:MGI:1918615
    See related
    Ensembl:ENSMUSG00000038240 AllianceGenome:MGI:1918615
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    kd; Gm60; Plmp; mDLP1; 5430420P03Rik
    Summary
    Enables protein heterodimerization activity. Contributes to all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity. Involved in cerebellum development; isoprenoid biosynthetic process; and ubiquinone biosynthetic process. Acts upstream of or within regulation of body fluid levels. Located in mitochondrion. Part of heterotetrameric polyprenyl diphosphate synthase complex. Is expressed in several structures, including endocrine gland; genitourinary system; heart; nervous system; and stomach. Used to study coenzyme Q10 deficiency disease. Human ortholog(s) of this gene implicated in primary coenzyme Q10 deficiency 3. Orthologous to human PDSS2 (decaprenyl diphosphate synthase subunit 2). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in colon adult (RPKM 2.3), adrenal adult (RPKM 2.0) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Pdss2 in Genome Data Viewer
    Location:
    10 B2; 10 22.91 cM
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (43095396..43340878)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (43218248..43464882)

    Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_26500 Neighboring gene sine oculis binding protein Neighboring gene predicted gene, 47815 Neighboring gene RIKEN cDNA 9030612E09 gene Neighboring gene STARR-seq mESC enhancer starr_26502 Neighboring gene STARR-seq mESC enhancer starr_26503 Neighboring gene predicted gene, 40631 Neighboring gene STARR-positive B cell enhancer mm9_chr10:43098751-43099051 Neighboring gene ribosomal protein S19, pseudogene 11 Neighboring gene STARR-seq mESC enhancer starr_26505 Neighboring gene STARR-positive B cell enhancer mm9_chr10:43137256-43137557 Neighboring gene STARR-positive B cell enhancer ABC_E9031 Neighboring gene STARR-seq mESC enhancer starr_26511 Neighboring gene ribosomal protein L41 pseudogene Neighboring gene BEN domain containing 3 Neighboring gene predicted gene, 47889

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Nutritional inhibition of genetically determined renal disease and autoimmunity with prolongation of life in kdkd mice. Fernandes G, et al. Proc Natl Acad Sci U S A, 1978 Jun. PMID 275859, Free PMC Article
    2. Spontaneous interstitial nephritis in kdkd mice. II. Characterization of a tubular antigen-specific, H-2K-restricted Lyt-2+ effector T cell that mediates destructive tubulointerstitial injury. Kelly CJ, et al. J Immunol, 1986 Jan. PMID 2416810
    3. Spontaneous interstitial nephritis in kdkd mice. I. An experimental model of autoimmune renal disease. Neilson EG, et al. J Immunol, 1984 Nov. PMID 6384368
    4. Coenzyme Q10 restores oocyte mitochondrial function and fertility during reproductive aging. Ben-Meir A, et al. Aging Cell, 2015 Oct. PMID 26111777, Free PMC Article
    5. Inhibiting cytosolic translation and autophagy improves health in mitochondrial disease. Peng M, et al. Hum Mol Genet, 2015 Sep 1. PMID 26041819, Free PMC Article

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PDSS2 Inhibits the Ferroptosis of Vascular Endothelial Cells in Atherosclerosis by Activating Nrf2.
      Title: PDSS2 Inhibits the Ferroptosis of Vascular Endothelial Cells in Atherosclerosis by Activating Nrf2.
    2. kidney-specific loss of mitochondria triggered by oxidative stress may be the cause of renal failure in Pdss2(kd/kd) mice
      Title: Tissue-specific oxidative stress and loss of mitochondria in CoQ-deficient Pdss2 mutant mice.
    3. During cerebellum development, Pdss2 knockout results in severe cerebellum hypoplasia by impairing cell migration and eliciting ectopic apoptosis, whereas Pdss2 knockout in Purkinje cells at postnatal stages leads to the development of cerebellar ataxia.
      Title: Cerebellar defects in Pdss2 conditional knockout mice during embryonic development and in adulthood.
    4. The authors report that homozygousPdss2 missense mutants also demonstrate significant neuromuscular deficits, as validated by behavioral and coordination assays.
      Title: Parkinson's disease-like neuromuscular defects occur in prenyl diphosphate synthase subunit 2 (Pdss2) mutant mice.
    5. Data show that focal segmental glomerulopathy-like kidney disease in Pdss2 mutant animals with primary coenzyme Q (CoQ) deficiency is significantly ameliorated by oral treatment with probucol.
      Title: Probucol ameliorates renal and metabolic sequelae of primary CoQ deficiency in Pdss2 mutant mice.
    6. Calorie restriction increased both ubiquinone homologues and mPDSS2 mRNA in skeletal muscle, but mCOQ7 was decreased.
      Title: Calorie restriction modifies ubiquinone and COQ transcript levels in mouse tissues.
    7. Dietary supplementation with coenzyme Q10 provides a dramatic rescue of both proteinuria and interstitial nephritis in the Pdss2kd/kd mutant mice.
      Title: Coenzyme Q10 supplementation rescues renal disease in Pdss2kd/kd mice with mutations in prenyl diphosphate synthase subunit 2.
    8. a presumed autoimmune kidney disease in mice with the missense Pdss2(kd/kd) genotype can be attributed to a mitochondrial CoQ biosynthetic defect
      Title: Primary coenzyme Q deficiency in Pdss2 mutant mice causes isolated renal disease.
    9. In kd/kd mice the tubular epithelial defect triggers autoimmune interstitial nephritis, whereas a defect in podocytes leads to proteinuria and glomerulosclerosis.
      Title: Glomerular and tubular epithelial defects in kd/kd mice lead to progressive renal failure.
    10. murine and human solanesyl and decaprenyl diphosphate synthases are heterotetramers composed of newly characterized hDPS1 (mSPS1) and hDLP1 (mDLP1).
      Title: Characterization of solanesyl and decaprenyl diphosphate synthases in mice and humans.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    Phenotypes

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    Associated conditions

    Description Tests
    kidney disease
    GeneReviews: Not available

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    contributes_to all-trans-decaprenyl-diphosphate synthase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    contributes_to all-trans-decaprenyl-diphosphate synthase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    contributes_to all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables prenyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein heterodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cerebellum development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in isoprenoid biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in isoprenoid biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in isoprenoid biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of body fluid levels IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in ubiquinone biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ubiquinone biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in ubiquinone biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ubiquinone biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of heterotetrameric polyprenyl diphosphate synthase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of heterotetrameric polyprenyl diphosphate synthase complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in mitochondrion HDA PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of polyprenyl diphosphate synthase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    all trans-polyprenyl-diphosphate synthase PDSS2
    Names
    all-trans-decaprenyl-diphosphate synthase subunit 2
    decaprenyl pyrophosphate synthase subunit 2
    decaprenyl pyrophosphate synthetase subunit 2
    decaprenyl-diphosphate synthase subunit 2
    prenyltransferase-like mitochondrial protein
    solanesyl-diphosphate synthase subunit 2
    NP_001161761.1
    NP_082048.2
    XP_006512915.1
    XP_006512916.1
    XP_006512917.1
    XP_036011908.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001168289.1 → NP_001161761.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform 2

      See identical proteins and their annotated locations for NP_001161761.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and includes an alternate exon in the 3' coding region, which results in a frameshift, compared to variant 1. The resulting protein (isoform 2) has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AK140091, BY733519
      Consensus CDS
      CCDS48552.1
      UniProtKB/TrEMBL
      E0CYM9
      Related
      ENSMUSP00000124864.2, ENSMUST00000159139.8
      Conserved Domains (1) summary
      cl00210
      Location:65 → 348
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

    2. NM_027772.2 → NP_082048.2  all trans-polyprenyl-diphosphate synthase PDSS2 isoform 1

      See identical proteins and their annotated locations for NP_082048.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC152922, BC147693, BY733519
      Consensus CDS
      CCDS35891.1
      UniProtKB/Swiss-Prot
      B2RWA7, B2RWF3, Q33DR3, Q3USU6, Q9D3K7
      UniProtKB/TrEMBL
      E0CYM9
      Related
      ENSMUSP00000093393.5, ENSMUST00000095725.11
      Conserved Domains (1) summary
      cl00210
      Location:69 → 401
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000076.7 Reference GRCm39 C57BL/6J

      Range
      43095396..43340878
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006512852.5 → XP_006512915.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X1

      See identical proteins and their annotated locations for XP_006512915.1

      UniProtKB/TrEMBL
      E0CYM9
      Conserved Domains (1) summary
      cl00210
      Location:69 → 390
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

    2. XM_006512854.5 → XP_006512917.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X3

      Conserved Domains (1) summary
      cl00210
      Location:69 → 232
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

    3. XM_036156015.1 → XP_036011908.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X4

      Conserved Domains (1) summary
      cl00210
      Location:69 → 241
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

    4. XM_006512853.5 → XP_006512916.1  all trans-polyprenyl-diphosphate synthase PDSS2 isoform X2

      UniProtKB/TrEMBL
      E0CYM9
      Related
      ENSMUSP00000124046.2, ENSMUST00000160823.8
      Conserved Domains (1) summary
      cl00210
      Location:69 → 320
      Isoprenoid_Biosyn_C1; Isoprenoid Biosynthesis enzymes, Class 1

    RNA

    1. XR_871439.4 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q33DR3.2 GenPept UniProtKB/Swiss-Prot:Q33DR3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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