1
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Shiver AL, Osadnik H, Peters JM, Mooney RA, Wu PI, Henry KK, Braberg H, Krogan NJ, Hu JC, Landick R, Huang KC, Gross CA. Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs. Mol Cell 2021; 81:2201-2215.e9. [PMID: 34019789 PMCID: PMC8484514 DOI: 10.1016/j.molcel.2021.04.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 01/25/2021] [Accepted: 04/29/2021] [Indexed: 11/16/2022]
Abstract
The multi-subunit bacterial RNA polymerase (RNAP) and its associated regulators carry out transcription and integrate myriad regulatory signals. Numerous studies have interrogated RNAP mechanism, and RNAP mutations drive Escherichia coli adaptation to many health- and industry-relevant environments, yet a paucity of systematic analyses hampers our understanding of the fitness trade-offs from altering RNAP function. Here, we conduct a chemical-genetic analysis of a library of RNAP mutants. We discover phenotypes for non-essential insertions, show that clustering mutant phenotypes increases their predictive power for drawing functional inferences, and demonstrate that some RNA polymerase mutants both decrease average cell length and prevent killing by cell-wall targeting antibiotics. Our findings demonstrate that RNAP chemical-genetic interactions provide a general platform for interrogating structure-function relationships in vivo and for identifying physiological trade-offs of mutations, including those relevant for disease and biotechnology. This strategy should have broad utility for illuminating the role of other important protein complexes.
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Affiliation(s)
- Anthony L Shiver
- Graduate Group in Biophysics, University of California San Francisco, San Francisco, CA 94158, USA; Department of Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hendrik Osadnik
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jason M Peters
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Rachel A Mooney
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peter I Wu
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Kemardo K Henry
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James C Hu
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA 94158, USA; California Institute of Quantitative Biology, University of California San Francisco, San Francisco, CA 94158, USA.
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2
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Structural visualization of transcription activated by a multidrug-sensing MerR family regulator. Nat Commun 2021; 12:2702. [PMID: 33976201 PMCID: PMC8113463 DOI: 10.1038/s41467-021-22990-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 04/08/2021] [Indexed: 01/25/2023] Open
Abstract
Bacterial RNA polymerase (RNAP) holoenzyme initiates transcription by recognizing the conserved -35 and -10 promoter elements that are optimally separated by a 17-bp spacer. The MerR family of transcriptional regulators activate suboptimal 19-20 bp spacer promoters in response to myriad cellular signals, ranging from heavy metals to drug-like compounds. The regulation of transcription by MerR family regulators is not fully understood. Here we report one crystal structure of a multidrug-sensing MerR family regulator EcmrR and nine cryo-electron microscopy structures that capture the EcmrR-dependent transcription process from promoter opening to initial transcription to RNA elongation. These structures reveal that EcmrR is a dual ligand-binding factor that reshapes the suboptimal 19-bp spacer DNA to enable optimal promoter recognition, sustains promoter remodeling to stabilize initial transcribing complexes, and finally dissociates from the promoter to reverse DNA remodeling and facilitate the transition to elongation. Our findings yield a comprehensive model for transcription regulation by MerR family factors and provide insights into the transition from transcription initiation to elongation.
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3
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de Dios R, Santero E, Reyes-Ramírez F. Extracytoplasmic Function σ Factors as Tools for Coordinating Stress Responses. Int J Mol Sci 2021; 22:ijms22083900. [PMID: 33918849 PMCID: PMC8103513 DOI: 10.3390/ijms22083900] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 01/03/2023] Open
Abstract
The ability of bacterial core RNA polymerase (RNAP) to interact with different σ factors, thereby forming a variety of holoenzymes with different specificities, represents a powerful tool to coordinately reprogram gene expression. Extracytoplasmic function σ factors (ECFs), which are the largest and most diverse family of alternative σ factors, frequently participate in stress responses. The classification of ECFs in 157 different groups according to their phylogenetic relationships and genomic context has revealed their diversity. Here, we have clustered 55 ECF groups with experimentally studied representatives into two broad classes of stress responses. The remaining 102 groups still lack any mechanistic or functional insight, representing a myriad of systems yet to explore. In this work, we review the main features of ECFs and discuss the different mechanisms controlling their production and activity, and how they lead to a functional stress response. Finally, we focus in more detail on two well-characterized ECFs, for which the mechanisms to detect and respond to stress are complex and completely different: Escherichia coli RpoE, which is the best characterized ECF and whose structural and functional studies have provided key insights into the transcription initiation by ECF-RNAP holoenzymes, and the ECF15-type EcfG, the master regulator of the general stress response in Alphaproteobacteria.
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4
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Shin Y, Qayyum MZ, Pupov D, Esyunina D, Kulbachinskiy A, Murakami KS. Structural basis of ribosomal RNA transcription regulation. Nat Commun 2021; 12:528. [PMID: 33483500 PMCID: PMC7822876 DOI: 10.1038/s41467-020-20776-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 12/14/2020] [Indexed: 01/30/2023] Open
Abstract
Ribosomal RNA (rRNA) is most highly expressed in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. Here, we determined cryo-electron microscopy structures of the Escherichia coli RNA polymerase (RNAP) σ70 holoenzyme during rRNA promoter recognition with and without DksA/ppGpp. RNAP contacts the UP element using dimerized α subunit carboxyl-terminal domains and scrunches the template DNA with the σ finger and β' lid to select the transcription start site favorable for rapid promoter escape. Promoter binding induces conformational change of σ domain 2 that opens a gate for DNA loading and ejects σ1.1 from the RNAP cleft to facilitate open complex formation. DksA/ppGpp binding also opens the DNA loading gate, which is not coupled to σ1.1 ejection and impedes open complex formation. These results provide a molecular basis for the exceptionally active rRNA transcription and its vulnerability to DksA/ppGpp.
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Affiliation(s)
- Yeonoh Shin
- grid.29857.310000 0001 2097 4281Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802 USA
| | - M. Zuhaib Qayyum
- grid.29857.310000 0001 2097 4281Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802 USA
| | - Danil Pupov
- grid.4886.20000 0001 2192 9124Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182 Russia
| | - Daria Esyunina
- grid.4886.20000 0001 2192 9124Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182 Russia
| | - Andrey Kulbachinskiy
- grid.4886.20000 0001 2192 9124Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182 Russia
| | - Katsuhiko S. Murakami
- grid.29857.310000 0001 2097 4281Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802 USA
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5
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Vishwakarma RK, Brodolin K. The σ Subunit-Remodeling Factors: An Emerging Paradigms of Transcription Regulation. Front Microbiol 2020; 11:1798. [PMID: 32849409 PMCID: PMC7403470 DOI: 10.3389/fmicb.2020.01798] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/09/2020] [Indexed: 11/13/2022] Open
Abstract
Transcription initiation is a key checkpoint and highly regulated step of gene expression. The sigma (σ) subunit of RNA polymerase (RNAP) controls all transcription initiation steps, from recognition of the -10/-35 promoter elements, upon formation of the closed promoter complex (RPc), to stabilization of the open promoter complex (RPo) and stimulation of the primary steps in RNA synthesis. The canonical mechanism to regulate σ activity upon transcription initiation relies on activators that recognize specific DNA motifs and recruit RNAP to promoters. This mini-review describes an emerging group of transcriptional regulators that form a complex with σ or/and RNAP prior to promoter binding, remodel the σ subunit conformation, and thus modify RNAP activity. Such strategy is widely used by bacteriophages to appropriate the host RNAP. Recent findings on RNAP-binding protein A (RbpA) from Mycobacterium tuberculosis and Crl from Escherichia coli suggest that activator-driven changes in σ conformation can be a widespread regulatory mechanism in bacteria.
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Affiliation(s)
- Rishi Kishore Vishwakarma
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, Montpellier, France
| | - Konstantin Brodolin
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, Montpellier, France
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6
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Structural basis for transcription activation by Crl through tethering of σ S and RNA polymerase. Proc Natl Acad Sci U S A 2019; 116:18923-18927. [PMID: 31484766 DOI: 10.1073/pnas.1910827116] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In bacteria, a primary σ-factor associates with the core RNA polymerase (RNAP) to control most transcription initiation, while alternative σ-factors are used to coordinate expression of additional regulons in response to environmental conditions. Many alternative σ-factors are negatively regulated by anti-σ-factors. In Escherichia coli, Salmonella enterica, and many other γ-proteobacteria, the transcription factor Crl positively regulates the alternative σS-regulon by promoting the association of σS with RNAP without interacting with promoter DNA. The molecular mechanism for Crl activity is unknown. Here, we determined a single-particle cryo-electron microscopy structure of Crl-σS-RNAP in an open promoter complex with a σS-regulon promoter. In addition to previously predicted interactions between Crl and domain 2 of σS (σS 2), the structure, along with p-benzoylphenylalanine cross-linking, reveals that Crl interacts with a structural element of the RNAP β'-subunit that we call the β'-clamp-toe (β'CT). Deletion of the β'CT decreases activation by Crl without affecting basal transcription, highlighting the functional importance of the Crl-β'CT interaction. We conclude that Crl activates σS-dependent transcription in part through stabilizing σS-RNAP by tethering σS 2 and the β'CT. We propose that Crl, and other transcription activators that may use similar mechanisms, be designated σ-activators.
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7
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Sun D, Liu C, Zhu J, Liu W. Connecting Metabolic Pathways: Sigma Factors in Streptomyces spp. Front Microbiol 2017; 8:2546. [PMID: 29312231 PMCID: PMC5742136 DOI: 10.3389/fmicb.2017.02546] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/07/2017] [Indexed: 11/13/2022] Open
Abstract
The gram-positive filamentous bacterium Streptomyces is one of the largest resources for bioactive metabolites, particularly antibiotics. Antibiotic production and other metabolic processes are tightly regulated at the transcriptional level. Sigma (σ) factors are components of bacterial RNA polymerases that determine promoter specificity. In Streptomyces, σ factors also play essential roles in signal transduction and in regulatory networks, thereby assisting in their survival in complex environments. However, our current understanding of σ factors in Streptomyces is still limited. In this mini-review, we demonstrate the roles of Streptomyces σ factors, illustrating that these serve as linkers of different metabolic pathways. Further investigations on σ factors may improve our knowledge of Streptomyces physiology and benefit exploitation of Streptomyces resources.
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Affiliation(s)
- Di Sun
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Cong Liu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jingrong Zhu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Weijie Liu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
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8
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Modulation of Global Transcriptional Regulatory Networks as a Strategy for Increasing Kanamycin Resistance of the Translational Elongation Factor-G Mutants in Escherichia coli. G3-GENES GENOMES GENETICS 2017; 7:3955-3966. [PMID: 29046437 PMCID: PMC5714492 DOI: 10.1534/g3.117.300284] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Evolve and resequence experiments have provided us a tool to understand bacterial adaptation to antibiotics. In our previous work, we used short-term evolution to isolate mutants resistant to the ribosome targeting antibiotic kanamycin, and reported that Escherichia coli develops low cost resistance to kanamycin via different point mutations in the translation Elongation Factor-G (EF-G). Furthermore, we had shown that the resistance of EF-G mutants could be increased by second site mutations in the genes rpoD/cpxA/topA/cyaA Mutations in three of these genes had been discovered in earlier screens for aminoglycoside resistance. In this work, we expand our understanding of these second site mutations, the goal being to understand how these mutations affect the activities of the mutated gene products to confer resistance. We show that the mutation in cpxA most likely results in an active Cpx stress response. Further evolution of an EF-G mutant in a higher concentration of kanamycin than what was used in our previous experiments identified the cpxA locus as a primary target for a significant increase in resistance. The mutation in cyaA results in a loss of catalytic activity and probably results in resistance via altered CRP function. Despite a reduction in cAMP levels, the CyaAN600Y mutant has a transcriptome indicative of increased CRP activity, pointing to an unknown role for CyaA and / or cAMP in gene expression. From the transcriptomes of double and single mutants, we describe the epistasis between the mutation in EF-G and these second site mutations. We show that the large scale transcriptomic changes in the topoisomerase I (FusAA608E-TopAS180L) mutant likely result from increased negative supercoiling in the cell. Finally, genes with known roles in aminoglycoside resistance were present among the misregulated genes in the mutants.
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9
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Santillán O, Ramírez-Romero MA, Lozano L, Checa A, Encarnación SM, Dávila G. Region 4 of Rhizobium etli Primary Sigma Factor (SigA) Confers Transcriptional Laxity in Escherichia coli. Front Microbiol 2016; 7:1078. [PMID: 27468278 PMCID: PMC4943231 DOI: 10.3389/fmicb.2016.01078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 06/27/2016] [Indexed: 11/13/2022] Open
Abstract
Sigma factors are RNA polymerase subunits engaged in promoter recognition and DNA strand separation during transcription initiation in bacteria. Primary sigma factors are responsible for the expression of housekeeping genes and are essential for survival. RpoD, the primary sigma factor of Escherichia coli, a γ-proteobacteria, recognizes consensus promoter sequences highly similar to those of some α-proteobacteria species. Despite this resemblance, RpoD is unable to sustain transcription from most of the α-proteobacterial promoters tested so far. In contrast, we have found that SigA, the primary sigma factor of Rhizobium etli, an α-proteobacteria, is able to transcribe E. coli promoters, although it exhibits only 48% identity (98% coverage) to RpoD. We have called this the transcriptional laxity phenomenon. Here, we show that SigA partially complements the thermo-sensitive deficiency of RpoD285 from E. coli strain UQ285 and that the SigA region σ4 is responsible for this phenotype. Sixteen out of 74 residues (21.6%) within region σ4 are variable between RpoD and SigA. Mutating these residues significantly improves SigA ability to complement E. coli UQ285. Only six of these residues fall into positions already known to interact with promoter DNA and to comprise a helix-turn-helix motif. The remaining variable positions are located on previously unexplored sites inside region σ4, specifically into the first two α-helices of the region. Neither of the variable positions confined to these helices seem to interact directly with promoter sequence; instead, we adduce that these residues participate allosterically by contributing to correct region folding and/or positioning of the HTH motif. We propose that transcriptional laxity is a mechanism for ensuring transcription in spite of naturally occurring mutations from endogenous promoters and/or horizontally transferred DNA sequences, allowing survival and fast environmental adaptation of α-proteobacteria.
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Affiliation(s)
- Orlando Santillán
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | | | - Luis Lozano
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Alberto Checa
- Programa de Genómica Funcional de Procariontes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Sergio M Encarnación
- Programa de Genómica Funcional de Procariontes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Guillermo Dávila
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico; Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de MéxicoJuriquilla, Mexico
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10
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Bird JG, Strobel EJ, Roberts JW. A universal transcription pause sequence is an element of initiation factor σ70-dependent pausing. Nucleic Acids Res 2016; 44:6732-40. [PMID: 27098041 PMCID: PMC5001585 DOI: 10.1093/nar/gkw285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/07/2016] [Indexed: 11/12/2022] Open
Abstract
The Escherichia coli σ70 initiation factor is required for a post-initiation, promoter-proximal pause essential for regulation of lambdoid phage late gene expression; potentially, σ70 acts at other sites during transcription elongation as well. The pause is induced by σ70 binding to a repeat of the promoter -10 sequence. After σ70 binding, further RNA synthesis occurs as DNA is drawn (or 'scrunched') into the enzyme complex, presumably exactly as occurs during initial synthesis from the promoter; this synthesis then pauses at a defined site several nucleotides downstream from the active center position when σ70 first engages the -10 sequence repeat. We show that the actual pause site in the stabilized, scrunched complex is the 'elemental pause sequence' recognized from its frequent occurrence in the E. coli genome. σ70 binding and the elemental pause sequence together, but neither alone, produce a substantial transcription pause.
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Affiliation(s)
- Jeremy G Bird
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Eric J Strobel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jeffrey W Roberts
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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11
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Bacterial RNA polymerase can retain σ70 throughout transcription. Proc Natl Acad Sci U S A 2016; 113:602-7. [PMID: 26733675 DOI: 10.1073/pnas.1513899113] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Production of a messenger RNA proceeds through sequential stages of transcription initiation and transcript elongation and termination. During each of these stages, RNA polymerase (RNAP) function is regulated by RNAP-associated protein factors. In bacteria, RNAP-associated σ factors are strictly required for promoter recognition and have historically been regarded as dedicated initiation factors. However, the primary σ factor in Escherichia coli, σ(70), can remain associated with RNAP during the transition from initiation to elongation, influencing events that occur after initiation. Quantitative studies on the extent of σ(70) retention have been limited to complexes halted during early elongation. Here, we used multiwavelength single-molecule fluorescence-colocalization microscopy to observe the σ(70)-RNAP complex during initiation from the λ PR' promoter and throughout the elongation of a long (>2,000-nt) transcript. Our results provide direct measurements of the fraction of actively transcribing complexes with bound σ(70) and the kinetics of σ(70) release from actively transcribing complexes. σ(70) release from mature elongation complexes was slow (0.0038 s(-1)); a substantial subpopulation of elongation complexes retained σ(70) throughout transcript elongation, and this fraction depended on the sequence of the initially transcribed region. We also show that elongation complexes containing σ(70) manifest enhanced recognition of a promoter-like pause element positioned hundreds of nucleotides downstream of the promoter. Together, the results provide a quantitative framework for understanding the postinitiation roles of σ(70) during transcription.
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12
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Chander M, Lee A, Vallery TK, Thandar M, Jiang Y, Hsu LM. Mechanisms of Very Long Abortive Transcript Release during Promoter Escape. Biochemistry 2015; 54:7393-408. [PMID: 26610896 DOI: 10.1021/acs.biochem.5b00712] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A phage T5 N25 promoter variant, DG203, undergoes the escape transition at the +16 to +19 positions after transcription initiation. By specifically examining the abortive activity of the initial transcribing complex at position +19 (ITC19), we observe the production of both GreB-sensitive and GreB-resistant VLAT19. This suggests that ITC19, which is perched on the brink of escape, is highly unstable and can achieve stabilization through either backtracking or forward translocation. Of the forward-tracked fraction, only a small percentage escapes normally (followed by stepwise elongation) to produce full-length RNA; the rest presumably hypertranslocates to release GreB-resistant VLATs. VLAT formation is dependent not only on consensus -35/-10 promoters with 17 bp spacing but also on sequence characteristics of the spacer DNA. Analysis of DG203 promoter variants containing different spacer sequences reveals that AT-rich spacers intrinsically elevate the level of VLAT formation. The AT-rich spacer of DG203 joined to the -10 box presents an UP element sequence capable of interacting with the polymerase α subunit C-terminal domain (αCTD) during the escape transition, which in turn enhances VLAT release. Utilization of the spacer/-10 region UP element by αCTD subunits requires a 10-15 bp hypertranslocation. We document the physical occurrence of hyper forward translocation using ExoIII footprinting analysis.
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Affiliation(s)
- Monica Chander
- Biology Department, Bryn Mawr College , Bryn Mawr, Pennsylvania 19010, United States
| | - Ahri Lee
- Program in Biochemistry, Mount Holyoke College , South Hadley, Massachusetts 01075, United States
| | - Tenaya K Vallery
- Program in Biochemistry, Mount Holyoke College , South Hadley, Massachusetts 01075, United States
| | - Mya Thandar
- Program in Biochemistry, Mount Holyoke College , South Hadley, Massachusetts 01075, United States
| | - Yunnan Jiang
- Program in Biochemistry, Mount Holyoke College , South Hadley, Massachusetts 01075, United States
| | - Lilian M Hsu
- Program in Biochemistry, Mount Holyoke College , South Hadley, Massachusetts 01075, United States
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13
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Paget MS. Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution. Biomolecules 2015; 5:1245-65. [PMID: 26131973 PMCID: PMC4598750 DOI: 10.3390/biom5031245] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/20/2015] [Accepted: 06/01/2015] [Indexed: 12/18/2022] Open
Abstract
Sigma factors are multi-domain subunits of bacterial RNA polymerase (RNAP) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in RNA synthesis. This review focuses on the structure and function of the major sigma-70 class that includes the housekeeping sigma factor (Group 1) that directs the bulk of transcription during active growth, and structurally-related alternative sigma factors (Groups 2-4) that control a wide variety of adaptive responses such as morphological development and the management of stress. A recurring theme in sigma factor control is their sequestration by anti-sigma factors that occlude their RNAP-binding determinants. Sigma factors are then released through a wide variety of mechanisms, often involving branched signal transduction pathways that allow the integration of distinct signals. Three major strategies for sigma release are discussed: regulated proteolysis, partner-switching, and direct sensing by the anti-sigma factor.
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Affiliation(s)
- Mark S Paget
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK.
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14
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Madhushani A, del Peso-Santos T, Moreno R, Rojo F, Shingler V. Transcriptional and translational control through the 5′-leader region of thedmpRmaster regulatory gene of phenol metabolism. Environ Microbiol 2014; 17:119-33. [DOI: 10.1111/1462-2920.12511] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/11/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Anjana Madhushani
- Department of Molecular Biology; Umeå University; Umeå SE 90187 Sweden
| | | | - Renata Moreno
- Departamento de Biotecnologia Microbiana; Centro Nacional de Biotecnologia; CSIC; Madrid Spain
| | - Fernando Rojo
- Departamento de Biotecnologia Microbiana; Centro Nacional de Biotecnologia; CSIC; Madrid Spain
| | - Victoria Shingler
- Department of Molecular Biology; Umeå University; Umeå SE 90187 Sweden
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15
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Key features of σS required for specific recognition by Crl, a transcription factor promoting assembly of RNA polymerase holoenzyme. Proc Natl Acad Sci U S A 2013; 110:15955-60. [PMID: 24043782 DOI: 10.1073/pnas.1311642110] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Bacteria use multiple sigma factors to coordinate gene expression in response to environmental perturbations. In Escherichia coli and other γ-proteobacteria, the transcription factor Crl stimulates σ(S)-dependent transcription during times of cellular stress by promoting the association of σ(S) with core RNA polymerase. The molecular basis for specific recognition of σ(S) by Crl, rather than the homologous and more abundant primary sigma factor σ(70), is unknown. Here we use bacterial two-hybrid analysis in vivo and p-benzoyl-phenylalanine cross-linking in vitro to define the features in σ(S) responsible for specific recognition by Crl. We identify residues in σ(S) conserved domain 2 (σ(S)2) that are necessary and sufficient to allow recognition of σ(70) conserved domain 2 by Crl, one near the promoter-melting region and the other at the position where a large nonconserved region interrupts the sequence of σ(70). We then use luminescence resonance energy transfer to demonstrate directly that Crl promotes holoenzyme assembly using these specificity determinants on σ(S). Our results explain how Crl distinguishes between sigma factors that are largely homologous and activates discrete sets of promoters even though it does not bind to promoter DNA.
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16
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Chlamydia trachomatis protein GrgA activates transcription by contacting the nonconserved region of σ66. Proc Natl Acad Sci U S A 2012; 109:16870-5. [PMID: 23027952 DOI: 10.1073/pnas.1207300109] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacterial RNA polymerase holoenzyme consists of a catalytic core enzyme in complex with a σ factor that is required for promoter-specific transcription initiation. Primary, or housekeeping, σ factors are responsible for most of the gene expression that occurs during the exponential phase of growth. Primary σ factors share four regions of conserved sequence, regions 1-4, which have been further subdivided. Many primary σ factors also contain a nonconserved region (NCR) located between subregions 1.2 and 2.1, which can vary widely in length. Interactions between the NCR of the primary σ factor of Escherichia coli, σ(70), and the β' subunit of the E. coli core enzyme have been shown to influence gene expression, suggesting that the NCR of primary σ factors represents a potential target for transcription regulation. Here, we report the identification and characterization of a previously undocumented Chlamydia trachomatis transcription factor, designated GrgA (general regulator of genes A). We demonstrate in vitro that GrgA is a DNA-binding protein that can stimulate transcription from a range of σ(66)-dependent promoters. We further show that GrgA activates transcription by contacting the NCR of the primary σ factor of C. trachomatis, σ(66). Our findings suggest GrgA serves as an important regulator of σ(66)-dependent transcription in C. trachomatis. Furthermore, because GrgA is present only in chlamydiae, our findings highlight how nonconserved regions of the bacterial RNA polymerase can be targets of regulatory factors that are unique to particular organisms.
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17
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Engineering of Rhodococcus cell catalysts for tolerance improvement by sigma factor mutation and active plasmid partition. ACTA ACUST UNITED AC 2012; 39:1421-30. [DOI: 10.1007/s10295-012-1146-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 05/03/2012] [Indexed: 10/28/2022]
Abstract
Abstract
Tolerance to various stresses is a key phenotype for cell catalysts, which are used widely in bioproduction of diverse valuable chemicals. Using the Rhodococcus ruber TH strain, which exhibits high nitrile hydratase activity, as the target cell catalyst for acrylamide production, we established a method to improve cell tolerance by stably introducing global transcription perturbation. The σ70 gene (sigA) of R. ruber was cloned and randomly mutated. An R. ruber TH3/pNV-sigAM library containing additional sigA mutants was constructed and used for survival selection. The TH3/M4N1-59 mutant was selected by acrylonitrile/acrylamide double stress and exhibited a 160 % extension of the half-life of nitrile hydratase upon exposure to 40 % acrylamide. A redesigned parDEM gene was introduced to Rhodococcus to accomplish stable inheritance of plasmids. A two-batch acrylonitrile hydration reaction was performed using the engineered cells as a catalyst. Compared to TH3, the acrylamide productivity of TH3/M4N1-59DEM catalysis increased by 27.8 and 37.5 % in the first and second bioreaction batches, respectively. These data suggest a novel method for increasing the bioconversion productivity of target chemicals through sigA mutation of the cell catalyst.
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18
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Affiliation(s)
- Sofia Österberg
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden;
| | | | - Victoria Shingler
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden;
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19
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Effects of substitutions at position 180 in the Escherichia coli RNA polymerase σ 70 subunit. J Biosci 2011; 36:43-54. [PMID: 21451247 DOI: 10.1007/s12038-011-9007-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In order to investigate the role of His180 residue, located in the non-conserved region of the σ 70 subunit of Escherichia coli RNA polymerase, two mutant variants of the protein with substitutions for either alanine or glutamic acid were constructed and purified using the IMPACT system. The ability of mutant σ 70 subunits to interact with core RNA polymerase was investigated using native gel-electrophoresis. The properties of the corresponding reconstituted holoenzymes, as provided by gel shift analysis of their complexes with single- and double-stranded promoter-like DNA and by in vitro transcription experiments, allowed one to deduce that His180 influences several steps of transcription initiation, including core binding, promoter DNA recognition and open complex formation.
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20
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Abstract
During transcription initiation in vitro, prokaryotic and eukaryotic RNA polymerase (RNAP) can engage in abortive initiation-the synthesis and release of short (2 to 15 nucleotides) RNA transcripts-before productive initiation. It has not been known whether abortive initiation occurs in vivo. Using hybridization with locked nucleic acid probes, we directly detected abortive transcripts in bacteria. In addition, we show that in vivo abortive initiation shows characteristics of in vitro abortive initiation: Abortive initiation increases upon stabilizing interactions between RNAP and either promoter DNA or sigma factor, and also upon deleting elongation factor GreA. Abortive transcripts may have functional roles in regulating gene expression in vivo.
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Affiliation(s)
- Seth R Goldman
- Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
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21
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Nickels BE. Genetic assays to define and characterize protein-protein interactions involved in gene regulation. Methods 2008; 47:53-62. [PMID: 18952173 DOI: 10.1016/j.ymeth.2008.10.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 10/06/2008] [Accepted: 10/08/2008] [Indexed: 11/18/2022] Open
Abstract
Transcription can be regulated during initiation, elongation, and termination by an enormous variety of regulatory factors. A critical step in obtaining a mechanistic understanding of regulatory factor function is the determination of whether the regulatory factor exerts its effect through direct contact with the transcription machinery. Here I describe the application of a transcription activation-based bacterial two-hybrid assay that is useful for the identification and genetic dissection of protein-protein interactions involved in gene regulation. I provide examples of how this two-hybrid system can be adapted for the study of "global" regulatory factors, sequence-specific DNA-binding proteins, and interactions that occur between two subunits of RNA polymerase (RNAP). These assays facilitate the isolation and characterization of informative amino acid substitutions within both regulatory factors and RNAP. Furthermore, these assays often enable the study of substitutions in essential domains of RNAP that would be lethal in their natural context.
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Affiliation(s)
- Bryce E Nickels
- Waksman Institute and Department of Genetics, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854, United States.
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22
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Yuan AH, Gregory BD, Sharp JS, McCleary KD, Dove SL, Hochschild A. Rsd family proteins make simultaneous interactions with regions 2 and 4 of the primary sigma factor. Mol Microbiol 2008; 70:1136-51. [PMID: 18826409 DOI: 10.1111/j.1365-2958.2008.06462.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial anti-sigma factors typically regulate sigma factor function by restricting the access of their cognate sigma factors to the RNA polymerase (RNAP) core enzyme. The Escherichia coli Rsd protein forms a complex with the primary sigma factor, sigma(70), inhibits sigma(70)-dependent transcription in vitro, and has been proposed to function as a sigma(70)-specific anti-sigma factor, thereby facilitating the utilization of alternative sigma factors. In prior work, Rsd has been shown to interact with conserved region 4 of sigma(70), but it is not known whether this interaction suffices to account for the regulatory functions of Rsd. Here we show that Rsd and the Rsd orthologue AlgQ, a global regulator of gene expression in Pseudomonas aeruginosa, interact with conserved region 2 of sigma(70). We show further that Rsd and AlgQ can interact simultaneously with regions 2 and 4 of sigma(70). Our findings establish that the abilities of Rsd and AlgQ to interact with sigma(70) region 2 are important determinants of their in vitro and in vivo activities.
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Affiliation(s)
- Andy H Yuan
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
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23
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Advances in bacterial promoter recognition and its control by factors that do not bind DNA. Nat Rev Microbiol 2008; 6:507-19. [PMID: 18521075 DOI: 10.1038/nrmicro1912] [Citation(s) in RCA: 238] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Early work identified two promoter regions, the -10 and -35 elements, that interact sequence specifically with bacterial RNA polymerase (RNAP). However, we now know that several additional promoter elements contact RNAP and influence transcription initiation. Furthermore, our picture of promoter control has evolved beyond one in which regulation results solely from activators and repressors that bind to DNA sequences near the RNAP binding site: many important transcription factors bind directly to RNAP without binding to DNA. These factors can target promoters by affecting specific kinetic steps on the pathway to open complex formation, thereby regulating RNA output from specific promoters.
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24
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Glaser BT, Bergendahl V, Thompson NE, Olson B, Burgess RR. LRET-Based HTS of a Small-Compound Library for Inhibitors of Bacterial RNA Polymerase. Assay Drug Dev Technol 2007; 5:759-68. [DOI: 10.1089/adt.2007.095] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Bryan T. Glaser
- McArdle Laboratory for Cancer Research, University of Wisconsin—Madison, Madison WI
| | - Veit Bergendahl
- McArdle Laboratory for Cancer Research, University of Wisconsin—Madison, Madison WI
- Genomics Center of Wisconsin, Madison, WI
| | - Nancy E. Thompson
- McArdle Laboratory for Cancer Research, University of Wisconsin—Madison, Madison WI
| | - Brian Olson
- McArdle Laboratory for Cancer Research, University of Wisconsin—Madison, Madison WI
- University of Wisconsin Paul P. Carbone Comprehensive Cancer Center, Madison, WI
| | - Richard R. Burgess
- McArdle Laboratory for Cancer Research, University of Wisconsin—Madison, Madison WI
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