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Nie H, Zhang Y, Li M, Wang W, Wang Z, Zheng J. Expression of microbial lipase in filamentous fungus Aspergillus niger: a review. 3 Biotech 2024; 14:172. [PMID: 38841267 PMCID: PMC11147998 DOI: 10.1007/s13205-024-03998-5] [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: 01/17/2024] [Accepted: 04/28/2024] [Indexed: 06/07/2024] Open
Abstract
Lipase has high economic importance and is widely used in biodiesel, food, detergents, cosmetics, and pharmaceutical industries. The rapid development of synthetic biology and system biology has not only paved the way for comprehensively understanding the efficient operation mechanism of Aspergillus niger cell factories but also introduced a new technological system for creating and optimizing high-efficiency A. niger cell factories. In this review, all relevant data on microbial lipase enzyme sources and general properties are gathered and updated. The relationship between A. niger strain morphology and protein production is discussed. The safety of A. niger strain is investigated to ensure product safety. The biotechnologies and factors influencing lipase expression in A. niger are summarized. This review focuses on various strategies to improve lipase expression in A. niger. The summary of these methods and the application of the gene editing technology CRISPR/Cas9 system can further improve the efficiency of constructing the engineered lipase-producing A. niger.
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Affiliation(s)
- Hongmei Nie
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Yueting Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Mengjiao Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Weili Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Zhao Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Jianyong Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
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Abstract
Our current food system relies on unsustainable practices, which often fail to provide healthy diets to a growing population. Therefore, there is an urgent demand for new sustainable nutrition sources and processes. Microorganisms have gained attention as a new food source solution, due to their low carbon footprint, low reliance on land, water and seasonal variations coupled with a favourable nutritional profile. Furthermore, with the emergence and use of new tools, specifically in synthetic biology, the uses of microorganisms have expanded showing great potential to fulfil many of our dietary needs. In this review, we look at the different applications of microorganisms in food, and examine the history, state-of-the-art and potential to disrupt current foods systems. We cover both the use of microbes to produce whole foods out of their biomass and as cell factories to make highly functional and nutritional ingredients. The technical, economical, and societal limitations are also discussed together with the current and future perspectives.
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Affiliation(s)
- Alicia E Graham
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.
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Roth MG, Westrick NM, Baldwin TT. Fungal biotechnology: From yesterday to tomorrow. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1135263. [PMID: 37746125 PMCID: PMC10512358 DOI: 10.3389/ffunb.2023.1135263] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/07/2023] [Indexed: 09/26/2023]
Abstract
Fungi have been used to better the lives of everyday people and unravel the mysteries of higher eukaryotic organisms for decades. However, comparing progress and development stemming from fungal research to that of human, plant, and bacterial research, fungi remain largely understudied and underutilized. Recent commercial ventures have begun to gain popularity in society, providing a new surge of interest in fungi, mycelia, and potential new applications of these organisms to various aspects of research. Biotechnological advancements in fungal research cannot occur without intensive amounts of time, investments, and research tool development. In this review, we highlight past breakthroughs in fungal biotechnology, discuss requirements to advance fungal biotechnology even further, and touch on the horizon of new breakthroughs with the highest potential to positively impact both research and society.
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Affiliation(s)
- Mitchell G. Roth
- Department of Plant Pathology, The Ohio State University, Wooster, OH, United States
| | - Nathaniel M. Westrick
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, United States
| | - Thomas T. Baldwin
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
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Wang S, Zhang P, Xue Y, Yan Q, Li X, Jiang Z. Characterization of a Novel Aspartic Protease from Rhizomucor miehei Expressed in Aspergillus niger and Its Application in Production of ACE-Inhibitory Peptides. Foods 2021; 10:foods10122949. [PMID: 34945499 PMCID: PMC8701012 DOI: 10.3390/foods10122949] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 11/16/2022] Open
Abstract
Rhizomucor miehei is an important fungus that produces aspartic proteases suitable for cheese processing. In this study, a novel aspartic protease gene (RmproB) was cloned from R. miehei CAU432 and expressed in Aspergillus niger. The amino acid sequence of RmproB shared the highest identity of 58.2% with the saccharopepsin PEP4 from Saccharomyces cerevisiae. High protease activity of 1242.2 U/mL was obtained through high density fermentation in 5 L fermentor. RmproB showed the optimal activity at pH 2.5 and 40 °C, respectively. It was stable within pH 1.5-6.5 and up to 45 °C. RmproB exhibited broad substrate specificity and had Km values of 3.16, 5.88, 5.43, and 1.56 mg/mL for casein, hemoglobin, myoglobin, and bovine serum albumin, respectively. RmproB also showed remarkable milk-clotting activity of 3894.1 SU/mg and identified the cleavage of Lys21-Ile22, Leu32-Ser33, Lys63-Pro64, Leu79-Ser80, Phe105-Met106, and Asp148-Ser149 bonds in κ-casein. Moreover, duck hemoglobin was hydrolyzed by RmproB to prepare angiotensin-I-converting enzyme (ACE) inhibitory peptides with high ACE-inhibitory activity (IC50 of 0.195 mg/mL). The duck hemoglobin peptides were further produced at kilo-scale with a yield of 62.5%. High-level expression and favorable biochemical characterization of RmproB make it a promising candidate for cheese processing and production of ACE-inhibitory peptides.
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Affiliation(s)
- Shounan Wang
- Department of Nutrition and Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (S.W.); (Y.X.)
| | - Peng Zhang
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Engineering, China Agricultural University, Beijing 100083, China; (P.Z.); (X.L.)
| | - Yibin Xue
- Department of Nutrition and Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (S.W.); (Y.X.)
| | - Qiaojuan Yan
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Engineering, China Agricultural University, Beijing 100083, China; (P.Z.); (X.L.)
- Correspondence: (Q.Y.); (Z.J.); Tel.: +86-10-6273-7689 (Z.J.); Fax: +86-10-8238-8508 (Z.J.)
| | - Xue Li
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Engineering, China Agricultural University, Beijing 100083, China; (P.Z.); (X.L.)
| | - Zhengqiang Jiang
- Department of Nutrition and Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (S.W.); (Y.X.)
- Correspondence: (Q.Y.); (Z.J.); Tel.: +86-10-6273-7689 (Z.J.); Fax: +86-10-8238-8508 (Z.J.)
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Filkin SY, Chertova NV, Vavilova EA, Zatsepin SS, Eldarov MA, Sadykhov EG, Fedorov AN, Lipkin AV. Optimization of the Production Method for Recombinant Chymosin in the Methylotrophic Yeast Komagataella phaffii. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820060058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Abstract
Aspergilli have been widely used in the production of organic acids, enzymes, and secondary metabolites for almost a century. Today, several GRAS (generally recognized as safe) Aspergillus species hold a central role in the field of industrial biotechnology with multiple profitable applications. Since the 1990s, research has focused on the use of Aspergillus species in the development of cell factories for the production of recombinant proteins mainly due to their natively high secretion capacity. Advances in the Aspergillus-specific molecular toolkit and combination of several engineering strategies (e.g., protease-deficient strains and fusions to carrier proteins) resulted in strains able to generate high titers of recombinant fungal proteins. However, the production of non-fungal proteins appears to still be inefficient due to bottlenecks in fungal expression and secretion machinery. After a brief overview of the different heterologous expression systems currently available, this review focuses on the filamentous fungi belonging to the genus Aspergillus and their use in recombinant protein production. We describe key steps in protein synthesis and secretion that may limit production efficiency in Aspergillus systems and present genetic engineering approaches and bioprocessing strategies that have been adopted in order to improve recombinant protein titers and expand the potential of Aspergilli as competitive production platforms.
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Havlik D, Brandt U, Bohle K, Fleißner A. Establishment of Neurospora crassa as a host for heterologous protein production using a human antibody fragment as a model product. Microb Cell Fact 2017; 16:128. [PMID: 28743272 PMCID: PMC5526295 DOI: 10.1186/s12934-017-0734-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/05/2017] [Indexed: 12/16/2022] Open
Abstract
Background Filamentous fungi are commonly used as production hosts for bulk enzymes in biotechnological applications. Their robust and quick growth combined with their ability to secrete large amounts of protein directly into the culture medium makes fungi appealing organisms for the generation of novel production systems. The red bread mold Neurospora crassa has long been established as a model system in basic research. It can be very easily genetically manipulated and a wealth of molecular tools and mutants are available. In addition, N. crassa is very fast growing and non-toxic. All of these features point to a high but so far untapped potential of this fungus for biotechnological applications. In this study, we used genetic engineering and bioprocess development in a design-build-test-cycle process to establish N. crassa as a production host for heterologous proteins. Results The human antibody fragment HT186-D11 was fused to a truncated version of the endogenous enzyme glucoamylase (GLA-1), which served as a carrier protein to achieve secretion into the culture medium. A modular expression cassette was constructed and tested under the control of different promoters. Protease activity was identified as a major limitation of the production strain, and the effects of different mutations causing protease deficiencies were compared. Furthermore, a parallel bioreactor system (1 L) was employed to develop and optimize a production process, including the comparison of different culture media and cultivation parameters. After successful optimization of the production strain and the cultivation conditions an exemplary scale up to a 10 L stirred tank reactor was performed. Conclusions The data of this study indicate that N. crassa is suited for the production and secretion of heterologous proteins. Controlling expression by the optimized promoter Pccg1nr in a fourfold protease deletion strain resulted in the successful secretion of the heterologous product with estimated yields of 3 mg/L of the fusion protein. The fungus could easily be cultivated in bioreactors and a first scale-up was successful. The system holds therefore much potential, warranting further efforts in optimization. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0734-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David Havlik
- Division of Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Inhoffenstr. 7, Braunschweig, 38124, Germany.,Institut für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.,Navigo Proteins GmbH, Heinrich-Damerow-Str. 1, 06120, Halle (Saale), Germany
| | - Ulrike Brandt
- Institut für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Kathrin Bohle
- Division of Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Inhoffenstr. 7, Braunschweig, 38124, Germany
| | - André Fleißner
- Institut für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.
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Liu WG, Wang YP, Zhang ZJ, Wang M, Lv QX, Liu HW, Meng LC, Lu M. Generation and characterization of caprine chymosin in corn seed. Protein Expr Purif 2017; 135:78-82. [DOI: 10.1016/j.pep.2017.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 04/25/2017] [Accepted: 05/15/2017] [Indexed: 10/19/2022]
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Behera B, Sethi B, Mishra R, Dutta S, Thatoi H. Microbial cellulases - Diversity & biotechnology with reference to mangrove environment: A review. J Genet Eng Biotechnol 2017; 15:197-210. [PMID: 30647656 PMCID: PMC6296582 DOI: 10.1016/j.jgeb.2016.12.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/01/2016] [Indexed: 11/21/2022]
Abstract
Cellulose is an abundant natural biopolymer on earth, found as a major constituent of plant cell wall in lignocellulosic form. Unlike other compounds cellulose is not easily soluble in water hence enzymatic conversion of cellulose has become a key technology for biodegradation of lignocellulosic materials. Microorganisms such as aerobic bacteria, fungi, yeast and actinomycetes produce cellulase that degrade cellulose by hydrolysing the β-1, 4-glycosidic linkages of cellulose. In contrast to aerobic bacteria, anaerobic bacteria lack the ability to effectively penetrate into the cellulosic material which leads to the development of complexed cellulase systems called cellulosome. Among the different environments, the sediments of mangrove forests are suitable for exploring cellulose degrading microorganisms because of continuous input of cellulosic carbon in the form of litter which then acts as a substrate for decomposition by microbe. Understanding the importance of cellulase, the present article overviews the diversity of cellulolytic microbes from different mangrove environments around the world. The molecular mechanism related to cellulase gene regulation, expression and various biotechnological application of cellulase is also discussed.
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Affiliation(s)
- B.C. Behera
- Department of Biotechnology, North Orissa University, Baripada 757003, Odisha, India
| | - B.K. Sethi
- Department of Biotechnology, MITS School of Biotechnology, Bhubaneswar 751024, India
| | - R.R. Mishra
- Department of Biotechnology, MITS School of Biotechnology, Bhubaneswar 751024, India
| | - S.K. Dutta
- Department of Zoology, North Orissa University, Baripada 757003, Odisha, India
| | - H.N. Thatoi
- Department of Biotechnology, North Orissa University, Baripada 757003, Odisha, India
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Jin FJ, Katayama T, Maruyama JI, Kitamoto K. Comparative genomic analysis identified a mutation related to enhanced heterologous protein production in the filamentous fungus Aspergillus oryzae. Appl Microbiol Biotechnol 2016; 100:9163-9174. [DOI: 10.1007/s00253-016-7714-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/14/2016] [Accepted: 06/27/2016] [Indexed: 11/27/2022]
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Production in stirred-tank bioreactor of recombinant bovine chymosin B by a high-level expression transformant clone of Pichia pastoris. Protein Expr Purif 2016; 123:112-21. [DOI: 10.1016/j.pep.2016.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 11/18/2022]
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Gene Expression Systems in Industrial Ascomycetes: Advancements and Applications. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Noseda DG, Blasco M, Recúpero M, Galvagno MÁ. Bioprocess and downstream optimization of recombinant bovine chymosin B in Pichia (Komagataella) pastoris under methanol-inducible AOXI promoter. Protein Expr Purif 2014; 104:85-91. [PMID: 25278015 DOI: 10.1016/j.pep.2014.09.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/16/2014] [Accepted: 09/19/2014] [Indexed: 11/29/2022]
Abstract
A clone of the methylotrophic yeast Pichia pastoris strain GS115 transformed with the bovine prochymosin B gene was used to optimize the production and downstream of recombinant bovine chymosin expressed under the methanol-inducible AOXI promoter. Cell growth and recombinant chymosin production were analyzed in flask cultures containing basal salts medium with biodiesel-byproduct glycerol as the carbon source, obtaining values of biomass level and milk-clotting activity similar to those achieved with analytical glycerol. The effect of biomass level at the beginning of methanol-induction phase on cell growth and chymosin expression was evaluated, determining that a high concentration of cells at the start of such period generated an increase in the production of chymosin. The impact of the specific growth rate on chymosin expression was studied throughout the induction stage by methanol exponential feeding fermentations in a lab-scale stirred bioreactor, achieving the highest production of heterologous chymosin with a constant specific growth rate of 0.01h(-1). By gel filtration chromatography performed at a semi-preparative scale, recombinant chymosin was purified from exponential fed-batch fermentation cultures, obtaining a specific milk-clotting activity of 6400IMCU/mg of chymosin and a purity level of 95%. The effect of temperature and pH on milk-clotting activity was analyzed, establishing that the optimal temperature and pH values for the purified recombinant chymosin are 37°C and 5.5, respectively. This study reported the features of a sustainable bioprocess for the production of recombinant bovine chymosin in P. pastoris by fermentation in stirred-tank bioreactors using biodiesel-derived glycerol as a low-cost carbon source.
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Affiliation(s)
- Diego Gabriel Noseda
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, 1650, Buenos Aires, Argentina.
| | - Martín Blasco
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, 1650, Buenos Aires, Argentina
| | - Matías Recúpero
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, 1650, Buenos Aires, Argentina
| | - Miguel Ángel Galvagno
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, 1650, Buenos Aires, Argentina; Departamento de Ingeniería Química, Facultad de Ingeniería, Universidad de Buenos Aires, Pabellón de Industrias, Ciudad Universitaria, 1428, Buenos Aires, Argentina
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Martín JF. Calcium-containing phosphopeptides pave the secretory pathway for efficient protein traffic and secretion in fungi. Microb Cell Fact 2014; 13:117. [PMID: 25205075 PMCID: PMC4180148 DOI: 10.1186/s12934-014-0117-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/01/2014] [Indexed: 02/07/2023] Open
Abstract
Casein phosphopeptides (CPPs) containing chelated calcium drastically increase the secretion of extracellular homologous and heterologous proteins in filamentous fungi. Casein phosphopeptides released by digestion of alpha - and beta-casein are rich in phosphoserine residues (SerP). They stimulate enzyme secretion in the gastrointestinal tract and enhance the immune response in mammals, and are used as food supplements. It is well known that casein phosphopeptides transport Ca2+ across the membranes and play an important role in Ca2+ homeostasis in the cells. Addition of CPPs drastically increases the production of heterologous proteins in Aspergillus as host for industrial enzyme production. Recent proteomics studies showed that CPPs alter drastically the vesicle-mediated secretory pathway in filamentous fungi, apparently because they change the calcium concentration in organelles that act as calcium reservoirs. In the organelles calcium homeostasis a major role is played by the pmr1 gene, that encodes a Ca2+/Mn2+ transport ATPase, localized in the Golgi complex; this transporter controls the balance between intra-Golgi and cytoplasmic Ca2+ concentrations. A Golgi-located casein kinase (CkiA) governs the ER to Golgi directionality of the movement of secretory proteins by interacting with the COPII coat of secretory vesicles when they reach the Golgi. Mutants defective in the casein-2 kinase CkiA show abnormal targeting of some secretory proteins, including cytoplasmic membrane amino acid transporters that in ckiA mutants are miss-targeted to vacuolar membranes. Interestingly, addition of CPPs increases a glyceraldehyde-3-phpshate dehydrogenase protein that is known to associate with microtubules and act as a vesicle/membrane fusogenic agent. In summary, CPPs alter the protein secretory pathway in fungi adapting it to a deregulated protein traffic through the organelles and vesicles what results in a drastic increase in secretion of heterologous and also of some homologous proteins.
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Affiliation(s)
- Juan F Martín
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
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Improvement of Heterologous Protein Production inAspergillus oryzaeby RNA Interference with α-Amylase Genes. Biosci Biotechnol Biochem 2014; 73:2370-3. [DOI: 10.1271/bbb.90177] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Adrio JL, Demain AL. Microbial enzymes: tools for biotechnological processes. Biomolecules 2014; 4:117-39. [PMID: 24970208 PMCID: PMC4030981 DOI: 10.3390/biom4010117] [Citation(s) in RCA: 283] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 01/02/2014] [Accepted: 01/02/2014] [Indexed: 11/29/2022] Open
Abstract
Microbial enzymes are of great importance in the development of industrial bioprocesses. Current applications are focused on many different markets including pulp and paper, leather, detergents and textiles, pharmaceuticals, chemical, food and beverages, biofuels, animal feed and personal care, among others. Today there is a need for new, improved or/and more versatile enzymes in order to develop more novel, sustainable and economically competitive production processes. Microbial diversity and modern molecular techniques, such as metagenomics and genomics, are being used to discover new microbial enzymes whose catalytic properties can be improved/modified by different strategies based on rational, semi-rational and random directed evolution. Most industrial enzymes are recombinant forms produced in bacteria and fungi.
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Affiliation(s)
- Jose L Adrio
- Neol Biosolutions SA, BIC Granada, Granada 18016, Spain.
| | - Arnold L Demain
- Research Institute for Scientists Emeriti (R.I.S.E.), Drew University, Madison, NJ 07940, USA.
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Preetha S, Boopathy R. Influence of culture conditions on the production of milk-clotting enzyme from Rhizomucor. World J Microbiol Biotechnol 2014; 10:527-30. [PMID: 24421126 DOI: 10.1007/bf00367659] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/11/1994] [Accepted: 04/14/1994] [Indexed: 11/28/2022]
Abstract
The ratio of milk-clotting activity to proteolytic activity (MC/PA) was used as an index to determine the quality of milk-clotting enzyme. Solid-state fermentation on wheat bran for 5 days at room temperature gave optimal production for enzyme by Rhizomucor miehei and R. pusillus. A ratio of wheat bran to moisture of 1:0.6 (w/v) gave best results. Adding skim milk powder to the media of R. miehei did not improve the MC/PA ratio but 4% (w/w) of the powder did improve the ratio with R. pusillus. Co-cultivation of R. miehei with R. pusillus did not change the MC/PA ratio.
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Cloning, expression and optimized production in a bioreactor of bovine chymosin B in Pichia (Komagataella) pastoris under AOX1 promoter. Protein Expr Purif 2013; 92:235-44. [PMID: 24141135 DOI: 10.1016/j.pep.2013.08.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 07/24/2013] [Accepted: 08/26/2013] [Indexed: 11/21/2022]
Abstract
The codon sequence optimized bovine prochymosin B gene was cloned under the control of the alcohol oxidase 1 promoter (AOX1) in the vector pPIC9K and integrated into the genome of the methylotrophic yeast Pichia (Komagataella) pastoris (P. pastoris) strain GS115. A transformant clone that showed resistance to over 4 mg G418/ml and displayed the highest milk-clotting activity was selected. Cell growth and recombinant bovine chymosin production were optimized in flask cultures during methanol induction phase achieving the highest coagulant activity with low pH values, a temperature of 25°C and with the addition of sorbitol and ascorbic acid at the beginning of this period. The scaling up of the fermentation process to lab-scale stirred bioreactor using optimized conditions, allowed to reach 240 g DCW/L of biomass level and 96 IMCU/ml of milk-clotting activity. The enzyme activity corresponded to 53 mg/L of recombinant bovine chymosin production after 120 h of methanol induction. Western blot analysis of the culture supernatant showed that recombinant chymosin did not suffer degradation during the protein production phase. By a procedure that included high performance gel filtration chromatography and 3 kDa fast ultrafiltration, the recombinant bovine chymosin was purified and concentrated from fermentation cultures, generating a specific activity of 800 IMCU/Total Abs(280 nm) and a total activity recovery of 56%. This study indicated that P. pastoris is a suitable expression system for bioreactor based fed-batch fermentation process for the efficient production of recombinant bovine chymosin under methanol-inducible AOX1 promoter.
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Rozhkova AM, Sereda AS, Tsurikova NV, Nurtaeva AK, Semenova MV, Rimareva LV, Rubtsova EA, Zorov IN, Sinitsyna OA, Sinitsyn AP. Creation of a heterologous gene expression system on the basis of Aspergillus awamori recombinant strain. APPL BIOCHEM MICRO+ 2011. [DOI: 10.1134/s0003683811030124] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Karmakar M, Ray R. Current Trends in Research and Application of Microbial Cellulases. ACTA ACUST UNITED AC 2011. [DOI: 10.3923/jm.2011.41.53] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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22
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Throndset W, Kim S, Bower B, Lantz S, Kelemen B, Pepsin M, Chow N, Mitchinson C, Ward M. Flow cytometric sorting of the filamentous fungus Trichoderma reesei for improved strains. Enzyme Microb Technol 2010. [DOI: 10.1016/j.enzmictec.2010.09.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Expression and export: recombinant protein production systems for Aspergillus. Appl Microbiol Biotechnol 2010; 87:1255-70. [DOI: 10.1007/s00253-010-2672-6] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 05/07/2010] [Accepted: 05/08/2010] [Indexed: 11/26/2022]
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24
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Kumar A, Grover S, Sharma J, Batish VK. Chymosin and other milk coagulants: sources and biotechnological interventions. Crit Rev Biotechnol 2010; 30:243-58. [DOI: 10.3109/07388551.2010.483459] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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25
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Shotgun proteomics of Aspergillus niger microsomes upon D-xylose induction. Appl Environ Microbiol 2010; 76:4421-9. [PMID: 20453123 DOI: 10.1128/aem.00482-10] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Protein secretion plays an eminent role in cell maintenance and adaptation to the extracellular environment of microorganisms. Although protein secretion is an extremely efficient process in filamentous fungi, the mechanisms underlying protein secretion have remained largely uncharacterized in these organisms. In this study, we analyzed the effects of the d-xylose induction of cellulase and hemicellulase enzyme secretion on the protein composition of secretory organelles in Aspergillus niger. We aimed to systematically identify the components involved in the secretion of these enzymes via mass spectrometry of enriched subcellular microsomal fractions. Under each condition, fractions enriched for secretory organelles were processed for tandem mass spectrometry, resulting in the identification of peptides that originate from 1,081 proteins, 254 of which-many of them hypothetical proteins-were predicted to play direct roles in the secretory pathway. d-Xylose induction led to an increase in specific small GTPases known to be associated with polarized growth, exocytosis, and endocytosis. Moreover, the endoplasmic-reticulum-associated degradation (ERAD) components Cdc48 and all 14 of the 20S proteasomal subunits were recruited to the secretory organelles. In conclusion, induction of extracellular enzymes results in specific changes in the secretory subproteome of A. niger, and the most prominent change found in this study was the recruitment of the 20S proteasomal subunits to the secretory organelles.
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Chill L, Trinh L, Azadi P, Ishihara M, Sonon R, Karnaukhova E, Ophir Y, Golding B, Shiloach J. Production, purification, and characterization of human alpha1 proteinase inhibitor from Aspergillus niger. Biotechnol Bioeng 2009; 102:828-44. [PMID: 18828177 DOI: 10.1002/bit.22099] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human alpha one proteinase inhibitor (alpha1-PI) was cloned and expressed in Aspergillus niger, filamentious fungus that can grow in defined media and can perform glycosylation. Submerged culture conditions were established using starch as carbon source, 30% dissolved oxygen concentration, pH 7.0 and 28 degrees C. Eight milligrams per liter of active alpha1-PI were secreted to the growth media in about 40 h. Controlling the protein proteolysis was found to be an important factor in the production. The effects of various carbon sources, pH and temperature on the production and stability of the protein were tested and the product was purified and characterized. Two molecular weights variants of the recombinant alpha1-PI were produced by the fungus; the difference is attributed to the glycosylated part of the molecule. The two glycoproteins were treated with PNGAse F and the released glycans were analyzed by HPAEC, MALDI/TOF-MS, NSI-MS(n), and GC-MS. The MALDI and NSI- full MS spectra of permethylated N-glycans revealed that the N-glycans of both variants contain a series of high-mannose type glycans with 5-20 hexose units. Monosaccharide analysis showed that these were composed of N-acetylglucos-amine, mannose, and galactose. Linkage analysis revealed that the galactosyl component was in the furanoic conformation, which was attaching in a terminal non-reducing position. The Galactofuranose-containing high-mannnose type N-glycans are typical structures, which recently have been found as part of several glycoproteins produced by Aspergillus niger.
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Affiliation(s)
- Liat Chill
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 14A Room 170, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
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27
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Approaches for refining heterologous protein production in filamentous fungi. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0128-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Isolation of Aspergillus oryzae mutants for heterologous protein production from a double proteinase gene disruptant. Appl Microbiol Biotechnol 2009; 82:1105-14. [DOI: 10.1007/s00253-008-1851-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 12/26/2008] [Accepted: 12/29/2008] [Indexed: 11/26/2022]
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30
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Demain AL, Vaishnav P. Production of recombinant proteins by microbes and higher organisms. Biotechnol Adv 2009; 27:297-306. [PMID: 19500547 DOI: 10.1016/j.biotechadv.2009.01.008] [Citation(s) in RCA: 584] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 01/14/2009] [Accepted: 01/21/2009] [Indexed: 02/08/2023]
Abstract
Large proteins are usually expressed in a eukaryotic system while smaller ones are expressed in prokaryotic systems. For proteins that require glycosylation, mammalian cells, fungi or the baculovirus system is chosen. The least expensive, easiest and quickest expression of proteins can be carried out in Escherichia coli. However, this bacterium cannot express very large proteins. Also, for S-S rich proteins, and proteins that require post-translational modifications, E. coli is not the system of choice. The two most utilized yeasts are Saccharomyces cerevisiae and Pichia pastoris. Yeasts can produce high yields of proteins at low cost, proteins larger than 50 kD can be produced, signal sequences can be removed, and glycosylation can be carried out. The baculoviral system can carry out more complex post-translational modifications of proteins. The most popular system for producing recombinant mammalian glycosylated proteins is that of mammalian cells. Genetically modified animals secrete recombinant proteins in their milk, blood or urine. Similarly, transgenic plants such as Arabidopsis thaliana and others can generate many recombinant proteins.
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Affiliation(s)
- Arnold L Demain
- Research Institute for Scientists Emeriti, Drew University, Madison, NJ 07940, USA
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31
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Richie DL, Hartl L, Aimanianda V, Winters MS, Fuller KK, Miley MD, White S, McCarthy JW, Latgé JP, Feldmesser M, Rhodes JC, Askew DS. A role for the unfolded protein response (UPR) in virulence and antifungal susceptibility in Aspergillus fumigatus. PLoS Pathog 2009; 5:e1000258. [PMID: 19132084 PMCID: PMC2606855 DOI: 10.1371/journal.ppat.1000258] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Accepted: 12/08/2008] [Indexed: 01/12/2023] Open
Abstract
Filamentous fungi rely heavily on the secretory pathway, both for the delivery of cell wall components to the hyphal tip and the production and secretion of extracellular hydrolytic enzymes needed to support growth on polymeric substrates. Increased demand on the secretory system exerts stress on the endoplasmic reticulum (ER), which is countered by the activation of a coordinated stress response pathway termed the unfolded protein response (UPR). To determine the contribution of the UPR to the growth and virulence of the filamentous fungal pathogen Aspergillus fumigatus, we disrupted the hacA gene, encoding the major transcriptional regulator of the UPR. The ΔhacA mutant was unable to activate the UPR in response to ER stress and was hypersensitive to agents that disrupt ER homeostasis or the cell wall. Failure to induce the UPR did not affect radial growth on rich medium at 37°C, but cell wall integrity was disrupted at 45°C, resulting in a dramatic loss in viability. The ΔhacA mutant displayed a reduced capacity for protease secretion and was growth-impaired when challenged to assimilate nutrients from complex substrates. In addition, the ΔhacA mutant exhibited increased susceptibility to current antifungal agents that disrupt the membrane or cell wall and had attenuated virulence in multiple mouse models of invasive aspergillosis. These results demonstrate the importance of ER homeostasis to the growth and virulence of A. fumigatus and suggest that targeting the UPR, either alone or in combination with other antifungal drugs, would be an effective antifungal strategy. The pathogenic mold Aspergillus fumigatus is the leading cause of airborne fungal infections in immunocompromised patients. The fungus normally resides in compost, an environment that challenges the organism to obtain nutrients by degrading complex organic polymers. This is accomplished by secreted enzymes, some of which may also contribute to nutrient acquisition during infection. Extracellular enzymes are folded in the endoplasmic reticulum (ER) prior to secretion. If the folding capacity of the ER is overwhelmed by increased secretory demand, the resulting ER stress triggers an adaptive response termed the unfolded protein response (UPR). In this study, we uncover a previously unknown function for the master transcriptional regulator of the UPR, HacA, in fungal virulence. In the absence of HacA, A. fumigatus was unable to secrete high levels of proteins and had reduced virulence in mice. In addition, loss of HacA caused a cell wall defect and increased susceptibility to two major classes of antifungal drugs used for the treatment of aspergillosis. These findings demonstrate that A. fumigatus relies on HacA for growth in the host environment and suggest that therapeutic targeting of the UPR could have merit against A. fumigatus, as well as other eukaryotic pathogens with highly developed secretory systems.
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Affiliation(s)
- Daryl L. Richie
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Lukas Hartl
- Unité des Aspergillus, Institut Pasteur, Paris, France
| | | | - Michael S. Winters
- Division of Infectious Diseases, Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Kevin K. Fuller
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Michael D. Miley
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Stephanie White
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Jason W. McCarthy
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | | | - Marta Feldmesser
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Judith C. Rhodes
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - David S. Askew
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail:
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32
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Developing Aspergillus as a host for heterologous expression. Biotechnol Adv 2009; 27:53-75. [DOI: 10.1016/j.biotechadv.2008.09.001] [Citation(s) in RCA: 204] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Revised: 09/04/2008] [Accepted: 09/07/2008] [Indexed: 12/11/2022]
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33
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Filamentous fungi for production of food additives and processing aids. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008. [PMID: 18253709 DOI: 10.1007/10_2007_094] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Filamentous fungi are metabolically versatile organisms with a very wide distribution in nature. They exist in association with other species, e.g. as lichens or mycorrhiza, as pathogens of animals and plants or as free-living species. Many are regarded as nature's primary degraders because they secrete a wide variety of hydrolytic enzymes that degrade waste organic materials. Many species produce secondary metabolites such as polyketides or peptides and an increasing range of fungal species is exploited commercially as sources of enzymes and metabolites for food or pharmaceutical applications. The recent availability of fungal genome sequences has provided a major opportunity to explore and further exploit fungi as sources of enzymes and metabolites. In this review chapter we focus on the use of fungi in the production of food additives but take a largely pre-genomic, albeit a mainly molecular, view of the topic.
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34
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Codon optimization increases steady-state mRNA levels in Aspergillus oryzae heterologous gene expression. Appl Environ Microbiol 2008; 74:6538-46. [PMID: 18791013 DOI: 10.1128/aem.01354-08] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We investigated the effect of codon optimization on the expression levels of heterologous proteins in Aspergillus oryzae, using the mite allergen Der f 7 as a model protein. A codon-optimized Der f 7 gene was synthesized according to the frequency of codon usage in A. oryzae by recursive PCR. Both native and optimized Der f 7 genes were expressed under the control of a high-level-expression promoter with their own signal peptides or in a fusion construct with A. oryzae glucoamylase (GlaA). Codon optimization markedly increased protein and mRNA production levels in both nonfused and GlaA-fused Der f 7 constructs. For constructs with native codons, analysis by 3' rapid amplification of cDNA ends revealed that poly(A) tracts tended to be added within the coding region, producing aberrant mRNAs that lack a termination codon. Insertion of a termination codon between the carrier GlaA and native Der f 7 proteins in the GlaA fusion construct resulted in increases in mRNA and secreted-carrier-GlaA levels. These results suggested that mRNAs without a termination codon as a result of premature polyadenylation are degraded, possibly through the nonstop mRNA decay pathway. We suggest that codon optimization in A. oryzae results in elimination of cryptic polyadenylation signals in native Der f 7, thereby circumventing the production of truncated transcripts and resulting in an increase in steady-state mRNA levels.
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35
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Desai RP, Leaf T, Hu Z, Hutchinson CR, Hong A, Byng G, Galazzo J, Licari P. Combining Classical, Genetic, and Process Strategies for Improved Precursor-Directed Production of 6-Deoxyerythronolide B Analogues. Biotechnol Prog 2008; 20:38-43. [PMID: 14763821 DOI: 10.1021/bp034171u] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A process for the production of erythromycin aglycone analogues has been developed by combining classical strain mutagenesis techniques with modern recombinant DNA methods and traditional process improvement strategies. A Streptomyces coelicolor strain expressing the heterologous 6-deoxyerythronolide B (6-dEB) synthase (DEBS) for the production of erythromycin aglycones was subjected to random mutagenesis and selection. Several strains exhibiting 2-fold higher productivities and reaching >3 g/L total macrolide aglycones were developed. These mutagenized strains were cured of the plasmid carrying the DEBS genes and a KS1 degrees mutant DEBS operon was introduced for the production of novel analogues when supplemented with a synthetic diketide precursor. The strains expressing the mutant DEBS were screened for improved 15-methyl-6-dEB production, and the best clone, strain B9, was found to be 50% more productive as compared to the parent host strain used for 15-methyl-6-dEB production. Strain B9 was evaluated in 5-L fermenters to confirm productivity in a scalable process. Although peak titers of 0.85 g/L 15-methyl-6-dEB by strain B9 confirmed improved productivity, it was hypothesized that the low solubility of 15-methyl-6-dEB limited productivity. The solubility of 15-methyl-6-dEB in water was determined to be 0.25-0.40 g/L, although higher titers are possible in fermentation medium. The incorporation of the hydrophobic resin XAD-16HP resulted in both the in situ adsorption of the product and the slow release of the diketide precursor. The resin-containing fermentation achieved 1.3 g/L 15-methyl-6-dEB, 50% higher than the resin-free process. By combining classical mutagenesis, recombinant DNA techniques, and process development, 15-methyl-6-dEB productivity was increased by over 100% in a scalable fermentation process.
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Affiliation(s)
- Ruchir P Desai
- Kosan Biosciences, Inc., 3832 Bay Center Place, Hayward, California 94545, USA.
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36
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Andersen MR, Nielsen ML, Nielsen J. Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Mol Syst Biol 2008; 4:178. [PMID: 18364712 PMCID: PMC2290933 DOI: 10.1038/msb.2008.12] [Citation(s) in RCA: 135] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Accepted: 01/28/2008] [Indexed: 11/09/2022] Open
Abstract
The release of the genome sequences of two strains of Aspergillus niger has allowed systems-level investigations of this important microbial cell factory. To this end, tools for doing data integration of multi-ome data are necessary, and especially interesting in the context of metabolism. On the basis of an A. niger bibliome survey, we present the largest model reconstruction of a metabolic network reported for a fungal species. The reconstructed gapless metabolic network is based on the reportings of 371 articles and comprises 1190 biochemically unique reactions and 871 ORFs. Inclusion of isoenzymes increases the total number of reactions to 2240. A graphical map of the metabolic network is presented. All levels of the reconstruction process were based on manual curation. From the reconstructed metabolic network, a mathematical model was constructed and validated with data on yields, fluxes and transcription. The presented metabolic network and map are useful tools for examining systemwide data in a metabolic context. Results from the validated model show a great potential for expanding the use of A. niger as a high-yield production platform.
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Affiliation(s)
- Mikael Rørdam Andersen
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
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37
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Abstract
Life on earth is not possible without microorganisms. Microbes have contributed to industrial science for over 100 years. They have given us diversity in enzymatic content and metabolic pathways. The advent of recombinant DNA brought many changes to industrial microbiology. New expression systems have been developed, biosynthetic pathways have been modified by metabolic engineering to give new metabolites, and directed evolution has provided enzymes with modified selectability, improved catalytic activity and stability. More and more genomes of industrial microorganisms are being sequenced giving valuable information about the genetic and enzymatic makeup of these valuable forms of life. Major tools such as functional genomics, proteomics, and metabolomics are being exploited for the discovery of new valuable small molecules for medicine and enzymes for catalysis.
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Affiliation(s)
- Arnold L Demain
- Research Institute for Scientists Emeriti (R.I.S.E.), Drew University, Madison, NJ 07940, USA.
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38
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Kumar A, Sharma J, Grover S, Kumar Mohanty A, Kumar Batish V. Molecular Cloning and Expression of Goat (Capra hircus) Prochymosin inE.coli. FOOD BIOTECHNOL 2007. [DOI: 10.1080/08905430701191163] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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39
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Masuda T, Kitabatake N. Developments in biotechnological production of sweet proteins. J Biosci Bioeng 2006; 102:375-89. [PMID: 17189164 DOI: 10.1263/jbb.102.375] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Accepted: 06/06/2006] [Indexed: 11/17/2022]
Abstract
Most proteins are tasteless and flavorless, while some proteins elicit a sweet-taste response on the human palate. Six proteins, thaumatin, monellin, mabinlin, brazzein, egg lysozyme, and neoculin (previously considered as curculin) have been identified as sweet-tasting proteins. However, no common features among them have been observed. Herein, recent advances in the research of sweet-tasting proteins and the production of such proteins by biotechnological approaches are reviewed. Information on the structure-sweetness relationship for these proteins would help not only in the clarification of the mechanism of interaction of sweet-tasting proteins with their receptors, but also in the design of more effective low-calorie sweeteners.
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Affiliation(s)
- Tetsuya Masuda
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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40
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El-Enshasy H, Kleine J, Rinas U. Agitation effects on morphology and protein productive fractions of filamentous and pelleted growth forms of recombinant Aspergillus niger. Process Biochem 2006. [DOI: 10.1016/j.procbio.2006.05.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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41
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van den Brink HJM, Petersen SG, Rahbek-Nielsen H, Hellmuth K, Harboe M. Increased production of chymosin by glycosylation. J Biotechnol 2006; 125:304-10. [PMID: 16621086 DOI: 10.1016/j.jbiotec.2006.02.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Revised: 02/22/2006] [Accepted: 02/27/2006] [Indexed: 10/24/2022]
Abstract
Filamentous fungi are well known in the industry as producers of large amounts of extracellular proteins. However, production levels of heterologous proteins are often disappointing low. In this paper it is shown that increasing glycosylation is a powerful strategy for increasing production levels of chymosin in filamentous fungi. Two different concepts based on glycosylation were tested. First, we improved a poorly used N-glycosylation site within the prochymosin molecule. The resulting highly glycosylated chymosin molecule was expressed in Aspergillus niger. It was shown that production of the glycosylated protein was much more efficient, giving a yield increase of more than 100% compared to production of the native chymosin molecule. In an alternative strategy the N-glycosylation site was located outside of the native chymosin molecule, on a linker separating prochymosin from its carrier molecule. Also in this case significantly increased production levels were obtained. This strategy might offer a powerful tool for increasing production levels of other heterologous proteins as well.
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42
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Mander GJ, Wang H, Bodie E, Wagner J, Vienken K, Vinuesa C, Foster C, Leeder AC, Allen G, Hamill V, Janssen GG, Dunn-Coleman N, Karos M, Lemaire HG, Subkowski T, Bollschweiler C, Turner G, Nüsslein B, Fischer R. Use of laccase as a novel, versatile reporter system in filamentous fungi. Appl Environ Microbiol 2006; 72:5020-6. [PMID: 16820501 PMCID: PMC1489370 DOI: 10.1128/aem.00060-06] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Accepted: 05/02/2006] [Indexed: 11/20/2022] Open
Abstract
Laccases are copper-containing enzymes which oxidize phenolic substrates and transfer the electrons to oxygen. Many filamentous fungi contain several laccase-encoding genes, but their biological roles are mostly not well understood. The main interest in laccases in biotechnology is their potential to be used to detoxify phenolic substances. We report here on a novel application of laccases as a reporter system in fungi. We purified a laccase enzyme from the ligno-cellulolytic ascomycete Stachybotrys chartarum. It oxidized the artificial substrate 2,2'-azino-di-(3-ethylbenzthiazolinsulfonate) (ABTS). The corresponding gene was isolated and expressed in Aspergillus nidulans, Aspergillus niger, and Trichoderma reesei. Heterologously expressed laccase activity was monitored in colorimetric enzyme assays and on agar plates with ABTS as a substrate. The use of laccase as a reporter was shown in a genetic screen for the isolation of improved T. reesei cellulase production strains. In addition to the laccase from S. charatarum, we tested the application of three laccases from A. nidulans (LccB, LccC, and LccD) as reporters. Whereas LccC oxidized ABTS (Km = 0.3 mM), LccD did not react with ABTS but with DMA/ADBP (3,5-dimethylaniline/4-amino-2,6-dibromophenol). LccB reacted with DMA/ADBP and showed weak activity with ABTS. The different catalytic properties of LccC and LccD allow simultaneous use of these two laccases as reporters in one fungal strain.
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Affiliation(s)
- Gerd J Mander
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
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43
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Kappeler SR, van den Brink HJM, Rahbek-Nielsen H, Farah Z, Puhan Z, Hansen EB, Johansen E. Characterization of recombinant camel chymosin reveals superior properties for the coagulation of bovine and camel milk. Biochem Biophys Res Commun 2006; 342:647-54. [PMID: 16488399 DOI: 10.1016/j.bbrc.2006.02.014] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Accepted: 02/06/2006] [Indexed: 11/16/2022]
Abstract
Enzymatic milk coagulation for cheese manufacturing involves the cleavage of the scissile bond in kappa-casein by an aspartic acid protease. Bovine chymosin is the preferred enzyme, combining a strong clotting activity with a low general proteolytic activity. In the present study, we report expression and enzymatic properties of recombinant camel chymosin expressed in Aspergillus niger. Camel chymosin was shown to have different characteristics than bovine chymosin. Camel chymosin exhibits a 70% higher clotting activity for bovine milk and has only 20% of the unspecific protease activity for bovine chymosin. This results in a sevenfold higher ratio of clotting to general proteolytic activity. The enzyme is more thermostable than bovine chymosin. Kinetic analysis showed that half-saturation is achieved with less than 50% of the substrate required for bovine chymosin and turnover rates are lower. While raw camel milk cannot be clotted with bovine chymosin, a high clotting activity was found with camel chymosin.
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Affiliation(s)
- Stefan R Kappeler
- Institute of Food Science, Swiss Federal Institute of Technology, CH-8092 Zurich, Switzerland
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44
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Semova N, Storms R, John T, Gaudet P, Ulycznyj P, Min XJ, Sun J, Butler G, Tsang A. Generation, annotation, and analysis of an extensive Aspergillus niger EST collection. BMC Microbiol 2006; 6:7. [PMID: 16457709 PMCID: PMC1434744 DOI: 10.1186/1471-2180-6-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2005] [Accepted: 02/02/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aspergillus niger, a saprophyte commonly found on decaying vegetation, is widely used and studied for industrial purposes. Despite its place as one of the most important organisms for commercial applications, the lack of available information about its genetic makeup limits research with this filamentous fungus. RESULTS We present here the analysis of 12,820 expressed sequence tags (ESTs) generated from A. niger cultured under seven different growth conditions. These ESTs identify about 5,108 genes of which 44.5% code for proteins sharing similarity (E < or = 1e(-5)) with GenBank entries of known function, 38% code for proteins that only share similarity with GenBank entries of unknown function and 17.5% encode proteins that do not have a GenBank homolog. Using the Gene Ontology hierarchy, we present a first classification of the A. niger proteins encoded by these genes and compare its protein repertoire with other well-studied fungal species. We have established a searchable web-based database that includes the EST and derived contig sequences and their annotation. Details about this project and access to the annotated A. niger database are available. CONCLUSION This EST collection and its annotation provide a significant resource for fundamental and applied research with A. niger. The gene set identified in this manuscript will be highly useful in the annotation of the genome sequence of A. niger, the genes described in the manuscript, especially those encoding hydrolytic enzymes will provide a valuable source for researchers interested in enzyme properties and applications.
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Affiliation(s)
- Natalia Semova
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Reginald Storms
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
- Department of Biology, Concordia University, Montreal, Canada
| | - Tricia John
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Pascale Gaudet
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
- Northwestern University, 676 N. St. Clair Street, Chicago, IL 60611
| | - Peter Ulycznyj
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Xiang Jia Min
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Jian Sun
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Greg Butler
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
- Department of Computer Science and Software Engineering, Concordia University, Montreal, Canada
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
- Department of Biology, Concordia University, Montreal, Canada
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Grimm LH, Kelly S, Krull R, Hempel DC. Morphology and productivity of filamentous fungi. Appl Microbiol Biotechnol 2005; 69:375-84. [PMID: 16317480 DOI: 10.1007/s00253-005-0213-5] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2005] [Revised: 10/06/2005] [Accepted: 10/10/2005] [Indexed: 10/25/2022]
Abstract
Cultivation processes involving filamentous fungi have been optimised for decades to obtain high product yields. Several bulk chemicals like citric acid and penicillin are produced this way. A simple adaptation of cultivation parameters for new production processes is not possible though. Models explaining the correlation between process-dependent growth behaviour and productivity are therefore necessary to prevent long-lasting empiric test series. Yet, filamentous growth consists of a complex microscopic differentiation process from conidia to hyphae resulting in various macroscopically visible appearances. Early approaches to model this morphologic development are recapitulated in this review to explain current trends in this area of research. Tailoring morphology by adjusting process parameters is one side of the coin, but an ideal morphology has not even been found. This article reviews several reasons for this fact starting with nutrient supply in a fungal culture and presents recent advances in the investigation of fungal metabolism. It illustrates the challenge to unfold the relationship between morphology and productivity.
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Affiliation(s)
- L H Grimm
- Institute of Biochemical Engineering, Technical University of Braunschweig, Gaussstrasse 17, 38106 Braunschweig, Germany
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Sims AH, Gent ME, Lanthaler K, Dunn-Coleman NS, Oliver SG, Robson GD. Transcriptome analysis of recombinant protein secretion by Aspergillus nidulans and the unfolded-protein response in vivo. Appl Environ Microbiol 2005; 71:2737-47. [PMID: 15870366 PMCID: PMC1087583 DOI: 10.1128/aem.71.5.2737-2747.2005] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Filamentous fungi have a high capacity for producing large amounts of secreted proteins, a property that has been exploited for commercial production of recombinant proteins. However, the secretory pathway, which is key to the production of extracellular proteins, is rather poorly characterized in filamentous fungi compared to yeast. We report the effects of recombinant protein secretion on gene expression levels in Aspergillus nidulans by directly comparing a bovine chymosin-producing strain with its parental wild-type strain in continuous culture by using expressed sequence tag microarrays. This approach demonstrated more subtle and specific changes in gene expression than those observed when mimicking the effects of protein overproduction by using a secretion blocker. The impact of overexpressing a secreted recombinant protein more closely resembles the unfolded-protein response in vivo.
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Affiliation(s)
- Andrew H Sims
- Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
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47
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Model-based prediction of substrate conversion and protein synthesis and excretion in recombinant Aspergillus niger biopellets. Chem Eng Sci 2005. [DOI: 10.1016/j.ces.2004.12.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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Liang Y, Li W, Ma Q, Zhang Y. Functional properties of PDIA from Aspergillus niger in renaturation of proteins. FEMS Microbiol Lett 2005; 245:363-8. [PMID: 15837393 DOI: 10.1016/j.femsle.2005.03.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2005] [Revised: 03/09/2005] [Accepted: 03/16/2005] [Indexed: 11/24/2022] Open
Abstract
Functional properties of protein disulfide isomerase A (PDIA) from Aspergillus niger were investigated using ribonuclease A, glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and prochymosin as substrates. PDIA was shown to function as an isomerase catalyzing the refolding of denatured and reduced ribonuclease A. PDIA also exhibited trx-independent chaperone activity preventing the aggregation of reduced, denatured GAPDH, an enzyme lacking disulfide bonds. Both isomerase activity and chaperone function of PDIA were essential for the efficient refolding of the reduced, denatured prochymosin.
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Affiliation(s)
- Yurong Liang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China
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Vega-Hernández MC, Gómez-Coello A, Villar J, Claverie-Martín F. Molecular cloning and expression in yeast of caprine prochymosin. J Biotechnol 2005; 114:69-79. [PMID: 15464600 DOI: 10.1016/j.jbiotec.2004.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2004] [Revised: 06/03/2004] [Accepted: 06/08/2004] [Indexed: 10/26/2022]
Abstract
We cloned and characterized a preprochymosin cDNA from the abomasum of milk-fed kid goats. This cDNA contained an open reading frame that predicts a polypeptide of 381 amino acid residues, with a signal peptide and a proenzyme region of 16 and 42 amino acids, respectively. Comparison of the caprine preprochymosin sequence with the corresponding sequences of lamb and calf revealed 99 and 94% identity at the amino acid level. The cDNA fragment encoding the mature portion of caprine prochymosin was fused in frame both to the killer toxin signal sequence and to the alpha-factor signal sequence-FLAG in two different yeast expression vectors. The recombinant plasmids were transformed into Kluyveromyces lactis and Saccharomyces cerevisiae cells, respectively. Culture supernatants of both yeast transformants showed milk-clotting activity after activation at acid pH. The FLAG-prochymosin fusion was purified from S. cerevisiae culture supernatants by affinity chromatography. Proteolytic activity assayed toward casein fractions indicated that the recombinant caprine chymosin specifically hydrolysed kappa-casein.
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Affiliation(s)
- Maria C Vega-Hernández
- Molecular Biology Laboratory, Research Unit, Nuestra Señora de Candelaria University Hospital, 38010, Santa Cruz de Tenerife, Spain
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Aro N, Pakula T, Penttilä M. Transcriptional regulation of plant cell wall degradation by filamentous fungi. FEMS Microbiol Rev 2004; 29:719-39. [PMID: 16102600 DOI: 10.1016/j.femsre.2004.11.006] [Citation(s) in RCA: 274] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2004] [Revised: 10/29/2004] [Accepted: 11/01/2004] [Indexed: 11/22/2022] Open
Abstract
Plant cell wall consists mainly of the large biopolymers cellulose, hemicellulose, lignin and pectin. These biopolymers are degraded by many microorganisms, in particular filamentous fungi, with the aid of extracellular enzymes. Filamentous fungi have a key role in degradation of the most abundant biopolymers found in nature, cellulose and hemicelluloses, and therefore are essential for the maintenance of the global carbon cycle. The production of plant cell wall degrading enzymes, cellulases, hemicellulases, ligninases and pectinases, is regulated mainly at the transcriptional level in filamentous fungi. The genes are induced in the presence of the polymers or molecules derived from the polymers and repressed under growth conditions where the production of these enzymes is not necessary, such as on glucose. The expression of the genes encoding the enzymes is regulated by various environmental and cellular factors, some of which are common while others are more unique to either a certain fungus or a class of enzymes. This review summarises our current knowledge on the transcriptional regulation, focusing on the recently characterized transcription factors that regulate genes coding for enzymes involved in the breakdown of plant cell wall biopolymers.
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Affiliation(s)
- Nina Aro
- VTT Biotechnology, Espoo, Finland.
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