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Lu Z, Chen Z, Liu Y, Hua X, Gao C, Liu J. Morphological Engineering of Filamentous Fungi: Research Progress and Perspectives. J Microbiol Biotechnol 2024; 34:1197-1205. [PMID: 38693049 PMCID: PMC11239417 DOI: 10.4014/jmb.2402.02007] [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: 02/05/2024] [Revised: 02/22/2024] [Accepted: 03/06/2024] [Indexed: 05/03/2024]
Abstract
Filamentous fungi are important cell factories for the production of high-value enzymes and chemicals for the food, chemical, and pharmaceutical industries. Under submerged fermentation, filamentous fungi exhibit diverse fungal morphologies that are influenced by environmental factors, which in turn affect the rheological properties and mass transfer of the fermentation system, and ultimately the synthesis of products. In this review, we first summarize the mechanisms of mycelial morphogenesis and then provide an overview of current developments in methods and strategies for morphological regulation, including physicochemical and metabolic engineering approaches. We also anticipate that rapid developments in synthetic biology and genetic manipulation tools will accelerate morphological engineering in the future.
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Affiliation(s)
- Zhengwu Lu
- College of Life Sciences, Linyi University, Linyi 276000, P. R. China
| | - Zhiqun Chen
- College of Life Sciences, Linyi University, Linyi 276000, P. R. China
| | - Yunguo Liu
- College of Life Sciences, Linyi University, Linyi 276000, P. R. China
| | - Xuexue Hua
- Shandong Fufeng Fermentation Co., Ltd., Linyi 276600, P. R. China
| | - Cuijuan Gao
- College of Life Sciences, Linyi University, Linyi 276000, P. R. China
| | - Jingjing Liu
- College of Life Sciences, Linyi University, Linyi 276000, P. R. China
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2
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Cairns TC, de Kanter T, Zheng XZ, Zheng P, Sun J, Meyer V. Regression modelling of conditional morphogene expression links and quantifies the impact of growth rate, fitness and macromorphology with protein secretion in Aspergillus niger. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:95. [PMID: 37268954 DOI: 10.1186/s13068-023-02345-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/18/2023] [Indexed: 06/04/2023]
Abstract
BACKGROUND Filamentous fungi are used as industrial cell factories to produce a diverse portfolio of proteins, organic acids, and secondary metabolites in submerged fermentation. Generating optimized strains for maximum product titres relies on a complex interplay of molecular, cellular, morphological, and macromorphological factors that are not yet fully understood. RESULTS In this study, we generate six conditional expression mutants in the protein producing ascomycete Aspergillus niger and use them as tools to reverse engineer factors which impact total secreted protein during submerged growth. By harnessing gene coexpression network data, we bioinformatically predicted six morphology and productivity associated 'morphogenes', and placed them under control of a conditional Tet-on gene switch using CRISPR-Cas genome editing. Strains were phenotypically screened on solid and liquid media following titration of morphogene expression, generating quantitative measurements of growth rate, filamentous morphology, response to various abiotic perturbations, Euclidean parameters of submerged macromorphologies, and total secreted protein. These data were built into a multiple linear regression model, which identified radial growth rate and fitness under heat stress as positively correlated with protein titres. In contrast, diameter of submerged pellets and cell wall integrity were negatively associated with productivity. Remarkably, our model predicts over 60% of variation in A. niger secreted protein titres is dependent on these four variables, suggesting that they play crucial roles in productivity and are high priority processes to be targeted in future engineering programs. Additionally, this study suggests A. niger dlpA and crzA genes are promising new leads for enhancing protein titres during fermentation. CONCLUSIONS Taken together this study has identified several potential genetic leads for maximizing protein titres, delivered a suite of chassis strains with user controllable macromorphologies during pilot fermentation studies, and has quantified four crucial factors which impact secreted protein titres in A. niger.
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Affiliation(s)
- Timothy C Cairns
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Straße Des 17. Juni 135, 10623, Berlin, Germany.
| | - Tom de Kanter
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Straße Des 17. Juni 135, 10623, Berlin, Germany
| | - Xiaomei Z 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, Beijing, 100049, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, 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, Beijing, 100049, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, 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, Beijing, 100049, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Vera Meyer
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Straße Des 17. Juni 135, 10623, Berlin, Germany.
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3
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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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Cairns TC, Zheng X, Feurstein C, Zheng P, Sun J, Meyer V. A Library of Aspergillus niger Chassis Strains for Morphology Engineering Connects Strain Fitness and Filamentous Growth With Submerged Macromorphology. Front Bioeng Biotechnol 2022; 9:820088. [PMID: 35111742 PMCID: PMC8801610 DOI: 10.3389/fbioe.2021.820088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/03/2021] [Indexed: 01/06/2023] Open
Abstract
Submerged fermentation using filamentous fungal cell factories is used to produce a diverse portfolio of useful molecules, including food, medicines, enzymes, and platform chemicals. Depending on strain background and abiotic culture conditions, different macromorphologies are formed during fermentation, ranging from dispersed hyphal fragments to approximately spherical pellets several millimetres in diameter. These macromorphologies are known to have a critical impact on product titres and rheological performance of the bioreactor. Pilot productivity screens in different macromorphological contexts is technically challenging, time consuming, and thus a significant limitation to achieving maximum product titres. To address this bottleneck, we developed a library of conditional expression mutants in the organic, protein, and secondary metabolite cell factory Aspergillus niger. Thirteen morphology-associated genes transcribed during fermentation were placed via CRISPR-Cas9 under control of a synthetic Tet-on gene switch. Quantitative analysis of submerged growth reveals that these strains have distinct and titratable macromorphologies for use as chassis during strain engineering programs. We also used this library as a tool to quantify how pellet formation is connected with strain fitness and filamentous growth. Using multiple linear regression modelling, we predict that pellet formation is dependent largely on strain fitness, whereas pellet Euclidian parameters depend on fitness and hyphal branching. Finally, we have shown that conditional expression of the putative kinase encoding gene pkh2 can decouple fitness, dry weight, pellet macromorphology, and culture heterogeneity. We hypothesize that further analysis of this gene product and the cell wall integrity pathway in which it is embedded will enable more precise engineering of A. niger macromorphology in future.
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Affiliation(s)
- Timothy C. Cairns
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- *Correspondence: Timothy C. Cairns, ; Jibin Sun, ; Vera Meyer,
| | - Xiaomei Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Claudia Feurstein
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- *Correspondence: Timothy C. Cairns, ; Jibin Sun, ; Vera Meyer,
| | - Vera Meyer
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- *Correspondence: Timothy C. Cairns, ; Jibin Sun, ; Vera Meyer,
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5
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Laible AR, Dinius A, Schrader M, Krull R, Kwade A, Briesen H, Schmideder S. Effects and interactions of metal oxides in microparticle-enhanced cultivation of filamentous microorganisms. Eng Life Sci 2021; 22:725-743. [PMID: 36514528 PMCID: PMC9731605 DOI: 10.1002/elsc.202100075] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/13/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
Filamentous microorganisms are used as molecular factories in industrial biotechnology. In 2007, a new approach to improve productivity in submerged cultivation was introduced: microparticle-enhanced cultivation (MPEC). Since then, numerous studies have investigated the influence of microparticles on the cultivation. Most studies considered MPEC a morphology engineering approach, in which altered morphology results in increased productivity. But sometimes similar morphological changes lead to decreased productivity, suggesting that this hypothesis is not a sufficient explanation for the effects of microparticles. Effects of surface chemistry on particles were paid little attention, as particles were often considered chemically-inert and bioinert. However, metal oxide particles strongly interact with their environment. This review links morphological, physical, and chemical properties of microparticles with effects on culture broth, filamentous morphology, and molecular biology. More precisely, surface chemistry effects of metal oxide particles lead to ion leaching, adsorption of enzymes, and generation of reactive oxygen species. Therefore, microparticles interfere with gene regulation, metabolism, and activity of enzymes. To enhance the understanding of microparticle-based morphology engineering, further interactions between particles and cells are elaborated. The presented description of phenomena occurring in MPEC eases the targeted choice of microparticles, and thus, contributes to improving the productivity of microbial cultivation technology.
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Affiliation(s)
- Andreas Reiner Laible
- School of Life SciencesChair of Process Systems EngineeringTechnische Universität MünchenFreisingGermany
| | - Anna Dinius
- Institute of Biochemical EngineeringTechnische Universität BraunschweigBraunschweigGermany,Center of Pharmaceutical EngineeringTechnische Universität BraunschweigBraunschweigGermany
| | - Marcel Schrader
- Center of Pharmaceutical EngineeringTechnische Universität BraunschweigBraunschweigGermany,Institute for Particle TechnologyTechnische Universität BraunschweigBraunschweigGermany
| | - Rainer Krull
- Institute of Biochemical EngineeringTechnische Universität BraunschweigBraunschweigGermany,Center of Pharmaceutical EngineeringTechnische Universität BraunschweigBraunschweigGermany
| | - Arno Kwade
- Center of Pharmaceutical EngineeringTechnische Universität BraunschweigBraunschweigGermany,Institute for Particle TechnologyTechnische Universität BraunschweigBraunschweigGermany
| | - Heiko Briesen
- School of Life SciencesChair of Process Systems EngineeringTechnische Universität MünchenFreisingGermany
| | - Stefan Schmideder
- School of Life SciencesChair of Process Systems EngineeringTechnische Universität MünchenFreisingGermany
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6
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Meyer V, Cairns T, Barthel L, King R, Kunz P, Schmideder S, Müller H, Briesen H, Dinius A, Krull R. Understanding and controlling filamentous growth of fungal cell factories: novel tools and opportunities for targeted morphology engineering. Fungal Biol Biotechnol 2021; 8:8. [PMID: 34425914 PMCID: PMC8383395 DOI: 10.1186/s40694-021-00115-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/02/2021] [Indexed: 02/20/2023] Open
Abstract
Filamentous fungal cell factories are efficient producers of platform chemicals, proteins, enzymes and natural products. Stirred-tank bioreactors up to a scale of several hundred m³ are commonly used for their cultivation. Fungal hyphae self-assemble into various cellular macromorphologies ranging from dispersed mycelia, loose clumps, to compact pellets. Development of these macromorphologies is so far unpredictable but strongly impacts productivities of fungal bioprocesses. Depending on the strain and the desired product, the morphological forms vary, but no strain- or product-related correlations currently exist to improve
process understanding of fungal production systems. However, novel genomic, genetic, metabolic, imaging and modelling tools have recently been established that will provide fundamental new insights into filamentous fungal growth and how it is balanced with product formation. In this primer, these tools will be highlighted and their revolutionary impact on rational morphology engineering and bioprocess control will be discussed.
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Affiliation(s)
- Vera Meyer
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.
| | - Timothy Cairns
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Lars Barthel
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Rudibert King
- Chair of Measurement and Control, Institute of Chemical and Process Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Philipp Kunz
- Chair of Measurement and Control, Institute of Chemical and Process Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Stefan Schmideder
- Chair of Process Systems Engineering, School of Life Sciences, Technical University of Munich, Gregor- Mendel-Str. 4, 85354, Freising, Germany
| | - Henri Müller
- Chair of Process Systems Engineering, School of Life Sciences, Technical University of Munich, Gregor- Mendel-Str. 4, 85354, Freising, Germany
| | - Heiko Briesen
- Chair of Process Systems Engineering, School of Life Sciences, Technical University of Munich, Gregor- Mendel-Str. 4, 85354, Freising, Germany
| | - Anna Dinius
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany.,Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Franz-Liszt-Str. 35a, 38106, Brunswick, Germany
| | - Rainer Krull
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany.,Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Franz-Liszt-Str. 35a, 38106, Brunswick, Germany
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7
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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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Böl M, Schrinner K, Tesche S, Krull R. Challenges of influencing cellular morphology by morphology engineering techniques and mechanical induced stress on filamentous pellet systems-A critical review. Eng Life Sci 2021; 21:51-67. [PMID: 33716605 PMCID: PMC7923580 DOI: 10.1002/elsc.202000060] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 11/30/2022] Open
Abstract
Filamentous microorganisms are main producers of organic acids, enzymes, and pharmaceutical agents such as antibiotics and other active pharmaceutical ingredients. With their complex cell morphology, ranging from dispersed mycelia to dense pellets, the cultivation is challenging. In recent years, various techniques for tailor-made cell morphologies of filamentous microorganisms have been developed to increase product formation and have been summarised under the term morphology engineering. These techniques, namely microparticle-enhanced cultivation, macroparticle-enhanced cultivation, and alteration of the osmolality of the culture medium by addition of inorganic salts, the salt-enhanced cultivation, are presented and discussed in this review. These techniques have already proven to be useful and now await further proof-of-concept. Furthermore, the mechanical behaviour of individual pellets is of special interest for a general understanding of pellet mechanics and the productivity of biotechnological processes with filamentous microorganisms. Correlating them with substrate uptake and finally with productivity would be a breakthrough not to be underestimated for the comprehensive characterisation of filamentous systems. So far, this research field is under-represented. First results on filamentous pellet mechanics are discussed and important future aspects, which the filamentous expert community should deal with, will be presented and critically discussed.
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Affiliation(s)
- Markus Böl
- Institute of Mechanics and AdaptronicsTechnische Universität BraunschweigBraunschweigGermany
- Center of Pharmaceutical Engineering (PVZ)Technische Universität BraunschweigBraunschweigGermany
| | - Kathrin Schrinner
- Center of Pharmaceutical Engineering (PVZ)Technische Universität BraunschweigBraunschweigGermany
- Institute of Biochemical EngineeringTechnische Universität BraunschweigBraunschweigGermany
| | - Sebastian Tesche
- Center of Pharmaceutical Engineering (PVZ)Technische Universität BraunschweigBraunschweigGermany
- Institute of Biochemical EngineeringTechnische Universität BraunschweigBraunschweigGermany
| | - Rainer Krull
- Center of Pharmaceutical Engineering (PVZ)Technische Universität BraunschweigBraunschweigGermany
- Institute of Biochemical EngineeringTechnische Universität BraunschweigBraunschweigGermany
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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] [Grants] [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
- 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
- Institute of Biotechnology, Chair of Applied and Molecular Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 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, Beijing, 100049 China
| | - Li Hui 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
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457 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, Beijing, 100049 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, Beijing, 100049 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
- Institute of Biotechnology, Chair of Applied and Molecular Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
- University of Chinese Academy of Sciences, Beijing, 100049 China
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10
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Evaluation of a cell model expressing βKlotho for screening FGF21 analogues. Cytotechnology 2019; 71:1033-1041. [PMID: 31535308 DOI: 10.1007/s10616-019-00344-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/06/2019] [Indexed: 10/26/2022] Open
Abstract
βKlotho as the major role is a necessary auxiliary protein when fibroblast growth factor 21 (FGF21) binds FGF21 receptors (FGFR) for activating intracellular signaling pathways that ultimately generate biological effects. To achieve the aim of high throughput screening of FGF21 analogues, we established 3T3-L1-βKlotho cells that could stably express βklotho protein. The glucose uptake, expression of GLUT1 mRNA and activation of FGF signaling molecules ERK1/2 phosphorylation were detected by GOD-POD assay, real-time PCR analysis and western blotting assay in 3T3-L1-βKlotho cells and 3T3-L1 adipocytes, respectively. The results showed that FGF21 increased glucose uptake significantly in a dose-dependent and time-dependent manner in 3T3-L1-βKlotho cells. 3T3-L1-βKlotho cells stimulated with FGF21 up-regulated the transcriptional levels of GLUT1 mRNA obviously. FGF21 activated the FGF signaling molecules ERK1/2 in 3T3-L1-βKlotho cells. In addition, the same results were obtained in 3T3-L1 adipocytes. Furthermore, FGF21-stimulated elevation of glucose uptake, GLUT1 mRNA transcription and the phosphorylation of ERK1/2 were dramatically attenuated by pretreatment of cells with FGFR specific inhibitor SU5402 in 3T3-L1-βKlotho cells. This study demonstrated that the cell model could be applied to high throughput screen FGF21 analogues.
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Tesche S, Rösemeier-Scheumann R, Lohr J, Hanke R, Büchs J, Krull R. Salt-enhanced cultivation as a morphology engineering tool for filamentous actinomycetes: Increased production of labyrinthopeptin A1 in Actinomadura namibiensis. Eng Life Sci 2019; 19:781-794. [PMID: 32624971 DOI: 10.1002/elsc.201900036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 08/03/2019] [Accepted: 08/23/2019] [Indexed: 12/11/2022] Open
Abstract
Salt-enhanced cultivation as a morphology engineering tool for the filamentous actinomycete Actinomadura namibiensis was evaluated in 500-mL shaking flasks (working volume 100 mL) with the aim of increasing the concentration of the pharmaceutically interesting peptide labyrinthopeptin A1. Among the inorganic salts added to a complex production medium, the addition of (NH4)2SO4 led to the highest amount of labyrinthopeptin A1 production. By using 50 mM (NH4)2SO4, the labyrinthopeptin A1 concentration increased up to sevenfold compared to the non-supplemented control, resulting in 325 mg L-1 labyrinthopeptin A1 after 10 days of cultivation. The performance of other ammonium- and sulfate-containing salts (e.g., NH4Cl, K2SO4) was much lower than the performance of (NH4)2SO4. A positive correlation between the uptake of glycerol as one of the main carbon sources and nongrowth-associated labyrinthopeptin productivity was found. The change in the cell morphology of A. namibiensis in conjunction with increased osmolality by the addition of 50 mM (NH4)2SO4, was quantified by image analysis. A. namibiensis always developed a heterogeneous morphology with pellets and loose mycelia present simultaneously. In contrast to the non-supplemented control, the morphology of (NH4)2SO4-supplemented cultures was characterized by smaller and circular pellets that were more stable against disintegration in the stationary production phase.
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Affiliation(s)
- Sebastian Tesche
- Institute of Biochemical Engineering Technische Universität Braunschweig Braunschweig Germany.,Center of Pharmaceutical Engineering (PVZ) Technische Universität Braunschweig Braunschweig Germany
| | - René Rösemeier-Scheumann
- Institute of Biochemical Engineering Technische Universität Braunschweig Braunschweig Germany.,Center of Pharmaceutical Engineering (PVZ) Technische Universität Braunschweig Braunschweig Germany
| | - Jonas Lohr
- Institute of Biochemical Engineering Technische Universität Braunschweig Braunschweig Germany.,Center of Pharmaceutical Engineering (PVZ) Technische Universität Braunschweig Braunschweig Germany
| | - René Hanke
- AVT - Chair of Biochemical Engineering RWTH Aachen University Aachen Germany
| | - Jochen Büchs
- AVT - Chair of Biochemical Engineering RWTH Aachen University Aachen Germany
| | - Rainer Krull
- Institute of Biochemical Engineering Technische Universität Braunschweig Braunschweig Germany.,Center of Pharmaceutical Engineering (PVZ) Technische Universität Braunschweig Braunschweig Germany
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12
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Jansen RP, Beuck C, Moch M, Klein B, Küsters K, Morschett H, Wiechert W, Oldiges M. A closer look at Aspergillus: online monitoring via scattered light enables reproducible phenotyping. Fungal Biol Biotechnol 2019; 6:11. [PMID: 31396392 PMCID: PMC6681481 DOI: 10.1186/s40694-019-0073-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 07/17/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Filamentously growing microorganisms offer unique advantages for biotechnological processes, such as extraordinary secretion capacities, going along with multiple obstacles due to their complex morphology. However, limited experimental throughput in bioprocess development still hampers taking advantage of their full potential. Miniaturization and automation are powerful tools to accelerate bioprocess development, but so far the application of such technologies has mainly been focused on non-filamentous systems. During cultivation, filamentous fungi can undergo remarkable morphological changes, creating challenging cultivation conditions. Depending on the process and product, only one specific state of morphology may be advantageous to achieve e.g. optimal productivity or yield. Different approaches to control morphology have been investigated, such as microparticle enhanced cultivation. However, the addition of solid microparticles impedes the optical measurements typically used by microbioreactor systems and thus alternatives are needed. RESULTS Aspergillus giganteus IfGB 0902 was used as a model system to develop a time-efficient and robust workflow allowing microscale cultivation with increased throughput. The effect of microtiter plate geometry, shaking frequency and medium additives (talc and calcium chloride) on homogeneity of culture morphology as well as reproducibility were analyzed via online biomass measurement, microscopic imaging and cell dry weight. While addition of talc severely affected online measurements, 2% (w v-1) calcium chloride was successfully applied to obtain a highly reproducible growth behavior with homogenous morphology. Furthermore, the influence of small amounts of complex components was investigated for the applied model strain. By correlation to cell dry weight, it could be shown that optical measurements are a suitable signal for biomass concentration. However, each correlation is only applicable for a specific set of cultivation parameters. These optimized conditions were used in micro as well as lab-scale bioreactor cultivation in order to verify the reproducibility and scalability of the setup. CONCLUSION A robust workflow for A. giganteus was developed, allowing for reproducible microscale cultivation with online monitoring, where calcium chloride is an useful alternative to microparticle enhanced cultivation in order to control the morphology. Independent of the cultivation volume, comparable phenotypes were observed in microtiter plates and in lab-scale bioreactor.
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Affiliation(s)
- Roman P. Jansen
- Forschungszentrum Jülich, Institute of Bio- and Geosciences-Biotechnology (IBG-1), Jülich, Germany
| | - Carina Beuck
- Forschungszentrum Jülich, Institute of Bio- and Geosciences-Biotechnology (IBG-1), Jülich, Germany
| | - Matthias Moch
- Forschungszentrum Jülich, Institute of Bio- and Geosciences-Biotechnology (IBG-1), Jülich, Germany
| | - Bianca Klein
- Forschungszentrum Jülich, Institute of Bio- and Geosciences-Biotechnology (IBG-1), Jülich, Germany
| | - Kira Küsters
- Forschungszentrum Jülich, Institute of Bio- and Geosciences-Biotechnology (IBG-1), Jülich, Germany
| | - Holger Morschett
- Forschungszentrum Jülich, Institute of Bio- and Geosciences-Biotechnology (IBG-1), Jülich, Germany
| | - Wolfgang Wiechert
- Forschungszentrum Jülich, Institute of Bio- and Geosciences-Biotechnology (IBG-1), Jülich, Germany
- Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, Aachen, Germany
| | - Marco Oldiges
- Forschungszentrum Jülich, Institute of Bio- and Geosciences-Biotechnology (IBG-1), Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
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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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Cairns TC, Nai C, Meyer V. How a fungus shapes biotechnology: 100 years of Aspergillus niger research. Fungal Biol Biotechnol 2018; 5:13. [PMID: 29850025 PMCID: PMC5966904 DOI: 10.1186/s40694-018-0054-5] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/12/2018] [Indexed: 12/20/2022] Open
Abstract
In 1917, a food chemist named James Currie made a promising discovery: any strain of the filamentous mould Aspergillus niger would produce high concentrations of citric acid when grown in sugar medium. This tricarboxylic acid, which we now know is an intermediate of the Krebs cycle, had previously been extracted from citrus fruits for applications in food and beverage production. Two years after Currie’s discovery, industrial-level production using A. niger began, the biochemical fermentation industry started to flourish, and industrial biotechnology was born. A century later, citric acid production using this mould is a multi-billion dollar industry, with A. niger additionally producing a diverse range of proteins, enzymes and secondary metabolites. In this review, we assess main developments in the field of A. niger biology over the last 100 years and highlight scientific breakthroughs and discoveries which were influential for both basic and applied fungal research in and outside the A. niger community. We give special focus to two developments of the last decade: systems biology and genome editing. We also summarize the current international A. niger research community, and end by speculating on the future of fundamental research on this fascinating fungus and its exploitation in industrial biotechnology.
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Affiliation(s)
- Timothy C Cairns
- Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Corrado Nai
- Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Vera Meyer
- Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
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16
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Fiedler MRM, Cairns TC, Koch O, Kubisch C, Meyer V. Conditional Expression of the Small GTPase ArfA Impacts Secretion, Morphology, Growth, and Actin Ring Position in Aspergillus niger. Front Microbiol 2018; 9:878. [PMID: 29867795 PMCID: PMC5952172 DOI: 10.3389/fmicb.2018.00878] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 04/16/2018] [Indexed: 12/26/2022] Open
Abstract
In filamentous fungi, growth and protein secretion occurs predominantly at the tip of long, thread like cells termed hyphae. This requires coordinated regulation of multiple processes, including vesicle trafficking, exocytosis, and endocytosis, which are facilitated by a complex cytoskeletal apparatus. In this study, functional analyses of the small GTPase ArfA from Aspergillus niger demonstrate that this protein functionally complements the Saccharomyces cerevisiae ARF1/2, and that this protein is essential for A. niger. Loss-of-function and gain-of-function analyses demonstrate that titration of arfA expression impacts hyphal growth rate, hyphal tip morphology, and protein secretion. Moreover, localization of the endocytic machinery, visualized via fluorescent tagging of the actin ring, was found to be abnormal in ArfA under- and overexpressed conditions. Finally, we provide evidence that the major secreted protein GlaA localizes at septal junctions, indicating that secretion in A. niger may occur at these loci, and that this process is likely impacted by arfA expression levels. Taken together, our results demonstrate that ArfA fulfills multiple functions in the secretory pathway of A. niger.
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Affiliation(s)
- Markus R M Fiedler
- Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Timothy C Cairns
- Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Oliver Koch
- Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Christin Kubisch
- Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Vera Meyer
- Department of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
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17
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Huth I, Schrader J, Holtmann D. Microtiter plate-based cultivation to investigate the growth of filamentous fungi. Eng Life Sci 2017; 17:1064-1070. [PMID: 32624733 DOI: 10.1002/elsc.201700041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/19/2017] [Accepted: 06/06/2017] [Indexed: 11/09/2022] Open
Abstract
Microscale bioprocessing techniques are rapidly emerging as a means to increase the speed of bioprocess design and to reduce material consumption. However, there is still a lack of suitable parallelized techniques to investigate the industrially important group of filamentous bacteria and fungi. Cultivation of filamentous organisms in shake flasks is still the favored technique for comparing and optimizing cultivation conditions of production strains at mL-scale. In this paper, the application of a microtiter plate-based cultivation system in combination with the filamentous fungus Aspergillus niger was investigated. A protocol for reproducible cultivation was developed and evaluated. Productivity of A. niger concerning the rose-like aroma compound 2-phenylethanol showed low standard deviations while regular and consistent morphologies appeared in the parallelized system. Furthermore, the effect of addition of microparticles on the morphology was investigated. The results can be used to accelerate the process development with A. niger and other filamentous organisms.
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Affiliation(s)
- Ina Huth
- DECHEMA-Forschungsinstitut Frankfurt am Main Germany
| | - Jens Schrader
- DECHEMA-Forschungsinstitut Frankfurt am Main Germany
| | - Dirk Holtmann
- DECHEMA-Forschungsinstitut Frankfurt am Main Germany
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