Combined genome and transcriptome sequencing to investigate the plant cell wall degrading enzyme system in the thermophilic fungus Malbranchea cinnamomea

Abstract

BackgroundGenome and transcriptome sequencing has greatly facilitated the understanding of biomass-degrading mechanisms in a number of fungal species. The information obtained enables the investigation and discovery of genes encoding proteins involved in plant cell wall degradation, which are crucial for saccharification of lignocellulosic biomass in second-generation biorefinery applications. The thermophilic fungus Malbranchea cinnamomea is an efficient producer of many industrially relevant enzymes and a detailed analysis of its genomic content will considerably enhance our understanding of its lignocellulolytic system and promote the discovery of novel proteins.ResultsThe 25-million-base-pair genome of M. cinnamomea FCH 10.5 was sequenced with 225× coverage. A total of 9437 protein-coding genes were predicted and annotated, among which 301 carbohydrate-active enzyme (CAZyme) domains were found. The putative CAZymes of M. cinnamomea cover cellulases, hemicellulases, chitinases and pectinases, equipping the fungus with the ability to grow on a wide variety of biomass types. Upregulation of 438 and 150 genes during growth on wheat bran and xylan, respectively, in comparison to growth on glucose was revealed. Among the most highly upregulated CAZymes on xylan were glycoside hydrolase family GH10 and GH11 xylanases, as well as a putative glucuronoyl esterase and a putative lytic polysaccharide monooxygenase (LPMO). AA9-domain-containing proteins were also found to be upregulated on wheat bran, as well as a putative cutinase and a protein harbouring a CBM9 domain. Several genes encoding secreted proteins of unknown function were also more abundant on wheat bran and xylan than on glucose.ConclusionsThe comprehensive combined genome and transcriptome analysis of M. cinnamomea provides a detailed insight into its response to growth on different types of biomass. In addition, the study facilitates the further exploration and exploitation of the repertoire of industrially relevant lignocellulolytic enzymes of this fungus.Electronic supplementary materialThe online version of this article (10.1186/s13068-017-0956-0) contains supplementary material, which is available to authorised users.

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

“…Such observations have also been reported in A. fumigatus on different lignocellulosic biomass sources (Miao et al, 2015 ; de Gouvêa et al, 2018 ), with many such GTs involved in the biosynthesis of fungal cell wall chitins and ergosterol glycosylation (Klutts et al, 2006 ; Castell-Miller et al, 2016 ). Additional DEGs likely to be not involved in the plant cell wall degradation included six GH18 putative chitinases, with activity likely associated with cell wall dynamics during fungal growth, as also observed in the ascomycete fungus Malbranchea cinnamomea (Hüttner et al, 2017 ).…”

The key genes and pathways related to male sterility of eggplant revealed by comparative transcriptome analysis

“…Glycosyltransferase (TRINITY_DN105743_c0_g1) and glycosyl hydrolases (TRINITY_DN56811_c0_g2) belonging to two types of enzymes in the carbohydrate metabolism pathway were down-regulated in the MS line in our study. The genes encoding the two enzyme families have been reported to be associated with cell-wall synthesis and degradation [ 45 – 47 ]. SPG2, a GT43 glycosyltansferase and UPEX1, a GT31 glycosyltransferase were involved in the formation of pollen wall primexine [ 48 , 49 ].…”

Genome sequence of Rhizomucor pusillus FCH 5.7, a thermophilic zygomycete involved in plant biomass degradation harbouring putative GH9 endoglucanases

“…After isolation, R. pusillus FCH 5.7 was cultivated on potato dextrose agar (PDA) at 50 °C and the species identified by internal transcribed spacer (ITS) sequencing, as described previously [ 9 ]. For whole genome sequencing, 5-day-old mycelium from PDA plates was used for the inoculation of basal liquid medium (4 g L −1 KH 2 PO 4 , 13.6 g L −1 (NH 4 ) 2 SO 4 , 0.8 g L −1 CaCl 2 ⋅2H 2 O, 0.6 g L −1 MgSO 4 ⋅7H 2 O, 6 g L −1 Bacto peptone, 10 mg L −1 FeSO 4 ⋅7H 2 O, 3.2 mg L −1 MnSO 4 ⋅H 2 O, 2.8 mg L −1 ZnSO 4 ⋅7H 2 O, 4 mg L −1 CoCl 2 ⋅6H 2 O, 200 mL L −1 Tween 80, pH 5.8) containing 20 g L −1 glucose as carbon source.…”

“…Cultivation was carried out in 125 mL liquid medium in baffled Erlenmeyer flasks (500 mL; 50 °C, 48 h, shaking at 250 rpm). The mycelium was harvested after two days of cultivation and DNA was extracted with cetyltrimethyl ammonium bromide (CTAB) buffer (2% CTAB, 100 mM TrisHCl, pH 8.0, 20 mM EDTA, 1.4 M NaCl) and purified from the supernatant by a combination of phenol-chloroform extraction and isopropanol precipitation and DNeasy Plant Mini Kit (Qiagen), as described previously [ 9 ]. Quality of the purified DNA was verified by agarose gel electrophoresis, Nanodrop (Thermo Scientific) and Qubit (Life Technologies) before genome sequencing.…”