1
|
Hosseini SH, Roussel MR. Analytic delay distributions for a family of gene transcription models. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2024; 21:6225-6262. [PMID: 39176425 DOI: 10.3934/mbe.2024273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Models intended to describe the time evolution of a gene network must somehow include transcription, the DNA-templated synthesis of RNA, and translation, the RNA-templated synthesis of proteins. In eukaryotes, the DNA template for transcription can be very long, often consisting of tens of thousands of nucleotides, and lengthy pauses may punctuate this process. Accordingly, transcription can last for many minutes, in some cases hours. There is a long history of introducing delays in gene expression models to take the transcription and translation times into account. Here we study a family of detailed transcription models that includes initiation, elongation, and termination reactions. We establish a framework for computing the distribution of transcription times, and work out these distributions for some typical cases. For elongation, a fixed delay is a good model provided elongation is fast compared to initiation and termination, and there are no sites where long pauses occur. The initiation and termination phases of the model then generate a nontrivial delay distribution, and elongation shifts this distribution by an amount corresponding to the elongation delay. When initiation and termination are relatively fast, the distribution of elongation times can be approximated by a Gaussian. A convolution of this Gaussian with the initiation and termination time distributions gives another analytic approximation to the transcription time distribution. If there are long pauses during elongation, because of the modularity of the family of models considered, the elongation phase can be partitioned into reactions generating a simple delay (elongation through regions where there are no long pauses), and reactions whose distribution of waiting times must be considered explicitly (initiation, termination, and motion through regions where long pauses are likely). In these cases, the distribution of transcription times again involves a nontrivial part and a shift due to fast elongation processes.
Collapse
Affiliation(s)
- S Hossein Hosseini
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Marc R Roussel
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| |
Collapse
|
2
|
Yakhnin A, Bubunenko M, Mandell Z, Lubkowska L, Husher S, Babitzke P, Kashlev M. Robust regulation of transcription pausing in Escherichia coli by the ubiquitous elongation factor NusG. Proc Natl Acad Sci U S A 2023; 120:e2221114120. [PMID: 37276387 PMCID: PMC10268239 DOI: 10.1073/pnas.2221114120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/09/2023] [Indexed: 06/07/2023] Open
Abstract
Transcription elongation by multi-subunit RNA polymerases (RNAPs) is regulated by auxiliary factors in all organisms. NusG/Spt5 is the only universally conserved transcription elongation factor shared by all domains of life. NusG is a component of antitermination complexes controlling ribosomal RNA operons, an essential antipausing factor, and a transcription-translation coupling factor in Escherichia coli. We employed RNET-seq for genome-wide mapping of RNAP pause sites in wild-type and NusG-depleted cells. We demonstrate that NusG is a major antipausing factor that suppresses thousands of backtracked and nonbacktracked pauses across the E. coli genome. The NusG-suppressed pauses were enriched immediately downstream from the translation start codon but were also abundant elsewhere in open reading frames, small RNA genes, and antisense transcription units. This finding revealed a strong similarity of NusG to Spt5, which stimulates the elongation rate of many eukaryotic genes. We propose a model in which promoting forward translocation and/or stabilization of RNAP in the posttranslocation register by NusG results in suppression of pausing in E. coli.
Collapse
Affiliation(s)
- Alexander V. Yakhnin
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Mikhail Bubunenko
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Zachary F. Mandell
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA16802
| | - Lucyna Lubkowska
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Sara Husher
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA16802
| | - Mikhail Kashlev
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| |
Collapse
|
3
|
Midha T, Mallory JD, Kolomeisky AB, Igoshin OA. Synergy among Pausing, Intrinsic Proofreading, and Accessory Proteins Results in Optimal Transcription Speed and Tolerable Accuracy. J Phys Chem Lett 2023; 14:3422-3429. [PMID: 37010247 DOI: 10.1021/acs.jpclett.3c00345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cleavage of dinucleotides after the misincorporational pauses serves as a proofreading mechanism that increases transcriptional elongation accuracy. The accuracy is further improved by accessory proteins such as GreA and TFIIS. However, it is not clear why RNAP pauses and why cleavage-factor-assisted proofreading is necessary despite transcriptional errors in vitro being of the same order as those in downstream translation. Here, we developed a chemical-kinetic model that incorporates most relevant features of transcriptional proofreading and uncovers how the balance between speed and accuracy is achieved. We found that long pauses are essential for high accuracy, whereas cleavage-factor-stimulated proofreading optimizes speed. Moreover, in comparison to the cleavage of a single nucleotide or three nucleotides, RNAP backtracking and dinucleotide cleavage improve both speed and accuracy. Our results thereby show how the molecular mechanism and the kinetic parameters of the transcriptional process were evolutionarily optimized to achieve maximal speed and tolerable accuracy.
Collapse
Affiliation(s)
- Tripti Midha
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Joel D Mallory
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Anatoly B Kolomeisky
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, United States
| | - Oleg A Igoshin
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| |
Collapse
|
4
|
Mitra P, Banerjee S, Khandavalli C, Deshmukh AS. The role of Toxoplasma TFIIS-like protein in the early stages of mRNA transcription. Biochim Biophys Acta Gen Subj 2022; 1866:130240. [PMID: 36058424 DOI: 10.1016/j.bbagen.2022.130240] [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: 06/24/2022] [Revised: 08/25/2022] [Accepted: 08/28/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND The mRNA transcription is a multistep process involving distinct sets of proteins associated with RNA polymerase II (RNAPII) through various stages. Recent studies have highlighted the role of RNAPII-associated proteins in facilitating the assembly of functional complexes in a crowded nuclear milieu. RNAPII dynamics and gene expression regulation have been primarily studied in model eukaryotes like yeasts and mammals and remain largely unchartered in protozoan parasites like Toxoplasma gondii, where considerable gene expression changes accompany stage differentiations. Here we report a key modulator of RNAPII activity, TFIIS in Toxoplasma gondii (TgTFIIS). METHODS A Pull-down assay demonstrated that TgTFIIS binds to RNAPII subunit TgRPB1. Truncation mutants of TFIIS help us define the regions critical for its binding to TgRPB1. Co-immunoprecipitation analysis confirmed the interaction between the native TgTFIIS and TgRPB1. Confocal microscopy revealed a predominantly nuclear localization. Native TgTFIIS was able to bind promoter DNA which was consistent with the CHIP results. RESULTS TgTFIIS complements initiation defects in yeast mutants, and the regions implicated in RNAPII binding appeared essential for this function. Interestingly, the C-terminal zinc finger domain necessary for its potential elongation function is dispensable for TgRPB1 binding. TgTFIIS was found to be associated with the promoter region along with its association with the ORF on an RNAPII transcribed gene. CONCLUSION The observations were in line with the potential role of TgTFIIS in early events of RNAPII transcription in addition to elongation. GENERAL SIGNIFICANCE The study elucidates the potential role of RNAPII-associated proteins in multiple steps of transcription.
Collapse
Affiliation(s)
- Pallabi Mitra
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India.
| | - Sneha Banerjee
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Chittiraju Khandavalli
- DBT-National Institute of Animal Biotechnology, Hyderabad, India; Dept. of Graduate Studies, Regional Centre for Biotechnology, Faridabad, Haryana, India
| | | |
Collapse
|
5
|
Abstract
Cellular life depends on transcription of DNA by RNA polymerase to express genetic information. RNA polymerase has evolved not just to read information from DNA and write it to RNA but also to sense and process information from the cellular and extracellular environments. Much of this information processing occurs during transcript elongation, when transcriptional pausing enables regulatory decisions. Transcriptional pauses halt RNA polymerase in response to DNA and RNA sequences and structures at locations and times that help coordinate interactions with small molecules and transcription factors important for regulation. Four classes of transcriptional pause signals are now evident after decades of study: elemental pauses, backtrack pauses, hairpin-stabilized pauses, and regulator-stabilized pauses. In this review, I describe current understanding of the molecular mechanisms of these four classes of pause signals, remaining questions about how RNA polymerase responds to pause signals, and the many exciting directions now open to understand pausing and the regulation of transcript elongation on a genome-wide scale. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Robert Landick
- Department of Biochemistry and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
| |
Collapse
|
6
|
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.
Collapse
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.)
| |
Collapse
|
7
|
Antosz W, Deforges J, Begcy K, Bruckmann A, Poirier Y, Dresselhaus T, Grasser KD. Critical Role of Transcript Cleavage in Arabidopsis RNA Polymerase II Transcriptional Elongation. THE PLANT CELL 2020; 32:1449-1463. [PMID: 32152189 PMCID: PMC7203918 DOI: 10.1105/tpc.19.00891] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/10/2020] [Accepted: 03/05/2020] [Indexed: 05/14/2023]
Abstract
Transcript elongation factors associate with elongating RNA polymerase II (RNAPII) to control the efficiency of mRNA synthesis and consequently modulate plant growth and development. Encountering obstacles during transcription such as nucleosomes or particular DNA sequences may cause backtracking and transcriptional arrest of RNAPII. The elongation factor TFIIS stimulates the intrinsic transcript cleavage activity of the polymerase, which is required for efficient rescue of backtracked/arrested RNAPII. A TFIIS mutant variant (TFIISmut) lacks the stimulatory activity to promote RNA cleavage, but instead efficiently inhibits unstimulated transcript cleavage by RNAPII. We could not recover viable Arabidopsis (Arabidopsis thaliana) tfIIs plants constitutively expressing TFIISmut. Induced, transient expression of TFIISmut in tfIIs plants provoked severe growth defects, transcriptomic changes and massive, transcription-related redistribution of elongating RNAPII within transcribed regions toward the transcriptional start site. The predominant site of RNAPII accumulation overlapped with the +1 nucleosome, suggesting that upon inhibition of RNA cleavage activity, RNAPII arrest prevalently occurs at this position. In the presence of TFIISmut, the amount of RNAPII was reduced, which could be reverted by inhibiting the proteasome, indicating proteasomal degradation of arrested RNAPII. Our findings suggest that polymerase backtracking/arrest frequently occurs in plant cells, and RNAPII-reactivation is essential for correct transcriptional output and proper growth/development.
Collapse
Affiliation(s)
- Wojciech Antosz
- Department of Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, D-93040 Regensburg, Germany
| | - Jules Deforges
- Department of Plant Molecular Biology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Kevin Begcy
- Environmental Horticulture Department, University of Florida, Gainesville, Florida 32611
| | - Astrid Bruckmann
- Department for Biochemistry I, Biochemistry Centre, University of Regensburg, D-93040 Regensburg, Germany
| | - Yves Poirier
- Department of Plant Molecular Biology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Thomas Dresselhaus
- Department of Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, D-93040 Regensburg, Germany
| | - Klaus D Grasser
- Department of Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, D-93040 Regensburg, Germany
| |
Collapse
|
8
|
Zatreanu D, Han Z, Mitter R, Tumini E, Williams H, Gregersen L, Dirac-Svejstrup AB, Roma S, Stewart A, Aguilera A, Svejstrup JQ. Elongation Factor TFIIS Prevents Transcription Stress and R-Loop Accumulation to Maintain Genome Stability. Mol Cell 2019; 76:57-69.e9. [PMID: 31519522 PMCID: PMC6863433 DOI: 10.1016/j.molcel.2019.07.037] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 05/28/2019] [Accepted: 07/26/2019] [Indexed: 01/08/2023]
Abstract
Although correlations between RNA polymerase II (RNAPII) transcription stress, R-loops, and genome instability have been established, the mechanisms underlying these connections remain poorly understood. Here, we used a mutant version of the transcription elongation factor TFIIS (TFIISmut), aiming to specifically induce increased levels of RNAPII pausing, arrest, and/or backtracking in human cells. Indeed, TFIISmut expression results in slower elongation rates, relative depletion of polymerases from the end of genes, and increased levels of stopped RNAPII; it affects mRNA splicing and termination as well. Remarkably, TFIISmut expression also dramatically increases R-loops, which may form at the anterior end of backtracked RNAPII and trigger genome instability, including DNA strand breaks. These results shed light on the relationship between transcription stress and R-loops and suggest that different classes of R-loops may exist, potentially with distinct consequences for genome stability.
Collapse
Affiliation(s)
- Diana Zatreanu
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Zhong Han
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Richard Mitter
- Bioinformatics and Biostatistics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Emanuela Tumini
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
| | - Hannah Williams
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Lea Gregersen
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - A Barbara Dirac-Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stefania Roma
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
| | - Aengus Stewart
- Bioinformatics and Biostatistics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andres Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Kang JY, Mishanina TV, Landick R, Darst SA. Mechanisms of Transcriptional Pausing in Bacteria. J Mol Biol 2019; 431:4007-4029. [PMID: 31310765 DOI: 10.1016/j.jmb.2019.07.017] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 12/21/2022]
Abstract
Pausing by RNA polymerase (RNAP) during transcription regulates gene expression in all domains of life. In this review, we recap the history of transcriptional pausing discovery, summarize advances in our understanding of the underlying causes of pausing since then, and describe new insights into the pausing mechanisms and pause modulation by transcription factors gained from structural and biochemical experiments. The accumulated evidence to date suggests that upon encountering a pause signal in the nucleic-acid sequence being transcribed, RNAP rearranges into an elemental, catalytically inactive conformer unable to load NTP substrate. The conformation, and as a consequence lifetime, of an elemental paused RNAP is modulated by backtracking, nascent RNA structure, binding of transcription regulators, or a combination of these mechanisms. We conclude the review by outlining open questions and directions for future research in the field of transcriptional pausing.
Collapse
Affiliation(s)
- Jin Young Kang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejon 34141, Republic of Korea.
| | - Tatiana V Mishanina
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, 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
| | - Seth A Darst
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
11
|
Abstract
In all living organisms, the flow of genetic information is a two-step process: first DNA is transcribed into RNA, which is subsequently used as template for protein synthesis during translation. In bacteria, archaea and eukaryotes, transcription is carried out by multi-subunit RNA polymerases (RNAPs) sharing a conserved architecture of the RNAP core. RNAPs catalyse the highly accurate polymerisation of RNA from NTP building blocks, utilising DNA as template, being assisted by transcription factors during the initiation, elongation and termination phase of transcription. The complexity of this highly dynamic process is reflected in the intricate network of protein-protein and protein-nucleic acid interactions in transcription complexes and the substantial conformational changes of the RNAP as it progresses through the transcription cycle.In this chapter, we will first briefly describe the early work that led to the discovery of multisubunit RNAPs. We will then discuss the three-dimensional organisation of RNAPs from the bacterial, archaeal and eukaryotic domains of life, highlighting the conserved nature, but also the domain-specific features of the transcriptional apparatus. Another section will focus on transcription factors and their role in regulating the RNA polymerase throughout the different phases of the transcription cycle. This includes a discussion of the molecular mechanisms and dynamic events that govern transcription initiation, elongation and termination.
Collapse
|
12
|
Belogurov GA, Artsimovitch I. The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase. J Mol Biol 2019; 431:3975-4006. [PMID: 31153902 DOI: 10.1016/j.jmb.2019.05.042] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 11/15/2022]
Abstract
Multi-subunit DNA-dependent RNA polymerases synthesize all classes of cellular RNAs, ranging from short regulatory transcripts to gigantic messenger RNAs. RNA polymerase has to make each RNA product in just one try, even if it takes millions of successive nucleotide addition steps. During each step, RNA polymerase selects a correct substrate, adds it to a growing chain, and moves one nucleotide forward before repeating the cycle. However, RNA synthesis is anything but monotonous: RNA polymerase frequently pauses upon encountering mechanical, chemical and torsional barriers, sometimes stepping back and cleaving off nucleotides from the growing RNA chain. A picture in which these intermittent dynamics enable processive, accurate, and controllable RNA synthesis is emerging from complementary structural, biochemical, computational, and single-molecule studies. Here, we summarize our current understanding of the mechanism and regulation of the on-pathway transcription elongation. We review the details of substrate selection, catalysis, proofreading, and translocation, focusing on rate-limiting steps, structural elements that modulate them, and accessory proteins that appear to control RNA polymerase translocation.
Collapse
Affiliation(s)
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|
13
|
The Role of Pyrophosphorolysis in the Initiation-to-Elongation Transition by E. coli RNA Polymerase. J Mol Biol 2019; 431:2528-2542. [PMID: 31029704 DOI: 10.1016/j.jmb.2019.04.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/13/2019] [Accepted: 04/15/2019] [Indexed: 02/02/2023]
Abstract
RNA polymerase can cleave a phosphodiester bond at the 3' end of a nascent RNA in the presence of pyrophosphate producing NTP. Pyrophosphorolysis has been characterized during elongation steps of transcription where its rate is significantly slower than the forward rate of NMP addition. In contrast, we report here that pyrophosphorolysis can occur in a millisecond time scale during the transition of Escherichia coli RNA polymerase from initiation to elongation at the psbA2 promoter. This rapid pyrophosphorolysis occurs during productive RNA synthesis as opposed to abortive RNA synthesis. Dissociation of σ70 or RNA extension beyond nine nucleotides dramatically reduces the rate of pyrophosphorolysis. We argue that the rapid pyrophosphorolysis allows iterative cycles of cleavage and re-synthesis of the 3' phosphodiester bond by the productive complexes in the early stage of transcription. This iterative process may provide an opportunity for the σ70 to dissociate from the RNA exit channel of the enzyme, enabling RNA to extend through the channel.
Collapse
|
14
|
Sanders TJ, Lammers M, Marshall CJ, Walker JE, Lynch ER, Santangelo TJ. TFS and Spt4/5 accelerate transcription through archaeal histone-based chromatin. Mol Microbiol 2019; 111:784-797. [PMID: 30592095 PMCID: PMC6417941 DOI: 10.1111/mmi.14191] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2018] [Indexed: 12/25/2022]
Abstract
RNA polymerase must surmount translocation barriers for continued transcription. In Eukarya and most Archaea, DNA-bound histone proteins represent the most common and troublesome barrier to transcription elongation. Eukaryotes encode a plethora of chromatin-remodeling complexes, histone-modification enzymes and transcription elongation factors to aid transcription through nucleosomes, while archaea seemingly lack machinery to remodel/modify histone-based chromatin and thus must rely on elongation factors to accelerate transcription through chromatin-barriers. TFS (TFIIS in Eukarya) and the Spt4-Spt5 complex are universally encoded in archaeal genomes, and here we demonstrate that both elongation factors, via different mechanisms, can accelerate transcription through archaeal histone-based chromatin. Histone proteins in Thermococcus kodakarensis are sufficiently abundant to completely wrap all genomic DNA, resulting in a consistent protein barrier to transcription elongation. TFS-enhanced cleavage of RNAs in backtracked transcription complexes reactivates stalled RNAPs and dramatically accelerates transcription through histone-barriers, while Spt4-Spt5 changes to clamp-domain dynamics play a lesser-role in stabilizing transcription. Repeated attempts to delete TFS, Spt4 and Spt5 from the T. kodakarensis genome were not successful, and the essentiality of both conserved transcription elongation factors suggests that both conserved elongation factors play important roles in transcription regulation in vivo, including mechanisms to accelerate transcription through downstream protein barriers.
Collapse
Affiliation(s)
- Travis J. Sanders
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Marshall Lammers
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Craig J. Marshall
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Julie E. Walker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
- Current address: Renewable and Sustainable Energy Institute, University of Colorado, Boulder, Colorado, 80303, USA
| | - Erin R. Lynch
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Thomas J. Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| |
Collapse
|
15
|
Saba J, Chua XY, Mishanina TV, Nayak D, Windgassen TA, Mooney RA, Landick R. The elemental mechanism of transcriptional pausing. eLife 2019; 8:e40981. [PMID: 30618376 PMCID: PMC6336406 DOI: 10.7554/elife.40981] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/19/2018] [Indexed: 12/20/2022] Open
Abstract
Transcriptional pausing underlies regulation of cellular RNA biogenesis. A consensus pause sequence that acts on RNA polymerases (RNAPs) from bacteria to mammals halts RNAP in an elemental paused state from which longer-lived pauses can arise. Although the structural foundations of pauses prolonged by backtracking or nascent RNA hairpins are recognized, the fundamental mechanism of the elemental pause is less well-defined. Here we report a mechanistic dissection that establishes the elemental pause signal (i) is multipartite; (ii) causes a modest conformational shift that puts γ-proteobacterial RNAP in an off-pathway state in which template base loading but not RNA translocation is inhibited; and (iii) allows RNAP to enter pretranslocated and one-base-pair backtracked states easily even though the half-translocated state observed in paused cryo-EM structures rate-limits pause escape. Our findings provide a mechanistic basis for the elemental pause and a framework to understand how pausing is modulated by sequence, cellular conditions, and regulators.
Collapse
Affiliation(s)
- Jason Saba
- Department of BiochemistryUniversity of Wisconsin-MadisonMadisonUnited States
| | - Xien Yu Chua
- Department of BiochemistryUniversity of Wisconsin-MadisonMadisonUnited States
| | - Tatiana V Mishanina
- Department of BiochemistryUniversity of Wisconsin-MadisonMadisonUnited States
| | - Dhananjaya Nayak
- Department of BiochemistryUniversity of Wisconsin-MadisonMadisonUnited States
| | - Tricia A Windgassen
- Department of BiochemistryUniversity of Wisconsin-MadisonMadisonUnited States
| | - Rachel Anne Mooney
- Department of BiochemistryUniversity of Wisconsin-MadisonMadisonUnited States
| | - Robert Landick
- Department of BiochemistryUniversity of Wisconsin-MadisonMadisonUnited States
- Department of BacteriologyUniversity of Wisconsin-MadisonMadisonUnited States
| |
Collapse
|
16
|
Parsa JY, Boudoukha S, Burke J, Homer C, Madhani HD. Polymerase pausing induced by sequence-specific RNA-binding protein drives heterochromatin assembly. Genes Dev 2018; 32:953-964. [PMID: 29967291 PMCID: PMC6075038 DOI: 10.1101/gad.310136.117] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 05/18/2018] [Indexed: 01/09/2023]
Abstract
In this study, Parsa et al. investigated the mechanisms underlying RNAi-independent heterochromatin assembly by the CTD–RRM protein Seb1 in S. pombe. They show that Seb1 promotes long-lived RNAPII pauses at pericentromeric repeat regions and that their presence correlates with the heterochromatin-triggering activities of the corresponding dg and dh DNA fragments, providing new insight into Seb1-mediated polymerase stalling as a signal necessary for heterochromatin nucleation. In Schizosaccharomyces pombe, transcripts derived from the pericentromeric dg and dh repeats promote heterochromatin formation via RNAi as well as an RNAi-independent mechanism involving the RNA polymerase II (RNAPII)-associated RNA-binding protein Seb1 and RNA processing activities. We show that Seb1 promotes long-lived RNAPII pauses at pericentromeric repeat regions and that their presence correlates with the heterochromatin-triggering activities of the corresponding dg and dh DNA fragments. Globally increasing RNAPII stalling by other means induces the formation of novel large ectopic heterochromatin domains. Such ectopic heterochromatin occurs even in cells lacking RNAi. These results uncover Seb1-mediated polymerase stalling as a signal necessary for heterochromatin nucleation.
Collapse
Affiliation(s)
- Jahan-Yar Parsa
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Selim Boudoukha
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Jordan Burke
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Christina Homer
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA.,Chan-Zuckerberg Biohub, San Francisco, California 94158, USA
| |
Collapse
|
17
|
Gabizon R, Lee A, Vahedian-Movahed H, Ebright RH, Bustamante CJ. Pause sequences facilitate entry into long-lived paused states by reducing RNA polymerase transcription rates. Nat Commun 2018; 9:2930. [PMID: 30050038 PMCID: PMC6062546 DOI: 10.1038/s41467-018-05344-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/21/2018] [Indexed: 11/25/2022] Open
Abstract
Transcription by RNA polymerase (RNAP) is interspersed with sequence-dependent pausing. The processes through which paused states are accessed and stabilized occur at spatiotemporal scales beyond the resolution of previous methods, and are poorly understood. Here, we combine high-resolution optical trapping with improved data analysis methods to investigate the formation of paused states at enhanced temporal resolution. We find that pause sites reduce the forward transcription rate of nearly all RNAP molecules, rather than just affecting the subset of molecules that enter long-lived pauses. We propose that the reduced rates at pause sites allow time for the elongation complex to undergo conformational changes required to enter long-lived pauses. We also find that backtracking occurs stepwise, with states backtracked by at most one base pair forming quickly, and further backtracking occurring slowly. Finally, we find that nascent RNA structures act as modulators that either enhance or attenuate pausing, depending on the sequence context.
Collapse
Affiliation(s)
- Ronen Gabizon
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA, 94720, USA
| | - Antony Lee
- Department of Physics, University of California, Berkeley, CA, 94720, USA
| | - Hanif Vahedian-Movahed
- Department of Chemistry and Waksman Institute, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Richard H Ebright
- Department of Chemistry and Waksman Institute, Rutgers University, Piscataway, NJ, 08854, USA
| | - Carlos J Bustamante
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA, 94720, USA.
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.
- Department of Molecular and Cell Biology, and Kavli Energy Nanoscience Institute, University of California, Berkeley, CA, 94720, USA.
| |
Collapse
|
18
|
Control of transcriptional pausing by biased thermal fluctuations on repetitive genomic sequences. Proc Natl Acad Sci U S A 2016; 113:E7409-E7417. [PMID: 27830653 DOI: 10.1073/pnas.1607760113] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the process of transcription elongation, RNA polymerase (RNAP) pauses at highly nonrandom positions across genomic DNA, broadly regulating transcription; however, molecular mechanisms responsible for the recognition of such pausing positions remain poorly understood. Here, using a combination of statistical mechanical modeling and high-throughput sequencing and biochemical data, we evaluate the effect of thermal fluctuations on the regulation of RNAP pausing. We demonstrate that diffusive backtracking of RNAP, which is biased by repetitive DNA sequence elements, causes transcriptional pausing. This effect stems from the increased microscopic heterogeneity of an elongation complex, and thus is entropy-dominated. This report shows a linkage between repetitive sequence elements encoded in the genome and regulation of RNAP pausing driven by thermal fluctuations.
Collapse
|
19
|
Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue. Nat Commun 2016; 7:11244. [PMID: 27091704 PMCID: PMC4838855 DOI: 10.1038/ncomms11244] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 03/03/2016] [Indexed: 12/19/2022] Open
Abstract
The dynamics of the RNA polymerase II (Pol II) backtracking process is poorly understood. We built a Markov State Model from extensive molecular dynamics simulations to identify metastable intermediate states and the dynamics of backtracking at atomistic detail. Our results reveal that Pol II backtracking occurs in a stepwise mode where two intermediate states are involved. We find that the continuous bending motion of the Bridge helix (BH) serves as a critical checkpoint, using the highly conserved BH residue T831 as a sensing probe for the 3′-terminal base paring of RNA:DNA hybrid. If the base pair is mismatched, BH bending can promote the RNA 3′-end nucleotide into a frayed state that further leads to the backtracked state. These computational observations are validated by site-directed mutagenesis and transcript cleavage assays, and provide insights into the key factors that regulate the preferences of the backward translocation. RNA Polymerase II can detect and cleave mis-incorporated nucleotides by a proofreading mechanism that requires backtracking of the enzyme. Here the authors show that Pol II backtracking occurs in a stepwise mode that involves two intermediate states where the fraying of the terminal RNA nucleotide is a prerequisite.
Collapse
|
20
|
Zhang J, Landick R. A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure. Trends Biochem Sci 2016; 41:293-310. [PMID: 26822487 DOI: 10.1016/j.tibs.2015.12.009] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/21/2015] [Accepted: 12/22/2015] [Indexed: 02/06/2023]
Abstract
The vectorial (5'-to-3' at varying velocity) synthesis of RNA by cellular RNA polymerases (RNAPs) creates a rugged kinetic landscape, demarcated by frequent, sometimes long-lived, pauses. In addition to myriad gene-regulatory roles, these pauses temporally and spatially program the co-transcriptional, hierarchical folding of biologically active RNAs. Conversely, these RNA structures, which form inside or near the RNA exit channel, interact with the polymerase and adjacent protein factors to influence RNA synthesis by modulating pausing, termination, antitermination, and slippage. Here, we review the evolutionary origin, mechanistic underpinnings, and regulatory consequences of this interplay between RNAP and nascent RNA structure. We categorize and rationalize the extensive linkage between the transcriptional machinery and its product, and provide a framework for future studies.
Collapse
Affiliation(s)
- Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.
| | - Robert Landick
- Departments of Biochemistry and Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
| |
Collapse
|
21
|
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.
Collapse
|
22
|
Čabart P, Jin H, Li L, Kaplan CD. Activation and reactivation of the RNA polymerase II trigger loop for intrinsic RNA cleavage and catalysis. Transcription 2015; 5:e28869. [PMID: 25764335 PMCID: PMC4574878 DOI: 10.4161/trns.28869] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In addition to RNA synthesis, multisubunit RNA polymerases (msRNAPs) support enzymatic reactions such as intrinsic transcript cleavage. msRNAP active sites from different species appear to exhibit differential intrinsic transcript cleavage efficiency and have likely evolved to allow fine-tuning of the transcription process. Here we show that a single amino-acid substitution in the trigger loop (TL) of Saccharomyces RNAP II, Rpb1 H1085Y, engenders a gain of intrinsic cleavage activity where the substituted tyrosine appears to participate in acid-base chemistry at alkaline pH for both intrinsic cleavage and nucleotidyl transfer. We extensively characterize this TL substitution for each of these reactions by examining the responses RNAP II enzymes to catalytic metals, altered pH, and factor inputs. We demonstrate that TFIIF stimulation of the first phosphodiester bond formation by RNAP II requires wild type TL function and that H1085Y substitution within the TL compromises or alters RNAP II responsiveness to both TFIIB and TFIIF. Finally, Mn(2+) stimulation of H1085Y RNAP II reveals possible allosteric effects of TFIIB on the active center and cooperation between TFIIB and TFIIF.
Collapse
Affiliation(s)
- Pavel Čabart
- a Department of Biochemistry and Biophysics; Texas A&M University; College Station, TX
| | | | | | | |
Collapse
|
23
|
Strobel EJ, Roberts JW. Two transcription pause elements underlie a σ70-dependent pause cycle. Proc Natl Acad Sci U S A 2015; 112:E4374-80. [PMID: 26216999 PMCID: PMC4538648 DOI: 10.1073/pnas.1512986112] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The movement of RNA polymerase (RNAP) during transcription elongation is modulated by DNA-encoded elements that cause the elongation complex to pause. One of the best-characterized pause sequences is a binding site for the σ(70) initiation factor that induces pausing at a site near lambdoid phage late-gene promoters. An essential component of this σ(70)-dependent pause is the elemental pause site (EPS), a sequence that itself induces transcription pausing throughout the Escherichia coli genome and underlies other complex regulatory pause elements, such as the ops and his operon pauses. Here, we identify and provide a detailed kinetic analysis of a transcription cycle analogous to abortive cycling that underlies the σ(70)-dependent pause. We show that, in σ(70)-dependent pausing, the elemental pause acts primarily to modulate the rate at which complexes attempt to disengage the σ(70):DNA interaction. Our findings establish the σ(70)-dependent pause-encoding region as a multipartite element in which several pause-inducing components make distinct mechanistic contributions to the induction and maintenance of a regulatory transcription pause.
Collapse
Affiliation(s)
- Eric J Strobel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Jeffrey W Roberts
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| |
Collapse
|
24
|
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.
Collapse
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.
| |
Collapse
|
25
|
A genetic assay for transcription errors reveals multilayer control of RNA polymerase II fidelity. PLoS Genet 2014; 10:e1004532. [PMID: 25232834 PMCID: PMC4168980 DOI: 10.1371/journal.pgen.1004532] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 06/11/2014] [Indexed: 11/19/2022] Open
Abstract
We developed a highly sensitive assay to detect transcription errors in vivo. The assay is based on suppression of a missense mutation in the active site tyrosine in the Cre recombinase. Because Cre acts as tetramer, background from translation errors are negligible. Functional Cre resulting from rare transcription errors that restore the tyrosine codon can be detected by Cre-dependent rearrangement of reporter genes. Hence, transient transcription errors are captured as stable genetic changes. We used this Cre-based reporter to screen for mutations of Saccharomyces cerevisiae RPB1 (RPO21) that increase the level of misincorporation during transcription. The mutations are in three domains of Rpb1, the trigger loop, the bridge helix, and in sites involved in binding to TFIIS. Biochemical characterization demonstrates that these variants have elevated misincorporation, and/or ability to extend mispaired bases, or defects in TFIIS mediated editing.
Collapse
|
26
|
Clayton CE. Networks of gene expression regulation in Trypanosoma brucei. Mol Biochem Parasitol 2014; 195:96-106. [PMID: 24995711 DOI: 10.1016/j.molbiopara.2014.06.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/19/2014] [Accepted: 06/23/2014] [Indexed: 10/25/2022]
Abstract
Regulation of gene expression in Kinetoplastids relies mainly on post-transcriptional mechanisms. Recent high-throughput analyses, combined with mathematical modelling, have demonstrated possibilities for transcript-specific regulation at every stage: trans splicing, polyadenylation, translation, and degradation of both the precursor and the mature mRNA. Different mRNA degradation pathways result in different types of degradation kinetics. The original idea that the fate of an mRNA - or even just its degradation kinetics - can be defined by a single "regulatory element" is an over-simplification. It is now clear that every mRNA can bind many different proteins, some of which may compete with each other. Superimposed upon this complexity are the interactions of those proteins with effectors of gene expression. The amount of protein that is made from a gene is therefore determined by a complex network of interactions.
Collapse
Affiliation(s)
- C E Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
| |
Collapse
|
27
|
Imashimizu M, Kashlev M. Unveiling translocation intermediates of RNA polymerase. Proc Natl Acad Sci U S A 2014; 111:7507-8. [PMID: 24828529 PMCID: PMC4040548 DOI: 10.1073/pnas.1406413111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Masahiko Imashimizu
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Mikhail Kashlev
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| |
Collapse
|
28
|
Coliphage HK022 Nun protein inhibits RNA polymerase translocation. Proc Natl Acad Sci U S A 2014; 111:E2368-75. [PMID: 24853501 DOI: 10.1073/pnas.1319740111] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Nun protein of coliphage HK022 arrests RNA polymerase (RNAP) in vivo and in vitro at pause sites distal to phage λ N-Utilization (nut) site RNA sequences. We tested the activity of Nun on ternary elongation complexes (TECs) assembled with templates lacking the λ nut sequence. We report that Nun stabilizes both translocation states of RNAP by restricting lateral movement of TEC along the DNA register. When Nun stabilized TEC in a pretranslocated register, immediately after NMP incorporation, it prevented binding of the next NTP and stimulated pyrophosphorolysis of the nascent transcript. In contrast, stabilization of TEC by Nun in a posttranslocated register allowed NTP binding and nucleotidyl transfer but inhibited pyrophosphorolysis and the next round of forward translocation. Nun binding to and action on the TEC requires a 9-bp RNA-DNA hybrid. We observed a Nun-dependent toe print upstream to the TEC. In addition, mutations in the RNAP β' subunit near the upstream end of the transcription bubble suppress Nun binding and arrest. These results suggest that Nun interacts with RNAP near the 5' edge of the RNA-DNA hybrid. By stabilizing translocation states through restriction of TEC lateral mobility, Nun represents a novel class of transcription arrest factors.
Collapse
|
29
|
Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms. Proc Natl Acad Sci U S A 2014; 111:6642-7. [PMID: 24733897 DOI: 10.1073/pnas.1405181111] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent evidence suggests that transcript elongation by RNA polymerase II (RNAPII) is regulated by mechanical cues affecting the entry into, and exit from, transcriptionally inactive states, including pausing and arrest. We present a single-molecule optical-trapping study of the interactions of RNAPII with transcription elongation factors TFIIS and TFIIF, which affect these processes. By monitoring the response of elongation complexes containing RNAPII and combinations of TFIIF and TFIIS to controlled mechanical loads, we find that both transcription factors are independently capable of restoring arrested RNAPII to productive elongation. TFIIS, in addition to its established role in promoting transcript cleavage, is found to relieve arrest by a second, cleavage-independent mechanism. TFIIF synergistically enhances some, but not all, of the activities of TFIIS. These studies also uncovered unexpected insights into the mechanisms underlying transient pauses. The direct visualization of pauses at near-base-pair resolution, together with the load dependence of the pause-entry phase, suggests that two distinct mechanisms may be at play: backtracking under forces that hinder transcription and a backtrack-independent activity under assisting loads. The measured pause lifetime distributions are inconsistent with prevailing views of backtracking as a purely diffusive process, suggesting instead that the extent of backtracking may be modulated by mechanisms intrinsic to RNAPII. Pauses triggered by inosine triphosphate misincorporation led to backtracking, even under assisting loads, and their lifetimes were reduced by TFIIS, particularly when aided by TFIIF. Overall, these experiments provide additional insights into how obstacles to transcription may be overcome by the concerted actions of multiple accessory factors.
Collapse
|
30
|
Yakhnin AV, Babitzke P. NusG/Spt5: are there common functions of this ubiquitous transcription elongation factor? Curr Opin Microbiol 2014; 18:68-71. [PMID: 24632072 DOI: 10.1016/j.mib.2014.02.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 02/06/2014] [Accepted: 02/13/2014] [Indexed: 11/18/2022]
Abstract
NusG/Spt5 is a transcription elongation factor that assists in DNA-templated RNA synthesis by cellular RNA polymerases (RNAP). The modular domain composition of NusG/Spt5 and the way it binds to RNAP are conserved in all three domains of life. NusG/Spt5 closes RNAP around the DNA binding channel, thereby increasing transcription processivity. Recruitment of additional factors to elongating RNAP may be another conserved function of this ubiquitous protein. Eukaryotic Spt5 couples RNA processing and chromatin modification to transcription elongation, whereas bacterial NusG participates in a wide variety of processes, including RNAP pausing and Rho-dependent termination. Elongating RNAP forms a transcriptional bubble in which ∼12bp of the two DNA strands are locally separated. Within this transcription bubble the growing 3'-end of nascent RNA forms an 8-9bp long hybrid with the template DNA strand. Because of their location in the transcriptional bubble, NusG and its paralog RfaH recognize specific sequences in the nontemplate DNA strand and regulate transcription elongation in response to these signals.
Collapse
Affiliation(s)
- Alexander V Yakhnin
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
| |
Collapse
|
31
|
Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics. Proc Natl Acad Sci U S A 2014; 111:3419-24. [PMID: 24550488 DOI: 10.1073/pnas.1401611111] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Transcription factors IIS (TFIIS) and IIF (TFIIF) are known to stimulate transcription elongation. Here, we use a single-molecule transcription elongation assay to study the effects of both factors. We find that these transcription factors enhance overall transcription elongation by reducing the lifetime of transcriptional pauses and that TFIIF also decreases the probability of pause entry. Furthermore, we observe that both factors enhance the processivity of RNA polymerase II through the nucleosomal barrier. The effects of TFIIS and TFIIF are quantitatively described using the linear Brownian ratchet kinetic model for transcription elongation and the backtracking model for transcriptional pauses, modified to account for the effects of the transcription factors. Our findings help elucidate the molecular mechanisms by which transcription factors modulate gene expression.
Collapse
|
32
|
Dangkulwanich M, Ishibashi T, Liu S, Kireeva ML, Lubkowska L, Kashlev M, Bustamante CJ. Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism. eLife 2013; 2:e00971. [PMID: 24066225 PMCID: PMC3778554 DOI: 10.7554/elife.00971] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 08/13/2013] [Indexed: 12/31/2022] Open
Abstract
During transcription elongation, RNA polymerase has been assumed to attain equilibrium between pre- and post-translocated states rapidly relative to the subsequent catalysis. Under this assumption, recent single-molecule studies proposed a branched Brownian ratchet mechanism that necessitates a putative secondary nucleotide binding site on the enzyme. By challenging individual yeast RNA polymerase II with a nucleosomal barrier, we separately measured the forward and reverse translocation rates. Surprisingly, we found that the forward translocation rate is comparable to the catalysis rate. This finding reveals a linear, non-branched ratchet mechanism for the nucleotide addition cycle in which translocation is one of the rate-limiting steps. We further determined all the major on- and off-pathway kinetic parameters in the elongation cycle. The resulting translocation energy landscape shows that the off-pathway states are favored thermodynamically but not kinetically over the on-pathway states, conferring the enzyme its propensity to pause and furnishing the physical basis for transcriptional regulation. DOI:http://dx.doi.org/10.7554/eLife.00971.001.
Collapse
Affiliation(s)
- Manchuta Dangkulwanich
- Jason L Choy Laboratory of Single-Molecule Biophysics , University of California, Berkeley , Berkeley , United States ; Department of Chemistry , University of California, Berkeley , Berkeley , United States
| | | | | | | | | | | | | |
Collapse
|
33
|
Imashimizu M, Oshima T, Lubkowska L, Kashlev M. Direct assessment of transcription fidelity by high-resolution RNA sequencing. Nucleic Acids Res 2013; 41:9090-104. [PMID: 23925128 PMCID: PMC3799451 DOI: 10.1093/nar/gkt698] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Cancerous and aging cells have long been thought to be impacted by transcription errors that cause genetic and epigenetic changes. Until now, a lack of methodology for directly assessing such errors hindered evaluation of their impact to the cells. We report a high-resolution Illumina RNA-seq method that can assess noncoded base substitutions in mRNA at 10−4–10−5 per base frequencies in vitro and in vivo. Statistically reliable detection of changes in transcription fidelity through ∼103 nt DNA sites assures that the RNA-seq can analyze the fidelity in a large number of the sites where errors occur. A combination of the RNA-seq and biochemical analyses of the positions for the errors revealed two sequence-specific mechanisms that increase transcription fidelity by Escherichia coli RNA polymerase: (i) enhanced suppression of nucleotide misincorporation that improves selectivity for the cognate substrate, and (ii) increased backtracking of the RNA polymerase that decreases a chance of error propagation to the full-length transcript after misincorporation and provides an opportunity to proofread the error. This method is adoptable to a genome-wide assessment of transcription fidelity.
Collapse
Affiliation(s)
- Masahiko Imashimizu
- Gene Regulation and Chromosome Biology Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA and Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | | | | | | |
Collapse
|
34
|
Nayak D, Voss M, Windgassen T, Mooney RA, Landick R. Cys-pair reporters detect a constrained trigger loop in a paused RNA polymerase. Mol Cell 2013; 50:882-93. [PMID: 23769674 DOI: 10.1016/j.molcel.2013.05.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 04/10/2013] [Accepted: 05/07/2013] [Indexed: 01/22/2023]
Abstract
Transcriptional pausing, which regulates transcript elongation in both prokaryotes and eukaryotes, is thought to involve formation of alternative RNA polymerase conformations in which nucleotide addition is inhibited in part by restriction of trigger loop (TL) folding. The polymorphous TL must convert from a random coil to a helical hairpin that contacts the nucleotide triphosphate (NTP) substrate to allow rapid nucleotide addition. Understanding the distribution of TL conformations in different enzyme states is made difficult by the TL's small size and sensitive energetics. Here, we report a Cys-pair reporter strategy to elucidate the relative occupancies of different TL conformations in E. coli RNA polymerase based on the ability of Cys residues engineered into the TL and surrounding regions to form disulfide bonds. Our results indicate that a paused complex stabilized by a nascent RNA hairpin favors nonproductive TL conformations that persist after NTP binding but can be reversed by the elongation factor RfaH.
Collapse
Affiliation(s)
- Dhananjaya Nayak
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | | | | | | |
Collapse
|