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• W2074405508 abstract "A remarkably large collection of evolutionarily conserved proteins has been implicated in processing of noncoding RNAs and biogenesis of ribonucleoproteins. To better define the physical and functional relationships among these proteins and their cognate RNAs, we performed 165 highly stringent affinity purifications of known or predicted RNA-related proteins from Saccharomyces cerevisiae. We systematically identified and estimated the relative abundance of stably associated polypeptides and RNA species using a combination of gel densitometry, protein mass spectrometry, and oligonucleotide microarray hybridization. Ninety-two discrete proteins or protein complexes were identified comprising 489 different polypeptides, many associated with one or more specific RNA molecules. Some of the pre-rRNA-processing complexes that were obtained are discrete subcomplexes of those previously described. Among these, we identified the IPI complex required for proper processing of the ITS2 region of the ribosomal RNA primary transcript. This study provides a high-resolution overview of the modular topology of noncoding RNA-processing machinery. A remarkably large collection of evolutionarily conserved proteins has been implicated in processing of noncoding RNAs and biogenesis of ribonucleoproteins. To better define the physical and functional relationships among these proteins and their cognate RNAs, we performed 165 highly stringent affinity purifications of known or predicted RNA-related proteins from Saccharomyces cerevisiae. We systematically identified and estimated the relative abundance of stably associated polypeptides and RNA species using a combination of gel densitometry, protein mass spectrometry, and oligonucleotide microarray hybridization. Ninety-two discrete proteins or protein complexes were identified comprising 489 different polypeptides, many associated with one or more specific RNA molecules. Some of the pre-rRNA-processing complexes that were obtained are discrete subcomplexes of those previously described. Among these, we identified the IPI complex required for proper processing of the ITS2 region of the ribosomal RNA primary transcript. This study provides a high-resolution overview of the modular topology of noncoding RNA-processing machinery. Advances in protein affinity purification and protein mass spectrometry have enabled the development of systems for large-scale examination of the polypeptide subunit compositions of protein complexes (Gavin et al., 2002Gavin A.C. Bosche M. Krause R. Grandi P. Marzioch M. Bauer A. Schultz J. Rick J.M. Michon A.M. Cruciat C.M. et al.Functional organization of the yeast proteome by systematic analysis of protein complexes.Nature. 2002; 415: 141-147Crossref PubMed Scopus (3786) Google Scholar, Ho et al., 2002Ho Y. Gruhler A. Heilbut A. Bader G.D. Moore L. Adams S.L. Millar A. Taylor P. Bennett K. Boutilier K. et al.Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.Nature. 2002; 415: 180-183Crossref PubMed Scopus (2923) Google Scholar). A large number of proteins, including the products of approximately 25% of essential yeast genes, are involved in synthesis and processing of noncoding RNAs or RNPs (Issel-Tarver et al., 2002Issel-Tarver L. Christie K.R. Dolinski K. Andrada R. Balakrishnan R. Ball C.A. Binkley G. Dong S. Dwight S.S. Fisk D.G. et al.Saccharomyces genome database.Methods Enzymol. 2002; 350: 329-346Crossref PubMed Scopus (107) Google Scholar). These RNAs are required for diverse cellular processes, including translation, telomere replication, transport across membranes, and processing of other RNAs. Many of these RNAs function as components of larger protein-containing macromolecular assemblies. Over 150 polypeptides have been established as being directly involved in rRNA processing and ribosome assembly (reviewed by Fatica and Tollervey 2002Fatica A. Tollervey D. Making ribosomes.Curr. Opin. Cell Biol. 2002; 14: 313-318Crossref PubMed Scopus (412) Google Scholar, Peng et al., 2003Peng W.T. Robinson M.D. Mnaimneh S. Krogan N.J. Cagney G. Morris Q. Davierwala A.P. Grigull J. Yang X. Zhang W. et al.A panoramic view of yeast non-coding RNA processing.Cell. 2003; 113: 919-933Abstract Full Text Full Text PDF PubMed Scopus (200) Google Scholar), and many of these are found in extremely large preribosomal particles. The processing of rRNA is a multistep process in which each step is likely to be catalyzed by a discrete subcomplex within the large preribosomal complexes. Therefore, mechanistic dissection of rRNA processing would be greatly facilitated by resolving the large preribosomal particles into discrete, functional subcomplexes. Here, we report the application of large-scale protein affinity purification, supported by three different analytical techniques, gel-based mass spectrometry (MS), gel-free tandem MS, and DNA microarrays, to systematically examine the protein and RNA compositions of macromolecular complexes known or predicted to be involved in the synthesis and processing of noncoding RNAs in yeast. Unlike all previous biochemical studies of preribosomal processing, we utilized prefractionation by high-speed centrifugation to deplete extracts of larger ribonucleoprotein assemblies (e.g., ribosomal and preribosomal complexes) as a means of defining some of the smaller, stable constituents of the RNA-processing machinery. Our results delineate an extended molecular interaction network of well-defined protein subcomplexes, including discrete components of the SSU processome (Dragon et al., 2002Dragon F. Gallagher J.E. Compagnone-Post P.A. Mitchell B.M. Porwancher K.A. Wehner K.A. Wormsley S. Settlage R.E. Shabanowitz J. Osheim Y. et al.A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis.Nature. 2002; 417: 967-970Crossref PubMed Scopus (520) Google Scholar) and pre-60S particle. Many of these protein complexes were physically associated with one or more specific RNA molecules, including, in some cases, the apparent substrate(s). To enable efficient affinity purification of proteins known or predicted to function in RNA-related processing, we created a total of 165 yeast strains bearing a C-terminal tandem affinity purification (TAP) tag (Rigaut et al., 1999Rigaut G. Shevchenko A. Rutz B. Wilm M. Mann M. Seraphin B. A generic protein purification method for protein complex characterization and proteome exploration.Nat. Biotechnol. 1999; 17: 1030-1032Crossref PubMed Scopus (2226) Google Scholar) fused to a single gene product. Of these, 91 proteins were chosen based on an extensive, manual survey of several on-line yeast protein function databases with the aim of having at least one protein representing each known RNA-processing category (Mewes et al., 2002; YPD [Incyte Genomics], SGD Issel-Tarver et al., 2002Issel-Tarver L. Christie K.R. Dolinski K. Andrada R. Balakrishnan R. Ball C.A. Binkley G. Dong S. Dwight S.S. Fisk D.G. et al.Saccharomyces genome database.Methods Enzymol. 2002; 350: 329-346Crossref PubMed Scopus (107) Google Scholar). As well, 88 protein baits were predicted to have a related function on the basis of transcriptional coregulation with established RNA-processing proteins (Wu et al., 2002Wu L.F. Hughes T.R. Davierwala A.P. Robinson M.D. Stoughton R. Altschuler S.J. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters.Nat. Genet. 2002; 31: 255-265Crossref PubMed Scopus (279) Google Scholar), while 28 baits had sequence homology to human nucleolar proteins (Andersen et al., 2002Andersen J.S. Lyon C.E. Fox A.H. Leung A.K. Lam Y.W. Steen H. Mann M. Lamond A.I. Directed proteomic analysis of the human nucleolus.Curr. Biol. 2002; 12: 1-11Abstract Full Text Full Text PDF PubMed Scopus (787) Google Scholar). Western blots were performed to confirm the success of the tagging procedures (see Experimental Procedures). The tagged proteins were isolated from log-phase cultures using a tandem affinity purification procedure (Rigaut et al., 1999Rigaut G. Shevchenko A. Rutz B. Wilm M. Mann M. Seraphin B. A generic protein purification method for protein complex characterization and proteome exploration.Nat. Biotechnol. 1999; 17: 1030-1032Crossref PubMed Scopus (2226) Google Scholar) that intrinsically minimizes nonspecific background (Krogan et al., 2002Krogan N.J. Kim M. Ahn S.H. Zhong G. Kobor M.S. Cagney G. Emili A. Shilatifard A. Buratowski S. Greenblatt J. RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach.Mol. Cell. Biol. 2002; 22: 6979-6992Crossref PubMed Scopus (389) Google Scholar; see Experimental Procedures). Furthermore, in order to specifically remove 90S and pre-60S ribosomal complexes, the extracts were subjected to a high-speed centrifugation step (180,000 g for 45 min) to pellet the 40S and 60S ribosomal subunits. When we used a strain with a TAP tag on Erb1, only two other proteins, Nop7 and Ytm1, were obtained in approximately equimolar stoichiometry (Figure 1A) in a complex previously described by Du and Stillman 2002Du Y.C. Stillman B. Yph1p, an ORC-interacting protein: potential links between cell proliferation control, DNA replication, and ribosome biogenesis.Cell. 2002; 109: 835-848Abstract Full Text Full Text PDF PubMed Scopus (149) Google Scholar. In contrast, reducing the time and speed of centrifugation resulted in the copurification of many other proteins (Figure 1B), a number of which were originally described as components of the pre-60S complex (data not shown) (Du and Stillman 2002Du Y.C. Stillman B. Yph1p, an ORC-interacting protein: potential links between cell proliferation control, DNA replication, and ribosome biogenesis.Cell. 2002; 109: 835-848Abstract Full Text Full Text PDF PubMed Scopus (149) Google Scholar, Bassler et al., 2001Bassler J. Grandi P. Gadal O. Lessmann T. Petfalski E. Tollervey D. Lechner J. Hurt E. Identification of a 60S preribosomal particle that is closely linked to nuclear export.Mol. Cell. 2001; 8: 517-529Abstract Full Text Full Text PDF PubMed Scopus (264) Google Scholar, Harnpicharnchai et al., 2001Harnpicharnchai P. Jakovljevic J. Horsey E. Miles T. Roman J. Rout M. Meagher D. Imai B. Guo Y. Brame C.J. et al.Composition and functional characterization of yeast 66S ribosome assembly intermediates.Mol. Cell. 2001; 8: 505-515Abstract Full Text Full Text PDF PubMed Scopus (242) Google Scholar). With the expectation of identifying many of the subcomplexes that had previously been described only as components of much larger assemblies, we therefore decided to purify the complexes using the higher-speed centrifugation step. Each polypeptide visible on a silver-stained SDS-polyacrylamide gel after purification from a tagged strain (and absent from a parallel control preparation from an untagged strain) was excised and identified by MALDI-TOF mass spectrometry. In parallel, a second portion of the affinity-purified protein preparation was digested with trypsin in solution and analyzed by gel-free capillary-scale reverse-phase liquid chromatography-electrospray ion-trap tandem MS (LC-MS/MS) in order to identify small and/or less abundant polypeptides. Finally, RNA was extracted from a third aliquot of many of the protein preparations, treated with DNase I, coupled directly to fluorescent dyes, and hybridized to an oligonucleotide microarray designed to detect a variety of noncoding and coding RNAs using a conventional two-color procedure (Peng et al., 2003Peng W.T. Robinson M.D. Mnaimneh S. Krogan N.J. Cagney G. Morris Q. Davierwala A.P. Grigull J. Yang X. Zhang W. et al.A panoramic view of yeast non-coding RNA processing.Cell. 2003; 113: 919-933Abstract Full Text Full Text PDF PubMed Scopus (200) Google Scholar). The entire analytical procedure is outlined schematically in Figure 1C. In traditional biochemical studies of protein complexes, a distinction is usually made between core components, which mediate the direct (e.g., catalytic) function of a complex and are therefore normally associated stably and recovered in stoichiometric yields, and peripheral components, which may modulate the activity of the core complex and which are often loosely or transiently associated and recovered in substoichiometric yields. We took three approaches to resolve core complexes and peripheral components. First, the relative stoichiometry of copurifying proteins was estimated from both densitometric scans of the images of silver-stained gels as well as by filtering and weighting the LC-MS/MS data according to the number and quality of independent peptide matches (see Experimental Procedures). Complete lists of the unfiltered and filtered MS identifications are shown in the Supplemental Data at http://www.molecule.org/cgi/content/full/13/2/225/DC1. Second, reciprocal tagging was performed in many cases to confirm interactions. Third, all of the data was assembled into a single spreadsheet in which the columns represent the individual purifications (“baits”), and the rows represent the associated proteins (“preys,” which include the bait if it is detected). The entries in the spreadsheet represent whether each particular prey was detected in association with each bait (i.e., 0 if it is not detected, 1 if it is detected, intermediate values for lower stoichiometry [for MALDI] or lower confidence [for LC-MS/MS]). Data in this format can then be displayed using 2D hierarchical clustering (Eisen et al., 1998Eisen M.B. Spellman P.T. Brown P.O. Botstein D. Cluster analysis and display of genome-wide expression patterns.Proc. Natl. Acad. Sci. USA. 1998; 95: 14863-14868Crossref PubMed Scopus (12828) Google Scholar). Figure 2A shows such a display in which a modified version of hierarchical clustering was applied (Biedl et al., 2001Biedl, T., Brejova, B., Demaine, E.D., Hamel, A.M., and Vinar, T. (2001). Optimal arrangement of leaves in the tree representing hierarchical clustering of gene expression data. Technical Report CS-2001-14, Department of Computer Science, University of Waterloo, April 2001.Google Scholar) such that (1) the adjacency of complexes with shared components was maximized and (2) complexes were positioned along a diagonal (see Supplemental Data for a more complete description, including a tabular version of Figure 2A with all baits and preys listed). In this way, nearly identical complexes retrieved by more than one tagged subunit appear as boxes along the diagonal. This display has 165 baits and 317 preys. The row and column orders were determined using only proteins identified by MALDI-TOF MS and achieving adequate approximate stoichiometry on a silver-stained gel; these are displayed in blue and presumably represent primarily core complexes. Next, additional proteins identified by LC-MS/MS on an aliquot of the same preparation were introduced without altering the x and y axes and displayed in red; these are more likely to represent accessory factors. Proteins meeting the minimum stoichiometry and confidence levels of both types of MS are shown in black. An additional 172 proteins were identified only by LC-MS/MS and are listed in the Supplemental Data. Although these could include false-positives, these identifications may represent proteins that are either low in abundance (substoichiometric) or are smaller proteins that ran off the gel and were not analyzed via MALDI-TOF MS. Boundaries between complexes (blue lines) were determined on the basis of similarity between clusters, which was defined as the proportion of shared subunits. A threshold of slightly more than half the subunits being shared maximized grouping of proteins known previously to appear in a complex and separation of those previously established to be in separate complexes (specifically, the value [precision x recall] was maximized, with precision being the average of [known subunits in complex/total subunits in complex] and recall being [known subunits in complex/all known subunits in the same complex]) (Figure 2A; see Supplemental Data for details). This resulted in the definition of 92 discrete clusters, including 56 complexes ranging in composition from 2 to 17 subunits, and 36 examples in which the bait protein alone was identified in the purified fraction. In these latter 36 cases, we cannot exclude the possibility that the tag prevents an as yet undiscovered stable interaction with some other protein. Initial manual inspection of our clustered dataset revealed obvious relationships between many of complexes and those described in the literature. To quantitatively assess this correspondence, we performed a statistical comparison of each of the 56 complexes to an assembly of 547 previously described protein purifications, including all of the interaction data reported in two recent large-scale yeast proteomics studies (Gavin et al., 2002Gavin A.C. Bosche M. Krause R. Grandi P. Marzioch M. Bauer A. Schultz J. Rick J.M. Michon A.M. Cruciat C.M. et al.Functional organization of the yeast proteome by systematic analysis of protein complexes.Nature. 2002; 415: 141-147Crossref PubMed Scopus (3786) Google Scholar, Ho et al., 2002Ho Y. Gruhler A. Heilbut A. Bader G.D. Moore L. Adams S.L. Millar A. Taylor P. Bennett K. Boutilier K. et al.Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.Nature. 2002; 415: 180-183Crossref PubMed Scopus (2923) Google Scholar), as well as all complexes cataloged in the MIPS online database (Mewes et al., 2002Mewes H.W. Frishman D. Guldener U. Mannhaupt G. Mayer K. Mokrejs M. Morgenstern B. Munsterkotter M. Rudd S. Weil B. Mips: a database for genomes and protein sequences.Nucleic Acids Res. 2002; 30: 31-34Crossref PubMed Scopus (743) Google Scholar) and a set of complexes derived from the recent literature on preribosomal assembly (see Supplemental Data; Grandi et al., 2002Grandi P. Rybin V. Bassler J. Petfalski E. Strauss D. Marzioch M. Schafer T. Kuster B. Tschochner H. Tollervey D. et al.90S pre-ribosomes include the 35S pre-rRNA, the U3 snoRNP, and 40S subunit processing factors but predominantly lack 60S synthesis factors.Mol. Cell. 2002; 10: 105-115Abstract Full Text Full Text PDF PubMed Scopus (369) Google Scholar, Nissan et al., 2002Nissan T.A. Bassler J. Petfalski E. Tollervey D. Hurt E. 60S pre-ribosome formation viewed from assembly in the nucleolus until export to the cytoplasm.EMBO J. 2002; 21: 5539-5547Crossref PubMed Scopus (281) Google Scholar, Dragon et al., 2002Dragon F. Gallagher J.E. Compagnone-Post P.A. Mitchell B.M. Porwancher K.A. Wehner K.A. Wormsley S. Settlage R.E. Shabanowitz J. Osheim Y. et al.A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis.Nature. 2002; 417: 967-970Crossref PubMed Scopus (520) Google Scholar, Robinson et al., 2002Robinson M.D. Grigull J. Mohammad N. Hughes T.R. FunSpec: a web-based cluster interpreter for yeast.BMC Bioinformatics. 2002; 3: 35Crossref PubMed Scopus (320) Google Scholar). For each of our 56 complexes, the most significant overlap with these 547 groups of proteins is indicated in Figure 2A. Of the 715 approximately stoichiometric pairwise protein-protein associations represented in Figure 2A, 225 (31%) and 77 (11%) were identified in the large-scale studies of Gavin et al., 2002Gavin A.C. Bosche M. Krause R. Grandi P. Marzioch M. Bauer A. Schultz J. Rick J.M. Michon A.M. Cruciat C.M. et al.Functional organization of the yeast proteome by systematic analysis of protein complexes.Nature. 2002; 415: 141-147Crossref PubMed Scopus (3786) Google Scholar and Ho et al., 2002Ho Y. Gruhler A. Heilbut A. Bader G.D. Moore L. Adams S.L. Millar A. Taylor P. Bennett K. Boutilier K. et al.Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.Nature. 2002; 415: 180-183Crossref PubMed Scopus (2923) Google Scholar, respectively. Among these multiprotein complexes were represented versions of RNA polymerase I (RNAPI), RNAPII, RNAPIII, snoRNPs, the SSU processome, pre-60S complexes, the exosome, RNases P and MRP, spliceosomal proteins, various nucleases, modifying enzymes, RNA binding proteins, nuclear transporters, and translation factors (Figures 2A and 2B). Clear differences were observed between our complexes and the various overlapping sets of preribosomal complexes (Dragon et al., 2002Dragon F. Gallagher J.E. Compagnone-Post P.A. Mitchell B.M. Porwancher K.A. Wehner K.A. Wormsley S. Settlage R.E. Shabanowitz J. Osheim Y. et al.A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis.Nature. 2002; 417: 967-970Crossref PubMed Scopus (520) Google Scholar, Du and Stillman 2002Du Y.C. Stillman B. Yph1p, an ORC-interacting protein: potential links between cell proliferation control, DNA replication, and ribosome biogenesis.Cell. 2002; 109: 835-848Abstract Full Text Full Text PDF PubMed Scopus (149) Google Scholar, Bassler et al., 2001Bassler J. Grandi P. Gadal O. Lessmann T. Petfalski E. Tollervey D. Lechner J. Hurt E. Identification of a 60S preribosomal particle that is closely linked to nuclear export.Mol. Cell. 2001; 8: 517-529Abstract Full Text Full Text PDF PubMed Scopus (264) Google Scholar, Harnpicharnchai et al., 2001Harnpicharnchai P. Jakovljevic J. Horsey E. Miles T. Roman J. Rout M. Meagher D. Imai B. Guo Y. Brame C.J. et al.Composition and functional characterization of yeast 66S ribosome assembly intermediates.Mol. Cell. 2001; 8: 505-515Abstract Full Text Full Text PDF PubMed Scopus (242) Google Scholar, Gavin et al., 2002Gavin A.C. Bosche M. Krause R. Grandi P. Marzioch M. Bauer A. Schultz J. Rick J.M. Michon A.M. Cruciat C.M. et al.Functional organization of the yeast proteome by systematic analysis of protein complexes.Nature. 2002; 415: 141-147Crossref PubMed Scopus (3786) Google Scholar). The SSU processome (Dragon et al., 2002Dragon F. Gallagher J.E. Compagnone-Post P.A. Mitchell B.M. Porwancher K.A. Wehner K.A. Wormsley S. Settlage R.E. Shabanowitz J. Osheim Y. et al.A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis.Nature. 2002; 417: 967-970Crossref PubMed Scopus (520) Google Scholar) represents the most striking example; in this case, three distinct and nonoverlapping subcomplexes were retrieved. Purification of Utp8-TAP, Utp9-TAP, or Utp10-TAP each resulted in the isolation of a virtually identical, stoichiometric seven-protein complex (Utp8, Utp9, Utp4, Utp10, Utp15, Nan1, and Pol5, a nucleolar DNA polymerase required for rRNA synthesis [Shimizu et al., 2002Shimizu K. Kawasaki Y. Hiraga S.I. Tawaramoto M. Nakashima N. Sugino A. The fifth essential DNA polymerase ϕ in Saccharomyces cerevisiae is localized to the nucleolus and plays an important role in synthesis or rRNA.Proc. Natl. Acad. Sci. USA. 2002; 99: 9133-9138Crossref PubMed Scopus (35) Google Scholar]) (Figure 3A), which we refer to as UTP A. In contrast, when Utp13-TAP, Utp18-TAP, or Utp21-TAP was purified, we isolated a different, stoichiometric, six-protein complex containing the proteins Dip2, Pwp2, Utp6, Utp13, Utp18, and Utp21 (Figure 3B), which we have named UTP B. Finally, Utp22-TAP copurified with Rrp7 and the four subunits of casein kinase II (Cka1, Cka2, Ckb1, and Ckb2) (Figure 3C) in a complex which we have termed UTP C. We have shown that utp22 has a classical UTP-like defect (Peng et al., 2003Peng W.T. Robinson M.D. Mnaimneh S. Krogan N.J. Cagney G. Morris Q. Davierwala A.P. Grigull J. Yang X. Zhang W. et al.A panoramic view of yeast non-coding RNA processing.Cell. 2003; 113: 919-933Abstract Full Text Full Text PDF PubMed Scopus (200) Google Scholar), while Rrp7 is required for the production of 40S ribosomal subunits from the 43S precursor (Baudin-Baillieu et al., 1997Baudin-Baillieu A. Tollervery D. Cullin C. Lacroute F. Functional analysis of Rrp7p, an essential yeast protein involved in pre-rRNA processing and ribosome assembly.Mol. Cell. Biol. 1997; 17: 5023-5032Crossref PubMed Scopus (56) Google Scholar). Casein kinase II (CKII) is multifunctional and has been implicated in the modification of ribosomal proteins in Trichosporon cutaneum (Wojda et al., 2002Wojda I. Cytrynska M. Frajnt M.F. Jakubowicz T. Protein kinases CKI and CKII are implicated in modification of ribosomal proteins of the yeast Trichosporon cutaneum.Acta Biochim. Pol. 2002; 49: 947-957PubMed Google Scholar). We have confirmed the UTP22-CKII interaction by reciprocal purification: Cka1-TAP and Ckb2-TAP both copurify with Utp22, as well as with many other proteins (data not shown). Depletion of subunits of UTP A, UTP B, and UTP C leads to similar defects in the processing of rRNA, as determined by hybridizing total cellular RNA to a custom microarray (Figure 5A) designed to detect stable RNAs and their various precursors (Peng et al., 2003Peng W.T. Robinson M.D. Mnaimneh S. Krogan N.J. Cagney G. Morris Q. Davierwala A.P. Grigull J. Yang X. Zhang W. et al.A panoramic view of yeast non-coding RNA processing.Cell. 2003; 113: 919-933Abstract Full Text Full Text PDF PubMed Scopus (200) Google Scholar; see Figure 3D). The relationships of the UTP A, UTP B, and UTP C complexes and other complexes we have purified to previous preparations of the SSU processome and pre-60S ribosomes are shown in Figure 4. In each case, our purifications produced distinct subcomplexes of these very large macromolecular assemblies.Figure 4A Comparison of Our Data to Recently Published PurificationsShow full captionEach column represents a tagged protein from a particular purification, and the colored squares represent an associated protein. Purifications are depicted in black (Bassler et al., 2001Bassler J. Grandi P. Gadal O. Lessmann T. Petfalski E. Tollervey D. Lechner J. Hurt E. Identification of a 60S preribosomal particle that is closely linked to nuclear export.Mol. Cell. 2001; 8: 517-529Abstract Full Text Full Text PDF PubMed Scopus (264) Google Scholar, Fatica and Tollervey 2002Fatica A. Tollervey D. Making ribosomes.Curr. Opin. Cell Biol. 2002; 14: 313-318Crossref PubMed Scopus (412) Google Scholar, Grandi et al., 2002Grandi P. Rybin V. Bassler J. Petfalski E. Strauss D. Marzioch M. Schafer T. Kuster B. Tschochner H. Tollervey D. et al.90S pre-ribosomes include the 35S pre-rRNA, the U3 snoRNP, and 40S subunit processing factors but predominantly lack 60S synthesis factors.Mol. Cell. 2002; 10: 105-115Abstract Full Text Full Text PDF PubMed Scopus (369) Google Scholar, Harnpicharnchai et al., 2001Harnpicharnchai P. Jakovljevic J. Horsey E. Miles T. Roman J. Rout M. Meagher D. Imai B. Guo Y. Brame C.J. et al.Composition and functional characterization of yeast 66S ribosome assembly intermediates.Mol. Cell. 2001; 8: 505-515Abstract Full Text Full Text PDF PubMed Scopus (242) Google Scholar, Nissan et al., 2002Nissan T.A. Bassler J. Petfalski E. Tollervey D. Hurt E. 60S pre-ribosome formation viewed from assembly in the nucleolus until export to the cytoplasm.EMBO J. 2002; 21: 5539-5547Crossref PubMed Scopus (281) Google Scholar), blue (Gavin et al., 2002Gavin A.C. Bosche M. Krause R. Grandi P. Marzioch M. Bauer A. Schultz J. Rick J.M. Michon A.M. Cruciat C.M. et al.Functional organization of the yeast proteome by systematic analysis of protein complexes.Nature. 2002; 415: 141-147Crossref PubMed Scopus (3786) Google Scholar), or red (our data). The associated proteins for our data are ordered diagonally and separated according to a previous classification of SSU processome and pre-60S ribosome. The UTP A, B, and C complexes from the SSU processome are highlighted in green as are the IPI and other complexes from the pre-60S ribosome.View Large Image Figure ViewerDownload Hi-res image Download (PPT) Each column represents a tagged protein from a particular purification, and the colored squares represent an associated protein. Purifications are depicted in black (Bassler et al., 2001Bassler J. Grandi P. Gadal O. Lessmann T. Petfalski E. Tollervey D. Lechner J. Hurt E. Identification of a 60S preribosomal particle that is closely linked to nuclear export.Mol. Cell. 2001; 8: 517-529Abstract Full Text Full Text PDF PubMed Scopus (264) Google Scholar, Fatica and Tollervey 2002Fatica A. Tollervey D. Making ribosomes.Curr. Opin. Cell Biol. 2002; 14: 313-318Crossref PubMed Scopus (412) Google Scholar, Grandi et al., 2002Grandi P. Rybin V. Bassler J. Petfalski E. Strauss D. Marzioch M. Schafer T. Kuster B. Tschochner H. Tollervey D. et al.90S pre-ribosomes include the 35S pre-rRNA, the U3 snoRNP, and 40S subunit processing factors but predominantly lack 60S synthesis factors.Mol. Cell. 2002; 10: 105-115Abstract Full Text Full Text PDF PubMed Scopus (369) Google Scholar, Harnpicharnchai et al., 2001Harnpicharnchai P. Jakovljevic J. Horsey E. Miles T. Roman J. Rout M. Meagher D. Imai B. Guo Y. Brame C.J. et al.Composition and functional characterization of yeast 66S ribosome assembly intermediates.Mol. Cell. 2001; 8: 505-515Abstract Full Text Full Text PDF PubMed Scopus (242) Google Scholar, Nissan et al., 2002Nissan T.A. Bassler J. Petfalski E. Tollervey D. Hurt E. 60S pre-ribosome formation viewed from assembly in the nucleolus until export to the cytoplasm.EMBO J. 2002; 21: 5539-5547Crossref PubMed Scopus (281) Google Scholar), blue (Gavin et al., 2002Gavin A.C. Bosche M. Krause R. Grandi P. Marzioch M. Bauer A. Schultz J. Rick J.M. Michon A.M. Cruciat C.M. et al.Functional organization of the yeast proteome by systematic analysis of protein complexes.Nature. 2002; 415: 141-147Crossref PubMed Scopus (3786) Google Scholar), or red (our data). The associated proteins for our data are ordered diagonally and separated according to a previous classification of SSU processome and pre-60S ribosome. The UTP A, B, and C comple" @default.
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• W2074405508 date "2004-01-01" @default.
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• W2074405508 title "High-Definition Macromolecular Composition of Yeast RNA-Processing Complexes" @default.
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• W2074405508 doi "https://doi.org/10.1016/s1097-2765(04)00003-6" @default.
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