1
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Clamp Interactions with +3/+6 Duplex and Upstream-to-Downstream Allosteric Effects in Late Steps of Forming a Stable RNA Polymerase-Promoter Open Complex. J Mol Biol 2023; 435:167990. [PMID: 36736885 DOI: 10.1016/j.jmb.2023.167990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/04/2023]
Abstract
Stable 37 °C open complexes (OC) of E. coli RNA polymerase (RNAP) at λPR and T7A1 promoters form at similar rates but have very different lifetimes. To understand the downstream interactions responsible for OC lifetime, how promoter sequence directs them and when they form, we report lifetimes of stable OC and unstable late (I2) intermediates for promoters with different combinations of λPR (L) and T7A1 (T) discriminators, core promoters and UP elements. I2 lifetimes are similarly short, while stable OC lifetimes differ greatly, determined largely by the discriminator and modulated by core-promoter and UP elements. The free energy change ΔG3o for I2 → stable OC is approximately -4 kcal more favorable for L-discriminator than for T-discriminator promoters. Downstream-truncation at +6 (DT+6) greatly destabilizes OC at L-discriminator but not T-discriminator promoters, making all ΔG3o values similar (approximately -4 kcal). Urea reduces OC lifetime greatly by affecting ΔG3o. We deduce that urea acts by disfavoring coupled folding of key elements of the β'-clamp, that I2 is an open-clamp OC, and that clamp-closing in I2 → stable OC involves coupled folding. Differences in ΔG3o between downstream-truncated and full-length promoters yield contributions to ΔG3o from interactions with downstream mobile elements (DME) including β-lobe and β'-jaw, more favorable for L-discriminator than for T-discriminator promoters. We deduce how competition between far-downstream DNA and σ70 region 1.1 affects ΔG3o values. We discuss variant-specific ΔG3o contributions in terms of the allosteric network by which differences in discriminator and -10 sequence are sensed and transmitted downstream to affect DME-duplex interactions in I2 → stable OC.
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2
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Pletnev P, Pupov D, Pshanichnaya L, Esyunina D, Petushkov I, Nesterchuk M, Osterman I, Rubtsova M, Mardanov A, Ravin N, Sergiev P, Kulbachinskiy A, Dontsova O. Rewiring of growth-dependent transcription regulation by a point mutation in region 1.1 of the housekeeping σ factor. Nucleic Acids Res 2020; 48:10802-10819. [PMID: 32997144 PMCID: PMC7641759 DOI: 10.1093/nar/gkaa798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 09/09/2020] [Accepted: 09/12/2020] [Indexed: 01/24/2023] Open
Abstract
In bacteria, rapid adaptation to changing environmental conditions depends on the interplay between housekeeping and alternative σ factors, responsible for transcription of specific regulons by RNA polymerase (RNAP). In comparison with alternative σ factors, primary σs contain poorly conserved region 1.1, whose functions in transcription are only partially understood. We found that a single mutation in region 1.1 in Escherichia coli σ70 rewires transcription regulation during cell growth resulting in profound phenotypic changes. Despite its destabilizing effect on promoter complexes, this mutation increases the activity of rRNA promoters and also decreases RNAP sensitivity to the major regulator of stringent response DksA. Using total RNA sequencing combined with single-cell analysis of gene expression we showed that changes in region 1.1 disrupt the balance between the "greed" and "fear" strategies thus making the cells more susceptible to environmental threats and antibiotics. Our results reveal an unexpected role of σ region 1.1 in growth-dependent transcription regulation and suggest that changes in this region may facilitate rapid switching of RNAP properties in evolving bacterial populations.
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Affiliation(s)
- Philipp Pletnev
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Danil Pupov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow,123182, Russia
| | | | - Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow,123182, Russia
| | - Ivan Petushkov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow,123182, Russia
| | - Mikhail Nesterchuk
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143028, Russia
| | - Ilya Osterman
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143028, Russia
| | - Maria Rubtsova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143028, Russia
| | - Andrey Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Nikolai Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Petr Sergiev
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143028, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.,Institute of Functional Genomics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow,123182, Russia
| | - Olga Dontsova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143028, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
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3
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Harbottle J, Zenkin N. Ureidothiophene inhibits interaction of bacterial RNA polymerase with -10 promotor element. Nucleic Acids Res 2020; 48:7914-7923. [PMID: 32652039 PMCID: PMC7430646 DOI: 10.1093/nar/gkaa591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/26/2020] [Accepted: 07/05/2020] [Indexed: 01/25/2023] Open
Abstract
Bacterial RNA polymerase is a potent target for antibiotics, which utilize a plethora of different modes of action, some of which are still not fully understood. Ureidothiophene (Urd) was found in a screen of a library of chemical compounds for ability to inhibit bacterial transcription. The mechanism of Urd action is not known. Here, we show that Urd inhibits transcription at the early stage of closed complex formation by blocking interaction of RNA polymerase with the promoter -10 element, while not affecting interactions with -35 element or steps of transcription after promoter closed complex formation. We show that mutation in the region 1.2 of initiation factor σ decreases sensitivity to Urd. The results suggest that Urd may directly target σ region 1.2, which allosterically controls the recognition of -10 element by σ region 2. Alternatively, Urd may block conformational changes of the holoenzyme required for engagement with -10 promoter element, although by a mechanism distinct from that of antibiotic fidaxomycin (lipiarmycin). The results suggest a new mode of transcription inhibition involving the regulatory domain of σ subunit, and potentially pinpoint a novel target for development of new antibacterials.
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Affiliation(s)
- John Harbottle
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle Upon Tyne NE2 4AX, UK
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle Upon Tyne NE2 4AX, UK
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4
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Bervoets I, Charlier D. Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology. FEMS Microbiol Rev 2019; 43:304-339. [PMID: 30721976 PMCID: PMC6524683 DOI: 10.1093/femsre/fuz001] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 01/21/2019] [Indexed: 12/15/2022] Open
Abstract
Gene expression occurs in two essential steps: transcription and translation. In bacteria, the two processes are tightly coupled in time and space, and highly regulated. Tight regulation of gene expression is crucial. It limits wasteful consumption of resources and energy, prevents accumulation of potentially growth inhibiting reaction intermediates, and sustains the fitness and potential virulence of the organism in a fluctuating, competitive and frequently stressful environment. Since the onset of studies on regulation of enzyme synthesis, numerous distinct regulatory mechanisms modulating transcription and/or translation have been discovered. Mostly, various regulatory mechanisms operating at different levels in the flow of genetic information are used in combination to control and modulate the expression of a single gene or operon. Here, we provide an extensive overview of the very diverse and versatile bacterial gene regulatory mechanisms with major emphasis on their combined occurrence, intricate intertwinement and versatility. Furthermore, we discuss the potential of well-characterized basal expression and regulatory elements in synthetic biology applications, where they may ensure orthogonal, predictable and tunable expression of (heterologous) target genes and pathways, aiming at a minimal burden for the host.
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Affiliation(s)
- Indra Bervoets
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Daniel Charlier
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
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5
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Bergkessel M, Babin BM, VanderVelde D, Sweredoski MJ, Moradian A, Eggleston-Rangel R, Hess S, Tirrell DA, Artsimovitch I, Newman DK. The dormancy-specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa. Mol Microbiol 2019; 112:992-1009. [PMID: 31254296 DOI: 10.1111/mmi.14337] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2019] [Indexed: 11/27/2022]
Abstract
Though most bacteria in nature are nutritionally limited and grow slowly, our understanding of core processes like transcription comes largely from studies in model organisms doubling rapidly. We previously identified a small protein of unknown function, SutA, in a screen of proteins synthesized in Pseudomonas aeruginosa during dormancy. SutA binds RNA polymerase (RNAP), causing widespread changes in gene expression, including upregulation of the ribosomal RNA genes. Here, using biochemical and structural methods, we examine how SutA interacts with RNAP and the functional consequences of these interactions. We show that SutA comprises a central α-helix with unstructured N- and C-terminal tails, and binds to the β1 domain of RNAP. It activates transcription from the rrn promoter by both the housekeeping sigma factor holoenzyme (Eσ70 ) and the stress sigma factor holoenzyme (EσS ) in vitro, but has a greater impact on EσS . In both cases, SutA appears to affect intermediates in the open complex formation and its N-terminal tail is required for activation. The small magnitudes of in vitro effects are consistent with a role in maintaining activity required for homeostasis during dormancy. Our results add SutA to a growing list of transcription regulators that use their intrinsically disordered regions to remodel transcription complexes.
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Affiliation(s)
- Megan Bergkessel
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Brett M Babin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David VanderVelde
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Annie Moradian
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Roxana Eggleston-Rangel
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Sonja Hess
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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6
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Hook-Barnard IG, Hinton DM. Transcription Initiation by Mix and Match Elements: Flexibility for Polymerase Binding to Bacterial Promoters. GENE REGULATION AND SYSTEMS BIOLOGY 2017. [DOI: 10.1177/117762500700100020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Bacterial RNA polymerase is composed of a core of subunits (β β′, α1, α2, ω), which have RNA synthesizing activity, and a specificity factor (σ), which identifies the start of transcription by recognizing and binding to sequence elements within promoter DNA. Four core promoter consensus sequences, the –10 element, the extended –10 (TGn) element, the –35 element, and the UP elements, have been known for many years; the importance of a nontemplate G at position -5 has been recognized more recently. However, the functions of these elements are not the same. The AT-rich UP elements, the –35 elements (–35TTGACA–30), and the extended –10 (15TGn–13) are recognized as double-stranded binding elements, whereas the –5 nontemplate G is recognized in the context of single-stranded DNA at the transcription bubble. Furthermore, the –10 element (–12TATAAT–7) is recognized as both double-stranded DNA for the T:A bp at position –12 and as nontemplate, single-stranded DNA from positions –11 to –7. The single-stranded sequences at positions –11 to –7 as well as the –5 contribute to later steps in transcription initiation that involve isomerization of polymerase and separation of the promoter DNA around the transcription start site. Recent work has demonstrated that the double-stranded elements may be used in various combinations to yield an effective promoter. Thus, while some minimal number of contacts is required for promoter function, polymerase allows the elements to be mixed and matched. Interestingly, which particular elements are used does not appear to fundamentally alter the transcription bubble generated in the stable complex. In this review, we discuss the multiple steps involved in forming a transcriptionally competent polymerase/promoter complex, and we examine what is known about polymerase recognition of core promoter elements. We suggest that considering promoter elements according to their involvement in early (polymerase binding) or later (polymerase isomerization) steps in transcription initiation rather than simply from their match to conventional promoter consensus sequences is a more instructive form of promoter classification.
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Affiliation(s)
- India G. Hook-Barnard
- Gene Expression and Regulation Section, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8 Room 2A-13, Bethesda, MD 20892-0830
| | - Deborah M. Hinton
- Gene Expression and Regulation Section, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8 Room 2A-13, Bethesda, MD 20892-0830
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7
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Hubin EA, Lilic M, Darst SA, Campbell EA. Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures. Nat Commun 2017; 8:16072. [PMID: 28703128 PMCID: PMC5511352 DOI: 10.1038/ncomms16072] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/25/2017] [Indexed: 11/25/2022] Open
Abstract
The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the αCTD may play a role in Mtb transcription regulation. Our results reveal the structure of an Actinobacteria-unique insert of the RNAP β′ subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σA, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli. Understanding of the mycobacterial transcription system is useful to the development of therapeutics against tuberculosis infection. Here the authors present the crystal structure of a complete M. smegmatis RNA polymerase open promoter complex that reveals unique features of the mycobacterial polymerase.
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Affiliation(s)
- Elizabeth A Hubin
- The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Mirjana Lilic
- The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Seth A Darst
- The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
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8
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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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9
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Koroleva ON, Dubrovin EV, Tolstova AP, Kuzmina NV, Laptinskaya TV, Yaminsky IV, Drutsa VL. A hypothetical hierarchical mechanism of the self-assembly of the Escherichia coli RNA polymerase σ(70) subunit. SOFT MATTER 2016; 12:1974-1982. [PMID: 26758573 DOI: 10.1039/c5sm02934a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Diverse morphology of aggregates of amyloidogenic proteins has been attracting much attention in the last few years, and there is still no complete understanding of the relationships between various types of aggregates. In this work, we propose the model, which universally explains the formation of morphologically different (wormlike and rodlike) aggregates on the example of a σ(70) subunit of RNA polymerase, which has been recently shown to form amyloid fibrils. Aggregates were studied using AFM in solution and depolarized dynamic light scattering. The obtained results demonstrate comparably low Young's moduli of the wormlike structures (7.8-12.3 MPa) indicating less structured aggregation of monomeric proteins than that typical for β-sheet formation. To shed light on the molecular interaction of the protein during the aggregation, early stages of fibrillization of the σ(70) subunit were modeled using all-atom molecular dynamics. Simulations have shown that the σ(70) subunit is able to form quasi-symmetric extended dimers, which may further interact with each other and grow linearly. The proposed general model explains different pathways of σ(70) subunit aggregation and may be valid for other amyloid proteins.
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Affiliation(s)
- O N Koroleva
- Faculty of Chemistry, Lomonosov Moscow State University, Leninskie gory, 1/3, Moscow, 119991 Russian Federation
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10
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Morichaud Z, Chaloin L, Brodolin K. Regions 1.2 and 3.2 of the RNA Polymerase σ Subunit Promote DNA Melting and Attenuate Action of the Antibiotic Lipiarmycin. J Mol Biol 2016; 428:463-76. [DOI: 10.1016/j.jmb.2015.12.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 12/22/2015] [Accepted: 12/22/2015] [Indexed: 01/24/2023]
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11
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E. coli RNA Polymerase Determinants of Open Complex Lifetime and Structure. J Mol Biol 2015; 427:2435-2450. [PMID: 26055538 DOI: 10.1016/j.jmb.2015.05.024] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/29/2015] [Accepted: 05/29/2015] [Indexed: 11/24/2022]
Abstract
In transcription initiation by Escherichia coli RNA polymerase (RNAP), initial binding to promoter DNA triggers large conformational changes, bending downstream duplex DNA into the RNAP cleft and opening 13bp to form a short-lived open intermediate (I2). Subsequent conformational changes increase lifetimes of λPR and T7A1 open complexes (OCs) by >10(5)-fold and >10(2)-fold, respectively. OC lifetime is a target for regulation. To characterize late conformational changes, we determine effects on OC dissociation kinetics of deletions in RNAP mobile elements σ(70) region 1.1 (σ1.1), β' jaw and β' sequence insertion 3 (SI3). In very stable OC formed by the wild type WT RNAP with λPR (RPO) and by Δσ1.1 RNAP with λPR or T7A1, we conclude that downstream duplex DNA is bound to the jaw in an assembly with SI3, and bases -4 to +2 of the nontemplate strand discriminator region are stably bound in a positively charged track in the cleft. We deduce that polyanionic σ1.1 destabilizes OC by competing for binding sites in the cleft and on the jaw with the polyanionic discriminator strand and downstream duplex, respectively. Examples of σ1.1-destabilized OC are the final T7A1 OC and the λPR I3 intermediate OC. Deleting σ1.1 and either β' jaw or SI3 equalizes OC lifetimes for λPR and T7A1. DNA closing rates are similar for both promoters and all RNAP variants. We conclude that late conformational changes that stabilize OC, like early ones that bend the duplex into the cleft, are primary targets of regulation, while the intrinsic DNA opening/closing step is not.
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12
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Abstract
Transcription initiation is a highly regulated step of gene expression. Here, we discuss the series of large conformational changes set in motion by initial specific binding of bacterial RNA polymerase (RNAP) to promoter DNA and their relevance for regulation. Bending and wrapping of the upstream duplex facilitates bending of the downstream duplex into the active site cleft, nucleating opening of 13 bp in the cleft. The rate-determining opening step, driven by binding free energy, forms an unstable open complex, probably with the template strand in the active site. At some promoters, this initial open complex is greatly stabilized by rearrangements of the discriminator region between the -10 element and +1 base of the nontemplate strand and of mobile in-cleft and downstream elements of RNAP. The rate of open complex formation is regulated by effects on the rapidly-reversible steps preceding DNA opening, while open complex lifetime is regulated by effects on the stabilization of the initial open complex. Intrinsic DNA opening-closing appears less regulated. This noncovalent mechanism and its regulation exhibit many analogies to mechanisms of enzyme catalysis.
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13
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Withers R, Doherty GP, Jordan M, Yang X, Dixon NE, Lewis PJ. AtfA, a new factor in global regulation of transcription in Acinetobacter spp. Mol Microbiol 2014; 93:1130-43. [PMID: 25047957 DOI: 10.1111/mmi.12723] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2014] [Indexed: 11/29/2022]
Abstract
Acinetobacter species are widely distributed bacteria in the environment, and have recently gained notoriety as opportunistic nosocomial pathogens. Here we characterize a novel RNA polymerase-interacting protein named acidic transcription factor A, AtfA. It is small and highly acidic, and is widely distributed throughout the γ proteobacteria, including other significant pathogens in the genera Moraxella, Pseudomonas, Legionella and Vibrio. In the model species A. baylyi ADP1, deletion of atfA significantly affects expression of over 500 genes, resulting in a large cell phenotype, reduced cell fitness, impaired biofilm formation and twitching motility, and increased sensitivity to antibiotics. Deletion of atfA also causes dramatically enhanced sensitivity to ethanol, which is an important growth promoter and virulence factor in Acinetobacter spp. The results suggest that auxiliary factors of RNA polymerase with important biological roles remain to be discovered.
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Affiliation(s)
- Ryan Withers
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
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14
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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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15
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Phage T7 Gp2 inhibition of Escherichia coli RNA polymerase involves misappropriation of σ70 domain 1.1. Proc Natl Acad Sci U S A 2013; 110:19772-7. [PMID: 24218560 DOI: 10.1073/pnas.1314576110] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Bacteriophage T7 encodes an essential inhibitor of the Escherichia coli host RNA polymerase (RNAP), the product of gene 2 (Gp2). We determined a series of X-ray crystal structures of E. coli RNAP holoenzyme with or without Gp2. The results define the structure and location of the RNAP σ(70) subunit domain 1.1(σ(1.1)(70)) inside the RNAP active site channel, where it must be displaced by the DNA upon formation of the open promoter complex. The structures and associated data, combined with previous results, allow for a complete delineation of the mechanism for Gp2 inhibition of E. coli RNAP. In the primary inhibition mechanism, Gp2 forms a protein-protein interaction with σ(1.1)(70), preventing the normal egress of σ(1.1)(70) from the RNAP active site channel. Gp2 thus misappropriates a domain of the RNAP holoenzyme, σ(1.1)(70), to inhibit the function of the enzyme.
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Fitness, stress resistance, and extraintestinal virulence in Escherichia coli. Infect Immun 2013; 81:2733-42. [PMID: 23690401 DOI: 10.1128/iai.01329-12] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The extraintestinal virulence of Escherichia coli is dependent on numerous virulence genes. However, there is growing evidence for a role of the metabolic properties and stress responses of strains in pathogenesis. We assessed the respective roles of these factors in strain virulence by developing phenotypic assays for measuring in vitro individual and competitive fitness and the general stress response, which we applied to 82 commensal and extraintestinal pathogenic E. coli strains previously tested in a mouse model of sepsis. Individual fitness properties, in terms of maximum growth rates in various media (Luria-Bertani broth with and without iron chelator, minimal medium supplemented with gluconate, and human urine) and competitive fitness properties, estimated as the mean relative growth rate per generation in mixed cultures with a reference fluorescent E. coli strain, were highly diverse between strains. The activity of the main general stress response regulator, RpoS, as determined by iodine staining of the colonies, H2O2 resistance, and rpoS sequencing, was also highly variable. No correlation between strain fitness and stress resistance and virulence in the mouse model was found, except that the maximum growth rate in urine was higher for virulent strains. Multivariate analysis showed that the number of virulence factors was the only independent factor explaining the virulence in mice. At the species level, growth capacity and stress resistance are heterogeneous properties that do not contribute significantly to the intrinsic virulence of the strains.
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Bochkareva A, Zenkin N. The σ70 region 1.2 regulates promoter escape by unwinding DNA downstream of the transcription start site. Nucleic Acids Res 2013; 41:4565-72. [PMID: 23430153 PMCID: PMC3632114 DOI: 10.1093/nar/gkt116] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The mechanisms of abortive synthesis and promoter escape during initiation of transcription are poorly understood. Here, we show that, after initiation of RNA synthesis, non-specific interaction of σ70 region 1.2, present in all σ70 family factors, with the non-template strand around position −4 relative to the transcription start site facilitates unwinding of the DNA duplex downstream of the transcription start site. This leads to stabilization of short RNA products and allows their extension, i.e. promoter escape. We show that this activity of σ70 region 1.2 is assisted by the β-lobe domain, but does not involve the β′-rudder or the β′-switch-2, earlier proposed to participate in promoter escape. DNA sequence independence of this function of σ70 region 1.2 suggests that it may be conserved in all σ70 family factors. Our results indicate that the abortive nature of initial synthesis is caused, at least in part, by failure to open the downstream DNA by the β-lobe and σ region 1.2.
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Affiliation(s)
- Aleksandra Bochkareva
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
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18
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Koroleva ON, Dubrovin EV, Khodak YA, Kuzmina NV, Yaminsky IV, Drutsa VL. The model of amyloid aggregation of Escherichia coli RNA polymerase σ70 subunit based on AFM data and in vitro assays. Cell Biochem Biophys 2013; 66:623-36. [PMID: 23306967 DOI: 10.1007/s12013-012-9507-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
To propose a model for recently described amyloid aggregation of E.coli RNA polymerase σ(70) subunit, we have investigated the role of its N-terminal region. For this purpose, three mutant variants of protein with deletions Δ1-73, Δ1-100 and Δ74-100 were constructed and studied in a series of in vitro assays and using atomic force microscopy (AFM). Specifically, all RNA polymerase holoenzymes, reconstituted with the use of mutant σ subunits, have shown reduced affinity for promoter-containing DNA and reduced activity in run-off transcription experiments (compared to that of WT species), thus substantiating the modern concept on the modulatory role of N-terminus in formation of open complex and transcription initiation. The ability of mutant proteins to form amyloid-like structures has been investigated using AFM, which revealed the increased propensity of mutant proteins to form rodlike aggregates with the effect being more pronounced for the mutant with the deletion Δ1-73 (10 fold increase). σ(70) subunit aggregation ability has shown complex dependence on the ionic surrounding, which we explain by Debye screening effect and the change of the internal state of the protein. Basing on the obtained data, we propose the model of amyloid fibril formation by σ(70) subunit, implying the involvement of N-terminal region according to the domain swapping mechanism.
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Affiliation(s)
- Olga N Koroleva
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
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19
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Miropolskaya N, Ignatov A, Bass I, Zhilina E, Pupov D, Kulbachinskiy A. Distinct functions of regions 1.1 and 1.2 of RNA polymerase σ subunits from Escherichia coli and Thermus aquaticus in transcription initiation. J Biol Chem 2012; 287:23779-89. [PMID: 22605342 DOI: 10.1074/jbc.m112.363242] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RNA polymerase (RNAP) from thermophilic Thermus aquaticus is characterized by higher temperature of promoter opening, lower promoter complex stability, and higher promoter escape efficiency than RNAP from mesophilic Escherichia coli. We demonstrate that these differences are in part explained by differences in the structures of the N-terminal regions 1.1 and 1.2 of the E. coli σ(70) and T. aquaticus σ(A) subunits. In particular, region 1.1 and, to a lesser extent, region 1.2 of the E. coli σ(70) subunit determine higher promoter complex stability of E. coli RNAP. On the other hand, nonconserved amino acid substitutions in region 1.2, but not region 1.1, contribute to the differences in promoter opening between E. coli and T. aquaticus RNAPs, likely through affecting the σ subunit contacts with DNA nucleotides downstream of the -10 element. At the same time, substitutions in σ regions 1.1 and 1.2 do not affect promoter escape by E. coli and T. aquaticus RNAPs. Thus, evolutionary substitutions in various regions of the σ subunit modulate different steps of the open promoter complex formation pathway, with regions 1.1 and 1.2 affecting promoter complex stability and region 1.2 involved in DNA melting during initiation.
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Kusumoto A, Asakura H, Kawamoto K. General stress sigma factor RpoS influences time required to enter the viable but non-culturable state in Salmonella enterica. Microbiol Immunol 2012; 56:228-37. [DOI: 10.1111/j.1348-0421.2012.00428.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Sheppard C, Cámara B, Shadrin A, Akulenko N, Liu M, Baldwin G, Severinov K, Cota E, Matthews S, Wigneshweraraj SR. Reprint of: Inhibition of Escherichia coli RNAp by T7 Gp2 protein: Role of Negatively Charged Strip of Amino Acid Residues in Gp2. J Mol Biol 2011; 412:832-41. [DOI: 10.1016/j.jmb.2011.07.064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 02/03/2011] [Accepted: 02/04/2011] [Indexed: 11/15/2022]
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22
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Sheppard C, Cámara B, Shadrin A, Akulenko N, Liu M, Baldwin G, Severinov K, Cota E, Matthews S, Wigneshweraraj SR. Inhibition of Escherichia coli RNAp by T7 Gp2 protein: role of negatively charged strip of amino acid residues in Gp2. J Mol Biol 2011; 407:623-32. [PMID: 21316373 DOI: 10.1016/j.jmb.2011.02.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 02/03/2011] [Accepted: 02/04/2011] [Indexed: 11/29/2022]
Abstract
Gp2, a 7 kDa protein encoded by T7 bacteriophage, is a potent inhibitor of Escherichia coli RNA polymerase (RNAp), the enzyme responsible for transcription of all bacterial genes and early viral genes. A prominent feature in the structure of Gp2 is a contiguous strip of seven negatively charged amino acid residues (negatively charged strip or NCS), located along one side of the molecule. The role of the NCS in Gp2 function is not known. Here, the in vivo and in vitro properties of altered forms of Gp2 with amino acid substitutions in the NCS are described. While mutations in the NCS do not compromise the folding or the ability of Gp2 to bind to the RNAp β' subunit, disruption of the NCS significantly attenuates Gp2 function in vivo and its ability to inhibit RNAp in vitro. Efficient inhibition of the RNAp by Gp2 also involves the amino terminal region 1 domain of the RNAp promoter specificity subunit σ(70), located in the vicinity of the primary Gp2 binding site in β'. The results are discussed in the context of hypothetical molecular mechanisms of RNAp inhibition by Gp2.
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Affiliation(s)
- Carol Sheppard
- Section of Microbiology, Faculty of Medicine & Centre for Molecular Microbiology and Infection, Imperial College London, SW7 2AZ, UK
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Reverse biological engineering of hrdB to enhance the production of avermectins in an industrial strain of Streptomyces avermitilis. Proc Natl Acad Sci U S A 2010; 107:11250-4. [PMID: 20534557 DOI: 10.1073/pnas.1006085107] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Avermectin and its analogues are produced by the actinomycete Streptomyces avermitilis and are widely used in the field of animal health, agriculture, and human health. Here we have adopted a practical approach to successfully improve avermectin production in an industrial overproducer. Transcriptional levels of the wild-type strain and industrial overproducer in production cultures were monitored using microarray analysis. The avermectin biosynthetic genes, especially the pathway-specific regulatory gene, aveR, were up-regulated in the high-producing strain. The upstream promoter region of aveR was predicted and proved to be directly recognized by sigma(hrdB) in vitro. A mutant library of hrdB gene was constructed by error-prone PCR and selected by high-throughput screening. As a result of evolved hrdB expressed in the modified avermectin high-producing strain, 6.38 g/L of avermectin B1a was produced with over 50% yield improvement, in which the transcription level of aveR was significantly increased. The relevant residues were identified to center in the conserved regions. Engineering of the hrdB gene can not only elicit the overexpression of aveR but also allows for simultaneous transcription of many other genes. The results indicate that manipulating the key genes revealed by reverse engineering can effectively improve the yield of the target metabolites, providing a route to optimize production in these complex regulatory systems.
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Rogozina A, Zaychikov E, Buckle M, Heumann H, Sclavi B. DNA melting by RNA polymerase at the T7A1 promoter precedes the rate-limiting step at 37 degrees C and results in the accumulation of an off-pathway intermediate. Nucleic Acids Res 2009; 37:5390-404. [PMID: 19578065 PMCID: PMC2760793 DOI: 10.1093/nar/gkp560] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The formation of a transcriptionally active complex by RNA polymerase involves a series of short-lived structural intermediates where protein conformational changes are coupled to DNA wrapping and melting. We have used time-resolved KMnO4 and hydroxyl-radical X-ray footprinting to directly probe conformational signatures of these complexes at the T7A1 promoter. Here we demonstrate that DNA melting from m12 to m4 precedes the rate-limiting step in the pathway and takes place prior to the formation of full downstream contacts. In addition, on the wild-type promoter, we can detect the accumulation of a stable off-pathway intermediate that results from the absence of sequence-specific contacts with the melted non-consensus –10 region. Finally, the comparison of the results obtained at 37°C with those at 20°C reveals significant differences in the structure of the intermediates resulting in a different pathway for the formation of a transcriptionally active complex.
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Affiliation(s)
- Anastasia Rogozina
- Max Planck Institute of Biochemistry, D82152 Martinsried bei Munchen, Germany
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Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms. Appl Environ Microbiol 2009; 75:4599-615. [PMID: 19429552 DOI: 10.1128/aem.02943-08] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We analyzed near-complete population (composite) genomic sequences for coexisting acidophilic iron-oxidizing Leptospirillum group II and III bacteria (phylum Nitrospirae) and an extrachromosomal plasmid from a Richmond Mine, Iron Mountain, CA, acid mine drainage biofilm. Community proteomic analysis of the genomically characterized sample and two other biofilms identified 64.6% and 44.9% of the predicted proteins of Leptospirillum groups II and III, respectively, and 20% of the predicted plasmid proteins. The bacteria share 92% 16S rRNA gene sequence identity and >60% of their genes, including integrated plasmid-like regions. The extrachromosomal plasmid carries conjugation genes with detectable sequence similarity to genes in the integrated conjugative plasmid, but only those on the extrachromosomal element were identified by proteomics. Both bacterial groups have genes for community-essential functions, including carbon fixation and biosynthesis of vitamins, fatty acids, and biopolymers (including cellulose); proteomic analyses reveal these activities. Both Leptospirillum types have multiple pathways for osmotic protection. Although both are motile, signal transduction and methyl-accepting chemotaxis proteins are more abundant in Leptospirillum group III, consistent with its distribution in gradients within biofilms. Interestingly, Leptospirillum group II uses a methyl-dependent and Leptospirillum group III a methyl-independent response pathway. Although only Leptospirillum group III can fix nitrogen, these proteins were not identified by proteomics. The abundances of core proteins are similar in all communities, but the abundance levels of unique and shared proteins of unknown function vary. Some proteins unique to one organism were highly expressed and may be key to the functional and ecological differentiation of Leptospirillum groups II and III.
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Koo BM, Rhodius VA, Campbell EA, Gross CA. Mutational analysis of Escherichia coli sigma28 and its target promoters reveals recognition of a composite -10 region, comprised of an 'extended -10' motif and a core -10 element. Mol Microbiol 2009; 72:830-43. [PMID: 19400790 PMCID: PMC2756079 DOI: 10.1111/j.1365-2958.2009.06691.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sigma28 controls the expression of flagella-related genes and is the most widely distributed alternative sigma factor, present in motile Gram-positive and Gram-negative bacteria. The distinguishing feature of sigma28 promoters is a long -10 region (GCCGATAA). Despite the fact that the upstream GC is highly conserved, previous studies have not indicated a functional role for this motif. Here we examine the functional relevance of the GCCG motif and determine which residues in sigma28 participate in its recognition. We find that the GCCG motif is a functionally important composite element. The upstream GC constitutes an extended -10 motif and is recognized by R91, a residue in Domain 3 of sigma28. The downstream CG is the upstream edge of -10 region of the promoter; two residues in Region 2.4, D81 and R84, participate in its recognition. Consistent with their role in base-specific recognition of the promoter, R91, D81 and D84 are universally conserved in sigma28 orthologues. Sigma28 is the second Group 3 sigma shown to use an extended -10 region in promoter recognition, raising the possibility that other Group 3 sigmas will do so as well.
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Affiliation(s)
- Byoung-Mo Koo
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Virgil A. Rhodius
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Elizabeth A. Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Carol A. Gross
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94158, USA
- Department of Cell and Tissue biology, University of California at San Francisco, San Francisco, CA 94158, USA
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Loziński T, Bolewska K, Wierzchowski KL. Equivalence of Mg2+ and Na+ ions in salt dependence of the equilibrium binding and dissociation rate constants of Escherichia coli RNA polymerase open complex. Biophys Chem 2009; 142:65-75. [PMID: 19345467 DOI: 10.1016/j.bpc.2009.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 03/05/2009] [Accepted: 03/05/2009] [Indexed: 10/21/2022]
Abstract
Conflicting experimental data on the influence of Mg(2+) ions on the salt dependence of formation/dissociation of open transcription complex (RPo) of Escherichia coli RNA polymerase led us to carry systematic measurements of the dissociation rate constant (k(d)) and thermodynamic stability of complexes at lambdaP(R) and Pa promoters in a broad range of [NaCl] and [MgCl(2)] at 25, 31 and 37 degrees C, using fluorescence detected abortive transcription assay. Values of k(d) determined in MgCl(2) in the presence of heparin, as a commonly used anionic competitor, were shown to depend on heparin concentration whereas in NaCl this effect was not observed. Kinetics of dissociation was therefore determined in the course of salt-induced down-shift of the binding equilibrium. Salt derivatives of k(d)'s (n(d)) appeared to be similar in NaCl (approximately 8.5) and MgCl(2) (approximately 10) for both complexes. Isotherms of fractional occupancy of promoters by RNAP as a function of ln [salt] were shown to conform to a sigmoid Boltzman function parameterized to include binding constant of RPo and a net change (n(obs)) in the number of electrolyte ions associated with complex components upon its formation/dissociation. The fitted values of n(obs) appeared also similar in NaCl and in MgCl(2): approximately 18 for RPo/lambdaP(R) and approximately 20 for RPo/Pa, respectively. Overall unfavorable vant'Hoff enthalpy (DeltaH(obs)) of RPo proved to be much higher in MgCl(2) than in NaCl by ca. 20 kcal/mol for both complexes, rendering them profoundly less stable in the former salt. In both salts, DeltaH(obs) was higher by approximately 30 kcal/mol for RPo/Pa relative to RPo/lambdaP(R). Similarity of n(obs) and n(d) values for the two salts indicates thermodynamic equivalence of Mg(2+) and Na(+) in [salt]-controlled binding equilibrium of RPo. This finding remains in disagreement with earlier data and suggests that salt effects on open complex stability should be sought in global compensating changes in distribution of all ionic species around the interacting complex components.
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Affiliation(s)
- Tomasz Loziński
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
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Sclavi B. Opening the DNA at the Promoter; The Energetic Challenge. RNA POLYMERASES AS MOLECULAR MOTORS 2009. [DOI: 10.1039/9781847559982-00038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Bianca Sclavi
- LBPA UMR 8113 du CNRS ENS Cachan 61 Avenue du Président Wilson 94235 Cachan France
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The promoter spacer influences transcription initiation via sigma70 region 1.1 of Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A 2009; 106:737-42. [PMID: 19139410 DOI: 10.1073/pnas.0808133106] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcription initiation is a dynamic process in which RNA polymerase (RNAP) and promoter DNA act as partners, changing in response to one another, to produce a polymerase/promoter open complex (RPo) competent for transcription. In Escherichia coli RNAP, region 1.1, the N-terminal 100 residues of sigma(70), is thought to occupy the channel that will hold the DNA downstream of the transcription start site; thus, region 1.1 must move from this channel as RPo is formed. Previous work has also shown that region 1.1 can modulate RPo formation depending on the promoter. For some promoters region 1.1 stimulates the formation of open complexes; at the P(minor) promoter, region 1.1 inhibits this formation. We demonstrate here that the AT-rich P(minor) spacer sequence, rather than promoter recognition elements or downstream DNA, determines the effect of region 1.1 on promoter activity. Using a P(minor) derivative that contains good sigma(70)-dependent DNA elements, we find that the presence of a more GC-rich spacer or a spacer with the complement of the P(minor) sequence results in a promoter that is no longer inhibited by region 1.1. Furthermore, the presence of the P(minor) spacer, the GC-rich spacer, or the complement spacer results in different mobilities of promoter DNA during gel electrophoresis, suggesting that the spacer regions impart differing conformations or curvatures to the DNA. We speculate that the spacer can influence the trajectory or flexibility of DNA as it enters the RNAP channel and that region 1.1 acts as a "gatekeeper" to monitor channel entry.
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Schwartz EC, Shekhtman A, Dutta K, Pratt MR, Cowburn D, Darst S, Muir TW. A full-length group 1 bacterial sigma factor adopts a compact structure incompatible with DNA binding. ACTA ACUST UNITED AC 2008; 15:1091-103. [PMID: 18940669 DOI: 10.1016/j.chembiol.2008.09.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 09/15/2008] [Accepted: 09/18/2008] [Indexed: 10/21/2022]
Abstract
The sigma factors are the key regulators of bacterial transcription initiation. Through direct read-out of promoter DNA sequence, they recruit the core RNA polymerase to sites of initiation, thereby dictating the RNA polymerase promoter-specificity. The group 1 sigma factors, which direct the vast majority of transcription initiation during log phase growth and are essential for viability, are autoregulated by an N-terminal sequence known as sigma1.1. We report the solution structure of Thermotoga maritima sigmaA sigma1.1. We additionally demonstrate by using chemical crosslinking strategies that sigma1.1 is in close proximity to the promoter recognition domains of sigmaA. We therefore propose that sigma1.1 autoinhibits promoter DNA binding of free sigmaA by stabilizing a compact organization of the sigma factor domains that is unable to bind DNA.
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Affiliation(s)
- Edmund C Schwartz
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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Nechaev S, Geiduschek EP. Dissection of the bacteriophage T4 late promoter complex. J Mol Biol 2008; 379:402-13. [PMID: 18455735 DOI: 10.1016/j.jmb.2008.03.071] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Revised: 03/13/2008] [Accepted: 03/31/2008] [Indexed: 11/29/2022]
Abstract
Activated transcription of the bacteriophage T4 late genes is generated by a mechanism that stands apart from the common modalities of transcriptional regulation: the activator is gp45, the viral replisome's sliding clamp; two sliding-clamp-binding proteins, gp33 and gp55, replace the host RNA polymerase (RNAP) sigma subunit. We have mutagenized, reconfigured and selectively disrupted individual interactions of the sliding clamp with gp33 and gp55 and have monitored effects on transcription. The C-terminal sliding-clamp-binding epitopes of gp33 and gp55 are perfectly interchangeable, but the functions of these two RNAP-sliding clamp connections differ: only the gp33-gp45 linkage is essential for activation, while loss of the gp55-gp45 linkage impairs but does not abolish activation. Formation of transcription-ready promoter complexes by the sliding-clamp-activated wild-type T4 RNAP resists competition by high concentrations of the polyanion heparin. This avid formation of promoter complexes requires both linkages of the T4 late RNAP to the sliding clamp. Preopening the promoter compensates for loss of the gp55-gp45 but not the gp33-gp45 linkage. We interpret the relationship of these findings and our prior analysis to the common model of transcriptional initiation in bacteria in terms of two parallel pathways, with two RNAP holoenzymes and two DNA templates: (1) gp55-RNAP and the T4 late promoter execute basal transcription; (2) gp55-gp33-RNAP and the T4 late promoter with its mobile enhancer, the T4 sliding clamp, execute activated transcription. gp55 and gp33 perform sigma-like functions, gp55 in promoter recognition and gp33 (as well as gp55) in enhancer recognition. gp33 operates the switch between these two pathways by repressing basal transcription.
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Affiliation(s)
- Sergei Nechaev
- Division of Biological Sciences and Center for Molecular Genetics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0634, USA.
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Abstract
In Pseudomonas aeruginosa, as in most bacterial species, the expression of genes is tightly controlled by a repertoire of transcriptional regulators, particularly the so-called sigma (sigma) factors. The basic understanding of these proteins in bacteria has initially been described in Escherichia coli where seven sigma factors are involved in core RNA polymerase interactions and promoter recognition. Now, 7 years have passed since the completion of the first genome sequence of the opportunistic pathogen P. aeruginosa. Information from the genome of P. aeruginosa PAO1 identified 550 transcriptional regulators and 24 putative sigma factors. Of the 24 sigma, 19 were of extracytoplasmic function (ECF). Here, basic knowledge of sigma and ECF proteins was reviewed with particular emphasis on their role in P. aeruginosa global gene regulation. Summarized data are obtained from in silico analysis of P. aeruginosasigma and ECF including rpoD (sigma(70)), RpoH (sigma(32)), RpoF (FliA or sigma(28)), RpoS (sigma(S) or sigma(38)), RpoN (NtrA, sigma(54) or sigma(N)), ECF including AlgU (RpoE or sigma(22)), PvdS, SigX and a collection of uncharacterized sigma ECF, some of which are implicated in iron transport. Coupled to systems biology, identification and functional genomics analysis of P. aeruginosasigma and ECF are expected to provide new means to prevent infection, new targets for antimicrobial therapy, as well as new insights into the infection process.
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Affiliation(s)
- Eric Potvin
- Centre de Recherche sur la Fonction, Structure et Ingénierie des Protéines, Faculté de Médecine, Pavillon Charles-Eugène Marchand, Université Laval, Sainte-Foy, Quebec, Canada
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Tsonis PA, Dwivedi B. Molecular mimicry: structural camouflage of proteins and nucleic acids. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2007; 1783:177-87. [PMID: 18068679 DOI: 10.1016/j.bbamcr.2007.11.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Revised: 11/05/2007] [Accepted: 11/06/2007] [Indexed: 11/28/2022]
Abstract
When it comes to protein specificity and function their three-dimensional structure is the ultimate determinant. Thus, sequences that participate in key parts, such as catalytic sites or DNA binding have been favored and maintained highly conserved during evolution. However, in a reversal of fortune, selection has favored conservation of shapes over sequence, especially when proteins look like nucleic acids. Proteins from pathogens evade the host's defenses because they are shaped as DNA; others use such a disguise for transcriptional regulation. Several factors are tRNA look-alikes so that they can efficiently control the process of protein synthesis. Molecular mimicry among RNAs could result in a new unexplored level in gene regulation. This comprehensive review outlines this important area and aims to emphasize that molecular mimicry could in fact be more widespread than initially thought and eventually adds a new layer of genetic regulation.
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Lysenko EA. Plant sigma factors and their role in plastid transcription. PLANT CELL REPORTS 2007; 26:845-59. [PMID: 17356883 DOI: 10.1007/s00299-007-0318-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 01/13/2007] [Accepted: 02/09/2007] [Indexed: 05/08/2023]
Abstract
Plant sigma factors determine the promoter specificity of the major RNA polymerase of plastids and thus regulate the first level of plastome gene expression. In plants, sigma factors are encoded by a small family of nuclear genes, and it is not yet clear if the family members are functionally redundant or each paralog plays a particular role. The review presents the analysis of the information on plant sigma factors obtained since their discovery a decade ago and focuses on similarities and differences in structure and functions of various paralogs. Special attention is paid to their interaction with promoters, the regulation of their expression, and their role in the development of a whole plant. The analysis suggests that though plant sigma factors are basically similar, at least some of them perform distinct functions. Finally, the work presents the scheme of this gene family evolution in higher plants.
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Affiliation(s)
- Eugene A Lysenko
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya ul. 35, 127276 Moscow, Russia.
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Vingadassalom D, Kolb A, Mayer C, Collatz E, Podglajen I. Probing the Importance of Selected Phylum-specific Amino Acids in σA of Bacteroides fragilis, a Primary σ Factor Naturally Devoid of an N-terminal Acidic Region 1.1. J Biol Chem 2007; 282:3442-9. [PMID: 17150963 DOI: 10.1074/jbc.m608855200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The sigmaA factor of Bacteroides fragilis is the prototype of a novel subgroup of primary sigma factors that are essential for growth and ensure the initiation of transcription of the housekeeping genes. This subgroup is confined to the phyla Bacteroidetes and Chlorobi. Its members carry a specific amino acid signature and are notably characterized by a short, basic N-terminal segment instead of the typical acidic region 1.1. Using in vitro mutagenesis, we investigated the importance of this basic segment and of several residues of the signature for the function of sigmaA. We have shown that the conserved residues Phe-61 and Lys-265, located in the core binding and DNA binding subregions 2.1 and 4.2, respectively, are critical for full function of the B. fragilis holoenzyme. With respect to the unusual subregion composition of sigmaA, we have shown that truncation of the basic N-terminal segment, or reversion of its charge, strongly affects the overall transcriptional activity of B. fragilis RNA polymerase in vitro. Our results indicate that the presence of the intact basic segment is required for the formation of RNA polymerase (RNAP)-promoter open complexes, the correct architecture of the transcription bubble, and efficient promoter clearance.
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Zenkin N, Kulbachinskiy A, Yuzenkova Y, Mustaev A, Bass I, Severinov K, Brodolin K. Region 1.2 of the RNA polymerase sigma subunit controls recognition of the -10 promoter element. EMBO J 2007; 26:955-64. [PMID: 17268549 PMCID: PMC1852845 DOI: 10.1038/sj.emboj.7601555] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Accepted: 12/19/2006] [Indexed: 01/24/2023] Open
Abstract
Recognition of the -10 promoter consensus element by region 2 of the bacterial RNA polymerase sigma subunit is a key step in transcription initiation. sigma also functions as an elongation factor, inducing transcription pausing by interacting with transcribed DNA non-template strand sequences that are similar to the -10 element sequence. Here, we show that the region 1.2 of Escherichia coli sigma70, whose function was heretofore unknown, is strictly required for efficient recognition of the non-template strand of -10-like pause-inducing DNA sequence by sigma region 2, and for sigma-dependent promoter-proximal pausing. Recognition of the fork-junction promoter DNA by RNA polymerase holoenzyme also requires sigma region 1.2 and thus resembles the pause-inducing sequence recognition. Our results, together with available structural data, support a model where sigma region 1.2 acts as a core RNA polymerase-dependent allosteric switch that modulates non-template DNA strand recognition by sigma region 2 during transcription initiation and elongation.
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Affiliation(s)
- Nikolay Zenkin
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
- Department of Molecular Biology and Biochemistry, Waksman Institute, Rutgers the State University of New Jersey, Piscataway, NJ, USA
| | | | - Yuliya Yuzenkova
- Department of Molecular Biology and Biochemistry, Waksman Institute, Rutgers the State University of New Jersey, Piscataway, NJ, USA
| | | | - Irina Bass
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin Severinov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
- Department of Molecular Biology and Biochemistry, Waksman Institute, Rutgers the State University of New Jersey, Piscataway, NJ, USA
| | - Konstantin Brodolin
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
- Present address: Centre de Biochimie Structurale, 29 rue de Navacelles 34090, Montpellier Cedex, France
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq. 2, Moscow 123182, Russia. Tel.: +7 495 196 00 15; Fax: +7 495 196 02 21; E-mail:
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Hook-Barnard I, Johnson XB, Hinton DM. Escherichia coli RNA polymerase recognition of a sigma70-dependent promoter requiring a -35 DNA element and an extended -10 TGn motif. J Bacteriol 2006; 188:8352-9. [PMID: 17012380 PMCID: PMC1698240 DOI: 10.1128/jb.00853-06] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Accepted: 09/25/2006] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli sigma70-dependent promoters have typically been characterized as either -10/-35 promoters, which have good matches to both the canonical -10 and the -35 sequences or as extended -10 promoters (TGn/-10 promoters), which have the TGn motif and an excellent match to the -10 consensus sequence. We report here an investigation of a promoter, P(minor), that has a nearly perfect match to the -35 sequence and has the TGn motif. However, P(minor) contains an extremely poor sigma70 -10 element. We demonstrate that P(minor) is active both in vivo and in vitro and that mutations in either the -35 or the TGn motif eliminate its activity. Mutation of the TGn motif can be compensated for by mutations that make the -10 element more canonical, thus converting the -35/TGn promoter to a -35/-10 promoter. Potassium permanganate footprinting on the nontemplate and template strands indicates that when polymerase is in a stable (open) complex with P(minor), the DNA is single stranded from positions -11 to +4. We also demonstrate that transcription from P(minor) incorporates nontemplated ribonucleoside triphosphates at the 5' end of the P(minor) transcript, which results in an anomalous assignment for the start site when primer extension analysis is used. P(minor) represents one of the few -35/TGn promoters that have been characterized and serves as a model for investigating functional differences between these promoters and the better-characterized -10/-35 and extended -10 promoters used by E. coli RNA polymerase.
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Affiliation(s)
- India Hook-Barnard
- Gene Expression and Regulation Section, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8, Room 2A-13, Bethesda, MD 20892-0830, USA
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Baxter K, Lee J, Minakhin L, Severinov K, Hinton DM. Mutational analysis of sigma70 region 4 needed for appropriation by the bacteriophage T4 transcription factors AsiA and MotA. J Mol Biol 2006; 363:931-44. [PMID: 16996538 PMCID: PMC1698951 DOI: 10.1016/j.jmb.2006.08.074] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2006] [Revised: 08/24/2006] [Accepted: 08/25/2006] [Indexed: 10/24/2022]
Abstract
Transcriptional activation of bacteriophage T4 middle promoters requires sigma70-containing Escherichia coli RNA polymerase, the T4 activator MotA, and the T4 co-activator AsiA. T4 middle promoters contain the sigma70 -10 DNA element. However, these promoters lack the sigma70 -35 element, having instead a MotA box centered at -30, which is bound by MotA. Previous work has indicated that AsiA and MotA interact with region 4 of sigma70, the C-terminal portion that normally contacts -35 DNA and the beta-flap structure in core. AsiA binding prevents the sigma70/beta-flap and sigma70/-35 DNA interactions, inhibiting transcription from promoters that require a -35 element. To test the importance of residues within sigma70 region 4 for MotA and AsiA function, we investigated how sigma70 region 4 mutants interact with AsiA, MotA, and the beta-flap and function in transcription assays in vitro. We find that alanine substitutions at residues 584-588 (region 4.2) do not impair the interaction of region 4 with the beta-flap or MotA, but they eliminate the interaction with AsiA and prevent AsiA inhibition and MotA/AsiA activation. In contrast, alanine substitutions at 551-552, 554-555 (region 4.1) eliminate the region 4/beta-flap interaction, significantly impair the AsiA/sigma70 interaction, and eliminate AsiA inhibition. However, the 4.1 mutant sigma70 is still fully competent for activation if both MotA and AsiA are present. A previous NMR structure shows AsiA binding to sigma70 region 4, dramatically distorting regions 4.1 and 4.2 and indirectly changing the conformation of the MotA interaction site at the sigma70 C terminus. Our analyses provide biochemical relevance for the sigma70 residues identified in the structure, indicate that the interaction of AsiA with sigma70 region 4.2 is crucial for activation, and support the idea that AsiA binding facilitates an interaction between MotA and the far C terminus of sigma70.
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Affiliation(s)
- Kimberly Baxter
- Gene Expression and Regulation Section, Laboratory of Molecular and Cellular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892-0830, USA
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Haugen SP, Berkmen MB, Ross W, Gaal T, Ward C, Gourse RL. rRNA Promoter Regulation by Nonoptimal Binding of σ Region 1.2: An Additional Recognition Element for RNA Polymerase. Cell 2006; 125:1069-82. [PMID: 16777598 DOI: 10.1016/j.cell.2006.04.034] [Citation(s) in RCA: 172] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2006] [Revised: 03/16/2006] [Accepted: 04/11/2006] [Indexed: 10/24/2022]
Abstract
Regulation of transcription initiation is generally attributable to activator/repressor proteins that bind to specific DNA sequences. However, regulators can also achieve specificity by binding directly to RNA polymerase (RNAP) and exploiting the kinetic variation intrinsic to different RNAP-promoter complexes. We report here a previously unknown interaction with Escherichia coli RNAP that defines an additional recognition element in bacterial promoters. The strength of this sequence-specific interaction varies at different promoters and affects the lifetime of the complex with RNAP. Selection of rRNA promoter mutants forming long-lived complexes, kinetic analyses of duplex and bubble templates, dimethylsulfate footprinting, and zero-Angstrom crosslinking demonstrated that sigma subunit region 1.2 directly contacts the nontemplate strand base two positions downstream of the -10 element (within the "discriminator" region). By making a nonoptimal sigma1.2-discriminator interaction, rRNA promoters create the short-lived complex required for specific responses to the RNAP binding factors ppGpp and DksA, ultimately accounting for regulation of ribosome synthesis.
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Affiliation(s)
- Shanil P Haugen
- Department of Bacteriology, University of Wisconsin-Madison, 420 Henry Mall, 53706, USA
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40
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Wigneshweraraj SR, Savalia D, Severinov K, Buck M. Interplay between the beta' clamp and the beta' jaw domains during DNA opening by the bacterial RNA polymerase at sigma54-dependent promoters. J Mol Biol 2006; 359:1182-95. [PMID: 16725156 DOI: 10.1016/j.jmb.2006.04.063] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2006] [Revised: 04/17/2006] [Accepted: 04/25/2006] [Indexed: 10/24/2022]
Abstract
The bacterial RNA polymerase (RNAP) is a multi-subunit, structurally flexible, complex molecular machine, in which activities associated with DNA opening for transcription-competent open promoter complex (OC) formation reside in the catalytic beta and beta' subunits and the dissociable sigma subunit. OC formation is a multi-step process that involves several structurally conserved mobile modules of beta, beta', and sigma. Here, we present evidence that two flexible modules of beta', the beta' jaw and the beta' clamp and a conserved regulatory Region I domain of sigma(54), jointly contribute to the maintenance of stable DNA strand separation around the trancription start site in OCs formed at sigma(54)-dependent promoters. Clearly, regulated interplay between the mobile modules of the beta' and the sigma subunits of the RNAP appears to be necessary for stable OC formation.
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Affiliation(s)
- Siva R Wigneshweraraj
- Imperial College London, Faculty of Life Sciences, Division of Biology, Sir Alexander Fleming Building, South Kensington Campus, UK
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41
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Imashimizu M, Hanaoka M, Seki A, Murakami KS, Tanaka K. The cyanobacterial principal sigma factor region 1.1 is involved in DNA-binding in the free form and in transcription activity as holoenzyme. FEBS Lett 2006; 580:3439-44. [PMID: 16712841 DOI: 10.1016/j.febslet.2006.05.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Revised: 05/07/2006] [Accepted: 05/08/2006] [Indexed: 11/29/2022]
Abstract
Cyanobacterial principal sigma factor, sigma(A), includes a specifically conserved cluster of basic amino acids in the amino-terminal extension called region 1.1. We found that the sigma(A) in a thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 binds DNA in the absence of the core RNA polymerase and that sigma(A) lacking region 1.1 is not able to bind DNA. This indicates that, in the cyanobacterium, region 1.1 participates in DNA-binding, rather than inhibiting the interaction between free sigma and DNA, as found in other principal sigma factors of eubacteria. The results of in vitro transcription assays with the reconstituted RNA polymerase showed that region 1.1 reduces transcription activity from the cpc promoter.
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Affiliation(s)
- Masahiko Imashimizu
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Japan
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42
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Hinton DM, Vuthoori S, Mulamba R. The bacteriophage T4 inhibitor and coactivator AsiA inhibits Escherichia coli RNA Polymerase more rapidly in the absence of sigma70 region 1.1: evidence that region 1.1 stabilizes the interaction between sigma70 and core. J Bacteriol 2006; 188:1279-85. [PMID: 16452409 PMCID: PMC1367253 DOI: 10.1128/jb.188.4.1279-1285.2006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The N-terminal region (region 1.1) of sigma70, the primary sigma subunit of Escherichia coli RNA polymerase, is a negatively charged domain that affects the DNA binding properties of sigma70 regions 2 and 4. Region 1.1 prevents the interaction of free sigma70 with DNA and modulates the formation of stable (open) polymerase/promoter complexes at certain promoters. The bacteriophage T4 AsiA protein is an inhibitor of sigma70-dependent transcription from promoters that require an interaction between sigma70 region 4 and the -35 DNA element and is the coactivator of transcription at T4 MotA-dependent promoters. Like AsiA, the T4 activator MotA also interacts with sigma70 region 4. We have investigated the effect of region 1.1 on AsiA inhibition and MotA/AsiA activation. We show that sigma70 region 1.1 is not required for MotA/AsiA activation at the T4 middle promoter P(uvsX). However, the rate of AsiA inhibition and of MotA/AsiA activation of polymerase is significantly increased when region 1.1 is missing. We also find that RNA polymerase reconstituted with sigma70 that lacks region 1.1 is less stable than polymerase with full-length sigma70. Our previous work has demonstrated that the AsiA-inhibited polymerase is formed when AsiA binds to region 4 of free sigma70 and then the AsiA/sigma70 complex binds to core. Our results suggest that in the absence of region 1.1, there is a shift in the dynamic equilibrium between polymerase holoenzyme and free sigma70 plus core, yielding more free sigma70 at any given time. Thus, the rate of AsiA inhibition and AsiA/MotA activation increases when RNA polymerase lacks region 1.1 because of the increased availability of free sigma70. Previous work has argued both for and against a direct interaction between regions 1.1 and 4. Using an E. coli two-hybrid assay, we do not detect an interaction between these regions. This result supports the idea that the ability of region 1.1 to prevent DNA binding by free sigma70 arises through an indirect effect.
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Affiliation(s)
- Deborah M Hinton
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8 Room 2A-13, Bethesda, Maryland 20892-0830, USA.
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Vingadassalom D, Kolb A, Mayer C, Rybkine T, Collatz E, Podglajen I. An unusual primary sigma factor in the Bacteroidetes phylum. Mol Microbiol 2005; 56:888-902. [PMID: 15853878 DOI: 10.1111/j.1365-2958.2005.04590.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The presence of housekeeping gene promoters with a unique consensus sequence in Bacteroides fragilis, previously described by Bayley et al. (2000, FEMS Microbiol Lett 193: 149-154), suggested the existence of a particular primary sigma factor. The single rpoD-like gene observed in the B. fragilis genome, and similarly in those of other members of the Bacteroidetes phylum, was found to be essential. It encodes a protein, sigma(ABfr), of only 32.7 kDa that is produced with equal abundance during all phases of growth and was concluded to be the primary sigma factor. sigma(ABfr) and its orthologues in the Bacteroidetes are unusual primary sigma factors in that they lack region 1.1, have a unique signature made up of 29 strictly identical amino acids and are the only RpoD factors that cluster with the RpoS factors. Although binding to the Escherichia coli core RNA polymerase, sigma(ABfr) does not support transcription initiation from any promoter when it is part of the heterologous holoenzyme, while in the reconstituted homologous holoenzyme it does so only from typical B. fragilis, including rrs, promoters but not from the lacUV5 or RNA I promoters.
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Affiliation(s)
- Didier Vingadassalom
- INSERM E0004, Laboratoire de Recherche Moléculaire sur les Antibiotiques, Université Paris VI, 75270 Paris, France
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Geszvain K, Gruber TM, Mooney RA, Gross CA, Landick R. A Hydrophobic Patch on the Flap-tip Helix of E.coli RNA Polymerase Mediates σ70 Region 4 Function. J Mol Biol 2004; 343:569-87. [PMID: 15465046 DOI: 10.1016/j.jmb.2004.08.063] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2004] [Revised: 08/19/2004] [Accepted: 08/19/2004] [Indexed: 11/15/2022]
Abstract
The Escherichia coli RNA polymerase beta subunit contains a flexible flap domain that interacts with region 4 of sigma(70) to position it for recognition of the -35 element of promoters. We report that this function depends on a hydrophobic patch on one face of the short stretch of alpha helix located at the tip of the flap domain, called the flap-tip helix. Disruption of the hydrophobic patch by the substitution of hydrophilic or charged amino acids resulted in a loss of the interaction between the flap and sigma region 4, as determined by protease sensitivity assays, and impaired transcription from -35-dependent promoters. We suggest that contact of the flap-tip helix hydrophobic patch to the sigma region 4 hydrophobic core is essential for stable interaction of the flap-tip helix with region 4. This contact allowed region 4.2 recognition of the -35 promoter element and appeared to stabilize region 4 interaction with the beta' Zn(2+) binding domain. Our studies failed to detect any role for sigma region 1.1 in establishing or maintaining the flap-sigma region 4 interaction, consistent with recent reports placing sigma region 1.1 in the downstream DNA channel.
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Affiliation(s)
- Kati Geszvain
- Department of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
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Hsu HH, Huang WC, Chen JP, Huang LY, Wu CF, Chang BY. Properties of Bacillus subtilis sigma A factors with region 1.1 and the conserved Arg-103 at the N terminus of region 1.2 deleted. J Bacteriol 2004; 186:2366-75. [PMID: 15060039 PMCID: PMC412165 DOI: 10.1128/jb.186.8.2366-2375.2004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2003] [Accepted: 12/17/2003] [Indexed: 11/20/2022] Open
Abstract
sigma factors in the sigma(70) family can be classified into the primary and alternative sigma factors according to their physiological functions and amino acid sequence similarities. The primary sigma factors are composed of four conserved regions, with the conserved region 1 being divided into two subregions. Region 1.1, which is absent from the alternative sigma factor, is poor in conservation; however, region 1.2 is well conserved. We investigated the importance of these two subregions to the function of Bacillus subtilis sigma(A), which belongs to a subgroup of the primary sigma factor lacking a 254-amino-acid spacer between regions 1 and 2. We found that deletion of not more than 100 amino acid residues from the N terminus of sigma(A), which removed part or all region 1.1, did not affect the overall transcription activity of the truncated sigma(A)-RNA polymerase in vitro, indicating that region 1.1 is not required for the functioning of sigma(A) in RNA polymerase holoenzyme. This finding is consistent with the complementation data obtained in vivo. However, region 1.1 is able to negatively modulate the promoter DNA-binding activity of the sigma(A)-RNA polymerase. Further deletion of the conserved Arg-103 at the N terminus of region 1.2 increased the content of stable secondary structures of the truncated sigma(A) and greatly reduced the transcription activity of the truncated sigma(A)-RNA polymerase by lowering the efficiency of transcription initiation after core binding of sigma(A). More importantly, the conserved Arg-103 was also demonstrated to be critical for the functioning of the full-length sigma(A) in RNA polymerase.
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Affiliation(s)
- Hsin-Hsien Hsu
- Institute of Biochemistry, National Chung-Hsing University, Taichung 40227, Taiwan, Republic of China
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46
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Zhi H, Jin DJ. Purification of highly-active and soluble Escherichia coli sigma 70 polypeptide overproduced at low temperature. Methods Enzymol 2004; 370:174-80. [PMID: 14712643 DOI: 10.1016/s0076-6879(03)70015-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Affiliation(s)
- Huijun Zhi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bldg. 37, Rm. 5144, Bethesda, Maryland 20892, USA
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47
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Subbarayan PR, Sarkar M. Escherichia coli rpoS gene has an internal secondary translation initiation region. Biochem Biophys Res Commun 2004; 313:294-9. [PMID: 14684159 DOI: 10.1016/j.bbrc.2003.11.132] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Sigma S (sigma(s)) encoded by rpoS in Escherichia coli is a stationary phase specific sigma subunit of the RNA polymerase holoenzyme. Widespread among the E. coli K12 strains is an amber mutation that prematurely terminates sigma(s). These rpoSAm mutants would be expected to show no sigma(s) activity. However, suppressor free rpoSAm mutants retain an intermediate catalase activity, a sigma S controlled function. By analyzing the sequence of the rpoS gene we hypothesize that a 277 amino acids long delta1-53 sigma(s) of about 30 kDa can be translated from an internal secondary translation initiation region (STIR, AGGGAGN11GUG) that is located downstream of the amber codon. By cloning this rpoSAm gene, following the expression, function, and N-terminal sequence of this mutant protein, we report the presence of a functional internal STIR in E. coli rpoS, from where a truncated but nevertheless functional form of sigma(s) can be synthesized.
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48
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Subbarayan PR, Sarkar M. A comparative study of variation in codon 33 of the rpoS gene in Escherichia coli K12 stocks: implications for the synthesis of sigma(s). Mol Genet Genomics 2003; 270:533-8. [PMID: 14618393 DOI: 10.1007/s00438-003-0944-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2003] [Accepted: 10/02/2003] [Indexed: 10/26/2022]
Abstract
The Escherichia coli rpoS gene encodes an RNA polymerase sigma factor (sigma S or sigma(S)) required for the expression of stationary-phase genes. In the first published rpoS sequence from E. coli K-12 codon 33 is given as CAG. However, several subsequent independent studies found the amber codon TAG at this position ( rpoSAm). Besides this amber codon, other codons such as TAT have also been found at this location in rpoS. Comparative genome analysis now leads us to propose TAG as the parental codon 33 in rpoS in E. coli K-12. Five different stocks of the strain W3110, which differ in the levels of sigma(S) protein they express, were investigated. We sequenced the rpoS gene from these, and found a T at nucleotide position 97 in four out of the five stocks and a G at position 99 in three out of the five. W1485, a parental strain of W3110, and W3350, a derivative of W3110, are also rpoSAm mutants. Such rpoSAm mutants would be expected to show no RpoS activity. The retention of partial or intermediate sigma(S) activity by suppressor-free rpoSAm mutants is therefore puzzling. We propose that a functional, N-terminally truncated, sigma(S) (Delta1-53sigma(S)) can be translated from a Secondary Translation Initiation Region (STIR) located downstream of the amber codon 33. It has recently been reported that a fragment of RpoS (Delta1-53sigma(S)) that lacks the first 53 amino acids is functional when synthesized in vivo. Taken together, our results support the hypothesis that the original codon 33 of the rpoS gene in E. coli K-12 strains is the amber codon TAG.
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Affiliation(s)
- P R Subbarayan
- Department of Medicine, Division of Hematology and Oncology (D8-4), University of Miami School of Medicine, 1550 NW 10th Avenue, Fox 431A, Miami, FL 33136, USA.,
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Fenton MS, Gralla JD. Roles for inhibitory interactions in the use of the -10 promoter element by sigma 70 holoenzyme. J Biol Chem 2003; 278:39669-74. [PMID: 12902332 DOI: 10.1074/jbc.m307412200] [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] [Indexed: 11/06/2022] Open
Abstract
A panel of seven -10 region DNA mutants was tested for holoenzyme binding against a panel of 13 region 2 mutants of sigma 70. No patterns were noticed that would indicate unique interactions between individual amino acids and individual -10 region bases. Instead, certain amino acid substitutions led to increased holoenzyme binding to DNA, implying that the wild type interactions are associated with an inhibitory component. These inhibitory interactions were stronger on DNA containing non-consensus sequences, like those of typical promoters. In addition, the DNA segment downstream from the -10 element was also inhibitory to binding when in duplex form but stimulated binding when in single strand form. Overall, the data suggest that -10 region duplex recognition and melting have a large component of overcoming unfavorable protein:DNA base interactions, particularly when the bases are non-consensus, and that this contributes to setting physiologically appropriate variations in transcription rate.
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Affiliation(s)
- Mike S Fenton
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, 90095-1569, USA
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Abstract
Promoter recognition in eubacteria is carried out by the initiation factor sigma, which binds RNA polymerase and initiates transcription. Cells have one housekeeping factor and a variable number of alternative sigma factors that possess different promoter-recognition properties. The cell can choose from its repertoire of sigmas to alter its transcriptional program in response to stress. Recent structural information illuminates the process of initiation and also shows that the two key sigma domains are structurally conserved, even among diverse family members. We use the sigma repertoire of Escherichia coli, Bacillus subtilis, Streptomyces coelicolor, and cyanobacteria to illustrate the different strategies utilized to organize transcriptional space using multiple sigma factors.
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Affiliation(s)
- Tanja M Gruber
- Department of Microbiology and Immunology, University of California, Genentech Hall, 600 16th St., San Francisco, San Francisco, California 94143, USA.
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