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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Chu-Tan JA, Cioanca AV, Feng ZP, Wooff Y, Schumann U, Aggio-Bruce R, Patel H, Rutar M, Hannan K, Panov K, Provis J, Natoli R. Functional microRNA targetome undergoes degeneration-induced shift in the retina. Mol Neurodegener 2021; 16:60. [PMID: 34465369 PMCID: PMC8406976 DOI: 10.1186/s13024-021-00478-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/03/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND MicroRNA (miRNA) play a significant role in the pathogenesis of complex neurodegenerative diseases including age-related macular degeneration (AMD), acting as post-transcriptional gene suppressors through their association with argonaute 2 (AGO2) - a key member of the RNA Induced Silencing Complex (RISC). Identifying the retinal miRNA/mRNA interactions in health and disease will provide important insight into the key pathways miRNA regulate in disease pathogenesis and may lead to potential therapeutic targets to mediate retinal degeneration. METHODS To identify the active miRnome targetome interactions in the healthy and degenerating retina, AGO2 HITS-CLIP was performed using a rodent model of photoreceptor degeneration. Analysis of publicly available single-cell RNA sequencing (scRNAseq) data was performed to identify the cellular location of AGO2 and key members of the microRNA targetome in the retina. AGO2 findings were verified by in situ hybridization (RNA) and immunohistochemistry (protein). RESULTS Analysis revealed a similar miRnome between healthy and damaged retinas, however, a shift in the active targetome was observed with an enrichment of miRNA involvement in inflammatory pathways. This shift was further demonstrated by a change in the seed binding regions of miR-124-3p, the most abundant retinal AGO2-bound miRNA, and has known roles in regulating retinal inflammation. Additionally, photoreceptor cluster miR-183/96/182 were all among the most highly abundant miRNA bound to AGO2. Following damage, AGO2 expression was localized to the inner retinal layers and more in the OLM than in healthy retinas, indicating a locational miRNA response to retinal damage. CONCLUSIONS This study provides important insight into the alteration of miRNA regulatory activity that occurs as a response to retinal degeneration and explores the miRNA-mRNA targetome as a consequence of retinal degenerations. Further characterisation of these miRNA/mRNA interactions in the context of the degenerating retina may provide an important insight into the active role these miRNA may play in diseases such as AMD.
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Affiliation(s)
- Joshua A. Chu-Tan
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
- The Australian National University Medical School, College of Health and Medicine, Canberra, ACT 2601 Australia
| | - Adrian V. Cioanca
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
| | - Zhi-Ping Feng
- The ANU Bioinformatics Consultancy, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
| | - Yvette Wooff
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
- The Australian National University Medical School, College of Health and Medicine, Canberra, ACT 2601 Australia
| | - Ulrike Schumann
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
| | - Riemke Aggio-Bruce
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
- The Australian National University Medical School, College of Health and Medicine, Canberra, ACT 2601 Australia
| | - Hardip Patel
- The ANU Bioinformatics Consultancy, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
| | - Matt Rutar
- School of Biomedical Sciences, The University of Melbourne, Parkville, Victoria 3010 Australia
- Faculty of Science and Technology, University of Canberra, Bruce, ACT 2617 Australia
| | - Katherine Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
| | - Konstantin Panov
- School of Biological Sciences Queen’s University Belfast, Belfast, BT9 5DL Northern Ireland
| | - Jan Provis
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
- The Australian National University Medical School, College of Health and Medicine, Canberra, ACT 2601 Australia
| | - Riccardo Natoli
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
- The Australian National University Medical School, College of Health and Medicine, Canberra, ACT 2601 Australia
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Ajuh P, Kuster B, Panov K, Zomerdijk JC, Mann M, Lamond AI. Functional analysis of the human CDC5L complex and identification of its components by mass spectrometry. EMBO J 2000; 19:6569-81. [PMID: 11101529 PMCID: PMC305846 DOI: 10.1093/emboj/19.23.6569] [Citation(s) in RCA: 165] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recently, we identified proteins that co-purify with the human spliceosome using mass spectrometry. One of the identified proteins, CDC5L, corresponds to the human homologue of the Schizosaccharomyces pombe CDC5(+) gene product. Here we show that CDC5L is part of a larger multiprotein complex in HeLa nuclear extract that incorporates into the spliceosome in an ATP-dependent step. We also show that this complex is required for the second catalytic step of pre-mRNA splicing. Immunodepletion of the CDC5L complex from HeLa nuclear extract inhibits the formation of pre-mRNA splicing products in vitro but does not prevent spliceosome assembly. The first catalytic step of pre-mRNA splicing is less affected by immunodepleting the complex. The purified CDC5L complex in HeLa nuclear extract restores pre-mRNA splicing activity when added to extracts that have been immunodepleted using anti-CDC5L antibodies. Using mass spectrometry and database searches, the major protein components of the CDC5L complex have been identified. This work reports a first purification and characterization of a functional, human non-snRNA spliceosome subunit containing CDC5L and at least five additional protein factors.
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MESH Headings
- Adenosine Triphosphate/metabolism
- Amino Acid Sequence
- Blotting, Western
- Catalysis
- Cell Cycle Proteins/chemistry
- Cell Cycle Proteins/isolation & purification
- Cell Nucleus/metabolism
- Chromatography, Affinity
- Cloning, Molecular
- DNA, Complementary/metabolism
- Databases, Factual
- Electrophoresis, Polyacrylamide Gel
- HeLa Cells
- Humans
- Models, Biological
- Molecular Sequence Data
- Precipitin Tests
- RNA Splicing
- RNA, Messenger/metabolism
- Recombinant Proteins/chemistry
- Ribosomes/metabolism
- Schizosaccharomyces
- Schizosaccharomyces pombe Proteins
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Spliceosomes/metabolism
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Affiliation(s)
- P Ajuh
- Department of Biochemistry, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
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