PXD046217

PXD046217 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-18 14:44:55	ID requested
⏵ 1	2024-05-22 23:47:48	announced

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]

submitter keyword: liver,Fish, mitochondria, prm, complex, allele

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

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/05/PXD046217

PRIDE project URI

• PRIDE
  1. PXD046217
     1. Label: PRIDE project
     2. Name: Xiphophorus Hybrid Liver Mitochondria PRM