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Theobald S, Vesth TC, Geib E, Nybo JL, Frisvad JC, Larsen TO, Kuo A, LaButti K, Lyhne EK, Kjærbølling I, Ledsgaard L, Barry K, Clum A, Chen C, Nolan M, Sandor L, Lipzen A, Mondo S, Pangilinan J, Salamov A, Riley R, Wiebenga A, Müller A, Kun RS, dos Santos Gomes AC, Henrissat B, Magnuson JK, Simmons BA, Mäkelä MR, Mortensen UH, Grigoriev IV, Brock M, Baker SE, de Vries RP, Andersen MR. Genomic Analysis of Aspergillus Section Terrei Reveals a High Potential in Secondary Metabolite Production and Plant Biomass Degradation. J Fungi (Basel) 2024; 10:507. [PMID: 39057392 PMCID: PMC11278011 DOI: 10.3390/jof10070507] [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: 06/11/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Aspergillus terreus has attracted interest due to its application in industrial biotechnology, particularly for the production of itaconic acid and bioactive secondary metabolites. As related species also seem to possess a prosperous secondary metabolism, they are of high interest for genome mining and exploitation. Here, we present draft genome sequences for six species from Aspergillus section Terrei and one species from Aspergillus section Nidulantes. Whole-genome phylogeny confirmed that section Terrei is monophyletic. Genome analyses identified between 70 and 108 key secondary metabolism genes in each of the genomes of section Terrei, the highest rate found in the genus Aspergillus so far. The respective enzymes fall into 167 distinct families with most of them corresponding to potentially unique compounds or compound families. Moreover, 53% of the families were only found in a single species, which supports the suitability of species from section Terrei for further genome mining. Intriguingly, this analysis, combined with heterologous gene expression and metabolite identification, suggested that species from section Terrei use a strategy for UV protection different to other species from the genus Aspergillus. Section Terrei contains a complete plant polysaccharide degrading potential and an even higher cellulolytic potential than other Aspergilli, possibly facilitating additional applications for these species in biotechnology.
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Affiliation(s)
- Sebastian Theobald
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
| | - Tammi C. Vesth
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
| | - Elena Geib
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (E.G.); (M.B.)
| | - Jane L. Nybo
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
| | - Jens C. Frisvad
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
| | - Thomas O. Larsen
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Ellen K. Lyhne
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
| | - Inge Kjærbølling
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
| | - Line Ledsgaard
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Cindy Chen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Matt Nolan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Laura Sandor
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Stephen Mondo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, 3584 Utrecht, The Netherlands; (A.W.); (A.M.); (R.S.K.); (A.C.d.S.G.)
| | - Astrid Müller
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, 3584 Utrecht, The Netherlands; (A.W.); (A.M.); (R.S.K.); (A.C.d.S.G.)
| | - Roland S. Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, 3584 Utrecht, The Netherlands; (A.W.); (A.M.); (R.S.K.); (A.C.d.S.G.)
| | - Ana Carolina dos Santos Gomes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, 3584 Utrecht, The Netherlands; (A.W.); (A.M.); (R.S.K.); (A.C.d.S.G.)
| | - Bernard Henrissat
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jon K. Magnuson
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (J.K.M.); (B.A.S.)
- US Department of Energy Joint Bioenergy Institute, 5885 Hollis St., Emeryville, CA 94608, USA
| | - Blake A. Simmons
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (J.K.M.); (B.A.S.)
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Miia R. Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland;
| | - Uffe H. Mortensen
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Matthias Brock
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (E.G.); (M.B.)
| | - Scott E. Baker
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (J.K.M.); (B.A.S.)
- US Department of Energy Joint Bioenergy Institute, 5885 Hollis St., Emeryville, CA 94608, USA
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, 3584 Utrecht, The Netherlands; (A.W.); (A.M.); (R.S.K.); (A.C.d.S.G.)
| | - Mikael R. Andersen
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
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Yun EJ, Lee SH, Kim S, Ryu HS, Kim KH. Catabolism of 2-keto-3-deoxy-galactonate and the production of its enantiomers. Appl Microbiol Biotechnol 2024; 108:403. [PMID: 38954014 PMCID: PMC11219438 DOI: 10.1007/s00253-024-13235-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024]
Abstract
2-Keto-3-deoxy-galactonate (KDGal) serves as a pivotal metabolic intermediate within both the fungal D-galacturonate pathway, which is integral to pectin catabolism, and the bacterial DeLey-Doudoroff pathway for D-galactose catabolism. The presence of KDGal enantiomers, L-KDGal and D-KDGal, varies across these pathways. Fungal pathways generate L-KDGal through the reduction and dehydration of D-galacturonate, whereas bacterial pathways produce D-KDGal through the oxidation and dehydration of D-galactose. Two distinct catabolic routes further metabolize KDGal: a nonphosphorolytic pathway that employs aldolase and a phosphorolytic pathway involving kinase and aldolase. Recent findings have revealed that L-KDGal, identified in the bacterial catabolism of 3,6-anhydro-L-galactose, a major component of red seaweeds, is also catabolized by Escherichia coli, which is traditionally known to be catabolized by specific fungal species, such as Trichoderma reesei. Furthermore, the potential industrial applications of KDGal and its derivatives, such as pyruvate and D- and L-glyceraldehyde, are underscored by their significant biological functions. This review comprehensively outlines the catabolism of L-KDGal and D-KDGal across different biological systems, highlights stereospecific methods for discriminating between enantiomers, and explores industrial application prospects for producing KDGal enantiomers. KEY POINTS: • KDGal is a metabolic intermediate in fungal and bacterial pathways • Stereospecific enzymes can be used to identify the enantiomeric nature of KDGal • KDGal can be used to induce pectin catabolism or produce functional materials.
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Affiliation(s)
- Eun Ju Yun
- Division of Biotechnology, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Sun-Hee Lee
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, Republic of Korea
| | - Subin Kim
- Division of Biotechnology, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Hae Seul Ryu
- Division of Biotechnology, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, Republic of Korea.
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Xu L, Li J, Gonzalez Ramos VM, Lyra C, Wiebenga A, Grigoriev IV, de Vries RP, Mäkelä MR, Peng M. Genome-wide prediction and transcriptome analysis of sugar transporters in four ascomycete fungi. BIORESOURCE TECHNOLOGY 2024; 391:130006. [PMID: 37952592 DOI: 10.1016/j.biortech.2023.130006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
The import of plant-derived small sugars by sugar transporters (STs) has received increasing interest due to its important biological role and great industrial potential. STs are important targets of genetic engineering to improve fungal plant biomass conversion. Comparatively analysis of the genome-wide prevalence and transcriptomics of STs was performed in four filamentous fungi: Aspergillus niger, Aspergillus nidulans, Penicillium subrubescens and Trichoderma reesei. Using phylogenetic analysis and literature mining, their predicted STs were divided into ten subfamilies with putative sugar specificities assigned. In addition, transcriptome analysis revealed complex expression profiles among different STs subfamilies and fungal species, indicating a sophisticated transcriptome regulation and functional diversity of fungal STs. Several STs showed strong co-expression with other genes involved in sugar utilization, encoding CAZymes and sugar catabolic enzymes. This study provides new insights into the diversity of STs at the genomic/transcriptomic level, facilitating their biochemical characterization and metabolic engineering.
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Affiliation(s)
- Li Xu
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
| | - Jiajia Li
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
| | | | - Christina Lyra
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland.
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - 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 94720, USA.
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland.
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
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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, Wiebenga A, Lipzen A, Ng V, Tejomurthula S, Zhang Y, Grigoriev IV, Peng M, de Vries RP. Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi. J Fungi (Basel) 2023; 9:860. [PMID: 37623631 PMCID: PMC10455118 DOI: 10.3390/jof9080860] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
Plant biomass is one of the most abundant renewable carbon sources, which holds great potential for replacing current fossil-based production of fuels and chemicals. In nature, fungi can efficiently degrade plant polysaccharides by secreting a broad range of carbohydrate-active enzymes (CAZymes), such as cellulases, hemicellulases, and pectinases. Due to the crucial role of plant biomass-degrading (PBD) CAZymes in fungal growth and related biotechnology applications, investigation of their genomic diversity and transcriptional dynamics has attracted increasing attention. In this project, we systematically compared the genome content of PBD CAZymes in six taxonomically distant species, Aspergillus niger, Aspergillus nidulans, Penicillium subrubescens, Trichoderma reesei, Phanerochaete chrysosporium, and Dichomitus squalens, as well as their transcriptome profiles during growth on nine monosaccharides. Considerable genomic variation and remarkable transcriptomic diversity of CAZymes were identified, implying the preferred carbon source of these fungi and their different methods of transcription regulation. In addition, the specific carbon utilization ability inferred from genomics and transcriptomics was compared with fungal growth profiles on corresponding sugars, to improve our understanding of the conversion process. This study enhances our understanding of genomic and transcriptomic diversity of fungal plant polysaccharide-degrading enzymes and provides new insights into designing enzyme mixtures and metabolic engineering of fungi for related industrial applications.
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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; (J.L.); (M.P.)
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (J.L.); (M.P.)
| | - Anna Lipzen
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA; (A.L.); (V.N.); (S.T.); (Y.Z.); (I.V.G.)
| | - Vivian Ng
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA; (A.L.); (V.N.); (S.T.); (Y.Z.); (I.V.G.)
| | - Sravanthi Tejomurthula
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA; (A.L.); (V.N.); (S.T.); (Y.Z.); (I.V.G.)
| | - Yu Zhang
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA; (A.L.); (V.N.); (S.T.); (Y.Z.); (I.V.G.)
| | - Igor V. Grigoriev
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA; (A.L.); (V.N.); (S.T.); (Y.Z.); (I.V.G.)
- Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (J.L.); (M.P.)
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (J.L.); (M.P.)
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Tomazeli EC, Alfaro M, Zambonelli A, Garde E, Pérez G, Jiménez I, Ramírez L, Salman H, Pisabarro AG. Transcriptome Metabolic Characterization of Tuber borchii SP1-A New Spanish Strain for In Vitro Studies of the Bianchetto Truffle. Int J Mol Sci 2023; 24:10981. [PMID: 37446159 DOI: 10.3390/ijms241310981] [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: 04/22/2023] [Revised: 06/16/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Truffles are ascomycete hypogeous fungi belonging to the Tuberaceae family of the Pezizales order that grow in ectomycorrhizal symbiosis with tree roots, and they are known for their peculiar aromas and flavors. The axenic culture of truffle mycelium is problematic because it is not possible in many cases, and the growth rate is meager when it is possible. This limitation has prompted searching and characterizing new strains that can be handled in laboratory conditions for basic and applied studies. In this work, a new strain of Tuber borchii (strain SP1) was isolated and cultured, and its transcriptome was analyzed under different in vitro culture conditions. The results showed that the highest growth of T. borchii SP1 was obtained using maltose-enriched cultures made with soft-agar and in static submerged cultures made at 22 °C. We analyzed the transcriptome of this strain cultured in different media to establish a framework for future comparative studies, paying particular attention to the central metabolic pathways, principal secondary metabolite gene clusters, and the genes involved in producing volatile aromatic compounds (VOCs). The results showed a transcription signal for around 80% of the annotated genes. In contrast, most of the transcription effort was concentrated on a limited number of genes (20% of genes account for 80% of the transcription), and the transcription profile of the central metabolism genes was similar in the different conditions analyzed. The gene expression profile suggests that T. borchii uses fermentative rather than respiratory metabolism in these cultures, even in aerobic conditions. Finally, there was a reduced expression of genes belonging to secondary metabolite clusters, whereas there was a significative transcription of those involved in producing volatile aromatic compounds.
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Affiliation(s)
- Emilia Chuina Tomazeli
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006 Pamplona, Spain
- Bionanoplus, 31194 Oricain, Spain
| | - Manuel Alfaro
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006 Pamplona, Spain
| | - Alessandra Zambonelli
- Department of Agro-Food Sciences and Technologies, University of Bologna (UNIBO), 40126 Bologna, Italy
| | - Edurne Garde
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006 Pamplona, Spain
| | - Gumer Pérez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006 Pamplona, Spain
| | - Idoia Jiménez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006 Pamplona, Spain
| | - Lucía Ramírez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006 Pamplona, Spain
| | | | - Antonio G Pisabarro
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006 Pamplona, Spain
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Wang Z, Kim W, Wang YW, Yakubovich E, Dong C, Trail F, Townsend JP, Yarden O. The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1214537. [PMID: 37746130 PMCID: PMC10512317 DOI: 10.3389/ffunb.2023.1214537] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/06/2023] [Indexed: 09/26/2023]
Abstract
Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera Fusarium, Neurospora, and Trichoderma are present. In this review, we examine recently published studies and data on the Sordariomycetes that have contributed novel insights to the field of fungal evolution via integrative analyses of the genetic, pathogenic, and other biological characteristics of the fungi. Some of these studies applied ancestral state analysis of gene expression among divergent lineages to infer regulatory network models, identify key genetic elements in fungal sexual development, and investigate the regulation of conidial germination and secondary metabolism. Such multispecies investigations address challenges in the study of fungal evolutionary genomics derived from studies that are often based on limited model genomes and that primarily focus on the aspects of biology driven by knowledge drawn from a few model species. Rapidly accumulating information and expanding capabilities for systems biological analysis of Big Data are setting the stage for the expansion of the concept of model systems from unitary taxonomic species/genera to inclusive clusters of well-studied models that can facilitate both the in-depth study of specific lineages and also investigation of trait diversity across lineages. The Sordariomycetes class, in particular, offers abundant omics data and a large and active global research community. As such, the Sordariomycetes can form a core omics clade, providing a blueprint for the expansion of our knowledge of evolution at the genomic scale in the exciting era of Big Data and artificial intelligence, and serving as a reference for the future analysis of different taxonomic levels within the fungal kingdom.
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Affiliation(s)
- Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Republic of Korea
| | - Yen-Wen Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Elizabeta Yakubovich
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Caihong Dong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Frances Trail
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
- Department of Ecology and Evolutionary Biology, Program in Microbiology, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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