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He S, Huang K, Li B, Lu G, Wang A. Functional Analysis of a Salicylate Hydroxylase in Sclerotinia sclerotiorum. J Fungi (Basel) 2023; 9:1169. [PMID: 38132770 PMCID: PMC10744347 DOI: 10.3390/jof9121169] [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: 10/21/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
Salicylic acid plays a crucial role during plant defense to Sclerotinia sclerotiorum. Some bacteria and a few fungi can produce salicylate hydroxylase to degrade SA to suppress plant defense and increase their virulence. But there has been no single salicylate hydroxylase in Sclerotinia sclerotiorum identified until now. In this study, we found that SS1G_02963 (SsShy1), among several predicted salicylate hydroxylases in S. sclerotiorum, was induced approximately 17.6-fold during infection, suggesting its potential role in virulence. SsShy1 could catalyze the conversion of SA to catechol when heterologous expression in E. coli. Moreover, overexpression of SsShy1 in Arabidopsis thaliana decreased the SA concentration and the resistance to S. sclerotiorum, confirming that SsShy1 is a salicylate hydroxylase. Deletion mutants of SsShy1 (∆Ssshy1) showed slower growth, less sclerotia production, more sensitivity to exogenous SA, and lower virulence to Brassica napus. The complemented strain with a functional SsShy1 gene recovered the wild-type phenotype. These results indicate that SsShy1 plays an important role in growth and sclerotia production of S. sclerotiorum, as well as the ability to metabolize SA affects the virulence of S. sclerotiorum.
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Affiliation(s)
- Shengfei He
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.H.); (K.H.); (B.L.); (G.L.)
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kun Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.H.); (K.H.); (B.L.); (G.L.)
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baoge Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.H.); (K.H.); (B.L.); (G.L.)
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.H.); (K.H.); (B.L.); (G.L.)
| | - Airong Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.H.); (K.H.); (B.L.); (G.L.)
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Sgro M, Chow N, Olyaei F, Arentshorst M, Geoffrion N, Ram AFJ, Powlowski J, Tsang A. Functional analysis of the protocatechuate branch of the β-ketoadipate pathway in Aspergillus niger. J Biol Chem 2023; 299:105003. [PMID: 37399977 PMCID: PMC10406623 DOI: 10.1016/j.jbc.2023.105003] [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: 02/06/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023] Open
Abstract
Bacteria and fungi catabolize plant-derived aromatic compounds by funneling into one of seven dihydroxylated aromatic intermediates, which then undergo ring fission and conversion to TCA cycle intermediates. Two of these intermediates, protocatechuic acid and catechol, converge on β-ketoadipate which is further cleaved to succinyl-CoA and acetyl-CoA. These β-ketoadipate pathways have been well characterized in bacteria. The corresponding knowledge of these pathways in fungi is incomplete. Characterization of these pathways in fungi would expand our knowledge and improve the valorization of lignin-derived compounds. Here, we used homology to characterize bacterial or fungal genes to predict the genes involved in the β-ketoadipate pathway for protocatechuate utilization in the filamentous fungus Aspergillus niger. We further used the following approaches to refine the assignment of the pathway genes: whole transcriptome sequencing to reveal genes upregulated in the presence of protocatechuic acid; deletion of candidate genes to observe their ability to grow on protocatechuic acid; determination by mass spectrometry of metabolites accumulated by deletion mutants; and enzyme assays of the recombinant proteins encoded by candidate genes. Based on the aggregate experimental evidence, we assigned the genes for the five pathway enzymes as follows: NRRL3_01405 (prcA) encodes protocatechuate 3,4-dioxygenase; NRRL3_02586 (cmcA) encodes 3-carboxy-cis,cis-muconate cyclase; NRRL3_01409 (chdA) encodes 3-carboxymuconolactone hydrolase/decarboxylase; NRRL3_01886 (kstA) encodes β-ketoadipate:succinyl-CoA transferase; and NRRL3_01526 (kctA) encodes β-ketoadipyl-CoA thiolase. Strain carrying ΔNRRL3_00837 could not grow on protocatechuic acid, suggesting that it is essential for protocatechuate catabolism. Its function is unknown as recombinant NRRL3_00837 did not affect the in vitro conversion of protocatechuic acid to β-ketoadipate.
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Affiliation(s)
- Michael Sgro
- Department of Biology, Concordia University, Montreal, Quebec, Canada; Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Nicholas Chow
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
| | - Farnaz Olyaei
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
| | - Mark Arentshorst
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, The Netherlands
| | - Nicholas Geoffrion
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Arthur F J Ram
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, The Netherlands
| | - Justin Powlowski
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada; Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
| | - Adrian Tsang
- Department of Biology, Concordia University, Montreal, Quebec, Canada; Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada.
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Hsu YS, Liu YH, Lin CH, Tsai CH, Wu WF. Dual bio-degradative pathways of di-2-ethylhexyl phthalate by a novel bacterium Burkholderia sp. SP4. World J Microbiol Biotechnol 2023; 39:44. [DOI: 10.1007/s11274-022-03490-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
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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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Ma Y, Jiang B, Liu K, Li R, Chen L, Liu Z, Xiang G, An J, Luo H, Wu J, Lv C, Pan Y, Ling T, Zhao M. Multi-omics analysis of the metabolism of phenolic compounds in tea leaves by Aspergillus luchuensis during fermentation of pu-erh tea. Food Res Int 2022; 162:111981. [DOI: 10.1016/j.foodres.2022.111981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/26/2022] [Accepted: 09/23/2022] [Indexed: 11/28/2022]
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Wang YS, Zheng W, Jiang N, Jin YX, Meng ZK, Sun MX, Zong YL, Xu T, Zhu J, Tan RX. Alteration of the Catalytic Reaction Trajectory of a Vicinal Oxygen Chelate Enzyme by Directed Evolution. Angew Chem Int Ed Engl 2022; 61:e202201321. [DOI: 10.1002/anie.202201321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Yi Shuang Wang
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Wan Zheng
- School of Medicine and Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Nan Jiang
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine School of Pharmacy Nanjing Medical University Nanjing 210023 China
| | - Yun Xia Jin
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Zi Kang Meng
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Meng Xin Sun
- School of Medicine and Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Yu Liang Zong
- School of Medicine and Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Tong Xu
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine School of Pharmacy Nanjing Medical University Nanjing 210023 China
| | - Jiapeng Zhu
- School of Medicine and Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Ren Xiang Tan
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy Nanjing University of Chinese Medicine Nanjing 210023 China
- State Key Laboratory of Pharmaceutical Biotechnology Institute of Functional Biomolecules School of Life Sciences Nanjing University Nanjing 210023 China
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Meier A, Worch S, Hartmann A, Marzec M, Mock HP, Bode R, Kunze G, Matthes F. Characterization of Catechol-1,2-Dioxygenase (Acdo1p) From Blastobotrys raffinosifermentans and Investigation of Its Role in the Catabolism of Aromatic Compounds. Front Microbiol 2022; 13:872298. [PMID: 35722288 PMCID: PMC9204233 DOI: 10.3389/fmicb.2022.872298] [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: 02/09/2022] [Accepted: 05/16/2022] [Indexed: 11/18/2022] Open
Abstract
Gallic acid, protocatechuic acid, catechol, and pyrogallol are only a few examples of industrially relevant aromatics. Today much attention is paid to the development of new microbial factories for the environmentally friendly biosynthesis of industrially relevant chemicals with renewable resources or organic pollutants as the starting material. The non–conventional yeast, Blastobotrys raffinosifermentans, possesses attractive properties for industrial bio-production processes such as thermo- and osmotolerance. An additional advantage is its broad substrate spectrum, with tannins at the forefront. The present study is dedicated to the characterization of catechol-1,2-dioxygenase (Acdo1p) and the analysis of its function in B. raffinosifermentans tannic acid catabolism. Acdo1p is a dimeric protein with higher affinity for catechol (KM = 0.004 ± 0.001 mM, kcat = 15.6 ± 0.4 s–1) than to pyrogallol (KM = 0.1 ± 0.02 mM, kcat = 10.6 ± 0.4 s–1). It is an intradiol dioxygenase and its reaction product with catechol as the substrate is cis,cis-muconic acid. B. raffinosifermentans G1212/YIC102-AYNI1-ACDO1-6H, which expresses the ACDO1 gene under the control of the strong nitrate-inducible AYNI1 promoter, achieved a maximum catechol-1,2-dioxygenase activity of 280.6 U/L and 26.9 U/g of dry cell weight in yeast grown in minimal medium with nitrate as the nitrogen source and 1.5% glucose as the carbon source. In the same medium with glucose as the carbon source, catechol-1,2-dioxygenase activity was not detected for the control strain G1212/YIC102 with ACDO1 expression under the regulation of its respective endogenous promoter. Gene expression analysis showed that ACDO1 is induced by gallic acid and protocatechuic acid. In contrast to the wild-type strain, the B. raffinosifermentans strain with a deletion of the ACDO1 gene was unable to grow on medium supplemented with gallic acid or protocatechuic acid as the sole carbon source. In summary, we propose that due to its substrate specificity, its thermal stability, and its ability to undergo long-term storage without significant loss of activity, B. raffinosifermentans catechol-1,2-dioxygenase (Acdo1p) is a promising enzyme candidate for industrial applications.
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Affiliation(s)
- Anna Meier
- Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Sebastian Worch
- Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Anja Hartmann
- Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Marek Marzec
- Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Hans-Peter Mock
- Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Rüdiger Bode
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Gotthard Kunze
- Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- *Correspondence: Gotthard Kunze,
| | - Falko Matthes
- Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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Wang YS, Zheng W, Jiang N, Jin YX, Meng ZK, Sun MX, Zong YL, Xu T, Zhu J, Tan RX. Alteration of the Catalytic Reaction Trajectory of a Vicinal Oxygen Chelate Enzyme by Directed Evolution. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yi Shuang Wang
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Wan Zheng
- School of Medicine and Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Nan Jiang
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine School of Pharmacy Nanjing Medical University Nanjing 210023 China
| | - Yun Xia Jin
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Zi Kang Meng
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Meng Xin Sun
- School of Medicine and Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Yu Liang Zong
- School of Medicine and Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Tong Xu
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine School of Pharmacy Nanjing Medical University Nanjing 210023 China
| | - Jiapeng Zhu
- School of Medicine and Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Ren Xiang Tan
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy Nanjing University of Chinese Medicine Nanjing 210023 China
- State Key Laboratory of Pharmaceutical Biotechnology Institute of Functional Biomolecules School of Life Sciences Nanjing University Nanjing 210023 China
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Ding Y, Gardiner DM, Kazan K. Transcriptome analysis reveals infection strategies employed by Fusarium graminearum as a root pathogen. Microbiol Res 2021; 256:126951. [PMID: 34972022 DOI: 10.1016/j.micres.2021.126951] [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: 03/09/2021] [Revised: 07/27/2021] [Accepted: 10/15/2021] [Indexed: 10/19/2022]
Abstract
The fungal pathogen Fusarium graminearum (Fg) infects both heads and roots of cereal crops causing several economically important diseases such as head blight, seedling blight, crown rot and root rot. Trichothecene mycotoxins such as deoxynivalenol (DON), a well-known virulence factor, produced by Fg during disease development is also an important health concern. Although how Fg infects above-ground tissues is relatively well studied, very little is known about molecular processes employed by the pathogen during below-ground infection. Also unknown is the role of DON during root infection. In the present study, we analyzed the transcriptome of Fg during root infection of the model cereal Brachypodium distachyon (Bd). We also compared our Fg transcriptome data obtained during Bd root infection with those reported during wheat head infection. These analyses suggested that both shared and unique infection strategies were employed by the pathogen during colonization of different host tissues. Several metabolite biosynthesis genes induced in Fg during root infection could be linked to phytohormone production, implying that the pathogen likely interferes with root specific defenses. In addition, to understand the role of DON in Fg root infection, we analyzed the transcriptome of the DON deficient Tri5 mutant. These analyses showed that the absence of DON had a significant effect on fungal transcriptional responses. Although DON was produced in infected roots, this mycotoxin did not act as a Fg virulence factor during root infection. Our results reveal new mechanistic insights into the below-ground strategies employed by Fg that may benefit the development of new genetic tools to combat this important cereal pathogen.
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Affiliation(s)
- Yi Ding
- The Plant Breeding Institute, School of Life & Environmental Sciences, Faculty of Science, The University of Sydney, Cobbitty, 2570, New South Wales, Australia; Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, 306 Carmody Road, St Lucia, 4067, Queensland, Australia.
| | - Donald M Gardiner
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, St Lucia, 4067, Queensland, Australia; Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, 306 Carmody Road, St Lucia, 4067, Queensland, Australia
| | - Kemal Kazan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, St Lucia, 4067, Queensland, Australia; Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, 306 Carmody Road, St Lucia, 4067, Queensland, Australia.
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Xu M, Zhang X, Yu J, Guo Z, Li Y, Song X, He K, Li G, Chi Y. Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in Aspergillus niger in Peanuts. Front Microbiol 2021; 12:719337. [PMID: 34489910 PMCID: PMC8418202 DOI: 10.3389/fmicb.2021.719337] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/30/2021] [Indexed: 01/10/2023] Open
Abstract
Aspergillus niger is a very destructive pathogen causing severe peanut root rot, especially in the seeding stage of peanuts (Arachis hypogaea), and often leading to the death of the plant. Protein lysine 2-hydroxyisobutyrylation (Khib) is a newly detected post-translational modification identified in several species. In this study, we identified 5041 Khib sites on 1,453 modified proteins in A. niger. Compared with five other species, A. niger has conserved and novel proteins. Bioinformatics analysis showed that Khib proteins are widely distributed in A. niger and are involved in many biological processes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that Khib proteins were significantly enriched in many cellular compartments and pathways, such as ribosomes and proteasome subunits. A total of 223 Khib proteins were part of the PPI network, thus, suggesting that Khib proteins are associated with a large range of protein interactions and diverse pathways in the life processes of A. niger. Several identified proteins are involved in pathogenesis regulation. Our research provides the first comprehensive report of Khib and an extensive database for potential functional studies on Khib proteins in this economically important fungus.
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Affiliation(s)
- Manlin Xu
- Shandong Peanut Research Institute, Qingdao, China
| | - Xia Zhang
- Shandong Peanut Research Institute, Qingdao, China
| | - Jing Yu
- Shandong Peanut Research Institute, Qingdao, China
| | - Zhiqing Guo
- Shandong Peanut Research Institute, Qingdao, China
| | - Ying Li
- Shandong Peanut Research Institute, Qingdao, China
| | - Xinying Song
- Shandong Peanut Research Institute, Qingdao, China
| | - Kang He
- Shandong Peanut Research Institute, Qingdao, China
| | - Guowei Li
- Institute of Crop Germplasm Resources, SAAS, Jinan, China
| | - Yucheng Chi
- Shandong Peanut Research Institute, Qingdao, China
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11
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Lubbers RJM, Dilokpimol A, Nousiainen PA, Cioc RC, Visser J, Bruijnincx PCA, de Vries RP. Vanillic acid and methoxyhydroquinone production from guaiacyl units and related aromatic compounds using Aspergillus niger cell factories. Microb Cell Fact 2021; 20:151. [PMID: 34344380 PMCID: PMC8336404 DOI: 10.1186/s12934-021-01643-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 07/22/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The aromatic compounds vanillin and vanillic acid are important fragrances used in the food, beverage, cosmetic and pharmaceutical industries. Currently, most aromatic compounds used in products are chemically synthesized, while only a small percentage is extracted from natural sources. The metabolism of vanillin and vanillic acid has been studied for decades in microorganisms and many studies have been conducted that showed that both can be produced from ferulic acid using bacteria. In contrast, the degradation of vanillin and vanillic acid by fungi is poorly studied and no genes involved in this metabolic pathway have been identified. In this study, we aimed to clarify this metabolic pathway in Aspergillus niger and identify the genes involved. RESULTS Using whole-genome transcriptome data, four genes involved in vanillin and vanillic acid metabolism were identified. These include vanillin dehydrogenase (vdhA), vanillic acid hydroxylase (vhyA), and two genes encoding novel enzymes, which function as methoxyhydroquinone 1,2-dioxygenase (mhdA) and 4-oxo-monomethyl adipate esterase (omeA). Deletion of these genes in A. niger confirmed their role in aromatic metabolism and the enzymatic activities of these enzymes were verified. In addition, we demonstrated that mhdA and vhyA deletion mutants can be used as fungal cell factories for the accumulation of vanillic acid and methoxyhydroquinone from guaiacyl lignin units and related aromatic compounds. CONCLUSIONS This study provides new insights into the fungal aromatic metabolic pathways involved in the degradation of guaiacyl units and related aromatic compounds. The identification of the involved genes unlocks new potential for engineering aromatic compound-producing fungal cell factories.
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Affiliation(s)
- Ronnie J M Lubbers
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Adiphol Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Paula A Nousiainen
- Department of Chemistry, University of Helsinki, A. I. Virtasen Aukio 1, P.O. Box 55, 00014, Helsinki, Finland
| | - Răzvan C Cioc
- Organic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Jaap Visser
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Pieter C A Bruijnincx
- Organic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands.
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Production of Protocatechuic Acid from p-Hydroxyphenyl (H) Units and Related Aromatic Compounds Using an Aspergillus niger Cell Factory. mBio 2021; 12:e0039121. [PMID: 34154420 PMCID: PMC8262893 DOI: 10.1128/mbio.00391-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Protocatechuic acid (3,4-dihydroxybenzoic acid) is a chemical building block for polymers and plastics. In addition, protocatechuic acid has many properties of great pharmaceutical interest. Much research has been performed in creating bacterial protocatechuic acid production strains, but no protocatechuic acid-producing fungal cell factories have been described. The filamentous fungus Aspergillus niger can produce protocatechuic acid as an intermediate of the benzoic acid metabolic pathway. Recently, the p-hydroxybenzoate-m-hydroxylase (phhA) and protocatechuate 3,4-dioxygenase (prcA) of A. niger have been identified. It has been shown that the prcA deletion mutant is still able to grow on protocatechuic acid. This led to the identification of an alternative pathway that converts protocatechuic acid to hydroxyquinol (1,3,4-trihydroxybenzene). However, the gene involved in the hydroxylation of protocatechuic acid to hydroxyquinol remained unidentified. Here, we describe the identification of protocatechuate hydroxylase (decarboxylating) (PhyA) by using whole-genome transcriptome data. The identification of phyA enabled the creation of a fungal cell factory that is able to accumulate protocatechuic acid from benzyl alcohol, benzaldehyde, benzoic acid, caffeic acid, cinnamic acid, cinnamyl alcohol, m-hydroxybenzoic acid, p-hydroxybenzyl alcohol, p-hydroxybenzaldehyde, p-hydroxybenzoic acid, p-anisyl alcohol, p-anisaldehyde, p-anisic acid, p-coumaric acid, and protocatechuic aldehyde. IMPORTANCE Aromatic compounds have broad applications and are used in many industries, such as the cosmetic, food, fragrance, paint, plastic, pharmaceutical, and polymer industries. The majority of aromatic compounds are synthesized from fossil sources, which are becoming limited. Plant biomass is the most abundant renewable resource on Earth and can be utilized to produce chemical building blocks, fuels, and bioplastics through fermentations with genetically modified microorganisms. Therefore, knowledge about the metabolic pathways and the genes and enzymes involved is essential to create efficient strategies for producing valuable aromatic compounds such as protocatechuic acid. Protocatechuic acid has many pharmaceutical properties but also can be used as a chemical building block to produce polymers and plastics. Here, we show that the fungus Aspergillus niger can be engineered to produce protocatechuic acid from plant-derived aromatic compounds and contributes to creating alternative methods for the production of platform chemicals. .
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Arentshorst M, Falco MD, Moisan MC, Reid ID, Spaapen TOM, van Dam J, Demirci E, Powlowski J, Punt PJ, Tsang A, Ram AFJ. Identification of a Conserved Transcriptional Activator-Repressor Module Controlling the Expression of Genes Involved in Tannic Acid Degradation and Gallic Acid Utilization in Aspergillus niger. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:681631. [PMID: 37744122 PMCID: PMC10512348 DOI: 10.3389/ffunb.2021.681631] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/23/2021] [Indexed: 09/26/2023]
Abstract
Tannic acid, a hydrolysable gallotannin present in plant tissues, consists of a central glucose molecule esterified with gallic acid molecules. Some microorganisms, including several Aspergillus species, can metabolize tannic acid by releasing gallic acid residues from tannic acid by secreting tannic acid specific esterases into the medium. The expression of these so-called tannases is induced by tannic acid or gallic acid. In this study, we identified a conserved transcriptional activator-repressor module involved in the regulation of predicted tannases and other genes involved in gallic acid metabolism. The transcriptional activator-repressor module regulating tannic acid utilization resembles the transcriptional activator-repressor modules regulating galacturonic acid and quinic acid utilization. Like these modules, the Zn(II)2Cys6 transcriptional activator (TanR) and the putative repressor (TanX) are located adjacent to each other. Deletion of the transcriptional activator (ΔtanR) results in inability to grow on gallic acid and severely reduces growth on tannic acid. Deletion of the putative repressor gene (ΔtanX) results in the constitutive expression of tannases as well as other genes with mostly unknown function. Known microbial catabolic pathways for gallic acid utilization involve so-called ring cleavage enzymes, and two of these ring cleavage enzymes show increased expression in the ΔtanX mutant. However, deletion of these two genes, and even deletion of all 17 genes encoding potential ring cleavage enzymes, did not result in a gallic acid non-utilizing phenotype. Therefore, in A. niger gallic acid utilization involves a hitherto unknown pathway. Transcriptome analysis of the ΔtanX mutant identified several genes and gene clusters that were significantly induced compared to the parental strain. The involvement of a selection of these genes and gene clusters in gallic acid utilization was examined by constructing gene deletion mutants and testing their ability to grow on gallic acid. Only the deletion of a gene encoding an FAD-dependent monooxygenase (NRRL3_04659) resulted in a strain that was unable to grow on gallic acid. Metabolomic studies showed accumulation of gallic acid in the ΔNRRL3_04659 mutant suggesting that this predicted monooxygenase is involved in the first step of gallic acid metabolism and is likely responsible for oxidation of the aromatic ring.
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Affiliation(s)
- Mark Arentshorst
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Marcos Di Falco
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Marie-Claude Moisan
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Ian D. Reid
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Tessa O. M. Spaapen
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Jisca van Dam
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Ebru Demirci
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Justin Powlowski
- Department of Chemistry & Biochemistry, Concordia University, Montreal, QC, Canada
| | - Peter J. Punt
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- Dutch DNA Biotech, Hugo R Kruytgebouw 4-Noord, Utrecht, Netherlands
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Arthur F. J. Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
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Lubbers RJM, Dilokpimol A, Visser J, de Vries RP. Aspergillus niger uses the peroxisomal CoA-dependent β-oxidative genes to degrade the hydroxycinnamic acids caffeic acid, ferulic acid, and p-coumaric acid. Appl Microbiol Biotechnol 2021; 105:4199-4211. [PMID: 33950281 PMCID: PMC8140964 DOI: 10.1007/s00253-021-11311-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/05/2021] [Accepted: 04/20/2021] [Indexed: 11/28/2022]
Abstract
Abstract Aromatic compounds are important molecules which are widely applied in many industries and are mainly produced from nonrenewable sources. Renewable sources such as plant biomass are interesting alternatives for the production of aromatic compounds. Ferulic acid and p-coumaric acid, a precursor for vanillin and p-vinyl phenol, respectively, can be released from plant biomass by the fungus Aspergillus niger. The degradation of hydroxycinnamic acids such as caffeic acid, ferulic acid, and p-coumaric acid has been observed in many fungi. In A. niger, multiple metabolic pathways were suggested for the degradation of hydroxycinnamic acids. However, no genes were identified for these hydroxycinnamic acid metabolic pathways. In this study, several pathway genes were identified using whole-genome transcriptomic data of A. niger grown on different hydroxycinnamic acids. The genes are involved in the CoA-dependent β-oxidative pathway in fungi. This pathway is well known for the degradation of fatty acids, but not for hydroxycinnamic acids. However, in plants, it has been shown that hydroxycinnamic acids are degraded through this pathway. We identified genes encoding hydroxycinnamate-CoA synthase (hcsA), multifunctional β-oxidation hydratase/dehydrogenase (foxA), 3-ketoacyl CoA thiolase (katA), and four thioesterases (theA-D) of A. niger, which were highly induced by all three tested hydroxycinnamic acids. Deletion mutants revealed that these genes were indeed involved in the degradation of several hydroxycinnamic acids. In addition, foxA and theB are also involved in the degradation of fatty acids. HcsA, FoxA, and KatA contained a peroxisomal targeting signal and are therefore predicted to be localized in peroxisomes. Key points • Metabolism of hydroxycinnamic acid was investigated in Aspergillus niger • Using transcriptome data, multiple CoA-dependent β-oxidative genes were identified. • Both foxA and theB are involved in hydroxycinnamate but also fatty acid metabolism. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11311-0.
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Affiliation(s)
- R J M Lubbers
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - A Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - J Visser
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - R P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.
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