1
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Struhl K. How is polyadenylation restricted to 3'-untranslated regions? Yeast 2024; 41:186-191. [PMID: 38041485 PMCID: PMC11001523 DOI: 10.1002/yea.3915] [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: 08/04/2023] [Revised: 10/30/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023] Open
Abstract
Polyadenylation occurs at numerous sites within 3'-untranslated regions (3'-UTRs) but rarely within coding regions. How does Pol II travel through long coding regions without generating poly(A) sites, yet then permits promiscuous polyadenylation once it reaches the 3'-UTR? The cleavage/polyadenylation (CpA) machinery preferentially associates with 3'-UTRs, but it is unknown how its recruitment is restricted to 3'-UTRs during Pol II elongation. Unlike coding regions, 3'-UTRs have long AT-rich stretches of DNA that may be important for restricting polyadenylation to 3'-UTRs. Recognition of the 3'-UTR could occur at the DNA (AT-rich), RNA (AU-rich), or RNA:DNA hybrid (rU:dA- and/or rA:dT-rich) level. Based on the nucleic acid critical for 3'-UTR recognition, there are three classes of models, not mutually exclusive, for how the CpA machinery is selectively recruited to 3'-UTRs, thereby restricting where polyadenylation occurs: (1) RNA-based models suggest that the CpA complex directly (or indirectly through one or more intermediary proteins) binds long AU-rich stretches that are exposed after Pol II passes through these regions. (2) DNA-based models suggest that the AT-rich sequence affects nucleosome depletion or the elongating Pol II machinery, resulting in dissociation of some elongation factors and subsequent recruitment of the CpA machinery. (3) RNA:DNA hybrid models suggest that preferential destabilization of the Pol II elongation complex at rU:dA- and/or rA:dT-rich duplexes bridging the nucleotide addition and RNA exit sites permits preferential association of the CpA machinery with 3'-UTRs. Experiments to provide evidence for one or more of these models are suggested.
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Affiliation(s)
- Kevin Struhl
- Dept. Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
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2
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Cui JZ, Chew ZH, Lim LHK. New insights into nucleic acid sensor AIM2: The potential benefit in targeted therapy for cancer. Pharmacol Res 2024; 200:107079. [PMID: 38272334 DOI: 10.1016/j.phrs.2024.107079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
The AIM2 inflammasome represents a multifaceted oligomeric protein complex within the innate immune system, with the capacity to perceive double-stranded DNA (dsDNA) and engage in diverse physiological reactions and disease contexts, including cancer. While originally conceived as a discerning DNA sensor, AIM2 has demonstrated its capability to discern various nucleic acid variations, encompassing RNA and DNA-RNA hybrids. Through its interaction with nucleic acids, AIM2 orchestrates the assembly of a complex involving multiple proteins, aptly named the AIM2 inflammasome, which facilitates the enzymatic cleavage of proinflammatory cytokines, namely pro-IL-1β and pro-IL-18. This process, in turn, underpins its pivotal biological role. In this review, we provide a systematic summary and discussion of the latest advancements in AIM2 sensing various types of nucleic acids. Additionally, we discuss the modulation of AIM2 activation, which can cause cell death, including pyroptosis, apoptosis, and autophagic cell death. Finally, we fully illustrate the evidence for the dual role of AIM2 in different cancer types, including both anti-tumorigenic and pro-tumorigenic functions. Considering the above information, we uncover the therapeutic promise of modulating the AIM2 inflammasome in cancer treatment.
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Affiliation(s)
- Jian-Zhou Cui
- Translational Immunology Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore; NUS-Cambridge Immunophenotyping Centre, Life Science Institute, National University of Singapore, Singapore.
| | - Zhi Huan Chew
- Translational Immunology Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore; Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lina H K Lim
- Translational Immunology Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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3
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Gupta S, Padmashali N, Pal D. INTERPIN: A repository for intrinsic transcription termination hairpins in bacteria. Biochimie 2023; 214:228-236. [PMID: 37499897 DOI: 10.1016/j.biochi.2023.07.018] [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: 03/09/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
The large-scale detection of putative intrinsic transcription terminators is limited to only a few bacteria currently. We discovered a group of hairpins, called cluster hairpins, present within 15 nucleotides from each other. These are expected to work in tandem to cause intrinsic transcription termination (ITT), while the single hairpin can do the same alone. Therefore, exploring these ITT sites and the hairpins across bacterial genomes becomes highly desirable. INTERPIN is the largest archived collection of in silico inferred ITT hairpins in bacteria, covering 12745 bacterial genomes and encompassing ten bacterial phyla for ∼25 million hairpins. Users can obtain details on operons, individual cluster, and single ITT hairpins that were screened therein. Integrated Genome Viewer (IGV) software interactively visualizes hairpin secondary and tertiary structures in the genomic context. We also discuss statistics for the occurrence of cluster or single hairpins and other termination alternatives while showing the validation of predicted hairpins against in vivo detected hairpins. The database is freely available at http://pallab.cds.iisc.ac.in/INTERPIN/. INTERPIN (database and software) can make predictions for both AT and GC-rich genomes, which has not been achieved by any other program so far. It can also be used to improve genome annotation as well as to get predictions to improve the understanding of the ITT pathway by further analysis.
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Affiliation(s)
- Swati Gupta
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, 560012, Karnataka, India
| | - Namrata Padmashali
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, 560012, Karnataka, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, 560012, Karnataka, India.
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4
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Han Z, Moore GA, Mitter R, Lopez Martinez D, Wan L, Dirac Svejstrup AB, Rueda DS, Svejstrup JQ. DNA-directed termination of RNA polymerase II transcription. Mol Cell 2023; 83:3253-3267.e7. [PMID: 37683646 PMCID: PMC7615648 DOI: 10.1016/j.molcel.2023.08.007] [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: 03/23/2023] [Revised: 06/27/2023] [Accepted: 08/09/2023] [Indexed: 09/10/2023]
Abstract
RNA polymerase II (RNAPII) transcription involves initiation from a promoter, transcriptional elongation through the gene, and termination in the terminator region. In bacteria, terminators often contain specific DNA elements provoking polymerase dissociation, but RNAPII transcription termination is thought to be driven entirely by protein co-factors. We used biochemical reconstitution, single-molecule studies, and genome-wide analysis in yeast to study RNAPII termination. Transcription into natural terminators by pure RNAPII results in spontaneous termination at specific sequences containing T-tracts. Single-molecule analysis indicates that termination involves pausing without backtracking. The "torpedo" Rat1-Rai1 exonuclease (XRN2 in humans) greatly stimulates spontaneous termination but is ineffectual on other paused RNAPIIs. By contrast, elongation factor Spt4-Spt5 (DSIF) suppresses termination. Genome-wide analysis further indicates that termination occurs by transcript cleavage at the poly(A) site exposing a new 5' RNA-end that allows Rat1-Rai1 loading, which then catches up with destabilized RNAPII at specific termination sites to end transcription.
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Affiliation(s)
- Zhong Han
- Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark; Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - George A Moore
- Single Molecule Imaging group, MRC-London Institute of Medical Sciences, and Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David Lopez Martinez
- Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark; Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Li Wan
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - A Barbara Dirac Svejstrup
- Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark; Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David S Rueda
- Single Molecule Imaging group, MRC-London Institute of Medical Sciences, and Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Jesper Q Svejstrup
- Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark; Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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5
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Miguel-Arribas A, Martín-María A, Alaerds ECW, Val-Calvo J, Yuste L, Rojo F, Abia D, Wu L, Meijer WJJ. Extraordinary long-stem confers resistance of intrinsic terminators to processive antitermination. Nucleic Acids Res 2023; 51:6073-6086. [PMID: 37125647 PMCID: PMC10325885 DOI: 10.1093/nar/gkad333] [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: 10/06/2022] [Revised: 03/14/2023] [Accepted: 04/20/2023] [Indexed: 05/02/2023] Open
Abstract
Many prokaryotic operons encode a processive antitermination (P-AT) system. Transcription complexes associated with an antitermination factor can bypass multiple transcription termination signals regardless of their sequences. However, to avoid compromising transcriptional regulation of downstream regions, the terminator at the end of the operon needs to be resistant to antitermination. So far, no studies on the mechanism of resistance to antitermination have been reported. The recently discovered conAn P-AT system is composed of two components that are encoded at the start of many conjugation operons on plasmids of Gram-positive bacteria. Here we report the identification of a conAn-resistant terminator, named TerR, in the conjugation operon of the Bacillus subtilis plasmid pLS20, re-defining the end of the conjugation operon. We investigated the various characteristics of TerR and show that its extraordinary long stem is the determining feature for resistance to antitermination. This is the first P-AT resistance mechanism to be reported.
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Affiliation(s)
- Andrés Miguel-Arribas
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Ana Martín-María
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Eef C W Alaerds
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Jorge Val-Calvo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Luis Yuste
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, C. Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Fernando Rojo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, C. Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular “Severo Ochoa”, (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle Upon Tyne, NE2 4AX, UK
| | - Wilfried J J Meijer
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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6
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Zhang Y, Han W, Wang L, Wang H, Jia Q, Chen T, Wang S, Li M. Correlative Escherichia coli Transcription Rate and Bubble Conformation Remodeled by NusA and NusG. J Phys Chem B 2023; 127:2909-2917. [PMID: 36977198 DOI: 10.1021/acs.jpcb.2c08771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Transcription is highly regulated by a variety of transcription factors, among which NusA and NusG act contradictorily in Escherichia coli (E. coli) that NusA stabilizes a paused RNA polymerase (RNAP) and NusG suppresses it. The mechanism of the NusA and NusG regulations on RNAP transcription has been addressed, but their effect on the conformational changes of the transcription bubble correlated with transcription kinetics remains elusive. By using single-molecule magnetic trap, we identify a reduction in the transcription rate of ∼40% events by NusA. Although the rest ∼60% of transcription events exhibit unaffected transcription rates, a NusA-enhanced standard deviation of the transcription rate is observed. NusA remodeling also increases the extent of DNA unwinding in the transcription bubble by 1-2 base pairs, which can be reduced by NusG. The NusG remodeling is more significant on the RNAP molecules with reduced transcription rates rather than those without. Our results provide a quantitative view on the mechanisms of transcriptional regulation by NusA and NusG factors.
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Affiliation(s)
- Yuqiong Zhang
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong 510631, China
- Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong 510631, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Weijing Han
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Lisha Wang
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Hao Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Qi Jia
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Tongsheng Chen
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong 510631, China
- Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong 510631, China
| | - Shuang Wang
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Ming Li
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
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7
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You L, Omollo EO, Yu C, Mooney RA, Shi J, Shen L, Wu X, Wen A, He D, Zeng Y, Feng Y, Landick R, Zhang Y. Structural basis for intrinsic transcription termination. Nature 2023; 613:783-789. [PMID: 36631609 PMCID: PMC10091898 DOI: 10.1038/s41586-022-05604-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/25/2022] [Indexed: 01/13/2023]
Abstract
Efficient and accurate termination is required for gene transcription in all living organisms1,2. Cellular RNA polymerases in both bacteria and eukaryotes can terminate their transcription through a factor-independent termination pathway3,4-called intrinsic termination transcription in bacteria-in which RNA polymerase recognizes terminator sequences, stops nucleotide addition and releases nascent RNA spontaneously. Here we report a set of single-particle cryo-electron microscopy structures of Escherichia coli transcription intrinsic termination complexes representing key intermediate states of the event. The structures show how RNA polymerase pauses at terminator sequences, how the terminator RNA hairpin folds inside RNA polymerase, and how RNA polymerase rewinds the transcription bubble to release RNA and then DNA. These macromolecular snapshots define a structural mechanism for bacterial intrinsic termination and a pathway for RNA release and DNA collapse that is relevant for factor-independent termination by all RNA polymerases.
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Affiliation(s)
- Linlin 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, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Expery O Omollo
- Department of Biochemistry and Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Chengzhi Yu
- 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, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Rachel A Mooney
- Department of Biochemistry and Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Jing Shi
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Liqiang Shen
- 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, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoxian 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, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Aijia Wen
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dingwei He
- 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, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Zeng
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu Feng
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Robert Landick
- Department of Biochemistry and Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
| | - 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, China.
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8
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Hall PM, Inman JT, Fulbright RM, Le TT, Brewer JJ, Lambert G, Darst SA, Wang MD. Polarity of the CRISPR roadblock to transcription. Nat Struct Mol Biol 2022; 29:1217-1227. [PMID: 36471058 PMCID: PMC9758054 DOI: 10.1038/s41594-022-00864-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 10/12/2022] [Indexed: 12/12/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) utility relies on a stable Cas effector complex binding to its target site. However, a Cas complex bound to DNA may be removed by motor proteins carrying out host processes and the mechanism governing this removal remains unclear. Intriguingly, during CRISPR interference, RNA polymerase (RNAP) progression is only fully blocked by a bound endonuclease-deficient Cas (dCas) from the protospacer adjacent motif (PAM)-proximal side. By mapping dCas-DNA interactions at high resolution, we discovered that the collapse of the dCas R-loop allows Escherichia coli RNAP read-through from the PAM-distal side for both Sp-dCas9 and As-dCas12a. This finding is not unique to RNAP and holds for the Mfd translocase. This mechanistic understanding allowed us to modulate the dCas R-loop stability by modifying the guide RNAs. This work highlights the importance of the R-loop in dCas-binding stability and provides valuable mechanistic insights for broad applications of CRISPR technology.
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Affiliation(s)
- Porter M Hall
- Biophysics Program, Cornell University, Ithaca, NY, USA
| | - James T Inman
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, USA
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA
| | - Robert M Fulbright
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, USA
| | - Tung T Le
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, USA
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA
| | - Joshua J Brewer
- Laboratory of Molecular Biophysics, Rockefeller University, New York, NY, USA
| | - Guillaume Lambert
- Department of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, Rockefeller University, New York, NY, USA
| | - Michelle D Wang
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, USA.
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA.
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9
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Abstract
In bacteria, transcription and translation take place in the same cellular compartment. Therefore, a messenger RNA can be translated as it is being transcribed, a process known as transcription-translation coupling. This process was already recognized at the dawn of molecular biology, yet the interplay between the two key players, the RNA polymerase and ribosome, remains elusive. Genetic data indicate that an RNA sequence can be translated shortly after it has been transcribed. The closer both processes are in time, the less accessible the RNA sequence is between the RNA polymerase and ribosome. This temporal coupling has important consequences for gene regulation. Biochemical and structural studies have detailed several complexes between the RNA polymerase and ribosome. The in vivo relevance of this physical coupling has not been formally demonstrated. We discuss how both temporal and physical coupling may mesh to produce the phenomenon we know as transcription-translation coupling.
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Affiliation(s)
- Gregor M Blaha
- Department of Biochemistry, University of California, Riverside, California, USA;
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA;
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
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10
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Mandell ZF, Vishwakarma RK, Yakhnin H, Murakami KS, Kashlev M, Babitzke P. Comprehensive transcription terminator atlas for Bacillus subtilis. Nat Microbiol 2022; 7:1918-1931. [PMID: 36192538 PMCID: PMC10024249 DOI: 10.1038/s41564-022-01240-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/26/2022] [Indexed: 01/12/2023]
Abstract
The transcriptome-wide contributions of Rho-dependent and intrinsic (Rho-independent) transcription termination mechanisms in bacteria are unclear. By sequencing released transcripts in a wild-type strain and strains containing deficiencies in NusA, NusG and/or Rho (10 strains), we produced an atlas of terminators for the model Gram-positive bacterium Bacillus subtilis. We found that NusA and NusG stimulate 77% and 19% of all intrinsic terminators, respectively, and that both proteins participate in Rho-dependent termination. We also show that Rho stimulates termination at 10% of the intrinsic terminators in vivo. We recapitulated Rho-stimulated intrinsic termination at 5 terminators in vitro and found that Rho requires the KOW domain of NusG to stimulate this process at one of these terminators. Computational analyses of our atlas using RNAstructure, MEME suite and DiffLogo, combined with in vitro transcription experiments, revealed that Rho stimulates intrinsic terminators with weak hairpins and/or U-rich tracts by remodelling the RNA upstream of the intrinsic terminator to prevent the formation of RNA structures that could otherwise compete with the terminator hairpin. We also identified 56 putative examples of 'hybrid Rho-dependent termination', wherein classical Rho-dependent termination occurs after readthrough of a Rho-stimulated intrinsic terminator.
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Affiliation(s)
- Zachary F Mandell
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Department of Molecular Biology and Genetics and Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Rishi K Vishwakarma
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Helen Yakhnin
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Mikhail Kashlev
- NCI RNA Biology Laboratory, Center for Cancer Research, NCI, Frederick, MD, USA
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA.
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11
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Dey S, Batisse C, Shukla J, Webster MW, Takacs M, Saint-André C, Weixlbaumer A. Structural insights into RNA-mediated transcription regulation in bacteria. Mol Cell 2022; 82:3885-3900.e10. [DOI: 10.1016/j.molcel.2022.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/07/2022] [Accepted: 09/19/2022] [Indexed: 11/06/2022]
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12
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Structural basis of transcriptional regulation by a nascent RNA element, HK022 putRNA. Nat Commun 2022; 13:4668. [PMID: 35970830 PMCID: PMC9378689 DOI: 10.1038/s41467-022-32315-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/26/2022] [Indexed: 12/16/2022] Open
Abstract
Transcription, in which RNA polymerases (RNAPs) produce RNA from DNA, is the first step of gene expression. As such, it is highly regulated either by trans-elements like protein factors and/or by cis-elements like specific sequences on the DNA. Lambdoid phage HK022 contains a cis-element, put, which suppresses pausing and termination during transcription of the early phage genes. The putRNA transcript solely performs the anti-pausing/termination activities by interacting directly with the E.coli RNAP elongation complex (EC) by an unknown structural mechanism. In this study, we reconstituted putRNA-associated ECs and determined the structures using cryo-electron microscopy. The determined structures of putRNA-associated EC, putRNA-absent EC, and σ70-bound EC suggest that the putRNA interaction with the EC counteracts swiveling, a conformational change previously identified to promote pausing and σ70 might modulate putRNA folding via σ70-dependent pausing during elongation.
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13
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Mandell ZF, Zemba D, Babitzke P. Factor-stimulated intrinsic termination: getting by with a little help from some friends. Transcription 2022; 13:96-108. [PMID: 36154805 PMCID: PMC9715273 DOI: 10.1080/21541264.2022.2127602] [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: 07/11/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 01/12/2023] Open
Abstract
Transcription termination is known to occur via two mechanisms in bacteria, intrinsic termination (also frequently referred to as Rho-independent or factor-independent termination) and Rho-dependent termination. Based primarily on in vitro studies using Escherichia coli RNA polymerase, it was generally assumed that intrinsic termination and Rho-dependent termination are distinct mechanisms and that the signals required for intrinsic termination are present primarily within the nucleic acids. In this review, we detail recent findings from studies in Bacillus subtilis showing that intrinsic termination in this organism is highly stimulated by NusA, NusG, and even Rho. In NusA-stimulated intrinsic termination, NusA facilitates the formation of weak terminator hairpins and compensates for distal U-rich tract interruptions. In NusG-stimulated intrinsic termination, NusG stabilizes a sequence-dependent pause at the point of termination, which extends the time frame for RNA hairpins with weak terminal base pairs to form in either a NusA-stimulated or a NusA-independent fashion. In Rho-stimulated intrinsic termination, Rho prevents the formation of antiterminator-like RNA structures that could otherwise compete with the terminator hairpin. Combined, NusA, NusG, and Rho stimulate approximately 97% of all intrinsic terminators in B. subtilis. Thus, the general view that intrinsic termination is primarily a factor-independent process needs to be revised to account for recent findings. Moreover, the historical distinction between Rho-dependent and intrinsic termination is overly simplistic and needs to be modernized.
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Affiliation(s)
- Zachary F. Mandell
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, United States
- Department of Molecular Biology and Genetics and Department of Biology, Johns Hopkins University, Baltimore, MD, United State
| | - Dani Zemba
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, United States
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, United States
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14
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Liu F, Sun F, Kuang GQ, Wang L, Yue GH. The Insertion in the 3' UTR of Pmel17 Is the Causal Variant for Golden Skin Color in Tilapia. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:566-573. [PMID: 35416601 DOI: 10.1007/s10126-022-10125-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Understanding of the relationships between genotypes and phenotypes is a central problem in biology. Although teleosts have colorful phenotypes, not much is known about their underlying mechanisms. Our previous study showed that golden skin color in Mozambique tilapia was mapped in the major locus containing the Pmel gene, and an insertion in 3' UTR of Pmel17 was fully correlated with the golden color. However, the molecular mechanism of how Pmel17 determines the golden skin color is unknown. In this study, knockout of Pmel17 with CRISPR/Cas9 in blackish tilapias resulted in golden coloration, and rescue of Pmel17 in golden tilapias recovered the wild-type blackish color, indicating that Pmel17 is the gene determining the golden and blackish color. Functional analysis in vitro showed that the insertion in the 3' UTR of Pmel17 reduced the transcripts of Pmel17. Our data supplies more evidence to support that Pmel17 is the gene for blackish and golden colors, and highlights that the insertion in the 3' UTR of Pmel17 is the causative mutation for the golden coloration.
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Affiliation(s)
- Feng Liu
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
- Shanghai Fisheries Institute, 265 Jiamusi Road, Shanghai, 200433, China
| | - Fei Sun
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Gang Qiao Kuang
- Department of Fisheries, Southwestern University, Rongchang Campus, 160 Xueyuan Road, Rongchang, Chongqing, 402460, China
| | - Le Wang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Gen Hua Yue
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive, Queenstown, 117543, Singapore.
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15
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Miguel-Arribas A, Wu LJ, Michaelis C, Yoshida KI, Grohmann E, Meijer WJJ. Conjugation Operons in Gram-Positive Bacteria with and without Antitermination Systems. Microorganisms 2022; 10:microorganisms10030587. [PMID: 35336162 PMCID: PMC8955417 DOI: 10.3390/microorganisms10030587] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 02/01/2023] Open
Abstract
Genes involved in the same cellular process are often clustered together in an operon whose expression is controlled by an upstream promoter. Generally, the activity of the promoter is strictly controlled. However, spurious transcription undermines this strict regulation, particularly affecting large operons. The negative effects of spurious transcription can be mitigated by the presence of multiple terminators inside the operon, in combination with an antitermination system. Antitermination systems modify the transcription elongation complexes and enable them to bypass terminators. Bacterial conjugation is the process by which a conjugative DNA element is transferred from a donor to a recipient cell. Conjugation involves many genes that are mostly organized in one or a few large operons. It has recently been shown that many conjugation operons present on plasmids replicating in Gram-positive bacteria possess a bipartite antitermination system that allows not only many terminators inside the conjugation operon to be bypassed, but also the differential expression of a subset of genes. Here, we show that some conjugation operons on plasmids belonging to the Inc18 family of Gram-positive broad host-range plasmids do not possess an antitermination system, suggesting that the absence of an antitermination system may have advantages. The possible (dis)advantages of conjugation operons possessing (or not) an antitermination system are discussed.
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Affiliation(s)
- Andrés Miguel-Arribas
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Instituto de Biología Molecular Eladio Viñuela (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain;
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Medical Faculty, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK;
| | - Claudia Michaelis
- School of Life Sciences and Technology, Berlin University of Applied Sciences, Seestrasse 64, 13347 Berlin, Germany;
| | - Ken-ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan;
| | - Elisabeth Grohmann
- School of Life Sciences and Technology, Berlin University of Applied Sciences, Seestrasse 64, 13347 Berlin, Germany;
- Correspondence: (E.G.); (W.J.J.M.); Tel.: +49-30-4504-3942 (E.G.); +34-91-196-4539 (W.J.J.M.)
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Instituto de Biología Molecular Eladio Viñuela (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain;
- Correspondence: (E.G.); (W.J.J.M.); Tel.: +49-30-4504-3942 (E.G.); +34-91-196-4539 (W.J.J.M.)
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16
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Wu H, Wei T, Yu B, Cheng R, Huang F, Lu X, Yan Y, Wang X, Liu C, Zhu B. A single mutation attenuates both the transcription termination and RNA-dependent RNA polymerase activity of T7 RNA polymerase. RNA Biol 2021; 18:451-466. [PMID: 34314299 PMCID: PMC8677023 DOI: 10.1080/15476286.2021.1954808] [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: 01/12/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 10/20/2022] Open
Abstract
Transcription termination is one of the least understood processes of gene expression. As the prototype model for transcription studies, the single-subunit T7 RNA polymerase (RNAP) is known to respond to two types of termination signals, but the mechanism underlying such termination, especially the specific elements of the polymerase involved, is still unclear, due to a lack of knowledge with respect to the structure of the termination complex. Here we applied phage-assisted continuous evolution to obtain variants of T7 RNAP that can bypass the typical class I T7 terminator with stem-loop structure. Through in vivo selection and in vitro characterization, we discovered a single mutation (S43Y) that significantly decreased the termination efficiency of T7 RNAP at all transcription terminators tested. Coincidently, the S43Y mutation almost eliminates the RNA-dependent RNAP (RdRp) activity of T7 RNAP without impeding the major DNA-dependent RNAP (DdRp) activity of the enzyme. S43 is located in a hinge region and regulates the transformation between transcription initiation and elongation of T7 RNAP. Steady-state kinetics analysis and an RNA binding assay indicate that the S43Y mutation increases the transcription efficiency while weakening RNA binding of the enzyme. As an enzymatic reagent for in vitro transcription, the T7 RNAP S43Y mutant reduces the undesired termination in run-off RNA synthesis and produces RNA with higher terminal homogeneity.
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Affiliation(s)
- Hui Wu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, HubeiChina
| | - Ting Wei
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, ShenzhenChina
| | - Bingbing Yu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, HubeiChina
| | - Rui Cheng
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, HubeiChina
| | - Fengtao Huang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, HubeiChina
| | - Xuelin Lu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, HubeiChina
| | - Yan Yan
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, HubeiChina
| | - Xionglue Wang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, HubeiChina
| | - Chenli Liu
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, ShenzhenChina
- University of Chinese Academy of Sciences, BeijingChina
| | - Bin Zhu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, HubeiChina
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17
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Du C, Wang Y, Gong S. Regulation of the ThiM riboswitch is facilitated by the trapped structure formed during transcription of the wild-type sequence. FEBS Lett 2021; 595:2816-2828. [PMID: 34644399 DOI: 10.1002/1873-3468.14202] [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: 06/18/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 11/09/2022]
Abstract
The ThiM riboswitch from Escherichia coli is a typical mRNA device that modulates downstream gene expression by sensing TPP. The helix-based RNA folding theory is used to investigate its detailed regulatory behaviors in cells. This RNA molecule is transcriptionally trapped in a state with the unstructured SD sequence in the absence of TPP, which induces downstream gene expression. As a key step to turn on gene expression, formation of this trapped state (the genetic ON state) highly depends on the co-transcriptional folding of its wild-type sequence. Instead of stabilities of the genetic ON and OFF states, the transcription rate, pause, and ligand levels are combined to affect the ThiM riboswitch-mediated gene regulation, which is consistent with a kinetic control model.
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Affiliation(s)
- Chengyi Du
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, China
| | - Yujie Wang
- Department of Physics and Telecommunication Engineering, Zhoukou Normal University, China
| | - Sha Gong
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, China
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18
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Lee CY, Myong S. Probing steps in DNA transcription using single-molecule methods. J Biol Chem 2021; 297:101086. [PMID: 34403697 PMCID: PMC8441165 DOI: 10.1016/j.jbc.2021.101086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/22/2022] Open
Abstract
Transcriptional regulation is one of the key steps in determining gene expression. Diverse single-molecule techniques have been applied to characterize the stepwise progression of transcription, yielding complementary results. These techniques include, but are not limited to, fluorescence-based microscopy with single or multiple colors, force measuring and manipulating microscopy using magnetic field or light, and atomic force microscopy. Here, we summarize and evaluate these current methodologies in studying and resolving individual steps in the transcription reaction, which encompasses RNA polymerase binding, initiation, elongation, mRNA production, and termination. We also describe the advantages and disadvantages of each method for studying transcription.
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Affiliation(s)
- Chun-Ying Lee
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA; Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, Illinois, USA.
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19
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Mandell ZF, Oshiro RT, Yakhnin AV, Vishwakarma R, Kashlev M, Kearns DB, Babitzke P. NusG is an intrinsic transcription termination factor that stimulates motility and coordinates gene expression with NusA. eLife 2021; 10:e61880. [PMID: 33835023 PMCID: PMC8060035 DOI: 10.7554/elife.61880] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 04/08/2021] [Indexed: 12/21/2022] Open
Abstract
NusA and NusG are transcription factors that stimulate RNA polymerase pausing in Bacillus subtilis. While NusA was known to function as an intrinsic termination factor in B. subtilis, the role of NusG in this process was unknown. To examine the individual and combinatorial roles that NusA and NusG play in intrinsic termination, Term-seq was conducted in wild type, NusA depletion, ΔnusG, and NusA depletion ΔnusG strains. We determined that NusG functions as an intrinsic termination factor that works alone and cooperatively with NusA to facilitate termination at 88% of the 1400 identified intrinsic terminators. Our results indicate that NusG stimulates a sequence-specific pause that assists in the completion of suboptimal terminator hairpins with weak terminal A-U and G-U base pairs at the bottom of the stem. Loss of NusA and NusG leads to global misregulation of gene expression and loss of NusG results in flagella and swimming motility defects.
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Affiliation(s)
- Zachary F Mandell
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
| | - Reid T Oshiro
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Alexander V Yakhnin
- NCI RNA Biology Laboratory, Center for Cancer Research, NCIFrederickUnited States
| | - Rishi Vishwakarma
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
| | - Mikhail Kashlev
- NCI RNA Biology Laboratory, Center for Cancer Research, NCIFrederickUnited States
| | - Daniel B Kearns
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
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20
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Imashimizu M, Tokunaga Y, Afek A, Takahashi H, Shimamoto N, Lukatsky DB. Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences. Biomolecules 2020; 10:biom10091299. [PMID: 32916947 PMCID: PMC7564750 DOI: 10.3390/biom10091299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/23/2020] [Accepted: 09/04/2020] [Indexed: 12/12/2022] Open
Abstract
In the process of transcription initiation by RNA polymerase, promoter DNA sequences affect multiple reaction pathways determining the productivity of transcription. However, the question of how the molecular mechanism of transcription initiation depends on the sequence properties of promoter DNA remains poorly understood. Here, combining the statistical mechanical approach with high-throughput sequencing results, we characterize abortive transcription and pausing during transcription initiation by Escherichia coli RNA polymerase at a genome-wide level. Our results suggest that initially transcribed sequences, when enriched with thymine bases, contain the signal for inducing abortive transcription, whereas certain repetitive sequence elements embedded in promoter regions constitute the signal for inducing pausing. Both signals decrease the productivity of transcription initiation. Based on solution NMR and in vitro transcription measurements, we suggest that repetitive sequence elements within the promoter DNA modulate the nonlocal base pair stability of its double-stranded form. This stability profoundly influences the reaction coordinates of the productive initiation via pausing.
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Affiliation(s)
- Masahiko Imashimizu
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan;
- Correspondence: (M.I.); (D.B.L.); Tel.: +81-3-3599-8232 (M.I.); +972-8642-8370 (D.B.L.)
| | - Yuji Tokunaga
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan;
| | - Ariel Afek
- Center for Genomic and Computational Biology, Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA;
| | - Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan;
- Molecular Chirality Research Center, Chiba University, Chiba 263-8522, Japan
- Plant Molecular Science Center, Chiba University, Chiba 260-8675, Japan
| | - Nobuo Shimamoto
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan;
| | - David B. Lukatsky
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Correspondence: (M.I.); (D.B.L.); Tel.: +81-3-3599-8232 (M.I.); +972-8642-8370 (D.B.L.)
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21
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Binas O, Schamber T, Schwalbe H. The conformational landscape of transcription intermediates involved in the regulation of the ZMP-sensing riboswitch from Thermosinus carboxydivorans. Nucleic Acids Res 2020; 48:6970-6979. [PMID: 32479610 PMCID: PMC7337938 DOI: 10.1093/nar/gkaa427] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/03/2020] [Accepted: 05/29/2020] [Indexed: 01/30/2023] Open
Abstract
Recently, prokaryotic riboswitches have been identified that regulate transcription in response to change of the concentration of secondary messengers. The ZMP (5-Aminoimidazole-4-carboxamide ribonucleotide (AICAR))-sensing riboswitch from Thermosinus carboxydivorans is a transcriptional ON-switch that is involved in purine and carbon-1 metabolic cycles. Its aptamer domain includes the pfl motif, which features a pseudoknot, impeding rho-independent terminator formation upon stabilization by ZMP interaction. We herein investigate the conformational landscape of transcriptional intermediates including the expression platform of this riboswitch and characterize the formation and unfolding of the important pseudoknot structure in the context of increasing length of RNA transcripts. NMR spectroscopic data show that even surprisingly short pre-terminator stems are able to disrupt ligand binding and thus metabolite sensing. We further show that the pseudoknot structure, a prerequisite for ligand binding, is preformed in transcription intermediates up to a certain length. Our results describe the conformational changes of 13 transcription intermediates of increasing length to delineate the change in structure as mRNA is elongated during transcription. We thus determine the length of the key transcription intermediate to which addition of a single nucleotide leads to a drastic drop in ZMP affinity.
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Affiliation(s)
- Oliver Binas
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/Main, Germany
| | - Tatjana Schamber
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/Main, Germany
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22
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Hudson AJ, Wieden HJ. Rapid generation of sequence-diverse terminator libraries and their parameterization using quantitative Term-Seq. Synth Biol (Oxf) 2019; 4:ysz026. [PMID: 32995547 PMCID: PMC7445774 DOI: 10.1093/synbio/ysz026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/03/2019] [Indexed: 01/09/2023] Open
Abstract
Synthetic biology and the rational design and construction of biological devices require vast numbers of characterized biological parts, as well as reliable design tools to build increasingly complex, multigene architectures. Design principles for intrinsic terminators have been established; however, additional sequence-structure studies are needed to refine parameters for termination-based genetic devices. We report a rapid single-pot method to generate libraries of thousands of randomized bidirectional intrinsic terminators and a modified quantitative Term-Seq (qTerm-Seq) method to simultaneously identify terminator sequences and measure their termination efficiencies (TEs). Using qTerm-Seq, we characterize hundreds of additional strong terminators (TE > 90%) with some terminators reducing transcription read-through by up to 1000-fold in Escherichia coli. Our terminator library and qTerm-Seq pipeline constitute a flexible platform enabling identification of terminator parts that can achieve transcription termination not only over a desired range but also to investigate their sequence-structure features, including for specific genetic and application contexts beyond the common in vivo systems such as E. coli.
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Affiliation(s)
- Andrew J Hudson
- Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, Lethbridge, Alberta, Canada.,Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Hans-Joachim Wieden
- Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, Lethbridge, Alberta, Canada.,Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
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23
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KIreeva M, Trang C, Matevosyan G, Turek-Herman J, Chasov V, Lubkowska L, Kashlev M. RNA-DNA and DNA-DNA base-pairing at the upstream edge of the transcription bubble regulate translocation of RNA polymerase and transcription rate. Nucleic Acids Res 2019; 46:5764-5775. [PMID: 29771376 PMCID: PMC6009650 DOI: 10.1093/nar/gky393] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 04/30/2018] [Indexed: 12/19/2022] Open
Abstract
Translocation of RNA polymerase (RNAP) along DNA may be rate-limiting for transcription elongation. The Brownian ratchet model posits that RNAP rapidly translocates back and forth until the post-translocated state is stabilized by NTP binding. An alternative model suggests that RNAP translocation is slow and poorly reversible. To distinguish between these two models, we take advantage of an observation that pyrophosphorolysis rates directly correlate with the abundance of the pre-translocated fraction. Pyrophosphorolysis by RNAP stabilized in the pre-translocated state by bacteriophage HK022 protein Nun was used as a reference point to determine the pre-translocated fraction in the absence of Nun. The stalled RNAP preferentially occupies the post-translocated state. The forward translocation rate depends, among other factors, on melting of the RNA–DNA base pair at the upstream edge of the transcription bubble. DNA–DNA base pairing immediately upstream from the RNA–DNA hybrid stabilizes the post-translocated state. This mechanism is conserved between E. coli RNAP and S. cerevisiae RNA polymerase II and is partially dependent on the lid domain of the catalytic subunit. Thus, the RNA–DNA hybrid and DNA reannealing at the upstream edge of the transcription bubble emerge as targets for regulation of the transcription elongation rate.
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Affiliation(s)
- Maria KIreeva
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Cyndi Trang
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Gayane Matevosyan
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Joshua Turek-Herman
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Vitaly Chasov
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Lucyna Lubkowska
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Mikhail Kashlev
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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24
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Structural basis for transcription antitermination at bacterial intrinsic terminator. Nat Commun 2019; 10:3048. [PMID: 31296855 PMCID: PMC6624301 DOI: 10.1038/s41467-019-10955-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/29/2019] [Indexed: 01/25/2023] Open
Abstract
Bacteriophages typically hijack the host bacterial transcriptional machinery to regulate their own gene expression and that of the host bacteria. The structural basis for bacteriophage protein-mediated transcription regulation—in particular transcription antitermination—is largely unknown. Here we report the 3.4 Å and 4.0 Å cryo-EM structures of two bacterial transcription elongation complexes (P7-NusA-TEC and P7-TEC) comprising the bacteriophage protein P7, a master host-transcription regulator encoded by bacteriophage Xp10 of the rice pathogen Xanthomonas oryzae pv. Oryzae (Xoo) and discuss the mechanisms by which P7 modulates the host bacterial RNAP. The structures together with biochemical evidence demonstrate that P7 prevents transcription termination by plugging up the RNAP RNA-exit channel and impeding RNA-hairpin formation at the intrinsic terminator. Moreover, P7 inhibits transcription initiation by restraining RNAP-clamp motions. Our study reveals the structural basis for transcription antitermination by phage proteins and provides insights into bacterial transcription regulation. Bacteriophages reprogram the host transcriptional machinery. Here the authors provide insights into the mechanism of how bacteriophages regulate host transcription by determining the cryo-EM structures of two bacterial transcription elongation complexes bound with the bacteriophage master host-transcription regulator protein P7.
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25
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Roberts JW. Mechanisms of Bacterial Transcription Termination. J Mol Biol 2019; 431:4030-4039. [PMID: 30978344 DOI: 10.1016/j.jmb.2019.04.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/28/2019] [Accepted: 04/02/2019] [Indexed: 01/28/2023]
Abstract
Bacterial transcription termination, described mostly for Escherichia coli, occurs in three recognized ways: intrinsic termination, an activity only of the core RNAP enzyme and transcript sequences that encode an RNA hairpin and terminal uridine-rich segment; termination by the enzyme Rho, an ATP-dependent RNA translocase that releases RNA by forcing uncharacterized structural changes in the elongating complex; and Mfd-dependent termination, the activity of an ATP-dependent DNA translocase that is thought to dissociate the elongation complex by exerting torque on a stalled RNAP. Intrinsic termination can be described in terms of the nucleic acid movements in the process, whereas the enzymatic mechanisms have been illuminated importantly by definitive structural and biochemical analysis of their activity.
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Affiliation(s)
- Jeffrey W Roberts
- Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA.
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26
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Wang S, Han Z, Libri D, Porrua O, Strick TR. Single-molecule characterization of extrinsic transcription termination by Sen1 helicase. Nat Commun 2019; 10:1545. [PMID: 30948716 PMCID: PMC6449345 DOI: 10.1038/s41467-019-09560-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 03/11/2019] [Indexed: 01/08/2023] Open
Abstract
Extrinsic transcription termination typically involves remodeling of RNA polymerase by an accessory helicase. In yeast this is accomplished by the Sen1 helicase homologous to human senataxin (SETX). To gain insight into these processes we develop a DNA scaffold construct compatible with magnetic-trapping assays and from which S. cerevisiae RNA polymerase II (Pol II), as well as E. coli RNA polymerase (ecRNAP), can efficiently initiate transcription without transcription factors, elongate, and undergo extrinsic termination. By stalling Pol II TECs on the construct we can monitor Sen1-induced termination in real-time, revealing the formation of an intermediate in which the Pol II transcription bubble appears half-rewound. This intermediate requires ~40 sec to form and lasts ~20 sec prior to final dissociation of the stalled Pol II. The experiments enabled by the scaffold construct permit detailed statistical and kinetic analysis of Pol II interactions with a range of cofactors in a multi-round, high-throughput fashion. Yeast’s Sen1 helicase is involved in the suppression of antisense transcription from bidirectional eukaryotic promoters. Here authors develop and utilize a quantitative single-molecule assay reporting on the kinetics of extrinsic eukaryotic transcription termination by the Sen1 helicase and a reaction intermediate in which the Pol II transcription bubble appears half-rewound.
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Affiliation(s)
- S Wang
- Molecular Motors and Machines group, Ecole normale supérieure, Institut de Biologie de l'Ecole normale supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005, Paris, France.,Biomolecular Nanomanipulation group, Institut Jacques Monod, CNRS, University Paris Diderot, Sorbonne Paris Cité, F-75205, Paris, France
| | - Z Han
- Metabolism and Function of RNA in the Nucleus, Institut Jacques Monod, CNRS, University Paris Diderot, Sorbonne Paris Cité, F-75205, Paris, France
| | - D Libri
- Metabolism and Function of RNA in the Nucleus, Institut Jacques Monod, CNRS, University Paris Diderot, Sorbonne Paris Cité, F-75205, Paris, France
| | - O Porrua
- Metabolism and Function of RNA in the Nucleus, Institut Jacques Monod, CNRS, University Paris Diderot, Sorbonne Paris Cité, F-75205, Paris, France
| | - T R Strick
- Molecular Motors and Machines group, Ecole normale supérieure, Institut de Biologie de l'Ecole normale supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005, Paris, France. .,Biomolecular Nanomanipulation group, Institut Jacques Monod, CNRS, University Paris Diderot, Sorbonne Paris Cité, F-75205, Paris, France. .,Programme Equipe Labellisées, Ligue Contre le Cancer, 75013, Paris, France.
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27
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Mishra S, Maraia RJ. RNA polymerase III subunits C37/53 modulate rU:dA hybrid 3' end dynamics during transcription termination. Nucleic Acids Res 2019; 47:310-327. [PMID: 30407541 PMCID: PMC6326807 DOI: 10.1093/nar/gky1109] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/22/2018] [Indexed: 12/18/2022] Open
Abstract
RNA polymerase (RNAP) III synthesizes tRNAs and other transcripts, and mutations to its subunits cause human disorders. The RNAP III subunit-heterodimer C37/53 functions in initiation, elongation and in termination-associated reinitiation with subunit C11. C37/53 is related to heterodimers associated with RNAPs I and II, and C11 is related to TFIIS and Rpa12.2, the active site RNA 3' cleavage factors for RNAPs II and I. Critical to termination is stability of the RNA:DNA hybrid bound in the active center, which is loose for RNAP III relative to other RNAPs. Here, we examined RNAP III lacking C37/53/C11 and various reconstituted forms during termination. First, we established a minimal terminator as 5T and 3A on the non-template and template DNA strands, respectively. We demonstrate that C11 stimulates termination, and does so independently of its RNA cleavage activity. We found that C37/53 sensitizes RNAP III termination to RNA:DNA hybrid strength and promotes RNA 3' end pairing/annealing with the template. The latter counteracts C11-insensitive arrest in the proximal part of the oligo(T)-tract, promoting oligo(rU:dA) extension toward greater hybrid instability and RNA release. The data also indicate that RNA 3' end engagement with the active site is a determinant of termination. Broader implications are also discussed.
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Affiliation(s)
- Saurabh Mishra
- Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard J Maraia
- Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
- Commissioned Corps, U.S. Public Health Service, Rockville, MD 20852, USA
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Bellecourt MJ, Ray-Soni A, Harwig A, Mooney RA, Landick R. RNA Polymerase Clamp Movement Aids Dissociation from DNA but Is Not Required for RNA Release at Intrinsic Terminators. J Mol Biol 2019; 431:696-713. [PMID: 30630008 DOI: 10.1016/j.jmb.2019.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 10/27/2022]
Abstract
In bacteria, disassembly of elongating transcription complexes (ECs) can occur at intrinsic terminators in a 2- to 3-nucleotide window after transcription of multiple kilobase pairs of DNA. Intrinsic terminators trigger pausing on weak RNA-DNA hybrids followed by formation of a strong, GC-rich stem-loop in the RNA exit channel of RNA polymerase (RNAP), inactivating nucleotide addition and inducing dissociation of RNA and RNAP from DNA. Although the movements of RNA and DNA during intrinsic termination have been studied extensively leading to multiple models, the effects of RNAP conformational changes remain less well defined. RNAP contains a clamp domain that closes around the nucleic acid scaffold during transcription initiation and can be displaced by either swiveling or opening motions. Clamp opening is proposed to promote termination by releasing RNAP-nucleic acid contacts. We developed a cysteine crosslinking assay to constrain clamp movements and study effects on intrinsic termination. We found that biasing the clamp into different conformations perturbed termination efficiency, but that perturbations were due primarily to changes in elongation rate, not the competing rate at which ECs commit to termination. After commitment, however, inhibiting clamp movements slowed release of DNA but not of RNA from the EC. We also found that restricting trigger-loop movements with the RNAP inhibitor microcin J25 prior to commitment inhibits termination, in agreement with a recently proposed multistate-multipath model of intrinsic termination. Together our results support views that termination commitment and DNA release are separate steps and that RNAP may remain associated with DNA after termination.
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Affiliation(s)
- Michael J Bellecourt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ananya Ray-Soni
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alex Harwig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Rachel Anne Mooney
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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29
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de Oliveira Martins E, Basílio Barbosa V, Weber G. DNA/RNA hybrid mesoscopic model shows strong stability dependence with deoxypyrimidine content and stacking interactions similar to RNA/RNA. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2018.11.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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30
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Koscielniak D, Wons E, Wilkowska K, Sektas M. Non-programmed transcriptional frameshifting is common and highly RNA polymerase type-dependent. Microb Cell Fact 2018; 17:184. [PMID: 30474557 PMCID: PMC6260861 DOI: 10.1186/s12934-018-1034-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/19/2018] [Indexed: 12/15/2022] Open
Abstract
Background The viral or host systems for a gene expression assume repeatability of the process and high quality of the protein product. Since level and fidelity of transcription primarily determines the overall efficiency, all factors contributing to their decrease should be identified and optimized. Among many observed processes, non-programmed insertion/deletion (indel) of nucleotide during transcription (slippage) occurring at homopolymeric A/T sequences within a gene can considerably impact its expression. To date, no comparative study of the most utilized Escherichia coli and T7 bacteriophage RNA polymerases (RNAP) propensity for this type of erroneous mRNA synthesis has been reported. To address this issue we evaluated the influence of shift-prone A/T sequences by assessing indel-dependent phenotypic changes. RNAP-specific expression profile was examined using two of the most potent promoters, ParaBAD of E. coli and φ10 of phage T7. Results Here we report on the first systematic study on requirements for efficient transcriptional slippage by T7 phage and cellular RNAPs considering three parameters: homopolymer length, template type, and frameshift directionality preferences. Using a series of out-of-frame gfp reporter genes fused to a variety of A/T homopolymeric sequences we show that T7 RNAP has an exceptional potential for generating frameshifts and is capable of slipping on as few as three adenine or four thymidine residues in a row, in a flanking sequence-dependent manner. In contrast, bacterial RNAP exhibits a relatively low ability to baypass indel mutations and requires a run of at least 7 tymidine and even more adenine residues. This difference comes from involvement of various intrinsic proofreading properties. Our studies demonstrate distinct preference towards a specific homopolymer in slippage induction. Whereas insertion slippage performed by T7 RNAP (but not deletion) occurs tendentiously on poly(A) rather than on poly(T) runs, strong bias towards poly(T) for the host RNAP is observed. Conclusions Intrinsic RNAP slippage properties involve trade-offs between accuracy, speed and processivity of transcription. Viral T7 RNAP manifests far greater inclinations to the transcriptional slippage than E. coli RNAP. This possibly plays an important role in driving bacteriophage adaptation and therefore could be considered as beneficial. However, from biotechnological and experimental viewpoint, this might create some problems, and strongly argues for employing bacterial expression systems, stocked with proofreading mechanisms. Electronic supplementary material The online version of this article (10.1186/s12934-018-1034-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dawid Koscielniak
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Ewa Wons
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Karolina Wilkowska
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Marian Sektas
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
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31
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Mihailovic MK, Vazquez-Anderson J, Li Y, Fry V, Vimalathas P, Herrera D, Lease RA, Powell WB, Contreras LM. High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites. Nat Commun 2018; 9:4084. [PMID: 30287822 PMCID: PMC6172242 DOI: 10.1038/s41467-018-06207-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 08/10/2018] [Indexed: 12/18/2022] Open
Abstract
Herein we introduce a high-throughput method, INTERFACE, to reveal the capacity of contiguous RNA nucleotides to establish in vivo intermolecular RNA interactions for the purpose of functional characterization of intracellular RNA. INTERFACE enables simultaneous accessibility interrogation of an unlimited number of regions by coupling regional hybridization detection to transcription elongation outputs measurable by RNA-seq. We profile over 900 RNA interfaces in 71 validated, but largely mechanistically under-characterized, Escherichia coli sRNAs in the presence and absence of a global regulator, Hfq, and find that two-thirds of tested sRNAs feature Hfq-dependent regions. Further, we identify in vivo hybridization patterns that hallmark functional regions to uncover mRNA targets. In this way, we biochemically validate 25 mRNA targets, many of which are not captured by typically tested, top-ranked computational predictions. We additionally discover direct mRNA binding activity within the GlmY terminator, highlighting the information value of high-throughput RNA accessibility data. Mapping RNA accessibility is valuable for identifying functional/regulatory RNA regions. Here the authors introduce INTERFACE, an intracellular method that quantifies antisense hybridization efficacy of any number of RNA regions simultaneously via a transcriptional elongation output, measurable via RNA-seq
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Affiliation(s)
- Mia K Mihailovic
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX, 78712, USA
| | - Jorge Vazquez-Anderson
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX, 78712, USA
| | - Yan Li
- Department of Operations Research and Financial Engineering, Princeton University, Sherrerd Hall, Charlton St., Princeton, NJ, 08544, USA
| | - Victoria Fry
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX, 78712, USA
| | - Praveen Vimalathas
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX, 78712, USA
| | - Daniel Herrera
- Department of Computer Science, University of Texas at Austin, 2317 Speedway Stop D9500, Austin, TX, 78712, USA
| | - Richard A Lease
- Department of Chemical and Biomolecular Engineering, The Ohio State University, 151W. Woodruff Ave, Columbus, OH, 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, 100W. 18th Ave, Columbus, OH, 43210, USA
| | - Warren B Powell
- Department of Operations Research and Financial Engineering, Princeton University, Sherrerd Hall, Charlton St., Princeton, NJ, 08544, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St., Stop C0400, Austin, TX, 78712, USA.
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32
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Trigger loop dynamics can explain stimulation of intrinsic termination by bacterial RNA polymerase without terminator hairpin contact. Proc Natl Acad Sci U S A 2017; 114:E9233-E9242. [PMID: 29078293 DOI: 10.1073/pnas.1706247114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In bacteria, intrinsic termination signals cause disassembly of the highly stable elongating transcription complex (EC) over windows of two to three nucleotides after kilobases of RNA synthesis. Intrinsic termination is caused by the formation of a nascent RNA hairpin adjacent to a weak RNA-DNA hybrid within RNA polymerase (RNAP). Although the contributions of RNA and DNA sequences to termination are largely understood, the roles of conformational changes in RNAP are less well described. The polymorphous trigger loop (TL), which folds into the trigger helices to promote nucleotide addition, also is proposed to drive termination by folding into the trigger helices and contacting the terminator hairpin after invasion of the hairpin in the RNAP main cleft [Epshtein V, Cardinale CJ, Ruckenstein AE, Borukhov S, Nudler E (2007) Mol Cell 28:991-1001]. To investigate the contribution of the TL to intrinsic termination, we developed a kinetic assay that distinguishes effects of TL alterations on the rate at which ECs terminate from effects of the TL on the nucleotide addition rate that indirectly affect termination efficiency by altering the time window in which termination can occur. We confirmed that the TL stimulates termination rate, but found that stabilizing either the folded or unfolded TL conformation decreased termination rate. We propose that conformational fluctuations of the TL (TL dynamics), not TL-hairpin contact, aid termination by increasing EC conformational diversity and thus access to favorable termination pathways. We also report that the TL and the TL sequence insertion (SI3) increase overall termination efficiency by stimulating pausing, which increases the flux of ECs into the termination pathway.
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33
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Abstract
RNA polymerase activity is regulated by nascent RNA sequences, DNA template sequences, and conserved transcription factors. Transcription factors promoting initiation and elongation have been characterized in each domain, but transcription termination factors have been identified only in bacteria and eukarya. Here we describe euryarchaeal termination activity (Eta), the first archaeal termination factor capable of disrupting the transcription elongation complex (TEC), detail the rate of and requirements for Eta-mediated transcription termination, and describe a role for Eta in transcription termination in vivo. Eta-mediated transcription termination is energy-dependent, requires upstream DNA sequences, and disrupts TECs to release the nascent RNA to solution. Deletion of TK0566 (encoding Eta) is possible, but results in slow growth and renders cells sensitive to DNA damaging agents. Our results suggest that the mechanisms used by termination factors in archaea, eukarya, and bacteria to disrupt the TEC may be conserved, and that Eta stimulates release of stalled or arrested TECs.
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34
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Olspert A, Carr JP, Firth AE. Mutational analysis of the Potyviridae transcriptional slippage site utilized for expression of the P3N-PIPO and P1N-PISPO proteins. Nucleic Acids Res 2016; 44:7618-29. [PMID: 27185887 PMCID: PMC5027478 DOI: 10.1093/nar/gkw441] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/05/2016] [Accepted: 05/06/2016] [Indexed: 12/02/2022] Open
Abstract
The Potyviridae comprise the largest and most important family of RNA plant viruses. An essential overlapping ORF, termed pipo, resides in an internal region of the main polyprotein ORF. Recently, expression of pipo was shown to depend on programmed transcriptional slippage at a conserved GAAAAAA sequence, resulting in the insertion of an extra A into a proportion of viral transcripts, fusing the pipo ORF in frame with the 5' third of the polyprotein ORF. However, the sequence features that mediate slippage have not been characterized. Using a duplicate copy of the pipo slip site region fused into a different genomic location where it can be freely mutated, we investigated the sequence requirements for transcriptional slippage. We find that the leading G is not strictly required, but increased flanking sequence GC content correlates with higher insertion rates. A homopolymeric hexamer is optimal for producing mainly single-nucleotide insertions. We also identify an overabundance of G to A substitutions immediately 3'-adjacent to GAAAAAA in insertion-free transcripts, which we infer to result from a 'to-fro' form of slippage during positive-strand synthesis. Analysis of wild-type and reverse complement sequences suggests that slippage occurs preferentially during synthesis of poly(A) and therefore occurs mainly during positive-strand synthesis.
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Affiliation(s)
- Allan Olspert
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - John P Carr
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
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Rijal K, Maraia RJ. Active Center Control of Termination by RNA Polymerase III and tRNA Gene Transcription Levels In Vivo. PLoS Genet 2016; 12:e1006253. [PMID: 27518095 PMCID: PMC4982682 DOI: 10.1371/journal.pgen.1006253] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/21/2016] [Indexed: 01/18/2023] Open
Abstract
The ability of RNA polymerase (RNAP) III to efficiently recycle from termination to reinitiation is critical for abundant tRNA production during cellular proliferation, development and cancer. Yet understanding of the unique termination mechanisms used by RNAP III is incomplete, as is its link to high transcription output. We used two tRNA-mediated suppression systems to screen for Rpc1 mutants with gain- and loss- of termination phenotypes in S. pombe. 122 point mutation mutants were mapped to a recently solved 3.9 Å structure of yeast RNAP III elongation complex (EC); they cluster in the active center bridge helix and trigger loop, as well as the pore and funnel, the latter of which indicate involvement of the RNA cleavage domain of the C11 subunit in termination. Purified RNAP III from a readthrough (RT) mutant exhibits increased elongation rate. The data strongly support a kinetic coupling model in which elongation rate is inversely related to termination efficiency. The mutants exhibit good correlations of terminator RT in vitro and in vivo, and surprisingly, amounts of transcription in vivo. Because assessing in vivo transcription can be confounded by various parameters, we used a tRNA reporter with a processing defect and a strong terminator. By ruling out differences in RNA decay rates, the data indicate that mutants with the RT phenotype synthesize more RNA than wild type cells, and than can be accounted for by their increased elongation rate. Finally, increased activity by the mutants appears unrelated to the RNAP III repressor, Maf1. The results show that the mobile elements of the RNAP III active center, including C11, are key determinants of termination, and that some of the mutations activate RNAP III for overall transcription. Similar mutations in spontaneous cancer suggest this as an unforeseen mechanism of RNAP III activation in disease.
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Affiliation(s)
- Keshab Rijal
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Richard J. Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
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36
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Porrua O, Boudvillain M, Libri D. Transcription Termination: Variations on Common Themes. Trends Genet 2016; 32:508-522. [DOI: 10.1016/j.tig.2016.05.007] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/28/2016] [Accepted: 05/31/2016] [Indexed: 11/29/2022]
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37
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Turowski TW, Leśniewska E, Delan-Forino C, Sayou C, Boguta M, Tollervey D. Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts. Genome Res 2016; 26:933-44. [PMID: 27206856 PMCID: PMC4937561 DOI: 10.1101/gr.205492.116] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/20/2016] [Indexed: 01/25/2023]
Abstract
RNA polymerase III (RNAPIII) synthesizes a range of highly abundant small stable RNAs, principally pre-tRNAs. Here we report the genome-wide analysis of nascent transcripts attached to RNAPIII under permissive and restrictive growth conditions. This revealed strikingly uneven polymerase distributions across transcription units, generally with a predominant 5' peak. This peak was higher for more heavily transcribed genes, suggesting that initiation site clearance is rate-limiting during RNAPIII transcription. Down-regulation of RNAPIII transcription under stress conditions was found to be uneven; a subset of tRNA genes showed low response to nutrient shift or loss of the major transcription regulator Maf1, suggesting potential "housekeeping" roles. Many tRNA genes were found to generate long, 3'-extended forms due to read-through of the canonical poly(U) terminators. The degree of read-through was anti-correlated with the density of U-residues in the nascent tRNA, and multiple, functional terminators can be located far downstream. The steady-state levels of 3'-extended pre-tRNA transcripts are low, apparently due to targeting by the nuclear surveillance machinery, especially the RNA binding protein Nab2, cofactors for the nuclear exosome, and the 5'-exonuclease Rat1.
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Affiliation(s)
- Tomasz W Turowski
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland; Institute of Biotechnology, Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
| | - Ewa Leśniewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Clementine Delan-Forino
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland
| | - Camille Sayou
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland
| | - Magdalena Boguta
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland
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38
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Abstract
The known diversity of metabolic strategies and physiological adaptations of archaeal species to extreme environments is extraordinary. Accurate and responsive mechanisms to ensure that gene expression patterns match the needs of the cell necessitate regulatory strategies that control the activities and output of the archaeal transcription apparatus. Archaea are reliant on a single RNA polymerase for all transcription, and many of the known regulatory mechanisms employed for archaeal transcription mimic strategies also employed for eukaryotic and bacterial species. Novel mechanisms of transcription regulation have become apparent by increasingly sophisticated in vivo and in vitro investigations of archaeal species. This review emphasizes recent progress in understanding archaeal transcription regulatory mechanisms and highlights insights gained from studies of the influence of archaeal chromatin on transcription.
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39
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Ray-Soni A, Bellecourt MJ, Landick R. Mechanisms of Bacterial Transcription Termination: All Good Things Must End. Annu Rev Biochem 2016; 85:319-47. [PMID: 27023849 DOI: 10.1146/annurev-biochem-060815-014844] [Citation(s) in RCA: 227] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Transcript termination is essential for accurate gene expression and the removal of RNA polymerase (RNAP) at the ends of transcription units. In bacteria, two mechanisms are responsible for proper transcript termination: intrinsic termination and Rho-dependent termination. Intrinsic termination is mediated by signals directly encoded within the DNA template and nascent RNA, whereas Rho-dependent termination relies upon the adenosine triphosphate-dependent RNA translocase Rho, which binds nascent RNA and dissociates the elongation complex. Although significant progress has been made in understanding these pathways, fundamental details remain undetermined. Among those that remain unresolved are the existence of an inactivated intermediate in the intrinsic termination pathway, the role of Rho-RNAP interactions in Rho-dependent termination, and the mechanisms by which accessory factors and nucleoid-associated proteins affect termination. We describe current knowledge, discuss key outstanding questions, and highlight the importance of defining the structural rearrangements of RNAP that are involved in the two mechanisms of transcript termination.
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Affiliation(s)
- Ananya Ray-Soni
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706; ,
| | - Michael J Bellecourt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706; ,
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706; , .,Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706;
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40
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Lass-Napiorkowska A, Heyduk T. Real-Time Observation of Backtracking by Bacterial RNA Polymerase. Biochemistry 2016; 55:647-58. [PMID: 26745324 DOI: 10.1021/acs.biochem.5b01184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA polymerase (RNAP) backtracking is a backward sliding of the enzyme along DNA and RNA. It plays important roles in many essential processes in bacteria and in eukaryotes. We describe here a fluorescence-based approach that allows a real-time observation of bacterial RNAP backtracking. A Cy3 fluorescence probe, when incorporated into a specific site in the nontemplate strand near the site of backtracking, allows RNAP movements to be monitored near the probe because of a robust enhancement of fluorescence caused by protein proximity. Using this approach, we showed that binding of NTP to the active site prior to phosphodiester bond formation inhibited backtracking, consistent with the coupling of NTP binding to translocation. The extent and the kinetics of backtracking did not show a simple correlation with the instability of the DNA-RNA hybrid, indicating a more complex dependence of backtracking on DNA template sequence. Experiments with transcription through an abasic site in DNA template or neutravidin bound to biotinylated template strand base illustrated an important role of backtracking in defining how RNAP reacts to such obstacles in the DNA template. The described approach will be a useful tool in deciphering the mechanism of backtracking and in studying factors that affect the backtracking.
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Affiliation(s)
- Agnieszka Lass-Napiorkowska
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine , Saint Louis, Missouri 63104, United States
| | - Tomasz Heyduk
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine , Saint Louis, Missouri 63104, United States
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Mondal S, Yakhnin AV, Sebastian A, Albert I, Babitzke P. NusA-dependent transcription termination prevents misregulation of global gene expression. Nat Microbiol 2016; 1:15007. [PMID: 27571753 DOI: 10.1038/nmicrobiol.2015.7] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/09/2015] [Indexed: 01/28/2023]
Abstract
Intrinsic transcription terminators consist of an RNA hairpin followed by a U-rich tract, and these signals can trigger termination without the involvement of additional factors. Although NusA is known to stimulate intrinsic termination in vitro, the in vivo targets and global impact of NusA are not known because it is essential for viability. Using genome-wide 3' end-mapping on an engineered Bacillus subtilis NusA depletion strain, we show that weak suboptimal terminators are the principle NusA substrates. Moreover, a subclass of weak non-canonical terminators was identified that completely depend on NusA for effective termination. NusA-dependent terminators tend to have weak hairpins and/or distal U-tract interruptions, supporting a model in which NusA is directly involved in the termination mechanism. Depletion of NusA altered global gene expression directly and indirectly via readthrough of suboptimal terminators. Readthrough of NusA-dependent terminators caused misregulation of genes involved in essential cellular functions, especially DNA replication and metabolism. We further show that nusA is autoregulated by a transcription attenuation mechanism that does not rely on antiterminator structures. Instead, NusA-stimulated termination in its 5' UTR dictates the extent of transcription into the operon, thereby ensuring tight control of cellular NusA levels.
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Affiliation(s)
- Smarajit Mondal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Alexander V Yakhnin
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Aswathy Sebastian
- Bioinformatics Consulting Center, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Istvan Albert
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Bioinformatics Consulting Center, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Abstract
The highly conserved Nus factors of bacteria were discovered as essential host proteins for the growth of temperate phage λ in Escherichia coli. Later, their essentiality and functions in transcription, translation, and, more recently, in DNA repair have been elucidated. Close involvement of these factors in various gene networks and circuits is also emerging from recent genomic studies. We have described a detailed overview of their biochemistry, structures, and various cellular functions, as well as their interactions with other macromolecules. Towards the end, we have envisaged different uncharted areas of studies with these factors, including their participation in pathogenicity.
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Imashimizu M, Shimamoto N, Oshima T, Kashlev M. Transcription elongation. Heterogeneous tracking of RNA polymerase and its biological implications. Transcription 2015; 5:e28285. [PMID: 25764114 PMCID: PMC4214235 DOI: 10.4161/trns.28285] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Regulation of transcription elongation via pausing of RNA polymerase has multiple physiological roles. The pausing mechanism depends on the sequence heterogeneity of the DNA being transcribed, as well as on certain interactions of polymerase with specific DNA sequences. In order to describe the mechanism of regulation, we introduce the concept of heterogeneity into the previously proposed alternative models of elongation, power stroke and Brownian ratchet. We also discuss molecular origins and physiological significances of the heterogeneity.
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Abstract
The Nus factors-NusA, NusB, NusE, and NusG-area set of well-conserved proteins in bacteria and are involved in transcription elongation, termination, antitermination, and translation processes. Originally, Escherichia coli host mutations defective for supporting bacteriophage λ N-mediated antitermination were mapped to the nusA (nusA1), nusB (nusB5, nusB101), and nusE (nusE71) genes, and hence, these genes were named nus for Nutilization substances (Nus). Subsequently,the Nus factors were purified and their roles in different host functions were elucidated. Except for NusB, deletion of which is conditionally lethal, all the other Nus factors are essential for E. coli. Among the Nus factors, NusA has the most varied functions. It specifically binds to RNA polymerase (RNAP), nascent RNA, and antiterminator proteins like N and Q and hence takes part in modulating transcription elongation, termination, and antitermination. It is also involved in DNA repair pathways. NusG interacts with RNAP and the transcription termination factor Rho and therefore is involved in both factor-dependent termination and transcription elongation processes. NusB and NusE are mostly important in antitermination at the ribosomal operon-transcription. NusE is a component of ribosome and may take part in facilitating the coupling between transcription and translation. This chapter emphasizes the structure-function relationship of these factors and their involvement in different fundamental cellular processes from a mechanistic angle.
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Zenkin N, Severinov K, Yuzenkova Y. Bacteriophage Xp10 anti-termination factor p7 induces forward translocation by host RNA polymerase. Nucleic Acids Res 2015; 43:6299-308. [PMID: 26038312 PMCID: PMC4513864 DOI: 10.1093/nar/gkv586] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 05/05/2015] [Accepted: 05/22/2015] [Indexed: 11/12/2022] Open
Abstract
Regulation of transcription elongation is based on response of RNA polymerase (RNAP) to various pause signals and is modulated by various accessory factors. Here we report that a 7 kDa protein p7 encoded by bacteriophage Xp10 acts as an elongation processivity factor of RNAP of host bacterium Xanthomonas oryzae, a major rice pathogen. Our data suggest that p7 stabilizes the upstream DNA duplex of the elongation complex thus disfavouring backtracking and promoting forward translocated states of the elongation complex. The p7-induced 'pushing' of RNAP and modification of RNAP contacts with the upstream edge of the transcription bubble lead to read-through of various types of pauses and termination signals and generally increase transcription processivity and elongation rate, contributing for transcription of an extremely long late genes operon of Xp10. Forward translocation was observed earlier upon the binding of unrelated bacterial elongation factor NusG, suggesting that this may be a general pathway of regulation of transcription elongation.
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Affiliation(s)
- Nikolay Zenkin
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Konstantin Severinov
- Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854-8020, USA Skolkovo Institute of Science and Technology, Skolkovo,143025, Russia Institute of Molecular Genetics, Russian Academy of Sciences, Moscow,123182, Russia Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Yulia Yuzenkova
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
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Imashimizu M, Takahashi H, Oshima T, McIntosh C, Bubunenko M, Court DL, Kashlev M. Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo. Genome Biol 2015; 16:98. [PMID: 25976475 PMCID: PMC4457086 DOI: 10.1186/s13059-015-0666-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 05/05/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Transcription elongation is frequently interrupted by pausing signals in DNA, with downstream effects on gene expression. Transcription errors also induce prolonged pausing, which can lead to a destabilized genome by interfering with DNA replication. Mechanisms of pausing associated with translocation blocks and misincorporation have been characterized in vitro, but not in vivo. RESULTS We investigate the pausing pattern of RNA polymerase (RNAP) in Escherichia coli by a novel approach, combining native elongating transcript sequencing (NET-seq) with RNase footprinting of the transcripts (RNET-seq). We reveal that the G-dC base pair at the 5' end of the RNA-DNA hybrid interferes with RNAP translocation. The distance between the 5' G-dC base pair and the 3' end of RNA fluctuates over a three-nucleotide width. Thus, the G-dC base pair can induce pausing in post-translocated, pre-translocated, and backtracked states of RNAP. Additionally, a CpG sequence of the template DNA strand spanning the active site of RNAP inhibits elongation and induces G-to-A errors, which leads to backtracking of RNAP. Gre factors efficiently proofread the errors and rescue the backtracked complexes. We also find that pausing events are enriched in the 5' untranslated region and antisense transcription of mRNA genes and are reduced in rRNA genes. CONCLUSIONS In E. coli, robust transcriptional pausing involves RNAP interaction with G-dC at the upstream end of the RNA-DNA hybrid, which interferes with translocation. CpG DNA sequences induce transcriptional pausing and G-to-A errors.
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Affiliation(s)
- Masahiko Imashimizu
- Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan.
| | - Taku Oshima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5, Ikoma, Nara, 630-0192, Japan.
| | - Carl McIntosh
- Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Mikhail Bubunenko
- Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Donald L Court
- Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Mikhail Kashlev
- Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
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Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators. Proc Natl Acad Sci U S A 2015; 112:E1984-93. [PMID: 25848054 DOI: 10.1073/pnas.1418384112] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli and yeast DNA-dependent RNA polymerases are shown to mediate efficient nascent transcript stem loop formation-dependent RNA-DNA hybrid realignment. The realignment was discovered on the heteropolymeric sequence T5C5 and yields transcripts lacking a C residue within a corresponding U5C4. The sequence studied is derived from a Roseiflexus insertion sequence (IS) element where the resulting transcriptional slippage is required for transposase synthesis. The stability of the RNA structure, the proximity of the stem loop to the slippage site, the length and composition of the slippage site motif, and the identity of its 3' adjacent nucleotides (nt) are crucial for transcripts lacking a single C. In many respects, the RNA structure requirements for this slippage resemble those for hairpin-dependent transcription termination. In a purified in vitro system, the slippage efficiency ranges from 5% to 75% depending on the concentration ratios of the nucleotides specified by the slippage sequence and the 3' nt context. The only previous proposal of stem loop mediated slippage, which was in Ebola virus expression, was based on incorrect data interpretation. We propose a mechanical slippage model involving the RNAP translocation state as the main motor in slippage directionality and efficiency. It is distinct from previously described models, including the one proposed for paramyxovirus, where following random movement efficiency is mainly dependent on the stability of the new realigned hybrid. In broadening the scope for utilization of transcription slippage for gene expression, the stimulatory structure provides parallels with programmed ribosomal frameshifting at the translation level.
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Distinct pathways of RNA polymerase regulation by a phage-encoded factor. Proc Natl Acad Sci U S A 2015; 112:2017-22. [PMID: 25646468 DOI: 10.1073/pnas.1416330112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Transcription antitermination is a common strategy of gene expression regulation, but only a few transcription antitermination factors have been studied in detail. Here, we dissect the transcription antitermination mechanism of Xanthomonas oryzae virus Xp10 protein p7, which binds host RNA polymerase (RNAP) and regulates both transcription initiation and termination. We show that p7 suppresses intrinsic termination by decreasing RNAP pausing and increasing the transcription complex stability, in cooperation with host-encoded factor NusA. Uniquely, the antitermination activity of p7 depends on the ω subunit of the RNAP core and is modulated by ppGpp. In contrast, the inhibition of transcription initiation by p7 does not require ω but depends on other RNAP sites. Our results suggest that p7, a bifunctional transcription factor, uses distinct mechanisms to control different steps of transcription. We propose that regulatory functions of the ω subunit revealed by our analysis may extend to its homologs in eukaryotic RNAPs.
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Koo CX, Kobiyama K, Shen YJ, LeBert N, Ahmad S, Khatoo M, Aoshi T, Gasser S, Ishii KJ. RNA polymerase III regulates cytosolic RNA:DNA hybrids and intracellular microRNA expression. J Biol Chem 2015; 290:7463-73. [PMID: 25623070 PMCID: PMC4367256 DOI: 10.1074/jbc.m115.636365] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
RNA:DNA hybrids form in the nuclei and mitochondria of cells as transcription-induced R-loops or G-quadruplexes, but exist only in the cytosol of virus-infected cells. Little is known about the existence of RNA:DNA hybrids in the cytosol of virus-free cells, in particular cancer or transformed cells. Here, we show that cytosolic RNA:DNA hybrids are present in various human cell lines, including transformed cells. Inhibition of RNA polymerase III (Pol III), but not DNA polymerase, abrogated cytosolic RNA:DNA hybrids. Cytosolic RNA:DNA hybrids bind to several components of the microRNA (miRNA) machinery-related proteins, including AGO2 and DDX17. Furthermore, we identified miRNAs that are specifically regulated by Pol III, providing a potential link between RNA:DNA hybrids and the miRNA machinery. One of the target genes, exportin-1, is shown to regulate cytosolic RNA:DNA hybrids. Taken together, we reveal previously unknown mechanism by which Pol III regulates the presence of cytosolic RNA:DNA hybrids and miRNA biogenesis in various human cells.
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Affiliation(s)
- Christine Xing'er Koo
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and the NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, the Laboratory of Adjuvant Innovation and
| | - Kouji Kobiyama
- the Laboratory of Adjuvant Innovation and the Laboratory of Vaccine Science, World Premier International Immunology Frontier Research Center (iFREC), Osaka University, Suita, Osaka 565-0871, Japan
| | - Yu J Shen
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and the NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456
| | - Nina LeBert
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and
| | - Shandar Ahmad
- the Laboratory of Bioinformatics, National Institute of Biomedical Innovation (NIBIO), Ibaraki, Osaka 567-0085, Japan, and
| | - Muznah Khatoo
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and
| | - Taiki Aoshi
- the Laboratory of Adjuvant Innovation and the Laboratory of Vaccine Science, World Premier International Immunology Frontier Research Center (iFREC), Osaka University, Suita, Osaka 565-0871, Japan
| | - Stephan Gasser
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and the NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456,
| | - Ken J Ishii
- the Laboratory of Adjuvant Innovation and the Laboratory of Vaccine Science, World Premier International Immunology Frontier Research Center (iFREC), Osaka University, Suita, Osaka 565-0871, Japan
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50
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Gong S, Wang Y, Zhang W. Kinetic regulation mechanism of pbuE riboswitch. J Chem Phys 2015; 142:015103. [DOI: 10.1063/1.4905214] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Sha Gong
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
| | - Yujie Wang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
| | - Wenbing Zhang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
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