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Glucose-lactose mixture feeds in industry-like conditions: a gene regulatory network analysis on the hyperproducing Trichoderma reesei strain Rut-C30

Aurélie Pirayre, View ORCID ProfileLaurent Duval, Corinne Blugeon, Cyril Firmo, Sandrine Perrin, Etienne Jourdier, Antoine Margeot, Frédérique Bidard
doi: https://doi.org/10.1101/2020.10.02.324319
Aurélie Pirayre
1IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau 92852 Rueil-Malmaison, France
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  • For correspondence: aurelie.pirayre@ifpen.fr
Laurent Duval
2ESIEE Paris, Université Paris-Est, Laboratoire d’Informatique Gaspard Monge (LIGM), 93162 Noisy-le-Grand, France
1IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau 92852 Rueil-Malmaison, France
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  • ORCID record for Laurent Duval
Corinne Blugeon
3Genomic facility, Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
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Cyril Firmo
3Genomic facility, Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
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Sandrine Perrin
3Genomic facility, Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
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Etienne Jourdier
1IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau 92852 Rueil-Malmaison, France
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Antoine Margeot
1IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau 92852 Rueil-Malmaison, France
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Frédérique Bidard
1IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau 92852 Rueil-Malmaison, France
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Abstract

Background The degradation of cellulose and hemicellulose molecules into simpler sugars such as glucose is part of the second generation biofuel production process. Hydrolysis of lignocellulosic substrates is usually performed by enzymes produced and secreted by the fungus Trichoderma reesei. Studies identifying transcription factors involved in the regulation of cellulase production have been conducted but no overview of the whole regulation network is available. A transcriptomic approach with mixtures of glucose and lactose, used as a substrate for cellulase induction, was used to help us decipher missing parts in the network.

Results Experimental results confirmed the impact of sugar mixture on the enzymatic cocktail composition. The transcriptomic study shows a temporal regulation of the main transcription factors and a lactose concentration impact on the transcriptional profile. A gene regulatory network (GRN) built using the BRANE Cut software reveals three sub-networks related to i a positive correlation between lactose concentration and cellulase production, ii a particular dependence of the lactose onto the β-glucosidase regulation and iii a negative regulation of the development process and growth.

Conclusions This work is the first investigating a transcriptomic study regarding the effects of pure and mixed carbon sources in a fed-batch mode. Our study expose a co-orchestration of xyr1, clr2 and ace3 for cellulase and hemicellulase induction and production, a fine regulation of the β-glucosidase and a decrease of growth in favor of cellulase production. These conclusions provide us with potential targets for further genetic engineering leading to better cellulase-producing strains.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 04, 2020.
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Glucose-lactose mixture feeds in industry-like conditions: a gene regulatory network analysis on the hyperproducing Trichoderma reesei strain Rut-C30
Aurélie Pirayre, Laurent Duval, Corinne Blugeon, Cyril Firmo, Sandrine Perrin, Etienne Jourdier, Antoine Margeot, Frédérique Bidard
bioRxiv 2020.10.02.324319; doi: https://doi.org/10.1101/2020.10.02.324319
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Glucose-lactose mixture feeds in industry-like conditions: a gene regulatory network analysis on the hyperproducing Trichoderma reesei strain Rut-C30
Aurélie Pirayre, Laurent Duval, Corinne Blugeon, Cyril Firmo, Sandrine Perrin, Etienne Jourdier, Antoine Margeot, Frédérique Bidard
bioRxiv 2020.10.02.324319; doi: https://doi.org/10.1101/2020.10.02.324319

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