Transcriptome and secretome analysis of Aspergillus fumigatus in the presence of sugarcane bagasse

Abstract

BackgroundSugarcane bagasse has been proposed as a lignocellulosic residue for second-generation ethanol (2G) produced by breaking down biomass into fermentable sugars. The enzymatic cocktails for biomass degradation are mostly produced by fungi, but low cost and high efficiency can consolidate 2G technologies. A. fumigatus plays an important role in plant biomass degradation capabilities and recycling. To gain more insight into the divergence in gene expression during steam-exploded bagasse (SEB) breakdown, this study profiled the transcriptome of A. fumigatus by RNA sequencing to compare transcriptional profiles of A. fumigatus grown on media containing SEB or fructose as the sole carbon source. Secretome analysis was also performed using SDS-PAGE and LC-MS/MS.ResultsThe maximum activities of cellulases (0.032 U mL-1), endo-1,4-β--xylanase (10.82 U mL-1) and endo-1,3-β glucanases (0.77 U mL-1) showed that functional CAZymes (carbohydrate-active enzymes) were secreted in the SEB culture conditions. Correlations between transcriptome and secretome data identified several CAZymes in A. fumigatus. Particular attention was given to CAZymes related to lignocellulose degradation and sugar transporters. Genes encoding glycoside hydrolase classes commonly expressed during the breakdown of cellulose, such as GH-5, 6, 7, 43, 45, and hemicellulose, such as GH-2, 10, 11, 30, 43, were found to be highly expressed in SEB conditions. Lytic polysaccharide monooxygenases (LPMO) classified as auxiliary activity families AA9 (GH61), CE (1, 4, 8, 15, 16), PL (1, 3, 4, 20) and GT (1, 2, 4, 8, 20, 35, 48) were also differentially expressed in this condition. Similarly, the most important enzymes related to biomass degradation, including endoxylanases, xyloglucanases, β-xylosidases, LPMOs, α-arabinofuranosidases, cellobiohydrolases, endoglucanases and β-glucosidases, were also identified in the secretome.ConclusionsThis is the first report of a transcriptome and secretome experiment of Aspergillus fumigatus in the degradation of pretreated sugarcane bagasse. The results suggest that this strain employs important strategies for this complex degradation process. It was possible to identify a set of genes and proteins that might be applied in several biotechnology fields. This knowledge can be exploited for the improvement of 2G ethanol production by the rational design of enzymatic cocktails.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4627-8) contains supplementary material, which is available to authorized users.

Transcriptome Profiling-Based Analysis of Carbohydrate-Active Enzymes in Aspergillus terreus Involved in Plant Biomass Degradation

“…Whilst the pectin content in SB and SH is considerably lower than for hollocellulose ( de Souza Moreira et al, 2013 ; Li et al, 2017 ), evidence was also observed for pectin degradation on both, with considerable exclusive up-regulation of genes on SH likely reflecting differences in pectin content between the different carbon sources. Up-regulation of genes related to pectinolytic activity have also been reported previously on SB for A. niger (PL4 family), A. fumigatus (PL4 family) and for A. tamarii (PL1, PL9, GH28 families) ( Borin et al, 2017 ; de Gouvêa et al, 2018 ; Midorikawa et al, 2018 ). Genome-predicted enzyme profiles in Aspergillus sections Aspergillus, Candidi and Flavi indicate the presence of pectin-degrading enzymes in the GH families 28, 43, 53, 78, and 142, in the CE family 8, and in the PL families 1, 3, 4, and 26, again with considerable conservation in up to 15 species ( Barrett et al, 2020 ).…”

“…With AA9, AA11, AA13, AA14, and AA16 exclusive to fungal genomes, multiple genes encoding LPMOs appear to be common in fungal genomes, particularly in Ascomycetes and Basidiomycetes ( Kracher et al, 2016 ). With previous reports of LPMOs in transcriptome and/or secretomes of A. niger , A. fumigatus, and A. tamarii following growth on sugarcane bagasse ( Borin et al, 2015 , 2017 ; de Gouvêa et al, 2018 ; Midorikawa et al, 2018 ), and recent characterization of seven AA9s in the secretome of A. terreus on soybean spent flakes ( Pierce et al, 2017 ), investigation here also highlights their involvement in the degradation of the SB and SH, with one AA3 gene and five LPMO AA9 genes up-regulated on both SB and SH lignocellulosic carbon sources, as well as exclusive AA3, AA7 and AA9-encoding genes on SB. Such data highlights potential conserved functional roles in biomass degradation, as reported in other fungi ( Isaken et al, 2014 ), as well as evidence for substrate specific activity, as documented recently for AA9 LPMOs ( Jagadeeswaran et al, 2016 ; Hüttner et al, 2019 ).…”

“…Similar up-regulation was previously observed in A. tamarii , where transcriptome analysis on SB in comparison to glucose revealed CAZyme-encoding DEGs within GH families 3, 5, 31, 43, and 92 ( Midorikawa et al, 2018 ). de Gouvêa et al (2018) also reported highly expressed genes in A. fumigatus on SB belonging to most of these GH families, when compared to growth on fructose. Genome-based prediction of fungal secretomes has also revealed predicted conserved enzyme profiles for families GH 3, 5, 10, and 43 across up to 14 species in taxonomic sections Aspergillus, Candidi, and Flavi for the genus Aspergillus , indicating likely conservation of such carbohydrate-active enzymes during speciation ( Barrett et al, 2020 ).…”

“…In this context, investigation has been considerable into furthering understanding of the molecular mechanisms involved in lignocellulose biodegradation by filamentous fungi. In the case of the genus Aspergillus , lignocellulose biodegradation potential has been investigated at the transcriptome level in species such as A. fumigatus ( Miao et al, 2015 ; Damasio et al, 2017 ; de Gouvêa et al, 2018 ), A. niger ( de Souza et al, 2011 ; Delmas et al, 2012 ; Pullan et al, 2014 ; van Munster et al, 2014 ; Brown et al, 2016 ), A. nidulans ( de Assis et al, 2015 ), A. sydowii ( Cong et al, 2017 ) and A. tamarii ( Midorikawa et al, 2018 ). Typically isolated from soil and decomposing lignocellulosic plant biomass ( Reddy and Singh, 2002 ; He et al, 2004 ; Chantasingh et al, 2006 ), ligninolytic enzyme activities have been investigated in A. terreus , across diverse biorefinery applications, from bioethanol ( Sethi et al, 2017 ), to lovastatin ( Jahromi et al, 2012 ) and organic acid production ( Jiménez-Quero et al, 2017 ).…”

“…Although likely to be abundant in fungal genomes, especially in those species adapted to lignocellulose decomposition, their comprehensive investigation has been restricted mostly to model organisms such as Saccharomyces cerevisiae ( Wieczorke et al, 1999 ). Within the genus Aspergillus , sugar transporter genes have recently been characterized in species such as A. niger , with 86 putative genes identified in silico , based on proteome and transcriptome analysis ( Peng et al, 2018 ), as well as A. nidulans , with 357 proteins in the major facilitator superfamily predicted in the annotated genome, albeit without validation of roles in sugar transport for the majority ( de Gouvêa et al, 2018 ). Lignocellulose contains both hexose (glucose) and pentose (mostly xylose) sugars which can be released by the enzymatic action of ligninolytic fungi.…”