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Hengelbrock A, Schmidt A, Strube J. Digital Twin Fundamentals of mRNA In Vitro Transcription in Variable Scale Toward Autonomous Operation. ACS Omega 2024; 9:8204-8220. [PMID: 38405539 PMCID: PMC10882708 DOI: 10.1021/acsomega.3c08732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/27/2024]
Abstract
The COVID-19 pandemic caused the rapid development of mRNA (messenger ribonucleic acid) vaccines and new RNA-based therapeutic methods. However, the approval rate for candidates has the potential to be increased, with a significant number failing so far due to efficacy, safety, and manufacturing deficiencies, hindering equitable vaccine distribution during pandemics. This study focuses on optimizing the production of mRNA, a critical component of mRNA-based vaccines, using a scalable machine by investigating the key mechanisms of mRNA in vitro transcription. First, kinetic parameters for the mRNA production process were determined. The validity of the determination and the robustness of the model are demonstrated by predicting different reactions with and without substrate limitations as well as different transcripts. The optimized reaction conditions, including temperature, urea concentration, and concentration of reaction-enhancing additives, resulted in a 55% increase in mRNA yield with a 33% reduction in truncated mRNA. Additionally, the feasibility of a segmented flow approach allowed for high-throughput screening (HTS), enabling the production of 20 vaccine candidates within a short time frame, representing a 10-fold increase in productivity, compared to nonsegmented reactions limited by the residence time in the plug flow reactor. The findings presented for the first time here contribute to the development of a fully continuous and efficient manufacturing process for mRNA and other cell and gene therapy drugs/vaccine candidates as presented in our previous work, which discussed the integration of process analytical technologies and predictive process models in a Biopharma 4.0 facility to enable the production of clinical and large-scale doses, ensuring a rapid and resilient supply of critical therapeutics. The results in this study especially highlight that the same machine and equipment can be used for screening and manufacturing different drug candidates in continuous operation. By streamlining production and adhering to quality standards, this approach enhances the industry's ability to respond swiftly to pandemics and public health emergencies, addressing the urgent need for accessible and effective vaccines.
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Affiliation(s)
- Alina Hengelbrock
- Institute for Separation
and Process Technology, Clausthal University
of Technology, Clausthal-Zellerfeld 38678, Germany
| | - Axel Schmidt
- Institute for Separation
and Process Technology, Clausthal University
of Technology, Clausthal-Zellerfeld 38678, Germany
| | - Jochen Strube
- Institute for Separation
and Process Technology, Clausthal University
of Technology, Clausthal-Zellerfeld 38678, Germany
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2
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Molodtsov V, Anikin M, McAllister WT. The presence of an RNA:DNA hybrid that is prone to slippage promotes termination by T7 RNA polymerase. J Mol Biol 2014; 426:3095-3107. [PMID: 24976131 DOI: 10.1016/j.jmb.2014.06.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 06/20/2014] [Accepted: 06/23/2014] [Indexed: 11/17/2022]
Abstract
Intrinsic termination signals for multisubunit bacterial RNA polymerases (RNAPs) encode a GC-rich stem-loop structure followed by a polyuridine [poly(U)] tract, and it has been proposed that steric clash of the stem-loop with the exit pore of the RNAP imposes a shearing force on the RNA in the downstream RNA:DNA hybrid, resulting in misalignment of the active site. The structurally unrelated T7 RNAP terminates at a similar type of signal (TΦ), suggesting a common mechanism for termination. In the absence of a hairpin (passive conditions), T7 RNAP slips efficiently in both homopolymeric A and U tracts, and we have found that replacement of the U tract in TΦ with a slippage-prone A tract still allows efficient termination. Under passive conditions, incorporation of a single G residue following a poly(U) tract (which is the situation during termination at TΦ) results in a "locked" complex that is unable to extend the transcript. Our results support a model in which transmission of the shearing force generated by steric clash of the hairpin with the exit pore is promoted by the presence of a slippery tracts downstream, resulting in alterations in the active site and the formation of a locked complex that represents an early step in the termination pathway.
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Affiliation(s)
- Vadim Molodtsov
- Graduate Program in Cell and Molecular Biology, Rowan University School of Osteopathic Medicine, 42 East Laurel Road, UDP 2200, Stratford, NJ 08084, USA; Department of Cell Biology, Rowan University School of Osteopathic Medicine, 42 East Laurel Road, UDP 2200, Stratford, NJ 08084, USA
| | - Michael Anikin
- Department of Cell Biology, Rowan University School of Osteopathic Medicine, 42 East Laurel Road, UDP 2200, Stratford, NJ 08084, USA
| | - William T McAllister
- Department of Cell Biology, Rowan University School of Osteopathic Medicine, 42 East Laurel Road, UDP 2200, Stratford, NJ 08084, USA.
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3
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Ibach J, Dietrich L, Koopmans KRM, Nöbel N, Skoupi M, Brakmann S. Identification of a T7 RNA polymerase variant that permits the enzymatic synthesis of fully 2'-O-methyl-modified RNA. J Biotechnol 2013; 167:287-95. [PMID: 23871655 DOI: 10.1016/j.jbiotec.2013.07.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 07/04/2013] [Accepted: 07/08/2013] [Indexed: 12/11/2022]
Abstract
T7 RNA polymerase is an important biocatalyst that is used in diverse biotechnological applications such as in vitro transcription or protein expression. The enzyme displays high substrate specificity which is payed by significant limitations regarding incorporation of synthetic nucleotide analogs. Of specific interest is enzymatic synthesis of 2'-O-methyl-modified RNA as these nucleic acids exhibit improved biochemical and pharmacokinetic properties that make them attractive for diagnostic and therapeutic purposes. We report here on the development of an activity-based selection/screening approach for assessing polymerase activities in the presence of 2'-O-methyl-modified nucleotides, and on the identification of one variant T7 RNA polymerase which is capable of synthesizing all-2'-O-methyl RNA.
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Affiliation(s)
- Jenny Ibach
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
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4
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Robins WP, Faruque SM, Mekalanos JJ. Coupling mutagenesis and parallel deep sequencing to probe essential residues in a genome or gene. Proc Natl Acad Sci U S A 2013; 110:E848-57. [PMID: 23401533 DOI: 10.1073/pnas.1222538110] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The sequence of a protein determines its function by influencing its folding, structure, and activity. Similarly, the most conserved residues of orthologous and paralogous proteins likely define those most important. The detection of important or essential residues is not always apparent via sequence alignments because these are limited by the depth of any given gene's phylogeny, as well as specificities that relate to each protein's unique biological origin. Thus, there is a need for robust and comprehensive ways of evaluating the importance of specific amino acid residues of proteins of known or unknown function. Here we describe an approach called Mut-seq, which allows the identification of virtually all of the essential residues present in a whole genome through the application of limited chemical mutagenesis, selection for function, and deep parallel genomic sequencing. Here we have applied this method to T7 bacteriophage and T7-like virus JSF7 of Vibrio cholerae.
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5
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Lin YR, Chiu CW, Chang FY, Lin CS. Characterization of a new phage, termed ϕA318, which is specific for Vibrio alginolyticus. Arch Virol 2012; 157:917-26. [PMID: 22327389 DOI: 10.1007/s00705-012-1244-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 12/14/2011] [Indexed: 10/14/2022]
Abstract
Vibrio alginolyticus is an opportunistic pathogen of animals and humans; its related strains can also produce tetrodotoxin and hemolysins. A new phage, ϕA318, which lysed its host V. alginolyticus with high efficiency, was characterized. The burst size of ϕA318 in V. alginolyticus was 72 PFU/bacterium at an MOI of 1 at room temperature; the plaque size was as large as 5 mm in diameter. Electron microscopy (EM) of the phage particles revealed a 50- to 55-nm isomorphous icosahedral head with a 12-nm non-contractile tail, similar to the T7-like phages of the family Podoviridae. Phylogenetic analysis based on complete sequences of the DNA-directed RNA polymerase gene revealed that ϕA318 had 28-47% amino acid identity to enterobacteria phages T7 and SP6, and other Vibrio phages, and the phylogenetic distance suggested that ϕA318 could be classified as a new T7-like bacteriophage. Nevertheless, several motifs in the ϕA318 phage RNA polymerase were highly conserved, including DFRGR (T7-421 motif), DG (T7-537 motif), PSEKPQDIYGAVS (T7-563 motif), RSMTKKPVMTL PYGS (T7-627 motif), and HDS (T7-811 motif). Genetic analysis indicated that phage ϕA318 is not a thermostable direct hemolysin producer. The results suggest that the MOI should be higher than 0.1 to prevent the chance of hemolysin production by the bacteria before they are lysed by the phage.
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Błaziak D, Guga P, Jagiełło A, Korczyński D, Maciaszek A, Nowicka A, Pietkiewicz A, Stec WJ. Stereoselective formation of a P-P bond in the reaction of 2-alkoxy-2-thio-1,3,2-oxathiaphospholanes with O,O-dialkyl H-phosphonates and H-thiophosphonates. Org Biomol Chem 2010; 8:5505-10. [PMID: 20944857 DOI: 10.1039/c0ob00104j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new method for the formation of organohypophosphates containing a P-P bond under mild conditions, based on the DBU-assisted reaction of 2-alkoxy-2-thio-1,3,2-oxathiaphospholanes with O,O-dialkyl H-phosphonates or H-thiophosphonates, has been elaborated. The resulting triesters of P(1)-thio- and P(1),P(2)-dithiohypophosphoric acids, respectively, having O-methyl or O-ethyl groups, can be selectively dealkylated to form the corresponding di- or monoesters. Appropriately protected 2'-deoxyguanosine-3'-O-(2-thio-1,3,2-oxathiaphospholane) was converted into the corresponding P(1)-thio- and P(1),P(2)-dithiohypophosphate esters in a highly stereoselective manner (98%+ and 90%+, respectively).
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Affiliation(s)
- Damian Błaziak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, 90-363, Łódź, Poland
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7
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Anikin M, Molodtsov V, Temiakov D, Mcallister WT. Transcript Slippage and Recoding. Recoding: Expansion of Decoding Rules Enriches Gene Expression 2010. [DOI: 10.1007/978-0-387-89382-2_19] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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8
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Davydova EK, Kaganman I, Kazmierczak KM, Rothman-Denes LB. Identification of bacteriophage N4 virion RNA polymerase-nucleic acid interactions in transcription complexes. J Biol Chem 2008; 284:1962-70. [PMID: 19015264 DOI: 10.1074/jbc.m807785200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacteriophage N4 mini-virion RNA polymerase (mini-vRNAP), the 1106-amino acid transcriptionally active domain of vRNAP, recognizes single-stranded DNA template-containing promoters composed of conserved sequences and a 3-base loop-5-base pair stem hairpin structure. The major promoter recognition determinants are a purine located at the center of the hairpin loop (-11G) and a base at the hairpin stem (-8G). Mini-vRNAP is an evolutionarily highly diverged member of the T7 family of RNAPs. A two-plasmid system was developed to measure the in vivo activity of mutant mini-vRNAP enzymes. Five mini-vRNAP derivatives, each containing a pair of cysteine residues separated by approximately 100 amino acids and single cysteine-containing enzymes, were generated. These reagents were used to determine the smallest catalytically active polypeptide and to map promoter, substrate, and RNA-DNA hybrid contact sites to single amino acid residues in the enzyme by using end-labeled 5-iododeoxyuridine- and azidophenacyl-substituted oligonucleotides, cross-linkable derivatives of the initiating nucleotide, and RNA products with 5-iodouridine incorporated at specific positions. Localization of functionally important amino acid residues in the recently determined crystal structures of apomini-vRNAP and the mini-vRNAP-promoter complex and comparison with the crystal structures of the T7 RNAP initiation and elongation complexes allowed us to predict major rearrangements in mini-vRNAP in the transition from transcription initiation to elongation similar to those observed in T7 RNAP, a task otherwise precluded by the lack of sequence homology between N4 mini-vRNAP and T7 RNAP.
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Affiliation(s)
- Elena K Davydova
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637, USA
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9
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Chopin A, Deveau H, Ehrlich SD, Moineau S, Chopin MC. KSY1, a lactococcal phage with a T7-like transcription. Virology 2007; 365:1-9. [PMID: 17467024 DOI: 10.1016/j.virol.2007.03.044] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 03/12/2007] [Accepted: 03/23/2007] [Indexed: 11/20/2022]
Abstract
The virulent lactococcal phage KSY1 possesses a large elongated capsid (223 nm long, 45 nm wide) and a short tail (32 nm). This phage of the Podoviridae group (C3 morphotype) has a linear 79,232-bp double-stranded DNA genome, which encodes 131 putative proteins and 3 tRNAs. This is the first description of the genome of a phage of this morphotype. KSY1 possesses a T7-like transcription system, including an RNA polymerase and a series of specific promoters, showing sequence homology to other known T7-like RNA polymerase promoters. Late stages of KSY1 multiplication are resistant to rifampicin. Otherwise, KSY1 shares limited similarity with other Podoviridae phages. Fourteen KSY1 structural proteins were identified by SDS-PAGE analysis. Among these proteins, those forming the distal tail structure and likely involved in host recognition are encoded by a 5-kb genomic region of KSY1. This region consists of a mosaic of DNA segments highly homologous to DNA of other lactococcal phages, suggesting an horizontal gene transfer.
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Affiliation(s)
- Alain Chopin
- Laboratoire de Génétique Microbienne, INRA, 78352 Jouy-en-Josas, France.
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10
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Polosa PL, Deceglie S, Falkenberg M, Roberti M, Di Ponzio B, Gadaleta MN, Cantatore P. Cloning of the sea urchin mitochondrial RNA polymerase and reconstitution of the transcription termination system. Nucleic Acids Res 2007; 35:2413-27. [PMID: 17392338 PMCID: PMC1874651 DOI: 10.1093/nar/gkm159] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Termination of transcription is a key process in the regulation of mitochondrial gene expression in animal cells. To investigate transcription termination in sea urchin mitochondria, we cloned the mitochondrial RNA polymerase (mtRNAP) of Paracentrotus lividus and used a recombinant form of the enzyme in a reconstituted transcription system, in the presence of the DNA-binding protein mtDBP. Cloning of mtRNAP was performed by a combination of PCR with degenerate primers and library screening. The enzyme contains 10 phage-like conserved motifs, two pentatricopeptide motifs and a serine-rich stretch. The protein expressed in insect cells supports transcription elongation in a promoter-independent assay. Addition of recombinant mtDBP caused arrest of the transcribing mtRNAP when the enzyme approached the mtDBP-binding site in the direction of transcription of mtDNA l-strand. When the polymerase encountered the protein-binding site in the opposite direction, termination occurred in a protein-independent manner, inside the mtDBP-binding site. Pulse-chase experiments show that mtDBP caused true transcription termination rather than pausing. These data indicate that mtDBP acts as polar termination factor and suggest that transcription termination in sea urchin mitochondria could take place by two alternative modes based on protein-mediated or sequence-dependent mechanisms.
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Affiliation(s)
- Paola Loguercio Polosa
- Dipartimento di Biochimica e Biologia Molecolare “Ernesto Quagliariello”, Università degli Studi di Bari, Istituto di Biomembrane e Bioenergetica, CNR, Via Orabona, 4, 70125 Bari, Italy and Department of Laboratory Medicine, Division of Metabolic Diseases, Karolinska Institutet, Novum, SE-141 86 Stockholm, Sweden
| | - Stefania Deceglie
- Dipartimento di Biochimica e Biologia Molecolare “Ernesto Quagliariello”, Università degli Studi di Bari, Istituto di Biomembrane e Bioenergetica, CNR, Via Orabona, 4, 70125 Bari, Italy and Department of Laboratory Medicine, Division of Metabolic Diseases, Karolinska Institutet, Novum, SE-141 86 Stockholm, Sweden
| | - Maria Falkenberg
- Dipartimento di Biochimica e Biologia Molecolare “Ernesto Quagliariello”, Università degli Studi di Bari, Istituto di Biomembrane e Bioenergetica, CNR, Via Orabona, 4, 70125 Bari, Italy and Department of Laboratory Medicine, Division of Metabolic Diseases, Karolinska Institutet, Novum, SE-141 86 Stockholm, Sweden
| | - Marina Roberti
- Dipartimento di Biochimica e Biologia Molecolare “Ernesto Quagliariello”, Università degli Studi di Bari, Istituto di Biomembrane e Bioenergetica, CNR, Via Orabona, 4, 70125 Bari, Italy and Department of Laboratory Medicine, Division of Metabolic Diseases, Karolinska Institutet, Novum, SE-141 86 Stockholm, Sweden
| | - Barbara Di Ponzio
- Dipartimento di Biochimica e Biologia Molecolare “Ernesto Quagliariello”, Università degli Studi di Bari, Istituto di Biomembrane e Bioenergetica, CNR, Via Orabona, 4, 70125 Bari, Italy and Department of Laboratory Medicine, Division of Metabolic Diseases, Karolinska Institutet, Novum, SE-141 86 Stockholm, Sweden
| | - Maria Nicola Gadaleta
- Dipartimento di Biochimica e Biologia Molecolare “Ernesto Quagliariello”, Università degli Studi di Bari, Istituto di Biomembrane e Bioenergetica, CNR, Via Orabona, 4, 70125 Bari, Italy and Department of Laboratory Medicine, Division of Metabolic Diseases, Karolinska Institutet, Novum, SE-141 86 Stockholm, Sweden
| | - Palmiro Cantatore
- Dipartimento di Biochimica e Biologia Molecolare “Ernesto Quagliariello”, Università degli Studi di Bari, Istituto di Biomembrane e Bioenergetica, CNR, Via Orabona, 4, 70125 Bari, Italy and Department of Laboratory Medicine, Division of Metabolic Diseases, Karolinska Institutet, Novum, SE-141 86 Stockholm, Sweden
- *To whom correspondence should be addressed. +39-080-5443378+39-080-5443403
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11
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Kennedy WP, Momand JR, Yin YW. Mechanism for de novo RNA synthesis and initiating nucleotide specificity by t7 RNA polymerase. J Mol Biol 2007; 370:256-68. [PMID: 17512007 DOI: 10.1016/j.jmb.2007.03.041] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 03/14/2007] [Accepted: 03/14/2007] [Indexed: 10/23/2022]
Abstract
DNA-directed RNA polymerases are capable of initiating synthesis of RNA without primers, the first catalytic stage of initiation is referred to as de novo RNA synthesis. De novo synthesis is a unique phase in the transcription cycle where the RNA polymerase binds two nucleotides rather than a nascent RNA polymer and a single nucleotide. For bacteriophage T7 RNA polymerase, transcription begins with a marked preference for GTP at the +1 and +2 positions. We determined the crystal structures of T7 RNA polymerase complexes captured during the de novo RNA synthesis. The DNA substrates in the structures in the complexes contain a common Phi 10 duplex promoter followed by a unique five base single-stranded extension of template DNA whose sequences varied at positions +1 and +2, thereby allowing for different pairs of initiating nucleotides GTP, ATP, CTP or UTP to bind. The structures show that the initiating nucleotides bind RNA polymerase in locations distinct from those described previously for elongation complexes. Selection bias in favor of GTP as an initiating nucleotide is accomplished by shape complementarity, extensive protein side-chain and strong base-stacking interactions for the guanine moiety in the enzyme active site. Consequently, an initiating GTP provides the largest stabilization force for the open promoter conformation.
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Affiliation(s)
- William P Kennedy
- Department of Chemistry and Biochemistry, Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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12
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Abstract
Plant plastids contain a circular genome of ∼150 kb organized into ∼35 transcription units. The plastid genome is organized into nucleoids and attached to plastid membranes. This relatively small genome is transcribed by at least two different RNA polymerases, one being of the prokaryotic type and plastid-encoded (PEP), the other one being of the phage-type and nucleus-encoded (NEP). The presumed localization of a second phage-type RNA polymerase in plastids is still questionable. There is strong evidence for a sequential action of NEP and PEP enzymes during plant development attributing a prevailing role of NEP during early plant and plastid development, although NEP is present in mature chloroplasts. In the present paper, we have analysed two different NEP enzymes from spinach with respect to subcellular and intra-plastidial localization in mature chloroplasts with the help of specific antibodies. Results show the presence of the two different NEP enzymes in mature chloroplasts. Both enzymes are entirely membrane bound but, unlike previously thought, this membrane binding is not mediated via DNA. This finding indicates that NEP enzymes are not found as elongating transcription complexes on the template DNA in mature chloroplasts and raises the question of their function in mature chloroplasts.
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Affiliation(s)
| | | | - Silva Lerbs-Mache
- To whom correspondence should be addressed. Tel: +33 04 76 63 57 44; Fax: +33 04 76 63 55 86;
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13
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Jiang M, Ma N, Vassylyev DG, McAllister WT. RNA displacement and resolution of the transcription bubble during transcription by T7 RNA polymerase. Mol Cell 2004; 15:777-88. [PMID: 15350221 DOI: 10.1016/j.molcel.2004.07.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2004] [Revised: 06/07/2004] [Accepted: 06/17/2004] [Indexed: 11/26/2022]
Abstract
Unlike DNA polymerases, RNA polymerases (RNAPs) must displace the nascent product from the template and restore the DNA to duplex form after passage of the transcription complex. To accomplish this, RNAPs establish a locally denatured "bubble" that encloses a short RNA:DNA hybrid. As the polymerase advances along the template, the RNA is displaced at the trailing edge of the bubble and the two DNA strands are reannealed. Structural analyses have revealed a number of elements that are likely to be involved in this process in T7 RNAP. In this work, we used genetic and biochemical methods to explore the roles of these elements during the transition from an initiation complex to an elongation complex. The results indicate that the transition is a multistep process and reveal a critical role for the nontemplate strand of the DNA.
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Affiliation(s)
- Manli Jiang
- Morse Institute of Molecular Genetics, Department of Microbiology and Immunology, SUNY Health Science Center at Brooklyn, 450 Clarkson Avenue, Brooklyn, NY 11203, USA
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14
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Affiliation(s)
- Elena K Davydova
- Department of Molecular Genetics and Cell Biology, University of Chicago, 920 E. 58th Street, Chicago, Illinois 60637, USA
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15
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Affiliation(s)
- Rui Sousa
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229-3900, USA
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16
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Abstract
Unlike DNA polymerases, an RNA polymerase must initiate transcription de novo, that is binding of the initiating (+1) nucleoside triphosphate must be achieved without benefit of the cooperative binding energetics of an associated primer. Since a single Watson-Crick base pair is not stable in solution, RNA polymerases might be expected to provide additional stabilizing interactions to facilitate binding and positioning of the initiating (priming) nucleoside triphosphate at position +1. Consistent with base-specific stabilizing interactions, of the 17 T7 RNA polymerase promoters in the phage genome, 15 begin with guanine. In this work, we demonstrate that the purine N-7 is important in the utilization of the initial substrate GTP. The fact that on a template encoding AG as the first two bases in the transcript (as in the remaining two of the T7 genome) transcription starts predominantly (but not exclusively) at the G at position +2 additionally implicates the purine O-6 as an important recognition element in the major groove. Finally, results suggest that these interactions serve primarily to position the initiating base in the active site. It is proposed that T7 RNA polymerase interacts directly with the Hoogsteen side of the initial priming GTP (most likely via an interaction with an arginine side chain in the protein) to provide the extra stability required at this unique step in transcription.
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Affiliation(s)
- Iaroslav Kuzmine
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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17
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Kukarin A, Rong M, McAllister WT. Exposure of T7 RNA polymerase to the isolated binding region of the promoter allows transcription from a single-stranded template. J Biol Chem 2003; 278:2419-24. [PMID: 12441338 DOI: 10.1074/jbc.m210058200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
While the binding region of the T7 promoter must be double-stranded (ds) to function, the non-template strand in the initiation region is dispensable, and a promoter that lacks this element allows efficient initiation. To determine whether the binding region serves merely to recruit the RNA polymerase (RNAP) to the vicinity of a melted initiation region or provides other functions, we utilized a GAL4-T7 RNAP fusion protein to provide an independent binding capacity to the RNAP. When the GAL4-T7 RNAP was recruited to a single-stranded (ss) promoter via a nearby Gal4 recognition sequence, no transcription was observed. However, transcription from the ss promoter could be activated by the addition, in trans, of a ds hairpin loop that contains only the binding region of the promoter. The same results were obtained in the absence of the GAL4 recognition sequence in the template and were also observed with wild type enzyme. Gel-shift experiments indicate that exposure of the RNAP to the isolated binding region facilitates recruitment of the ss template, but that the binding region is displaced from the complex prior to initiation. We conclude that exposure of the RNAP to the isolated binding region reorganizes the enzyme, allowing it to bind to the ss template. These findings have potential implications with regard to mechanisms of promoter binding and melting.
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Affiliation(s)
- Alexander Kukarin
- Morse Institute of Molecular Genetics, Department of Microbiology and Immunology, SUNY Downstate Medical Center, Brooklyn, New York 11203, USA
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Abstract
We have used synthetic oligomers of DNA and RNA to assemble nucleic acid scaffolds that, when mixed with T7 RNA polymerase, allow the formation of functional transcription complexes. Manipulation of the scaffold structure allows the contribution of each element in the scaffold to transcription activity to be independently determined. The minimal scaffold that allows efficient extension after challenge with 200 mm NaCl consists of an 8-nt RNA primer hybridized to a DNA template (T strand) that extends 5-10 nt downstream. Constructs in which the RNA-DNA hybrid is less than or greater than 8 bp are less salt-resistant, and the hybrid cannot be extended beyond 12-13 bp. Although the presence of a complementary nontemplate strand downstream of the primer does not affect salt resistance, the presence of DNA upstream decreases resistance. The addition of a 4-nt unpaired "tail" to the 5' end of the primer increases salt resistance, as does the presence of an unpaired nontemplate strand in the region that contains the 8-bp hybrid (thereby generating an artificial transcription "bubble"). Scaffold complexes having these features remain active for over 1 week in the absence of salt and exhibit many of the properties of halted elongation complexes, including resistance to salt challenge, a similar trypsin cleavage pattern, and a similar pattern of RNA-RNA polymerase cross-linking.
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Affiliation(s)
- Dmitri Temiakov
- Morse Institute of Molecular Genetics, Department of Microbiology and Immunology, State University of New York Health Science Center at Brooklyn, Brooklyn, New York 11203-2098, USA
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19
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Ma K, Temiakov D, Jiang M, Anikin M, McAllister WT. Major conformational changes occur during the transition from an initiation complex to an elongation complex by T7 RNA polymerase. J Biol Chem 2002; 277:43206-15. [PMID: 12186873 DOI: 10.1074/jbc.m206658200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To examine changes that occur during the transition from an initiation complex (IC) to an elongation complex (EC) in T7 RNA polymerase (RNAP), we used nucleic acid-protein cross-linking methods to probe interactions of the RNAP with RNA and DNA in a halted EC. As the RNA is displaced from the RNA-DNA hybrid approximately 9 bp upstream from the active site (at -9) it interacts with a region within the specificity loop (residues 744-750) and is directed toward a positively charged surface that surrounds residues Lys-302 and Lys-303. Surprisingly, the template and non-template strands of the DNA at the upstream edge of the hybrid (near the site where the RNA is displaced) interact with a region in the N-terminal domain of the RNAP (residues 172-191) that is far away from the specificity loop before isomerization (in the IC). To bring these two regions of the RNAP into proximity, major conformational changes must occur during the transition from an IC to an EC. The observed nucleic acid-protein interactions help to explain the behavior of a number of mutant RNAPs that are affected at various stages in the initiation process and in termination.
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Affiliation(s)
- Kaiyu Ma
- Morse Institute of Molecular Genetics, Department of Microbiology and Immunology, State University of New York Health Science Center, Brooklyn, New York 11203-2098, USA
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20
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Abstract
In vitro, bacteriophage N4 virion RNA polymerase (vRNAP) recognizes in vivo sites of transcription initiation on single-stranded templates. N4 vRNAP promoters are comprised of a hairpin structure and conserved sequences. Here, we show that vRNAP consists of a single 3500 amino acid polypeptide, and we define and characterize a transcriptionally active 1106 amino acid domain (mini-vRNAP). Biochemical and genetic characterization of this domain indicates that, despite its peculiar promoter specificity and lack of extensive sequence similarity to other DNA-dependent RNA polymerases, mini-vRNAP is related to the family of T7-like RNA polymerases.
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Affiliation(s)
- K.M. Kazmierczak
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637 and Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA Present address: Lilly Research Laboratories, Indianapolis, IN 46285, USA Corresponding author e-mail: K.M.Kazmierczak and E.K.Davydova contributed equally to this work
| | - E.K. Davydova
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637 and Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA Present address: Lilly Research Laboratories, Indianapolis, IN 46285, USA Corresponding author e-mail: K.M.Kazmierczak and E.K.Davydova contributed equally to this work
| | - A.A. Mustaev
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637 and Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA Present address: Lilly Research Laboratories, Indianapolis, IN 46285, USA Corresponding author e-mail: K.M.Kazmierczak and E.K.Davydova contributed equally to this work
| | - L.B. Rothman-Denes
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637 and Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA Present address: Lilly Research Laboratories, Indianapolis, IN 46285, USA Corresponding author e-mail: K.M.Kazmierczak and E.K.Davydova contributed equally to this work
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21
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Willis SH, Kazmierczak KM, Carter RH, Rothman-Denes LB. N4 RNA polymerase II, a heterodimeric RNA polymerase with homology to the single-subunit family of RNA polymerases. J Bacteriol 2002; 184:4952-61. [PMID: 12193610 PMCID: PMC135322 DOI: 10.1128/jb.184.18.4952-4961.2002] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriophage N4 middle genes are transcribed by a phage-coded, heterodimeric, rifampin-resistant RNA polymerase, N4 RNA polymerase II (N4 RNAPII). Sequencing and transcriptional analysis revealed that the genes encoding the two subunits comprising N4 RNAPII are translated from a common transcript initiating at the N4 early promoter Pe3. These genes code for proteins of 269 and 404 amino acid residues with sequence similarity to the single-subunit, phage-like RNA polymerases. The genes encoding the N4 RNAPII subunits, as well as a synthetic construct encoding a fusion polypeptide, have been cloned and expressed. Both the individually expressed subunits and the fusion polypeptide reconstitute functional enzymes in vivo and in vitro.
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Affiliation(s)
- S H Willis
- Department of Molecular Genetics, The University of Chicago, Chicago, Illinois 60637, USA
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