Proteomic snapshot analyses of preribosomal ribonucleoprotein complexes formed at various stages of ribosome biogenesis in yeast and mammalian cells

Publisher Website
Google Scholar
Abstract
I. Introduction 288 II. Transcription and Processing of the Pre‐rRNA in the Ribosome Biogenesis of Yeast Cells: A Model for Eukaryotic Cells 290 III. Trans‐Acting Factors Involved in the Pre‐rRNA Processing and Assembly in Yeast Cells 291 A. Trans‐Acting Proteins That Act with snoRNAs 291 B. Trans‐Acting Factors Involved in the rRNA Cleavages 293 C. Trans‐Acting Factors Involved in the rRNA Editing and Conformational Rearrangement 296 IV. Isolation and Proteomic Characterization of Pre‐rRNP Complexes Formed During Ribosome Biogenesis in Yeast Cells 296 A. Experimental Approaches to Characterize Pre‐rRNP Complexes 296 B. 90S Pre‐rRNP Complexes Formed at Very Early Stages of Ribosome Biogenesis 299 C. Pre‐rRNP Complexes Formed at Early/Middle Stages of Ribosome Biogenesis 302 D. Pre‐rRNP Complexes Formed at Later Stages of Ribosome Biogenesis 303 V. Isolation and Proteomic Characterization of Pre‐rRNP Complexes Involved in Mammalian Ribosome Biogenesis 304 A. Ribosome Biogenesis in Mammalian Cells 304 B. Proteomic Analysis of the Pre‐rRNP Complexes Associated with Nucleolin: A Major Nucleolar Protein 305 C. Reverse‐Tagging Methodology Applied to Human Trans‐Acting Proteins Involved in Ribosome Biogenesis 310 D. Isolation and Proteomic Analysis of Human Parvulin‐Associating Pre‐rRNP Complexes 310 VI. Proteomic Analysis of the Nucleolus of Mammalian Cells 312 VII. Conclusions 312 VIII. Abbreviations 314 References 314 Proteomic technologies powered by advancements in mass spectrometry and bioinformatics and coupled with accumulated genome sequence data allow a comprehensive study of cell function through large‐scale and systematic protein identifications of protein constituents of the cell and tissues, as well as of multi‐protein complexes that carry out many cellular function in a higher‐order network in the cell. One of the most extensively analyzed cellular functions by proteomics is the production of ribosome, the protein‐synthesis machinery, in the nucle(ol)us—the main site of ribosome biogenesis. The use of tagged proteins as affinity bait, coupled with mass spectrometric identification, enabled us to isolate synthetic intermediates of ribosomes that might represent snapshots of nascent ribosomes at particular stages of ribosome biogenesis and to identify their constituents—some of which showed dynamic changes for association with the intermediates at various stages of ribosome biogenesis. In this review, in conjunction with the results from yeast cells, our proteomic approach to analyze ribosome biogenesis in mammalian cells is described. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 22:287–317, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mas.10057