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Pang B, Song M, Yang J, Mo H, Wang K, Chen X, Huang Y, Gu R, Guan C. Efficient production of a highly active lysozyme from European flat oyster Ostrea edulis. J Biotechnol 2024; 391:40-49. [PMID: 38848819 DOI: 10.1016/j.jbiotec.2024.05.011] [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: 03/25/2024] [Revised: 05/21/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024]
Abstract
Lysozyme, an antimicrobial agent, is extensively employed in the food and healthcare sectors to facilitate the breakdown of peptidoglycan. However, the methods to improve its catalytic activity and secretory expression still need to be studied. In the present study, twelve lysozymes from different origins were heterologously expressed using the Komagataella phaffii expression system. Among them, the lysozyme from the European flat oyster Ostrea edulis (oeLYZ) showed the highest activity. Via a semi-rational approach to reduce the structural free energy, the double mutant Y15A/S39R (oeLYZdm) with the catalytic activity 1.8-fold greater than that of the wild type was generated. Subsequently, different N-terminal fusion tags were employed to enhance oeLYZdm expression. The fusion with peptide tag 6×Glu resulted in a remarkable increase in the recombinant oeLYZdm expression, from 2.81 × 103 U mL-1 to 2.11 × 104 U mL-1 in shake flask culture, and eventually reaching 2.05 × 105 U mL-1 in a 3-L fermenter. The work produced the greatest amount of heterologous oeLYZ expression in microbial systems that are known to exist. Reducing the structural free energy and employing the N-terminal fusion tags are effective strategies to improve the catalytic activity and secretory expression of lysozyme.
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Affiliation(s)
- Bo Pang
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; Key Lab of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Manxi Song
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; Key Lab of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Jiahao Yang
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; Key Lab of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Haobin Mo
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; Key Lab of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Kai Wang
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; Key Lab of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Xia Chen
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; Key Lab of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Yujun Huang
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; Key Lab of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Ruixia Gu
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; Key Lab of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou, Jiangsu 225127, China
| | - Chengran Guan
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 225127, China; Key Lab of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou, Jiangsu 225127, China.
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Vijayakumar VE, Venkataraman K. A Systematic Review of the Potential of Pichia pastoris (Komagataella phaffii) as an Alternative Host for Biologics Production. Mol Biotechnol 2024; 66:1621-1639. [PMID: 37400712 DOI: 10.1007/s12033-023-00803-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/20/2023] [Indexed: 07/05/2023]
Abstract
The methylotrophic yeast Pichia pastoris is garnering interest as a chassis cell factory for the manufacture of recombinant proteins because it effectively satisfies the requirements of both laboratory and industrial set up. The optimisation of P. pastoris cultivation is still necessary due to strain- and product-specific problems such as promoter strength, methanol utilisation type, and culturing conditions to realize the high yields of heterologous protein(s) of interest. Techniques integrating genetic and process engineering have been used to overcome these problems. Insight into the Pichia as an expression system utilizing MUT pathway and the development of methanol free systems are highlighted in this systematic review. Recent developments in the improved production of proteins in P. pastoris by (i) diverse genetic engineering such as codon optimization and gene dosage; (ii) cultivating tactics including co-expression of chaperones; (iii) advances in the use of the 2A peptide system, and (iv) CRISPR/Cas technologies are widely discussed. We believe that by combining these strategies, P. pastoris will become a formidable platform for the production of high value therapeutic proteins.
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Affiliation(s)
- Vijay Elakkya Vijayakumar
- Centre for Bio-Separation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Krishnan Venkataraman
- Centre for Bio-Separation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India.
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Zhong YJ, Luo YY, Xia H, Zhao QW, Mao XM. Cytokinetic engineering enhances the secretory production of recombinant human lysozyme in Komagataella phaffii. Microb Cell Fact 2024; 23:179. [PMID: 38890717 PMCID: PMC11184742 DOI: 10.1186/s12934-024-02434-w] [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: 12/31/2023] [Accepted: 05/21/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Human lysozyme (hLYZ) is a natural antibacterial protein with broad applications in food and pharmaceutical industries. Recombinant production of hLYZ in Komagataella phaffii (K. phaffii) has attracted considerable attention, but there are very limited strategies for its hyper-production in yeast. RESULTS Here through Atmospheric and Room Temperature Plasma (ARTP)-based mutagenesis and transcriptomic analysis, the expression of two genes MYO1 and IQG1 encoding the cytokinesis core proteins was identified downregulated along with higher hLYZ production. Deletion of either gene caused severe cytokinesis defects, but significantly enhanced hLYZ production. The highest hLYZ yield of 1,052,444 ± 23,667 U/mL bioactivity and 4.12 ± 0.11 g/L total protein concentration were obtained after high-density fed-batch fermentation in the Δmyo1 mutant, representing the best production of hLYZ in yeast. Furthermore, O-linked mannose glycans were characterized on this recombinant hLYZ. CONCLUSIONS Our work suggests that cytokinesis-based morphology engineering is an effective way to enhance the production of hLYZ in K. phaffii.
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Affiliation(s)
- Yong-Jun Zhong
- School of Pharmaceutical Sciences, Taizhou University, Jiaojiang, Zhejiang Province, 318000, China
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China
| | - Yang-Yang Luo
- Polytechnic Institute, Zhejiang University, Hangzhou, 310015, China
- Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Haiyang Xia
- School of Pharmaceutical Sciences, Taizhou University, Jiaojiang, Zhejiang Province, 318000, China
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China
| | - Qing-Wei Zhao
- Department of Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310058, China.
| | - Xu-Ming Mao
- Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.
- Department of Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China.
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310058, China.
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Xu K, Ma C, Wu C, Wu D. The molecular modification, expression, and the antibacterial effects studies of human lysozyme. Biosci Biotechnol Biochem 2024; 88:546-554. [PMID: 38409797 DOI: 10.1093/bbb/zbae023] [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: 11/30/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024]
Abstract
Human lysozyme (hLYZ) has attracted considerable research attention due to its natural and efficient antibacterial abilities and widespread uses. In this study, hLYZ was modified to enhance its enzyme activity and expressed in a Pichia pastoris expression system. A combination mutant HZM(2R-K)-N88D/V110S demonstrated the highest enzyme activity (6213 ± 164 U/mL) in shake flasks, which was 4.07-fold higher when compared with the original strain. Moreover, the recombinant P. pastoris was inducted in a 3 L bioreactor plus methanol/sorbitol co-feeding. After 120 h induction, the antibacterial activity of hLYZ reached 2.23 ± 0.12 × 105 U/mL, with the specific activity increasing to 1.89 × 105 U/mg, which is currently the highest specific activity obtained through recombinant expression of hLYZ. Also, hLYZ supernatants showed 2-fold inhibitory effects toward Staphylococcus aureus and Micrococcus lysodeikticus when compared with HZM(2R-K). Our research generated a hLYZ mutant with high antibacterial capabilities and provided a method for screening of high-quality enzymes.
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Affiliation(s)
- Kewei Xu
- SINOPEC Key Laboratory of Petroleum Accumulation Mechanisms, Wuxi, Jiangsu, China
- Wuxi Research Institute of Petroleum Geology, Research Institute of Petroleum Exploration & Production, SINOPEC, Wuxi, Jiangsu, China
| | - Chuanyuan Ma
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Changyun Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Dan Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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Tian X, Cao H, Yan J, Li C, Li F, Li Y, Huang F, Bao C, Cao Y, Rao Z. Effect of dietary supplementation with recombinant human lysozyme on growth performance, antioxidative characteristics, and intestinal health in broiler chickens. J Anim Sci 2024; 102:skae121. [PMID: 38745481 PMCID: PMC11161903 DOI: 10.1093/jas/skae121] [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: 12/01/2023] [Accepted: 05/03/2024] [Indexed: 05/16/2024] Open
Abstract
Lysozyme is often used as a feed additive to act as an antibacterial protein that boosts the immune system of livestock and poultry while protecting against pathogens. To investigate the effects of recombinant human lysozyme (rhLYZ) from Pichia pastoris and chlortetracycline on broiler chicken's production performance, antioxidant characteristics, and intestinal microbiota, a total of 200, 1-d-old male Arbor Acres broiler chickens (46.53 ± 0.42 g) were selected for a 42-d experiment. Dietary treatments included a basal diet of corn-soybean meal supplemented with either 0 mg/kg (CON), 50 mg/kg aureomycin (ANT), 20 mg/kg rhLYZ (LOW), 60 mg/kg rhLYZ (MEDIUM), or 180 mg/kg rhLYZ (HIGH). Compared with CON, MEDIUM diet increased (P < 0.05) average daily gain (67.40 g) of broilers from day 22 to 42. In the early (1.29) and overall phases (1.69), MEDIUM led to a reduction (P < 0.05) in the feed conversion ratio of broiler chickens. Furthermore, in comparison to the CON and ANT, MEDIUM exhibited reduced (P < 0.05) levels of INF-γ and tumor necrosis factor-α in the serum. In the cecum, the abundance of Monoglobus and Family_XIII_AD3011_group was lower (P < 0.05) in the MEDIUM treatment compared to CON. Overall, supplementation of 60 mg/kg of rhLYZ improved growth performance, nutrient utilization efficiency, and serum immune function, while also influencing the composition of intestinal microbiota. This suggests lysozyme's potential to replace antibiotic additives in feed.
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Affiliation(s)
- Xuefeng Tian
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Heng Cao
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Juntong Yan
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Chunyue Li
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Feiyu Li
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yunke Li
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Fei Huang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Chengling Bao
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yunhe Cao
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhenghua Rao
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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Wang Y, Wang B, Gao Y, Nakanishi H, Gao XD, Li Z. Highly efficient expression and secretion of human lysozyme using multiple strategies in Pichia pastoris. Biotechnol J 2023; 18:e2300259. [PMID: 37470505 DOI: 10.1002/biot.202300259] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Human lysozyme (hLYZ), an emerging antibacterial agent, has extensive application in the food and pharmaceutical industries. However, the source of hLYZ is particularly limited. RESULTS To achieve highly efficient expression and secretion of hLYZ in Pichia pastoris, multiple strategies including G418 sulfate screening, signal sequence optimization, vacuolar sorting receptor VPS10 disruption, and chaperones/transcription factors co-expression were applied. The maximal enzyme activity of extracellular hLYZ in a shaking flask was 81,600 ± 5230 U mL-1 , which was about five times of original strain. To further reduce the cost, the optimal medium RDMY was developed and the highest hLYZ activity reached 352,000 ± 16,696.5 U mL-1 in a 5 L fermenter. CONCLUSION This research provides a very useful and cost-effective approach for the hLYZ production in P. pastoris and can also be applied to the production of other recombinant proteins.
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Affiliation(s)
- Yasen Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Buqing Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Yahui Gao
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hideki Nakanishi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Zijie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
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Biko OD, Viljoen-Bloom M, van Zyl WH. Medium optimization for enhanced production of recombinant lignin peroxidase in Pichia pastoris. Biotechnol Lett 2023; 45:105-113. [PMID: 36400875 DOI: 10.1007/s10529-022-03321-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/24/2022] [Accepted: 10/28/2022] [Indexed: 11/21/2022]
Abstract
OBJECTIVES Different cultivation conditions and parameters were evaluated to improve the production and secretion of a recombinant Phanerochaete chrysosporium lipH8 gene in Komagataella phaffii (Pichia pastoris). RESULTS The recombinant lipH8 gene with its native secretion signal was successfully cloned and expressed in Komagataella phaffii (Pichia pastoris) under the control of the alcohol oxidase 1 promoter (PAOX1). The results revealed that co-feeding with sorbitol and methanol increased rLiP secretion by 5.9-fold compared to the control conditions. The addition of 1 mM FeSO4 increased LiP activity a further 6.0-fold during the induction phase. Moreover, the combination of several optimal conditions and parameters yielded an extracellular rLiP activity of 20.05 U l-1, which is more than ten-fold higher relative to standard growth conditions (BMM10 medium, pH 6 and 30 °C). CONCLUSION Extracellular activity of a recombinant LiP expressed in P. pastoris increased more than ten-fold when co-feeding sorbitol and methanol as carbon sources, together with urea as nitrogen source, FeSO4 supplementation, lower pH and lower cultivation temperature.
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Affiliation(s)
- Odwa D Biko
- Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Marinda Viljoen-Bloom
- Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Willem H van Zyl
- Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa.
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Li Z, Wang X, Zhang Y, Yu Z, Zhang T, Dai X, Pan X, Jing R, Yan Y, Liu Y, Gao S, Li F, Huang Y, Tian J, Yao J, Xing X, Shi T, Ning J, Yao B, Huang H, Jiang Y. Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates. THE ISME JOURNAL 2022; 16:2775-2787. [PMID: 35986094 PMCID: PMC9666518 DOI: 10.1038/s41396-022-01306-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
Understanding the biodiversity and genetics of gut microbiomes has important implications for host physiology and industrial enzymes, whereas most studies have been focused on bacteria and archaea, and to a lesser extent on fungi and viruses. One group, still underexplored and elusive, is ciliated protozoa, despite its importance in shaping microbiota populations. Integrating single-cell sequencing and an assembly-and-identification pipeline, we acquired 52 high-quality ciliate genomes of 22 rumen morphospecies from 11 abundant morphogenera. With these genomes, we resolved the taxonomic and phylogenetic framework that revised the 22 morphospecies into 19 species spanning 13 genera and reassigned the genus Dasytricha from Isotrichidae to a new family Dasytrichidae. Comparative genomic analyses revealed that extensive horizontal gene transfers and gene family expansion provided rumen ciliate species with a broad array of carbohydrate-active enzymes (CAZymes) to degrade all major kinds of plant and microbial carbohydrates. In particular, the genomes of Diplodiniinae and Ophryoscolecinae species encode as many CAZymes as gut fungi, and ~80% of their degradative CAZymes act on plant cell-wall. The activities of horizontally transferred cellulase and xylanase of ciliates were experimentally verified and were 2-9 folds higher than those of the inferred corresponding bacterial donors. Additionally, the new ciliate dataset greatly facilitated rumen metagenomic analyses by allowing ~12% of the metagenomic sequencing reads to be classified as ciliate sequences.
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Affiliation(s)
- Zongjun Li
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiangnan Wang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yu Zhang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Tingting Zhang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xuelei Dai
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiangyu Pan
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ruoxi Jing
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
- College of Animal Engineering, Yangling Vocational & Technical College, Yangling, 712100, China
| | - Yueyang Yan
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yangfan Liu
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shan Gao
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Fei Li
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Youqin Huang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Jian Tian
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Junhu Yao
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - XvPeng Xing
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Tao Shi
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jifeng Ning
- College of Information Engineering, Northwest A&F University, Yangling, 712100, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Yu Jiang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
- Center for Functional Genomics, Institute of Future Agriculture, Northwest A&F University, Yangling, 712100, China.
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Pathway engineering facilitates efficient protein expression in Pichia pastoris. Appl Microbiol Biotechnol 2022; 106:5893-5912. [PMID: 36040488 DOI: 10.1007/s00253-022-12139-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/02/2022]
Abstract
Pichia pastoris has been recognized as an important platform for the production of various heterologous proteins in recent years. The strong promoter AOX1, induced by methanol, with the help of the α-pre-pro signal sequence, can lead to a high expression level of extracellular protein. However, this combination was not always efficient, as protein secretion in P. pastoris involves numerous procedures mediated by several cellular proteins, including folding assisted by endoplasmic reticulum (ER) molecular chaperones, degradation through ubiquitination, and an efficient vesicular transport system. Efficient protein expression requires the cooperation of various intracellular pathways. This article summarizes the process of protein secretion, modification, and transportation in P. pastoris. In addition, the roles played by the key proteins in these processes and the corresponding co-expression effects are also listed. It is expected to lay the foundation for the industrial protein production of P. pastoris. KEY POINTS: • Mechanisms of chaperones in protein folding and their co-expression effects are summarized. • Protein glycosylation modifications are comprehensively reviewed. • Current dilemmas in the overall protein secretion pathway of Pichia pastoris and corresponding solutions are demonstrated.
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Cui L, Huang H, Zhang H, Wang X, Qin X, Tu T, Zhang J, Su X, Yu H, Bai Y, Luo H, Yao B, Wang Y. Recombinant expression of hen egg white lysozyme with the assistance of xylanase fusion partner in Pichia pastoris. Bioengineered 2022; 13:13860-13871. [PMID: 35726822 PMCID: PMC9275996 DOI: 10.1080/21655979.2022.2084496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Due to its bacteriolytic activity, hen egg white lysozyme (HEWL) is widely used in the feed, food, and pharmaceutical industries. However, its application is hindered by low protein expression levels in microbial expression systems. In this work, a novel fusion protein expression strategy was proposed for increasing the expression level of HEWL. First, HEWL, fused with a highly expressed fusion protein partner xylanase XynCDBFV, is expressed in Pichia pastoris. Secondly, a linker including endogenous protease cleavage sites was introduced between two fusion proteins in order to separate them directly during the secretion process. Finally, the results show that the supernatant of XynCDBFV-HEWL has a higher HEWL expression level and activity compared with HEWL only. It should be noted that the expression of HEWL reaches to about 3.5 g/L, and the activity of HEWL against Micrococcus lysodeikticus reaches to 1.50 × 105 U/mL in a fed-batch fermentation, which is currently the highest level of recombinant expression of an egg white-derived lysozyme. Taken together, we acquired bioactive HEWL for large-scale recombinant production in Pichia pastoris using a novel fusion protein expression strategy, which could then be used for a variety of applications.
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Affiliation(s)
- Lin Cui
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P.R.China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P.R.China
| | - Honglian Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P.R.China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P.R.China
| | - Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P.R.China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P.R.China
| | - Jie Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P.R.China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P.R.China
| | - Huimin Yu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P.R.China
| | - Yingguo Bai
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P.R.China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P.R.China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P.R.China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P.R.China
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Bustos C, Quezada J, Veas R, Altamirano C, Braun-Galleani S, Fickers P, Berrios J. Advances in Cell Engineering of the Komagataella phaffii Platform for Recombinant Protein Production. Metabolites 2022; 12:346. [PMID: 35448535 PMCID: PMC9027633 DOI: 10.3390/metabo12040346] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 12/11/2022] Open
Abstract
Komagataella phaffii (formerly known as Pichia pastoris) has become an increasingly important microorganism for recombinant protein production. This yeast species has gained high interest in an industrial setting for the production of a wide range of proteins, including enzymes and biopharmaceuticals. During the last decades, relevant bioprocess progress has been achieved in order to increase recombinant protein productivity and to reduce production costs. More recently, the improvement of cell features and performance has also been considered for this aim, and promising strategies with a direct and substantial impact on protein productivity have been reported. In this review, cell engineering approaches including metabolic engineering and energy supply, transcription factor modulation, and manipulation of routes involved in folding and secretion of recombinant protein are discussed. A lack of studies performed at the higher-scale bioreactor involving optimisation of cultivation parameters is also evidenced, which highlights new research aims to be considered.
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Affiliation(s)
- Cristina Bustos
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Av. de la Faculté 2B, 5030 Gembloux, Belgium;
| | - Johan Quezada
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Rhonda Veas
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Claudia Altamirano
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Stephanie Braun-Galleani
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Av. de la Faculté 2B, 5030 Gembloux, Belgium;
| | - Julio Berrios
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
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Kastberg LLB, Ard R, Jensen MK, Workman CT. Burden Imposed by Heterologous Protein Production in Two Major Industrial Yeast Cell Factories: Identifying Sources and Mitigation Strategies. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:827704. [PMID: 37746199 PMCID: PMC10512257 DOI: 10.3389/ffunb.2022.827704] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/10/2022] [Indexed: 09/26/2023]
Abstract
Production of heterologous proteins, especially biopharmaceuticals and industrial enzymes, in living cell factories consumes cellular resources. Such resources are reallocated from normal cellular processes toward production of the heterologous protein that is often of no benefit to the host cell. This competition for resources is a burden to host cells, has a negative impact on cell fitness, and may consequently trigger stress responses. Importantly, this often causes a reduction in final protein titers. Engineering strategies to generate more burden resilient production strains offer sustainable opportunities to increase production and profitability for this growing billion-dollar global industry. We review recently reported impacts of burden derived from resource competition in two commonly used protein-producing yeast cell factories: Saccharomyces cerevisiae and Komagataella phaffii (syn. Pichia pastoris). We dissect possible sources of burden in these organisms, from aspects related to genetic engineering to protein translation and export of soluble protein. We also summarize advances as well as challenges for cell factory design to mitigate burden and increase overall heterologous protein production from metabolic engineering, systems biology, and synthetic biology perspectives. Lastly, future profiling and engineering strategies are highlighted that may lead to constructing robust burden-resistant cell factories. This includes incorporation of systems-level data into mathematical models for rational design and engineering dynamical regulation circuits in production strains.
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Affiliation(s)
| | - Ryan Ard
- Department of Biology, University of British Columbia, Kelowna, BC, Canada
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Christopher T. Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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13
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Liu K, Ouyang Y, Lin R, Ge C, Zhou M. Strong negative correlation between codon usage bias and protein structural disorder impedes protein expression after codon optimization. J Biotechnol 2022; 343:15-24. [PMID: 34763006 DOI: 10.1016/j.jbiotec.2021.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/14/2021] [Accepted: 11/04/2021] [Indexed: 11/18/2022]
Abstract
As a common phenomenon existing in almost all genomes, codon usage bias has been studied for a long time. Codon optimization is a frequently used strategy to accelerate protein synthesis rate. Besides regulating protein translation speed, codon usage bias has also be reported to affect co-translation folding and transcription. P. pastoris is a well-developed expression system, whose efficiency is tightly correlated with commercial value. However, few studies focus on the role of codon usage bias in affecting protein expression in P. pastoris. Besides, many genes in P. pastoris genome show significant negative correlation between codon usage bias and protein structural disorder tendency. It's not known whether this feature is important for their expression. In order to answer these questions, we picked 4P. pastoris gene candidates with strong negative correlation between codon usage bias and protein structural disorder. We then performed full-length codon optimization which completely eliminated the correlation. Protein and RNA assays were then used to compare protein and mRNA levels before and after codon optimization. As a result, codon optimization failed to elevate their protein expression levels, and even resulted in a decrease. As represented by the trypsin sensitivity assays, codon optimization also altered the protein structure of 0616 and 0788. Besides protein, codon optimization also affected mRNA levels. Shown by in vitro and in vivo RNA degradation assays, the mRNA stability of 0616, 0788 and 0135 were also altered by codon optimization. For each gene, the detailed effect may be related with its specific sequence and protein structure. Our results suggest that codon usage bias is an important factor to regulate gene expression level, as well as mRNA and protein stabilities in P. pastoris. "Extreme" codon optimization in genes with strong negative correlation between codon usage bias and protein structural disorder tendency may not be favored. Compromised strategies should be tried if expression is not successful. Besides, codon optimization may affect protein structural conformation more severely in structural disordered proteins.
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Affiliation(s)
- Kunshan Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yaqi Ouyang
- 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
| | - Chenyu Ge
- 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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14
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Raschmanová H, Weninger A, Knejzlík Z, Melzoch K, Kovar K. Engineering of the unfolded protein response pathway in Pichia pastoris: enhancing production of secreted recombinant proteins. Appl Microbiol Biotechnol 2021; 105:4397-4414. [PMID: 34037840 PMCID: PMC8195892 DOI: 10.1007/s00253-021-11336-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/30/2021] [Accepted: 05/06/2021] [Indexed: 12/14/2022]
Abstract
Folding and processing of proteins in the endoplasmic reticulum (ER) are major impediments in the production and secretion of proteins from Pichia pastoris (Komagataella sp.). Overexpression of recombinant genes can overwhelm the innate secretory machinery of the P. pastoris cell, and incorrectly folded proteins may accumulate inside the ER. To restore proper protein folding, the cell naturally triggers an unfolded protein response (UPR) pathway, which upregulates the expression of genes coding for chaperones and other folding-assisting proteins (e.g., Kar2p, Pdi1, Ero1p) via the transcription activator Hac1p. Unfolded/misfolded proteins that cannot be repaired are degraded via the ER-associated degradation (ERAD) pathway, which decreases productivity. Co-expression of selected UPR genes, along with the recombinant gene of interest, is a common approach to enhance the production of properly folded, secreted proteins. Such an approach, however, is not always successful and sometimes, protein productivity decreases because of an unbalanced UPR. This review summarizes successful chaperone co-expression strategies in P. pastoris that are specifically related to overproduction of foreign proteins and the UPR. In addition, it illustrates possible negative effects on the cell's physiology and productivity resulting from genetic engineering of the UPR pathway. We have focused on Pichia's potential for commercial production of valuable proteins and we aim to optimize molecular designs so that production strains can be tailored to suit a specific heterologous product. KEY POINTS: • Chaperones co-expressed with recombinant genes affect productivity in P. pastoris. • Enhanced UPR may impair strain physiology and promote protein degradation. • Gene copy number of the target gene and the chaperone determine the secretion rate.
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Affiliation(s)
- Hana Raschmanová
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic.
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland.
| | - Astrid Weninger
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Zdeněk Knejzlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Karel Melzoch
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Karin Kovar
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
- daspool Association, Wädenswil, Switzerland
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15
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Du C, Zhao X, Song W, He N, Jiang S, Zhou Y, Zhang G. Combined strategies to improve the expression of acidic mammalian chitinase in Pichia pastoris for the production of N, N'-diacetylchitobiose. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2020.107907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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