1
|
Nguyen L, Schmelzer B, Wilkinson S, Mattanovich D. From natural to synthetic: Promoter engineering in yeast expression systems. Biotechnol Adv 2024; 77:108446. [PMID: 39245291 DOI: 10.1016/j.biotechadv.2024.108446] [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: 07/12/2024] [Revised: 09/04/2024] [Accepted: 09/05/2024] [Indexed: 09/10/2024]
Abstract
Synthetic promoters are particularly relevant for application not only in yeast expression systems designed for high-level heterologous protein production but also in other applications such as metabolic engineering, cell biological research, and stage-specific gene expression control. By designing synthetic promoters, researcher can create customized expression systems tailored to specific needs, whether it is maximizing protein production or precisely controlling gene expression at different stages of a process. While recognizing the limitations of endogenous promoters, they also provide important information needed to design synthetic promoters. In this review, emphasis will be placed on some key approaches to identify endogenous, and to generate synthetic promoters in yeast expression systems. It shows the connection between endogenous and synthetic promoters, highlighting how their interplay contributes to promoter development. Furthermore, this review illustrates recent developments in biotechnological advancements and discusses how this field will evolve in order to develop custom-made promoters for diverse applications. This review offers detailed information, explores the transition from endogenous to synthetic promoters, and presents valuable perspectives on the next generation of promoter design strategies.
Collapse
Affiliation(s)
- Ly Nguyen
- BOKU University, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, 1190 Vienna, Austria
| | - Bernhard Schmelzer
- BOKU University, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, 1190 Vienna, Austria
| | | | - Diethard Mattanovich
- BOKU University, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, 1190 Vienna, Austria; Austrian Centre of Industrial Biotechnology, 1190 Vienna, Austria.
| |
Collapse
|
2
|
Unver Y, Ari B, Acar M, Yildiz Arslan S. A self-inducible heterologous protein expression system in Komagataella phaffii ( Pichia pastoris). 3 Biotech 2024; 14:193. [PMID: 39131177 PMCID: PMC11306816 DOI: 10.1007/s13205-024-04039-x] [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: 04/17/2024] [Accepted: 07/30/2024] [Indexed: 08/13/2024] Open
Abstract
Komagataella phaffii (previously described as Pichia pastoris) is a yeast that produces high-level heterologous proteins with a wide range of applications in medicine and industry. The methanol-induced alcohol oxidase I promoter (PAOX1) is frequently used for protein expression in this yeast. However, limitations on the use of methanol have been observed in large-scale production, including its flammability, toxicity, and need for special handling. Here, we propose to develop a system using recombinant cells constitutively expressing pectinmethyl esterase for expression of two reporter proteins, GFP and azurin, under the control of PAOX1 using pectin in production medium. So, this system is coherent with yeast culture medium containing pectin and heterologous gene inserted downstream of PAOX1 can be successfully expressed without the addition of methanol. Therefore, this novel Self-inducibLe heterologous protein EXpression (SILEX) system, which does not require the addition of methanol, can be used for the production of any protein. It can also be adapted for large-scale production. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04039-x.
Collapse
Affiliation(s)
- Yagmur Unver
- Department of Molecular Biology and Genetics, Faculty of Science, Atatürk University, Erzurum, Turkey
| | - Betul Ari
- Department of Molecular Biology and Genetics, Graduate School of Natural and Applied Sciences, Atatürk University, Erzurum, Turkey
| | - Melek Acar
- Department of Molecular Biology and Genetics, Graduate School of Natural and Applied Sciences, Atatürk University, Erzurum, Turkey
| | - Seyda Yildiz Arslan
- Department of Molecular Biology and Genetics, Graduate School of Natural and Applied Sciences, Atatürk University, Erzurum, Turkey
| |
Collapse
|
3
|
Xu L, Bai X, Joong Oh E. Strategic approaches for designing yeast strains as protein secretion and display platforms. Crit Rev Biotechnol 2024:1-18. [PMID: 39138023 DOI: 10.1080/07388551.2024.2385996] [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: 04/02/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 08/15/2024]
Abstract
Yeast has been established as a versatile platform for expressing functional molecules, owing to its well-characterized biology and extensive genetic modification tools. Compared to prokaryotic systems, yeast possesses advanced cellular mechanisms that ensure accurate protein folding and post-translational modifications. These capabilities are particularly advantageous for the expression of human-derived functional proteins. However, designing yeast strains as an expression platform for proteins requires the integration of molecular and cellular functions. By delving into the complexities of yeast-based expression systems, this review aims to empower researchers with the knowledge to fully exploit yeast as a functional platform to produce a diverse range of proteins. This review includes an exploration of the host strains, gene cassette structures, as well as considerations for maximizing the efficiency of the expression system. Through this in-depth analysis, the review anticipates stimulating further innovation in the field of yeast biotechnology and protein engineering.
Collapse
Affiliation(s)
- Luping Xu
- Department of Food Science, Purdue University, West Lafayette, IN, USA
- Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
| | | | - Eun Joong Oh
- Department of Food Science, Purdue University, West Lafayette, IN, USA
- Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
4
|
Liu M, Zhou S, Cao Y, Yang K, Xiao Y, Wang W. Characterization of MAP c21873-1 as a new counter-selectable marker for unmarked genetic modification of Pichia pastoris. Microb Cell Fact 2024; 23:224. [PMID: 39118053 PMCID: PMC11312372 DOI: 10.1186/s12934-024-02496-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: 04/18/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Selection markers are useful in genetic modification of yeast Pichia pastoris. However, the leakage of the promoter caused undesired expression of selection markers especially those toxic proteins like MazF, halting the cell growth and hampering the genetic manipulation in procaryotic system. In this study, a new counter-selectable marker-based strategy has been established for seamless modification with high efficiency and low toxicity. RESULTS At first, the leaky expression of the enhanced green fluorescent protein (EGFP) as a reporter gene under the control of six inducible promoters of P. pastoris was investigated in two hosts Escherichia coli and P. pastoris, respectively. The results demonstrated that the DAS1 and FDH1 promoters (PDAS1 and PFDH1) had the highest leakage expression activities in procaryotes and eukaryotes, and the DAS2 promoter (PDAS2) was inducible with medium strength but low leakage expression activity, all of which were selected for further investigation. Next, Mirabilis antiviral proteins (MAPs) c21873-1, c21873-1T (truncated form of c21873-1) and c23467 were mined as the new counter-selectable markers, and hygromycin B (Hyg B) resistance gene was used as the positive-selectable marker, respectively. Then, modular plasmids with MAP-target gene-Hyg B cassettes were constructed and used to transform into P. pastoris cells after linearization, and the target genes were integrated into its genome at the BmT1 locus through single-crossover homologous recombination (HR). After counter-selection induced by methanol medium, the markers c21873-1 and c21873-1T were recycled efficiently. But c23467 failed to be recycled due to its toxic effect on the P. pastoris cells. At last, the counter-selectable marker c21873-1 under the tightly regulated PDAS2 enabled the encoding genes of reporter EGFP and tested proteins to be integrated into the target locus and expressed successfully. CONCLUSIONS We have developed MAP c21873-1 as a novel counter-selectable marker which could perform efficient gene knock-in by site-directed HR. Upon counter-selection, the marker could be recycled for repeated use, and no undesirable sequences were introduced except for the target gene. This unmarked genetic modification strategy may be extended to other genetic modification including but not limited to gene knock-out and site-directed mutagenesis in future.
Collapse
Affiliation(s)
- Minzhi Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
- Key Laboratory of Biosynthesis of Natural Products of National Health Commission of the Peoples Republic of China, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Sihan Zhou
- Key Laboratory of Biosynthesis of Natural Products of National Health Commission of the Peoples Republic of China, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Yunsong Cao
- Key Laboratory of Biosynthesis of Natural Products of National Health Commission of the Peoples Republic of China, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Keqin Yang
- Key Laboratory of Biosynthesis of Natural Products of National Health Commission of the Peoples Republic of China, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Yao Xiao
- Key Laboratory of Biosynthesis of Natural Products of National Health Commission of the Peoples Republic of China, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Wei Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
- Key Laboratory of Biosynthesis of Natural Products of National Health Commission of the Peoples Republic of China, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
| |
Collapse
|
5
|
Sauvageau D, Stein LY, Arenas E, Das S, Iacobelli M, Lawley M, Lazic M, Rondón FL, Weiblen C. Industrializing methanotrophs and other methylotrophic bacteria: from bioengineering to product recovery. Curr Opin Biotechnol 2024; 88:103167. [PMID: 38901110 DOI: 10.1016/j.copbio.2024.103167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/23/2024] [Accepted: 06/05/2024] [Indexed: 06/22/2024]
Abstract
Microbes that use the single-carbon substrates methanol and methane offer great promise to bioindustry along with substantial environmental benefits. Methanotrophs and other methylotrophs can be engineered and optimized to produce a wide range of products, from biopolymers to biofuels and beyond. While significant limitations remain, including delivery of single-carbon feedstock to bioreactors, efficient growth, and scale-up, these challenges are being addressed and notable improvements have been rapid. Development of expression chassis, use of genome-scale and regulatory models based on omics data, improvements in bioreactor design and operation, and development of green product recovery schemes are enabling the rapid development of single-carbon bioconversion in the industrial space.
Collapse
Affiliation(s)
- Dominic Sauvageau
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada.
| | - Lisa Y Stein
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Elizabeth Arenas
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Shibashis Das
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada
| | - Maryssa Iacobelli
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Mark Lawley
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada
| | - Marina Lazic
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Fabián L Rondón
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Cerrise Weiblen
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, AB T6G 2E9, Canada
| |
Collapse
|
6
|
Adame M, Vázquez H, Juárez-López D, Corzo G, Amezcua M, López D, González Z, Schcolnik-Cabrera A, Morales-Martínez A, Villegas E. Expression and characterization of scFv-6009FV in Pichia pastoris with improved ability to neutralize the neurotoxin Cn2 from Centruroides noxius. Int J Biol Macromol 2024; 275:133461. [PMID: 38945343 DOI: 10.1016/j.ijbiomac.2024.133461] [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: 05/07/2024] [Revised: 06/11/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024]
Abstract
Small single-chain variable fragments (scFv) are promising biomolecules to inhibit and neutralize toxins and to act as antivenoms. In this work, we aimed to produce a functional scFv-6009FV in the yeast Pichia pastoris, which inhibits the pure Cn2 neurotoxin and the whole venom of Centruroides noxius. We were able to achieve yields of up to 31.6 ± 2 mg/L in flasks. Furthermore, the protein showed a structure of 6.1 % α-helix, 49.1 % β-sheet, and 44.8 % of random coil by CD. Mass spectrometry confirmed the amino acid sequence and showed no glycosylation profile for this molecule. Purified scFv-6009FV allowed us to develop anti-scFvs in rabbits, which were then used in affinity columns to purify other scFvs. Determination of its half-maximal inhibitory concentration value (IC50) was 40 % better than the scFvs produced by E. coli as a control. Finally, we found that scFv-6009FV was able to inhibit ex vivo the pure Cn2 toxin and the whole venom from C. noxius in murine rescue experiments. These results demonstrated that under the conditions assayed here, P. pastoris is suited to produce scFv-6009FV that, compared to scFvs produced by E. coli, maintains the characteristics of an antibody and neutralizes the Cn2 toxin more effectively.
Collapse
Affiliation(s)
- Mariel Adame
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Hilda Vázquez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Daniel Juárez-López
- Instituto de Investigaciones Biomédicas, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Gerardo Corzo
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Mónica Amezcua
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Daniela López
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Zuriel González
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | | | - Adriana Morales-Martínez
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Elba Villegas
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México.
| |
Collapse
|
7
|
Lin X, Ding W, Zheng S, Wu L, Chen X, Xie C, Liu D, Yao D. Novel transcriptional regulation of the GAP promoter in Pichia pastoris towards high expression of heterologous proteins. Microb Cell Fact 2024; 23:206. [PMID: 39044288 PMCID: PMC11267847 DOI: 10.1186/s12934-024-02435-9] [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: 11/08/2023] [Accepted: 05/21/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND Pichia pastoris (Komagataella phaffii) is a promising production host, but the usage of methanol limits its application in the medicine and food industries. RESULTS To improve the constitutive expression of heterologous proteins in P. pastoris, four new potential transcription regulators (Loc1p, Msn2p, Gsm1p, Hot1p) of the glyceraldehyde triphosphate dehydrogenase promoter (pGAP) were revealed in this study by using cellulase E4 as reporter gene. On this basis, a series of P. pastoris strains with knockout or overexpression of transcription factors were constructed and the deletion of transcription factor binding sites on pGAP was confirmed. The results showed that Loc1p and Msn2p can inhibit the activity of pGAP, while Gsm1p and Hot1p can enhance the activity of pGAP; Loc1p, Gsm1p and Hot1p can bind directly to pGAP, while Msn2p must be treated to expose the C-terminal domain to bind to pGAP. Moreover, manipulating a single transcription factor led to a 0.96-fold to 2.43-fold increase in xylanase expression. In another model protein, aflatoxin oxidase, knocking out Loc1 based on AFO-∆Msn2 strain resulted in a 0.63-fold to 1.4-fold increase in expression. It can be demonstrated that the combined use of transcription factors can further improve the expression of exogenous proteins in P. pastoris. CONCLUSION These findings will contribute to the construction of pGAP-based P. pastoris systems towards high expression of heterologous proteins, hence improving the application potential of yeast.
Collapse
Affiliation(s)
- Xiangna Lin
- Institute of Biomedicine, Jinan University, Guangzhou City, 510632, Guangdong Province, China
- National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou City, 510632, Guangdong Province, China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou City, 510632, Guangdong Province, China
| | - Weiqiu Ding
- Institute of Biomedicine, Jinan University, Guangzhou City, 510632, Guangdong Province, China
- National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou City, 510632, Guangdong Province, China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou City, 510632, Guangdong Province, China
| | - Shaoyan Zheng
- Institute of Biomedicine, Jinan University, Guangzhou City, 510632, Guangdong Province, China
- National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou City, 510632, Guangdong Province, China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou City, 510632, Guangdong Province, China
| | - Lianna Wu
- Institute of Biomedicine, Jinan University, Guangzhou City, 510632, Guangdong Province, China
- National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou City, 510632, Guangdong Province, China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou City, 510632, Guangdong Province, China
| | - Xue Chen
- Institute of Biomedicine, Jinan University, Guangzhou City, 510632, Guangdong Province, China
- National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou City, 510632, Guangdong Province, China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou City, 510632, Guangdong Province, China
| | - Chunfang Xie
- Department of Bioengineering, Jinan University, Guangzhou City, 510632, Guangdong Province, China
| | - Daling Liu
- Department of Bioengineering, Jinan University, Guangzhou City, 510632, Guangdong Province, China
| | - Dongsheng Yao
- Institute of Biomedicine, Jinan University, Guangzhou City, 510632, Guangdong Province, China.
- National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou City, 510632, Guangdong Province, China.
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou City, 510632, Guangdong Province, China.
| |
Collapse
|
8
|
Zhang S, Ma T, Zheng FH, Aslam M, Wang YJ, Chi ZM, Liu GL. Customizable and stable multilocus chromosomal integration: a novel glucose-dependent selection system in Aureobasidium spp. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:81. [PMID: 38886802 PMCID: PMC11181563 DOI: 10.1186/s13068-024-02531-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND Non-conventional yeasts hold significant potential as biorefinery cell factories for microbial bioproduction. Currently, gene editing systems used for these yeasts rely on antibiotic and auxotrophic selection mechanisms. However, the drawbacks of antibiotics, including high costs, environmental concerns, and the dissemination of resistance genes, make them unsuitable for large-scale industrial fermentation. For auxotrophic selection system, the engineered strains harboring auxotrophic marker genes are typically supplemented with complex nutrient-rich components instead of precisely defined synthetic media in large-scale industrial fermentations, thus lack selection pressure to ensure the stability of heterologous metabolic pathways. Therefore, it is a critical to explore alternative selection systems that can be adapted for large-scale industrial fermentation. RESULTS Here, a novel glucose-dependent selection system was developed in a high pullulan-producing non-conventional strain A. melanogenum P16. The system comprised a glucose-deficient chassis cell Δpfk obtained through the knockout of the phosphofructokinase gene (PFK) and a series of chromosomal integration plasmids carrying a selection marker PFK controlled by different strength promoters. Utilizing the green fluorescent protein gene (GFP) as a reporter gene, this system achieved a 100% positive rate of transformation, and the chromosomal integration numbers of GFP showed an inverse relationship with promoter strength, with a customizable copy number ranging from 2 to 54. More importantly, the chromosomal integration numbers of target genes remained stable during successive inoculation and fermentation process, facilitated simply by using glucose as a cost-effective and environmental-friendly selectable molecule to maintain a constant and rigorous screening pressure. Moreover, this glucose-dependent selection system exhibited no significant effect on cell growth and product synthesis, and the glucose-deficient related selectable marker PFK has universal application potential in non-conventional yeasts. CONCLUSION Here, we have developed a novel glucose-dependent selection system to achieve customizable and stable multilocus chromosomal integration of target genes. Therefore, this study presents a promising new tool for genetic manipulation and strain enhancement in non-conventional yeasts, particularly tailored for industrial fermentation applications.
Collapse
Affiliation(s)
- Shuo Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, 266003, Shandong, China
| | - Tao Ma
- MOE Key Laboratory of Evolution and Marine Biodiversity, College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, 266003, Shandong, China
| | - Fu-Hui Zheng
- MOE Key Laboratory of Evolution and Marine Biodiversity, College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, 266003, Shandong, China
| | - Muhammad Aslam
- Faculty of Basic Sciences, Bolan University of Medical and Health Sciences, Quetta, 87600, Pakistan
| | - Yu-Jie Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, 266003, Shandong, China
| | - Zhen-Ming Chi
- MOE Key Laboratory of Evolution and Marine Biodiversity, College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, 266003, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, No.1 Wenhai Road, Qingdao, 266237, China
| | - Guang-Lei Liu
- MOE Key Laboratory of Evolution and Marine Biodiversity, College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, 266003, Shandong, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, No.1 Wenhai Road, Qingdao, 266237, China.
| |
Collapse
|
9
|
Younes M, Aquilina G, Degen G, Engel K, Fowler P, Frutos Fernandez MJ, Fürst P, Gundert‐Remy U, Gürtler R, Husøy T, Manco M, Mennes W, Passamonti S, Moldeus P, Shah R, Waalkens‐Berendsen I, Wright M, Barat Baviera JM, Gott D, Herman L, Leblanc J, Wölfle D, Entrena JA, Gagliardi G, Rincon AM, Ruggeri L, Smeraldi C, Tard A, Castle L. Safety of soy leghemoglobin from genetically modified Komagataella phaffii as a food additive. EFSA J 2024; 22:e8822. [PMID: 38946918 PMCID: PMC11211803 DOI: 10.2903/j.efsa.2024.8822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024] Open
Abstract
The EFSA Panel on Food Additive and Flavourings (FAF Panel) provides a scientific opinion on the safety of soy leghemoglobin from genetically modified Komagataella phaffii as a food additive in accordance with Regulation (EC) No 1331/2008. The proposed food additive, LegH Prep, is intended to be used as a colour in meat analogue products. The yeast Komagataella phaffii strain MXY0541 has been genetically modified to produce soy leghemoglobin; the safety of the genetic modification is under assessment by the EFSA GMO Panel (EFSA-GMO-NL-2019-162). The amount of haem iron provided by soy leghemoglobin from its proposed uses in meat analogue products is comparable to that provided by similar amounts of different types of meat. The exposure to iron from the proposed food additive, both at the mean and 95th percentile exposure, will be below the 'safe levels of intake' established by the NDA Panel for all population groups. Considering that the components of the proposed food additive will be digested to small peptide, amino acids and haem B; the recipient (non GM) strain qualifies for qualified presumption of safety status; no genotoxicity concern has been identified and no adverse effects have been identified at the highest dose tested in the available toxicological studies, the Panel concluded that there was no need to set a numerical acceptable daily intake (ADI) and that the food additive does not raise a safety concern at the proposed use in food category 12.9 and maximum use level. The Panel concluded that the use of soy leghemoglobin from genetically modified Komagataella phaffii MXY0541 as a new food additive does not raise a safety concern at the proposed use and use level. This safety evaluation of the proposed food additive remains provisional subject to the ongoing safety assessment of the genetic modification of the production strain by the GMO Panel (EFSA-GMO-NL-2019-162).
Collapse
|
10
|
Krishna S, Jung ST, Lee EY. Escherichia coli and Pichia pastoris: microbial cell-factory platform for -full-length IgG production. Crit Rev Biotechnol 2024:1-23. [PMID: 38797692 DOI: 10.1080/07388551.2024.2342969] [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: 12/13/2023] [Accepted: 03/18/2024] [Indexed: 05/29/2024]
Abstract
Owing to the unmet demand, the pharmaceutical industry is investigating an alternative host to mammalian cells to produce antibodies for a variety of therapeutic and research applications. Regardless of some disadvantages, Escherichia coli and Pichia pastoris are the preferred microbial hosts for antibody production. Despite the fact that the production of full-length antibodies has been successfully demonstrated in E. coli, which has mostly been used to produce antibody fragments, such as: antigen-binding fragments (Fab), single-chain fragment variable (scFv), and nanobodies. In contrast, Pichia, a eukaryotic microbial host, is mostly used to produce glycosylated full-length antibodies, though hypermannosylated glycan is a major challenge. Advanced strategies, such as the introduction of human-like glycosylation in endotoxin-edited E. coli and cell-free system-based glycosylation, are making progress in creating human-like glycosylation profiles of antibodies in these microbes. This review begins by explaining the structural and functional requirements of antibodies and continues by describing and analyzing the potential of E. coli and P. pastoris as hosts for providing a favorable environment to create a fully functional antibody. In addition, authors compare these microbes on certain features and predict their future in antibody production. Briefly, this review analyzes, compares, and highlights E. coli and P. pastoris as potential hosts for antibody production.
Collapse
Affiliation(s)
- Shyam Krishna
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Sang Taek Jung
- BK21 Graduate Program, Department of Biomedical Sciences, Graduate School, Korea University, Seoul, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| |
Collapse
|
11
|
Tsuda M, Nonaka K. Recent progress on heterologous protein production in methylotrophic yeast systems. World J Microbiol Biotechnol 2024; 40:200. [PMID: 38730212 PMCID: PMC11087369 DOI: 10.1007/s11274-024-04008-9] [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: 03/04/2024] [Accepted: 04/27/2024] [Indexed: 05/12/2024]
Abstract
Recombinant protein production technology is widely applied to the manufacture of biologics used as drug substances and industrial proteins such as recombinant enzymes and bioactive proteins. Various heterologous protein production systems have been developed using prokaryotic and eukaryotic hosts. Especially methylotrophic yeast in eukaryotic hosts is suggested to be particularly valuable because such systems have the following advantages: protein secretion into culture broth, eukaryotic quality control systems, a post-translational modification system, rapid growth, and established recombinant DNA tools and technologies such as strong promoters, effective selection markers, and gene knock-in and -out systems. Many methylotrophic yeasts such as the genera Candida, Ogataea, and Komagataella have been studied since methylotrophic yeast was first isolated in 1969. The methanol-consumption-related genes in methylotrophic yeast are strongly and strictly regulated under methanol-containing conditions. The well-regulated gene expression systems under the methanol-inducible gene promoter lead to the potential application of heterologous protein production in methylotrophic yeast. In this review, we describe the recent progress of heterologous protein production technology in methylotrophic yeast and introduce Ogataea minuta as an alternative production host as a substitute for K. phaffii and O. polymorpha.
Collapse
Affiliation(s)
- Masashi Tsuda
- Biologics Technology Research Laboratories I, Daiichi Sankyo Co., Ltd., 2716-1 Kurakake, Akaiwa, Chiyoda, Gunma, 370-0503, Japan.
| | - Koichi Nonaka
- Biologics Technology Research Laboratories I, Daiichi Sankyo Co., Ltd., 2716-1 Kurakake, Akaiwa, Chiyoda, Gunma, 370-0503, Japan
| |
Collapse
|
12
|
Steimann T, Heite Z, Germer A, Blank LM, Büchs J, Mann M, Magnus JB. Understanding exopolysaccharide byproduct formation in Komagataella phaffii fermentation processes for recombinant protein production. Microb Cell Fact 2024; 23:131. [PMID: 38711081 DOI: 10.1186/s12934-024-02403-3] [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: 02/13/2024] [Accepted: 04/24/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Komagataella phaffii (Pichia pastoris) has emerged as a common and robust biotechnological platform organism, to produce recombinant proteins and other bioproducts of commercial interest. Key advantage of K. phaffii is the secretion of recombinant proteins, coupled with a low host protein secretion. This facilitates downstream processing, resulting in high purity of the target protein. However, a significant but often overlooked aspect is the presence of an unknown polysaccharide impurity in the supernatant. Surprisingly, this impurity has received limited attention in the literature, and its presence and quantification are rarely addressed. RESULTS This study aims to quantify this exopolysaccharide in high cell density recombinant protein production processes and identify its origin. In stirred tank fed-batch fermentations with a maximal cell dry weight of 155 g/L, the polysaccharide concentration in the supernatant can reach up to 8.7 g/L. This level is similar to the achievable target protein concentration. Importantly, the results demonstrate that exopolysaccharide production is independent of the substrate and the protein production process itself. Instead, it is directly correlated with biomass formation and proportional to cell dry weight. Cell lysis can confidently be ruled out as the source of this exopolysaccharide in the culture medium. Furthermore, the polysaccharide secretion can be linked to a mutation in the HOC1 gene, featured by all derivatives of strain NRRL Y-11430, leading to a characteristic thinner cell wall. CONCLUSIONS This research sheds light on a previously disregarded aspect of K. phaffii fermentations, emphasizing the importance of monitoring and addressing the exopolysaccharide impurity in biotechnological applications, independent of the recombinant protein produced.
Collapse
Affiliation(s)
- Thomas Steimann
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Zoe Heite
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Andrea Germer
- iAMB-Institute of Applied Microbiology, RWTH Aachen University, Worringer Weg 1, 52074, Aachen, Germany
| | - Lars Mathias Blank
- iAMB-Institute of Applied Microbiology, RWTH Aachen University, Worringer Weg 1, 52074, Aachen, Germany
| | - Jochen Büchs
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Marcel Mann
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Jørgen Barsett Magnus
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany.
| |
Collapse
|
13
|
Weiss F, Requena-Moreno G, Pichler C, Valero F, Glieder A, Garcia-Ortega X. Scalable protein production by Komagataella phaffii enabled by ARS plasmids and carbon source-based selection. Microb Cell Fact 2024; 23:116. [PMID: 38643119 PMCID: PMC11031860 DOI: 10.1186/s12934-024-02368-3] [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: 01/30/2024] [Accepted: 03/18/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Most recombinant Komagataella phaffii (Pichia pastoris) strains for protein production are generated by genomic integration of expression cassettes. The clonal variability in gene copy numbers, integration loci and consequently product titers limit the aptitude for high throughput applications in drug discovery, enzyme engineering or most comparative analyses of genetic elements such as promoters or secretion signals. Circular episomal plasmids with an autonomously replicating sequence (ARS), an alternative which would alleviate some of these limitations, are inherently unstable in K. phaffii. Permanent selection pressure, mostly enabled by antibiotic resistance or auxotrophy markers, is crucial for plasmid maintenance and hardly scalable for production. The establishment and use of extrachromosomal ARS plasmids with key genes of the glycerol metabolism (glycerol kinase 1, GUT1, and triosephosphate isomerase 1, TPI1) as selection markers was investigated to obtain a system with high transformation rates that can be directly used for scalable production processes in lab scale bioreactors. RESULTS In micro-scale deep-well plate experiments, ARS plasmids employing the Ashbya gossypii TEF1 (transcription elongation factor 1) promoter to regulate transcription of the marker gene were found to deliver high transformation efficiencies and the best performances with the reporter protein (CalB, lipase B of Candida antarctica) for both, the GUT1- and TPI1-based, marker systems. The GUT1 marker-bearing strain surpassed the reference strain with integrated expression cassette by 46% upon re-evaluation in shake flask cultures regarding CalB production, while the TPI1 system was slightly less productive compared to the control. In 5 L bioreactor methanol-free fed-batch cultivations, the episomal production system employing the GUT1 marker led to 100% increased CalB activity in the culture supernatant compared to integration construct. CONCLUSIONS For the first time, a scalable and methanol-independent expression system for recombinant protein production for K. phaffii using episomal expression vectors was demonstrated. Expression of the GUT1 selection marker gene of the new ARS plasmids was refined by employing the TEF1 promoter of A. gossypii. Additionally, the antibiotic-free marker toolbox for K. phaffii was expanded by the TPI1 marker system, which proved to be similarly suited for the use in episomal plasmids as well as integrative expression constructs for the purpose of recombinant protein production.
Collapse
Affiliation(s)
- Florian Weiss
- Christian Doppler Laboratory for Innovative Pichia pastoris host and vector systems, Institute of Molecular Biotechnology, Graz University of Technology, Graz, A-8010, Austria
| | - Guillermo Requena-Moreno
- Christian Doppler Laboratory for Innovative Pichia Pastoris Host and Vector Systems, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, 08193, Spain
| | - Carsten Pichler
- Christian Doppler Laboratory for Innovative Pichia pastoris host and vector systems, Institute of Molecular Biotechnology, Graz University of Technology, Graz, A-8010, Austria
| | - Francisco Valero
- Christian Doppler Laboratory for Innovative Pichia Pastoris Host and Vector Systems, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, 08193, Spain
| | - Anton Glieder
- Christian Doppler Laboratory for Innovative Pichia pastoris host and vector systems, Institute of Molecular Biotechnology, Graz University of Technology, Graz, A-8010, Austria.
| | - Xavier Garcia-Ortega
- Christian Doppler Laboratory for Innovative Pichia Pastoris Host and Vector Systems, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, 08193, Spain
| |
Collapse
|
14
|
Wang X, Xu M, Ren X, Li M, Wang C, Yang F, Li X. High-Level Expression and Biochemical Characterization of a Maltotetraose Amylase in Pichia pastoris X-33 for Maltotetraose Production. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04871-0. [PMID: 38407782 DOI: 10.1007/s12010-024-04871-0] [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] [Accepted: 02/12/2024] [Indexed: 02/27/2024]
Abstract
Maltotetraose amylase, which catalyzes the hydrolysis of amylaceous polysaccharides into maltooligosaccharides with maltotetraose as the main product, is extensively used in the food industry. However, the lack of efficient expression system for maltotetraose amylase has hampered its production and application. In this study, high-level production of a maltotetraose amylase mutant (referred to as Pp-Mta∆CBM) from Pseudomonas saccharophila was achieved in Pichia pastoris X-33. First, the gene of maltotetraose amylase with the carbohydrate-binding module (CBM) removed was codon-optimized and cloned into the pPICZαA vector, followed by transformation into P. pastoris X-33 for expression. Using the promoter PAOX1 and signal peptide α-factor, high-level production of Pp-Mta∆CBM with minimal extracellular impurity proteins was achieved, resulting in an extracellular activity of 367.9 U/mL after 7 days of cultivation in shake flasks. Next, the expressed Pp-Mta∆CBM was purified and characterized. This recombinant enzyme was glycosylated and has maximum activity at 55 ℃ and pH 7.0. Its Km for soluble starch was 4.1 g/L, and its kcat was 3237.6 s-1. Finally, the Pp-Mta∆CBM was found to produce a maximum maltotetraose yield of 57.1% in the presence of 200 g/L of substrate. The findings presented in this study demonstrate the efficient production of Pp-Mta∆CBM in P. pastoris, providing a new expression system for maltotetraose amylase and laying the foundation for its scale-up production and industrial application.
Collapse
Affiliation(s)
- Xinyu Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Ming Xu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Xiaopeng Ren
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Mingyu Li
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Conggang Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China.
| | - Fan Yang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China.
| | - Xianzhen Li
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| |
Collapse
|
15
|
Khlebodarova TM, Bogacheva NV, Zadorozhny AV, Bryanskaya AV, Vasilieva AR, Chesnokov DO, Pavlova EI, Peltek SE. Komagataella phaffii as a Platform for Heterologous Expression of Enzymes Used for Industry. Microorganisms 2024; 12:346. [PMID: 38399750 PMCID: PMC10892927 DOI: 10.3390/microorganisms12020346] [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: 01/15/2024] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
In the 1980s, Escherichia coli was the preferred host for heterologous protein expression owing to its capacity for rapid growth in complex media; well-studied genetics; rapid and direct transformation with foreign DNA; and easily scalable fermentation. Despite the relative ease of use of E. coli for achieving the high expression of many recombinant proteins, for some proteins, e.g., membrane proteins or proteins of eukaryotic origin, this approach can be rather ineffective. Another microorganism long-used and popular as an expression system is baker's yeast, Saccharomyces cerevisiae. In spite of a number of obvious advantages of these yeasts as host cells, there are some limitations on their use as expression systems, for example, inefficient secretion, misfolding, hyperglycosylation, and aberrant proteolytic processing of proteins. Over the past decade, nontraditional yeast species have been adapted to the role of alternative hosts for the production of recombinant proteins, e.g., Komagataella phaffii, Yarrowia lipolytica, and Schizosaccharomyces pombe. These yeast species' several physiological characteristics (that are different from those of S. cerevisiae), such as faster growth on cheap carbon sources and higher secretion capacity, make them practical alternative hosts for biotechnological purposes. Currently, the K. phaffii-based expression system is one of the most popular for the production of heterologous proteins. Along with the low secretion of endogenous proteins, K. phaffii efficiently produces and secretes heterologous proteins in high yields, thereby reducing the cost of purifying the latter. This review will discuss practical approaches and technological solutions for the efficient expression of recombinant proteins in K. phaffii, mainly based on the example of enzymes used for the feed industry.
Collapse
Affiliation(s)
- Tamara M. Khlebodarova
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Natalia V. Bogacheva
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Andrey V. Zadorozhny
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alla V. Bryanskaya
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Asya R. Vasilieva
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Danil O. Chesnokov
- Sector of Genetics of Industrial Microorganisms of Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.O.C.); (E.I.P.)
| | - Elena I. Pavlova
- Sector of Genetics of Industrial Microorganisms of Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.O.C.); (E.I.P.)
| | - Sergey E. Peltek
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| |
Collapse
|
16
|
Wang J, Bao C, Cao H, Huang F, Liu Y, Cao Y. Multi-copy expression of a protease-resistant xylanase with high xylan degradation ability and its application in broilers fed wheat-based diets. Int J Biol Macromol 2024; 257:128633. [PMID: 38070812 DOI: 10.1016/j.ijbiomac.2023.128633] [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: 09/09/2023] [Revised: 11/27/2023] [Accepted: 12/03/2023] [Indexed: 01/26/2024]
Abstract
The acidic thermostable xylanase (AT-xynA) has great potential in the feed industry, but its low activity is not conductive to large-scale production, and its application in poultry diets still needs to be further evaluated. In Experiment1, AT-xynA activity increased 3.10 times by constructing multi-copy strains, and the highest activity reached 10,018.29 ± 91.18 U/mL. AT-xynA showed protease resistance, high specificity for xylan substrates, xylobiose and xylotriose were the main hydrolysates. In Experiment2, 192 broilers were assigned into 3 treatments including a wheat-based diet, and the diets supplemented with AT-xynA during the entire period (XY-42) or exclusively during the early stage (XY-21). AT-xynA improved growth performance, while the performance of XY-21 and XY-42 was identical. To further clarify the mechanism underlying the particular effectiveness of AT-xynA during the early stage, 128 broilers were allotted into 2 treatments including a wheat-based diet and the diet supplemented with AT-xynA for 42 d in Experiment3. AT-xynA improved intestinal digestive function and microbiota composition, the benefits were stronger in younger broilers than older ones. Overall, the activity of AT-xynA exhibiting protease resistance and high xylan degradation ability increased by constructing multi-copy strains, and AT-xynA was particularly effective in improving broiler performance during the early stage.
Collapse
Affiliation(s)
- Jian Wang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, People's Republic of China; Department of Nutrition and Health, China Agricultural University, Beijing 100091, People's Republic of China
| | - Chengling Bao
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Heng Cao
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Fei Huang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Yajing Liu
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Yunhe Cao
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, People's Republic of China.
| |
Collapse
|
17
|
Fernandes Fidelis C, Silva de Araújo L, Prates-Patarroyo PA, Martins-Kalks KH, Licursi de Oliveira L, Vargas Viloria MI, Tafur-Gómez GA, Patarroyo Salcedo JH. Immunisation with Neospora caninum subunits rsNcSAG4 and rsNcGRA1 (NcSAG4 and NcGRA1 epitopes construct) in BALB/c mice: the profile of the immune response and controlling the vertical transmission. Parasitol Res 2023; 123:58. [PMID: 38110570 PMCID: PMC10728228 DOI: 10.1007/s00436-023-08020-0] [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: 04/17/2023] [Accepted: 11/21/2023] [Indexed: 12/20/2023]
Abstract
Neospora caninum is an apicomplexan protozoan that causes neosporosis, which has a high economic impact on cattle herds with no available vaccine. During infection, the secretion of dense granules and the expression of surface antigens play an important role in hosting immunomodulation. However, some epitopes of those antigens are immunogenic, and using these fractions could improve the subunit antigens in vaccine design. This study evaluates the recombinant peptides rsNcGRA1 and rsNcSAG4 derived from NcGRA1 and NcSAG4 native antigens as vaccine candidates produced by a fermentative process in the yeast culture system of Komagataella phaffii strain Km71, confirmed by colony PCR, SDS-PAGE, and western blotting. The assay was conducted in BALB/c mice using the peptides at low (25 μg) and standard (50 μg) dosages in monovalent and combined administrations at three time points with saponin as an adjuvant assessing the immunogenicity by antibodies response and cytokine production. We challenge the females after pregnancy confirmation using 2 × 105 NC-1 tachyzoites previously propagated in Vero cells. We assessed the chronic infection in dams and vertical transmission in the offspring by PCR and histopathology. Mice, especially those immunised with combined peptides and monovalent rsNcGRA1 at a standard dose, controlling the chronic infection in dams with the absence of clinical manifestations, showed an immune response with induction of IgG1, a proper balance between Th1/Th2 cytokines and reduced vertical transmission in the pups. In contrast, dams inoculated with a placebo vaccine showed clinical signs, low-scored brain lesions, augmented chronic infection with 80% positivity, 31% mortality in pups, and 81% vertical transmission. These findings indicate that rsNcGRA1 peptides in monovalent and combined with rsNCSAG4 at standard dose are potential vaccine candidates and improve the protective immune response against neosporosis in mice.
Collapse
Affiliation(s)
- Cintia Fernandes Fidelis
- Laboratório de Biologia e Controle de Hematozoários e Vetores, Departamento de Veterinária, Instituto de Biotecnologia Aplicada à Agropecuária - BIOAGRO, Universidade Federal de Viçosa - UFV, CEP, Viçosa, MG, 36570-900, Brazil
| | - Leandro Silva de Araújo
- Laboratório de Biologia e Controle de Hematozoários e Vetores, Departamento de Veterinária, Instituto de Biotecnologia Aplicada à Agropecuária - BIOAGRO, Universidade Federal de Viçosa - UFV, CEP, Viçosa, MG, 36570-900, Brazil
| | - Pablo A Prates-Patarroyo
- Laboratório de Biologia e Controle de Hematozoários e Vetores, Departamento de Veterinária, Instituto de Biotecnologia Aplicada à Agropecuária - BIOAGRO, Universidade Federal de Viçosa - UFV, CEP, Viçosa, MG, 36570-900, Brazil
| | - Karlos H Martins-Kalks
- Laboratório de Biologia e Controle de Hematozoários e Vetores, Departamento de Veterinária, Instituto de Biotecnologia Aplicada à Agropecuária - BIOAGRO, Universidade Federal de Viçosa - UFV, CEP, Viçosa, MG, 36570-900, Brazil
| | - Leandro Licursi de Oliveira
- Laboratório de Imunoquímica e Glicobiologia, Departamento de Biologia Geral, Universidade Federal de Viçosa - UFV, CEP, Viçosa, MG, 36570-900, Brazil
| | - Marlene Isabel Vargas Viloria
- Laboratório de Biologia e Controle de Hematozoários e Vetores, Departamento de Veterinária, Instituto de Biotecnologia Aplicada à Agropecuária - BIOAGRO, Universidade Federal de Viçosa - UFV, CEP, Viçosa, MG, 36570-900, Brazil
| | - Gabriel A Tafur-Gómez
- Universidad de Ciencias Aplicadas y Ambientales - U.D.C.A, Bogotá, 111166, Colombia.
| | - Joaquín Hernán Patarroyo Salcedo
- Laboratório de Biologia e Controle de Hematozoários e Vetores, Departamento de Veterinária, Instituto de Biotecnologia Aplicada à Agropecuária - BIOAGRO, Universidade Federal de Viçosa - UFV, CEP, Viçosa, MG, 36570-900, Brazil.
- Patsos Biotecnologia, Parque tecnológico de Viçosa, CEP, Viçosa, MG, 36570-900, Brazil.
| |
Collapse
|
18
|
Miroshnichenko S, Pykhtina M, Kotliarova A, Chepurnov A, Beklemishev A. Engineering a New IFN-ApoA-I Fusion Protein with Low Toxicity and Prolonged Action. Molecules 2023; 28:8014. [PMID: 38138504 PMCID: PMC10745500 DOI: 10.3390/molecules28248014] [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: 10/28/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Recombinant human interferon alpha-2b (rIFN) is widely used in antiviral and anticancer immunotherapy. However, the high efficiency of interferon therapy is accompanied by a number of side effects; this problem requires the design of a new class of interferon molecules with reduced cytotoxicity. In this work, IFN was modified via genetic engineering methods by merging it with the blood plasma protein apolipoprotein A-I in order to reduce acute toxicity and improve the pharmacokinetics of IFN. The chimeric protein was obtained via biosynthesis in the yeast P. pastoris. The yield of ryIFN-ApoA-I protein when cultivated on a shaker in flasks was 30 mg/L; protein purification was carried out using reverse-phase chromatography to a purity of 95-97%. The chimeric protein demonstrated complete preservation of the biological activity of IFN in the model of vesicular stomatitis virus and SARS-CoV-2. In addition, the chimeric form had reduced cytotoxicity towards Vero cells and increased cell viability under viral load conditions compared with commercial IFN-a2b preparations. Analysis of the pharmacokinetic profile of ryIFN-ApoA-I after a single subcutaneous injection in mice showed a 1.8-fold increased half-life of the chimeric protein compared with ryIFN.
Collapse
Affiliation(s)
- Svetlana Miroshnichenko
- Federal Research Center of Fundamental and Translational Medicine (FRC FTM), Timakova str., 2, 630117 Novosibirsk, Russia; (S.M.); (A.C.); (A.B.)
| | - Mariya Pykhtina
- Federal Research Center of Fundamental and Translational Medicine (FRC FTM), Timakova str., 2, 630117 Novosibirsk, Russia; (S.M.); (A.C.); (A.B.)
| | - Anastasiia Kotliarova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev Ave., 9, 630090 Novosibirsk, Russia;
| | - Alexander Chepurnov
- Federal Research Center of Fundamental and Translational Medicine (FRC FTM), Timakova str., 2, 630117 Novosibirsk, Russia; (S.M.); (A.C.); (A.B.)
| | - Anatoly Beklemishev
- Federal Research Center of Fundamental and Translational Medicine (FRC FTM), Timakova str., 2, 630117 Novosibirsk, Russia; (S.M.); (A.C.); (A.B.)
| |
Collapse
|
19
|
Eskandari A, Nezhad NG, Leow TC, Rahman MBA, Oslan SN. Current achievements, strategies, obstacles, and overcoming the challenges of the protein engineering in Pichia pastoris expression system. World J Microbiol Biotechnol 2023; 40:39. [PMID: 38062216 DOI: 10.1007/s11274-023-03851-6] [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: 10/11/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023]
Abstract
Yeasts serve as exceptional hosts in the manufacturing of functional protein engineering and possess industrial or medical utilities. Considerable focus has been directed towards yeast owing to its inherent benefits and recent advancements in this particular cellular host. The Pichia pastoris expression system is widely recognized as a prominent and widely accepted instrument in molecular biology for the purpose of generating recombinant proteins. The advantages of utilizing the P. pastoris system for protein production encompass the proper folding process occurring within the endoplasmic reticulum (ER), as well as the subsequent secretion mediated by Kex2 as a signal peptidase, ultimately leading to the release of recombinant proteins into the extracellular environment of the cell. In addition, within the P. pastoris expression system, the ease of purifying recombinant protein arises from its restricted synthesis of endogenous secretory proteins. Despite its achievements, scientists often encounter persistent challenges when attempting to utilize yeast for the production of recombinant proteins. This review is dedicated to discussing the current achievements in the usage of P. pastoris as an expression host. Furthermore, it sheds light on the strategies employed in the expression system and the optimization and development of the fermentative process of this yeast. Finally, the impediments (such as identifying high expression strains, improving secretion efficiency, and decreasing hyperglycosylation) and successful resolution of certain difficulties are put forth and deliberated upon in order to assist and promote the expression of complex proteins in this prevalent recombinant host.
Collapse
Affiliation(s)
- Azadeh Eskandari
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | | | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
| |
Collapse
|
20
|
Irshad B, Lu C, Nederstigt AE, Hu P, Xue L, Lin-Cereghino J, Franz AH, Harrison JS, Lin-Cereghino GP. The effect of the bgs13 mutation on the structure of the reporter protein beta-lactoglobulin: Influence on folding and aggregation in Pichia pastoris. Protein Expr Purif 2023; 212:106355. [PMID: 37598731 PMCID: PMC10528908 DOI: 10.1016/j.pep.2023.106355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/22/2023]
Abstract
Pichia pastoris, a methylotrophic yeast used for recombinant protein expression, has the capability of performing many eukaryotic post-translational modifications, growing to high cell densities, and producing proteins in a cost-effective manner. However, P. pastoris's secretion properties are not always efficient, and its secretory pathway mechanisms have not been thoroughly elucidated. A previously identified mutant strain, bgs13, was found to efficiently secrete most recombinant proteins tested, raising the possibility that this bgs13 mutant is a universal super secreter. In this study, we used a reporter protein, β-lactoglobulin (b-LG), to perform structural analysis of the protein secreted from wild type and mutant bgs13 strains to investigate the secretory mechanism. Primary, secondary, and tertiary structures of b-LG were examined using Edman sequencing, circular dichroism, tryptophan fluorescence, and temperature induced aggregation analysis. Our results demonstrate that the bgs13 produced more b-LG than the wt strain and that this protein was functionally folded similar to the wt. Surprisingly, we also found that the bgs13 b-LG was more resistant to aggregation, providing another example of the superior qualities of this strain for enhanced secreted protein production.
Collapse
Affiliation(s)
- Bushra Irshad
- Department of Biological Sciences, University of the Pacific, Stockton, CA, 95211, USA
| | - Cai Lu
- Department of Chemistry, University of the Pacific, Stockton, CA, 95211, USA
| | - Anneroos E Nederstigt
- Biomolecular Mass Spectrometry and Proteomics, Utrecht University, Utrecht, the Netherlands
| | - Priscilla Hu
- Department of Biological Sciences, University of the Pacific, Stockton, CA, 95211, USA
| | - Liang Xue
- Department of Chemistry, University of the Pacific, Stockton, CA, 95211, USA
| | - Joan Lin-Cereghino
- Department of Biological Sciences, University of the Pacific, Stockton, CA, 95211, USA
| | - Andreas H Franz
- Department of Chemistry, University of the Pacific, Stockton, CA, 95211, USA
| | - Joseph S Harrison
- Department of Chemistry, University of the Pacific, Stockton, CA, 95211, USA.
| | - Geoff P Lin-Cereghino
- Department of Biological Sciences, University of the Pacific, Stockton, CA, 95211, USA.
| |
Collapse
|
21
|
Liu Y, Jiang B, Wang K. A review of fermented bee products: Sources, nutritional values, and health benefits. Food Res Int 2023; 174:113506. [PMID: 37986501 DOI: 10.1016/j.foodres.2023.113506] [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: 07/31/2023] [Revised: 09/15/2023] [Accepted: 09/22/2023] [Indexed: 11/22/2023]
Abstract
Bee products have garnered considerable interest due to their abundant nutritional content and versatile biological activities. The utilization of bee products as fermentation materials has shown favorable potential for increasing nutrients, altering texture, and endorsing unique tastes. This review critically examines the existing literature on fermented bee products, with a specific emphasis on the impact of fermentation on their nutritional composition and potential health benefits. The raw materials, strains, conditions, and methodologies employed in the fermentation of bee products, as well as the utilization of bee products as fermentation raw materials/excipients, are reviewed. We also present a special focus on the nutritional composition and content of bioactive substances, such as polyphenols and volatile organic compounds, in fermented bee products. Additionally, the influence of fermentation on bee product ingredients and their health benefits is summarized. Fermented bee products substantially benefit human health, with superior antioxidant, anti-inflammatory, and anti-allergic properties compared to non-fermented bee products. Finally, this article discusses the types, strains, health benefits, production processes, and market prospects of fermented bee products, which are expected to become an important part of human food culture as functional food or nutritional supplements. The aforementioned findings highlight the remarkable nutritional value and bioactive properties exhibited by fermented bee products.
Collapse
Affiliation(s)
- Yang Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Bokai Jiang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Kai Wang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China.
| |
Collapse
|
22
|
Joseph JA, Akkermans S, Van Impe JF. Macroscopic modeling of the growth and substrate consumption of wild type and genetically modified Pichia pastoris. Biotechnol J 2023; 18:e2300164. [PMID: 37688402 DOI: 10.1002/biot.202300164] [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: 04/13/2023] [Revised: 08/15/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023]
Abstract
Pichia pastoris is a popular yeast platform to generate several industrially relevant products which have applications in a wide range of sectors. The complexities in the processes due to the addition of a foreign gene are not widely explored. Since these complexities can be dependent on the strain characteristics, promoter, and type of protein produced, it is vital to investigate the growth and substrate consumption patterns of the host to facilitate customized process optimization. In this study, the growth rates of P. pastoris GS115 wild type (WT) and genetically modified (GM) strains grown on glycerol and methanol in batch cultivation mode were estimated and the model providing the best representation of the true growth kinetics based on substrate consumption was identified. It was observed that the growth of P. pastoris exhibits Haldane kinetics on glycerol rather than the most commonly used Monod kinetics due to the inability of the latter to describe growth inhibition at high concentrations of glycerol. Whereas, the cardinal parameter model, a newly proposed model for this application, was found to be the best fitting to describe the growth of P. pastoris on methanol due to its ability to describe methanol toxicity. Interestingly, the findings from this study concluded that in both substrates, the genetically engineered strain exhibited a higher growth rate compared to the WT strain. Such an observation has not been established yet in other published works, indicating an opportunity to further optimize the carbon source feeding strategies when the host is grown in fed-batch mode.
Collapse
Affiliation(s)
- Jewel Ann Joseph
- BioTeC+, Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Ghent, Belgium
| | - Simen Akkermans
- BioTeC+, Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Ghent, Belgium
| | - Jan F Van Impe
- BioTeC+, Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Ghent, Belgium
| |
Collapse
|
23
|
Guo X, Ma Y, Wang H, Yin H, Shi X, Chen Y, Gao G, Sun L, Wang J, Wang Y, Fan D. Status and developmental trends in recombinant collagen preparation technology. Regen Biomater 2023; 11:rbad106. [PMID: 38173768 PMCID: PMC10761200 DOI: 10.1093/rb/rbad106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024] Open
Abstract
Recombinant collagen is a pivotal topic in foundational biological research and epitomizes the application of critical bioengineering technologies. These technological advancements have profound implications across diverse areas such as regenerative medicine, organ replacement, tissue engineering, cosmetics and more. Thus, recombinant collagen and its preparation methodologies rooted in genetically engineered cells mark pivotal milestones in medical product research. This article provides a comprehensive overview of the current genetic engineering technologies and methods used in the production of recombinant collagen, as well as the conventional production process and quality control detection methods for this material. Furthermore, the discussion extends to foresee the strides in physical transfection and magnetic control sorting studies, envisioning an enhanced preparation of recombinant collagen-seeded cells to further fuel recombinant collagen production.
Collapse
Affiliation(s)
- Xiaolei Guo
- Center for Medical Device Evaluation, National Medical Products Administration, Beijing 100081, China
| | - Yuan Ma
- State Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Hang Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Hongping Yin
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Xinli Shi
- Center for Medical Device Evaluation, National Medical Products Administration, Beijing 100081, China
| | - Yiqin Chen
- State Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Guobiao Gao
- Center for Medical Device Evaluation, National Medical Products Administration, Beijing 100081, China
| | - Lei Sun
- Center for Medical Device Evaluation, National Medical Products Administration, Beijing 100081, China
| | - Jiadao Wang
- State Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Yunbing Wang
- National Engineering Research Center for Biomaterials & College of Biomedical Engineering, Sichuan University, Chengdu 610064, China
| | - Daidi Fan
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710127, China
| |
Collapse
|
24
|
Aza P, Camarero S. Fungal Laccases: Fundamentals, Engineering and Classification Update. Biomolecules 2023; 13:1716. [PMID: 38136587 PMCID: PMC10741624 DOI: 10.3390/biom13121716] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Multicopper oxidases (MCOs) share a common catalytic mechanism of activation by oxygen and cupredoxin-like folding, along with some common structural determinants. Laccases constitute the largest group of MCOs, with fungal laccases having the greatest biotechnological applicability due to their superior ability to oxidize a wide range of aromatic compounds and lignin, which is enhanced in the presence of redox mediators. The adaptation of these versatile enzymes to specific application processes can be achieved through the directed evolution of the recombinant enzymes. On the other hand, their substrate versatility and the low sequence homology among laccases make their exact classification difficult. Many of the ever-increasing amounts of MCO entries from fungal genomes are automatically (and often wrongly) annotated as laccases. In a recent comparative genomic study of 52 basidiomycete fungi, MCO classification was revised based on their phylogeny. The enzymes clustered according to common structural motifs and theoretical activities, revealing three novel groups of laccase-like enzymes. This review provides an overview of the structure, catalytic activity, and oxidative mechanism of fungal laccases and how their biotechnological potential as biocatalysts in industry can be greatly enhanced by protein engineering. Finally, recent information on newly identified MCOs with laccase-like activity is included.
Collapse
Affiliation(s)
| | - Susana Camarero
- Margarita Salas Center for Biological Research, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain;
| |
Collapse
|
25
|
Lisov A, Belova O, Lisova Z, Nagel A, Shadrin A, Andreeva-Kovalevskaya Z, Nagornykh M, Zakharova M, Leontievsky A. Two β-glucanases from bacterium Cellulomonas flavigena: expression in Pichia pastoris, properties, biotechnological potential. Prep Biochem Biotechnol 2023; 53:1313-1321. [PMID: 37093814 DOI: 10.1080/10826068.2023.2201934] [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] [Indexed: 04/25/2023]
Abstract
In the genome of Cellulomonas flavigena, two genes that potentially encode endoglucanases - Cfla_2912 and Cfla_2913 were identified. We cloned the genes and created Pichia pastoris-based recombinant producers of two proteins that were expressed from the AOX1 promoter. Each of the endoglucanase molecules contains a GH6 catalytic domain, CBM2 carbohydrate-binding module, and TAT signal peptide. The fermentation of the producers was carried out in a 10 L fermenter; Cfla_2912 and Cfla_2913 were purified using affinity chromatography. The yield comprised 10.3 mg/ml (430 U/ml) for Cfla_2913 and 9 mg/ml (370 U/ml) for Cfla_2912. Cfla_2912 and Cfla_2913 were found to have a high activity against barley β-glucan and lichenan, a weak activity against carboxymethyl cellulose (CMC), phosphoric-acid treated cellulose, and no activity against laminarin, xylan, soluble starch, microcrystalline cellulose, cellobiose, and cellotriose. Thus, the proteins exhibited β-glucanase activity. Both proteins had a neutral pH optimum of about 7.0 and were more stable at neutral and slightly alkaline pH ranging from 7.0 to 9.0. Cfla_2912 and Cfla_2913 showed a moderate thermal stability. The products of barley β-glucan hydrolysis by Cfla_2912 and Cfla_2913 were trisaccharide, tetrasaccharide, and cellobiose. Cfla_2912 and Cfla_2913 efficiently hydrolyzed cereal polysaccharides, which indicate that they may have biotechnological potential.
Collapse
Affiliation(s)
- Alexander Lisov
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Oksana Belova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Zoya Lisova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Nagel
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Shadrin
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Zhanna Andreeva-Kovalevskaya
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Maxim Nagornykh
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Marina Zakharova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Leontievsky
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
26
|
Zha J, Liu D, Ren J, Liu Z, Wu X. Advances in Metabolic Engineering of Pichia pastoris Strains as Powerful Cell Factories. J Fungi (Basel) 2023; 9:1027. [PMID: 37888283 PMCID: PMC10608127 DOI: 10.3390/jof9101027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023] Open
Abstract
Pichia pastoris is the most widely used microorganism for the production of secreted industrial proteins and therapeutic proteins. Recently, this yeast has been repurposed as a cell factory for the production of chemicals and natural products. In this review, the general physiological properties of P. pastoris are summarized and the readily available genetic tools and elements are described, including strains, expression vectors, promoters, gene editing technology mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9, and adaptive laboratory evolution. Moreover, the recent achievements in P. pastoris-based biosynthesis of proteins, natural products, and other compounds are highlighted. The existing issues and possible solutions are also discussed for the construction of efficient P. pastoris cell factories.
Collapse
Affiliation(s)
- Jian Zha
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (D.L.); (J.R.); (Z.L.)
| | | | | | | | - Xia Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (D.L.); (J.R.); (Z.L.)
| |
Collapse
|
27
|
Bao C, Liu Y, Li F, Cao H, Dong B, Cao Y. Expression and Characterization of Laccase Lac1 from Coriolopsis trogii Strain Mafic-2001 in Pichia pastoris and Its Degradation of Lignin. Appl Biochem Biotechnol 2023; 195:6150-6167. [PMID: 36847985 DOI: 10.1007/s12010-023-04390-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2023] [Indexed: 03/01/2023]
Abstract
The laccase gene (Lac1) was cloned from Coriolopsis trogii strain Mafic-2001. Full-length sequence of Lac1 containing 11 exons and 10 introns is composed of 2140 nucleotides (nts). mRNA of Lac1 encoded for a protein of 517 aa. Nucleotide sequence of the laccase was optimized and expressed in Pichia pastoris X-33. SDS-PAGE analysis showed that the molecular weight of the purified recombinant laccase rLac1 was about 70 kDa. The optimum temperature and pH of rLac1 were 40 ℃ and 3.0, respectively. rLac1 showed high residual activity (90%) in the solutions after 1 h incubation at the pH ranging from 2.5 to 8.0. rLac1 maintained over 60% of laccase activity at the temperatures ranging from 20 to 60 °C, and kept higher than 50% of its activity at 40 °C for 2 h. The activity of rLac1 was promoted by Cu2+ and inhibited by Fe2+. Under optimal conditions, lignin degradation rates of rLac1 on the substrates of rice straw, corn stover, and palm kernel cake were 50.24%, 55.49%, and 24.43% (the lignin contents of substrates untreated with rLac1 were 100%), respectively. Treated with rLac1, the structures of agricultural residues (rice straw, corn stover, and palm kernel cake) were obviously loosened which was reflected by the analysis of scanning electron microscopy and Fourier transform infrared spectroscopy. Based on the specific activity of rLac1 on the degradation of lignin, rLac1 from Coriolopsis trogii strain Mafic-2001 has the potential for in-depth utilization of agricultural residues.
Collapse
Affiliation(s)
- Chengling Bao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yajing Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Feiyu Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Heng Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Bing Dong
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yunhe Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
| |
Collapse
|
28
|
Cardoso SL, Souza PM, Rodrigues K, Mota IDS, Filho EF, Fávaro LCDL, Saldanha-Araujo F, Homem-de-Mello M, Pessoa A, Silveira D, Fonseca-Bazzo YM, Magalhães PO. l-Asparaginase Type II from Fusarium proliferatum: Heterologous Expression and In Silico Analysis. Pharmaceutics 2023; 15:2352. [PMID: 37765320 PMCID: PMC10534586 DOI: 10.3390/pharmaceutics15092352] [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: 07/29/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
The search for new drug-producing microorganisms is one of the most promising situations in current world scientific scenarios. The use of molecular biology as well as the cloning of protein and compound genes is already well established as the gold standard method of increasing productivity. Aiming at this increase in productivity, this work aims at the cloning, purification and in silico analysis of l-asparaginase from Fusarium proliferatum in Komagataella phaffii (Pichia pastoris) protein expression systems. The l-asparaginase gene (NCBI OQ439985) has been cloned into Pichia pastoris strains. Enzyme production was analyzed via the quantification of aspartic B-hydroxamate, followed by purification on a DEAE FF ion exchange column. The in silico analysis was proposed based on the combined use of various technological tools. The enzymatic activity found intracellularly was 2.84 IU/g. A purification factor of 1.18 was observed. The in silico analysis revealed the position of five important amino acid residues for enzymatic activity, and likewise, it was possible to predict a monomeric structure with a C-score of 1.59. The production of the enzyme l-asparaginase from F. proliferatum in P. pastoris was demonstrated in this work, being of great importance for the analysis of new methodologies in search of the production of important drugs in therapy.
Collapse
Affiliation(s)
- Samuel Leite Cardoso
- Health Science School, University of Brasilia, Brasilia 70910-900, Brazil; (S.L.C.); (P.M.S.); (I.d.S.M.); (F.S.-A.); (M.H.-d.-M.); (D.S.); (Y.M.F.-B.)
| | - Paula Monteiro Souza
- Health Science School, University of Brasilia, Brasilia 70910-900, Brazil; (S.L.C.); (P.M.S.); (I.d.S.M.); (F.S.-A.); (M.H.-d.-M.); (D.S.); (Y.M.F.-B.)
| | - Kelly Rodrigues
- Brazilian Agricultural Research Corporation—EMBRAPA Agroenergia, Brasilia 70770-901, Brazil; (K.R.); (L.C.d.L.F.)
| | - Isabella de Souza Mota
- Health Science School, University of Brasilia, Brasilia 70910-900, Brazil; (S.L.C.); (P.M.S.); (I.d.S.M.); (F.S.-A.); (M.H.-d.-M.); (D.S.); (Y.M.F.-B.)
| | | | - Léia Cecilia de Lima Fávaro
- Brazilian Agricultural Research Corporation—EMBRAPA Agroenergia, Brasilia 70770-901, Brazil; (K.R.); (L.C.d.L.F.)
| | - Felipe Saldanha-Araujo
- Health Science School, University of Brasilia, Brasilia 70910-900, Brazil; (S.L.C.); (P.M.S.); (I.d.S.M.); (F.S.-A.); (M.H.-d.-M.); (D.S.); (Y.M.F.-B.)
| | - Mauricio Homem-de-Mello
- Health Science School, University of Brasilia, Brasilia 70910-900, Brazil; (S.L.C.); (P.M.S.); (I.d.S.M.); (F.S.-A.); (M.H.-d.-M.); (D.S.); (Y.M.F.-B.)
| | - Adalberto Pessoa
- Department of Biochemical and Pharmaceutical Technology, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Dâmaris Silveira
- Health Science School, University of Brasilia, Brasilia 70910-900, Brazil; (S.L.C.); (P.M.S.); (I.d.S.M.); (F.S.-A.); (M.H.-d.-M.); (D.S.); (Y.M.F.-B.)
| | - Yris Maria Fonseca-Bazzo
- Health Science School, University of Brasilia, Brasilia 70910-900, Brazil; (S.L.C.); (P.M.S.); (I.d.S.M.); (F.S.-A.); (M.H.-d.-M.); (D.S.); (Y.M.F.-B.)
| | - Pérola Oliveira Magalhães
- Health Science School, University of Brasilia, Brasilia 70910-900, Brazil; (S.L.C.); (P.M.S.); (I.d.S.M.); (F.S.-A.); (M.H.-d.-M.); (D.S.); (Y.M.F.-B.)
| |
Collapse
|
29
|
Xifeng W, Jiahua Z, Ningxing L, Guowu Z, Yunxia S, Xuepeng C, Jun Q, Xianzhu X, Qingling M. The regulatory roles of Fasciola hepatica GSTO1 protein in inflammatory cytokine expression and apoptosis in murine macrophages. Acta Trop 2023; 245:106977. [PMID: 37399980 DOI: 10.1016/j.actatropica.2023.106977] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 06/22/2023] [Accepted: 06/24/2023] [Indexed: 07/05/2023]
Abstract
Fascioliasis, a global zoonotic parasitic disease, is mainly caused by Fasciola hepatica (F. hepatica) parasitizing in the livers of hosts, mainly humans and herbivores. Glutathione S-transferase (GST) is one of the important excretory- secretory products (ESPs) from F. hepatica, however, the regulatory roles of its Omega subtype in the immunomodulatory effects remain unknown. Here, we expressed F. hepatica recombinant GSTO1 protein (rGSTO1) in Pichia pastoris and analyzed its antioxidant properties. Then, the interaction between F. hepatica rGSTO1 and RAW264.7 macrophages and its effects on inflammatory responses and cell apoptosis were further explored. The results revealed that GSTO1 of F. hepatica owned the potent ability to resist oxidative stress. F. hepatica rGSTO1 could interact with RAW264.7 macrophages and inhibit its cell viability, furthermore, it may suppress the production of pro-inflammatory cytokines IL-1β, IL-6 and TNF-α, but promote the expression of anti-inflammatory cytokine IL-10. In addition, F. hepatica rGSTO1 may down-regulate the ratio of Bcl-2/Bax, and increase the expression of pro-apoptotic protein caspase-3, thereby eliciting the apoptosis of macrophages. Notably, F. hepatica rGSTO1 inhibited the activation of nuclear factor-κB (NF-κB) and mitogen‑activated protein kinases (MAPKs p38, ERK and JNK) pathways in LPS-activated RAW264.7 cells, exerting potent modulatory effects on macrophages. These findings suggested that F. hepatica GSTO1 can modulate the host immune response, which provided new insights into the immune evasion mechanism of F. hepatica infection in host.
Collapse
Affiliation(s)
- Wang Xifeng
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Zhang Jiahua
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Li Ningxing
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Zhang Guowu
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Shang Yunxia
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Cai Xuepeng
- State Key Lab of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Qiao Jun
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Xia Xianzhu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin 130062, China.
| | - Meng Qingling
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China.
| |
Collapse
|
30
|
Aloysia D’Cor N, Siddaiah P, Mohapatra S, Dhaded SM, I. V. P, Kar S, V. N. T, Muley P, Chhatwal J, Patnaik BN, Vidor E, Moureau A, Patel DM, Midde VJ, Jagga SR, Peesapati S, Noriega F. Safety and immunogenicity of a new formulation of a pentavalent DTwP-HepB-Hib vaccine in healthy Indian infants-A randomized study. PLoS One 2023; 18:e0284898. [PMID: 37582114 PMCID: PMC10426953 DOI: 10.1371/journal.pone.0284898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 04/11/2023] [Indexed: 08/17/2023] Open
Abstract
BACKGROUND Pentavalent vaccines (DTP-HepB-Hib) have been introduced in many countries in their routine public immunization programmes to protect against diphtheria (D), tetanus (T), pertussis (P), hepatitis B (Hep B) and Hemophilus influenzae type b (Hib) diseases. This study compared the safety and immunogenicity of a new formulation of a whole-cell Bordetella pertussis (wP) based pentavalent vaccine (DTwP-HepB-Hib). The new formulation was developed using well-characterized hepatitis B and pertussis whole cell vaccine components. METHODS This was a phase III, observer-blind, randomized, non-inferiority, multi-center study conducted in India among 460 infants who were followed up for safety and immunogenicity for 28 days after administration of three doses of either investigational or licensed comparator formulations at 6-8, 10-12 and 14-16 weeks of age. RESULTS The investigational formulation of DTwP-HepB-Hib vaccine was non-inferior to the licensed formulation in terms of hepatitis B seroprotection rate (% of subjects with HepB antibodies ≥10mIU/mL were 99.1% versus 99.0%, respectively, corresponding to a difference of 0.1% (95% CI, -2.47 to 2.68)) and pertussis immune responses (adjusted geometric mean concentrations of antibodies for anti-PT were 76.7 EU/mL versus 63.3 EU/mL, with a ratio of aGMTs of 1.21 (95% CI, 0.89-1.64), and for anti-FIM were 1079 EU/mL versus 1129 EU/mL, with a ratio of aGMTs of 0.95 (95% CI, 0.73-1.24), respectively). The immune responses to other valences (D, T, and Hib) in the two formulations were also similar. The safety profile of both formulations was found to be similar and were well tolerated. CONCLUSIONS The investigational DTwP-HepB-Hib vaccine formulation was immunogenic and well-tolerated when administered as three dose primary series in infants. CLINICAL TRIAL REGISTRATION Clinical Trials Registry India number: CTRI/2018/12/016692.
Collapse
Affiliation(s)
| | - Prashanth Siddaiah
- Dept. of Pediatrics, Mysore Medical College and Research Institute, Mysore, India
| | - Satyajit Mohapatra
- Dept. of Pharmacology, SRM Medical College Hospital & Research Center, Chennai, India
| | - Sangappa Malappa Dhaded
- Dept. of Pediatrics, KLES Dr Prabhakar Kore Hospital & Medical Research Centre, Belagavi, India
| | - Padmavathi I. V.
- Dept. of Pediatrics, Government Victoria Hospital, Visakhapatnam, India
| | - Sonali Kar
- Dept. of Community Medicine, Kalinga Institute of Medical Sciences, Bhubaneswar, India
| | - Tripathi V. N.
- Dept. of Pediatrics, Prakhar Hospital Pvt. Ltd., Kanpur, India
| | - Prasad Muley
- Dept. of Pediatrics, SBKS Medical College, Vadodara, India
| | - Jugesh Chhatwal
- Dept. of Pediatrics, Christian Medical College & Hospital, Ludhiana, India
| | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Zazulya AZ, Semkiv MV, Stec M, Cyske Z, Gaffke L, Pierzynowska K, Węgrzyn G, Sibirny AA. The Komagatella phaffii ACG1 gene, encoding β-1,6-N-acetylglucosaminyltransferase, is involved in the autophagy of cytosolic and peroxisomal proteins. Yeast 2023; 40:367-376. [PMID: 36814084 DOI: 10.1002/yea.3846] [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: 11/24/2022] [Revised: 01/31/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
The methylotrophic yeast Komagataella phaffii is considered one of the most effective producers of recombinant proteins of industrial importance. Effective producers should be characterized by the maximal reduction of degradation of the cytosolic recombinant proteins. The mechanisms of degradation of cytosolic proteins in K. phaffii have not been elucidated; however, data suggest that they are partially degraded in the autophagic pathway. To identify factors that influence this process, a developed system for the selection of recombinant strains of K. phaffii with impaired autophagic degradation of the heterologous model cytosolic protein (yeast β-galactosidase) was used for insertional tagging of the genes involved in cytosolic proteins degradation. In one of the obtained strains, the insertion cassette disrupted the open reading frame of the gene encoding β-1,6-N-acetylglucosaminyltransferase. A recombinant strain with deletion of this gene was also obtained. The rate of degradation of the β-galactosidase enzyme was two times slower in the insertion mutant and 1.5 times slower in the deletion strain as compared to the parental strain with native β-1,6-N-acetylglucosaminyltransferase. The rate of degradation of native K. phaffii cytosolic and peroxisomal enzymes, formaldehyde dehydrogenase, formate dehydrogenase, and alcohol oxidase, respectively, showed similar trends to that of β-galactosidase-slower degradation in the deletion and insertional mutants as compared to the wild-type strain, but faster protein degradation relative to the strain completely defective in autophagy. We conclude that K. phaffii gene designated ACG1, encoding β-1,6-N-acetylglucosaminyltransferase, is involved in autophagy of the cytosolic and peroxisomal proteins.
Collapse
Affiliation(s)
- Anastasiya Z Zazulya
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Science of Ukraine, Lviv, Ukraine
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Marta V Semkiv
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Science of Ukraine, Lviv, Ukraine
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Maxim Stec
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Science of Ukraine, Lviv, Ukraine
| | - Zuzanna Cyske
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Science of Ukraine, Lviv, Ukraine
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Karolina Pierzynowska
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Science of Ukraine, Lviv, Ukraine
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Andriy A Sibirny
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Science of Ukraine, Lviv, Ukraine
- Department of Biotechnology and Microbiology, University of Rzeszow, Rzeszow, Poland
| |
Collapse
|
32
|
Robainas-Del-Pino Y, Viader-Salvadó JM, Herrera-Estala AL, Guerrero-Olazarán M. Functional characterization of the Komagataella phaffii 1033 gene promoter and transcriptional terminator. World J Microbiol Biotechnol 2023; 39:246. [PMID: 37420160 DOI: 10.1007/s11274-023-03682-5] [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: 10/22/2022] [Accepted: 06/16/2023] [Indexed: 07/09/2023]
Abstract
The methylotrophic yeast Komagataella phaffii (syn. Pichia pastoris) is a widely used host for extracellularly producing heterologous proteins via an expression cassette integrated into the yeast genome. A strong promoter in the expression cassette is not always the most favorable choice for heterologous protein production, especially if the correct folding of the protein and/or post-translational processing is the limiting step. The transcriptional terminator is another regulatory element in the expression cassette that can modify the expression levels of the heterologous gene. In this work, we identified and functionally characterized the promoter (P1033) and transcriptional terminator (T1033) of a constitutive gene (i.e., the 1033 gene) with a weak non-methanol-dependent transcriptional activity. We constructed two K. phaffii strains with two combinations of the regulatory DNA elements from the 1033 and AOX1 genes (i.e., P1033-TAOX1 and P1033-T1033 pairs) and evaluated the impact of the regulatory element combinations on the transcript levels of the heterologous gene and endogenous 1033 and GAPDH genes in cells grown in glucose or glycerol, and on the extracellular product/biomass yield. The results indicate that the P1033 has a 2-3% transcriptional activity of the GAP promoter and it is tunable by cell growth and the carbon source. The combinations of the regulatory elements rendered different transcriptional activity of the heterologous and endogenous genes that were dependent on the carbon source. The promoter-terminator pair and the carbon source affected the heterologous gene translation and/or protein secretion pathway. Moreover, low heterologous gene-transcript levels along with glycerol cultures increased translation and/or protein secretion.
Collapse
Affiliation(s)
- Yanelis Robainas-Del-Pino
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico
| | - José María Viader-Salvadó
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico.
| | - Ana Lucía Herrera-Estala
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico
| | - Martha Guerrero-Olazarán
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico.
| |
Collapse
|
33
|
Wang P, Hu J, Min S, Chen C, Zhu Y, Pan Y, Wei D, Wang X. Recombinant Phaseolus vulgaris phytohemagglutinin L-form expressed in the Bacillus brevis exerts in vitro and in vivo anti-tumor activity through potentiation of apoptosis and immunomodulation. Int Immunopharmacol 2023; 120:110322. [PMID: 37269742 DOI: 10.1016/j.intimp.2023.110322] [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: 03/17/2023] [Revised: 04/27/2023] [Accepted: 05/08/2023] [Indexed: 06/05/2023]
Abstract
Leukocyte phytohemagglutinin (PHA-L) is a tetrameric isomer of phytohemagglutinin (PHA) purified from the red kidney bean (Phaseolus vulgaris) and is a well-known human lymphocyte mitogen. Due to its antitumor and immunomodulatory effects, PHA-L may serve as a potential antineoplastic agent in future cancer therapeutics. However, various negative consequences of PHA have been reported in the literature as a result of the restricted acquisition methods, including oral toxicity, hemagglutinating activity, and immunogenicity. There is a critical need to explore a new method to obtain PHA-L with high purity, high activity and low toxicity. In this report active recombinant PHA-L protein was successfully prepared by Bacillus brevius expression system, and the antitumor and immunomodulatory activities of recombinant PHA-L were characterized by in vitro and in vivo experiments. The results showed that recombinant PHA-L protein had stronger antitumor effect, and its anti-tumor mechanism was realized through direct cytotoxicity and immune regulation. Importantly, compared with natural PHA-L, the recombinant PHA-L protein showed the lower erythrocyte agglutination toxicity in vitro and immunogenicity in mice. Altogether, our study provides a new strategy and important experimental basis for the development of drugs with dual effects of immune regulation and direct antitumor activity.
Collapse
Affiliation(s)
- Peipei Wang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Junmei Hu
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Shitong Min
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Congliang Chen
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yue Zhu
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yan Pan
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Dapeng Wei
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Xia Wang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China.
| |
Collapse
|
34
|
Laval F, Coppin G, Twizere JC, Vidal M. Homo cerevisiae-Leveraging Yeast for Investigating Protein-Protein Interactions and Their Role in Human Disease. Int J Mol Sci 2023; 24:9179. [PMID: 37298131 PMCID: PMC10252790 DOI: 10.3390/ijms24119179] [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: 05/01/2023] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Understanding how genetic variation affects phenotypes represents a major challenge, particularly in the context of human disease. Although numerous disease-associated genes have been identified, the clinical significance of most human variants remains unknown. Despite unparalleled advances in genomics, functional assays often lack sufficient throughput, hindering efficient variant functionalization. There is a critical need for the development of more potent, high-throughput methods for characterizing human genetic variants. Here, we review how yeast helps tackle this challenge, both as a valuable model organism and as an experimental tool for investigating the molecular basis of phenotypic perturbation upon genetic variation. In systems biology, yeast has played a pivotal role as a highly scalable platform which has allowed us to gain extensive genetic and molecular knowledge, including the construction of comprehensive interactome maps at the proteome scale for various organisms. By leveraging interactome networks, one can view biology from a systems perspective, unravel the molecular mechanisms underlying genetic diseases, and identify therapeutic targets. The use of yeast to assess the molecular impacts of genetic variants, including those associated with viral interactions, cancer, and rare and complex diseases, has the potential to bridge the gap between genotype and phenotype, opening the door for precision medicine approaches and therapeutic development.
Collapse
Affiliation(s)
- Florent Laval
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; (F.L.); (G.C.)
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- TERRA Teaching and Research Centre, University of Liège, 5030 Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, 4000 Liège, Belgium
| | - Georges Coppin
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; (F.L.); (G.C.)
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, 4000 Liège, Belgium
| | - Jean-Claude Twizere
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; (F.L.); (G.C.)
- TERRA Teaching and Research Centre, University of Liège, 5030 Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, 4000 Liège, Belgium
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; (F.L.); (G.C.)
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
35
|
Karaoğlan M. Alternative secretory signal sequences for recombinant protein production in Pichia pastoris. Enzyme Microb Technol 2023; 168:110256. [PMID: 37196384 DOI: 10.1016/j.enzmictec.2023.110256] [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: 02/24/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
Extracellular protein production is primarily preferred to facilitate the downstream processes in recombinant protein production. Secretion of recombinant proteins is mediated by the processing of signal peptides in their N-terminal portion by the secretory mechanism of host expression systems. These molecular elements involved in secretion are functionally interchangeable between different species and secretion sequence screening is one of the widely used approaches to improve extracellular protein production. In this study, α-mating and protein internal repeats (PIR) secretion sequences isolated from different yeasts (Kluyveromyces lactis, Kluyveromyces marxianus and Hansenula polymorpha) were tested in Pichia pastoris for the production of two different proteins (α-amylase and xylanase) and compared with the well-known secretory signals, S. cerevisiae α-mating factor (Sc-MF) and P. pastoris protein internal repeats PIR (PpPIR). The results obtained showed the potential of signal sequences tested. Among the tested peptides, the highest yields were achieved with H. polymorpha protein internal repeats (HpPIR) and K. lactis α-mating factor (Kl-MF) for xylanase and K. marxianus protein internal repeats (KmPIR) and K. lactis α-mating factor (Kl-MF) for amylase. In further studies, these sequences can be evaluated as alternatives in the production of different proteins in P. pastoris and in the production of recombinant proteins in different expression systems.
Collapse
Affiliation(s)
- Mert Karaoğlan
- Department of Food Engineering, Erzincan Binali Yıldırım University, Erzincan, Türkiye.
| |
Collapse
|
36
|
Saraiva A, Carrascosa C, Ramos F, Raheem D, Pedreiro S, Vega A, Raposo A. Brazzein and Monellin: Chemical Analysis, Food Industry Applications, Safety and Quality Control, Nutritional Profile and Health Impacts. Foods 2023; 12:foods12101943. [PMID: 37238762 DOI: 10.3390/foods12101943] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/30/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
Recently, customers have been keener to buy products manufactured using all-natural ingredients with positive health properties, but without losing flavor. In this regard, the objective of the current study is to review the consumption of brazzein and monellin, their nutritional profiles and health effects, and their potential applications in the food industry. This poses challenges with sustainability and important quality and safety indicators, as well as the chemical processes used to determine them. To better understand the utilization of brazzein and monellin, the chemical analysis of these two natural sweet proteins was also reviewed by placing particular emphasis on their extraction methods, purification and structural characterization. Protein engineering is considered a means to improve the thermal stability of brazzein and monellin to enhance their application in food processing, especially where high temperatures are applied. When the quality and safety of these sweet proteins are well-investigated and the approval from safety authorities is secured, the market for brazzein and monellin as food ingredient substitutes for free sugar will be guaranteed in the future. Ultimately, the review on these two natural peptide sweeteners increases the body of knowledge on alleviating problems of obesity, diabetes and other non-communicable diseases.
Collapse
Affiliation(s)
- Ariana Saraiva
- Department of Animal Pathology and Production, Bromatology and Food Technology, Faculty of Veterinary, Universidad de Las Palmas de Gran Canaria, Trasmontaña s/n, 35413 Arucas, Spain
| | - Conrado Carrascosa
- Department of Animal Pathology and Production, Bromatology and Food Technology, Faculty of Veterinary, Universidad de Las Palmas de Gran Canaria, Trasmontaña s/n, 35413 Arucas, Spain
| | - Fernando Ramos
- Faculty of Pharmacy, University of Coimbra, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
- Associated Laboratory for Green Chemistry (LAQV) of the Network of Chemistry and Technology (REQUIMTE), Rua D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal
| | - Dele Raheem
- Arctic Centre, University of Lapland, 96101 Rovaniemi, Finland
| | - Sónia Pedreiro
- Faculty of Pharmacy, University of Coimbra, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
- Associated Laboratory for Green Chemistry (LAQV) of the Network of Chemistry and Technology (REQUIMTE), Rua D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal
| | - Angelo Vega
- Department of Animal Pathology and Production, Bromatology and Food Technology, Faculty of Veterinary, Universidad de Las Palmas de Gran Canaria, Trasmontaña s/n, 35413 Arucas, Spain
| | - António Raposo
- CBIOS (Research Center for Biosciences and Health Technologies), Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisboa, Portugal
| |
Collapse
|
37
|
Erden-Karaoğlan F, Karaoğlan M. Improvement of recombinant L-Asparaginase production in Pichia pastoris. 3 Biotech 2023; 13:164. [PMID: 37159589 PMCID: PMC10163189 DOI: 10.1007/s13205-023-03600-4] [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: 10/20/2022] [Accepted: 04/29/2023] [Indexed: 05/11/2023] Open
Abstract
Pichia pastoris is a successful expression system that is frequently preferred in the secretion of proteins for both basic research and industrial purposes. In this study, recombinant Rhizomucor miehei (RmASNase) L-asparaginase was produced in Pichia pastoris. The impact of gene copy number on increasing protein production was examined with six clones harboring various gene copy numbers (1-5 and 5 +). The results demonstrated that the clone with three copies of the expression cassette integrated had the highest production level. Also, biochemical characterization of the enzyme was performed. It was determined that the optimum pH and temperature values of the purified enzyme were pH 7.0 and 50 °C, respectively. Stability analyses of the enzyme showed that it maintains its activity of 80% in the pH range of 5-9 and 67% in the temperature range of 20-50 °C. Ca+2 and Mn+2 ions increased the enzyme activity to 121% and 138%, respectively. In future studies, it is also possible to improve the activity and stability values of the enzyme with advanced molecular techniques and to increase production efficiency by producing at fermenter scale and under optimum conditions.
Collapse
Affiliation(s)
- Fidan Erden-Karaoğlan
- Department of Food Engineering, Erzincan Binali Yıldırım University, Erzincan, Türkiye
| | - Mert Karaoğlan
- Department of Food Engineering, Erzincan Binali Yıldırım University, Erzincan, Türkiye
| |
Collapse
|
38
|
Deng H, Li M, Zhang Q, Gao C, Song Z, Chen C, Wang Z, Feng X. The Broad-Spectrum Endolysin LySP2 Improves Chick Survival after Salmonella Pullorum Infection. Viruses 2023; 15:v15040836. [PMID: 37112818 PMCID: PMC10142873 DOI: 10.3390/v15040836] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/19/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Salmonella pullorum causes typical “Bacillary White Diarrhea” and loss of appetite in chicks, which leads to the death of chicks in severe cases; thus, it is still a critical issue in China. Antibiotics are conventional medicines used for Salmonella infections; however, due to the extensive long-term use and even abuse of antibiotics, drug resistance becomes increasingly severe, making treating pullorum disease more difficult. Most of the endolysins are hydrolytic enzymes produced by bacteriophages to cleave the host’s cell wall during the final stage of the lytic cycle. A virulent bacteriophage, YSP2, of Salmonella was isolated in a previous study. A Pichia pastoris expression strain that can express the Salmonella bacteriophage endolysin was constructed efficiently, and the Gram-negative bacteriophage endolysin, LySP2, was obtained in this study. Compared with the parental phage YSP2, which can only lyse Salmonella, LySP2 can lyse Salmonella and Escherichia. The survival rate of Salmonella-infected chicks treated with LySP2 can reach up to 70% and reduce Salmonella abundance in the liver and intestine. The treatment group showed that LySP2 significantly improved the health of infected chicks and alleviated organ damage caused by Salmonella infection. In this study, the Salmonella bacteriophage endolysin was expressed efficiently by Pichia pastoris, and the endolysin LySP2 showed good potential for the treatment of pullorum disease caused by Salmonella pullorum.
Collapse
Affiliation(s)
- Hewen Deng
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
| | - Mengjiao Li
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
| | - Qiuyang Zhang
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
| | - Chencheng Gao
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
| | - Zhanyun Song
- Changchun Customs District, Changchun 130000, China
| | - Chunhua Chen
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
| | - Zhuo Wang
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
| | - Xin Feng
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
- Correspondence: ; Tel.: +86-135-0430-0193
| |
Collapse
|
39
|
Selection of the methylotrophic yeast Ogataea minuta as a high-producing host for heterologous protein expression. J Biosci Bioeng 2023; 135:196-202. [PMID: 36702678 DOI: 10.1016/j.jbiosc.2022.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/28/2022] [Accepted: 12/11/2022] [Indexed: 01/26/2023]
Abstract
Three Ogataea minuta var. minuta strains have been deposited as NBRC 0975, NBRC 10402, and NBRC 10746 in the National Institute of Technology and Evaluation (NITE) Biological Resource Center (NBRC) collection. We investigated the ability to produce secretory proteins and several genotypic and phenotypic characteristics in order to select the best strain for heterologous protein expression. NBRC 10746 showed the best performance as evaluated by Cypridina noctiluca luciferase expression. Subsequently, clone #5-30 named tat06213, which was obtained by single-colony isolation from NBRC 10746, was established as a promising host for heterologous protein expression. To deepen our understanding of the characteristics of O.minuta var. minuta strains, sequence analysis of the D1/D2 domain of large subunit rRNA was conducted and the resulting phylogenetic tree derived from the D1/D2 domain showed that NBRC 10402 and NBRC 10746 were grouped into a different cluster far from NBRC 0975. Furthermore, a chromosome structure topology with electrophoretic karyotype and AOX1 loci analyzed by pulsed-field gel electrophoresis with Southern blotting showed different chromosome patterns and AOX1-hybridization loci among the strains. Additionally, the sequences of the promoter regions of the cloned AOX1 genes were not identical among the three strains. These findings might explain the differences in heterologous protein expression among the tested O. minuta var. minuta strains.
Collapse
|
40
|
Tan H, Wang L, Wang H, Cheng Y, Li X, Wan H, Liu C, Liu T, Li Q. Engineering Komagataella phaffii to biosynthesize cordycepin from methanol which drives global metabolic alterations at the transcription level. Synth Syst Biotechnol 2023; 8:242-252. [PMID: 37007278 PMCID: PMC10060148 DOI: 10.1016/j.synbio.2023.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/18/2023] Open
Abstract
Cordycepin has the potential to be an alternative to the disputed herbicide glyphosate. However, current laborious and time-consuming production strategies at low yields based on Cordyceps militaris lead to extremely high cost and restrict its application in the field of agriculture. In this study, Komagataella phaffii (syn. Pichia pastoris) was engineered to biosynthesize cordycepin from methanol, which could be converted from CO2. Combined with fermentation optimization, cordycepin content in broth reached as high as 2.68 ± 0.04 g/L within 168 h, around 15.95 mg/(L·h) in productivity. Additionally, a deaminated product of cordycepin was identified at neutral or weakly alkaline starting pH during fermentation. Transcriptome analysis found the yeast producing cordycepin was experiencing severe inhibition in methanol assimilation and peroxisome biogenesis, responsible for delayed growth and decreased carbon flux to pentose phosphate pathway (PPP) which led to lack of precursor supply. Amino acid interconversion and disruption in RNA metabolism were also due to accumulation of cordycepin. The study provided a unique platform for the manufacture of cordycepin based on the emerging non-conventional yeast and gave practical strategies for further optimization of the microbial cell factory.
Collapse
|
41
|
Zhao J, Zhou P, Zhang L, Liu W, Liu W, Zhang Y, Li Y, Shi Z, Gao J. N-region of Cry1Ia: A novel fusion tag for Escherichia coli and Pichia pastoris. J Biotechnol 2023; 366:54-64. [PMID: 36822476 DOI: 10.1016/j.jbiotec.2023.02.006] [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: 11/29/2022] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023]
Abstract
Secretory signal peptides (SPs) can increase enhanced green fluorescent protein (eGFP) expression in cytosol. In this study, SPs Iasp (Cry1Ia), Vasp (Vip3A), and their local sequences were used as fusion tags to compare their effects on eGFP expression in Escherichia coli MC4100 and Pichia pastoris GS115. In E coli, the solubility was almost opposite between the proteins encoded by Vegfp and Iegfp. This may be because the overall hydrophobicity of the SPs differed. When the hydrophobic H-region and C-region were removed, the negative effects on eGFP solubility of the N-regions of both SPs (IaN and VN) were significantly reduced without compromise on the expression level. IaN promotes eGFP protein yield 7.1-fold more than Iasp, and using this peptide in tandem (Ia3N) further enhanced fluorescent fusion protein solubility with an efficacy similar to that of a polycationic tag. Furthermore, the GS-IaNeGFP strain produced the highest fluorescent signal intensity when these fusion proteins were expressed in P. pastoris, and the expression was higher than in other strains, including eGFP. In conclusion, we revealed the potential of the N-region of Iasp as a fusion tag in both prokaryotic and eukaryotic cells and further demonstrated the value of the N-regions of abundant SPs.
Collapse
Affiliation(s)
- Juanli Zhao
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Pu Zhou
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Luyao Zhang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Wenhui Liu
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Wei Liu
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Yuqi Zhang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Yi Li
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Zongyong Shi
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China.
| | - Jianhua Gao
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China.
| |
Collapse
|
42
|
Anju MV, Archana K, Anooja VV, Athira PP, Neelima S, Singh ISB, Philip R. A novel anti-lipopolysaccharide factor from blue swimmer crab Portunus pelagicus and its cytotoxic effect on the prokaryotic expression host, E. coli on heterologous expression. J Genet Eng Biotechnol 2023; 21:22. [PMID: 36805357 PMCID: PMC9941410 DOI: 10.1186/s43141-023-00478-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/04/2023] [Indexed: 02/22/2023]
Abstract
BACKGROUND Invertebrates like crabs employ their own immune systems to fight against a number of invasive infections. Anti-lipopolysaccharide factors (ALFs) are an important class of antimicrobial peptides (AMPs) exhibiting binding and neutralizing activities against lipopolysaccharides. RESULTS This study identified and characterized a novel homolog of ALF (Pp-ALF) from the blue swimmer crab Portunus pelagicus. Pp-ALF has a 369bp open-reading frame encoding a protein with 123 amino acids. The deduced protein featured an LPS-binding domain and a signal peptide. The predicted tertiary structure of Pp-ALF contains three α helices packed against four β sheets. The deduced amino acid sequence of Pp-ALF had a net positive charge of +10.75 and an isoelectric point of 9.8. Phylogenetic analysis revealed that Pp-ALF has a strong ancestral relationship with crab ALFs. CONCLUSION Antibacterial, antiviral, antifungal, anticancer, and antibiofilm activities of Pp-ALF could be revealed by in silico prediction tools. Recombinant expression of Pp-ALF was unsuccessful in the Escherichia coli Rosetta-gami expression system due to the cytotoxic effect of the peptide to the host. The toxic effect of Pp-ALF to the host was displayed by membrane permeabilization and death of the host cells by fluorescent staining with Syto9-Propidium Iodide and CTC-DAPI- FITC.
Collapse
Affiliation(s)
- M V Anju
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala, 682016, India
| | - K Archana
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala, 682016, India
| | - V V Anooja
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala, 682016, India
| | - P P Athira
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala, 682016, India
| | - S Neelima
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala, 682016, India
| | - I S Bright Singh
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, 682016, India
| | - Rosamma Philip
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala, 682016, India.
| |
Collapse
|
43
|
Gómez-Ramírez IV, Corrales-García LL, Possani LD, Riaño-Umbarila L, Becerril B. Expression in Pichia pastoris of human antibody fragments that neutralize venoms of Mexican scorpions. Toxicon 2023; 223:107012. [PMID: 36592762 DOI: 10.1016/j.toxicon.2022.107012] [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: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022]
Abstract
The methylotrophic yeast Pichia pastoris has been one of the most widely used organisms in recent years as an expression system for a wide variety of recombinant proteins with therapeutic potential. Its popularity as an alternative system to Escherichia coli is mainly due to the easy genetic manipulation and the ability to produce high levels of heterologous proteins, either intracellularly or extracellularly. Being a eukaryotic organism, P. pastoris carries out post-translational modifications that allow it to produce soluble and correctly folded recombinant proteins. This work, evaluated the expression capacity in P. pastoris of two single-chain variable fragments (scFvs) of human origin, 10FG2 and LR. These scFvs were previously obtained by directed evolution against scorpion venom toxins and are able to neutralize different toxins and venoms of Mexican species. The yield obtained in P. pastoris was higher than that obtained in bacterial periplasm (E. coli), and most importantly, biochemical and functional properties were not modified. These results confirm that P. pastoris yeast can be a good expression system for the production of antibody fragments of a new recombinant antivenom.
Collapse
Affiliation(s)
- Ilse V Gómez-Ramírez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, UNAM, Apartado Postal 510-3, Cuernavaca, Morelos, 62250, Mexico
| | - Ligia Luz Corrales-García
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, UNAM, Apartado Postal 510-3, Cuernavaca, Morelos, 62250, Mexico; Departamento de Alimentos, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, AA 1226, Medellín, 050010, Colombia
| | - Lourival D Possani
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, UNAM, Apartado Postal 510-3, Cuernavaca, Morelos, 62250, Mexico
| | - Lidia Riaño-Umbarila
- Investigadora por México, CONACyT, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca, Morelos, 62250, Mexico.
| | - Baltazar Becerril
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, UNAM, Apartado Postal 510-3, Cuernavaca, Morelos, 62250, Mexico.
| |
Collapse
|
44
|
Quintero Barbosa JS, Rojas HYT, Gonzalez J, Espejo-Mojica AJ, Díaz CJA, Gutierrez MF. Characterization and expression of domains of Alphaherpesvirus bovine 1/5 envelope glycoproteins B in Komagataella phaffi. BMC Vet Res 2023; 19:28. [PMID: 36721143 PMCID: PMC9887784 DOI: 10.1186/s12917-023-03590-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/25/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Bovine herpes virus (BoHV 1 and BoHV-5) are the causative agents of infectious bovine rhinotracheitis (IBR). IBR is responsible for important economic losses in the cattle industry. The envelope glycoprotein B (gB) is essential for BoHV infection of cattle's upper respiratory and genital tract. gB is one of the main candidate antigens for a potential recombinant vaccine since it induces a strong and persistent immune response. RESULTS In this study, gB of BoHV-1 and BoHV-5 was characterized in terms of function, structure, and antigenicity through bioinformatics tools. gB showed conserved sequence and structure, so, both domains named PH Like 1 and 2 domains of each virus were selected for the design of a bivalent vaccine candidate. The immunoinformatic study showed that these two domains have epitopes recognizable by B and T lymphocytes, followed by this, the cDNA domains from BoHV-1/5 gB (Domains-gB) were transformed into the yeast Komagataella phaffii GS115 (previously known as Pichia pastoris). A recombinant protein with molecular weight of about 110 kDa was obtained from the culture media. The vaccine candidate protein (Domains-gB) was recognized by a monoclonal antibody from a commercial ELISA kit used for IBR diagnostic, which may suggest that the epitopes are conserved of the entire infectious virus. CONCLUSION Overall, it was shown that the recombinant domains of BoHV-1/5 gB have antigenic and immunogenic properties similar to the native gB. This vaccine candidate is promising to be used in future studies to assess its immunogenicity in an animal model.
Collapse
Affiliation(s)
- Juan Sebastián Quintero Barbosa
- grid.41312.350000 0001 1033 6040Virology Laboratory, Infectious Diseases Group, Microbiology Department, Faculty of Science Pontificia, Universidad Javeriana, Bogotá, D.C Colombia
| | - Heidy Yohana Triana Rojas
- grid.41312.350000 0001 1033 6040Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá, D.C Colombia
| | - Janneth Gonzalez
- grid.41312.350000 0001 1033 6040Nutrition and Biochemistry Department, Faculty of Science, Pontificia Universidad Javeriana, Bogotá, D.C Colombia
| | - Angela Johana Espejo-Mojica
- grid.41312.350000 0001 1033 6040Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá, D.C Colombia
| | - Carlos Javier Alméciga Díaz
- grid.41312.350000 0001 1033 6040Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá, D.C Colombia
| | - María Fernanda Gutierrez
- grid.41312.350000 0001 1033 6040Virology Laboratory, Infectious Diseases Group, Microbiology Department, Faculty of Science Pontificia, Universidad Javeriana, Bogotá, D.C Colombia
| |
Collapse
|
45
|
Ávila-Fernández Á, Montiel S, Rodríguez-Alegría ME, Caspeta L, López Munguía A. Simultaneous enzyme production, Levan-type FOS synthesis and sugar by-products elimination using a recombinant Pichia pastoris strain expressing a levansucrase-endolevanase fusion enzyme. Microb Cell Fact 2023; 22:18. [PMID: 36703199 PMCID: PMC9881289 DOI: 10.1186/s12934-022-02009-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/21/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Although Levan-type fructooligosaccharides (L-FOS) have been shown to exhibit prebiotic properties, no efficient methods for their large-scale production have been proposed. One alternative relies on the simultaneous levan synthesis from sucrose, followed by endolevanase hydrolysis. For this purpose, several options have been described, particularly through the synthesis of the corresponding enzymes in recombinant Escherichia coli. Major drawbacks still consist in the requirement of GRAS microorganisms for enzyme production, but mainly, the elimination of glucose and fructose, the reaction by-products. RESULTS The expression of a fusion enzyme between Bacillus licheniformis endolevanase (LevB1) and B. subtilis levansucrase (SacB) in Pichia pastoris cultures, coupled with the simultaneous synthesis of L-FOS from sucrose and the elimination of the residual monosaccharides, in a single one-pot process was developed. The proof of concept at 250 mL flask-level, resulted in 8.62 g of monosaccharide-free L-FOS and 12.83 gDCW of biomass, after 3 successive sucrose additions (30 g in total), that is a 28.7% yield (w L-FOS/w sucrose) over a period of 288 h. At a 1.5 L bioreactor-level, growth considerably increased and, after 59 h and two sucrose additions, 72.9 g of monosaccharide-free L-FOS and 22.77 gDCW of biomass were obtained from a total of 160 g of sucrose fed, corresponding to a 45.5% yield (w L-FOS/w sucrose), 1.6 higher than the flask system. The L-FOS obtained at flask-level had a DP lower than 20 fructose units, while at bioreactor-level smaller oligosaccharides were obtained, with a DP lower than 10, as a consequence of the lower endolevanase activity in the flask-level. CONCLUSION We demonstrate here in a novel system, that P. pastoris cultures can simultaneously be used as comprehensive system to produce the enzyme and the enzymatic L-FOS synthesis with growth sustained by sucrose by-products. This system may be now the center of an optimization strategy for an efficient production of glucose and fructose free L-FOS, to make them available for their application as prebiotics. Besides, P. pastoris biomass also constitutes an interesting source of unicellular protein.
Collapse
Affiliation(s)
- Ángela Ávila-Fernández
- grid.441115.40000 0001 2293 8305Centro de Investigación, DACS-Universidad Juárez Autónoma de Tabasco, Av. Gregorio Méndez No. 2838-A. Col. Tamulte ´, 86150 Villahermosa, Centro, Tabasco Mexico
| | - Silvia Montiel
- grid.9486.30000 0001 2159 0001Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, UNAM, Av. Universidad, 2001 Chamilpa, Cuernavaca, Mor. Mexico
| | - María Elena Rodríguez-Alegría
- grid.9486.30000 0001 2159 0001Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, UNAM, Av. Universidad, 2001 Chamilpa, Cuernavaca, Mor. Mexico
| | - Luis Caspeta
- grid.9486.30000 0001 2159 0001Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, UNAM, Av. Universidad, 2001 Chamilpa, Cuernavaca, Mor. Mexico
| | - Agustín López Munguía
- grid.9486.30000 0001 2159 0001Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, UNAM, Av. Universidad, 2001 Chamilpa, Cuernavaca, Mor. Mexico
| |
Collapse
|
46
|
Cheng J, Ahmad B, Raza MA, Guo H, Ahmat M, Wei X, Zhang L, Li Z, Cheng Q, Zhang J, Wang J, Si D, Zhang Y, Zhang R. Yeast Expressed Hybrid Peptide CLP Abridged Pro-Inflammatory Cytokine Levels by Endotoxin Neutralization. Microorganisms 2023; 11:microorganisms11010131. [PMID: 36677423 PMCID: PMC9860938 DOI: 10.3390/microorganisms11010131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
The aim of this study was to apply a strategy to express a recombinant CLP peptide and explore its application as a product derived from natural compounds. The amphiphilic CLP peptide was hybridized from three parent peptides (CM4, LL37, and TP5) and was considered to have potent endotoxin-neutralizing activity with minimal cytotoxic and hemolytic activity. To achieve high secretion expression, an expression vector of pPICZαA-HSA-CLP was constructed by the golden gate cloning strategy before being transformed into Pichia pastoris and integrated into the genome. The recombinant CLP was purified through the Ni-NTA affinity chromatography and analyzed by SDS-PAGE and mass spectrometry. The Limulus amebocyte lysate (LAL) test exhibited that the hybrid peptide CLP inhibited lipopolysaccharides (LPS) in a dose-dependent manner and was significantly (p < 0.05) more efficient compared to the parent peptides. In addition, it essentially diminished (p < 0.05) the levels of nitric oxide and pro-inflammatory cytokines (including TNF-α, IL6, and IL-1β) in LPS-induced mouse RAW264.7 macrophages. As an attendant to the control and the parental peptide LL37, the number of LPS-induced apoptotic cells was diminished compared to the control parental peptide LL37 (p < 0.05) with the treatment of CLP. Consequently, we concluded that the hybrid peptide CLP might be used as a therapeutic agent.
Collapse
Affiliation(s)
- Junhao Cheng
- Laboratory of Feed Biotechnology, State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Baseer Ahmad
- Laboratory of Feed Biotechnology, State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Faculty of Veterinary and Animal Sciences, Muhammad Nawaz Shareef University of Agriculture, Multan 2500, Pakistan
| | - Muhammad Asif Raza
- Faculty of Veterinary and Animal Sciences, Muhammad Nawaz Shareef University of Agriculture, Multan 2500, Pakistan
| | - Henan Guo
- Laboratory of Feed Biotechnology, State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Marhaba Ahmat
- Laboratory of Feed Biotechnology, State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xubiao Wei
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100193, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100193, China
| | - Lulu Zhang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100193, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100193, China
| | - Zhongxuan Li
- College of Bioengineering, Sichuan University of Science & Engineering, Chengdu 610017, China
| | - Qiang Cheng
- Laboratory of Feed Biotechnology, State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jing Zhang
- Laboratory of Feed Biotechnology, State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Junyong Wang
- Laboratory of Feed Biotechnology, State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Dayong Si
- Laboratory of Feed Biotechnology, State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yueping Zhang
- Laboratory of Feed Biotechnology, State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Correspondence: (Y.Z.); (R.Z.)
| | - Rijun Zhang
- Laboratory of Feed Biotechnology, State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Correspondence: (Y.Z.); (R.Z.)
| |
Collapse
|
47
|
Zou C, Lu L, Wang S, Zhang C, Chen X, Lin Y, Huang Y. The α-mating factor secretion signals and endogenous signal peptides for recombinant protein secretion in Komagataella phaffii. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:140. [PMID: 36527112 PMCID: PMC9756452 DOI: 10.1186/s13068-022-02243-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND The budding yeast Komagataella phaffii (Pichia pastoris) is widely employed to secrete proteins of academic and industrial interest. For secretory proteins, signal peptides are the sorting signal to direct proteins from cytosol to extracellular matrix, and their secretion efficiency directly impacts the yields of the targeted proteins in fermentation broth. Although the α-mating factor (MF) secretion signal from S. cerevisiae, the most common and widely used signal sequence for protein secretion, works in most cases, limitation exists as some proteins cannot be secreted efficiently. As the optimal choice of secretion signals is often protein specific, more secretion signals need to be developed to augment protein expression levels in K. phaffii. RESULTS In this study, the secretion efficiency of 40 α-MF secretion signals from various yeast species and 32 endogenous signal peptides from K. phaffii were investigated using enhanced green fluorescent protein (EGFP) as the model protein. All of the evaluated α-MF secretion signals successfully directed EGFP secretion except for the secretion signals of the yeast D. hansenii CBS767 and H. opuntiae. The secretion efficiency of α-MF secretion signal from Wickerhamomyces ciferrii was higher than that from S. cerevisiae. 24 out of 32 endogenous signal peptides successfully mediated EGFP secretion. The signal peptides of chr3_1145 and FragB_0048 had similar efficiency to S. cerevisiae α-MF secretion signal for EGFP secretion and expression. CONCLUSIONS The screened α-MF secretion signals and endogenous signal peptides in this study confer an abundance of signal peptide selection for efficient secretion and expression of heterologous proteins in K. phaffii.
Collapse
Affiliation(s)
- Chenwei Zou
- grid.411503.20000 0000 9271 2478Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, 350007 China
| | - Lingfang Lu
- grid.411503.20000 0000 9271 2478Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, 350007 China
| | - Shengyan Wang
- grid.411503.20000 0000 9271 2478Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, 350007 China
| | - Chenshan Zhang
- grid.411503.20000 0000 9271 2478Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, 350007 China
| | - Xuequn Chen
- grid.411504.50000 0004 1790 1622Central Laboratory at the Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122 Fujian People’s Republic of China
| | - Yao Lin
- grid.411504.50000 0004 1790 1622Central Laboratory at the Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122 Fujian People’s Republic of China
| | - Yide Huang
- grid.411503.20000 0000 9271 2478Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, 350007 China ,grid.411503.20000 0000 9271 2478Engineering Research Center of Industrial Microbiology, College of Life Sciences, Fujian Normal University, Fuzhou, 350007 China
| |
Collapse
|
48
|
Offei B, Braun-Galleani S, Venkatesh A, Casey WT, O’Connor KE, Byrne KP, Wolfe KH. Identification of genetic variants of the industrial yeast Komagataella phaffii (Pichia pastoris) that contribute to increased yields of secreted heterologous proteins. PLoS Biol 2022; 20:e3001877. [PMID: 36520709 PMCID: PMC9754263 DOI: 10.1371/journal.pbio.3001877] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 10/13/2022] [Indexed: 12/23/2022] Open
Abstract
The yeast Komagataella phaffii (formerly called Pichia pastoris) is used widely as a host for secretion of heterologous proteins, but only a few isolates of this species exist and all the commonly used expression systems are derived from a single genetic background, CBS7435 (NRRL Y-11430). We hypothesized that other genetic backgrounds could harbor variants that affect yields of secreted proteins. We crossed CBS7435 with 2 other K. phaffii isolates and mapped quantitative trait loci (QTLs) for secretion of a heterologous protein, β-glucosidase, by sequencing individual segregant genomes. A major QTL mapped to a frameshift mutation in the mannosyltransferase gene HOC1, which gives CBS7435 a weaker cell wall and higher protein secretion than the other isolates. Inactivation of HOC1 in the other isolates doubled β-glucosidase secretion. A second QTL mapped to an amino acid substitution in IRA1 that tripled β-glucosidase secretion in 1-week batch cultures but reduced cell viability, and its effects are specific to this heterologous protein. Our results demonstrate that QTL analysis is a powerful method for dissecting the basis of biotechnological traits in nonconventional yeasts, and a route to improving their industrial performance.
Collapse
Affiliation(s)
- Benjamin Offei
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Stephanie Braun-Galleani
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Anjan Venkatesh
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - William T. Casey
- Bioplastech Ltd., NovaUCD, Belfield Innovation Park, University College Dublin, Dublin, Ireland
| | - Kevin E. O’Connor
- UCD Earth Institute and School of Biomolecular & Biomedical Science, University College Dublin, Dublin, Ireland
- BiOrbic Bioeconomy SFI Research Centre, University College Dublin, Dublin, Ireland
| | - Kevin P. Byrne
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Kenneth H. Wolfe
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
- * E-mail:
| |
Collapse
|
49
|
Bajoria S, Kaur K, Kumru OS, Van Slyke G, Doering J, Novak H, Rodriguez Aponte SA, Dalvie NC, Naranjo CA, Johnston RS, Silverman JM, Kleanthous H, Love JC, Mantis NJ, Joshi SB, Volkin DB. Antigen-adjuvant interactions, stability, and immunogenicity profiles of a SARS-CoV-2 receptor-binding domain (RBD) antigen formulated with aluminum salt and CpG adjuvants. Hum Vaccin Immunother 2022; 18:2079346. [PMID: 35666264 PMCID: PMC9621007 DOI: 10.1080/21645515.2022.2079346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/16/2022] [Indexed: 02/07/2023] Open
Abstract
Low-cost, refrigerator-stable COVID-19 vaccines will facilitate global access and improve vaccine coverage in low- and middle-income countries. To this end, subunit-based approaches targeting the receptor-binding domain (RBD) of SARS-CoV-2 Spike protein remain attractive. Antibodies against RBD neutralize SARS-CoV-2 by blocking viral attachment to the host cell receptor, ACE2. Here, a yeast-produced recombinant RBD antigen (RBD-L452K-F490W or RBD-J) was formulated with various combinations of aluminum-salt (Alhydrogel®, AH; AdjuPhos®, AP) and CpG 1018 adjuvants. We assessed the effect of antigen-adjuvant interactions on the stability and mouse immunogenicity of various RBD-J preparations. While RBD-J was 50% adsorbed to AH and <15% to AP, addition of CpG resulted in complete AH binding, yet no improvement in AP adsorption. ACE2 competition ELISA analyses of formulated RBD-J stored at varying temperatures (4, 25, 37°C) revealed that RBD-J was destabilized by AH, an effect exacerbated by CpG. DSC studies demonstrated that aluminum-salt and CpG adjuvants decrease the conformational stability of RBD-J and suggest a direct CpG-RBD-J interaction. Although AH+CpG-adjuvanted RBD-J was the least stable in vitro, the formulation was most potent at eliciting SARS-CoV-2 pseudovirus neutralizing antibodies in mice. In contrast, RBD-J formulated with AP+CpG showed minimal antigen-adjuvant interactions, a better stability profile, but suboptimal immune responses. Interestingly, the loss of in vivo potency associated with heat-stressed RBD-J formulated with AH+CpG after one dose was abrogated by a booster. Our findings highlight the importance of elucidating the key interrelationships between antigen-adjuvant interactions, storage stability, and in vivo performance to enable successful formulation development of stable and efficacious subunit vaccines.
Collapse
Affiliation(s)
- Sakshi Bajoria
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Kawaljit Kaur
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Ozan S. Kumru
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Greta Van Slyke
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Jennifer Doering
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Hayley Novak
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Sergio A. Rodriguez Aponte
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Neil C. Dalvie
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Christopher A. Naranjo
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ryan S. Johnston
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - J. Christopher Love
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Nicholas J. Mantis
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Sangeeta B. Joshi
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - David B. Volkin
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| |
Collapse
|
50
|
Allampalli P, Rathinavelu S, Mohan N, Sivaprakasam S. Deployment of metabolic heat rate based soft sensor for estimation and control of specific growth rate in glycoengineered Pichia pastoris for human interferon alpha 2b production. J Biotechnol 2022; 359:194-206. [DOI: 10.1016/j.jbiotec.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 09/10/2022] [Accepted: 10/11/2022] [Indexed: 11/28/2022]
|