Mitochondrial Nucleotide Transporters #694
Comments
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@Devlin-Moyer these rxns mentioned in the beginning are missing in the tasks/actions.
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oops, looks like I forgot those; I'll add them to the list of new reactions to add |
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@Devlin-Moyer very nice findings! it has been nearly 10 years since the publication of this paper, are there any new isoenzymes of these transporters reported recently? |
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not that I can tell; the only more recent papers that mention either gene that I can find were looking for something else and happened to find that one or both was over- or under-expressed in response to some perturbation. |
good to know this. I assume it was found manually, if it's possible to get it done by script automatically? |
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yea all the papers I've found for all my issues were ones I found manually, either by directly searching on Google Scholar or looking at references on Uniprot pages for specific proteins; I have no thoughts or experience on any sort of automated paper-finding script |
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fixed in #709 |
According to this paper (specifically Figure 4 and Table 1 from that paper), SLC25A33 (
ENSG00000171612) and SLC25A36 (ENSG00000114120) can transport pyrimidine (d)NTPs, (d)NDPs, and (d)NMPs from the cytosol into the mitochondria. To be specific:ENSG00000114120ENSG00000114120ENSG00000114120ENSG00000114120ENSG00000114120ENSG00000114120ENSG00000114120ENSG00000114120ENSG00000114120ENSG00000114120ENSG00000114120ENSG00000114120ENSG00000114120ENSG00000114120ENSG00000114120 or ENSG00000171612ENSG00000114120ENSG00000114120ENSG00000114120ENSG00000114120ENSG00000114120ENSG00000171612ENSG00000171612ENSG00000171612ENSG00000171612ENSG00000171612ENSG00000171612ENSG00000171612ENSG00000171612ENSG00000171612ENSG00000171612ENSG00000171612ENSG00000171612ENSG00000114120 or ENSG00000171612ENSG00000114120 or ENSG00000171612ENSG00000171612ENSG00000114120 or ENSG00000171612The only one of those reactions that is already represented in Human-GEM is
MAR08301: dTTP [c] ⇒ dTTP [m], but it is irreversible has no genes associated with it; it should be made reversible and have its GPR set toENSG00000171612.There are also
MAR07823: dCTP [c] ⇒ dCTP [m],MAR07926: dGTP [c] ⇒ dGTP [m], andMAR09019: CDP [c] ⇒ CDP [m], none of which have any associated genes. Adding all of the reactions in the table above would allow all three of these metabolites to be exchanged and actually have evidence supporting their existence, so I thinkMAR07823,MAR07926, andMAR09019should be removed. Similarly, I thinkMAR04843: GDP [c] + GTP [m] ⇔ GDP [m] + GTP [c]should also be removed in favor of the reactions in the above table; it is currently associated with ALDH1A3, ALDH3A1, and ALDH3B2, but none of those known to exchange GTP and GDP between the cytosol and mitochondria. The only reference associated withMAR04843just shows that GTP, GDP, and GMP can be transported into mitochondria from their surroundings and does not identify which gene(s) is/are responsible or even whether this transport is antiport, symport, or uniport.There are also a large number of reactions that exchange (d)NTPs and (d)NDPs catalyzed by SLC15A19 that should all be removed, but I address that in #695.
Proposed Changes
ENSG00000171612(name: SLC25A33) andENSG00000114120(name: SLC25A36)MAR08301reversible and change its GPR toENSG00000171612MAR07823MAR07926MAR09019MAR04843CTP [c] + CDP [m] <-> CTP [m] + CDP [c], GPR:ENSG00000114120CTP [c] + CMP [m] <-> CTP [m] + CMP [c], GPR:ENSG00000114120CTP [c] + dCTP [m] <-> CTP [m] + dCTP [c], GPR:ENSG00000114120CTP [c] + dCDP [m] <-> CTP [m] + dCDP [c], GPR:ENSG00000114120CTP [c] + dCMP [m] <-> CTP [m] + dCMP [c], GPR:ENSG00000114120CTP [c] + GTP [m] <-> CTP [m] + GTP [c], GPR:ENSG00000114120CTP [c] + GDP [m] <-> CTP [m] + GDP [c], GPR:ENSG00000114120CTP [c] + GMP [m] <-> CTP [m] + GMP [c], GPR:ENSG00000114120CTP [c] + dGTP [m] <-> CTP [m] + dGTP [c], GPR:ENSG00000114120CTP [c] + dGDP [m] <-> CTP [m] + dGDP [c], GPR:ENSG00000114120CTP [c] + dGMP [m] <-> CTP [m] + dGMP [c], GPR:ENSG00000114120CTP [c] + ITP [m] <-> CTP [m] + ITP [c], GPR:ENSG00000114120CTP [c] + IDP [m] <-> CTP [m] + IDP [c], GPR:ENSG00000114120CTP [c] + IMP [m] <-> CTP [m] + IMP [c], GPR:ENSG00000114120CTP [c] + UTP [m] <-> CTP [m] + UTP [c], GPR:ENSG00000114120 or ENSG00000171612CTP [c] + UDP [m] <-> CTP [m] + UDP [c], GPR:ENSG00000114120CTP [c] + UMP [m] <-> CTP [m] + UMP [c], GPR:ENSG00000114120CTP [c] + dUTP [m] <-> CTP [m] + dUTP [c], GPR:ENSG00000114120CTP [c] + dUDP [m] <-> CTP [m] + dUDP [c], GPR:ENSG00000114120CTP [c] + dUMP [m] <-> CTP [m] + dUMP [c], GPR:ENSG00000114120UTP [c] + CDP [m] <-> UTP [m] + CDP [c], GPR:ENSG00000171612UTP [c] + dCTP [m] <-> UTP [m] + dCTP [c], GPR:ENSG00000171612UTP [c] + dCDP [m] <-> UTP [m] + dCDP [c], GPR:ENSG00000171612UTP [c] + GTP [m] <-> UTP [m] + GTP [c], GPR:ENSG00000171612UTP [c] + GDP [m] <-> UTP [m] + GDP [c], GPR:ENSG00000171612UTP [c] + dGTP [m] <-> UTP [m] + dGTP [c], GPR:ENSG00000171612UTP [c] + dGDP [m] <-> UTP [m] + dGDP [c], GPR:ENSG00000171612UTP [c] + ITP [m] <-> UTP [m] + ITP [c], GPR:ENSG00000171612UTP [c] + dTTP [m] <-> UTP [m] + dTTP [c], GPR:ENSG00000171612UTP [c] + dTDP [m] <-> UTP [m] + dTDP [c], GPR:ENSG00000171612UTP [c] + UDP [m] <-> UTP [m] + UDP [c], GPR:ENSG00000171612UTP [c] + dUTP [m] <-> UTP [m] + dUTP [c], GPR:ENSG00000171612CTP [c] <-> CTP [m], GPR:ENSG00000114120 or ENSG00000171612GTP [c] <-> GTP [m], GPR:ENSG00000114120 or ENSG00000171612UTP [c] <-> UTP [m], GPR:ENSG00000114120 or ENSG00000171612The text was updated successfully, but these errors were encountered: