1
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Naumann TA, Sollenberger KG, Hao G. Production of selenomethionine labeled polyglycine hydrolases in Pichia pastoris. Protein Expr Purif 2022; 194:106076. [PMID: 35240278 DOI: 10.1016/j.pep.2022.106076] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 01/05/2023]
Abstract
Producing recombinant proteins with incorporated selenomethionine (SeMet) facilitates solving X-ray crystallographic structures of novel proteins. Production of SeMet labeled proteins in the yeast Pichia pastoris (syn. Komagataella phaffii) is difficult because SeMet is mildly toxic, reducing protein expression levels. To counteract this yield loss for a novel protease, Epicoccum sorghi chitinase modifying protein (Es-cmp), a novel disease promoting protease secreted by these plant pathogenic fungi, we isolated a yeast strain that secreted more protein. By comparing the expression level of 48 strains we isolated one that produced significantly more protein. This strain was found to be gene dosed, having four copies of the expression cassette. After optimization the strain produced Es-cmp in defined media with SeMet at levels nearly equal to that of the original strain in complex media. Also, we produced SeMet labeled protein for a homologous protease from the fungus Fusarium vanettenii, Fvan-cmp, by directly selecting a gene dosed strain on agar plates with increased zeocin. Linearization of plasmid with PmeI before electroporation led to high numbers of 1 mg/mL zeocin resistant clones with significantly increased expression compared to those selected on 0.1 mg/mL. The gene dosed strains expressing Es-cmp and Fvan-cmp allowed production of 8.5 and 16.8 mg of SeMet labeled protein from 500 mL shake flask cultures. The results demonstrate that selection of P. pastoris expression strains by plating after transformation on agar with 1 mg/mL zeocin rather than the standard 0.1 mg/mL directly selects gene dosed strains that can facilitate production of selenomethionine labeled proteins.
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Affiliation(s)
- Todd A Naumann
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agriculture Utilization Research, Peoria, IL, 61604, USA.
| | - Kurt G Sollenberger
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agriculture Utilization Research, Peoria, IL, 61604, USA
| | - Guixia Hao
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agriculture Utilization Research, Peoria, IL, 61604, USA
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2
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Abstract
Gene transcription by RNA polymerase II (Pol II) is the first step in the expression of the eukaryotic genome and a focal point for cellular regulation during development, differentiation, and responses to the environment. Two decades after the determination of the structure of Pol II, the mechanisms of transcription have been elucidated with studies of Pol II complexes with nucleic acids and associated proteins. Here we provide an overview of the nearly 200 available Pol II complex structures and summarize how these structures have elucidated promoter-dependent transcription initiation, promoter-proximal pausing and release of Pol II into active elongation, and the mechanisms that Pol II uses to navigate obstacles such as nucleosomes and DNA lesions. We predict that future studies will focus on how Pol II transcription is interconnected with chromatin transitions, RNA processing, and DNA repair.
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Affiliation(s)
- Sara Osman
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;,
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;,
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3
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Wenzel S, Imasaki T, Takagi Y. A practical method for efficient and optimal production of Seleno-methionine-labeled recombinant protein complexes in the insect cells. Protein Sci 2019; 28:808-822. [PMID: 30663186 DOI: 10.1002/pro.3575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/04/2019] [Accepted: 01/07/2019] [Indexed: 11/07/2022]
Abstract
The use of Seleno-methionine (SeMet) incorporated protein crystals for single or multi-wavelength anomalous diffraction (SAD or MAD) to facilitate phasing has become almost synonymous with modern X-ray crystallography. The anomalous signals from SeMets can be used for phasing as well as sequence markers for subsequent model building. The production of large quantities of SeMet incorporated recombinant proteins is relatively straightforward when expressed in Escherichia coli. In contrast, production of SeMet substituted recombinant proteins expressed in the insect cells is not as robust due to the toxicity of SeMet in eukaryotic systems. Previous protocols for SeMet-incorporation in the insect cells are laborious, and more suited for secreted proteins. In addition, these protocols have generally not addressed the SeMet toxicity issue, and typically result in low recovery of the labeled proteins. Here we report that SeMet toxicity can be circumvented by fully infecting insect cells with baculovirus. Quantitatively controlling infection levels using our Titer Estimation of Quality Control (TEQC) method allow for the incorporation of substantial amounts of SeMet, resulting in an efficient and optimal production of labeled recombinant protein complexes. With the method described here, we were able to consistently reach incorporation levels of about 75% and protein yield of 60-90% compared with native protein expression.
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Affiliation(s)
- Sabine Wenzel
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana, 46202
| | - Tsuyoshi Imasaki
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana, 46202
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana, 46202
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4
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Jun S, XiaoFeng J, Yuan Z, Mi S. Expression, purification, crystallization, and diffraction analysis of a selenomethionyl lipase Lip8 from Yarrowia lipolytica. Prep Biochem Biotechnol 2018; 48:213-217. [DOI: 10.1080/10826068.2016.1188316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Sheng Jun
- Laboratory of Enzyme Engineering, Yellow Sea Fisheries Research Institute, Qingdao, P. R. China
| | - Ji XiaoFeng
- Laboratory of Enzyme Engineering, Yellow Sea Fisheries Research Institute, Qingdao, P. R. China
| | - Zheng Yuan
- Laboratory of Enzyme Engineering, Yellow Sea Fisheries Research Institute, Qingdao, P. R. China
| | - Sun Mi
- Laboratory of Enzyme Engineering, Yellow Sea Fisheries Research Institute, Qingdao, P. R. China
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5
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Structure determination of transient transcription complexes. Biochem Soc Trans 2017; 44:1177-82. [PMID: 27528766 DOI: 10.1042/bst20160079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Indexed: 11/17/2022]
Abstract
The determination of detailed 3D structures of large and transient multicomponent complexes remains challenging. Here I describe the approaches that were used and developed by our laboratory to achieve structure solution of eukaryotic transcription complexes. I hope this collection serves as a resource for structural biologists seeking solutions for difficult structure determination projects.
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6
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Incorporation of non-canonical amino acids into proteins in yeast. Fungal Genet Biol 2016; 89:137-156. [DOI: 10.1016/j.fgb.2016.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 12/22/2022]
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7
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Routledge SJ, Mikaliunaite L, Patel A, Clare M, Cartwright SP, Bawa Z, Wilks MDB, Low F, Hardy D, Rothnie AJ, Bill RM. The synthesis of recombinant membrane proteins in yeast for structural studies. Methods 2015; 95:26-37. [PMID: 26431670 DOI: 10.1016/j.ymeth.2015.09.027] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 12/22/2022] Open
Abstract
Historically, recombinant membrane protein production has been a major challenge meaning that many fewer membrane protein structures have been published than those of soluble proteins. However, there has been a recent, almost exponential increase in the number of membrane protein structures being deposited in the Protein Data Bank. This suggests that empirical methods are now available that can ensure the required protein supply for these difficult targets. This review focuses on methods that are available for protein production in yeast, which is an important source of recombinant eukaryotic membrane proteins. We provide an overview of approaches to optimize the expression plasmid, host cell and culture conditions, as well as the extraction and purification of functional protein for crystallization trials in preparation for structural studies.
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Affiliation(s)
- Sarah J Routledge
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK; School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Lina Mikaliunaite
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Anjana Patel
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Michelle Clare
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Stephanie P Cartwright
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Zharain Bawa
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Martin D B Wilks
- Smallpeice Enterprises Ltd, 27 Newbold Terrace East, Leamington Spa, Warwickshire CV32 4ES, UK
| | - Floren Low
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - David Hardy
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Alice J Rothnie
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Roslyn M Bill
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
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8
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Abstract
High-throughput, automated or semiautomated methodologies implemented by companies and structural genomics initiatives have accelerated the process of acquiring structural information for proteins via x-ray crystallography. This has enabled the application of structure-based drug design technologies to a variety of new structures that have potential pharmacologic relevance. Although there remain major challenges to applying these approaches more broadly to all classes of drug discovery targets, clearly the continued development and implementation of these structure-based drug design methodologies by the scientific community at large will help to address and provide solutions to these hurdles. The result will be a growing number of protein structures of important pharmacologic targets that will help to streamline the process of identification and optimization of lead compounds for drug development. These lead agonist and antagonist pharmacophores should, in turn, help to alleviate one of the current critical bottlenecks in the drug discovery process; that is, defining the functional relevance of potential novel targets to disease modification. The prospect of generating an increasing number of potential drug candidates will serve to highlight perhaps the most significant future bottleneck for drug development, the cost and complexity of the drug approval process.
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Affiliation(s)
- Leslie W Tari
- ActiveSight, 4045 Sorrento Valley Blvd, San Diego, CA 92121, USA.
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9
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Structure of the mediator head module bound to the carboxy-terminal domain of RNA polymerase II. Proc Natl Acad Sci U S A 2012; 109:17931-5. [PMID: 23071300 DOI: 10.1073/pnas.1215241109] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The X-ray crystal structure of the Head module, one-third of the Mediator of transcriptional regulation, has been determined as a complex with the C-terminal domain (CTD) of RNA polymerase II. The structure reveals multiple points of interaction with an extended conformation of the CTD; it suggests a basis for regulation by phosphorylation of the CTD. Biochemical studies show a requirement for Mediator-CTD interaction for transcription.
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10
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Abstract
Dyneins are microtubule-based motor proteins that power ciliary beating, transport intracellular cargos, and help to construct the mitotic spindle. Evolved from ring-shaped hexameric AAA-family adenosine triphosphatases (ATPases), dynein's large size and complexity have posed challenges for understanding its structure and mechanism. Here, we present a 6 angstrom crystal structure of a functional dimer of two ~300-kilodalton motor domains of yeast cytoplasmic dynein. The structure reveals an unusual asymmetric arrangement of ATPase domains in the ring-shaped motor domain, the manner in which the mechanical element interacts with the ATPase ring, and an unexpected interaction between two coiled coils that create a base for the microtubule binding domain. The arrangement of these elements provides clues as to how adenosine triphosphate-driven conformational changes might be transmitted across the motor domain.
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Affiliation(s)
- Andrew P Carter
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California-San Francisco, 600 16th Street, San Francisco, CA 94158, USA.
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11
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Mutation of high-affinity methionine permease contributes to selenomethionyl protein production in Saccharomyces cerevisiae. Appl Environ Microbiol 2010; 76:6351-9. [PMID: 20693451 DOI: 10.1128/aem.01026-10] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The production of selenomethionine (SeMet) derivatives of recombinant proteins allows phase determination by single-wavelength or multiwavelength anomalous dispersion phasing in X-ray crystallography, and this popular approach has permitted the crystal structures of numerous proteins to be determined. Although yeast is an ideal host for the production of large amounts of eukaryotic proteins that require posttranslational modification, the toxic effects of SeMet often interfere with the preparation of protein derivatives containing this compound. We previously isolated a mutant strain (SMR-94) of the methylotrophic yeast Pichia pastoris that is resistant to both SeMet and selenate and demonstrated its applicability for the production of proteins suitable for X-ray crystallographic analysis. However, the molecular basis for resistance to SeMet by the SMR-94 strain remains unclear. Here, we report the characterization of SeMet-resistant mutants of Saccharomyces cerevisiae and the identification of a mutant allele of the MUP1 gene encoding high-affinity methionine permease, which confers SeMet resistance. Although the total methionine uptake by the mup1 mutant (the SRY5-7 strain) decreased to 47% of the wild-type level, it was able to incorporate SeMet into the overexpressed epidermal growth factor peptide with 73% occupancy, indicating the importance of the moderate uptake of SeMet by amino acid permeases other than Mup1p for the alleviation of SeMet toxicity. In addition, under standard culture conditions, the mup1 mutant showed higher productivity of the SeMet derivative relative to other SeMet-resistant mutants. Based on these results, we conclude that the mup1 mutant would be useful for the preparation of selenomethionyl proteins for X-ray crystallography.
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12
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Walden H. Selenium incorporation using recombinant techniques. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:352-7. [PMID: 20382987 PMCID: PMC2852298 DOI: 10.1107/s0907444909038207] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Accepted: 09/21/2009] [Indexed: 11/29/2022]
Abstract
An overview of techniques for recombinant incorporation of selenium and subsequent purification and crystallization of the resulting labelled protein. Using selenomethionine to phase macromolecular structures is common practice in structure determination, along with the use of selenocysteine. Selenium is consequently the most commonly used heavy atom for MAD. In addition to the well established recombinant techniques for the incorporation of selenium in prokaryal expression systems, there have been recent advances in selenium labelling in eukaryal expression, which will be discussed. Tips and things to consider for the purification and crystallization of seleno-labelled proteins are also included.
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Affiliation(s)
- Helen Walden
- Protein Structure and Function Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields, London WC2A 3PX, England.
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13
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Berntsson RPA, Alia Oktaviani N, Fusetti F, Thunnissen AMWH, Poolman B, Slotboom DJ. Selenomethionine incorporation in proteins expressed in Lactococcus lactis. Protein Sci 2009; 18:1121-7. [PMID: 19388077 DOI: 10.1002/pro.97] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Lactococcus lactis is a promising host for (membrane) protein overproduction. Here, we describe a protocol for incorporation of selenomethionine (SeMet) into proteins expressed in L. lactis. Incorporation efficiencies of SeMet in the membrane protein complex OpuA (an ABC transporter) and the soluble protein OppA, both from L. lactis, were monitored by mass spectrometry. Both proteins incorporated SeMet with high efficiencies (>90%), which greatly extends the usefulness of the expression host L. lactis for X-ray crystallography purposes. The crystal structure of ligand-free OppA was determined at 2.4 A resolution by a semiautomatic approach using selenium single-wavelength anomalous diffraction phasing.
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Affiliation(s)
- Ronnie P-A Berntsson
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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14
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Kitajima T, Yagi E, Kubota T, Chiba Y, Nishikawa S, Jigami Y. Use of novel selenomethionine-resistant yeast to produce selenomethionyl protein suitable for structural analysis. FEMS Yeast Res 2009; 9:439-45. [DOI: 10.1111/j.1567-1364.2009.00484.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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15
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Genome-wide screen of Saccharomyces cerevisiae null allele strains identifies genes involved in selenomethionine resistance. Proc Natl Acad Sci U S A 2008; 105:17682-7. [PMID: 19004804 DOI: 10.1073/pnas.0805642105] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Selenomethionine (SeMet) is a potentially toxic amino acid, and yet it is a valuable tool in the preparation of labeled proteins for multiwavelength anomalous dispersion or single-wavelength anomalous dispersion phasing in X-ray crystallography. The mechanism by which high levels of SeMet exhibits its toxic effects in eukaryotic cells is not fully understood. Attempts to use Saccharomyces cerevisiae for the preparation of fully substituted SeMet proteins for X-ray crystallography have been limited. A screen of the viable S. cerevisiae haploid null allele strain collection for resistance to SeMet was performed. Deletion of the CYS3 gene encoding cystathionine gamma-lyase resulted in the highest resistance to SeMet. In addition, deletion of SSN2 resulted in both increased resistance to SeMet as well as reduced levels of Cys3p. A methionine auxotrophic strain lacking CYS3 was able to grow in media with SeMet as the only source of Met, achieving essentially 100% occupancy in total proteins. The CYS3 deletion strain provides advantages for an easy and cost-effective method to prepare SeMet-substituted protein in yeast and perhaps other eukaryotic systems.
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16
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Wiltschi B, Wenger W, Nehring S, Budisa N. Expanding the genetic code ofSaccharomyces cerevisiaewith methionine analogues. Yeast 2008; 25:775-86. [DOI: 10.1002/yea.1632] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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17
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Cronin CN, Lim KB, Rogers J. Production of selenomethionyl-derivatized proteins in baculovirus-infected insect cells. Protein Sci 2007; 16:2023-9. [PMID: 17660253 PMCID: PMC2206972 DOI: 10.1110/ps.072931407] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A protocol is described for the production of both intracellularly expressed and secreted selenomethionyl-derivatized recombinant proteins in baculovirus-infected insect cells. The method results in the production of recombinant soluble proteins with an SeMet occupancy of approximately 75% and with a recovery of approximately 20% that of native protein expression. The method is independent of the percentage methionine content of the protein and is reliable and consistent. Similar results are obtained using either Spodoptera frugiperda Sf9 or Trichoplusia ni High Five insect cells as the expression host, and when cultures are grown in either shake flasks or in Wave BioReactors.
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Affiliation(s)
- Ciarán N Cronin
- Pfizer, Inc., 10777 Science Center Drive, San Diego, CA 92121, USA.
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18
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Malkowski MG, Quartley E, Friedman AE, Babulski J, Kon Y, Wolfley J, Said M, Luft JR, Phizicky EM, DeTitta GT, Grayhack EJ. Blocking S-adenosylmethionine synthesis in yeast allows selenomethionine incorporation and multiwavelength anomalous dispersion phasing. Proc Natl Acad Sci U S A 2007; 104:6678-83. [PMID: 17426150 PMCID: PMC1850019 DOI: 10.1073/pnas.0610337104] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Indexed: 11/18/2022] Open
Abstract
Saccharomyces cerevisiae is an ideal host from which to obtain high levels of posttranslationally modified eukaryotic proteins for x-ray crystallography. However, extensive replacement of methionine by selenomethionine for anomalous dispersion phasing has proven intractable in yeast. We report a general method to incorporate selenomethionine into proteins expressed in yeast based on manipulation of the appropriate metabolic pathways. sam1(-) sam2(-) mutants, in which the conversion of methionine to S-adenosylmethionine is blocked, exhibit reduced selenomethionine toxicity compared with wild-type yeast, increased production of protein during growth in selenomethionine, and efficient replacement of methionine by selenomethionine, based on quantitative mass spectrometry and x-ray crystallography. The structure of yeast tryptophanyl-tRNA synthetase was solved to 1.8 A by using multiwavelength anomalous dispersion phasing with protein that was expressed and purified from the sam1(-) sam2(-) strain grown in selenomethionine. Six of eight selenium residues were located in the structure.
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Affiliation(s)
- Michael G. Malkowski
- *Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203; and
- Department of Structural Biology, State University of New York, 700 Ellicott Street, Buffalo, NY 14203
| | | | | | | | - Yoshiko Kon
- Center for Pediatric Biomedical Research and
- Biochemistry and Biophysics, University of Rochester Medical School, Rochester, NY 14642
| | - Jennifer Wolfley
- *Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203; and
| | - Meriem Said
- *Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203; and
| | - Joseph R. Luft
- *Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203; and
- Department of Structural Biology, State University of New York, 700 Ellicott Street, Buffalo, NY 14203
| | - Eric M. Phizicky
- Center for Pediatric Biomedical Research and
- Biochemistry and Biophysics, University of Rochester Medical School, Rochester, NY 14642
| | - George T. DeTitta
- *Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203; and
- Department of Structural Biology, State University of New York, 700 Ellicott Street, Buffalo, NY 14203
| | - Elizabeth J. Grayhack
- Center for Pediatric Biomedical Research and
- Biochemistry and Biophysics, University of Rochester Medical School, Rochester, NY 14642
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19
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Doublié S. Production of selenomethionyl proteins in prokaryotic and eukaryotic expression systems. Methods Mol Biol 2007; 363:91-108. [PMID: 17272838 DOI: 10.1007/978-1-59745-209-0_5] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The use of selenomethionine as a phasing tool was first reported in 1990. Engineering of selenomethionyl proteins for structure determination is now routine. In fact, selenium is by far the most commonly used anomalous scatterer for multiwavelength anomalous diffraction studies. The past few years have seen new developments, which demonstrated the feasibility of expressing selenomethionyl protein in eukaryotic systems. In this chapter, the different methods available for producing selenomethionine-labeled proteins in bacteria, as well as in yeast and mammalian cells will be presented, along with tips for purifying and crystallizing selenomethionyl proteins.
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Affiliation(s)
- Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA
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20
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Abstract
Selenomethionine incorporation is a standard method for determining the phases in protein crystallography by single- or multiwavelength anomalous dispersion. Recombinant expression of selenomethionine-containing protein in non-auxotrophic Pichia pastoris strains yield an incorporation of about 50%. The expression of a mutated variant of Penicillium minioluteum dextranase in P. pastoris is used to illustrate the method utilized to obtain selenomethionyl-substituted protein and to show the phasing power of the acquired anomalous signal. The dextranase structure was solved using the anomalous signal achieved from 50% selenomethionine incorporation.
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Affiliation(s)
- Anna M Larsson
- Department of Cell and Molecular Biology, University of Uppsala, Uppsala, Sweden
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21
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Abstract
This year's Nobel laureate in chemistry is Roger Kornberg. Patrick Cramer gives a personal account of how the Kornberg laboratory determined the structure of the RNA polymerase II core enzyme.
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Affiliation(s)
- Patrick Cramer
- Gene Center Munich, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, D-81377 Munich, Germany.
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22
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Laible PD, Hata AN, Crawford AE, Hanson DK. Incorporation of selenomethionine into induced intracytoplasmic membrane proteins of Rhodobacter species. ACTA ACUST UNITED AC 2006; 6:95-102. [PMID: 16211505 DOI: 10.1007/s10969-005-1936-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2004] [Accepted: 01/16/2005] [Indexed: 10/25/2022]
Abstract
Efficient multiple- or single-wavelength anomalous dispersion (MAD/SAD) techniques that use tunable X-ray sources at third-generation synchrotrons exploit the anomalous scattering of certain heavy atoms for determination of experimental phases. Development of methods for the in vivo substitution of methionine by selenomethionine (SeMet) has revolutionized the process for determination of structures of soluble proteins in recent years. Herein, we report methods for biosynthetic incorporation of SeMet into induced intracytoplasmic membrane proteins of two species of the Rhodobacter genus of purple non-sulfur photosynthetic bacteria. Amino acid analysis of a membrane protein complex that was purified to homogeneity determined that the extent of SeMet incorporation was extensive and approached quantitative replacement. Diffraction-quality crystals were obtained from SeMet-labeled membrane proteins purified from 2 l of culture. These methods augment the potential utility of photosynthetic bacteria and their inducible membrane systems for the production of foreign membrane proteins for structure determination.
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Affiliation(s)
- Philip D Laible
- Biosciences Division, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA
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23
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Abstract
The vast majority of mammalian glycosyltransferases are endoplasmic reticulum (ER) and Golgi resident type II membrane proteins. As such, producing large quantities of properly folded and active enzymes for X-ray crystallographic analysis is a challenge. Described here are the methods that we have developed to facilitate the structural characterization of these enzymes. The approach involves the production of a soluble Protein A-tagged form of the catalytic domain in a mammalian cell expression system. Production is scaled up in a perfusion-fed bioreactor with media flow rates of 3-5 liters/day. Expression levels are typically in the 1- to 4-mg/liter range and a simple and efficient purification method based on immunoglobulin G (IgG)-Sepharose affinity chromatography has been developed. Our approach to delimiting the catalytic domain and deglycosylating it when necessary is also discussed. Finally, we describe the selenomethionine labeling protocol used in our X-ray crystal structure determination of leukocyte-type Core 2 beta1,6-N-acetylglucosaminyltransferase.
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Affiliation(s)
- John E Pak
- Department of Molecular and Medical Genetics, University of Toronto, Ontario, Canada
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Chen CY, Cheng CH, Chen YC, Lee JC, Chou SH, Huang W, Chuang WJ. Preparation of amino-acid-type selective isotope labeling of protein expressed in Pichia pastoris. Proteins 2005; 62:279-87. [PMID: 16283643 DOI: 10.1002/prot.20742] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We report the culture conditions for successful amino-acid-type selective (AATS) isotope labeling of protein expressed in Pichia pastoris (P. pastoris). Rhodostomin (Rho), a six disulfide-bonded protein expressed in P. pastoris with the correct fold, was used to optimize the culture conditions. The concentrations of [alpha-15N] selective amino acid, nonlabeled amino acids, and ammonium chloride, as well as induction time, were optimized to avoid scrambling and to increase the incorporation rate and protein yield. The optimized protocol was successfully applied to produce AATS isotope-labeled Rho. The labeling of [alpha-15N]Cys has a 50% incorporation rate, and all 12 cysteine resonances were observed in HSQC spectrum. The labeling of [alpha-15N]Leu, -Lys, and -Met amino acids has an incorporation rate greater than 65%, and the expected number of resonances in the HSQC spectra were observed. In contrast, the labeling of [alpha-15N]Asp and -Gly amino acids has a low incorporation rate and the scrambling problem. In addition, the culture condition was successfully applied to label dendroaspin (Den), a four disulfide-bonded protein expressed in P. pastoris. Therefore, the described condition should be generally applicable to other proteins produced in the P. pastoris expression system. This is the first report to present a protocol for AATS isotope labeling of protein expressed in P. pastoris for NMR study.
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Affiliation(s)
- Chiu-Yueh Chen
- Department of Biochemistry and Institute of Basic Medical Science, National Cheng Kung University College of Medicine, Tainan 701, Taiwan
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25
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Laurila MRL, Salgado PS, Makeyev EV, Nettelship J, Stuart DI, Grimes JM, Bamford DH. Gene silencing pathway RNA-dependent RNA polymerase of Neurospora crassa: yeast expression and crystallization of selenomethionated QDE-1 protein. J Struct Biol 2005; 149:111-5. [PMID: 15629662 DOI: 10.1016/j.jsb.2004.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Revised: 10/01/2004] [Indexed: 11/18/2022]
Abstract
The RNA-dependent RNA polymerase, QDE-1, is a component of the RNA silencing pathway in Neurospora crassa. The enzymatically active carboxy-terminal fragment QDE-1 DeltaN has been expressed in Saccharomyces cerevisiae in the presence and absence of selenomethionine (SeMet). The level of SeMet incorporation was estimated by mass spectrometry to be approximately 98%. Both native and SeMet proteins were crystallized in space group P2(1) with unit cell parameters a=101.2, b=122.5, c=114.4A, beta=108.9 degrees , and 2 molecules per asymmetric unit. The native and SeMet crystals diffract to 2.3 and 3.2A, respectively, the latter are suitable for MAD structure determination.
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Affiliation(s)
- Minni R L Laurila
- Institute of Biotechnology, Faculty of Biosciences, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 5, 00014 Helsinki, Finland
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26
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Folschweiller N, Pacaud K, Celia H, Potier N, Cobessi D, Van Dorsselaer A, Pattus F. In vivo incorporation of selenomethionine in proteins using Pseudomonas aeruginosa as expression host: case study—the outer membrane receptor FpvA. Protein Expr Purif 2004; 38:79-83. [PMID: 15477085 DOI: 10.1016/j.pep.2004.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2004] [Revised: 07/24/2004] [Indexed: 11/23/2022]
Abstract
The number of protein structures solved using multiwavelength anomalous diffraction methods coupled with selenomethionine substitution has grown dramatically over the last years. We show using the outer membrane pyoverdin receptor FpvA that Pseudomonas aeruginosa can be used for producing proteins with a high level of selenomethionine incorporation. To circumvent problems encountered with mass spectroscopy analysis of purified membrane proteins, in-gel trypsin digestion of FpvA coupled with MALDI mass spectrometry analysis of the resulting peptides was used to determine the extent of selenomethionine incorporation. Selenomethionine incorporation greater than 95% was achieved using P. aeruginosa as an overexpression system.
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Affiliation(s)
- Nicolas Folschweiller
- Récepteurs et Protéines Membranaires, UPR CNRS 9050, BP10413, F-67412 Illkirch, France
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27
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Strub MP, Hoh F, Sanchez JF, Strub JM, Böck A, Aumelas A, Dumas C. Selenomethionine and selenocysteine double labeling strategy for crystallographic phasing. Structure 2004; 11:1359-67. [PMID: 14604526 DOI: 10.1016/j.str.2003.09.014] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A protocol for the quantitative incorporation of both selenomethionine and selenocysteine into recombinant proteins overexpressed in Escherichia coli is described. This methodology is based on the use of a suitable cysteine auxotrophic strain and a minimal medium supplemented with selenium-labeled methionine and cysteine. The proteins chosen for these studies are the cathelin-like motif of protegrin-3 and a nucleoside-diphosphate kinase. Analysis of the purified proteins by electrospray mass spectrometry and X-ray crystallography revealed that both cysteine and methionine residues were isomorphously replaced by selenocysteine and selenomethionine. Moreover, selenocysteines allowed the formation of unstrained and stable diselenide bridges in place of the canonical disulfide bonds. In addition, we showed that NDP kinase contains a selenocysteine adduct on Cys122. This novel selenium double-labeling method is proposed as a general approach to increase the efficiency of the MAD technique used for phase determination in protein crystallography.
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Affiliation(s)
- Marie Paule Strub
- Centre de Biochimie Structurale, UMR CNRS 5048, UMR 554 INSERM, Université Montpellier I, 34090 Cedex, Montpellier, France
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28
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Affiliation(s)
- Patrick Cramer
- Institute of Biochemistry and Gene Center, University of Munich, 81377 Munich, Germany
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29
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Abstract
Transcription of the genetic information in all cells is carried out by multisubunit RNA polymerases (RNAPs). Comparison of the crystal structures of a bacterial and a eukaryotic RNAP reveals a conserved core that comprises the active site and a multifunctional clamp. Together with a further structure of eukaryotic RNAP bound to DNA and RNA, these results elucidate many aspects of the transcription mechanism, including initiation, elongation, nucleotide addition, processivity and proofreading.
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Affiliation(s)
- Patrick Cramer
- Institute of Biochemistry, Gene Center, University of Munich, Feodor-Lynen-Strasse 25, 81377, Munich, Germany.
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30
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Current awareness on yeast. Yeast 2001; 18:1269-76. [PMID: 11561294 DOI: 10.1002/yea.689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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31
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Heinemann U, Illing G, Oschkinat H. High-throughput three-dimensional protein structure determination. Curr Opin Biotechnol 2001; 12:348-54. [PMID: 11551462 DOI: 10.1016/s0958-1669(00)00226-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the wake of finished genomic sequencing projects, high-throughput analysis techniques are being developed in various fields of functional genomics. Of special interest in this regard is the three-dimensional structure analysis of proteins by X-ray crystallography and NMR spectroscopy, which has been characterized by distinctly low-throughput in the past. A number of recent advances in instrumentation and software are promising to radically change this situation, leaving the production of suitable protein samples as the sole rate-limiting step in structural analyses.
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Affiliation(s)
- U Heinemann
- Forschungsgruppe Kristallographie, Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, D-13125 Berlin, Germany.
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32
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Cramer P, Bushnell DA, Kornberg RD. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 2001; 292:1863-76. [PMID: 11313498 DOI: 10.1126/science.1059493] [Citation(s) in RCA: 933] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Structures of a 10-subunit yeast RNA polymerase II have been derived from two crystal forms at 2.8 and 3.1 angstrom resolution. Comparison of the structures reveals a division of the polymerase into four mobile modules, including a clamp, shown previously to swing over the active center. In the 2.8 angstrom structure, the clamp is in an open state, allowing entry of straight promoter DNA for the initiation of transcription. Three loops extending from the clamp may play roles in RNA unwinding and DNA rewinding during transcription. A 2.8 angstrom difference Fourier map reveals two metal ions at the active site, one persistently bound and the other possibly exchangeable during RNA synthesis. The results also provide evidence for RNA exit in the vicinity of the carboxyl-terminal repeat domain, coupling synthesis to RNA processing by enzymes bound to this domain.
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MESH Headings
- Amino Acid Sequence
- Binding Sites
- Conserved Sequence
- Crystallography, X-Ray
- DNA, Fungal/chemistry
- DNA, Fungal/metabolism
- Fourier Analysis
- Hydrogen Bonding
- Magnesium/metabolism
- Metals/metabolism
- Models, Molecular
- Molecular Sequence Data
- Promoter Regions, Genetic
- Protein Conformation
- Protein Structure, Quaternary
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Protein Subunits
- RNA Polymerase II/chemistry
- RNA Polymerase II/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Fungal/biosynthesis
- RNA, Fungal/chemistry
- RNA, Fungal/metabolism
- RNA, Messenger/biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
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Affiliation(s)
- P Cramer
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
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