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Zhang S, Lin R, Cui L, Jiang T, Shi J, Lu C, Li P, Zhou M. Alter codon bias of the P. pastoris genome to overcome a bottleneck in codon optimization strategy development and improve protein expression. Microbiol Res 2024; 282:127629. [PMID: 38330819 DOI: 10.1016/j.micres.2024.127629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/27/2023] [Accepted: 01/21/2024] [Indexed: 02/10/2024]
Abstract
Apart from its role in translation, codon bias is also an important mechanism to regulate mRNA levels. The traditional frequency-based codon optimization strategy is rather efficient in organisms such as N. crassa, but much less in yeast P. pastoris which is a popular host for heterologous protein expression. This is because that unlike N. crassa, the preferred codons of P. pastoris are actually AU-rich and hence codon optimization for extremely low GC content comes with issues of pre-mature transcriptional termination or low RNA stability in spite of translational advantages. To overcome this bottleneck, we focused on three reporter genes in P. pastoris first and confirmed the great advantage of GC-prone codon optimization on mRNA levels. Then we altered the codon bias profile of P. pastoris by introducing additional rare tRNA gene copies. Prior to that we constructed IPTG-regulated tRNA species to enable chassis cells to switch between different codon bias status. As demonstrated again with reporter genes, protein yield of luc and 0788 was successfully increased by 4-5 folds in chassis cells. In summary, here we provide an alternative codon optimization strategy for genes with unsatisfactory performance under traditional codon frequency-based optimization.
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Affiliation(s)
- Siyu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ru Lin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Luyao Cui
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Tianyi Jiang
- China Innovation Center of Roche, Shanghai 201203, China
| | - Jiacheng Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Chaoyu Lu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Pengfei Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Mian Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
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An R, Zhang R, Guo Y, Geng J, Si M, Wang S, Gao M, Wang J. Biological Activity of Optimized Codon Bovine Type III Interferon Expressed in Pichia pastoris. Viruses 2023; 15:v15051101. [PMID: 37243187 DOI: 10.3390/v15051101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Type III interferons (IFN-λs) exhibit potent antiviral activity and immunomodulatory effects in specific cells. Nucleotide fragments of the bovine ifn-λ (boifn-λ) gene were synthetized after codon optimization. The boifn-λ gene was then amplified by splicing using overlap extension PCR (SOE PCR), resulting in the serendipitous acquisition of the mutated boIFN-λ3V18M. The recombinant plasmid pPICZαA-boIFN-λ3/λ3V18M was constructed, and the corresponding proteins were expressed in Pichia pastoris with a high-level extracellular soluble form. Dominant expression strains of boIFN-λ3/λ3V18M were selected by Western blot and ELISA and cultured on a large scale, and the recombinant proteins purified by ammonium sulfate precipitation and ion exchange chromatography yielded 1.5g/L and 0.3 g/L, with 85% and 92% purity, respectively. The antiviral activity of boIFN-λ3/λ3V18M exceeded 106 U/mg, and they were neutralized with IFN-λ3 polyclonal antibodies, were susceptible to trypsin, and retained stability within defined pH and temperature ranges. Furthermore, boIFN-λ3/λ3V18M exerted antiproliferative effects on MDBK cells without cytotoxicity at 104 U/mL. Overall, boIFN-λ3 and boIFN-λ3V18M did not differ substantially in biological activity, except for reduced glycosylation of the latter. The development of boIFN-λ3 and comparative evaluation with the mutant provide theoretical insights into the antiviral mechanisms of boIFN-λs and provide material for therapeutic development.
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Affiliation(s)
- Ran An
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Runxiang Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Yongli Guo
- Heilongjiang Provincial Key Laboratory for Infection and Immunity, Department of Immunology, Harbin Medical University, Harbin 150030, China
| | - Jinfeng Geng
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Minglu Si
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Shuangfeng Wang
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Mingchun Gao
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Junwei Wang
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
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Yu HY, Gao DM, Zhou W, Xia BB, He ZY, Wu B, Jiang MZ, Wang ML, Zhao J. Acute and Sub-chronic Toxicity Study of Recombinant Bovine Interferon Alpha in Rodents. J Vet Res 2021; 65:183-192. [PMID: 34250303 PMCID: PMC8256469 DOI: 10.2478/jvetres-2021-0023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 04/09/2020] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION Recombinant bovine interferon alpha (rBoIFN-α) has been demonstrated to have antiviral activity. However, no conduct of acute or chronic toxicity tests has been reported. MATERIAL AND METHODS Specific pathogen-free Sprague Dawley rats were administered doses at different concentrations through intraperitoneal or intravenous injection. After the administration (single for an acute toxicity test over 14 days or daily for a sub-chronic toxicity test over 30 days), the rats' behaviour and other indicators and the degree of toxic reaction were continuously monitored. Blood was collected for haematological and serum biochemical examinations. At the end of the experiments, the rats were sacrificed for necropsy and histopathological tissue analysis. RESULTS The external performance, behaviour characteristics, and changes in body temperature and body weight of the rats in each subgroup were comparable to the normal control subgroup. Except for a few cases, there were no lesions in the viscera's pathological structures, and the blood parameters and biochemical indicators were not noticeably different from those of the control subgroup. CONCLUSION This study suggests that rBoIFN-α seems to be safe for rats, and its use may foster the development of the cattle industry in China by protecting livestock health.
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Affiliation(s)
- Hai-Yang Yu
- Department of Microbiology, Anhui Medical University, Hefei, Anhui Province, 230032, P.R. China
| | - Dong-Mei Gao
- Department of Clinical Laboratory, Third Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, 230032, P.R. China
| | - Wei Zhou
- Wuhu Interferon Bio-products Industry Research Institute Co., Ltd, Wuhu, Anhui Province, 241007, P.R. China
| | - Bing-Bing Xia
- Wuhu Interferon Bio-products Industry Research Institute Co., Ltd, Wuhu, Anhui Province, 241007, P.R. China
| | - Zhi-Yuan He
- Wuhu Interferon Bio-products Industry Research Institute Co., Ltd, Wuhu, Anhui Province, 241007, P.R. China
| | - Bo Wu
- Wuhu Interferon Bio-products Industry Research Institute Co., Ltd, Wuhu, Anhui Province, 241007, P.R. China
| | - Min-Zhi Jiang
- Wuhu Interferon Bio-products Industry Research Institute Co., Ltd, Wuhu, Anhui Province, 241007, P.R. China
| | - Ming-Li Wang
- Department of Microbiology, Anhui Medical University, Hefei, Anhui Province, 230032, P.R. China
- Wuhu Interferon Bio-products Industry Research Institute Co., Ltd, Wuhu, Anhui Province, 241007, P.R. China
| | - Jun Zhao
- Department of Microbiology, Anhui Medical University, Hefei, Anhui Province, 230032, P.R. China
- Wuhu Interferon Bio-products Industry Research Institute Co., Ltd, Wuhu, Anhui Province, 241007, P.R. China
- Wuhu Overseas Students Pioneer Park, Wuhu, Anhui Province, 241000, P.R. China
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Quintana ME, Cardoso NP, Pereyra R, Barone LJ, Barrionuevo FM, Mansilla FC, Turco CS, Capozzo AV. Interferon lambda protects cattle against bovine viral diarrhea virus infection. Vet Immunol Immunopathol 2020; 230:110145. [PMID: 33160262 DOI: 10.1016/j.vetimm.2020.110145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 10/25/2020] [Accepted: 10/29/2020] [Indexed: 01/15/2023]
Abstract
Interferon lambda (IFN-λ) plays an important role in inducing an antiviral state in mucosal surfaces and has been used as an effective biotherapeutic against several viral diseases. Here we performed a proof of concept study on the activity of a biologically active recombinant bovine IFN-λ (rIFN-λ) produced in eukaryotic cells against Bovine Viral Diarrhea Virus (BVDV) in cattle. We first confirmed the lack of toxicity of different concentrations of rIFN-λ in bovine peripheral blood cells and the safety of its subcutaneous application in calves in doses up to 12 IU/kg. The antiviral activity of the rIFN-λ against BVDV was assessed in calves that were inoculated with 6 IU/kg of rIFN-λ (n = 4) or mock-treated (n = 2) two days before and after challenge with a BVDV type-2 non-cytopathic strain. Mock-treated animals developed respiratory disease, shedded the virus from 4 to 7 days post-infection (dpi) and had viremia between 4 and 14 dpi. Conversely, calves treated with rIFN-λ did not develop clinical symptoms. The virus was not found in nasal secretions or sera. Only one animal had a positive viral RNA detection in serum at 7 dpi. All infected animals treated with rIFN-λ increased systemic type-I IFNs levels at 4 dpi. The antiviral treatment induced an earlier onset of the anti-BVDV neutralizing antibodies. Altogether, these results constitute the proof-of-principle of bovine IFN-λ as an antiviral biotherapeutic to protect cattle against the clinical disease caused by BVDV.
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Affiliation(s)
- María Eugenia Quintana
- Instituto de Virología e Innovaciones Tecnológicas. IVIT, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Instituto Nacional de Tecnología Agropecuaria (INTA). Nicolás Repetto y Los Reseros s/n. Hurlingham, Buenos Aires, Argentina
| | - Nancy Patricia Cardoso
- Instituto de Virología e Innovaciones Tecnológicas. IVIT, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Instituto Nacional de Tecnología Agropecuaria (INTA). Nicolás Repetto y Los Reseros s/n. Hurlingham, Buenos Aires, Argentina
| | - Rodrigo Pereyra
- Área de Investigación en Sanidad Animal IIACS-CIAP- Estación Experimental Agropecuaria EEA, INTA Cerrillos, Salta, Argentina
| | - Lucas José Barone
- Instituto de Virología e Innovaciones Tecnológicas. IVIT, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Instituto Nacional de Tecnología Agropecuaria (INTA). Nicolás Repetto y Los Reseros s/n. Hurlingham, Buenos Aires, Argentina
| | - Florencia Mariel Barrionuevo
- Instituto de Virología e Innovaciones Tecnológicas. IVIT, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Instituto Nacional de Tecnología Agropecuaria (INTA). Nicolás Repetto y Los Reseros s/n. Hurlingham, Buenos Aires, Argentina
| | - Florencia Celeste Mansilla
- Instituto de Virología e Innovaciones Tecnológicas. IVIT, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Instituto Nacional de Tecnología Agropecuaria (INTA). Nicolás Repetto y Los Reseros s/n. Hurlingham, Buenos Aires, Argentina
| | - Cecilia Soledad Turco
- Instituto de Virología e Innovaciones Tecnológicas. IVIT, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Instituto Nacional de Tecnología Agropecuaria (INTA). Nicolás Repetto y Los Reseros s/n. Hurlingham, Buenos Aires, Argentina
| | - Alejandra Victoria Capozzo
- Instituto de Virología e Innovaciones Tecnológicas. IVIT, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Instituto Nacional de Tecnología Agropecuaria (INTA). Nicolás Repetto y Los Reseros s/n. Hurlingham, Buenos Aires, Argentina.
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Yu HY, Liu J, He ZY, Zhou W, Xia BB, Wang M, Chen J, Wang ML, Jiang GT, Zhao J. Soluble Expression, Rapid Purification and Antiviral Activity of Recimbinant Bovine Interferon-α in Escherichia coli. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820020143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Deng J, Li J, Ma M, Zhao P, Ming F, Lu Z, Shi J, Fan Q, Liang Q, Jia J, Li J, Zhang S, Zhang L. Co-expressing GroEL-GroES, Ssa1-Sis1 and Bip-PDI chaperones for enhanced intracellular production and partial-wall breaking improved stability of porcine growth hormone. Microb Cell Fact 2020; 19:35. [PMID: 32070347 PMCID: PMC7027120 DOI: 10.1186/s12934-020-01304-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/09/2020] [Indexed: 12/18/2022] Open
Abstract
Porcine growth hormone (pGH) is a class of peptide hormones secreted from the pituitary gland, which can significantly improve growth and feed utilization of pigs. However, it is unstable and volatile in vitro. It needs to be encapsulated in liposomes when feeding livestock, whose high cost greatly limits its application in pig industry. Therefore we attempted to express pGH as intracellular soluble protein in Pichia pastoris and feed these yeasts with partial wall-breaking for swine, which could release directly pGH in intestine tract in case of being degraded in intestinal tract with low cost. In order to improve the intracellular soluble expression of pGH protein in Pichia pastoris and stability in vitro, we optimized the pGH gene, and screened molecular chaperones from E. coli and Pichia pastoris respectively for co-expressing with pGH. In addition, we had also explored conditions of mechanical crushing and fermentation. The results showed that the expression of intracellular soluble pGH protein was significantly increased after gene optimized and co-expressed with Ssa1-Sis1 chaperone from Pichia pastoris. Meanwhile, the optimal conditions of partial wall-breaking and fermentation of Pichia pastoris were confirmed, the data showed that the intracellular expression of the optimized pGH protein co-expressed with Ssa1-Sis1 could reach 340 mg/L with optimal conditions of partial wall-breaking and fermentation. Animal experiments verified that the optimized pGH protein co-expression with Ssa1-Sis1 had the best promoting effects on the growth of piglets. Our study demonstrated that Ssa1-Sis1 could enhance the intracellular soluble expression of pGH protein in Pichia pastoris and that partial wall-breaking of yeast could prevent pGH from degradation in vitro, release targetedly in the intestine and play its biological function effectively. Our study could provide a new idea to cut the cost effectively, establishing a theoretical basis for the clinic application of unstable substances in vitro.
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Affiliation(s)
- Jinbo Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Jiaoqing Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Miaopeng Ma
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Peijing Zhao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Feiping Ming
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Zhipeng Lu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Juqing Shi
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Qin Fan
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Qianyi Liang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Junhao Jia
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Jiayi Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Shuxia Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China
| | - Linghua Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Microbiological Staff Room, College of Life Sciences, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, 510642, Guangdong, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China.
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Karbalaei M, Rezaee SA, Farsiani H. Pichia pastoris: A highly successful expression system for optimal synthesis of heterologous proteins. J Cell Physiol 2020; 235:5867-5881. [PMID: 32057111 PMCID: PMC7228273 DOI: 10.1002/jcp.29583] [Citation(s) in RCA: 256] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 01/09/2020] [Indexed: 01/09/2023]
Abstract
One of the most important branches of genetic engineering is the expression of recombinant proteins using biological expression systems. Nowadays, different expression systems are used for the production of recombinant proteins including bacteria, yeasts, molds, mammals, plants, and insects. Yeast expression systems such as Saccharomyces cerevisiae (S. cerevisiae) and Pichia pastoris (P. pastoris) are more popular. P. pastoris expression system is one of the most popular and standard tools for the production of recombinant protein in molecular biology. Overall, the benefits of protein production by P. pastoris system include appropriate folding (in the endoplasmic reticulum) and secretion (by Kex2 as signal peptidase) of recombinant proteins to the external environment of the cell. Moreover, in the P. pastoris expression system due to its limited production of endogenous secretory proteins, the purification of recombinant protein is easy. It is also considered a unique host for the expression of subunit vaccines which could significantly affect the growing market of medical biotechnology. Although P. pastoris expression systems are impressive and easy to use with well‐defined process protocols, some degree of process optimization is required to achieve maximum production of the target proteins. Methanol and sorbitol concentration, Mut forms, temperature and incubation time have to be adjusted to obtain optimal conditions, which might vary among different strains and externally expressed protein. Eventually, optimal conditions for the production of a recombinant protein in P. pastoris expression system differ according to the target protein.
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Affiliation(s)
- Mohsen Karbalaei
- Department of Microbiology and Virology, School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
| | - Seyed A Rezaee
- School of Medicine, Mashhad University of Medical Sciences, Inflammation and Inflammatory Diseases Research Centre, Mashhad, Iran
| | - Hadi Farsiani
- Mashhad University of Medical Sciences, Antimicrobial Resistance Research Center, Mashhad, Iran
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