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Nayarisseri A, Bhrdwaj A, Khan A, Sharma K, Shaheen U, Selvaraj C, Khan MA, Abhirami R, Pravin MA, Shri GR, Raje D, Singh SK. Promoter–motif extraction from co-regulated genes and their relevance to co-expression using E. coli as a model. Brief Funct Genomics 2023; 22:204-216. [PMID: 37053503 DOI: 10.1093/bfgp/elac043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/29/2022] [Accepted: 10/26/2022] [Indexed: 02/04/2023] Open
Abstract
Abstract
Gene expression varies due to the intrinsic stochasticity of transcription or as a reaction to external perturbations that generate cellular mutations. Co-regulation, co-expression and functional similarity of substances have been employed for indoctrinating the process of the transcriptional paradigm. The difficult process of analysing complicated proteomes and biological switches has been made easier by technical improvements, and microarray technology has flourished as a viable platform. Therefore, this research enables Microarray to cluster genes that are co-expressed and co-regulated into specific segments. Copious search algorithms have been employed to ascertain diacritic motifs or a combination of motifs that are performing regular expression, and their relevant information corresponding to the gene patterns is also documented. The associated genes co-expression and relevant cis-elements are further explored by engaging Escherichia coli as a model organism. Various clustering algorithms have also been used to generate classes of genes with similar expression profiles. A promoter database ‘EcoPromDB’ has been developed by referring RegulonDB database; this promoter database is freely available at www.ecopromdb.eminentbio.com and is divided into two sub-groups, depending upon the results of co-expression and co-regulation analyses.
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Affiliation(s)
- Anuraj Nayarisseri
- Eminent Biosciences In silico Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
- LeGene Biosciences Pvt Ltd Bioinformatics Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Anushka Bhrdwaj
- Eminent Biosciences In silico Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Arshiya Khan
- Eminent Biosciences In silico Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Khushboo Sharma
- Eminent Biosciences In silico Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Uzma Shaheen
- Eminent Biosciences In silico Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
| | - Chandrabose Selvaraj
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Mohammad Aqueel Khan
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Rajaram Abhirami
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Muthuraja Arun Pravin
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Gurunathan Rubha Shri
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Dhanjay Raje
- Eminent Biosciences In silico Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
| | - Sanjeev Kumar Singh
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
- Department of Data Sciences, Centre of Biomedical Research , SGPGIMS Campus, Raebareli Rd, Lucknow 226014, India
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Basov A, Drobotenko M, Svidlov A, Gerasimenko E, Malyshko V, Elkina A, Baryshev M, Dzhimak S. Inequality in the Frequency of the Open States Occurrence Depends on Single 2H/ 1H Replacement in DNA. Molecules 2020; 25:E3753. [PMID: 32824686 PMCID: PMC7463606 DOI: 10.3390/molecules25163753] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/04/2020] [Accepted: 08/15/2020] [Indexed: 12/15/2022] Open
Abstract
In the present study, the effect of 2H/1H isotopic exchange in hydrogen bonds between nitrogenous base pairs on occurrence and open states zones dynamics is investigated. These processes are studied using mathematical modeling, taking into account the number of open states between base pairs. The calculations of the probability of occurrence of open states in different parts of the gene were done depending on the localization of the deuterium atom. The mathematical modeling study demonstrated significant inequality (dependent on single 2H/1H replacement in DNA) among three parts of the gene similar in length of the frequency of occurrence of the open states. In this paper, the new convenient approach of the analysis of the abnormal frequency of open states in different parts of the gene encoding interferon alpha 17 was presented, which took into account both rising and decreasing of them that allowed to make a prediction of the functional instability of the specific DNA regions. One advantage of the new algorithm is diminishing the number of both false positive and false negative results in data filtered by this approach compared to the pure fractile methods, such as deciles or quartiles.
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Affiliation(s)
- Alexander Basov
- Kuban State Medical University, 350063 Krasnodar, Russia; (A.B.); (V.M.)
- Kuban State University, 350040 Krasnodar, Russia; (M.D.); (A.S.); (M.B.); (S.D.)
| | - Mikhail Drobotenko
- Kuban State University, 350040 Krasnodar, Russia; (M.D.); (A.S.); (M.B.); (S.D.)
| | - Alexandr Svidlov
- Kuban State University, 350040 Krasnodar, Russia; (M.D.); (A.S.); (M.B.); (S.D.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
| | | | - Vadim Malyshko
- Kuban State Medical University, 350063 Krasnodar, Russia; (A.B.); (V.M.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
| | - Anna Elkina
- Kuban State University, 350040 Krasnodar, Russia; (M.D.); (A.S.); (M.B.); (S.D.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
| | - Mikhail Baryshev
- Kuban State University, 350040 Krasnodar, Russia; (M.D.); (A.S.); (M.B.); (S.D.)
- Kuban State Technological University, 350042 Krasnodar, Russia;
| | - Stepan Dzhimak
- Kuban State University, 350040 Krasnodar, Russia; (M.D.); (A.S.); (M.B.); (S.D.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
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3
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Duchi D, Gryte K, Robb NC, Morichaud Z, Sheppard C, Brodolin K, Wigneshweraraj S, Kapanidis AN. Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes. Nucleic Acids Res 2019; 46:677-688. [PMID: 29177430 PMCID: PMC5778504 DOI: 10.1093/nar/gkx1146] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 10/31/2017] [Indexed: 12/16/2022] Open
Abstract
Transcription initiation is a major step in gene regulation for all organisms. In bacteria, the promoter DNA is first recognized by RNA polymerase (RNAP) to yield an initial closed complex. This complex subsequently undergoes conformational changes resulting in DNA strand separation to form a transcription bubble and an RNAP-promoter open complex; however, the series and sequence of conformational changes, and the factors that influence them are unclear. To address the conformational landscape and transitions in transcription initiation, we applied single-molecule Förster resonance energy transfer (smFRET) on immobilized Escherichia coli transcription open complexes. Our results revealed the existence of two stable states within RNAP–DNA complexes in which the promoter DNA appears to adopt closed and partially open conformations, and we observed large-scale transitions in which the transcription bubble fluctuated between open and closed states; these transitions, which occur roughly on the 0.1 s timescale, are distinct from the millisecond-timescale dynamics previously observed within diffusing open complexes. Mutational studies indicated that the σ70 region 3.2 of the RNAP significantly affected the bubble dynamics. Our results have implications for many steps of transcription initiation, and support a bend-load-open model for the sequence of transitions leading to bubble opening during open complex formation.
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Affiliation(s)
- Diego Duchi
- Gene Machines Group, Biological Physics Research Unit, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Kristofer Gryte
- Gene Machines Group, Biological Physics Research Unit, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Nicole C Robb
- Gene Machines Group, Biological Physics Research Unit, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Zakia Morichaud
- CNRS UMR 9004, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Carol Sheppard
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Konstantin Brodolin
- CNRS UMR 9004, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | | | - Achillefs N Kapanidis
- Gene Machines Group, Biological Physics Research Unit, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
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Li L, Fang C, Zhuang N, Wang T, Zhang Y. Structural basis for transcription initiation by bacterial ECF σ factors. Nat Commun 2019; 10:1153. [PMID: 30858373 PMCID: PMC6411747 DOI: 10.1038/s41467-019-09096-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/01/2019] [Indexed: 01/07/2023] Open
Abstract
Bacterial RNA polymerase employs extra-cytoplasmic function (ECF) σ factors to regulate context-specific gene expression programs. Despite being the most abundant and divergent σ factor class, the structural basis of ECF σ factor-mediated transcription initiation remains unknown. Here, we determine a crystal structure of Mycobacterium tuberculosis (Mtb) RNAP holoenzyme comprising an RNAP core enzyme and the ECF σ factor σH (σH-RNAP) at 2.7 Å, and solve another crystal structure of a transcription initiation complex of Mtb σH-RNAP (σH-RPo) comprising promoter DNA and an RNA primer at 2.8 Å. The two structures together reveal the interactions between σH and RNAP that are essential for σH-RNAP holoenzyme assembly as well as the interactions between σH-RNAP and promoter DNA responsible for stringent promoter recognition and for promoter unwinding. Our study establishes that ECF σ factors and primary σ factors employ distinct mechanisms for promoter recognition and for promoter unwinding.
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Affiliation(s)
- Lingting Li
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,0000 0004 1797 8419grid.410726.6University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chengli Fang
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,0000 0004 1797 8419grid.410726.6University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ningning Zhuang
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Tiantian Wang
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,0000 0004 1797 8419grid.410726.6University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yu Zhang
- 0000000119573309grid.9227.eKey Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China
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An Evolutionary/Biochemical Connection between Promoter- and Primer-Dependent Polymerases Revealed by Systematic Evolution of Ligands by Exponential Enrichment. J Bacteriol 2018; 200:JB.00579-17. [PMID: 29339418 DOI: 10.1128/jb.00579-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/11/2018] [Indexed: 01/06/2023] Open
Abstract
DNA polymerases (DNAPs) recognize 3' recessed termini on duplex DNA and carry out nucleotide catalysis. Unlike promoter-specific RNA polymerases (RNAPs), no sequence specificity is required for binding or initiation of catalysis. Despite this, previous results indicate that viral reverse transcriptases bind much more tightly to DNA primers that mimic the polypurine tract. In the current report, primer sequences that bind with high affinity to Taq and Klenow polymerases were identified using a modified systematic evolution of ligands by exponential enrichment (SELEX) approach. Two Taq-specific primers that bound ∼10 (Taq1) and over 100 (Taq2) times more stably than controls to Taq were identified. TaqI contained 8 nucleotides (5'-CACTAAAG-3') that matched the phage T3 RNAP "core" promoter. Both primers dramatically outcompeted primers with similar binding thermodynamics in PCRs. Similarly, exonuclease- Klenow polymerase also selected a high-affinity primer that contained a related core promoter sequence from phage T7 RNAP (5'-ACTATAG-3'). For both Taq and Klenow, even small modifications to the sequence resulted in large losses in binding affinity, suggesting that binding was highly sequence specific. The results are discussed in the context of possible effects on multiprimer (multiplex) PCR assays, molecular information theory, and the evolution of RNAPs and DNAPs.IMPORTANCE This work further demonstrates that primer-dependent DNA polymerases can have strong sequence biases leading to dramatically tighter binding to specific sequences. These may be related to biological function or be a consequence of the structural architecture of the enzyme. New sequence specificity for Taq and Klenow polymerases were uncovered, and among them were sequences that contained the core promoter elements from T3 and T7 phage RNA polymerase promoters. This suggests the intriguing possibility that phage RNA polymerases exploited intrinsic binding affinities of ancestral DNA polymerases to develop their promoters. Conversely, DNA polymerases could have evolved from related RNA polymerases and retained the intrinsic binding preference despite there being no clear function for such a preference in DNA biology.
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6
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Raindlová V, Janoušková M, Slavíčková M, Perlíková P, Boháčová S, Milisavljevič N, Šanderová H, Benda M, Barvík I, Krásný L, Hocek M. Influence of major-groove chemical modifications of DNA on transcription by bacterial RNA polymerases. Nucleic Acids Res 2016; 44:3000-12. [PMID: 27001521 PMCID: PMC4838386 DOI: 10.1093/nar/gkw171] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/04/2016] [Indexed: 12/11/2022] Open
Abstract
DNA templates containing a set of base modifications in the major groove (5-substituted pyrimidines or 7-substituted 7-deazapurines bearing H, methyl, vinyl, ethynyl or phenyl groups) were prepared by PCR using the corresponding base-modified 2′-deoxyribonucleoside triphosphates (dNTPs). The modified templates were used in an in vitro transcription assay using RNA polymerase from Bacillus subtilis and Escherichia coli. Some modified nucleobases bearing smaller modifications (H, Me in 7-deazapurines) were perfectly tolerated by both enzymes, whereas bulky modifications (Ph at any nucleobase) and, surprisingly, uracil blocked transcription. Some middle-sized modifications (vinyl or ethynyl) were partly tolerated mostly by the E. coli enzyme. In all cases where the transcription proceeded, full length RNA product with correct sequence was obtained indicating that the modifications of the template are not mutagenic and the inhibition is probably at the stage of initiation. The results are promising for the development of bioorthogonal reactions for artificial chemical switching of the transcription.
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Affiliation(s)
- Veronika Raindlová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Martina Janoušková
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, CZ-14220 Prague 4, Czech Republic
| | - Michaela Slavíčková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Pavla Perlíková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Soňa Boháčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Nemanja Milisavljevič
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Hana Šanderová
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, CZ-14220 Prague 4, Czech Republic
| | - Martin Benda
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, CZ-14220 Prague 4, Czech Republic
| | - Ivan Barvík
- Division of Biomolecular Physics, Institute of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Libor Krásný
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, CZ-14220 Prague 4, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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Arimbasseri AG, Maraia RJ. A high density of cis-information terminates RNA Polymerase III on a 2-rail track. RNA Biol 2015; 13:166-71. [PMID: 26636900 DOI: 10.1080/15476286.2015.1116677] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Transcription termination delineates the 3' ends of transcripts, prevents otherwise runaway RNA polymerase (RNAP) from intruding into downstream genes and regulatory elements, and enables release of the RNAP for recycling. While other eukaryotic RNAPs require complex cis-signals and/or accessory factors to achieve these activities, RNAP III does so autonomously with high efficiency and precision at a simple oligo(dT) stretch of 5-6 bp. A basis for this high density cis-information is that both template and nontemplate strands of the RNAP III terminator carry distinct signals for different stages of termination. High-density cis-information is a feature of the RNAP III system that is also reflected by dual functionalities of the tRNA promoters as both DNA and RNA elements. We review emerging developments in RNAP III termination and single strand nontemplate DNA use by other RNAPs. Use of nontemplate signals by RNAPs and associated transcription factors may be prevalent in gene regulation.
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Affiliation(s)
- Aneeshkumar G Arimbasseri
- a Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development , Bethesda , MD , USA
| | - Richard J Maraia
- a Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development , Bethesda , MD , USA.,b Commissioned Corps, U. S. Public Health Service , Washington, DC
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Bae B, Feklistov A, Lass-Napiorkowska A, Landick R, Darst SA. Structure of a bacterial RNA polymerase holoenzyme open promoter complex. eLife 2015; 4. [PMID: 26349032 PMCID: PMC4593229 DOI: 10.7554/elife.08504] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/03/2015] [Indexed: 01/17/2023] Open
Abstract
Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the −10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstream of the −10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Addition of an RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σA dissociation. DOI:http://dx.doi.org/10.7554/eLife.08504.001 Inside cells, molecules of double-stranded DNA encode the instructions needed to make proteins. To make a protein, the two strands of DNA that make up a gene are separated and one strand acts as a template to make molecules of messenger ribonucleic acid (or mRNA for short). This process is called transcription. The mRNA is then used as a template to assemble the protein. An enzyme called RNA polymerase carries out transcription and is found in all cells ranging from bacteria to humans and other animals. Bacteria have the simplest form of RNA polymerase and provide an excellent system to study how it controls transcription. It is made up of several proteins that work together to make RNA using DNA as a template. However, it requires the help of another protein called sigma factor to direct it to regions of DNA called promoters, which are just before the start of the gene. When RNA polymerase and the sigma factor interact the resulting group of proteins is known as the RNA polymerase ‘holoenzyme’. Transcription takes place in several stages. To start with, the RNA polymerase holoenzyme locates and binds to promoter DNA. Next, it separates the two strands of DNA and exposes a portion of the template strand. At this point, the DNA and the holoenzyme are said to be in an ‘open promoter complex’ and the section of promoter DNA that is within it is known as a ‘transcription bubble’. However, it is not clear how RNA polymerase holoenzyme interacts with DNA in the open promoter complex. Bae, Feklistov et al. have now used X-ray crystallography to reveal the three-dimensional structure of the open promoter complex with an entire transcription bubble from a bacterium called Thermus aquaticus. The experiments show that there are several important interactions between RNA polymerase holoenzyme and promoter DNA. In particular, the sigma factor inserts into a region of the DNA at the start of the transcription bubble. This rearranges the DNA in a manner that allows the DNA to be exposed and contact the main part of the RNA polymerase. If the holoenyzyme fails to contact the DNA in this way, the holoenzyme does not bind properly to the promoter and transcription does not start. These findings build on previous work to provide a detailed structural framework for understanding how the RNA polymerase holoenzyme and DNA interact to form the open promoter complex. Another study by Bae et al.—which involved some of the same researchers as this study—reveals how another protein called CarD also binds to DNA at the start of the transcription bubble to stabilize the open promoter complex. DOI:http://dx.doi.org/10.7554/eLife.08504.002
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Affiliation(s)
- Brian Bae
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| | - Andrey Feklistov
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
| | - Agnieszka Lass-Napiorkowska
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-madison, Madison, United States.,Department of Bacteriology, University of Wisconsin-Madison, Madison, United States
| | - Seth A Darst
- Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States
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Bick MJ, Malik S, Mustaev A, Darst SA. TFIIB is only ∼9 Å away from the 5'-end of a trimeric RNA primer in a functional RNA polymerase II preinitiation complex. PLoS One 2015; 10:e0119007. [PMID: 25774659 PMCID: PMC4361453 DOI: 10.1371/journal.pone.0119007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 01/27/2015] [Indexed: 11/18/2022] Open
Abstract
Recent X-ray crystallographic studies of Pol II in complex with the general transcription factor (GTF) IIB have begun to provide insights into the mechanism of transcription initiation. These structures have also shed light on the architecture of the transcription preinitiation complex (PIC). However, structural characterization of a functional PIC is still lacking, and even the topological arrangement of the GTFs in the Pol II complex is a matter of contention. We have extended our activity-based affinity crosslinking studies, initially developed to investigate the interaction of bacterial RNA polymerase with σ, to the eukaryotic transcription machinery. Towards that end, we sought to identify GTFs that are within the Pol II active site in a functioning PIC. We provide biochemical evidence that TFIIB is located within ∼9 Å of the -2 site of promoter DNA, where it is positioned to play a role in de novo transcription initiation.
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Affiliation(s)
- Matthew J. Bick
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, United States of America
| | - Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, United States of America
| | - Arkady Mustaev
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, University Heights, Newark, NJ, United States of America
| | - Seth A. Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, United States of America
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Campagne S, Allain FHT, Vorholt JA. Extra Cytoplasmic Function sigma factors, recent structural insights into promoter recognition and regulation. Curr Opin Struct Biol 2015; 30:71-78. [PMID: 25678040 DOI: 10.1016/j.sbi.2015.01.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/20/2015] [Indexed: 10/24/2022]
Abstract
Bacterial transcription initiation is controlled by sigma factors, the RNA polymerase (RNAP) subunits responsive for promoter specificity. While the primary sigma factor ensures the bulk of transcription during growth, a major strategy used by bacteria to regulate gene expression consists of modifying the RNAP promoter specificity by means of alternative sigma factors. Among these factors, Extra Cytoplasmic Function sigma factors (σ(ECF)) constitute the most abundant group and are generally kept inactive by specific anti-sigma factors that are directly or indirectly sensitive to environmental stimuli. When activated by anti-sigma factor release, σ(ECF) turn on the transcription of dedicated regulons, which trigger adaptive responses for the survival of the cell. Recent structural studies have deciphered the molecular basis for σ(ECF) promoter recognition and original regulatory mechanisms.
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Feklistov A, Darst SA. Crystallographic analysis of an RNA polymerase σ-subunit fragment complexed with -10 promoter element ssDNA: quadruplex formation as a possible tool for engineering crystal contacts in protein-ssDNA complexes. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:950-5. [PMID: 23989139 PMCID: PMC3758139 DOI: 10.1107/s1744309113020368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 07/23/2013] [Indexed: 11/10/2022]
Abstract
Structural studies of -10 promoter element recognition by domain 2 of the RNA polymerase σ subunit [Feklistov & Darst (2011), Cell, 147, 1257-1269] reveal an unusual crystal-packing arrangement dominated by G-quartets. The 3'-terminal GGG motif of the oligonucleotide used in crystallization participates in G-quadruplex formation with GGG motifs from symmetry-related complexes. Stacking between neighboring G-quadruplexes results in the formation of pseudo-continuous four-stranded columns running throughout the length of the crystal (G-columns). Here, a new crystal form is presented with a different arrangement of G-columns and it is proposed that the fortuitous finding of G-quartet packing could be useful in engineering crystal contacts in protein-ssDNA complexes.
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Affiliation(s)
- Andrey Feklistov
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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Abstract
Transcription initiation is a key event in the regulation of gene expression. RNA polymerase (RNAP), the central enzyme of transcription, is able to efficiently locate promoters in the genome, carry out promoter opening, and initiate RNA synthesis. All the substeps of transcription initiation are subject to complex cellular regulation. Understanding the molecular details of each step in the promoter-opening pathway is essential for a complete mechanistic and quantitative picture of gene expression. In this minireview, primarily using bacterial RNAP as an example, I briefly summarize some of the key recent advances in our understanding of the mechanisms of promoter search and promoter opening.
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Affiliation(s)
- Andrey Feklistov
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, New York 10065, USA.
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Zhang Y, Feng Y, Chatterjee S, Tuske S, Ho MX, Arnold E, Ebright RH. Structural basis of transcription initiation. Science 2012; 338:1076-80. [PMID: 23086998 DOI: 10.1126/science.1227786] [Citation(s) in RCA: 262] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
During transcription initiation, RNA polymerase (RNAP) binds and unwinds promoter DNA to form an RNAP-promoter open complex. We have determined crystal structures at 2.9 and 3.0 Å resolution of functional transcription initiation complexes comprising Thermus thermophilus RNA polymerase, σ(A), and a promoter DNA fragment corresponding to the transcription bubble and downstream double-stranded DNA of the RNAP-promoter open complex. The structures show that σ recognizes the -10 element and discriminator element through interactions that include the unstacking and insertion into pockets of three DNA bases and that RNAP recognizes the -4/+2 region through interactions that include the unstacking and insertion into a pocket of the +2 base. The structures further show that interactions between σ and template-strand single-stranded DNA (ssDNA) preorganize template-strand ssDNA to engage the RNAP active center.
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Affiliation(s)
- Yu Zhang
- Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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