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Wang Y, Wang T, Chen X, Lu Y. IRES-mediated Pichia pastoris cell-free protein synthesis. BIORESOUR BIOPROCESS 2023; 10:35. [PMID: 38647944 PMCID: PMC10992869 DOI: 10.1186/s40643-023-00653-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/15/2023] [Indexed: 04/25/2024] Open
Abstract
Cell-free protein synthesis (CFPS) system is an ideal platform for fast and convenient protein research and has been used for macromolecular assembly, unnatural amino acid embedding, glycoprotein production, and more. To realize the construction of an efficient eukaryotic CFPS platform with the advantages of low cost and short time, a CFPS system based on the yeast Pichia pastoris was built in this study. The internal ribosomal entry site (IRES) can independently initiate translation and thus promote protein synthesis. The Kozak sequences can facilitate translation initiation. Therefore, the screening of IRES and its combination with Kozak was performed, in which cricket paralysis virus (CRPV) exhibited as the best translation initiation element from 14 different IRESs. Furthermore, the system components and reaction environment were explored. The protein yield was nearly doubled by the addition of RNase inhibitor. The cell extract amount, energy regeneration system (phosphocreatine and phosphocreatine kinase), and metal ions (K+ and Mg2+) were optimized to achieve the best protein synthesis yield. This P. pastoris CFPS system can extend the eukaryotic CFPS platform, providing an enabling technology for fast prototyping design and functional protein synthesis.
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Affiliation(s)
- Yanan Wang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Ting Wang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xinjie Chen
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China.
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China.
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Gurramkonda C, Rao A, Borhani S, Pilli M, Deldari S, Ge X, Pezeshk N, Han TC, Tolosa M, Kostov Y, Tolosa L, Wood DW, Vattem K, Frey DD, Rao G. Improving the recombinant human erythropoietin glycosylation using microsome supplementation in CHO cell-free system. Biotechnol Bioeng 2018; 115:1253-1264. [PMID: 29384203 DOI: 10.1002/bit.26554] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 11/28/2017] [Accepted: 01/22/2018] [Indexed: 12/19/2022]
Abstract
Cell-Free Protein Synthesis (CFPS) offers many advantages for the production of recombinant therapeutic proteins using the CHO cell-free system. However, many complex proteins are still difficult to express using this method. To investigate the current bottlenecks in cell-free glycoprotein production, we chose erythropoietin (40% glycosylated), an essential endogenous hormone which stimulates the development of red blood cells. Here, we report the production of recombinant erythropoietin (EPO) using CHO cell-free system. Using this method, EPO was expressed and purified with a twofold increase in yield when the cell-free reaction was supplemented with CHO microsomes. The protein was purified to near homogeneity using an ion-metal affinity column. We were able to analyze the expressed and purified products (glycosylated cell-free EPO runs at 25-28 kDa, and unglycosylated protein runs at 20 kDa on an SDS-PAGE), identifying the presence of glycan moieties by PNGase shift assay. The purified protein was predicted to have ∼2,300 IU in vitro activity. Additionally, we tested the presence and absence of sugars on the cell-free EPO using a lectin-based assay system. The results obtained in this study indicate that microsomes augmented in vitro production of the glycoprotein is useful for the rapid production of single doses of a therapeutic glycoprotein drug and to rapidly screen glycoprotein constructs in the development of these types of drugs. CFPS is useful for implementing a lectin-based method for rapid screening and detection of glycan moieties, which is a critical quality attribute in the industrial production of therapeutic glycoproteins.
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Affiliation(s)
- Chandrasekhar Gurramkonda
- Center for Advanced Sensor Technology (CAST) and Department of Chemical Biochemical and Environmental Engineering (CBEE), University of Maryland Baltimore County, Baltimore, Maryland
| | - Aniruddha Rao
- Center for Advanced Sensor Technology (CAST) and Department of Chemical Biochemical and Environmental Engineering (CBEE), University of Maryland Baltimore County, Baltimore, Maryland
| | - Shayan Borhani
- Center for Advanced Sensor Technology (CAST) and Department of Chemical Biochemical and Environmental Engineering (CBEE), University of Maryland Baltimore County, Baltimore, Maryland
| | - Manohar Pilli
- Center for Advanced Sensor Technology (CAST) and Department of Chemical Biochemical and Environmental Engineering (CBEE), University of Maryland Baltimore County, Baltimore, Maryland
| | - Sevda Deldari
- Center for Advanced Sensor Technology (CAST) and Department of Chemical Biochemical and Environmental Engineering (CBEE), University of Maryland Baltimore County, Baltimore, Maryland
| | - Xudong Ge
- Center for Advanced Sensor Technology (CAST) and Department of Chemical Biochemical and Environmental Engineering (CBEE), University of Maryland Baltimore County, Baltimore, Maryland
| | - Niloufar Pezeshk
- Center for Advanced Sensor Technology (CAST) and Department of Chemical Biochemical and Environmental Engineering (CBEE), University of Maryland Baltimore County, Baltimore, Maryland
| | - Tzu-Chiang Han
- Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, Ohio
| | - Michael Tolosa
- Center for Advanced Sensor Technology (CAST) and Department of Chemical Biochemical and Environmental Engineering (CBEE), University of Maryland Baltimore County, Baltimore, Maryland
| | - Yordan Kostov
- Center for Advanced Sensor Technology (CAST) and Department of Chemical Biochemical and Environmental Engineering (CBEE), University of Maryland Baltimore County, Baltimore, Maryland
| | - Leah Tolosa
- Center for Advanced Sensor Technology (CAST) and Department of Chemical Biochemical and Environmental Engineering (CBEE), University of Maryland Baltimore County, Baltimore, Maryland
| | - David W Wood
- Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, Ohio
| | | | - Douglas D Frey
- Center for Advanced Sensor Technology (CAST) and Department of Chemical Biochemical and Environmental Engineering (CBEE), University of Maryland Baltimore County, Baltimore, Maryland
| | - Govind Rao
- Center for Advanced Sensor Technology (CAST) and Department of Chemical Biochemical and Environmental Engineering (CBEE), University of Maryland Baltimore County, Baltimore, Maryland
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Tran K, Gurramkonda C, Cooper MA, Pilli M, Taris JE, Selock N, Han T, Tolosa M, Zuber A, Peñalber‐Johnstone C, Dinkins C, Pezeshk N, Kostov Y, Frey DD, Tolosa L, Wood DW, Rao G. Cell‐free production of a therapeutic protein: Expression, purification, and characterization of recombinant streptokinase using a CHO lysate. Biotechnol Bioeng 2017; 115:92-102. [DOI: 10.1002/bit.26439] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/09/2017] [Accepted: 08/21/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Kevin Tran
- Center for Advanced Sensor TechnologyUniversity of Maryland Baltimore CountyBaltimoreMaryland
| | | | - Merideth A. Cooper
- Department of Chemical and Biomolecular EngineeringOhio State UniversityColumbusOhio
| | - Manohar Pilli
- Center for Advanced Sensor TechnologyUniversity of Maryland Baltimore CountyBaltimoreMaryland
| | - Joseph E. Taris
- Department of Chemical and Biomolecular EngineeringOhio State UniversityColumbusOhio
| | - Nicholas Selock
- Center for Advanced Sensor TechnologyUniversity of Maryland Baltimore CountyBaltimoreMaryland
| | - Tzu‐Chiang Han
- Department of Chemical and Biomolecular EngineeringOhio State UniversityColumbusOhio
| | - Michael Tolosa
- Center for Advanced Sensor TechnologyUniversity of Maryland Baltimore CountyBaltimoreMaryland
| | - Adil Zuber
- Center for Advanced Sensor TechnologyUniversity of Maryland Baltimore CountyBaltimoreMaryland
| | | | - Christina Dinkins
- Center for Advanced Sensor TechnologyUniversity of Maryland Baltimore CountyBaltimoreMaryland
| | - Niloufar Pezeshk
- Center for Advanced Sensor TechnologyUniversity of Maryland Baltimore CountyBaltimoreMaryland
| | - Yordan Kostov
- Center for Advanced Sensor TechnologyUniversity of Maryland Baltimore CountyBaltimoreMaryland
| | - Douglas D. Frey
- Center for Advanced Sensor TechnologyUniversity of Maryland Baltimore CountyBaltimoreMaryland
| | - Leah Tolosa
- Center for Advanced Sensor TechnologyUniversity of Maryland Baltimore CountyBaltimoreMaryland
| | - David W. Wood
- Department of Chemical and Biomolecular EngineeringOhio State UniversityColumbusOhio
| | - Govind Rao
- Center for Advanced Sensor TechnologyUniversity of Maryland Baltimore CountyBaltimoreMaryland
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Wong TY, Schwartzbach SD. Protein Mis-Termination Initiates Genetic Diseases, Cancers, and Restricts Bacterial Genome Expansion. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2015; 33:255-285. [PMID: 26087060 DOI: 10.1080/10590501.2015.1053461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein termination is an important cellular process. Protein termination relies on the stop-codons in the mRNA interacting properly with the releasing factors on the ribosome. One third of inherited diseases, including cancers, are associated with the mutation of the stop-codons. Many pathogens and viruses are able to manipulate their stop-codons to express their virulence. The influence of stop-codons is not limited to the primary reading frame of the genes. Stop-codons in the second and third reading frames are referred as premature stop signals (PSC). Stop-codons and PSCs together are collectively referred as stop-signals. The ratios of the stop-signals (referred as translation stop-signals ratio or TSSR) of genetically related bacteria, despite their great differences in gene contents, are much alike. This nearly identical Genomic-TSSR value of genetically related bacteria may suggest that bacterial genome expansion is limited by their unique stop-signals bias. We review the protein termination process and the different types of stop-codon mutation in plants, animals, microbes, and viruses, with special emphasis on the role of PSCs in directing bacterial evolution in their natural environments. Knowing the limit of genomic boundary could facilitate the formulation of new strategies in controlling the spread of diseases and combat antibiotic-resistant bacteria.
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Affiliation(s)
- Tit-Yee Wong
- a Department of Biological Sciences , University of Memphis , Memphis , Tennessee , USA
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Lyophilized Escherichia coli-based cell-free systems for robust, high-density, long-term storage. Biotechniques 2014; 56:186-93. [DOI: 10.2144/000114158] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/03/2014] [Indexed: 11/23/2022] Open
Abstract
Cell-free protein synthesis (CFPS) is a versatile tool for rapid recombinant protein production and engineering. One drawback of cell-free technology is the necessity to store the major components—cell extracts and energy systems—below freezing in bulky aqueous solutions. Here we describe simple methods for lyophilizing extracts and preparing powdered energy systems for CFPS. These techniques allow for high-density storage of cell-free systems that are more robust against temperature and bacterial degradation. Our methods have the potential to decrease storage expenses, allow for longer shelf-life of cell extracts at room temperature, and enable durable portable protein production technologies.
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Shrestha P, Smith MT, Bundy BC. Cell-free unnatural amino acid incorporation with alternative energy systems and linear expression templates. N Biotechnol 2013; 31:28-34. [PMID: 24103470 DOI: 10.1016/j.nbt.2013.09.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 09/17/2013] [Accepted: 09/27/2013] [Indexed: 01/12/2023]
Abstract
Site-specific incorporation of unnatural amino acids (uAAs) during protein synthesis expands the proteomic code through the addition of unique residue chemistry. This field provides a unique tool to improve pharmacokinetics, cancer treatments, vaccine development, proteomics and protein engineering. The limited ability to predict the characteristics of proteins with uAA-incorporation creates a need for a low-cost system with the potential for rapid screening. Escherichia coli-based cell-free protein synthesis is a compelling platform for uAA incorporation due to the open and accessible nature of the reaction environment. However, typical cell-free systems can be expensive due to the high cost of energizing reagents. By employing alternative energy sources, we reduce the cost of uAA-incorporation in CFPS by 55%. While alternative energy systems reduce cost, the time investment to develop gene libraries can remain cumbersome. Cell-free systems allow the direct use of PCR products known as linear expression templates, thus alleviating tedious plasmid library preparations steps. We report the specific costs of CFPS with uAA incorporation, demonstrate that LETs are suitable expression templates with uAA-incorporation, and consider the substantial reduction in labor intensity using LET-based expression for CFPS uAA incorporation.
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Affiliation(s)
- Prashanta Shrestha
- Department of Chemical Engineering, Brigham Young University, 350 Clyde Building, Provo, UT 84602, USA
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Ahn JH, Keum JW, Kim DM. Expression screening of fusion partners from an E. coli genome for soluble expression of recombinant proteins in a cell-free protein synthesis system. PLoS One 2011; 6:e26875. [PMID: 22073212 PMCID: PMC3206877 DOI: 10.1371/journal.pone.0026875] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Accepted: 10/05/2011] [Indexed: 12/04/2022] Open
Abstract
While access to soluble recombinant proteins is essential for a number of proteome studies, preparation of purified functional proteins is often limited by the protein solubility. In this study, potent solubility-enhancing fusion partners were screened from the repertoire of endogenous E. coli proteins. Based on the presumed correlation between the intracellular abundance and folding efficiency of proteins, PCR-amplified ORFs of a series of highly abundant E. coli proteins were fused with aggregation-prone heterologous proteins and then directly expressed for quantitative estimation of the expression efficiency of soluble translation products. Through two-step screening procedures involving the expression of 552 fusion constructs targeted against a series of cytokine proteins, we were able to discover a number of endogenous E. coli proteins that dramatically enhanced the soluble expression of the target proteins. This strategy of cell-free expression screening can be extended to quantitative, global analysis of genomic resources for various purposes.
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Affiliation(s)
- Jin-Ho Ahn
- Department of Fine Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Jung-Won Keum
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
| | - Dong-Myung Kim
- Department of Fine Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, Republic of Korea
- * E-mail:
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Ahn JH, Kang TJ, Kim DM. Tuning the expression level of recombinant proteins by modulating mRNA stability in a cell-free protein synthesis system. Biotechnol Bioeng 2008; 101:422-7. [DOI: 10.1002/bit.21884] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Ahn JH, Keum JW, Kim DM. High-Throughput, Combinatorial Engineering of Initial Codons for Tunable Expression of Recombinant Proteins. J Proteome Res 2008; 7:2107-13. [DOI: 10.1021/pr700856s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jin-Ho Ahn
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 151-742, Korea, School of Chemical and Biological Engineering, Seoul National University, Seoul 151-742, Korea, and Department of Fine Chemical Engineering and Chemistry, Chungnam National University, Daejeon 305-764, Korea
| | - Jung-Won Keum
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 151-742, Korea, School of Chemical and Biological Engineering, Seoul National University, Seoul 151-742, Korea, and Department of Fine Chemical Engineering and Chemistry, Chungnam National University, Daejeon 305-764, Korea
| | - Dong-Myung Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 151-742, Korea, School of Chemical and Biological Engineering, Seoul National University, Seoul 151-742, Korea, and Department of Fine Chemical Engineering and Chemistry, Chungnam National University, Daejeon 305-764, Korea
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Ahn JH, Hwang MY, Lee KH, Choi CY, Kim DM. Use of signal sequences as an in situ removable sequence element to stimulate protein synthesis in cell-free extracts. Nucleic Acids Res 2006; 35:e21. [PMID: 17185295 PMCID: PMC1849898 DOI: 10.1093/nar/gkl917] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
This study developed a method to boost the expression of recombinant proteins in a cell-free protein synthesis system without leaving additional amino acid residues. It was found that the nucleotide sequences of the signal peptides serve as an efficient downstream box to stimulate protein synthesis when they were fused upstream of the target genes. The extent of stimulation was critically affected by the identity of the second codons of the signal sequences. Moreover, the yield of the synthesized protein was enhanced by as much as 10 times in the presence of an optimal second codon. The signal peptides were in situ cleaved and the target proteins were produced in their native sizes by carrying out the cell-free synthesis reactions in the presence of Triton X-100, most likely through the activation of signal peptidase in the S30 extract. The amplification of the template DNA and the addition of the signal sequences were accomplished by PCR. Hence, elevated levels of recombinant proteins were generated within several hours.
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Affiliation(s)
- Jin-Ho Ahn
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, College of Engineering, Seoul National UniversitySeoul 151-742, Korea
| | - Mi-Yeon Hwang
- School of Chemical and Biological Engineering, College of Engineering, Seoul National UniversitySeoul 151-742, Korea
| | - Kyung-Ho Lee
- Department of Fine Chemical Engineering and Chemistry, Chungnam National UniversityDaejeon 305-764, Korea
| | - Cha-Yong Choi
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, College of Engineering, Seoul National UniversitySeoul 151-742, Korea
- School of Chemical and Biological Engineering, College of Engineering, Seoul National UniversitySeoul 151-742, Korea
| | - Dong-Myung Kim
- Department of Fine Chemical Engineering and Chemistry, Chungnam National UniversityDaejeon 305-764, Korea
- To whom correspondence should be addressed. Tel: +82 42 821 5899; Fax: +82 42 823 7692;
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Biochemical reactions on a microfluidic chip based on a precise fluidic handling method at the nanoliter scale. BIOTECHNOL BIOPROC E 2006. [DOI: 10.1007/bf02931899] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Son JM, Ahn JH, Hwang MY, Park CG, Choi CY, Kim DM. Enhancing the efficiency of cell-free protein synthesis through the polymerase-chain-reaction-based addition of a translation enhancer sequence and the in situ removal of the extra amino acid residues. Anal Biochem 2005; 351:187-92. [PMID: 16430851 DOI: 10.1016/j.ab.2005.11.047] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2005] [Revised: 11/30/2005] [Accepted: 11/30/2005] [Indexed: 10/25/2022]
Abstract
A method for the rapid generation of intact proteins in a cell-free protein synthesis system was developed. The productivity of the recombinant proteins from the polymerase-chain-reaction-amplified templates was enhanced remarkably using an optimized translation enhancer sequence. The extra amino acid residues derived from the translation enhancer sequence were effectively removed by utilizing the appropriate detergent and peptide cleavage enzyme in the reaction mixture. These results demonstrate the versatility of cell-free protein synthesis in providing optimized and customized reaction conditions for the efficient production of the desired proteins.
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Affiliation(s)
- Jeong-Mi Son
- School of Chemical and Biological Engineering, Seoul National University, Seoul 151-742, Republic of Korea
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