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PXD046217

PXD046217 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleXiphophorus Hybrid Liver Mitochondria PRM
DescriptionHybrids between species contain a mixture of two divergent proteomes, the combination of which may lead to dysfunctional protein-protein interactions. We performed an integrative study on hybrids between the swordtail fishes Xiphophorus malinche and Xiphophorus birchmanni, and found that the combination of X. birchmanni ndufs5 (a nuclear-encoded subunit of mitochondrial Complex I) with X. malinche mtDNA (which codes for multiple Complex I subunits) was lethal. We reasoned that if this lethality was due to dysfunctional protein-protein interactions in Complex I causing improper assembly, then in heterozygotes which possess one functional and one dysfunctional allele, the dysfunctional allele might be more likely to exist in an improperly integrated/folded state, and thus be more likely to be degraded by protein quality control mechanisms. This preferential degradation would be measurable as a bias in the proteome towards the compatible allele of ndufs5, and so we sought to measure the relative abundance of peptides derived from the X. malinche and X. birchmanni alleles of ndufs5 in hybrids heterozygous at ndufs5, with X. malinche ancestry in the mtDNA. Peptides derived from each allele are distinguishable by multiple amino acids, and we used heavy-labeled spike-ins to target multiple ndufs5 peptides from each species in 5 hybrids. We successfully detected one pair of birchmanni/malinche peptides, and compared their relative abundance using peak integration, then compared the ratio to that observed in the heavy-labeled spike-in, for which the true ratio was known. We found that the endogenous peptides were skewed towards the allele from the same species as the mtDNA (X. malinche), consistent with our hypothesis.
HostingRepositoryPRIDE
AnnounceDate2024-05-23
AnnouncementXMLSubmission_2024-05-22_23:47:47.533.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD046217
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterBen Moran
SpeciesList scientific name: Xiphophorus malinche x Xiphophorus birchmanni; NCBI TaxID: 1500961;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-10-18 14:44:55ID requested
12024-05-22 23:47:48announced
Publication List
10.1038/s41586-023-06895-8;
10.6019/PXD046217;
Moran BM, Payne CY, Powell DL, Iverson ENK, Donny AE, Banerjee SM, Langdon QK, Gunn TR, Rodriguez-Soto RA, Madero A, Baczenas JJ, Kleczko KM, Liu F, Matney R, Singhal K, Leib RD, Hernandez-Perez O, Corbett-Detig R, Frydman J, Gifford C, Schartl M, Havird JC, Schumer M, A lethal mitonuclear incompatibility in complex I of natural hybrids. Nature, 626(7997):119-127(2024) [pubmed]
Keyword List
submitter keyword: liver,Fish, mitochondria, prm, complex, allele
Contact List
Molly E Schumer
contact affiliationDepartment of Biology, Stanford University, USA
contact emailschumer@stanford.edu
lab head
Ben Moran
contact affiliationStanford University
contact emailbenmoran@stanford.edu
dataset submitter
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Dataset FTP location
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