1
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Correll CC, Rudloff U, Schmit JD, Ball DA, Karpova TS, Balzer E, Dundr M. Crossing boundaries of light microscopy resolution discerns novel assemblies in the nucleolus. Histochem Cell Biol 2024:10.1007/s00418-024-02297-7. [PMID: 38758429 DOI: 10.1007/s00418-024-02297-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
Abstract
The nucleolus is the largest membraneless organelle and nuclear body in mammalian cells. It is primarily involved in the biogenesis of ribosomes, essential macromolecular machines responsible for synthesizing all proteins required by the cell. The assembly of ribosomes is evolutionarily conserved and accounts for the most energy-consuming cellular process needed for cell growth, proliferation, and homeostasis. Despite the significance of this process, the substructural mechanistic principles of the nucleolar function in preribosome biogenesis have only recently begun to emerge. Here, we provide a new perspective using advanced super-resolution microscopy and single-molecule MINFLUX nanoscopy on the mechanistic principles governing ribosomal RNA-seeded nucleolar formation and the resulting tripartite suborganization of the nucleolus driven, in part, by liquid-liquid phase separation. With recent advances in the cryogenic electron microscopy (cryoEM) structural analysis of ribosome biogenesis intermediates, we highlight the current understanding of the step-wise assembly of preribosomal subunits in the nucleolus. Finally, we address how novel anticancer drug candidates target early steps in ribosome biogenesis to exploit these essential dependencies for growth arrest and tumor control.
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Affiliation(s)
- Carl C Correll
- Center for Proteomics and Molecular Therapeutics and Biochemistry and Molecular Biology, Chicago Medical School, Rosalind Franklin University of Medicine & Science, North Chicago, IL, 60064, USA
| | - Udo Rudloff
- Rare Tumor Initiative, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, KS, 66506, USA
| | - David A Ball
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tatiana S Karpova
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eric Balzer
- Nikon Instruments Inc., Melville, NY, 11747, USA
| | - Miroslav Dundr
- Rare Tumor Initiative, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
- Center for Cancer Cell Biology, Chicago Medical School, Rosalind Franklin University of Medicine & Science, North Chicago, IL, 60064, USA.
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2
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LeDoux MS. Polymerase I as a Target for Treating Neurodegenerative Disorders. Biomedicines 2024; 12:1092. [PMID: 38791054 PMCID: PMC11118182 DOI: 10.3390/biomedicines12051092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/06/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
Polymerase I (Pol I) is at the epicenter of ribosomal RNA (rRNA) synthesis. Pol I is a target for the treatment of cancer. Given the many cellular commonalities between cancer and neurodegeneration (i.e., different faces of the same coin), it seems rational to consider targeting Pol I or, more generally, rRNA synthesis for the treatment of disorders associated with the death of terminally differentiated neurons. Principally, ribosomes synthesize proteins, and, accordingly, Pol I can be considered the starting point for protein synthesis. Given that cellular accumulation of abnormal proteins such as α-synuclein and tau is an essential feature of neurodegenerative disorders such as Parkinson disease and fronto-temporal dementia, reduction of protein production is now considered a viable target for treatment of these and closely related neurodegenerative disorders. Abnormalities in polymerase I activity and rRNA production may also be associated with nuclear and nucleolar stress, DNA damage, and childhood-onset neuronal death, as is the case for the UBTF E210K neuroregression syndrome. Moreover, restraining the activity of Pol I may be a viable strategy to slow aging. Before starting down the road of Pol I inhibition for treating non-cancerous disorders of the nervous system, many questions must be answered. First, how much Pol I inhibition can neurons tolerate, and for how long? Should inhibition of Pol I be continuous or pulsed? Will cells compensate for Pol I inhibition by upregulating the number of active rDNAs? At present, we have no effective and safe disease modulatory treatments for Alzheimer disease, α-synucleinopathies, or tauopathies, and novel therapeutic targets and approaches must be explored.
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Affiliation(s)
- Mark S. LeDoux
- Department of Psychology and College of Health Sciences, University of Memphis, Memphis, TN 38152, USA; or
- Veracity Neuroscience LLC, Memphis, TN 38157, USA
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3
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Lewis JS, van Oijen AM, Spenkelink LM. Embracing Heterogeneity: Challenging the Paradigm of Replisomes as Deterministic Machines. Chem Rev 2023; 123:13419-13440. [PMID: 37971892 PMCID: PMC10790245 DOI: 10.1021/acs.chemrev.3c00436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/15/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023]
Abstract
The paradigm of cellular systems as deterministic machines has long guided our understanding of biology. Advancements in technology and methodology, however, have revealed a world of stochasticity, challenging the notion of determinism. Here, we explore the stochastic behavior of multi-protein complexes, using the DNA replication system (replisome) as a prime example. The faithful and timely copying of DNA depends on the simultaneous action of a large set of enzymes and scaffolding factors. This fundamental cellular process is underpinned by dynamic protein-nucleic acid assemblies that must transition between distinct conformations and compositional states. Traditionally viewed as a well-orchestrated molecular machine, recent experimental evidence has unveiled significant variability and heterogeneity in the replication process. In this review, we discuss recent advances in single-molecule approaches and single-particle cryo-EM, which have provided insights into the dynamic processes of DNA replication. We comment on the new challenges faced by structural biologists and biophysicists as they attempt to describe the dynamic cascade of events leading to replisome assembly, activation, and progression. The fundamental principles uncovered and yet to be discovered through the study of DNA replication will inform on similar operating principles for other multi-protein complexes.
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Affiliation(s)
- Jacob S. Lewis
- Macromolecular
Machines Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Antoine M. van Oijen
- Molecular
Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Lisanne M. Spenkelink
- Molecular
Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
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4
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Schwank K, Schmid C, Fremter T, Engel C, Milkereit P, Griesenbeck J, Tschochner H. Features of yeast RNA polymerase I with special consideration of the lobe binding subunits. Biol Chem 2023; 404:979-1002. [PMID: 37823775 DOI: 10.1515/hsz-2023-0184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/13/2023] [Indexed: 10/13/2023]
Abstract
Ribosomal RNAs (rRNAs) are structural components of ribosomes and represent the most abundant cellular RNA fraction. In the yeast Saccharomyces cerevisiae, they account for more than 60 % of the RNA content in a growing cell. The major amount of rRNA is synthesized by RNA polymerase I (Pol I). This enzyme transcribes exclusively the rRNA gene which is tandemly repeated in about 150 copies on chromosome XII. The high number of transcribed rRNA genes, the efficient recruitment of the transcription machinery and the dense packaging of elongating Pol I molecules on the gene ensure that enough rRNA is generated. Specific features of Pol I and of associated factors confer promoter selectivity and both elongation and termination competence. Many excellent reviews exist about the state of research about function and regulation of Pol I and how Pol I initiation complexes are assembled. In this report we focus on the Pol I specific lobe binding subunits which support efficient, error-free, and correctly terminated rRNA synthesis.
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Affiliation(s)
- Katrin Schwank
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Catharina Schmid
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Tobias Fremter
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Christoph Engel
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Philipp Milkereit
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Joachim Griesenbeck
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Herbert Tschochner
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
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5
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Daiß JL, Griesenbeck J, Tschochner H, Engel C. Synthesis of the ribosomal RNA precursor in human cells: mechanisms, factors and regulation. Biol Chem 2023; 404:1003-1023. [PMID: 37454246 DOI: 10.1515/hsz-2023-0214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
The ribosomal RNA precursor (pre-rRNA) comprises three of the four ribosomal RNAs and is synthesized by RNA polymerase (Pol) I. Here, we describe the mechanisms of Pol I transcription in human cells with a focus on recent insights gained from structure-function analyses. The comparison of Pol I-specific structural and functional features with those of other Pols and with the excessively studied yeast system distinguishes organism-specific from general traits. We explain the organization of the genomic rDNA loci in human cells, describe the Pol I transcription cycle regarding structural changes in the enzyme and the roles of human Pol I subunits, and depict human rDNA transcription factors and their function on a mechanistic level. We disentangle information gained by direct investigation from what had apparently been deduced from studies of the yeast enzymes. Finally, we provide information about how Pol I mutations may contribute to developmental diseases, and why Pol I is a target for new cancer treatment strategies, since increased rRNA synthesis was correlated with rapidly expanding cell populations.
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Affiliation(s)
- Julia L Daiß
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Joachim Griesenbeck
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Herbert Tschochner
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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6
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Yang DL, Huang K, Deng D, Zeng Y, Wang Z, Zhang Y. DNA-dependent RNA polymerases in plants. THE PLANT CELL 2023; 35:3641-3661. [PMID: 37453082 PMCID: PMC10533338 DOI: 10.1093/plcell/koad195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 06/09/2023] [Accepted: 05/29/2023] [Indexed: 07/18/2023]
Abstract
DNA-dependent RNA polymerases (Pols) transfer the genetic information stored in genomic DNA to RNA in all organisms. In eukaryotes, the typical products of nuclear Pol I, Pol II, and Pol III are ribosomal RNAs, mRNAs, and transfer RNAs, respectively. Intriguingly, plants possess two additional Pols, Pol IV and Pol V, which produce small RNAs and long noncoding RNAs, respectively, mainly for silencing transposable elements. The five plant Pols share some subunits, but their distinct functions stem from unique subunits that interact with specific regulatory factors in their transcription cycles. Here, we summarize recent advances in our understanding of plant nucleus-localized Pols, including their evolution, function, structures, and transcription cycles.
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Affiliation(s)
- Dong-Lei Yang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Kun Huang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Deyin Deng
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou 311300, China
| | - Yuan Zeng
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhenxing Wang
- College of Horticulture, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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7
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Chu J, Romero A, Taulbee J, Aran K. Development of Single Molecule Techniques for Sensing and Manipulation of CRISPR and Polymerase Enzymes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300328. [PMID: 37226388 PMCID: PMC10524706 DOI: 10.1002/smll.202300328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/20/2023] [Indexed: 05/26/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and polymerases are powerful enzymes and their diverse applications in genomics, proteomics, and transcriptomics have revolutionized the biotechnology industry today. CRISPR has been widely adopted for genomic editing applications and Polymerases can efficiently amplify genomic transcripts via polymerase chain reaction (PCR). Further investigations into these enzymes can reveal specific details about their mechanisms that greatly expand their use. Single-molecule techniques are an effective way to probe enzymatic mechanisms because they may resolve intermediary conformations and states with greater detail than ensemble or bulk biosensing techniques. This review discusses various techniques for sensing and manipulation of single biomolecules that can help facilitate and expedite these discoveries. Each platform is categorized as optical, mechanical, or electronic. The methods, operating principles, outputs, and utility of each technique are briefly introduced, followed by a discussion of their applications to monitor and control CRISPR and Polymerases at the single molecule level, and closing with a brief overview of their limitations and future prospects.
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Affiliation(s)
- Josephine Chu
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Andres Romero
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Jeffrey Taulbee
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Kiana Aran
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
- Cardea, San Diego, CA, 92121, USA
- University of California Berkeley, Berkeley, CA, 94720, USA
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8
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McNamar R, Freeman E, Baylor KN, Fakhouri AM, Huang S, Knutson BA, Rothblum LI. PAF49: An RNA Polymerase I subunit essential for rDNA transcription and stabilization of PAF53. J Biol Chem 2023; 299:104951. [PMID: 37356716 PMCID: PMC10365956 DOI: 10.1016/j.jbc.2023.104951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/30/2023] [Accepted: 06/09/2023] [Indexed: 06/27/2023] Open
Abstract
The application of genetic and biochemical techniques in yeast has informed our knowledge of transcription in mammalian cells. Such systems have allowed investigators to determine whether a gene was essential and to determine its function in rDNA transcription. However, there are significant differences in the nature of the transcription factors essential for transcription by Pol I in yeast and mammalian cells, and yeast RNA polymerase I contains 14 subunits while mammalian polymerase contains 13 subunits. We previously reported the adaptation of the auxin-dependent degron that enabled a combination of a "genetics-like" approach and biochemistry to study mammalian rDNA transcription. Using this system, we studied the mammalian orthologue of yeast RPA34.5, PAF49, and found that it is essential for rDNA transcription and cell division. The auxin-induced degradation of PAF49 induced nucleolar stress and the accumulation of P53. Interestingly, the auxin-induced degradation of AID-tagged PAF49 led to the degradation of its binding partner, PAF53, but not vice versa. A similar pattern of co-dependent expression was also found when we studied the non-essential, yeast orthologues. An analysis of the domains of PAF49 that are essential for rDNA transcription demonstrated a requirement for both the dimerization domain and an "arm" of PAF49 that interacts with PolR1B. Further, we demonstrate this interaction can be disrupted to inhibit Pol I transcription in normal and cancer cells which leads to the arrest of normal cells and cancer cell death. In summary, we have shown that both PAF53 and PAF49 are necessary for rDNA transcription and cell growth.
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Affiliation(s)
- Rachel McNamar
- Department of Cell Biology, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma, USA
| | - Emma Freeman
- Department of Cell and Development Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kairo N Baylor
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Aula M Fakhouri
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Sui Huang
- Department of Cell and Development Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Bruce A Knutson
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Lawrence I Rothblum
- Department of Cell Biology, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma, USA.
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9
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Dash S, Lamb MC, Lange JJ, McKinney MC, Tsuchiya D, Guo F, Zhao X, Corbin TJ, Kirkman M, Delventhal K, Moore EL, McKinney S, Shiang R, Trainor PA. rRNA transcription is integral to phase separation and maintenance of nucleolar structure. PLoS Genet 2023; 19:e1010854. [PMID: 37639467 PMCID: PMC10513380 DOI: 10.1371/journal.pgen.1010854] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/21/2023] [Accepted: 07/03/2023] [Indexed: 08/31/2023] Open
Abstract
Transcription of ribosomal RNA (rRNA) by RNA Polymerase (Pol) I in the nucleolus is necessary for ribosome biogenesis, which is intimately tied to cell growth and proliferation. Perturbation of ribosome biogenesis results in tissue specific disorders termed ribosomopathies in association with alterations in nucleolar structure. However, how rRNA transcription and ribosome biogenesis regulate nucleolar structure during normal development and in the pathogenesis of disease remains poorly understood. Here we show that homozygous null mutations in Pol I subunits required for rRNA transcription and ribosome biogenesis lead to preimplantation lethality. Moreover, we discovered that Polr1a-/-, Polr1b-/-, Polr1c-/- and Polr1d-/- mutants exhibit defects in the structure of their nucleoli, as evidenced by a decrease in number of nucleolar precursor bodies and a concomitant increase in nucleolar volume, which results in a single condensed nucleolus. Pharmacological inhibition of Pol I in preimplantation and midgestation embryos, as well as in hiPSCs, similarly results in a single condensed nucleolus or fragmented nucleoli. We find that when Pol I function and rRNA transcription is inhibited, the viscosity of the granular compartment of the nucleolus increases, which disrupts its phase separation properties, leading to a single condensed nucleolus. However, if a cell progresses through mitosis, the absence of rRNA transcription prevents reassembly of the nucleolus and manifests as fragmented nucleoli. Taken together, our data suggests that Pol I function and rRNA transcription are required for maintaining nucleolar structure and integrity during development and in the pathogenesis of disease.
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Affiliation(s)
- Soma Dash
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Maureen C. Lamb
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Jeffrey J. Lange
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Mary C. McKinney
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Dai Tsuchiya
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Fengli Guo
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Xia Zhao
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Timothy J. Corbin
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - MaryEllen Kirkman
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Kym Delventhal
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Emma L. Moore
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Rita Shiang
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Paul A. Trainor
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
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10
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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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11
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Belkevich AE, Pascual HG, Fakhouri AM, Ball DG, Knutson BA. Distinct Interaction Modes for the Eukaryotic RNA Polymerase Alpha-like Subunits. Mol Cell Biol 2023; 43:269-282. [PMID: 37222571 PMCID: PMC10251799 DOI: 10.1080/10985549.2023.2210023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/26/2023] [Accepted: 04/12/2023] [Indexed: 05/25/2023] Open
Abstract
Eukaryotic DNA-dependent RNA polymerases (Pols I-III) encode two distinct alpha-like heterodimers where one is shared between Pols I and III, and the other is unique to Pol II. Human alpha-like subunit mutations are associated with several diseases including Treacher Collins Syndrome (TCS), 4H leukodystrophy, and primary ovarian sufficiency. Yeast is commonly used to model human disease mutations, yet it remains unclear whether the alpha-like subunit interactions are functionally similar between yeast and human homologs. To examine this, we mutated several regions of the yeast and human small alpha-like subunits and used biochemical and genetic assays to establish the regions and residues required for heterodimerization with their corresponding large alpha-like subunits. Here we show that different regions of the small alpha-like subunits serve differential roles in heterodimerization, in a polymerase- and species-specific manner. We found that the small human alpha-like subunits are more sensitive to mutations, including a "humanized" yeast that we used to characterize the molecular consequence of the TCS-causingPOLR1D G52E mutation. These findings help explain why some alpha subunit associated disease mutations have little to no effect when made in their yeast orthologs and offer a better yeast model to assess the molecular basis of POLR1D associated disease mutations.
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Affiliation(s)
- Alana E. Belkevich
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Haleigh G. Pascual
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Aula M. Fakhouri
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - David G. Ball
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Bruce A. Knutson
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
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12
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Smallwood K, Watt KEN, Ide S, Baltrunaite K, Brunswick C, Inskeep K, Capannari C, Adam MP, Begtrup A, Bertola DR, Demmer L, Demo E, Devinsky O, Gallagher ER, Guillen Sacoto MJ, Jech R, Keren B, Kussmann J, Ladda R, Lansdon LA, Lunke S, Mardy A, McWalters K, Person R, Raiti L, Saitoh N, Saunders CJ, Schnur R, Skorvanek M, Sell SL, Slavotinek A, Sullivan BR, Stark Z, Symonds JD, Wenger T, Weber S, Whalen S, White SM, Winkelmann J, Zech M, Zeidler S, Maeshima K, Stottmann RW, Trainor PA, Weaver KN. POLR1A variants underlie phenotypic heterogeneity in craniofacial, neural, and cardiac anomalies. Am J Hum Genet 2023; 110:809-825. [PMID: 37075751 PMCID: PMC10183370 DOI: 10.1016/j.ajhg.2023.03.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/21/2023] [Indexed: 04/21/2023] Open
Abstract
Heterozygous pathogenic variants in POLR1A, which encodes the largest subunit of RNA Polymerase I, were previously identified as the cause of acrofacial dysostosis, Cincinnati-type. The predominant phenotypes observed in the cohort of 3 individuals were craniofacial anomalies reminiscent of Treacher Collins syndrome. We subsequently identified 17 additional individuals with 12 unique heterozygous variants in POLR1A and observed numerous additional phenotypes including neurodevelopmental abnormalities and structural cardiac defects, in combination with highly prevalent craniofacial anomalies and variable limb defects. To understand the pathogenesis of this pleiotropy, we modeled an allelic series of POLR1A variants in vitro and in vivo. In vitro assessments demonstrate variable effects of individual pathogenic variants on ribosomal RNA synthesis and nucleolar morphology, which supports the possibility of variant-specific phenotypic effects in affected individuals. To further explore variant-specific effects in vivo, we used CRISPR-Cas9 gene editing to recapitulate two human variants in mice. Additionally, spatiotemporal requirements for Polr1a in developmental lineages contributing to congenital anomalies in affected individuals were examined via conditional mutagenesis in neural crest cells (face and heart), the second heart field (cardiac outflow tract and right ventricle), and forebrain precursors in mice. Consistent with its ubiquitous role in the essential function of ribosome biogenesis, we observed that loss of Polr1a in any of these lineages causes cell-autonomous apoptosis resulting in embryonic malformations. Altogether, our work greatly expands the phenotype of human POLR1A-related disorders and demonstrates variant-specific effects that provide insights into the underlying pathogenesis of ribosomopathies.
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Affiliation(s)
- Kelly Smallwood
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Kristina Baltrunaite
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Chad Brunswick
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Katherine Inskeep
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Corrine Capannari
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Margaret P Adam
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | | | - Laurie Demmer
- Atrium Health's Levine Children's Hospital, Charlotte, NC, USA
| | - Erin Demo
- Sibley Heart Center, Atlanta, GA, USA
| | - Orrin Devinsky
- Department of Neurology, Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, USA
| | - Emily R Gallagher
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | - Robert Jech
- Department of Neurology, Charles University, 1st Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Boris Keren
- Genetic Department, APHP, Sorbonne Université, Pitié-Salpêtrière Hospital, 47-83 Boulevard de l'Hôpital, 75013 Paris, France
| | - Jennifer Kussmann
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO, USA
| | - Roger Ladda
- Department of Pediatrics, Penn State Health Children's Hospital, Hershey, PA, USA
| | - Lisa A Lansdon
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO, USA; Genomic Medicine Center, Children's Mercy Research Institute, 2401 Gillham Road, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, USA
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Flemington Road, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Australian Genomics, Melbourne, VIC, Australia
| | - Anne Mardy
- Department of Women's Health, University of Texas Austin Dell Medical Center, Austin, TX, USA
| | | | | | - Laura Raiti
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Flemington Road, Melbourne, VIC, Australia
| | | | - Carol J Saunders
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO, USA; Genomic Medicine Center, Children's Mercy Research Institute, 2401 Gillham Road, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, USA
| | | | - Matej Skorvanek
- Department of Neurology, P.J. Safarik University, Kosice, Slovak Republic; Department of Neurology, University Hospital of L. Pasteur, Kosice, Slovak Republic
| | - Susan L Sell
- Department of Pediatrics, Penn State Health Children's Hospital, Hershey, PA, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Bonnie R Sullivan
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO, USA
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Flemington Road, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia; Australian Genomics, Melbourne, VIC, Australia
| | - Joseph D Symonds
- Paediatric Neuroscience Research Group, Royal Hospital for Children, Glasgow G667AB, UK
| | - Tara Wenger
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sacha Weber
- CCA-AHU de génétique clinique et de neurogénétique, Service de Génétique et de Neurologie, CHU de Caen, Caen, France
| | - Sandra Whalen
- Genetic Department, APHP, Sorbonne Université, Pitié-Salpêtrière Hospital, 47-83 Boulevard de l'Hôpital, 75013 Paris, France
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Flemington Road, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany; Lehrstuhl für Neurogenetik, Technische Universität München, Munich, Germany; Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Shimriet Zeidler
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Rolf W Stottmann
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University School of Medicine, Columbus, OH, USA
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - K Nicole Weaver
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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13
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Ibars E, Codina-Fabra J, Bellí G, Casas C, Tarrés M, Solé-Soler R, Lorite NP, Ximénez-Embún P, Muñoz J, Colomina N, Torres-Rosell J. Ubiquitin proteomics identifies RNA polymerase I as a target of the Smc5/6 complex. Cell Rep 2023; 42:112463. [PMID: 37141096 DOI: 10.1016/j.celrep.2023.112463] [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: 05/30/2022] [Revised: 12/29/2022] [Accepted: 04/18/2023] [Indexed: 05/05/2023] Open
Abstract
Ubiquitination controls numerous cellular processes, and its deregulation is associated with many pathologies. The Nse1 subunit in the Smc5/6 complex contains a RING domain with ubiquitin E3 ligase activity and essential functions in genome integrity. However, Nse1-dependent ubiquitin targets remain elusive. Here, we use label-free quantitative proteomics to analyze the nuclear ubiquitinome of nse1-C274A RING mutant cells. Our results show that Nse1 impacts the ubiquitination of several proteins involved in ribosome biogenesis and metabolism that, importantly, extend beyond canonical functions of Smc5/6. In addition, our analysis suggests a connection between Nse1 and RNA polymerase I (RNA Pol I) ubiquitination. Specifically, Nse1 and the Smc5/6 complex promote ubiquitination of K408 and K410 in the clamp domain of Rpa190, a modification that induces its degradation in response to blocks in transcriptional elongation. We propose that this mechanism contributes to Smc5/6-dependent segregation of the rDNA array, the locus transcribed by RNA Pol I.
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Affiliation(s)
- Eva Ibars
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Joan Codina-Fabra
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Gemma Bellí
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Celia Casas
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Marc Tarrés
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Roger Solé-Soler
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Neus P Lorite
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Pilar Ximénez-Embún
- Proteomics Unit, Spanish National Cancer Research Center (CNIO), Madrid, Spain; ProteoRed-ISCIII, Madrid, Spain
| | - Javier Muñoz
- Proteomics Unit, Spanish National Cancer Research Center (CNIO), Madrid, Spain; ProteoRed-ISCIII, Madrid, Spain
| | - Neus Colomina
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain
| | - Jordi Torres-Rosell
- Departament de Ciencies Mediques Basiques, Institut de Recerca Biomedica de Lleida, Universitat de Lleida, 25198 Lleida, Spain.
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14
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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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15
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Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes. Nat Rev Mol Cell Biol 2023; 24:414-429. [PMID: 36732602 DOI: 10.1038/s41580-022-00573-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 02/04/2023]
Abstract
One of the first biological machineries to be created seems to have been the ribosome. Since then, organisms have dedicated great efforts to optimize this apparatus. The ribosomal RNA (rRNA) contained within ribosomes is crucial for protein synthesis and maintenance of cellular function in all known organisms. In eukaryotic cells, rRNA is produced from ribosomal DNA clusters of tandem rRNA genes, whose organization in the nucleolus, maintenance and transcription are strictly regulated to satisfy the substantial demand for rRNA required for ribosome biogenesis. Recent studies have elucidated mechanisms underlying the integrity of ribosomal DNA and regulation of its transcription, including epigenetic mechanisms and a unique recombination and copy-number control system to stably maintain high rRNA gene copy number. In this Review, we disucss how the crucial maintenance of rRNA gene copy number through control of gene amplification and of rRNA production by RNA polymerase I are orchestrated. We also discuss how liquid-liquid phase separation controls the architecture and function of the nucleolus and the relationship between rRNA production, cell senescence and disease.
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16
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Regulation of RNA Polymerase I Stability and Function. Cancers (Basel) 2022; 14:cancers14235776. [PMID: 36497261 PMCID: PMC9737084 DOI: 10.3390/cancers14235776] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
RNA polymerase I is a highly processive enzyme with fast initiation and elongation rates. The structure of Pol I, with its in-built RNA cleavage ability and incorporation of subunits homologous to transcription factors, enables it to quickly and efficiently synthesize the enormous amount of rRNA required for ribosome biogenesis. Each step of Pol I transcription is carefully controlled. However, cancers have highjacked these control points to switch the enzyme, and its transcription, on permanently. While this provides an exceptional benefit to cancer cells, it also creates a potential cancer therapeutic vulnerability. We review the current research on the regulation of Pol I transcription, and we discuss chemical biology efforts to develop new targeted agents against this process. Lastly, we highlight challenges that have arisen from the introduction of agents with promiscuous mechanisms of action and provide examples of agents with specificity and selectivity against Pol I.
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17
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Jacobs RQ, Fuller KB, Cooper SL, Carter ZI, Laiho M, Lucius AL, Schneider DA. RNA Polymerase I Is Uniquely Vulnerable to the Small-Molecule Inhibitor BMH-21. Cancers (Basel) 2022; 14:5544. [PMID: 36428638 PMCID: PMC9688676 DOI: 10.3390/cancers14225544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer cells require robust ribosome biogenesis to maintain rapid cell growth during tumorigenesis. Because RNA polymerase I (Pol I) transcription of the ribosomal DNA (rDNA) is the first and rate-limiting step of ribosome biogenesis, it has emerged as a promising anti-cancer target. Over the last decade, novel cancer therapeutics targeting Pol I have progressed to clinical trials. BMH-21 is a first-in-class small molecule that inhibits Pol I transcription and represses cancer cell growth. Several recent studies have uncovered key mechanisms by which BMH-21 inhibits ribosome biosynthesis but the selectivity of BMH-21 for Pol I has not been directly measured. Here, we quantify the effects of BMH-21 on Pol I, RNA polymerase II (Pol II), and RNA polymerase III (Pol III) in vitro using purified components. We found that BMH-21 directly impairs nucleotide addition by Pol I, with no or modest effect on Pols II and III, respectively. Additionally, we found that BMH-21 does not affect the stability of any of the Pols' elongation complexes. These data demonstrate that BMH-21 directly exploits unique vulnerabilities of Pol I.
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Affiliation(s)
- Ruth Q. Jacobs
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kaila B. Fuller
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Stephanie L. Cooper
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Marikki Laiho
- Department of Radiation Oncology and Molecular Radiation Sciences and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Aaron L. Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David A. Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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18
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Pitts S, Liu H, Ibrahim A, Garg A, Felgueira CM, Begum A, Fan W, Teh S, Low JY, Ford B, Schneider DA, Hay R, Laiho M. Identification of an E3 ligase that targets the catalytic subunit of RNA Polymerase I upon transcription stress. J Biol Chem 2022; 298:102690. [PMID: 36372232 PMCID: PMC9727647 DOI: 10.1016/j.jbc.2022.102690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/14/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022] Open
Abstract
RNA Polymerase I (Pol I) synthesizes rRNA, which is the first and rate-limiting step in ribosome biogenesis. Factors governing the stability of the polymerase complex are not known. Previous studies characterizing Pol I inhibitor BMH-21 revealed a transcriptional stress-dependent pathway for degradation of the largest subunit of Pol I, RPA194. To identify the E3 ligase(s) involved, we conducted a cell-based RNAi screen for ubiquitin pathway genes. We establish Skp-Cullin-F-box protein complex F-box protein FBXL14 as an E3 ligase for RPA194. We show that FBXL14 binds to RPA194 and mediates RPA194 ubiquitination and degradation in cancer cells treated with BMH-21. Mutation analysis in yeast identified lysines 1150, 1153, and 1156 on Rpa190 relevant for the protein degradation. These results reveal the regulated turnover of Pol I, showing that the stability of the catalytic subunit is controlled by the F-box protein FBXL14 in response to transcription stress.
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Affiliation(s)
- Stephanie Pitts
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hester Liu
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Adel Ibrahim
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, United Kingdom
| | - Amit Garg
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, United Kingdom
| | - Catarina Mendes Felgueira
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Asma Begum
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Wenjun Fan
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Selina Teh
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jin-Yih Low
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brittany Ford
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - David A. Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ronald Hay
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, United Kingdom
| | - Marikki Laiho
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland,For correspondence: Marikki Laiho
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19
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Daiß JL, Pilsl M, Straub K, Bleckmann A, Höcherl M, Heiss FB, Abascal-Palacios G, Ramsay EP, Tlučková K, Mars JC, Fürtges T, Bruckmann A, Rudack T, Bernecky C, Lamour V, Panov K, Vannini A, Moss T, Engel C. The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. Life Sci Alliance 2022; 5:5/11/e202201568. [PMID: 36271492 PMCID: PMC9438803 DOI: 10.26508/lsa.202201568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 06/20/2022] [Accepted: 08/09/2022] [Indexed: 11/24/2022] Open
Abstract
We characterize the human RNA polymerase I by evolutionary biochemistry and cryo-EM revealing a built-in structural domain that apparently serves as transcription factor–binding platform in metazoans. Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a major determinant of cellular growth, and dysregulation is observed in many cancer types. Here, we present the purification of human Pol I from cells carrying a genomic GFP fusion on the largest subunit allowing the structural and functional analysis of the enzyme across species. In contrast to yeast, human Pol I carries a single-subunit stalk, and in vitro transcription indicates a reduced proofreading activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native state rationalizes the effects of disease-associated mutations and uncovers an additional domain that is built into the sequence of Pol I subunit RPA1. This “dock II” domain resembles a truncated HMG box incapable of DNA binding which may serve as a downstream transcription factor–binding platform in metazoans. Biochemical analysis, in situ modelling, and ChIP data indicate that Topoisomerase 2a can be recruited to Pol I via the domain and cooperates with the HMG box domain–containing factor UBF. These adaptations of the metazoan Pol I transcription system may allow efficient release of positive DNA supercoils accumulating downstream of the transcription bubble.
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Affiliation(s)
- Julia L Daiß
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Michael Pilsl
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Kristina Straub
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Andrea Bleckmann
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Mona Höcherl
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Florian B Heiss
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Guillermo Abascal-Palacios
- Division of Structural Biology, The Institute of Cancer Research, London, UK
- Biofisika Institute (CSIC, UPV/EHU), Leioa, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Ewan P Ramsay
- Division of Structural Biology, The Institute of Cancer Research, London, UK
- Fondazione Human Technopole, Structural Biology Research Centre, Milan, Italy
| | | | - Jean-Clement Mars
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec, Canada
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada
- Borden Laboratory, IRIC, Université de Montréal, Montréal, Québec, Canada
| | - Torben Fürtges
- Protein Crystallography, Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Astrid Bruckmann
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Till Rudack
- Protein Crystallography, Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Carrie Bernecky
- Institute of Science and Technology, Klosterneuburg, Austria
| | - Valérie Lamour
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Integrated Structural Biology, Illkirch, France
- Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Konstantin Panov
- School of Biological Sciences and PGJCCR, Queen’s University Belfast, Belfast, UK
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London, UK
- Fondazione Human Technopole, Structural Biology Research Centre, Milan, Italy
| | - Tom Moss
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec, Canada
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada
| | - Christoph Engel
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
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20
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Falcon KT, Watt KEN, Dash S, Zhao R, Sakai D, Moore EL, Fitriasari S, Childers M, Sardiu ME, Swanson S, Tsuchiya D, Unruh J, Bugarinovic G, Li L, Shiang R, Achilleos A, Dixon J, Dixon MJ, Trainor PA. Dynamic regulation and requirement for ribosomal RNA transcription during mammalian development. Proc Natl Acad Sci U S A 2022; 119:e2116974119. [PMID: 35881792 PMCID: PMC9351356 DOI: 10.1073/pnas.2116974119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 05/11/2022] [Indexed: 01/28/2023] Open
Abstract
Ribosomal RNA (rRNA) transcription by RNA polymerase I (Pol I) is a critical rate-limiting step in ribosome biogenesis, which is essential for cell survival. Despite its global function, disruptions in ribosome biogenesis cause tissue-specific birth defects called ribosomopathies, which frequently affect craniofacial development. Here, we describe a cellular and molecular mechanism underlying the susceptibility of craniofacial development to disruptions in Pol I transcription. We show that Pol I subunits are highly expressed in the neuroepithelium and neural crest cells (NCCs), which generate most of the craniofacial skeleton. High expression of Pol I subunits sustains elevated rRNA transcription in NCC progenitors, which supports their high tissue-specific levels of protein translation, but also makes NCCs particularly sensitive to rRNA synthesis defects. Consistent with this model, NCC-specific deletion of Pol I subunits Polr1a, Polr1c, and associated factor Tcof1 in mice cell-autonomously diminishes rRNA synthesis, which leads to p53 protein accumulation, resulting in NCC apoptosis and craniofacial anomalies. Furthermore, compound mutations in Pol I subunits and associated factors specifically exacerbate the craniofacial anomalies characteristic of the ribosomopathies Treacher Collins syndrome and Acrofacial Dysostosis-Cincinnati type. Mechanistically, we demonstrate that diminished rRNA synthesis causes an imbalance between rRNA and ribosomal proteins. This leads to increased binding of ribosomal proteins Rpl5 and Rpl11 to Mdm2 and concomitantly diminished binding between Mdm2 and p53. Altogether, our results demonstrate a dynamic spatiotemporal requirement for rRNA transcription during mammalian cranial NCC development and corresponding tissue-specific threshold sensitivities to disruptions in rRNA transcription in the pathogenesis of congenital craniofacial disorders.
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Affiliation(s)
- Karla T. Falcon
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | | | - Soma Dash
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Ruonan Zhao
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Daisuke Sakai
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Biology, Kanazawa Medical University, Uchinada, Ishikawa 920-0293, Japan
| | - Emma L. Moore
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | | | | | - Mihaela E. Sardiu
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS 66160
| | - Selene Swanson
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Dai Tsuchiya
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - George Bugarinovic
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Orthopedic Surgery, Stanford University, Stanford, CA 94305
| | - Lin Li
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23284
| | - Rita Shiang
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23284
| | - Annita Achilleos
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, Nicosia 2408, Cyprus
| | - Jill Dixon
- Faculty of Biology, Medicine, and Health, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Michael J. Dixon
- Faculty of Biology, Medicine, and Health, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Paul A. Trainor
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160
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21
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Xie J, Aiello U, Clement Y, Haidara N, Girbig M, Schmitzova J, Pena V, Müller CW, Libri D, Porrua O. An integrated model for termination of RNA polymerase III transcription. SCIENCE ADVANCES 2022; 8:eabm9875. [PMID: 35857496 PMCID: PMC9278858 DOI: 10.1126/sciadv.abm9875] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
RNA polymerase III (RNAPIII) synthesizes essential and abundant noncoding RNAs such as transfer RNAs. Controlling RNAPIII span of activity by accurate and efficient termination is a challenging necessity to ensure robust gene expression and to prevent conflicts with other DNA-associated machineries. The mechanism of RNAPIII termination is believed to be simpler than that of other eukaryotic RNA polymerases, solely relying on the recognition of a T-tract in the nontemplate strand. Here, we combine high-resolution genome-wide analyses and in vitro transcription termination assays to revisit the mechanism of RNAPIII transcription termination in budding yeast. We show that T-tracts are necessary but not always sufficient for termination and that secondary structures of the nascent RNAs are important auxiliary cis-acting elements. Moreover, we show that the helicase Sen1 plays a key role in a fail-safe termination pathway. Our results provide a comprehensive model illustrating how multiple mechanisms cooperate to ensure efficient RNAPIII transcription termination.
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Affiliation(s)
- Juanjuan Xie
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Umberto Aiello
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Yves Clement
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Nouhou Haidara
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Mathias Girbig
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, 69117 Heidelberg, Germany
- Joint PhD degree from EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Jana Schmitzova
- Max Planck Institute for Biophysical Chemistry, Macromolecular Crystallography, Am Fassberg 11, 37077 Goettingen, Germany
| | - Vladimir Pena
- Max Planck Institute for Biophysical Chemistry, Macromolecular Crystallography, Am Fassberg 11, 37077 Goettingen, Germany
| | - Christoph W. Müller
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Domenico Libri
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
- Corresponding author. (D.L.); (O.P.)
| | - Odil Porrua
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
- Corresponding author. (D.L.); (O.P.)
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22
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Wang Q, Daiß JL, Xu Y, Engel C. Snapshots of RNA polymerase III in action - A mini review. Gene 2022; 821:146282. [PMID: 35149153 DOI: 10.1016/j.gene.2022.146282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/20/2022] [Accepted: 02/03/2022] [Indexed: 11/04/2022]
Abstract
RNA polymerase (Pol) III is responsible for the transcription of tRNAs, 5S rRNA, U6 snRNA, and other non-coding RNAs. Transcription factors such as TFIIIA, -B, -C, SNAPc, and Maf1 are required for promoter recognition, promoter opening, and Pol III activity regulation. Recent developments in cryo-electron microscopy and advanced purification approaches for endogenous multi-subunit complexes accelerated structural studies resulting in detailed structural insights which allowed an in-depth understanding of the molecular mechanisms underlying Pol III transcription. Here, we summarize structural data on Pol III and its regulating factors providing a three-dimensional framework to guide further analysis of RNA polymerase III.
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Affiliation(s)
- Qianmin Wang
- State Key Laboratory of Oncogenes and Related Genes, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Institute of Precision Medicine, Shanghai, China; Present address: Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Julia L Daiß
- Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany
| | - Youwei Xu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Christoph Engel
- Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany.
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23
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Structural insights into nuclear transcription by eukaryotic DNA-dependent RNA polymerases. Nat Rev Mol Cell Biol 2022; 23:603-622. [PMID: 35505252 DOI: 10.1038/s41580-022-00476-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2022] [Indexed: 02/07/2023]
Abstract
The eukaryotic transcription apparatus synthesizes a staggering diversity of RNA molecules. The labour of nuclear gene transcription is, therefore, divided among multiple DNA-dependent RNA polymerases. RNA polymerase I (Pol I) transcribes ribosomal RNA, Pol II synthesizes messenger RNAs and various non-coding RNAs (including long non-coding RNAs, microRNAs and small nuclear RNAs) and Pol III produces transfer RNAs and other short RNA molecules. Pol I, Pol II and Pol III are large, multisubunit protein complexes that associate with a multitude of additional factors to synthesize transcripts that largely differ in size, structure and abundance. The three transcription machineries share common characteristics, but differ widely in various aspects, such as numbers of RNA polymerase subunits, regulatory elements and accessory factors, which allows them to specialize in transcribing their specific RNAs. Common to the three RNA polymerases is that the transcription process consists of three major steps: transcription initiation, transcript elongation and transcription termination. In this Review, we outline the common principles and differences between the Pol I, Pol II and Pol III transcription machineries and discuss key structural and functional insights obtained into the three stages of their transcription processes.
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24
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Targeting Ribosome Biogenesis in Cancer: Lessons Learned and Way Forward. Cancers (Basel) 2022; 14:cancers14092126. [PMID: 35565259 PMCID: PMC9100539 DOI: 10.3390/cancers14092126] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/18/2022] [Accepted: 04/22/2022] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Cells need to produce ribosomes to sustain continuous proliferation and expand in numbers, a feature that is even more prominent in uncontrollably proliferating cancer cells. Certain cancer cell types are expected to depend more on ribosome biogenesis based on their genetic background, and this potential vulnerability can be exploited in designing effective, targeted cancer therapies. This review provides information on anti-cancer molecules that target the ribosome biogenesis machinery and indicates avenues for future research. Abstract Rapid growth and unrestrained proliferation is a hallmark of many cancers. To accomplish this, cancer cells re-wire and increase their biosynthetic and metabolic activities, including ribosome biogenesis (RiBi), a complex, highly energy-consuming process. Several chemotherapeutic agents used in the clinic impair this process by interfering with the transcription of ribosomal RNA (rRNA) in the nucleolus through the blockade of RNA polymerase I or by limiting the nucleotide building blocks of RNA, thereby ultimately preventing the synthesis of new ribosomes. Perturbations in RiBi activate nucleolar stress response pathways, including those controlled by p53. While compounds such as actinomycin D and oxaliplatin effectively disrupt RiBi, there is an ongoing effort to improve the specificity further and find new potent RiBi-targeting compounds with improved pharmacological characteristics. A few recently identified inhibitors have also become popular as research tools, facilitating our advances in understanding RiBi. Here we provide a comprehensive overview of the various compounds targeting RiBi, their mechanism of action, and potential use in cancer therapy. We discuss screening strategies, drug repurposing, and common problems with compound specificity and mechanisms of action. Finally, emerging paths to discovery and avenues for the development of potential biomarkers predictive of therapeutic outcomes across cancer subtypes are also presented.
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