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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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Zhuo R, Chen Y, Xing M, Zhang Z, Tian S, Li B. Ena Proteins Respond to PacC-Mediated pH Signaling Pathway and Play a Crucial Role in Patulin Biosynthesis. J Fungi (Basel) 2023; 9:806. [PMID: 37623577 PMCID: PMC10455529 DOI: 10.3390/jof9080806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023] Open
Abstract
Penicillium expansum is a main producer of patulin that causes severe postharvest decay and food safety issues in the fruit industry. Development, pathogenicity, and patulin production of P. expansum are strongly influenced by the PacC-pH signaling pathway. Global transcription factor PacC regulates various fungal biological processes through a complicated molecular network. In the present study, three Ena family genes (PeEnas), PeEnaA, PeEnaB, and PeEnaC, as important downstream targets of PePacC, were identified in P. expansum. Deletion of PeEnaA, PeEnaB, and PeEnaC showed little effect on mycelial growth under alkaline or high salinity conditions, but double and triple deletion of these genes impaired the virulence of P. expansum on apple fruit. Notably, patulin biosynthesis of P. expansum was distinctly inhibited in the deletion mutants of PeEnas. PeEnas regulated expressions of the patulin gene cluster, AP1, CreA, Sge1, and Hog1 at the transcriptional level and played roles in maintaining membrane potential. Overexpression of PeEnaC in ΔPePacC restored the patulin production defect of ΔPePacC. Our results indicated that, as downstream targets of PePacC, the PeEna family proteins play a crucial role in patulin biosynthesis in P. expansum.
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Affiliation(s)
- Ruiling Zhuo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Mengyang Xing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhanquan Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Boqiang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture, Beijing 100093, China
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Ma J, Ma Y, Li Y, Sun Z, Sun X, Padmakumar V, Cheng Y, Zhu W. Characterization of feruloyl esterases from Pecoramyces sp. F1 and the synergistic effect in biomass degradation. World J Microbiol Biotechnol 2022; 39:17. [PMID: 36409385 DOI: 10.1007/s11274-022-03466-3] [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: 06/01/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022]
Abstract
Feruloyl esterase (FAE; EC 3.1.1.73) cleaves the ester bond between ferulic acid (FA) and sugar, to assist the release of FAs and degradation of plant cell walls. In this study, two FAEs (Fae13961 and Fae16537) from the anaerobic fungus Pecoramyces sp. F1 were heterologously expressed in Pichia pastoris (P. pastoris). Compared with Fae16537, Fae13961 had higher catalytic efficiency. The optimum temperature and pH of both the FAEs were 45 ℃ and 7.0, respectively. They showed good stability-Fae16537 retained up to 80% activity after incubation at 37 ℃ for 24 h. The FAEs activity was enhanced by Ca2+ and reduced by Zn2+, Mn2+, Fe2+ and Fe3+. Additionally, the effect of FAEs on the hydrolytic efficiency of xylanase and cellulase was also determined. The FAE Fae13961 had synergistic effect with xylanase and it promoted the degradation of xylan substrates by xylanase, but it did not affect the degradation of cellulose substrates by cellulase. When Fae13961 was added in a mixture of xylanase and cellulase to degrade complex agricultural biomass, it significantly enhanced the mixture's ability to disintegrate complex substrates. These FAEs could serve as superior auxiliary enzymes for other lignocellulosic enzymes in the process of degradation of agricultural residues for industrial applications.
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Affiliation(s)
- Jing Ma
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuping Ma
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhanying Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoni Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | | | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
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Arentshorst M, Reijngoud J, van Tol DJC, Reid ID, Arendsen Y, Pel HJ, van Peij NNME, Visser J, Punt PJ, Tsang A, Ram AFJ. Utilization of ferulic acid in Aspergillus niger requires the transcription factor FarA and a newly identified Far-like protein (FarD) that lacks the canonical Zn(II) 2Cys 6 domain. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:978845. [PMID: 37746181 PMCID: PMC10512302 DOI: 10.3389/ffunb.2022.978845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 10/17/2022] [Indexed: 09/26/2023]
Abstract
The feruloyl esterase B gene (faeB) is specifically induced by hydroxycinnamic acids (e.g. ferulic acid, caffeic acid and coumaric acid) but the transcriptional regulation network involved in faeB induction and ferulic acid metabolism has only been partially addressed. To identify transcription factors involved in ferulic acid metabolism we constructed and screened a transcription factor knockout library of 239 Aspergillus niger strains for mutants unable to utilize ferulic acid as a carbon source. The ΔfarA transcription factor mutant, already known to be involved in fatty acid metabolism, could not utilize ferulic acid and other hydroxycinnamic acids. In addition to screening the transcription factor mutant collection, a forward genetic screen was performed to isolate mutants unable to express faeB. For this screen a PfaeB-amdS and PfaeB-lux613 dual reporter strain was engineered. The rationale of the screen is that in this reporter strain ferulic acid induces amdS (acetamidase) expression via the faeB promoter resulting in lethality on fluoro-acetamide. Conidia of this reporter strain were UV-mutagenized and plated on fluoro-acetamide medium in the presence of ferulic acid. Mutants unable to induce faeB are expected to be fluoro-acetamide resistant and can be positively selected for. Using this screen, six fluoro-acetamide resistant mutants were obtained and phenotypically characterized. Three mutants had a phenotype identical to the farA mutant and sequencing the farA gene in these mutants indeed showed mutations in FarA which resulted in inability to growth on ferulic acid as well as on short and long chain fatty acids. The growth phenotype of the other three mutants was similar to the farA mutants in terms of the inability to grow on ferulic acid, but these mutants grew normally on short and long chain fatty acids. The genomes of these three mutants were sequenced and allelic mutations in one particular gene (NRRL3_09145) were found. The protein encoded by NRRL3_09145 shows similarity to the FarA and FarB transcription factors. However, whereas FarA and FarB contain both the Zn(II)2Cys6 domain and a fungal-specific transcription factor domain, the protein encoded by NRRL3_09145 (FarD) lacks the canonical Zn(II)2Cys6 domain and possesses only the fungal specific transcription factor domain.
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Affiliation(s)
- Mark Arentshorst
- Microbial Sciences, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Jos Reijngoud
- Microbial Sciences, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Daan J. C. van Tol
- Microbial Sciences, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Ian D. Reid
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Yvonne Arendsen
- DSM Biosciences and Process Innovation, Center for Biotech Innovation, Delft, Netherlands
| | - Herman J. Pel
- DSM Biosciences and Process Innovation, Center for Biotech Innovation, Delft, Netherlands
| | | | - Jaap Visser
- Microbial Sciences, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- Fungal Genetics and Technology Consultancy, Wageningen, AJ, Netherlands
| | - Peter J. Punt
- Microbial Sciences, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Arthur F. J. Ram
- Microbial Sciences, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
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