PXD073587

PXD073587 is an original dataset announced via ProteomeXchange.

Title	Phosphorylation patterns of pre-ribosomal proteins associated with exosome subunits
Description	This project investigates the phosphorylation landscape of protein factors associated with distinct assemblies of the RNA exosome in Saccharomyces cerevisiae. The RNA exosome is a conserved 3′–5′ exoribonuclease complex essential for pre-rRNA processing, ribosome biogenesis, and RNA quality control. Although its structural organization and cofactors have been well characterized, the regulatory contribution of post-translational modifications, particularly phosphorylation, to exosome recruitment and function remains poorly understood. To address this, we performed comparative phosphoproteomic analyses of protein complexes co-purified with either the nuclear subunit Rrp6 or the core subunit Rrp46. Yeast strains expressing TAP-tagged Rrp6 or Rrp46 were grown in controlled conditions and used for tandem affinity purification (TAP)–based co-immunoprecipitation. A wild-type W303 strain served as a negative control to subtract background interactors. Cell lysates were obtained by cryogenic milling and clarified by ultracentrifugation before incubation with IgG-Sepharose. After TEV protease elution, proteins were lyophilized and subjected to in-solution digestion with sequencing-grade trypsin. Phosphopeptides were enriched using TiO₂ spin tips and analyzed by nano-LC–MS/MS on an LTQ-Orbitrap Velos operated in data-dependent acquisition mode. Raw files were processed with MaxQuant (v2.6.7.0) using standard parameters for phosphosite identification and a 1% FDR cutoff. Across biological triplicates, the dataset comprises 756 phosphorylated peptides and 111 high-confidence phosphosites functionally linked to rRNA maturation, pre-ribosomal particle assembly, nucleocytoplasmic transport, exosome cofactors, and ribosome biogenesis. Principal component analysis confirmed strong replicate clustering. Comparative analysis revealed phosphorylation events exclusive to either Rrp6- or Rrp46-associated complexes, as well as shared sites indicative of constitutive regulatory functions. Several phosphosites mapped to core exosome subunits (Csl4, Rrp4, Rrp6) and cofactors such as Mpp6, Mtr4, and Ski7, highlighting regulatory hotspots potentially involved in exosome recruitment dynamics and cytoplasmic versus nuclear functions. Functional interrogation of selected residues (e.g., Ski7-S90 and Rrp4-S152) demonstrated differential growth phenotypes upon alanine substitution, supporting their biological relevance. Together, these data provide a comprehensive phosphoproteomic profile of exosome-associated assemblies at distinct stages of ribosome maturation. The dataset enables exploration of post-translational regulatory mechanisms governing exosome recruitment, activity modulation, and interaction with ribosomal precursors and cofactors. The high-resolution phosphosite map supplied here offers an important resource for understanding dynamic control of RNA metabolism in eukaryotes and supports future mechanistic studies on exosome regulation and ribosome biogenesis.
HostingRepository	PRIDE
AnnounceDate	2026-08-20
AnnouncementXML	Submission_2026-08-19_22:38:28.120.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Felipe Almeida
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: NEWT:4932;
ModificationList	phosphorylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2026-01-26 13:11:48	ID requested
⏵ 1	2026-08-19 22:38:28	announced

10.1021/ACS.JPROTEOME.6C00095;

submitter keyword: Affinity purification–mass spectrometry

Phosphosite mapping

SSU processome

Ribosome assembly factors;

Carla Columbano de Oliveira
contact affiliation	Department of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000, São Paulo, SP, Brazil.
contact email	ccoliv@iq.usp.br
lab head
Felipe Almeida
contact affiliation	Laboratory of Chemistry and Function of Proteins and Peptides
contact email	flp_astolpho@uenf.br
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/2026/08/PXD073587

PRIDE project URI

• PRIDE
  1. PXD073587
     1. Label: PRIDE project
     2. Name: Phosphorylation patterns of pre-ribosomal proteins associated with exosome subunits