Disorders of Mitochondrial Homeostatis, Dynamics, Protein Import, and Quality Control (Homo sapiens)

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Description

This pathway lists several genes involved in mechanisms involved in disorders of mitochondrial homeostatis, dynamics, protein import, and quality control. This pathway was inspired by Figure 46.1 of Edition 5, Chapter 46 of the book of Blau (ISBN 9783030677268). Genes linked to a disease in this book chapter are depicted in red.

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Quality Tags

Ontology Terms

 

Bibliography

  1. Becirovic T, Zhang B, Lindskog C, Norberg E, Vakifahmetoglu-Norberg H, Kaminskyy VO, Kochetkova E; ''Deubiquitinase USP9x regulates the proline biosynthesis pathway in non-small cell lung cancer.''; Cell Death Discov, 2024 PubMed Europe PMC Scholia
  2. Poerschke S, Oeljeklaus S, Cruz-Zaragoza LD, Schenzielorz A, Dahal D, Hillen HS, Das H, Kremer LS, Valpadashi A, Breuer M, Sattmann J, Richter-Dennerlein R, Warscheid B, Dennerlein S, Rehling P; ''Identification of TMEM126A as OXA1L-interacting protein reveals cotranslational quality control in mitochondria.''; Mol Cell, 2024 PubMed Europe PMC Scholia
  3. Park I, Kim KE, Kim J, Kim AK, Bae S, Jung M, Choi J, Mishra PK, Kim TM, Kwak C, Kang MG, Yoo CM, Mun JY, Liu KH, Lee KS, Kim JS, Suh JM, Rhee HW; ''Mitochondrial matrix RTN4IP1/OPA10 is an oxidoreductase for coenzyme Q synthesis.''; Nat Chem Biol, 2024 PubMed Europe PMC Scholia
  4. Pontifex CS, Zaman M, Fanganiello RD, Shutt TE, Pfeffer G; ''Valosin-Containing Protein (VCP): A Review of Its Diverse Molecular Functions and Clinical Phenotypes.''; Int J Mol Sci, 2024 PubMed Europe PMC Scholia
  5. Blau, Nenad, Duran, Marinus, Gibson, K. Michael, Dionisi-Vici, Carlo; ''Physician's Guidee to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases'''; , 2014

History

View all...
CompareRevisionActionTimeUserComment
136157view14:30, 20 December 2024Egonwmim-translocation and RoundedRectangle
136141view16:34, 19 December 2024DeSlChanged two lines to graphical ones
136140view16:31, 19 December 2024DeSlAdded last molecular interactions for VCP
136138view16:22, 19 December 2024DeSlAdded molecular interactions for TMEM126A and VCP
136130view15:42, 19 December 2024DeSlAdded IDs for datanodes missing
136129view15:40, 19 December 2024DeSlAdded LOHN1 ID
136128view15:37, 19 December 2024DeSlUpdated the description
136127view15:35, 19 December 2024DeSlAdded all OMIM IDs for this chapter!!
136125view14:27, 19 December 2024DeSlMore OMIM annotations :D
136123view13:54, 19 December 2024DeSlAdded OMIM links for mitochondrial degradation and more from biogenesis
136121view13:08, 19 December 2024DeSlAdded more OMIM links for mitochondrial biogenesis
136120view12:46, 19 December 2024DeSlAdded several OMIM links to mitochondrial biogenesis section
136114view11:11, 19 December 2024DeSlAdded OMIM links for 5 fusion proteins; annotated OPA3 en MSTO1
136113view10:54, 19 December 2024DeSlAdded OMIM IDs for first 5 IMDs
136112view10:47, 19 December 2024DeSlConnected first proteins to IMDs
136111view10:36, 19 December 2024DeSlAdded USP9X mediation of proline through PYCR3
136110view09:37, 19 December 2024DeSlAdded more details on RTN4IP1 involvement in COQ3 biotinylated.
136109view09:25, 19 December 2024DeSlAdded 4 missing proteins from chapter, linked one to current literature and PW model
136098view07:37, 18 December 2024EgonwTypo in the chapter figure?
136089view09:44, 15 December 2024EgonwAdded a reference to the book
136088view09:42, 15 December 2024EgonwModified description
136087view09:38, 15 December 2024EgonwOntology Term : 'mitochondrial disease pathway' added !
136086view09:38, 15 December 2024EgonwOntology Term : 'disease pathway' added !
136085view07:45, 15 December 2024EgonwCompleted the first draft
136084view17:42, 14 December 2024EgonwAnother bit
136083view17:34, 14 December 2024EgonwAnother bit
136081view17:01, 14 December 2024EgonwMore genes (identifiers based on gene name)
136080view16:55, 14 December 2024EgonwNew pathway

External references

DataNodes

View all...
NameTypeDatabase referenceComment
AFG3L2GeneProductENSG00000141385 (Ensembl)
AGKGeneProductENSG00000006530 (Ensembl)
AIFM1GeneProductENSG00000156709 (Ensembl)
ATAD3AGeneProductENSG00000197785 (Ensembl)
C1QBPGeneProductENSG00000108561 (Ensembl)
CLPBGeneProductENSG00000162129 (Ensembl)
CLPPGeneProductENSG00000125656 (Ensembl)
COQ3ProteinQ9NZJ6 (Uniprot-TrEMBL)
COQ5ProteinQ5HYK3 (Uniprot-TrEMBL) "Given that we identified COQ5 as part of the interactome of RTN4IP1-TurboID, it will be intriguing to further investigate whether RTN4IP1 can assist this reaction of COQ5." DOI: https://doi.org/10.1038/s41589-023-01452-w
CoQ BiosynthesisPathwayWP5037 (WikiPathways)
DNAJC19GeneProductENSG00000205981 (Ensembl)
DNM1LGeneProductENSG00000087470 (Ensembl)
GDAP1L1GeneProductGDAP1L1 (HGNC)
GFERGeneProductGFER (HGNC)
HSPA9GeneProductENSG00000113013 (Ensembl)
HSPD1GeneProductENSG00000144381 (Ensembl)
HTRA2GeneProductENSG00000115317 (Ensembl)
LONP1ProteinP36776 (Uniprot-TrEMBL)
MARCHF5ProteinQ9NX47 (Uniprot-TrEMBL) MITOL/March5
MCL1ProteinQ07820 (Uniprot-TrEMBL)
MFFGeneProductENSG00000168958 (Ensembl)
MFN1ProteinQ8IWA4 (Uniprot-TrEMBL)
MFN2GeneProductENSG00000116688 (Ensembl)
MICOS13GeneProductENSG00000174917 (Ensembl)
MICU1GeneProductENSG00000107745 (Ensembl)
MIPEPGeneProductENSG00000027001 (Ensembl)
MSTO1?ProteinQ9BUK6 (Uniprot-TrEMBL)
MSTO1ProteinQ9BUK6 (Uniprot-TrEMBL)
NADPHMetaboliteCHEBI:16474 (ChEBI) cofactor to PYCR3
NPLOC4ProteinQ8TAT6 (Uniprot-TrEMBL) AKA NPL4
OPA1GeneProductENSG00000198836 (Ensembl)
OPA3?ProteinQ9H6K4 (Uniprot-TrEMBL)
OPA3ProteinQ9H6K4 (Uniprot-TrEMBL)
OXA1LProteinQ15070 (Uniprot-TrEMBL)
PAM16GeneProductENSG00000217930 (Ensembl)
PINK1GeneProductENSG00000158828 (Ensembl)
PITRM1GeneProductENSG00000107959 (Ensembl)
PMPCAGeneProductENSG00000165688 (Ensembl)
PMPCBGeneProductENSG00000105819 (Ensembl)
PPA2GeneProductENSG00000138777 (Ensembl)
PRKNGeneProductENSG00000185345 (Ensembl)
PYCR1ProteinP32322 (Uniprot-TrEMBL) Active in Cytosol
PYCR2ProteinQ96C36 (Uniprot-TrEMBL) Active in Cytosol
PYCR3ProteinQ53H96 (Uniprot-TrEMBL) Active in Cytosol
ProlineMetaboliteCHEBI:26271 (ChEBI)
RTN4IP1ProteinQ8WWV3 (Uniprot-TrEMBL)
  • also known as optic atrophy-10 (OPA10); NADPH oxidoreductase, enriched in the mitochondrial matrix of muscle tissues. DOI: https://doi.org/10.1038/s41589-023-01452-w
  • "COQ3 was the most strongly biotinylated protein by RTN4IP1-TurboID, suggesting a potential involvement of RTN4IP1 in the CoQ production pathway within the mitochondria" DOI: https://doi.org/10.1038/s41589-023-01452-w
SACS?ProteinQ9NZJ4 (Uniprot-TrEMBL)
SASK1Protein
SFXN4GeneProductENSG00000183605 (Ensembl)
SLC25A46GeneProductENSG00000164209 (Ensembl)
SPG7GeneProductENSG00000197912 (Ensembl)
STAT2GeneProductENSG00000170581 (Ensembl)
TCA cyclePathwayWP78 (WikiPathways)
TIMM50GeneProductENSG00000105197 (Ensembl)
TIMM8AGeneProductENSG00000126953 (Ensembl)
TIMMDC1GeneProductENSG00000113845 (Ensembl)
TMEM126AProteinQ9H061 (Uniprot-TrEMBL)
TRAK1GeneProductENSG00000182606 (Ensembl)
TXN2GeneProductENSG00000100348 (Ensembl)
TXNRD2GeneProductENSG00000184470 (Ensembl)
UBXD1/UBXN6ProteinQ9BZV1 (Uniprot-TrEMBL)
UBXN1ProteinQ04323 (Uniprot-TrEMBL)
UFD1ProteinQ92890 (Uniprot-TrEMBL)
USP9XProteinQ93008 (Uniprot-TrEMBL)
  • Ubiquitin-specific peptidase 9 X-linked
  • "Collectively, these findings suggest that USP9x regulates the proline biosynthesis pathway and the proline cycle via PYCR3, which affects PPP and mitochondrial respiration." DOI: https://doi.org/10.1038/s41420-024-02111-2
Urea CyclePathwayWP4571 (WikiPathways)
VCPProteinP55072 (Uniprot-TrEMBL)
XPNPEP3 GeneProductENSG00000196236 (Ensembl) Listed as XNPEP3 in the chapter.
YME1L1GeneProductENSG00000136758 (Ensembl)
YME1L1ProteinQ96TA2 (Uniprot-TrEMBL) Not in Figure, but added in Table 46.35
arginineMetaboliteCHEBI:29016 (ChEBI)
biotinMetaboliteCHEBI:15956 (ChEBI)
glutamateMetaboliteCHEBI:14321 (ChEBI)
inner membrane translocation insertionPathwayWP2717 (WikiPathways)
ornithineMetaboliteCHEBI:18257 (ChEBI)
p47ProteinP08567 (Uniprot-TrEMBL)
pyrroline-5- carboxylateMetaboliteCHEBI:15893 (ChEBI) AKA P5C
α-KetoglutarateMetaboliteCHEBI:30915 (ChEBI) aka 2-oxoglutaric acid

Annotated Interactions

No annotated interactions

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