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

Genome 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 sacc...

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Published inBiotechnology for biofuels Vol. 10; no. 1; p. 265
Main Authors Hüttner, Silvia, Nguyen, Thanh Thuy, Granchi, Zoraide, Chin-A-Woeng, Thomas, Ahrén, Dag, Larsbrink, Johan, Thanh, Vu Nguyen, Olsson, Lisbeth
Format Journal Article
LanguageEnglish
Published England BioMed Central Ltd 13.11.2017
BioMed Central
BMC
Subjects
Bacteria, Thermophilic
Biodegradation
Biologi
Biological Sciences
Biomass
biorefining
Carbohydrate-active enzymes
Carbohydrates
Carbon
Carbon sources
Cell walls
Cellular control mechanisms
Cellulase
Cellulose
chitinase
cutinase
Deoxyribonucleic acid
DNA
Enzymes
Fungi
Gene expression
gene expression regulation
Gene sequencing
genes
Genetic aspects
Genetics
Genetics and Genomics
Genetik
Genetik och genomik
Genomes
Genotype
glucose
glycosides
lignocellulases
Lignocellulose
Malbranchea
Malbranchea cinnamomea
Malbranchea pulchella
Mass transfer
Natural Sciences
Naturvetenskap
Neurospora crassa
Plant biomass
Polymers
Properties
protein secretion
Rice
Risk reduction
saccharification
Thermophilic fungi
transcriptomics
Wheat bran
Xylan
xylanases
Xylan
Malbranchea pulchella
Cellulase
Plant biomass
Carbohydrate-active enzymes
Wheat bran
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Abstract Genome 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 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. The 25-million-base-pair genome of 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 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. The comprehensive combined genome and transcriptome analysis of 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.
AbstractList Most enzymes used today in biomass conversion are mesophilic, but higher process temperatures could enable faster reaction rates, lower viscosity, better cell wall disintegration and enzyme penetration into the raw material, increased mass transfer and reduced risk of contamination [11-14].[...]thermophilic organisms, with growth optima between 45 and 80 °C [15], are promising sources of thermostable enzymes and have hitherto not been as extensively explored as their mesophilic counterparts [16].[ Table Omitted - see PDF ] Table 1 Comparison of the numbers of CAZymes in M. cinnamomea with those in other fungi Phylum Species GH GT PL CE AA CBM All ASC Yarrowia lipolytica a 42 45 0 1 10 8 106 Saccharomyces cerevisiae a 45 65 0 2 6 15 133 Kluyveromyces lactis a 47 63 0 1 0 11 122 Arthrobotrys oligospora a 205 87 15 30 33 180 550 Malbranchea cinnamomea b 137 62 4 24 42 32 301 Penicillium chrysogenum a 222 103 9 22 22 51 429 Aspergillus nidulans a 264 92 21 31 33 44 485 Aspergillus niger a 253 121 8 23 68 55 528 Aspergillus oryzae a 307 117 23 29 30 37 543 Leptosphaeria maculans a 220 98 19 33 33 53 456 Thielavia terrestris a 212 91 4 28 58 80 473 Myceliophthora thermophila a 195 87 8 28 50 50 418 Podospora anserina a 213 92 8 41 105 104 563 Neurospora crassa a 174 78 4 22 35 42 355 Magnaporthe grisea a 265 105 4 52 92 114 632 Fusarium graminearum a 253 110 21 45 72 87 588 BAS Rhodosporidium toruloides a 75 101 4 10 17 11 218 Sporisorium reilianum a 104 66 3 12 21 6 212 Schizophyllum commune c,d 237 77 5 40 70 39 468 Piriformospora indica a 206 73 16 45 57 141 538 Phanerochaete chrysosporium e,f 170 70 1 20 81 71 413 Postia placenta g,h 174 102 2 22 22 22 344 ZYG Rhizopus oryzae i,j 123 145 6 48 10 38 370 OOM Phytophthora infestans a 283 157 67 21 0 37 565 ASC Ascomycota, BAS Basidiomycota, ZYG Zygomycota, OOM Oomycota a[7]; bthis study; c[76]; d[77]; e[78]; f[79]; g[80]; h[81]; i[48]; j[82] The concerted action of members from various CAZy families is required for the efficient degradation of plant cell wall polymers.The intensity of the shading indicates the coverage between query and subject in the dbCAN search. a Twenty putative proteins with at least one catalytic CAZy domain in addition to one or several CBM domains were found in the M. cinnamomea genome. b Eight putative proteins without predicted catalytic domains, but one or more CBM domains were present in the genome CAZymes expressed during growth on glucose, wheat bran and xylan To investigate how gene expression is influenced by growth on an easily metabolised carbon source, where mostly constitutive genes are predicted to be expressed compared to growth on a more complex carbon sources, RNAseq analysis was conducted on M. cinnamomea cultivated on glucose, wheat bran and beechwood xylan.GH72 enzymes are known to be involved in elongation and remodelling of the ?-1,3-glucan of the fungal cell wall [53].[...]MalCi_235.14 is not likely to be involved in plant biomass degradation, but may be important for hyphal growth during an abundance of nutrients.
Background: Genome 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. Results: The 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. Conclusions: The 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.
Background: Genome 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. Results: The 25-million-base-pair genome of M. cinnamomea FCH 10.5 was sequenced with 225x 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. Conclusions: The 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.
Abstract Background Genome 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. Results The 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. Conclusions The 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.
Genome 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.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.The 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.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.The 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.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.
Genome 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 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. The 25-million-base-pair genome of 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 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. The comprehensive combined genome and transcriptome analysis of 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.
ArticleNumber 265
Audience Academic
Author Ahrén, Dag
Nguyen, Thanh Thuy
Granchi, Zoraide
Chin-A-Woeng, Thomas
Thanh, Vu Nguyen
Olsson, Lisbeth
Hüttner, Silvia
Larsbrink, Johan
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Strategiska forskningsområden (SFO)
Biologiska institutionen
Strategic research areas (SRA)
Lunds universitet
Naturvetenskapliga fakulteten
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MEMEG
BECC: Biodiversity and Ecosystem services in a Changing Climate
Faculty of Science
Lund University
Profilområden och andra starka forskningsmiljöer
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– name: Strategiska forskningsområden (SFO)
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– name: MEMEG
– name: BECC: Biodiversity and Ecosystem services in a Changing Climate
– name: Biologiska institutionen
– name: Profile areas and other strong research environments
– name: Strategic research areas (SRA)
– name: Department of Biology
– name: Faculty of Science
– name: Lunds universitet
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Issue 1
Keywords Xylan
Malbranchea pulchella
Cellulase
Plant biomass
Carbohydrate-active enzymes
Wheat bran
Language English
License Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
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Snippet Genome and transcriptome sequencing has greatly facilitated the understanding of biomass-degrading mechanisms in a number of fungal species. The information...
Most enzymes used today in biomass conversion are mesophilic, but higher process temperatures could enable faster reaction rates, lower viscosity, better cell...
BACKGROUND: Genome and transcriptome sequencing has greatly facilitated the understanding of biomass-degrading mechanisms in a number of fungal species. The...
Background: Genome and transcriptome sequencing has greatly facilitated the understanding of biomass-degrading mechanisms in a number of fungal species. The...
Abstract Background Genome and transcriptome sequencing has greatly facilitated the understanding of biomass-degrading mechanisms in a number of fungal...
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SubjectTerms Bacteria, Thermophilic
Biodegradation
Biologi
Biological Sciences
Biomass
biorefining
Carbohydrate-active enzymes
Carbohydrates
Carbon
Carbon sources
Cell walls
Cellular control mechanisms
Cellulase
Cellulose
chitinase
cutinase
Deoxyribonucleic acid
DNA
Enzymes
Fungi
Gene expression
gene expression regulation
Gene sequencing
genes
Genetic aspects
Genetics
Genetics and Genomics
Genetik
Genetik och genomik
Genomes
Genotype
glucose
glycosides
lignocellulases
Lignocellulose
Malbranchea
Malbranchea cinnamomea
Malbranchea pulchella
Mass transfer
Natural Sciences
Naturvetenskap
Neurospora crassa
Plant biomass
Polymers
Properties
protein secretion
Rice
Risk reduction
saccharification
Thermophilic fungi
transcriptomics
Wheat bran
Xylan
xylanases
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Title Combined genome and transcriptome sequencing to investigate the plant cell wall degrading enzyme system in the thermophilic fungus Malbranchea cinnamomea
URI https://www.ncbi.nlm.nih.gov/pubmed/29158777
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Volume 10
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