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Dalldorf C, Rychel K, Szubin R, Hefner Y, Patel A, Zielinski DC, Palsson BO. The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. mSystems 2024; 9:e0030524. [PMID: 38829048 DOI: 10.1128/msystems.00305-24] [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: 02/29/2024] [Accepted: 04/24/2024] [Indexed: 06/05/2024] Open
Abstract
Fast growth phenotypes are achieved through optimal transcriptomic allocation, in which cells must balance tradeoffs in resource allocation between diverse functions. One such balance between stress readiness and unbridled growth in E. coli has been termed the fear versus greed (f/g) tradeoff. Two specific RNA polymerase (RNAP) mutations observed in adaptation to fast growth have been previously shown to affect the f/g tradeoff, suggesting that genetic adaptations may be primed to control f/g resource allocation. Here, we conduct a greatly expanded study of the genetic control of the f/g tradeoff across diverse conditions. We introduced 12 RNA polymerase (RNAP) mutations commonly acquired during adaptive laboratory evolution (ALE) and obtained expression profiles of each. We found that these single RNAP mutation strains resulted in large shifts in the f/g tradeoff primarily in the RpoS regulon and ribosomal genes, likely through modifying RNAP-DNA interactions. Two of these mutations additionally caused condition-specific transcriptional adaptations. While this tradeoff was previously characterized by the RpoS regulon and ribosomal expression, we find that the GAD regulon plays an important role in stress readiness and ppGpp in translation activity, expanding the scope of the tradeoff. A phylogenetic analysis found the greed-related genes of the tradeoff present in numerous bacterial species. The results suggest that the f/g tradeoff represents a general principle of transcriptome allocation in bacteria where small genetic changes can result in large phenotypic adaptations to growth conditions.IMPORTANCETo increase growth, E. coli must raise ribosomal content at the expense of non-growth functions. Previous studies have linked RNAP mutations to this transcriptional shift and increased growth but were focused on only two mutations found in the protein's central region. RNAP mutations, however, commonly occur over a large structural range. To explore RNAP mutations' impact, we have introduced 12 RNAP mutations found in laboratory evolution experiments and obtained expression profiles of each. The mutations nearly universally increased growth rates by adjusting said tradeoff away from non-growth functions. In addition to this shift, a few caused condition-specific adaptations. We explored the prevalence of this tradeoff across phylogeny and found it to be a widespread and conserved trend among bacteria.
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Affiliation(s)
| | - Kevin Rychel
- Department of Bioengineering, University of California San Diego, La Jolla, USA
| | - Richard Szubin
- Department of Bioengineering, University of California San Diego, La Jolla, USA
| | - Ying Hefner
- Department of Bioengineering, University of California San Diego, La Jolla, USA
| | - Arjun Patel
- Department of Bioengineering, University of California San Diego, La Jolla, USA
| | - Daniel C Zielinski
- Department of Bioengineering, University of California San Diego, La Jolla, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, USA
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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2
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Su BG, Vos SM. Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing. Mol Cell 2024; 84:1243-1256.e5. [PMID: 38401543 PMCID: PMC10997474 DOI: 10.1016/j.molcel.2024.01.023] [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: 10/11/2023] [Revised: 12/17/2023] [Accepted: 01/25/2024] [Indexed: 02/26/2024]
Abstract
Metazoan gene expression regulation involves pausing of RNA polymerase (Pol II) in the promoter-proximal region of genes and is stabilized by DSIF and NELF. Upon depletion of elongation factors, NELF appears to accompany elongating Pol II past pause sites; however, prior work indicates that NELF prevents Pol II elongation. Here, we report cryoelectron microscopy structures of Pol II-DSIF-NELF complexes with NELF in two distinct conformations corresponding to paused and poised states. The paused NELF state supports Pol II stalling, whereas the poised NELF state enables transcription elongation as it does not support a tilted RNA-DNA hybrid. Further, the poised NELF state can accommodate TFIIS binding to Pol II, allowing for Pol II reactivation at paused or backtracking sites. Finally, we observe that the NELF-A tentacle interacts with the RPB2 protrusion and is necessary for pausing. Our results define how NELF can support pausing, reactivation, and elongation by Pol II.
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Affiliation(s)
- Bonnie G Su
- Department of Biology, Massachusetts Institute of Technology, Building 68, 31 Ames St., Cambridge, MA 02139, USA
| | - Seychelle M Vos
- Department of Biology, Massachusetts Institute of Technology, Building 68, 31 Ames St., Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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3
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Baquero F, Beis K, Craik DJ, Li Y, Link AJ, Rebuffat S, Salomón R, Severinov K, Zirah S, Hegemann JD. The pearl jubilee of microcin J25: thirty years of research on an exceptional lasso peptide. Nat Prod Rep 2024; 41:469-511. [PMID: 38164764 DOI: 10.1039/d3np00046j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Covering: 1992 up to 2023Since their discovery, lasso peptides went from peculiarities to be recognized as a major family of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products that were shown to be spread throughout the bacterial kingdom. Microcin J25 was first described in 1992, making it one of the earliest known lasso peptides. No other lasso peptide has since then been studied to such an extent as microcin J25, yet, previous review articles merely skimmed over all the research done on this exceptional lasso peptide. Therefore, to commemorate the 30th anniversary of its first report, we give a comprehensive overview of all literature related to microcin J25. This review article spans the early work towards the discovery of microcin J25, its biosynthetic gene cluster, and the elucidation of its three-dimensional, threaded lasso structure. Furthermore, the current knowledge about the biosynthesis of microcin J25 and lasso peptides in general is summarized and a detailed overview is given on the biological activities associated with microcin J25, including means of self-immunity, uptake into target bacteria, inhibition of the Gram-negative RNA polymerase, and the effects of microcin J25 on mitochondria. The in vitro and in vivo models used to study the potential utility of microcin J25 in a (veterinary) medicine context are discussed and the efforts that went into employing the microcin J25 scaffold in bioengineering contexts are summed up.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- Network Center for Research in Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire OX11 0FA, UK
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, 4072 Brisbane, Queensland, Australia
| | - Yanyan Li
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - A James Link
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Raúl Salomón
- Instituto de Química Biológica "Dr Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, San Miguel de Tucumán, Argentina
| | - Konstantin Severinov
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany.
- Department of Pharmacy, Campus E8 1, Saarland University, 66123 Saarbrücken, Germany
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4
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do Prado PFV, Ahrens FM, Liebers M, Ditz N, Braun HP, Pfannschmidt T, Hillen HS. Structure of the multi-subunit chloroplast RNA polymerase. Mol Cell 2024; 84:910-925.e5. [PMID: 38428434 DOI: 10.1016/j.molcel.2024.02.003] [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: 09/25/2023] [Revised: 01/26/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Chloroplasts contain a dedicated genome that encodes subunits of the photosynthesis machinery. Transcription of photosynthesis genes is predominantly carried out by a plastid-encoded RNA polymerase (PEP), a nearly 1 MDa complex composed of core subunits with homology to eubacterial RNA polymerases (RNAPs) and at least 12 additional chloroplast-specific PEP-associated proteins (PAPs). However, the architecture of this complex and the functions of the PAPs remain unknown. Here, we report the cryo-EM structure of a 19-subunit PEP complex from Sinapis alba (white mustard). The structure reveals that the PEP core resembles prokaryotic and nuclear RNAPs but contains chloroplast-specific features that mediate interactions with the PAPs. The PAPs are unrelated to known transcription factors and arrange around the core in a unique fashion. Their structures suggest potential functions during transcription in the chemical environment of chloroplasts. These results reveal structural insights into chloroplast transcription and provide a framework for understanding photosynthesis gene expression.
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Affiliation(s)
- Paula F V do Prado
- University Medical Center Göttingen, Department of Cellular Biochemistry, Humboldtallee 23, 37073 Göttingen, Germany; Max Planck Institute for Multidisciplinary Sciences, Research Group Structure and Function of Molecular Machines, Am Fassberg 11, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Frederik M Ahrens
- Institute of Botany, Plant Physiology, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Monique Liebers
- Institute of Botany, Plant Physiology, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Noah Ditz
- Institute of Plant Genetics, Plant Molecular Biology and Plant Proteomics, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Hans-Peter Braun
- Institute of Plant Genetics, Plant Molecular Biology and Plant Proteomics, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Thomas Pfannschmidt
- Institute of Botany, Plant Physiology, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany.
| | - Hauke S Hillen
- University Medical Center Göttingen, Department of Cellular Biochemistry, Humboldtallee 23, 37073 Göttingen, Germany; Max Planck Institute for Multidisciplinary Sciences, Research Group Structure and Function of Molecular Machines, Am Fassberg 11, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37075 Göttingen, Germany; Göttingen Center for Molecular Biosciences (GZMB), Research Group Structure and Function of Molecular Machines, University of Göttingen, 37077 Göttingen, Germany.
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Fenstermaker TK, Petruk S, Mazo A. An emerging paradigm in epigenetic marking: coordination of transcription and replication. Transcription 2024; 15:22-37. [PMID: 38378467 DOI: 10.1080/21541264.2024.2316965] [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: 12/22/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
DNA replication and RNA transcription both utilize DNA as a template and therefore need to coordinate their activities. The predominant theory in the field is that in order for the replication fork to proceed, transcription machinery has to be evicted from DNA until replication is complete. If that does not occur, these machineries collide, and these collisions elicit various repair mechanisms which require displacement of one of the enzymes, often RNA polymerase, in order for replication to proceed. This model is also at the heart of the epigenetic bookmarking theory, which implies that displacement of RNA polymerase during replication requires gradual re-building of chromatin structure, which guides recruitment of transcriptional proteins and resumption of transcription. We discuss these theories but also bring to light newer data that suggest that these two processes may not be as detrimental to one another as previously thought. This includes findings suggesting that these processes can occur without fork collapse and that RNA polymerase may only be transiently displaced during DNA replication. We discuss potential mechanisms by which RNA polymerase may be retained at the replication fork and quickly rebind to DNA post-replication. These discoveries are important, not only as new evidence as to how these two processes are able to occur harmoniously but also because they have implications on how transcriptional programs are maintained through DNA replication. To this end, we also discuss the coordination of replication and transcription in light of revising the current epigenetic bookmarking theory of how the active gene status can be transmitted through S phase.
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Affiliation(s)
- Tyler K Fenstermaker
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Alexander Mazo
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
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6
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Duan B, Qiu C, Lockless SW, Sze SH, Kaplan CD. Higher-order epistasis within Pol II trigger loop haplotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576280. [PMID: 38293233 PMCID: PMC10827151 DOI: 10.1101/2024.01.20.576280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
RNA polymerase II (Pol II) has a highly conserved domain, the trigger loop (TL), that controls transcription fidelity and speed. We previously probed pairwise genetic interactions between residues within and surrounding the TL and identified widespread incompatibility between TLs of different species when placed in the Saccharomyces cerevisiae Pol II context, indicating epistasis between the TL and its surrounding context. We sought to understand the nature of this incompatibility and probe higher order epistasis internal to the TL. We have employed deep mutational scanning with selected natural TL variants ("haplotypes"), and all possible intermediate substitution combinations between them and the yeast Pol II TL. We identified both positive and negative higher-order residue interactions within example TL haplotypes. Intricate higher-order epistasis formed by TL residues was sometimes only apparent from analysis of intermediate genotypes, emphasizing complexity of epistatic interactions. Furthermore, we distinguished TL substitutions with distinct classes of epistatic patterns, suggesting specific TL residues that potentially influence TL evolution. Our examples of complex residue interactions suggest possible pathways for epistasis to facilitate Pol II evolution.
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Affiliation(s)
- Bingbing Duan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Chenxi Qiu
- Department of Genetics, Harvard Medical School, Boston, MA 02215
| | - Steve W Lockless
- Department of Biology, Texas A&M University, College Station, TX 77843
| | - Sing-Hoi Sze
- Department of Computer Science & Engineering, Texas A&M University, College Station, TX 77843
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
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7
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Zhou RW, Gordon IJ, Hei Y, Wang B. Synthetase and Hydrolase Specificity Collectively Excludes 2'-Deoxyguanosine from Bacterial Alarmone. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.06.574488. [PMID: 38260349 PMCID: PMC10802352 DOI: 10.1101/2024.01.06.574488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
In response to starvation, virtually all bacteria pyrophosphorylate the 3'-hydroxy group of GTP or GDP to produce two messenger nucleotides collectively denoted as (p)ppGpp. Also known as alarmones, (p)ppGpp reprograms bacterial physiology to arrest growth and promote survival. Intriguingly, although cellular concentration of dGTP is two orders of magnitude lower than that of GTP, alarmone synthetases are highly selective against using 2'-deoxyguanosine (2dG) nucleotides as substrates. We thus hypothesize that production of 2dG alarmone, (p)pp(dG)pp, is highly deleterious, which drives a strong negative selection to exclude 2dG nucleotides from alarmone signaling. In this work, we show that the B. subtilis SasB synthetase prefers GDP over dGDP with 65,000-fold higher kcat/Km, a specificity stricter than RNA polymerase selecting against 2'-deoxynucleotides. Using comparative chemical proteomics, we found that although most known alarmone-binding proteins in Escherichia coli cannot distinguish ppGpp from pp(dG)pp, hydrolysis of pp(dG)pp by the essential hydrolase, SpoT, is 1,000-fold slower. This inability to degrade 2'-deoxy-3'-pyrophosphorylated substrate is a common feature of the alarmone hydrolase family. We further show that SpoT is a binuclear metallopyrophoshohydrolase and that hydrolysis of ppGpp and pp(dG)pp shares the same metal dependence. Our results support a model in which 2'-OH directly coordinates the Mn2+ at SpoT active center to stabilize the hydrolysis-productive conformation of ppGpp. Taken together, our study reveals a vital role of 2'-OH in alarmone degradation, provides new insight on the catalytic mechanism of alarmone hydrolases, and leads to the conclusion that 2dG nucleotides must be strictly excluded from alarmone synthesis because bacteria lack the key machinery to down-regulate such products.
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Affiliation(s)
- Rich W Zhou
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Isis J Gordon
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yuanyuan Hei
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Boyuan Wang
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
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Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y. Structural visualization of transcription initiation in action. Science 2023; 382:eadi5120. [PMID: 38127763 DOI: 10.1126/science.adi5120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 11/11/2023] [Indexed: 12/23/2023]
Abstract
Transcription initiation is a complex process, and its mechanism is incompletely understood. We determined the structures of de novo transcribing complexes TC2 to TC17 with RNA polymerase II halted on G-less promoters when nascent RNAs reach 2 to 17 nucleotides in length, respectively. Connecting these structures generated a movie and a working model. As initially synthesized RNA grows, general transcription factors (GTFs) remain bound to the promoter and the transcription bubble expands. Nucleoside triphosphate (NTP)-driven RNA-DNA translocation and template-strand accumulation in a nearly sealed channel may promote the transition from initially transcribing complexes (ITCs) (TC2 to TC9) to early elongation complexes (EECs) (TC10 to TC17). Our study shows dynamic processes of transcription initiation and reveals why ITCs require GTFs and bubble expansion for initial RNA synthesis, whereas EECs need GTF dissociation from the promoter and bubble collapse for promoter escape.
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Affiliation(s)
- Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Weida Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Qianmin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xinxin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yulei Ren
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xuechun Qu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Wanjun Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
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9
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Oh J, Shan Z, Hoshika S, Xu J, Chong J, Benner SA, Lyumkis D, Wang D. A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase. Nat Commun 2023; 14:8219. [PMID: 38086811 PMCID: PMC10716388 DOI: 10.1038/s41467-023-43735-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
Artificially Expanded Genetic Information Systems (AEGIS) add independently replicable unnatural nucleotide pairs to the natural G:C and A:T/U pairs found in native DNA, joining the unnatural pairs through alternative modes of hydrogen bonding. Whether and how AEGIS pairs are recognized and processed by multi-subunit cellular RNA polymerases (RNAPs) remains unknown. Here, we show that E. coli RNAP selectively recognizes unnatural nucleobases in a six-letter expanded genetic system. High-resolution cryo-EM structures of three RNAP elongation complexes containing template-substrate UBPs reveal the shared principles behind the recognition of AEGIS and natural base pairs. In these structures, RNAPs are captured in an active state, poised to perform the chemistry step. At this point, the unnatural base pair adopts a Watson-Crick geometry, and the trigger loop is folded into an active conformation, indicating that the mechanistic principles underlying recognition and incorporation of natural base pairs also apply to AEGIS unnatural base pairs. These data validate the design philosophy of AEGIS unnatural basepairs. Further, we provide structural evidence supporting a long-standing hypothesis that pair mismatch during transcription occurs via tautomerization. Together, our work highlights the importance of Watson-Crick complementarity underlying the design principles of AEGIS base pair recognition.
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Affiliation(s)
- Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Pharmacy, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Zelin Shan
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd Box 7, Alachua, FL, 32615, USA
| | - Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd Box 7, Alachua, FL, 32615, USA.
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute 10550 N Torrey Pines Road, La Jolla, CA, 92037, USA.
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA.
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
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10
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Kim D, Lee MS, Kim ND, Lee S, Lee HS. Identification of α-amanitin effector proteins in hepatocytes by limited proteolysis-coupled mass spectrometry. Chem Biol Interact 2023; 386:110778. [PMID: 37879594 DOI: 10.1016/j.cbi.2023.110778] [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: 06/29/2023] [Revised: 10/02/2023] [Accepted: 10/22/2023] [Indexed: 10/27/2023]
Abstract
The misuse of poisonous mushrooms containing amatoxins causes acute liver failure (ALF) in patients and is a cause of significant mortality. Although the toxic mechanisms of α-amanitin (α-AMA) and its interactions with RNA polymerase II (RNAP II) have been studied, α-AMA effector proteins that can interact with α-AMA in hepatocytes have not been systematically studied. Limited proteolysis-coupled mass spectrometry (LiP-MS) is an advanced technology that can quickly identify protein-ligand interactions based on global comparative proteomics. This study identified the α-AMA effector proteins found in human hepatocytes, following the detection of conformotypic peptides using LiP-MS coupled with tandem mass tag (TMT) technology. Proteins that are classified into protein processing in the endoplasmic reticulum and the ribosome during the KEGG pathway can be identified through affinity evaluation, according to α-AMA concentration-dependent LiP-MS and LiP-MS in hepatocytes derived from humans and mice, respectively. The possibility of interaction between α-AMA and proteins containing conformotypic peptides was evaluated through molecular docking studies. The results of this study suggest a novel path for α-AMA to induce hepatotoxicity through interactions with various proteins involved in protein synthesis, as well as with RNAP II.
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Affiliation(s)
- Doeun Kim
- College of Pharmacy, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Min Seo Lee
- BK21 Four-sponsored Advanced Program for SmartPharma Leaders, College of Pharmacy, The Catholic University of Korea, Bucheon, 14662, Republic of Korea
| | - Nam Doo Kim
- Voronoibio Inc., Incheon, 21984, Republic of Korea
| | - Sangkyu Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| | - Hye Suk Lee
- BK21 Four-sponsored Advanced Program for SmartPharma Leaders, College of Pharmacy, The Catholic University of Korea, Bucheon, 14662, Republic of Korea.
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11
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Khitun A, Brion C, Moqtaderi Z, Geisberg JV, Churchman LS, Struhl K. Elongation rate of RNA polymerase II affects pausing patterns across 3' UTRs. J Biol Chem 2023; 299:105289. [PMID: 37748648 PMCID: PMC10598743 DOI: 10.1016/j.jbc.2023.105289] [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: 06/09/2023] [Revised: 09/01/2023] [Accepted: 09/20/2023] [Indexed: 09/27/2023] Open
Abstract
Yeast mRNAs are polyadenylated at multiple sites in their 3' untranslated regions (3' UTRs), and poly(A) site usage is regulated by the rate of transcriptional elongation by RNA polymerase II (Pol II). Slow Pol II derivatives favor upstream poly(A) sites, and fast Pol II derivatives favor downstream poly(A) sites. Transcriptional elongation and polyadenylation are linked at the nucleotide level, presumably reflecting Pol II dwell time at each residue that influences the level of polyadenylation. Here, we investigate the effect of Pol II elongation rate on pausing patterns and the relationship between Pol II pause sites and poly(A) sites within 3' UTRs. Mutations that affect Pol II elongation rate alter sequence preferences at pause sites within 3' UTRs, and pausing preferences differ between 3' UTRs and coding regions. In addition, sequences immediately flanking the pause sites show preferences that are largely independent of Pol II speed. In wild-type cells, poly(A) sites are preferentially located < 50 nucleotides upstream from Pol II pause sites, but this spatial relationship is diminished in cells harboring Pol II speed mutants. Based on a random forest classifier, Pol II pause sites are modestly predicted by the distance to poly(A) sites but are better predicted by the chromatin landscape in Pol II speed derivatives. Transcriptional regulatory proteins can influence the relationship between Pol II pausing and polyadenylation but in a manner distinct from Pol II elongation rate derivatives. These results indicate a complex relationship between Pol II pausing and polyadenylation.
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Affiliation(s)
- Alexandra Khitun
- Departments of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Christian Brion
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Zarmik Moqtaderi
- Departments of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph V Geisberg
- Departments of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Kevin Struhl
- Departments of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.
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12
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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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13
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Lin G, Barnes CO, Weiss S, Dutagaci B, Qiu C, Feig M, Song J, Lyubimov A, Cohen AE, Kaplan CD, Calero G. Structural basis of transcription: RNA Polymerase II substrate binding and metal coordination at 3.0 Å using a free-electron laser. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.559052. [PMID: 37790421 PMCID: PMC10543002 DOI: 10.1101/2023.09.22.559052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Catalysis and translocation of multi-subunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near atomic resolution and precise arrangement of key active site components have been elusive. Here we present the free electron laser (FEL) structure of a matched ATP-bound Pol II, revealing the full active site interaction network at the highest resolution to date, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg2+, and a putative third (site C) Mg2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structure indicate that the third Mg2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/bridge helix (BH) interactions induce conformational changes that could propel translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the hyperactive Rpb1 T834P bridge helix mutant reveals rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.
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Affiliation(s)
- Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261 USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena CA 91125 USA
| | - Simon Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261 USA
| | - Bercem Dutagaci
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing MI 48824 USA
| | - Chenxi Qiu
- Department of Genetics, Harvard Medical School, Boston MA 02115 USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing MI 48824 USA
| | - Jihnu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Artem Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260 USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261 USA
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14
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Dollinger R, Deng EB, Schultz J, Wu S, Deorio HR, Gilmour DS. Assessment of the roles of Spt5-nucleic acid contacts in promoter proximal pausing of RNA polymerase II. J Biol Chem 2023; 299:105106. [PMID: 37517697 PMCID: PMC10482750 DOI: 10.1016/j.jbc.2023.105106] [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: 03/27/2023] [Revised: 07/10/2023] [Accepted: 07/18/2023] [Indexed: 08/01/2023] Open
Abstract
Promoter proximal pausing of RNA polymerase II (Pol II) is a critical transcriptional regulatory mechanism in metazoans that requires the transcription factor DRB sensitivity-inducing factor (DSIF) and the inhibitory negative elongation factor (NELF). DSIF, composed of Spt4 and Spt5, establishes the pause by recruiting NELF to the elongation complex. However, the role of DSIF in pausing beyond NELF recruitment remains unclear. We used a highly purified in vitro system and Drosophila nuclear extract to investigate the role of DSIF in promoter proximal pausing. We identified two domains of Spt5, the KOW4 and NGN domains, that facilitate Pol II pausing. The KOW4 domain promotes pausing through its interaction with the nascent RNA while the NGN domain does so through a short helical motif that is in close proximity to the non-transcribed DNA template strand. Removal of this sequence in Drosophila has a male-specific dominant negative effect. The alpha-helical motif is also needed to support fly viability. We also show that the interaction between the Spt5 KOW1 domain and the upstream DNA helix is required for DSIF association with the Pol II elongation complex. Disruption of the KOW1-DNA interaction is dominant lethal in vivo. Finally, we show that the KOW2-3 domain of Spt5 mediates the recruitment of NELF to the elongation complex. In summary, our results reveal additional roles for DSIF in transcription regulation and identify specific domains important for facilitating Pol II pausing.
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Affiliation(s)
- Roberta Dollinger
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Eilene B Deng
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Josie Schultz
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sharon Wu
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Haley R Deorio
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David S Gilmour
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA.
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15
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Zhang HW, Huang K, Gu ZX, Wu XX, Wang JW, Zhang Y. A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex. Nat Commun 2023; 14:3118. [PMID: 37253723 DOI: 10.1038/s41467-023-38619-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/10/2023] [Indexed: 06/01/2023] Open
Abstract
De novo DNA methylation in plants relies on transcription of RNA polymerase V (Pol V) along with KTF1, which produce long non-coding RNAs for recruitment and assembly of the DNA methylation machinery. Here, we report a cryo-EM structure of the Pol V transcription elongation complex bound to KTF1. The structure reveals the conformation of the structural motifs in the active site of Pol V that accounts for its inferior RNA-extension ability. The structure also reveals structural features of Pol V that prevent it from interacting with the transcription factors of Pol II and Pol IV. The KOW5 domain of KTF1 binds near the RNA exit channel of Pol V providing a scaffold for the proposed recruitment of Argonaute proteins to initiate the assembly of the DNA methylation machinery. The structure provides insight into the Pol V transcription elongation process and the role of KTF1 during Pol V transcription-coupled DNA methylation.
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Affiliation(s)
- Hong-Wei 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
- University of Chinese Academy of Sciences, Beijing, 100049, 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
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhan-Xi Gu
- 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
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Xian Wu
- 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
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, 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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16
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Dalldorf C, Rychel K, Szubin R, Hefner Y, Patel A, Zielinski DC, Palsson BO. The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions. RESEARCH SQUARE 2023:rs.3.rs-2729651. [PMID: 37090546 PMCID: PMC10120744 DOI: 10.21203/rs.3.rs-2729651/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Fit phenotypes are achieved through optimal transcriptomic allocation. Here, we performed a high-resolution, multi-scale study of the transcriptomic tradeoff between two key fitness phenotypes, stress response (fear) and growth (greed), in Escherichia coli. We introduced twelve RNA polymerase (RNAP) mutations commonly acquired during adaptive laboratory evolution (ALE) and found that single mutations resulted in large shifts in the fear vs. greed tradeoff, likely through destabilizing the rpoB-rpoC interface. RpoS and GAD regulons drive the fear response while ribosomal proteins and the ppGpp regulon underlie greed. Growth rate selection pressure during ALE results in endpoint strains that often have RNAP mutations, with synergistic mutations reflective of particular conditions. A phylogenetic analysis found the tradeoff in numerous bacteria species. The results suggest that the fear vs. greed tradeoff represents a general principle of transcriptome allocation in bacteria where small genetic changes can result in large phenotypic adaptations to growth conditions.
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Affiliation(s)
- Christopher Dalldorf
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Kevin Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Ying Hefner
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Arjun Patel
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Daniel C. Zielinski
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
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17
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Duan B, Qiu C, Sze SH, Kaplan C. Widespread epistasis shapes RNA Polymerase II active site function and evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530048. [PMID: 36909581 PMCID: PMC10002619 DOI: 10.1101/2023.02.27.530048] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Multi-subunit RNA Polymerases (msRNAPs) are responsible for transcription in all kingdoms of life. At the heart of these msRNAPs is an ultra-conserved active site domain, the trigger loop (TL), coordinating transcription speed and fidelity by critical conformational changes impacting multiple steps in substrate selection, catalysis, and translocation. Previous studies have observed several different types of genetic interactions between eukaryotic RNA polymerase II (Pol II) TL residues, suggesting that the TL's function is shaped by functional interactions of residues within and around the TL. The extent of these interaction networks and how they control msRNAP function and evolution remain to be determined. Here we have dissected the Pol II TL interaction landscape by deep mutational scanning in Saccharomyces cerevisiae Pol II. Through analysis of over 15000 alleles, representing all single mutants, a rationally designed subset of double mutants, and evolutionarily observed TL haplotypes, we identify interaction networks controlling TL function. Substituting residues creates allele-specific networks and propagates epistatic effects across the Pol II active site. Furthermore, the interaction landscape further distinguishes alleles with similar growth phenotypes, suggesting increased resolution over the previously reported single mutant phenotypic landscape. Finally, co-evolutionary analyses reveal groups of co-evolving residues across Pol II converge onto the active site, where evolutionary constraints interface with pervasive epistasis. Our studies provide a powerful system to understand the plasticity of RNA polymerase mechanism and evolution, and provide the first example of pervasive epistatic landscape in a highly conserved and constrained domain within an essential enzyme.
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Affiliation(s)
- Bingbing Duan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Chenxi Qiu
- Department of Genetics, Harvard Medical School, Boston, MA 02215
| | - Sing-Hoi Sze
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX 77843
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843
| | - Craig Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
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18
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Xie G, Du X, Hu H, Li S, Cao X, Jacobsen SE, Du J. Structure and mechanism of the plant RNA polymerase V. Science 2023; 379:1209-1213. [PMID: 36893216 PMCID: PMC10041816 DOI: 10.1126/science.adf8231] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
In addition to the conserved RNA polymerases I to III (Pols I to III) in eukaryotes, two atypical polymerases, Pols IV and V, specifically produce noncoding RNA in the RNA-directed DNA methylation pathway in plants. Here, we report on the structures of cauliflower Pol V in the free and elongation conformations. A conserved tyrosine residue of NRPE2 stacks with a double-stranded DNA branch of the transcription bubble to potentially attenuate elongation by inducing transcription stalling. The nontemplate DNA strand is captured by NRPE2 to enhance backtracking, thereby increasing 3'-5' cleavage, which likely underpins Pol V's high fidelity. The structures also illuminate the mechanism of Pol V transcription stalling and enhanced backtracking, which may be important for Pol V's retention on chromatin to serve its function in tethering downstream factors for RNA-directed DNA methylation.
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Affiliation(s)
- Guohui Xie
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xuan Du
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Medical School, Shenzhen 518060, China
| | - Hongmiao Hu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Sisi Li
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Medical School, Shenzhen 518060, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Jiamu Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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19
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Chung C, Verheijen BM, Navapanich Z, McGann EG, Shemtov S, Lai GJ, Arora P, Towheed A, Haroon S, Holczbauer A, Chang S, Manojlovic Z, Simpson S, Thomas KW, Kaplan C, van Hasselt P, Timmers M, Erie D, Chen L, Gout JF, Vermulst M. Evolutionary conservation of the fidelity of transcription. Nat Commun 2023; 14:1547. [PMID: 36941254 PMCID: PMC10027832 DOI: 10.1038/s41467-023-36525-w] [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: 12/15/2021] [Accepted: 02/03/2023] [Indexed: 03/23/2023] Open
Abstract
Accurate transcription is required for the faithful expression of genetic information. However, relatively little is known about the molecular mechanisms that control the fidelity of transcription, or the conservation of these mechanisms across the tree of life. To address these issues, we measured the error rate of transcription in five organisms of increasing complexity and found that the error rate of RNA polymerase II ranges from 2.9 × 10-6 ± 1.9 × 10-7/bp in yeast to 4.0 × 10-6 ± 5.2 × 10-7/bp in worms, 5.69 × 10-6 ± 8.2 × 10-7/bp in flies, 4.9 × 10-6 ± 3.6 × 10-7/bp in mouse cells and 4.7 × 10-6 ± 9.9 × 10-8/bp in human cells. These error rates were modified by various factors including aging, mutagen treatment and gene modifications. For example, the deletion or modification of several related genes increased the error rate substantially in both yeast and human cells. This research highlights the evolutionary conservation of factors that control the fidelity of transcription. Additionally, these experiments provide a reasonable estimate of the error rate of transcription in human cells and identify disease alleles in a subunit of RNA polymerase II that display error-prone transcription. Finally, we provide evidence suggesting that the error rate and spectrum of transcription co-evolved with our genetic code.
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Affiliation(s)
- Claire Chung
- School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Bert M Verheijen
- School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Zoe Navapanich
- School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Eric G McGann
- School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Sarah Shemtov
- School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Guan-Ju Lai
- School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Payal Arora
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Atif Towheed
- Children's hospital of Philadelphia, Center for Mitochondrial and Epigenomic Medicine, Philadelphia, PA, USA
| | - Suraiya Haroon
- Children's hospital of Philadelphia, Center for Mitochondrial and Epigenomic Medicine, Philadelphia, PA, USA
| | - Agnes Holczbauer
- Children's hospital of Philadelphia, Center for Mitochondrial and Epigenomic Medicine, Philadelphia, PA, USA
| | - Sharon Chang
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Zarko Manojlovic
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stephen Simpson
- College of Life Sciences and Agriculture, University of New Hampshire, Durham, NH, USA
| | - Kelley W Thomas
- College of Life Sciences and Agriculture, University of New Hampshire, Durham, NH, USA
| | - Craig Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peter van Hasselt
- Department of Metabolic Disease, University of Utrecht, Utrecht, the Netherlands
| | - Marc Timmers
- Department of Urology, Medical Center - University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dorothy Erie
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Lin Chen
- Department of Molecular and Cellular Biology, University of Southern California, Los Angeles, CA, USA
| | - Jean-Franćois Gout
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Marc Vermulst
- School of Gerontology, University of Southern California, Los Angeles, CA, USA.
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20
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Deng S. The origin of genetic and metabolic systems: Evolutionary structuralinsights. Heliyon 2023; 9:e14466. [PMID: 36967965 PMCID: PMC10036676 DOI: 10.1016/j.heliyon.2023.e14466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
DNA is derived from reverse transcription and its origin is related to reverse transcriptase, DNA polymerase and integrase. The gene structure originated from the evolution of the first RNA polymerase. Thus, an explanation of the origin of the genetic system must also explain the evolution of these enzymes. This paper proposes a polymer structure model, termed the stable complex evolution model, which explains the evolution of enzymes and functional molecules. Enzymes evolved their functions by forming locally tightly packed complexes with specific substrates. A metabolic reaction can therefore be considered to be the result of adaptive evolution in this way when a certain essential molecule is lacking in a cell. The evolution of the primitive genetic and metabolic systems was thus coordinated and synchronized. According to the stable complex model, almost all functional molecules establish binding affinity and specific recognition through complementary interactions, and functional molecules therefore have the nature of being auto-reactive. This is thermodynamically favorable and leads to functional duplication and self-organization. Therefore, it can be speculated that biological systems have a certain tendency to maintain functional stability or are influenced by an inherent selective power. The evolution of dormant bacteria may support this hypothesis, and inherent selectivity can be unified with natural selection at the molecular level.
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21
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Dutagaci B, Duan B, Qiu C, Kaplan CD, Feig M. Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning. PLoS Comput Biol 2023; 19:e1010999. [PMID: 36947548 PMCID: PMC10069792 DOI: 10.1371/journal.pcbi.1010999] [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: 08/15/2022] [Revised: 04/03/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023] Open
Abstract
Catalysis and fidelity of multisubunit RNA polymerases rely on a highly conserved active site domain called the trigger loop (TL), which achieves roles in transcription through conformational changes and interaction with NTP substrates. The mutations of TL residues cause distinct effects on catalysis including hypo- and hyperactivity and altered fidelity. We applied molecular dynamics simulation (MD) and machine learning (ML) techniques to characterize TL mutations in the Saccharomyces cerevisiae RNA Polymerase II (Pol II) system. We did so to determine relationships between individual mutations and phenotypes and to associate phenotypes with MD simulated structural alterations. Using fitness values of mutants under various stress conditions, we modeled phenotypes along a spectrum of continual values. We found that ML could predict the phenotypes with 0.68 R2 correlation from amino acid sequences alone. It was more difficult to incorporate MD data to improve predictions from machine learning, presumably because MD data is too noisy and possibly incomplete to directly infer functional phenotypes. However, a variational auto-encoder model based on the MD data allowed the clustering of mutants with different phenotypes based on structural details. Overall, we found that a subset of loss-of-function (LOF) and lethal mutations tended to increase distances of TL residues to the NTP substrate, while another subset of LOF and lethal substitutions tended to confer an increase in distances between TL and bridge helix (BH). In contrast, some of the gain-of-function (GOF) mutants appear to cause disruption of hydrophobic contacts among TL and nearby helices.
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Affiliation(s)
- Bercem Dutagaci
- Department of Molecular and Cell Biology, University of California Merced, Merced, California, United States of America
| | - Bingbing Duan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Chenxi Qiu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Craig D. Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
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22
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Investigation of Multi-Subunit Mycobacterium tuberculosis DNA-Directed RNA Polymerase and Its Rifampicin Resistant Mutants. Int J Mol Sci 2023; 24:ijms24043313. [PMID: 36834726 PMCID: PMC9965755 DOI: 10.3390/ijms24043313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
Emerging Mycobacterium tuberculosis (Mtb) resistant strains have continued to limit the efficacies of existing antitubercular therapies. More specifically, mutations in the RNA replicative machinery of Mtb, RNA polymerase (RNAP), have been widely linked to rifampicin (RIF) resistance, which has led to therapeutic failures in many clinical cases. Moreover, elusive details on the underlying mechanisms of RIF-resistance caused by Mtb-RNAP mutations have hampered the development of new and efficient drugs that are able to overcome this challenge. Therefore, in this study we attempt to resolve the molecular and structural events associated with RIF-resistance in nine clinically reported missense Mtb RNAP mutations. Our study, for the first time, investigated the multi-subunit Mtb RNAP complex and findings revealed that the mutations commonly disrupted structural-dynamical attributes that may be essential for the protein's catalytic functions, particularly at the βfork loop 2, β'zinc-binding domain, the β' trigger loop and β'jaw, which in line with previous experimental reports, are essential for RNAP processivity. Complementarily, the mutations considerably perturbed the RIF-BP, which led to alterations in the active orientation of RIF needed to obstruct RNA extension. Consequentially, essential interactions with RIF were lost due to the mutation-induced repositioning with corresponding reductions in the binding affinity of the drug observed in majority of the mutants. We believe these findings will significantly aid future efforts in the discovery of new treatment options with the potential to overcome antitubercular resistance.
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23
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Oh J, Kimoto M, Xu H, Chong J, Hirao I, Wang D. Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase. Nat Commun 2023; 14:195. [PMID: 36635281 PMCID: PMC9836923 DOI: 10.1038/s41467-022-35755-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/23/2022] [Indexed: 01/14/2023] Open
Abstract
Bacteriophage T7 RNA polymerase (T7 RNAP) is widely used for synthesizing RNA molecules with synthetic modifications and unnatural base pairs (UBPs) for a variety of biotechnical and therapeutic applications. However, the molecular basis of transcription recognition of UBPs by T7 RNAP remains poorly understood. Here we focused on a representative UBP, 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and pyrrole 2-carbaldehyde (Pa), and investigated how the hydrophobic Ds-Pa pair is recognized by T7 RNAP. Our kinetic assays revealed that T7 RNAP selectively recognizes the Ds or Pa base in the templates and preferentially incorporates their cognate unnatural base nucleotide substrate (PaTP or DsTP) over natural NTPs. Our structural studies reveal that T7 RNAP recognizes the unnatural substrates at the pre-insertion state in a distinct manner compared to natural substrates. These results provide mechanistic insights into transcription recognition of UBP by T7 RNAP and provide valuable information for designing the next generation of UBPs.
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Affiliation(s)
- Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Michiko Kimoto
- Institute of Bioengineering and Bioimaging (IBB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Xenolis Pte. Ltd., Singapore, Singapore
| | - Haoqing Xu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Ichiro Hirao
- Institute of Bioengineering and Bioimaging (IBB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- Xenolis Pte. Ltd., Singapore, Singapore.
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
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24
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Unarta IC, Goonetilleke EC, Wang D, Huang X. Nucleotide addition and cleavage by RNA polymerase II: Coordination of two catalytic reactions using a single active site. J Biol Chem 2022; 299:102844. [PMID: 36581202 PMCID: PMC9860460 DOI: 10.1016/j.jbc.2022.102844] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
RNA polymerase II (Pol II) incorporates complementary ribonucleotides into the growing RNA chain one at a time via the nucleotide addition cycle. The nucleotide addition cycle, however, is prone to misincorporation of noncomplementary nucleotides. Thus, to ensure transcriptional fidelity, Pol II backtracks and then cleaves the misincorporated nucleotides. These two reverse reactions, nucleotide addition and cleavage, are catalyzed in the same active site of Pol II, which is different from DNA polymerases or other endonucleases. Recently, substantial progress has been made to understand how Pol II effectively performs its dual role in the same active site. Our review highlights these recent studies and provides an overall model of the catalytic mechanisms of Pol II. In particular, RNA extension follows the two-metal-ion mechanism, and several Pol II residues play important roles to facilitate the catalysis. In sharp contrast, the cleavage reaction is independent of any Pol II residues. Interestingly, Pol II relies on its residues to recognize the misincorporated nucleotides during the backtracking process, prior to cleavage. In this way, Pol II efficiently compartmentalizes its two distinct catalytic functions using the same active site. Lastly, we also discuss a new perspective on the potential third Mg2+ in the nucleotide addition and intrinsic cleavage reactions.
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Affiliation(s)
- Ilona Christy Unarta
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eshani C Goonetilleke
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Dong Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA; Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA.
| | - Xuhui Huang
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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25
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Stephanie F, Tambunan USF, Siahaan TJ. M. tuberculosis Transcription Machinery: A Review on the Mycobacterial RNA Polymerase and Drug Discovery Efforts. Life (Basel) 2022; 12:1774. [PMID: 36362929 PMCID: PMC9695777 DOI: 10.3390/life12111774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/24/2022] [Accepted: 11/01/2022] [Indexed: 09/08/2023] Open
Abstract
Mycobacterium tuberculosis (MTB) is the main source of tuberculosis (TB), one of the oldest known diseases in the human population. Despite the drug discovery efforts of past decades, TB is still one of the leading causes of mortality and claimed more than 1.5 million lives worldwide in 2020. Due to the emergence of drug-resistant strains and patient non-compliance during treatments, there is a pressing need to find alternative therapeutic agents for TB. One of the important areas for developing new treatments is in the inhibition of the transcription step of gene expression; it is the first step to synthesize a copy of the genetic material in the form of mRNA. This further translates to functional protein synthesis, which is crucial for the bacteria living processes. MTB contains a bacterial DNA-dependent RNA polymerase (RNAP), which is the key enzyme for the transcription process. MTB RNAP has been targeted for designing and developing antitubercular agents because gene transcription is essential for the mycobacteria survival. Initiation, elongation, and termination are the three important sequential steps in the transcription process. Each step is complex and highly regulated, involving multiple transcription factors. This review is focused on the MTB transcription machinery, especially in the nature of MTB RNAP as the main enzyme that is regulated by transcription factors. The mechanism and conformational dynamics that occur during transcription are discussed and summarized. Finally, the current progress on MTB transcription inhibition and possible drug target in mycobacterial RNAP are also described to provide insight for future antitubercular drug design and development.
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Affiliation(s)
- Filia Stephanie
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Usman Sumo Friend Tambunan
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Teruna J. Siahaan
- Department of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, Lawrence, KS 66045, USA
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26
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Johnson RS, Strausbauch M, McCloud C. An NTP-driven mechanism for the nucleotide addition cycle of Escherichia coli RNA polymerase during transcription. PLoS One 2022; 17:e0273746. [PMID: 36282801 PMCID: PMC9595533 DOI: 10.1371/journal.pone.0273746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/15/2022] [Indexed: 11/06/2022] Open
Abstract
The elementary steps of transcription as catalyzed by E. coli RNA polymerase during one and two rounds of the nucleotide addition cycle (NAC) were resolved in rapid kinetic studies. Modelling of stopped-flow kinetic data of pyrophosphate release in a coupled enzyme assay during one round of the NAC indicates that the rate of pyrophosphate release is significantly less than that for nucleotide incorporation. Upon modelling of the stopped-flow kinetic data for pyrophosphate release during two rounds of the NAC, it was observed that the presence of the next nucleotide for incorporation increases the rate of release of the first pyrophosphate equivalent; incorrect nucleotides for incorporation had no effect on the rate of pyrophosphate release. Although the next nucleotide for incorporation increases the rate of pyrophosphate release, it is still significantly less than the rate of incorporation of the first nucleotide. The results from the stopped-flow kinetic studies were confirmed by using quench-flow followed by thin-layer chromatography (QF-TLC) with only the first nucleotide for incorporation labeled on the gamma phosphate with 32P to monitor pyrophosphate release. Collectively, the results are consistent with an NTP-driven model for the NAC in which the binding of the next cognate nucleotide for incorporation causes a synergistic conformational change in the enzyme that triggers the more rapid release of pyrophosphate, translocation of the enzyme along the DNA template strand and nucleotide incorporation.
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Affiliation(s)
- Ronald S. Johnson
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
- * E-mail:
| | - Mark Strausbauch
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Christopher McCloud
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
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27
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Cui R, Li H, Zhao J, Li X, Gan J, Ma J. Structural insights into the dual activities of the two-barrel RNA polymerase QDE-1. Nucleic Acids Res 2022; 50:10169-10186. [PMID: 36039765 PMCID: PMC9508822 DOI: 10.1093/nar/gkac727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/01/2022] [Accepted: 08/27/2022] [Indexed: 11/19/2022] Open
Abstract
Neurospora crassa protein QDE-1, a member of the two-barrel polymerase superfamily, possesses both DNA- and RNA-dependent RNA polymerase (DdRP and RdRP) activities. The dual activities are essential for the production of double-stranded RNAs (dsRNAs), the precursors of small interfering RNAs (siRNAs) in N. crassa. Here, we report five complex structures of N-terminal truncated QDE-1 (QDE-1ΔN), representing four different reaction states: DNA/RNA-templated elongation, the de novo initiation of RNA synthesis, the first step of nucleotide condensation during de novo initiation and initial NTP loading. The template strand is aligned by a bridge-helix and double-psi beta-barrels 2 (DPBB2), the RNA product is held by DPBB1 and the slab domain. The DNA template unpairs with the RNA product at position –7, but the RNA template remains paired. The NTP analog coordinates with cations and is precisely positioned at the addition site by a rigid trigger loop and a proline-containing loop in the active center. The unique C-terminal tail from the QDE-1 dimer partner inserts into the substrate-binding cleft and plays regulatory roles in RNA synthesis. Collectively, this work elucidates the conserved mechanisms for DNA/RNA-dependent dual activities by QDE-1 and other two-barrel polymerase superfamily members.
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Affiliation(s)
- Ruixue Cui
- Huashan Hospital affiliated to Fudan University, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hao Li
- Huashan Hospital affiliated to Fudan University, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jin Zhao
- Huashan Hospital affiliated to Fudan University, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xuhang Li
- Huashan Hospital affiliated to Fudan University, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jinbiao Ma
- Huashan Hospital affiliated to Fudan University, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute of Complex Systems, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
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28
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Giacomini T, Scala M, Nobile G, Severino M, Tortora D, Nobili L, Accogli A, Torella A, Capra V, Mancardi MM, Nigro V. De novo POLR2A p.(Ile457Thr) variant associated with early-onset encephalopathy and cerebellar atrophy: expanding the phenotypic spectrum. Brain Dev 2022; 44:480-485. [PMID: 35461703 DOI: 10.1016/j.braindev.2022.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 03/15/2022] [Accepted: 04/05/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Heterozygous POLR2A variants have been recently reported in patients with a neurodevelopmental syndrome characterized by profound infantile-onset hypotonia. POLR2A encodes the highly conserved RBP1 protein, an essential subunit of the DNA-dependent RNA polymerase II. CASE PRESENTATION We investigated a 12-year-old girl presenting with an early-onset encephalopathy characterized by psychomotor delay, facial dysmorphism, refractory epilepsy with variable seizure types, behavioural abnormalities, and sleep disorder. Brain MRI showed a slowly progressive cerebellar atrophy. Trio-exome sequencing (Trio-ES) revealed the de novo germline variant NM_000937.5:c.1370T>C; p.(Ile457Thr) in POLR2A. This variant was previously reported in a subject with profound generalized hypotonia and muscular atrophy by Haijes et al. Our patient displayed instead a severe epileptic phenotype with refractory hypotonic seizures with impaired consciousness, myoclonic jerks, and drop attacks. CONCLUSION This case expands the clinical spectrum of POLR2A-related syndrome, highlighting its phenotypic variability and supporting the relevance of epilepsy as a core feature of this emerging condition.
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Affiliation(s)
- Thea Giacomini
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genoa, Genoa, Italy; Neuroradiology Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genoa, Genoa, Italy.
| | - Giulia Nobile
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genoa, Genoa, Italy.
| | | | - Domenico Tortora
- Neuroradiology Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | - Lino Nobili
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genoa, Genoa, Italy; Unit of Child Neuropsychiatry, IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | - Andrea Accogli
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genoa, Genoa, Italy.
| | - Annalaura Torella
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy; Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy.
| | - Valeria Capra
- Medical Genetic Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | | | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy; Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy.
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- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
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29
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Arba M, Paradis N, Wahyudi ST, Brunt DJ, Hausman KR, Lakernick PM, Singh M, Wu C. Unraveling the binding mechanism of the active form of Remdesivir to RdRp of SARS-CoV-2 and designing new potential analogues: Insights from molecular dynamics simulations. Chem Phys Lett 2022; 799:139638. [PMID: 35475235 PMCID: PMC9020840 DOI: 10.1016/j.cplett.2022.139638] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 01/18/2023]
Abstract
The binding of the active form of Remdesivir (RTP) to RNA-dependent RNA Polymerase (RdRp) of SARS-CoV-2 was studied using molecular dynamics simulation. The RTP maintained the interactions observed in the experimental cryo-EM structure. Next, we designed new analogues of RTP, which not only binds to the RNA primer strand in a similar pose as that of RTP, but also binds more strongly than RTP does as predicted by MM-PBSA binding energy. This suggest that these analogues might be able to covalently link to the primer strand as RTP, but their 3' modification would terminate the primer strand growth.
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Affiliation(s)
- Muhammad Arba
- Faculty of Pharmacy, Universitas Halu Oleo, Kendari 93232, Indonesia
| | - Nicholas Paradis
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, United States
| | - Setyanto T Wahyudi
- Department of Physics, Faculty of Mathematic and Natural Sciences, IPB University, Bogor 16680, Indonesia
| | - Dylan J Brunt
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, United States
| | - Katherine R Hausman
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, United States
| | - Phillip M Lakernick
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, United States
| | - Mursalin Singh
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, United States
| | - Chun Wu
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ 08028, United States
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30
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Garcia J, Carvalho A, das Neves RP, Malheiro R, Rodrigues DF, Figueiredo PR, Bovolini A, Duarte JA, Costa VM, Carvalho F. Antidotal effect of cyclosporine A against α-amanitin toxicity in CD-1 mice, at clinical relevant doses. Food Chem Toxicol 2022; 166:113198. [PMID: 35671903 DOI: 10.1016/j.fct.2022.113198] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 12/12/2022]
Abstract
Amanita phalloides is one of the most toxic mushrooms worldwide, being responsible for the majority of human fatal cases of mushroom intoxications. α-Amanitin, the most deleterious toxin of A. phalloides, inhibits RNA polymerase II (RNAP II), causing hepatic and renal failure. Herein, we used cyclosporine A after it showed potential to displace RNAP II α-amanitin in silico. That potential was not confirmed either by the incorporation of ethynyl-UTP or by the monitoring of fluorescent RNAP II levels. Nevertheless, concomitant incubation of cyclosporine A with α-amanitin, for a short period, provided significant protection against its toxicity in differentiated HepaRG cells. In mice, the concomitant administration of α-amanitin [0.45 mg/kg intraperitoneal (i.p.)] with cyclosporine A (10 mg/kg i.p. plus 2 × 10 mg/kg cyclosporine A i.p. at 8 and 12 h post α-amanitin) resulted in the full survival of α-amanitin-intoxicated mice, up to 30 days after the toxin's administration. Since α-amanitin is a substrate of the organic-anion-transporting polypeptide 1B3 and cyclosporine A inhibits this transporter and is a potent anti-inflammatory agent, we hypothesize that these mechanisms are responsible for the protection observed. These results indicate a potential antidotal effect of cyclosporine A, and its safety profile advocates for its use at an early stage of α-amanitin intoxications.
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Affiliation(s)
- Juliana Garcia
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal; Laboratório Associado i4HB - Instituto para a Saúde e a Bioeconomia, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, 4050-313, Porto, Portugal
| | - Alexandra Carvalho
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517, Coimbra, Portugal; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789, Coimbra, Portugal
| | - Ricardo Pires das Neves
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517, Coimbra, Portugal
| | - Rui Malheiro
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal; Laboratório Associado i4HB - Instituto para a Saúde e a Bioeconomia, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, 4050-313, Porto, Portugal
| | - Daniela F Rodrigues
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal; Laboratório Associado i4HB - Instituto para a Saúde e a Bioeconomia, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, 4050-313, Porto, Portugal
| | - Pedro R Figueiredo
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517, Coimbra, Portugal
| | | | - José Alberto Duarte
- CIAFEL, Faculty of Sport, University of Porto, Porto, Portugal; TOXRUN - Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, 4585-116, Gandra, Portugal
| | - Vera Marisa Costa
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal; Laboratório Associado i4HB - Instituto para a Saúde e a Bioeconomia, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, 4050-313, Porto, Portugal.
| | - Félix Carvalho
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal; Laboratório Associado i4HB - Instituto para a Saúde e a Bioeconomia, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, 4050-313, Porto, Portugal.
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31
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Du X, Yang Z, Ariza AJF, Wang Q, Xie G, Li S, Du J. Structure of plant RNA-DEPENDENT RNA POLYMERASE 2, an enzyme involved in small interfering RNA production. THE PLANT CELL 2022; 34:2140-2149. [PMID: 35188193 PMCID: PMC9134047 DOI: 10.1093/plcell/koac067] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
In plants, the biogenesis of small interfering RNA (siRNA) requires a family of RNA-dependent RNA polymerases that convert single-stranded RNA (ssRNA) into double-stranded RNA (dsRNA), which is subsequently cleaved into defined lengths by Dicer endonucleases. Here, we determined the structure of maize (Zea mays) RNA-DEPENDENT RNA POLYMERASE 2 (ZmRDR2) in the closed and open conformations. The core catalytic region of ZmRDR2 possesses the canonical DNA-dependent RNA polymerase (DdRP) catalytic sites, pointing to a shared RNA production mechanism between DdRPs and plant RDR-family proteins. Apo-ZmRDR2 adopts a highly compact structure, representing an inactive closed conformation. By contrast, adding RNA induced a significant conformational change in the ZmRDR2 Head domain that opened the RNA binding tunnel, suggesting this is an active elongation conformation of ZmRDR2. Overall, our structural studies trapped both the active and inactive conformations of ZmRDR2, providing insights into the molecular mechanism of dsRNA synthesis during plant siRNA production.
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Affiliation(s)
| | | | - Alfredo Jose Florez Ariza
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, USA
- Biophysics Graduate Group, University of California, Berkeley, California 94720, USA
| | - Qian Wang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guohui Xie
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Sisi Li
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen 518060, China
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32
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Aranda J, Wieczór M, Terrazas M, Brun-Heath I, Orozco M. Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2. CHEM CATALYSIS 2022; 2:1084-1099. [PMID: 35465139 PMCID: PMC9016896 DOI: 10.1016/j.checat.2022.03.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/08/2022] [Accepted: 03/24/2022] [Indexed: 01/21/2023]
Abstract
We combine molecular dynamics, statistical mechanics, and hybrid quantum mechanics/molecular mechanics simulations to describe mechanistically the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp). Our study analyzes the binding mode of both natural triphosphate substrates as well as remdesivir triphosphate (the active form of drug), which is bound preferentially over ATP by RdRp while being poorly recognized by human RNA polymerase II (RNA Pol II). A comparison of incorporation rates between natural and antiviral nucleotides shows that remdesivir is incorporated more slowly into the nascent RNA compared with ATP, leading to an RNA duplex that is structurally very similar to an unmodified one, arguing against the hypothesis that remdesivir is a competitive inhibitor of ATP. We characterize the entire mechanism of reaction, finding that viral RdRp is highly processive and displays a higher catalytic rate of incorporation than human RNA Pol II. Overall, our study provides the first detailed explanation of the replication mechanism of RdRp.
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Affiliation(s)
- Juan Aranda
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Milosz Wieczór
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Physical Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Montserrat Terrazas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Inorganic and Organic Chemistry, Section of Organic Chemistry, IBUB, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Isabelle Brun-Heath
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Departament de Bioquímica i Biomedicine, Universitat de Barcelona, Universitat de Barcelona, Avinguda Diagonal 645, 08028 Barcelona, Spain
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Abstract
Biochemistry and molecular biology rely on the recognition of structural complementarity between molecules. Molecular interactions must be both quickly reversible, i.e., tenuous, and specific. How the cell reconciles these conflicting demands is the subject of this article. The problem and its theoretical solution are discussed within the wider theoretical context of the thermodynamics of stochastic processes (stochastic thermodynamics). The solution-an irreversible reaction cycle that decreases internal error at the expense of entropy export into the environment-is shown to be widely employed by biological processes that transmit genetic and regulatory information. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Hinrich Boeger
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California;
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34
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Bou-Nader C, Bothra A, Garboczi DN, Leppla SH, Zhang J. Structural basis of R-loop recognition by the S9.6 monoclonal antibody. Nat Commun 2022; 13:1641. [PMID: 35347133 PMCID: PMC8960830 DOI: 10.1038/s41467-022-29187-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 03/02/2022] [Indexed: 12/31/2022] Open
Abstract
R-loops are ubiquitous, dynamic nucleic-acid structures that play fundamental roles in DNA replication and repair, chromatin and transcription regulation, as well as telomere maintenance. The DNA-RNA hybrid–specific S9.6 monoclonal antibody is widely used to map R-loops. Here, we report crystal structures of a S9.6 antigen-binding fragment (Fab) free and bound to a 13-bp hybrid duplex. We demonstrate that S9.6 exhibits robust selectivity in binding hybrids over double-stranded (ds) RNA and in categorically rejecting dsDNA. S9.6 asymmetrically recognizes a compact epitope of two consecutive RNA nucleotides via their 2′-hydroxyl groups and six consecutive DNA nucleotides via their backbone phosphate and deoxyribose groups. Recognition is mediated principally by aromatic and basic residues of the S9.6 heavy chain, which closely track the curvature of the hybrid minor groove. These findings reveal the molecular basis for S9.6 recognition of R-loops, detail its binding specificity, identify a new hybrid-recognition strategy, and provide a framework for S9.6 protein engineering. The S9.6 monoclonal antibody is widely used to map R-loops genome wide. Here, Bou-Nader et al., define the nucleic acid-binding specificity of S9.6 and report its crystal structures free and bound to a hybrid, which reveal the asymmetric recognition of the RNA and DNA strands and its A-form conformation.
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Affiliation(s)
- Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892, USA
| | - Ankur Bothra
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA
| | - David N Garboczi
- Structural Biology Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA
| | - Stephen H Leppla
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA.
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892, USA.
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35
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Evans DR, Qiao Y, Trost B, Calli K, Martell S, Jones SJM, Scherer SW, Lewis MES. Complex Autism Spectrum Disorder with Epilepsy, Strabismus and Self-Injurious Behaviors in a Patient with a De Novo Heterozygous POLR2A Variant. Genes (Basel) 2022; 13:genes13030470. [PMID: 35328024 PMCID: PMC8955435 DOI: 10.3390/genes13030470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 02/01/2023] Open
Abstract
Autism spectrum disorder (ASD) describes a complex and heterogenous group of neurodevelopmental disorders. Whole genome sequencing continues to shed light on the multifactorial etiology of ASD. Dysregulated transcriptional pathways have been implicated in neurodevelopmental disorders. Emerging evidence suggests that de novo POLR2A variants cause a newly described phenotype called ‘Neurodevelopmental Disorder with Hypotonia and Variable Intellectual and Behavioral Abnormalities’ (NEDHIB). The variable phenotype manifests with a spectrum of features; primarily early onset hypotonia and delay in developmental milestones. In this study, we investigate a patient with complex ASD involving epilepsy and strabismus. Whole genome sequencing of the proband−parent trio uncovered a novel de novo POLR2A variant (c.1367T>C, p. Val456Ala) in the proband. The variant appears deleterious according to in silico tools. We describe the phenotype in our patient, who is now 31 years old, draw connections between the previously reported phenotypes and further delineate this emerging neurodevelopmental phenotype. This study sheds new insights into this neurodevelopmental disorder, and more broadly, the genetic etiology of ASD.
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Affiliation(s)
- Daniel R. Evans
- Department of Family Practice, University of British Columbia (UBC), Victoria, BC V8R 1J8, Canada;
| | - Ying Qiao
- Medical Genetics, University of British Columbia (UBC), Vancouver, BC V6H 3N1, Canada; (Y.Q.); (K.C.); (S.M.); (S.J.M.J.)
- BC Children’s Hospital Research Institute, Vancouver, BC V6H 3N1, Canada
- iTARGET Autism, Vancouver, BC V6H 3N1, Canada
| | - Brett Trost
- The Centre for Applied Genomics and McLaughlin Centre, Hospital for Sick Children, University of Toronto, Toronto, ON M5G 0A4, Canada; (B.T.); (S.W.S.)
| | - Kristina Calli
- Medical Genetics, University of British Columbia (UBC), Vancouver, BC V6H 3N1, Canada; (Y.Q.); (K.C.); (S.M.); (S.J.M.J.)
- BC Children’s Hospital Research Institute, Vancouver, BC V6H 3N1, Canada
- iTARGET Autism, Vancouver, BC V6H 3N1, Canada
| | - Sally Martell
- Medical Genetics, University of British Columbia (UBC), Vancouver, BC V6H 3N1, Canada; (Y.Q.); (K.C.); (S.M.); (S.J.M.J.)
- BC Children’s Hospital Research Institute, Vancouver, BC V6H 3N1, Canada
- iTARGET Autism, Vancouver, BC V6H 3N1, Canada
| | - Steven J. M. Jones
- Medical Genetics, University of British Columbia (UBC), Vancouver, BC V6H 3N1, Canada; (Y.Q.); (K.C.); (S.M.); (S.J.M.J.)
- iTARGET Autism, Vancouver, BC V6H 3N1, Canada
- Michael Smith Genome Sciences Centre, Vancouver, BC V6H 3N1, Canada
| | - Stephen W. Scherer
- The Centre for Applied Genomics and McLaughlin Centre, Hospital for Sick Children, University of Toronto, Toronto, ON M5G 0A4, Canada; (B.T.); (S.W.S.)
| | - M. E. Suzanne Lewis
- Medical Genetics, University of British Columbia (UBC), Vancouver, BC V6H 3N1, Canada; (Y.Q.); (K.C.); (S.M.); (S.J.M.J.)
- BC Children’s Hospital Research Institute, Vancouver, BC V6H 3N1, Canada
- iTARGET Autism, Vancouver, BC V6H 3N1, Canada
- Correspondence:
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36
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Gong P. Within and Beyond the Nucleotide Addition Cycle of Viral RNA-dependent RNA Polymerases. Front Mol Biosci 2022; 8:822218. [PMID: 35083282 PMCID: PMC8784604 DOI: 10.3389/fmolb.2021.822218] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Abstract
Nucleotide addition cycle (NAC) is a fundamental process utilized by nucleic acid polymerases when carrying out nucleic acid biosynthesis. An induced-fit mechanism is usually taken by these polymerases upon NTP/dNTP substrate binding, leading to active site closure and formation of a phosphodiester bond. In viral RNA-dependent RNA polymerases, the post-chemistry translocation is stringently controlled by a structurally conserved motif, resulting in asymmetric movement of the template-product duplex. This perspective focuses on viral RdRP NAC and related mechanisms that have not been structurally clarified to date. Firstly, RdRP movement along the template strand in the absence of catalytic events may be relevant to catalytic complex dissociation or proofreading. Secondly, pyrophosphate or non-cognate NTP-mediated cleavage of the product strand 3′-nucleotide can also play a role in reactivating paused or arrested catalytic complexes. Furthermore, non-cognate NTP substrates, including NTP analog inhibitors, can not only alter NAC when being misincorporated, but also impact on subsequent NACs. Complications and challenges related to these topics are also discussed.
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Affiliation(s)
- Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, China
- *Correspondence: Peng Gong,
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37
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Agapov A, Olina A, Kulbachinskiy A. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3018-3041. [PMID: 35323981 PMCID: PMC8989532 DOI: 10.1093/nar/gkac174] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 02/26/2022] [Accepted: 03/03/2022] [Indexed: 11/14/2022] Open
Abstract
Cellular DNA is continuously transcribed into RNA by multisubunit RNA polymerases (RNAPs). The continuity of transcription can be disrupted by DNA lesions that arise from the activities of cellular enzymes, reactions with endogenous and exogenous chemicals or irradiation. Here, we review available data on translesion RNA synthesis by multisubunit RNAPs from various domains of life, define common principles and variations in DNA damage sensing by RNAP, and consider existing controversies in the field of translesion transcription. Depending on the type of DNA lesion, it may be correctly bypassed by RNAP, or lead to transcriptional mutagenesis, or result in transcription stalling. Various lesions can affect the loading of the templating base into the active site of RNAP, or interfere with nucleotide binding and incorporation into RNA, or impair RNAP translocation. Stalled RNAP acts as a sensor of DNA damage during transcription-coupled repair. The outcome of DNA lesion recognition by RNAP depends on the interplay between multiple transcription and repair factors, which can stimulate RNAP bypass or increase RNAP stalling, and plays the central role in maintaining the DNA integrity. Unveiling the mechanisms of translesion transcription in various systems is thus instrumental for understanding molecular pathways underlying gene regulation and genome stability.
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Affiliation(s)
- Aleksei Agapov
- Correspondence may also be addressed to Aleksei Agapov. Tel: +7 499 196 0015; Fax: +7 499 196 0015;
| | - Anna Olina
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute” Moscow 123182, Russia
| | - Andrey Kulbachinskiy
- To whom correspondence should be addressed. Tel: +7 499 196 0015; Fax: +7 499 196 0015;
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38
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Connell Z, Parnell TJ, McCullough LL, Hill CP, Formosa T. The interaction between the Spt6-tSH2 domain and Rpb1 affects multiple functions of RNA Polymerase II. Nucleic Acids Res 2021; 50:784-802. [PMID: 34967414 PMCID: PMC8789061 DOI: 10.1093/nar/gkab1262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 11/29/2021] [Accepted: 12/09/2021] [Indexed: 11/21/2022] Open
Abstract
The conserved transcription elongation factor Spt6 makes several contacts with the RNA Polymerase II (RNAPII) complex, including a high-affinity interaction between the Spt6 tandem SH2 domain (Spt6-tSH2) and phosphorylated residues of the Rpb1 subunit in the linker between the catalytic core and the C-terminal domain (CTD) heptad repeats. This interaction contributes to generic localization of Spt6, but we show here that it also has gene-specific roles. Disrupting the interface affected transcription start site selection at a subset of genes whose expression is regulated by this choice, and this was accompanied by changes in a distinct pattern of Spt6 accumulation at these sites. Splicing efficiency was also diminished, as was apparent progression through introns that encode snoRNAs. Chromatin-mediated repression was impaired, and a distinct role in maintaining +1 nucleosomes was identified, especially at ribosomal protein genes. The Spt6-tSH2:Rpb1 interface therefore has both genome-wide functions and local roles at subsets of genes where dynamic decisions regarding initiation, transcript processing, or termination are made. We propose that the interaction modulates the availability or activity of the core elongation and histone chaperone functions of Spt6, contributing to coordination between RNAPII and its accessory factors as varying local conditions call for dynamic responses.
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Affiliation(s)
- Zaily Connell
- Dept of Biochemistry, University of Utah School of Medicine 15 N Medical Drive, Rm 4100, Salt Lake City, UT 84112, USA
| | - Timothy J Parnell
- Huntsman Cancer Institute, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
| | - Laura L McCullough
- Dept of Biochemistry, University of Utah School of Medicine 15 N Medical Drive, Rm 4100, Salt Lake City, UT 84112, USA
| | - Christopher P Hill
- Dept of Biochemistry, University of Utah School of Medicine 15 N Medical Drive, Rm 4100, Salt Lake City, UT 84112, USA
| | - Tim Formosa
- Dept of Biochemistry, University of Utah School of Medicine 15 N Medical Drive, Rm 4100, Salt Lake City, UT 84112, USA
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39
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Huang K, Wu XX, Fang CL, Xu ZG, Zhang HW, Gao J, Zhou CM, You LL, Gu ZX, Mu WH, Feng Y, Wang JW, Zhang Y. Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA. Science 2021; 374:1579-1586. [DOI: 10.1126/science.abj9184] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- 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
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Xian Wu
- 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
| | - Cheng-Li Fang
- 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
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhou-Geng Xu
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hong-Wei 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
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Gao
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chuan-Miao Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lin-Lin You
- 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
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhan-Xi Gu
- 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
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Hui Mu
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yu Feng
- Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, 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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40
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Schuster J, de Guidi C, Fatima A, Sobol M, Dahl N. Syndromic RNA polymerase II insufficiency: Generation of a human induced pluripotent stem cell line (UUIGPi002A-5) with a heterozygous disruption of POLR2A. Stem Cell Res 2021; 57:102577. [PMID: 34688129 DOI: 10.1016/j.scr.2021.102577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/17/2021] [Indexed: 11/30/2022] Open
Abstract
Heterozygous variants in POLR2A, encoding the largest subunit of RNA polymerase II, cause severe neurodevelopmental and multisystem abnormalities in humans. Using CRISPR/Cas9 we generated the human iPSC line KICRi002A-5 with a heterozygous truncating 4 bp insertion in exon 5 of the POLR2A gene. Analysis using qRT-PCR confirmed reduced POLR2A mRNA in KICRi002A-5 vs. the isogenic WT iPSC line. The edited iPSC line expressed pluripotency markers and exhibited differentiation capacity into the three germ layers. Assessment of genomic integrity revealed a normal karyotype and OFF-target editing was excluded. The iPSC line KICRi002A-5 provides a useful resource to study mechanisms underlying developmental defects caused by RBP1 insufficiency.
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Affiliation(s)
- Jens Schuster
- Uppsala University, Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala, Sweden.
| | - Claudia de Guidi
- Uppsala University, Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala, Sweden
| | - Ambrin Fatima
- Uppsala University, Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala, Sweden
| | - Maria Sobol
- Uppsala University, Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala, Sweden
| | - Niklas Dahl
- Uppsala University, Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala, Sweden.
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41
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Palo MZ, Zhu J, Mishanina TV, Landick R. Conserved Trigger Loop Histidine of RNA Polymerase II Functions as a Positional Catalyst Primarily through Steric Effects. Biochemistry 2021; 60:3323-3336. [PMID: 34705427 DOI: 10.1021/acs.biochem.1c00528] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In all domains of life, multisubunit RNA polymerases (RNAPs) catalyze both the extension of mRNA transcripts by nucleotide addition and the hydrolysis of RNA, which enables proofreading by removal of misincorporated nucleotides. A highly conserved catalytic module within RNAPs called the trigger loop (TL) functions as the key controller of these activities. The TL is proposed to act as a positional catalyst of phosphoryl transfer and transcript cleavage via electrostatic and steric contacts with substrates in its folded helical form. The function of a near-universally conserved TL histidine that contacts NTP phosphates is of particular interest. Despite its exceptional conservation, substitutions of the TL His with Gln support efficient catalysis in bacterial and yeast RNAPs. Unlike bacterial TLs, which contain a nearby Arg, the TL His is the only acid-base catalyst candidate in the eukaryotic RNAPII TL. Nonetheless, replacement of the TL His with Leu is reported to support cell growth in yeast, suggesting that even hydrogen bonding and polarity at this position may be dispensable for efficient catalysis by RNAPII. To test how a TL His-to-Leu substitution affects the enzymatic functions of RNAPII, we compared its rates of nucleotide addition, pyrophosphorolysis, and RNA hydrolysis to those of the wild-type RNAPII enzyme. The His-to-Leu substitution slightly reduced rates of phosphoryl transfer with little if any effect on intrinsic transcript cleavage. These findings indicate that the highly conserved TL His is neither an obligate acid-base catalyst nor a polar contact for NTP phosphates but instead functions as a positional catalyst mainly through steric effects.
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Affiliation(s)
- Michael Z Palo
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Junqiao Zhu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Tatiana V Mishanina
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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42
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Gaul L, Svejstrup JQ. Transcription-coupled repair and the transcriptional response to UV-Irradiation. DNA Repair (Amst) 2021; 107:103208. [PMID: 34416541 DOI: 10.1016/j.dnarep.2021.103208] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 02/07/2023]
Abstract
Lesions in genes that result in RNA polymerase II (RNAPII) stalling or arrest are particularly toxic as they are a focal point of genome instability and potently block further transcription of the affected gene. Thus, cells have evolved the transcription-coupled nucleotide excision repair (TC-NER) pathway to identify damage-stalled RNAPIIs, so that the lesion can be rapidly repaired and transcription can continue. However, despite the identification of several factors required for TC-NER, how RNAPII is remodelled, modified, removed, or whether this is even necessary for repair remains enigmatic, and theories are intensely contested. Recent studies have further detailed the cellular response to UV-induced ubiquitylation and degradation of RNAPII and its consequences for transcription and repair. These advances make it pertinent to revisit the TC-NER process in general and with specific discussion of the fate of RNAPII stalled at DNA lesions.
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Affiliation(s)
- Liam Gaul
- Department of Cellular and Molecular Medicine, Panum Institute, Blegdamsvej 3B, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Jesper Q Svejstrup
- Department of Cellular and Molecular Medicine, Panum Institute, Blegdamsvej 3B, University of Copenhagen, 2200, Copenhagen N, Denmark.
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43
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Zhao D, Liu W, Chen K, Wu Z, Yang H, Xu Y. Structure of the human RNA polymerase I elongation complex. Cell Discov 2021; 7:97. [PMID: 34671025 PMCID: PMC8528822 DOI: 10.1038/s41421-021-00335-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/06/2021] [Indexed: 01/29/2023] Open
Abstract
Eukaryotic RNA polymerase I (Pol I) transcribes ribosomal DNA and generates RNA for ribosome synthesis. Pol I accounts for the majority of cellular transcription activity and dysregulation of Pol I transcription leads to cancers and ribosomopathies. Despite extensive structural studies of yeast Pol I, structure of human Pol I remains unsolved. Here we determined the structures of the human Pol I in the pre-translocation, post-translocation, and backtracked states at near-atomic resolution. The single-subunit peripheral stalk lacks contacts with the DNA-binding clamp and is more flexible than the two-subunit stalk in yeast Pol I. Compared to yeast Pol I, human Pol I possesses a more closed clamp, which makes more contacts with DNA. The Pol I structure in the post-cleavage backtracked state shows that the C-terminal zinc ribbon of RPA12 inserts into an open funnel and facilitates “dinucleotide cleavage” on mismatched DNA–RNA hybrid. Critical disease-associated mutations are mapped on Pol I regions that are involved in catalysis and complex organization. In summary, the structures provide new sights into human Pol I complex organization and efficient proofreading.
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Affiliation(s)
- Dan Zhao
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Weida Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Ke Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Zihan Wu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Huirong Yang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China.
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China. .,The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology of China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China. .,Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China. .,State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia, China.
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44
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Research progress of azido-containing Pt(IV) antitumor compounds. Eur J Med Chem 2021; 227:113927. [PMID: 34695775 DOI: 10.1016/j.ejmech.2021.113927] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/10/2021] [Accepted: 10/13/2021] [Indexed: 12/11/2022]
Abstract
Cancer is a long-known incurable disease, and the medical use of cisplatin has been a significant discovery. However, the side-effects of cisplatin necessitate the development of new and improved drug. Therefore, in this study, we focused on the photoactivatable Pt(IV) compounds Pt[(X1)(X2)(Y1)(Y2)(N3)2], which have a completely novel mechanism of action. Pt(IV) can efficiently overcome the side-effects of cisplatin and other drugs. Here, we have demonstrated, summarized and discussed the effects and mechanism of these compounds. Compared to the relevant articles in the literature, we have provided a more detailed introduction and a made comprehensive classification of these compounds. We believe that our results can effectively provide a reference for the development of these drugs.
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45
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Britt HM, Cragnolini T, Thalassinos K. Integration of Mass Spectrometry Data for Structural Biology. Chem Rev 2021; 122:7952-7986. [PMID: 34506113 DOI: 10.1021/acs.chemrev.1c00356] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mass spectrometry (MS) is increasingly being used to probe the structure and dynamics of proteins and the complexes they form with other macromolecules. There are now several specialized MS methods, each with unique sample preparation, data acquisition, and data processing protocols. Collectively, these methods are referred to as structural MS and include cross-linking, hydrogen-deuterium exchange, hydroxyl radical footprinting, native, ion mobility, and top-down MS. Each of these provides a unique type of structural information, ranging from composition and stoichiometry through to residue level proximity and solvent accessibility. Structural MS has proved particularly beneficial in studying protein classes for which analysis by classic structural biology techniques proves challenging such as glycosylated or intrinsically disordered proteins. To capture the structural details for a particular system, especially larger multiprotein complexes, more than one structural MS method with other structural and biophysical techniques is often required. Key to integrating these diverse data are computational strategies and software solutions to facilitate this process. We provide a background to the structural MS methods and briefly summarize other structural methods and how these are combined with MS. We then describe current state of the art approaches for the integration of structural MS data for structural biology. We quantify how often these methods are used together and provide examples where such combinations have been fruitful. To illustrate the power of integrative approaches, we discuss progress in solving the structures of the proteasome and the nuclear pore complex. We also discuss how information from structural MS, particularly pertaining to protein dynamics, is not currently utilized in integrative workflows and how such information can provide a more accurate picture of the systems studied. We conclude by discussing new developments in the MS and computational fields that will further enable in-cell structural studies.
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Affiliation(s)
- Hannah M Britt
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
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46
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Obligate movements of an active site-linked surface domain control RNA polymerase elongation and pausing via a Phe pocket anchor. Proc Natl Acad Sci U S A 2021; 118:2101805118. [PMID: 34470825 DOI: 10.1073/pnas.2101805118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The catalytic trigger loop (TL) in RNA polymerase (RNAP) alternates between unstructured and helical hairpin conformations to admit and then contact the NTP substrate during transcription. In many bacterial lineages, the TL is interrupted by insertions of two to five surface-exposed, sandwich-barrel hybrid motifs (SBHMs) of poorly understood function. The 188-amino acid, two-SBHM insertion in Escherichia coli RNAP, called SI3, occupies different locations in elongating, NTP-bound, and paused transcription complexes, but its dynamics during active transcription and pausing are undefined. Here, we report the design, optimization, and use of a Cys-triplet reporter to measure the positional bias of SI3 in different transcription complexes and to determine the effect of restricting SI3 movement on nucleotide addition and pausing. We describe the use of H2O2 as a superior oxidant for RNAP disulfide reporters. NTP binding biases SI3 toward the closed conformation, whereas transcriptional pausing biases SI3 toward a swiveled position that inhibits TL folding. We find that SI3 must change location in every round of nucleotide addition and that restricting its movements inhibits both transcript elongation and pausing. These dynamics are modulated by a crucial Phe pocket formed by the junction of the two SBHM domains. This SI3 Phe pocket captures a Phe residue in the RNAP jaw when the TL unfolds, explaining the similar phenotypes of alterations in the jaw and SI3. Our findings establish that SI3 functions by modulating TL folding to aid transcriptional regulation and to reset secondary channel trafficking in every round of nucleotide addition.
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47
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de Martín Garrido N, Orekhova M, Lai Wan Loong Y, Litvinova A, Ramlaul K, Artamonova T, Melnikov A, Serdobintsev P, Aylett CHS, Yakunina M. Structure of the bacteriophage PhiKZ non-virion RNA polymerase. Nucleic Acids Res 2021; 49:7732-7739. [PMID: 34181731 PMCID: PMC8287921 DOI: 10.1093/nar/gkab539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/04/2021] [Accepted: 06/24/2021] [Indexed: 11/18/2022] Open
Abstract
Bacteriophage ΦKZ (PhiKZ) is the archetype of a family of massive bacterial viruses. It is considered to have therapeutic potential as its host, Pseudomonas aeruginosa, is an opportunistic, intrinsically antibiotic resistant, pathogen that kills tens of thousands worldwide each year. ΦKZ is an incredibly interesting virus, expressing many systems that the host already possesses. On infection, it forms a ‘nucleus’, erecting a barrier around its genome to exclude host endonucleases and CRISPR-Cas systems. ΦKZ infection is independent of the host transcriptional apparatus. It expresses two different multi-subunit RNA polymerases (RNAPs): the virion RNAP (vRNAP) is injected with the viral DNA during infection to transcribe early genes, including those encoding the non-virion RNAP (nvRNAP), which transcribes all further genes. ΦKZ nvRNAP is formed by four polypeptides thought to represent homologues of the eubacterial β/β′ subunits, and a fifth with unclear homology, but essential for transcription. We have resolved the structure of ΦKZ nvRNAP to better than 3.0 Å, shedding light on its assembly, homology, and the biological role of the fifth subunit: it is an embedded, integral member of the complex, the position, structural homology and biochemical role of which imply that it has evolved from an ancestral homologue to σ-factor.
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Affiliation(s)
| | | | | | - Anna Litvinova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Kailash Ramlaul
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, UK
| | - Tatyana Artamonova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Alexei S Melnikov
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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48
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Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II. Nat Chem Biol 2021; 17:906-914. [PMID: 34140682 PMCID: PMC8319059 DOI: 10.1038/s41589-021-00817-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/10/2021] [Indexed: 02/05/2023]
Abstract
The development of unnatural base pairs (UBPs) has greatly increased the information storage capacity of DNA, allowing for transcription of unnatural RNA by the heterologously expressed T7 RNA polymerase (RNAP) in Escherichia coli. However, little is known about how UBPs are transcribed by cellular RNA polymerases. Here, we investigated how synthetic unnatural nucleotides, NaM and TPT3, are recognized by eukaryotic RNA polymerase II (Pol II) and found that Pol II is able to selectively recognize UBPs with high fidelity when dTPT3 is in the template strand and rNaMTP acts as the nucleotide substrate. Our structural analysis and molecular dynamics simulation provide structural insights into transcriptional processing of UBPs in a stepwise manner. Intriguingly, we identified a novel 3'-RNA binding site after rNaM addition, termed the swing state. These results may pave the way for future studies in the design of transcription and translation strategies in higher organisms with expanded genetic codes.
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49
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Shin Y, Murakami KS. Watching the bacterial RNA polymerase transcription reaction by time-dependent soak-trigger-freeze X-ray crystallography. Enzymes 2021; 49:305-314. [PMID: 34696836 DOI: 10.1016/bs.enz.2021.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
RNA polymerase (RNAP) is the central enzyme of gene expression, which transcribes DNA to RNA. All cellular organisms synthesize RNA with highly conserved multi-subunit DNA-dependent RNAPs, except mitochondrial RNA transcription, which is carried out by a single-subunit RNAP. Over 60 years of extensive research has elucidated the structures and functions of cellular RNAPs. In this review, we introduce a brief structural feature of bacterial RNAP, the most well characterized model enzyme, and a novel experimental approach known as "Time-dependent soak-trigger-freeze X-ray crystallography" which can be used to observe the RNA synthesis reaction at atomic resolution in real time. This principle methodology can be used for elucidating fundamental mechanisms of cellular RNAP transcription.
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Affiliation(s)
- Yeonoh Shin
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, United States.
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50
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Adasme MF, Linnemann KL, Bolz SN, Kaiser F, Salentin S, Haupt VJ, Schroeder M. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA. Nucleic Acids Res 2021; 49:W530-W534. [PMID: 33950214 PMCID: PMC8262720 DOI: 10.1093/nar/gkab294] [Citation(s) in RCA: 603] [Impact Index Per Article: 201.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/24/2021] [Accepted: 04/13/2021] [Indexed: 12/19/2022] Open
Abstract
With the growth of protein structure data, the analysis of molecular interactions between ligands and their target molecules is gaining importance. PLIP, the protein–ligand interaction profiler, detects and visualises these interactions and provides data in formats suitable for further processing. PLIP has proven very successful in applications ranging from the characterisation of docking experiments to the assessment of novel ligand–protein complexes. Besides ligand–protein interactions, interactions with DNA and RNA play a vital role in many applications, such as drugs targeting DNA or RNA-binding proteins. To date, over 7% of all 3D structures in the Protein Data Bank include DNA or RNA. Therefore, we extended PLIP to encompass these important molecules. We demonstrate the power of this extension with examples of a cancer drug binding to a DNA target, and an RNA–protein complex central to a neurological disease. PLIP is available online at https://plip-tool.biotec.tu-dresden.de and as open source code. So far, the engine has served over a million queries and the source code has been downloaded several thousand times.
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Affiliation(s)
- Melissa F Adasme
- Biotechnology Center (BIOTEC), CMCB, Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | - Katja L Linnemann
- Biotechnology Center (BIOTEC), CMCB, Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | - Sarah Naomi Bolz
- Biotechnology Center (BIOTEC), CMCB, Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | | | - Sebastian Salentin
- Biotechnology Center (BIOTEC), CMCB, Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | | | - Michael Schroeder
- Biotechnology Center (BIOTEC), CMCB, Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany
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