The SSU processome interactome in Saccharomyces cerevisiae reveals novel protein subcomplexes

Ribosome assembly is an evolutionarily conserved and energy intensive process required for cellular growth, proliferation, and maintenance. In yeast, assembly of the small ribosomal subunit (SSU) requires approximately 75 assembly factors that act in coordination to form the SSU processome, a 6 MDa ribonucleoprotein complex. The SSU processome is required for processing, modifying, and folding the preribosomal RNA (rRNA) to prepare it for incorporation into the mature SSU. Although the protein composition of the SSU processome has been known for some time, the interaction network of the proteins required for its assembly has remained poorly defined. Here, we have used a semi-high-throughput yeast two-hybrid (Y2H) assay and coimmunoprecipitation validation method to produce a high-confidence interactome of SSU processome assembly factors (SPAFs), providing essential insight into SSU assembly and ribosome biogenesis. Further, we used glycerol density-gradient sedimentation to reveal the presence of protein subcomplexes that have not previously been observed. Our work not only provides essential insight into SSU assembly and ribosome biogenesis, but also serves as an important resource for future investigations into how defects in biogenesis and assembly cause congenital disorders of ribosomes known as ribosomopathies.

• Publication year

  2018

• Venue

  RNA: A publication of the RNA Society

• Publication date

  2018-01-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1261/rna.062927.117PMID 29054886PMCID 5733573
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Integrating the genomic architecture of human nucleolar organizer regions with the biophysical properties of nucleoli

  2017cited by this paper
• Interaction network of the ribosome assembly machinery from a eukaryotic thermophile

  2017influential reference
• Molecular architecture of the 90S small subunit pre-ribosome

  2017influential reference
• Architecture of the yeast small subunit processome

  2016cited by this paper
• Integrative structural analysis of the UTPB complex, an early assembly factor for eukaryotic small ribosomal subunits

  2016influential reference
• UtpA and UtpB chaperone nascent pre-ribosomal RNA and U3 snoRNA to initiate eukaryotic ribosome assembly

  2016influential reference
• Nucleolar organizer regions: genomic ‘dark matter’ requiring illumination

  2016cited by this paper
• Stepwise and dynamic assembly of the earliest precursors of small ribosomal subunits in yeast

  2016influential reference
• Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome.

  2016cited by this paper
• Cotranscriptional events in eukaryotic ribosome synthesis

  2015influential reference
• Ribosomopathies: Global process, tissue specific defects

  2015cited by this paper
• Processing of preribosomal RNA in Saccharomyces cerevisiae

  2015cited by this paper
• Stage-specific assembly events of the 6-MDa small-subunit processome initiate eukaryotic ribosome biogenesis

  2015influential reference
• A protein interaction map of the LSU processome

  2015cited by this paper
• Ribosomopathies: how a common root can cause a tree of pathologies

  2015cited by this paper
• Determinants of mammalian nucleolar architecture

  2015cited by this paper
• Human diseases of the SSU processome.

  2014cited by this paper
• In Vitro Reconstitution of Yeast tUTP/UTP A and UTP B Subcomplexes Provides New Insights into Their Modular Architecture

  2014influential reference
• Ribosomopathies: Mechanisms of Disease

  2014cited by this paper
• The roles of SSU processome components and surveillance factors in the initial processing of human ribosomal RNA

  2014cited by this paper
• Structure of Utp21 Tandem WD Domain Provides Insight into the Organization of the UTPB Complex Involved in Ribosome Synthesis

  2014cited by this paper
• The Human Plasma Membrane Peripherome: Visualization and Analysis of Interactions

  2014cited by this paper
• The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

  2013influential reference
• Mysterious Ribosomopathies

  2013cited by this paper
• Yeast and human RNA helicases involved in ribosome biogenesis: current status and perspectives.

  2013cited by this paper
• Chromatin states at ribosomal DNA loci.

  2013cited by this paper
• Ribosome Biogenesis in the Yeast Saccharomyces cerevisiae

  2013cited by this paper
• Dynamic protein-protein interaction wiring of the human spliceosome.

  2012cited by this paper
• clusterMaker: a multi-algorithm clustering plugin for Cytoscape

  2011cited by this paper
• The small subunit processome in ribosome biogenesis—progress and prospects

  2011cited by this paper
• Assembling a Protein-Protein Interaction Map of the SSU Processome from Existing Datasets

  2011cited by this paper
• Yeast protein-protein interaction assays and screens.

  2011cited by this paper
• Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile.

  2011cited by this paper
• Elucidation of the assembly events required for the recruitment of Utp20, Imp4 and Bms1 onto nascent pre-ribosomes

  2011cited by this paper
• The initial U3 snoRNA:pre-rRNA base pairing interaction required for pre-18S rRNA folding revealed by in vivo chemical probing

  2011cited by this paper
• A second base pair interaction between U3 small nucleolar RNA and the 5′-ETS region is required for early cleavage of the yeast pre-ribosomal RNA

  2011cited by this paper
• The DEAD-box RNA helicase-like Utp25 is an SSU processome component.

  2010cited by this paper
• Small epitope-linker modules for PCR-based C-terminal tagging in Saccharomyces cerevisiae

  2009cited by this paper
• Systems biology: Untangling the protein web

  2009influential reference
• Identifying functional modules in the physical interactome of Saccharomyces cerevisiae

  2007cited by this paper
• Examining protein protein interactions using endogenously tagged yeast arrays: the cross-and-capture system.

  2007cited by this paper
• A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality

  2007cited by this paper
• The 90S Preribosome Is a Multimodular Structure That Is Assembled through a Hierarchical Mechanism

  2007cited by this paper
• Comprehensive analysis of diverse ribonucleoprotein complexes

  2007influential reference
• Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

  2006cited by this paper
• Biochemical and genetic analysis of the yeast proteome with a movable ORF collection.

  2005influential reference
• High-definition macromolecular composition of yeast RNA-processing complexes.

  2004influential reference
• Pre-18S ribosomal RNA is structurally compacted into the SSU processome prior to being cleaved from nascent transcripts in Saccharomyces cerevisiae.

  2004cited by this paper
• RNA polymerase I transcription and pre-rRNA processing are linked by specific SSU processome components.

  2004cited by this paper
• Cytoscape: a software environment for integrated models of biomolecular interaction networks.

  2003influential reference
• Detection of functional modules from protein interaction networks

  2003cited by this paper
• A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis

  2002cited by this paper
• Protein-protein interactions between large proteins: two-hybrid screening using a functionally classified library composed of long cDNAs.

  2002cited by this paper
• Components of an Interdependent Unit within the SSU Processome Regulate and Mediate Its Activity

  2002cited by this paper
• 90S pre-ribosomes include the 35S pre-rRNA, the U3 snoRNP, and 40S subunit processing factors but predominantly lack 60S synthesis factors.

  2002cited by this paper
• The tandem affinity purification (TAP) method: a general procedure of protein complex purification.

  2001cited by this paper
• Interactions of Isw2 Chromatin Remodeling Complex with Nucleosomal Arrays: Analyses Using Recombinant Yeast Histones and Immobilized Templates

  2001cited by this paper
• A common core RNP structure shared between the small nucleoar box C/D RNPs and the spliceosomal U4 snRNP.

  2000cited by this paper
• Base Pairing between U3 Small Nucleolar RNA and the 5′ End of 18S rRNA Is Required for Pre-rRNA Processing

  1999cited by this paper
• The economics of ribosome biosynthesis in yeast.

  1999cited by this paper
• Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast.

  1996influential reference
• Functional base-pairing interaction between highly conserved elements of U3 small nucleolar RNA and the small ribosomal subunit RNA.

  1996cited by this paper
• Base pairing between U3 and the pre‐ribosomal RNA is required for 18S rRNA synthesis.

  1995cited by this paper
• Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds.

  1995cited by this paper
• Mutational analysis of an essential binding site for the U3 snoRNA in the 5' external transcribed spacer of yeast pre-rRNA.

  1994cited by this paper
• Gene RRN4 in Saccharomyces cerevisiae encodes the A12.2 subunit of RNA polymerase I and is essential only at high temperatures

  1993cited by this paper
• The p21 Cdk-interacting protein Cip1 is a potent inhibitor of G1 cyclin-dependent kinases.

  1993influential reference
• Identification and functional analysis of two U3 binding sites on yeast pre‐ribosomal RNA.

  1992cited by this paper
• A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae.

  1989cited by this paper
• Improved silver staining of plant proteins, RNA and DNA in polyacrylamide gels

  1987cited by this paper
• Genetics

  1981cited by this paper
• Molecular Systems Biology Peer Review Process File toward an Understanding of the Protein Interaction Network of Human Liver Transaction Report

  year unknowncited by this paper

• How the concentric organization of the nucleolus and chromatin ensures accuracy of ribosome biogenesis and drives transport.

  2025cites this paper
• WDR75: An essential protein for ribosome assembly undergoing purifying selection

  2025cites this paper
• In‐Cell Proteomics Enables High‐Resolution Temporal Profiling of Cell Cycle Progression and DNA Damage Response in Saccharomyces cerevisiae

  2025cites this paper
• An artifact of recombinatorial cloning challenges established beliefs of plasmid cotransformation, selection, and maintenance.

  2025cites this paper
• Domain definition and preliminary functional exploration of the endonuclease NOBP-1 in Strongyloides stercoralis

  2023cites this paper
• RNA folding and functions of RNA helicases in ribosome biogenesis

  2022cites this paper
• The SSU Processome Component Utp25p is a Pseudohelicase

  2022cites this paper
• The dual nature of the nucleolus

  2022cites this paper
• Production of nascent ribosome precursors within the nucleolar microenvironment of Saccharomyces cerevisiae.

  2022cites this paper
• An oomycete effector targets a plant RNA helicase involved in root development and defense.

  2021cites this paper
• The nucleolus as a polarized coaxial cable in which the rDNA axis is surrounded by dynamic subunit-specific phases.

  2021cites this paper
• Blocking a dead-end assembly pathway creates a point of regulation for the DEAD-box ATPase Has1 and prevents platform misassembly

  2021cites this paper
• The ARRE RING-Type E3 Ubiquitin Ligase Negatively Regulates Cuticular Wax Biosynthesis in Arabidopsis thaliana by Controlling ECERIFERUM1 and ECERIFERUM3 Protein Levels

  2021cites this paper
• A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis

  2021cites this paper
• Synergistic defects in pre-rRNA processing from mutations in the U3-specific protein Rrp9 and U3 snoRNA

  2020cites this paper
• Bud23 promotes the final disassembly of the small subunit Processome in Saccharomyces cerevisiae

  2020cites this paper
• Bud23 promotes the progression of the Small Subunit Processome to the pre-40S ribosome in Saccharomyces cerevisiae

  2020cites this paper
• Eukaryotic Ribosome Assembly.

  2019cites this paper
• Assembly and structure of the SSU processome-a nucleolar precursor of the small ribosomal subunit.

  2018cites this paper
• Ribosome assembly coming into focus

  2018cites this paper
• Utp14 interaction with the small subunit processome

  2018cites this paper