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Jadhav R, Mach RL, Mach-Aigner AR. Protein secretion and associated stress in industrially employed filamentous fungi. Appl Microbiol Biotechnol 2024; 108:92. [PMID: 38204136 PMCID: PMC10781871 DOI: 10.1007/s00253-023-12985-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024]
Abstract
Application of filamentous fungi for the production of commercial enzymes such as amylase, cellulase, or xylanase is on the rise due to the increasing demand to degrade several complex carbohydrates as raw material for biotechnological processes. Also, protein production by fungi for food and feed gains importance. In any case, the protein production involves both cellular synthesis and secretion outside of the cell. Unfortunately, the secretion of proteins or enzymes can be hampered due to accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) as a result of too high synthesis of enzymes or (heterologous) protein expression. To cope with this ER stress, the cell generates a response known as unfolded protein response (UPR). Even though this mechanism should re-establish the protein homeostasis equivalent to a cell under non-stress conditions, the enzyme expression might still suffer from repression under secretory stress (RESS). Among eukaryotes, Saccharomyces cerevisiae is the only fungus, which is studied quite extensively to unravel the UPR pathway. Several homologs of the proteins involved in this signal transduction cascade are also found in filamentous fungi. Since RESS seems to be absent in S. cerevisiae and was only reported in Trichoderma reesei in the presence of folding and glycosylation inhibitors such as dithiothreitol and tunicamycin, more in-depth study about this mechanism, specifically in filamentous fungi, is the need of the hour. Hence, this review article gives an overview on both, protein secretion and associated stress responses in fungi. KEY POINTS: • Enzymes produced by filamentous fungi are crucial in industrial processes • UPR mechanism is conserved among many fungi, but mediated by different proteins • RESS is not fully understood or studied in industrially relevant filamentous fungi.
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Affiliation(s)
- Reshma Jadhav
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
| | - Robert L Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
| | - Astrid R Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria.
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria.
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2
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He J, Tang M, Zhong F, Deng J, Li W, Zhang L, Lin Q, Xia X, Li J, Guo T. Current trends and possibilities of typical microbial protein production approaches: a review. Crit Rev Biotechnol 2024:1-18. [PMID: 38566484 DOI: 10.1080/07388551.2024.2332927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 01/17/2024] [Indexed: 04/04/2024]
Abstract
Global population growth and demographic restructuring are driving the food and agriculture sectors to provide greater quantities and varieties of food, of which protein resources are particularly important. Traditional animal-source proteins are becoming increasingly difficult to meet the demand of the current consumer market, and the search for alternative protein sources is urgent. Microbial proteins are biomass obtained from nonpathogenic single-celled organisms, such as bacteria, fungi, and microalgae. They contain large amounts of proteins and essential amino acids as well as a variety of other nutritive substances, which are considered to be promising sustainable alternatives to traditional proteins. In this review, typical approaches to microbial protein synthesis processes were highlighted and the characteristics and applications of different types of microbial proteins were described. Bacteria, fungi, and microalgae can be individually or co-cultured to obtain protein-rich biomass using starch-based raw materials, organic wastes, and one-carbon compounds as fermentation substrates. Microbial proteins have been gradually used in practical applications as foods, nutritional supplements, flavor modifiers, and animal feeds. However, further development and application of microbial proteins require more advanced biotechnological support, screening of good strains, and safety considerations. This review contributes to accelerating the practical application of microbial proteins as a promising alternative protein resource and provides a sustainable solution to the food crisis facing the world.
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Affiliation(s)
- JinTao He
- Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - Min Tang
- Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - FeiFei Zhong
- Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
- Changsha Institute for Food and Drug Control, Changsha, China
| | - Jing Deng
- Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - Wen Li
- Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
- Hunan Provincial Engineering Technology Research Center of Seasonings Green Manufacturing, Changsha, China
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing, China
| | - Lin Zhang
- Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - QinLu Lin
- Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
- Hunan Provincial Engineering Technology Research Center of Seasonings Green Manufacturing, Changsha, China
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing, China
| | - Xu Xia
- Huaihua Academy of Agricultural Sciences, Huaihua, China
| | - Juan Li
- Hunan Province Key Laboratory of Edible Forestry Resources Safety and Processing Utilization, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - Ting Guo
- Jiangsu Academy of Agricultural Sciences, Nanjing, China
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3
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Yang W, Su Y, Wang R, Zhang H, Jing H, Meng J, Zhang G, Huang L, Guo L, Wang J, Gao W. Microbial production and applications of β-glucosidase-A review. Int J Biol Macromol 2024; 256:127915. [PMID: 37939774 DOI: 10.1016/j.ijbiomac.2023.127915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/03/2023] [Accepted: 11/04/2023] [Indexed: 11/10/2023]
Abstract
β-Glucosidase exists in all areas of living organisms, and microbial β-glucosidase has become the main source of its production because of its unique physicochemical properties and the advantages of high-yield production by fermentation. With the rise of the green circular economy, the production of enzymes through the fermentation of waste as the substrate has become a popular trend. Lignocellulosic biomass is an easily accessible and sustainable feedstock that exists in nature, and the production of biofuels from lignocellulosic biomass requires the involvement of β-glucosidase. This review proposes ways to improve β-glucosidase yield and catalytic efficiency. Optimization of growth conditions and purification strategies of enzymes can increase enzyme yield, and enzyme immobilization, genetic engineering, protein engineering, and whole-cell catalysis provide solutions to enhance the catalytic efficiency and activity of β-glucosidase. Besides, the diversified industrial applications, challenges and prospects of β-glucosidase are also described.
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Affiliation(s)
- Wenqi Yang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Yaowu Su
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Rubing Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Huanyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Hongyan Jing
- Traditional Chinese Medicine College, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jie Meng
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Guoqi Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Luqi Huang
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Lanping Guo
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs.
| | - Juan Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China.
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China.
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4
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Liu D, Garrigues S, de Vries RP. Heterologous protein production in filamentous fungi. Appl Microbiol Biotechnol 2023; 107:5019-5033. [PMID: 37405433 PMCID: PMC10386965 DOI: 10.1007/s00253-023-12660-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/06/2023]
Abstract
Filamentous fungi are able to produce a wide range of valuable proteins and enzymes for many industrial applications. Recent advances in fungal genomics and experimental technologies are rapidly changing the approaches for the development and use of filamentous fungi as hosts for the production of both homologous and heterologous proteins. In this review, we highlight the benefits and challenges of using filamentous fungi for the production of heterologous proteins. We review various techniques commonly employed to improve the heterologous protein production in filamentous fungi, such as strong and inducible promoters, codon optimization, more efficient signal peptides for secretion, carrier proteins, engineering of glycosylation sites, regulation of the unfolded protein response and endoplasmic reticulum associated protein degradation, optimization of the intracellular transport process, regulation of unconventional protein secretion, and construction of protease-deficient strains. KEY POINTS: • This review updates the knowledge on heterologous protein production in filamentous fungi. • Several fungal cell factories and potential candidates are discussed. • Insights into improving heterologous gene expression are given.
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Affiliation(s)
- Dujuan Liu
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Sandra Garrigues
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Department of Food Biotechnology, Instituto de Agroquímica Y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.
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5
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Tiwari P, Dufossé L. Focus and Insights into the Synthetic Biology-Mediated Chassis of Economically Important Fungi for the Production of High-Value Metabolites. Microorganisms 2023; 11:1141. [PMID: 37317115 PMCID: PMC10222946 DOI: 10.3390/microorganisms11051141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 06/16/2023] Open
Abstract
Substantial progress has been achieved and knowledge gaps addressed in synthetic biology-mediated engineering of biological organisms to produce high-value metabolites. Bio-based products from fungi are extensively explored in the present era, attributed to their emerging importance in the industrial sector, healthcare, and food applications. The edible group of fungi and multiple fungal strains defines attractive biological resources for high-value metabolites comprising food additives, pigments, dyes, industrial chemicals, and antibiotics, including other compounds. In this direction, synthetic biology-mediated genetic chassis of fungal strains to enhance/add value to novel chemical entities of biological origin is opening new avenues in fungal biotechnology. While substantial success has been achieved in the genetic manipulation of economically viable fungi (including Saccharomyces cerevisiae) in the production of metabolites of socio-economic relevance, knowledge gaps/obstacles in fungal biology and engineering need to be remedied for complete exploitation of valuable fungal strains. Herein, the thematic article discusses the novel attributes of bio-based products from fungi and the creation of high-value engineered fungal strains to promote yield, bio-functionality, and value-addition of the metabolites of socio-economic value. Efforts have been made to discuss the existing limitations in fungal chassis and how the advances in synthetic biology provide a plausible solution.
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Affiliation(s)
- Pragya Tiwari
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea;
| | - Laurent Dufossé
- Chemistry and Biotechnology of Natural Products, CHEMBIOPRO, Université de La Réunion, ESIROI Agroalimentaire, 15 Avenue René Cassin, F-97490 Saint-Denis, France
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Jo C, Zhang J, Tam JM, Church GM, Khalil AS, Segrè D, Tang TC. Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability. Mater Today Bio 2023; 19:100560. [PMID: 36756210 PMCID: PMC9900623 DOI: 10.1016/j.mtbio.2023.100560] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023] Open
Abstract
Filamentous fungi drive carbon and nutrient cycling across our global ecosystems, through its interactions with growing and decaying flora and their constituent microbiomes. The remarkable metabolic diversity, secretion ability, and fiber-like mycelial structure that have evolved in filamentous fungi have been increasingly exploited in commercial operations. The industrial potential of mycelial fermentation ranges from the discovery and bioproduction of enzymes and bioactive compounds, the decarbonization of food and material production, to environmental remediation and enhanced agricultural production. Despite its fundamental impact in ecology and biotechnology, molds and mushrooms have not, to-date, significantly intersected with synthetic biology in ways comparable to other industrial cell factories (e.g. Escherichia coli,Saccharomyces cerevisiae, and Komagataella phaffii). In this review, we summarize a suite of synthetic biology and computational tools for the mining, engineering and optimization of filamentous fungi as a bioproduction chassis. A combination of methods across genetic engineering, mutagenesis, experimental evolution, and computational modeling can be used to address strain development bottlenecks in established and emerging industries. These include slow mycelium growth rate, low production yields, non-optimal growth in alternative feedstocks, and difficulties in downstream purification. In the scope of biomanufacturing, we then detail previous efforts in improving key bottlenecks by targeting protein processing and secretion pathways, hyphae morphogenesis, and transcriptional control. Bringing synthetic biology practices into the hidden world of molds and mushrooms will serve to expand the limited panel of host organisms that allow for commercially-feasible and environmentally-sustainable bioproduction of enzymes, chemicals, therapeutics, foods, and materials of the future.
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Affiliation(s)
- Charles Jo
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Jing Zhang
- Biological Design Center, Boston University, Boston, MA, USA
- Graduate Program in Bioinformatics, Boston, MA, USA
| | - Jenny M. Tam
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Ahmad S. Khalil
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Daniel Segrè
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- Graduate Program in Bioinformatics, Boston, MA, USA
- Department of Biology, Boston University, Boston, MA, USA
- Department of Physics, Boston University, Boston, MA, USA
| | - Tzu-Chieh Tang
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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7
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Zhang J, Hong Y, Li K, Sun Y, Yao C, Ling J, Zhong Y. Enhancing the production of a heterologous Trametes laccase (LacA) by replacement of the major cellulase CBH1 in Trichoderma reesei. J Ind Microbiol Biotechnol 2023; 50:kuad002. [PMID: 36690343 PMCID: PMC10124127 DOI: 10.1093/jimb/kuad002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023]
Abstract
The laccases from white-rot fungi exhibit high redox potential in treating phenolic compounds. However, their application in commercial purposes has been limited because of the relatively low productivity of the native hosts. Here, the laccase A-encoding gene lacA of Trametes sp. AH28-2 was overexpressed under the control of the strong promoter of cbh1 (Pcbh1), the gene encoding the endogenous cellobiohydrolase 1 (CBH1), in the industrial workhorse fungus Trichoderma reesei. Firstly, the lacA expression cassette was randomly integrated into the T. reesei chromosome by genetic transformation. The lacA gene was successfully transcribed, but the laccase couldn't be detected in the liquid fermentation condition. Meanwhile, it was found that the endoplasmic reticulum-associated degradation (ERAD) was strongly activated, indicating that the expression of LacA probably triggered intense endoplasmic reticulum (ER) stress. Subsequently, the lacA expression cassette was added with the downstream region of cbh1 (Tcbh1) to construct the new expression cassette lacA::Δcbh1, which could replace the cbh1 locus in the genome via homologous recombination. After genetic transformation, the lacA gene was integrated into the cbh1 locus and transcribed. And the unfolded protein response (UPR) and ERAD were only slightly induced, for which the loss of endogenous cellulase CBH1 released the pressure of secretion. Finally, the maximum laccase activity of 168.3 U/l was obtained in the fermentation broth. These results demonstrated that the reduction of secretion pressure by deletion of endogenous protein-encoding genes would be an efficient strategy for the secretion of heterologous target proteins in industrial fungi. ONE-SENTENCE SUMMARY The reduction of the secretion pressure by deletion of the endogenous cbh1 gene can contribute to heterologous expression of the laccase (LacA) from Trametes sp. AH28-2 in Trichoderma reesei.
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Affiliation(s)
- Jiaxin Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Yu Hong
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Kehang Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Yu Sun
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Cheng Yao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Jianya Ling
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Yaohua Zhong
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
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Shi Z, Zhao Y, Liu S, Wang Y, Yu Q. Size-Dependent Impact of Magnetic Nanoparticles on Growth and Sporulation of Aspergillus niger. Molecules 2022; 27:molecules27185840. [PMID: 36144576 PMCID: PMC9502663 DOI: 10.3390/molecules27185840] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 08/31/2022] [Accepted: 09/07/2022] [Indexed: 12/03/2022] Open
Abstract
Magnetic nanoparticles (MNPs) are becoming important DNA nanocarriers for genetic engineering of industrial fungi. However, the biological effect of MNPs on industrial fungi remains unknown. In this study, we prepared three kinds of magnetic nanoparticles with different sizes (i.e., 10 nm, 20 nm, and 200 nm) to investigate their impact on the growth and sporulation of the important industrial fungus Aspergillus niger. Transmission electron microscopy, X-ray diffraction analysis and Zeta potential analysis revealed that the three kinds of MNPs, including MNP10, MNP20 and MNP200, had uniform size distribution, regular Fe3O4 X-ray diffraction (XRD) patterns and similar Zeta potentials. Interestingly, although the three kinds of MNPs did not obviously inhibit growth of the fungus, the MNP20 at 500 mg/L strongly attenuated sporulation, leading to a remarkable decrease in spore numbers on culturing plates. Further investigation showed that MNP20 at the high concentration led to drastic chitin accumulation in the cell wall, indicating cell wall disruption of the MNP20-treated fungal cells. Moreover, the MNPs did not cause unusual iron dissolution and reactive oxygen species (ROS) accumulation, and the addition of ferrous ion, ferric ion or the reactive oxygen species scavenger N-acetyl-L-cysteine (NAC) had no impact on the sporulation of the fungus, suggesting that both iron dissolution and ROS accumulation did not contribute to attenuated sporulation by MNP20. This study revealed the size-dependent effect of MNPs on fungal sporulation, which was associated with MNP-induced cell wall disruption.
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Affiliation(s)
- Zhishang Shi
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yan Zhao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shuo Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
- Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yanting Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
- Correspondence:
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Dong M, Wang S, Xu F, Xiao G, Bai J, Wang J, Sun X. Integrative transcriptome and proteome analyses of Trichoderma longibrachiatum LC and its cellulase hyper-producing mutants generated by heavy ion mutagenesis reveal the key genes involved in cellulolytic enzymes regulation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:63. [PMID: 35658919 PMCID: PMC9166314 DOI: 10.1186/s13068-022-02161-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/18/2022] [Indexed: 01/10/2023]
Abstract
Background The major challenge of facing the efficient utilization of biomass is the high cost of cellulolytic enzyme, while the Trichoderma longibrachiatum plays an essential role in the production of industrial enzymes and biomass recycling. Results The cellulase hyper‑producing mutants of LC-M4 and LC-M16 derived from the wild type T. longibrachiatum LC strain through heavy ion mutagenesis exhibited the high-efficiency secretion ability of cellulase and hemicellulose. The FPase activities of LC-M4 (4.51 IU/mL) and LC-M16 (4.16 IU/mL) mutants increased by 46.91% and 35.5% when compared to the LC strain, respectively. Moreover, these two cellulase hyper-producing mutants showed faster growth rate on the cellulosic substrates (Avicel and CMC-Na) plate than that of LC strain. Therefore, an integrative transcriptome and proteome profiling analysis of T. longibrachiatum LC and its cellulase hyper‑producing mutant LC-M4 and LC-M16 were employed to reveal the key genes involved in cellulolytic enzymes regulation. It was showed that the transcriptome and proteome profiles changed dramatically between the wild strain and mutant strains. Notably, the overlapped genes obtained from integrative analysis identified that the protein processing in ER involved in protein secretory pathway, starch and sucrose metabolism pathway and N-glycan biosynthesis pathway were significantly changed both in cellulase hyper-producing mutants and thereby improving the enzyme secretion efficiency, which maybe the main reason of cellulase hyper-production in LC-M4 and LC-M16 mutants. In addition, the three DEGs/DEPs (PDI, Sec61, VIP36) related with protein secretion in ER and two DEGs/DEPs (OST, MOGS) related with N-glycan biosynthesis were identified as key candidate genes participating in enzyme protein biosynthesis and secretion. Conclusions In this study, a hypothetical secretory model of cellulase protein in filamentous fungi was established on the basis of DEGs/DEPs and key genes identified from the omics analysis, which were of great guidance on the rational genetic engineering and/or breeding of filamentous fungi for improving cellulase production. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02161-7.
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Affiliation(s)
- Miaoyin Dong
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Rd, Lanzhou, 730000, Gansu, People's Republic of China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, People's Republic of China
| | - Shuyang Wang
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Rd, Lanzhou, 730000, Gansu, People's Republic of China. .,Institute of Biology, Gansu Academy of Sciences, 197 Dingxi South Rd, Lanzhou, 730000, Gansu, People's Republic of China. .,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, People's Republic of China.
| | - Fuqiang Xu
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Rd, Lanzhou, 730000, Gansu, People's Republic of China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, People's Republic of China
| | - Guoqing Xiao
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Rd, Lanzhou, 730000, Gansu, People's Republic of China. .,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, People's Republic of China.
| | - Jin Bai
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Rd, Lanzhou, 730000, Gansu, People's Republic of China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, People's Republic of China
| | - Junkai Wang
- College of Physics and Electronic Engineering, Northwest Normal University, 967Anning East Rd, Lanzhou, 730000, Gansu, People's Republic of China
| | - Xisi Sun
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Rd, Lanzhou, 730000, Gansu, People's Republic of China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, People's Republic of China
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Lübeck M, Lübeck PS. Fungal Cell Factories for Efficient and Sustainable Production of Proteins and Peptides. Microorganisms 2022; 10:753. [PMID: 35456803 PMCID: PMC9025306 DOI: 10.3390/microorganisms10040753] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 01/12/2023] Open
Abstract
Filamentous fungi are a large and diverse taxonomically group of microorganisms found in all habitats worldwide. They grow as a network of cells called hyphae. Since filamentous fungi live in very diverse habitats, they produce different enzymes to degrade material for their living, for example hydrolytic enzymes to degrade various kinds of biomasses. Moreover, they produce defense proteins (antimicrobial peptides) and proteins for attaching surfaces (hydrophobins). Many of them are easy to cultivate in different known setups (submerged fermentation and solid-state fermentation) and their secretion of proteins and enzymes are often much larger than what is seen from yeast and bacteria. Therefore, filamentous fungi are in many industries the preferred production hosts of different proteins and enzymes. Edible fungi have traditionally been used as food, such as mushrooms or in fermented foods. New trends are to use edible fungi to produce myco-protein enriched foods. This review gives an overview of the different kinds of proteins, enzymes, and peptides produced by the most well-known fungi used as cell factories for different purposes and applications. Moreover, we describe some of the challenges that are important to consider when filamentous fungi are optimized as efficient cell factories.
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Affiliation(s)
- Mette Lübeck
- Department of Chemistry and Bioscience, Aalborg University, DK-9100 Aalborg, Denmark;
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Li Q, Lu J, Zhang G, Liu S, Zhou J, Du G, Chen J. Recent advances in the development of Aspergillus for protein production. BIORESOURCE TECHNOLOGY 2022; 348:126768. [PMID: 35091037 DOI: 10.1016/j.biortech.2022.126768] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Aspergillus had been widely used in the industrial production of recombinant proteins. In addition to the safety and broad substrate utilization spectrum, its efficient post-translational modification and strong protein secretion capacity have significant advantages for developing an excellent protein-producing cell factory in industrial production. However, the difficulties in genetic manipulation of Aspergillus and varying expression levels of different heterologous proteins hampered its further development and application. Recently, the development of CRISPR genome editing and high-throughput screening platforms has facilitated the Aspergillus development of a wide range of modifications and applications. Meanwhile, multi-omics analysis and multiplexed genetic engineering have promoted effective knowledge mining. This paper provides a comprehensive and updated review of these advances, including high-throughput screening, genome editing, protein expression modules, and fermentation optimization. It also highlights and discusses the latest significant progress, aiming to provide a practical guide for implementing Aspergillus as an efficient protein-producing cell factory.
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Affiliation(s)
- Qinghua Li
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jinchang Lu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Guoqiang Zhang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Song Liu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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Chai S, Zhu Z, Tian E, Xiao M, Wang Y, Zou G, Zhou Z. Building a Versatile Protein Production Platform Using Engineered Trichoderma reesei. ACS Synth Biol 2022; 11:486-496. [PMID: 34928572 DOI: 10.1021/acssynbio.1c00570] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Trichoderma reesei has an extremely high capacity for synthesizing and secreting proteins, thus exhibiting promise as an expression platform for heterologous proteins. However, T. reesei secretes large amounts of native proteins, which hinders its widespread application for heterologous protein production. Here, we designed and built a series of T. reesei chassis using an iterative gene deletion approach based on an efficient genome editing system. Donor DNAs with specially designed construct facilitated screening of positive deletion strains without ectopic insertion. Finally, marker-free T. reesei chassis with lower rates of native protein secretion and low levels of extracellular protease activity were constructed after 11 consecutive rounds of gene deletion. Higher production levels of three heterologous proteins─a bacterial xylanase XYL7, a fungal immunomodulatory protein LZ8, and the human serum albumin HSA─were achieved with these chassis using the cbh1 promoter. It is possible that diverse high-value proteins might be produced at a high yield using this engineered platform.
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Affiliation(s)
- Shunxing Chai
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19(A) Yuquan Rd, Beijing 100049, China
| | - Zhihua Zhu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19(A) Yuquan Rd, Beijing 100049, China
| | - Ernuo Tian
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
| | - Meili Xiao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19(A) Yuquan Rd, Beijing 100049, China
| | - Yan Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
| | - Gen Zou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, 1000 Jinqi Rd, Shanghai 201403, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
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Sun Y, Qian Y, Zhang J, Yao C, Wang Y, Liu H, Zhong Y. Development of a novel expression platform for heterologous protein production via deleting the p53-like regulator Vib1 in Trichoderma reesei. Enzyme Microb Technol 2022; 155:109993. [DOI: 10.1016/j.enzmictec.2022.109993] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/03/2022] [Accepted: 01/11/2022] [Indexed: 02/06/2023]
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Yan S, Xu Y, Yu XW. From induction to secretion: a complicated route for cellulase production in Trichoderma reesei. BIORESOUR BIOPROCESS 2021; 8:107. [PMID: 38650205 PMCID: PMC10991602 DOI: 10.1186/s40643-021-00461-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/16/2021] [Indexed: 11/10/2022] Open
Abstract
The filamentous fungus Trichoderma reesei has been widely used for cellulase production that has extensive applications in green and sustainable development. Increasing costs and depletion of fossil fuels provoke the demand for hyper-cellulase production in this cellulolytic fungus. To better manipulate T. reesei for enhanced cellulase production and to lower the cost for large-scale fermentation, it is wise to have a comprehensive understanding of the crucial factors and complicated biological network of cellulase production that could provide new perspectives for further exploration and modification. In this review, we summarize recent progress and give an overview of the cellular process of cellulase production in T. reesei, including the carbon source-dependent cellulase induction, complicated transcriptional regulation network, and efficient protein assembly and trafficking. Among that, the key factors involved in cellulase production were emphasized, shedding light on potential perspectives for further engineering.
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Affiliation(s)
- Su Yan
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Xiao-Wei Yu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China.
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China.
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Gabriel R, Mueller R, Floerl L, Hopson C, Harth S, Schuerg T, Fleissner A, Singer SW. CAZymes from the thermophilic fungus Thermoascus aurantiacus are induced by C5 and C6 sugars. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:169. [PMID: 34384463 PMCID: PMC8359064 DOI: 10.1186/s13068-021-02018-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Filamentous fungi are excellent lignocellulose degraders, which they achieve through producing carbohydrate active enzymes (CAZymes). CAZyme production is highly orchestrated and gene expression analysis has greatly expanded understanding of this important biotechnological process. The thermophilic fungus Thermoascus aurantiacus secretes highly active thermostable enzymes that enable saccharifications at higher temperatures; however, the genome-wide measurements of gene expression in response to CAZyme induction are not understood. RESULTS A fed-batch system with plant biomass-derived sugars D-xylose, L-arabinose and cellobiose established that these sugars induce CAZyme expression in T. aurantiacus. The C5 sugars induced both cellulases and hemicellulases, while cellobiose specifically induced cellulases. A minimal medium formulation was developed to enable gene expression studies of T. aurantiacus with these inducers. It was found that d-xylose and L-arabinose strongly induced a wide variety of CAZymes, auxiliary activity (AA) enzymes and carbohydrate esterases (CEs), while cellobiose facilitated lower expression of mostly cellulase genes. Furthermore, putative orthologues of different unfolded protein response genes were up-regulated during the C5 sugar feeding together with genes in the C5 sugar assimilation pathways. CONCLUSION This work has identified two additional CAZyme inducers for T. aurantiacus, L-arabinose and cellobiose, along with D-xylose. A combination of biochemical assays and RNA-seq measurements established that C5 sugars induce a suite of cellulases and hemicellulases, providing paths to produce broad spectrum thermotolerant enzymatic mixtures.
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Affiliation(s)
- Raphael Gabriel
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Institut Für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Rebecca Mueller
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Institut Für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Lena Floerl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190, Vienna, Austria
- Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Cynthia Hopson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Department of Chemical Engineering and Materials, Faculty of Chemistry, Complutense University of Madrid, Av. Complutense s/n, 28040, Madrid, Spain
| | - Simon Harth
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Frankfurt Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Timo Schuerg
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Andre Fleissner
- Institut Für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106, Braunschweig, Germany
| | - Steven W Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA.
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.
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González-López MDC, Jijón-Moreno S, Dautt-Castro M, Ovando-Vázquez C, Ziv T, Horwitz BA, Casas-Flores S. Secretome Analysis of Arabidopsis- Trichoderma atroviride Interaction Unveils New Roles for the Plant Glutamate:Glyoxylate Aminotransferase GGAT1 in Plant Growth Induced by the Fungus and Resistance against Botrytis cinerea. Int J Mol Sci 2021; 22:6804. [PMID: 34202732 PMCID: PMC8268252 DOI: 10.3390/ijms22136804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/02/2021] [Accepted: 06/10/2021] [Indexed: 11/16/2022] Open
Abstract
The establishment of plant-fungus mutualistic interaction requires bidirectional molecular crosstalk. Therefore, the analysis of the interacting organisms secretomes would help to understand how such relationships are established. Here, a gel-free shotgun proteomics approach was used to identify the secreted proteins of the plant Arabidopsis thaliana and the mutualistic fungus Trichoderma atroviride during their interaction. A total of 126 proteins of Arabidopsis and 1027 of T. atroviride were identified. Among them, 118 and 780 were differentially modulated, respectively. Bioinformatic analysis unveiled that both organisms' secretomes were enriched with enzymes. In T. atroviride, glycosidases, aspartic endopeptidases, and dehydrogenases increased in response to Arabidopsis. Additionally, amidases, protein-serine/threonine kinases, and hydro-lyases showed decreased levels. Furthermore, peroxidases, cysteine endopeptidases, and enzymes related to the catabolism of secondary metabolites increased in the plant secretome. In contrast, pathogenesis-related proteins and protease inhibitors decreased in response to the fungus. Notably, the glutamate:glyoxylate aminotransferase GGAT1 was secreted by Arabidopsis during its interaction with T. atroviride. Our study showed that GGAT1 is partially required for plant growth stimulation and on the induction of the plant systemic resistance by T. atroviride. Additionally, GGAT1 seems to participate in the negative regulation of the plant systemic resistance against B. cinerea through a mechanism involving H2O2 production.
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Affiliation(s)
- María del Carmen González-López
- Laboratorio de Genómica Funcional y Comparativa, División de Biología Molecular, IPICYT, Camino a la Presa San José No. 2055. Col. Lomas 4ª. Section, San Luis Potosí C.P. 78216, Mexico; (M.d.C.G.-L.); (S.J.-M.); (M.D.-C.); (C.O.-V.)
| | - Saúl Jijón-Moreno
- Laboratorio de Genómica Funcional y Comparativa, División de Biología Molecular, IPICYT, Camino a la Presa San José No. 2055. Col. Lomas 4ª. Section, San Luis Potosí C.P. 78216, Mexico; (M.d.C.G.-L.); (S.J.-M.); (M.D.-C.); (C.O.-V.)
| | - Mitzuko Dautt-Castro
- Laboratorio de Genómica Funcional y Comparativa, División de Biología Molecular, IPICYT, Camino a la Presa San José No. 2055. Col. Lomas 4ª. Section, San Luis Potosí C.P. 78216, Mexico; (M.d.C.G.-L.); (S.J.-M.); (M.D.-C.); (C.O.-V.)
| | - Cesaré Ovando-Vázquez
- Laboratorio de Genómica Funcional y Comparativa, División de Biología Molecular, IPICYT, Camino a la Presa San José No. 2055. Col. Lomas 4ª. Section, San Luis Potosí C.P. 78216, Mexico; (M.d.C.G.-L.); (S.J.-M.); (M.D.-C.); (C.O.-V.)
- Centro Nacional de Supercómputo, IPICYT, Camino a la Presa San José No. 2055. Col. Lomas 4ª. Section, San Luis Potosí C.P. 78216, Mexico
| | - Tamar Ziv
- Smoler Protein Center, Faculty of Biology, Technion—Israel Institute of Technology, Haifa 32000, Israel;
| | - Benjamin A. Horwitz
- Faculty of Biology, Technion—Israel Institute of Technology, Haifa 32000, Israel;
| | - Sergio Casas-Flores
- Laboratorio de Genómica Funcional y Comparativa, División de Biología Molecular, IPICYT, Camino a la Presa San José No. 2055. Col. Lomas 4ª. Section, San Luis Potosí C.P. 78216, Mexico; (M.d.C.G.-L.); (S.J.-M.); (M.D.-C.); (C.O.-V.)
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Tesei D, Chiang AJ, Kalkum M, Stajich JE, Mohan GBM, Sterflinger K, Venkateswaran K. Effects of Simulated Microgravity on the Proteome and Secretome of the Polyextremotolerant Black Fungus Knufia chersonesos. Front Genet 2021; 12:638708. [PMID: 33815472 PMCID: PMC8012687 DOI: 10.3389/fgene.2021.638708] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/19/2021] [Indexed: 11/13/2022] Open
Abstract
Black fungi are a group of melanotic microfungi characterized by remarkable polyextremotolerance. Due to a broad ecological plasticity and adaptations at the cellular level, it is predicted that they may survive in a variety of extreme environments, including harsh niches on Earth and Mars, and in outer space. However, the molecular mechanisms aiding survival, especially in space, are yet to be fully elucidated. Based on these premises, the rock-inhabiting black fungus Knufia chersonesos (Wt) and its non-melanized mutant (Mut) were exposed to simulated microgravity-one of the prevalent features characterizing space conditions-by growing the cultures in high-aspect-ratio vessels (HARVs). Qualitative and quantitative proteomic analyses were performed on the mycelia and supernatant of culture medium (secretome) to assess alterations in cell physiology in response to low-shear simulated microgravity (LSSMG) and to ultimately evaluate the role of cell-wall melanization in stress survival. Differential expression was observed for proteins involved in carbohydrate and lipid metabolic processes, transport, and ribosome biogenesis and translation via ribosomal translational machinery. However, no evidence of significant activation of stress components or starvation response was detected, except for the scytalone dehydratase, enzyme involved in the synthesis of dihydroxynaphthalene (DNH) melanin, which was found to be upregulated in the secretome of the wild type and downregulated in the mutant. Differences in protein modulation were observed between K. chersonesos Wt and Mut, with several proteins being downregulated under LSSMG in the Mut when compared to the Wt. Lastly, no major morphological alterations were observed following exposure to LSSMG. Similarly, the strains' survivability was not negatively affected. This study is the first to characterize the response to simulated microgravity in black fungi, which might have implications on future astrobiological missions.
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Affiliation(s)
- Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Abby J. Chiang
- Department of Molecular Imaging and Therapy, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Markus Kalkum
- Department of Molecular Imaging and Therapy, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - Ganesh Babu Malli Mohan
- Department of Biotechnology, Centre for Research and Infectious Diseases, SASTRA Deemed University, Thanjavur, India
| | - Katja Sterflinger
- Institute for Natural Sciences and Technology in the Arts, Academy of Fine Arts Vienna, Vienna, Austria
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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Wei H, Wu M, Fan A, Su H. Recombinant protein production in the filamentous fungus Trichoderma. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Takahashi JA, Barbosa BVR, Martins BDA, P. Guirlanda C, A. F. Moura M. Use of the Versatility of Fungal Metabolism to Meet Modern Demands for Healthy Aging, Functional Foods, and Sustainability. J Fungi (Basel) 2020; 6:E223. [PMID: 33076336 PMCID: PMC7711925 DOI: 10.3390/jof6040223] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/22/2020] [Accepted: 09/27/2020] [Indexed: 01/27/2023] Open
Abstract
Aging-associated, non-transmissible chronic diseases (NTCD) such as cancer, dyslipidemia, and neurodegenerative disorders have been challenged through several strategies including the consumption of healthy foods and the development of new drugs for existing diseases. Consumer health consciousness is guiding market trends toward the development of additives and nutraceutical products of natural origin. Fungi produce several metabolites with bioactivity against NTCD as well as pigments, dyes, antioxidants, polysaccharides, and enzymes that can be explored as substitutes for synthetic food additives. Research in this area has increased the yields of metabolites for industrial applications through improving fermentation conditions, application of metabolic engineering techniques, and fungal genetic manipulation. Several modern hyphenated techniques have impressively increased the rate of research in this area, enabling the analysis of a large number of species and fermentative conditions. This review thus focuses on summarizing the nutritional, pharmacological, and economic importance of fungi and their metabolites resulting from applications in the aforementioned areas, examples of modern techniques for optimizing the production of fungi and their metabolites, and methodologies for the identification and analysis of these compounds.
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Affiliation(s)
- Jacqueline A. Takahashi
- Department of Chemistry, Exact Sciences Institute, Universidade Federal de Minas Gerais, Pres. Antônio Carlos Avenue, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil; (B.V.R.B.); (B.d.A.M.)
| | - Bianca V. R. Barbosa
- Department of Chemistry, Exact Sciences Institute, Universidade Federal de Minas Gerais, Pres. Antônio Carlos Avenue, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil; (B.V.R.B.); (B.d.A.M.)
| | - Bruna de A. Martins
- Department of Chemistry, Exact Sciences Institute, Universidade Federal de Minas Gerais, Pres. Antônio Carlos Avenue, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil; (B.V.R.B.); (B.d.A.M.)
| | - Christiano P. Guirlanda
- Department of Food Science, Faculty of Pharmacy, Universidade Federal de Minas Gerais, Pres. Antônio Carlos Avenue, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil; (C.P.G.); (M.A.F.M.)
| | - Marília A. F. Moura
- Department of Food Science, Faculty of Pharmacy, Universidade Federal de Minas Gerais, Pres. Antônio Carlos Avenue, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil; (C.P.G.); (M.A.F.M.)
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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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Li C, Zhou J, Du G, Chen J, Takahashi S, Liu S. Developing Aspergillus niger as a cell factory for food enzyme production. Biotechnol Adv 2020; 44:107630. [PMID: 32919011 DOI: 10.1016/j.biotechadv.2020.107630] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 09/05/2020] [Accepted: 09/05/2020] [Indexed: 02/06/2023]
Abstract
Aspergillus niger has become one of the most important hosts for food enzyme production due to its unique food safety characteristics and excellent protein secretion systems. A series of food enzymes such as glucoamylase have been commercially produced by A. niger strains, making this species a suitable platform for the engineered of strains with improved enzyme production. However, difficulties in genetic manipulations and shortage of expression strategies limit the progress in this regard. Moreover, several mycotoxins have recently been detected in some A. niger strains, which raises the necessity for a regulatory approval process for food enzyme production. With robust strains, processing engineering strategies are also needed for producing the enzymes on a large scale, which is also challenging for A. niger, since its culture is aerobic, and non-Newtonian fluid properties are developed during submerged culture, making mixing and aeration very energy-intensive. In this article, the progress and challenges of developing A. niger for the production of food enzymes are reviewed, including its genetic manipulations, strategies for more efficient production of food enzymes, and elimination of mycotoxins for product safety.
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Affiliation(s)
- Cen Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Guocheng Du
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Song Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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Zubieta MP, Gerhardt JA, Rubio MV, Terrasan CRF, Persinoti GF, Antoniel EP, Contesini FJ, Prade RA, Damasio A. Improvement of homologous GH10 xylanase production by deletion of genes with predicted function in the Aspergillus nidulans secretion pathway. Microb Biotechnol 2020; 13:1245-1253. [PMID: 32212325 PMCID: PMC7264891 DOI: 10.1111/1751-7915.13556] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 03/01/2020] [Indexed: 12/20/2022] Open
Abstract
Filamentous fungi are important cell factories for large-scale enzyme production. However, production levels are often low, and this limitation has stimulated research focusing on the manipulation of genes with predicted function in the protein secretory pathway. This pathway is the major route for the delivery of proteins to the cell exterior, and a positive relationship between the production of recombinant enzymes and the unfolded protein response (UPR) pathway has been observed. In this study, Aspergillus nidulans was exposed to UPR-inducing chemicals and differentially expressed genes were identified by RNA-seq. Twelve target genes were deleted in A. nidulans recombinant strains producing homologous and heterologous GH10 xylanases. The knockout of pbnA (glycosyltransferase), ydjA (Hsp40 co-chaperone), trxA (thioredoxin) and cypA (cyclophilin) improved the production of the homologous xylanase by 78, 171, 105 and 125% respectively. Interestingly, these deletions decreased the overall protein secretion, suggesting that the production of the homologous xylanase was specifically altered. However, the production of the heterologous xylanase and the secretion of total proteins were not altered by deleting the same genes. Considering the results, this approach demonstrated the possibility of rationally increase the production of a homologous enzyme, indicating that trxA, cypA, ydjA and pbnA are involved in protein production by A. nidulans.
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Affiliation(s)
- Mariane P. Zubieta
- Department of Biochemistry and Tissue BiologyInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSPBrazil
- Microbiology and Molecular GeneticsOklahoma State UniversityStillwaterOKUSA
| | - Jaqueline A. Gerhardt
- Department of Biochemistry and Tissue BiologyInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSPBrazil
| | - Marcelo V. Rubio
- Department of Biochemistry and Tissue BiologyInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSPBrazil
| | - César R. F. Terrasan
- Department of Biochemistry and Tissue BiologyInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSPBrazil
| | - Gabriela F. Persinoti
- Brazilian Biorenewables National Laboratory (LNBR)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasSPBrazil
| | - Everton P. Antoniel
- Department of Biochemistry and Tissue BiologyInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSPBrazil
| | - Fabiano J. Contesini
- Department of Biochemistry and Tissue BiologyInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSPBrazil
| | - Rolf A. Prade
- Microbiology and Molecular GeneticsOklahoma State UniversityStillwaterOKUSA
| | - André Damasio
- Department of Biochemistry and Tissue BiologyInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSPBrazil
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Wiltschi B, Cernava T, Dennig A, Galindo Casas M, Geier M, Gruber S, Haberbauer M, Heidinger P, Herrero Acero E, Kratzer R, Luley-Goedl C, Müller CA, Pitzer J, Ribitsch D, Sauer M, Schmölzer K, Schnitzhofer W, Sensen CW, Soh J, Steiner K, Winkler CK, Winkler M, Wriessnegger T. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnol Adv 2020; 40:107520. [DOI: 10.1016/j.biotechadv.2020.107520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
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