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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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Kaimenyi D, Rij M, Wendland J. Improved gene-targeting efficiency upon starvation in Saccharomycopsis. Fungal Genet Biol 2023; 167:103809. [PMID: 37169215 DOI: 10.1016/j.fgb.2023.103809] [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: 03/24/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
Commonly used fungal transformation protocols rely on the use of either electroporation or the lithium acetate/single strand carrier DNA/Polyethylene glycol/heat shock method. We have used the latter method previously in establishing DNA-mediated transformation in Saccharomycopsis schoenii, a CTG-clade yeast that exhibits necrotrophic mycoparasitism. To elucidate the molecular mechanisms of predation by Saccharomycopsis we aim at gene-function analyses to identify virulence-related pathways and genes. However, in spite of a satisfactory transformation efficiency our efforts were crippled by high frequency of ectopic integration of disruption cassettes. Here, we show that overnight starvation of S. schoenii cells, while reducing the number of transformants, resulted in a substantial increase in gene-targeting via homologous recombination. To demonstrate this, we have deleted the S. schoenii CHS1, HIS3 and LEU2 genes and determined the required size of the flanking homology regions. Additionally, we complemented the S. schoenii leu2 mutant with heterologous LEU2 gene from Saccharomycopsis fermentans. To demonstrate the usefulness of our approach we also generated a S. fermentans leu2 strain, suggesting that this approach may have broader applicability.
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Affiliation(s)
- Davies Kaimenyi
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse, 1, 65366 Geisenheim, Germany
| | - Mareike Rij
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse, 1, 65366 Geisenheim, Germany
| | - Jürgen Wendland
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse, 1, 65366 Geisenheim, Germany; Geisenheim Yeast Breeding Center, Hochschule Geisenheim University, Von-Lade-Strasse, 1, 65366 Geisenheim, Germany.
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Cairns T, Zheng X, Feurstein C, Zheng P, Sun J, Meyer V. Quantitative phenotypic screens of Aspergillus niger mutants in solid and liquid culture. STAR Protoc 2022; 3:101883. [PMID: 36595891 PMCID: PMC9706620 DOI: 10.1016/j.xpro.2022.101883] [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: 09/08/2022] [Revised: 10/08/2022] [Accepted: 11/03/2022] [Indexed: 11/27/2022] Open
Abstract
This protocol describes procedures for quantifying Aspergillus niger growth in both solid and liquid culture. Firstly, by comparing radial growth between mutant and progenitor isolates on solid agar supplemented with sublethal stressors, susceptibility coefficients can be calculated. Secondly, analysis of macromorphological growth types in liquid culture allows full quantification of how a gene of interest affects submerged growth. By combining these assays, an extensive and quantitative dataset of how a gene of interest impacts growth in this fungus is possible. For complete details on the use and execution of this protocol, please refer to Cairns et al. (2019)1 and Cairns et al. (2022).2.
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Affiliation(s)
- Timothy Cairns
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, 10263 Berlin, Germany,Tianjin Institute of Industrial 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,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Claudia Feurstein
- 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
| | - 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
| | - Vera Meyer
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, 10263 Berlin, Germany,Corresponding author
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