Genome-wide prediction and transcriptome analysis of sugar transporters in four ascomycete fungi

Li Xu; Jiajia Li; Victor M Gonzalez Ramos; Christina Lyra; Ad Wiebenga; Igor V Grigoriev; Ronald P de Vries; Miia R Mäkelä; Mao Peng

doi:10.1016/j.biortech.2023.130006

Genome-wide prediction and transcriptome analysis of sugar transporters in four ascomycete fungi

Bioresour Technol. 2024 Jan;391(Pt B):130006. doi: 10.1016/j.biortech.2023.130006. Epub 2023 Nov 10.

Authors

Li Xu¹, Jiajia Li², Victor M Gonzalez Ramos³, Christina Lyra⁴, Ad Wiebenga⁵, Igor V Grigoriev⁶, Ronald P de Vries⁷, Miia R Mäkelä⁸, Mao Peng⁹

Affiliations

¹ Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands. Electronic address: l.xu@wi.knaw.nl.
² Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands. Electronic address: j.li@wi.knaw.nl.
³ Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland. Electronic address: victor.gonzalez@helsinki.fi.
⁴ Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland. Electronic address: christina.lyra@helsinki.fi.
⁵ Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
⁶ 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. Electronic address: ivgrigoriev@lbl.gov.
⁷ Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands. Electronic address: r.devries@wi.knaw.nl.
⁸ Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland. Electronic address: miia.r.makela@helsinki.fi.
⁹ Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands. Electronic address: m.peng@wi.knaw.nl.

PMID: 37952592
DOI: 10.1016/j.biortech.2023.130006

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.

Keywords: Fungi; Genome; Prediction; Sugar transporter; Transcriptome.

MeSH terms

Ascomycota* / metabolism
Fungal Proteins* / genetics
Fungal Proteins* / metabolism
Gene Expression Profiling
Phylogeny
Sugars
Transcriptome / genetics

Substances

Fungal Proteins
Sugars