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Hu YY, Xiao S, Zhou GC, Chen X, Wang B, Wang JH. Bioactive peptides in dry-cured ham: A comprehensive review of preparation methods, metabolic stability, safety, health benefits, and regulatory frameworks. Food Res Int 2024; 186:114367. [PMID: 38729727 DOI: 10.1016/j.foodres.2024.114367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/29/2024] [Accepted: 04/17/2024] [Indexed: 05/12/2024]
Abstract
Dry-cured hams contain abundant bioactive peptides with significant potential for the development of functional foods. However, the limited bioavailability of food-derived bioactive peptides has hindered their utilization in health food development. Moreover, there is insufficient regulatory information regarding bioactive peptides and related products globally. This review summarizes diverse bioactive peptides derived from dry-cured ham and by-products originating from various countries and regions. The bioactivity, preparation techniques, bioavailability, and metabolic stability of these bioactive peptides are described, as well as the legal and regulatory frameworks in various countries. The primary objectives of this review are to dig deeper into the functionality of dry-cured ham and provide theoretical support for the commercialization of bioactive peptides from food sources, especially the dry-cured ham.
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Affiliation(s)
- Yao-Yao Hu
- School of Life Healthy and Technology, Dongguan University of Technology, Dongguan 523808, China; College of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Shan Xiao
- School of Life Healthy and Technology, Dongguan University of Technology, Dongguan 523808, China; College of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China.
| | - Gui-Cheng Zhou
- School of Life Healthy and Technology, Dongguan University of Technology, Dongguan 523808, China; College of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Xuan Chen
- School of Life Healthy and Technology, Dongguan University of Technology, Dongguan 523808, China
| | - Bo Wang
- School of Life Healthy and Technology, Dongguan University of Technology, Dongguan 523808, China; Regional Brand Innovation & Development Institute of Dongguan Prepared Dishes
| | - Ji-Hui Wang
- School of Life Healthy and Technology, Dongguan University of Technology, Dongguan 523808, China; College of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China; Regional Brand Innovation & Development Institute of Dongguan Prepared Dishes
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2
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Kordi M, Talkhounche PG, Vahedi H, Farrokhi N, Tabarzad M. Heterologous Production of Antimicrobial Peptides: Notes to Consider. Protein J 2024; 43:129-158. [PMID: 38180586 DOI: 10.1007/s10930-023-10174-w] [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] [Accepted: 11/28/2023] [Indexed: 01/06/2024]
Abstract
Heavy and irresponsible use of antibiotics in the last century has put selection pressure on the microbes to evolve even faster and develop more resilient strains. In the confrontation with such sometimes called "superbugs", the search for new sources of biochemical antibiotics seems to have reached the limit. In the last two decades, bioactive antimicrobial peptides (AMPs), which are polypeptide chains with less than 100 amino acids, have attracted the attention of many in the control of microbial pathogens, more than the other types of antibiotics. AMPs are groups of components involved in the immune response of many living organisms, and have come to light as new frontiers in fighting with microbes. AMPs are generally produced in minute amounts within organisms; therefore, to address the market, they have to be either produced on a large scale through recombinant DNA technology or to be synthesized via chemical methods. Here, heterologous expression of AMPs within bacterial, fungal, yeast, plants, and insect cells, and points that need to be considered towards their industrialization will be reviewed.
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Affiliation(s)
- Masoumeh Kordi
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Parnian Ghaedi Talkhounche
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Helia Vahedi
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Naser Farrokhi
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran.
| | - Maryam Tabarzad
- Protein Technology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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3
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Nguyen HLT, Nguyen NQT, Le TT, Pham XDT, Pham HL, Le HNT, Phan TN, Dinh NT. Improved expression and purification of highly-active 3 chymotrypsin-like protease from SARS-CoV-2. Protein Expr Purif 2024; 215:106414. [PMID: 38072143 DOI: 10.1016/j.pep.2023.106414] [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: 10/04/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/31/2023]
Abstract
Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is the causative pathogen of coronavirus disease-19 (COVID-19). The COVID-19 pandemic has resulted in millions of deaths and widespread socio-economic damage worldwide. Therefore, numerous studies have been conducted to identify effective measures to control the spreading of the virus. Among various potential targets, the 3 chymotrypsin-like protease (3CLpro), also known as Mpro, stands out as the key protease of SARS-CoV-2, playing an essential role in virus replication and assembly, is the most prospective. In this study, we modified the commercial vector, pETM33-Nsp5-Mpro (plasmid # 156475, Addgene, USA), by inserting an autocleavage site (AVLQ) of 3CLpro and 6 × His-tag encoding sequences before and after the Nsp5-Mpro sequence, respectively. This modification enabled the expression of 3CLpro as an authentic N terminal protease (au3CLpro), which was purified to electrophoretic homogeneity by a single-step chromatography using two tandem Glutathione- and Ni-Sepharose columns. The enzyme au3CLpro demonstrated significantly higher activity (3169 RFU/min/μg protein) and catalytic efficiency (Kcat/Km of 0.007 μM-1.s-1) than that of the 3CLpro (com3CLpro) expressed from the commercial vector (pETM33-Nsp5-Mpro) with specific activity 889 RFU/min/μg and Kcat/Km of 0.0015 μM-1.s-1, respectively. Optimal conditions for au3CLpro activity included a 50 mM Tris-HCl buffer at pH 7, containing 150 mM NaCl and 0.1 mg/ml BSA at 37 °C.
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Affiliation(s)
- Hong-Loan T Nguyen
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam; Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Nhu-Quynh T Nguyen
- Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - The-Thai Le
- Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Xuan-Dieu T Pham
- Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Hai-Long Pham
- Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Hong-Nhung T Le
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam; Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Tuan-Nghia Phan
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam; Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Nho-Thai Dinh
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam; Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam.
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4
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Xu K, Yu S, Wang K, Tan Y, Zhao X, Liu S, Zhou J, Wang X. AI and Knowledge-Based Method for Rational Design of Escherichia coli Sigma70 Promoters. ACS Synth Biol 2024; 13:402-407. [PMID: 38176073 DOI: 10.1021/acssynbio.3c00578] [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: 01/06/2024]
Abstract
Expanding sigma70 promoter libraries can support the engineering of metabolic pathways and enhance recombinant protein expression. Herein, we developed an artificial intelligence (AI) and knowledge-based method for the rational design of sigma70 promoters. Strong sigma70 promoters were identified by using high-throughput screening (HTS) with enhanced green fluorescent protein (eGFP) as a reporter gene. The features of these strong promoters were adopted to guide promoter design based on our previous reported deep learning model. In the following case study, the obtained strong promoters were used to express collagen and microbial transglutaminase (mTG), resulting in increased expression levels by 81.4% and 33.4%, respectively. Moreover, these constitutive promoters achieved soluble expression of mTG-activating protease and contributed to active mTG expression in Escherichia coli. The results suggested that the combined method may be effective for promoter engineering.
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Affiliation(s)
- Kangjie Xu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shangyang Yu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Kun Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yameng Tan
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xinyi Zhao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Song Liu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xinglong Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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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.
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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.
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6
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Lappöhn CA, Oestreich AM, Stei R, Weber LG, Maerz L, Wolff MW. Process intensification for the production of a C-tagged antimicrobial peptide in Escherichia coli - First steps toward a platform technology. J Biosci Bioeng 2023; 136:358-365. [PMID: 37770299 DOI: 10.1016/j.jbiosc.2023.09.003] [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: 05/05/2023] [Revised: 09/06/2023] [Accepted: 09/06/2023] [Indexed: 09/30/2023]
Abstract
The production of antimicrobial peptides/proteins (AMPs) in sufficient quantities for clinical evaluation is challenging because complex peptides are unsuitable for chemical synthesis, natural sources have low yields, and heterologous systems often have low expression levels or require product-specific process adaptations. Here we describe the production of a complex AMP, the insect metalloproteinase inhibitor (IMPI), by adding a C-terminal C-tag to increase the yield compared to the unmodified peptide. We used a design of experiments approach for process intensification in Escherichia coli Rosetta-gami 2(DE3)pLysS cells and achieved a yield of 260 mg L-1, which is up to 30-fold higher than previously reported. The C-tag also enhanced product purity but had no effect on IMPI activity, making tag removal unnecessary and therefore simplifying process analytics and downstream processing. We have confirmed that the C-tag is compatible with the peptide and could form the basis of a platform technology for the expression, purification and detection of diverse AMPs produced in E. coli.
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Affiliation(s)
- Carolin A Lappöhn
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen (THM), Wiesenstr. 14, 35390 Giessen, Germany
| | - Arne M Oestreich
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen (THM), Wiesenstr. 14, 35390 Giessen, Germany
| | - Robin Stei
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen (THM), Wiesenstr. 14, 35390 Giessen, Germany
| | - Linus G Weber
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen (THM), Wiesenstr. 14, 35390 Giessen, Germany
| | - Lea Maerz
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen (THM), Wiesenstr. 14, 35390 Giessen, Germany
| | - Michael W Wolff
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen (THM), Wiesenstr. 14, 35390 Giessen, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Ohlebergsweg 12, 35392 Giessen, Germany.
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Puan SL, Erriah P, Baharudin MMAA, Yahaya NM, Kamil WNIWA, Ali MSM, Ahmad SA, Oslan SN, Lim S, Sabri S. Antimicrobial peptides from Bacillus spp. and strategies to enhance their yield. Appl Microbiol Biotechnol 2023; 107:5569-5593. [PMID: 37450018 DOI: 10.1007/s00253-023-12651-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
Antibiotic resistance is a growing concern that is affecting public health globally. The search for alternative antimicrobial agents has become increasingly important. Antimicrobial peptides (AMPs) produced by Bacillus spp. have emerged as a promising alternative to antibiotics, due to their broad-spectrum antimicrobial activity against resistant pathogens. In this review, we provide an overview of Bacillus-derived AMPs, including their classification into ribosomal (bacteriocins) and non-ribosomal peptides (lipopeptides and polyketides). Additionally, we delve into the molecular mechanisms of AMP production and describe the key biosynthetic gene clusters involved. Despite their potential, the low yield of AMPs produced under normal laboratory conditions remains a challenge to large-scale production. This review thus concludes with a comprehensive summary of recent studies aimed at enhancing the productivity of Bacillus-derived AMPs. In addition to medium optimization and genetic manipulation, various molecular strategies have been explored to increase the production of recombinant antimicrobial peptides (AMPs). These include the selection of appropriate expression systems, the engineering of expression promoters, and metabolic engineering. Bacillus-derived AMPs offer great potential as alternative antimicrobial agents, and this review provides valuable insights on the strategies to enhance their production yield, which may have significant implications for combating antibiotic resistance. KEY POINTS: • Bacillus-derived AMP is a potential alternative therapy for resistant pathogens • Bacillus produces two main classes of AMPs: ribosomal and non-ribosomal peptides • AMP yield can be enhanced using culture optimization and molecular approaches.
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Affiliation(s)
- Sheau Ling Puan
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Pirasannah Erriah
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Mohamad Malik Al-Adil Baharudin
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Normi Mohd Yahaya
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, 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
| | - Wan Nur Ismah Wan Ahmad Kamil
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, 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
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, 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
| | - Sooa Lim
- Department of Pharmaceutical Engineering, Hoseo University, 31499, Asan-Si, Chungnam, Republic of Korea
| | - Suriana Sabri
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
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Tang R, Tan H, Dai Y, Li L, Huang Y, Yao H, Cai Y, Yu G. Application of antimicrobial peptides in plant protection: making use of the overlooked merits. FRONTIERS IN PLANT SCIENCE 2023; 14:1139539. [PMID: 37538059 PMCID: PMC10394246 DOI: 10.3389/fpls.2023.1139539] [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: 01/07/2023] [Accepted: 04/07/2023] [Indexed: 08/05/2023]
Abstract
Pathogen infection is one of the major causes of yield loss in the crop field. The rapid increase of antimicrobial resistance in plant pathogens has urged researchers to develop both new pesticides and management strategies for plant protection. The antimicrobial peptides (AMPs) showed potential on eliminating plant pathogenic fungi and bacteria. Here, we first summarize several overlooked advantages and merits of AMPs, which includes the steep dose-response relations, fast killing ability, broad synergism, slow resistance selection. We then discuss the possible application of AMPs for plant protection with above merits, and highlight how AMPs can be incorporated into a more efficient integrated management system that both increases the crop yield and reduce resistance evolution of pathogens.
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Choyam S, Kammara R. Understanding the Necessity of Regulatory Protein Machinery in Heterologous Expression of Class-III Type of Ocins. Protein J 2023:10.1007/s10930-023-10106-8. [PMID: 36976382 DOI: 10.1007/s10930-023-10106-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2023] [Indexed: 03/29/2023]
Abstract
To date, there have been no or just a few reports of successful cloning and expression to create biologically active ocins or bacteriocins. Cloning, expression, and production of class I ocins are problematic because of their structural arrangements, coordinated functions, size, and posttranslational modifications. Mass synthesis of these molecules is necessary for commercialization and to restrict the excessive use of conventional antibiotics, which encourages the development of antibiotic-resistant bacteria. In the case of class III ocins, there are no reports of obtaining biological active proteins to date. Being able to obtain biologically active proteins requires an understanding of mechanistic features due to their expanding importance and broad spectrum of activity. As a result, we intend to clone and express the class III type. The class I types that are devoid of posttranslational modifications were transformed into class III through fusion. Therefore, this construct resembles a class III type ocin. With the exception of Zoocin, expression of the proteins was found to be physiologically ineffective after cloning. But, few cell morphological changes such as elongation, aggregation, and the formation of terminal hyphae were observed. However, it was discovered that the target indicator had been altered to Vibrio spp. in a few. All the three ocins were subjected to in-silico structure prediction/analysis. Finally, we confirm the existence of unidentified additional intrinsic factors for successful expression to obtain biologically active protein.
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Affiliation(s)
- Shilja Choyam
- Department of Microbiology and Fermentation Technology, CSIR-CFTRI, Mysore, India
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Song Y, Wang Y, Yan S, Nakamura K, Kikukawa T, Ayabe T, Aizawa T. Efficient recombinant production of mouse-derived cryptdin family peptides by a novel facilitation strategy for inclusion body formation. Microb Cell Fact 2023; 22:9. [PMID: 36635697 PMCID: PMC9838031 DOI: 10.1186/s12934-023-02016-2] [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: 01/01/2023] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND A number of antimicrobial peptides (AMPs) hold promise as new drugs owing to their potent bactericidal activity and because they are often refractory to the development of drug resistance. Cryptdins (Crps) are a family of antimicrobial peptides found in the small intestine of mice, comprising six isoforms containing three sets of disulfide bonds. Although Crp4 is actively being investigated, there have been few studies to date on the other Crp isoforms. A prerequisite for detailed characterization of the other Crp isoforms is establishment of efficient sample preparation methods. RESULTS To avoid degradation during recombinant expression of Crps in E. coli, co-expression of Crps with the aggregation-prone protein human α-lactalbumin (HLA) was used to promote the formation of stable inclusion bodies. Using this method, the production of Crp4 and Crp6 by the BL21 strain was effective, but the expression of other Crp isoforms was not as efficient. The results of a cell-free system study suggested that Crps were degraded, even though a substantial amounts of Crps were synthesized. Therefore, using the Origami™ B strain, we were able to significantly increase the expression efficiency of Crps by promoting the formation of erroneous intermolecular disulfide bonds between HLA and Crps, thereby promoting protein aggregation and inclusion body formation, which prevented degradation. The various Crp isoforms were successfully refolded in vitro and purified using reversed-phase HPLC. In addition, the yield was further improved by deformylation of formyl-Crps. We measured the antibacterial activity of Crps against both Gram-positive and Gram-negative bacteria. Each Crp isoform exhibited a completely different trend in antimicrobial activity, although conformational analysis by circular dichroism did not reveal any significant steric differences. CONCLUSION In this study, we established a novel and efficient method for the production of the cryptdin family of cysteine-containing antimicrobial peptides. Additionally, we found that there were notable differences in the antibacterial activities of the various Crp family members. The expression system established in this study is expected to provide new insights regarding the mechanisms underlying the different antibacterial activities of the Crp family of peptides.
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Affiliation(s)
- Yuchi Song
- grid.39158.360000 0001 2173 7691Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido Japan
| | - Yi Wang
- grid.39158.360000 0001 2173 7691Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido Japan
| | - Shaonan Yan
- grid.39158.360000 0001 2173 7691Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido Japan
| | - Kiminori Nakamura
- grid.39158.360000 0001 2173 7691Innate Immunity Laboratory, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido Japan
| | - Takashi Kikukawa
- grid.39158.360000 0001 2173 7691Laboratory of Biological Information Analysis Science, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido Japan
| | - Tokiyoshi Ayabe
- grid.39158.360000 0001 2173 7691Innate Immunity Laboratory, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido Japan
| | - Tomoyasu Aizawa
- grid.39158.360000 0001 2173 7691Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido Japan
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Deo S, Turton KL, Kainth T, Kumar A, Wieden HJ. Strategies for improving antimicrobial peptide production. Biotechnol Adv 2022; 59:107968. [PMID: 35489657 DOI: 10.1016/j.biotechadv.2022.107968] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/18/2022] [Accepted: 04/25/2022] [Indexed: 01/10/2023]
Abstract
Antimicrobial peptides (AMPs) found in a wide range of animal, insect, and plant species are host defense peptides forming an integral part of their innate immunity. Although the exact mode of action of some AMPs is yet to be deciphered, many exhibit membrane lytic activity or interact with intracellular targets. The ever-growing threat of antibiotic resistance has brought attention to research on AMPs to enhance their clinical use as a therapeutic alternative. AMPs have several advantages over antibiotics such as broad range of antimicrobial activities including anti-fungal, anti-viral and anti-bacterial, and have not reported to contribute to resistance development. Despite the numerous studies to develop efficient production methods for AMPs, limitations including low yield, degradation, and loss of activity persists in many recombinant approaches. In this review, we outline available approaches for AMP production and various expression systems used to achieve higher yield and quality. In addition, recent advances in recombinant strategies, suitable fusion protein partners, and other molecular engineering strategies for improved AMP production are surveyed.
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Affiliation(s)
- Soumya Deo
- Department of Microbiology, Buller building, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Kristi L Turton
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Dr. W., Lethbridge, AB T1K 3M4, Canada
| | - Tajinder Kainth
- Department of Microbiology, Buller building, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ayush Kumar
- Department of Microbiology, Buller building, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Hans-Joachim Wieden
- Department of Microbiology, Buller building, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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12
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Abdelhamid AG, Campbell EP, Hawkins Z, Yousef AE. Efficient Production of Broad-Spectrum Antimicrobials by Paenibacillus polymyxa OSY-EC Using Acid Whey-Based Medium and Novel Antimicrobial Concentration Approach. Front Bioeng Biotechnol 2022; 10:869778. [PMID: 35646844 PMCID: PMC9141042 DOI: 10.3389/fbioe.2022.869778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Production of some antimicrobial peptides by bacterial producers is a resource-intensive process, thus, using inexpensive growth media and simplifying antimicrobial extraction and down-stream processing are highly desirable. Acid whey, a dairy industry waste, is explored as a medium for production of broad-spectrum antimicrobials from selected bacteriocinogenic bacteria. Neutralized and yeast extract-supplemented acid whey was suitable for production of antimicrobials by four tested strains, but Paenibacillus polymyxa OSY-EC was the most prolific antimicrobial producer. Concentrating synthesized antimicrobials during culture incubation using beads of polymeric adsorbent resin, followed by solvent extraction and freeze-drying, resulted in antimicrobials-rich powder (AMRP). Under these conditions, P. polymyxa OSY-EC produced paenibacillin, polymyxin E, and fusaricidin, which are active against Gram-positive and Gram-negative bacteria and fungi, respectively. When media containing 2x and 4x minimum inhibitory concentrations of AMRP were inoculated with Listeria innocua and Escherichia coli, microbial populations decreased by ≥4-log CFU ml-1 in tryptic soy broth and ≥3.5-log CFU ml-1 in milk. The antimicrobial mechanism of action of AMRP solutions was attributed to the disruption of cytoplasmic membrane of indicator strains, L. innocua and E. coli. These findings exemplify promising strategies for valorization of acid whey via microbial bioreactions to yield potent antimicrobials.
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Affiliation(s)
- Ahmed G. Abdelhamid
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha, Egypt
| | - Emily P. Campbell
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States
| | - Zach Hawkins
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Ahmed E. Yousef
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
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13
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Schwarz S, Gerlach D, Fan R, Czermak P. GbpA as a secretion and affinity purification tag for an antimicrobial peptide produced in Vibrio natriegens. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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14
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Shariati FS, Norouzian D, Valizadeh V, Ahangari Cohan R, Keramati M. Rapid screening of high expressing Escherichia coli colonies using a novel dicistronic-autoinducible system. Microb Cell Fact 2021; 20:223. [PMID: 34895227 PMCID: PMC8666062 DOI: 10.1186/s12934-021-01711-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/23/2021] [Indexed: 11/25/2022] Open
Abstract
Background Identification of high-expressing colonies is one of the main concerns in the upstream process of recombinant protein development. The common method to screen high-producing colonies is SDS-PAGE, a laborious and time-consuming process, which is based on a random and qualitative way. The current study describes the design and development of a rapid screening system composed of a dicistronic expression system containing a reporter (enhanced green fluorescent protein, eGFP), protein model (staphylokinase, SAK), and a self-inducible system containing heat shock protein 27 (Hsp27). Results Dicistronic-autoinducible system expressed eGFP and SAK successfully in 5-ml and 1-L culture volumes. High expressing colonies were identified during 6 h via fluorescent signals. In addition, the biological activity of the protein model was confirmed semi-quantitatively and quantitatively through radial caseinolytic and chromogenic methods, respectively. There was a direct correlation between eGFP fluorescent intensity and SAK activity. The correlation and linearity of expression between the two genes were respectively confirmed with Pearson correlation and linear regression. Additionally, the precision, limit of detection (LOD), and limit of quantification (LOQ) were determined. The expression of eGFP and SAK was stable during four freeze–thaw cycles. In addition, the developed protocol showed that the transformants can be inoculated directly to the culture, saving time and reducing the error-prone step of colony picking. Conclusion The developed system is applicable for rapid screening of high-expressing colonies in most research laboratories. This system can be investigated for other recombinant proteins expressed in E. coli with a potential capability for automation and use at larger scales. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01711-2.
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Affiliation(s)
- Fatemeh Sadat Shariati
- Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran
| | - Dariush Norouzian
- Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran
| | - Vahideh Valizadeh
- Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran
| | - Reza Ahangari Cohan
- Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran.
| | - Malihe Keramati
- Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran.
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15
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Campbell EP, Hussein WE, Huang E, Yousef AE. Enhancing titre and production stability of paenibacillin from Paenibacillus polymyxa by sequential drug resistance screening. J Appl Microbiol 2021; 131:2876-2885. [PMID: 34048127 DOI: 10.1111/jam.15165] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 05/08/2021] [Accepted: 05/23/2021] [Indexed: 11/29/2022]
Abstract
AIMS Paenibacillin is a naturally biosynthesized antimicrobial lantibiotic peptide which is produced by wild-type Paenibacillus polymyxa OSY-DF in low but detectable levels. The aim was to increase paenibacillin titre and production consistency through sequential drug resistance screening. METHODS AND RESULTS Spontaneous mutants of P. polymyxa OSY-DF were isolated by subjecting the bacterium to two rounds of screening for resistance to rifampicin, which targets RNA polymerase, and gentamicin, which targets ribosomes. Changes in antimicrobial production of the mutants were monitored using a bioassay method. A spontaneous mutant, P. polymyxa OSY-EC, capable of producing high paenibacillin titre, was selected and compared phenotypically to the wild-type strain. The mutant was found to produce paenibacillin at five-fold higher titre than the wild type. The mutant constantly produced paenibacillin while the wild type produced the antimicrobial agent variably. Fourier transformation mid-infrared spectroscopy revealed an interclass distance of 6·4 between the wild type and the mutant strain, suggesting significant phenotypic change during the mutation. CONCLUSIONS P. polymyxa OSY-EC, a spontaneous mutant capable of consistent production of high paenibacillin titre, was isolated from the wild type after sequential screening on rationally selected antibiotics. SIGNIFICANCE AND IMPACT OF THE STUDY The study will help make paenibacillin available for large-scale testing by interested researchers and industries seeking applications that improve food safety and quality.
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Affiliation(s)
- E P Campbell
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, USA
| | - W E Hussein
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, USA
| | - E Huang
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, USA
| | - A E Yousef
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, USA.,Department of Microbiology, The Ohio State University, Columbus, OH, USA
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16
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Liu Y, Shi J, Tong Z, Jia Y, Yang B, Wang Z. The revitalization of antimicrobial peptides in the resistance era. Pharmacol Res 2020; 163:105276. [PMID: 33161137 DOI: 10.1016/j.phrs.2020.105276] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 01/14/2023]
Abstract
The antibiotic resistance crisis is becoming incredibly thorny due to the indiscriminate employment of antibiotics in agriculture and aquaculture, such as growth promoters, and the emergence of bacteria that are capable of enduring antibiotic treatment in an endless stream. Hence, to reverse this situation, vigorous efforts should be made in the process of identifying other alternative strategies with a lower frequency of resistance. Antimicrobial peptides (AMPs), originated from host defense peptides, are generally produced by a variety of organisms as defensive weapons to protect the host from other pathogenic bacteria. The unique ability of AMPs to control bacterial infections, as well as low propensity to acquire resistance, provides the basis for it to become one of the promising antibacterial substances. Herein, we present new insights into the biological functions, structural properties, distinct mechanisms of action of AMPs and their resistance determinants. Besides, we separately discuss natural and synthetic AMPs, including their source, screening pathway and antibacterial activity. Lastly, challenges and perspectives to identify novel potent AMPs are highlighted, which will expand our understanding of the chemical space of antimicrobials and provide a pipeline for discovering the next-generation of AMPs.
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Affiliation(s)
- Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009, China.
| | - Jingru Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Ziwen Tong
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Yuqian Jia
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Bingqing Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
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17
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Guevara Agudelo FA, Muñoz Molina LC, Navarrette Ospina J, Salazar Pulido LM, Pinilla Bermúdez G. Innovaciones en la terapia antimicrobiana. NOVA 2020. [DOI: 10.22490/24629448.3921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
La resistencia microbiana ha llevado a la búsqueda de innovadoras alternativas para su contención y dentro de las más promisorias están el uso de péptidos sintéticos, no sólo por sus características intrínsecas antimicrobianas, sino por las interacciones sinérgicas y antagónicas que presenta con otros mediadores inmunológicos. Estas propiedades han permitido crear péptidos sintéticos reguladores de defensa innata que representan un nuevo enfoque inmunomodulador para el tratamiento de infecciones; sin embargo, sólo los diseñados con alto score antimicrobiano, han demostrado eficacia en estudios clínicos de Fase 3. Debido a su amplio espectro de actividad, un único péptido puede actuar contra bacterias Gram negativas, Gram positivas, hongos, e incluso virus y parásitos, aumentando el interés por investigar estas dinámicas moléculas.
Por otra parte, se encuentra el sistema CRISPR, para la edición de genomas bacterianos, permitirá reducir su actividad virulenta y diseñar antimicrobianos basados en nucleasas CRISPR-Cas 9 programables contra dianas específicas, las que representan un promisorio camino en el estudio de nuevas alternativas con alto potencial para eliminar la resistencia a antibióticos de bacterias altamente patógenas. Asimismo, se aborda la terapia con fagos, referida a la accion de virus que infectan bacterias, usados solos o en cocteles para aumentar el espectro de acción de estos, aprovechando su abundacia en la naturaleza, ya que se ha considerado que cada bacteria tiene un virus específico que podría emplearse como potente agente antibacteriano.
Finalmente, mientras se usen como principal medio de contención solo tratamientos convencionales antimicrobianos, incluso de manera oportuna y acertada, la microevolución en las bacterias se asegurará de seguir su curs
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18
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Sampaio de Oliveira KB, Leite ML, Rodrigues GR, Duque HM, da Costa RA, Cunha VA, de Loiola Costa LS, da Cunha NB, Franco OL, Dias SC. Strategies for recombinant production of antimicrobial peptides with pharmacological potential. Expert Rev Clin Pharmacol 2020; 13:367-390. [PMID: 32357080 DOI: 10.1080/17512433.2020.1764347] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION The need to develop new drugs for the control of pathogenic microorganisms has redoubled efforts to prospect for antimicrobial peptides (AMPs) from natural sources and to characterize its structure and function. These molecules present a broad spectrum of action against different microorganisms and frequently present promiscuous action, with anticancer and immunomodulatory activities. Furthermore, AMPs can be used as biopharmaceuticals in the treatment of hospital-acquired infections and other serious diseases with relevant social and economic impacts.Areas covered: The low yield and the therefore difficult extraction and purification process in AMPs are problems that limit their industrial application and scientific research. Thus, optimized heterologous expression systems were developed to significantly boost AMP yields, allow high efficiency in purification and structural optimization for the increase of therapeutic activity.Expert opinion: This review provides an update on recent developments in the recombinant production of ribosomal and non-ribosomal synthesis of AMPs and on strategies to increase the expression of genes encoding AMPs at the transcriptional and translational levels and regulation of the post-translational modifications. Moreover, there are detailed reports of AMPs that have already reached marketable status or are in the pipeline under advanced stages of preclinical testing.
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Affiliation(s)
- Kamila Botelho Sampaio de Oliveira
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Michel Lopes Leite
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Gisele Regina Rodrigues
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Harry Morales Duque
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Rosiane Andrade da Costa
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Victor Albuquerque Cunha
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Lorena Sousa de Loiola Costa
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Nicolau Brito da Cunha
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Octavio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil.,Universidade de Brasília, Pós-graduação em Patologia Molecular, Campus Darcy Ribeiro , Brasília, Brazil.,S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco , Campo Grande, Mato Grosso do Sul, Brazil
| | - Simoni Campos Dias
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil.,Universidade de Brasília, Pós-graduação em Biologia Animal, Campus Darcy Ribeiro , Brasília, Brazil
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19
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Markina NM, Kotlobay AA, Tsarkova AS. Heterologous Metabolic Pathways: Strategies for Optimal Expression in Eukaryotic Hosts. Acta Naturae 2020; 12:28-39. [PMID: 32742725 PMCID: PMC7385092 DOI: 10.32607/actanaturae.10966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 04/29/2020] [Indexed: 11/20/2022] Open
Abstract
Heterologous pathways are linked series of biochemical reactions occurring in a host organism after the introduction of foreign genes. Incorporation of metabolic pathways into host organisms is a major strategy used to increase the production of valuable secondary metabolites. Unfortunately, simple introduction of the pathway genes into the heterologous host in most cases does not result in successful heterologous expression. Extensive modification of heterologous genes and the corresponding enzymes on many different levels is required to achieve high target metabolite production rates. This review summarizes the essential techniques used to create heterologous biochemical pathways, with a focus on the key challenges arising in the process and the major strategies for overcoming them.
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Affiliation(s)
- N. M. Markina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Planta LLC, Moscow, 121205 Russia
| | - A. A. Kotlobay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - A. S. Tsarkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
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20
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Neshani A, Tanhaeian A, Zare H, Akbari Eidgahi MR, Ghazvini K. Preparation and evaluation of a new biopesticide solution candidate for plant disease control using pexiganan gene and Pichia pastoris expression system. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100509] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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21
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Der Torossian Torres M, de la Fuente-Nunez C. Reprogramming biological peptides to combat infectious diseases. Chem Commun (Camb) 2019; 55:15020-15032. [PMID: 31782426 DOI: 10.1039/c9cc07898c] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
With the rapid spread of resistance among parasites and bacterial pathogens, antibiotic-resistant infections have drawn much attention worldwide. Consequently, there is an urgent need to develop new strategies to treat neglected diseases and drug-resistant infections. Here, we outline several new strategies that have been developed to counter pathogenic microorganisms by designing and constructing antimicrobial peptides (AMPs). In addition to traditional discovery and design mechanisms guided by chemical biology, synthetic biology and computationally-based approaches offer useful tools for the discovery and generation of bioactive peptides. We believe that the convergence of such fields, coupled with systematic experimentation in animal models, will help translate biological peptides into the clinic. The future of anti-infective therapeutics is headed towards specifically designed molecules whose form is driven by computer-based frameworks. These molecules are selective, stable, and active at therapeutic doses.
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Affiliation(s)
- Marcelo Der Torossian Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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22
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Eichmann J, Oberpaul M, Weidner T, Gerlach D, Czermak P. Selection of High Producers From Combinatorial Libraries for the Production of Recombinant Proteins in Escherichia coli and Vibrio natriegens. Front Bioeng Biotechnol 2019; 7:254. [PMID: 31637238 PMCID: PMC6788121 DOI: 10.3389/fbioe.2019.00254] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/20/2019] [Indexed: 11/13/2022] Open
Abstract
The optimization of recombinant protein production in bacteria is an important stage of process development, especially for difficult-to-express proteins that are particularly sensitive or recalcitrant. The optimal expression level must be neither too low, which would limit yields, nor too high, which would promote the formation of insoluble inclusion bodies. Expression can be optimized by testing different combinations of elements such as ribosome binding sites and N-terminal affinity tags, but the rate of protein synthesis is strongly dependent on mRNA secondary structures so the combined effects of these elements must be taken into account. This substantially increases the complexity of high-throughput expression screening. To address this limitation, we generated libraries of constructs systematically combining different ribosome binding sites, N-terminal affinity tags, and periplasmic translocation sequences representing two secretion pathways. Each construct also contained a green fluorescent protein (GFP) tag to allow the identification of high producers and a thrombin cleavage site enabling the removal of fusion tags. To achieve proof of principle, we generated libraries of 200 different combinations of elements for the expression of an antimicrobial peptide (AMPs), an antifungal peptide, and the enzyme urate oxidase (uricase) in Escherichia coli and Vibrio natriegens. High producers for all three difficult-to-express products were enriched by fluorescence-activated cell sorting. Our results indicated that the E. coli ssYahJ secretion signal is recognized in V. natriegens and efficiently mediates translocation to the periplasm. Our combinatorial library approach therefore allows the cross-species direct selection of high-producer clones for difficult-to-express proteins by systematically evaluating the combined impact of multiple construct elements.
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Affiliation(s)
- Joel Eichmann
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany.,Faculty of Biology and Chemistry, Justus-Liebig University of Giessen, Giessen, Germany
| | - Markus Oberpaul
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Tobias Weidner
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Doreen Gerlach
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Peter Czermak
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany.,Faculty of Biology and Chemistry, Justus-Liebig University of Giessen, Giessen, Germany.,Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
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23
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Liu Q, Shi X, Song L, Liu H, Zhou X, Wang Q, Zhang Y, Cai M. CRISPR-Cas9-mediated genomic multiloci integration in Pichia pastoris. Microb Cell Fact 2019; 18:144. [PMID: 31434578 PMCID: PMC6704636 DOI: 10.1186/s12934-019-1194-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/14/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Pichia pastoris (syn. Komagataella phaffii) is a widely used generally recognized as safe host for heterologous expression of proteins in both industry and academia. Recently, it has been shown to be a potentially good chassis host for the production of high-value pharmaceuticals and chemicals. Nevertheless, limited availability of selective markers and low efficiency of homologous recombination make this process difficult and time-consuming, particularly in the case of multistep biosynthetic pathways. Therefore, it is crucial to develop an efficient and marker-free multiloci gene knock-in method in P. pastoris. RESULTS A non-homologous-end-joining defective strain (Δku70) was first constructed using the CRISPR-Cas9 based gene deficiency approach. It was then used as a parent strain for multiloci gene integration. Ten guide RNA (gRNA) targets were designed within 100 bp upstream of the promoters or downstream of terminator, and then tested using an eGFP reporter and confirmed as suitable single-locus integration sites. Three high-efficiency gRNA targets (PAOX1UP-g2, PTEF1UP-g1, and PFLD1UP-g1) were selected for double- and triple-locus co-integration. The integration efficiency ranged from 57.7 to 70% and 12.5 to 32.1% for double-locus and triple-locus integration, respectively. In addition, biosynthetic pathways of 6-methylsalicylic acid and 3-methylcatechol were successfully assembled using the developed method by one-step integration of functional genes. The desired products were obtained, which further established the effectiveness and applicability of the developed CRISPR-Cas9-mediated gene co-integration method in P. pastoris. CONCLUSIONS A CRISPR-Cas9-mediated multiloci gene integration method was developed with efficient gRNA targets in P. pastoris. Using this method, multiple gene cassettes can be simultaneously integrated into the genome without employing selective markers. The multiloci integration strategy is beneficial for pathway assembly of complicated pharmaceuticals and chemicals expressed in P. pastoris.
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Affiliation(s)
- Qi Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Xiaona Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Lili Song
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Haifeng Liu
- Chinare Resources Angde Biotech Pharmaceutical Co., Ltd., 78 E-jiao Street, Liaocheng, China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
- Chinare Resources Angde Biotech Pharmaceutical Co., Ltd., 78 E-jiao Street, Liaocheng, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
- Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai, 200237 China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
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24
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Joachim M, Maguire N, Schäfer J, Gerlach D, Czermak P. Process Intensification for an Insect Antimicrobial Peptide Elastin-Like Polypeptide Fusion Produced in Redox-Engineered Escherichia coli. Front Bioeng Biotechnol 2019; 7:150. [PMID: 31316976 PMCID: PMC6610315 DOI: 10.3389/fbioe.2019.00150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/06/2019] [Indexed: 12/31/2022] Open
Abstract
Peptides and proteins containing disulfide bonds can be produced in Escherichia coli by targeting the oxidizing periplasm, co-expressing isomerases or chaperons, refolding from inclusion bodies, or by using redox-engineered E. coli strains. Thus far, protein expression in glutathione reductase and thioredoxin reductase deficient (Δgor ΔtrxB) E. coli strains has required a complex medium. However, a chemically defined medium suitable for large-scale production would be preferable for industrial applications. Recently, we developed a minimal medium supplemented with iron (M9i) for high-density cultivation using E. coli Rosetta gami B(DE3)pLysS cells. Here we show that M9i is suitable for the production of insect metalloproteinase inhibitor (IMPI), which contains five disulfide bonds, in the same E. coli strain. We demonstrated the scalability of the new fed-batch process by combining the scale-up criteria of constant dissolved oxygen (DO) and matching volumetric power inputs (P/V) at the borders of the stirrer cascade. Process intensification was achieved by investigating production feed rates and different induction times. We improved product titers by ~200-fold compared to the standard process in complex medium while maintaining the activity of the IMPI protein. Our results show for the first time that it is possible to produce active proteins containing multiple disulfide bonds in a Δgor ΔtrxB E. coli strain using M9i medium. The success of scale-up and process intensification shows that the industrial production of complex recombinant proteins in such strains using chemically defined M9i minimal medium is feasible.
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Affiliation(s)
- Mathias Joachim
- Department of Life Science Engineering, Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany.,Faculty of Biology and Chemistry, Justus Liebig University, Giessen, Germany
| | - Nicolas Maguire
- Department of Bioresources of Fraunhofer, Institute for Molecular Biology and Applied Ecology IME, Giessen, Germany
| | - Johannes Schäfer
- Department of Life Science Engineering, Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Doreen Gerlach
- Department of Bioresources of Fraunhofer, Institute for Molecular Biology and Applied Ecology IME, Giessen, Germany
| | - Peter Czermak
- Department of Life Science Engineering, Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany.,Faculty of Biology and Chemistry, Justus Liebig University, Giessen, Germany.,Department of Bioresources of Fraunhofer, Institute for Molecular Biology and Applied Ecology IME, Giessen, Germany
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25
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Ortega C, Abreu C, Oppezzo P, Correa A. Overview of High-Throughput Cloning Methods for the Post-genomic Era. Methods Mol Biol 2019; 2025:3-32. [PMID: 31267446 DOI: 10.1007/978-1-4939-9624-7_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The advent of new DNA sequencing technologies leads to a dramatic increase in the number of available genome sequences and therefore of target genes with potential for functional analysis. The insertion of these sequences into proper expression vectors requires a simple an efficient cloning method. In addition, when expressing a target protein, quite often it is necessary to evaluate different DNA constructs to achieve a soluble and homogeneous expression of the target with satisfactory yields. The development of new molecular methods made possible the cloning of a huge number of DNA sequences in a high-throughput manner, necessary for meeting the increasing demands for soluble protein expression and characterization. In this chapter several molecular methods suitable for high-throughput cloning are reviewed.
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Affiliation(s)
- Claudia Ortega
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Cecilia Abreu
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Molecular, Cellular and Animal Technology Program, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Pablo Oppezzo
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Agustín Correa
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay.
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26
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Hoffmann D, Eckhardt D, Gerlach D, Vilcinskas A, Czermak P. Downstream processing of Cry4AaCter-induced inclusion bodies containing insect-derived antimicrobial peptides produced in Escherichia coli. Protein Expr Purif 2018; 155:120-129. [PMID: 30529536 DOI: 10.1016/j.pep.2018.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 11/30/2022]
Abstract
The Cry4AaCter tag is a pull-down tag which promotes the formation of inclusion bodies (IBs) that can be resolubilized in an alkaline buffer. Here, we used the Cry4AaCter tag to create a platform for the production of antimicrobial peptides (AMPs) in Escherichia coli featuring a uniform resolubilization process independent of the peptide fused to the pull-down tag. The Cry4AaCter tag conserves the bioactivity of fusion proteins and thus allows the purification of simple AMPs and more complex AMPs stabilized by disulfide bonds. We developed a downstream process (DSP) for the purification of IBs containing the mutated Galleria mellonella insect metalloprotease inhibitor IMPI(I38V), which has a globular structure stabilized by five disulfide bonds. IMPI(I38V) is a potent inhibitor of the M4 metalloproteases used as virulence factors by several human pathogens. We used a single crossflow filtration for the washing and resolubilization of the Cry4AaCter-induced IBs and obtained bioactive IMPI(I38V) after tag removal. We achieved a 68-fold higher protein yield using our IB system compared to an alternative DSP approach in which a GST-fusion strategy was used to produce soluble IMPI(I38V). The Cry4AaCter-based process was transferable to gloverin (another G. mellonella AMP) and the visible marker green fluorescent protein, which accumulated in fluorescent IBs, confirming it is a broadly applicable strategy for the recovery of functional proteins.
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Affiliation(s)
- Daniel Hoffmann
- University of Applied Sciences Mittelhessen, Institute of Bioprocess Engineering and Pharmaceutical Technology, Wiesenstrasse 14, 35390, Giessen, Germany
| | - Dustin Eckhardt
- University of Applied Sciences Mittelhessen, Institute of Bioprocess Engineering and Pharmaceutical Technology, Wiesenstrasse 14, 35390, Giessen, Germany
| | - Doreen Gerlach
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Project Group Bioresources, Heinrich-Buff-Ring 26, 35392, Giessen, Germany
| | - Andreas Vilcinskas
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Project Group Bioresources, Heinrich-Buff-Ring 26, 35392, Giessen, Germany; Justus Liebig University, Heinrich-Buff-Ring, 35392, Giessen, Germany
| | - Peter Czermak
- University of Applied Sciences Mittelhessen, Institute of Bioprocess Engineering and Pharmaceutical Technology, Wiesenstrasse 14, 35390, Giessen, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Project Group Bioresources, Heinrich-Buff-Ring 26, 35392, Giessen, Germany; Justus Liebig University, Heinrich-Buff-Ring, 35392, Giessen, Germany; Kansas State University, Faculty of Chemical Engineering, 1005 Durland Hall 1701A Platt Street, Manhattan, KS, 66506, USA.
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27
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Wibowo D, Zhao CX. Recent achievements and perspectives for large-scale recombinant production of antimicrobial peptides. Appl Microbiol Biotechnol 2018; 103:659-671. [DOI: 10.1007/s00253-018-9524-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/10/2018] [Accepted: 11/14/2018] [Indexed: 02/07/2023]
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28
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Zitzmann J, Schreiber C, Eichmann J, Bilz RO, Salzig D, Weidner T, Czermak P. Single-cell cloning enables the selection of more productive Drosophila melanogaster S2 cells for recombinant protein expression. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2018; 19:e00272. [PMID: 29998071 PMCID: PMC6037645 DOI: 10.1016/j.btre.2018.e00272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/18/2018] [Accepted: 06/22/2018] [Indexed: 11/16/2022]
Abstract
The generation of monoclonal cell lines is an important early process development step for recombinant protein production. Although single-cell cloning is an established method in mammalian cell lines, straightforward protocols are not yet available for insect cells. We describe a new method for the generation of monoclonal insect cells without using fetal bovine serum and/or feeder cells pretreated by irradiation or exposure to mitomycin. Highly productive clones of Drosophila melanogaster S2 cells were prepared in a two-step procedure, comprising the establishment of a polyclonal population and subsequent single cell isolation by limiting dilution. Necessary growth factors were provided by co-cultivation of single transformants with untransfected feeder cells, which were later removed by antibiotic selection. Enhanced expression of EGFP and two target peptides was confirmed by flow cytometry and dot/western blotting. Highly productive clones were stable, showed a uniform expression profile and typically a sixfold to tenfold increase in cell-specific productivity.
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Key Words
- AMP, antimicrobial peptide/protein
- BR021, Harmonia axyridis antimicrobial peptide BR021
- BSA, bovine serum albumin
- D. melanogaster S2 cells
- DMSO, dimethyl sulfoxide
- EGFP, enhanced green fluorescent protein
- FACS, fluorescence activated cell sorting
- FBS, fetal bovine serum
- GMP, good manufacturing practice
- GmGlv, Galleria mellonella antimicrobial peptide Gloverin
- Insect cell culture
- Monoclonal cell line
- OD600, optical density at 600nm
- PBS, phosphate-buffered saline
- PCR, polymerase chain reaction
- PVDF, polyvinylidene difluoride
- RMCE, recombinase mediated cassette exchange
- Recombinant protein expression
- SDS-PAGE, sodium dodecylsulfate polyacrylamide gel electrophoresis
- SFM, serum free medium
- Sf9, clonal isolate of Spodoptera frugiperda Sf21 cells
- Single-cell cloning
- Stably transformed
- rS2, recombinant Drosophila melanogaster Schneider 2 cells
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Affiliation(s)
- Jan Zitzmann
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Christine Schreiber
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Joel Eichmann
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Roberto Otmar Bilz
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Denise Salzig
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Tobias Weidner
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Peter Czermak
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
- Department of Chemical Engineering, Kansas State University, Manhattan KS, USA
- Faculty of Biology and Chemistry, Justus-Liebig University of Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Project group Bioresources, Giessen, Germany
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29
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Metabolic engineering of Pichia pastoris. Metab Eng 2018; 50:2-15. [PMID: 29704654 DOI: 10.1016/j.ymben.2018.04.017] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/16/2018] [Accepted: 04/23/2018] [Indexed: 12/11/2022]
Abstract
Besides its use for efficient production of recombinant proteins the methylotrophic yeast Pichia pastoris (syn. Komagataella spp.) has been increasingly employed as a platform to produce metabolites of varying origin. We summarize here the impressive methodological developments of the last years to model and analyze the metabolism of P. pastoris, and to engineer its genome and metabolic pathways. Efficient methods to insert, modify or delete genes via homologous recombination and CRISPR/Cas9, supported by modular cloning techniques, have been reported. An outstanding early example of metabolic engineering in P. pastoris was the humanization of protein glycosylation. More recently the cell metabolism was engineered also to enhance the productivity of heterologous proteins. The last few years have seen an increased number of metabolic pathway design and engineering in P. pastoris, mainly towards the production of complex (secondary) metabolites. In this review, we discuss the potential role of P. pastoris as a platform for metabolic engineering, its strengths, and major requirements for future developments of chassis strains based on synthetic biology principles.
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30
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Prielhofer R, Barrero JJ, Steuer S, Gassler T, Zahrl R, Baumann K, Sauer M, Mattanovich D, Gasser B, Marx H. GoldenPiCS: a Golden Gate-derived modular cloning system for applied synthetic biology in the yeast Pichia pastoris. BMC SYSTEMS BIOLOGY 2017; 11:123. [PMID: 29221460 PMCID: PMC5723102 DOI: 10.1186/s12918-017-0492-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 11/13/2017] [Indexed: 01/05/2023]
Abstract
BACKGROUND State-of-the-art strain engineering techniques for the host Pichia pastoris (syn. Komagataella spp.) include overexpression of homologous and heterologous genes, and deletion of host genes. For metabolic and cell engineering purposes the simultaneous overexpression of more than one gene would often be required. Very recently, Golden Gate based libraries were adapted to optimize single expression cassettes for recombinant proteins in P. pastoris. However, an efficient toolbox allowing the overexpression of multiple genes at once was not available for P. pastoris. METHODS With the GoldenPiCS system, we provide a flexible modular system for advanced strain engineering in P. pastoris based on Golden Gate cloning. For this purpose, we established a wide variety of standardized genetic parts (20 promoters of different strength, 10 transcription terminators, 4 genome integration loci, 4 resistance marker cassettes). RESULTS All genetic parts were characterized based on their expression strength measured by eGFP as reporter in up to four production-relevant conditions. The promoters, which are either constitutive or regulatable, cover a broad range of expression strengths in their active conditions (2-192% of the glyceraldehyde-3-phosphate dehydrogenase promoter P GAP ), while all transcription terminators and genome integration loci led to equally high expression strength. These modular genetic parts can be readily combined in versatile order, as exemplified for the simultaneous expression of Cas9 and one or more guide-RNA expression units. Importantly, for constructing multigene constructs (vectors with more than two expression units) it is not only essential to balance the expression of the individual genes, but also to avoid repetitive homologous sequences which were otherwise shown to trigger "loop-out" of vector DNA from the P. pastoris genome. CONCLUSIONS GoldenPiCS, a modular Golden Gate-derived P. pastoris cloning system, is very flexible and efficient and can be used for strain engineering of P. pastoris to accomplish pathway expression, protein production or other applications where the integration of various DNA products is required. It allows for the assembly of up to eight expression units on one plasmid with the ability to use different characterized promoters and terminators for each expression unit. GoldenPiCS vectors are available at Addgene.
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Affiliation(s)
- Roland Prielhofer
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Juan J Barrero
- Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria.,Present Address: Department of Chemical, Biological, and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Stefanie Steuer
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Present Address: Novartis, Vienna, Austria
| | - Thomas Gassler
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Richard Zahrl
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Kristin Baumann
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Michael Sauer
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Brigitte Gasser
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria.
| | - Hans Marx
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
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31
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Zahrl RJ, Peña DA, Mattanovich D, Gasser B. Systems biotechnology for protein production in Pichia pastoris. FEMS Yeast Res 2017; 17:4093073. [DOI: 10.1093/femsyr/fox068] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 08/22/2017] [Indexed: 12/31/2022] Open
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