PXD009990

PXD009990 is an original dataset announced via ProteomeXchange.

Title	Direct proteome labelling in fruit flies with SILAF reveals differential phosphorylation of mitochondrial proteins upon loss of OXPHOS subunits
Description	Drosophila melanogaster has been a workhorse of genetics and cell biology for more than a century. However, proteomic-based methods have been limited due to the complexity and dynamic range of the fly proteome and the lack of efficient labelling methods. Here, we advanced a chemically defined food source into direct stable-isotope labelling of amino acids in flies (SILAF). It allows for the rapid and cost-efficient generation of a large number of larvae or flies, with full incorporation of lysine-[13C6] after six labelling days. SILAF followed by fractionation and enrichment gave proteomic insights at a depth of 7,196 proteins and 8,451 phosphorylation sites, which substantiated metabolic regulation on enzymatic level. We applied SILAF to quantify the mitochondrial phosphoproteome of an early-stage leucine-rich PPR motif-containing protein (LRPPRC)-knockdown fly model of mitochondrial disease that almost exclusively affects protein levels of the oxidative phosphorylation (OXPHOS) system. While the mitochondrial compartment was hypo-phosphorylated, two conserved phospho-sites on OXPHOS subunits NDUFB10 and NDUFA4 were significantly upregulated upon impaired OXPHOS function. The ease and versatility of the method actuates the fruit fly as an appealing model in proteomic and post-translational modification studies and it enlarges potential metabolic applications based on heavy amino acid diets.
HostingRepository	PRIDE
AnnounceDate	2021-02-10
AnnouncementXML	Submission_2021-02-10_00:02:23.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Florian Schober
SpeciesList	scientific name: Drosophila melanogaster (Fruit fly); NCBI TaxID: 7227;
ModificationList	6x(13)C labeled L-lysine; 13C(6)15N(4); phosphorylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2018-06-01 01:42:44	ID requested
⏵ 1	2021-02-10 00:02:23	announced

Dataset with its publication pending

submitter keyword: SILAC, SILAF, Drosophila, Drosophila melanogaster, fly, fruit fly, Methods development, OXPHOS, LRPPRC, bsf, holidic

Anna Wredenberg
contact affiliation	MBB, Karolinska Institutet, Stockholm/Sweden
contact email	anna.wredenberg@ki.se
lab head
Florian Schober
contact affiliation	MMK, Karolinska Institute
contact email	florian.schober@ki.se
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD009990
     1. Label: PRIDE project
     2. Name: Direct proteome labelling in fruit flies with SILAF reveals differential phosphorylation of mitochondrial proteins upon loss of OXPHOS subunits