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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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2
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Sharma P, Bano A, Singh SP, Sharma S, Xia C, Nadda AK, Lam SS, Tong YW. Engineered microbes as effective tools for the remediation of polyaromatic aromatic hydrocarbons and heavy metals. CHEMOSPHERE 2022; 306:135538. [PMID: 35792210 DOI: 10.1016/j.chemosphere.2022.135538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/04/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
Heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) have become a major concern to human health and the environment due to rapid industrialization and urbanization. Traditional treatment measures for removing toxic substances from the environment have largely failed, and thus development and advancement in newer remediation techniques are of utmost importance. Rising environmental pollution with HMs and PAHs prompted the research on microbes and the development of genetically engineered microbes (GEMs) for reducing pollution via the bioremediation process. The enzymes produced from a variety of microbes can effectively treat a range of pollutants, but evolutionary trends revealed that various emerging pollutants are resistant to microbial or enzymatic degradation. Naturally, existing microbes can be engineered using various techniques including, gene engineering, directed evolution, protein engineering, media engineering, strain engineering, cell wall modifications, rationale hybrid design, and encapsulation or immobilization process. The immobilization of microbes and enzymes using a variety of nanomaterials, membranes, and supports with high specificity toward the emerging pollutants is also an effective strategy to capture and treat the pollutants. The current review focuses on successful bioremediation techniques and approaches that make use of GEMs or engineered enzymes. Such engineered microbes are more potent than natural strains and have greater degradative capacities, as well as rapid adaptation to various pollutants as substrates or co-metabolizers. The future for the implementation of genetic engineering to produce such organisms for the benefit of the environment andpublic health is indeed long and valuable.
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Affiliation(s)
- Pooja Sharma
- Environmental Research Institute, National University of Singapore, 1 Create Way, 138602, Singapore; Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore
| | - Ambreen Bano
- IIRC-3, Plant-Microbe Interaction and Molecular Immunology Laboratory, Department of Biosciences, Faculty of Sciences, Integral University, Lucknow, UP, India
| | - Surendra Pratap Singh
- Plant Molecular Biology Laboratory, Department of Botany, Dayanand Anglo-Vedic (PG) College, Chhatrapati Shahu Ji Maharaj University, Kanpur, 208001, India
| | - Swati Sharma
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
| | - Changlei Xia
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, College of Materials Science and Engineering, Nanjing Forestry University, Nanjing, Jiangsu 210037, China; Dehua Tubao New Decoration Material Co., Ltd., Huzhou, Zhejiang 313200, China
| | - Ashok Kumar Nadda
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173 234, India.
| | - Su Shiung Lam
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia; Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand 248007, India.
| | - Yen Wah Tong
- Environmental Research Institute, National University of Singapore, 1 Create Way, 138602, Singapore; Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive, 117585, Singapore.
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3
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Igbokwe VC, Ezugworie FN, Onwosi CO, Aliyu GO, Obi CJ. Biochemical biorefinery: A low-cost and non-waste concept for promoting sustainable circular bioeconomy. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 305:114333. [PMID: 34952394 DOI: 10.1016/j.jenvman.2021.114333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 12/11/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
The transition from a fossil-based linear economy to a circular bioeconomy is no longer an option but rather imperative, given worldwide concerns about the depletion of fossil resources and the demand for innovative products that are ecocompatible. As a critical component of sustainable development, this discourse has attracted wide attention at the regional and international levels. Biorefinery is an indispensable technology to implement the blueprint of the circular bioeconomy. As a low-cost, non-waste innovative concept, the biorefinery concept will spur a myriad of new economic opportunities across a wide range of sectors. Consequently, scaling up biorefinery processes is of the essence. Despite several decades of research and development channeled into upscaling biorefinery processes, the commercialization of biorefinery technology appears unrealizable. In this review, challenges limiting the commercialization of biorefinery technologies are discussed, with a particular focus on biofuels, biochemicals, and biomaterials. To counteract these challenges, various process intensification strategies such as consolidated bioprocessing, integrated biorefinery configurations, the use of highly efficient bioreactors, simultaneous saccharification and fermentation, have been explored. This study also includes an overview of biomass pretreatment-generated inhibitory compounds as platform chemicals to produce other essential biocommodities. There is a detailed examination of the technological, economic, and environmental considerations of a sustainable biorefinery. Finally, the prospects for establishing a viable circular bioeconomy in Nigeria are briefly discussed.
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Affiliation(s)
- Victor C Igbokwe
- Bioconversion and Renewable Energy Research Unit, University of Nigeria, Nsukka, Enugu State, Nigeria; Department of Materials Science and Engineering, Université de Pau et des Pays de l'Adour, 64012, Pau Cedex, France
| | - Flora N Ezugworie
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria; Bioconversion and Renewable Energy Research Unit, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Chukwudi O Onwosi
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria; Bioconversion and Renewable Energy Research Unit, University of Nigeria, Nsukka, Enugu State, Nigeria.
| | - Godwin O Aliyu
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria; Bioconversion and Renewable Energy Research Unit, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Chinonye J Obi
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria
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4
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Song L, Yang D, Liu R, Liu S, Dai L, Dai X. Microbial production of lactic acid from food waste: Latest advances, limits, and perspectives. BIORESOURCE TECHNOLOGY 2022; 345:126052. [PMID: 34592459 DOI: 10.1016/j.biortech.2021.126052] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
A significant amount of food waste (FW) is produced every year. If it is not disposed of timeously, human health and the ecological environment can be negatively affected. Lactic acid (LA), a high value-added product, can be produced by fermentation from FW as a substrate, realizing the concurrent treatment and recycling of FW, which has attracted increasing research interest. In this paper, the latest advances and deficiencies were presented from the following aspects: microorganisms involved in LA fermentation and the metabolic pathways of Lactobacillus, fermentation conditions, and methods of enhanced biotransformation and LA separation. The limitations of the LA fermentation of FW are mainly associated with low LA concentration and yield, the low purity of L(+)-LA, and the high separation costs. The establishment of biorefineries of FW with lactic acid as the target product is the future development direction, but there are still many research studies to be done.
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Affiliation(s)
- Liang Song
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Donghai Yang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Rui Liu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Shiyu Liu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Lingling Dai
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xiaohu Dai
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
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5
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da Silva DB, Fernandes BS, da Silva AJ. Effect of initial pH and substrate concentration on the lactic acid production from cassava wastewater fermentation by an enriched culture of acidogenic microorganisms. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2021; 93:1925-1933. [PMID: 33073475 DOI: 10.1002/wer.1467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 10/05/2020] [Accepted: 10/10/2020] [Indexed: 06/11/2023]
Abstract
Recently, cassava processing wastewater has been considered an alternative substrate for lactic acid production due to its appreciable carbohydrate levels. The authors carried out different batch reactor trials aiming to favor the production of lactic acid through the fermentation of non-sterilized cassava wastewater by an enriched culture of acidogenic microorganisms. To this end, the impact of different initial pHs (4.5, 5.0, 5.7, 6.5, and 7.0) and different initial substrate concentrations (10, 15.8, 30, 44.2, and 50 g/L) in terms of glucose on lactic acid production yield (Y) was evaluated by applying the design of experiment (DoE) known as central composite rotatable design (CCRD). The highest rate of lactic acid production (40 g/L) occurred with an initial pH of 6.5 and an initial substrate concentration of 50 g/L. The maximum yield was higher in trials T1, T2, T4, T5, and T8, reaching values of 0.80, 0.62, 0.60, 0.96, and 0.70 g/g, respectively. The maximum lactic acid productivity (P), of 0.60 and 0.73 g L-1 hr-1 , was observed in trials T5 and T8, respectively. The enriched culture of acidogenic microorganisms was shown to favor the production of lactic acid, since the production of other acids, such as acetic and propionic acid, did not exceed 3.5 and 4.5 g/L, respectively. © 2020 Water Environment Federation PRACTITIONER POINTS: Cassava wastewater presented potential to lactic acid production. The CCRD showed that highest lactic acid concentrations (40 g/L). The adoption of cassava wastewater or manipueira as a substrate resulted in important information on the tendency to obtain value-added products such as lactic acid.
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Affiliation(s)
- Douglas B da Silva
- School of Agricultural Engineering, State University of Campinas, Campinas, Brazil
| | | | - Ariovaldo J da Silva
- School of Agricultural Engineering, State University of Campinas, Campinas, Brazil
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6
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Sharma P, Sirohi R, Tong YW, Kim SH, Pandey A. Metal and metal(loids) removal efficiency using genetically engineered microbes: Applications and challenges. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125855. [PMID: 34492804 DOI: 10.1016/j.jhazmat.2021.125855] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 06/13/2023]
Abstract
The environment is being polluted in different many with metal and metalloid pollution, mostly due to anthropogenic activity, which is directly affecting human and environmental health. Metals and metalloids are highly toxic at low concentrations and contribute primarily to the survival equilibrium of activities in the environment. However, because of non-degradable, they persist in nature and these metal and metalloids bioaccumulate in the food chain. Genetically engineered microorganisms (GEMs) mediated techniques for the removal of metals and metalloids are considered an environmentally safe and economically feasible strategy. Various forms of GEMs, including fungi, algae, and bacteria have been produced by recombinant DNA and RNA technologies, which have been used to eliminate metal and metalloids compounds from the polluted areas. Besides, GEMs have the potentiality to produce enzymes and other metabolites that are capable of tolerating metals stress and detoxify the pollutants. Thus, the aim of this review is to discuss the use of GEMs as advanced tools to produce metabolites, signaling molecules, proteins through genetic expression during metal and metalloids interaction, which help in the breakdown of persistent pollutants in the environment.
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Affiliation(s)
- Pooja Sharma
- Centre for Energy and Environmental Sustainability, Lucknow 226029, Uttar Pradesh, India
| | - Ranjna Sirohi
- Department of Chemical & Biological Engineering, Korea University, Seoul 136713, Republic of Korea
| | - Yen Wah Tong
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
| | - Sang Hyoun Kim
- Department of Chemical and Environmental Engineering, Yonsei University, Seoul, Republic of Korea
| | - Ashok Pandey
- Centre for Energy and Environmental Sustainability, Lucknow 226029, Uttar Pradesh, India; Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow 226001, Uttar Pradesh, India.
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7
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Accelerated glucose metabolism in hyphae-dispersed Aspergillus oryzae is suitable for biological production. J Biosci Bioeng 2021; 132:140-147. [PMID: 33896702 DOI: 10.1016/j.jbiosc.2021.03.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/28/2021] [Accepted: 03/28/2021] [Indexed: 11/23/2022]
Abstract
Recently, a hyphae-dispersed type of filamentous fungus Aspergillus oryzae was constructed via genetic engineering, and industrial applications are expected due to the ease of handling and to the level of protein production properties. In this study, we constructed cellulase-expressing strains using wild-type and hyphae-dispersed strains to investigate the correlation between protein productivity and metabolism. Compared with the original strain, the hyphae-dispersed cellulase-expressing strain showed elevated cellulase activity, rapid glucose consumption, increased mycelial dry weight, an increased expression of cellulase genes, and activated respiration activity. Comparative metabolomic analysis showed fewer metabolites in the glycolysis and TCA cycles in the dispersed strains than in the original strains. These results indicate that the flux of carbohydrate metabolism in the hyphae-dispersed strains is smoother than that in the original strains. Such efficient metabolic flux would contribute to efficient energy conversion and to sufficient energy supply to anabolisms, such as mycelial growth and protein production. Our findings suggest that the hyphae-dispersed strains could be a useful host not only for protein production but also for the biological production of various chemicals such as organic acids.
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Ji L, Wang J, Luo Q, Ding Q, Tang W, Chen X, Liu L. Enhancing L-malate production of Aspergillus oryzae by nitrogen regulation strategy. Appl Microbiol Biotechnol 2021; 105:3101-3113. [PMID: 33818672 DOI: 10.1007/s00253-021-11149-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/14/2021] [Accepted: 01/26/2021] [Indexed: 12/01/2022]
Abstract
Regulating morphology engineering and fermentation of Aspergillus oryzae makes it possible to increase the titer of L-malate. However, the existing L-malate-producing strain has limited L-malate production capacity and the fermentation process is insufficiently mature, which cannot meet the needs of industrial L-malate production. To further increase the L-malate production capacity of A. oryzae, we screened out a mutant strain (FMME-S-38) that produced 79.8 g/L L-malate in 250-mL shake flasks, using a newly developed screening system based on colony morphology on the plate. We further compared the extracellular nitrogen (N1) and intracellular nitrogen (N2) contents of the control and mutant strain (FMME-S-38) to determine the relationship between the curve of nitrogen content (N1 and N2) and the L-malate titer. This correlation was then used to optimize the conditions for developing a novel nitrogen supply strategy (initial tryptone concentration of 6.5 g/L and feeding with 3 g/L tryptone at 24 h). Fermentation in a 7.5-L fermentor under the optimized conditions further increased the titer and productivity of L-malate to 143.3 g/L and 1.19 g/L/h, respectively, corresponding to 164.9 g/L and 1.14 g/L/h in a 30-L fermentor. This nitrogen regulation-based strategy cannot only enhance industrial-scale L-malate production but also has generalizability and the potential to increase the production of similar metabolites.Key Points• Construction of a new screening system based on colony morphology on the plate.• A novel nitrogen regulation strategy used to regulate the production of L-malate.• A nitrogen supply strategy used to maximize the production of L-malate.
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Affiliation(s)
- Lihao Ji
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Ju Wang
- College of Food Engineering, Anhui Science and Technology University, Chuzhou, 233100, Anhui, China
| | - Qiuling Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Qiang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wenxiu Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China. .,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.
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Pant G, Garlapati D, Agrawal U, Prasuna RG, Mathimani T, Pugazhendhi A. Biological approaches practised using genetically engineered microbes for a sustainable environment: A review. JOURNAL OF HAZARDOUS MATERIALS 2021; 405:124631. [PMID: 33278727 DOI: 10.1016/j.jhazmat.2020.124631] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 10/28/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
Conventional methods used to remediate toxic substances from the environment have failed drastically, and thereby, advancement in newer remediation techniques can be one of the ways to improve the quality of bioremediation. The increased environmental pollution led to the exploration of microorganisms and construction of genetically engineered microbes (GEMs) for pollution abatement through bioremediation. The present review deals with the successful bioremediation techniques and approaches practised using genetically modified or engineered microbes. In the present scenario, physical and chemical strategies have been practised for the remediation of domestic and industrial wastes but these techniques are expensive and toxic to the environment. Involving engineered microbes can provide a much safer and cost effective strategy in comparison with the other techniques. With the aid of biotechnology and genetic engineering, GEMs are designed by transforming microbes with a more potent protein to overexpress the desired character. GEMs such as bacteria, fungi and algae have been used to degrade oil spills, camphor, hexane, naphthalene, toluene, octane, xylene, halobenzoates, trichloroethylene etc. These engineered microbes are more potent than the natural strains and have higher degradative capacities with quick adaptation for various pollutants as substrates or cometabolize. The road ahead for the implementation of genetic engineering to produce such organisms for the welfare of the environment and finally, public health is indeed long and worthwhile.
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Affiliation(s)
- Gaurav Pant
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh, India
| | - Deviram Garlapati
- National Centre for Coastal Research, Ministry of Earth Sciences (MoES), Govt. of India, Chennai 600 100, Tamil Nadu, India
| | - Urvashi Agrawal
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh, India
| | - R Gyana Prasuna
- Department of Microbiology & FST, GITAM Institute of Science, GITAM University, Visakhapatnam, Andhra Pradesh, India
| | - Thangavel Mathimani
- Department of Energy and Environment, National Institute of Technology, Tiruchirappalli 620 015, Tamil Nadu, India
| | - Arivalagan Pugazhendhi
- Innovative Green Product Synthesis and Renewable Environment Development Research Group, Faculty of Environment and Labour Safety, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
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10
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Chroumpi T, Mäkelä MR, de Vries RP. Engineering of primary carbon metabolism in filamentous fungi. Biotechnol Adv 2020; 43:107551. [DOI: 10.1016/j.biotechadv.2020.107551] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 10/24/2022]
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11
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Zhang S, Wakai S, Sasakura N, Tsutsumi H, Hata Y, Ogino C, Kondo A. Pyruvate metabolism redirection for biological production of commodity chemicals in aerobic fungus Aspergillus oryzae. Metab Eng 2020; 61:225-237. [DOI: 10.1016/j.ymben.2020.06.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/03/2020] [Accepted: 06/22/2020] [Indexed: 01/31/2023]
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12
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Abstract
Biodegradable polylactic acid material is manufactured from lactic acid, mainly produced by microbial fermentation. The high production cost of lactic acid still remains the major limitation for its application, indicating that the cost of carbon sources for the production of lactic acid has to be minimized. In addition, a lack of source availability of food crop and lignocellulosic biomass has encouraged researchers and industries to explore new feedstocks for microbial lactic acid fermentation. Seaweeds have attracted considerable attention as a carbon source for microbial fermentation owing to their non-terrestrial origin, fast growth, and photoautotrophic nature. The proximate compositions study of red, brown, and green seaweeds indicated that Gracilaria sp. has the highest carbohydrate content. The conditions were optimized for the saccharification of the seaweeds, and the results indicated that Gracilaria sp. yielded the highest reducing sugar content. Optimal lactic acid fermentation parameters, such as cell inoculum, agitation, and temperature, were determined to be 6% (v/v), 0 rpm, and 30 °C, respectively. Gracilaria sp. hydrolysates fermented by lactic acid bacteria at optimal conditions yielded a final lactic acid concentration of 19.32 g/L.
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Alternative transcription start sites of the enolase-encoding gene enoA are stringently used in glycolytic/gluconeogenic conditions in Aspergillus oryzae. Curr Genet 2020; 66:729-747. [PMID: 32072240 DOI: 10.1007/s00294-020-01053-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 12/24/2019] [Accepted: 01/07/2020] [Indexed: 10/25/2022]
Abstract
Gene expression using alternative transcription start sites (TSSs) is an important transcriptional regulatory mechanism for environmental responses in eukaryotes. Here, we identify two alternative TSSs in the enolase-encoding gene (enoA) in Aspergillus oryzae, an industrially important filamentous fungus. TSS use in enoA is strictly dependent on the difference in glycolytic and gluconeogenic carbon sources. Transcription from the upstream TSS (uTSS) or downstream TSS (dTSS) predominantly occurs under gluconeogenic or glycolytic conditions, respectively. In addition to enoA, most glycolytic genes involved in reversible reactions possess alternative TSSs. The fbaA gene, which encodes fructose-bisphosphate aldolase, also shows stringent alternative TSS selection, similar to enoA. Alignment of promoter sequences of enolase-encoding genes in Aspergillus predicted two conserved regions that contain a putative cis-element required for enoA transcription from each TSS. However, uTSS-mediated transcription of the acuN gene, an enoA ortholog in Aspergillus nidulans, is not strictly dependent on carbon source, unlike enoA. Furthermore, enoA transcript levels in glycolytic conditions are higher than in gluconeogenic conditions. Conversely, acuN is more highly transcribed in gluconeogenic conditions. This suggests that the stringent usage of alternative TSSs and higher transcription in glycolytic conditions in enoA may reflect that the A. oryzae evolutionary genetic background was domesticated by exclusive growth in starch-rich environments. These findings provide novel insights into the complexity and diversity of transcriptional regulation of glycolytic/gluconeogenic genes among Aspergilli.
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14
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Villena GK, Kitazono AA, Hernández-Macedo M L. Bioengineering Fungi and Yeast for the Production of Enzymes, Metabolites, and Value-Added Compounds. Fungal Biol 2020. [DOI: 10.1007/978-3-030-41870-0_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Wakai S, Nakashima N, Ogino C, Tsutsumi H, Hata Y, Kondo A. Modified expression of multi-cellulases in a filamentous fungus Aspergillus oryzae. BIORESOURCE TECHNOLOGY 2019; 276:146-153. [PMID: 30623869 DOI: 10.1016/j.biortech.2018.12.117] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/28/2018] [Accepted: 12/29/2018] [Indexed: 06/09/2023]
Abstract
Aspergillus oryzae, a filamentous fungus, can secrete large amounts of enzymes extracellularly. We constructed a genetically engineered A. oryzae that simultaneously produced cellobiohydrolase, endoglucanase, and β-glucosidase by integrating multiple copies of the genes encoding these cellulases into fungal chromosomes. The resulting strain possessed 5-16 copies of each cellulase gene within the chromosome and showed approximately 10-fold higher activity versus single integration strains. Copy number polymorphisms were attributed to differences in flanking region sequence for the integrated gene fragments. Furthermore, we found that the P-sodM/T-glaB set demonstrated the strongest transcription levels per gene copy number. We therefore modified promoter/terminator set and cellulase gene combinations based on this polymorphism and transcription level data, with the resulting transformant showing 40-fold higher cellulolytic activity versus the single integration strain. This designed expression method could be useful for the overexpression of multiple enzymes and pathway flux control-mediated metabolic engineering in A. oryzae.
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Affiliation(s)
- Satoshi Wakai
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Nanami Nakashima
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Hiroko Tsutsumi
- Research Institute, Gekkeikan Sake Co. Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto, Kyoto 612-8385, Japan
| | - Yoji Hata
- Research Institute, Gekkeikan Sake Co. Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto, Kyoto 612-8385, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan.
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Khlestkin VK, Peltek SE, Kolchanov NA. Review of direct chemical and biochemical transformations of starch. Carbohydr Polym 2018; 181:460-476. [DOI: 10.1016/j.carbpol.2017.10.035] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/04/2017] [Accepted: 10/07/2017] [Indexed: 01/19/2023]
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17
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Wakai S, Arazoe T, Ogino C, Kondo A. Future insights in fungal metabolic engineering. BIORESOURCE TECHNOLOGY 2017; 245:1314-1326. [PMID: 28483354 DOI: 10.1016/j.biortech.2017.04.095] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
Filamentous fungi exhibit versatile abilities, including organic acid fermentation, protein production, and secondary metabolism, amongst others, and thus have applications in the medical and food industries. Previous genomic analyses of several filamentous fungi revealed their further potential as host microorganisms for bioproduction. Recent advancements in molecular genetics, marker recycling, and genome editing could be used to alter transformation and metabolism, based on optimized design carbolated with computer science. In this review, we detail the current applications of filamentous fungi and describe modern molecular genetic tools that could be used to expand the role of these microorganisms in bioproduction. The present review shed light on the possibility of filamentous fungi as host microorganisms in the field of bioproduction in the future.
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Affiliation(s)
- Satoshi Wakai
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Takayoshi Arazoe
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan.
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Liu J, Li J, Shin HD, Du G, Chen J, Liu L. Metabolic engineering of Aspergillus oryzae for efficient production of l -malate directly from corn starch. J Biotechnol 2017; 262:40-46. [DOI: 10.1016/j.jbiotec.2017.09.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/04/2017] [Accepted: 09/28/2017] [Indexed: 11/25/2022]
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Yu XC, Ma SL, Xu Y, Fu CH, Jiang CY, Zhou CY. Construction and application of a novel genetically engineered Aspergillus oryzae for expressing proteases. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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Tang J, Wang XC, Hu Y, Zhang Y, Li Y. Effect of pH on lactic acid production from acidogenic fermentation of food waste with different types of inocula. BIORESOURCE TECHNOLOGY 2017; 224:544-552. [PMID: 27939870 DOI: 10.1016/j.biortech.2016.11.111] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/27/2016] [Accepted: 11/28/2016] [Indexed: 06/06/2023]
Abstract
Effect of acidic pH (4, 5, 6 and uncontrolled) on lactic acid (LA) fermentation from food waste was investigated by batch fermentation experiments using methanogenic sludge, fresh food waste and anaerobic activated sludge as inocula. Results showed that due to the increase of hydrolysis, substrate degradation rate and enzyme activity, the optimal LA concentration and yield were obtained at pH 5, regardless of the inoculum used. The highest LA concentration (28.4g/L) and yield (0.46g/g-TS) were obtained with fresh food waste as inoculum. Moreover, after the substrate was completely utilized, the lactic acid bacteria population sharply decreased, and the LA produced was converted to volatile fatty acids (VFAs) at pH 6 within a short period. The VFA components varied with the inoculum supplied. Microbial community analysis using high-throughput pyrosequencing revealed that diversity decreased and a high abundance of Lactobacillus (83.4-98.5%) accumulated during fermentation with all inocula.
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Affiliation(s)
- Jialing Tang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Key Lab of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; International Science & Technology Cooperation Center for Urban Alternative Water Resources Development, Xi'an 710055, China
| | - Xiaochang C Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Key Lab of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; International Science & Technology Cooperation Center for Urban Alternative Water Resources Development, Xi'an 710055, China.
| | - Yisong Hu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; International Science & Technology Cooperation Center for Urban Alternative Water Resources Development, Xi'an 710055, China
| | - Yongmei Zhang
- International Science & Technology Cooperation Center for Urban Alternative Water Resources Development, Xi'an 710055, China; Taiyuan University of Technology, Shanxi Province, Taiyuan 030054, China
| | - Yuyou Li
- Department of Civil and Environmental Engineering, Tohoku University, Sendai 9808579, Japan
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Biorefinery-Based Lactic Acid Fermentation: Microbial Production of Pure Monomer Product. SYNTHESIS, STRUCTURE AND PROPERTIES OF POLY(LACTIC ACID) 2017. [DOI: 10.1007/12_2016_11] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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22
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Kawaguchi H, Hasunuma T, Ogino C, Kondo A. Bioprocessing of bio-based chemicals produced from lignocellulosic feedstocks. Curr Opin Biotechnol 2016; 42:30-39. [PMID: 26970511 DOI: 10.1016/j.copbio.2016.02.031] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 02/17/2016] [Accepted: 02/24/2016] [Indexed: 10/22/2022]
Abstract
The feedstocks used for the production of bio-based chemicals have recently expanded from edible sugars to inedible and more recalcitrant forms of lignocellulosic biomass. To produce bio-based chemicals from renewable polysaccharides, several bioprocessing approaches have been developed and include separate hydrolysis and fermentation (SHF), simultaneous saccharification and fermentation (SSF), and consolidated bioprocessing (CBP). In the last decade, SHF, SSF, and CBP have been used to generate macromolecules and aliphatic and aromatic compounds that are capable of serving as sustainable, drop-in substitutes for petroleum-based chemicals. The present review focuses on recent progress in the bioprocessing of microbially produced chemicals from renewable feedstocks, including starch and lignocellulosic biomass. In particular, the technological feasibility of bio-based chemical production is discussed in terms of the feedstocks and different bioprocessing approaches, including the consolidation of enzyme production, enzymatic hydrolysis of biomass, and fermentation.
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Affiliation(s)
- Hideo Kawaguchi
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tomohisa Hasunuma
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Biomass Engineering Research Division, RIKEN, 1-7-22 Suehiro, Turumi, Yokohama, Kanagawa 230-0045, Japan.
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Expression of Lactate Dehydrogenase in Aspergillus niger for L-Lactic Acid Production. PLoS One 2015; 10:e0145459. [PMID: 26683313 PMCID: PMC4684279 DOI: 10.1371/journal.pone.0145459] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/03/2015] [Indexed: 11/19/2022] Open
Abstract
Different engineered organisms have been used to produce L-lactate. Poor yields of lactate at low pH and expensive downstream processing remain as bottlenecks. Aspergillus niger is a prolific citrate producer and a remarkably acid tolerant fungus. Neither a functional lactate dehydrogenase (LDH) from nor lactate production by A. niger is reported. Its genome was also investigated for the presence of a functional ldh. The endogenous A. niger citrate synthase promoter relevant to A. niger acidogenic metabolism was employed to drive constitutive expression of mouse lactate dehydrogenase (mldhA). An appraisal of different branches of the A. niger pyruvate node guided the choice of mldhA for heterologous expression. A high copy number transformant C12 strain, displaying highest LDH specific activity, was analyzed under different growth conditions. The C12 strain produced 7.7 g/l of extracellular L-lactate from 60 g/l of glucose, in non-neutralizing minimal media. Significantly, lactate and citrate accumulated under two different growth conditions. Already an established acidogenic platform, A. niger now promises to be a valuable host for lactate production.
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Hara KY, Araki M, Okai N, Wakai S, Hasunuma T, Kondo A. Development of bio-based fine chemical production through synthetic bioengineering. Microb Cell Fact 2014; 13:173. [PMID: 25494636 PMCID: PMC4302092 DOI: 10.1186/s12934-014-0173-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 11/23/2014] [Indexed: 01/23/2023] Open
Abstract
Fine chemicals that are physiologically active, such as pharmaceuticals, cosmetics, nutritional supplements, flavoring agents as well as additives for foods, feed, and fertilizer are produced by enzymatically or through microbial fermentation. The identification of enzymes that catalyze the target reaction makes possible the enzymatic synthesis of the desired fine chemical. The genes encoding these enzymes are then introduced into suitable microbial hosts that are cultured with inexpensive, naturally abundant carbon sources, and other nutrients. Metabolic engineering create efficient microbial cell factories for producing chemicals at higher yields. Molecular genetic techniques are then used to optimize metabolic pathways of genetically and metabolically well-characterized hosts. Synthetic bioengineering represents a novel approach to employ a combination of computer simulation and metabolic analysis to design artificial metabolic pathways suitable for mass production of target chemicals in host strains. In the present review, we summarize recent studies on bio-based fine chemical production and assess the potential of synthetic bioengineering for further improving their productivity.
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Affiliation(s)
- Kiyotaka Y Hara
- Organization of Advanced Science and Technology, Kobe University, Nada, Kobe, Japan.
| | - Michihiro Araki
- Organization of Advanced Science and Technology, Kobe University, Nada, Kobe, Japan.
| | - Naoko Okai
- Organization of Advanced Science and Technology, Kobe University, Nada, Kobe, Japan.
| | - Satoshi Wakai
- Organization of Advanced Science and Technology, Kobe University, Nada, Kobe, Japan.
| | - Tomohisa Hasunuma
- Organization of Advanced Science and Technology, Kobe University, Nada, Kobe, Japan.
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe, 657-8501, Japan.
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