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Zheng Y, Kan CH, Tsang TF, Liu Y, Liu T, Tsang MW, Lam LY, Yang X, Ma C. Discovery of Inhibitors Targeting Protein-Protein Interaction between Bacterial RNA Polymerase and NusG as Novel Antimicrobials. J Med Chem 2024. [PMID: 39196895 DOI: 10.1021/acs.jmedchem.4c01386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2024]
Abstract
Bacterial RNA polymerase (RNAP), the core enzyme responsible for bacterial transcription, requires the NusG factor for efficient transcription elongation and termination. As the primary binding site for NusG, the RNAP clamp-helix (CH) domain represents a potential protein-protein interaction (PPI) target for novel antimicrobial agent design and discovery. In this study, we designed a pharmacophore model based on the essential amino acids of the CH for binding to NusG, such as R270, R278, and R281 (Escherichia coli numbering), and identified a hit compound with mild antimicrobial activity. Subsequent rational design and synthesis of this hit compound led to improved antimicrobial activity against Streptococcus pneumoniae, with the minimum inhibitory concentration (MIC) reduced from 128 to 1 μg/mL. Additional characterization of the antimicrobial activity, inhibitory activity against RNAP-NusG interaction, and cell-based transcription and fluorescent assays of the optimized compounds demonstrated their potential for further lead optimization.
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Affiliation(s)
- Yingbo Zheng
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Cheuk Hei Kan
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Tsz Fung Tsang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Yanpeng Liu
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Tiankuang Liu
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Man Wai Tsang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Long Yin Lam
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Xiao Yang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Cong Ma
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
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2
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El Sayyed H, Pambos OJ, Stracy M, Gottesman ME, Kapanidis AN. Single-molecule tracking reveals the functional allocation, in vivo interactions, and spatial organization of universal transcription factor NusG. Mol Cell 2024; 84:926-937.e4. [PMID: 38387461 DOI: 10.1016/j.molcel.2024.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 12/14/2023] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
During transcription elongation, NusG aids RNA polymerase by inhibiting pausing, promoting anti-termination on rRNA operons, coupling transcription with translation on mRNA genes, and facilitating Rho-dependent termination. Despite extensive work, the in vivo functional allocation and spatial distribution of NusG remain unknown. Using single-molecule tracking and super-resolution imaging in live E. coli cells, we found NusG predominantly in a chromosome-associated population (binding to RNA polymerase in elongation complexes) and a slowly diffusing population complexed with the 30S ribosomal subunit; the latter provides a "30S-guided" path for NusG into transcription elongation. Only ∼10% of NusG is fast diffusing, with its mobility suggesting non-specific interactions with DNA for >50% of the time. Antibiotic treatments and deletion mutants revealed that chromosome-associated NusG participates mainly in rrn anti-termination within phase-separated transcriptional condensates and in transcription-translation coupling. This study illuminates the multiple roles of NusG and offers a guide on dissecting multi-functional machines via in vivo imaging.
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Affiliation(s)
- Hafez El Sayyed
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK; Kavli Institute of Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, Oxford, UK.
| | - Oliver J Pambos
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK; Kavli Institute of Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, Oxford, UK
| | - Mathew Stracy
- Sir William Dunn School of Pathology, University of Oxford, South Parks Rd, Oxford, UK
| | - Max E Gottesman
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY, USA
| | - Achillefs N Kapanidis
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK; Kavli Institute of Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, Oxford, UK.
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3
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Ye J, Yang X, Ma C. Ligand-Based Drug Design of Novel Antimicrobials against Staphylococcus aureus by Targeting Bacterial Transcription. Int J Mol Sci 2022; 24:ijms24010339. [PMID: 36613782 PMCID: PMC9820117 DOI: 10.3390/ijms24010339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Staphylococcus aureus is a common human commensal pathogen that causes a wide range of infectious diseases. Due to the generation of antimicrobial resistance, the pathogen becomes resistant to more and more antibiotics, resulting in methicillin-resistant S. aureus (MRSA) and even multidrug-resistant S. aureus (MDRSA), namely 'superbugs'. This situation highlights the urgent need for novel antimicrobials. Bacterial transcription, which is responsible for bacterial RNA synthesis, is a valid but underutilized target for developing antimicrobials. Previously, we reported a novel class of antimicrobials, coined nusbiarylins, that inhibited bacterial transcription by interrupting the protein-protein interaction (PPI) between two transcription factors NusB and NusE. In this work, we developed a ligand-based workflow based on the chemical structures of nusbiarylins and their activity against S. aureus. The ligand-based models-including the pharmacophore model, 3D QSAR, AutoQSAR, and ADME/T calculation-were integrated and used in the following virtual screening of the ChemDiv PPI database. As a result, four compounds, including J098-0498, 1067-0401, M013-0558, and F186-026, were identified as potential antimicrobials against S. aureus, with predicted pMIC values ranging from 3.8 to 4.2. The docking study showed that these molecules bound to NusB tightly with the binding free energy ranging from -58 to -66 kcal/mol.
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Affiliation(s)
- Jiqing Ye
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, China
| | - Xiao Yang
- Department of Microbiology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Correspondence: (X.Y.); (C.M.)
| | - Cong Ma
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
- Correspondence: (X.Y.); (C.M.)
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4
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Thornburg ZR, Bianchi DM, Brier TA, Gilbert BR, Earnest TM, Melo MC, Safronova N, Sáenz JP, Cook AT, Wise KS, Hutchison CA, Smith HO, Glass JI, Luthey-Schulten Z. Fundamental behaviors emerge from simulations of a living minimal cell. Cell 2022; 185:345-360.e28. [PMID: 35063075 PMCID: PMC9985924 DOI: 10.1016/j.cell.2021.12.025] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/01/2021] [Accepted: 12/17/2021] [Indexed: 01/18/2023]
Abstract
We present a whole-cell fully dynamical kinetic model (WCM) of JCVI-syn3A, a minimal cell with a reduced genome of 493 genes that has retained few regulatory proteins or small RNAs. Cryo-electron tomograms provide the cell geometry and ribosome distributions. Time-dependent behaviors of concentrations and reaction fluxes from stochastic-deterministic simulations over a cell cycle reveal how the cell balances demands of its metabolism, genetic information processes, and growth, and offer insight into the principles of life for this minimal cell. The energy economy of each process including active transport of amino acids, nucleosides, and ions is analyzed. WCM reveals how emergent imbalances lead to slowdowns in the rates of transcription and translation. Integration of experimental data is critical in building a kinetic model from which emerges a genome-wide distribution of mRNA half-lives, multiple DNA replication events that can be compared to qPCR results, and the experimentally observed doubling behavior.
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Affiliation(s)
- Zane R. Thornburg
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - David M. Bianchi
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Troy A. Brier
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Benjamin R. Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tyler M. Earnest
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Marcelo C.R. Melo
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Nataliya Safronova
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, 01307 Dresden, Germany
| | - James P. Sáenz
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, 01307 Dresden, Germany
| | | | - Kim S. Wise
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | | | | | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; NSF Center for the Physics of Living Cells, Urbana, IL 61801, USA; NIH Center for Macromolecular Modeling and Bioinformatics, Urbana, IL 61801, USA.
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5
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Capacity of soybean carbohydrate metabolism in Leuconostoc mesenteroides, Lactococcus lactis and Streptococcus thermophilus. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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6
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A multiplex CRISPR interference tool for virulence gene interrogation in Legionella pneumophila. Commun Biol 2021; 4:157. [PMID: 33542442 PMCID: PMC7862264 DOI: 10.1038/s42003-021-01672-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/27/2020] [Indexed: 11/08/2022] Open
Abstract
Catalytically inactive dCas9 imposes transcriptional gene repression by sterically precluding RNA polymerase activity at a given gene to which it was directed by CRISPR (cr)RNAs. This gene silencing technology, known as CRISPR interference (CRISPRi), has been employed in various bacterial species to interrogate genes, mostly individually or in pairs. Here, we developed a multiplex CRISPRi platform in the pathogen Legionella pneumophila capable of silencing up to ten genes simultaneously. Constraints on precursor-crRNA expression were overcome by combining a strong promoter with a boxA element upstream of a CRISPR array. Using crRNAs directed against virulence protein-encoding genes, we demonstrated that CRISPRi is fully functional not only during growth in axenic media, but also during macrophage infection, and that gene depletion by CRISPRi recapitulated the growth defect of deletion strains. By altering the position of crRNA-encoding spacers within the CRISPR array, our platform achieved the gradual depletion of targets that was mirrored by the severity in phenotypes. Multiplex CRISPRi thus holds great promise for probing large sets of genes in bulk in order to decipher virulence strategies of L. pneumophila and other bacterial pathogens.
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7
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Stringer AM, Baniulyte G, Lasek-Nesselquist E, Seed KD, Wade JT. Transcription termination and antitermination of bacterial CRISPR arrays. eLife 2020; 9:e58182. [PMID: 33124980 PMCID: PMC7665894 DOI: 10.7554/elife.58182] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022] Open
Abstract
A hallmark of CRISPR-Cas immunity systems is the CRISPR array, a genomic locus consisting of short, repeated sequences ('repeats') interspersed with short, variable sequences ('spacers'). CRISPR arrays are transcribed and processed into individual CRISPR RNAs that each include a single spacer, and direct Cas proteins to complementary sequences in invading nucleic acid. Most bacterial CRISPR array transcripts are unusually long for untranslated RNA, suggesting the existence of mechanisms to prevent premature transcription termination by Rho, a conserved bacterial transcription termination factor that rapidly terminates untranslated RNA. We show that Rho can prematurely terminate transcription of bacterial CRISPR arrays, and we identify a widespread antitermination mechanism that antagonizes Rho to facilitate complete transcription of CRISPR arrays. Thus, our data highlight the importance of transcription termination and antitermination in the evolution of bacterial CRISPR-Cas systems.
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Affiliation(s)
- Anne M Stringer
- Wadsworth Center, New York State Department of HealthAlbanyUnited States
| | - Gabriele Baniulyte
- Department of Biomedical Sciences, School of Public Health, University at AlbanyAlbanyUnited States
| | | | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Joseph T Wade
- Wadsworth Center, New York State Department of HealthAlbanyUnited States
- Department of Biomedical Sciences, School of Public Health, University at AlbanyAlbanyUnited States
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8
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NusG controls transcription pausing and RNA polymerase translocation throughout the Bacillus subtilis genome. Proc Natl Acad Sci U S A 2020; 117:21628-21636. [PMID: 32817529 DOI: 10.1073/pnas.2006873117] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcription is punctuated by RNA polymerase (RNAP) pausing. These pauses provide time for diverse regulatory events that can modulate gene expression. Transcription elongation factors dramatically affect RNAP pausing in vitro, but the genome-wide role of such factors on pausing has not been examined. Using native elongating transcript sequencing followed by RNase digestion (RNET-seq), we analyzed RNAP pausing in Bacillus subtilis genome-wide and identified an extensive role of NusG in pausing. This universally conserved transcription elongation factor is known as Spt5 in archaeal and eukaryotic organisms. B. subtilis NusG shifts RNAP to the posttranslocation register and induces pausing at 1,600 sites containing a consensus TTNTTT motif in the nontemplate DNA strand within the paused transcription bubble. The TTNTTT motif is necessary but not sufficient for NusG-dependent pausing. Approximately one-fourth of these pause sites were localized to untranslated regions and could participate in posttranscription initiation control of gene expression as was previously shown for tlrB and the trpEDCFBA operon. Most of the remaining pause sites were identified in protein-coding sequences. NusG-dependent pausing was confirmed for all 10 pause sites that we tested in vitro. Putative pause hairpins were identified for 225 of the 342 strongest NusG-dependent pause sites, and some of these hairpins were shown to function in vitro. NusG-dependent pausing in the ribD riboswitch provides time for cotranscriptional binding of flavin mononucleotide, which decreases the concentration required for termination upstream of the ribD coding sequence. Our phylogenetic analysis implicates NusG-dependent pausing as a widespread mechanism in bacteria.
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9
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Chen M, Fredrick K. RNA Polymerase's Relationship with the Ribosome: Not So Physical, Most of the Time. J Mol Biol 2020; 432:3981-3986. [PMID: 32198117 DOI: 10.1016/j.jmb.2020.03.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/03/2020] [Accepted: 03/11/2020] [Indexed: 01/19/2023]
Abstract
In bacteria, the rates of transcription elongation and translation elongation are coordinated, changing together in response to growth conditions. It has been proposed that this is due to physical coupling of RNA polymerase and the lead ribosome on nascent mRNA, an interaction important for preventing premature transcription termination by Rho factor. Recent studies challenge this view and provide evidence that coordination is indirect, mediated in Escherichia coli by the alarmone (p)ppGpp. Here, we discuss these new findings and how they shape our understanding of the functional relationship between RNA polymerase and the ribosome as well as the basis of transcriptional polarity.
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Affiliation(s)
- Menglin Chen
- Department of Microbiology, Ohio State Biochemistry Program, and Center for RNA Biology, The Ohio State University, 484 W. 12(th) Ave, Columbus, OH, 43210, USA
| | - Kurt Fredrick
- Department of Microbiology, Ohio State Biochemistry Program, and Center for RNA Biology, The Ohio State University, 484 W. 12(th) Ave, Columbus, OH, 43210, USA.
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10
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Dudenhoeffer BR, Schneider H, Schweimer K, Knauer SH. SuhB is an integral part of the ribosomal antitermination complex and interacts with NusA. Nucleic Acids Res 2020; 47:6504-6518. [PMID: 31127279 PMCID: PMC6614797 DOI: 10.1093/nar/gkz442] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 12/20/2022] Open
Abstract
The synthesis of ribosomal RNA (rRNA) is a tightly regulated central process in all cells. In bacteria efficient expression of all seven rRNA operons relies on the suppression of termination signals (antitermination) and the proper maturation of the synthesized rRNA. These processes depend on N-utilization substance (Nus) factors A, B, E and G, as well as ribosomal protein S4 and inositol monophosphatase SuhB, but their structural basis is only poorly understood. Combining nuclear magnetic resonance spectroscopy and biochemical approaches we show that Escherichia coli SuhB can be integrated into a Nus factor-, and optionally S4-, containing antitermination complex halted at a ribosomal antitermination signal. We further demonstrate that SuhB specifically binds to the acidic repeat 2 (AR2) domain of the multi-domain protein NusA, an interaction that may be involved in antitermination or posttranscriptional processes. Moreover, we show that SuhB interacts with RNA and weakly associates with RNA polymerase (RNAP). We finally present evidence that SuhB, the C-terminal domain of the RNAP α-subunit, and the N-terminal domain of NusG share binding sites on NusA-AR2 and that all three can release autoinhibition of NusA, indicating that NusA-AR2 serves as versatile recruitment platform for various factors in transcription regulation.
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Affiliation(s)
| | - Hans Schneider
- Biopolymers, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Kristian Schweimer
- Biopolymers, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Stefan H Knauer
- Biopolymers, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
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11
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Nusbiarylins, a new class of antimicrobial agents: Rational design of bacterial transcription inhibitors targeting the interaction between the NusB and NusE proteins. Bioorg Chem 2019; 92:103203. [PMID: 31446238 DOI: 10.1016/j.bioorg.2019.103203] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/15/2019] [Accepted: 08/14/2019] [Indexed: 01/03/2023]
Abstract
Discovery of antibiotics of a novel mode of action is highly required in the fierce battlefield with multi-drug resistant bacterial infections. Previously we have validated the protein-protein interaction between bacterial NusB and NusE proteins as an unprecedented antimicrobial target and reported the identification of a first-in-class inhibitor of bacterial ribosomal RNA synthesis with antimicrobial activities. In this paper, derivatives of the hit compound were rationally designed based on the pharmacophore model for chemical synthesis, followed by biological evaluations. Some of the derivatives demonstrated the improved antimicrobial activity with the minimum inhibitory concentration (MIC) at 1-2 μg/mL against clinically significant bacterial pathogens. Time-kill kinetics, confocal microscope, ATP production, cytotoxicity, hemolytic property and cell permeability using Caco-2 cells of a representative compound were also measured. This series of compounds were named "nusbiarylins" based on their target protein NusB and the biaryl structure and were expected to be further developed towards novel antimicrobial drug candidates in the near future.
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12
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Lima J, Auffret MD, Stewart RD, Dewhurst RJ, Duthie CA, Snelling TJ, Walker AW, Freeman TC, Watson M, Roehe R. Identification of Rumen Microbial Genes Involved in Pathways Linked to Appetite, Growth, and Feed Conversion Efficiency in Cattle. Front Genet 2019; 10:701. [PMID: 31440274 PMCID: PMC6694183 DOI: 10.3389/fgene.2019.00701] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 07/03/2019] [Indexed: 12/18/2022] Open
Abstract
The rumen microbiome is essential for the biological processes involved in the conversion of feed into nutrients that can be utilized by the host animal. In the present research, the influence of the rumen microbiome on feed conversion efficiency, growth rate, and appetite of beef cattle was investigated using metagenomic data. Our aim was to explore the associations between microbial genes and functional pathways, to shed light on the influence of bacterial enzyme expression on host phenotypes. Two groups of cattle were selected on the basis of their high and low feed conversion ratio. Microbial DNA was extracted from rumen samples, and the relative abundances of microbial genes were determined via shotgun metagenomic sequencing. Using partial least squares analyses, we identified sets of 20, 14, 17, and 18 microbial genes whose relative abundances explained 63, 65, 66, and 73% of the variation of feed conversion efficiency, average daily weight gain, residual feed intake, and daily feed intake, respectively. The microbial genes associated with each of these traits were mostly different, but highly correlated traits such as feed conversion ratio and growth rate showed some overlapping genes. Consistent with this result, distinct clusters of a coabundance network were enriched with microbial genes identified to be related with feed conversion ratio and growth rate or daily feed intake and residual feed intake. Microbial genes encoding for proteins related to cell wall biosynthesis, hemicellulose, and cellulose degradation and host-microbiome crosstalk (e.g., aguA, ptb, K01188, and murD) were associated with feed conversion ratio and/or average daily gain. Genes related to vitamin B12 biosynthesis, environmental information processing, and bacterial mobility (e.g., cobD, tolC, and fliN) were associated with residual feed intake and/or daily feed intake. This research highlights the association of the microbiome with feed conversion processes, influencing growth rate and appetite, and it emphasizes the opportunity to use relative abundances of microbial genes in the prediction of these performance traits, with potential implementation in animal breeding programs and dietary interventions.
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Affiliation(s)
- Joana Lima
- Beef and Sheep Research Centre, Future Farming Systems Group, Scotland’s Rural College, Edinburgh, United Kingdom
| | - Marc D. Auffret
- Beef and Sheep Research Centre, Future Farming Systems Group, Scotland’s Rural College, Edinburgh, United Kingdom
| | - Robert D. Stewart
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
| | - Richard J. Dewhurst
- Beef and Sheep Research Centre, Future Farming Systems Group, Scotland’s Rural College, Edinburgh, United Kingdom
| | - Carol-Anne Duthie
- Beef and Sheep Research Centre, Future Farming Systems Group, Scotland’s Rural College, Edinburgh, United Kingdom
| | | | - Alan W. Walker
- The Rowett Institute, University of Aberdeen, Aberdeen, United Kingdom
| | - Tom C. Freeman
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
| | - Mick Watson
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
| | - Rainer Roehe
- Beef and Sheep Research Centre, Future Farming Systems Group, Scotland’s Rural College, Edinburgh, United Kingdom
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13
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Abstract
In every cell from bacteria to mammals, NusG-like proteins bind transcribing RNA polymerase to modulate the rate of nascent RNA synthesis and to coordinate it with numerous cotranscriptional processes that ultimately determine the transcript fate. Housekeeping NusG factors regulate expression of the bulk of the genome, whereas their highly specialized paralogs control just a few targets. In every cell from bacteria to mammals, NusG-like proteins bind transcribing RNA polymerase to modulate the rate of nascent RNA synthesis and to coordinate it with numerous cotranscriptional processes that ultimately determine the transcript fate. Housekeeping NusG factors regulate expression of the bulk of the genome, whereas their highly specialized paralogs control just a few targets. In Escherichia coli, NusG stimulates silencing of horizontally acquired genes, while its paralog RfaH counters NusG action by activating a subset of these genes. Acting alone or as part of regulatory complexes, NusG factors can promote uninterrupted RNA synthesis, bring about transcription pausing or premature termination, modulate RNA processing, and facilitate translation. Recent structural and mechanistic studies of NusG homologs from all domains of life reveal molecular details of multifaceted interactions that underpin their unexpectedly diverse regulatory roles. NusG proteins share conserved binding sites on RNA polymerase and many effects on the transcription elongation complex but differ in their mechanisms of recruitment, interactions with nucleic acids and secondary partners, and regulatory outcomes. Strikingly, some can alternate between autoinhibited and activated states that possess dramatically different secondary structures to achieve exquisite target specificity.
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14
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Mata Martin C, Sun Z, Zhou YN, Jin DJ. Extrachromosomal Nucleolus-Like Compartmentalization by a Plasmid-Borne Ribosomal RNA Operon and Its Role in Nucleoid Compaction. Front Microbiol 2018; 9:1115. [PMID: 29922250 PMCID: PMC5996182 DOI: 10.3389/fmicb.2018.01115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/11/2018] [Indexed: 02/01/2023] Open
Abstract
In the fast-growing Escherichia coli cells, RNA polymerase (RNAP) molecules are concentrated and form foci at clusters of ribosomal RNA (rRNA) operons resembling eukaryotic nucleolus. The bacterial nucleolus-like organization, spatially compartmentalized at the surface of the compact bacterial chromosome (nucleoid), serves as transcription factories for rRNA synthesis and ribosome biogenesis, which influences the organization of the nucleoid. Unlike wild type that has seven rRNA operons in the genome in a mutant that has six (Δ6rrn) rRNA operons deleted in the genome, there are no apparent transcription foci and the nucleoid becomes uncompacted, indicating that formation of RNAP foci requires multiple copies of rRNA operons clustered in space and is critical for nucleoid compaction. It has not been determined, however, whether a multicopy plasmid-borne rRNA operon (prrnB) could substitute the multiple chromosomal rRNA operons for the organization of the bacterial nucleolus-like structure in the mutants of Δ6rrn and Δ7rrn that has all seven rRNA operons deleted in the genome. We hypothesized that extrachromosomal nucleolus-like structures are similarly organized and functional in trans from prrnB in these mutants. In this report, using multicolor images of three-dimensional superresolution Structured Illumination Microscopy (3D-SIM), we determined the distributions of both RNAP and NusB that are a transcription factor involved in rRNA synthesis and ribosome biogenesis, prrnB clustering, and nucleoid structure in these two mutants in response to environmental cues. Our results found that the extrachromosomal nucleolus-like organization tends to be spatially located at the poles of the mutant cells. In addition, formation of RNAP foci at the extrachromosomal nucleolus-like structure condenses the nucleoid, supporting the idea that active transcription at the nucleolus-like organization is a driving force in nucleoid compaction.
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Affiliation(s)
| | | | | | - Ding Jun Jin
- Transcription Control Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
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15
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Segev E, Pasternak Z, Ben Sasson T, Jurkevitch E, Gonen M. Automatic identification of optimal marker genes for phenotypic and taxonomic groups of microorganisms. PLoS One 2018; 13:e0195537. [PMID: 29718935 PMCID: PMC5931505 DOI: 10.1371/journal.pone.0195537] [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: 11/01/2017] [Accepted: 03/23/2018] [Indexed: 11/18/2022] Open
Abstract
Finding optimal markers for microorganisms important in the medical, agricultural, environmental or ecological fields is of great importance. Thousands of complete microbial genomes now available allow us, for the first time, to exhaustively identify marker proteins for groups of microbial organisms. In this work, we model the biological task as the well-known mathematical “hitting set” problem, solving it based on both greedy and randomized approximation algorithms. We identify unique markers for 17 phenotypic and taxonomic microbial groups, including proteins related to the nitrite reductase enzyme as markers for the non-anammox nitrifying bacteria group, and two transcription regulation proteins, nusG and yhiF, as markers for the Archaea and Escherichia/Shigella taxonomic groups, respectively. Additionally, we identify marker proteins for three subtypes of pathogenic E. coli, which previously had no known optimal markers. Practically, depending on the completeness of the database this algorithm can be used for identification of marker genes for any microbial group, these marker genes may be prime candidates for the understanding of the genetic basis of the group's phenotype or to help discover novel functions which are uniquely shared among a group of microbes. We show that our method is both theoretically and practically efficient, while establishing an upper bound on its time complexity and approximation ratio; thus, it promises to remain efficient and permit the identification of marker proteins that are specific to phenotypic or taxonomic groups, even as more and more bacterial genomes are being sequenced.
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Affiliation(s)
- Elad Segev
- Department of Mathematics, Holon Institute of Technology, Holon, Israel
- * E-mail:
| | - Zohar Pasternak
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Tom Ben Sasson
- Department of Mathematics and Computer Science, The Open University of Israel, Raanana, Israel
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Mira Gonen
- Department of Computer Science, Ariel University, Ariel, Israel
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16
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Saxena S, Myka KK, Washburn R, Costantino N, Court DL, Gottesman ME. Escherichia coli transcription factor NusG binds to 70S ribosomes. Mol Microbiol 2018; 108:495-504. [PMID: 29575154 DOI: 10.1111/mmi.13953] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2018] [Indexed: 10/17/2022]
Abstract
Transcription and translation are coupled processes in bacteria. A role of transcription elongation cofactor NusG in coupling has been suggested by in vitro structural studies. NMR revealed association of the NusG carboxy-terminal domain with S10 (NusE), implying a direct role for NusG as a bridge linking RNAP and the lead ribosome. Here we present the first in vitro and in vivo evidence of full-length NusG association with mature 70S ribosomes. Binding did not require accessory factors in vitro. Mutating the NusG:S10 binding interface at NusG F165 or NusE M88 and D97 residues weakened NusG:S10 association in vivo and completely abolished it in vitro, supporting the specificity of this interaction. Mutations in the binding interface increased sensitivity to chloramphenicol. This phenotype was suppressed by rpoB*35, an RNAP mutation that reduces replisome-RNAP clashes. We propose that weakened NusG:S10 interaction leads to uncoupling when translation is inhibited, with resulting RNAP backtracking, replication blocks and formation of lethal DNA double-strand breaks.
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Affiliation(s)
- Shivalika Saxena
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Kamila K Myka
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Robert Washburn
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Nina Costantino
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Donald L Court
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Max E Gottesman
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
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17
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Baniulyte G, Singh N, Benoit C, Johnson R, Ferguson R, Paramo M, Stringer AM, Scott A, Lapierre P, Wade JT. Identification of regulatory targets for the bacterial Nus factor complex. Nat Commun 2017; 8:2027. [PMID: 29229908 PMCID: PMC5725501 DOI: 10.1038/s41467-017-02124-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 11/08/2017] [Indexed: 11/21/2022] Open
Abstract
Nus factors are broadly conserved across bacterial species, and are often essential for viability. A complex of five Nus factors (NusB, NusE, NusA, NusG and SuhB) is considered to be a dedicated regulator of ribosomal RNA folding, and has been shown to prevent Rho-dependent transcription termination. Here, we identify an additional cellular function for the Nus factor complex in Escherichia coli: repression of the Nus factor-encoding gene, suhB. This repression occurs primarily by translation inhibition, followed by Rho-dependent transcription termination. Thus, the Nus factor complex can prevent or promote Rho activity depending on the gene context. Conservation of putative NusB/E binding sites upstream of Nus factor genes suggests that Nus factor autoregulation occurs in many bacterial species. Additionally, many putative NusB/E binding sites are also found upstream of other genes in diverse species, and we demonstrate Nus factor regulation of one such gene in Citrobacter koseri. We conclude that Nus factors have an evolutionarily widespread regulatory function beyond ribosomal RNA, and that they are often autoregulatory.
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Affiliation(s)
- Gabriele Baniulyte
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Rensselaer, NY, 12144, USA
| | - Navjot Singh
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
| | - Courtney Benoit
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
| | - Richard Johnson
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Rensselaer, NY, 12144, USA
| | - Robert Ferguson
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
| | - Mauricio Paramo
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
| | - Anne M Stringer
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
| | - Ashley Scott
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA.
- Department of Biomedical Sciences, School of Public Health, University at Albany, Rensselaer, NY, 12144, USA.
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18
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Drögemüller J, Schneider C, Schweimer K, Strauß M, Wöhrl BM, Rösch P, Knauer SH. Thermotoga maritima NusG: domain interaction mediates autoinhibition and thermostability. Nucleic Acids Res 2016; 45:446-460. [PMID: 27899597 PMCID: PMC5224480 DOI: 10.1093/nar/gkw1111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 10/24/2016] [Accepted: 11/03/2016] [Indexed: 11/14/2022] Open
Abstract
NusG, the only universally conserved transcription factor, comprises an N- and a C-terminal domain (NTD, CTD) that are flexibly connected and move independently in Escherichia coli and other organisms. In NusG from the hyperthermophilic bacterium Thermotoga maritima (tmNusG), however, NTD and CTD interact tightly. This closed state stabilizes the CTD, but masks the binding sites for the interaction partners Rho, NusE and RNA polymerase (RNAP), suggesting that tmNusG is autoinhibited. Furthermore, tmNusG and some other bacterial NusGs have an additional domain, DII, of unknown function. Here we demonstrate that tmNusG is indeed autoinhibited and that binding to RNAP may stabilize the open conformation. We identified two interdomain salt bridges as well as Phe336 as major determinants of the domain interaction. By successive weakening of this interaction we show that after domain dissociation tmNusG-CTD can bind to Rho and NusE, similar to the Escherichia coli NusG-CTD, indicating that these interactions are conserved in bacteria. Furthermore, we show that tmNusG-DII interacts with RNAP as well as nucleic acids with a clear preference for double stranded DNA. We suggest that tmNusG-DII supports tmNusG recruitment to the transcription elongation complex and stabilizes the tmNusG:RNAP complex, a necessary adaptation to high temperatures.
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Affiliation(s)
- Johanna Drögemüller
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Christin Schneider
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Kristian Schweimer
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Martin Strauß
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Birgitta M Wöhrl
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Paul Rösch
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Stefan H Knauer
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
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19
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Abstract
UNLABELLED A complex of highly conserved proteins consisting of NusB, NusE, NusA, and NusG is required for robust expression of rRNA in Escherichia coli. This complex is proposed to prevent Rho-dependent transcription termination by a process known as "antitermination." The mechanism of this antitermination in rRNA is poorly understood but requires association of NusB and NusE with a specific RNA sequence in rRNA known as BoxA. Here, we identify a novel member of the rRNA antitermination machinery: the inositol monophosphatase SuhB. We show that SuhB associates with elongating RNA polymerase (RNAP) at rRNA in a NusB-dependent manner. Although we show that SuhB is required for BoxA-mediated antitermination in a reporter system, our data indicate that the major function of the NusB/E/A/G/SuhB complex is not to prevent Rho-dependent termination of rRNA but rather to promote correct rRNA maturation. This occurs through formation of a SuhB-mediated loop between NusB/E/BoxA and RNAP/NusA/G. Thus, we have reassigned the function of these proteins at rRNA and identified another key player in this complex. IMPORTANCE As RNA polymerase transcribes the rRNA operons in E. coli, it complexes with a set of proteins called Nus that confer enhanced rates of transcription elongation, correct folding of rRNA, and rRNA assembly with ribosomal proteins to generate a fully functional ribosome. Four Nus proteins were previously known, NusA, NusB, NusE, and NusG; here, we discover and describe a fifth, SuhB, that is an essential component of this complex. We demonstrate that the main function of this SuhB-containing complex is not to prevent premature transcription termination within the rRNA operon, as had been long claimed, but to enable rRNA maturation and a functional ribosome fully competent for translation.
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20
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Bacterial Transcription as a Target for Antibacterial Drug Development. Microbiol Mol Biol Rev 2016; 80:139-60. [PMID: 26764017 DOI: 10.1128/mmbr.00055-15] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Transcription, the first step of gene expression, is carried out by the enzyme RNA polymerase (RNAP) and is regulated through interaction with a series of protein transcription factors. RNAP and its associated transcription factors are highly conserved across the bacterial domain and represent excellent targets for broad-spectrum antibacterial agent discovery. Despite the numerous antibiotics on the market, there are only two series currently approved that target transcription. The determination of the three-dimensional structures of RNAP and transcription complexes at high resolution over the last 15 years has led to renewed interest in targeting this essential process for antibiotic development by utilizing rational structure-based approaches. In this review, we describe the inhibition of the bacterial transcription process with respect to structural studies of RNAP, highlight recent progress toward the discovery of novel transcription inhibitors, and suggest additional potential antibacterial targets for rational drug design.
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21
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Imashimizu M, Shimamoto N, Oshima T, Kashlev M. Transcription elongation. Heterogeneous tracking of RNA polymerase and its biological implications. Transcription 2015; 5:e28285. [PMID: 25764114 PMCID: PMC4214235 DOI: 10.4161/trns.28285] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Regulation of transcription elongation via pausing of RNA polymerase has multiple physiological roles. The pausing mechanism depends on the sequence heterogeneity of the DNA being transcribed, as well as on certain interactions of polymerase with specific DNA sequences. In order to describe the mechanism of regulation, we introduce the concept of heterogeneity into the previously proposed alternative models of elongation, power stroke and Brownian ratchet. We also discuss molecular origins and physiological significances of the heterogeneity.
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22
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Structural and biochemical insights into the DNA-binding mode of MjSpt4p:Spt5 complex at the exit tunnel of RNAPII. J Struct Biol 2015; 192:418-425. [PMID: 26433031 DOI: 10.1016/j.jsb.2015.09.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/27/2015] [Accepted: 09/30/2015] [Indexed: 12/20/2022]
Abstract
Spt5 (NusG in bacteria) is the only RNA polymerase-associated factor known to be conserved in all three domains of life. In archaea and eukaryotes, Spt5 associates with Spt4, an elongation factor that is absent in bacteria, to form a functional heterodimeric complex. Previous studies suggest that the Spt4:Spt5 complex interacts directly with DNA at the double-stranded DNA exit tunnel of RNA polymerase to regulate gene transcription. In this study, the DNA-binding ability of Spt4:Spt5 from the archaeon Methanocaldococcus jannaschii was confirmed via nuclear magnetic resonance chemical shift perturbation and fluorescence polarization assays. Crystallographic analysis of the full-length MjSpt4:Spt5 revealed two distinct conformations of the C-terminal KOW domain of Spt5. A similar alkaline region was found on the Spt4:Spt5 surface in both crystal forms, and identified as double-stranded DNA binding patch through mutagenesis-fluorescence polarization assays. Based on these structural and biochemical data, the Spt4:Spt5-DNA binding model was built for the first time.
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23
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Washburn RS, Gottesman ME. Regulation of transcription elongation and termination. Biomolecules 2015; 5:1063-78. [PMID: 26035374 PMCID: PMC4496710 DOI: 10.3390/biom5021063] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/20/2015] [Accepted: 05/21/2015] [Indexed: 11/16/2022] Open
Abstract
This article will review our current understanding of transcription elongation and termination in E. coli. We discuss why transcription elongation complexes pause at certain template sites and how auxiliary host and phage transcription factors affect elongation and termination. The connection between translation and transcription elongation is described. Finally we present an overview indicating where progress has been made and where it has not.
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Affiliation(s)
- Robert S Washburn
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.
| | - Max E Gottesman
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA.
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24
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Jin DJ, Cagliero C, Martin CM, Izard J, Zhou YN. The dynamic nature and territory of transcriptional machinery in the bacterial chromosome. Front Microbiol 2015; 6:497. [PMID: 26052320 PMCID: PMC4440401 DOI: 10.3389/fmicb.2015.00497] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/06/2015] [Indexed: 11/16/2022] Open
Abstract
Our knowledge of the regulation of genes involved in bacterial growth and stress responses is extensive; however, we have only recently begun to understand how environmental cues influence the dynamic, three-dimensional distribution of RNA polymerase (RNAP) in Escherichia coli on the level of single cell, using wide-field fluorescence microscopy and state-of-the-art imaging techniques. Live-cell imaging using either an agarose-embedding procedure or a microfluidic system further underscores the dynamic nature of the distribution of RNAP in response to changes in the environment and highlights the challenges in the study. A general agreement between live-cell and fixed-cell images has validated the formaldehyde-fixing procedure, which is a technical breakthrough in the study of the cell biology of RNAP. In this review we use a systems biology perspective to summarize the advances in the cell biology of RNAP in E. coli, including the discoveries of the bacterial nucleolus, the spatial compartmentalization of the transcription machinery at the periphery of the nucleoid, and the segregation of the chromosome territories for the two major cellular functions of transcription and replication in fast-growing cells. Our understanding of the coupling of transcription and bacterial chromosome (or nucleoid) structure is also summarized. Using E. coli as a simple model system, co-imaging of RNAP with DNA and other factors during growth and stress responses will continue to be a useful tool for studying bacterial growth and adaptation in changing environment.
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Affiliation(s)
- Ding J Jin
- Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health Frederick, MD, USA
| | - Cedric Cagliero
- Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health Frederick, MD, USA
| | - Carmen M Martin
- Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health Frederick, MD, USA
| | - Jerome Izard
- Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health Frederick, MD, USA
| | - Yan N Zhou
- Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, National Institutes of Health Frederick, MD, USA
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25
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Cagliero C, Zhou YN, Jin DJ. Spatial organization of transcription machinery and its segregation from the replisome in fast-growing bacterial cells. Nucleic Acids Res 2015; 42:13696-705. [PMID: 25416798 PMCID: PMC4267616 DOI: 10.1093/nar/gku1103] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In a fast-growing Escherichia coli cell, most RNA polymerase (RNAP) is allocated to rRNA synthesis forming transcription foci at clusters of rrn operons or bacterial nucleolus, and each of the several nascent nucleoids contains multiple pairs of replication forks. The composition of transcription foci has not been determined. In addition, how the transcription machinery is three-dimensionally organized to promote cell growth in concord with replication machinery in the nucleoid remains essentially unknown. Here, we determine the spatial and functional landscapes of transcription and replication machineries in fast-growing E. coli cells using super-resolution-structured illumination microscopy. Co-images of RNAP and DNA reveal spatial compartmentation and duplication of the transcription foci at the surface of the bacterial chromosome, encompassing multiple nascent nucleoids. Transcription foci cluster with NusA and NusB, which are the rrn anti-termination system and are associated with nascent rRNAs. However, transcription foci tend to separate from SeqA and SSB foci, which track DNA replication forks and/or the replisomes, demonstrating that transcription machinery and replisome are mostly located in different chromosomal territories to maintain harmony between the two major cellular functions in fast-growing cells. Our study suggests that bacterial chromosomes are spatially and functionally organized, analogous to eukaryotes.
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Affiliation(s)
| | | | - Ding Jun Jin
- To whom correspondence should be addressed. Tel: +1 301 846 7684; Fax: +1 301 846 1489;
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26
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Replication Restart after Replication-Transcription Conflicts Requires RecA in Bacillus subtilis. J Bacteriol 2015; 197:2374-82. [PMID: 25939832 DOI: 10.1128/jb.00237-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 04/27/2015] [Indexed: 01/29/2023] Open
Abstract
UNLABELLED Efficient duplication of genomes depends on reactivation of replication forks outside the origin. Replication restart can be facilitated by recombination proteins, especially if single- or double-strand breaks form in the DNA. Each type of DNA break is processed by a distinct pathway, though both depend on the RecA protein. One common obstacle that can stall forks, potentially leading to breaks in the DNA, is transcription. Though replication stalling by transcription is prevalent, the nature of DNA breaks and the prerequisites for replication restart in response to these encounters remain unknown. Here, we used an engineered site-specific replication-transcription conflict to identify and dissect the pathways required for the resolution and restart of replication forks stalled by transcription in Bacillus subtilis. We found that RecA, its loader proteins RecO and AddAB, and the Holliday junction resolvase RecU are required for efficient survival and replication restart after conflicts with transcription. Genetic analyses showed that RecO and AddAB act in parallel to facilitate RecA loading at the site of the conflict but that they can each partially compensate for the other's absence. Finally, we found that RecA and either RecO or AddAB are required for the replication restart and helicase loader protein, DnaD, to associate with the engineered conflict region. These results suggest that conflicts can lead to both single-strand gaps and double-strand breaks in the DNA and that RecA loading and Holliday junction resolution are required for replication restart at regions of replication-transcription conflicts. IMPORTANCE Head-on conflicts between replication and transcription occur when a gene is expressed from the lagging strand. These encounters stall the replisome and potentially break the DNA. We investigated the necessary mechanisms for Bacillus subtilis cells to overcome a site-specific engineered conflict with transcription of a protein-coding gene. We found that the recombination proteins RecO and AddAB both load RecA onto the DNA in response to the head-on conflict. Additionally, RecA loading by one of the two pathways was required for both replication restart and efficient survival of the collision. Our findings suggest that both single-strand gaps and double-strand DNA breaks occur at head-on conflict regions and demonstrate a requirement for recombination to restart replication after collisions with transcription.
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27
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Tomar SK, Artsimovitch I. NusG-Spt5 proteins-Universal tools for transcription modification and communication. Chem Rev 2013; 113:8604-19. [PMID: 23638618 PMCID: PMC4259564 DOI: 10.1021/cr400064k] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sushil Kumar Tomar
- Department of Microbiology and The Center for RNA Biology, The Ohio State University , Columbus, Ohio 43210, United States
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28
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Drögemüller J, Stegmann CM, Mandal A, Steiner T, Burmann BM, Gottesman ME, Wöhrl BM, Rösch P, Wahl MC, Schweimer K. An autoinhibited state in the structure of Thermotoga maritima NusG. Structure 2013; 21:365-75. [PMID: 23415559 DOI: 10.1016/j.str.2012.12.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 11/19/2012] [Accepted: 12/21/2012] [Indexed: 01/05/2023]
Abstract
NusG is a conserved regulatory protein interacting with RNA polymerase (RNAP) and other proteins to form multicomponent complexes that modulate transcription. The crystal structure of Thermotoga maritima NusG (TmNusG) shows a three-domain architecture, comprising well-conserved amino-terminal (NTD) and carboxy-terminal (CTD) domains with an additional, species-specific domain inserted into the NTD. NTD and CTD directly contact each other, occluding a surface of the NTD for binding to RNAP and a surface on the CTD interacting either with transcription termination factor Rho or transcription antitermination factor NusE. NMR spectroscopy confirmed the intramolecular NTD-CTD interaction up to the optimal growth temperature of Thermotoga maritima. The domain interaction involves a dynamic equilibrium between open and closed states and contributes significantly to the overall fold stability of the protein. Wild-type TmNusG and deletion variants could not replace endogenous Escherichia coli NusG, suggesting that the NTD-CTD interaction of TmNusG represents an autoinhibited state.
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Affiliation(s)
- Johanna Drögemüller
- Lehrstuhl Biopolymere und Forschungszentrum für Biomakromoleküle, Universität Bayreuth, Universitätsstrasse 30, Bayreuth, Germany
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29
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Bubunenko M, Court DL, Refaii AA, Saxena S, Korepanov A, Friedman DI, Gottesman ME, Alix JH. Nus transcription elongation factors and RNase III modulate small ribosome subunit biogenesis in Escherichia coli. Mol Microbiol 2013; 87:382-93. [PMID: 23190053 PMCID: PMC3545037 DOI: 10.1111/mmi.12105] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2012] [Indexed: 01/02/2023]
Abstract
Escherichia coli NusA and NusB proteins bind specific sites, such as those in the leader and spacer sequences that flank the 16S region of the ribosomal RNA transcript, forming a complex with RNA polymerase that suppresses Rho-dependent transcription termination. Although antitermination has long been the accepted role for Nus factors in rRNA synthesis, we propose that another major role for the Nus-modified transcription complex in rrn operons is as an RNA chaperone insuring co-ordination of 16S rRNA folding and RNase III processing that results in production of proper 30S ribosome subunits. This contrarian proposal is based on our studies of nusA and nusB cold-sensitive mutations that have altered translation and at low temperature accumulate 30S subunit precursors. Both phenotypes are suppressed by deletion of RNase III. We argue that these results are consistent with the idea that the nus mutations cause altered rRNA folding that leads to abnormal 30S subunits and slow translation. According to this idea, functional Nus proteins stabilize an RNA loop between their binding sites in the 5' RNA leader and on the transcribing RNA polymerase, providing a topological constraint on the RNA that aids normal rRNA folding and processing.
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Affiliation(s)
- Mikhail Bubunenko
- Frederick National Laboratory for Cancer Research, Basic Research Program, SAIC-Frederick, Inc., Frederick, Maryland 21702, USA
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Donald L. Court
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Abdalla Al Refaii
- CNRS UPR9073, associated with University of Paris Diderot, Sorbonne Paris Cite Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris
| | - Shivalika Saxena
- Columbia University Medical Center, Departments of Microbiology and Biochemistry and Molecular Biophysics, New York, New York 10032, USA
| | - Alexey Korepanov
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - David I. Friedman
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Max E. Gottesman
- Columbia University Medical Center, Departments of Microbiology and Biochemistry and Molecular Biophysics, New York, New York 10032, USA
| | - Jean-Hervé Alix
- CNRS UPR9073, associated with University of Paris Diderot, Sorbonne Paris Cite Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris
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Werner F. A nexus for gene expression-molecular mechanisms of Spt5 and NusG in the three domains of life. J Mol Biol 2012; 417:13-27. [PMID: 22306403 PMCID: PMC3382729 DOI: 10.1016/j.jmb.2012.01.031] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 01/10/2012] [Accepted: 01/13/2012] [Indexed: 11/25/2022]
Abstract
Evolutionary related multisubunit RNA polymerases (RNAPs) transcribe the genomes of all living organisms. Whereas the core subunits of RNAPs are universally conserved in all three domains of life—indicative of a common evolutionary descent—this only applies to one RNAP-associated transcription factor—Spt5, also known as NusG in bacteria. All other factors that aid RNAP during the transcription cycle are specific for the individual domain or only conserved between archaea and eukaryotes. Spt5 and its bacterial homologue NusG regulate gene expression in several ways by (i) modulating transcription processivity and promoter proximal pausing, (ii) coupling transcription and RNA processing or translation, and (iii) recruiting termination factors and thereby silencing laterally transferred DNA and protecting the genome against double-stranded DNA breaks. This review discusses recent discoveries that identify Spt5-like factors as evolutionary conserved nexus for the regulation and coordination of the machineries responsible for information processing in the cell.
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Affiliation(s)
- Finn Werner
- RNAP Laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK.
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31
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Viktorovskaya OV, Appling FD, Schneider DA. Yeast transcription elongation factor Spt5 associates with RNA polymerase I and RNA polymerase II directly. J Biol Chem 2011; 286:18825-33. [PMID: 21467036 PMCID: PMC3099699 DOI: 10.1074/jbc.m110.202119] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 03/23/2011] [Indexed: 11/06/2022] Open
Abstract
Spt5 is a transcription factor conserved in all three domains of life. Spt5 homologues from bacteria and archaea bind the largest subunit of their respective RNA polymerases. Here we demonstrate that Spt5 directly associates with RNA polymerase (Pol) I and RNA Pol II in yeast through its central region containing conserved NusG N-terminal homology and KOW domains. Deletion analysis of SPT5 supports our biochemical data, demonstrating the importance of the KOW domains in Spt5 function. Far Western blot analysis implicates A190 of Pol I as well as Rpb1 of Pol II in binding Spt5. Three additional subunits of Pol I may also participate in this interaction. One of these subunits, A49, has known roles in transcription elongation by Pol I. Interestingly, spt5 truncation mutations suppress the cold-sensitive phenotype of rpa49Δ strain, which lacks the A49 subunit in the Pol I complex. Finally, we observed that Spt5 directly binds to an essential Pol I transcription initiation factor, Rrn3, and to the ribosomal RNA. Based on these data, we propose a model in which Spt5 is recruited to the rDNA early in transcription and propose that it plays an important role in ribosomal RNA synthesis through direct binding to the Pol I complex.
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MESH Headings
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- Models, Biological
- Pol1 Transcription Initiation Complex Proteins/genetics
- Pol1 Transcription Initiation Complex Proteins/metabolism
- Protein Binding
- Protein Structure, Tertiary
- RNA Polymerase I/genetics
- RNA Polymerase I/metabolism
- RNA Polymerase II/genetics
- RNA Polymerase II/metabolism
- RNA, Fungal/biosynthesis
- RNA, Fungal/genetics
- RNA, Ribosomal/biosynthesis
- RNA, Ribosomal/genetics
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Transcription, Genetic/physiology
- Transcriptional Elongation Factors/genetics
- Transcriptional Elongation Factors/metabolism
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Affiliation(s)
- Olga V. Viktorovskaya
- From the Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294-0024
| | - Francis D. Appling
- From the Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294-0024
| | - David A. Schneider
- From the Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294-0024
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32
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Domain interactions of the transcription–translation coupling factor Escherichia coli NusG are intermolecular and transient. Biochem J 2011; 435:783-9. [DOI: 10.1042/bj20101679] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The bacterial transcription factor NusG (N-utilization substance G) is suggested to act as a key coupling factor between transcription and translation [Burmann, Schweimer, Luo, Wahl, Stitt, Gottesman and Rösch (2010) Science 328, 501–504] and contributes to phage λ-mediated antitermination in Escherichia coli that enables read-through of early transcription termination sites. E. coli NusG consists of two structurally and functionally distinct domains that are connected through a flexible linker. The homologous Aquifex aeolicus NusG, with a secondary structure that is highly similar to E. coli NusG shows direct interaction between its N- and C-terminal domains in a domain-swapped dimer. In the present study, we performed NMR paramagnetic relaxation enhancement measurements and identified interdomain interactions that were concentration dependent and thus probably not only weak and transient, but also predominantly intermolecular. This notion of two virtually independent domains in a monomeric protein was supported by 15N-relaxation measurements. Thus we suggest that a regulatory role of NusG interdomain interactions is highly unlikely.
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33
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Cruz-García C, Murray AE, Rodrigues JLM, Gralnick JA, McCue LA, Romine MF, Löffler FE, Tiedje JM. Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1. BMC Microbiol 2011; 11:64. [PMID: 21450087 PMCID: PMC3078092 DOI: 10.1186/1471-2180-11-64] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Accepted: 03/30/2011] [Indexed: 11/17/2022] Open
Abstract
Background EtrA in Shewanella oneidensis MR-1, a model organism for study of adaptation to varied redox niches, shares 73.6% and 50.8% amino acid sequence identity with the oxygen-sensing regulators Fnr in E. coli and Anr in Pseudomonas aeruginosa, respectively; however, its regulatory role of anaerobic metabolism in Shewanella spp. is complex and not well understood. Results The expression of the nap genes, nrfA, cymA and hcp was significantly reduced in etrA deletion mutant EtrA7-1; however, limited anaerobic growth and nitrate reduction occurred, suggesting that multiple regulators control nitrate reduction in this strain. Dimethyl sulfoxide (DMSO) and fumarate reductase gene expression was down-regulated at least 2-fold in the mutant, which, showed lower or no reduction of these electron acceptors when compared to the wild type, suggesting both respiratory pathways are under EtrA control. Transcript analysis further suggested a role of EtrA in prophage activation and down-regulation of genes implicated in aerobic metabolism. Conclusion In contrast to previous studies that attributed a minor regulatory role to EtrA in Shewanella spp., this study demonstrates that EtrA acts as a global transcriptional regulator and, in conjunction with other regulators, fine-tunes the expression of genes involved in anaerobic metabolism in S. oneidensis strain MR-1. Transcriptomic and sequence analyses of the genes differentially expressed showed that those mostly affected by the mutation belonged to the "Energy metabolism" category, while stress-related genes were indirectly regulated in the mutant possibly as a result of a secondary perturbation (e.g. oxidative stress, starvation). We also conclude based on sequence, physiological and expression analyses that this regulator is more appropriately termed Fnr and recommend this descriptor be used in future publications.
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Affiliation(s)
- Claribel Cruz-García
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824-1325, USA.
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Grohmann D, Werner F. Hold on!: RNA polymerase interactions with the nascent RNA modulate transcription elongation and termination. RNA Biol 2010; 7:310-5. [PMID: 20473037 DOI: 10.4161/rna.7.3.11912] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Evolutionary related multisubunit RNA polymerases from all three domains of life, Eukarya, Archaea and Bacteria, have common structural and functional properties. We have recently shown that two RNAP subunits, F/E (RPB4/7)-which are conserved between eukaryotes and Archaea but have no bacterial homologues-interact with the nascent RNA chain and thereby profoundly modulate RNAP activity. Overall F/E increases transcription processivity, but it also stimulates transcription termination in a sequence-dependent manner. In addition to RNA-binding, these two apparently opposed processes are likely to involve an allosteric mechanism of the RNAP clamp. Spt4/5 is the only known RNAP-associated transcription factor that is conserved in all three domains of life, and it stimulates elongation similar to RNAP subunits F/E. Spt4/5 enhances processivity in a fashion that is independent of the nontemplate DNA strand, by interacting with the RNAP clamp. Whereas the molecular mechanism of Spt4/5 is universally conserved in evolution, the added functionality of F/E-like complexes has emerged after the split of the bacterial and archaeoeukaryotic lineages. Interestingly, bacteriophage-encoded antiterminator proteins could, in theory, fulfil an analogous function in the bacterial RNAP.
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Affiliation(s)
- Dina Grohmann
- UCL Institute for Structural and Molecular Biology, Division of Biosciences, London, UK
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Herbert KM, Zhou J, Mooney RA, Porta AL, Landick R, Block SM. E. coli NusG inhibits backtracking and accelerates pause-free transcription by promoting forward translocation of RNA polymerase. J Mol Biol 2010; 399:17-30. [PMID: 20381500 DOI: 10.1016/j.jmb.2010.03.051] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 03/25/2010] [Accepted: 03/26/2010] [Indexed: 10/19/2022]
Abstract
NusG is an essential transcription factor in Escherichia coli that is capable of increasing the overall rate of transcription. Transcript elongation by RNA polymerase (RNAP) is frequently interrupted by pauses of varying durations, and NusG is known to decrease the occupancy of at least some paused states. However, it has not been established whether NusG enhances transcription chiefly by (1) increasing the rate of elongation between pauses, (2) reducing the lifetimes of pauses, or (3) reducing the rate of entry into paused states. Here, we studied transcription by single molecules of RNAP under various conditions of ribonucleoside triphosphate concentration, applied load, and temperature, using an optical trapping assay capable of distinguishing pauses as brief as 1 s. We found that NusG increases the rate of elongation, that is, the pause-free velocity along the template. Because pauses are off-pathway states that compete with elongation, we observed a concomitant decrease in the rate of entry into short-lifetime, paused states. The effects on short pauses and elongation were comparatively modest, however. More dramatic was the effect of NusG on suppressing entry into long-lifetime ("stabilized") pauses. Because a significant fraction of the time required for the transcription of a typical gene may be occupied by long pauses, NusG is capable of exerting a significant modulatory effect on the rates of RNA synthesis. The observed properties of NusG were consistent with a unified model where the function of this accessory factor is to promote transcriptionally downstream motion of the enzyme along the DNA template, which has the effect of forward-biasing RNAP from the pre-translocated state toward the post-translocated state.
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36
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Hirtreiter A, Damsma GE, Cheung ACM, Klose D, Grohmann D, Vojnic E, Martin ACR, Cramer P, Werner F. Spt4/5 stimulates transcription elongation through the RNA polymerase clamp coiled-coil motif. Nucleic Acids Res 2010; 38:4040-51. [PMID: 20197319 PMCID: PMC2896526 DOI: 10.1093/nar/gkq135] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Spt5 is the only known RNA polymerase-associated factor that is conserved in all three domains of life. We have solved the structure of the Methanococcus jannaschii Spt4/5 complex by X-ray crystallography, and characterized its function and interaction with the archaeal RNAP in a wholly recombinant in vitro transcription system. Archaeal Spt4 and Spt5 form a stable complex that associates with RNAP independently of the DNA–RNA scaffold of the elongation complex. The association of Spt4/5 with RNAP results in a stimulation of transcription processivity, both in the absence and the presence of the non-template strand. A domain deletion analysis reveals the molecular anatomy of Spt4/5—the Spt5 Nus-G N-terminal (NGN) domain is the effector domain of the complex that both mediates the interaction with RNAP and is essential for its elongation activity. Using a mutagenesis approach, we have identified a hydrophobic pocket on the Spt5 NGN domain as binding site for RNAP, and reciprocally the RNAP clamp coiled-coil motif as binding site for Spt4/5.
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Affiliation(s)
- Angela Hirtreiter
- Division of Biosciences, University College London, Institute for Structural and Molecular Biology, Darwin Building, Gower Street, London WC1E 6BT, UK
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SigN is responsible for differentiation and stress responses based on comparative proteomic analyses of Streptomyces coelicolor wild-type and sigN deletion strains. Microbiol Res 2010; 165:221-31. [DOI: 10.1016/j.micres.2009.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 05/12/2009] [Accepted: 05/16/2009] [Indexed: 11/17/2022]
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38
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Belogurov GA, Sevostyanova A, Svetlov V, Artsimovitch I. Functional regions of the N-terminal domain of the antiterminator RfaH. Mol Microbiol 2010; 76:286-301. [PMID: 20132437 PMCID: PMC2871177 DOI: 10.1111/j.1365-2958.2010.07056.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RfaH is a bacterial elongation factor that increases expression of distal genes in several long, horizontally acquired operons. RfaH is recruited to the transcription complex during RNA chain elongation through specific interactions with a DNA element called ops. Following recruitment, RfaH remains bound to RNA polymerase (RNAP) and acts as an antiterminator by reducing RNAP pausing and termination at some factor-independent and Rho-dependent signals. RfaH consists of two domains connected by a flexible linker. The N-terminal RfaH domain (RfaHN) recognizes the ops element, binds to the RNAP and reduces pausing and termination in vitro. Functional analysis of single substitutions in this domain reported here suggests that three separate RfaHN regions mediate these functions. We propose that a polar patch on one side of RfaHN interacts with the non-template DNA strand during recruitment, whereas a hydrophobic surface on the opposite side of RfaHN remains bound to the β′ subunit clamp helices domain throughout transcription of the entire operon. The third region is apparently dispensable for RfaH binding to the transcription complex but is required for the antitermination modification of RNAP.
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Affiliation(s)
- Georgiy A Belogurov
- Department of Microbiology and The RNA Group, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
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39
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Lambert C, Chang CY, Capeness MJ, Sockett RE. The first bite--profiling the predatosome in the bacterial pathogen Bdellovibrio. PLoS One 2010; 5:e8599. [PMID: 20062540 PMCID: PMC2797640 DOI: 10.1371/journal.pone.0008599] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 11/09/2009] [Indexed: 11/18/2022] Open
Abstract
Bdellovibrio bacteriovorus is a Gram-negative bacterium that is a pathogen of other Gram-negative bacteria, including many bacteria which are pathogens of humans, animals and plants. As such Bdellovibrio has potential as a biocontrol agent, or living antibiotic. B. bacteriovorus HD100 has a large genome and it is not yet known which of it encodes the molecular machinery and genetic control of predatory processes. We have tried to fill this knowledge-gap using mixtures of predator and prey mRNAs to monitor changes in Bdellovibrio gene expression at a timepoint of early-stage prey infection and prey killing in comparison to control cultures of predator and prey alone and also in comparison to Bdellovibrio growing axenically (in a prey-or host independent “HI” manner) on artificial media containing peptone and tryptone. From this we have highlighted genes of the early predatosome with predicted roles in prey killing and digestion and have gained insights into possible regulatory mechanisms as Bdellovibrio enter and establish within the prey bdelloplast. Approximately seven percent of all Bdellovibrio genes were significantly up-regulated at 30 minutes of infection- but not in HI growth- implicating the role of these genes in prey digestion. Five percent were down-regulated significantly, implicating their role in free-swimming, attack-phase physiology. This study gives the first post- genomic insight into the predatory process and reveals some of the important genes that Bdellovibrio expresses inside the prey bacterium during the initial attack.
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Affiliation(s)
- Carey Lambert
- Institute of Genetics, School of Biology, Nottingham University, Queen's Medical Centre, Nottingham, United Kingdom
| | - Chien-Yi Chang
- Institute of Genetics, School of Biology, Nottingham University, Queen's Medical Centre, Nottingham, United Kingdom
| | - Michael J. Capeness
- Institute of Genetics, School of Biology, Nottingham University, Queen's Medical Centre, Nottingham, United Kingdom
| | - R. Elizabeth Sockett
- Institute of Genetics, School of Biology, Nottingham University, Queen's Medical Centre, Nottingham, United Kingdom
- * E-mail:
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40
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Crystal structure of the human transcription elongation factor DSIF hSpt4 subunit in complex with the hSpt5 dimerization interface. Biochem J 2009; 425:373-80. [DOI: 10.1042/bj20091422] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The eukaryotic transcription elongation factor DSIF [DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) sensitivity-inducing factor] is composed of two subunits, hSpt4 and hSpt5, which are homologous to the yeast factors Spt4 and Spt5. DSIF is involved in regulating the processivity of RNA polymerase II and plays an essential role in transcriptional activation of eukaryotes. At several eukaryotic promoters, DSIF, together with NELF (negative elongation factor), leads to promoter-proximal pausing of RNA polymerase II. In the present paper we describe the crystal structure of hSpt4 in complex with the dimerization region of hSpt5 (amino acids 176–273) at a resolution of 1.55 Å (1 Å=0.1 nm). The heterodimer shows high structural similarity to its homologue from Saccharomyces cerevisiae. Furthermore, hSpt5-NGN is structurally similar to the NTD (N-terminal domain) of the bacterial transcription factor NusG. A homologue for hSpt4 has not yet been found in bacteria. However, the archaeal transcription factor RpoE” appears to be distantly related. Although a comparison of the NusG-NTD of Escherichia coli with hSpt5 revealed a similarity of the three-dimensional structures, interaction of E. coli NusG-NTD with hSpt4 could not be observed by NMR titration experiments. A conserved glutamate residue, which was shown to be crucial for dimerization in yeast, is also involved in the human heterodimer, but is substituted for a glutamine residue in Escherichia coli NusG. However, exchanging the glutamine for glutamate proved not to be sufficient to induce hSpt4 binding.
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41
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Burmann BM, Luo X, Rösch P, Wahl MC, Gottesman ME. Fine tuning of the E. coli NusB:NusE complex affinity to BoxA RNA is required for processive antitermination. Nucleic Acids Res 2009; 38:314-26. [PMID: 19854945 PMCID: PMC2800207 DOI: 10.1093/nar/gkp736] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phage lambda propagation in Escherichia coli host cells requires transcription antitermination on the lambda chromosome mediated by lambdaN protein and four host Nus factors, NusA, B, E (ribosomal S10) and G. Interaction of E. coli NusB:NusE heterodimer with the single stranded BoxA motif of lambdanutL or lambdanutR RNA is crucial for this reaction. Similarly, binding of NusB:NusE to a BoxA motif is essential to suppress transcription termination in the ribosomal RNA (rrn) operons. We used fluorescence anisotropy to measure the binding properties of NusB and of NusB:NusE heterodimer to BoxA-containing RNAs differing in length and sequence. Our results demonstrate that BoxA is necessary and sufficient for binding. We also studied the gain-of-function D118N NusB mutant that allows lambda growth in nusA1 or nusE71 mutants. In vivo lambda burst-size determinations, CD thermal unfolding measurements and X-ray crystallography of this as well as various other NusB D118 mutants showed the importance of size and polarity of amino acid 118 for RNA binding and other interactions. Our work suggests that the affinity of the NusB:NusE complex to BoxA RNA is precisely tuned to maximize control of transcription termination.
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Affiliation(s)
- Björn M Burmann
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Bayreuth, Germany
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42
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Mooney RA, Schweimer K, Rösch P, Gottesman M, Landick R. Two structurally independent domains of E. coli NusG create regulatory plasticity via distinct interactions with RNA polymerase and regulators. J Mol Biol 2009; 391:341-58. [PMID: 19500594 DOI: 10.1016/j.jmb.2009.05.078] [Citation(s) in RCA: 154] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 05/27/2009] [Accepted: 05/29/2009] [Indexed: 11/25/2022]
Abstract
NusG is a conserved regulatory protein that interacts with elongation complexes (ECs) of RNA polymerase, DNA, and RNA to modulate transcription in multiple and sometimes opposite ways. In Escherichia coli, NusG suppresses pausing and increases elongation rate, enhances termination by E. coli rho and phage HK022 Nun protein, and promotes antitermination by lambdaN and in ribosomal RNA operons. We report NMR studies that suggest that E. coli NusG consists of two largely independent N- and C-terminal structural domains, NTD and CTD, respectively. Based on tests of the functions of the NTD and CTD and variants of NusG in vivo and in vitro, we find that NTD alone is sufficient to suppress pausing and enhance transcript elongation in vitro. However, neither domain alone can enhance rho-dependent termination or support antitermination, indicating that interactions of both domains with ECs are required for these processes. We propose that the two domains of NusG mediate distinct interactions with ECs: the NTD interacts with RNA polymerase and the CTD interacts with rho and other regulators, providing NusG with different combinations of interactions to effect different regulatory outcomes.
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Affiliation(s)
- Rachel Anne Mooney
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
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43
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Connolly K, Culver G. Deconstructing ribosome construction. Trends Biochem Sci 2009; 34:256-63. [PMID: 19376708 DOI: 10.1016/j.tibs.2009.01.011] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Revised: 01/13/2009] [Accepted: 01/14/2009] [Indexed: 12/30/2022]
Abstract
The ribosome is an essential ribonucleoprotein enzyme, and its biogenesis is a fundamental process in all living cells. Recent X-ray crystal structures of the bacterial ribosome and new technologies have allowed a greater interrogation of in vitro ribosome assembly; however, substantially less is known about ribosome biogenesis in vivo. Ongoing investigations are focused on elucidating the cellular processes that facilitate biogenesis of the ribosomal subunits, and many extraribosomal factors, including modification enzymes, remodeling enzymes and GTPases, are being uncovered. Moreover, specific roles for ribosome biogenesis factors in subunit maturation are now being elaborated. Ultimately, such studies will reveal a more complete understanding of processes at work in in vivo ribosome biogenesis.
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Affiliation(s)
- Keith Connolly
- Departments of Biology and of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14627, USA
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44
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Abstract
Gene expression is a fundamental process that is highly conserved from humans to bacteria. The first step in gene expression, transcription, is performed by structurally conserved DNA-dependent RNA polymerases (RNAPs), which results in the synthesis of an RNA molecule from a DNA template. In bacteria, a single species of RNAP is responsible for transcribing both stable RNA (i.e. t- and rRNA) and protein-encoding genes (i.e. mRNA), unlike eukaryotic systems, which use three distinct RNAP species to transcribe the different gene classes (RNAP I transcribes most rRNA, RNAP II transcribes mRNA, and RNAP III transcribes tRNA and 5S rRNA). The versatility of bacterial RNAP is dependent on both dynamic interactions with co-factors and the coding sequence of the template DNA, which allows RNAP to respond appropriately to the transcriptional needs of the cell. Although the majority of the research on gene expression has focused on the initiation stage, regulation of the elongation phase is essential for cell viability and represents an important topic for study. The elongation factors that associate with RNAP are unique and highly conserved among prokaryotes, making disruption of their interactions a potentially important target for antibiotic development. One of the most significant advances in molecular biology over the last decade has been the use of green fluorescent protein (GFP) and its spectral variants to observe the subcellular localization of proteins in live intact cells. This review discusses transcription dynamics with respect to RNAP and its associated transcription elongation factors in the two best-studied prokaryotes, Escherichia coli and Bacillus subtilis.
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Affiliation(s)
- P J Lewis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - G P Doherty
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - J Clarke
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
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Abstract
Transcription antitermination in the ribosomal operons of Escherichia coli results in the modification of RNA polymerase by specific proteins, altering its basic properties. For such alterations to occur, signal sequences in rrn operons are required as well as individual interacting proteins. In this study we tested putative rrn transcription antitermination-inducing sequences from five different bacteria for their abilities to function in E. coli. We further examined their response to the lack of one known rrn transcription antitermination protein from E. coli, NusB. We monitored antitermination activity by assessing the ability of RNA polymerase to read through a factor-dependent terminator. We found that, in general, the closer the regulatory sequence matched that of E. coli, the more likely there was to be a successful antitermination-proficient modification of the transcription complex. The rrn leader sequences from Pseudomonas aeruginosa, Bacillus subtilis, and Caulobacter crescentus all provided various levels of, but functionally significant antitermination properties to, RNA polymerase, while those of Mycobacterium tuberculosis and Thermotoga maritima did not. Possible RNA folding structures of presumed antitermination sequences and specific critical bases are discussed in light of our results. An unexpected finding was that when using the Caulobacter crescentus rrn leader sequence, there was little effect on terminator readthrough in the absence of NusB. All other hybrid antitermination system activities required this factor. Possible reasons for this finding are discussed.
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46
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Liu J, Pei H, Mei S, Li J, Zhou L, Xiang H. Replication initiator DnaA interacts with an anti-terminator NusG in T. tengcongensis. Biochem Biophys Res Commun 2008; 371:573-7. [PMID: 18457667 DOI: 10.1016/j.bbrc.2008.04.131] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 04/25/2008] [Indexed: 01/15/2023]
Abstract
DnaA plays a central role in initiation of DNA replication at oriC in bacteria, and is also a transcription regulator which interacts with the DnaA box relative to a specific gene. Through screening the interaction between TtDnaA and the transcription machinery in Thermoanaerobacter tengcongensis by yeast two-hybrid assays, we found for the first time that the TtDnaA could interact with an anti-terminator, TtNusG2, in this thermophilic bacterium. The direct interaction between TtDnaA and TtNusG2 was verified by surface plasmon resonance (SPR) assay in vitro, and was further confirmed by co-immunoprecipitation assay in vivo. Moreover, we demonstrated that domain I and domain III of TtDnaA were responsible for the interaction with TtNusG2. These findings might expand our understanding of cooperation of two fundamental processes, replication and transcription, in this bacterium.
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Affiliation(s)
- Jingfang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing 100101, PR China
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Bubunenko M, Baker T, Court DL. Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli. J Bacteriol 2007; 189:2844-53. [PMID: 17277072 PMCID: PMC1855809 DOI: 10.1128/jb.01713-06] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Accepted: 01/18/2007] [Indexed: 11/20/2022] Open
Abstract
We describe here details of the method we used to identify and distinguish essential from nonessential genes on the bacterial Escherichia coli chromosome. Three key features characterize our method: high-efficiency recombination, precise replacement of just the open reading frame of a chromosomal gene, and the presence of naturally occurring duplications within the bacterial genome. We targeted genes encoding functions critical for processes of transcription and translation. Proteins from three complexes were evaluated to determine if they were essential to the cell by deleting their individual genes. The transcription elongation Nus proteins and termination factor Rho, which are involved in rRNA antitermination, the ribosomal proteins of the small 30S ribosome subunit, and minor ribosome-associated proteins were analyzed. It was concluded that four of the five bacterial transcription antitermination proteins are essential, while all four of the minor ribosome-associated proteins examined (RMF, SRA, YfiA, and YhbH), unlike most ribosomal proteins, are dispensable. Interestingly, although most 30S ribosomal proteins were essential, the knockouts of six ribosomal protein genes, rpsF (S6), rpsI (S9), rpsM (S13), rpsO (S15), rpsQ (S17), and rpsT (S20), were viable.
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Affiliation(s)
- Mikhail Bubunenko
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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48
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Marchi P, Longhi V, Zangrossi S, Gaetani E, Briani F, Dehò G. Autogenous regulation of Escherichia coli polynucleotide phosphorylase during cold acclimation by transcription termination and antitermination. Mol Genet Genomics 2007; 278:75-84. [PMID: 17384964 DOI: 10.1007/s00438-007-0231-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Accepted: 03/06/2007] [Indexed: 10/23/2022]
Abstract
Adaptation of Escherichia coli at low temperature implicates a drastic reprogramming of gene expression patterns. Mechanisms operating downstream of transcription initiation, such as control of transcription termination, mRNA stability and translatability, play a major role in controlling gene expression in the cold acclimation phase. It was previously shown that Rho-dependent transcription termination within pnp, the gene encoding polynucleotide phosphorylase (PNPase), was suppressed in pnp nonsense mutants, whereas it was restored by complementation with wild type allele. Using a tRNA gene as a reporter and the strong Rho-dependent transcription terminator t ( imm ) of bacteriophage P4 as a tester, here we show that specific sites in the 5'-untranslated region of pnp mRNA are required for PNPase-sensitive cold-induced suppression of Rho-dependent transcription termination. We suggest that suppression of Rho-dependent transcription termination within pnp and its restoration by PNPase is an autogenous regulatory circuit that modulates pnp expression during cold acclimation.
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Affiliation(s)
- Paolo Marchi
- Dipartimento di Scienze biomolecolari e Biotecnologie, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
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49
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Vassylyeva MN, Svetlov V, Klyuyev S, Devedjiev YD, Artsimovitch I, Vassylyev DG. Crystallization and preliminary crystallographic analysis of the transcriptional regulator RfaH from Escherichia coli and its complex with ops DNA. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1027-30. [PMID: 17012804 PMCID: PMC2225194 DOI: 10.1107/s174430910603658x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Accepted: 09/09/2006] [Indexed: 11/10/2022]
Abstract
The bacterial transcriptional factor and virulence regulator RfaH binds to rapidly moving transcription elongation complexes through specific interactions with the exposed segment of the non-template DNA strand. To elucidate this unusual mechanism of recruitment, determination of the three-dimensional structure of RfaH and its complex with DNA was initiated. To this end, the Escherichia coli rfaH gene was cloned and expressed. The purified protein was crystallized by the sitting-drop vapor-diffusion technique. The space group was P6(1)22 or P6(5)22, with unit-cell parameters a = b = 45.46, c = 599.93 A. A complex of RfaH and a nine-nucleotide oligodeoxyribonucleotide was crystallized by the same technique, but under different crystallization conditions, yielding crystals that belonged to space group P1 (unit-cell parameters a = 36.79, b = 44.01, c = 62.37 A, alpha = 80.62, beta = 75.37, gamma = 75.41 degrees ). Complete diffraction data sets were collected for RfaH and its complex with DNA at 2.4 and 1.6 A resolution, respectively. Crystals of selenomethionine-labeled proteins in both crystal forms were obtained by cross-microseeding using the native microcrystals. The structure determination of RfaH and its complex with DNA is in progress.
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Affiliation(s)
- Marina N. Vassylyeva
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA
| | - Vladimir Svetlov
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Sergiy Klyuyev
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA
| | - Yancho D. Devedjiev
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
- Correspondence e-mail: ,
| | - Dmitry G. Vassylyev
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA
- Correspondence e-mail: ,
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50
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Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA. Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress. Genes Dev 2006; 20:1776-89. [PMID: 16818608 PMCID: PMC1522074 DOI: 10.1101/gad.1428206] [Citation(s) in RCA: 238] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The heat-shock response (HSR), a universal cellular response to heat, is crucial for cellular adaptation. In Escherichia coli, the HSR is mediated by the alternative sigma factor, sigma32. To determine its role, we used genome-wide expression analysis and promoter validation to identify genes directly regulated by sigma32 and screened ORF overexpression libraries to identify sigma32 inducers. We triple the number of genes validated to be transcribed by sigma32 and provide new insights into the cellular role of this response. Our work indicates that the response is propagated as the regulon encodes numerous global transcriptional regulators, reveals that sigma70 holoenzyme initiates from 12% of sigma32 promoters, which has important implications for global transcriptional wiring, and identifies a new role for the response in protein homeostasis, that of protecting complex proteins. Finally, this study suggests that the response protects the cell membrane and responds to its status: Fully 25% of sigma32 regulon members reside in the membrane and alter its functionality; moreover, a disproportionate fraction of overexpressed proteins that induce the response are membrane localized. The intimate connection of the response to the membrane rationalizes why a major regulator of the response resides in that cellular compartment.
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Affiliation(s)
- Gen Nonaka
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California 94143, USA
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