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Mueller A, Xu L, Heine C, Flach T, Mäkelä MR, de Vries RP. Genome Mining Reveals a Surprising Number of Sugar Reductases in Aspergillus niger. J Fungi (Basel) 2023; 9:1138. [PMID: 38132739 PMCID: PMC10744612 DOI: 10.3390/jof9121138] [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: 10/26/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023] Open
Abstract
Metabolic engineering of filamentous fungi has received increasing attention in recent years, especially in the context of creating better industrial fungal cell factories to produce a wide range of valuable enzymes and metabolites from plant biomass. Recent studies into the pentose catabolic pathway (PCP) in Aspergillus niger have revealed functional redundancy in most of the pathway steps. In this study, a closer examination of the A. niger genome revealed five additional paralogs for the three original pentose reductases (LarA, XyrA, XyrB). Analysis of these genes using phylogeny, in vitro and in vivo functional analysis of the enzymes, and gene expression revealed that all can functionally replace LarA, XyrA, and XyrB. However, they are also active on several other sugars, suggesting a role for them in other pathways. This study therefore reveals the diversity of primary carbon metabolism in fungi, suggesting an intricate evolutionary process that distinguishes different species. In addition, through this study, the metabolic toolkit for synthetic biology and metabolic engineering of A. niger and other fungal cell factories has been expanded.
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Affiliation(s)
- Astrid Mueller
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (A.M.); (L.X.); (C.H.); (T.F.)
| | - Li Xu
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (A.M.); (L.X.); (C.H.); (T.F.)
| | - Claudia Heine
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (A.M.); (L.X.); (C.H.); (T.F.)
| | - Tila Flach
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (A.M.); (L.X.); (C.H.); (T.F.)
| | - Miia R. Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland;
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (A.M.); (L.X.); (C.H.); (T.F.)
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Li J, Chroumpi T, Garrigues S, Kun RS, Meng J, Salazar-Cerezo S, Aguilar-Pontes MV, Zhang Y, Tejomurthula S, Lipzen A, Ng V, Clendinen CS, Tolić N, Grigoriev IV, Tsang A, Mäkelä MR, Snel B, Peng M, de Vries RP. The Sugar Metabolic Model of Aspergillus niger Can Only Be Reliably Transferred to Fungi of Its Phylum. J Fungi (Basel) 2022; 8:jof8121315. [PMID: 36547648 PMCID: PMC9781776 DOI: 10.3390/jof8121315] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Fungi play a critical role in the global carbon cycle by degrading plant polysaccharides to small sugars and metabolizing them as carbon and energy sources. We mapped the well-established sugar metabolic network of Aspergillus niger to five taxonomically distant species (Aspergillus nidulans, Penicillium subrubescens, Trichoderma reesei, Phanerochaete chrysosporium and Dichomitus squalens) using an orthology-based approach. The diversity of sugar metabolism correlates well with the taxonomic distance of the fungi. The pathways are highly conserved between the three studied Eurotiomycetes (A. niger, A. nidulans, P. subrubescens). A higher level of diversity was observed between the T. reesei and A. niger, and even more so for the two Basidiomycetes. These results were confirmed by integrative analysis of transcriptome, proteome and metabolome, as well as growth profiles of the fungi growing on the corresponding sugars. In conclusion, the establishment of sugar pathway models in different fungi revealed the diversity of fungal sugar conversion and provided a valuable resource for the community, which would facilitate rational metabolic engineering of these fungi as microbial cell factories.
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Affiliation(s)
- Jiajia Li
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Tania Chroumpi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Sandra Garrigues
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Roland S. Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Jiali Meng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Sonia Salazar-Cerezo
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | | | - Yu Zhang
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Sravanthi Tejomurthula
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Anna Lipzen
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Vivian Ng
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Chaevien S. Clendinen
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Nikola Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Igor V. Grigoriev
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94598, USA
| | - Adrian Tsang
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada
| | - Miia R. Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Correspondence:
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Meng J, Németh Z, Peng M, Fekete E, Garrigues S, Lipzen A, Ng V, Savage E, Zhang Y, Grigoriev IV, Mäkelä MR, Karaffa L, de Vries RP. GalR, GalX and AraR co-regulate d-galactose and l-arabinose utilization in Aspergillus nidulans. Microb Biotechnol 2022; 15:1839-1851. [PMID: 35213794 PMCID: PMC9151342 DOI: 10.1111/1751-7915.14025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 11/27/2022] Open
Abstract
Filamentous fungi produce a wide variety of enzymes in order to efficiently degrade plant cell wall polysaccharides. The production of these enzymes is controlled by transcriptional regulators, which also control the catabolic pathways that convert the released monosaccharides. Two transcriptional regulators, GalX and GalR, control d-galactose utilization in the model filamentous fungus Aspergillus nidulans, while the arabinanolytic regulator AraR regulates l-arabinose catabolism. d-Galactose and l-arabinose are commonly found together in polysaccharides, such as arabinogalactan, xylan and rhamnogalacturonan I. Therefore, the catabolic pathways that convert d-galactose and l-arabinose are often also likely to be active simultaneously. In this study, we investigated the interaction between GalX, GalR and AraR in d-galactose and l-arabinose catabolism. For this, we generated single, double and triple mutants of the three regulators, and analysed their growth and enzyme and gene expression profiles. Our results clearly demonstrated that GalX, GalR and AraR co-regulate d-galactose catabolism in A. nidulans. GalX has a prominent role on the regulation of genes of d-galactose oxido-reductive pathway, while AraR can compensate for the absence of GalR and/or GalX.
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Affiliation(s)
- Jiali Meng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Zoltán Németh
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1., Debrecen, H-4032, Hungary
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1., Debrecen, H-4032, Hungary
| | - Sandra Garrigues
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Vivian Ng
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Emily Savage
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Yu Zhang
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, 00790, Finland
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1., Debrecen, H-4032, Hungary.,Institute of Metagenomics, University of Debrecen, Egyetem tér 1., Debrecen, H-4032, Hungary
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
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Kun RS, Garrigues S, Di Falco M, Tsang A, de Vries RP. Blocking utilization of major plant biomass polysaccharides leads Aspergillus niger towards utilization of minor components. Microb Biotechnol 2021; 14:1683-1698. [PMID: 34114741 PMCID: PMC8313289 DOI: 10.1111/1751-7915.13835] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 11/28/2022] Open
Abstract
Fungi produce a wide range of enzymes that allow them to grow on diverse plant biomass. Wheat bran is a low-cost substrate with high potential for biotechnological applications. It mainly contains cellulose and (arabino)xylan, as well as starch, proteins, lipids and lignin to a lesser extent. In this study, we dissected the regulatory network governing wheat bran degradation in Aspergillus niger to assess the relative contribution of the regulators to the utilization of this plant biomass substrate. Deletion of genes encoding transcription factors involved in (hemi-)cellulose utilization (XlnR, AraR, ClrA and ClrB) individually and in combination significantly reduced production of polysaccharide-degrading enzymes, but retained substantial growth on wheat bran. Proteomic analysis suggested the ability of A. niger to grow on other carbon components, such as starch, which was confirmed by the additional deletion of the amylolytic regulator AmyR. Growth was further reduced but not impaired, indicating that other minor components provide sufficient energy for residual growth, displaying the flexibility of A. niger, and likely other fungi, in carbon utilization. Better understanding of the complexity and flexibility of fungal regulatory networks will facilitate the generation of more efficient fungal cell factories that use plant biomass as a substrate.
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Affiliation(s)
- Roland S. Kun
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
| | - Sandra Garrigues
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
| | - Marcos Di Falco
- Centre for Structural and Functional GenomicsConcordia University7141 Sherbrooke Street WestMontrealQCH4B 1R6Canada
| | - Adrian Tsang
- Centre for Structural and Functional GenomicsConcordia University7141 Sherbrooke Street WestMontrealQCH4B 1R6Canada
| | - Ronald P. de Vries
- Fungal PhysiologyWesterdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8Utrecht3584 CTThe Netherlands
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