PXD019329

PXD019329 is an original dataset announced via ProteomeXchange.

Title	Separation and Paired Proteome Profiling of Plant Chloroplast and Cytoplasmic Ribosomes
Description	Conventional preparation methods of plant ribosomes fail to resolve non-translating chloroplast or cytoplasmic ribosome subunits from translating fractions. We established preparation of these ribosome complexes from Arabidopsis thaliana leaf, root, and seed tissues by optimized sucrose density gradient centrifugation of protease protected plant extracts. The method co-purified non-translating 30S and 40S ribosome subunits, separated non-translating 50S from 60S subunits, and resolved assembled monosomes from low oligomeric polysomes. Combining ribosome fractionation with microfluidic rRNA analysis and proteomics, we characterized the rRNA and ribosomal protein (RP) composition. The identity of cytoplasmic and chloroplast ribosome complexes and the presence of ribosome biogenesis factors in the 60S - 80S sedimentation interval were verified. In vivo cross-linking of leaf tissue stabilized ribosome biogenesis complexes but induced polysome run-off. Omitting cross-linking, the established paired fractionation and proteome analysis monitored relative abundances of plant chloroplast and cytoplasmic ribosome fractions and enabled analysis of RP composition and ribosome associated proteins including transiently associated biogenesis factors.
HostingRepository	PRIDE
AnnounceDate	2021-09-09
AnnouncementXML	Submission_2021-09-08_23:34:50.724.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Michal Gorka
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-05-21 15:53:38	ID requested
⏵ 1	2021-09-08 23:34:51	announced

Firmino AAP, Gorka M, Graf A, Skirycz A, Martinez-Seidel F, Zander K, Kopka J, Beine-Golovchuk O, Separation and Paired Proteome Profiling of Plant Chloroplast and Cytoplasmic Ribosomes. Plants (Basel), 9(7):(2020) [pubmed]

submitter keyword: in vivo protein complex stabilization, plant proteomics, ribo-proteome, ribosome complexes, tissue specific separation

Joachim Kopka
contact affiliation	Prof. Dr. Joachim Kopka Max-Planck-Institut für Molekulare Pflanzenphysiologie Potsdam Science Park Am Mühlenberg 1 14476 Potsdam, German
contact email	kopka@mpimp-golm.mpg.de
lab head
Michal Gorka
contact affiliation	Max Planck Institute for Molecular Plant Physiology
contact email	gorka@mpimp-golm.mpg.de
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/2021/09/PXD019329

PRIDE project URI

• PRIDE
  1. PXD019329
     1. Label: PRIDE project
     2. Name: Separation and Paired Proteome Profiling of Plant Chloroplast and Cytoplasmic Ribosomes