1
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Zhang R, Chen Y, Wang W, Chen J, Liu D, Zhang L, Xiang Q, Zhao K, Ma M, Yu X, Chen Q, Penttinen P, Gu Y. Combined transcriptomic and metabolomic analysis revealed that pH changes affected the expression of carbohydrate and ribosome biogenesis-related genes in Aspergillus niger SICU-33. Front Microbiol 2024; 15:1389268. [PMID: 38962137 PMCID: PMC11220263 DOI: 10.3389/fmicb.2024.1389268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/03/2024] [Indexed: 07/05/2024] Open
Abstract
The process of carbohydrate metabolism and genetic information transfer is an important part of the study on the effects of the external environment on microbial growth and development. As one of the most significant environmental parameters, pH has an important effect on mycelial growth. In this study, the effects of environmental pH on the growth and nutrient composition of Aspergillus niger (A. niger) filaments were determined. The pH values of the medium were 5, 7, and 9, respectively, and the molecular mechanism was further investigated by transcriptomics and metabolomics methods. The results showed that pH 5 and 9 significantly inhibited filament growth and polysaccharide accumulation of A. niger. Further, the mycelium biomass of A. niger and the crude polysaccharide content was higher when the medium's pH was 7. The DEGs related to ribosome biogenesis were the most abundant, and the downregulated expression of genes encoding XRN1, RRM, and RIO1 affected protein translation, modification, and carbohydrate metabolism in fungi. The dynamic changes of pargyline and choline were in response to the oxidative metabolism of A. niger SICU-33. The ribophorin_I enzymes and DL-lactate may be important substances related to pH changes during carbohydrate metabolism of A.niger SICU-33. The results of this study provide useful transcriptomic and metabolomic information for further analyzing the bioinformatic characteristics of A. niger and improving the application in ecological agricultural fermentation.
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Affiliation(s)
- Runji Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yulan Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Wenxian Wang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Juan Chen
- Liangshan Tobacco Corporation of Sichuan Province, Xichang, China
| | - Dongyang Liu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- Liangshan Tobacco Corporation of Sichuan Province, Xichang, China
| | - Lingzi Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Quanju Xiang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Ke Zhao
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Menggen Ma
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiumei Yu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Qiang Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Petri Penttinen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yunfu Gu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
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2
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Wu X, Zhang T, Zhang K, Zhang R, Shi M, Gu C, Shi T, Lu L, Xue F, Xu Q, Zhang C. The forced activation of asexual conidiation in Aspergillus niger simplifies bioproduction. Synth Syst Biotechnol 2024; 9:277-284. [PMID: 38496318 PMCID: PMC10942867 DOI: 10.1016/j.synbio.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/22/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Aspergillus niger is an efficient cell factory for organic acids production, particularly l-malic acid, through genetic manipulation. However, the traditional method of collecting A. niger spores for inoculation is labor-intensive and resource-consuming. In our study, we used the CRISPR-Cas9 system to replace the promoter of brlA, a key gene in Aspergillus conidiation, with a xylose-inducible promoter xylP in l-malic acid-producing A. niger strain RG0095, generating strain brlAxylP. When induced with xylose in submerged liquid culture, brlAxylP exhibited significant upregulation of conidiation-related genes. This induction allowed us to easily collect an abundance of brlAxylP spores (>7.1 × 106/mL) in liquid xylose medium. Significantly, the submerged conidiation approach preserves the substantial potential of A. niger as a foundational cellular platform for the biosynthesis of organic acids, including but not limited to l-malic acid. In summary, our study offers a simplified submerged conidiation strategy to streamline the preparation stage and reduce labor and material costs for industrial organic acid production using Aspergillus species.
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Affiliation(s)
- Xingyu Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Tingting Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Ke Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Rui Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Man Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Chenlei Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Tianqiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Ling Lu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Feng Xue
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Qing Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Chi Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
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3
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Amina R, Habiba R, Abouddihaj B. Camel urine as a potential source of bioactive molecules showing their efficacy against pathogens: A systematic review. Saudi J Biol Sci 2024; 31:103966. [PMID: 38495380 PMCID: PMC10940778 DOI: 10.1016/j.sjbs.2024.103966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/20/2024] [Accepted: 02/24/2024] [Indexed: 03/19/2024] Open
Abstract
Camels are highly suited for severe desert conditions and able to provide most of the natural products like urine, which has been used as alternative medicine to treat diverse infections and disorders. There is, however, a shortage and paucity of scientific reviews highlighting the antifungal, antibacterial and antiviral effects of camel urine. By better understanding its antimicrobial characteristics, our overarching aim is to provide an exhaustive overview of this valuable natural product by synthesizing and summarizing data on the efficacy of this biofluid and also describing the potential substances exhibiting antimicrobial properties. We searched three databases in order to point out relevant articles (Web of Science, Scopus and Google Scholar) until December 2022. Research articles of interest evaluating the antimicrobial effects of camel urine were selected. Overall, camel urine furnished promising antibacterial activities against gram-positive bacteria, namely Staphylococcus aureus (30 mm), Bacillus cereus (22 mm), Bacillus subtilis (25 mm) and Micrococcus luteus (21 mm), as well as gram-negative bacteria, especially Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter cloacae, and Salmonella spp., without forgetting its efficiency on Mycobacterium tuberculosis as well. The excretion also showed its potency against H1N1 virus, vesicular stomatitis virus and middle east respiratory syndrome coronavirus. Similarly, the camel urine featured strong antifungal activity against Candida albicans, Aspergillus niger, Aspergillus flavus and dermatophytes with a minimal inhibitory concentration of 0.625 μg/ml against Trichophyton violaceum, 2.5 μg/ml against Microsporum canis and 1.25 μg/ml against Trichophyton rubrum and Trichophyton mentagrophytes. This comprehensive review will be valuable for researchers interested in investigating the potential of camel urine in the development of novel broad-spectrum key molecules targeting a wide range of drug-resistant pathogenic microorganisms.
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Affiliation(s)
- Ressmi Amina
- Laboratory of Biotechnology and Sustainable Development of Natural Resources, Life Sciences Department, Polydisciplinary Faculty, Sultan Moulay Slimane University, Beni Mellal 23023, Morocco
| | - Raqraq Habiba
- Laboratory of Biotechnology and Sustainable Development of Natural Resources, Life Sciences Department, Polydisciplinary Faculty, Sultan Moulay Slimane University, Beni Mellal 23023, Morocco
| | - Barguigua Abouddihaj
- Laboratory of Biotechnology and Sustainable Development of Natural Resources, Life Sciences Department, Polydisciplinary Faculty, Sultan Moulay Slimane University, Beni Mellal 23023, Morocco
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4
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Xu L, Li J, Gonzalez Ramos VM, Lyra C, Wiebenga A, Grigoriev IV, de Vries RP, Mäkelä MR, Peng M. Genome-wide prediction and transcriptome analysis of sugar transporters in four ascomycete fungi. BIORESOURCE TECHNOLOGY 2024; 391:130006. [PMID: 37952592 DOI: 10.1016/j.biortech.2023.130006] [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: 10/14/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
The import of plant-derived small sugars by sugar transporters (STs) has received increasing interest due to its important biological role and great industrial potential. STs are important targets of genetic engineering to improve fungal plant biomass conversion. Comparatively analysis of the genome-wide prevalence and transcriptomics of STs was performed in four filamentous fungi: Aspergillus niger, Aspergillus nidulans, Penicillium subrubescens and Trichoderma reesei. Using phylogenetic analysis and literature mining, their predicted STs were divided into ten subfamilies with putative sugar specificities assigned. In addition, transcriptome analysis revealed complex expression profiles among different STs subfamilies and fungal species, indicating a sophisticated transcriptome regulation and functional diversity of fungal STs. Several STs showed strong co-expression with other genes involved in sugar utilization, encoding CAZymes and sugar catabolic enzymes. This study provides new insights into the diversity of STs at the genomic/transcriptomic level, facilitating their biochemical characterization and metabolic engineering.
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Affiliation(s)
- Li Xu
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
| | - Jiajia Li
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
| | | | - Christina Lyra
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland.
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Igor V Grigoriev
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland.
| | - Mao Peng
- 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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Książek E. Citric Acid: Properties, Microbial Production, and Applications in Industries. Molecules 2023; 29:22. [PMID: 38202605 PMCID: PMC10779990 DOI: 10.3390/molecules29010022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Citric acid finds broad applications in various industrial sectors, such as the pharmaceutical, food, chemical, and cosmetic industries. The bioproduction of citric acid uses various microorganisms, but the most commonly employed ones are filamentous fungi such as Aspergillus niger and yeast Yarrowia lipolytica. This article presents a literature review on the properties of citric acid, the microorganisms and substrates used, different fermentation techniques, its industrial utilization, and the global citric acid market. This review emphasizes that there is still much to explore, both in terms of production process techniques and emerging new applications of citric acid.
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Affiliation(s)
- Ewelina Książek
- Department of Agroenginieering and Quality Analysis, Faculty of Production Engineering, Wroclaw University of Economics and Business, Komandorska 118-120, 53-345 Wrocław, Poland
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6
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Zhang K, Zhang TT, Guo RR, Ye Q, Zhao HL, Huang XH. The regulation of key flavor of traditional fermented food by microbial metabolism: A review. Food Chem X 2023; 19:100871. [PMID: 37780239 PMCID: PMC10534219 DOI: 10.1016/j.fochx.2023.100871] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/27/2023] [Accepted: 09/06/2023] [Indexed: 10/03/2023] Open
Abstract
The beneficial microorganisms in food are diverse and complex in structure. These beneficial microorganisms can produce different and unique flavors in the process of food fermentation. The unique flavor of these fermented foods is mainly produced by different raw and auxiliary materials, fermentation technology, and the accumulation of flavor substances by dominant microorganisms during fermentation. The succession and metabolic accumulation of microbial flora significantly impacts the distinctive flavor of fermented foods. The investigation of the role of microbial flora changes in the production of flavor substances during fermentation can reveal the potential connection between microbial flora succession and the formation of key flavor compounds. This paper reviewed the evolution of microbial flora structure as food fermented and the key volatile compounds that contribute to flavor in the food system and their potential relationship. Further, it was a certain guiding significance for food industrial production.
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Affiliation(s)
- Ke Zhang
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian Technology Innovation Center for Chinese Prepared Food, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
- School of Food and Biological Engineering, Hefei University of Technology, Engineering Research Center of Bio-Process, Ministry of Education, Hefei 230601, Anhui, China
| | - Ting-Ting Zhang
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian Technology Innovation Center for Chinese Prepared Food, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
| | - Ren-Rong Guo
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian Technology Innovation Center for Chinese Prepared Food, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
| | - Quan Ye
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian Technology Innovation Center for Chinese Prepared Food, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
| | - Hui-Lin Zhao
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian Technology Innovation Center for Chinese Prepared Food, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
| | - Xu-Hui Huang
- SKL of Marine Food Processing & Safety Control, National Engineering Research Center of Seafood, Collaborative Innovation Center of Seafood Deep Processing, Dalian Technology Innovation Center for Chinese Prepared Food, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
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7
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Zheng X, Du P, Gao K, Du Y, Cairns TC, Ni X, Chen M, Zhao W, Ma X, Yang H, Zheng P, Sun J. Genome-wide transcription landscape of citric acid producing Aspergillus niger in response to glucose gradient. Front Bioeng Biotechnol 2023; 11:1282314. [PMID: 37941722 PMCID: PMC10628723 DOI: 10.3389/fbioe.2023.1282314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023] Open
Abstract
Aspergillus niger is the main industrial workhorse for global citric acid production. This fungus has complex sensing and signaling pathways to respond to environmental nutrient fluctuations. As the preferred primary carbon source, glucose also acts as a critical signal to trigger intracellular bioprocesses. Currently, however, there is still a knowledge gap in systems-level understanding of metabolic and cellular responses to this vital carbon source. In this study, we determined genome-wide transcriptional changes of citric acid-producing Aspergillus niger in response to external glucose gradient. It demonstrated that external glucose fluctuation led to transcriptional reprogramming of many genes encoding proteins involved in fundamental cellular process, including ribosomal biogenesis, carbon transport and catabolism, glucose sensing and signaling. The major glucose catabolism repressor creA maintained a stable expression independent of external glucose, while creB and creD showed significant downregulation and upregulation by the glucose increase. Notably, several high-affinity glucose transporters encoding genes, including mstA, were greatly upregulated when glucose was depleted, while the expression of low-affinity glucose transporter mstC was glucose-independent, which showed clear concordance with their protein levels detected by in situ fluorescence labeling assay. In addition, we also observed that the citric acid exporter cexA was observed to be transcriptionally regulated by glucose availability, which was correlated with extracellular citric acid secretion. These discoveries not only deepen our understanding of the transcriptional regulation of glucose but also shed new light on the adaptive evolutionary mechanism of citric acid production of A. niger.
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Affiliation(s)
- Xiaomei Zheng
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Du
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Kaiyue Gao
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yimou Du
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Timothy C. Cairns
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Xiaomeng Ni
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Meiling Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Wei Zhao
- Shan Dong Fuyang Biological Technology Co., Ltd., Dezhou, China
| | - Xinrong Ma
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Hongjiang Yang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Ping Zheng
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jibin Sun
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
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8
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Wu T, Li J, Tian C. Fungal carboxylate transporters: recent manipulations and applications. Appl Microbiol Biotechnol 2023; 107:5909-5922. [PMID: 37561180 DOI: 10.1007/s00253-023-12720-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023]
Abstract
Carboxylic acids containing acidic groups with additional keto/hydroxyl-groups or unsaturated bond have displayed great applicability in the food, agricultural, cosmetic, textile, and pharmaceutical industries. The traditional approach for carboxylate production through chemical synthesis is based on petroleum derivatives, resulting in concerns for the environmental complication and energy crisis, and increasing attention has been attracted to the eco-friendly and renewable bio-based synthesis for carboxylate production. The efficient and specific export of target carboxylic acids through the microbial membrane is essential for high productivity, yield, and titer of bio-based carboxylates. Therefore, understanding the characteristics, regulations, and efflux mechanisms of carboxylate transporters will efficiently increase industrial biotechnological production of carboxylic acids. Several transporters from fungi have been reported and used for improved synthesis of target products. The transport activity and substrate specificity are two key issues that need further improvement in the application of carboxylate transporters. This review presents developments in the structural and functional diversity of carboxylate transporters, focusing on the modification and regulation of carboxylate transporters to alter the transport activity and substrate specificity, providing new strategy for transporter engineering in constructing microbial cell factory for carboxylate production. KEY POINTS: • Structures of multiple carboxylate transporters have been predicted. • Carboxylate transporters can efficiently improve production. • Modification engineering of carboxylate transporters will be more popular in the future.
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Affiliation(s)
- Taju Wu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- School of Life Science, Bengbu Medical College, Bengbu, 233030, China
| | - Jingen Li
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
| | - Chaoguang Tian
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
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9
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Zhou S, Ding N, Han R, Deng Y. Metabolic engineering and fermentation optimization strategies for producing organic acids of the tricarboxylic acid cycle by microbial cell factories. BIORESOURCE TECHNOLOGY 2023; 379:128986. [PMID: 37001700 DOI: 10.1016/j.biortech.2023.128986] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
The organic acids of the tricarboxylic acid (TCA) pathway are important platform compounds and are widely used in many areas. The high-productivity strains and high-efficient and low-cost fermentation are required to satisfy a huge market size. The high metabolic flux of the TCA pathway endows microorganisms potential to produce high titers of these organic acids. Coupled with metabolic engineering and fermentation optimization, the titer of the organic acids has been significantly improved in recent years. Herein, we discuss and compare the recent advances in synthetic pathway engineering, cofactor engineering, transporter engineering, and fermentation optimization strategies to maximize the biosynthesis of organic acids. Such engineering strategies were mainly based on the TCA pathway and glyoxylate pathway. Furthermore, organic-acid-secretion enhancement and renewable-substrate-based fermentation are often performed to assist the biosynthesis of organic acids. Further strategies are also discussed to construct high-productivity and acid-resistant strains for industrial large-scale production.
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Affiliation(s)
- Shenghu Zhou
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Nana Ding
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, China
| | - Runhua Han
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Yu Deng
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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10
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Liu J, Zhang S, Li W, Wang G, Xie Z, Cao W, Gao W, Liu H. Engineering a Phosphoketolase Pathway to Supplement Cytosolic Acetyl-CoA in Aspergillus niger Enables a Significant Increase in Citric Acid Production. J Fungi (Basel) 2023; 9:jof9050504. [PMID: 37233215 DOI: 10.3390/jof9050504] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/19/2023] [Accepted: 04/19/2023] [Indexed: 05/27/2023] Open
Abstract
Citric acid is widely used in the food, chemical and pharmaceutical industries. Aspergillus niger is the workhorse used for citric acid production in industry. A canonical citrate biosynthesis that occurred in mitochondria was well established; however, some research suggested that the cytosolic citrate biosynthesis pathway may play a role in this chemical production. Here, the roles of cytosolic phosphoketolase (PK), acetate kinase (ACK) and acetyl-CoA synthetase (ACS) in citrate biosynthesis were investigated by gene deletion and complementation in A. niger. The results indicated that PK, ACK and ACS were important for cytosolic acetyl-CoA accumulation and had significant effects on citric acid biosynthesis. Subsequently, the functions of variant PKs and phosphotransacetylase (PTA) were evaluated, and their efficiencies were determined. Finally, an efficient PK-PTA pathway was reconstructed in A. niger S469 with Ca-PK from Clostridium acetobutylicum and Ts-PTA from Thermoanaerobacterium saccharolyticum. The resultant strain showed an increase of 96.4% and 88% in the citrate titer and yield, respectively, compared with the parent strain in the bioreactor fermentation. These findings indicate that the cytosolic citrate biosynthesis pathway is important for citric acid biosynthesis, and increasing the cytosolic acetyl-CoA level can significantly enhance citric acid production.
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Affiliation(s)
- Jiao Liu
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Shanshan Zhang
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wenhao Li
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Guanyi Wang
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Zhoujie Xie
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wei Cao
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Weixia Gao
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Hao Liu
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science & Technology, Tianjin 300457, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
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11
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Ghosh S, Rusyn I, Dmytruk OV, Dmytruk KV, Onyeaka H, Gryzenhout M, Gafforov Y. Filamentous fungi for sustainable remediation of pharmaceutical compounds, heavy metal and oil hydrocarbons. Front Bioeng Biotechnol 2023; 11:1106973. [PMID: 36865030 PMCID: PMC9971017 DOI: 10.3389/fbioe.2023.1106973] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/31/2023] [Indexed: 02/16/2023] Open
Abstract
This review presents a comprehensive summary of the latest research in the field of bioremediation with filamentous fungi. The main focus is on the issue of recent progress in remediation of pharmaceutical compounds, heavy metal treatment and oil hydrocarbons mycoremediation that are usually insufficiently represented in other reviews. It encompasses a variety of cellular mechanisms involved in bioremediation used by filamentous fungi, including bio-adsorption, bio-surfactant production, bio-mineralization, bio-precipitation, as well as extracellular and intracellular enzymatic processes. Processes for wastewater treatment accomplished through physical, biological, and chemical processes are briefly described. The species diversity of filamentous fungi used in pollutant removal, including widely studied species of Aspergillus, Penicillium, Fusarium, Verticillium, Phanerochaete and other species of Basidiomycota and Zygomycota are summarized. The removal efficiency of filamentous fungi and time of elimination of a wide variety of pollutant compounds and their easy handling make them excellent tools for the bioremediation of emerging contaminants. Various types of beneficial byproducts made by filamentous fungi, such as raw material for feed and food production, chitosan, ethanol, lignocellulolytic enzymes, organic acids, as well as nanoparticles, are discussed. Finally, challenges faced, future prospects, and how innovative technologies can be used to further exploit and enhance the abilities of fungi in wastewater remediation, are mentioned.
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Affiliation(s)
- Soumya Ghosh
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa,*Correspondence: Soumya Ghosh, ,
| | - Iryna Rusyn
- Department of Ecology and Sustainaible Environmental Management, Viacheslav Chornovil Institute of Sustainable Development, Lviv Polytechnic National University, Lviv, Ukraine
| | - Olena V. Dmytruk
- Institute of Cell Biology NAS of Ukraine, Lviv, Ukraine,Institute of Biology and Biotechnology, University of Rzeszow, Rzeszow, Poland
| | - Kostyantyn V. Dmytruk
- Institute of Cell Biology NAS of Ukraine, Lviv, Ukraine,Institute of Biology and Biotechnology, University of Rzeszow, Rzeszow, Poland
| | - Helen Onyeaka
- School of Chemical Engineering, University of Birmingham, Birmingham, United Kingdom
| | - Marieka Gryzenhout
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
| | - Yusufjon Gafforov
- Mycology Laboratory, Institute of Botany, Academy of Sciences of Republic of Uzbekistan, Tashkent, Uzbekistan,AKFA University, Tashkent, Uzbekistan
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12
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Recent advances and perspectives on production of value-added organic acids through metabolic engineering. Biotechnol Adv 2023; 62:108076. [PMID: 36509246 DOI: 10.1016/j.biotechadv.2022.108076] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
Organic acids are important consumable materials with a wide range of applications in the food, biopolymer and chemical industries. The global consumer organic acids market is estimated to increase to $36.86 billion by 2026. Conventionally, organic acids are produced from the chemical catalysis process with petrochemicals as raw materials, which posts severe environmental concerns and conflicts with our sustainable development goals. Most of the commonly used organic acids can be produced from various organisms. As a state-of-the-art technology, large-scale fermentative production of important organic acids with genetically-modified microbes has become an alternative to the chemical route to meet the market demand. Despite the fact that bio-based organic acid production from renewable cheap feedstock provides a viable solution, low productivity has impeded their industrial-scale application. With our deeper understanding of strain genetics, physiology and the availability of strain engineering tools, new technologies including synthetic biology, various metabolic engineering strategies, omics-based system biology tools, and high throughput screening methods are gradually established to bridge our knowledge gap. And they were further applied to modify the cellular reaction networks of potential microbial hosts and improve the strain performance, which facilitated the commercialization of consumable organic acids. Here we present the recent advances of metabolic engineering strategies to improve the production of important organic acids including fumaric acid, citric acid, itaconic acid, adipic acid, muconic acid, and we also discuss the current challenges and future perspectives on how we can develop a cost-efficient, green and sustainable process to produce these important chemicals from low-cost feedstocks.
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13
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Zheng X, Cairns T, Zheng P, Meyer V, Sun J. Protocol for gene characterization in Aspergillus niger using 5S rRNA-CRISPR-Cas9-mediated Tet-on inducible promoter exchange. STAR Protoc 2022; 3:101838. [PMID: 36595926 PMCID: PMC9678785 DOI: 10.1016/j.xpro.2022.101838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/29/2022] [Accepted: 10/18/2022] [Indexed: 11/19/2022] Open
Abstract
This protocol presents an efficient genetic strategy to investigate gene function in the fungus Aspergillus niger. We combined 5S rRNA-CRISPR-Cas9 technology with Tet-on gene switch to generate conditional-expression mutants via precisely replacing native promoter with inducible promoter. We describe the design and DNA preparation for sgRNAs and donor DNA. We then detail the steps for DNA co-transformation into A. niger protoplasts by PEG-mediated transformation, followed by homozygote isolation. Finally, we describe the genome verification and strain validation of the isolates. For complete details on the use and execution of this protocol, please refer to Zheng et al. (2019).1.
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Affiliation(s)
- Xiaomei Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China,University of Chinese Academy of Sciences, Beijing 100049, China,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China,Corresponding author
| | - Timothy Cairns
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China,Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, 10263 Berlin, Germany
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China,University of Chinese Academy of Sciences, Beijing 100049, China,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China,Corresponding author
| | - Vera Meyer
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, 10263 Berlin, Germany
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China,University of Chinese Academy of Sciences, Beijing 100049, China,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China,Corresponding author
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14
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Borin GP, Oliveira JVDC. Assessing the intracellular primary metabolic profile of Trichoderma reesei and Aspergillus niger grown on different carbon sources. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:998361. [PMID: 37746225 PMCID: PMC10512294 DOI: 10.3389/ffunb.2022.998361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/29/2022] [Indexed: 09/26/2023]
Abstract
Trichoderma reesei and Aspergillus niger are efficient biological platforms for the production of various industrial products, including cellulases and organic acids. Nevertheless, despite the extensive research on these fungi, integrated analyses of omics-driven approaches are still missing. In this study, the intracellular metabolic profile of T. reesei RUT-C30 and A. niger N402 strains grown on glucose, lactose, carboxymethylcellulose (CMC), and steam-exploded sugarcane bagasse (SEB) as carbon sources for 48 h was analysed by proton nuclear magnetic resonance. The aim was to verify the changes in the primary metabolism triggered by these substrates and use transcriptomics data from the literature to better understand the dynamics of the observed alterations. Glucose and CMC induced higher fungal growth whereas fungi grown on lactose showed the lowest dry weight. Metabolic profile analysis revealed that mannitol, trehalose, glutamate, glutamine, and alanine were the most abundant metabolites in both fungi regardless of the carbon source. These metabolites are of particular interest for the mobilization of carbon and nitrogen, and stress tolerance inside the cell. Their concomitant presence indicates conserved mechanisms adopted by both fungi to assimilate carbon sources of different levels of recalcitrance. Moreover, the higher levels of galactose intermediates in T. reesei suggest its better adaptation in lactose, whereas glycolate and malate in CMC might indicate activation of the glyoxylate shunt. Glycerol and 4-aminobutyrate accumulated in A. niger grown on CMC and lactose, suggesting their relevant role in these carbon sources. In SEB, a lower quantity and diversity of metabolites were identified compared to the other carbon sources, and the metabolic changes and higher xylanase and pNPGase activities indicated a better utilization of bagasse by A. niger. Transcriptomic analysis supported the observed metabolic changes and pathways identified in this work. Taken together, we have advanced the knowledge about how fungal primary metabolism is affected by different carbon sources, and have drawn attention to metabolites still unexplored. These findings might ultimately be considered for developing more robust and efficient microbial factories.
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Affiliation(s)
- Gustavo Pagotto Borin
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
| | - Juliana Velasco de Castro Oliveira
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
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15
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Jiang C, Wang H, Liu M, Wang L, Yang R, Wang P, Lu Z, Zhou Y, Zheng Z, Zhao G. Identification of chitin synthase activator in Aspergillus niger and its application in citric acid fermentation. Appl Microbiol Biotechnol 2022; 106:6993-7011. [PMID: 36149454 DOI: 10.1007/s00253-022-12174-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 11/02/2022]
Abstract
The biosynthesis of citric acid (CA) using Aspergillus niger as a carrier is influenced by mycelium morphology, which is determined by the expression level of morphology-related genes. As a key component of the fungal cell wall, chitin content has an important effect on morphogenesis, and to investigate the effects of this on fermentation performance, we used RNA interference to knockdown chitin synthase C (CHSC) and chitin synthase activator (CHS3) to obtain the single-gene mutant strains A. niger chs3 and chsC and the double mutant A. niger chs3C. We found that the CA fermentation performance of the two single mutants was significantly better than that of the double mutant. The mutant A. niger chs3-4 exhibited CA production potential compared to that of the parent strain in scale-up fermentation; we determined certain characteristics of CA high-yielding strain fermentation pellets. In addition, when chsC alone was silenced, there was very little change in chs3 mRNA levels, whereas those of chsC were significantly reduced when only chs3 was silenced. As this may be because of a synergistic effect between chsC and chs3, and we speculated that the latent activation target of CHS3 is CHSC, our results confirmed this hypothesis. This study is the first application of a separation and combination silence strategy of chitin synthase and chitin synthase activator in the morphology of A. niger CA fermentation. Furthermore, it provides new insights into the method for the morphological study of A. niger fermentation and the interaction of homologous genes. KEY POINTS: • The function of chitin synthase C (chsC) and chitin synthase activator (chs3) is tightly interrelated. • Mycelial morphology was optimized by knockdown of CHS3, resulting in the overproduction of citric acid. • The separation and combination silence strategies are promising tools for the interaction of homologous housekeeping genes.
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Affiliation(s)
- Chunxu Jiang
- Hefei Institutes of Physical Science, Comprehensive Laboratory Building, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1138, Hefei Anhui, 230031, People's Republic of China.,University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Han Wang
- Hefei Institutes of Physical Science, Comprehensive Laboratory Building, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1138, Hefei Anhui, 230031, People's Republic of China.
| | - Menghan Liu
- COFCO Biotechnology Co, Ltd. No. 1, Zhongliang Avenue, Bengbu Anhui, 233010, People's Republic of China
| | - Li Wang
- Hefei Institutes of Physical Science, Comprehensive Laboratory Building, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1138, Hefei Anhui, 230031, People's Republic of China
| | - Ruwen Yang
- COFCO Biotechnology Co, Ltd. No. 1, Zhongliang Avenue, Bengbu Anhui, 233010, People's Republic of China
| | - Peng Wang
- Hefei Institutes of Physical Science, Comprehensive Laboratory Building, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1138, Hefei Anhui, 230031, People's Republic of China
| | - Zongmei Lu
- COFCO Biotechnology Co, Ltd. No. 1, Zhongliang Avenue, Bengbu Anhui, 233010, People's Republic of China
| | - Yong Zhou
- COFCO Biotechnology Co, Ltd. No. 1, Zhongliang Avenue, Bengbu Anhui, 233010, People's Republic of China.
| | - Zhiming Zheng
- Hefei Institutes of Physical Science, Comprehensive Laboratory Building, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1138, Hefei Anhui, 230031, People's Republic of China.
| | - Genhai Zhao
- Hefei Institutes of Physical Science, Comprehensive Laboratory Building, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1138, Hefei Anhui, 230031, People's Republic of China.
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16
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Cao W, Zhang L, Wu L, Zhang M, Liu J, Xie Z, Liu H. Identification and genetic characterization of mitochondrial citrate transporters in Aspergillus niger. Front Microbiol 2022; 13:1009491. [PMID: 36177470 PMCID: PMC9512666 DOI: 10.3389/fmicb.2022.1009491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Aspergillus niger is a major cell factory for citric acid production, and the process of citrate export from mitochondria to cytoplasm is predicted to be one of rate-limiting steps in citric acid accumulation. Currently, the mitochondrial citrate transporters (Ctps) in A. niger are not fully characterized. Here, six putative Ctp encoding genes (ctpA to ctpF) were identified based on their homology with a mitochondrial citrate transporter ScCtp1 from Saccharomyces cerevisiae. Disruption of individual ctpA to ctpF caused varying degrees of decline in citric acid accumulation at different fermentation stages, whereas a mutant strain S1696 with disruption of all six ctps showed complete loss of citiric acid production. S1696 also exhibited delayed growth, reduced conidia formation, and decreased pigmentogenesis. Exogenous addition of citrate partially restored the conidia formation and pigmentogenesis in S1696 mutant. Reintroduction of individual ctps (ctpA to ctpF) into S1696 at the amyA locus showed that ctpA, ctpB, and ctpD restored the citric acid titers to 88.5, 93.8, and 94.6% of the parent strain, respectively. Additionally, the formation of conidia and pigment production was partially restored after reintroduction of ctpA, ctpB, or ctpD. Overexpression of respective ctpA, ctpB, and ctpD in the parent strain resulted in increases in citric acid accumulation by 32.8, 19.3, and 24.2%, respectively. These results demonstrate that CtpA, CtpB, and CtpD play important roles in citric acid transport across the mitochondrial membrane and function in a redundant manner. Enhancement of citric acid transport process can serve as a target for boosting citric acid accumulation in A. niger.
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Affiliation(s)
- Wei Cao
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science and Technology, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Licheng Zhang
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Liu Wu
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Mingyi Zhang
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Jiao Liu
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science and Technology, Tianjin, China
| | - Zhoujie Xie
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science and Technology, Tianjin, China
| | - Hao Liu
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science and Technology, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- *Correspondence: Hao Liu,
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17
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Sikander A, Kelly S, Kuchta K, Sievers A, Willner T, Hursthouse AS. Chemical and Microbial Leaching of Valuable Metals from PCBs and Tantalum Capacitors of Spent Mobile Phones. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph191610006. [PMID: 36011640 PMCID: PMC9408593 DOI: 10.3390/ijerph191610006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/01/2022] [Accepted: 08/11/2022] [Indexed: 05/25/2023]
Abstract
We compared chemical and microbial leaching for multi-metal extraction from printed circuit boards (PCBs) and tantalum capacitor scrap. A mixed consortium of acidophiles and heterotrophic fungal strains were used in the experiments and compared to chemical leaching using specific acids (sulfuric, citric and oxalic acids). Under optimum conditions, 100% extraction efficiency of Cu, and nearly 85% of Zn, Fe, Al and Ni were achieved from PCB and tantalum capacitor scrap samples using sulfuric acid. The mixed consortium of acidophiles successfully mobilized, Ni and Cu (99% and 96%, respectively) while Fe, Zn, Al and Mn reached an extraction yield of 89, 77, 70 and 43%, respectively, from the PCB samples. For the tantalum capacitor samples, acidophiles mobilized 92% Cu, 88% Ni, 78% Fe, 77% Al, 70% Zn and 57% Mn. Metal mobilization from PCBs and tantalum capacitor scrap by A. niger filtrate showed efficient solubilization of Cu, Fe, Al, Mn, Ni, Pb and Zn at an efficiency of 52, 29, 75, 5, 61, 21 and 35% from PCB samples and 61, 25, 69, 23, 68, 15 and 45% from tantalum capacitor samples, respectively. Microbial leaching proved viable as a method to extract base metals but was less specific for tantalum and precious metals in electronic waste. The implications of these results for further processing of waste electronic and electrical equipment (WEEE) are considered in potential hybrid treatment strategies.
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Affiliation(s)
- Asma Sikander
- Department of Process Engineering, Hamburg University of Applied Sciences, Ulmenliet 20, 21033 Hamburg, Germany
- School of Computing, Engineering & Physical Sciences, University of the West of the Scotland, Scotland PA1 2BE, UK
| | - Steven Kelly
- School of Health Life Sciences, University of the West of Scotland, Scotland G72 0LH, UK
| | - Kerstin Kuchta
- Institute for Environmental Engineering and Energy Economics, TUHH—Hamburg University of Technology, 21079 Hamburg, Germany
| | - Anika Sievers
- Department of Process Engineering, Hamburg University of Applied Sciences, Ulmenliet 20, 21033 Hamburg, Germany
| | - Thomas Willner
- Department of Process Engineering, Hamburg University of Applied Sciences, Ulmenliet 20, 21033 Hamburg, Germany
| | - Andrew S. Hursthouse
- School of Computing, Engineering & Physical Sciences, University of the West of the Scotland, Scotland PA1 2BE, UK
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18
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Fekete E, Bíró V, Márton A, Bakondi-Kovács I, Németh Z, Sándor E, Kovács B, Fábián I, Kubicek CP, Tsang A, Karaffa L. Bioreactor as the root cause of the “manganese effect” during Aspergillus niger citric acid fermentations. Front Bioeng Biotechnol 2022; 10:935902. [PMID: 35992333 PMCID: PMC9386146 DOI: 10.3389/fbioe.2022.935902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022] Open
Abstract
High-yield citric acid production by the filamentous Ascomycete fungus Aspergillus niger requires a combination of extreme nutritional conditions, of which maintaining a low manganese (II) ion concentration (<5 μg L−1) is a key feature. Technical-scale production of citric acid predominantly uses stainless-steel tank fermenters, but glass bioreactors used for strain improvement and manufacturing process development also contain stainless steel components, in which manganese is an essential alloying element. We show here that during citric acid fermentations manganese (II) ions were leaching from the bioreactor into the growth media, resulting in altered fungal physiology and morphology, and significant reduction of citric acid yields. The leaching of manganese (II) ions was dependent on the fermentation time, the acidity of the culture broth and the sterilization protocol applied. Manganese (II) ion leaching was partially mitigated by electrochemical polishing of stainless steel components of the bioreactor. High concentrations of manganese (II) ions during early cultivation led to a reduction in citric acid yield. However, the effect of manganese (II) ions on the reduction of citric acid yield diminished towards the second half of the fermentation. Since maintaining low concentrations of manganese (II) ions is costly, the results of this study can potentially be used to modify protocols to reduce the cost of citric acid production.
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Affiliation(s)
- Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Vivien Bíró
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
- Juhász-Nagy Pál Doctoral School of Biology and Environmental Sciences, University of Debrecen, Debrecen, Hungary
| | - Alexandra Márton
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
- Juhász-Nagy Pál Doctoral School of Biology and Environmental Sciences, University of Debrecen, Debrecen, Hungary
| | - István Bakondi-Kovács
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
- Juhász-Nagy Pál Doctoral School of Biology and Environmental Sciences, University of Debrecen, Debrecen, Hungary
| | - Zoltán Németh
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Erzsébet Sándor
- Institute of Food Science, Faculty of Agricultural and Food Science and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Béla Kovács
- Institute of Food Science, Faculty of Agricultural and Food Science and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - István Fábián
- Department of Inorganic and Analytical Chemistry, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
- MTA-DE Redox and Homogeneous Catalytic Reaction Mechanism Research Group, Debrecen, Hungary
| | - Christian P. Kubicek
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
- Institute of Metagenomics, University of Debrecen, Debrecen, Hungary
- *Correspondence: Levente Karaffa,
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19
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Evaluation of Aspergillus niger Six Constitutive Strong Promoters by Fluorescent-Auxotrophic Selection Coupled with Flow Cytometry: A Case for Citric Acid Production. J Fungi (Basel) 2022; 8:jof8060568. [PMID: 35736051 PMCID: PMC9224621 DOI: 10.3390/jof8060568] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 02/05/2023] Open
Abstract
Aspergillus niger is an important industrial workhorse for the biomanufacturing of organic acids, proteins, etc. Well-controlled genetic regulatory elements, including promoters, are vital for strain engineering, but available strong promoters for A. niger are limited. Herein, to efficiently assess promoters, we developed an accurate and intuitive fluorescent-auxotrophic selection workflow based on mCherry, pyrG, CRISPR/Cas9 system, and flow cytometry. With this workflow, we characterized six endogenous constitutive promoters in A. niger. The endogenous glyceraldehyde-3-phosphate dehydrogenase promoter PgpdAg showed a 2.28-fold increase in promoter activity compared with the most frequently used strong promoter PgpdAd from A. nidulans. Six predicted conserved motifs, including the gpdA-box, were verified to be essential for the PgpdAg activity. To demonstrate its application, the promoter PgpdAg was used for enhancing the expression of citrate exporter cexA in a citric acid-producing isolate D353.8. Compared with the cexA controlled by PgpdAd, the transcription level of the cexA gene driven by PgpdAg increased by 2.19-fold, which is consistent with the promoter activity assessment. Moreover, following cexA overexpression, several genes involved in carbohydrate transport and metabolism were synergically upregulated, resulting in up to a 2.48-fold increase in citric acid titer compared with that of the parent strain. This study provides an intuitive workflow to speed up the quantitative evaluation of A. niger promoters and strong constitutive promoters for fungal cell factory construction and strain engineering.
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20
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Strong PJ, Self R, Allikian K, Szewczyk E, Speight R, O'Hara I, Harrison MD. Filamentous fungi for future functional food and feed. Curr Opin Biotechnol 2022; 76:102729. [PMID: 35525176 DOI: 10.1016/j.copbio.2022.102729] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/16/2022] [Accepted: 03/29/2022] [Indexed: 11/19/2022]
Abstract
In this review, we offer our opinion of current and expected trends regarding the use of mushrooms and mycelia in food and feed. Mushrooms have provided food for millennia and production methods and species diversity have recently expanded. Beyond mushrooms, cultured fungal mycelia are now harvested as a primary product for food. Mushrooms and mycelia provide dietary protein, lipids and fatty acids, vitamins, fibre, and flavour, and can improve the organoleptic properties of processed foods (including meat analogues). Further, they are often key ingredients in nutritional or therapeutic supplements because of diverse specialised metabolites. Mycelia can also improve feed conversion efficiency, gut health, and wellbeing in livestock. New molecular tools, coupled with quality genetic data, are improving production technologies, enabling the synthesis of specialised metabolites, and creating new processing and valorisation opportunities. Production systems for submerged culture are capital intensive, but investment is required considering the scale of the protein market.
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Affiliation(s)
- Peter James Strong
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia; School of Biology and Environmental Sciences, Faculty of Science, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia; ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland 4000, Australia.
| | - Rachel Self
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia; School of Biology and Environmental Sciences, Faculty of Science, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia
| | - Kathrine Allikian
- Nourish Ingredients, Unit 2, 6 Pelle Street, Mitchell, Canberra, Australian Capital Territory 2911, Australia
| | - Edyta Szewczyk
- Bolt Threads, 5858 Horton St, Suite 400, Emeryville, CA 94608, United States
| | - Robert Speight
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia; School of Biology and Environmental Sciences, Faculty of Science, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia; ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Ian O'Hara
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia; ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland 4000, Australia; School of Mechanical, Medical and Process Engineering, Faculty of Engineering, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia
| | - Mark D Harrison
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia; School of Biology and Environmental Sciences, Faculty of Science, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4001, Australia
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21
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CRISPR/Cas9-Based Genome Editing and Its Application in Aspergillus Species. J Fungi (Basel) 2022; 8:jof8050467. [PMID: 35628723 PMCID: PMC9143064 DOI: 10.3390/jof8050467] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 02/04/2023] Open
Abstract
Aspergillus, a genus of filamentous fungi, is extensively distributed in nature and plays crucial roles in the decomposition of organic materials as an important environmental microorganism as well as in the traditional fermentation and food processing industries. Furthermore, due to their strong potential to secrete a large variety of hydrolytic enzymes and other natural products by manipulating gene expression and/or introducing new biosynthetic pathways, several Aspergillus species have been widely exploited as microbial cell factories. In recent years, with the development of next-generation genome sequencing technology and genetic engineering methods, the production and utilization of various homo-/heterologous-proteins and natural products in Aspergillus species have been well studied. As a newly developed genome editing technology, the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system has been used to edit and modify genes in Aspergilli. So far, the CRISPR/Cas9-based approach has been widely employed to improve the efficiency of gene modification in the strain type Aspergillus nidulans and other industrially important and pathogenic Aspergillus species, including Aspergillus oryzae, Aspergillus niger, and Aspergillus fumigatus. This review highlights the current development of CRISPR/Cas9-based genome editing technology and its application in basic research and the production of recombination proteins and natural products in the Aspergillus species.
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22
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Zheng X, Cairns TC, Ni X, Zhang L, Zhai H, Meyer V, Zheng P, Sun J. Comprehensively dissecting the hub regulation of PkaC on high-productivity and pellet macromorphology in citric acid producing Aspergillus niger. Microb Biotechnol 2022; 15:1867-1882. [PMID: 35213792 PMCID: PMC9151341 DOI: 10.1111/1751-7915.14020] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 01/20/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
Abstract
Aspergillus niger, an important industrial workhorse for citric acid production, is characterized by polar hyphal growth with complex pelleted, clumped or dispersed macromorphologies in submerged culture. Although organic acid titres are dramatically impacted by these growth types, studies that assess productivity and macromorphological changes are limited. Herein, we functionally analysed the role of the protein kinase A (PKA)/cyclic adenosine monophosphate (cAMP) signalling cascade during fermentation by disrupting and conditionally expressing the pkaC gene. pkaC played multiple roles during hyphal, colony and conidiophore growth. By overexpressing pkaC, we could concomitantly modify hyphal growth at the pellet surface and improve citric acid titres up to 1.87‐fold. By quantitatively analysing hundreds of pellets during pilot fermentation experiments, we provide the first comprehensive correlation between A. niger pellet surface morphology and citric acid production. Finally, by intracellular metabolomics analysis and weighted gene coexpression network analysis (WGCNA) following titration of pkaC expression, we unveil the metabolomic and transcriptomic basis underpin hyperproductivity and pellet growth. Taken together, this study confirms pkaC as hub regulator linking submerged macromorphology and citric acid production and provides high‐priority genetic leads for future strain engineering programmes.
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Affiliation(s)
- Xiaomei Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Timothy C Cairns
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Institute of Biotechnology, Chair of Applied and Molecular Microbiology, Technische Universität Berlin, Berlin, 13355, Germany
| | - Xiaomei Ni
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Lihui Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Huanhuan Zhai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Vera Meyer
- Institute of Biotechnology, Chair of Applied and Molecular Microbiology, Technische Universität Berlin, Berlin, 13355, Germany
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
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23
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Pooresmaeil M, Javanbakht S, Namazi H, Shaabani A. Application or function of citric acid in drug delivery platforms. Med Res Rev 2021; 42:800-849. [PMID: 34693555 DOI: 10.1002/med.21864] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 08/02/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022]
Abstract
Nontoxic materials with natural origin are promising materials in the designing and preparation of the new drug delivery systems (DDSs). Today's, citric acid (CA) has attracted a great deal of attention because of its special features; green nature, biocompatibility, low price, biodegradability, and commercially available property. So, CA has been employed in the preparation of the various platforms to induce a suitable property on their structure. Recently, several research groups investigated the CA-based platforms in different forms like tablets, dendrimers, hyperbranched polymers, (co)polymer, hydrogels, and nanoparticles as efficient DDSs. By considering an increasing amount of published articles in this field, for the first time, in this review, an overview of the published works regarding CA applications in the design of various DDSs is presented with a detailed and insightful discussion.
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Affiliation(s)
- Malihe Pooresmaeil
- Polymer Research Laboratory, Department of Organic and Biochemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran
| | | | - Hassan Namazi
- Polymer Research Laboratory, Department of Organic and Biochemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran.,Research Center for Pharmaceutical Nanotechnology (RCPN), Tabriz University of Medical Science, Tabriz, Iran
| | - Ahmad Shaabani
- Faculty of Chemistry, Shahid Beheshti University, Tehran, Iran
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24
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Melaku M, Zhong R, Han H, Wan F, Yi B, Zhang H. Butyric and Citric Acids and Their Salts in Poultry Nutrition: Effects on Gut Health and Intestinal Microbiota. Int J Mol Sci 2021; 22:10392. [PMID: 34638730 PMCID: PMC8508690 DOI: 10.3390/ijms221910392] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/19/2021] [Accepted: 09/22/2021] [Indexed: 12/26/2022] Open
Abstract
Intestinal dysfunction of farm animals, such as intestinal inflammation and altered gut microbiota, is the critical problem affecting animal welfare, performance and farm profitability. China has prohibited the use of antibiotics to improve feed efficiency and growth performance for farm animals, including poultry, in 2020. With the advantages of maintaining gut homeostasis, enhancing digestion, and absorption and modulating gut microbiota, organic acids are regarded as promising antibiotic alternatives. Butyric and citric acids as presentative organic acids positively impact growth performance, welfare, and intestinal health of livestock mainly by reducing pathogenic bacteria and maintaining the gastrointestinal tract (GIT) pH. This review summarizes the discovery of butyric acid (BA), citric acid (CA) and their salt forms, molecular structure and properties, metabolism, biological functions and their applications in poultry nutrition. The research findings about BA, CA and their salts on rats, pigs and humans are also briefly reviewed. Therefore, this review will fill the knowledge gaps of the scientific community and may be of great interest for poultry nutritionists, researchers and feed manufacturers about these two weak organic acids and their effects on intestinal health and gut microbiota community, with the hope of providing safe, healthy and nutrient-rich poultry products to consumers.
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Affiliation(s)
- Mebratu Melaku
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.M.); (R.Z.); (H.H.); (F.W.)
- Department of Animal Production and Technology, College of Agriculture, Woldia University, Woldia P.O. Box 400, Ethiopia
| | - Ruqing Zhong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.M.); (R.Z.); (H.H.); (F.W.)
| | - Hui Han
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.M.); (R.Z.); (H.H.); (F.W.)
| | - Fan Wan
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.M.); (R.Z.); (H.H.); (F.W.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Bao Yi
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.M.); (R.Z.); (H.H.); (F.W.)
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.M.); (R.Z.); (H.H.); (F.W.)
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25
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Hasan H, Abd Rahim MH, Campbell L, Carter D, Abbas A, Montoya A. Increasing Lovastatin Production by Re-routing the Precursors Flow of Aspergillus terreus via Metabolic Engineering. Mol Biotechnol 2021; 64:90-99. [PMID: 34546548 DOI: 10.1007/s12033-021-00393-w] [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: 06/12/2021] [Accepted: 09/08/2021] [Indexed: 12/11/2022]
Abstract
Lovastatin is an anti-cholesterol medicine that is commonly prescribed to manage cholesterol levels, and minimise the risk of suffering from heart-related diseases. Aspergillus terreus (ATCC 20542) supplied with carbohydrates or sugar alcohols can produce lovastatin. The present work explored the application of metabolic engineering in A. terreus to re-route the precursor flow towards the lovastatin biosynthetic pathway by simultaneously overexpressing the gene for acetyl-CoA carboxylase (acc) to increase the precursor flux, and eliminate ( +)-geodin biosynthesis (a competing secondary metabolite) by removing the gene for emodin anthrone polyketide synthase (gedC). Alterations to metabolic flux in the double mutant (gedCΔ*accox) strain and the effects of using two different substrate formulations were examined. The gedCΔ*accox strain, when cultivated with a mixture of glycerol and lactose, significantly (p < 0.05) increased the levels of metabolic precursors malonyl-CoA (48%) and acetyl-CoA (420%), completely inhibited the (+)-geodin biosynthesis, and increased the level of lovastatin [152 mg/L; 143% higher than the wild-type (WT) strain]. The present work demonstrated how the manipulation of A. terreus metabolic pathways could increase the efficiency of carbon flux towards lovastatin, thus elevating its overall production and enabling the use of glycerol as a substrate source. As such, the present work also provides a framework model for other medically or industrially important fungi to synthesise valuable compounds using sustainable carbon sources.
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Affiliation(s)
- Hanan Hasan
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, Australia. .,Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia. .,Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Muhamad Hafiz Abd Rahim
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, Australia.,Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Leona Campbell
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Dee Carter
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Ali Abbas
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, Australia
| | - Alejandro Montoya
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, Australia
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26
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Afroz MM, Kashem MNH, Piash KMPS, Islam N. Saccharomyces Cerevisiae as an Untapped Source of Fungal Chitosan for Antimicrobial Action. Appl Biochem Biotechnol 2021; 193:3765-3786. [PMID: 34406627 DOI: 10.1007/s12010-021-03639-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 08/10/2021] [Indexed: 01/01/2023]
Abstract
Despite being widely available, Saccharomyces cerevisiae has not been widely explored for direct extraction of chitosan biopolymer for antimicrobial applications. In our study, S. cerevisiae from Baker's yeast and Aspergillus niger from moldy onion extracts are studied as alternative sources of chitosan; and S cerevisiae chitosan tested for antimicrobial efficacy. The properties of S. cerevisiae chitosan are compared with moldy onion chitosan and shrimp chitosan extracted from shrimp shells. Chitosan extracted from S. cerevisiae is tested for antimicrobial efficacy against Staphylococcus Aureus. The maximum yields of fungal chitosan are 20.85 ± 0.35 mg/g dry S. cerevisiae biomass at 4th day using a culture broth containing sodium acetate, and 16.15 ± 0.95 mg/g dry A. niger biomass at 12th day. The degree of deacetylation (DD%) of the extracted fungal chitosan samples from S. cerevisiae and A. niger is found to be 63.4%, and 61.2% respectively, using Fourier Transform Infrared Spectroscopy. At a concentration of 2 g/L, S. cerevisiae chitosan shows the maximum inhibition zone diameter of 15.48 ± 0.07 mm. Baker's yeast S cerevisiae biomass and A. niger from moldy onions has not been previously explored as a source of extractible fungal chitosan. This study gives insight that S. cerevisiae and A. niger from agricultural or industrial wastes could be a potential biomass source for production of the chitosan biopolymer. The S. cerevisiae chitosan displayed effective antimicrobial properties against S aureus, indicating the viablitiy of S cerevisae as a resource for extraction of high-quality chitosan.
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Affiliation(s)
- Md Masirul Afroz
- Department of Chemical Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
- Department of Chemical Engineering, University of Wyoming, Laramie, WY, USA
| | - Md Nayeem Hasan Kashem
- Department of Chemical Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX, USA
| | | | - Nafisa Islam
- Department of Chemical Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh.
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27
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Something old, something new: challenges and developments in Aspergillus niger biotechnology. Essays Biochem 2021; 65:213-224. [PMID: 33955461 PMCID: PMC8314004 DOI: 10.1042/ebc20200139] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022]
Abstract
The filamentous ascomycete fungus Aspergillus niger is a prolific secretor of organic acids, proteins, enzymes and secondary metabolites. Throughout the last century, biotechnologists have developed A. niger into a multipurpose cell factory with a product portfolio worth billions of dollars each year. Recent technological advances, from genome editing to other molecular and omics tools, promise to revolutionize our understanding of A. niger biology, ultimately to increase efficiency of existing industrial applications or even to make entirely new products. However, various challenges to this biotechnological vision, many several decades old, still limit applications of this fungus. These include an inability to tightly control A. niger growth for optimal productivity, and a lack of high-throughput cultivation conditions for mutant screening. In this mini-review, we summarize the current state-of-the-art for A. niger biotechnology with special focus on organic acids (citric acid, malic acid, gluconic acid and itaconic acid), secreted proteins and secondary metabolites, and discuss how new technological developments can be applied to comprehensively address a variety of old and persistent challenges.
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28
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Soares-Silva I, Ribas D, Sousa-Silva M, Azevedo-Silva J, Rendulić T, Casal M. Membrane transporters in the bioproduction of organic acids: state of the art and future perspectives for industrial applications. FEMS Microbiol Lett 2021; 367:5873408. [PMID: 32681640 PMCID: PMC7419537 DOI: 10.1093/femsle/fnaa118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 07/17/2020] [Indexed: 12/16/2022] Open
Abstract
Organic acids such as monocarboxylic acids, dicarboxylic acids or even more complex molecules such as sugar acids, have displayed great applicability in the industry as these compounds are used as platform chemicals for polymer, food, agricultural and pharmaceutical sectors. Chemical synthesis of these compounds from petroleum derivatives is currently their major source of production. However, increasing environmental concerns have prompted the production of organic acids by microorganisms. The current trend is the exploitation of industrial biowastes to sustain microbial cell growth and valorize biomass conversion into organic acids. One of the major bottlenecks for the efficient and cost-effective bioproduction is the export of organic acids through the microbial plasma membrane. Membrane transporter proteins are crucial elements for the optimization of substrate import and final product export. Several transporters have been expressed in organic acid-producing species, resulting in increased final product titers in the extracellular medium and higher productivity levels. In this review, the state of the art of plasma membrane transport of organic acids is presented, along with the implications for industrial biotechnology.
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Affiliation(s)
- I Soares-Silva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - D Ribas
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - M Sousa-Silva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - J Azevedo-Silva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - T Rendulić
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
| | - M Casal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
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29
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Turning Inside Out: Filamentous Fungal Secretion and Its Applications in Biotechnology, Agriculture, and the Clinic. J Fungi (Basel) 2021; 7:jof7070535. [PMID: 34356914 PMCID: PMC8307877 DOI: 10.3390/jof7070535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/14/2021] [Accepted: 06/25/2021] [Indexed: 12/15/2022] Open
Abstract
Filamentous fungi are found in virtually every marine and terrestrial habitat. Vital to this success is their ability to secrete a diverse range of molecules, including hydrolytic enzymes, organic acids, and small molecular weight natural products. Industrial biotechnologists have successfully harnessed and re-engineered the secretory capacity of dozens of filamentous fungal species to make a diverse portfolio of useful molecules. The study of fungal secretion outside fermenters, e.g., during host infection or in mixed microbial communities, has also led to the development of novel and emerging technological breakthroughs, ranging from ultra-sensitive biosensors of fungal disease to the efficient bioremediation of polluted environments. In this review, we consider filamentous fungal secretion across multiple disciplinary boundaries (e.g., white, green, and red biotechnology) and product classes (protein, organic acid, and secondary metabolite). We summarize the mechanistic understanding for how various molecules are secreted and present numerous applications for extracellular products. Additionally, we discuss how the control of secretory pathways and the polar growth of filamentous hyphae can be utilized in diverse settings, including industrial biotechnology, agriculture, and the clinic.
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30
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Zhou J, Zhuang Y, Xia J. Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions. Microb Cell Fact 2021; 20:125. [PMID: 34193117 PMCID: PMC8247156 DOI: 10.1186/s12934-021-01614-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/16/2021] [Indexed: 11/26/2022] Open
Abstract
Background Genome-scale metabolic model (GSMM) is a powerful tool for the study of cellular metabolic characteristics. With the development of multi-omics measurement techniques in recent years, new methods that integrating multi-omics data into the GSMM show promising effects on the predicted results. It does not only improve the accuracy of phenotype prediction but also enhances the reliability of the model for simulating complex biochemical phenomena, which can promote theoretical breakthroughs for specific gene target identification or better understanding the cell metabolism on the system level. Results Based on the basic GSMM model iHL1210 of Aspergillus niger, we integrated large-scale enzyme kinetics and proteomics data to establish a GSMM based on enzyme constraints, termed a GEM with Enzymatic Constraints using Kinetic and Omics data (GECKO). The results show that enzyme constraints effectively improve the model’s phenotype prediction ability, and extended the model’s potential to guide target gene identification through predicting metabolic phenotype changes of A. niger by simulating gene knockout. In addition, enzyme constraints significantly reduced the solution space of the model, i.e., flux variability over 40.10% metabolic reactions were significantly reduced. The new model showed also versatility in other aspects, like estimating large-scale \documentclass[12pt]{minimal}
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\begin{document}$$k_{{cat}}$$\end{document}kcat values, predicting the differential expression of enzymes under different growth conditions. Conclusions This study shows that incorporating enzymes’ abundance information into GSMM is very effective for improving model performance with A. niger. Enzyme-constrained model can be used as a powerful tool for predicting the metabolic phenotype of A. niger by incorporating proteome data. In the foreseeable future, with the fast development of measurement techniques, and more precise and rich proteomics quantitative data being obtained for A. niger, the enzyme-constrained GSMM model will show greater application space on the system level. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01614-2.
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Affiliation(s)
- Jingru Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, 300308, China.
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31
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32
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Yoshioka I, Kirimura K. Rapid and marker-free gene replacement in citric acid-producing Aspergillus tubingensis (A. niger) WU-2223L by the CRISPR/Cas9 system-based genome editing technique using DNA fragments encoding sgRNAs. J Biosci Bioeng 2021; 131:579-588. [PMID: 33612423 DOI: 10.1016/j.jbiosc.2021.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/11/2021] [Accepted: 01/30/2021] [Indexed: 01/19/2023]
Abstract
Strains belonging to Aspergillus section Nigri, including Aspergillus niger, are used for industrial production of citric acid from carbohydrates such as molasses and starch. The objective of this study was to construct the genome editing system that could enable rapid and efficient gene replacement in citric acid-producing fungi for genetic breeding. Using the citric acid-hyperproducer A. tubingensis (formerly A. niger) WU-2223L as a model strain, we developed a CRISPR/Cas9 system-based genome editing technique involving co-transformation of Cas9 and the DNA fragment encoding single guide RNA (sgRNA). Using this system, ATP-sulfurylase gene (sC) knock-out strain derived from WU-2223L was generated; the knock-out efficiency was 29 transformants when 5 μg Cas9 was added to 5 × 105 protoplasts. In the gene replacement method based on this system, a DNA fragment encoding sgRNAs that target both the gene of interest and marker gene was used, and replacement of nitrate reductase gene (niaD) using sC gene as a marker gene was attempted. More than 90% of the sC-knock-out transformants exhibited replaced niaD, indicating efficient gene replacement. Moreover, one-step marker rescue of the sC marker gene was accomplished by excising the knock-in donor via intramolecular homologous recombination, enabling marker-free genome editing and drastically shortening the gene replacement period by circumventing the transformation procedure to recover the sC gene. Thus, we succeeded in constructing a CRISPR/Cas9 system-based rapid and marker-free gene replacement system for the citric acid-hyperproducer strain WU-2223L.
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Affiliation(s)
- Isato Yoshioka
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Kohtaro Kirimura
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan.
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33
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Cheng JT, Yu JH, Sun CF, Cao F, Ying YM, Zhan ZJ, Li WJ, Chen XA, Zhao QW, Li YQ, Gan LS, Mao XM. A Cell Factory of a Fungicolous Fungus Calcarisporium arbuscula for Efficient Production of Natural Products. ACS Synth Biol 2021; 10:698-706. [PMID: 33720696 DOI: 10.1021/acssynbio.0c00371] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fungal natural products are rich sources of clinical drugs. Particularly, the fungicolous fungi have a large number of biosynthetic gene clusters (BGCs) to produce numerous bioactive natural products, but most BGCs are silent in the laboratory. We have shown that a fungicolous fungus Calcarisporium arbuscula NRRL 3705 predominantly produces the highly reduced polyketide-type mycotoxins aurovertins. Here after evaluation of the aurovertin-null mutant ΔaurA as an efficient host, we further screened two strong promoters aurBp and A07068p based on RNA-Seq, and successfully activated an endogenous gene cluster from C. arbuscula as well as three additional exogenous BGCs from other fungi to produce polyketide-type natural products. Thus, we showed an efficient expression system from the fungicolous fungus C. arbuscula, which will be highly beneficial and complementary to the conventional Aspergillus and Penicillium fungal cell factories, and provides a useful toolkit for genome-wide mining of bioactive natural products from fungicolous fungi.
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Affiliation(s)
- Jin-Tao Cheng
- Institute of Pharmaceutical Biotechnology & Research Center for Clinical Pharmacy, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, P. R. China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, P. R. China
| | - Jia-Hui Yu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong 529020, P. R. China
| | - Chen-Fan Sun
- Institute of Pharmaceutical Biotechnology & Research Center for Clinical Pharmacy, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, P. R. China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, P. R. China
| | - Fei Cao
- Institute of Pharmaceutical Biotechnology & Research Center for Clinical Pharmacy, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, P. R. China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, P. R. China
| | - You-Min Ying
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Zha-Jun Zhan
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Wen-Ju Li
- Jinan Samuel Pharmaceutical Co., Ltd of Shandong Province, Jinan, 250100, P. R. China
| | - Xin-Ai Chen
- Institute of Pharmaceutical Biotechnology & Research Center for Clinical Pharmacy, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, P. R. China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, P. R. China
| | - Qing-Wei Zhao
- Institute of Pharmaceutical Biotechnology & Research Center for Clinical Pharmacy, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Yong-Quan Li
- Institute of Pharmaceutical Biotechnology & Research Center for Clinical Pharmacy, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, P. R. China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, P. R. China
| | - Li-She Gan
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong 529020, P. R. China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Xu-Ming Mao
- Institute of Pharmaceutical Biotechnology & Research Center for Clinical Pharmacy, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, P. R. China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, P. R. China
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Salihu R, Abd Razak SI, Ahmad Zawawi N, Rafiq Abdul Kadir M, Izzah Ismail N, Jusoh N, Riduan Mohamad M, Hasraf Mat Nayan N. Citric acid: A green cross-linker of biomaterials for biomedical applications. Eur Polym J 2021. [DOI: 10.1016/j.eurpolymj.2021.110271] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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35
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Mores S, Vandenberghe LPDS, Magalhães Júnior AI, de Carvalho JC, de Mello AFM, Pandey A, Soccol CR. Citric acid bioproduction and downstream processing: Status, opportunities, and challenges. BIORESOURCE TECHNOLOGY 2021; 320:124426. [PMID: 33249260 DOI: 10.1016/j.biortech.2020.124426] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 06/12/2023]
Abstract
Citric acid (CA) has been widely used in different industrial sectors, being produced through fermentation of low-cost feedstock. The development of downstream processes, easier to operate, environmentally friendly, and more economic than precipitation, is certainly a challenge in CA bioproduction. Large volumes of by-products generated in precipitation require treatment before disposal. Adsorption, extraction, and membrane separation have been shown to have a lower environmental impact than precipitation, but the technological maturity of these methods is still limited. However, reactive extraction and adsorption have great potential for industrial applications. This review shows that there is still much to be explored, both about the factors that are intrinsic to the techniques, but also in their combination for new processes' development. This review reports the most recent advances on CA bioproduction, with significant information about recovery and purification methods involving this highly industrially demanded organic acid.
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Affiliation(s)
- Sabrina Mores
- Federal University of Paraná (UFPR). Department of Bioprocess Engineering and Biotechnology. P.O. Box 19011, ZIP Code 81531-990, Curitiba, Paraná, Brazil
| | - Luciana Porto de Souza Vandenberghe
- Federal University of Paraná (UFPR). Department of Bioprocess Engineering and Biotechnology. P.O. Box 19011, ZIP Code 81531-990, Curitiba, Paraná, Brazil.
| | - Antonio Irineudo Magalhães Júnior
- Federal University of Paraná (UFPR). Department of Bioprocess Engineering and Biotechnology. P.O. Box 19011, ZIP Code 81531-990, Curitiba, Paraná, Brazil
| | - Júlio César de Carvalho
- Federal University of Paraná (UFPR). Department of Bioprocess Engineering and Biotechnology. P.O. Box 19011, ZIP Code 81531-990, Curitiba, Paraná, Brazil
| | - Ariane Fátima Murawski de Mello
- Federal University of Paraná (UFPR). Department of Bioprocess Engineering and Biotechnology. P.O. Box 19011, ZIP Code 81531-990, Curitiba, Paraná, Brazil
| | - Ashok Pandey
- Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, 226 001, India
| | - Carlos Ricardo Soccol
- Federal University of Paraná (UFPR). Department of Bioprocess Engineering and Biotechnology. P.O. Box 19011, ZIP Code 81531-990, Curitiba, Paraná, Brazil
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Songserm P, Srimongkol P, Thitiprasert S, Tanasupawat S, Cheirsilp B, Assabumrungrat S, Karnchanatat A, Thongchul N. Differential Gene Expression Analysis
of Aspergillus terreus Reveals Metabolic
Response and Transcription Suppression under Dissolved Oxygen and
pH Stress. J EVOL BIOCHEM PHYS+ 2020. [DOI: 10.1134/s0022093020060101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Li J, Rong L, Zhao Y, Li S, Zhang C, Xiao D, Foo JL, Yu A. Next-generation metabolic engineering of non-conventional microbial cell factories for carboxylic acid platform chemicals. Biotechnol Adv 2020; 43:107605. [DOI: 10.1016/j.biotechadv.2020.107605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/30/2020] [Accepted: 07/27/2020] [Indexed: 01/21/2023]
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Abstract
Microbial citric acid has high economic importance and widely used in beverage, food, detergents, cosmetics and pharmaceutical industries. The filamentous fungus Aspergillus niger is a work horse and important cell factory in industry for the production of citric acid. Although in-depth literatures and reviews have been published to explain the biochemistry, biotechnology and genetic engineering study of citric acid production by Aspergillus niger separately but the present review compiled, all the aspects with upto date brief summary of the subject describing microorganisms, substrates and their pre-treatment, screening, fermentation techniques, metabolic engineering, biochemistry, product recovery and numerous biotechnological application of citric acid for simple understanding of microbial citric acid production. The availability of genome sequence of this organism has facilitated numerous studies in gene function, gene regulation, primary and secondary metabolism. An attempt has been also made to address the molecular mechanisms and application of recent advanced techniques such as CRISPR/Cas9 systems in enhancement of citric acid production.
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Affiliation(s)
- Bikash Chandra Behera
- School of Biological sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India
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39
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Cao W, Yan L, Li M, Liu X, Xu Y, Xie Z, Liu H. Identification and engineering a C4-dicarboxylate transporter for improvement of malic acid production in Aspergillus niger. Appl Microbiol Biotechnol 2020; 104:9773-9783. [DOI: 10.1007/s00253-020-10932-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 08/12/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022]
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40
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de Oliveira F, Ferreira LC, Neto ÁB, Simas Teixeira MF, de Carvalho Santos Ebinuma V. Biosynthesis of natural colorant by Talaromyces amestolkiae: Mycelium accumulation and colorant formation in incubator shaker and in bioreactor. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107694] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Zhao J, Fang H, Zhang D. Expanding application of CRISPR-Cas9 system in microorganisms. Synth Syst Biotechnol 2020; 5:269-276. [PMID: 32913902 PMCID: PMC7451738 DOI: 10.1016/j.synbio.2020.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/24/2020] [Accepted: 08/04/2020] [Indexed: 11/08/2022] Open
Abstract
The development of CRISPR-Cas9 based genetic manipulation tools represents a huge breakthrough in life sciences and has been stimulating research on metabolic engineering, synthetic biology, and systems biology. The CRISPR-Cas9 and its derivative tools are one of the best choices for precise genome editing, multiplexed genome editing, and reversible gene expression control in microorganisms. However, challenges remain for applying CRISPR-Cas9 in novel microorganisms, especially those industrial microorganism hosts that are intractable using traditional genetic manipulation tools. How to further extend CRISPR-Cas9 to these microorganisms is being an urgent matter. In this review, we first introduce the mechanism and application of CRISPR-Cas9, then discuss how to optimize CRISPR-Cas9 as genome editing tools, including but not limited to how to reduce off-target effects and Cas9 related toxicity, and how to increase on-target efficiency by optimizing crRNA and sgRNA design.
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Affiliation(s)
- Jing Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Huan Fang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
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42
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Xu Y, Zhou Y, Cao W, Liu H. Improved Production of Malic Acid in Aspergillus niger by Abolishing Citric Acid Accumulation and Enhancing Glycolytic Flux. ACS Synth Biol 2020; 9:1418-1425. [PMID: 32379964 DOI: 10.1021/acssynbio.0c00096] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microbial fermentation was widely explored to produce malic acid. Previously, Aspergillus niger has been successfully engineered, and a high titer of malic acid was achieved with strain S575, but it also produced a high level of byproduct citric acid. Here, the capability of A. niger in malic acid biosynthesis was further improved by eliminating the accumulation of citric acid and enhancing glycolytic flux. Characterization of variant mutants suggested that disruption of cexA, a gene encoding citric acid transporter located on cell membrane, abolished citric acid accumulation. However, cexA-deficient strain S895 showed significantly decreased malic acid production. Further analysis of S895 indicated that the transcription level of genes involved in glucose transportation and glycolytic pathway was significantly reduced, and the corresponding enzyme activity was also lower than those of S575. Individual overexpression of genes encoding glucose transporter MstC and key enzymes (hexokinase HxkA, 6-phosphofructo-2-kinase PfkA, and pyruvate kinase PkiA) involved in irreversible reactions of glycolic pathway increased malic acid production. Accordingly, genes of mstC, hxkA, pfkA, and pkiA were overexpressed altogether in S895, and the resultant strain S1149 was constructed. The titer of malic acid in fed-batch fermentation with S1149 reached 201.13 g/L. Compared with S575, the byproduct of citric acid was completely abolished in S1149, and the ratio of malic acid/glucose was increased from 1.27 to 1.64 mol/mol, the highest yield reported so far, and the fermentation period was shortened from 9 to 8 days. Thus, a strain with great industrial application potential was developed by engineering nine genes in A. niger, and a pilot fermentation technology was exploited.
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Affiliation(s)
- Yongxue Xu
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, 300457 Tianjin, China
| | - Yutao Zhou
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, 300457 Tianjin, China
| | - Wei Cao
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, 300457 Tianjin, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science & Technology, 300457 Tianjin, China
| | - Hao Liu
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science & Technology, 300457 Tianjin, China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin University of Science & Technology, 300457 Tianjin, China
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43
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Fatma Z, Schultz JC, Zhao H. Recent advances in domesticating non‐model microorganisms. Biotechnol Prog 2020; 36:e3008. [DOI: 10.1002/btpr.3008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/14/2020] [Accepted: 04/18/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Zia Fatma
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | - J. Carl Schultz
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
- Departments of Chemistry, Biochemistry, and Bioengineering University of Illinois at Urbana‐Champaign Urbana Illinois USA
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Zhang L, Zheng X, Cairns TC, Zhang Z, Wang D, Zheng P, Sun J. Disruption or reduced expression of the orotidine-5'-decarboxylase gene pyrG increases citric acid production: a new discovery during recyclable genome editing in Aspergillus niger. Microb Cell Fact 2020; 19:76. [PMID: 32209089 PMCID: PMC7092557 DOI: 10.1186/s12934-020-01334-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/16/2020] [Indexed: 11/15/2022] Open
Abstract
Background Aspergillus niger is a filamentous fungus used for the majority of global citric acid production. Recent developments in genome editing now enable biotechnologists to engineer and optimize A. niger. Currently, however, genetic-leads for maximizing citric acid titers in industrial A. niger isolates is limited. Results In this study, we try to engineer two citric acid A. niger production isolates, WT-D and D353, to serve as platform strains for future high-throughput genome engineering. Consequently, we used genome editing to simultaneously disrupt genes encoding the orotidine-5′-decarboxylase (pyrG) and non-homologous end-joining component (kusA) to enable use of the pyrG selection/counter selection system, and to elevate homologous recombination rates, respectively. During routine screening of these pyrG mutant strains, we unexpectedly observed a 2.17-fold increase in citric acid production when compared to the progenitor controls, indicating that inhibition of uridine/pyrimidine synthesis may increase citric acid titers. In order to further test this hypothesis, the pyrG gene was placed under the control of a tetracycline titratable cassette, which confirmed that reduced expression of this gene elevated citric acid titers in both shake flask and bioreactor fermentation. Subsequently, we conducted intracellular metabolomics analysis, which demonstrated that pyrG disruption enhanced the glycolysis flux and significantly improved abundance of citrate and its precursors. Conclusions In this study, we deliver two citric acid producing isolates which are amenable to high throughput genetic manipulation due to pyrG/kusA deletion. Strikingly, we demonstrate for the first time that A. niger pyrG is a promising genetic lead for generating citric acid hyper-producing strains. Our data support the hypothesis that uridine/pyrimidine biosynthetic pathway offer future avenues for strain engineering efforts.![]()
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Affiliation(s)
- Lihui Zhang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Xiaomei Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Timothy C Cairns
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Zhidan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Depei Wang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China.
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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45
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Amato A, Becci A, Beolchini F. Citric acid bioproduction: the technological innovation change. Crit Rev Biotechnol 2020; 40:199-212. [DOI: 10.1080/07388551.2019.1709799] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Alessia Amato
- Department of Life and Environmental Science, Università Politecnica delle Marche, Ancona, Italy
| | - Alessandro Becci
- Department of Life and Environmental Science, Università Politecnica delle Marche, Ancona, Italy
| | - Francesca Beolchini
- Department of Life and Environmental Science, Università Politecnica delle Marche, Ancona, Italy
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46
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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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47
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Cairns TC, Feurstein C, Zheng X, Zhang LH, Zheng P, Sun J, Meyer V. Functional exploration of co-expression networks identifies a nexus for modulating protein and citric acid titres in Aspergillus niger submerged culture. Fungal Biol Biotechnol 2019; 6:18. [PMID: 31728200 PMCID: PMC6842248 DOI: 10.1186/s40694-019-0081-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/21/2019] [Indexed: 01/10/2023] Open
Abstract
Background Filamentous fungal cell factories are used to produce numerous proteins, enzymes, and organic acids. Protein secretion and filamentous growth are tightly coupled at the hyphal tip. Additionally, both these processes require ATP and amino acid precursors derived from the citric acid cycle. Despite this interconnection of organic acid production and protein secretion/filamentous growth, few studies in fungi have identified genes which may concomitantly impact all three processes. Results We applied a novel screen of a global co-expression network in the cell factory Aspergillus niger to identify candidate genes which may concomitantly impact macromorphology, and protein/organic acid fermentation. This identified genes predicted to encode the Golgi localized ArfA GTPase activating protein (GAP, AgeB), and ArfA guanine nucleotide exchange factors (GEFs SecG and GeaB) to be co-expressed with citric acid cycle genes. Consequently, we used CRISPR-based genome editing to place the titratable Tet-on expression system upstream of ageB, secG, and geaB in A. niger. Functional analysis revealed that ageB and geaB are essential whereas secG was dispensable for early filamentous growth. Next, gene expression was titrated during submerged cultivations under conditions for either protein or organic acid production. ArfA regulators played varied and culture-dependent roles on pellet formation. Notably, ageB or geaB expression levels had major impacts on protein secretion, whereas secG was dispensable. In contrast, reduced expression of each predicted ArfA regulator resulted in an absence of citric acid in growth media. Finally, titrated expression of either GEFs resulted in an increase in oxaloacetic acid concentrations in supernatants. Conclusion Our data suggest that the Golgi may play an underappreciated role in modulating organic acid titres during industrial applications, and that this is SecG, GeaB and AgeB dependent in A. niger. These data may lead to novel avenues for strain optimization in filamentous fungi for improved protein and organic acid titres.
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Affiliation(s)
- Timothy C Cairns
- 1Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China.,2Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China
| | - Claudia Feurstein
- 1Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China.,2Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China.,3Institute of Biotechnology, Chair of Applied and Molecular Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Xiaomei Zheng
- 1Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China.,2Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China.,4University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Li Hui Zhang
- 1Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China.,2Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China.,5College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457 China
| | - Ping Zheng
- 1Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China.,2Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China.,4University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jibin Sun
- 1Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China.,2Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China.,4University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Vera Meyer
- 1Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China.,2Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People's Republic of China.,3Institute of Biotechnology, Chair of Applied and Molecular Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany.,4University of Chinese Academy of Sciences, Beijing, 100049 China
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Kayacan Y, Griffiths A, Wendland J. A script for initiating molecular biology studies with non-conventional yeasts based on Saccharomycopsis schoenii. Microbiol Res 2019; 229:126342. [PMID: 31536874 DOI: 10.1016/j.micres.2019.126342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 02/07/2023]
Abstract
Non-conventional yeasts (NCYs), i.e. all yeasts other than Saccharomyces cerevisiae, are emerging as novel production strains and gain more and more attention to exploit their unique properties. Yet, these yeasts can hardly compete against the advanced methodology and genetic tool kit available for exploiting and engineering S. cerevisiae. Currently, for many NCYs one has to start from scratch to initiate molecular genetic manipulations, which is often time consuming and not straight-forward. More so because utilization of S. cerevisiae tools based on short-flank mediated homologous recombination or plasmid biology are not readily applicable in NCYs. Here we present a script with discrete steps that will lead to the development of a basic and expandable molecular toolkit for ascomycetous NCYs and will allow genetic engineering of novel platform strains. For toolkit development the highly efficient in vivo recombination efficiency of S. cerevisiae is utilized in the generation and initial testing of tools. The basic toolkit includes promoters, reporter genes, selectable markers based on dominant antibiotic resistance genes and the generation of long-flanking homology disruption cassettes. The advantage of having pretested molecular tools that function in a heterologous host facilitate NCY strain manipulations. We demonstrate the usefulness of this script on Saccharomycopsis schoenii, a predator yeast with useful properties in fermentation and fungal biocontrol.
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Affiliation(s)
- Yeseren Kayacan
- Vrije Universiteit Brussel, Functional Yeast Genomics, BE-1050 Brussels, Belgium
| | - Adam Griffiths
- Vrije Universiteit Brussel, Functional Yeast Genomics, BE-1050 Brussels, Belgium
| | - Jürgen Wendland
- Hochschule Geisenheim University, Department of Microbiology and Biochemistry, von-Lade-Strasse 1, D-65366 Geisenheim, Germany; Vrije Universiteit Brussel, Functional Yeast Genomics, BE-1050 Brussels, Belgium.
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Cairns TC, Zheng X, Zheng P, Sun J, Meyer V. Moulding the mould: understanding and reprogramming filamentous fungal growth and morphogenesis for next generation cell factories. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:77. [PMID: 30988699 PMCID: PMC6446404 DOI: 10.1186/s13068-019-1400-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/09/2019] [Indexed: 05/21/2023]
Abstract
Filamentous fungi are harnessed as cell factories for the production of a diverse range of organic acids, proteins, and secondary metabolites. Growth and morphology have critical implications for product titres in both submerged and solid-state fermentations. Recent advances in systems-level understanding of the filamentous lifestyle and development of sophisticated synthetic biological tools for controlled manipulation of fungal genomes now allow rational strain development programs based on data-driven decision making. In this review, we focus on Aspergillus spp. and other industrially utilised fungi to summarise recent insights into the multifaceted and dynamic relationship between filamentous growth and product titres from genetic, metabolic, modelling, subcellular, macromorphological and process engineering perspectives. Current progress and knowledge gaps with regard to mechanistic understanding of product secretion and export from the fungal cell are discussed. We highlight possible strategies for unlocking lead genes for rational strain optimizations based on omics data, and discuss how targeted genetic manipulation of these candidates can be used to optimise fungal morphology for improved performance. Additionally, fungal signalling cascades are introduced as critical processes that can be genetically targeted to control growth and morphology during biotechnological applications. Finally, we review progress in the field of synthetic biology towards chassis cells and minimal genomes, which will eventually enable highly programmable filamentous growth and diversified production capabilities. Ultimately, these advances will not only expand the fungal biotechnology portfolio but will also significantly contribute to a sustainable bio-economy.
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Affiliation(s)
- Timothy C. Cairns
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Xiaomei Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Vera Meyer
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
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Cairns TC, Feurstein C, Zheng X, Zheng P, Sun J, Meyer V. A quantitative image analysis pipeline for the characterization of filamentous fungal morphologies as a tool to uncover targets for morphology engineering: a case study using aplD in Aspergillus niger. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:149. [PMID: 31223339 PMCID: PMC6570962 DOI: 10.1186/s13068-019-1473-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/20/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Fungal fermentation is used to produce a diverse repertoire of enzymes, chemicals, and drugs for various industries. During submerged cultivation, filamentous fungi form a range of macromorphologies, including dispersed mycelia, clumped aggregates, or pellets, which have critical implications for rheological aspects during fermentation, gas/nutrient transfer, and, thus, product titres. An important component of strain engineering efforts is the ability to quantitatively assess fungal growth phenotypes, which will drive novel leads for morphologically optimized production strains. RESULTS In this study, we developed an automated image analysis pipeline to quantify the morphology of pelleted and dispersed growth (MPD) which rapidly and reproducibly measures dispersed and pelleted macromorphologies from any submerged fungal culture. It (i) enables capture and analysis of several hundred images per user/day, (ii) is designed to quantitatively assess heterogeneous cultures consisting of dispersed and pelleted forms, (iii) gives a quantitative measurement of culture heterogeneity, (iv) automatically generates key Euclidian parameters for individual fungal structures including particle diameter, aspect ratio, area, and solidity, which are also assembled into a previously described dimensionless morphology number MN, (v) has an in-built quality control check which enables end-users to easily confirm the accuracy of the automated calls, and (vi) is easily adaptable to user-specified magnifications and macromorphological definitions. To concomitantly provide proof of principle for the utility of this image analysis pipeline, and provide new leads for morphologically optimized fungal strains, we generated a morphological mutant in the cell factory Aspergillus niger based on CRISPR-Cas technology. First, we interrogated a previously published co-expression networks for A. niger to identify a putative gamma-adaptin encoding gene (aplD) that was predicted to play a role in endosome cargo trafficking. Gene editing was used to generate a conditional aplD expression mutant under control of the titratable Tet-on system. Reduced aplD expression caused a hyperbranched growth phenotype and diverse defects in pellet formation with a putative increase in protein secretion. This possible protein hypersecretion phenotype could be correlated with increased dispersed mycelia, and both decreased pellet diameter and MN. CONCLUSION The MPD image analysis pipeline is a simple, rapid, and flexible approach to quantify diverse fungal morphologies. As an exemplar, we have demonstrated that the putative endosomal transport gene aplD plays a crucial role in A. niger filamentous growth and pellet formation during submerged culture. This suggests that endocytic components are underexplored targets for engineering fungal cell factories.
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Affiliation(s)
- Timothy C. Cairns
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Claudia Feurstein
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Xiaomei Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Vera Meyer
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
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