Carbohydrate-active enzymes in  Trichoderma harzianum : a bioinformatic analysis bioprospecting for key enzymes for the biofuels industry

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Abstract

Background

Trichoderma harzianum is used in biotechnology applications due to its ability to produce powerful enzymes for the conversion of lignocellulosic substrates into soluble sugars. Active enzymes involved in carbohydrate metabolism are defined as carbohydrate-active enzymes (CAZymes), and the most abundant family in the CAZy database is the glycoside hydrolases. The enzymes of this family play a fundamental role in the decomposition of plant biomass.

Results

In this study, the CAZymes of T. harzianum were identified and classified using bioinformatic approaches after which the expression profiles of all annotated CAZymes were assessed via RNA-Seq, and a phylogenetic analysis was performed. A total of 430 CAZymes (3.7% of the total proteins for this organism) were annotated in T. harzianum, including 259 glycoside hydrolases (GHs), 101 glycosyl transferases (GTs), 6 polysaccharide lyases (PLs), 22 carbohydrate esterases (CEs), 42 auxiliary activities (AAs) and 46 carbohydrate-binding modules (CBMs). Among the identified T. harzianum CAZymes, 47% were predicted to harbor a signal peptide sequence and were therefore classified as secreted proteins. The GH families were the CAZyme class with the greatest number of expressed genes, including GH18 (23 genes), GH3 (17 genes), GH16 (16 genes), GH2 (13 genes) and GH5 (12 genes). A phylogenetic analysis of the proteins in the AA9/GH61, CE5 and GH55 families showed high functional variation among the proteins.

Conclusions

Identifying the main proteins used by T. harzianum for biomass degradation can ensure new advances in the biofuel production field. Herein, we annotated and characterized the expression levels of all of the CAZymes from T. harzianum, which may contribute to future studies focusing on the functional and structural characterization of the identified proteins.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4181-9) contains supplementary material, which is available to authorized users.

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Most cited references 35

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Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes

Anthony Levasseur, Elodie Drula, Vincent Lombard … (2013)

Background Since its inception, the carbohydrate-active enzymes database (CAZy; http://www.cazy.org) has described the families of enzymes that cleave or build complex carbohydrates, namely the glycoside hydrolases (GH), the polysaccharide lyases (PL), the carbohydrate esterases (CE), the glycosyltransferases (GT) and their appended non-catalytic carbohydrate-binding modules (CBM). The recent discovery that members of families CBM33 and family GH61 are in fact lytic polysaccharide monooxygenases (LPMO), demands a reclassification of these families into a suitable category. Results Because lignin is invariably found together with polysaccharides in the plant cell wall and because lignin fragments are likely to act in concert with (LPMO), we have decided to join the families of lignin degradation enzymes to the LPMO families and launch a new CAZy class that we name “Auxiliary Activities” in order to accommodate a range of enzyme mechanisms and substrates related to lignocellulose conversion. Comparative analyses of these auxiliary activities in 41 fungal genomes reveal a pertinent division of several fungal groups and subgroups combining their phylogenetic origin and their nutritional mode (white vs. brown rot). Conclusions The new class introduced in the CAZy database extends the traditional CAZy families, and provides a better coverage of the full extent of the lignocellulose breakdown machinery.

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Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

Christian P. Kubicek, Alfredo Herrera-Estrella, Verena Seidl-Seiboth … (2011)

Background Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma. Results Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei. Conclusions The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.

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Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

Zhongtao Zhao, Huiquan Liu, Chenfang Wang … (2013)

Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 103 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also revealed a complex history of lineage-specific expansions and attritions for the PL1 family. Conclusions Our study provides insights into the variety and expansion of fungal CAZyme classes and revealed the relationship of CAZyme size and diversity with their nutritional strategy and host specificity.

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Author and article information

Contributors

Jaire Alves Ferreira Filho: jaire_hp@yahoo.com.br

Maria Augusta Crivelente Horta: marau_ch@yahoo.com.br

Lilian Luzia Beloti: llbeloti@gmail.com

Clelton Aparecido dos Santos: cleltonsto@gmail.com

Anete Pereira de Souza: anete@unicamp.br

Journal

Journal ID (nlm-ta): BMC Genomics

Journal ID (iso-abbrev): BMC Genomics

Title: BMC Genomics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2164

Publication date (Electronic): 12 October 2017

Publication date PMC-release: 12 October 2017

Publication date Collection: 2017

Volume: 18

Electronic Location Identifier: 779

Affiliations

[1 ]ISNI 0000 0001 0723 2494, GRID grid.411087.b, Center for Molecular Biology and Genetic Engineering (CBMEG), , University of Campinas (UNICAMP), ; Campinas, SP Brazil

[2 ]ISNI 0000 0001 0723 2494, GRID grid.411087.b, Graduate Program in Genetics and Molecular Biology, Institute of Biology, UNICAMP, ; Campinas, SP Brazil

[3 ]ISNI 0000 0001 0723 2494, GRID grid.411087.b, Department of Plant Biology, Institute of Biology, UNICAMP, ; Campinas, SP Brazil

Article

Publisher ID: 4181

DOI: 10.1186/s12864-017-4181-9

PMC ID: 5639747

PubMed ID: 29025413

SO-VID: ecf95dd0-62c7-4e49-b291-6017a0f42b8a

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.

History

Date received : 28 May 2017

Date accepted : 5 October 2017

Funding

Funded by: Fundação de Amparo à Pesquisa do Estado de São Paulo (BR)

Award ID: 2015/09202-0

Award Recipient : Anete Pereira de Souza

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: trichoderma harzianum,cazymes,glycoside hydrolases,phylogeny,rna-seq,cellulases

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ScienceOpen disciplines: Genetics

Keywords: trichoderma harzianum, cazymes, glycoside hydrolases, phylogeny, rna-seq, cellulases

Carbohydrate-active enzymes in Trichoderma harzianum: a bioinformatic analysis bioprospecting for key enzymes for the biofuels industry

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Genes & Diseases

Most cited references 35

Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes

Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

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