1
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Zhang TM, Zhu XN, Qin SW, Guo XF, Xing XK, Zhao LF, Tan SK. Potential and application of abortive transcripts as a novel molecular marker of cancers. World J Exp Med 2024; 14:92343. [PMID: 38948416 PMCID: PMC11212745 DOI: 10.5493/wjem.v14.i2.92343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/25/2024] [Accepted: 05/14/2024] [Indexed: 06/19/2024] Open
Abstract
Abortive transcript (AT) is a 2-19 nt long non-coding RNA that is produced in the abortive initiation stage. Abortive initiation was found to be closely related to RNA polymerase through in vitro experiments. Therefore, the distribution of AT length and the scale of abortive initiation are correlated to the promoter, discriminator, and transcription initiation sequence, and can be affected by transcription elongation factors. AT plays an important role in the occurrence and development of various diseases. Here we summarize the discovery of AT, the factors responsible for AT formation, the detection methods and biological functions of AT, to provide new clues for finding potential targets in the early diagnosis and treatment of cancers.
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Affiliation(s)
- Tian-Miao Zhang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin 541199, Guangxi Zhuang Autonomous Region, China
| | - Xiao-Nian Zhu
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin 541199, Guangxi Zhuang Autonomous Region, China
| | - Shao-Wei Qin
- School of Leisure and Health, Guilin Tourism University, Guilin 541006, Guangxi Zhuang Autonomous Region, China
| | - Xue-Feng Guo
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin 541199, Guangxi Zhuang Autonomous Region, China
| | - Xue-Kun Xing
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin 541199, Guangxi Zhuang Autonomous Region, China
| | - Li-Feng Zhao
- School of Leisure and Health, Guilin Tourism University, Guilin 541006, Guangxi Zhuang Autonomous Region, China
| | - Sheng-Kui Tan
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin 541199, Guangxi Zhuang Autonomous Region, China
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2
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Qin S, Wu H, Li C, Yang J, Yan W, He Z, Xing X, Zhang J, Xu X, Zhao L, Su X. Detection of Naturally occurring abortive transcripts by Base-Stacking Hybridization Assisted Ligation and PCR amplification. Biosens Bioelectron 2024; 251:116099. [PMID: 38330773 DOI: 10.1016/j.bios.2024.116099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/13/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
Abortive transcripts (ATs) refer to nascent 2-10 nucleotides (nt) RNAs released by RNA polymerases before synthesizing productive RNAs. The quantitative detection of ATs is important for studying transcription initiation and the biological function of ATs; however, no method is available for the qualitative and quantitative assessment of such ultra-short oligonucleotides (typically shorter than 11 nt) in vivo at present, even with the LNA probes, the detection limit can only reach 11 nt. Here, we demonstrated the base stacking hybridization assisted ligation (BSHAL) technique, combined with TaqMan-MGB qPCR, can detect 4-10 nt ATs with a specificity of nucleotide resolution and a sensitivity of approximately 10 pM. By this technique, we detected endogenous ATs in cell lines, mice plasmas, and mice liver tissues, respectively, and proved that naturally occurring ATs do exist. We found that the 8 nt ATs of HMSB and Gapdh could be used as reference ATs for data normalization in Homo and mouse respectively, and 8 nt ATs of Afp and Gpc3 were suitable for use as plasma biomarkers of Hepatocellular carcinoma in mouse, indicate ATs are promising biomarkers. This study offers opportunities to study ATs and other ultra-short oligonucleotides in biological samples.
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Affiliation(s)
- Shaowei Qin
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Haizhu Wu
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Cailin Li
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Jiarui Yang
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, The Johns Hopkins University, Baltimore, 21218, USA
| | - Weiwei Yan
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Zhigui He
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Xuekun Xing
- College of Public Health, Guilin Medical University, Guilin, 541199, China
| | - Jiayang Zhang
- College of Public Health, Guilin Medical University, Guilin, 541199, China
| | - Xianglin Xu
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Lifeng Zhao
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China.
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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3
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Meier D, Rauch C, Wagner M, Klemm P, Blumenkamp P, Müller R, Ellenberger E, Karia KM, Vecchione S, Serrania J, Lechner M, Fritz G, Goesmann A, Becker A. A MoClo-Compatible Toolbox of ECF Sigma Factor-Based Regulatory Switches for Proteobacterial Chassis. BIODESIGN RESEARCH 2024; 6:0025. [PMID: 38384496 PMCID: PMC10880074 DOI: 10.34133/bdr.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/04/2023] [Indexed: 02/23/2024] Open
Abstract
The construction of complex synthetic gene circuits with predetermined and reliable output depends on orthogonal regulatory parts that do not inadvertently interfere with the host machinery or with other circuit components. Previously, extracytoplasmic function sigma factors (ECFs), a diverse group of alternative sigma factors with distinct promoter specificities, were shown to have great potential as context-independent regulators, but so far, they have only been used in a few model species. Here, we show that the alphaproteobacterium Sinorhizobium meliloti, which has been proposed as a plant-associated bacterial chassis for synthetic biology, has a similar phylogenetic ECF acceptance range as the gammaproteobacterium Escherichia coli. A common set of orthogonal ECF-based regulators that can be used in both bacterial hosts was identified and used to create 2-step delay circuits. The genetic circuits were implemented in single copy in E. coli by chromosomal integration using an established method that utilizes bacteriophage integrases. In S. meliloti, we demonstrated the usability of single-copy pABC plasmids as equivalent carriers of the synthetic circuits. The circuits were either implemented on a single pABC or modularly distributed on 3 such plasmids. In addition, we provide a toolbox containing pABC plasmids compatible with the Golden Gate (MoClo) cloning standard and a library of basic parts that enable the construction of ECF-based circuits in S. meliloti and in E. coli. This work contributes to building a context-independent and species-overarching ECF-based toolbox for synthetic biology applications.
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Affiliation(s)
- Doreen Meier
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Christian Rauch
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Marcel Wagner
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Paul Klemm
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Patrick Blumenkamp
- Bioinformatics and Systems Biology,
Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Raphael Müller
- Bioinformatics and Systems Biology,
Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Eric Ellenberger
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Kinnari M. Karia
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Stefano Vecchione
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Javier Serrania
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Marcus Lechner
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Georg Fritz
- The University of Western Australia, School of Molecular Sciences, Perth, Australia
| | - Alexander Goesmann
- Bioinformatics and Systems Biology,
Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
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4
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Pal S, Biswas D. Promoter-proximal regulation of gene transcription: Key factors involved and emerging role of general transcription factors in assisting productive elongation. Gene 2023:147571. [PMID: 37331491 DOI: 10.1016/j.gene.2023.147571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023]
Abstract
The pausing of RNA polymerase II (Pol II) at the promoter-proximal sites is a key rate-limiting step in gene expression. Cells have dedicated a specific set of proteins that sequentially establish pause and then release the Pol II from promoter-proximal sites. A well-controlled pausing and subsequent release of Pol II is crucial for thefine tuning of expression of genes including signal-responsive and developmentally-regulated ones. The release of paused Pol II broadly involves its transition from initiation to elongation. In this review article, we will discuss the phenomenon of Pol II pausing, the underlying mechanism, and also the role of different known factors, with an emphasis on general transcription factors, involved in this overall regulation. We will further discuss some recent findings suggesting a possible role (underexplored) of initiation factors in assisting the transition of transcriptionally-engaged paused Pol II into productive elongation.
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Affiliation(s)
- Sujay Pal
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata - 32, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata - 32, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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5
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Schmitz C, Madej M, Nowakowska Z, Cuppari A, Jacula A, Ksiazek M, Mikruta K, Wisniewski J, Pudelko-Malik N, Saran A, Zeytuni N, Mlynarz P, Lamont RJ, Usón I, Siksnys V, Potempa J, Solà M. Response regulator PorX coordinates oligonucleotide signalling and gene expression to control the secretion of virulence factors. Nucleic Acids Res 2022; 50:12558-12577. [PMID: 36464236 PMCID: PMC9757075 DOI: 10.1093/nar/gkac1103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/27/2022] [Accepted: 11/08/2022] [Indexed: 12/07/2022] Open
Abstract
The PglZ family of proteins belongs to the alkaline phosphatase superfamily, which consists of metallohydrolases with limited sequence identity but similar metal-coordination architectures in otherwise divergent active sites. Proteins with a well-defined PglZ domain are ubiquitous among prokaryotes as essential components of BREX phage defence systems and two-component systems (TCSs). Whereas other members of the alkaline phosphatase superfamily are well characterized, the activity, structure and biological function of PglZ family proteins remain unclear. We therefore investigated the structure and function of PorX, an orphan response regulator of the Porphyromonas gingivalis TCS containing a putative PglZ effector domain. The crystal structure of PorX revealed a canonical receiver domain, a helical bundle, and an unprecedented PglZ domain, similar to the general organization of the phylogenetically related BREX-PglZ proteins. The PglZ domain of PorX features an active site cleft suitable for large substrates. An extensive search for substrates revealed that PorX is a phosphodiesterase that acts on cyclic and linear oligonucleotides, including signalling molecules such as cyclic oligoadenylates. These results, combined with mutagenesis, biophysical and enzymatic analysis, suggest that PorX coordinates oligonucleotide signalling pathways and indirectly regulates gene expression to control the secretion of virulence factors.
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Affiliation(s)
- Claus Schmitz
- Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Barcelona E-08028, Spain
| | - Mariusz Madej
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków PL-30-387, Poland
| | - Zuzanna Nowakowska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków PL-30-387, Poland
| | - Anna Cuppari
- Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Barcelona E-08028, Spain
| | - Anna Jacula
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków PL-30-387, Poland
| | - Miroslaw Ksiazek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków PL-30-387, Poland
| | - Katarzyna Mikruta
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków PL-30-387, Poland
| | - Jerzy Wisniewski
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw PL-50-370, Poland
| | - Natalia Pudelko-Malik
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw PL-50-370, Poland
| | - Anshu Saran
- Department of Anatomy and Cell Biology, McGill University, Montréal, Quebec H3A 0C7, Canada
| | - Natalie Zeytuni
- Department of Anatomy and Cell Biology, McGill University, Montréal, Quebec H3A 0C7, Canada
| | - Piotr Mlynarz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw PL-50-370, Poland
| | - Richard J Lamont
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY 40202, USA
| | - Isabel Usón
- Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Barcelona E-08028, Spain
- ICREA Institució Catalana de Recerca i Estudis Avançats, Barcelona E-08010, Spain
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków PL-30-387, Poland
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY 40202, USA
| | - Maria Solà
- Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Barcelona E-08028, Spain
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6
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Shao W, Bi X, Pan Y, Gao B, Wu J, Yin Y, Liu Z, Peng M, Zhang W, Jiang X, Ren W, Xu Y, Wu Z, Wang K, Zhan G, Lu JY, Han X, Li T, Wang J, Li G, Deng H, Li B, Shen X. Phase separation of RNA-binding protein promotes polymerase binding and transcription. Nat Chem Biol 2022; 18:70-80. [PMID: 34916619 DOI: 10.1038/s41589-021-00904-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/22/2021] [Indexed: 01/27/2023]
Abstract
An RNA-involved phase-separation model has been proposed for transcription control. However, the molecular links that connect RNA to the transcription machinery remain missing. Here we find that RNA-binding proteins (RBPs) constitute half of the chromatin proteome in embryonic stem cells (ESCs), some being colocalized with RNA polymerase (Pol) II at promoters and enhancers. Biochemical analyses of representative RBPs show that the paraspeckle protein PSPC1 inhibits the RNA-induced premature release of Pol II, and makes use of RNA as multivalent molecules to enhance the formation of transcription condensates and subsequent phosphorylation and release of Pol II. This synergistic interplay enhances polymerase engagement and activity via the RNA-binding and phase-separation activities of PSPC1. In ESCs, auxin-induced acute degradation of PSPC1 leads to genome-wide defects in Pol II binding and nascent transcription. We propose that promoter-associated RNAs and their binding proteins synergize the phase separation of polymerase condensates to promote active transcription.
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Affiliation(s)
- Wen Shao
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Xianju Bi
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Yixuan Pan
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Boyang Gao
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Jun Wu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yafei Yin
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Zhimin Liu
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Mengyuan Peng
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenhao Zhang
- Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xu Jiang
- Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wenlin Ren
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Yanhui Xu
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Zhongyang Wu
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Kaili Wang
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Ge Zhan
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - J Yuyang Lu
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Xue Han
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Tong Li
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Guohong Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Haiteng Deng
- Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Bing Li
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xiaohua Shen
- School of Medicine and School of Life Sciences, Tsinghua University; Tsinghua-Peking Joint Center for Life Sciences, Beijing, China.
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7
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Abstract
To exert their functions, RNAs adopt diverse structures, ranging from simple secondary to complex tertiary and quaternary folds. In vivo, RNA folding starts with RNA transcription, and a wide variety of processes are coupled to co-transcriptional RNA folding events, including the regulation of fundamental transcription dynamics, gene regulation by mechanisms like attenuation, RNA processing or ribonucleoprotein particle formation. While co-transcriptional RNA folding and associated co-transcriptional processes are by now well accepted as pervasive regulatory principles in all organisms, investigations into the role of the transcription machinery in co-transcriptional folding processes have so far largely focused on effects of the order in which RNA regions are produced and of transcription kinetics. Recent structural and structure-guided functional analyses of bacterial transcription complexes increasingly point to an additional role of RNA polymerase and associated transcription factors in supporting co-transcriptional RNA folding by fostering or preventing strategic contacts to the nascent transcripts. In general, the results support the view that transcription complexes can act as RNA chaperones, a function that has been suggested over 30 years ago. Here, we discuss transcription complexes as RNA chaperones based on recent examples from bacterial transcription.
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Affiliation(s)
- Nelly Said
- Freie Universität Berlin, Department Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Berlin, Germany
| | - Markus C Wahl
- Freie Universität Berlin, Department Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Berlin, Germany.,Helmholtz-Zentrum Berlin Für Materialien Und Energie, Macromolecular Crystallography, Berlin, Germany
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8
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Single-cell measurement of plasmid copy number and promoter activity. Nat Commun 2021; 12:1475. [PMID: 33674569 PMCID: PMC7935883 DOI: 10.1038/s41467-021-21734-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 02/08/2021] [Indexed: 01/31/2023] Open
Abstract
Accurate measurements of promoter activities are crucial for predictably building genetic systems. Here we report a method to simultaneously count plasmid DNA, RNA transcripts, and protein expression in single living bacteria. From these data, the activity of a promoter in units of RNAP/s can be inferred. This work facilitates the reporting of promoters in absolute units, the variability in their activity across a population, and their quantitative toll on cellular resources, all of which provide critical insights for cellular engineering.
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9
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Kunthavai PC, Kannan M, Ragunathan P. Structural analysis of alternate sigma factor ComX with RpoC, RpoB and its cognate CIN promoter reveals a distinctive promoter melting mechanism. J Biomol Struct Dyn 2021; 40:6272-6285. [PMID: 33554755 DOI: 10.1080/07391102.2021.1882338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Alternate sigma factors play a major role in the survival of pathogenic bacteria such as Streptococcus pyogenes in adverse environment conditions. Stress induced sigma factors mediate gene expression under conditions of pathogenesis, dormancy and unusual environmental cues. In the present work, ComX, an alternate sigma factor from S. pyogenes has been characterized. The structures of ComX, RpoB β subunit and RpoC β' subunit of RNA polymerase have been predicted using comparative and homology modelling respectively and validated. Attempts have been made to study RpoB-RpoC-ComX complex interactions with Double Strand (DS) and Single Strand (SS) promoter regions. Stability of these complexes and the promoter melting mechanism have been analysed using Molecular Dynamic (MD) simulations. This study suggests that ComX, although identifies promoter analogous to the alternate sigma factor SigH of M. tuberculosis, follows a distinctive promoter flip out mechanism.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- P C Kunthavai
- Centre of Advanced study in Crystallography and Biophysics, University of Madras, Chennai, India
| | - Muthu Kannan
- Department of Biological sciences, National University of Singapore, Singapore, Singapore
| | - Preethi Ragunathan
- Centre of Advanced study in Crystallography and Biophysics, University of Madras, Chennai, India
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10
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Mejía-Almonte C, Busby SJW, Wade JT, van Helden J, Arkin AP, Stormo GD, Eilbeck K, Palsson BO, Galagan JE, Collado-Vides J. Redefining fundamental concepts of transcription initiation in bacteria. Nat Rev Genet 2020; 21:699-714. [PMID: 32665585 PMCID: PMC7990032 DOI: 10.1038/s41576-020-0254-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2020] [Indexed: 12/15/2022]
Abstract
Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles. In this Expert Recommendation, we suggest precise, updated definitions that support a logical, consistent conceptual framework of bacterial gene regulation, focusing on transcription initiation. The resulting concepts can be formalized by ontologies for computational modelling, laying the foundation for improved bioinformatics tools, knowledge-based resources and scientific communication. Thus, this work will help researchers construct better predictive models, with different formalisms, that will be useful in engineering, synthetic biology, microbiology and genetics.
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Affiliation(s)
- Citlalli Mejía-Almonte
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México
| | | | - Joseph T Wade
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Jacques van Helden
- Aix-Marseille University, INSERM UMR S 1090, Theory and Approaches of Genome Complexity (TAGC), Marseille, France
- CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Evry, France
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Gary D Stormo
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - James E Galagan
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Julio Collado-Vides
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
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11
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Diverse and unified mechanisms of transcription initiation in bacteria. Nat Rev Microbiol 2020; 19:95-109. [PMID: 33122819 DOI: 10.1038/s41579-020-00450-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
Transcription of DNA is a fundamental process in all cellular organisms. The enzyme responsible for transcription, RNA polymerase, is conserved in general architecture and catalytic function across the three domains of life. Diverse mechanisms are used among and within the different branches to regulate transcription initiation. Mechanistic studies of transcription initiation in bacteria are especially amenable because the promoter recognition and melting steps are much less complicated than in eukaryotes or archaea. Also, bacteria have critical roles in human health as pathogens and commensals, and the bacterial RNA polymerase is a proven target for antibiotics. Recent biophysical studies of RNA polymerases and their inhibition, as well as transcription initiation and transcription factors, have detailed the mechanisms of transcription initiation in phylogenetically diverse bacteria, inspiring this Review to examine unifying and diverse themes in this process.
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12
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Miura M, Chen H. CUT&RUN detects distinct DNA footprints of RNA polymerase II near the transcription start sites. Chromosome Res 2020; 28:381-393. [PMID: 33070289 PMCID: PMC7691310 DOI: 10.1007/s10577-020-09643-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 11/30/2022]
Abstract
CUT&RUN is a powerful tool to study protein-DNA interactions in vivo. DNA fragments cleaved by the targeted micrococcal nuclease identify the footprints of DNA-binding proteins on the chromatin. We performed CUT&RUN on human lung carcinoma cell line A549 maintained in a multi-well cell culture plate to profile RNA polymerase II. Long (> 270 bp) DNA fragments released by CUT&RUN corresponded to the bimodal peak around the transcription start sites, as previously seen with chromatin immunoprecipitation. However, we found that short (< 120 bp) fragments identify a well-defined peak localised at the transcription start sites. This distinct DNA footprint of short fragments, which constituted only about 5% of the total reads, suggests the transient positioning of RNA polymerase II before promoter-proximal pausing, which has not been detected in the physiological settings by standard chromatin immunoprecipitation. We showed that the positioning of the large-size-class DNA footprints around the short-fragment peak was associated with the directionality of transcription, demonstrating the biological significance of distinct CUT&RUN footprints of RNA polymerase II.
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Affiliation(s)
- Michi Miura
- State Key Laboratory for Emerging Infectious Diseases and Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China.
| | - Honglin Chen
- State Key Laboratory for Emerging Infectious Diseases and Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
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13
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Zuo Y, De S, Feng Y, Steitz TA. Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation. iScience 2020; 23:101445. [PMID: 32829286 PMCID: PMC7452309 DOI: 10.1016/j.isci.2020.101445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/27/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023] Open
Abstract
In bacteria, the dissociable σ subunit of the RNA polymerase (RNAP) is responsible for initiating RNA synthesis from specific DNA sites. As nascent RNA grows, downstream DNA unwinds and is pulled into the RNAP, causing stress accumulation and initiation complex destabilization. Processive transcription elongation requires at least partial separation of the σ factor from the RNAP core enzyme. Here, we present a series of transcription complexes captured between the early initiation and elongation phases via in-crystal RNA synthesis and cleavage. Crystal structures of these complexes indicate that stress accumulation during transcription initiation is not due to clashing of the growing nascent RNA with the σ3.2 loop, but results from scrunching of the template strand DNA that is contained inside the RNAP by the σ3 domain. Our results shed light on how scrunching of template-strand DNA drives both abortive initiation and σ-RNAP core separation to transition transcription from initiation to elongation.
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Affiliation(s)
- Yuhong Zuo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Swastik De
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Howard Hughes Medical Institute, New Haven, CT 06510, USA
| | - Yingang Feng
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Laoshan District, Qingdao, Shandong 266101, China
| | - Thomas A. Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Howard Hughes Medical Institute, New Haven, CT 06510, USA
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
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14
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Balzer Le S, Onsager I, Lorentzen JA, Lale R. Dual UTR-A novel 5' untranslated region design for synthetic biology applications. Synth Biol (Oxf) 2020; 5:ysaa006. [PMID: 32995550 PMCID: PMC7476403 DOI: 10.1093/synbio/ysaa006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 04/29/2020] [Accepted: 05/29/2020] [Indexed: 01/07/2023] Open
Abstract
Bacterial 5' untranslated regions of mRNA (UTR) involve in a complex regulation of gene expression; however, the exact sequence features contributing to gene regulation are not yet fully understood. In this study, we report the design of a novel 5' UTR, dual UTR, utilizing the transcriptional and translational characteristics of 5' UTRs in a single expression cassette. The dual UTR consists of two 5' UTRs, each separately leading to either increase in transcription or translation of the reporter, that are separated by a spacer region, enabling de novo translation initiation. We rationally create dual UTRs with a wide range of expression profiles and demonstrate the functionality of the novel design concept in Escherichia coli and Pseudomonas putida using different promoter systems and coding sequences. Overall, we demonstrate the application potential of dual UTR design concept in various synthetic biology applications ranging from fine-tuning of gene expression to maximization of protein production.
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Affiliation(s)
- Simone Balzer Le
- PhotoSynLab, Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Ingerid Onsager
- PhotoSynLab, Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Jon Andreas Lorentzen
- PhotoSynLab, Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Rahmi Lale
- PhotoSynLab, Department of Biotechnology, Faculty of Natural Sciences, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
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15
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Cook PR, Marenduzzo D. Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations. Nucleic Acids Res 2019; 46:9895-9906. [PMID: 30239812 PMCID: PMC6212781 DOI: 10.1093/nar/gky763] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 09/14/2018] [Indexed: 12/29/2022] Open
Abstract
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and topologically-associating domains (TADs), to contact domains stabilized by cohesin and CTCF. However, molecular mechanisms underlying this folding, and the way folding affects transcriptional activity, remain obscure. Here we review physical principles driving proteins bound to long polymers into clusters surrounded by loops, and present a parsimonious yet comprehensive model for the way the organization determines function. We argue that clusters of active RNA polymerases and their transcription factors are major architectural features; then, contact domains, TADs and compartments just reflect one or more loops and clusters. We suggest tethering a gene close to a cluster containing appropriate factors—a transcription factory—increases the firing frequency, and offer solutions to many current puzzles concerning the actions of enhancers, super-enhancers, boundaries and eQTLs (expression quantitative trait loci). As a result, the activity of any gene is directly influenced by the activity of other transcription units around it in 3D space, and this is supported by Brownian-dynamics simulations of transcription factors binding to cognate sites on long polymers.
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Affiliation(s)
- Peter R Cook
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Davide Marenduzzo
- SUPA, School of Physics, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
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16
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Abstract
In all living organisms, the flow of genetic information is a two-step process: first DNA is transcribed into RNA, which is subsequently used as template for protein synthesis during translation. In bacteria, archaea and eukaryotes, transcription is carried out by multi-subunit RNA polymerases (RNAPs) sharing a conserved architecture of the RNAP core. RNAPs catalyse the highly accurate polymerisation of RNA from NTP building blocks, utilising DNA as template, being assisted by transcription factors during the initiation, elongation and termination phase of transcription. The complexity of this highly dynamic process is reflected in the intricate network of protein-protein and protein-nucleic acid interactions in transcription complexes and the substantial conformational changes of the RNAP as it progresses through the transcription cycle.In this chapter, we will first briefly describe the early work that led to the discovery of multisubunit RNAPs. We will then discuss the three-dimensional organisation of RNAPs from the bacterial, archaeal and eukaryotic domains of life, highlighting the conserved nature, but also the domain-specific features of the transcriptional apparatus. Another section will focus on transcription factors and their role in regulating the RNA polymerase throughout the different phases of the transcription cycle. This includes a discussion of the molecular mechanisms and dynamic events that govern transcription initiation, elongation and termination.
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17
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Agarwal S, Franco E. Enzyme-Driven Assembly and Disassembly of Hybrid DNA-RNA Nanotubes. J Am Chem Soc 2019; 141:7831-7841. [PMID: 31042366 DOI: 10.1021/jacs.9b01550] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Living cells have the ability to control the dynamics of responsive assemblies such as the cytoskeleton by temporally activating and deactivating inert precursors. While DNA nanotechnology has demonstrated many synthetic supramolecular assemblies that rival biological ones in size and complexity, dynamic control of their formation is still challenging. Taking inspiration from nature, we developed a DNA-RNA nanotube system whose assembly and disassembly can be temporally controlled at physiological temperature using transcriptional programs. Nanotubes assemble when inert DNA monomers are directly and selectively activated by RNA molecules that become embedded in the structure, producing hybrid DNA-RNA assemblies. The reactions and molecular programs controlling nanotube formation are fueled by enzymes that produce or degrade RNA. We show that the speed of assembly and disassembly of the nanotubes can be controlled by tuning various reaction parameters in the transcriptional programs. We anticipate that these hybrid structures are a starting point to build integrated biological circuits and functional scaffolds inside natural and artificial cells, where RNA produced by gene networks could fuel the assembly of nucleic acid components on demand.
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Affiliation(s)
- Siddharth Agarwal
- Department of Mechanical Engineering , University of California at Riverside , Riverside , California 90095 , United States
| | - Elisa Franco
- Department of Mechanical Engineering , University of California at Riverside , Riverside , California 90095 , United States
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18
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Fouqueau T, Blombach F, Cackett G, Carty AE, Matelska DM, Ofer S, Pilotto S, Phung DK, Werner F. The cutting edge of archaeal transcription. Emerg Top Life Sci 2018; 2:517-533. [PMID: 33525828 PMCID: PMC7289017 DOI: 10.1042/etls20180014] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/01/2018] [Accepted: 10/04/2018] [Indexed: 12/26/2022]
Abstract
The archaeal RNA polymerase (RNAP) is a double-psi β-barrel enzyme closely related to eukaryotic RNAPII in terms of subunit composition and architecture, promoter elements and basal transcription factors required for the initiation and elongation phase of transcription. Understanding archaeal transcription is, therefore, key to delineate the universally conserved fundamental mechanisms of transcription as well as the evolution of the archaeo-eukaryotic transcription machineries. The dynamic interplay between RNAP subunits, transcription factors and nucleic acids dictates the activity of RNAP and ultimately gene expression. This review focusses on recent progress in our understanding of (i) the structure, function and molecular mechanisms of known and less characterized factors including Elf1 (Elongation factor 1), NusA (N-utilization substance A), TFS4, RIP and Eta, and (ii) their evolution and phylogenetic distribution across the expanding tree of Archaea.
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Affiliation(s)
- Thomas Fouqueau
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Fabian Blombach
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Gwenny Cackett
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Alice E Carty
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Dorota M Matelska
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Sapir Ofer
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Simona Pilotto
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Duy Khanh Phung
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Finn Werner
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
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19
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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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20
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Interplay between σ region 3.2 and secondary channel factors during promoter escape by bacterial RNA polymerase. Biochem J 2017; 474:4053-4064. [DOI: 10.1042/bcj20170436] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 11/01/2017] [Accepted: 11/03/2017] [Indexed: 12/29/2022]
Abstract
In bacterial RNA polymerase (RNAP), conserved region 3.2 of the σ subunit was proposed to contribute to promoter escape by interacting with the 5′-end of nascent RNA, thus facilitating σ dissociation. RNAP activity during transcription initiation can also be modulated by protein factors that bind within the secondary channel and reach the enzyme active site. To monitor the kinetics of promoter escape in real time, we used a molecular beacon assay with fluorescently labeled σ70 subunit of Escherichia coli RNAP. We show that substitutions and deletions in σ region 3.2 decrease the rate of promoter escape and lead to accumulation of inactive complexes during transcription initiation. Secondary channel factors differentially regulate this process depending on the promoter and mutations in σ region 3.2. GreA generally increase the rate of promoter escape; DksA also stimulates promoter escape on certain templates, while GreB either stimulates or inhibits this process depending on the template. When observed, the stimulation of promoter escape correlates with the accumulation of stressed transcription complexes with scrunched DNA, while changes in the RNA 5′-end structure modulate promoter clearance. Thus, the initiation-to-elongation transition is controlled by a complex interplay between RNAP-binding protein factors and the growing RNA chain.
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21
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The special existences: nanoRNA and nanoRNase. Microbiol Res 2017; 207:134-139. [PMID: 29458847 DOI: 10.1016/j.micres.2017.11.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/23/2017] [Accepted: 11/25/2017] [Indexed: 12/21/2022]
Abstract
To adapt to a wide range of nutritional and environmental changes, cells must adjust their gene expression profiles. This process is completed by the frequent transcription and rapid degradation of mRNA. mRNA decay is initiated by a series of endo- and exoribonucleases. These enzymes leave behind 2- to 5-nt-long oligoribonucleotides termed "nanoRNAs" that are degraded by specific nanoRNases; the degradation of nanoRNA is essential because nanoRNA can mediate the priming of transcription initiation that is harmful for the cell via an unknown mechanism. Identified nanoRNases include Orn in E. coli, NrnA and NrnB in B. subtilis, and NrnC in Bartonella. Even though these nanoRNases can degrade nanoRNA specifically into mononucleotides, the biochemical features, structural features and functional mechanisms of these enzymes are different. Sequence analysis has identified homologs of these nanoRNases in different bacteria, including Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, Firmicutes and Cyanobacteria. However, there are several bacteria, such as those belonging to the class Thermolithobacteria, that do not have homologs of these nanoRNases. In this paper, the source of nanoRNA, the features of different kinds of nanoRNases and the distribution of these enzymes in prokaryotes are described in detail.
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22
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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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23
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Stewart JM, Subramanian HKK, Franco E. Self-assembly of multi-stranded RNA motifs into lattices and tubular structures. Nucleic Acids Res 2017; 45:5449-5457. [PMID: 28204562 PMCID: PMC5435959 DOI: 10.1093/nar/gkx063] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 01/31/2017] [Indexed: 01/20/2023] Open
Abstract
Rational design of nucleic acid molecules yields self-assembling scaffolds with increasing complexity, size and functionality. It is an open question whether design methods tailored to build DNA nanostructures can be adapted to build RNA nanostructures with comparable features. Here we demonstrate the formation of RNA lattices and tubular assemblies from double crossover (DX) tiles, a canonical motif in DNA nanotechnology. Tubular structures can exceed 1 μm in length, suggesting that this DX motif can produce very robust lattices. Some of these tubes spontaneously form with left-handed chirality. We obtain assemblies by using two methods: a protocol where gel-extracted RNA strands are slowly annealed, and a one-pot transcription and anneal procedure. We identify the tile nick position as a structural requirement for lattice formation. Our results demonstrate that stable RNA structures can be obtained with design tools imported from DNA nanotechnology. These large assemblies could be potentially integrated with a variety of functional RNA motifs for drug or nanoparticle delivery, or for colocalization of cellular components.
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Affiliation(s)
- Jaimie Marie Stewart
- Department of Bioengineering, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Hari K K Subramanian
- Department of Mechanical Engineering, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Elisa Franco
- Department of Mechanical Engineering, University of California, 900 University Avenue, Riverside, CA 92521, USA
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24
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Structural Basis for the Bidirectional Activity of Bacillus nanoRNase NrnA. Sci Rep 2017; 7:11085. [PMID: 28894100 PMCID: PMC5593865 DOI: 10.1038/s41598-017-09403-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/24/2017] [Indexed: 12/21/2022] Open
Abstract
NanoRNAs are RNA fragments 2 to 5 nucleotides in length that are generated as byproducts of RNA degradation and abortive transcription initiation. Cells have specialized enzymes to degrade nanoRNAs, such as the DHH phosphoesterase family member NanoRNase A (NrnA). This enzyme was originally identified as a 3′ → 5′ exonuclease, but we show here that NrnA is bidirectional, degrading 2–5 nucleotide long RNA oligomers from the 3′ end, and longer RNA substrates from the 5′ end. The crystal structure of Bacillus subtilis NrnA reveals a dynamic bi-lobal architecture, with the catalytic N-terminal DHH domain linked to the substrate binding C-terminal DHHA1 domain via an extended linker. Whereas this arrangement is similar to the structure of RecJ, a 5′ → 3′ DHH family DNase and other DHH family nanoRNases, Bacillus NrnA has gained an extended substrate-binding patch that we posit is responsible for its 3′ → 5′ activity.
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25
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Alhadid Y, Chung S, Lerner E, Taatjes DJ, Borukhov S, Weiss S. Studying transcription initiation by RNA polymerase with diffusion-based single-molecule fluorescence. Protein Sci 2017; 26:1278-1290. [PMID: 28370550 PMCID: PMC5477543 DOI: 10.1002/pro.3160] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/11/2017] [Accepted: 03/13/2017] [Indexed: 01/30/2023]
Abstract
Over the past decade, fluorescence-based single-molecule studies significantly contributed to characterizing the mechanism of RNA polymerase at different steps in transcription, especially in transcription initiation. Transcription by bacterial DNA-dependent RNA polymerase is a multistep process that uses genomic DNA to synthesize complementary RNA molecules. Transcription initiation is a highly regulated step in E. coli, but it has been challenging to study its mechanism because of its stochasticity and complexity. In this review, we describe how single-molecule approaches have contributed to our understanding of transcription and have uncovered mechanistic details that were not observed in conventional assays because of ensemble averaging.
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Affiliation(s)
- Yazan Alhadid
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, California, 90095
| | - SangYoon Chung
- Department of Chemistry & Biochemistry, University of California, Los Angeles, California, 90095
| | - Eitan Lerner
- Department of Chemistry & Biochemistry, University of California, Los Angeles, California, 90095
| | - Dylan J Taatjes
- Department of Chemistry & Biochemistry, University of Colorado, Boulder, Colorado, 80303
| | - Sergei Borukhov
- Rowan University School of Osteopathic Medicine, Stratford, New Jersey, 08084
| | - Shimon Weiss
- Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, California, 90095
- Department of Chemistry & Biochemistry, University of California, Los Angeles, California, 90095
- Molecular Biology Institute (MBI), University of California, Los Angeles, California, 90095
- California NanoSystems Institute, University of California, Los Angeles, California, 90095
- Department of Physiology, University of California, Los Angeles, California, 90095
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26
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Marcus JI, Hassoun S, Nair NU. Computational prediction of functional abortive RNA in E. coli. Genomics 2017; 109:196-203. [PMID: 28347827 DOI: 10.1016/j.ygeno.2017.03.003] [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: 09/30/2016] [Revised: 02/24/2017] [Accepted: 03/22/2017] [Indexed: 11/26/2022]
Abstract
Failure by RNA polymerase to break contacts with promoter DNA results in release of bound RNA and re-initiation of transcription. These abortive RNAs were assumed to be non-functional but have recently been shown to affect termination in bacteriophage T7. Little is known about the functional role of these RNA in other genetic models. Using a computational approach, we investigated whether abortive RNA could exert function in E. coli. Fragments generated from 3780 transcription units were used as query sequences within their respective transcription units to search for possible binding sites. Sites that fell within known regulatory features were then ranked based upon the free energy of hybridization to the abortive. We further hypothesize about mechanisms of regulatory action for a select number of likely matches. Future experimental validation of these putative abortive-mRNA pairs may confirm our findings and promote exploration of functional abortive RNAs (faRNAs) in natural and synthetic systems.
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Affiliation(s)
- Jeremy I Marcus
- Department of Computer Science, Tufts University, Medford, MA 02155, United States
| | - Soha Hassoun
- Department of Computer Science, Tufts University, Medford, MA 02155, United States; Department of Chemical and Biological Engineering, Tufts University, Medford, MA 02155, United States
| | - Nikhil U Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA 02155, United States.
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27
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Lerner E, Ingargiola A, Lee JJ, Borukhov S, Michalet X, Weiss S. Different types of pausing modes during transcription initiation. Transcription 2017; 8:242-253. [PMID: 28332923 DOI: 10.1080/21541264.2017.1308853] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
In many cases, initiation is rate limiting to transcription. This due in part to the multiple cycles of abortive transcription that delay promoter escape and the transition from initiation to elongation. Pausing of transcription in initiation can further delay promoter escape. The previously hypothesized pausing in initiation was confirmed by two recent studies from Duchi et al. 1 and from Lerner, Chung et al. 2 In both studies, pausing is attributed to a lack of forward translocation of the nascent transcript during initiation. However, the two works report on different pausing mechanisms. Duchi et al. report on pausing that occurs during initiation predominantly on-pathway of transcript synthesis. Lerner, Chung et al. report on pausing during initiation as a result of RNAP backtracking, which is off-pathway to transcript synthesis. Here, we discuss these studies, together with additional experimental results from single-molecule FRET focusing on a specific distance within the transcription bubble. We show that the results of these studies are complementary to each other and are consistent with a model involving two types of pauses in initiation: a short-lived pause that occurs in the translocation of a 6-mer nascent transcript and a long-lived pause that occurs as a result of 1-2 nucleotide backtracking of a 7-mer transcript.
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Affiliation(s)
- Eitan Lerner
- a Department of Chemistry & Biochemistry , University of California , Los Angeles , CA , USA
| | - Antonino Ingargiola
- a Department of Chemistry & Biochemistry , University of California , Los Angeles , CA , USA
| | - Jookyung J Lee
- b Rowan University School of Osteopathic Medicine , Stratford , NJ , USA
| | - Sergei Borukhov
- b Rowan University School of Osteopathic Medicine , Stratford , NJ , USA
| | - Xavier Michalet
- a Department of Chemistry & Biochemistry , University of California , Los Angeles , CA , USA
| | - Shimon Weiss
- a Department of Chemistry & Biochemistry , University of California , Los Angeles , CA , USA.,c Molecular Biology Institute , University of California , Los Angeles , CA , USA.,d Department of Physiology , University of California , Los Angeles , CA , USA
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28
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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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29
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Backtracked and paused transcription initiation intermediate of Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A 2016; 113:E6562-E6571. [PMID: 27729537 DOI: 10.1073/pnas.1605038113] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Initiation is a highly regulated, rate-limiting step in transcription. We used a series of approaches to examine the kinetics of RNA polymerase (RNAP) transcription initiation in greater detail. Quenched kinetics assays, in combination with gel-based assays, showed that RNAP exit kinetics from complexes stalled at later stages of initiation (e.g., from a 7-base transcript) were markedly slower than from earlier stages (e.g., from a 2- or 4-base transcript). In addition, the RNAP-GreA endonuclease accelerated transcription kinetics from otherwise delayed initiation states. Further examination with magnetic tweezers transcription experiments showed that RNAP adopted a long-lived backtracked state during initiation and that the paused-backtracked initiation intermediate was populated abundantly at physiologically relevant nucleoside triphosphate (NTP) concentrations. The paused intermediate population was further increased when the NTP concentration was decreased and/or when an imbalance in NTP concentration was introduced (situations that mimic stress). Our results confirm the existence of a previously hypothesized paused and backtracked RNAP initiation intermediate and suggest it is biologically relevant; furthermore, such intermediates could be exploited for therapeutic purposes and may reflect a conserved state among paused, initiating eukaryotic RNA polymerase II enzymes.
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30
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Šimčíková M, Alves CPA, Brito L, Prather KLJ, Prazeres DMF, Monteiro GA. Improvement of DNA minicircle production by optimization of the secondary structure of the 5′-UTR of ParA resolvase. Appl Microbiol Biotechnol 2016; 100:6725-6737. [DOI: 10.1007/s00253-016-7565-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 04/08/2016] [Accepted: 04/16/2016] [Indexed: 01/10/2023]
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31
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Liu B, Zuo Y, Steitz TA. Structures of E. coli σS-transcription initiation complexes provide new insights into polymerase mechanism. Proc Natl Acad Sci U S A 2016; 113:4051-6. [PMID: 27035955 PMCID: PMC4839411 DOI: 10.1073/pnas.1520555113] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In bacteria, multiple σ factors compete to associate with the RNA polymerase (RNAP) core enzyme to form a holoenzyme that is required for promoter recognition. During transcription initiation RNAP remains associated with the upstream promoter DNA via sequence-specific interactions between the σ factor and the promoter DNA while moving downstream for RNA synthesis. As RNA polymerase repetitively adds nucleotides to the 3'-end of the RNA, a pyrophosphate ion is generated after each nucleotide incorporation. It is currently unknown how the release of pyrophosphate affects transcription. Here we report the crystal structures of E coli transcription initiation complexes (TICs) containing the stress-responsive σ(S) factor, a de novo synthesized RNA oligonucleotide, and a complete transcription bubble (σ(S)-TIC) at about 3.9-Å resolution. The structures show the 3D topology of the σ(S) factor and how it recognizes the promoter DNA, including likely specific interactions with the template-strand residues of the -10 element. In addition, σ(S)-TIC structures display a highly stressed pretranslocated initiation complex that traps a pyrophosphate at the active site that remains closed. The position of the pyrophosphate and the unusual phosphodiester linkage between the two terminal RNA residues suggest an unfinished nucleotide-addition reaction that is likely at equilibrium between nucleotide addition and pyrophosphorolysis. Although these σ(S)-TIC crystals are enzymatically active, they are slow in nucleotide addition, as suggested by an NTP soaking experiment. Pyrophosphate release completes the nucleotide addition reaction and is associated with extensive conformational changes around the secondary channel but causes neither active site opening nor transcript translocation.
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Affiliation(s)
- Bin Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Yuhong Zuo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520;
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520; Department of Chemistry, Yale University, New Haven, CT 06520
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32
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Sheshukova EV, Shindyapina AV, Komarova TV, Dorokhov YL. “Matreshka” genes with alternative reading frames. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416020149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Affiliation(s)
- P. B. Persson
- Institute of Vegetative Physiology; Charité-Universitaetsmedizin Berlin; Berlin Germany
| | - M. Mueller
- Institute of Vegetative Physiology; Charité-Universitaetsmedizin Berlin; Berlin Germany
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34
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Goldman SR, Nair NU, Wells CD, Nickels BE, Hochschild A. The primary σ factor in Escherichia coli can access the transcription elongation complex from solution in vivo. eLife 2015; 4. [PMID: 26371553 PMCID: PMC4604602 DOI: 10.7554/elife.10514] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/14/2015] [Indexed: 11/13/2022] Open
Abstract
The σ subunit of bacterial RNA polymerase (RNAP) confers on the enzyme the ability to initiate promoter-specific transcription. Although σ factors are generally classified as initiation factors, σ can also remain associated with, and modulate the behavior of, RNAP during elongation. Here we establish that the primary σ factor in Escherichia coli, σ70, can function as an elongation factor in vivo by loading directly onto the transcription elongation complex (TEC) in trans. We demonstrate that σ70 can bind in trans to TECs that emanate from either a σ70-dependent promoter or a promoter that is controlled by an alternative σ factor. We further demonstrate that binding of σ70 to the TEC in trans can have a particularly large impact on the dynamics of transcription elongation during stationary phase. Our findings establish a mechanism whereby the primary σ factor can exert direct effects on the composition of the entire transcriptome, not just that portion that is produced under the control of σ70-dependent promoters. DOI:http://dx.doi.org/10.7554/eLife.10514.001 Proteins are made following instructions that are encoded by sections of DNA called genes. In the first step of protein production, an enzyme called RNA polymerase uses the gene as a template to make molecules of messenger ribonucleic acid (mRNA). This process—known as transcription—starts when RNA polymerase binds to a site at the start of a gene. The enzyme then moves along the DNA, assembling the mRNA as it goes. This stage of transcription is known as elongation and continues until the RNA polymerase reaches the end of the gene. In bacteria, RNA polymerase needs a family of proteins called sigma factors to help it identify and bind to the start sites associated with the genes that will be transcribed. In the well studied bacterium known as E. coli, the primary sigma factor that is required for transcription initiation on most genes is called sigma 70. Recent research has shown that sigma 70 also influences the activity of RNA polymerase during elongation. During this stage, the RNA polymerase and several other proteins interact to form a complex called the transcription elongation complex (or TEC for short). However, it is not clear how sigma 70 gains access to this complex: does it simply remain with RNA polymerase after transcription starts, or is it freshly incorporated into the TEC during elongation? Goldman, Nair et al. found that sigma 70 is able to incorporate into TECs during elongation and causes them to pause at specific sites in the gene. Sigma 70 can even incorporate into TECs on genes where transcription was initiated by a different sigma factor. These findings indicate that sigma 70 can directly influence the transcription of all genes, not just the genes with start sites that are recognized by this sigma factor. Goldman et al. also observed that in cells that were growing and dividing rapidly, the pauses that occurred due to sigma 70 associating with TECs were of shorter duration than those in cells that were growing slowly. This implies that the growth status of the cells modulates the pausing of RNA polymerase during transcription. In the future, it will be important to understand how much influence the primary sigma factor has on RNA polymerase during elongation in E. coli and other bacteria. DOI:http://dx.doi.org/10.7554/eLife.10514.002
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Affiliation(s)
- Seth R Goldman
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States.,Department of Genetics, Waksman Institute, Rutgers University, New Brunswick, United States
| | - Nikhil U Nair
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Christopher D Wells
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Bryce E Nickels
- Department of Genetics, Waksman Institute, Rutgers University, New Brunswick, United States
| | - Ann Hochschild
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
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35
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Bae B, Feklistov A, Lass-Napiorkowska A, Landick R, Darst SA. Structure of a bacterial RNA polymerase holoenzyme open promoter complex. eLife 2015; 4. [PMID: 26349032 PMCID: PMC4593229 DOI: 10.7554/elife.08504] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/03/2015] [Indexed: 01/17/2023] Open
Abstract
Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the −10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstream of the −10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Addition of an RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σA dissociation. DOI:http://dx.doi.org/10.7554/eLife.08504.001 Inside cells, molecules of double-stranded DNA encode the instructions needed to make proteins. To make a protein, the two strands of DNA that make up a gene are separated and one strand acts as a template to make molecules of messenger ribonucleic acid (or mRNA for short). This process is called transcription. The mRNA is then used as a template to assemble the protein. An enzyme called RNA polymerase carries out transcription and is found in all cells ranging from bacteria to humans and other animals. Bacteria have the simplest form of RNA polymerase and provide an excellent system to study how it controls transcription. It is made up of several proteins that work together to make RNA using DNA as a template. However, it requires the help of another protein called sigma factor to direct it to regions of DNA called promoters, which are just before the start of the gene. When RNA polymerase and the sigma factor interact the resulting group of proteins is known as the RNA polymerase ‘holoenzyme’. Transcription takes place in several stages. To start with, the RNA polymerase holoenzyme locates and binds to promoter DNA. Next, it separates the two strands of DNA and exposes a portion of the template strand. At this point, the DNA and the holoenzyme are said to be in an ‘open promoter complex’ and the section of promoter DNA that is within it is known as a ‘transcription bubble’. However, it is not clear how RNA polymerase holoenzyme interacts with DNA in the open promoter complex. Bae, Feklistov et al. have now used X-ray crystallography to reveal the three-dimensional structure of the open promoter complex with an entire transcription bubble from a bacterium called Thermus aquaticus. The experiments show that there are several important interactions between RNA polymerase holoenzyme and promoter DNA. In particular, the sigma factor inserts into a region of the DNA at the start of the transcription bubble. This rearranges the DNA in a manner that allows the DNA to be exposed and contact the main part of the RNA polymerase. If the holoenyzyme fails to contact the DNA in this way, the holoenzyme does not bind properly to the promoter and transcription does not start. These findings build on previous work to provide a detailed structural framework for understanding how the RNA polymerase holoenzyme and DNA interact to form the open promoter complex. Another study by Bae et al.—which involved some of the same researchers as this study—reveals how another protein called CarD also binds to DNA at the start of the transcription bubble to stabilize the open promoter complex. DOI:http://dx.doi.org/10.7554/eLife.08504.002
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Affiliation(s)
- Brian Bae
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| | - Andrey Feklistov
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| | - Agnieszka Lass-Napiorkowska
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-madison, Madison, United States.,Department of Bacteriology, University of Wisconsin-Madison, Madison, United States
| | - Seth A Darst
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
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36
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Aseev LV, Bylinkina NS, Boni IV. Regulation of the rplY gene encoding 5S rRNA binding protein L25 in Escherichia coli and related bacteria. RNA (NEW YORK, N.Y.) 2015; 21:851-61. [PMID: 25749694 PMCID: PMC4408793 DOI: 10.1261/rna.047381.114] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 12/22/2014] [Indexed: 05/09/2023]
Abstract
Ribosomal protein (r-protein) L25 is one of the three r-proteins (L25, L5, L18) that interact with 5S rRNA in eubacteria. Specific binding of L25 with a certain domain of 5S r-RNA, a so-called loop E, has been studied in detail, but information about regulation of L25 synthesis has remained totally lacking. In contrast to the rplE (L5) and rplR (L18) genes that belong to the polycistronic spc-operon and are regulated at the translation level by r-protein S8, the rplY (L25) gene forms an independent transcription unit. The main goal of this work was to study the regulation of the rplY expression in vivo. We show that the rplY promoter is down-regulated by ppGpp and its cofactor DksA in response to amino acid starvation. At the level of translation, the rplY expression is subjected to the negative feedback control. The 5'-untranslated region of the rplY mRNA comprises specific sequence/structure features, including an atypical SD-like sequence, which are highly conserved in a subset of gamma-proteobacterial families. Despite the lack of a canonical SD element, the rplY'-'lacZ single-copy reporter showed unusually high translation efficiency. Expression of the rplY gene in trans decreased the translation yield, indicating the mechanism of autogenous repression. Site-directed mutagenesis of the rplY 5' UTR revealed an important role of the conserved elements in the translation control. Thus, the rplY expression regulation represents one more example of regulatory pathways that control ribosome biogenesis in Escherichia coli and related bacteria.
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Affiliation(s)
- Leonid V Aseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Natalia S Bylinkina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia Moscow Institute of Physics and Technology, 141700, Moscow Region, Dolgoprudny, Russia
| | - Irina V Boni
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
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37
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Zuo Y, Steitz TA. Crystal structures of the E. coli transcription initiation complexes with a complete bubble. Mol Cell 2015; 58:534-40. [PMID: 25866247 DOI: 10.1016/j.molcel.2015.03.010] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/12/2015] [Accepted: 03/06/2015] [Indexed: 11/15/2022]
Abstract
During transcription initiation, RNA polymerase binds to promoter DNA to form an initiation complex containing a DNA bubble and enters into abortive cycles of RNA synthesis before escaping the promoter to transit into the elongation phase for processive RNA synthesis. Here we present the crystal structures of E. coli transcription initiation complexes containing a complete transcription bubble and de novo synthesized RNA oligonucleotides at about 6-Å resolution. The structures show how RNA polymerase recognizes DNA promoters that contain spacers of different lengths and reveal a bridging interaction between the 5'-triphosphate of the nascent RNA and the σ factor that may function to stabilize the short RNA-DNA hybrids during the early stage of transcription initiation. The conformation of the RNA oligonucleotides and the paths of the DNA strands in the complete initiation complexes provide insights into the mechanism that controls both the abortive and productive RNA synthesis.
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Affiliation(s)
- Yuhong Zuo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, New Haven, CT 06510, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA.
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38
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Gehring AM, Santangelo TJ. Manipulating archaeal systems to permit analyses of transcription elongation-termination decisions in vitro. Methods Mol Biol 2015; 1276:263-79. [PMID: 25665569 DOI: 10.1007/978-1-4939-2392-2_15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcription elongation by multisubunit RNA polymerases (RNAPs) is processive, but neither uniform nor continuous. Regulatory events during elongation include pausing, backtracking, arrest, and transcription termination, and it is critical to determine whether the absence of continued synthesis is transient or permanent. Here we describe mechanisms to generate large quantities of stable archaeal elongation complexes on a solid support to permit (1) single-round transcription, (2) walking of RNAP to any defined template position, and (3) discrimination of transcripts that are associated with RNAP from those that are released to solution. This methodology is based on untagged proteins transcribing biotin- and digoxigenin-labeled DNA templates in association with paramagnetic particles.
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Affiliation(s)
- Alexandra M Gehring
- Department of Biochemistry and Molecular Biology, 383 MRB, Colorado State University, Fort Collins, CO, 80523, USA
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39
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Baranovskiy AG, Zhang Y, Suwa Y, Babayeva ND, Gu J, Pavlov YI, Tahirov TH. Crystal structure of the human primase. J Biol Chem 2014; 290:5635-46. [PMID: 25550159 DOI: 10.1074/jbc.m114.624742] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
DNA replication in bacteria and eukaryotes requires the activity of DNA primase, a DNA-dependent RNA polymerase that lays short RNA primers for DNA polymerases. Eukaryotic and archaeal primases are heterodimers consisting of small catalytic and large accessory subunits, both of which are necessary for RNA primer synthesis. Understanding of RNA synthesis priming in eukaryotes is currently limited due to the lack of crystal structures of the full-length primase and its complexes with substrates in initiation and elongation states. Here we report the crystal structure of the full-length human primase, revealing the precise overall organization of the enzyme, the relative positions of its functional domains, and the mode of its interaction with modeled DNA and RNA. The structure indicates that the dramatic conformational changes in primase are necessary to accomplish the initiation and then elongation of RNA synthesis. The presence of a long linker between the N- and C-terminal domains of p58 provides the structural basis for the bulk of enzyme's conformational flexibility. Deletion of most of this linker affected the initiation and elongation steps of the primer synthesis.
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Affiliation(s)
- Andrey G Baranovskiy
- From the Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Yinbo Zhang
- From the Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198, the Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198, and
| | - Yoshiaki Suwa
- From the Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Nigar D Babayeva
- From the Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Jianyou Gu
- From the Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Youri I Pavlov
- From the Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198, the Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198, and the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Tahir H Tahirov
- From the Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198,
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40
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Zhang X, Jin H, Yang Z, Lei J. Effects of elongation delay in transcription dynamics. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2014; 11:1431-1448. [PMID: 25365608 DOI: 10.3934/mbe.2014.11.1431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In the transcription process, elongation delay is induced by the movement of RNA polymerases (RNAP) along the DNA sequence, and can result in changes in the transcription dynamics. This paper studies the transcription dynamics that involved the elongation delay and effects of cell division and DNA replication. The stochastic process of gene expression is modeled with delay chemical master equation with periodic coefficients, and is studied numerically through the stochastic simulation algorithm with delay. We show that the average transcription level approaches to a periodic dynamics over cell cycles at homeostasis, and the elongation delay can reduce the transcription level and increase the transcription noise. Moreover, the transcription elongation can induce bimodal distribution of mRNA levels that can be measured by the techniques of flow cytometry.
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Affiliation(s)
- Xuan Zhang
- School of Mathematics and Systems Science, Beihang University, Beijing 100191, China.
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41
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Aseev LV, Koledinskaya LS, Boni IV. Dissecting the extended "-10" Escherichia coli rpsB promoter activity and regulation in vivo. BIOCHEMISTRY (MOSCOW) 2014; 79:776-84. [PMID: 25365487 DOI: 10.1134/s0006297914080057] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
As we have shown previously, transcription of the rpsB-tsf operon encoding essential components of the translation machinery, a ribosomal protein S2 and an elongation factor Ts, is driven by a single promoter PrpsB, which is highly conserved among γ-proteobacteria. PrpsB belongs to the extended "-10" promoter class; it comprises a TGTG-extension upstream of the "-10" hexamer TATAAA, a suboptimal "-35" region TTGGTG, and a GC-rich discriminator GCGCGC that separates the "-10" element from the transcription start site. In this work, we examined an impact of site-directed mutations in the rpsB promoter region on expression of the reporter gene PrpsB-lacZ within the E. coli chromosome as well as promoter regulation by transcription factors ppGpp and DksA upon amino acid starvation. The results show that the transcription level largely depends on both the TGTG-extension and the TTG-element in the "-35" region, as mutations in these sequences dramatically decrease the activity of the promoter. Upon induction of amino acid starvation, the rpsB promoter is negatively regulated by ppGpp due to the presence of the GC-rich discriminator, whose substitution for the AT-rich element abolished stringent control. These and other data obtained demonstrate the necessity of a natural combination of all the conserved promoter elements for efficient and regulated transcription of the essential rpsB-tsf operon.
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Affiliation(s)
- L V Aseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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42
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Kinetics of promoter escape by bacterial RNA polymerase: effects of promoter contacts and transcription bubble collapse. Biochem J 2014; 463:135-44. [PMID: 24995916 DOI: 10.1042/bj20140179] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Promoter escape by RNA polymerase, the transition between the initiation and elongation, is a critical step that defines transcription output at many promoters. In the present study we used a real-time fluorescence assay for promoter melting and escape to study the determinants of the escape. Perturbation of core promoter-polymerase contacts had opposing effects on the rates of melting and escape, demonstrating a direct role of core promoter elements sequence in setting not only the kinetics of promoter melting, but also the kinetics of promoter escape. The start of RNA synthesis is accompanied by an enlargement of the transcription bubble and pulling in of the downstream DNA into the enzyme, resulting in DNA scrunching. Promoter escape results in collapse of the enlarged bubble. To test whether the energy that could be potentially released by the collapse of the bubble plays a role in determining escape kinetics, we measured the rates of promoter escape in promoter constructs, in which the amount of this energy was perturbed by introducing sequence mismatches. We found no significant changes in the rate of promoter escape with these promoter constructs suggesting that the energy released upon bubble collapse does not play a critical role in determining the kinetics of promoter escape.
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Burmann BM, Rösch P. The role of E. coli Nus-factors in transcription regulation and transcription:translation coupling: From structure to mechanism. Transcription 2014; 2:130-134. [PMID: 21922055 DOI: 10.4161/trns.2.3.15671] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 03/31/2011] [Accepted: 03/31/2011] [Indexed: 11/19/2022] Open
Abstract
Bacterial transcription mediated by RNA polymerase (RNAP) is a highly regulated process and RNAP action is modulated during the different phases of initiation, elongation and termination by proteins such as the Escherichia coli Nus transcription-factors. Here we discuss the structural interplay and the mechanistic role of the Nus-factors that are directly involved in the processivity of elongation, transcription:translation coupling and termination, as well as the varying effects of these proteins on transcription under the influence of additional signals.
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Affiliation(s)
- Björn M Burmann
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle; Universität Bayreuth; Bayreuth, Germany
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Yuzenkova Y, Gamba P, Herber M, Attaiech L, Shafeeq S, Kuipers OP, Klumpp S, Zenkin N, Veening JW. Control of transcription elongation by GreA determines rate of gene expression in Streptococcus pneumoniae. Nucleic Acids Res 2014; 42:10987-99. [PMID: 25190458 PMCID: PMC4176173 DOI: 10.1093/nar/gku790] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 08/18/2014] [Accepted: 08/20/2014] [Indexed: 01/28/2023] Open
Abstract
Transcription by RNA polymerase may be interrupted by pauses caused by backtracking or misincorporation that can be resolved by the conserved bacterial Gre-factors. However, the consequences of such pausing in the living cell remain obscure. Here, we developed molecular biology and transcriptome sequencing tools in the human pathogen Streptococcus pneumoniae and provide evidence that transcription elongation is rate-limiting on highly expressed genes. Our results suggest that transcription elongation may be a highly regulated step of gene expression in S. pneumoniae. Regulation is accomplished via long-living elongation pauses and their resolution by elongation factor GreA. Interestingly, mathematical modeling indicates that long-living pauses cause queuing of RNA polymerases, which results in 'transcription traffic jams' on the gene and thus blocks its expression. Together, our results suggest that long-living pauses and RNA polymerase queues caused by them are a major problem on highly expressed genes and are detrimental for cell viability. The major and possibly sole function of GreA in S. pneumoniae is to prevent formation of backtracked elongation complexes.
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Affiliation(s)
- Yulia Yuzenkova
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Pamela Gamba
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Martijn Herber
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Laetitia Attaiech
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Sulman Shafeeq
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Oscar P Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Stefan Klumpp
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Jan-Willem Veening
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
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45
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Baboo S, Cook PR. "Dark matter" worlds of unstable RNA and protein. Nucleus 2014; 5:281-6. [PMID: 25482115 PMCID: PMC4152340 DOI: 10.4161/nucl.29577] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 06/10/2014] [Accepted: 06/13/2014] [Indexed: 12/11/2022] Open
Abstract
Astrophysicists use the term "dark matter" to describe the majority of the matter and/or energy in the universe that is hidden from view, and biologists now apply it to the new families of RNA they are uncovering. We review evidence for an analogous hidden world containing peptides. The critical experiments involved pulse-labeling human cells with tagged amino acids for periods as short as five seconds. Results are extraordinary in two respects: both nucleus and cytoplasm become labeled, and most signals disappear with a half-life of less than one minute. Just as the synthesis of each mature mRNA is regulated by the abortive production of hundreds of shorter transcripts that are quickly degraded, it seems that the synthesis of each full-length protein in the stable proteome is regulated by an apparently wasteful production and degradation of shorter peptides. Some of the nuclear synthesis is probably a byproduct of nuclear ribosomes proofreading newly-made RNA for inappropriately-placed termination codons (a process that triggers "nonsense-mediated decay"). We speculate that some "dark-matter" peptides will play other important roles in the cell.
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Affiliation(s)
- Sabyasachi Baboo
- Sir William Dunn School of Pathology; University of Oxford; Oxford, UK
| | - Peter R Cook
- Sir William Dunn School of Pathology; University of Oxford; Oxford, UK
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Baboo S, Bhushan B, Jiang H, Grovenor CRM, Pierre P, Davis BG, Cook PR. Most human proteins made in both nucleus and cytoplasm turn over within minutes. PLoS One 2014; 9:e99346. [PMID: 24911415 PMCID: PMC4050049 DOI: 10.1371/journal.pone.0099346] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 05/13/2014] [Indexed: 12/25/2022] Open
Abstract
In bacteria, protein synthesis can be coupled to transcription, but in eukaryotes it is believed to occur solely in the cytoplasm. Using pulses as short as 5 s, we find that three analogues – L-azidohomoalanine, puromycin (detected after attaching fluors using ‘click’ chemistry or immuno-labeling), and amino acids tagged with ‘heavy’ 15N and 13C (detected using secondary ion mass spectrometry) – are incorporated into the nucleus and cytoplasm in a process sensitive to translational inhibitors. The nuclear incorporation represents a significant fraction of the total, and labels in both compartments have half-lives of less than a minute; results are consistent with most newly-made peptides being destroyed soon after they are made. As nascent RNA bearing a premature termination codon (detected by fluorescence in situ hybridization) is also eliminated by a mechanism sensitive to a translational inhibitor, the nuclear turnover of peptides is probably a by-product of proof-reading the RNA for stop codons (a process known as nonsense-mediated decay). We speculate that the apparently-wasteful turnover of this previously-hidden (‘dark-matter’) world of peptide is involved in regulating protein production.
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Affiliation(s)
- Sabyasachi Baboo
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Bhaskar Bhushan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Haibo Jiang
- Department of Materials, University of Oxford, Oxford, United Kingdom
| | | | - Philippe Pierre
- Centre d′Immunologie de Marseille-Luminy, Aix-Marseille Université, Marseille, France
- Institut National de la Santé et de la Recherche Médicale, U1104, Marseille, France
- Centre National de la Recherche Scientifique, Unités Mixtes de Recherche 7280, Marseille, France
| | - Benjamin G. Davis
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Peter R. Cook
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- * E-mail:
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Tang GQ, Nandakumar D, Bandwar RP, Lee KS, Roy R, Ha T, Patel SS. Relaxed rotational and scrunching changes in P266L mutant of T7 RNA polymerase reduce short abortive RNAs while delaying transition into elongation. PLoS One 2014; 9:e91859. [PMID: 24651161 PMCID: PMC3961267 DOI: 10.1371/journal.pone.0091859] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 02/14/2014] [Indexed: 12/02/2022] Open
Abstract
Abortive cycling is a universal feature of transcription initiation catalyzed by DNA-dependent RNA polymerases (RNAP). In bacteriophage T7 RNAP, mutation of proline 266 to leucine (P266L) in the C-linker region connecting the N-terminal promoter binding domain with the C-terminal catalytic domain drastically reduces short abortive products (4–7 nt) while marginally increasing long abortives (9–11 nt). Here we have investigated the transcription initiation pathway of P266L with the goal of understanding the mechanistic basis for short and long abortive synthesis. We show that the P266L mutation does not alter the affinity for the promoter, mildly affects promoter opening, and increases the +1/+2 GTP Kd by 2-fold. However, unlike wild-type T7 RNAP that undergoes stepwise rotation of the promoter binding domain and DNA scrunching during initial transcription, the P266L mutant does not undergo coupled rotational/scrunching movements until 7 nt RNA synthesis. The lack of rotation/scrunching correlates with greater stabilities of the initiation complexes of the P266L and decreased short abortive products. The results indicate that the increased flexibility in the C-linker due to P266L mutation enables T7 RNAP to absorb the stress from the growing RNA:DNA hybrid thereby decreasing short abortive products. Increased C-linker flexibility, however, has an adverse effect of delaying the transition into elongation by 1–2 nt, which gives rise to long abortive products. However, a mutation in the upstream promoter region greatly decreases long abortive products in P266L reactions, rendering the combination of P266L and A-15C promoter a desirable pair for efficient in vitro transcription for RNA production. We conclude that the conformational rigidity in the C-linker region conferred by the proline at position 266 is responsible for the undesirable short abortive products, but the rigidity is critical for efficient promoter clearance and transition into elongation.
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Affiliation(s)
- Guo-Qing Tang
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Divya Nandakumar
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Rajiv P. Bandwar
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Kyung Suk Lee
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Rahul Roy
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Taekjip Ha
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Howard Hughes Medical Institutes, Urbana, Illinois, United States of America
| | - Smita S. Patel
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
- * E-mail:
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Sharma A, Leach RN, Gell C, Zhang N, Burrows PC, Shepherd DA, Wigneshweraraj S, Smith DA, Zhang X, Buck M, Stockley PG, Tuma R. Domain movements of the enhancer-dependent sigma factor drive DNA delivery into the RNA polymerase active site: insights from single molecule studies. Nucleic Acids Res 2014; 42:5177-90. [PMID: 24553251 PMCID: PMC4005640 DOI: 10.1093/nar/gku146] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recognition of bacterial promoters is regulated by two distinct classes of sequence-specific sigma factors, σ70 or σ54, that differ both in their primary sequence and in the requirement of the latter for activation via enhancer-bound upstream activators. The σ54 version controls gene expression in response to stress, often mediating pathogenicity. Its activator proteins are members of the AAA+ superfamily and use adenosine triphosphate (ATP) hydrolysis to remodel initially auto-inhibited holoenzyme promoter complexes. We have mapped this remodeling using single-molecule fluorescence spectroscopy. Initial remodeling is nucleotide-independent and driven by binding both ssDNA during promoter melting and activator. However, DNA loading into the RNA polymerase active site depends on co-operative ATP hydrolysis by the activator. Although the coupled promoter recognition and melting steps may be conserved between σ70 and σ54, the domain movements of the latter have evolved to require an activator ATPase.
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Affiliation(s)
- Amit Sharma
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Robert N. Leach
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Christopher Gell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Nan Zhang
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Patricia C. Burrows
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Dale A. Shepherd
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Sivaramesh Wigneshweraraj
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - David Alastair Smith
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Xiaodong Zhang
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Martin Buck
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
| | - Peter G. Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
- *To whom correspondence should be addressed. Tel: +44 1133 433092; Fax: +44 1133 437897;
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK, Department of Life Sciences, Sir Alexander Fleming Building, Imperial College, London SW72AZ, UK and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK
- Correspondence may also be addressed to Roman Tuma. Tel: +44 1133 433080; Fax: +44 1133 437897;
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Strobel EJ, Roberts JW. Regulation of promoter-proximal transcription elongation: enhanced DNA scrunching drives λQ antiterminator-dependent escape from a σ70-dependent pause. Nucleic Acids Res 2014; 42:5097-108. [PMID: 24550164 PMCID: PMC4005639 DOI: 10.1093/nar/gku147] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
During initial transcription, RNA polymerase remains bound at the promoter and synthesizes RNA without movement along the DNA template, drawing downstream DNA into itself in a process called scrunching and thereby storing energy to sever the bonds that hold the enzyme at the promoter. We show that DNA scrunching also is the driving force behind the escape of RNA polymerase from a regulatory pause of the late gene operon of bacteriophage λ, and that this process is enhanced by the activity of the Q(λ) antiterminator. Furthermore, we show that failure of transcription complexes to escape the pause results in backtracking and arrest in a process analogous to abortive initiation. We identify a sequence element that modulates both abortive synthesis and the formation of arrested elongation complexes.
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Affiliation(s)
- Eric J Strobel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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50
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Ang J, Harris E, Hussey BJ, Kil R, McMillen DR. Tuning response curves for synthetic biology. ACS Synth Biol 2013; 2:547-67. [PMID: 23905721 PMCID: PMC3805330 DOI: 10.1021/sb4000564] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Indexed: 01/07/2023]
Abstract
Synthetic biology may be viewed as an effort to establish, formalize, and develop an engineering discipline in the context of biological systems. The ability to tune the properties of individual components is central to the process of system design in all fields of engineering, and synthetic biology is no exception. A large and growing number of approaches have been developed for tuning the responses of cellular systems, and here we address specifically the issue of tuning the rate of response of a system: given a system where an input affects the rate of change of an output, how can the shape of the response curve be altered experimentally? This affects a system's dynamics as well as its steady-state properties, both of which are critical in the design of systems in synthetic biology, particularly those with multiple components. We begin by reviewing a mathematical formulation that captures a broad class of biological response curves and use this to define a standard set of varieties of tuning: vertical shifting, horizontal scaling, and the like. We then survey the experimental literature, classifying the results into our defined categories, and organizing them by regulatory level: transcriptional, post-transcriptional, and post-translational.
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Affiliation(s)
- Jordan Ang
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - Edouard Harris
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - Brendan J. Hussey
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - Richard Kil
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - David R. McMillen
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
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