1
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Chauvier A, Walter NG. Beyond ligand binding: Single molecule observation reveals how riboswitches integrate multiple signals to balance bacterial gene regulation. Curr Opin Struct Biol 2024; 88:102893. [PMID: 39067113 DOI: 10.1016/j.sbi.2024.102893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/26/2024] [Accepted: 07/09/2024] [Indexed: 07/30/2024]
Abstract
Riboswitches are specialized RNA structures that orchestrate gene expression in response to sensing specific metabolite or ion ligands, mostly in bacteria. Upon ligand binding, these conformationally dynamic RNA motifs undergo structural changes that control critical gene expression processes such as transcription termination and translation initiation, thereby enabling cellular homeostasis and adaptation. Because RNA folds rapidly and co-transcriptionally, riboswitches make use of the low complexity of RNA sequences to adopt alternative, transient conformations on the heels of the transcribing RNA polymerase (RNAP), resulting in kinetic partitioning that defines the regulatory outcome. This review summarizes single molecule microscopy evidence that has begun to unveil a sophisticated network of dynamic, kinetically balanced interactions between riboswitch architecture and the gene expression machinery that, together, integrate diverse cellular signals.
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Affiliation(s)
- Adrien Chauvier
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA. https://twitter.com/adrienchauvier
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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2
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Carlero D, Fukuda S, Bocanegra R, Ando T, Martin-Benito J, Ibarra B. Conformational Dynamics of Influenza A Virus Ribonucleoprotein Complexes during RNA Synthesis. ACS NANO 2024. [PMID: 39013014 DOI: 10.1021/acsnano.4c01362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Viral ribonucleoproteins (vRNPs) are the cornerstones of viral proliferation, as they form the macromolecular complexes that are responsible for the transcription and replication of most single-stranded RNA viruses. The influenza A virus (IAV) polymerase catalyzes RNA synthesis within the context of vRNPs where genomic viral RNA (vRNA) is packaged by the viral nucleoprotein (NP). We used high-speed atomic force microscopy and electron microscopy to study the conformational dynamics of individual IAV recombinant RNPs (rRNPs) during RNA synthesis. The rRNPs present an annular organization that allows for the real-time tracking of conformational changes in the NP-vRNA template caused by the advancing polymerase. We demonstrate that the rRNPs undergo a well-defined conformational cycle during RNA synthesis, which can be interpreted in light of previous transcription models. We also present initial estimations of the average RNA synthesis rate in the rRNP and its dependence on the nucleotide concentration and stability of the nascent RNA secondary structures. Furthermore, we provide evidence that rRNPs can perform consecutive cycles of RNA synthesis, accounting for their ability to recycle and generate multiple copies of RNA.
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Affiliation(s)
- Diego Carlero
- Centro Nacional de Biotecnología Campus de Cantoblanco, 28049, Madrid, Spain
| | - Shingo Fukuda
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Rebeca Bocanegra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, 28049, Madrid, Spain
- IMDEA Nanociencia & CNB-CSIC-IMDEA Nanociencia Associated Unit "Unidad de Nanobiotecnología", 28049, Madrid, Spain
| | - Toshio Ando
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Jaime Martin-Benito
- IMDEA Nanociencia & CNB-CSIC-IMDEA Nanociencia Associated Unit "Unidad de Nanobiotecnología", 28049, Madrid, Spain
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, 28049, Madrid, Spain
- IMDEA Nanociencia & CNB-CSIC-IMDEA Nanociencia Associated Unit "Unidad de Nanobiotecnología", 28049, Madrid, Spain
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3
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Seffouh A, Nikolay R, Ortega J. Critical steps in the assembly process of the bacterial 50S ribosomal subunit. Nucleic Acids Res 2024; 52:4111-4123. [PMID: 38554105 PMCID: PMC11077053 DOI: 10.1093/nar/gkae199] [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: 09/14/2023] [Revised: 03/02/2024] [Accepted: 03/07/2024] [Indexed: 04/01/2024] Open
Abstract
During assembly, ribosomal particles in bacteria fold according to energy landscapes comprised of multiple parallel pathways. Cryo-electron microscopy studies have identified a critical maturation step that occurs during the late assembly stages of the 50S subunit in Bacillus subtilis. This step acts as a point of convergency for all the parallel assembly pathways of the subunit, where an assembly intermediate accumulates in a 'locked' state, causing maturation to pause. Assembly factors then act on this critical step to 'unlock' the last maturation steps involving the functional sites. Without these factors, the 50S subunit fails to complete its assembly, causing cells to die due to a lack of functional ribosomes to synthesize proteins. In this review, we analyze these findings in B. subtilis and examine other cryo-EM studies that have visualized assembly intermediates in different bacterial species, to determine if convergency points in the ribosome assembly process are a common theme among bacteria. There are still gaps in our knowledge, as these methodologies have not yet been applied to diverse species. However, identifying and characterizing these convergency points can reveal how different bacterial species implement unique mechanisms to regulate critical steps in the ribosome assembly process.
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Affiliation(s)
- Amal Seffouh
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
- Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Rainer Nikolay
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Joaquin Ortega
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
- Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada
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Sheng K, Dong X, Aiyer S, Lee J, Marquardt SD, Lyumkis D, Williamson JR. Domain consolidation in Bacterial 50S assembly revealed by Anti-Sense Oligonucleotide Probing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593220. [PMID: 38765969 PMCID: PMC11100757 DOI: 10.1101/2024.05.08.593220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Investigating the intricate and rapid folding kinetics of large RNA-protein complexes (RNPs), like the bacterial ribosome, remains a formidable challenge in structural biology. Previous genetic approaches to probe assembly have focused on modulating the expression of either r-proteins or assembly factors. Here, anti-sense oligonucleotides (ASOs) were used to disrupt native RNA/RNA and RNA/protein interactions, in order to generate novel folding intermediates. In an in vitro co-transcriptional assembly assay, 8 assembly inhibitor ASOs were identified. Using cryo-electron microscopy, 38 new intermediate structures were determined resulting from the specific inhibitions. In particular a novel intermediate class provided compelling evidence of independent rRNA domain folding before proper interdomain docking. Three PNAs targeting domain-I of 23S-rRNA further subdivided the previously identified assembly core into smaller blocks representing the earliest steps in assembly. The resulting assembly graph reveals template-directed RNA foldon docking and domain consolidation, which provides a hierarchical view of the RNP assembly process.
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Affiliation(s)
- Kai Sheng
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiyu Dong
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sriram Aiyer
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joan Lee
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Dmitry Lyumkis
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Chauvier A, Walter NG. Regulation of bacterial gene expression by non-coding RNA: It is all about time! Cell Chem Biol 2024; 31:71-85. [PMID: 38211587 DOI: 10.1016/j.chembiol.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024]
Abstract
Commensal and pathogenic bacteria continuously evolve to survive in diverse ecological niches by efficiently coordinating gene expression levels in their ever-changing environments. Regulation through the RNA transcript itself offers a faster and more cost-effective way to adapt than protein-based mechanisms and can be leveraged for diagnostic or antimicrobial purposes. However, RNA can fold into numerous intricate, not always functional structures that both expand and obscure the plethora of roles that regulatory RNAs serve within the cell. Here, we review the current knowledge of bacterial non-coding RNAs in relation to their folding pathways and interactions. We posit that co-transcriptional folding of these transcripts ultimately dictates their downstream functions. Elucidating the spatiotemporal folding of non-coding RNAs during transcription therefore provides invaluable insights into bacterial pathogeneses and predictive disease diagnostics. Finally, we discuss the implications of co-transcriptional folding andapplications of RNAs for therapeutics and drug targets.
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Affiliation(s)
- Adrien Chauvier
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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Li J, Xie S, Zhang B, He W, Zhang Y, Wang J, Yang L. UTP23 Is a Promising Prognostic Biomarker and Is Associated with Immune Infiltration in Breast Cancer. Crit Rev Eukaryot Gene Expr 2024; 34:1-15. [PMID: 38305284 DOI: 10.1615/critreveukaryotgeneexpr.2023048311] [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: 02/03/2024]
Abstract
Breast cancer is one of the malignant tumors with a high incidence and mortality rate among women worldwide, and its prevalence is increasing year by year, posing a serious health risk to women. UTP23 (UTP23 Small Subunit Processome Component) is a nucleolar protein that is essential for ribosome production. As we all know, disruption of ribosome structure and function results in improper protein function, affecting the body's normal physiological processes and promoting cancer growth. However, little research has shown a connection between UTP23 and cancer. We analyzed the mRNA expression of UTP23 in normal tissue and breast cancer using The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) database, and the protein expression of UTP23 using The Human Protein Atlas (HPA) database. Next, we examined the relationship between UTP23 high expression and Overall Survival (OS) using Kaplan-Meier Plotters and enriched 980 differentially expressed genes in UTP23 high and low expression samples using GO/KEGG and GSEA to identify potential biological functions of UTP23 and signaling pathways that it might influence. Finally, we also investigated the relationship between UTP23 and immune infiltration and examined the effect of UTP23 on the proliferation of human breast cancer cell lines by knocking down UTP23. We found that UTP23 levels in breast cancer patient samples were noticeably greater than those in healthy individuals and that high UTP23 levels were strongly linked with poor prognoses (P = 0.008). Functional enrichment analysis revealed that UTP23 expression was connected to the humoral immune response. Besides, UTP23 expression was found to be positively correlated with immune cell infiltration. Furthermore, UTP23 knockdown has been shown to inhibit the proliferation of human breast cancer cells MDA-MB-231 and HCC-1806. Taken together, our study demonstrated that UTP23 is a promising target in detecting and treating breast cancer and is intimately linked to immune infiltration.
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Affiliation(s)
- Jindong Li
- Department of Pharmacy, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, Jiangsu Province, China
| | - Siman Xie
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing, Jiangsu Province, China
| | - Benteng Zhang
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing, Jiangsu Province, China
| | - Weiping He
- Department of Pharmacy, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, Jiangsu Province, China
| | - Yan Zhang
- Department of Pharmacy, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, Jiangsu Province, China
| | - Jun Wang
- Taizhou People's Hospital Affiliated to Nanjing Medical University
| | - Li Yang
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, Jiangsu Province, China
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Peterson M, Braga RM, Floris DL, Nielsen JA. Evidence for a Compensatory Relationship between Left- and Right-Lateralized Brain Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570817. [PMID: 38106130 PMCID: PMC10723397 DOI: 10.1101/2023.12.08.570817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The two hemispheres of the human brain are functionally asymmetric. At the network level, the language network exhibits left-hemisphere lateralization. While this asymmetry is widely replicated, the extent to which other functional networks demonstrate lateralization remains a subject of Investigation. Additionally, it is unknown how the lateralization of one functional network may affect the lateralization of other networks within individuals. We quantified lateralization for each of 17 networks by computing the relative surface area on the left and right cerebral hemispheres. After examining the ecological, convergent, and external validity and test-retest reliability of this surface area-based measure of lateralization, we addressed two hypotheses across multiple datasets (Human Connectome Project = 553, Human Connectome Project-Development = 343, Natural Scenes Dataset = 8). First, we hypothesized that networks associated with language, visuospatial attention, and executive control would show the greatest lateralization. Second, we hypothesized that relationships between lateralized networks would follow a dependent relationship such that greater left-lateralization of a network would be associated with greater right-lateralization of a different network within individuals, and that this pattern would be systematic across individuals. A language network was among the three networks identified as being significantly left-lateralized, and attention and executive control networks were among the five networks identified as being significantly right-lateralized. Next, correlation matrices, an exploratory factor analysis, and confirmatory factor analyses were used to test the second hypothesis and examine the organization of lateralized networks. We found general support for a dependent relationship between highly left- and right-lateralized networks, meaning that across subjects, greater left lateralization of a given network (such as a language network) was linked to greater right lateralization of another network (such as a ventral attention/salience network) and vice versa. These results further our understanding of brain organization at the macro-scale network level in individuals, carrying specific relevance for neurodevelopmental conditions characterized by disruptions in lateralization such as autism and schizophrenia.
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Affiliation(s)
- Madeline Peterson
- Department of Psychology, Brigham Young University, Provo, UT, 84602, USA
| | - Rodrigo M. Braga
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Dorothea L. Floris
- Methods of Plasticity Research, Department of Psychology, University of Zurich, Zurich, Switzerland
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Jared A. Nielsen
- Department of Psychology, Brigham Young University, Provo, UT, 84602, USA
- Neuroscience Center, Brigham Young University, Provo, UT, 84604, USA
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Gor K, Duss O. Emerging Quantitative Biochemical, Structural, and Biophysical Methods for Studying Ribosome and Protein-RNA Complex Assembly. Biomolecules 2023; 13:biom13050866. [PMID: 37238735 DOI: 10.3390/biom13050866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Ribosome assembly is one of the most fundamental processes of gene expression and has served as a playground for investigating the molecular mechanisms of how protein-RNA complexes (RNPs) assemble. A bacterial ribosome is composed of around 50 ribosomal proteins, several of which are co-transcriptionally assembled on a ~4500-nucleotide-long pre-rRNA transcript that is further processed and modified during transcription, the entire process taking around 2 min in vivo and being assisted by dozens of assembly factors. How this complex molecular process works so efficiently to produce an active ribosome has been investigated over decades, resulting in the development of a plethora of novel approaches that can also be used to study the assembly of other RNPs in prokaryotes and eukaryotes. Here, we review biochemical, structural, and biophysical methods that have been developed and integrated to provide a detailed and quantitative understanding of the complex and intricate molecular process of bacterial ribosome assembly. We also discuss emerging, cutting-edge approaches that could be used in the future to study how transcription, rRNA processing, cellular factors, and the native cellular environment shape ribosome assembly and RNP assembly at large.
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Affiliation(s)
- Kavan Gor
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, 69117 Heidelberg, Germany
| | - Olivier Duss
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
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Zhou C, Bei J, Qiu Y, Chang Q, Nyong E, Vasilakis N, Yang J, Krishnan B, Khanipov K, Jin Y, Fang X, Gaitas A, Gong B. Exosomally Targeting microRNA23a Ameliorates Microvascular Endothelial Barrier Dysfunction Following Rickettsial Infection. Front Immunol 2022; 13:904679. [PMID: 35812423 PMCID: PMC9260018 DOI: 10.3389/fimmu.2022.904679] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/23/2022] [Indexed: 11/25/2022] Open
Abstract
Spotted fever group rickettsioses caused by Rickettsia (R) are devastating human infections, which mainly target microvascular endothelial cells (ECs) and can induce lethal EC barrier dysfunction in the brain and lungs. Our previous evidence reveals that exosomes (Exos) derived from rickettsial-infected ECs, namely R-ECExos, can induce disruption of the tight junctional (TJ) protein ZO-1 and barrier dysfunction of human normal recipient brain microvascular endothelial cells (BMECs). However, the underlying mechanism remains elusive. Given that we have observed that microRNA23a (miR23a), a negative regulator of endothelial ZO-1 mRNA, is selectively sorted into R-ECExos, the aim of the present study was to characterize the potential functional role of exosomal miR23a delivered by R-ECExos in normal recipient BMECs. We demonstrated that EC-derived Exos (ECExos) have the capacity to deliver oligonucleotide RNAs to normal recipient BMECs in an RNase-abundant environment. miR23a in ECExos impairs normal recipient BMEC barrier function, directly targeting TJ protein ZO-1 mRNAs. In separate studies using a traditional in vitro model and a novel single living-cell biomechanical assay, our group demonstrated that miR23a anti-sense oligonucleotide-enriched ECExos ameliorate R-ECExo-provoked recipient BMEC dysfunction in association with stabilization of ZO-1 in a dose-dependent manner. These results suggest that Exo-based therapy could potentially prove to be a promising strategy to improve vascular barrier function during bacterial infection and concomitant inflammation.
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Affiliation(s)
- Changcheng Zhou
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Jiani Bei
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Yuan Qiu
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Qing Chang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Emmanuel Nyong
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
- Department of Preventive Medicine and Population Health, The University of Texas Medical Branch, Galveston, TX, United States
- Center for Vector Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, TX, United States
- The Center of Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, United States
- Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, United States
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, United States
| | - Jun Yang
- Department of Internal Medicine, Endocrinology, University of Texas Medical Branch, Galveston, TX, United States
| | - Balaji Krishnan
- Mitchell Center for Neurodegenerative Diseases, Department of Neurology, University of Texas Medical Branch, Galveston, TX, United States
| | - Kamil Khanipov
- Department of Pharmacology, University of Texas Medical Branch, Galveston, TX, United States
| | - Yang Jin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University Medical Campus, Boston, MA, United States
| | - Xiang Fang
- Mitchell Center for Neurodegenerative Diseases, Department of Neurology, University of Texas Medical Branch, Galveston, TX, United States
| | - Angelo Gaitas
- The Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Bin Gong
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
- Center for Vector Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, TX, United States
- The Center of Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, United States
- Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, United States
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, United States
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10
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Krause L, Willing F, Andreou AZ, Klostermeier D. The domains of yeast eIF4G, eIF4E and the cap fine-tune eIF4A activities through an intricate network of stimulatory and inhibitory effects. Nucleic Acids Res 2022; 50:6497-6510. [PMID: 35689631 PMCID: PMC9226541 DOI: 10.1093/nar/gkac437] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/19/2022] [Accepted: 05/23/2022] [Indexed: 12/13/2022] Open
Abstract
Translation initiation in eukaryotes starts with the recognition of the mRNA 5'-cap by eIF4F, a hetero-trimeric complex of eIF4E, the cap-binding protein, eIF4A, a DEAD-box helicase, and eIF4G, a scaffold protein. eIF4G comprises eIF4E- and eIF4A-binding domains (4E-BD, 4A-BD) and three RNA-binding regions (RNA1-RNA3), and interacts with eIF4A, eIF4E, and with the mRNA. Within the eIF4F complex, the helicase activity of eIF4A is increased. We showed previously that RNA3 of eIF4G is important for the stimulation of the eIF4A conformational cycle and its ATPase and helicase activities. Here, we dissect the interplay between the eIF4G domains and the role of the eIF4E/cap interaction in eIF4A activation. We show that RNA2 leads to an increase in the fraction of eIF4A in the closed state, an increased RNA affinity, and faster RNA unwinding. This stimulatory effect is partially reduced when the 4E-BD is present. eIF4E binding to the 4E-BD then further inhibits the helicase activity and closing of eIF4A, but does not affect the RNA-stimulated ATPase activity of eIF4A. The 5'-cap renders the functional interaction of mRNA with eIF4A less efficient. Overall, the activity of eIF4A at the 5'-cap is thus fine-tuned by a delicately balanced network of stimulatory and inhibitory interactions.
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Affiliation(s)
- Linda Krause
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany
| | - Florian Willing
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany
| | - Alexandra Zoi Andreou
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, 48149 Muenster, Germany
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11
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Cimicata G, Fridkin G, Bose T, Eyal Z, Halfon Y, Breiner-Goldstein E, Fox T, Zimmerman E, Bashan A, de Val N, Wlodawer A, Yonath A. Structural Studies Reveal the Role of Helix 68 in the Elongation Step of Protein Biosynthesis. mBio 2022; 13:e0030622. [PMID: 35348349 PMCID: PMC9040758 DOI: 10.1128/mbio.00306-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 02/04/2023] Open
Abstract
The ribosome, a multicomponent assembly consisting of RNA and proteins, is a pivotal macromolecular machine that translates the genetic code into proteins. The large ribosomal subunit rRNA helix 68 (H68) is a key element in the protein synthesis process, as it coordinates the coupled movements of the actors involved in translocation, including the tRNAs and L1 stalk. Examination of cryo-electron microscopy (cryo-EM) structures of ribosomes incubated for various time durations at physiological temperatures led to the identification of functionally relevant H68 movements. These movements assist the transition of the L1 stalk between its open and closed states. H68 spatial flexibility and its significance to the protein synthesis process were confirmed through its effective targeting with antisense PNA oligomers. Our results suggest that H68 is actively involved in ribosome movements that are central to the elongation process. IMPORTANCE The mechanism that regulates the translocation step in ribosomes during protein synthesis is not fully understood. In this work, cryo-EM techniques used to image ribosomes from Staphylococcus aureus after incubation at physiological temperature allowed the identification of a conformation of the helix 68 that has never been observed so far. We then propose a mechanism in which such helix, switching between two different conformations, actively coordinates the translocation step, shedding light on the dynamics of ribosomal components. In addition, the relevance of helix 68 to ribosome function and its potential as an antibiotic target was proved by inhibiting Staphylococcus aureus ribosomes activity in vitro using oligomers with sequence complementarity.
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Affiliation(s)
- Giuseppe Cimicata
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Gil Fridkin
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Tanaya Bose
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Zohar Eyal
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Yehuda Halfon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Elinor Breiner-Goldstein
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Tara Fox
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Ella Zimmerman
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Anat Bashan
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Alexander Wlodawer
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Ada Yonath
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
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12
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Kelly SL, Szyjka CE, Strobel EJ. Purification of synchronized E. coli transcription elongation complexes by reversible immobilization on magnetic beads. J Biol Chem 2022; 298:101789. [PMID: 35247385 PMCID: PMC8969151 DOI: 10.1016/j.jbc.2022.101789] [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: 01/10/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 10/26/2022] Open
Abstract
Synchronized transcription elongation complexes (TECs) are a fundamental tool for in vitro studies of transcription and RNA folding. Transcription elongation can be synchronized by omitting one or more nucleoside triphosphates (NTPs) from an in vitro transcription reaction so that RNA polymerase can only transcribe to the first occurrence of the omitted nucleotide(s) in the coding DNA strand. This approach was developed over four decades ago and has been applied extensively in biochemical investigations of RNA polymerase enzymes, but has not been optimized for RNA-centric assays. In this work, we describe the development of a system for isolating synchronized TECs from an in vitro transcription reaction. Our approach uses a custom 5' leader sequence, called C3-SC1, to reversibly capture synchronized TECs on magnetic beads. We first show using electrophoretic mobility shift and high-resolution in vitro transcription assays that complexes isolated by this procedure, called C3-SC1TECs, are >95% pure, >98% active, highly synchronous (94% of complexes chase in <15s upon addition of saturating NTPs), and compatible with solid-phase transcription; the yield of this purification is ∼8%. We then show that C3-SC1TECs perturb, but do not interfere with, the function of ZTP (5-aminoimidazole-4-carboxamide riboside 5'-triphosphate)-sensing and ppGpp (guanosine-3',5'-bisdiphosphate)-sensing transcriptional riboswitches. For both riboswitches, transcription using C3-SC1TECs improved the efficiency of transcription termination in the absence of ligand but did not inhibit ligand-induced transcription antitermination. Given these properties, C3-SC1TECs will likely be useful for developing biochemical and biophysical RNA assays that require high-performance, quantitative bacterial in vitro transcription.
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Affiliation(s)
- Skyler L Kelly
- Department of Biological Sciences, The University at Buffalo, Buffalo, NY 14260, USA
| | - Courtney E Szyjka
- Department of Biological Sciences, The University at Buffalo, Buffalo, NY 14260, USA
| | - Eric J Strobel
- Department of Biological Sciences, The University at Buffalo, Buffalo, NY 14260, USA.
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13
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Nemashkalo A, Phipps ME, Hennelly SP, Goodwin PM. Real-time, single-molecule observation of biomolecular interactions inside nanophotonic zero mode waveguides. NANOTECHNOLOGY 2022; 33:165101. [PMID: 34959227 DOI: 10.1088/1361-6528/ac467c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
Living cells rely on numerous protein-protein, RNA-protein and DNA-protein interactions for processes such as gene expression, biomolecular assembly, protein and RNA degradation. Single-molecule microscopy and spectroscopy are ideal tools for real-time observation and quantification of nucleic acids-protein and protein-protein interactions. One of the major drawbacks of conventional single-molecule imaging methods is low throughput. Methods such as sequencing by synthesis utilizing nanofabrication and single-molecule spectroscopy have brought high throughput into the realm of single-molecule biology. The Pacific Biosciences RS2 sequencer utilizes sequencing by synthesis within nanophotonic zero mode waveguides. A number of years ago this instrument was unlocked by Pacific Biosciences for custom use by researchers allowing them to monitor biological interactions at the single-molecule level with high throughput. In this capability letter we demonstrate the use of the RS2 sequencer for real-time observation of DNA-to-RNA transcription and RNA-protein interactions. We use a relatively complex model-transcription of structured ribosomal RNA fromE. coliand interactions of ribosomal RNA with ribosomal proteins. We also show evidence of observation of transcriptional pausing without the application of an external force (as is required for single-molecule pausing studies using optical traps). Overall, in the unlocked, custom mode, the RS2 sequencer can be used to address a wide variety of biological assembly and interaction questions at the single-molecule level with high throughput. This instrument is available for use at the Center for Integrated Nanotechnologies Gateway located at Los Alamos National Laboratory.
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Affiliation(s)
- A Nemashkalo
- MPA-CINT (Materials Physics and Applications, Center for Integrated Nanotechnologies, Los Alamos National Laboratory), United States of America
| | - M E Phipps
- MPA-CINT (Materials Physics and Applications, Center for Integrated Nanotechnologies, Los Alamos National Laboratory), United States of America
| | - S P Hennelly
- B-11 (Bioenergy and Biome Sciences, Los Alamos National Laboratory), United States of America
| | - P M Goodwin
- MPA-CINT (Materials Physics and Applications, Center for Integrated Nanotechnologies, Los Alamos National Laboratory), United States of America
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14
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Abstract
Cotranscriptional folding is a fundamental step in RNA biogenesis and the basis for many RNA-mediated gene regulation systems. Understanding how RNA folds as it is synthesized requires experimental methods that can systematically identify intermediate RNA structures that form during transcription. Cotranscriptional RNA chemical probing experiments achieve this by applying high-throughput RNA structure probing to an in vitro transcribed array of cotranscriptionally folded intermediate transcripts. In this chapter, we present guidelines and procedures for integrating single-round in vitro transcription using E. coli RNA polymerase with high-throughput RNA chemical probing workflows. We provide an overview of key concepts including DNA template design, transcription roadblocking strategies, single-round in vitro transcription with E. coli RNA polymerase, and RNA chemical probing and describe procedures for DNA template preparation, cotranscriptional RNA chemical probing, RNA purification, and 3' adapter ligation. The end result of these procedures is a purified RNA library that can be prepared for Illumina sequencing using established high-throughput RNA structure probing library construction strategies.
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Affiliation(s)
- Courtney E Szyjka
- Department of Biological Sciences, The University at Buffalo, Buffalo, NY, USA
| | - Eric J Strobel
- Department of Biological Sciences, The University at Buffalo, Buffalo, NY, USA.
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15
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Iizuka R, Yamazaki H, Uemura S. Zero-mode waveguides and nanopore-based sequencing technologies accelerate single-molecule studies. Biophys Physicobiol 2022; 19:e190032. [DOI: 10.2142/biophysico.bppb-v19.0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/26/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Ryo Iizuka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Hirohito Yamazaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
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16
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Forman-Kay JD, Ditlev JA, Nosella ML, Lee HO. What are the distinguishing features and size requirements of biomolecular condensates and their implications for RNA-containing condensates? RNA (NEW YORK, N.Y.) 2022; 28:36-47. [PMID: 34772786 PMCID: PMC8675286 DOI: 10.1261/rna.079026.121] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Exciting recent work has highlighted that numerous cellular compartments lack encapsulating lipid bilayers (often called "membraneless organelles"), and that their structure and function are central to the regulation of key biological processes, including transcription, RNA splicing, translation, and more. These structures have been described as "biomolecular condensates" to underscore that biomolecules can be significantly concentrated in them. Many condensates, including RNA granules and processing bodies, are enriched in proteins and nucleic acids. Biomolecular condensates exhibit a range of material states from liquid- to gel-like, with the physical process of liquid-liquid phase separation implicated in driving or contributing to their formation. To date, in vitro studies of phase separation have provided mechanistic insights into the formation and function of condensates. However, the link between the often micron-sized in vitro condensates with nanometer-sized cellular correlates has not been well established. Consequently, questions have arisen as to whether cellular structures below the optical resolution limit can be considered biomolecular condensates. Similarly, the distinction between condensates and discrete dynamic hub complexes is debated. Here we discuss the key features that define biomolecular condensates to help understand behaviors of structures containing and generating RNA.
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Affiliation(s)
- Julie D Forman-Kay
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jonathon A Ditlev
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Michael L Nosella
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Hyun O Lee
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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17
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Liu J, Yang LZ, Chen LL. Understanding lncRNA-protein assemblies with imaging and single-molecule approaches. Curr Opin Genet Dev 2021; 72:128-137. [PMID: 34933201 DOI: 10.1016/j.gde.2021.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 11/24/2022]
Abstract
Long non-coding RNAs (lncRNAs) associate with RNA-binding proteins (RBPs) to form lncRNA-protein complexes that act in a wide range of biological processes. Understanding the molecular mechanism of how a lncRNA-protein complex is assembled and regulated is key for their cellular functions. In this mini-review, we outline molecular methods used to identify lncRNA-protein interactions from large-scale to individual levels using bulk cells as well as those recently developed imaging and single-molecule approaches that are capable of visualizing RNA-protein assemblies in single cells and in real-time. Focusing on the latter group of approaches, we discuss their applications and limitations, which nevertheless have enabled quantification and comprehensive dissection of RNA-protein interactions possible.
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Affiliation(s)
- Jiaquan Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
| | - Liang-Zhong Yang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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18
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Dynamic competition between a ligand and transcription factor NusA governs riboswitch-mediated transcription regulation. Proc Natl Acad Sci U S A 2021; 118:2109026118. [PMID: 34782462 DOI: 10.1073/pnas.2109026118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 11/18/2022] Open
Abstract
Cotranscriptional RNA folding is widely assumed to influence the timely control of gene expression, but our understanding remains limited. In bacteria, the fluoride (F-)-sensing riboswitch is a transcriptional control element essential to defend against toxic F- levels. Using this model riboswitch, we find that its ligand F- and essential bacterial transcription factor NusA compete to bind the cotranscriptionally folding RNA, opposing each other's modulation of downstream pausing and termination by RNA polymerase. Single-molecule fluorescence assays probing active transcription elongation complexes discover that NusA unexpectedly binds highly reversibly, frequently interrogating the complex for emerging, cotranscriptionally folding RNA duplexes. NusA thus fine-tunes the transcription rate in dependence of the ligand-responsive higher-order structure of the riboswitch. At the high NusA concentrations found intracellularly, this dynamic modulation is expected to lead to adaptive bacterial transcription regulation with fast response times.
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19
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Abstract
To exert their functions, RNAs adopt diverse structures, ranging from simple secondary to complex tertiary and quaternary folds. In vivo, RNA folding starts with RNA transcription, and a wide variety of processes are coupled to co-transcriptional RNA folding events, including the regulation of fundamental transcription dynamics, gene regulation by mechanisms like attenuation, RNA processing or ribonucleoprotein particle formation. While co-transcriptional RNA folding and associated co-transcriptional processes are by now well accepted as pervasive regulatory principles in all organisms, investigations into the role of the transcription machinery in co-transcriptional folding processes have so far largely focused on effects of the order in which RNA regions are produced and of transcription kinetics. Recent structural and structure-guided functional analyses of bacterial transcription complexes increasingly point to an additional role of RNA polymerase and associated transcription factors in supporting co-transcriptional RNA folding by fostering or preventing strategic contacts to the nascent transcripts. In general, the results support the view that transcription complexes can act as RNA chaperones, a function that has been suggested over 30 years ago. Here, we discuss transcription complexes as RNA chaperones based on recent examples from bacterial transcription.
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Affiliation(s)
- Nelly Said
- Freie Universität Berlin, Department Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Berlin, Germany
| | - Markus C Wahl
- Freie Universität Berlin, Department Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Berlin, Germany.,Helmholtz-Zentrum Berlin Für Materialien Und Energie, Macromolecular Crystallography, Berlin, Germany
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20
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Rodgers ML, Woodson SA. A roadmap for rRNA folding and assembly during transcription. Trends Biochem Sci 2021; 46:889-901. [PMID: 34176739 PMCID: PMC8526401 DOI: 10.1016/j.tibs.2021.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/14/2021] [Accepted: 05/27/2021] [Indexed: 01/11/2023]
Abstract
Ribonucleoprotein (RNP) assembly typically begins during transcription when folding of the newly synthesized RNA is coupled with the recruitment of RNA-binding proteins (RBPs). Upon binding, the proteins induce structural rearrangements in the RNA that are crucial for the next steps of assembly. Focusing primarily on bacterial ribosome assembly, we discuss recent work showing that early RNA-protein interactions are more dynamic than previously supposed, and remain so, until sufficient proteins are recruited to each transcript to consolidate an entire domain of the RNP. We also review studies showing that stable assembly of an RNP competes against modification and processing of the RNA. Finally, we discuss how transcription sets the timeline for competing and cooperative RNA-RBP interactions that determine the fate of the nascent RNA. How this dance is coordinated is the focus of this review.
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Affiliation(s)
- Margaret L Rodgers
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Sarah A Woodson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.
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21
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Mawer JSP, Massen J, Reichert C, Grabenhorst N, Mylonas C, Tessarz P. Nhp2 is a reader of H2AQ105me and part of a network integrating metabolism with rRNA synthesis. EMBO Rep 2021; 22:e52435. [PMID: 34409714 PMCID: PMC8490984 DOI: 10.15252/embr.202152435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 01/16/2023] Open
Abstract
Ribosome biogenesis is an essential cellular process that requires integration of extracellular cues, such as metabolic state, with intracellular signalling, transcriptional regulation and chromatin accessibility at the ribosomal DNA. Here, we demonstrate that the recently identified histone modification, methylation of H2AQ105 (H2AQ105me), is an integral part of a dynamic chromatin network at the rDNA locus. Its deposition depends on a functional mTor signalling pathway and acetylation of histone H3 at position K56, thus integrating metabolic and proliferative signals. Furthermore, we identify a first epigenetic reader of this modification, the ribonucleoprotein Nhp2, which specifically recognizes H2AQ105me. Based on functional and proteomic data, we suggest that Nhp2 functions as an adapter to bridge rDNA chromatin with components of the small subunit processome to efficiently coordinate transcription of rRNA with its post‐transcriptional processing. We support this by showing that an H2AQ105A mutant has a mild defect in early processing of rRNA.
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Affiliation(s)
- Julia S P Mawer
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Jennifer Massen
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Christina Reichert
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Niklas Grabenhorst
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Constantine Mylonas
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Peter Tessarz
- Max Planck Research Group "Chromatin and Ageing", Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cologne Excellence Cluster on Stress Responses in ageing-associated Diseases (CECAD), Cologne, Germany
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22
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Nikulin AD. Characteristic Features of Protein Interaction with Single- and Double-Stranded RNA. BIOCHEMISTRY (MOSCOW) 2021; 86:1025-1040. [PMID: 34488578 DOI: 10.1134/s0006297921080125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The review discusses differences between the specific protein interactions with single- and double-stranded RNA molecules using the data on the structure of RNA-protein complexes. Proteins interacting with the single-stranded RNAs form contacts with RNA bases, which ensures recognition of specific nucleotide sequences. Formation of such contacts with the double-stranded RNAs is hindered, so that the proteins recognize unique conformations of the RNA spatial structure and interact mainly with the RNA sugar-phosphate backbone.
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Affiliation(s)
- Alexey D Nikulin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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23
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Abstract
Spotted fever group rickettsioses (SFRs) are devastating human infections. Vascular endothelial cells (ECs) are the primary targets of rickettsial infection. Edema resulting from EC barrier dysfunction occurs in the brain and lungs in most cases of lethal SFR, but the underlying mechanisms remain unclear. The aim of the study was to explore the potential role of Rickettsia-infected, EC-derived exosomes (Exos) during infection. Using size exclusion chromatography (SEC), we purified Exos from conditioned, filtered, bacterium-free media collected from Rickettsia parkeri-infected human umbilical vein ECs (HUVECs) (R-ECExos) and plasma of Rickettsia australis- or R. parkeri-infected mice (R-plsExos). We observed that rickettsial infection increased the release of heterogeneous plsExos, but endothelial exosomal size, morphology, and production were not significantly altered following infection. Compared to normal plsExos and ECExos, both R-plsExos and R-ECExos induced dysfunction of recipient normal brain microvascular ECs (BMECs). The effect of R-plsExos on mouse recipient BMEC barrier function is dose dependent. The effect of R-ECExos on human recipient BMEC barrier function is dependent on the exosomal RNA cargo. Next-generation sequencing analysis and stem-loop quantitative reverse transcription-PCR (RT-qPCR) validation revealed that rickettsial infection triggered the selective enrichment of endothelial exosomal mir-23a and mir-30b, which potentially target the endothelial barrier. To our knowledge, this is the first report on the functional role of extracellular vesicles following infection by obligately intracellular bacteria.
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24
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Feng XA, Poyton MF, Ha T. Multicolor single-molecule FRET for DNA and RNA processes. Curr Opin Struct Biol 2021; 70:26-33. [PMID: 33894656 DOI: 10.1016/j.sbi.2021.03.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 03/10/2021] [Indexed: 12/31/2022]
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) is a useful tool for observing the dynamics of protein-nucleic acid interactions. Although most smFRET measurements have used two fluorophores, multicolor smFRET measurements using more than two fluorophores offer more information about how protein-nucleic acid complexes dynamically move, assemble, and disassemble. Multicolor smFRET experiments include three or more fluorophores and at least one donor-acceptor pair. This review highlights how multicolor smFRET is being used to probe the dynamics of three different classes of biochemical processes-protein-DNA interactions, chromatin remodeling, and protein translation.
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Affiliation(s)
- Xinyu A Feng
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Matthew F Poyton
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA; Howard Hughes Medical Institute, Baltimore, MD, USA.
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25
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A translational riboswitch coordinates nascent transcription-translation coupling. Proc Natl Acad Sci U S A 2021; 118:2023426118. [PMID: 33850018 DOI: 10.1073/pnas.2023426118] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bacterial messenger RNA (mRNA) synthesis by RNA polymerase (RNAP) and first-round translation by the ribosome are often coupled to regulate gene expression, yet how coupling is established and maintained is ill understood. Here, we develop biochemical and single-molecule fluorescence approaches to probe the dynamics of RNAP-ribosome interactions on an mRNA with a translational preQ1-sensing riboswitch in its 5' untranslated region. Binding of preQ1 leads to the occlusion of the ribosome binding site (RBS), inhibiting translation initiation. We demonstrate that RNAP poised within the mRNA leader region promotes ribosomal 30S subunit binding, antagonizing preQ1-induced RBS occlusion, and that the RNAP-30S bridging transcription factors NusG and RfaH distinctly enhance 30S recruitment and retention, respectively. We further find that, while 30S-mRNA interaction significantly impedes RNAP in the absence of translation, an actively translating ribosome promotes productive transcription. A model emerges wherein mRNA structure and transcription factors coordinate to dynamically modulate the efficiency of transcription-translation coupling.
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26
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Scull CE, Dandpat SS, Romero RA, Walter NG. Transcriptional Riboswitches Integrate Timescales for Bacterial Gene Expression Control. Front Mol Biosci 2021; 7:607158. [PMID: 33521053 PMCID: PMC7838592 DOI: 10.3389/fmolb.2020.607158] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/11/2020] [Indexed: 12/16/2022] Open
Abstract
Transcriptional riboswitches involve RNA aptamers that are typically found in the 5' untranslated regions (UTRs) of bacterial mRNAs and form alternative secondary structures upon binding to cognate ligands. Alteration of the riboswitch's secondary structure results in perturbations of an adjacent expression platform that controls transcription elongation and termination, thus turning downstream gene expression "on" or "off." Riboswitch ligands are typically small metabolites, divalent cations, anions, signaling molecules, or other RNAs, and can be part of larger signaling cascades. The interconnectedness of ligand binding, RNA folding, RNA transcription, and gene expression empowers riboswitches to integrate cellular processes and environmental conditions across multiple timescales. For a successful response to an environmental cue that may determine a bacterium's chance of survival, a coordinated coupling of timescales from microseconds to minutes must be achieved. This review focuses on recent advances in our understanding of how riboswitches affect such critical gene expression control across time.
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Affiliation(s)
| | | | | | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States
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27
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Çetin B, Song GJ, O'Leary SE. Heterogeneous Dynamics of Protein-RNA Interactions across Transcriptome-Derived Messenger RNA Populations. J Am Chem Soc 2020; 142:21249-21253. [PMID: 33315378 DOI: 10.1021/jacs.0c09841] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Dynamic RNA-protein interactions underpin numerous molecular control mechanisms in biology. However, relatively little is known about the kinetic landscape of protein interactions with full-length RNAs. The extent to which interaction kinetics vary for the same RNA element across the transcriptome and the molecular determinants of variability therefore remain poorly defined. Moreover, it is unclear how one protein-RNA interaction might be transduced by RNA to kinetically impact a second. We report a parallelized, real-time single-molecule fluorescence assay for protein interaction kinetics on eukaryotic mRNA populations obtained from cells. We observed ∼100-fold heterogeneity for interactions of the translation initiation factor eIF4E with the universal mRNA 5' cap structure, dominated by steric effects on barrier-height variability for association. We also found that an RNA helicase, eIF4A, independently accelerated eIF4E-cap association. These data support a kinetic mechanism for how mRNA can determine the sensitivity of its translation to reduction in cellular eIF4E concentrations. They also support the view that global RNA structure significantly modulates protein-RNA interaction dynamics and can facilitate real-time communication between protein interactions at distinct sites.
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Affiliation(s)
- Burak Çetin
- Graduate Program in Cell, Molecular, and Developmental Biology, University of California, Riverside, California 92521, United States
| | - Gary J Song
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Seán E O'Leary
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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28
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Bacic L, Sabantsev A, Deindl S. Recent advances in single-molecule fluorescence microscopy render structural biology dynamic. Curr Opin Struct Biol 2020; 65:61-68. [PMID: 32634693 DOI: 10.1016/j.sbi.2020.05.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 01/30/2023]
Abstract
Single-molecule fluorescence microscopy has long been appreciated as a powerful tool to study the structural dynamics that enable biological function of macromolecules. Recent years have witnessed the development of more complex single-molecule fluorescence techniques as well as powerful combinations with structural approaches to obtain mechanistic insights into the workings of various molecular machines and protein complexes. In this review, we highlight these developments that together bring us one step closer to a dynamic understanding of biological processes in atomic details.
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Affiliation(s)
- Luka Bacic
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anton Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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29
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Zhou G, Loper J, Geman S. Base-pair ambiguity and the kinetics of RNA folding. BMC Bioinformatics 2019; 20:666. [PMID: 31830902 PMCID: PMC6909616 DOI: 10.1186/s12859-019-3303-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/02/2019] [Indexed: 01/28/2023] Open
Abstract
Background A pairings of nucleotide sequences. Given this forbidding free-energy landscape, mechanisms have evolved that contribute to a directed and efficient folding process, including catalytic proteins and error-detecting chaperones. Among structural RNA molecules we make a distinction between “bound” molecules, which are active as part of ribonucleoprotein (RNP) complexes, and “unbound,” with physiological functions performed without necessarily being bound in RNP complexes. We hypothesized that unbound molecules, lacking the partnering structure of a protein, would be more vulnerable than bound molecules to kinetic traps that compete with native stem structures. We defined an “ambiguity index”—a normalized function of the primary and secondary structure of an individual molecule that measures the number of kinetic traps available to nucleotide sequences that are paired in the native structure, presuming that unbound molecules would have lower indexes. The ambiguity index depends on the purported secondary structure, and was computed under both the comparative (“gold standard”) and an equilibrium-based prediction which approximates the minimum free energy (MFE) structure. Arguing that kinetically accessible metastable structures might be more biologically relevant than thermodynamic equilibrium structures, we also hypothesized that MFE-derived ambiguities would be less effective in separating bound and unbound molecules. Results We have introduced an intuitive and easily computed function of primary and secondary structures that measures the availability of complementary sequences that could disrupt the formation of native stems on a given molecule—an ambiguity index. Using comparative secondary structures, the ambiguity index is systematically smaller among unbound than bound molecules, as expected. Furthermore, the effect is lost when the presumably more accurate comparative structure is replaced instead by the MFE structure. Conclusions A statistical analysis of the relationship between the primary and secondary structures of non-coding RNA molecules suggests that stem-disrupting kinetic traps are substantially less prevalent in molecules not participating in RNP complexes. In that this distinction is apparent under the comparative but not the MFE secondary structure, the results highlight a possible deficiency in structure predictions when based upon assumptions of thermodynamic equilibrium.
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Affiliation(s)
| | - Jackson Loper
- Data Science Institute, Columbia University, New York, NY, USA
| | - Stuart Geman
- Division of Applied Mathematics, Brown University, Providence, RI, USA
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Duss O, Stepanyuk GA, Puglisi JD, Williamson JR. Transient Protein-RNA Interactions Guide Nascent Ribosomal RNA Folding. Cell 2019; 179:1357-1369.e16. [PMID: 31761533 DOI: 10.1016/j.cell.2019.10.035] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/18/2019] [Accepted: 10/28/2019] [Indexed: 11/28/2022]
Abstract
Ribosome assembly is an efficient but complex and heterogeneous process during which ribosomal proteins assemble on the nascent rRNA during transcription. Understanding how the interplay between nascent RNA folding and protein binding determines the fate of transcripts remains a major challenge. Here, using single-molecule fluorescence microscopy, we follow assembly of the entire 3' domain of the bacterial small ribosomal subunit in real time. We find that co-transcriptional rRNA folding is complicated by the formation of long-range RNA interactions and that r-proteins self-chaperone the rRNA folding process prior to stable incorporation into a ribonucleoprotein (RNP) complex. Assembly is initiated by transient rather than stable protein binding, and the protein-RNA binding dynamics gradually decrease during assembly. This work questions the paradigm of strictly sequential and cooperative ribosome assembly and suggests that transient binding of RNA binding proteins to cellular RNAs could provide a general mechanism to shape nascent RNA folding during RNP assembly.
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Affiliation(s)
- Olivier Duss
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Galina A Stepanyuk
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Rodgers ML, Woodson SA. Transcription Increases the Cooperativity of Ribonucleoprotein Assembly. Cell 2019; 179:1370-1381.e12. [PMID: 31761536 DOI: 10.1016/j.cell.2019.11.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/12/2019] [Accepted: 11/01/2019] [Indexed: 11/17/2022]
Abstract
The synthesis of new ribosomes begins during transcription of the rRNA and is widely assumed to follow an orderly 5' to 3' gradient. To visualize co-transcriptional assembly of ribosomal protein-RNA complexes in real time, we developed a single-molecule platform that simultaneously monitors transcription and protein association with the elongating transcript. Unexpectedly, the early assembly protein uS4 binds newly made pre-16S rRNA only transiently, likely due to non-native folding of the rRNA during transcription. Stable uS4 binding became more probable only in the presence of additional ribosomal proteins that bind upstream and downstream of protein uS4 by allowing productive assembly intermediates to form earlier. We propose that dynamic sampling of elongating RNA by multiple proteins overcomes heterogeneous RNA folding, preventing assembly bottlenecks and initiating assembly within the transcription time window. This may be a common feature of transcription-coupled RNP assembly.
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Affiliation(s)
- Margaret L Rodgers
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sarah A Woodson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.
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Choi J, Grosely R, Puglisi EV, Puglisi JD. Expanding single-molecule fluorescence spectroscopy to capture complexity in biology. Curr Opin Struct Biol 2019; 58:233-240. [PMID: 31213390 PMCID: PMC6778503 DOI: 10.1016/j.sbi.2019.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/03/2019] [Accepted: 05/08/2019] [Indexed: 11/16/2022]
Abstract
Fundamental biological processes are driven by diverse molecular machineries. In recent years, single-molecule fluorescence spectroscopy has matured as a unique tool in biology to study how structural dynamics of molecular complexes drive various biochemical reactions. In this review, we highlight underlying developments in single-molecule fluorescence methods that enable deep biological investigations. Recent progress in these methods points toward increasing complexity of measurements to capture biological processes in a living cell, where multiple processes often occur simultaneously and are mechanistically coupled.
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Affiliation(s)
- Junhong Choi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305-4090, USA
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
| | - Elisabetta V Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
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Scull CE, Schneider DA. Coordinated Control of rRNA Processing by RNA Polymerase I. Trends Genet 2019; 35:724-733. [PMID: 31358304 DOI: 10.1016/j.tig.2019.07.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/25/2019] [Accepted: 07/01/2019] [Indexed: 11/19/2022]
Abstract
Ribosomal RNA (rRNA) is co- and post-transcriptionally processed into active ribosomes. This process is dynamically regulated by direct covalent modifications of the polymerase that synthesizes the rRNA, RNA polymerase I (Pol I), and by interactions with cofactors that influence initiation, elongation, and termination activities of Pol I. The rate of transcription elongation by Pol I directly influences processing of nascent rRNA, and changes in Pol I transcription rate result in alternative rRNA processing events that lead to cellular signaling alterations and stress. It is clear that in divergent species, there exists robust organization of nascent rRNA processing events during transcription elongation. This review evaluates the current state of our understanding of the complex relationship between transcription elongation and rRNA processing.
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Affiliation(s)
- Catherine E Scull
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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