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Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA. Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy. Nat Struct Mol Biol 2024:10.1038/s41594-024-01349-9. [PMID: 38951624 DOI: 10.1038/s41594-024-01349-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 06/06/2024] [Indexed: 07/03/2024]
Abstract
During formation of the transcription-competent open complex (RPo) by bacterial RNA polymerases (RNAPs), transient intermediates pile up before overcoming a rate-limiting step. Structural descriptions of these interconversions in real time are unavailable. To address this gap, here we use time-resolved cryogenic electron microscopy (cryo-EM) to capture four intermediates populated 120 ms or 500 ms after mixing Escherichia coli σ70-RNAP and the λPR promoter. Cryo-EM snapshots revealed that the upstream edge of the transcription bubble unpairs rapidly, followed by stepwise insertion of two conserved nontemplate strand (nt-strand) bases into RNAP pockets. As the nt-strand 'read-out' extends, the RNAP clamp closes, expelling an inhibitory σ70 domain from the active-site cleft. The template strand is fully unpaired by 120 ms but remains dynamic, indicating that yet unknown conformational changes complete RPo formation in subsequent steps. Given that these events likely describe DNA opening at many bacterial promoters, this study provides insights into how DNA sequence regulates steps of RPo formation.
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Affiliation(s)
- Ruth M Saecker
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Andreas U Mueller
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Brandon Malone
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
- Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY, USA
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - William C Budell
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Venkata P Dandey
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Kashyap Maruthi
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Joshua H Mendez
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Nina Molina
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Edward T Eng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Laura Y Yen
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Clinton S Potter
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Chan Zuckerberg Imaging Institute, San Francisco, CA, USA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Chan Zuckerberg Imaging Institute, San Francisco, CA, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA.
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Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA. Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584744. [PMID: 38559232 PMCID: PMC10979975 DOI: 10.1101/2024.03.13.584744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
During formation of the transcription-competent open complex (RPo) by bacterial RNA polymerases (RNAP), transient intermediates pile up before overcoming a rate-limiting step. Structural descriptions of these interconversions in real time are unavailable. To address this gap, time-resolved cryo-electron microscopy (cryo-EM) was used to capture four intermediates populated 120 or 500 milliseconds (ms) after mixing Escherichia coli σ70-RNAP and the λPR promoter. Cryo-EM snapshots revealed the upstream edge of the transcription bubble unpairs rapidly, followed by stepwise insertion of two conserved nontemplate strand (nt-strand) bases into RNAP pockets. As nt-strand "read-out" extends, the RNAP clamp closes, expelling an inhibitory σ70 domain from the active-site cleft. The template strand is fully unpaired by 120 ms but remains dynamic, indicating yet unknown conformational changes load it in subsequent steps. Because these events likely describe DNA opening at many bacterial promoters, this study provides needed insights into how DNA sequence regulates steps of RPo formation.
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Affiliation(s)
- Ruth M. Saecker
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
| | - Andreas U. Mueller
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
| | - Brandon Malone
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
| | - William C. Budell
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Venkata P. Dandey
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Kashyap Maruthi
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Joshua H. Mendez
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Nina Molina
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
| | - Edward T. Eng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Laura Y. Yen
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Clinton S. Potter
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY USA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY USA
| | - Seth A. Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
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3
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Roy NS, Debnath S, Chakraborty A, Chakraborty P, Bera I, Ghosh R, Ghoshal N, Chakrabarti S, Roy S. Enhanced basepair dynamics pre-disposes protein-assisted flips of key bases in DNA strand separation during transcription initiation. Phys Chem Chem Phys 2018; 20:9449-9459. [DOI: 10.1039/c8cp01119b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Localized separation of strands of duplex DNA is a necessary step in many DNA-dependent processes, including transcription and replication.
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Affiliation(s)
- Neeladri Sekhar Roy
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Subrata Debnath
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Abhijit Chakraborty
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | | | - Indrani Bera
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Raka Ghosh
- Department of Biophysics
- Bose Institute
- Kolkata 700054
- India
| | - Nanda Ghoshal
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Saikat Chakrabarti
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Siddhartha Roy
- Department of Biophysics
- Bose Institute
- Kolkata 700054
- India
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4
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Molecular Mechanisms of Transcription Initiation at gal Promoters and their Multi-Level Regulation by GalR, CRP and DNA Loop. Biomolecules 2015; 5:2782-807. [PMID: 26501343 PMCID: PMC4693257 DOI: 10.3390/biom5042782] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 09/25/2015] [Indexed: 11/16/2022] Open
Abstract
Studying the regulation of transcription of the gal operon that encodes the amphibolic pathway of d-galactose metabolism in Escherichia coli discerned a plethora of principles that operate in prokaryotic gene regulatory processes. In this chapter, we have reviewed some of the more recent findings in gal that continues to reveal unexpected but important mechanistic details. Since the operon is transcribed from two overlapping promoters, P1 and P2, regulated by common regulatory factors, each genetic or biochemical experiment allowed simultaneous discernment of two promoters. Recent studies range from genetic, biochemical through biophysical experiments providing explanations at physiological, mechanistic and single molecule levels. The salient observations highlighted here are: the axiom of determining transcription start points, discovery of a new promoter element different from the known ones that influences promoter strength, occurrence of an intrinsic DNA sequence element that overrides the transcription elongation pause created by a DNA-bound protein roadblock, first observation of a DNA loop and determination its trajectory, and piggybacking proteins and delivering to their DNA target.
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5
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Karpen ME, deHaseth PL. Base flipping in open complex formation at bacterial promoters. Biomolecules 2015; 5:668-78. [PMID: 25927327 PMCID: PMC4496690 DOI: 10.3390/biom5020668] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/16/2015] [Accepted: 04/14/2015] [Indexed: 12/18/2022] Open
Abstract
In the process of transcription initiation, the bacterial RNA polymerase binds double-stranded (ds) promoter DNA and subsequently effects strand separation of 12 to 14 base pairs (bp), including the start site of transcription, to form the so-called "open complex" (also referred to as RP(o)). This complex is competent to initiate RNA synthesis. Here we will review the role of σ70 and its homologs in the strand separation process, and evidence that strand separation is initiated at the -11A (the A of the non-template strand that is 11 bp upstream from the transcription start site) of the promoter. By using the fluorescent adenine analog, 2-aminopurine, it was demonstrated that the -11A on the non-template strand flips out of the DNA helix and into a hydrophobic pocket where it stacks with tyrosine 430 of σ70. Open complexes are remarkably stable, even though in vivo, and under most experimental conditions in vitro, dsDNA is much more stable than its strand-separated form. Subsequent structural studies of other researchers have confirmed that in the open complex the -11A has flipped into a hydrophobic pocket of σ70. It was also revealed that RPo was stabilized by three additional bases of the non-template strand being flipped out of the helix and into hydrophobic pockets, further preventing re-annealing of the two complementary DNA strands.
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Affiliation(s)
- Mary E Karpen
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, 312 Padnos Hall, Allendale, MI 49401, USA.
| | - Pieter L deHaseth
- Center for RNA Molecular Biology, Case Western Reserve University, 2109 Adelbert Road, Cleveland, OH 44106, USA.
- Department of Biochemistry, Case Western Reserve University, 2109 Adelbert Road, Cleveland, OH 44106, USA.
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6
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Rammohan J, Ruiz Manzano A, Garner AL, Stallings CL, Galburt EA. CarD stabilizes mycobacterial open complexes via a two-tiered kinetic mechanism. Nucleic Acids Res 2015; 43:3272-85. [PMID: 25697505 PMCID: PMC4381055 DOI: 10.1093/nar/gkv078] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 01/21/2015] [Indexed: 11/28/2022] Open
Abstract
CarD is an essential and global transcriptional regulator in mycobacteria. While its biological role is unclear, CarD functions by interacting directly with RNA polymerase (RNAP) holoenzyme promoter complexes. Here, using a fluorescent reporter of open complex, we quantitate RPo formation in real time and show that Mycobacterium tuberculosis CarD has a dramatic effect on the energetics of RNAP bound complexes on the M. tuberculosis rrnAP3 ribosomal RNA promoter. The data reveal that Mycobacterium bovis RNAP exhibits an unstable RPo that is stabilized by CarD and suggest that CarD uses a two-tiered, concentration-dependent mechanism by associating with open and closed complexes with different affinities. Specifically, the kinetics of open-complex formation can be explained by a model where, at saturating concentrations of CarD, the rate of bubble collapse is slowed and the rate of opening is accelerated. The kinetics and open-complex stabilities of CarD mutants further clarify the roles played by the key residues W85, K90 and R25 previously shown to affect CarD-dependent gene regulation in vivo. In contrast to M. bovis RNAP, Escherichia coli RNAP efficiently forms RPo on rrnAP3, suggesting an important difference between the polymerases themselves and highlighting how transcriptional machinery can vary across bacterial genera.
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Affiliation(s)
- Jayan Rammohan
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ana Ruiz Manzano
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ashley L Garner
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Christina L Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eric A Galburt
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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7
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Differential role of base pairs on gal promoters strength. J Mol Biol 2014; 427:792-806. [PMID: 25543084 DOI: 10.1016/j.jmb.2014.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 12/16/2014] [Accepted: 12/18/2015] [Indexed: 11/23/2022]
Abstract
Sequence alignments of promoters in prokaryotes postulated that the frequency of occurrence of a base pair at a given position of promoter elements reflects its contribution to intrinsic promoter strength. We directly assessed the contribution of the four base pairs in each position in the intrinsic promoter strength by keeping the context constant in Escherichia coli cAMP-CRP (cAMP receptor protein) regulated gal promoters by in vitro transcription assays. First, we show that base pair frequency within known consensus elements correlates well with promoter strength. Second, we observe some substitutions upstream of the ex-10 TG motif that are important for promoter function. Although the galP1 and P2 promoters overlap, only three positions where substitutions inactivated both promoters were found. We propose that RNA polymerase binds to the -12T base pair as part of double-stranded DNA while opening base pairs from -11A to +3 to form the single-stranded transcription bubble DNA during isomerization. The cAMP-CRP complex rescued some deleterious substitutions in the promoter region. The base pair roles and their flexibilities reported here for E. coli gal promoters may help construction of synthetic promoters in gene circuitry experiments in which overlapping promoters with differential controls may be warranted.
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8
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Feklístov A, Sharon BD, Darst SA, Gross CA. Bacterial sigma factors: a historical, structural, and genomic perspective. Annu Rev Microbiol 2014; 68:357-76. [PMID: 25002089 DOI: 10.1146/annurev-micro-092412-155737] [Citation(s) in RCA: 327] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Transcription initiation is the crucial focal point of gene expression in prokaryotes. The key players in this process, sigma factors (σs), associate with the catalytic core RNA polymerase to guide it through the essential steps of initiation: promoter recognition and opening, and synthesis of the first few nucleotides of the transcript. Here we recount the key advances in σ biology, from their discovery 45 years ago to the most recent progress in understanding their structure and function at the atomic level. Recent data provide important structural insights into the mechanisms whereby σs initiate promoter opening. We discuss both the housekeeping σs, which govern transcription of the majority of cellular genes, and the alternative σs, which direct RNA polymerase to specialized operons in response to environmental and physiological cues. The review concludes with a genome-scale view of the extracytoplasmic function σs, the most abundant group of alternative σs.
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9
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Holt AK, Senear DF. The cooperative binding energetics of CytR and cAMP receptor protein support a quantitative model of differential activation and repression of CytR-regulated class III Escherichia coli promoters. Biochemistry 2013; 52:8209-18. [PMID: 24138566 DOI: 10.1021/bi401063c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
cAMP receptor protein (CRP) and CytR mediate positive and negative control of nine genes in Escherichia coli, most of which are involved in nucleoside catabolism and recycling. Five promoters share a common architecture in which tandem CRP sites flank an intervening CytR operator (CytO). CytR and CRP bind cooperatively to these promoters to form a three-protein, DNA-bound complex that controls activation and repression, the levels of which vary markedly among the promoters. To understand the specific combinatorial control mechanisms that are responsible for this outcome, we have used quantitative DNase I footprinting to generate individual site isotherms for each site of protein-DNA interaction. The intrinsic affinities of each transcription factor for its respective site and the specific patterns of cooperativity and competition underlying the molecular interactions at each promoter were determined by a global analysis of these titration data. Here we present results obtained for nupGP and tsxP2, adding to results published previously for deoP2, udpP, and cddP. These data allowed us to correlate the reported levels of activation, repression, and induction with the ligation states of these five promoters under physiologically relevant conditions. A general pattern of transcriptional regulation emerges that allows for complex patterns of regulation in this seemingly simple system.
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Affiliation(s)
- Allison K Holt
- Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697, United States
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10
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Kim H, Tang GQ, Patel SS, Ha T. Opening-closing dynamics of the mitochondrial transcription pre-initiation complex. Nucleic Acids Res 2011; 40:371-80. [PMID: 21911357 PMCID: PMC3245942 DOI: 10.1093/nar/gkr736] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Promoter recognition and local melting of DNA are key steps of transcription initiation catalyzed by RNA polymerase and initiation factors. From single molecule fluorescence resonance energy transfer studies of the yeast (Saccharomyces cerevisiae) mitochondrial RNA polymerase Rpo41 and its transcription factor Mtf1, we show that the pre-initiation complex is highly dynamic and undergoes repetitive opening-closing transitions that are modulated by Mtf1 and ATP. We found that Rpo41 alone has the intrinsic ability to bend the promoter but only very briefly. Mtf1 enhances bending/opening transition and suppresses closing transition, indicating its dual roles of nucleating promoter opening and stabilizing the open state. The cognate initiating ATP prolongs the lifetime of the open state, plausibly explaining the 'ATP sensing mechanism' suggested for the system. We discovered short-lived opening trials upon initial binding of Rpo41-Mtf1 before the establishment of the opening/closing equilibrium, which may aid in promoter selection before the formation of stable pre-initiation complex. The dynamics of open complex formation provides unique insights into the interplay between RNA polymerase and transcription factors in regulating initiation.
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Affiliation(s)
- Hajin Kim
- Physics Department and Center for Physics of Living Cells, University of Illinois, Urbana-Champaign, Howard Hughes Medical Institute, Urbana, IL 61801, USA
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11
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Liang J, Matsika S. Pathways for fluorescence quenching in 2-aminopurine π-stacked with pyrimidine nucleobases. J Am Chem Soc 2011; 133:6799-808. [PMID: 21486032 DOI: 10.1021/ja2007998] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Fluorescent analogues of nucleobases are very useful as probes to study DNA dynamics, because natural DNA does not fluoresce significantly. In many of these analogues, such as 2-aminopurine (2AP), the fluorescence is quenched when incorporated into DNA through processes that are not well understood. This work uses theoretical studies to examine fluorescence quenching pathways in 2AP-containing dimers. The singlet excited states of π-stacked dimer systems containing 2AP and a pyrimidine base, thymine or cytosine, have been studied using ab initio computational methods. Computed relaxation pathways along the excited-state surfaces reveal novel mechanisms that can lead to fluorescence quenching in the π-stacked dimers. The placement of 2AP on the 5' or 3' terminus of the dimers has different effects on the excitation energies and the relaxation pathways on the S(1) excited state. Conical intersections between the ground and first excited states exist when 2AP is placed at the 3' side, whereas the placement of 2AP at the 5' side leads to the switching of a bright state to a dark state. Both of these processes can lead to fluorescence quenching and may contribute to the fluorescence quenching observed in 2AP when incorporated in DNA.
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Affiliation(s)
- Jingxin Liang
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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12
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Ji SC, Wang X, Yun SH, Jeon HJ, Lee HJ, Kim H, Lim HM. In vivo transcription dynamics of the galactose operon: a study on the promoter transition from P1 to P2 at onset of stationary phase. PLoS One 2011; 6:e17646. [PMID: 21445255 PMCID: PMC3060815 DOI: 10.1371/journal.pone.0017646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2010] [Accepted: 02/09/2011] [Indexed: 12/04/2022] Open
Abstract
Quantitative analyses of the 5′ end of gal transcripts indicate that transcription from the galactose operon P1 promoter is higher during cell division. When cells are no longer dividing, however, transcription is initiated more often from the P2 promoter. Escherichia coli cells divide six times before the onset of the stationary phase when grown in LB containing 0.5% galactose at 37°C. Transcription from the two promoters increases, although at different rates, during early exponential phase (until the third cell division, OD600 0.4), and then reaches a plateau. The steady-state transcription from P1 continues in late exponential phase (the next three cell divisions, OD600 3.0), after which transcription from this promoter decreases. However, steady-state transcription from P2 continues 1 h longer into the stationary phase, before decreasing. This longer steady-state P2 transcription constitutes the promoter transition from P1 to P2 at the onset of the stationary phase. The intracellular cAMP concentration dictates P1 transcription dynamics; therefore, promoter transition may result from a lack of cAMP-CRP complex binding to the gal operon. The decay rate of gal-specific transcripts is constant through the six consecutive cell divisions that comprise the exponential growth phase, increases at the onset of the stationary phase, and is too low to be measured during the stationary phase. These data suggest that a regulatory mechanism coordinates the synthesis and decay of gal mRNAs to maintain the observed gal transcription. Our analysis indicates that the increase in P1 transcription is the result of cAMP-CRP binding to increasing numbers of galactose operons in the cell population.
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Affiliation(s)
- Sang Chun Ji
- Department of Biological Science, College of Biological Sciences and Biotechnology, Chungnam National University, Taejon, Republic of Korea
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13
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McCullagh E, Farlow J, Fuller C, Girard J, Lipinski-Kruszka J, Lu D, Noriega T, Rollins G, Spitzer R, Todhunter M, El-Samad H. Not all quiet on the noise front. Nat Chem Biol 2009; 5:699-704. [PMID: 19763097 DOI: 10.1038/nchembio.222] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Phenotypic diversity exists even within isogenic populations of cells. Such nongenetic individuality may have wide implications for our understanding of many biological processes. The field of study concerned with the investigation of nongenetic individuality, also known as the 'biology of noise', is ripe with exciting scientific opportunities and challenges.
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Affiliation(s)
- Emma McCullagh
- TETRAD Graduate Program, University of California, San Francisco, California, USA
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14
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Tang GQ, Paratkar S, Patel SS. Fluorescence mapping of the open complex of yeast mitochondrial RNA polymerase. J Biol Chem 2008; 284:5514-22. [PMID: 19116203 DOI: 10.1074/jbc.m807880200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mitochondrial RNA polymerase (mtRNAP) of Saccharomyces cerevisiae, consisting of a complex of Rpo41 and Mtf1, is homologous to the phage single polypeptide T7/T3 RNA polymerases. The yeast mtRNAP recognizes a conserved nonanucleotide sequence to initiate specific transcription. In this work, we have defined the region of the nonanucleotide that is melted by the mtRNAP using 2-aminopurine (2AP) fluorescence that is sensitive to changes in base stacking interactions. We show that mtRNAP spontaneously melts the promoter from -4 to +2 forming a bubble around the transcription start site at +1. The location and size of the DNA bubble in this open complex of the mtRNAP closely resembles that of the T7 RNA polymerase. We show that DNA melting requires the simultaneous presence of Rpo41 and Mtf1. Adding the initiating nucleotide ATP does not expand the size of the initially melted DNA, but the initiating nucleotide differentially affects base stacking interactions at -1 and -2. Thus, the promoter structure upstream of the transcription start site is slightly rearranged during early initiation from its structure in the pre-initiation stage. Unlike on the duplex promoter, Rpo41 alone was able to form a competent open complex on a pre-melted promoter. The results indicate that Rpo41 contains the elements for recognizing the melted promoter through interactions with the template strand. We propose that Mtf1 plays a role in base pair disruption during the early stages of open complex formation.
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Affiliation(s)
- Guo-Qing Tang
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA
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15
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Schroeder LA, Gries TJ, Saecker RM, Record MT, Harris ME, DeHaseth PL. Evidence for a tyrosine-adenine stacking interaction and for a short-lived open intermediate subsequent to initial binding of Escherichia coli RNA polymerase to promoter DNA. J Mol Biol 2008; 385:339-49. [PMID: 18976666 DOI: 10.1016/j.jmb.2008.10.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Revised: 09/30/2008] [Accepted: 10/03/2008] [Indexed: 11/18/2022]
Abstract
Bacterial RNA polymerase and a "sigma" transcription factor form an initiation-competent "open" complex at a promoter by disruption of about 14 base pairs. Strand separation is likely initiated at the highly conserved -11 A-T base pair. Amino acids in conserved region 2.3 of the main Escherichia coli sigma factor, sigma(70), are involved in this process, but their roles are unclear. To monitor the fates of particular bases upon addition of RNA polymerase, promoters bearing single substitutions of the fluorescent A-analog 2-aminopurine (2-AP) at -11 and two other positions in promoter DNA were examined. Evidence was obtained for an open intermediate on the pathway to open complex formation, in which these 2-APs are no longer stacked onto their neighboring bases. The tyrosine at residue 430 in region 2.3 of sigma(70) was shown to be involved in quenching the fluorescence of a 2-AP substituted at -11, presumably through a stacking interaction. These data refine the structural model for open complex formation and reveal a novel interaction involved in DNA melting by RNA polymerase.
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Affiliation(s)
- Lisa A Schroeder
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106-4973, USA
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16
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Wade JT, Struhl K. The transition from transcriptional initiation to elongation. Curr Opin Genet Dev 2008; 18:130-6. [PMID: 18282700 DOI: 10.1016/j.gde.2007.12.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Accepted: 12/20/2007] [Indexed: 11/26/2022]
Abstract
Transcription is the first step in gene expression, and its regulation underlies multicellular development and the response to environmental changes. Most studies of transcriptional regulation have focused on the recruitment of RNA polymerase to promoters. However, recent work has shown that, for many promoters, post-recruitment steps in transcriptional initiation are likely to be rate limiting. The rate at which RNA polymerase transitions from transcriptional initiation to elongation varies dramatically between promoters and between organisms and is the target of multiple regulatory proteins that can function to both repress and activate transcription.
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Affiliation(s)
- Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, United States.
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17
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Reppas NB, Wade JT, Church GM, Struhl K. The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol Cell 2007; 24:747-757. [PMID: 17157257 DOI: 10.1016/j.molcel.2006.10.030] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 10/10/2006] [Accepted: 10/24/2006] [Indexed: 10/23/2022]
Abstract
We perform a genome-wide analysis of the transition between transcriptional initiation and elongation in Escherichia coli by determining the association of core RNA polymerase (RNAP) and the promoter-recognition factor sigma70 with respect to RNA transcripts. We identify 1286 sigma70-associated promoters, including many internal to known operons, and demonstrate that sigma70 is usually released very rapidly from elongating RNAP complexes. On average, RNAP density is higher at the promoter than in the coding sequence, although the ratio is highly variable among different transcribed regions. Strikingly, a significant fraction of RNAP-bound promoters is not associated with transcriptional activity, perhaps due to an intrinsic energetic barrier to promoter escape. Thus, the transition from transcriptional initiation to elongation is highly variable, often rate limiting, and in some cases is essentially blocked such that RNAP is effectively "poised" to transcribe only under the appropriate environmental conditions. The genomic pattern of RNAP density in E. coli differs from that in yeast and mammalian cells.
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Affiliation(s)
- Nikos B Reppas
- Harvard University Biophysics Program, Harvard Medical School, Boston, Massachusetts 02115; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Joseph T Wade
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115.
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18
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Somsen OJG, Keukens LB, de Keijzer MN, van Hoek A, van Amerongen H. Structural heterogeneity in DNA: temperature dependence of 2-aminopurine fluorescence in dinucleotides. Chemphyschem 2007; 6:1622-7. [PMID: 16082664 DOI: 10.1002/cphc.200400648] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The fluorescent base analogue 2-aminopurine is a sensitive probe for local dynamics of DNA. Its fluorescence is quenched by interaction with the neighboring bases, but the underlying mechanisms are still under investigation. We studied 2-aminopurine fluorescence in dinucleotides with each of the natural bases. Consistently, two of the four fluorescence-decay components depend strongly on temperature. Our results indicate that these components are due to the excited-state dynamics of a single conformational state. We propose a variation of the gating model in which transient unstacking occurs in the excited state.
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Affiliation(s)
- Oscar J G Somsen
- Wageningen University, Laboratory of Biophysics, P.O. Box 8128, 6700 ET Wageningen, The Netherlands.
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19
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Abstract
Information theory was used to build a promoter model that accounts for the -10, the -35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base -7, rather than -11, of the -10 may be flipping to initiate transcription. We found that the sequence conservation of sigma70 binding sites is 6.5 +/- 0.1 bits. Some promoters lack a -35 region, but have a 6.7 +/- 0.2 bit extended -10, almost the same information as the bipartite promoter. These results and similarities between the contacts in the extended -10 binding and the -35 suggest that the flexible bipartite sigma factor evolved from a simpler polymerase. Binding predicted by the bipartite model is enriched around 35 bases upstream of the translational start. This distance is the smallest 5' mRNA leader necessary for ribosome binding, suggesting that selective pressure minimizes transcript length. The promoter model was combined with models of the transcription factors Fur and Lrp to locate new promoters, to quantify promoter strengths, and to predict activation and repression. Finally, the DNA-bending proteins Fis, H-NS and IHF frequently have sites within one DNA persistence length from the -35, so bending allows distal activators to reach the polymerase.
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Affiliation(s)
| | | | | | - Thomas D. Schneider
- To whom correspondence should be addressed. Tel: +1 301 846 5581; Fax: +1 301 846 5598;
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Brodolin K, Zenkin N, Severinov K. Remodeling of the sigma70 subunit non-template DNA strand contacts during the final step of transcription initiation. J Mol Biol 2005; 350:930-7. [PMID: 15978618 DOI: 10.1016/j.jmb.2005.05.048] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2005] [Revised: 05/18/2005] [Accepted: 05/19/2005] [Indexed: 10/25/2022]
Abstract
Transcription initiation in bacteria requires melting of approximately 13 bp of promoter DNA. The mechanism of the melting process is not fully understood. Escherichia coli RNA polymerase bearing a deletion of the beta subunit lobe I (amino acid residues 186-433) initiates melting of the -10 promoter element but cannot propagate the melting downstream, towards the transcription initiation start site (+1). However, in the presence of nucleotides, stable downstream melting is induced. Here, we studied lacUV5 promoter complexes formed by the mutant enzyme by cross-linking RNA polymerase subunits to single-stranded DNA in the transcription bubble. In the absence of NTPs, a contact between the sigma70 subunit and the non-template strand of the -10 promoter element was detected. This contact disappeared in the presence of NTPs. Instead, a new sigma70-DNA contact as well as stable beta' and beta subunit contacts with the non-template DNA downstream of the -10 promoter element were established. In terms of the two-step (upstream initiation/downstream propagation) model of promoter melting, our data suggest that beta lobe I induces the propagation of promoter melting by directing downstream promoter DNA duplex towards the downstream DNA-binding channel (beta' clamp). Establishment of downstream contacts leads to remodeling of upstream interactions between sigma70 and the -10 promoter element that might facilitate promoter escape and sigma release.
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Affiliation(s)
- Konstantin Brodolin
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq. 2, Moscow 123182, Russia.
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Roy S, Semsey S, Liu M, Gussin GN, Adhya S. GalR represses galP1 by inhibiting the rate-determining open complex formation through RNA polymerase contact: a GalR negative control mutant. J Mol Biol 2005; 344:609-18. [PMID: 15533432 DOI: 10.1016/j.jmb.2004.09.070] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Revised: 09/23/2004] [Accepted: 09/23/2004] [Indexed: 11/19/2022]
Abstract
GalR represses the galP1 promoter by a DNA looping-independent mechanism. Equilibrium binding of GalR and RNA polymerase to DNA, and real-time kinetics of base-pair distortion (isomerization) showed that the equilibrium dissociation constant of RNA polymerase-P1 closed complexes is largely unaffected in the presence of saturating GalR, indicating that mutual antagonism (steric hindrance) of the regulator and the RNA polymerase does not occur at this promoter. In fluorescence kinetics with 2-AP labeled P1 DNA, GalR inhibited the slower of the two-step base-pair distortion process. We isolated a negative control GalR mutant, S29R, which while bound to the operator DNA was incapable of repression of P1. Based on these results and previous demonstration that repression requires the C-terminal domain of the alpha subunit (alpha-CTD) of RNA polymerase, we propose that GalR establishes contact with alpha-CTD at the last resolved isomerization intermediate, forming a kinetic trap.
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Affiliation(s)
- Siddhartha Roy
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Lee HJ, Lim HM, Adhya S. An unsubstituted C2 hydrogen of adenine is critical and sufficient at the -11 position of a promoter to signal base pair deformation. J Biol Chem 2004; 279:16899-902. [PMID: 14990576 DOI: 10.1074/jbc.c400054200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The conserved A:T base pair at the -11 position of the promoters in Escherichia coli is very sensitive to substitutions. In vitro transcription with the galP1 promoter having a natural or unnatural base in either strand at position -11 showed that only a purine base with no side group at C2 in the nontemplate strand is transcriptionally potent; neither a purine with an amino group at C2 nor a pyrimidine support transcription. The amino group at C6 in the omnipresent adenine at -11 does not play any role in promoting transcription. The nature of the base, complementary or noncomplementary, at -11 in the template strand also does not influence transcription. We propose that the adenine, by becoming extrahelical, interacts with an amino acid(s) of the 2.3-2.4 region of sigma for which an unsubstituted C2 hydrogen is critical.
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Affiliation(s)
- Hee Jung Lee
- Department of Biology, College of Natural Sciences, Chungnam National University, Taejon 305-764, Republic of Korea
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