Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose.

Autor: van Munster JM; 1School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK.; 2Manchester Institute of Biotechnology (MIB) & School of Chemistry, The University of Manchester, Manchester, M1 7DN UK., Daly P; 1School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK.; 3Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.; 11Present Address: Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China., Blythe MJ; 4Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK., Ibbett R; 5School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK., Kokolski M; 1School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK., Gaddipati S; 5School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK., Lindquist E; 6US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA., Singan VR; 6US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA., Barry KW; 6US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA., Lipzen A; 6US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA., Ngan CY; 6US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA., Petzold CJ; 7Joint BioEnergy Institute, Emeryville, CA 94608 USA., Chan LJG; 7Joint BioEnergy Institute, Emeryville, CA 94608 USA., Arvas M; 8VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 VTT Espoo, Finland., Raulo R; 1School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK., Pullan ST; 1School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK.; 9Present Address: Public Health England, National Infection Service, Salisbury, UK., Delmas S; 1School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK.; 10Present Address: Laboratory of Computational and Quantitative Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, 75005 Paris, France., Grigoriev IV; 6US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA., Tucker GA; 5School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK., Simmons BA; 7Joint BioEnergy Institute, Emeryville, CA 94608 USA., Archer DB; 1School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK.
Jazyk: angličtina
Zdroj: Biotechnology for biofuels [Biotechnol Biofuels] 2020 Apr 13; Vol. 13, pp. 69. Date of Electronic Publication: 2020 Apr 13 (Print Publication: 2020).
DOI: 10.1186/s13068-020-01702-2
Abstrakt: Background: Understanding how fungi degrade lignocellulose is a cornerstone of improving renewables-based biotechnology, in particular for the production of hydrolytic enzymes. Considerable progress has been made in investigating fungal degradation during time-points where CAZyme expression peaks. However, a robust understanding of the fungal survival strategies over its life time on lignocellulose is thereby missed. Here we aimed to uncover the physiological responses of the biotechnological workhorse and enzyme producer Aspergillus niger over its life time to six substrates important for biofuel production.
Results: We analysed the response of A. niger to the feedstock Miscanthus and compared it with our previous study on wheat straw, alone or in combination with hydrothermal or ionic liquid feedstock pretreatments. Conserved (substrate-independent) metabolic responses as well as those affected by pretreatment and feedstock were identified via multivariate analysis of genome-wide transcriptomics combined with targeted transcript and protein analyses and mapping to a metabolic model. Initial exposure to all substrates increased fatty acid beta-oxidation and lipid metabolism transcripts. In a strain carrying a deletion of the ortholog of the Aspergillus nidulans fatty acid beta-oxidation transcriptional regulator farA, there was a reduction in expression of selected lignocellulose degradative CAZyme-encoding genes suggesting that beta-oxidation contributes to adaptation to lignocellulose. Mannan degradation expression was wheat straw feedstock-dependent and pectin degradation was higher on the untreated substrates. In the later life stages, known and novel secondary metabolite gene clusters were activated, which are of high interest due to their potential to synthesize bioactive compounds.
Conclusion: In this study, which includes the first transcriptional response of Aspergilli to Miscanthus , we highlighted that life time as well as substrate composition and structure (via variations in pretreatment and feedstock) influence the fungal responses to lignocellulose. We also demonstrated that the fungal response contains physiological stages that are conserved across substrates and are typically found outside of the conditions with high CAZyme expression, as exemplified by the stages that are dominated by lipid and secondary metabolism.
Competing Interests: Competing interestsThe authors declare that they have no competing interests.
(© The Author(s) 2020.)
Databáze: MEDLINE
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