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Joron K, Zamel J, Kalisman N, Lerner E. Evidence for a compact σ 70 conformation in vitro and in vivo. iScience 2024; 27:110140. [PMID: 38957792 PMCID: PMC11217687 DOI: 10.1016/j.isci.2024.110140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/28/2024] [Accepted: 05/27/2024] [Indexed: 07/04/2024] Open
Abstract
The initiation of transcription in Escherichia coli (E. coli) is facilitated by promoter specificity factors, also known as σ factors, which may bind a promoter only as part of a complex with RNA polymerase (RNAP). By performing in vitro cross-linking mass spectrometry (CL-MS) of apo-σ70, we reveal structural features suggesting a compact conformation compared to the known RNAP-bound extended conformation. Then, we validate the existence of the compact conformation using in vivo CL-MS by identifying cross-links similar to those found in vitro, which deviate from the extended conformation only during the stationary phase of bacterial growth. Conclusively, we provide information in support of a compact conformation of apo-σ70 that exists in live cells, which might represent a transcriptionally inactive form that can be activated upon binding to RNAP.
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Affiliation(s)
- Khalil Joron
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, Edmond J. Safra Campus, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Joanna Zamel
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, Edmond J. Safra Campus, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nir Kalisman
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, Edmond J. Safra Campus, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Center for Nanoscience and Nanotechnology, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Eitan Lerner
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, Edmond J. Safra Campus, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Center for Nanoscience and Nanotechnology, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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Turecka K, Firczuk M, Werel W. Alteration of the -35 and -10 sequences and deletion the upstream sequence of the -35 region of the promoter A1 of the phage T7 in dsDNA confirm the contribution of non-specific interactions with E. coli RNA polymerase to the transcription initiation process. Front Mol Biosci 2024; 10:1335409. [PMID: 38259683 PMCID: PMC10800924 DOI: 10.3389/fmolb.2023.1335409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Transcription initiation is a multi-step process, in which the RNA polymerase holoenzyme binds to the specific promoter sequences to form a closed complex, which, through intermediate stages, isomerizes into an open complex capable of initiating the productive phase of transcription. The aim of this work was to determine the contribution of the -10 and -35 regions of the promoter, as well as the role of non-specific interactions, in the binding of RNA polymerase and the formation of an active initiation complex capable of transcription. Therefore, fragments of promoter DNA, derived from the strong promoter A1 of the phage T7, containing completely and partially altered elements -35 and -10, and devoid of an upstream region, were constructed using genetic engineering methods. Functional analyses of modified promoter fragments were carried out, checking their ability to form binary complexes with Escherichia coli RNA polymerase (RNAP) and the efficiency of converting binary complexes into triple complexes characteristic of the productive phase of transcription. The obtained results suggest that, in relation to the A1 promoter of the T7 phage, the most important role of the -35 region is carrying the open complex through the next phases of transcription initiation. The weakening of specific impacts within the region -35 is a reason for the defect associated with the transformation of the open complex, formed by a DNA fragment containing the completely altered -35 region, into elongation and the impairment of RNA synthesis. This leads to breaking contacts with the RNA polymerase holoenzyme, and destabilization and disintegration of the complex in the initial phase of productive transcription. This confirms the hypothesis of the so-called stressed intermediate state associated with the stage of transition from the open complex to the elongation complex. The experiments carried out in this work confirm also that the process of promoter localization and recognition, as well as the formation of binary complexes, is sequential in nature, and that the region located upstream of the -35 hexamer, and the hexamer itself, plays here an additive role.
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Affiliation(s)
- Katarzyna Turecka
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland
| | | | - Władysław Werel
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland
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3
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Identification and Characterization of the Alternative σ 28 Factor in Treponema denticola. J Bacteriol 2022; 204:e0024822. [PMID: 36043861 PMCID: PMC9487585 DOI: 10.1128/jb.00248-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
FliA (also known as σ28), a member of the bacterial σ70 family of transcription factors, directs RNA polymerase to flagellar late (class 3) promoters and initiates transcription. FliA has been studied in several bacteria, yet its role in spirochetes has not been established. In this report, we identify and functionally characterize a FliA homolog (TDE2683) in the oral spirochete Treponema denticola. Computational, genetic, and biochemical analyses demonstrated that TDE2683 has a structure similar to that of the σ28 of Escherichia coli, binds to σ28-dependent promoters, and can functionally replace the σ28 of E. coli. However, unlike its counterparts from other bacteria, TDE2683 cannot be deleted, suggesting its essential role in the survival of T. denticola. In vitro site-directed mutagenesis revealed that E221 and V231, two conserved residues in the σ4 region of σ28, are indispensable for the binding activity of TDE2683 to the σ28-dependent promoter. We then mutated these two residues in T. denticola and found that the mutations impair the expression of flagellin and chemotaxis genes and bacterial motility as well. Cryo-electron tomography analysis further revealed that the mutations disrupt the flagellar symmetry (i.e., number and placement) of T. denticola. Collectively, these results indicate that TDE2683 is a σ28 transcription factor that regulates the class 3 gene expression and controls the flagellar symmetry of T. denticola. To the best of our knowledge, this is the first report establishing the functionality of FliA in spirochetes. IMPORTANCE Spirochetes are a group of medically important but understudied bacteria. One of the unique aspects of spirochetes is that they have periplasmic flagella (PF, also known as endoflagella) which give rise to their unique spiral shape and distinct swimming behaviors and play a critical role in the pathophysiology of spirochetes. PF are structurally similar to external flagella, but the underpinning mechanism that regulates PF biosynthesis and assembly remains largely unknown. By using the oral spirochete Treponema denticola as a model, this report provides several lines of evidence that FliA, a σ28 transcriptional factor, regulates the late flagellin gene (class 3) expression, PF assembly, and flagellar symmetry as well, which provides insights into flagellar regulation and opens an avenue to investigate the role of σ28 in spirochetes.
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4
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Lin ES, Huang YH, Huang CY. Characterization of the Chimeric PriB-SSBc Protein. Int J Mol Sci 2021; 22:ijms221910854. [PMID: 34639195 PMCID: PMC8509808 DOI: 10.3390/ijms221910854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 01/27/2023] Open
Abstract
PriB is a primosomal protein required for the replication fork restart in bacteria. Although PriB shares structural similarity with SSB, they bind ssDNA differently. SSB consists of an N-terminal ssDNA-binding/oligomerization domain (SSBn) and a flexible C-terminal protein–protein interaction domain (SSBc). Apparently, the largest difference in structure between PriB and SSB is the lack of SSBc in PriB. In this study, we produced the chimeric PriB-SSBc protein in which Klebsiella pneumoniae PriB (KpPriB) was fused with SSBc of K. pneumoniae SSB (KpSSB) to characterize the possible SSBc effects on PriB function. The crystal structure of KpSSB was solved at a resolution of 2.3 Å (PDB entry 7F2N) and revealed a novel 114-GGRQ-117 motif in SSBc that pre-occupies and interacts with the ssDNA-binding sites (Asn14, Lys74, and Gln77) in SSBn. As compared with the ssDNA-binding properties of KpPriB, KpSSB, and PriB-SSBc, we observed that SSBc could significantly enhance the ssDNA-binding affinity of PriB, change the binding behavior, and further stimulate the PriA activity (an initiator protein in the pre-primosomal step of DNA replication), but not the oligomerization state, of PriB. Based on these experimental results, we discuss reasons why the properties of PriB can be retrofitted when fusing with SSBc.
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Affiliation(s)
- En-Shyh Lin
- Department of Beauty Science, National Taichung University of Science and Technology, No. 193, Sec.1, San-Min Rd., Taichung City 403, Taiwan;
| | - Yen-Hua Huang
- School of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec.1, Chien-Kuo N. Rd., Taichung City 402, Taiwan;
| | - Cheng-Yang Huang
- School of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec.1, Chien-Kuo N. Rd., Taichung City 402, Taiwan;
- Department of Medical Research, Chung Shan Medical University Hospital, No. 110, Sec.1, Chien-Kuo N. Rd., Taichung City 402, Taiwan
- Correspondence:
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5
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Abstract
Chloroplasts, the sites of photosynthesis and sources of reducing power, are at the core of the success story that sets apart autotrophic plants from most other living organisms. Along with their fellow organelles (e.g., amylo-, chromo-, etio-, and leucoplasts), they form a group of intracellular biosynthetic machines collectively known as plastids. These plant cell constituents have their own genome (plastome), their own (70S) ribosomes, and complete enzymatic equipment covering the full range from DNA replication via transcription and RNA processive modification to translation. Plastid RNA synthesis (gene transcription) involves the collaborative activity of two distinct types of RNA polymerases that differ in their phylogenetic origin as well as their architecture and mode of function. The existence of multiple plastid RNA polymerases is reflected by distinctive sets of regulatory DNA elements and protein factors. This complexity of the plastid transcription apparatus thus provides ample room for regulatory effects at many levels within and beyond transcription. Research in this field offers insight into the various ways in which plastid genes, both singly and groupwise, can be regulated according to the needs of the entire cell. Furthermore, it opens up strategies that allow to alter these processes in order to optimize the expression of desired gene products.
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Affiliation(s)
- Jennifer Ortelt
- Department of Biology and Biotechnology, University of Bochum, Bochum, Germany
| | - Gerhard Link
- Department of Biology and Biotechnology, University of Bochum, Bochum, Germany.
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Rangel-Chávez CP, Galán-Vásquez E, Pescador-Tapia A, Delaye L, Martínez-Antonio A. RNA polymerases in strict endosymbiont bacteria with extreme genome reduction show distinct erosions that might result in limited and differential promoter recognition. PLoS One 2021; 16:e0239350. [PMID: 34324516 PMCID: PMC8321222 DOI: 10.1371/journal.pone.0239350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 06/22/2021] [Indexed: 11/26/2022] Open
Abstract
Strict endosymbiont bacteria present high degree genome reduction, retain smaller proteins, and in some instances, lack complete functional domains compared to free-living counterparts. Until now, the mechanisms underlying these genetic reductions are not well understood. In this study, the conservation of RNA polymerases, the essential machinery for gene expression, is analyzed in endosymbiont bacteria with extreme genome reductions. We analyzed the RNA polymerase subunits to identify and define domains, subdomains, and specific amino acids involved in precise biological functions known in Escherichia coli. We also perform phylogenetic analysis and three-dimensional models over four lineages of endosymbiotic proteobacteria with the smallest genomes known to date: Candidatus Hodgkinia cicadicola, Candidatus Tremblaya phenacola, Candidatus Tremblaya Princeps, Candidatus Nasuia deltocephalinicola, and Candidatus Carsonella ruddii. We found that some Hodgkinia strains do not encode for the RNA polymerase α subunit. The rest encode genes for α, β, β', and σ subunits to form the RNA polymerase. However, 16% shorter, on average, respect their orthologous in E. coli. In the α subunit, the amino-terminal domain is the most conserved. Regarding the β and β' subunits, both the catalytic core and the assembly domains are the most conserved. However, they showed compensatory amino acid substitutions to adapt to changes in the σ subunit. Precisely, the most erosive diversity occurs within the σ subunit. We identified broad amino acid substitution even in those recognizing and binding to the -10-box promoter element. In an overall conceptual image, the RNA polymerase from Candidatus Nasuia conserved the highest similarity with Escherichia coli RNA polymerase and their σ70. It might be recognizing the two main promoter elements (-10 and -35) and the two promoter accessory elements (-10 extended and UP-element). In Candidatus Carsonella, the RNA polymerase could recognize all the promoter elements except the -10-box extended. In Candidatus Tremblaya and Hodgkinia, due to the α carboxyl-terminal domain absence, they might not recognize the UP-promoter element. We also identified the lack of the β flap-tip helix domain in most Hodgkinia's that suggests the inability to bind the -35-box promoter element.
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Affiliation(s)
- Cynthia Paola Rangel-Chávez
- Biological Engineering Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute, Irapuato Gto, México
| | - Edgardo Galán-Vásquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, CDMX, México
| | - Azucena Pescador-Tapia
- Biological Engineering Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute, Irapuato Gto, México
| | - Luis Delaye
- Evolutionary Genomics Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute, Irapuato Gto, México
| | - Agustino Martínez-Antonio
- Biological Engineering Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute, Irapuato Gto, México
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7
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Diverse and unified mechanisms of transcription initiation in bacteria. Nat Rev Microbiol 2020; 19:95-109. [PMID: 33122819 DOI: 10.1038/s41579-020-00450-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
Transcription of DNA is a fundamental process in all cellular organisms. The enzyme responsible for transcription, RNA polymerase, is conserved in general architecture and catalytic function across the three domains of life. Diverse mechanisms are used among and within the different branches to regulate transcription initiation. Mechanistic studies of transcription initiation in bacteria are especially amenable because the promoter recognition and melting steps are much less complicated than in eukaryotes or archaea. Also, bacteria have critical roles in human health as pathogens and commensals, and the bacterial RNA polymerase is a proven target for antibiotics. Recent biophysical studies of RNA polymerases and their inhibition, as well as transcription initiation and transcription factors, have detailed the mechanisms of transcription initiation in phylogenetically diverse bacteria, inspiring this Review to examine unifying and diverse themes in this process.
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8
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Tamizi AA, Abu-Bakar N, Samsuddin AF, Rozano L, Ahmad-Redzuan R, Abdul-Murad AM. Characterisation and Mutagenesis Study of An Alternative Sigma Factor Gene ( hrpL) from Erwinia mallotivora Reveal Its Central Role in Papaya Dieback Disease. BIOLOGY 2020; 9:biology9100323. [PMID: 33023069 PMCID: PMC7600996 DOI: 10.3390/biology9100323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 11/26/2022]
Abstract
Simple Summary Erwinia mallotivora is the causal agent of papaya dieback disease in Malaysia, and its pathogenicity is less appreciated, especially from the molecular perspective. Our previous investigations proved that the hrpL/rpoE gene was one of the significant differentially expressed genes (DEGs) during early infection of E. mallotivora in papaya, suggesting this particular gene is important for infection. In this study, an in-depth analysis was performed using bioinformatics software on hrpL from E. mallotivora (EmhrpL) and its encoded protein (EmHrpL) obtaining crucial information including the conserved function and sequence motif, protein structural similarity with related homologs, and the possibility of being inhibited by a cognate inhibitor. Moreover, knockout (insertional mutational on DNA sequence) of the hrpL gene had caused mutant E. mallotivora (ΔEmhrpL) to be avirulent in four-month-old papaya plants. Here, the conclusion was that EmHrpL is indeed a necessary factor in E. mallotivora pathogenicity, and the findings on the potential inhibitor of this protein are useful for future studies to formulate a papaya dieback disease management programme. Abstract The alternative sigma (σ) factor E, RpoE or HrpL, has been reported to be involved in stress- and pathogenicity-related transcription initiation in Escherichia coli and many other Gram-negative bacteria, including Erwinia spp. and Pseudomonas spp. A previous study identified the hrpL/rpoE transcript as one of the significant differentially expressed genes (DEGs) during early E. mallotivora infection in papaya and those data serve as the basis of the current project. Here, the full coding DNA sequence (CDS) of hrpL from E. mallotivora (EmhrpL) was determined to be 549 bp long, and it encoded a 21.3 kDa HrpL protein that possessed two highly conserved sigma-70 (σ70) motifs—σR2 and σR4. Nucleotide sequence alignment revealed the hrpL from E. mallotivora shared high sequence similarity to rpoE/hrpL from E. tracheiphila (83%), E. pyrifoliae (81%), and E. tasmaniensis (80%). Phylogenetics analysis indicated hrpL from E. mallotivora to be monophyletic with rpoEs/hrpLs from Pantoea vagans, E. herbicola, and E. tracheiphila. Structural analysis postulated that the E. mallotivora’s alternative σ factor was non-transmembranic and was an extracytoplasmic function (ECF) protein—characteristics shared by other σ factors in different bacterial species. Notably, the protein–protein interaction (PPI) study through molecular docking suggested the σ factor could be possibly inhibited by an anti-σ. Finally, a knockout of hrpL in E. mallotivora (ΔEmhrpL) resulted in avirulence in four-month-old papaya plants. These findings have revealed that the hrpL is a necessary element in E. mallotivora pathogenicity and also predicted that the gene can be inhibited by an anti-σ.
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Affiliation(s)
- Amin-Asyraf Tamizi
- Agri-Omics and Bioinformatics Programme, Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute Headquarters, Serdang 43400, Selangor, Malaysia; (A.-A.T.); (L.R.); (R.A.-R.)
| | - Norliza Abu-Bakar
- Agri-Omics and Bioinformatics Programme, Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute Headquarters, Serdang 43400, Selangor, Malaysia; (A.-A.T.); (L.R.); (R.A.-R.)
- Correspondence: ; Tel.: +60-3-8953-6102
| | - Aimera-Farhana Samsuddin
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (A.-F.S.); (A.-M.A.-M.)
| | - Lina Rozano
- Agri-Omics and Bioinformatics Programme, Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute Headquarters, Serdang 43400, Selangor, Malaysia; (A.-A.T.); (L.R.); (R.A.-R.)
| | - Rohaiza Ahmad-Redzuan
- Agri-Omics and Bioinformatics Programme, Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute Headquarters, Serdang 43400, Selangor, Malaysia; (A.-A.T.); (L.R.); (R.A.-R.)
| | - Abdul-Munir Abdul-Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (A.-F.S.); (A.-M.A.-M.)
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9
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Gleizer S, Ben-Nissan R, Bar-On YM, Antonovsky N, Noor E, Zohar Y, Jona G, Krieger E, Shamshoum M, Bar-Even A, Milo R. Conversion of Escherichia coli to Generate All Biomass Carbon from CO 2. Cell 2020; 179:1255-1263.e12. [PMID: 31778652 PMCID: PMC6904909 DOI: 10.1016/j.cell.2019.11.009] [Citation(s) in RCA: 241] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/17/2019] [Accepted: 11/04/2019] [Indexed: 01/11/2023]
Abstract
The living world is largely divided into autotrophs that convert CO2 into biomass and heterotrophs that consume organic compounds. In spite of widespread interest in renewable energy storage and more sustainable food production, the engineering of industrially relevant heterotrophic model organisms to use CO2 as their sole carbon source has so far remained an outstanding challenge. Here, we report the achievement of this transformation on laboratory timescales. We constructed and evolved Escherichia coli to produce all its biomass carbon from CO2. Reducing power and energy, but not carbon, are supplied via the one-carbon molecule formate, which can be produced electrochemically. Rubisco and phosphoribulokinase were co-expressed with formate dehydrogenase to enable CO2 fixation and reduction via the Calvin-Benson-Bassham cycle. Autotrophic growth was achieved following several months of continuous laboratory evolution in a chemostat under intensifying organic carbon limitation and confirmed via isotopic labeling.
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Affiliation(s)
- Shmuel Gleizer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Roee Ben-Nissan
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yinon M Bar-On
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Niv Antonovsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yehudit Zohar
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ghil Jona
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eyal Krieger
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Melina Shamshoum
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Arren Bar-Even
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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10
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Wei Z, Chen C, Liu YJ, Dong S, Li J, Qi K, Liu S, Ding X, Ortiz de Ora L, Muñoz-Gutiérrez I, Li Y, Yao H, Lamed R, Bayer EA, Cui Q, Feng Y. Alternative σI/anti-σI factors represent a unique form of bacterial σ/anti-σ complex. Nucleic Acids Res 2019; 47:5988-5997. [PMID: 31106374 PMCID: PMC6582324 DOI: 10.1093/nar/gkz355] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/21/2019] [Accepted: 04/26/2019] [Indexed: 12/18/2022] Open
Abstract
The σ70 family alternative σI factors and their cognate anti-σI factors are widespread in Clostridia and Bacilli and play a role in heat stress response, virulence, and polysaccharide sensing. Multiple σI/anti-σI factors exist in some lignocellulolytic clostridial species, specifically for regulation of components of a multienzyme complex, termed the cellulosome. The σI and anti-σI factors are unique, because the C-terminal domain of σI (SigIC) and the N-terminal inhibitory domain of anti-σI (RsgIN) lack homology to known proteins. Here, we report structure and interaction studies of a pair of σI and anti-σI factors, SigI1 and RsgI1, from the cellulosome-producing bacterium, Clostridium thermocellum. In contrast to other known anti-σ factors that have N-terminal helical structures, RsgIN has a β-barrel structure. Unlike other anti-σ factors that bind both σ2 and σ4 domains of the σ factors, RsgIN binds SigIC specifically. Structural analysis showed that SigIC contains a positively charged surface region that recognizes the promoter -35 region, and the synergistic interactions among multiple interfacial residues result in the specificity displayed by different σI/anti-σI pairs. We suggest that the σI/anti-σI factors represent a distinctive mode of σ/anti-σ complex formation, which provides the structural basis for understanding the molecular mechanism of the intricate σI/anti-σI system.
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Affiliation(s)
- Zhen Wei
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Chen
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Jie Li
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuan Qi
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiyue Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoke Ding
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Lizett Ortiz de Ora
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Iván Muñoz-Gutiérrez
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Yifei Li
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Hongwei Yao
- High-Field Nuclear Magnetic Resonance Center, Xiamen University, 422 South Siming Road, Xiamen 361005, China
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- To whom correspondence should be addressed. Tel: +86 532 80662706; Fax: +86 532 80662707;
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11
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Inniss NL, Prehna G, Morrison DA. The pneumococcal σ X activator, ComW, is a DNA-binding protein critical for natural transformation. J Biol Chem 2019; 294:11101-11118. [PMID: 31160340 DOI: 10.1074/jbc.ra119.007571] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/19/2019] [Indexed: 11/06/2022] Open
Abstract
Natural genetic transformation via horizontal gene transfer enables rapid adaptation to dynamic environments and contributes to both antibiotic resistance and vaccine evasion among bacterial populations. In Streptococcus pneumoniae (pneumococcus), transformation occurs when cells enter competence, a transient state in which cells express the competence master regulator, SigX (σΧ), an alternative σ factor (σ), and a competence co-regulator, ComW. Together, ComW and σX facilitate expression of the genes required for DNA uptake and genetic recombination. SigX activity depends on ComW, as ΔcomW cells transcribe late genes and transform at levels 10- and 10,000-fold below that of WT cells, respectively. Previous findings suggest that ComW functions during assembly of the RNA polymerase-σX holoenzyme to help promote transcription from σX-targeted promoters. However, it remains unknown how ComW facilitates holoenzyme assembly. As ComW seems to be unique to Gram-positive cocci and has no sequence similarity with known transcriptional activators, here we used Rosetta to generate an ab initio model of pneumococcal ComW's 3D-structure. Using this model as a basis for further biochemical, biophysical, and genetic investigations into the molecular features important for its function, we report that ComW is a predicted globular protein and that it interacts with DNA, independently of DNA sequence. We also identified conserved motifs in ComW and show that key residues in these motifs contribute to DNA binding. Lastly, we provide evidence that ComW's DNA-binding activity is important for transformation in pneumococcus. Our findings begin to fill the gaps in understanding how ComW regulates σΧ activity during bacterial natural transformation.
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Affiliation(s)
- Nicole L Inniss
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Gerd Prehna
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Donald A Morrison
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607
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12
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Mazumder A, Kapanidis AN. Recent Advances in Understanding σ70-Dependent Transcription Initiation Mechanisms. J Mol Biol 2019; 431:3947-3959. [PMID: 31082441 PMCID: PMC7057261 DOI: 10.1016/j.jmb.2019.04.046] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/26/2019] [Accepted: 04/29/2019] [Indexed: 11/23/2022]
Abstract
Prokaryotic transcription is one of the most studied biological systems, with relevance to many fields including the development and use of antibiotics, the construction of synthetic gene networks, and the development of many cutting-edge methodologies. Here, we discuss recent structural, biochemical, and single-molecule biophysical studies targeting the mechanisms of transcription initiation in bacteria, including the formation of the open complex, the reaction of initial transcription, and the promoter escape step that leads to elongation. We specifically focus on the mechanisms employed by the RNA polymerase holoenzyme with the housekeeping sigma factor σ70. The recent progress provides answers to long-held questions, identifies intriguing new behaviours, and opens up fresh questions for the field of transcription.
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Affiliation(s)
- Abhishek Mazumder
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.
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13
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14
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Narayanan A, Vago FS, Li K, Qayyum MZ, Yernool D, Jiang W, Murakami KS. Cryo-EM structure of Escherichia coli σ 70 RNA polymerase and promoter DNA complex revealed a role of σ non-conserved region during the open complex formation. J Biol Chem 2018; 293:7367-7375. [PMID: 29581236 DOI: 10.1074/jbc.ra118.002161] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/13/2018] [Indexed: 11/06/2022] Open
Abstract
First step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In Escherichia coli, a primary σ70 factor forms the RNAP holoenzyme to express housekeeping genes. The σ70 contains a large insertion between the conserved regions 1.2 and 2.1, the σ non-conserved region (σNCR), but its function remains to be elucidated. In this study, we determined the cryo-EM structures of the E. coli RNAP σ70 holoenzyme and its complex with promoter DNA (open complex, RPo) at 4.2 and 5.75 Å resolutions, respectively, to reveal native conformations of RNAP and DNA. The RPo structure presented here found an interaction between the σNCR and promoter DNA just upstream of the -10 element, which was not observed in a previously determined E. coli RNAP transcription initiation complex (RPo plus short RNA) structure by X-ray crystallography because of restraint of crystal packing effects. Disruption of the σNCR and DNA interaction by the amino acid substitutions (R157A/R157E) influences the DNA opening around the transcription start site and therefore decreases the transcription activity of RNAP. We propose that the σNCR and DNA interaction is conserved in proteobacteria, and RNAP in other bacteria replaces its role with a transcription factor.
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Affiliation(s)
- Anoop Narayanan
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802; Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, Indiana 47906
| | - Frank S Vago
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, Indiana 47906
| | - Kunpeng Li
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, Indiana 47906
| | - M Zuhaib Qayyum
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Dinesh Yernool
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, Indiana 47906
| | - Wen Jiang
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, Indiana 47906.
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802.
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15
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Roy NS, Debnath S, Chakraborty A, Chakraborty P, Bera I, Ghosh R, Ghoshal N, Chakrabarti S, Roy S. Enhanced basepair dynamics pre-disposes protein-assisted flips of key bases in DNA strand separation during transcription initiation. Phys Chem Chem Phys 2018; 20:9449-9459. [DOI: 10.1039/c8cp01119b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Localized separation of strands of duplex DNA is a necessary step in many DNA-dependent processes, including transcription and replication.
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Affiliation(s)
- Neeladri Sekhar Roy
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Subrata Debnath
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Abhijit Chakraborty
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | | | - Indrani Bera
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Raka Ghosh
- Department of Biophysics
- Bose Institute
- Kolkata 700054
- India
| | - Nanda Ghoshal
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Saikat Chakrabarti
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Siddhartha Roy
- Department of Biophysics
- Bose Institute
- Kolkata 700054
- India
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16
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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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17
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Chen J, Wassarman KM, Feng S, Leon K, Feklistov A, Winkelman JT, Li Z, Walz T, Campbell EA, Darst SA. 6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase. Mol Cell 2017; 68:388-397.e6. [PMID: 28988932 DOI: 10.1016/j.molcel.2017.09.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/11/2017] [Accepted: 09/05/2017] [Indexed: 01/25/2023]
Abstract
Noncoding RNAs (ncRNAs) regulate gene expression in all organisms. Bacterial 6S RNAs globally regulate transcription by binding RNA polymerase (RNAP) holoenzyme and competing with promoter DNA. Escherichia coli (Eco) 6S RNA interacts specifically with the housekeeping σ70-holoenzyme (Eσ70) and plays a key role in the transcriptional reprogramming upon shifts between exponential and stationary phase. Inhibition is relieved upon 6S RNA-templated RNA synthesis. We report here the 3.8 Å resolution structure of a complex between 6S RNA and Eσ70 determined by single-particle cryo-electron microscopy and validation of the structure using footprinting and crosslinking approaches. Duplex RNA segments have A-form C3' endo sugar puckers but widened major groove widths, giving the RNA an overall architecture that mimics B-form promoter DNA. Our results help explain the specificity of Eco 6S RNA for Eσ70 and show how an ncRNA can mimic B-form DNA to directly regulate transcription by the DNA-dependent RNAP.
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Affiliation(s)
- James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Karen M Wassarman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Shili Feng
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Katherine Leon
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Andrey Feklistov
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Jared T Winkelman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zongli Li
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA.
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA.
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18
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Wenholz DS, Zeng M, Ma C, Mielczarek M, Yang X, Bhadbhade M, Black DSC, Lewis PJ, Griffith R, Kumar N. Small molecule inhibitors of bacterial transcription complex formation. Bioorg Med Chem Lett 2017; 27:4302-4308. [PMID: 28866270 DOI: 10.1016/j.bmcl.2017.08.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/16/2017] [Accepted: 08/16/2017] [Indexed: 11/26/2022]
Abstract
Knoevenagel condensation was employed to generate a set of molecules potentially capable of inhibiting the RNA polymerase-σ70/σA interaction in bacteria. Synthesis was achieved via reactions between a variety of indole-7-carbaldehydes and rhodanine, N-allylrhodanine, barbituric acid or thiobarbituric acid. A library of structurally diverse compounds was examined by enzyme-linked immunosorbent assay (ELISA) to assess the inhibition of the targeted protein-protein interaction. Inhibition of bacterial growth was also evaluated using Bacillus subtilis and Escherichia coli cultures. The structure-activity relationship studies demonstrated the significance of particular structural features of the synthesized molecules for RNA polymerase-σ70/σA interaction inhibition and antibacterial activity. Docking was investigated as an in silico method for the further development of the compounds.
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Affiliation(s)
- Daniel S Wenholz
- School of Chemistry, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Ming Zeng
- School of Chemistry, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Cong Ma
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong
| | | | - Xiao Yang
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong
| | - Mohan Bhadbhade
- School of Chemistry, UNSW Sydney, Kensington, NSW 2052, Australia
| | - David St C Black
- School of Chemistry, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Peter J Lewis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Renate Griffith
- School of Medical Sciences, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Naresh Kumar
- School of Chemistry, UNSW Sydney, Kensington, NSW 2052, Australia; Australian Centre for Nanomedicine, UNSW Sydney, Kensington, NSW 2052, Australia.
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19
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Cavaliere P, Norel F. Recent advances in the characterization of Crl, the unconventional activator of the stress sigma factor σS/RpoS. Biomol Concepts 2017; 7:197-204. [PMID: 27180360 DOI: 10.1515/bmc-2016-0006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 03/29/2016] [Indexed: 11/15/2022] Open
Abstract
The bacterial RNA polymerase (RNAP) holoenzyme is a multisubunit core enzyme associated with a σ factor that is required for promoter-specific transcription initiation. Besides a primary σ responsible for most of the gene expression during active growth, bacteria contain alternative σ factors that control adaptive responses. A recurring strategy in the control of σ factor activity is their sequestration by anti-sigma factors that occlude the RNAP binding determinants, reducing their activity. In contrast, the unconventional transcription factor Crl binds specifically to the alternative σ factor σS/RpoS, and favors its association with the core RNAP, thereby increasing its activity. σS is the master regulator of the general stress response that protects many Gram-negative bacteria from several harmful environmental conditions. It is also required for biofilm formation and virulence of Salmonella enterica serovar Typhimurium. In this report, we discuss current knowledge on the regulation and function of Crl in Salmonella and Escherichia coli, two bacterial species in which Crl has been studied. We review recent advances in the structural characterization of the Crl-σS interaction that have led to a better understanding of this unusual mechanism of σ regulation.
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20
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Davis MC, Kesthely CA, Franklin EA, MacLellan SR. The essential activities of the bacterial sigma factor. Can J Microbiol 2016; 63:89-99. [PMID: 28117604 DOI: 10.1139/cjm-2016-0576] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Transcription is the first and most heavily regulated step in gene expression. Sigma (σ) factors are general transcription factors that reversibly bind RNA polymerase (RNAP) and mediate transcription of all genes in bacteria. σ Factors play 3 major roles in the RNA synthesis initiation process: they (i) target RNAP holoenzyme to specific promoters, (ii) melt a region of double-stranded promoter DNA and stabilize it as a single-stranded open complex, and (iii) interact with other DNA-binding transcription factors to contribute complexity to gene expression regulation schemes. Recent structural studies have demonstrated that when σ factors bind promoter DNA, they capture 1 or more nucleotides that are flipped out of the helical DNA stack and this stabilizes the promoter open-complex intermediate that is required for the initiation of RNA synthesis. This review describes the structure and function of the σ70 family of σ proteins and the essential roles they play in the transcription process.
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Affiliation(s)
- Maria C Davis
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada.,Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Christopher A Kesthely
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada.,Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Emily A Franklin
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada.,Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Shawn R MacLellan
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada.,Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
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21
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Xue X, Davis MC, Steeves T, Bishop A, Breen J, MacEacheron A, Kesthely CA, Hsu F, MacLellan SR. Characterization of a protein-protein interaction within the SigO-RsoA two-subunit σ factor: the σ70 region 2.3-like segment of RsoA mediates interaction with SigO. MICROBIOLOGY-SGM 2016; 162:1857-1869. [PMID: 27558998 DOI: 10.1099/mic.0.000358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
σ factors are single subunit general transcription factors that reversibly bind core RNA polymerase and mediate gene-specific transcription in bacteria. Previously, an atypical two-subunit σ factor was identified that activates transcription from a group of related promoters in Bacillus subtilis. Both of the subunits, named SigO and RsoA, share primary sequence similarity with the canonical σ70 family of σ factors and interact with each other and with RNA polymerase subunits. Here we show that the σ70 region 2.3-like segment of RsoA is unexpectedly sufficient for interaction with the amino-terminus of SigO and the β' subunit. A mutational analysis of RsoA identified aromatic residues conserved amongst all RsoA homologues, and often amongst canonical σ factors, that are particularly important for the SigO-RsoA interaction. In a canonical σ factor, region 2.3 amino acids bind non-template strand DNA, trapping the promoter in a single-stranded state required for initiation of transcription. Accordingly, we speculate that RsoA region 2.3 protein-binding activity likely arose from a motif that, at least in its ancestral protein, participated in DNA-binding interactions.
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Affiliation(s)
- Xiaowei Xue
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Maria C Davis
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Thomas Steeves
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Adam Bishop
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Jillian Breen
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | | | | | - FoSheng Hsu
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Shawn R MacLellan
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
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22
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Uncovering ancient transcription systems with a novel evolutionary indicator. Sci Rep 2016; 6:27922. [PMID: 27307191 PMCID: PMC4910066 DOI: 10.1038/srep27922] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 05/26/2016] [Indexed: 11/08/2022] Open
Abstract
TBP and TFIIB are evolutionarily conserved transcription initiation factors in archaea and eukaryotes. Information about their ancestral genes would be expected to provide insight into the origin of the RNA polymerase II-type transcription apparatus. In obtaining such information, the nucleotide sequences of current genes of both archaea and eukaryotes should be included in the analysis. However, the present methods of evolutionary analysis require that a subset of the genes should be excluded as an outer group. To overcome this limitation, we propose an innovative concept for evolutionary analysis that does not require an outer group. This approach utilizes the similarity in intramolecular direct repeats present in TBP and TFIIB as an evolutionary measure revealing the degree of similarity between the present offspring genes and their ancestors. Information on the properties of the ancestors and the order of emergence of TBP and TFIIB was also revealed. These findings imply that, for evolutionarily early transcription systems billions of years ago, interaction of RNA polymerase II with transcription initiation factors and the regulation of its enzymatic activity was required prior to the accurate positioning of the enzyme. Our approach provides a new way to discuss mechanistic and system evolution in a quantitative manner.
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23
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Liu B, Zuo Y, Steitz TA. Structures of E. coli σS-transcription initiation complexes provide new insights into polymerase mechanism. Proc Natl Acad Sci U S A 2016; 113:4051-6. [PMID: 27035955 PMCID: PMC4839411 DOI: 10.1073/pnas.1520555113] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In bacteria, multiple σ factors compete to associate with the RNA polymerase (RNAP) core enzyme to form a holoenzyme that is required for promoter recognition. During transcription initiation RNAP remains associated with the upstream promoter DNA via sequence-specific interactions between the σ factor and the promoter DNA while moving downstream for RNA synthesis. As RNA polymerase repetitively adds nucleotides to the 3'-end of the RNA, a pyrophosphate ion is generated after each nucleotide incorporation. It is currently unknown how the release of pyrophosphate affects transcription. Here we report the crystal structures of E coli transcription initiation complexes (TICs) containing the stress-responsive σ(S) factor, a de novo synthesized RNA oligonucleotide, and a complete transcription bubble (σ(S)-TIC) at about 3.9-Å resolution. The structures show the 3D topology of the σ(S) factor and how it recognizes the promoter DNA, including likely specific interactions with the template-strand residues of the -10 element. In addition, σ(S)-TIC structures display a highly stressed pretranslocated initiation complex that traps a pyrophosphate at the active site that remains closed. The position of the pyrophosphate and the unusual phosphodiester linkage between the two terminal RNA residues suggest an unfinished nucleotide-addition reaction that is likely at equilibrium between nucleotide addition and pyrophosphorolysis. Although these σ(S)-TIC crystals are enzymatically active, they are slow in nucleotide addition, as suggested by an NTP soaking experiment. Pyrophosphate release completes the nucleotide addition reaction and is associated with extensive conformational changes around the secondary channel but causes neither active site opening nor transcript translocation.
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Affiliation(s)
- Bin Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Yuhong Zuo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520;
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520; Department of Chemistry, Yale University, New Haven, CT 06520
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24
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Thach O, Mielczarek M, Ma C, Kutty SK, Yang X, Black DS, Griffith R, Lewis PJ, Kumar N. From indole to pyrrole, furan, thiophene and pyridine: Search for novel small molecule inhibitors of bacterial transcription initiation complex formation. Bioorg Med Chem 2016; 24:1171-82. [DOI: 10.1016/j.bmc.2016.01.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/11/2016] [Accepted: 01/19/2016] [Indexed: 10/22/2022]
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25
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Binder SC, Eckweiler D, Schulz S, Bielecka A, Nicolai T, Franke R, Häussler S, Meyer-Hermann M. Functional modules of sigma factor regulons guarantee adaptability and evolvability. Sci Rep 2016; 6:22212. [PMID: 26915971 PMCID: PMC4768184 DOI: 10.1038/srep22212] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 02/10/2016] [Indexed: 01/30/2023] Open
Abstract
The focus of modern molecular biology turns from assigning functions to individual genes towards understanding the expression and regulation of complex sets of molecules. Here, we provide evidence that alternative sigma factor regulons in the pathogen Pseudomonas aeruginosa largely represent insulated functional modules which provide a critical level of biological organization involved in general adaptation and survival processes. Analysis of the operational state of the sigma factor network revealed that transcription factors functionally couple the sigma factor regulons and significantly modulate the transcription levels in the face of challenging environments. The threshold quality of newly evolved transcription factors was reached faster and more robustly in in silico testing when the structural organization of sigma factor networks was taken into account. These results indicate that the modular structures of alternative sigma factor regulons provide P. aeruginosa with a robust framework to function adequately in its environment and at the same time facilitate evolutionary change. Our data support the view that widespread modularity guarantees robustness of biological networks and is a key driver of evolvability.
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Affiliation(s)
- Sebastian C Binder
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Denitsa Eckweiler
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, 30265 Hannover, Germany.,Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Sebastian Schulz
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, 30265 Hannover, Germany.,Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Agata Bielecka
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, 30265 Hannover, Germany.,Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Tanja Nicolai
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, 30265 Hannover, Germany.,Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany.,Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, 38124 Braunschweig, Germany
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26
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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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27
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Si HM, Zhang F, Wu AN, Han RZ, Xu GC, Ni Y. DNA microarray of global transcription factor mutant reveals membrane-related proteins involved in n-butanol tolerance in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:114. [PMID: 27252779 PMCID: PMC4888631 DOI: 10.1186/s13068-016-0527-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 05/11/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND Escherichia coli has been explored as a platform host strain for biofuels production such as butanol. However, the severe toxicity of butanol is considered to be one major limitation for butanol production from E. coli. The goal of this study is therefore to construct butanol-tolerant E. coli strains and clarify the tolerance mechanisms. RESULTS A recombinant E. coli strain harboring σ(70) mutation capable of tolerating 2 % (v/v) butanol was isolated by the global transcription machinery engineering (gTME) approach. DNA microarrays were employed to assess the transcriptome profile of butanol-tolerant strain B8. Compared with the wild-type strain, 329 differentially expressed genes (197 up-regulated and 132 down-regulated) (p < 0.05; FC ≥ 2) were identified. These genes are involved in carbohydrate metabolism, energy metabolism, two-component signal transduction system, oxidative stress response, lipid and cell envelope biogenesis and efflux pump. CONCLUSIONS Several membrane-related proteins were proved to be involved in butanol tolerance of E. coli. Two down-regulated genes, yibT and yghW, were identified to be capable of affecting butanol tolerance by regulating membrane fatty acid composition. Another down-regulated gene ybjC encodes a predicted inner membrane protein. In addition, a number of up-regulated genes, such as gcl and glcF, contribute to supplement metabolic intermediates for glyoxylate and TCA cycles to enhance energy supply. Our results could serve as a practical strategy for the construction of platform E. coli strains as biofuel producer.
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Affiliation(s)
- Hai-Ming Si
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Fa Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - An-Ning Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Rui-Zhi Han
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Guo-Chao Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Ye Ni
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu China
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28
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Tolstova AP, Dubrovin EV, Koroleva ON. Investigation of σ70 subunit structure dependence in Escherichia coli RNA polymerase on ionic strength by the molecular dynamics simulation method. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915060251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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29
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Mekler V, Severinov K. Use of RNA polymerase molecular beacon assay to measure RNA polymerase interactions with model promoter fragments. Methods Mol Biol 2015; 1276:199-210. [PMID: 25665565 DOI: 10.1007/978-1-4939-2392-2_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
RNA polymerase-promoter interactions that keep the transcription initiation complex together are complex and multipartite, and formation of the RNA polymerase-promoter complex proceeds through multiple intermediates. Short promoter fragments can be used as a tool to dissect RNA polymerase-promoter interactions and to pinpoint elements responsible for specific properties of the entire promoter complex. A recently developed fluorometric molecular beacon assay allows one to monitor the enzyme interactions with various DNA probes and quantitatively characterize partial RNA polymerase-promoter interactions. Here, we present detailed protocols for the preparation of an Escherichia coli molecular beacon and its application to study RNA polymerase interactions with model promoter fragments.
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Affiliation(s)
- Vladimir Mekler
- Waksman Institute of Microbiology, Rutgers, State University of New Jersey, Piscataway, NJ, 08854, USA,
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30
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Bae B, Feklistov A, Lass-Napiorkowska A, Landick R, Darst SA. Structure of a bacterial RNA polymerase holoenzyme open promoter complex. eLife 2015; 4. [PMID: 26349032 PMCID: PMC4593229 DOI: 10.7554/elife.08504] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/03/2015] [Indexed: 01/17/2023] Open
Abstract
Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the −10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstream of the −10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Addition of an RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σA dissociation. DOI:http://dx.doi.org/10.7554/eLife.08504.001 Inside cells, molecules of double-stranded DNA encode the instructions needed to make proteins. To make a protein, the two strands of DNA that make up a gene are separated and one strand acts as a template to make molecules of messenger ribonucleic acid (or mRNA for short). This process is called transcription. The mRNA is then used as a template to assemble the protein. An enzyme called RNA polymerase carries out transcription and is found in all cells ranging from bacteria to humans and other animals. Bacteria have the simplest form of RNA polymerase and provide an excellent system to study how it controls transcription. It is made up of several proteins that work together to make RNA using DNA as a template. However, it requires the help of another protein called sigma factor to direct it to regions of DNA called promoters, which are just before the start of the gene. When RNA polymerase and the sigma factor interact the resulting group of proteins is known as the RNA polymerase ‘holoenzyme’. Transcription takes place in several stages. To start with, the RNA polymerase holoenzyme locates and binds to promoter DNA. Next, it separates the two strands of DNA and exposes a portion of the template strand. At this point, the DNA and the holoenzyme are said to be in an ‘open promoter complex’ and the section of promoter DNA that is within it is known as a ‘transcription bubble’. However, it is not clear how RNA polymerase holoenzyme interacts with DNA in the open promoter complex. Bae, Feklistov et al. have now used X-ray crystallography to reveal the three-dimensional structure of the open promoter complex with an entire transcription bubble from a bacterium called Thermus aquaticus. The experiments show that there are several important interactions between RNA polymerase holoenzyme and promoter DNA. In particular, the sigma factor inserts into a region of the DNA at the start of the transcription bubble. This rearranges the DNA in a manner that allows the DNA to be exposed and contact the main part of the RNA polymerase. If the holoenyzyme fails to contact the DNA in this way, the holoenzyme does not bind properly to the promoter and transcription does not start. These findings build on previous work to provide a detailed structural framework for understanding how the RNA polymerase holoenzyme and DNA interact to form the open promoter complex. Another study by Bae et al.—which involved some of the same researchers as this study—reveals how another protein called CarD also binds to DNA at the start of the transcription bubble to stabilize the open promoter complex. DOI:http://dx.doi.org/10.7554/eLife.08504.002
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Affiliation(s)
- Brian Bae
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| | - Andrey Feklistov
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| | - Agnieszka Lass-Napiorkowska
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-madison, Madison, United States.,Department of Bacteriology, University of Wisconsin-Madison, Madison, United States
| | - Seth A Darst
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
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31
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Structural biology of bacterial RNA polymerase. Biomolecules 2015; 5:848-64. [PMID: 25970587 PMCID: PMC4496699 DOI: 10.3390/biom5020848] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/10/2015] [Accepted: 04/13/2015] [Indexed: 11/17/2022] Open
Abstract
Since its discovery and characterization in the early 1960s (Hurwitz, J. The discovery of RNA polymerase. J. Biol. Chem. 2005, 280, 42477-42485), an enormous amount of biochemical, biophysical and genetic data has been collected on bacterial RNA polymerase (RNAP). In the late 1990s, structural information pertaining to bacterial RNAP has emerged that provided unprecedented insights into the function and mechanism of RNA transcription. In this review, I list all structures related to bacterial RNAP (as determined by X-ray crystallography and NMR methods available from the Protein Data Bank), describe their contributions to bacterial transcription research and discuss the role that small molecules play in inhibiting bacterial RNA transcription.
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32
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Mekler V, Severinov K. RNA polymerase molecular beacon as tool for studies of RNA polymerase-promoter interactions. Methods 2015; 86:19-26. [PMID: 25956222 DOI: 10.1016/j.ymeth.2015.04.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/27/2015] [Accepted: 04/28/2015] [Indexed: 10/23/2022] Open
Abstract
The molecular details of formation of transcription initiation complex upon the interaction of bacterial RNA polymerase (RNAP) with promoters are not completely understood. One way to address this problem is to understand how RNAP interacts with different parts of promoter DNA. A recently developed fluorometric RNAP molecular beacon assay allows one to monitor the RNAP interactions with various unlabeled DNA probes and quantitatively characterize partial RNAP-promoter interactions. This paper focuses on methodological aspects of application of this powerful assay to study the mechanism of transcription initiation complex formation by Escherichia coli RNA polymerase σ(70) holoenzyme and its regulation by bacterial and phage encoded factors.
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Affiliation(s)
- Vladimir Mekler
- Waksman Institute of Microbiology, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA; Skolkovo Institute of Science and Technology, 143025 Skolkovo, Russia; Institutes of Gene Biology and Molecular Genetics, Russian Academy of Sciences, 119334 Moscow, Russia.
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33
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Synthesis and biological activity of novel mono-indole and mono-benzofuran inhibitors of bacterial transcription initiation complex formation. Bioorg Med Chem 2015; 23:1763-75. [DOI: 10.1016/j.bmc.2015.02.037] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 02/12/2015] [Accepted: 02/17/2015] [Indexed: 11/23/2022]
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34
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Acid-adapted strains of Escherichia coli K-12 obtained by experimental evolution. Appl Environ Microbiol 2015; 81:1932-41. [PMID: 25556191 DOI: 10.1128/aem.03494-14] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Enteric bacteria encounter a wide range of pHs throughout the human intestinal tract. We conducted experimental evolution of Escherichia coli K-12 to isolate clones with increased fitness during growth under acidic conditions (pH 4.5 to 4.8). Twenty-four independent populations of E. coli K-12 W3110 were evolved in LBK medium (10 g/liter tryptone, 5 g/liter yeast extract, 7.45 g/liter KCl) buffered with homopiperazine-N,N'-bis-2-(ethanosulfonic acid) and malate at pH 4.8. At generation 730, the pH was decreased to 4.6 with HCl. By 2,000 generations, all populations had achieved higher endpoint growth than the ancestor at pH 4.6 but not at pH 7.0. All evolving populations showed a progressive loss of activity of lysine decarboxylase (CadA), a major acid stress enzyme. This finding suggests a surprising association between acid adaptation and moderation of an acid stress response. At generation 2,000, eight clones were isolated from four populations, and their genomes were sequenced. Each clone showed between three and eight missense mutations, including one in a subunit of the RNA polymerase holoenzyme (rpoB, rpoC, or rpoD). Missense mutations were found in adiY, the activator of the acid-inducible arginine decarboxylase (adiA), and in gcvP (glycine decarboxylase), a possible acid stress component. For tests of fitness relative to that of the ancestor, lacZ::kan was transduced into each strain. All acid-evolved clones showed a high fitness advantage at pH 4.6. With the cytoplasmic pH depressed by benzoate (at external pH 6.5), acid-evolved clones showed decreased fitness; thus, there was no adaptation to cytoplasmic pH depression. At pH 9.0, acid-evolved clones showed no fitness advantage. Thus, our acid-evolved clones showed a fitness increase specific to low external pH.
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35
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Differential role of base pairs on gal promoters strength. J Mol Biol 2014; 427:792-806. [PMID: 25543084 DOI: 10.1016/j.jmb.2014.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 12/16/2014] [Accepted: 12/18/2015] [Indexed: 11/23/2022]
Abstract
Sequence alignments of promoters in prokaryotes postulated that the frequency of occurrence of a base pair at a given position of promoter elements reflects its contribution to intrinsic promoter strength. We directly assessed the contribution of the four base pairs in each position in the intrinsic promoter strength by keeping the context constant in Escherichia coli cAMP-CRP (cAMP receptor protein) regulated gal promoters by in vitro transcription assays. First, we show that base pair frequency within known consensus elements correlates well with promoter strength. Second, we observe some substitutions upstream of the ex-10 TG motif that are important for promoter function. Although the galP1 and P2 promoters overlap, only three positions where substitutions inactivated both promoters were found. We propose that RNA polymerase binds to the -12T base pair as part of double-stranded DNA while opening base pairs from -11A to +3 to form the single-stranded transcription bubble DNA during isomerization. The cAMP-CRP complex rescued some deleterious substitutions in the promoter region. The base pair roles and their flexibilities reported here for E. coli gal promoters may help construction of synthetic promoters in gene circuitry experiments in which overlapping promoters with differential controls may be warranted.
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36
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37
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Degen D, Feng Y, Zhang Y, Ebright KY, Ebright YW, Gigliotti M, Vahedian-Movahed H, Mandal S, Talaue M, Connell N, Arnold E, Fenical W, Ebright RH. Transcription inhibition by the depsipeptide antibiotic salinamide A. eLife 2014; 3:e02451. [PMID: 24843001 PMCID: PMC4029172 DOI: 10.7554/elife.02451] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 04/18/2014] [Indexed: 12/12/2022] Open
Abstract
We report that bacterial RNA polymerase (RNAP) is the functional cellular target of the depsipeptide antibiotic salinamide A (Sal), and we report that Sal inhibits RNAP through a novel binding site and mechanism. We show that Sal inhibits RNA synthesis in cells and that mutations that confer Sal-resistance map to RNAP genes. We show that Sal interacts with the RNAP active-center 'bridge-helix cap' comprising the 'bridge-helix N-terminal hinge', 'F-loop', and 'link region'. We show that Sal inhibits nucleotide addition in transcription initiation and elongation. We present a crystal structure that defines interactions between Sal and RNAP and effects of Sal on RNAP conformation. We propose that Sal functions by binding to the RNAP bridge-helix cap and preventing conformational changes of the bridge-helix N-terminal hinge necessary for nucleotide addition. The results provide a target for antibacterial drug discovery and a reagent to probe conformation and function of the bridge-helix N-terminal hinge.DOI: http://dx.doi.org/10.7554/eLife.02451.001.
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Affiliation(s)
- David Degen
- Waksman Institute, Rutgers University, Piscataway, United States
| | - Yu Feng
- Waksman Institute, Rutgers University, Piscataway, United States
| | - Yu Zhang
- Waksman Institute, Rutgers University, Piscataway, United States
| | | | - Yon W Ebright
- Waksman Institute, Rutgers University, Piscataway, United States
| | | | | | - Sukhendu Mandal
- Waksman Institute, Rutgers University, Piscataway, United States
| | - Meliza Talaue
- Center for Biodefense, New Jersey Medical School, Rutgers University, Newark, United States
| | - Nancy Connell
- Center for Biodefense, New Jersey Medical School, Rutgers University, Newark, United States
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, United States
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, United States
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38
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Mielczarek M, Devakaram RV, Ma C, Yang X, Kandemir H, Purwono B, Black DS, Griffith R, Lewis PJ, Kumar N. Synthesis and biological activity of novel bis-indole inhibitors of bacterial transcription initiation complex formation. Org Biomol Chem 2014; 12:2882-94. [DOI: 10.1039/c4ob00460d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of novel bis-indole amides and glyoxylamides as bacterial transcription complex formation inhibitors and their structure–activity relationships are discussed.
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Affiliation(s)
- Marcin Mielczarek
- School of Chemistry
- The University of New South Wales
- Sydney, Australia
| | - Ruth V. Devakaram
- School of Chemistry
- The University of New South Wales
- Sydney, Australia
| | - Cong Ma
- School of Environmental and Life Sciences
- University of Newcastle
- Callaghan, Australia
| | - Xiao Yang
- School of Environmental and Life Sciences
- University of Newcastle
- Callaghan, Australia
| | - Hakan Kandemir
- School of Chemistry
- The University of New South Wales
- Sydney, Australia
| | - Bambang Purwono
- School of Chemistry
- The University of New South Wales
- Sydney, Australia
| | - David StC. Black
- School of Chemistry
- The University of New South Wales
- Sydney, Australia
| | - Renate Griffith
- School of Medical Sciences
- Department of Pharmacology
- The University of New South Wales
- Sydney, Australia
| | - Peter J. Lewis
- School of Environmental and Life Sciences
- University of Newcastle
- Callaghan, Australia
| | - Naresh Kumar
- School of Chemistry
- The University of New South Wales
- Sydney, Australia
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39
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Abstract
Chloroplasts, the sites of photosynthesis and sources of reducing power, are at the core of the success story that sets apart autotrophic plants from most other living organisms. Along with their fellow organelles (e.g., amylo-, chromo-, etio-, and leucoplasts), they form a group of intracellular biosynthetic machines collectively known as plastids. These plant cell constituents have their own genome (plastome), their own (70S) ribosomes, and complete enzymatic equipment covering the full range from DNA replication via transcription and RNA processive modification to translation. Plastid RNA synthesis (gene transcription) involves the collaborative activity of two distinct types of RNA polymerases that differ in their phylogenetic origin as well as their architecture and mode of function. The existence of multiple plastid RNA polymerases is reflected by distinctive sets of regulatory DNA elements and protein factors. This complexity of the plastid transcription apparatus thus provides ample room for regulatory effects at many levels within and beyond transcription. Research in this field offers insight into the various ways in which plastid genes, both singly and groupwise, can be regulated according to the needs of the entire cell. Furthermore, it opens up strategies that allow to alter these processes in order to optimize the expression of desired gene products.
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Affiliation(s)
- Jennifer Ortelt
- Plant Cell Physiology and Molecular Biology, University of Bochum, Bochum, Germany
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40
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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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41
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Mapping the Spatial Neighborhood of the Regulatory 6S RNA Bound to Escherichia coli RNA Polymerase Holoenzyme. J Mol Biol 2013; 425:3649-61. [DOI: 10.1016/j.jmb.2013.07.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 06/28/2013] [Accepted: 07/04/2013] [Indexed: 11/15/2022]
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Tare P, Mallick B, Nagaraja V. Co-evolution of specific amino acid in sigma 1.2 region and nucleotide base in the discriminator to act as sensors of small molecule effectors of transcription initiation in mycobacteria. Mol Microbiol 2013; 90:569-83. [PMID: 23998628 DOI: 10.1111/mmi.12384] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2013] [Indexed: 11/30/2022]
Abstract
The transcription from rrn and a number of other promoters is regulated by initiating ribonucleotides (iNTPs) and guanosine tetra/penta phosphate [(p)ppGpp], either by strengthening or by weakening of the RNA polymerase (RNAP)-promoter interactions during initiation. Studies in Escherichia coli revealed the importance of a sequence termed discriminator, located between -10 and the transcription start site of the responsive promoters in this mode of regulation. Instability of the open complex at these promoters is attributed to the lack of stabilizing interactions between the suboptimal discriminator and the 1.2 region of sigma 70 (Sig70) in RNAP holoenzyme. We demonstrate a different pattern of interaction between the promoters and sigma A (SigA) of Mycobacterium tuberculosis to execute similar regulation. Instead of cytosine and methionine, thymine at three nucleotides downstream to -10 element and leucine 232 in SigA are found to be essential for iNTPs and pppGpp mediated response at the rrn and gyr promoters of the organism. The specificity of the interaction is substantiated by mutational replacements, either in the discriminator or in SigA, which abolish the nucleotide mediated regulation in vitro or in vivo. Specific yet distinct bases and the amino acids appear to have 'co-evolved' to retain the discriminator-sigma 1.2 region regulatory switch operated by iNTPs/pppGpp during the transcription initiation in different bacteria.
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Affiliation(s)
- Priyanka Tare
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
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Key features of σS required for specific recognition by Crl, a transcription factor promoting assembly of RNA polymerase holoenzyme. Proc Natl Acad Sci U S A 2013; 110:15955-60. [PMID: 24043782 DOI: 10.1073/pnas.1311642110] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Bacteria use multiple sigma factors to coordinate gene expression in response to environmental perturbations. In Escherichia coli and other γ-proteobacteria, the transcription factor Crl stimulates σ(S)-dependent transcription during times of cellular stress by promoting the association of σ(S) with core RNA polymerase. The molecular basis for specific recognition of σ(S) by Crl, rather than the homologous and more abundant primary sigma factor σ(70), is unknown. Here we use bacterial two-hybrid analysis in vivo and p-benzoyl-phenylalanine cross-linking in vitro to define the features in σ(S) responsible for specific recognition by Crl. We identify residues in σ(S) conserved domain 2 (σ(S)2) that are necessary and sufficient to allow recognition of σ(70) conserved domain 2 by Crl, one near the promoter-melting region and the other at the position where a large nonconserved region interrupts the sequence of σ(70). We then use luminescence resonance energy transfer to demonstrate directly that Crl promotes holoenzyme assembly using these specificity determinants on σ(S). Our results explain how Crl distinguishes between sigma factors that are largely homologous and activates discrete sets of promoters even though it does not bind to promoter DNA.
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Affiliation(s)
- Helen Cook
- Department of Systems Biology; Center for Biological Sequence Analysis; The Technical University of Denmark; 2800 Kgs Lyngby Denmark
| | - David W. Ussery
- Department of Systems Biology; Center for Biological Sequence Analysis; The Technical University of Denmark; 2800 Kgs Lyngby Denmark
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Ganguly A, Chatterji D. A comparative kinetic and thermodynamic perspective of the σ-competition model in Escherichia coli. Biophys J 2013; 103:1325-33. [PMID: 22995505 DOI: 10.1016/j.bpj.2012.08.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 08/01/2012] [Accepted: 08/02/2012] [Indexed: 11/17/2022] Open
Abstract
Transcription is the most fundamental step in gene expression in any living organism. Various environmental cues help in the maturation of core RNA polymerase (RNAP; α(2)ββ'ω) with different σ-factors, leading to the directed recruitment of RNAP to different promoter DNA sequences. Thus it is essential to determine the σ-factors that affect the preferential partitioning of core RNAP among various σ-actors, and the role of σ-switching in transcriptional gene regulation. Further, the macromolecular assembly of holo RNAP takes place in an extremely crowded environment within a cell, and thus far the kinetics and thermodynamics of this molecular recognition process have not been well addressed. In this study we used a site-directed bioaffinity immobilization method to evaluate the relative binding affinities of three different Escherichia coli σ-factors to the same core RNAP with variations in temperature and ionic strength while emulating the crowded cellular milieu. Our data indicate that the interaction of core RNAP-σ is susceptible to changes in external stimuli such as osmolytic and thermal stress, and the degree of susceptibility varies among different σ-factors. This allows for a reversible σ-switching from housekeeping factors to alternate σ-factors when the organism senses a change in its physiological conditions.
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Affiliation(s)
- Abantika Ganguly
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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Murakami KS. X-ray crystal structure of Escherichia coli RNA polymerase σ70 holoenzyme. J Biol Chem 2013; 288:9126-34. [PMID: 23389035 DOI: 10.1074/jbc.m112.430900] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli RNA polymerase (RNAP) is the most studied bacterial RNAP and has been used as the model RNAP for screening and evaluating potential RNAP-targeting antibiotics. However, the x-ray crystal structure of E. coli RNAP has been limited to individual domains. Here, I report the x-ray structure of the E. coli RNAP σ(70) holoenzyme, which shows σ region 1.1 (σ1.1) and the α subunit C-terminal domain for the first time in the context of an intact RNAP. σ1.1 is positioned at the RNAP DNA-binding channel and completely blocks DNA entry to the RNAP active site. The structure reveals that σ1.1 contains a basic patch on its surface, which may play an important role in DNA interaction to facilitate open promoter complex formation. The α subunit C-terminal domain is positioned next to σ domain 4 with a fully stretched linker between the N- and C-terminal domains. E. coli RNAP crystals can be prepared from a convenient overexpression system, allowing further structural studies of bacterial RNAP mutants, including functionally deficient and antibiotic-resistant RNAPs.
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Affiliation(s)
- Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
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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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Debnath S, Roy NS, Bera I, Ghoshal N, Roy S. Indirect read-out of the promoter DNA by RNA polymerase in the closed complex. Nucleic Acids Res 2012; 41:366-77. [PMID: 23118489 PMCID: PMC3592454 DOI: 10.1093/nar/gks1018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transcription is initiated when RNA polymerase recognizes the duplex promoter DNA in the closed complex. Due to its transient nature, the closed complex has not been well characterized. How the initial promoter recognition occurs may offer important clues to regulation of transcription initiation. In this article, we have carried out single-base pair substitution experiments on two Escherichia coli promoters belonging to two different classes, the -35 and the extended -10, under conditions which stabilize the closed complex. Single-base pair substitution experiments indicate modest base-specific effects on the stability of the closed complex of both promoters. Mutations of base pairs in the -10 region affect the closed complexes of two promoters differently, suggesting different modes of interaction of the RNA polymerase and the promoter in the two closed complexes. Two residues on σ(70) which have been suggested to play important role in promoter recognition, Q437 and R436, were mutated and found to have different effects on the closed-complex stability. DNA circular dichroism (CD) and FRET suggest that the promoter DNA in the closed complex is distorted. Modeling suggests two different orientations of the recognition helix of the RNA polymerase in the closed complex. We propose that the RNA polymerase recognizes the sequence dependent conformation of the promoter DNA in the closed complex.
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Affiliation(s)
- Subrata Debnath
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4 Raja Subodh Mullick Road, Kolkata 700032, India
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Malkhed V, Mustyala KK, Potlapally SR, Vuruputuri U. Modeling of Alternate RNA Polymerase Sigma D Factor and Identification of Novel Inhibitors by Virtual Screening. Cell Mol Bioeng 2012. [DOI: 10.1007/s12195-012-0238-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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50
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Liu J, Li J, Wu Z, Pei H, Zhou J, Xiang H. Identification and characterization of the cognate anti-sigma factor and specific promoter elements of a T. tengcongensis ECF sigma factor. PLoS One 2012; 7:e40885. [PMID: 22815853 PMCID: PMC3397946 DOI: 10.1371/journal.pone.0040885] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 06/14/2012] [Indexed: 11/18/2022] Open
Abstract
Extracytoplasmic function (ECF) σ factors, the largest group of alternative σ factors, play important roles in response to environmental stresses. Tt-RpoE1 is annotated as an ECF σ factor in Thermoanaerobacter tengcongensis. In this study, we revealed that the Tt-tolB gene located downstream of the Tt-rpoE1 gene encoded the cognate anti-σ factor, which could inhibit the transcription activity of Tt-RpoE1 by direct interaction with Tt-RpoE1 via its N-terminal domain. By in vitro transcription assay, the auto-regulation ability of Tt-RpoE1 was determined, and band shift assay showed that Tt-RpoE1 preferred to bind a fork-junction promoter DNA. With truncation or base-specific scanning mutations, the contribution of the nucleotides in −35 and −10 regions to interaction between Tt-RpoE1 and promoter DNA was explored. The promoter recognition pattern of Tt-RpoE1 was determined as 5′ tGTTACN16CGTC 3′, which was further confirmed by in vitro transcription assays. This result showed that the Tt-RpoE1-recognized promoter possessed a distinct −10 motif (−13CGTC−10) as the recognition determinant, which is distinguished from the −10 element recognized by σ70. Site-directed mutagenesis in Region 2.4 of Tt-RpoE1 indicated that the “D” residue of DXXR motif was responsible for recognizing the −12G nucleotide. Our results suggested that distinct −10 motif may be an efficient and general strategy used by ECF σ factors in adaptive response regulation of the related genes.
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Affiliation(s)
- Jingfang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Zhenfang Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Huadong Pei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
- * E-mail:
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