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Zhang Y, Pang Y, Zhang K, Song X, Gao J, Zhang S, Deng W. RNA polymerase I subunit RPA43 activates rRNA expression and cell proliferation but inhibits cell migration. Biochim Biophys Acta Gen Subj 2023:130411. [PMID: 37343605 DOI: 10.1016/j.bbagen.2023.130411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/21/2023] [Accepted: 06/13/2023] [Indexed: 06/23/2023]
Abstract
The products synthesized by RNA polymerase I (Pol I) play fundamental roles in several cellular processes, including ribosomal biogenesis, protein synthesis, cell metabolism, and growth. Deregulation of Pol I products can cause various diseases such as ribosomopathies, leukaemia, and solid tumours. However, the detailed mechanism of Pol I-directed transcription remains elusive, and the roles of Pol I subunits in rRNA synthesis and cellular activities still need clarification. In this study, we found that RPA43 expression levels positively correlate with Pol I product accumulation and cell proliferation, indicating that RPA43 activates these processes. Unexpectedly, RPA43 depletion promoted HeLa cell migration, suggesting that RPA43 functions as a negative regulator in cell migration. Mechanistically, RPA43 positively modulates the recruitment of Pol I transcription machinery factors to the rDNA promoter by activating the transcription of the genes encoding Pol I transcription machinery factors. RPA43 inhibits cell migration by dampening the expression of c-JUN and Integrin. Collectively, we found that RPA43 plays opposite roles in cell proliferation and migration except for driving Pol I-dependent transcription. These findings provide novel insights into the regulatory mechanism of Pol I-mediated transcription and cell proliferation and a potential pathway to developing anti-cancer drugs using RPA43 as a target.
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Affiliation(s)
- Yue Zhang
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei province 430065, China
| | - Yaoyu Pang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7GE, UK
| | - Kewei Zhang
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei province 430065, China
| | - Xiaoye Song
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei province 430065, China
| | - Junwei Gao
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei province 430065, China
| | - Shuting Zhang
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei province 430065, China
| | - Wensheng Deng
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei province 430065, China.
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2
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Watt KE, Macintosh J, Bernard G, Trainor PA. RNA Polymerases I and III in development and disease. Semin Cell Dev Biol 2023; 136:49-63. [PMID: 35422389 PMCID: PMC9550887 DOI: 10.1016/j.semcdb.2022.03.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 12/18/2022]
Abstract
Ribosomes are macromolecular machines that are globally required for the translation of all proteins in all cells. Ribosome biogenesis, which is essential for cell growth, proliferation and survival, commences with transcription of a variety of RNAs by RNA Polymerases I and III. RNA Polymerase I (Pol I) transcribes ribosomal RNA (rRNA), while RNA Polymerase III (Pol III) transcribes 5S ribosomal RNA and transfer RNAs (tRNA) in addition to a wide variety of small non-coding RNAs. Interestingly, despite their global importance, disruptions in Pol I and Pol III function result in tissue-specific developmental disorders, with craniofacial anomalies and leukodystrophy/neurodegenerative disease being among the most prevalent. Furthermore, pathogenic variants in genes encoding subunits shared between Pol I and Pol III give rise to distinct syndromes depending on whether Pol I or Pol III function is disrupted. In this review, we discuss the global roles of Pol I and III transcription, the consequences of disruptions in Pol I and III transcription, disorders arising from pathogenic variants in Pol I and Pol III subunits, and mechanisms underpinning their tissue-specific phenotypes.
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Affiliation(s)
- Kristin En Watt
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Julia Macintosh
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada; Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Geneviève Bernard
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada; Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada; Departments of Pediatrics and Human Genetics, McGill University, Montreal, QC, Canada; Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, QC, Canada.
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Anatomy & Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA.
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3
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Azouzi C, Jaafar M, Dez C, Abou Merhi R, Lesne A, Henras AK, Gadal O. Coupling Between Production of Ribosomal RNA and Maturation: Just at the Beginning. Front Mol Biosci 2021; 8:778778. [PMID: 34765647 PMCID: PMC8575686 DOI: 10.3389/fmolb.2021.778778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/12/2021] [Indexed: 01/28/2023] Open
Abstract
Ribosomal RNA (rRNA) production represents the most active transcription in the cell. Synthesis of the large rRNA precursors (35S/47S in yeast/human) is achieved by up to hundreds of RNA polymerase I (Pol I) enzymes simultaneously transcribing a single rRNA gene. In this review, we present recent advances in understanding the coupling between rRNA production and nascent rRNA folding. Mapping of the distribution of Pol I along ribosomal DNA at nucleotide resolution, using either native elongating transcript sequencing (NET-Seq) or crosslinking and analysis of cDNAs (CRAC), revealed frequent Pol I pausing, and CRAC results revealed a direct coupling between pausing and nascent RNA folding. High density of Pol I per gene imposes topological constraints that establish a defined pattern of polymerase distribution along the gene, with a persistent spacing between transcribing enzymes. RNA folding during transcription directly acts as an anti-pausing mechanism, implying that proper folding of the nascent rRNA favors elongation in vivo. Defects in co-transcriptional folding of rRNA are likely to induce Pol I pausing. We propose that premature termination of transcription, at defined positions, can control rRNA production in vivo.
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Affiliation(s)
- Chaima Azouzi
- Laboratoire de Biologie Moléculaire, Cellulaire et du Développement (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Mariam Jaafar
- Laboratoire de Biologie Moléculaire, Cellulaire et du Développement (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Christophe Dez
- Laboratoire de Biologie Moléculaire, Cellulaire et du Développement (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Raghida Abou Merhi
- Genomic Stability and Biotherapy (GSBT) Laboratory, Faculty of Sciences, Rafik Hariri Campus, Lebanese University, Beirut, Lebanon
| | - Annick Lesne
- CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, Sorbonne Université, Paris, France.,Institut de Génétique Moléculaire de Montpellier, IGMM, CNRS, Université Montpellier, Montpellier, France
| | - Anthony K Henras
- Laboratoire de Biologie Moléculaire, Cellulaire et du Développement (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Olivier Gadal
- Laboratoire de Biologie Moléculaire, Cellulaire et du Développement (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France
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4
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Tafur L, Sadian Y, Hanske J, Wetzel R, Weis F, Müller CW. The cryo-EM structure of a 12-subunit variant of RNA polymerase I reveals dissociation of the A49-A34.5 heterodimer and rearrangement of subunit A12.2. eLife 2019; 8:43204. [PMID: 30913026 PMCID: PMC6435322 DOI: 10.7554/elife.43204] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/09/2019] [Indexed: 11/13/2022] Open
Abstract
RNA polymerase (Pol) I is a 14-subunit enzyme that solely transcribes pre-ribosomal RNA. Cryo-electron microscopy (EM) structures of Pol I initiation and elongation complexes have given first insights into the molecular mechanisms of Pol I transcription. Here, we present cryo-EM structures of yeast Pol I elongation complexes (ECs) bound to the nucleotide analog GMPCPP at 3.2 to 3.4 Å resolution that provide additional insight into the functional interplay between the Pol I-specific transcription-like factors A49-A34.5 and A12.2. Strikingly, most of the nucleotide-bound ECs lack the A49-A34.5 heterodimer and adopt a Pol II-like conformation, in which the A12.2 C-terminal domain is bound in a previously unobserved position at the A135 surface. Our structural and biochemical data suggest a mechanism where reversible binding of the A49-A34.5 heterodimer could contribute to the regulation of Pol I transcription initiation and elongation.
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Affiliation(s)
- Lucas Tafur
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Collaboration for joint PhD degree, European Molecular Biology Laboratory and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Yashar Sadian
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jonas Hanske
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rene Wetzel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Felix Weis
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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5
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Gómez-Herreros F, Margaritis T, Rodríguez-Galán O, Pelechano V, Begley V, Millán-Zambrano G, Morillo-Huesca M, Muñoz-Centeno MC, Pérez-Ortín JE, de la Cruz J, Holstege FCP, Chávez S. The ribosome assembly gene network is controlled by the feedback regulation of transcription elongation. Nucleic Acids Res 2017. [PMID: 28637236 PMCID: PMC5737610 DOI: 10.1093/nar/gkx529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ribosome assembly requires the concerted expression of hundreds of genes, which are transcribed by all three nuclear RNA polymerases. Transcription elongation involves dynamic interactions between RNA polymerases and chromatin. We performed a synthetic lethal screening in Saccharomyces cerevisiae with a conditional allele of SPT6, which encodes one of the factors that facilitates this process. Some of these synthetic mutants corresponded to factors that facilitate pre-rRNA processing and ribosome biogenesis. We found that the in vivo depletion of one of these factors, Arb1, activated transcription elongation in the set of genes involved directly in ribosome assembly. Under these depletion conditions, Spt6 was physically targeted to the up-regulated genes, where it helped maintain their chromatin integrity and the synthesis of properly stable mRNAs. The mRNA profiles of a large set of ribosome biogenesis mutants confirmed the existence of a feedback regulatory network among ribosome assembly genes. The transcriptional response in this network depended on both the specific malfunction and the role of the regulated gene. In accordance with our screening, Spt6 positively contributed to the optimal operation of this global network. On the whole, this work uncovers a feedback control of ribosome biogenesis by fine-tuning transcription elongation in ribosome assembly factor-coding genes.
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Affiliation(s)
- Fernando Gómez-Herreros
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Thanasis Margaritis
- Molecular Cancer Research, University Medical Center Utrecht, & Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Olga Rodríguez-Galán
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Vicent Pelechano
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed. Facultad de Biológicas, Universitat de València. Burjassot, Spain.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Victoria Begley
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Gonzalo Millán-Zambrano
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Macarena Morillo-Huesca
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Mari Cruz Muñoz-Centeno
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - José E Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed. Facultad de Biológicas, Universitat de València. Burjassot, Spain
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Frank C P Holstege
- Molecular Cancer Research, University Medical Center Utrecht, & Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
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6
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Torreira E, Louro JA, Pazos I, González-Polo N, Gil-Carton D, Duran AG, Tosi S, Gallego O, Calvo O, Fernández-Tornero C. The dynamic assembly of distinct RNA polymerase I complexes modulates rDNA transcription. eLife 2017; 6. [PMID: 28262097 PMCID: PMC5362265 DOI: 10.7554/elife.20832] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 03/06/2017] [Indexed: 12/31/2022] Open
Abstract
Cell growth requires synthesis of ribosomal RNA by RNA polymerase I (Pol I). Binding of initiation factor Rrn3 activates Pol I, fostering recruitment to ribosomal DNA promoters. This fundamental process must be precisely regulated to satisfy cell needs at any time. We present in vivo evidence that, when growth is arrested by nutrient deprivation, cells induce rapid clearance of Pol I–Rrn3 complexes, followed by the assembly of inactive Pol I homodimers. This dual repressive mechanism reverts upon nutrient addition, thus restoring cell growth. Moreover, Pol I dimers also form after inhibition of either ribosome biogenesis or protein synthesis. Our mutational analysis, based on the electron cryomicroscopy structures of monomeric Pol I alone and in complex with Rrn3, underscores the central role of subunits A43 and A14 in the regulation of differential Pol I complexes assembly and subsequent promoter association. DOI:http://dx.doi.org/10.7554/eLife.20832.001
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Affiliation(s)
- Eva Torreira
- IPSBB Unit, Centro de Investigaciones Biológicas, Madrid, Spain
| | | | - Irene Pazos
- Institute for Research in Biomedicine, Barcelona, Spain.,The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Noelia González-Polo
- Instituto de Biología Funcional y Genómica, CSIC-Universidad de Salamanca, Salamanca, Spain
| | - David Gil-Carton
- Structural Biology Unit, Cooperative Center for Research in Biosciences CIC bioGUNE, Derio, Spain
| | - Ana Garcia Duran
- Institute for Research in Biomedicine, Barcelona, Spain.,The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sébastien Tosi
- Institute for Research in Biomedicine, Barcelona, Spain.,The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Oriol Gallego
- Institute for Research in Biomedicine, Barcelona, Spain.,The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica, CSIC-Universidad de Salamanca, Salamanca, Spain
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7
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Zhang Y, Najmi SM, Schneider DA. Transcription factors that influence RNA polymerases I and II: To what extent is mechanism of action conserved? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:246-255. [PMID: 27989933 DOI: 10.1016/j.bbagrm.2016.10.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/07/2016] [Accepted: 10/25/2016] [Indexed: 01/05/2023]
Abstract
In eukaryotic cells, nuclear RNA synthesis is accomplished by at least three unique, multisubunit RNA polymerases. The roles of these enzymes are generally partitioned into the synthesis of the three major classes of RNA: rRNA, mRNA, and tRNA for RNA polymerases I, II, and III respectively. Consistent with their unique cellular roles, each enzyme has a complement of specialized transcription factors and enzymatic properties. However, not all transcription factors have evolved to affect only one eukaryotic RNA polymerase. In fact, many factors have been shown to influence the activities of multiple nuclear RNA polymerases. This review focuses on a subset of these factors, specifically addressing the mechanisms by which these proteins influence RNA polymerases I and II.
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Affiliation(s)
- Yinfeng Zhang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Saman M Najmi
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
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8
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Spt6 Is Essential for rRNA Synthesis by RNA Polymerase I. Mol Cell Biol 2015; 35:2321-31. [PMID: 25918242 DOI: 10.1128/mcb.01499-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/19/2015] [Indexed: 01/04/2023] Open
Abstract
Spt6 (suppressor of Ty6) has many roles in transcription initiation and elongation by RNA polymerase (Pol) II. These effects are mediated through interactions with histones, transcription factors, and the RNA polymerase. Two lines of evidence suggest that Spt6 also plays a role in rRNA synthesis. First, Spt6 physically associates with a Pol I subunit (Rpa43). Second, Spt6 interacts physically and genetically with Spt4/5, which directly affects Pol I transcription. Utilizing a temperature-sensitive allele, spt6-1004, we show that Spt6 is essential for Pol I occupancy of the ribosomal DNA (rDNA) and rRNA synthesis. Our data demonstrate that protein levels of an essential Pol I initiation factor, Rrn3, are reduced when Spt6 is inactivated, leading to low levels of Pol I-Rrn3 complex. Overexpression of RRN3 rescues Pol I-Rrn3 complex formation; however, rRNA synthesis is not restored. These data suggest that Spt6 is involved in either recruiting the Pol I-Rrn3 complex to the rDNA or stabilizing the preinitiation complex. The findings presented here identify an unexpected, essential role for Spt6 in synthesis of rRNA.
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9
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Inositol pyrophosphates regulate RNA polymerase I-mediated rRNA transcription in Saccharomyces cerevisiae. Biochem J 2015; 466:105-14. [PMID: 25423617 PMCID: PMC4325516 DOI: 10.1042/bj20140798] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosome biogenesis is an essential cellular process regulated by the metabolic state of a cell. We examined whether inositol pyrophosphates, energy-rich derivatives of inositol that act as metabolic messengers, play a role in ribosome synthesis in the budding yeast, Saccharomyces cerevisiae. Yeast strains lacking the inositol hexakisphosphate (IP6) kinase Kcs1, which is required for the synthesis of inositol pyrophosphates, display increased sensitivity to translation inhibitors and decreased protein synthesis. These phenotypes are reversed on expression of enzymatically active Kcs1, but not on expression of the inactive form. The kcs1Δ yeast cells exhibit reduced levels of ribosome subunits, suggesting that they are defective in ribosome biogenesis. The rate of rRNA synthesis, the first step of ribosome biogenesis, is decreased in kcs1Δ yeast strains, suggesting that RNA polymerase I (Pol I) activity may be reduced in these cells. We determined that the Pol I subunits, A190, A43 and A34.5, can accept a β-phosphate moiety from inositol pyrophosphates to undergo serine pyrophosphorylation. Although there is impaired rRNA synthesis in kcs1Δ yeast cells, we did not find any defect in recruitment of Pol I on rDNA, but observed that the rate of transcription elongation was compromised. Taken together, our findings highlight inositol pyrophosphates as novel regulators of rRNA transcription. Inositol pyrophosphates are phosphate-rich metabolic messengers that regulate many cellular processes. We observed that RNA polymerase I is pyrophosphorylated by inositol pyrophosphates, and its transcription elongation activity was reduced in budding yeast strains devoid of inositol pyrophosphates.
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10
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Viktorovskaya OV, Schneider DA. Functional divergence of eukaryotic RNA polymerases: unique properties of RNA polymerase I suit its cellular role. Gene 2014; 556:19-26. [PMID: 25445273 DOI: 10.1016/j.gene.2014.10.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/16/2014] [Accepted: 10/17/2014] [Indexed: 02/08/2023]
Abstract
Eukaryotic cells express at least three unique nuclear RNA polymerases. The selective advantage provided by this enhanced complexity is a topic of fundamental interest in cell biology. It has long been known that the gene targets and transcription initiation pathways for RNA polymerases (Pols) I, II and III are distinct; however, recent genetic, biochemical and structural data suggest that even the core enzymes have evolved unique properties. Among the three eukaryotic RNA polymerases, Pol I is considered the most divergent. Transcription of the ribosomal DNA by Pol I is unmatched in its high rate of initiation, complex organization within the nucleolus and functional connection to ribosome assembly. Furthermore, ribosome synthesis is intimately linked to cell growth and proliferation. Thus, there is intense selective pressure on Pol I. This review describes key features of Pol I transcription, discusses catalytic activities of the enzyme and focuses on recent advances in understanding its unique role among eukaryotic RNA polymerases.
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Affiliation(s)
- Olga V Viktorovskaya
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, United States
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, United States.
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11
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RNA polymerase I structure and transcription regulation. Nature 2013; 502:650-5. [DOI: 10.1038/nature12712] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 09/24/2013] [Indexed: 01/25/2023]
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12
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Jennebach S, Herzog F, Aebersold R, Cramer P. Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage. Nucleic Acids Res 2012; 40:5591-601. [PMID: 22396529 PMCID: PMC3384336 DOI: 10.1093/nar/gks220] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
RNA polymerase (Pol) I contains a 10-subunit catalytic core that is related to the core of Pol II and includes subunit A12.2. In addition, Pol I contains the heterodimeric subcomplexes A14/43 and A49/34.5, which are related to the Pol II subcomplex Rpb4/7 and the Pol II initiation factor TFIIF, respectively. Here we used lysine-lysine crosslinking, mass spectrometry (MS) and modeling based on five crystal structures, to extend the previous homology model of the Pol I core, to confirm the location of A14/43 and to position A12.2 and A49/34.5 on the core. In the resulting model of Pol I, the C-terminal ribbon (C-ribbon) domain of A12.2 reaches the active site via the polymerase pore, like the C-ribbon of the Pol II cleavage factor TFIIS, explaining why the intrinsic RNA cleavage activity of Pol I is strong, in contrast to the weak cleavage activity of Pol II. The A49/34.5 dimerization module resides on the polymerase lobe, like TFIIF, whereas the A49 tWH domain resides above the cleft, resembling parts of TFIIE. This indicates that Pol I and also Pol III are distantly related to a Pol II-TFIIS-TFIIF-TFIIE complex.
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Affiliation(s)
- Stefan Jennebach
- Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
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13
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SPPS: a sequence-based method for predicting probability of protein-protein interaction partners. PLoS One 2012; 7:e30938. [PMID: 22292078 PMCID: PMC3266917 DOI: 10.1371/journal.pone.0030938] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 12/26/2011] [Indexed: 01/20/2023] Open
Abstract
Background The molecular network sustained by different types of interactions among proteins is widely manifested as the fundamental driving force of cellular operations. Many biological functions are determined by the crosstalk between proteins rather than by the characteristics of their individual components. Thus, the searches for protein partners in global networks are imperative when attempting to address the principles of biology. Results We have developed a web-based tool “Sequence-based Protein Partners Search” (SPPS) to explore interacting partners of proteins, by searching over a large repertoire of proteins across many species. SPPS provides a database containing more than 60,000 protein sequences with annotations and a protein-partner search engine in two modes (Single Query and Multiple Query). Two interacting proteins of human FBXO6 protein have been found using the service in the study. In addition, users can refine potential protein partner hits by using annotations and possible interactive network in the SPPS web server. Conclusions SPPS provides a new type of tool to facilitate the identification of direct or indirect protein partners which may guide scientists on the investigation of new signaling pathways. The SPPS server is available to the public at http://mdl.shsmu.edu.cn/SPPS/.
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