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Genome-wide effects on Escherichia coli transcription from ppGpp binding to its two sites on RNA polymerase. Proc Natl Acad Sci U S A 2019; 116:8310-8319. [PMID: 30971496 DOI: 10.1073/pnas.1819682116] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The second messenger nucleotide ppGpp dramatically alters gene expression in bacteria to adjust cellular metabolism to nutrient availability. ppGpp binds to two sites on RNA polymerase (RNAP) in Escherichia coli, but it has also been reported to bind to many other proteins. To determine the role of the RNAP binding sites in the genome-wide effects of ppGpp on transcription, we used RNA-seq to analyze transcripts produced in response to elevated ppGpp levels in strains with/without the ppGpp binding sites on RNAP. We examined RNAs rapidly after ppGpp production without an accompanying nutrient starvation. This procedure enriched for direct effects of ppGpp on RNAP rather than for indirect effects on transcription resulting from starvation-induced changes in metabolism or on secondary events from the initial effects on RNAP. The transcriptional responses of all 757 genes identified after 5 minutes of ppGpp induction depended on ppGpp binding to RNAP. Most (>75%) were not reported in earlier studies. The regulated transcripts encode products involved not only in translation but also in many other cellular processes. In vitro transcription analysis of more than 100 promoters from the in vivo dataset identified a large collection of directly regulated promoters, unambiguously demonstrated that most effects of ppGpp on transcription in vivo were direct, and allowed comparison of DNA sequences from inhibited, activated, and unaffected promoter classes. Our analysis greatly expands our understanding of the breadth of the stringent response and suggests promoter sequence features that contribute to the specific effects of ppGpp.
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102
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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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103
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104
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Li L, Fang C, Zhuang N, Wang T, Zhang Y. Structural basis for transcription initiation by bacterial ECF σ factors. Nat Commun 2019; 10:1153. [PMID: 30858373 PMCID: PMC6411747 DOI: 10.1038/s41467-019-09096-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/01/2019] [Indexed: 01/07/2023] Open
Abstract
Bacterial RNA polymerase employs extra-cytoplasmic function (ECF) σ factors to regulate context-specific gene expression programs. Despite being the most abundant and divergent σ factor class, the structural basis of ECF σ factor-mediated transcription initiation remains unknown. Here, we determine a crystal structure of Mycobacterium tuberculosis (Mtb) RNAP holoenzyme comprising an RNAP core enzyme and the ECF σ factor σH (σH-RNAP) at 2.7 Å, and solve another crystal structure of a transcription initiation complex of Mtb σH-RNAP (σH-RPo) comprising promoter DNA and an RNA primer at 2.8 Å. The two structures together reveal the interactions between σH and RNAP that are essential for σH-RNAP holoenzyme assembly as well as the interactions between σH-RNAP and promoter DNA responsible for stringent promoter recognition and for promoter unwinding. Our study establishes that ECF σ factors and primary σ factors employ distinct mechanisms for promoter recognition and for promoter unwinding.
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Affiliation(s)
- Lingting Li
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,0000 0004 1797 8419grid.410726.6University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chengli Fang
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,0000 0004 1797 8419grid.410726.6University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ningning Zhuang
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Tiantian Wang
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,0000 0004 1797 8419grid.410726.6University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yu Zhang
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China
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105
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Structural basis of ECF-σ-factor-dependent transcription initiation. Nat Commun 2019; 10:710. [PMID: 30755604 PMCID: PMC6372665 DOI: 10.1038/s41467-019-08443-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/11/2019] [Indexed: 01/24/2023] Open
Abstract
Extracytoplasmic (ECF) σ factors, the largest class of alternative σ factors, are related to primary σ factors, but have simpler structures, comprising only two of six conserved functional modules in primary σ factors: region 2 (σR2) and region 4 (σR4). Here, we report crystal structures of transcription initiation complexes containing Mycobacterium tuberculosis RNA polymerase (RNAP), M. tuberculosis ECF σ factor σL, and promoter DNA. The structures show that σR2 and σR4 of the ECF σ factor occupy the same sites on RNAP as in primary σ factors, show that the connector between σR2 and σR4 of the ECF σ factor–although shorter and unrelated in sequence–follows the same path through RNAP as in primary σ factors, and show that the ECF σ factor uses the same strategy to bind and unwind promoter DNA as primary σ factors. The results define protein-protein and protein-DNA interactions involved in ECF-σ-factor-dependent transcription initiation. No structural data have been available for RNA polymerase holoenzymes or transcription initiation complexes that contain extracytoplasmic σ factors. Here the authors report the crystal structures of transcription initiation complexes comprising Mycobacterium tuberculosis RNA polymerase, extracytoplasmic σ factor σL and promoter DNA.
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106
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Distinct Modes of Promoter Recognition by Two Iron Starvation σ Factors with Overlapping Promoter Specificities. J Bacteriol 2019; 201:JB.00507-18. [PMID: 30455278 DOI: 10.1128/jb.00507-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/06/2018] [Indexed: 01/28/2023] Open
Abstract
OrbS and PvdS are extracytoplasmic function (ECF) σ factors that regulate transcription of operons required for the biosynthesis of the siderophores ornibactin and pyoverdine in the Burkholderia cepacia complex and Pseudomonas spp., respectively. Here we show that promoter recognition by OrbS requires specific tetrameric -35 and -10 element sequences that are strikingly similar to those of the consensus PvdS-dependent promoter. However, whereas Pseudomonas aeruginosa PvdS can serve OrbS-dependent promoters, OrbS cannot utilize PvdS-dependent promoters. To identify features present at OrbS-dependent promoters that facilitate recognition by OrbS, we carried out a detailed analysis of the nucleotide sequence requirements for promoter recognition by both OrbS and PvdS. This revealed that DNA sequence features located outside the sigma binding elements are required for efficient promoter utilization by OrbS. In particular, the presence of an A-tract extending downstream from the -35 element at OrbS-dependent promoters was shown to be an important contributor to OrbS specificity. Our observations demonstrate that the nature of the spacer sequence can have a major impact on promoter recognition by some ECF σ factors through modulation of the local DNA architecture.IMPORTANCE ECF σ factors regulate subsets of bacterial genes in response to environmental stress signals by directing RNA polymerase to promoter sequences known as the -35 and -10 elements. In this work, we identify the -10 and -35 elements that are recognized by the ECF σ factor OrbS. Furthermore, we demonstrate that efficient promoter utilization by this σ factor also requires a polyadenine tract located downstream of the -35 region. We propose that the unique architecture of A-tract DNA imposes conformational features on the -35 element that facilitates efficient recognition by OrbS. Our results show that sequences located between the core promoter elements can make major contributions to promoter recognition by some ECF σ factors.
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107
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Liu Y, Song M, Ding S, Zhu K. Discovery of Linear Low-Cationic Peptides to Target Methicillin-Resistant Staphylococcus aureus in Vivo. ACS Infect Dis 2019; 5:123-130. [PMID: 30372023 DOI: 10.1021/acsinfecdis.8b00230] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development and rapid spread of multidrug resistant (MDR) bacteria cause severe public crises. New antibacterial compounds are urgently needed to treat bacterial infections. By circumventing the disadvantages of cationic peptides here, we engineered a short, linear, low-cationic peptide bacaucin-1a, which exhibited remarkable antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA). Bacaucin-1a was efficient in the prevention of MRSA associated infections in both in vitro and in vivo models with a unique mode of action. The discovery of low-cationic antibiotic candidates will extend our antibiotic pipeline in the fight against antibiotic resistant bacteria.
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Affiliation(s)
- Yuan Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, China 100193
| | - Meirong Song
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, China 100193
| | - Shuangyang Ding
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, China 100193
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, China 100193
| | - Kui Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, China 100193
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, China 100193
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, China 100193
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108
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Dienemann C, Schwalb B, Schilbach S, Cramer P. Promoter Distortion and Opening in the RNA Polymerase II Cleft. Mol Cell 2019; 73:97-106.e4. [DOI: 10.1016/j.molcel.2018.10.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/04/2018] [Accepted: 10/09/2018] [Indexed: 12/14/2022]
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109
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Esyunina D, Pupov D, Kulbachinskiy A. Dual role of the σ factor in primer RNA synthesis by bacterial RNA polymerase. FEBS Lett 2018; 593:361-368. [PMID: 30536890 DOI: 10.1002/1873-3468.13312] [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: 10/10/2018] [Revised: 11/28/2018] [Accepted: 11/30/2018] [Indexed: 11/08/2022]
Abstract
Bacterial RNA polymerase (RNAP) serves as a primase during replication of single-stranded plasmids and filamentous phages. Primer RNA (prRNA) synthesis from the origin regions of these replicons depends on the σ factor that normally participates in promoter recognition. However, it was proposed that σ may not be required for origin recognition but is rather involved in RNA extension by RNAP. Here, by analyzing the natural replication origin of bacteriophage M13 and synthetic ssDNA templates, we show that interactions of σ with promoter-like motifs stabilize priming complexes and can control prRNA synthesis by trapping RNAP on the template. Thus, the σ factor is involved in both DNA recognition and RNA priming, unifying its functions in transcription initiation from double- and single-stranded templates.
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Affiliation(s)
- Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Danil Pupov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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Bharanikumar R, Premkumar KAR, Palaniappan A. PromoterPredict: sequence-based modelling of Escherichia coli σ 70 promoter strength yields logarithmic dependence between promoter strength and sequence. PeerJ 2018; 6:e5862. [PMID: 30425888 PMCID: PMC6228582 DOI: 10.7717/peerj.5862] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 10/03/2018] [Indexed: 11/20/2022] Open
Abstract
We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ70 factor of RNA polymerase. σ70 promoters are ubiquitously used in recombinant DNA technology, but characterizing their strength is demanding in terms of both time and money. We parsed a comprehensive database of bacterial promoters for the -35 and -10 hexamer regions of σ70-binding promoters and used these sequences to construct the respective position weight matrices (PWM). Next we used a well-characterized set of promoters to train a multivariate linear regression model and learn the mapping between PWM scores of the -35 and -10 hexamers and the promoter strength. We found that the log of the promoter strength is significantly linearly associated with a weighted sum of the -10 and -35 sequence profile scores. We applied our model to 100 sets of 100 randomly generated promoter sequences to generate a sampling distribution of mean strengths of random promoter sequences and obtained a mean of 6E-4 ± 1E-7. Our model was further validated by cross-validation and on independent datasets of characterized promoters. PromoterPredict accepts -10 and -35 hexamer sequences and returns the predicted promoter strength. It is capable of dynamic learning from user-supplied data to refine the model construction and yield more robust estimates of promoter strength. PromoterPredict is available as both a web service (https://promoterpredict.com) and standalone tool (https://github.com/PromoterPredict). Our work presents an intuitive generalization applicable to modelling the strength of other promoter classes.
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Affiliation(s)
- Ramit Bharanikumar
- Biotechnology, Sri Venkateswara College of Engineering (Autonomous), Sriperumbudur, Tamil Nadu, India
| | - Keshav Aditya R Premkumar
- Computer Science and Engineering, Sri Venkateswara College of Engineering (Autonomous), Sriperumbudur, Tamil Nadu, India
| | - Ashok Palaniappan
- Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India
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111
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Rivera-Osorio A, Osorio A, Poggio S, Dreyfus G, Camarena L. Architecture of divergent flagellar promoters controlled by CtrA in Rhodobacter sphaeroides. BMC Microbiol 2018; 18:129. [PMID: 30305031 PMCID: PMC6180460 DOI: 10.1186/s12866-018-1264-y] [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: 12/05/2017] [Accepted: 09/26/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rhodobacter sphaeroides has two sets of flagellar genes, fla1 and fla2, that are responsible for the synthesis of two different flagellar structures. The expression of the fla2 genes is under control of CtrA. In several α-proteobacteria CtrA is also required for the expression of the flagellar genes, but the architecture of CtrA-dependent promoters has only been studied in detail in Caulobacter crescentus. In many cases the expression of fla genes originates from divergent promoters located a few base pairs apart, suggesting a particular arrangement of the cis-acting sites. RESULTS Here we characterized several control regions of the R. sphaeroides fla2 genes and analyzed in detail two regions containing the divergent promoters flgB2p-fliI2p, and fliL2p-fliF2p. Binding sites for CtrA of these promoters were identified in silico and tested by site directed mutagenesis. We conclude that each one of these promoter regions has a particular arrangement, either a single CtrA binding site for activation of fliL2p and fliF2p, or two independent sites for activation of flgB2p and fliI2p. ChIP experiments confirmed that CtrA binds to the control region containing the flgB2 and fliI2 promoters, supporting the notion that CtrA directly controls the expression of the fla2 genes. The flgB and fliI genes are syntenic and show a short intercistronic region in closely related bacterial species. We analyzed these regions and found that the arrangement of the CtrA binding sites varies considerably. CONCLUSIONS The results in this work reveal the arrangement of the fla2 divergent promoters showing that CtrA promotes transcriptional activation using more than a single architecture.
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Affiliation(s)
- Anet Rivera-Osorio
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| | - Aurora Osorio
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| | - Sebastian Poggio
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| | - Georges Dreyfus
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México.
| | - Laura Camarena
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México.
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112
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Structural basis of mitochondrial transcription. Nat Struct Mol Biol 2018; 25:754-765. [PMID: 30190598 DOI: 10.1038/s41594-018-0122-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/29/2018] [Indexed: 01/17/2023]
Abstract
The mitochondrial genome is transcribed by a single-subunit DNA-dependent RNA polymerase (mtRNAP) and its auxiliary factors. Structural studies have elucidated how mtRNAP cooperates with its dedicated transcription factors to direct RNA synthesis: initiation factors TFAM and TFB2M assist in promoter-DNA binding and opening by mtRNAP while the elongation factor TEFM increases polymerase processivity to the levels required for synthesis of long polycistronic mtRNA transcripts. Here, we review the emerging body of structural and functional studies of human mitochondrial transcription, provide a molecular movie that can be used for teaching purposes and discuss the open questions to guide future directions of investigation.
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Mishra A, Siwach P, Misra P, Jayaram B, Bansal M, Olson WK, Thayer KM, Beveridge DL. Toward a Universal Structural and Energetic Model for Prokaryotic Promoters. Biophys J 2018; 115:1180-1189. [PMID: 30172386 DOI: 10.1016/j.bpj.2018.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/28/2018] [Accepted: 08/02/2018] [Indexed: 01/04/2023] Open
Abstract
With almost no consensus promoter sequence in prokaryotes, recruitment of RNA polymerase (RNAP) to precise transcriptional start sites (TSSs) has remained an unsolved puzzle. Uncovering the underlying mechanism is critical for understanding the principle of gene regulation. We attempted to search the hidden code in ∼16,500 promoters of 12 prokaryotes representing two kingdoms in their structure and energetics. Twenty-eight fundamental parameters of DNA structure including backbone angles, basepair axis, and interbasepair and intrabasepair parameters were used, and information was extracted from x-ray crystallography data. Three parameters (solvation energy, hydrogen-bond energy, and stacking energy) were selected for creating energetics profiles using in-house programs. DNA of promoter regions was found to be inherently designed to undergo a change in every parameter undertaken for the study, in all prokaryotes. The change starts from some distance upstream of TSSs and continues past some distance from TSS, hence giving a signature state to promoter regions. These signature states might be the universal hidden codes recognized by RNAP. This observation was reiterated when randomly selected promoter sequences (with little sequence conservation) were subjected to structure generation; all developed into very similar three-dimensional structures quite distinct from those of conventional B-DNA and coding sequences. Fine structural details at important motifs (viz. -11, -35, and -75 positions relative to TSS) of promoters reveal novel to our knowledge and pointed insights for RNAP interaction at these locations; it could be correlated with how some particular structural changes at the -11 region may allow insertion of RNAP amino acids in interbasepair space as well as facilitate the flipping out of bases from the DNA duplex.
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Affiliation(s)
- Akhilesh Mishra
- Supercomputing Facility for Bioinformatics & Computational Biology; Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - Priyanka Siwach
- Supercomputing Facility for Bioinformatics & Computational Biology; Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana, India
| | - Pallavi Misra
- Supercomputing Facility for Bioinformatics & Computational Biology
| | - Bhyravabhotla Jayaram
- Supercomputing Facility for Bioinformatics & Computational Biology; Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India; Department of Chemistry, Indian Institute of Technology, Delhi, India.
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Wilma K Olson
- Department of Chemistry & Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers, Piscataway, New Jersey
| | - Kelly M Thayer
- Department of Chemistry, Vassar College, Poughkeepsie, New York
| | - David L Beveridge
- Departments of Chemistry, Molecular Biology, and Biochemistry and Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
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114
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Nedialkov Y, Svetlov D, Belogurov GA, Artsimovitch I. Locking the nontemplate DNA to control transcription. Mol Microbiol 2018; 109:445-457. [PMID: 29758107 PMCID: PMC6173972 DOI: 10.1111/mmi.13983] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2018] [Indexed: 12/31/2022]
Abstract
Universally conserved NusG/Spt5 factors reduce RNA polymerase pausing and arrest. In a widely accepted model, these proteins bridge the RNA polymerase clamp and lobe domains across the DNA channel, inhibiting the clamp opening to promote pause-free RNA synthesis. However, recent structures of paused transcription elongation complexes show that the clamp does not open and suggest alternative mechanisms of antipausing. Among these mechanisms, direct contacts of NusG/Spt5 proteins with the nontemplate DNA in the transcription bubble have been proposed to prevent unproductive DNA conformations and thus inhibit arrest. We used Escherichia coli RfaH, whose interactions with DNA are best characterized, to test this idea. We report that RfaH stabilizes the upstream edge of the transcription bubble, favoring forward translocation, and protects the upstream duplex DNA from exonuclease cleavage. Modeling suggests that RfaH loops the nontemplate DNA around its surface and restricts the upstream DNA duplex mobility. Strikingly, we show that RfaH-induced DNA protection and antipausing activity can be mimicked by shortening the nontemplate strand in elongation complexes assembled on synthetic scaffolds. We propose that remodeling of the nontemplate DNA controls recruitment of regulatory factors and R-loop formation during transcription elongation across all life.
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Affiliation(s)
- Yuri Nedialkov
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210
| | - Dmitri Svetlov
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | | | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210
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115
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Glyde R, Ye F, Jovanovic M, Kotta-Loizou I, Buck M, Zhang X. Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation. Mol Cell 2018; 70:1111-1120.e3. [PMID: 29932903 PMCID: PMC6028918 DOI: 10.1016/j.molcel.2018.05.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/25/2018] [Accepted: 05/18/2018] [Indexed: 12/15/2022]
Abstract
Gene transcription is carried out by multi-subunit RNA polymerases (RNAPs). Transcription initiation is a dynamic multi-step process that involves the opening of the double-stranded DNA to form a transcription bubble and delivery of the template strand deep into the RNAP for RNA synthesis. Applying cryoelectron microscopy to a unique transcription system using σ54 (σN), the major bacterial variant sigma factor, we capture a new intermediate state at 4.1 Å where promoter DNA is caught at the entrance of the RNAP cleft. Combining with new structures of the open promoter complex and an initial de novo transcribing complex at 3.4 and 3.7 Å, respectively, our studies reveal the dynamics of DNA loading and mechanism of transcription bubble stabilization that involves coordinated, large-scale conformational changes of the universally conserved features within RNAP and DNA. In addition, our studies reveal a novel mechanism of strand separation by σ54.
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Affiliation(s)
- Robert Glyde
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Fuzhou Ye
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Milija Jovanovic
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Martin Buck
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Xiaodong Zhang
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK.
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116
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Engel C, Neyer S, Cramer P. Distinct Mechanisms of Transcription Initiation by RNA Polymerases I and II. Annu Rev Biophys 2018; 47:425-446. [DOI: 10.1146/annurev-biophys-070317-033058] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA polymerases I and II (Pol I and Pol II) are the eukaryotic enzymes that catalyze DNA-dependent synthesis of ribosomal RNA and messenger RNA, respectively. Recent work shows that the transcribing forms of both enzymes are similar and the fundamental mechanisms of RNA chain elongation are conserved. However, the mechanisms of transcription initiation and its regulation differ between Pol I and Pol II. Recent structural studies of Pol I complexes with transcription initiation factors provided insights into how the polymerase recognizes its specific promoter DNA, how it may open DNA, and how initiation may be regulated. Comparison with the well-studied Pol II initiation system reveals a distinct architecture of the initiation complex and visualizes promoter- and gene-class-specific aspects of transcription initiation. On the basis of new structural studies, we derive a model of the Pol I transcription cycle and provide a molecular movie of Pol I transcription that can be used for teaching.
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Affiliation(s)
- Christoph Engel
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- Current affiliation: Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Simon Neyer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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117
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Zuber PK, Artsimovitch I, NandyMazumdar M, Liu Z, Nedialkov Y, Schweimer K, Rösch P, Knauer SH. The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand. eLife 2018; 7:36349. [PMID: 29741479 PMCID: PMC5995543 DOI: 10.7554/elife.36349] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/05/2018] [Indexed: 12/31/2022] Open
Abstract
RfaH, a transcription regulator of the universally conserved NusG/Spt5 family, utilizes a unique mode of recruitment to elongating RNA polymerase to activate virulence genes. RfaH function depends critically on an ops sequence, an exemplar of a consensus pause, in the non-template DNA strand of the transcription bubble. We used structural and functional analyses to elucidate the role of ops in RfaH recruitment. Our results demonstrate that ops induces pausing to facilitate RfaH binding and establishes direct contacts with RfaH. Strikingly, the non-template DNA forms a hairpin in the RfaH:ops complex structure, flipping out a conserved T residue that is specifically recognized by RfaH. Molecular modeling and genetic evidence support the notion that ops hairpin is required for RfaH recruitment. We argue that both the sequence and the structure of the non-template strand are read out by transcription factors, expanding the repertoire of transcriptional regulators in all domains of life.
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Affiliation(s)
- Philipp K Zuber
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Bayreuth, Germany
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, United States.,The Center for RNA Biology, The Ohio State University, Columbus, United States
| | - Monali NandyMazumdar
- Department of Microbiology, The Ohio State University, Columbus, United States.,The Center for RNA Biology, The Ohio State University, Columbus, United States
| | - Zhaokun Liu
- Department of Microbiology, The Ohio State University, Columbus, United States.,The Center for RNA Biology, The Ohio State University, Columbus, United States
| | - Yuri Nedialkov
- Department of Microbiology, The Ohio State University, Columbus, United States.,The Center for RNA Biology, The Ohio State University, Columbus, United States
| | - Kristian Schweimer
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Bayreuth, Germany
| | - Paul Rösch
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Bayreuth, Germany
| | - Stefan H Knauer
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Bayreuth, Germany
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118
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Salas-Navarrete C, Hernández-Chávez G, Flores N, Martínez LM, Martinez A, Bolívar F, Barona-Gomez F, Gosset G. Increasing pinosylvin production in Escherichia coli by reducing the expression level of the gene fabI -encoded enoyl-acyl carrier protein reductase. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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119
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Wassarman KM. 6S RNA, a Global Regulator of Transcription. Microbiol Spectr 2018; 6:10.1128/microbiolspec.RWR-0019-2018. [PMID: 29916345 PMCID: PMC6013841 DOI: 10.1128/microbiolspec.rwr-0019-2018] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Indexed: 01/06/2023] Open
Abstract
6S RNA is a small RNA regulator of RNA polymerase (RNAP) that is present broadly throughout the bacterial kingdom. Initial functional studies in Escherichia coli revealed that 6S RNA forms a complex with RNAP resulting in regulation of transcription, and cells lacking 6S RNA have altered survival phenotypes. The last decade has focused on deepening the understanding of several aspects of 6S RNA activity, including (i) addressing questions of how broadly conserved 6S RNAs are in diverse organisms through continued identification and initial characterization of divergent 6S RNAs; (ii) the nature of the 6S RNA-RNAP interaction through examination of variant proteins and mutant RNAs, cross-linking approaches, and ultimately a cryo-electron microscopic structure; (iii) the physiological consequences of 6S RNA function through identification of the 6S RNA regulon and promoter features that determine 6S RNA sensitivity; and (iv) the mechanism and cellular impact of 6S RNA-directed synthesis of product RNAs (i.e., pRNA synthesis). Much has been learned about this unusual RNA, its mechanism of action, and how it is regulated; yet much still remains to be investigated, especially regarding potential differences in behavior of 6S RNAs in diverse bacteria.
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Affiliation(s)
- Karen M Wassarman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53562
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120
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Dulin D, Bauer DLV, Malinen AM, Bakermans JJW, Kaller M, Morichaud Z, Petushkov I, Depken M, Brodolin K, Kulbachinskiy A, Kapanidis AN. Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria. Nat Commun 2018; 9:1478. [PMID: 29662062 PMCID: PMC5902446 DOI: 10.1038/s41467-018-03902-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 03/20/2018] [Indexed: 01/25/2023] Open
Abstract
Transcription in bacteria is controlled by multiple molecular mechanisms that precisely regulate gene expression. It has been recently shown that initial RNA synthesis by the bacterial RNA polymerase (RNAP) is interrupted by pauses; however, the pausing determinants and the relationship of pausing with productive and abortive RNA synthesis remain poorly understood. Using single-molecule FRET and biochemical analysis, here we show that the pause encountered by RNAP after the synthesis of a 6-nt RNA (ITC6) renders the promoter escape strongly dependent on the NTP concentration. Mechanistically, the paused ITC6 acts as a checkpoint that directs RNAP to one of three competing pathways: productive transcription, abortive RNA release, or a new unscrunching/scrunching pathway. The cyclic unscrunching/scrunching of the promoter generates a long-lived, RNA-bound paused state; the abortive RNA release and DNA unscrunching are thus not as tightly linked as previously thought. Finally, our new model couples the pausing with the abortive and productive outcomes of initial transcription.
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Affiliation(s)
- David Dulin
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK.
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Hartmannstrasse 14, 91052, Erlangen, Germany.
| | - David L V Bauer
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - Anssi M Malinen
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
- Department of Biochemistry, University of Turku, 20014, Turku, Finland
| | - Jacob J W Bakermans
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - Martin Kaller
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - Zakia Morichaud
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR9004 CNRS-Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, France
| | - Ivan Petushkov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Konstantin Brodolin
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR9004 CNRS-Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, France
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK.
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121
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An Evolutionary/Biochemical Connection between Promoter- and Primer-Dependent Polymerases Revealed by Systematic Evolution of Ligands by Exponential Enrichment. J Bacteriol 2018; 200:JB.00579-17. [PMID: 29339418 DOI: 10.1128/jb.00579-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/11/2018] [Indexed: 01/06/2023] Open
Abstract
DNA polymerases (DNAPs) recognize 3' recessed termini on duplex DNA and carry out nucleotide catalysis. Unlike promoter-specific RNA polymerases (RNAPs), no sequence specificity is required for binding or initiation of catalysis. Despite this, previous results indicate that viral reverse transcriptases bind much more tightly to DNA primers that mimic the polypurine tract. In the current report, primer sequences that bind with high affinity to Taq and Klenow polymerases were identified using a modified systematic evolution of ligands by exponential enrichment (SELEX) approach. Two Taq-specific primers that bound ∼10 (Taq1) and over 100 (Taq2) times more stably than controls to Taq were identified. TaqI contained 8 nucleotides (5'-CACTAAAG-3') that matched the phage T3 RNAP "core" promoter. Both primers dramatically outcompeted primers with similar binding thermodynamics in PCRs. Similarly, exonuclease- Klenow polymerase also selected a high-affinity primer that contained a related core promoter sequence from phage T7 RNAP (5'-ACTATAG-3'). For both Taq and Klenow, even small modifications to the sequence resulted in large losses in binding affinity, suggesting that binding was highly sequence specific. The results are discussed in the context of possible effects on multiprimer (multiplex) PCR assays, molecular information theory, and the evolution of RNAPs and DNAPs.IMPORTANCE This work further demonstrates that primer-dependent DNA polymerases can have strong sequence biases leading to dramatically tighter binding to specific sequences. These may be related to biological function or be a consequence of the structural architecture of the enzyme. New sequence specificity for Taq and Klenow polymerases were uncovered, and among them were sequences that contained the core promoter elements from T3 and T7 phage RNA polymerase promoters. This suggests the intriguing possibility that phage RNA polymerases exploited intrinsic binding affinities of ancestral DNA polymerases to develop their promoters. Conversely, DNA polymerases could have evolved from related RNA polymerases and retained the intrinsic binding preference despite there being no clear function for such a preference in DNA biology.
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122
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Roy NS, Debnath S, Chakraborty A, Chakraborty P, Bera I, Ghosh R, Ghoshal N, Chakrabarti S, Roy S. Enhanced basepair dynamics pre-disposes protein-assisted flips of key bases in DNA strand separation during transcription initiation. Phys Chem Chem Phys 2018; 20:9449-9459. [DOI: 10.1039/c8cp01119b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Localized separation of strands of duplex DNA is a necessary step in many DNA-dependent processes, including transcription and replication.
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Affiliation(s)
- Neeladri Sekhar Roy
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Subrata Debnath
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Abhijit Chakraborty
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | | | - Indrani Bera
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Raka Ghosh
- Department of Biophysics
- Bose Institute
- Kolkata 700054
- India
| | - Nanda Ghoshal
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Saikat Chakrabarti
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Siddhartha Roy
- Department of Biophysics
- Bose Institute
- Kolkata 700054
- India
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123
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Schramm FD, Heinrich K, Thüring M, Bernhardt J, Jonas K. An essential regulatory function of the DnaK chaperone dictates the decision between proliferation and maintenance in Caulobacter crescentus. PLoS Genet 2017; 13:e1007148. [PMID: 29281627 PMCID: PMC5760092 DOI: 10.1371/journal.pgen.1007148] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 01/09/2018] [Accepted: 12/11/2017] [Indexed: 11/19/2022] Open
Abstract
Hsp70 chaperones are well known for their important functions in maintaining protein homeostasis during thermal stress conditions. In many bacteria the Hsp70 homolog DnaK is also required for growth in the absence of stress. The molecular reasons underlying Hsp70 essentiality remain in most cases unclear. Here, we demonstrate that DnaK is essential in the α-proteobacterium Caulobacter crescentus due to its regulatory function in gene expression. Using a suppressor screen we identified mutations that allow growth in the absence of DnaK. All mutations reduced the activity of the heat shock sigma factor σ32, demonstrating that the DnaK-dependent inactivation of σ32 is a growth requirement. While most mutations occurred in the rpoH gene encoding σ32, we also identified mutations affecting σ32 activity or stability in trans, providing important new insight into the regulatory mechanisms controlling σ32 activity. Most notably, we describe a mutation in the ATP dependent protease HslUV that induces rapid degradation of σ32, and a mutation leading to increased levels of the house keeping σ70 that outcompete σ32 for binding to the RNA polymerase. We demonstrate that σ32 inhibits growth and that its unrestrained activity leads to an extensive reprogramming of global gene expression, resulting in upregulation of repair and maintenance functions and downregulation of the growth-promoting functions of protein translation, DNA replication and certain metabolic processes. While this re-allocation from proliferative to maintenance functions could provide an advantage during heat stress, it leads to growth defects under favorable conditions. We conclude that Caulobacter has co-opted the DnaK chaperone system as an essential regulator of gene expression under conditions when its folding activity is dispensable. Molecular chaperones of the Hsp70 family belong to the most conserved cellular machineries throughout the tree of life. These proteins play key roles in maintaining protein homeostasis, especially under heat stress conditions. In diverse bacteria the Hsp70 homolog DnaK is essential for growth even in the absence of stress. However, the molecular mechanisms underlying the essential nature of DnaK have in most cases not been studied. We found in the α-proteobacterium Caulobacter crescentus that the function of DnaK as a folding catalyst is dispensable in the absence of stress. Instead, its sole essential function under such conditions is to inhibit the activity of the heat shock sigma factor σ32. Our findings highlight that some bacteria have co-opted chaperones as essential regulators of gene expression under conditions when their folding activity is not required. Furthermore, our work illustrates that essential genes can perform different essential functions in discrete growth conditions.
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Affiliation(s)
- Frederic D. Schramm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
| | - Kristina Heinrich
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
| | - Marietta Thüring
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
| | - Jörg Bernhardt
- Institute of Microbiology, Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
| | - Kristina Jonas
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
- * E-mail:
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124
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Hillen HS, Morozov YI, Sarfallah A, Temiakov D, Cramer P. Structural Basis of Mitochondrial Transcription Initiation. Cell 2017; 171:1072-1081.e10. [PMID: 29149603 DOI: 10.1016/j.cell.2017.10.036] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/18/2017] [Accepted: 10/22/2017] [Indexed: 12/31/2022]
Abstract
Transcription in human mitochondria is driven by a single-subunit, factor-dependent RNA polymerase (mtRNAP). Despite its critical role in both expression and replication of the mitochondrial genome, transcription initiation by mtRNAP remains poorly understood. Here, we report crystal structures of human mitochondrial transcription initiation complexes assembled on both light and heavy strand promoters. The structures reveal how transcription factors TFAM and TFB2M assist mtRNAP to achieve promoter-dependent initiation. TFAM tethers the N-terminal region of mtRNAP to recruit the polymerase to the promoter whereas TFB2M induces structural changes in mtRNAP to enable promoter opening and trapping of the DNA non-template strand. Structural comparisons demonstrate that the initiation mechanism in mitochondria is distinct from that in the well-studied nuclear, bacterial, or bacteriophage transcription systems but that similarities are found on the topological and conceptual level. These results provide a framework for studying the regulation of gene expression and DNA replication in mitochondria.
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Affiliation(s)
- Hauke S Hillen
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Yaroslav I Morozov
- Department of Cell Biology, Rowan University, School of Osteopathic Medicine, 2 Medical Center Dr., Stratford, NJ 08084, USA
| | - Azadeh Sarfallah
- Department of Cell Biology, Rowan University, School of Osteopathic Medicine, 2 Medical Center Dr., Stratford, NJ 08084, USA
| | - Dmitry Temiakov
- Department of Cell Biology, Rowan University, School of Osteopathic Medicine, 2 Medical Center Dr., Stratford, NJ 08084, USA.
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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125
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Interaction of intramembrane metalloprotease SpoIVFB with substrate Pro-σ K. Proc Natl Acad Sci U S A 2017; 114:E10677-E10686. [PMID: 29180425 DOI: 10.1073/pnas.1711467114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Intramembrane proteases (IPs) cleave membrane-associated substrates in nearly all organisms and regulate diverse processes. A better understanding of how these enzymes interact with their substrates is necessary for rational design of IP modulators. We show that interaction of Bacillus subtilis IP SpoIVFB with its substrate Pro-σK depends on particular residues in the interdomain linker of SpoIVFB. The linker plus either the N-terminal membrane domain or the C-terminal cystathione-β-synthase (CBS) domain of SpoIVFB was sufficient for the interaction but not for cleavage of Pro-σK Chemical cross-linking and mass spectrometry of purified, inactive SpoIVFB-Pro-σK complex indicated residues of the two proteins in proximity. A structural model of the complex was built via partial homology and by using constraints based on cross-linking data. In the model, the Proregion of Pro-σK loops into the membrane domain of SpoIVFB, and the rest of Pro-σK interacts extensively with the linker and the CBS domain of SpoIVFB. The extensive interaction is proposed to allow coordination between ATP binding by the CBS domain and Pro-σK cleavage by the membrane domain.
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126
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Schroeder JW, Yeesin P, Simmons LA, Wang JD. Sources of spontaneous mutagenesis in bacteria. Crit Rev Biochem Mol Biol 2017; 53:29-48. [PMID: 29108429 DOI: 10.1080/10409238.2017.1394262] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mutations in an organism's genome can arise spontaneously, that is, in the absence of exogenous stress and prior to selection. Mutations are often neutral or deleterious to individual fitness but can also provide genetic diversity driving evolution. Mutagenesis in bacteria contributes to the already serious and growing problem of antibiotic resistance. However, the negative impacts of spontaneous mutagenesis on human health are not limited to bacterial antibiotic resistance. Spontaneous mutations also underlie tumorigenesis and evolution of drug resistance. To better understand the causes of genetic change and how they may be manipulated in order to curb antibiotic resistance or the development of cancer, we must acquire a mechanistic understanding of the major sources of mutagenesis. Bacterial systems are particularly well-suited to studying mutagenesis because of their fast growth rate and the panoply of available experimental tools, but efforts to understand mutagenic mechanisms can be complicated by the experimental system employed. Here, we review our current understanding of mutagenic mechanisms in bacteria and describe the methods used to study mutagenesis in bacterial systems.
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Affiliation(s)
- Jeremy W Schroeder
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
| | - Ponlkrit Yeesin
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
| | - Lyle A Simmons
- b Department of Molecular, Cellular, and Developmental Biology , University of Michigan , Ann Arbor , MI , USA
| | - Jue D Wang
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
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127
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Miropolskaya N, Feklistov A, Nikiforov V, Kulbachinskiy A. Site-specific aptamer inhibitors of Thermus RNA polymerase. Biochem Biophys Res Commun 2017; 495:110-115. [PMID: 29097207 DOI: 10.1016/j.bbrc.2017.10.151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 10/28/2017] [Indexed: 11/19/2022]
Abstract
Bacterial RNA polymerase (RNAP) is an RNA-synthesizing molecular machine and a target for antibiotics. In transcription, RNAP can interact with DNA sequence-specifically, during promoter recognition by the σ-containing holoenzyme, or nonspecifically, during productive RNA elongation by the core RNAP. We describe high-affinity single-stranded DNA aptamers that are specifically recognized by the core RNAP from Thermus aquaticus. The aptamers interact with distinct epitopes inside the RNAP main channel, including the rifamycin pocket, and sense the binding of other RNAP ligands such as rifamycin and the σA subunit. The aptamers inhibit RNAP activity and can thus be used for functional studies of transcription and development of novel RNAP inhibitors.
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Affiliation(s)
- Nataliya Miropolskaya
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia
| | - Andrey Feklistov
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Vadim Nikiforov
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia.
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128
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Real-time observation of polymerase-promoter contact remodeling during transcription initiation. Nat Commun 2017; 8:1178. [PMID: 29079833 PMCID: PMC5660091 DOI: 10.1038/s41467-017-01041-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 08/11/2017] [Indexed: 01/22/2023] Open
Abstract
Critical contacts made between the RNA polymerase (RNAP) holoenzyme and promoter DNA modulate not only the strength of promoter binding, but also the frequency and timing of promoter escape during transcription. Here, we describe a single-molecule optical-trapping assay to study transcription initiation in real time, and use it to map contacts formed between σ70 RNAP holoenzyme from E. coli and the T7A1 promoter, as well as to observe the remodeling of those contacts during the transition to the elongation phase. The strong binding contacts identified in certain well-known promoter regions, such as the −35 and −10 elements, do not necessarily coincide with the most highly conserved portions of these sequences. Strong contacts formed within the spacer region (−10 to −35) and with the −10 element are essential for initiation and promoter escape, respectively, and the holoenzyme releases contacts with promoter elements in a non-sequential fashion during escape. Contacts between RNA polymerase and promoter DNA modulate the strength of binding and the frequency of promoter escape during transcription. Here, the authors describe a single molecule optical-trapping assay to study transcription initiation and observe the dynamic remodeling of enzyme contacts in real time.
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129
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Chen J, Wassarman KM, Feng S, Leon K, Feklistov A, Winkelman JT, Li Z, Walz T, Campbell EA, Darst SA. 6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase. Mol Cell 2017; 68:388-397.e6. [PMID: 28988932 DOI: 10.1016/j.molcel.2017.09.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/11/2017] [Accepted: 09/05/2017] [Indexed: 01/25/2023]
Abstract
Noncoding RNAs (ncRNAs) regulate gene expression in all organisms. Bacterial 6S RNAs globally regulate transcription by binding RNA polymerase (RNAP) holoenzyme and competing with promoter DNA. Escherichia coli (Eco) 6S RNA interacts specifically with the housekeeping σ70-holoenzyme (Eσ70) and plays a key role in the transcriptional reprogramming upon shifts between exponential and stationary phase. Inhibition is relieved upon 6S RNA-templated RNA synthesis. We report here the 3.8 Å resolution structure of a complex between 6S RNA and Eσ70 determined by single-particle cryo-electron microscopy and validation of the structure using footprinting and crosslinking approaches. Duplex RNA segments have A-form C3' endo sugar puckers but widened major groove widths, giving the RNA an overall architecture that mimics B-form promoter DNA. Our results help explain the specificity of Eco 6S RNA for Eσ70 and show how an ncRNA can mimic B-form DNA to directly regulate transcription by the DNA-dependent RNAP.
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Affiliation(s)
- James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Karen M Wassarman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Shili Feng
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Katherine Leon
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Andrey Feklistov
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Jared T Winkelman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zongli Li
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA.
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA.
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130
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Characterization of a Minimal Type of Promoter Containing the -10 Element and a Guanine at the -14 or -13 Position in Mycobacteria. J Bacteriol 2017; 199:JB.00385-17. [PMID: 28784819 DOI: 10.1128/jb.00385-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/03/2017] [Indexed: 11/20/2022] Open
Abstract
Three key promoter elements, i.e., -10, -35, and T-15G-14N, are recognized by the σ subunit of RNA polymerase. Among them, promoters with the -10 element and either -35 or T-15G-14N are known to initiate transcription efficiently, but recent systematic analyses have identified a large group of promoters in Mycobacterium tuberculosis that contain only a -10 consensus. How these promoters initiate transcription remains poorly understood. Here, we show that promoters containing the -10 element and an upstream G located at the -14 or -13 position can successfully initiate transcription in mycobacteria. Importantly, this new type of promoter is active in the absence of other promoter consensuses, suggesting that it is a minimal promoter type. Mutation of the upstream G in promoters decreased the efficiencies of their binding with RNA polymerase and their abilities to initiate transcription in both in vitro and in vivo analyses. A glutamic acid in σ region 3.0 is essential for recognizing G-14 and G-13 and is conserved in both principal and principal-like σ factors in mycobacteria, indicating that recognition of this minimal type of promoter might be a common mechanism for transcription initiation. Consistently, more than 70% of the identified promoters in M. tuberculosis contained G-14 or G-13 upstream of the conserved -10 element, and thousands of promoters in representative mycobacterial species have been predicted using the -10 consensus and G-14 or G-13 Altogether, our study presents a universal mechanism for transcription initiation from a minimal promoter in mycobacteria, which might also be applicable to other bacteria.IMPORTANCE In contrast to the detailed information for recognizing classic promoters in the model organism Escherichia coli, very little is known about how transcription is initiated in the human pathogen Mycobacterium tuberculosis In this study, we characterized a new type of promoter in mycobacteria that requires only a -10 consensus and an upstream G-14 or G-13 Residues important for recognizing the -10 element and the upstream G are conserved in σA and σB from mycobacterial species. According to such features, thousands of promoters in mycobacteria can be predicted using the -10 consensus and G-14 or G-13, which suggests that transcription from this new type of promoter might be widespread. Our findings provide insightful information for characterizing promoters in mycobacteria.
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131
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Sokolova M, Borukhov S, Lavysh D, Artamonova T, Khodorkovskii M, Severinov K. A non-canonical multisubunit RNA polymerase encoded by the AR9 phage recognizes the template strand of its uracil-containing promoters. Nucleic Acids Res 2017; 45:5958-5967. [PMID: 28402520 PMCID: PMC5449584 DOI: 10.1093/nar/gkx264] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 04/04/2017] [Indexed: 12/22/2022] Open
Abstract
AR9 is a giant Bacillus subtilis phage whose uracil-containing double-stranded DNA genome encodes distant homologs of β and β’ subunits of bacterial RNA polymerase (RNAP). The products of these genes are thought to assemble into two non-canonical multisubunit RNAPs - a virion RNAP (vRNAP) that is injected into the host along with phage DNA to transcribe early phage genes, and a non-virion RNAP (nvRNAP), which is synthesized during the infection and transcribes late phage genes. We purified the AR9 nvRNAP from infected B. subtilis cells and characterized its transcription activity in vitro. The AR9 nvRNAP requires uracils rather than thymines at specific conserved positions of late viral promoters. Uniquely, the nvRNAP recognizes the template strand of its promoters and is capable of specific initiation of transcription from both double- and single-stranded DNA. While the AR9 nvRNAP does not contain homologs of bacterial RNAP α subunits, it contains, in addition to the β and β’-like subunits, a phage protein gp226. The AR9 nvRNAP lacking gp226 is catalytically active but unable to bind to promoter DNA. Thus, gp226 is required for promoter recognition by the AR9 nvRNAP and may represent a new group of transcription initiation factors.
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Affiliation(s)
- Maria Sokolova
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia.,Peter the Great St.Petersburg Polytechnic University, Saint-Petersburg, 195251, Russia
| | - Sergei Borukhov
- Department of Cell Biology, Rowan University School of Osteopathic Medicine at Stratford, Stratford, NJ 08084-1489, USA
| | - Daria Lavysh
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.,Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, 214019, Russia
| | - Tatjana Artamonova
- Peter the Great St.Petersburg Polytechnic University, Saint-Petersburg, 195251, Russia
| | - Mikhail Khodorkovskii
- Peter the Great St.Petersburg Polytechnic University, Saint-Petersburg, 195251, Russia
| | - Konstantin Severinov
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia.,Peter the Great St.Petersburg Polytechnic University, Saint-Petersburg, 195251, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.,Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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132
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Gouge J, Guthertz N, Kramm K, Dergai O, Abascal-Palacios G, Satia K, Cousin P, Hernandez N, Grohmann D, Vannini A. Molecular mechanisms of Bdp1 in TFIIIB assembly and RNA polymerase III transcription initiation. Nat Commun 2017; 8:130. [PMID: 28743884 PMCID: PMC5526994 DOI: 10.1038/s41467-017-00126-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/02/2017] [Indexed: 12/14/2022] Open
Abstract
Initiation of gene transcription by RNA polymerase (Pol) III requires the activity of TFIIIB, a complex formed by Brf1 (or Brf2), TBP (TATA-binding protein), and Bdp1. TFIIIB is required for recruitment of Pol III and to promote the transition from a closed to an open Pol III pre-initiation complex, a process dependent on the activity of the Bdp1 subunit. Here, we present a crystal structure of a Brf2-TBP-Bdp1 complex bound to DNA at 2.7 Å resolution, integrated with single-molecule FRET analysis and in vitro biochemical assays. Our study provides a structural insight on how Bdp1 is assembled into TFIIIB complexes, reveals structural and functional similarities between Bdp1 and Pol II factors TFIIA and TFIIF, and unravels essential interactions with DNA and with the upstream factor SNAPc. Furthermore, our data support the idea of a concerted mechanism involving TFIIIB and RNA polymerase III subunits for the closed to open pre-initiation complex transition.Transcription initiation by RNA polymerase III requires TFIIIB, a complex formed by Brf1/Brf2, TBP and Bdp1. Here, the authors describe the crystal structure of a Brf2-TBP-Bdp1 complex bound to a DNA promoter and characterize the role of Bdp1 in TFIIIB assembly and pre-initiation complex formation.
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Affiliation(s)
- Jerome Gouge
- The Institute of Cancer Research, London, SW7 3RP, UK
| | | | - Kevin Kramm
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, University of Regensburg, 93053, Regensburg, Germany
| | - Oleksandr Dergai
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | | | | | - Pascal Cousin
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Dina Grohmann
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, University of Regensburg, 93053, Regensburg, Germany
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133
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Hubin EA, Lilic M, Darst SA, Campbell EA. Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures. Nat Commun 2017; 8:16072. [PMID: 28703128 PMCID: PMC5511352 DOI: 10.1038/ncomms16072] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/25/2017] [Indexed: 11/25/2022] Open
Abstract
The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the αCTD may play a role in Mtb transcription regulation. Our results reveal the structure of an Actinobacteria-unique insert of the RNAP β′ subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σA, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli. Understanding of the mycobacterial transcription system is useful to the development of therapeutics against tuberculosis infection. Here the authors present the crystal structure of a complete M. smegmatis RNA polymerase open promoter complex that reveals unique features of the mycobacterial polymerase.
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Affiliation(s)
- Elizabeth A Hubin
- The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Mirjana Lilic
- The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Seth A Darst
- The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
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134
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Abstract
Transcription initiation is highly regulated in bacterial cells, allowing adaptive gene regulation in response to environment cues. One class of promoter specificity factor called sigma54 enables such adaptive gene expression through its ability to lock the RNA polymerase down into a state unable to melt out promoter DNA for transcription initiation. Promoter DNA opening then occurs through the action of specialized transcription control proteins called bacterial enhancer-binding proteins (bEBPs) that remodel the sigma54 factor within the closed promoter complexes. The remodelling of sigma54 occurs through an ATP-binding and hydrolysis reaction carried out by the bEBPs. The regulation of bEBP self-assembly into typically homomeric hexamers allows regulated gene expression since the self-assembly is required for bEBP ATPase activity and its direct engagement with the sigma54 factor during the remodelling reaction. Crystallographic studies have now established that in the closed promoter complex, the sigma54 factor occupies the bacterial RNA polymerase in ways that will physically impede promoter DNA opening and the loading of melted out promoter DNA into the DNA-binding clefts of the RNA polymerase. Large-scale structural re-organizations of sigma54 require contact of the bEBP with an amino-terminal glutamine and leucine-rich sequence of sigma54, and lead to domain movements within the core RNA polymerase necessary for making open promoter complexes and synthesizing the nascent RNA transcript.
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135
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Gaal T, Bratton BP, Sanchez-Vazquez P, Sliwicki A, Sliwicki K, Vegel A, Pannu R, Gourse RL. Colocalization of distant chromosomal loci in space in E. coli: a bacterial nucleolus. Genes Dev 2017; 30:2272-2285. [PMID: 27898392 PMCID: PMC5110994 DOI: 10.1101/gad.290312.116] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 10/05/2016] [Indexed: 01/20/2023]
Abstract
Gaal et al. examined the relative positions of the ribosomal RNA operons in space. The results show that E. coli bacterial chromosome folding in three dimensions is not dictated entirely by genetic position but rather includes functionally related, genetically distant loci that come into close proximity, with rRNA operons forming a structure reminiscent of the eukaryotic nucleolus. The spatial organization of DNA within the bacterial nucleoid remains unclear. To investigate chromosome organization in Escherichia coli, we examined the relative positions of the ribosomal RNA (rRNA) operons in space. The seven rRNA operons are nearly identical and separated from each other by as much as 180° on the circular genetic map, a distance of ≥2 million base pairs. By inserting binding sites for fluorescent proteins adjacent to the rRNA operons and then examining their positions pairwise in live cells by epifluorescence microscopy, we found that all but rrnC are in close proximity. Colocalization of the rRNA operons required the rrn P1 promoter region but not the rrn P2 promoter or the rRNA structural genes and occurred with and without active transcription. Non-rRNA operon pairs did not colocalize, and the magnitude of their physical separation generally correlated with that of their genetic separation. Our results show that E. coli bacterial chromosome folding in three dimensions is not dictated entirely by genetic position but rather includes functionally related, genetically distant loci that come into close proximity, with rRNA operons forming a structure reminiscent of the eukaryotic nucleolus.
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Affiliation(s)
- Tamas Gaal
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Benjamin P Bratton
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | | | - Alexander Sliwicki
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kristine Sliwicki
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Andrew Vegel
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Rachel Pannu
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Richard L Gourse
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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136
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Feklistov A, Bae B, Hauver J, Lass-Napiorkowska A, Kalesse M, Glaus F, Altmann KH, Heyduk T, Landick R, Darst SA. RNA polymerase motions during promoter melting. Science 2017; 356:863-866. [PMID: 28546214 PMCID: PMC5696265 DOI: 10.1126/science.aam7858] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/27/2017] [Indexed: 12/17/2022]
Abstract
All cellular RNA polymerases (RNAPs), from those of bacteria to those of man, possess a clamp that can open and close, and it has been assumed that the open RNAP separates promoter DNA strands and then closes to establish a tight grip on the DNA template. Here, we resolve successive motions of the initiating bacterial RNAP by studying real-time signatures of fluorescent reporters placed on RNAP and DNA in the presence of ligands locking the clamp in distinct conformations. We report evidence for an unexpected and obligatory step early in the initiation involving a transient clamp closure as a prerequisite for DNA melting. We also present a 2.6-angstrom crystal structure of a late-initiation intermediate harboring a rotationally unconstrained downstream DNA duplex within the open RNAP active site cleft. Our findings explain how RNAP thermal motions control the promoter search and drive DNA melting in the absence of external energy sources.
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Affiliation(s)
- Andrey Feklistov
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Brian Bae
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jesse Hauver
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Agnieszka Lass-Napiorkowska
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, USA
| | - Markus Kalesse
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Brunswick, Germany
| | - Florian Glaus
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Vladimir-Prelog-Weg 1-5/10 8093 Zürich, Switzerland
| | - Karl-Heinz Altmann
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Vladimir-Prelog-Weg 1-5/10 8093 Zürich, Switzerland
| | - Tomasz Heyduk
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, 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
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137
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Albersmeier A, Pfeifer-Sancar K, Rückert C, Kalinowski J. Genome-wide determination of transcription start sites reveals new insights into promoter structures in the actinomycete Corynebacterium glutamicum. J Biotechnol 2017; 257:99-109. [PMID: 28412515 DOI: 10.1016/j.jbiotec.2017.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/06/2017] [Accepted: 04/11/2017] [Indexed: 12/21/2022]
Abstract
The genome-wide identification of transcription start sites, enabled by high-throughput sequencing of a cDNA library enriched for native 5' transcript ends, is ideally suited for the analysis of promoters. Here, the transcriptome of Corynebacterium glutamicum, a non-pathogenic soil bacterium from the actinomycetes branch that is used in industry for the production of amino acids, was analysed by transcriptome sequencing of the 5'-ends of native transcripts. Total RNA samples were harvested from the exponential phase of growth, therefore the study mainly addressed promoters recognized by the main house-keeping sigma factor σA. The identification of 2454 transcription start sites (TSS) allowed the detailed analysis of most promoters recognized by σA and furthermore enabled us to form different promoter groups according to their location relative to protein-coding regions. These groups included leaderless transcripts (546 promoters), short-leadered (<500 bases) transcripts (917), and long-leadered (>500 bases) transcripts (173) as well as intragenic (557) and antisense transcripts (261). All promoters and the individual groups were searched for information, e.g. conserved residues and promoter motifs, and general design features as well as group-specific preferences were identified. A purine was found highly favored as TSS, whereas the -1 position was dominated by pyrimidines. The spacer between TSS and -10 region were consistently 6-7 bases and the -10 promoter motif was generally visible, whereas a recognizable -35 region was only occurring in a smaller fraction of promoters (7.5%) and enriched for leadered and antisense transcripts but depleted for leaderless transcripts. Promoters showing an extended -10 region were especially frequent in case of non-canonical -10 motifs (45.5%). Two bases downstream of the -10 core region, a G was conserved, exceeding 40% abundance in most groups. This fraction reached 74.6% for a group of putative σB-dependent promoters, thus giving a hint to a specific property of these promoters. In addition, the high number of promoters analysed allowed finding of subtle signals only showing up significantly with this large set. This included the observation of a periodically changing A+T-content with maxima spaced by a full turn of the DNA helix. This periodic structure includes the A+T-rich UP-element of bacterial promoters known before but was found to extend up to -100, indicating hitherto unknown constraints influencing promoter architecture and possibly also promoter function.
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Affiliation(s)
- Andreas Albersmeier
- Microbial Genomics Biotechnology, Centrum für Biotechnologie Universität Bielefeld, Sequenz 1, 33615 Bielefeld, Germany
| | - Katharina Pfeifer-Sancar
- Microbial Genomics Biotechnology, Centrum für Biotechnologie Universität Bielefeld, Sequenz 1, 33615 Bielefeld, Germany
| | - Christian Rückert
- Microbial Genomics Biotechnology, Centrum für Biotechnologie Universität Bielefeld, Sequenz 1, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics Biotechnology, Centrum für Biotechnologie Universität Bielefeld, Sequenz 1, 33615 Bielefeld, Germany.
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138
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Mechanism of transcription initiation and promoter escape by E. coli RNA polymerase. Proc Natl Acad Sci U S A 2017; 114:E3032-E3040. [PMID: 28348246 DOI: 10.1073/pnas.1618675114] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To investigate roles of the discriminator and open complex (OC) lifetime in transcription initiation by Escherichia coli RNA polymerase (RNAP; α2ββ'ωσ70), we compare productive and abortive initiation rates, short RNA distributions, and OC lifetime for the λPR and T7A1 promoters and variants with exchanged discriminators, all with the same transcribed region. The discriminator determines the OC lifetime of these promoters. Permanganate reactivity of thymines reveals that strand backbones in open regions of long-lived λPR-discriminator OCs are much more tightly held than for shorter-lived T7A1-discriminator OCs. Initiation from these OCs exhibits two kinetic phases and at least two subpopulations of ternary complexes. Long RNA synthesis (constrained to be single round) occurs only in the initial phase (<10 s), at similar rates for all promoters. Less than half of OCs synthesize a full-length RNA; the majority stall after synthesizing a short RNA. Most abortive cycling occurs in the slower phase (>10 s), when stalled complexes release their short RNA and make another without escaping. In both kinetic phases, significant amounts of 8-nt and 10-nt transcripts are produced by longer-lived, λPR-discriminator OCs, whereas no RNA longer than 7 nt is produced by shorter-lived T7A1-discriminator OCs. These observations and the lack of abortive RNA in initiation from short-lived ribosomal promoter OCs are well described by a quantitative model in which ∼1.0 kcal/mol of scrunching free energy is generated per translocation step of RNA synthesis to overcome OC stability and drive escape. The different length-distributions of abortive RNAs released from OCs with different lifetimes likely play regulatory roles.
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139
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Structural insights into the regulation of Bacillus subtilis SigW activity by anti-sigma RsiW. PLoS One 2017; 12:e0174284. [PMID: 28319136 PMCID: PMC5358783 DOI: 10.1371/journal.pone.0174284] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/06/2017] [Indexed: 11/19/2022] Open
Abstract
Bacillus subtilis SigW is localized to the cell membrane and is inactivated by the tight interaction with anti-sigma RsiW under normal growth conditions. Whereas SigW is discharged from RsiW binding and thus initiates the transcription of its regulon under diverse stress conditions such as antibiotics and alkaline shock. The release and activation of SigW in response to extracytoplasmic signals is induced by the regulated intramembrane proteolysis of RsiW. As a ZAS (Zinc-containing anti-sigma) family protein, RsiW has a CHCC zinc binding motif, which implies that its anti-sigma activity may be regulated by the state of zinc coordination in addition to the proteolytic cleavage of RsiW. To understand the regulation mode of SigW activity by RsiW, we determined the crystal structures of SigW in complex with the cytoplasmic domain of RsiW, and compared the conformation of the CHCC motif in the reduced/zinc binding and the oxidized states. The structures revealed that RsiW inhibits the promoter binding of SigW by interacting with the surface groove of SigW. The interaction between SigW and RsiW is not disrupted by the oxidation of the CHCC motif in RsiW, suggesting that SigW activity might not be regulated by the zinc coordination states of the CHCC motif.
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140
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Structural Basis of RNA Polymerase I Transcription Initiation. Cell 2017; 169:120-131.e22. [DOI: 10.1016/j.cell.2017.03.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/16/2017] [Accepted: 03/01/2017] [Indexed: 11/19/2022]
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141
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Crystal structure of Aquifex aeolicus σ N bound to promoter DNA and the structure of σ N-holoenzyme. Proc Natl Acad Sci U S A 2017; 114:E1805-E1814. [PMID: 28223493 DOI: 10.1073/pnas.1619464114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacterial σ factors confer promoter specificity to the RNA polymerase (RNAP). One alternative σ factor, σN, is unique in its structure and functional mechanism, forming transcriptionally inactive promoter complexes that require activation by specialized AAA+ ATPases. We report a 3.4-Å resolution X-ray crystal structure of a σN fragment in complex with its cognate promoter DNA, revealing the molecular details of promoter recognition by σN The structure allowed us to build and refine an improved σN-holoenzyme model based on previously published 3.8-Å resolution X-ray data. The improved σN-holoenzyme model reveals a conserved interdomain interface within σN that, when disrupted by mutations, leads to transcription activity without activator intervention (so-called bypass mutants). Thus, the structure and stability of this interdomain interface are crucial for the role of σN in blocking transcription activity and in maintaining the activator sensitivity of σN.
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142
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Alekseev S, Nagy Z, Sandoz J, Weiss A, Egly JM, Le May N, Coin F. Transcription without XPB Establishes a Unified Helicase-Independent Mechanism of Promoter Opening in Eukaryotic Gene Expression. Mol Cell 2017; 65:504-514.e4. [DOI: 10.1016/j.molcel.2017.01.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/07/2016] [Accepted: 01/06/2017] [Indexed: 10/20/2022]
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143
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Hubin EA, Fay A, Xu C, Bean JM, Saecker RM, Glickman MS, Darst SA, Campbell EA. Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA. eLife 2017; 6. [PMID: 28067618 PMCID: PMC5302886 DOI: 10.7554/elife.22520] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/07/2017] [Indexed: 02/07/2023] Open
Abstract
RbpA and CarD are essential transcription regulators in mycobacteria. Mechanistic analyses of promoter open complex (RPo) formation establish that RbpA and CarD cooperatively stimulate formation of an intermediate (RP2) leading to RPo; formation of RP2 is likely a bottleneck step at the majority of mycobacterial promoters. Once RPo forms, CarD also disfavors its isomerization back to RP2. We determined a 2.76 Å-resolution crystal structure of a mycobacterial transcription initiation complex (TIC) with RbpA as well as a CarD/RbpA/TIC model. Both CarD and RbpA bind near the upstream edge of the −10 element where they likely facilitate DNA bending and impede transcription bubble collapse. In vivo studies demonstrate the essential role of RbpA, show the effects of RbpA truncations on transcription and cell physiology, and indicate additional functions for RbpA not evident in vitro. This work provides a framework to understand the control of mycobacterial transcription by RbpA and CarD. DOI:http://dx.doi.org/10.7554/eLife.22520.001
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Affiliation(s)
| | - Allison Fay
- Immunology Program, Sloan-Kettering Institute, New York, United States
| | - Catherine Xu
- The Rockefeller University, New York, United States
| | - James M Bean
- Immunology Program, Sloan-Kettering Institute, New York, United States
| | | | - Michael S Glickman
- Immunology Program, Sloan-Kettering Institute, New York, United States.,Division of Infectious Diseases, Memorial Sloan-Kettering Cancer Center, New York, United States
| | - Seth A Darst
- The Rockefeller University, New York, United States
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144
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RNA polymerase gate loop guides the nontemplate DNA strand in transcription complexes. Proc Natl Acad Sci U S A 2016; 113:14994-14999. [PMID: 27956639 DOI: 10.1073/pnas.1613673114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Upon RNA polymerase (RNAP) binding to a promoter, the σ factor initiates DNA strand separation and captures the melted nontemplate DNA, whereas the core enzyme establishes interactions with the duplex DNA in front of the active site that stabilize initiation complexes and persist throughout elongation. Among many core RNAP elements that participate in these interactions, the β' clamp domain plays the most prominent role. In this work, we investigate the role of the β gate loop, a conserved and essential structural element that lies across the DNA channel from the clamp, in transcription regulation. The gate loop was proposed to control DNA loading during initiation and to interact with NusG-like proteins to lock RNAP in a closed, processive state during elongation. We show that the removal of the gate loop has large effects on promoter complexes, trapping an unstable intermediate in which the RNAP contacts with the nontemplate strand discriminator region and the downstream duplex DNA are not yet fully established. We find that although RNAP lacking the gate loop displays moderate defects in pausing, transcript cleavage, and termination, it is fully responsive to the transcription elongation factor NusG. Together with the structural data, our results support a model in which the gate loop, acting in concert with initiation or elongation factors, guides the nontemplate DNA in transcription complexes, thereby modulating their regulatory properties.
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145
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Del Peso Santos T, Shingler V. Inter-sigmulon communication through topological promoter coupling. Nucleic Acids Res 2016; 44:9638-9649. [PMID: 27422872 PMCID: PMC5175336 DOI: 10.1093/nar/gkw639] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/01/2016] [Accepted: 07/06/2016] [Indexed: 12/03/2022] Open
Abstract
Divergent transcription from within bacterial intergenic regions frequently involves promoters dependent on alternative σ-factors. This is the case for the non-overlapping σ70- and σ54-dependent promoters that control production of the substrate-responsive regulator and enzymes for (methyl)phenol catabolism. Here, using an array of in vivo and in vitro assays, we identify transcription-driven supercoiling arising from the σ54-promoter as the mechanism underlying inter-promoter communication that results in stimulation of the activity of the σ70-promoter. The non-overlapping 'back-to-back' configuration of a powerful σ54-promoter and weak σ70-promoter within this system offers a previously unknown means of inter-sigmulon communication that renders the σ70-promoter subservient to signals that elicit σ54-dependent transcription without it possessing a cognate binding site for the σ54-RNA polymerase holoenzyme. This mode of control has the potential to be a prevalent, but hitherto unappreciated, mechanism by which bacteria adjust promoter activity to gain appropriate transcriptional control.
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Affiliation(s)
| | - Victoria Shingler
- Department of Molecular Biology, Umeå University, Umeå SE 90187, Sweden
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146
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Abstract
Repeating sequences generated from RNA gene fusions/ligations dominate ancient life, indicating central importance of building structural complexity in evolving biological systems. A simple and coherent story of life on earth is told from tracking repeating motifs that generate α/β proteins, 2-double-Ψ-β-barrel (DPBB) type RNA polymerases (RNAPs), general transcription factors (GTFs), and promoters. A general rule that emerges is that biological complexity that arises through generation of repeats is often bounded by solubility and closure (i.e., to form a pseudo-dimer or a barrel). Because the first DNA genomes were replicated by DNA template-dependent RNA synthesis followed by RNA template-dependent DNA synthesis via reverse transcriptase, the first DNA replication origins were initially 2-DPBB type RNAP promoters. A simplifying model for evolution of promoters/replication origins via repetition of core promoter elements is proposed. The model can explain why Pribnow boxes in bacterial transcription (i.e., (-12)TATAATG(-6)) so closely resemble TATA boxes (i.e., (-31)TATAAAAG(-24)) in archaeal/eukaryotic transcription. The evolution of anchor DNA sequences in bacterial (i.e., (-35)TTGACA(-30)) and archaeal (BRE(up); BRE for TFB recognition element) promoters is potentially explained. The evolution of BRE(down) elements of archaeal promoters is potentially explained.
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Affiliation(s)
- Zachary F Burton
- a Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA
| | - Kristopher Opron
- b Department of Mathematics , Michigan State University , E. Lansing , MI , USA
| | - Guowei Wei
- b Department of Mathematics , Michigan State University , E. Lansing , MI , USA
| | - James H Geiger
- c Department of Chemistry , Michigan State University , E. Lansing , MI , USA
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147
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Lee J, Borukhov S. Bacterial RNA Polymerase-DNA Interaction-The Driving Force of Gene Expression and the Target for Drug Action. Front Mol Biosci 2016; 3:73. [PMID: 27882317 PMCID: PMC5101437 DOI: 10.3389/fmolb.2016.00073] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/24/2016] [Indexed: 11/17/2022] Open
Abstract
DNA-dependent multisubunit RNA polymerase (RNAP) is the key enzyme of gene expression and a target of regulation in all kingdoms of life. It is a complex multifunctional molecular machine which, unlike other DNA-binding proteins, engages in extensive and dynamic interactions (both specific and nonspecific) with DNA, and maintains them over a distance. These interactions are controlled by DNA sequences, DNA topology, and a host of regulatory factors. Here, we summarize key recent structural and biochemical studies that elucidate the fine details of RNAP-DNA interactions during initiation. The findings of these studies help unravel the molecular mechanisms of promoter recognition and open complex formation, initiation of transcript synthesis and promoter escape. We also discuss most current advances in the studies of drugs that specifically target RNAP-DNA interactions during transcription initiation and elongation.
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Affiliation(s)
- Jookyung Lee
- Department of Cell Biology, Rowan University School of Osteopathic Medicine Stratford, NJ, USA
| | - Sergei Borukhov
- Department of Cell Biology, Rowan University School of Osteopathic Medicine Stratford, NJ, USA
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148
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Davis MC, Kesthely CA, Franklin EA, MacLellan SR. The essential activities of the bacterial sigma factor. Can J Microbiol 2016; 63:89-99. [PMID: 28117604 DOI: 10.1139/cjm-2016-0576] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Transcription is the first and most heavily regulated step in gene expression. Sigma (σ) factors are general transcription factors that reversibly bind RNA polymerase (RNAP) and mediate transcription of all genes in bacteria. σ Factors play 3 major roles in the RNA synthesis initiation process: they (i) target RNAP holoenzyme to specific promoters, (ii) melt a region of double-stranded promoter DNA and stabilize it as a single-stranded open complex, and (iii) interact with other DNA-binding transcription factors to contribute complexity to gene expression regulation schemes. Recent structural studies have demonstrated that when σ factors bind promoter DNA, they capture 1 or more nucleotides that are flipped out of the helical DNA stack and this stabilizes the promoter open-complex intermediate that is required for the initiation of RNA synthesis. This review describes the structure and function of the σ70 family of σ proteins and the essential roles they play in the transcription process.
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Affiliation(s)
- Maria C Davis
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada.,Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Christopher A Kesthely
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada.,Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Emily A Franklin
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada.,Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Shawn R MacLellan
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada.,Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
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149
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Klein G, Stupak A, Biernacka D, Wojtkiewicz P, Lindner B, Raina S. Multiple Transcriptional Factors Regulate Transcription of the rpoE Gene in Escherichia coli under Different Growth Conditions and When the Lipopolysaccharide Biosynthesis Is Defective. J Biol Chem 2016; 291:22999-23019. [PMID: 27629414 DOI: 10.1074/jbc.m116.748954] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Indexed: 12/22/2022] Open
Abstract
The RpoE σ factor is essential for the viability of Escherichia coli RpoE regulates extracytoplasmic functions including lipopolysaccharide (LPS) translocation and some of its non-stoichiometric modifications. Transcription of the rpoE gene is positively autoregulated by EσE and by unknown mechanisms that control the expression of its distally located promoter(s). Mapping of 5' ends of rpoE mRNA identified five new transcriptional initiation sites (P1 to P5) located distal to EσE-regulated promoter. These promoters are activated in response to unique signals. Of these P2, P3, and P4 defined major promoters, recognized by RpoN, RpoD, and RpoS σ factors, respectively. Isolation of trans-acting factors, in vitro transcriptional and gel retardation assays revealed that the RpoN-recognized P2 promoter is positively regulated by a QseE/F two-component system and NtrC activator, whereas the RpoD-regulated P3 promoter is positively regulated by a Rcs system in response to defects in LPS core biosynthesis, overproduction of certain lipoproteins, and the global regulator CRP. Strains synthesizing Kdo2-LA LPS caused up to 7-fold increase in the rpoEP3 activity, which was abrogated in Δ(waaC rcsB). Overexpression of a novel 73-nucleotide sRNA rirA (RfaH interacting RNA) generated by the processing of 5' UTR of the waaQ mRNA induces the rpoEP3 promoter activity concomitant with a decrease in LPS content and defects in the O-antigen incorporation. In the presence of RNA polymerase, RirA binds LPS regulator RfaH known to prevent premature transcriptional termination of waaQ and rfb operons. RirA in excess could titrate out RfaH causing LPS defects and the activation of rpoE transcription.
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Affiliation(s)
- Gracjana Klein
- From the Unit of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdansk, Poland and
| | - Anna Stupak
- From the Unit of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdansk, Poland and
| | - Daria Biernacka
- From the Unit of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdansk, Poland and
| | - Pawel Wojtkiewicz
- From the Unit of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdansk, Poland and
| | - Buko Lindner
- the Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, 23845 Borstel, Germany
| | - Satish Raina
- From the Unit of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233, Gdansk, Poland and
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150
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Xue X, Davis MC, Steeves T, Bishop A, Breen J, MacEacheron A, Kesthely CA, Hsu F, MacLellan SR. Characterization of a protein-protein interaction within the SigO-RsoA two-subunit σ factor: the σ70 region 2.3-like segment of RsoA mediates interaction with SigO. MICROBIOLOGY-SGM 2016; 162:1857-1869. [PMID: 27558998 DOI: 10.1099/mic.0.000358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
σ factors are single subunit general transcription factors that reversibly bind core RNA polymerase and mediate gene-specific transcription in bacteria. Previously, an atypical two-subunit σ factor was identified that activates transcription from a group of related promoters in Bacillus subtilis. Both of the subunits, named SigO and RsoA, share primary sequence similarity with the canonical σ70 family of σ factors and interact with each other and with RNA polymerase subunits. Here we show that the σ70 region 2.3-like segment of RsoA is unexpectedly sufficient for interaction with the amino-terminus of SigO and the β' subunit. A mutational analysis of RsoA identified aromatic residues conserved amongst all RsoA homologues, and often amongst canonical σ factors, that are particularly important for the SigO-RsoA interaction. In a canonical σ factor, region 2.3 amino acids bind non-template strand DNA, trapping the promoter in a single-stranded state required for initiation of transcription. Accordingly, we speculate that RsoA region 2.3 protein-binding activity likely arose from a motif that, at least in its ancestral protein, participated in DNA-binding interactions.
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Affiliation(s)
- Xiaowei Xue
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Maria C Davis
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Thomas Steeves
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Adam Bishop
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Jillian Breen
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | | | | | - FoSheng Hsu
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Shawn R MacLellan
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
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