PXD046217 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Xiphophorus Hybrid Liver Mitochondria PRM |
Description | Hybrids 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. |
HostingRepository | PRIDE |
AnnounceDate | 2024-05-23 |
AnnouncementXML | Submission_2024-05-22_23:47:47.533.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD046217 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Ben Moran |
SpeciesList | scientific name: Xiphophorus malinche x Xiphophorus birchmanni; NCBI TaxID: 1500961; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-10-18 14:44:55 | ID requested | |
⏵ 1 | 2024-05-22 23:47:48 | announced | |
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 affiliation | Department of Biology, Stanford University, USA |
contact email | schumer@stanford.edu |
lab head | |
Ben Moran |
contact affiliation | Stanford University |
contact email | benmoran@stanford.edu |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD046217
- Label: PRIDE project
- Name: Xiphophorus Hybrid Liver Mitochondria PRM