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Analysis of the Transcriptome in Aspergillus tamarii During Enzymatic Degradation of Sugarcane Bagasse

The production of bioethanol from non-food agricultural residues represents an alternative energy source to fossil fuels for incorporation into the world's economy. Within the context of bioconversion of plant biomass into renewable energy using improved enzymatic cocktails, Illumina RNA-seq tr...

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Autores principales: Midorikawa, Glaucia Emy Okida, Correa, Camila Louly, Noronha, Eliane Ferreira, Filho, Edivaldo Ximenes Ferreira, Togawa, Roberto Coiti, Costa, Marcos Mota do Carmo, Silva-Junior, Orzenil Bonfim, Grynberg, Priscila, Miller, Robert Neil Gerard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6153317/
https://www.ncbi.nlm.nih.gov/pubmed/30280097
http://dx.doi.org/10.3389/fbioe.2018.00123
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author Midorikawa, Glaucia Emy Okida
Correa, Camila Louly
Noronha, Eliane Ferreira
Filho, Edivaldo Ximenes Ferreira
Togawa, Roberto Coiti
Costa, Marcos Mota do Carmo
Silva-Junior, Orzenil Bonfim
Grynberg, Priscila
Miller, Robert Neil Gerard
author_facet Midorikawa, Glaucia Emy Okida
Correa, Camila Louly
Noronha, Eliane Ferreira
Filho, Edivaldo Ximenes Ferreira
Togawa, Roberto Coiti
Costa, Marcos Mota do Carmo
Silva-Junior, Orzenil Bonfim
Grynberg, Priscila
Miller, Robert Neil Gerard
author_sort Midorikawa, Glaucia Emy Okida
collection PubMed
description The production of bioethanol from non-food agricultural residues represents an alternative energy source to fossil fuels for incorporation into the world's economy. Within the context of bioconversion of plant biomass into renewable energy using improved enzymatic cocktails, Illumina RNA-seq transcriptome profiling was conducted on a strain of Aspergillus tamarii, efficient in biomass polysaccharide degradation, in order to identify genes encoding proteins involved in plant biomass saccharification. Enzyme production and gene expression was compared following growth in liquid and semi-solid culture with steam-exploded sugarcane bagasse (SB) (1% w/v) and glucose (1% w/v) employed as contrasting sole carbon sources. Enzyme production following growth in liquid minimum medium supplemented with SB resulted in 0.626 and 0.711 UI.mL(−1) xylanases after 24 and 48 h incubation, respectively. Transcriptome profiling revealed expression of over 7120 genes, with groups of genes modulated according to solid or semi-solid culture, as well as according to carbon source. Gene ontology analysis of genes expressed following SB hydrolysis revealed enrichment in xyloglucan metabolic process and xylan, pectin and glucan catabolic process, indicating up-regulation of genes involved in xylanase secretion. According to carbohydrate-active enzyme (CAZy) classification, 209 CAZyme-encoding genes were identified with significant differential expression on liquid or semi-solid SB, in comparison to equivalent growth on glucose as carbon source. Up-regulated CAZyme-encoding genes related to cellulases (CelA, CelB, CelC, CelD) and hemicellulases (XynG1, XynG2, XynF1, XylA, AxeA, arabinofuranosidase) showed up to a 10-fold log2FoldChange in expression levels. Five genes from the AA9 (GH61) family, related to lytic polysaccharide monooxygenase (LPMO), were also identified with significant expression up-regulation. The transcription factor gene XlnR, involved in induction of hemicellulases, showed up-regulation on liquid and semi-solid SB culture. Similarly, the gene ClrA, responsible for regulation of cellulases, showed increased expression on liquid SB culture. Over 150 potential transporter genes were also identified with increased expression on liquid and semi-solid SB culture. This first comprehensive analysis of the transcriptome of A. tamarii contributes to our understanding of genes and regulatory systems involved in cellulose and hemicellulose degradation in this fungus, offering potential for application in improved enzymatic cocktail development for plant biomass degradation in biorefinery applications.
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spelling pubmed-61533172018-10-02 Analysis of the Transcriptome in Aspergillus tamarii During Enzymatic Degradation of Sugarcane Bagasse Midorikawa, Glaucia Emy Okida Correa, Camila Louly Noronha, Eliane Ferreira Filho, Edivaldo Ximenes Ferreira Togawa, Roberto Coiti Costa, Marcos Mota do Carmo Silva-Junior, Orzenil Bonfim Grynberg, Priscila Miller, Robert Neil Gerard Front Bioeng Biotechnol Bioengineering and Biotechnology The production of bioethanol from non-food agricultural residues represents an alternative energy source to fossil fuels for incorporation into the world's economy. Within the context of bioconversion of plant biomass into renewable energy using improved enzymatic cocktails, Illumina RNA-seq transcriptome profiling was conducted on a strain of Aspergillus tamarii, efficient in biomass polysaccharide degradation, in order to identify genes encoding proteins involved in plant biomass saccharification. Enzyme production and gene expression was compared following growth in liquid and semi-solid culture with steam-exploded sugarcane bagasse (SB) (1% w/v) and glucose (1% w/v) employed as contrasting sole carbon sources. Enzyme production following growth in liquid minimum medium supplemented with SB resulted in 0.626 and 0.711 UI.mL(−1) xylanases after 24 and 48 h incubation, respectively. Transcriptome profiling revealed expression of over 7120 genes, with groups of genes modulated according to solid or semi-solid culture, as well as according to carbon source. Gene ontology analysis of genes expressed following SB hydrolysis revealed enrichment in xyloglucan metabolic process and xylan, pectin and glucan catabolic process, indicating up-regulation of genes involved in xylanase secretion. According to carbohydrate-active enzyme (CAZy) classification, 209 CAZyme-encoding genes were identified with significant differential expression on liquid or semi-solid SB, in comparison to equivalent growth on glucose as carbon source. Up-regulated CAZyme-encoding genes related to cellulases (CelA, CelB, CelC, CelD) and hemicellulases (XynG1, XynG2, XynF1, XylA, AxeA, arabinofuranosidase) showed up to a 10-fold log2FoldChange in expression levels. Five genes from the AA9 (GH61) family, related to lytic polysaccharide monooxygenase (LPMO), were also identified with significant expression up-regulation. The transcription factor gene XlnR, involved in induction of hemicellulases, showed up-regulation on liquid and semi-solid SB culture. Similarly, the gene ClrA, responsible for regulation of cellulases, showed increased expression on liquid SB culture. Over 150 potential transporter genes were also identified with increased expression on liquid and semi-solid SB culture. This first comprehensive analysis of the transcriptome of A. tamarii contributes to our understanding of genes and regulatory systems involved in cellulose and hemicellulose degradation in this fungus, offering potential for application in improved enzymatic cocktail development for plant biomass degradation in biorefinery applications. Frontiers Media S.A. 2018-09-18 /pmc/articles/PMC6153317/ /pubmed/30280097 http://dx.doi.org/10.3389/fbioe.2018.00123 Text en Copyright © 2018 Midorikawa, Correa, Noronha, Filho, Togawa, Costa, Silva-Junior, Grynberg and Miller. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Bioengineering and Biotechnology
Midorikawa, Glaucia Emy Okida
Correa, Camila Louly
Noronha, Eliane Ferreira
Filho, Edivaldo Ximenes Ferreira
Togawa, Roberto Coiti
Costa, Marcos Mota do Carmo
Silva-Junior, Orzenil Bonfim
Grynberg, Priscila
Miller, Robert Neil Gerard
Analysis of the Transcriptome in Aspergillus tamarii During Enzymatic Degradation of Sugarcane Bagasse
title Analysis of the Transcriptome in Aspergillus tamarii During Enzymatic Degradation of Sugarcane Bagasse
title_full Analysis of the Transcriptome in Aspergillus tamarii During Enzymatic Degradation of Sugarcane Bagasse
title_fullStr Analysis of the Transcriptome in Aspergillus tamarii During Enzymatic Degradation of Sugarcane Bagasse
title_full_unstemmed Analysis of the Transcriptome in Aspergillus tamarii During Enzymatic Degradation of Sugarcane Bagasse
title_short Analysis of the Transcriptome in Aspergillus tamarii During Enzymatic Degradation of Sugarcane Bagasse
title_sort analysis of the transcriptome in aspergillus tamarii during enzymatic degradation of sugarcane bagasse
topic Bioengineering and Biotechnology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6153317/
https://www.ncbi.nlm.nih.gov/pubmed/30280097
http://dx.doi.org/10.3389/fbioe.2018.00123
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