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Gregorio NE, Levine MZ, Oza JP. A User's Guide to Cell-Free Protein Synthesis. Methods Protoc 2019; 2:E24. [PMID: 31164605 PMCID: PMC6481089 DOI: 10.3390/mps2010024] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 02/06/2023] Open
Abstract
Cell-free protein synthesis (CFPS) is a platform technology that provides new opportunities for protein expression, metabolic engineering, therapeutic development, education, and more. The advantages of CFPS over in vivo protein expression include its open system, the elimination of reliance on living cells, and the ability to focus all system energy on production of the protein of interest. Over the last 60 years, the CFPS platform has grown and diversified greatly, and it continues to evolve today. Both new applications and new types of extracts based on a variety of organisms are current areas of development. However, new users interested in CFPS may find it challenging to implement a cell-free platform in their laboratory due to the technical and functional considerations involved in choosing and executing a platform that best suits their needs. Here we hope to reduce this barrier to implementing CFPS by clarifying the similarities and differences amongst cell-free platforms, highlighting the various applications that have been accomplished in each of them, and detailing the main methodological and instrumental requirement for their preparation. Additionally, this review will help to contextualize the landscape of work that has been done using CFPS and showcase the diversity of applications that it enables.
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Affiliation(s)
- Nicole E Gregorio
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
| | - Max Z Levine
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
| | - Javin P Oza
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
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2
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Alhmidi H, John A, Mana TC, Koganti S, Cadnum JL, Shelton MB, Donskey CJ. Evaluation of Viral Surrogate Markers for Study of Pathogen Dissemination During Simulations of Patient Care. Open Forum Infect Dis 2017; 4:ofx128. [PMID: 28752103 DOI: 10.1093/ofid/ofx128] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/16/2017] [Indexed: 11/12/2022] Open
Abstract
During patient care simulations, cauliflower mosaic virus DNA and bacteriophage MS2 performed similarly as surrogate markers of pathogen dissemination. These markers disseminated to the environment in a manner similar to Clostridium difficile spores but were more frequently detected on skin and clothing of personnel after personal protective equipment removal.
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Affiliation(s)
| | - Amrita John
- Geriatric Research, Education and Clinical Center, Louis Stokes Veterans Affairs Medical Center.,Department of Medicine, Division of Infectious Diseases and HIV Medicine, University Hospitals Case Medical Center, and
| | | | | | | | - Melissa B Shelton
- Research Service, and.,Department of Medicine, Division of Infectious Diseases and HIV Medicine, University Hospitals Case Medical Center, and
| | - Curtis J Donskey
- Geriatric Research, Education and Clinical Center, Louis Stokes Veterans Affairs Medical Center.,Case Western Reserve University School of Medicine, Cleveland, Ohio
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3
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Austin RS, Hiu S, Waese J, Ierullo M, Pasha A, Wang TT, Fan J, Foong C, Breit R, Desveaux D, Moses A, Provart NJ. New BAR tools for mining expression data and exploring Cis-elements in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:490-504. [PMID: 27401965 DOI: 10.1111/tpj.13261] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/23/2016] [Accepted: 07/01/2016] [Indexed: 05/21/2023]
Abstract
Identifying sets of genes that are specifically expressed in certain tissues or in response to an environmental stimulus is useful for designing reporter constructs, generating gene expression markers, or for understanding gene regulatory networks. We have developed an easy-to-use online tool for defining a desired expression profile (a modification of our Expression Angler program), which can then be used to identify genes exhibiting patterns of expression that match this profile as closely as possible. Further, we have developed another online tool, Cistome, for predicting or exploring cis-elements in the promoters of sets of co-expressed genes identified by such a method, or by other methods. We present two use cases for these tools, which are freely available on the Bio-Analytic Resource at http://BAR.utoronto.ca.
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Affiliation(s)
- Ryan S Austin
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Shu Hiu
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jamie Waese
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Matthew Ierullo
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Ting Ting Wang
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jim Fan
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Curtis Foong
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Robert Breit
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Darrell Desveaux
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Alan Moses
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
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Hadfield J, Linderme D, Shepherd DN, Bezuidenhout M, Lefeuvre P, Martin DP, Varsani A. Complete genome sequence of a dahlia common mosaic virus isolate from New Zealand. Arch Virol 2011; 156:2297-301. [DOI: 10.1007/s00705-011-1112-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 09/12/2011] [Indexed: 10/17/2022]
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5
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Shinozaki A, Sato N, Hayashi Y. Peroxisomal targeting signals in green algae. PROTOPLASMA 2009; 235:57-66. [PMID: 19214701 DOI: 10.1007/s00709-009-0031-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 01/05/2009] [Indexed: 05/27/2023]
Abstract
Peroxisomal enzymatic proteins contain targeting signals (PTS) to enable their import into peroxisomes. These targeting signals have been identified as PTS1 and PTS2 in mammalian, yeast, and higher plant cells; however, no PTS2-like amino acid sequences have been observed in enzymes from the genome database of Cyanidiochyzon merolae (Bangiophyceae), a primitive red algae. In studies on the evolution of PTS, it is important to know when their sequences came to be the peroxisomal targeting signals for all living organisms. To this end, we identified a number of genes in the genome database of the green algae Chlamydomonas reinhardtii, which contains amino acid sequences similar to those found in plant PTS. In order to determine whether these sequences function as PTS in green algae, we expressed modified green fluorescent proteins (GFP) fused to these putative PTS peptides under the cauliflower mosaic virus 35S promoter. To confirm whether granular structures containing GFP-PTS fusion proteins accumulated in the peroxisomes of Closterium ehrenbergii, we observed these cells after the peroxisomes were stained with 3, 3'-diaminobenzidine. Our results confirm that the GFP-PTS fusion proteins indeed accumulated in the peroxisomes of these green algae. These findings suggest that the peroxisomal transport system for PTS1 and PTS2 is conserved in green algal cells and that our fusion proteins can be used to visualize peroxisomes in live cells.
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Affiliation(s)
- Akiko Shinozaki
- Graduate School of Science and Technology, Niigata University, 8050 Ikarashi, Ninotyou, Niigata city, Niigata, 950-2181, Japan
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Tepfer M, Gaubert S, Leroux-Coyau M, Prince S, Houdebine LM. Transient expression in mammalian cells of transgenes transcribed from theCauliflower mosaic virus35S promoter. ACTA ACUST UNITED AC 2004; 3:91-7. [PMID: 15612506 DOI: 10.1051/ebr:2004010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Gene constructs containing the Cauliflower mosaic virus (CaMV) 35S promoter and a sequence coding either for a green fluorescent protein (GFP) or for firefly luciferase were transfected into Chinese hamster ovary (CHO) cells. Both reporter genes were expressed to significant levels. The 35S promoter was 40 times less active than the human eF1 alpha promoter, which is known to be one of the most potent promoters in mammalian cells. The 35S promoter must therefore be considered to be a promoter of significant potency in mammalian cells. RT-PCR analysis suggested that transcription initiation in CHO cells occurred between the TATA box and the transcription start site of the 35S promoter that function in plant cells. Further analysis by 5'RACE confirmed that transcription was initiated in CHO cells at different sites located essentially between the TATA box and the plant transcription start site, showing that 35S promoter activity in animal cells is due to the presence of promoter elements that are functional in mammalian cells, but that are not those used in plants. The data reported here raise the possibility that genes controlled by the 35S promoter, which is commonly used in transgenic plants, have the potential for expression in animal cells.
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Affiliation(s)
- Mark Tepfer
- Laboratoire de Biologie Cellulaire, INRA-Versailles, 78026 Versailles Cedex, France.
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Shi BJ, Palukaitis P, Symons RH. Stable and unstable mutations in the 5' non-translated regions of tomato aspermy virus RNAs 1 and 2 generated de novo from infectious cDNA clones containing a cauliflower mosaic virus 35S promoter. Virus Genes 2004; 28:277-83. [PMID: 15266109 DOI: 10.1023/b:viru.0000025775.20862.50] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Tomato aspermy virus RNAs derived from infectious cDNA clones exhibited a number of sequence alterations in the 5' non-translated region (NTR). These included a deletion of the first four residues in both RNAs 1 and 2, transversion of residue 5 from a G to a U in RNA 1, and transversion of A to C at position of 50 of RNA 1. These alterations were not stable in the infected plants while the insertion of a U residue between nucleotides 1 and 5 of RNA 1 was stable in the infected plants. Generation of these sequence alternations was not dependent upon either the host species or the concentration of the inoculum. The sequence alterations also did not occur on passage of wildtype virus. Rather, the sequence alterations related to transcription from the cauliflower mosaic virus 35S RNA promoter-driving infectious cDNAs. The alternations observed had no impact on symptoms or infectivity, but did affect the accumulation of specific viral RNAs. The data also demonstrated the existence of some plasticity in the sequence of the 5' NTR.
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Affiliation(s)
- Bu-Jun Shi
- Department of Plant Science, Waite Institute, Adelaide University, Glen Osmond, SA 5064, Australia
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Abstract
▪ Abstract In vitro transcription systems provide a powerful tool for detailed analysis of transcription reactions including initiation, elongation, and termination. Despite problems inherent to plant cells, efforts have been made to develop plant in vitro transcription systems in the past decade. These efforts have finally culminated in the development of reliable in vitro systems from suspension-cell cultures of both monocot and dicot plants. These systems can be useful in elucidating the specific mechanisms involved in the process of plant transcription and thus can potentially open a new era of transcription studies in plants.
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Affiliation(s)
- Masahiro Sugiura
- Center for Gene Research, Nagoya University, Nagoya, 464-01, Japan
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Schweizer P, Mösinger E. Initiator-dependent transcription in vitro by a wheat germ chromatin extract. PLANT MOLECULAR BIOLOGY 1994; 25:115-130. [PMID: 8003692 DOI: 10.1007/bf00024203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The development of plant in vitro transcription systems transcribing faithfully and efficiently from a broad range of plant nuclear promoters has remained a challenge. We examined the nucleotide sequence requirements for faithful and efficient transcription in a wheat germ chromatin extract (Yamazaki et al., Plant Mol Biol Rep 8: 114-123). The wheat germ chromatin extract was tested with a series of chimeric promoter constructs containing plant promoter sequences upstream from the TATA box, TATA boxes, and cap-site sequences (from -10 to +14, relative to the major in vivo initiation site) in different combinations. The plant extract transcribed faithfully from several chimeric promoters containing the capsite sequence of the parsley chalcone synthase promoter. The transcription was sensitive to the RNA polymerase II-specific inhibitor alpha-amanitin and was only dependent on the chalcone synthase cap-site sequence which therefore fulfils the operational criteria for a plant initiator element. Mutations of the putative chalcone synthase initiator element defined a core sequence '5'TAACAAC' around the initiation site that was necessary for efficient transcription in vitro. In contrast to the extract, purified wheat germ RNA polymerase II showed no preference for transcription from the major chalcone synthase in vivo initiation site.
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Affiliation(s)
- P Schweizer
- Sandoz Agro Ltd., Agrobiological Research Station, Witterswil, Switzerland
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Affiliation(s)
- P Schweizer
- Institute de Biologie Végétale, Université de Fribourg, Switzerland
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Hohn T, Fütterer J. Transcriptional and translational control of gene expression in cauliflower mosaic virus. Curr Opin Genet Dev 1992; 2:90-6. [PMID: 1633431 DOI: 10.1016/s0959-437x(05)80328-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cauliflower mosaic virus sequences have developed as a powerful tool for the study of various aspects of gene expression in plants. Analysis of the promoter/enhancer region has led to the discovery of several transcription factors and factor-binding sites. Studies on RNA processing and polyadenylation reveal a viral strategy to obtain terminal redundancy of retrovirus pregenomic RNA. Striking differences between plant and vertebrate polyadenylation signals have been disclosed. The mechanisms for translation of the polycistronic 35S RNA are novel in the eukaryotic field and may give new insight to translational control in general.
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Affiliation(s)
- T Hohn
- Friedrich-Miescher-Institute, Basel, Switzerland
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12
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Gustavsson HO, Rask L, Josefsson LG. Transcription in vitro of a napin gene, napA, from Brassica napus with a HeLa cell nuclear extract. Hereditas 1991; 115:191-3. [PMID: 1810908 DOI: 10.1111/j.1601-5223.1991.tb03555.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- H O Gustavsson
- Department of Cell Research, Swedish University of Agricultural Sciences, Uppsala
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Verdier JM, Stalder R, Roberge M, Amati B, Sentenac A, Gasser SM. Preparation and characterization of yeast nuclear extracts for efficient RNA polymerase B (II)-dependent transcription in vitro. Nucleic Acids Res 1990; 18:7033-9. [PMID: 2263463 PMCID: PMC332766 DOI: 10.1093/nar/18.23.7033] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We present a reproducible method for the preparation of nuclear extracts from the yeast Saccharomyces cerevisiae that support efficient RNA polymerase B (II)-dependent transcription. Extracts from both a crude nuclear fraction and Percoll-purified nuclei are highly active for site-specific initiation and transcription of a G-free cassette under the Adenovirus major late promoter. At optimal extract concentrations transcription is at least 5 times more efficient with the yeast extracts than with HeLa whole cell extracts. We show that the transcriptional activity is sensitive to alpha-amanitin and to depletion of factor(s) recognizing the TATA-box of the promoter. The in vitro reaction showed maximal activity after 45 min, was very sensitive to Cl-, but was not affected by high concentrations of potassium. We find that the efficiency of in vitro transcription in nuclear extracts is reproducibly high when spheroplasting is performed with a partially purified beta 1,3-glucanase (lyticase). Therefore a simplified method to isolate the lyticase from the supernatant of Oerskovia xanthineolytica is also presented.
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Affiliation(s)
- J M Verdier
- Centre d'Etudes Nucléaires de Saclay, Service de Biochimie, Gif-sur-Yvette, France
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Burke C, Yu XB, Marchitelli L, Davis EA, Ackerman S. Transcription factor IIA of wheat and human function similarly with plant and animal viral promoters. Nucleic Acids Res 1990; 18:3611-20. [PMID: 2362810 PMCID: PMC331017 DOI: 10.1093/nar/18.12.3611] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Eucaryotic transcription initiation by RNA polymerase II involves protein:DNA interactions during the formation of a transcription complex. In addition to RNA polymerase II there are at least five other general transcription factors necessary for initiation with the adenovirus major late promoter. One of these, TFIIA, is involved in the earliest events during transcription complex assembly. We have purified TFIIA from wheat germ and characterized it in an in vitro transcription system. Wheat TFIIA is a single polypeptide of Mr approximately 35 kd which functionally replaces human (HeLa) TFIIA to form a wheat/HeLa transcription system. [This polypeptide can be eluted from a SDS-polyacrylamide gel, refolded to a native conformation, and will function as wheat TFIIA in the heterologous system.] The heterologous system requires a lower optimal incubation temperature than the HeLa system. Biochemical characterization, using the adenovirus major late promoter, indicates that transcription reaction parameters for both wheat and HeLa TFIIA are similar but the kinetics of transcription for both TFIIAs are somewhat dissimilar. A plant viral promoter, the cauliflower mosaic virus 35S promoter, accurately and efficiently directs in vitro transcription in both the wheat/HeLa and HeLa systems with identical transcription kinetics. We conclude that TFIIA function has been conserved during evolution.
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Affiliation(s)
- C Burke
- Biology Department, University of Massachusetts, Boston, MA 02125
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