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Citation for Study 21560

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

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

This study is part of submission 21560 (Status: Published).

Citation

Ferreira filho J.A., Horta M.C., Beloti L.L., Dos santos C.A., & De souza A.P. 2017. Carbohydrate-active enzymes in Trichoderma harzianum: a bioinformatic analysis bioprospecting for key enzymes for the biofuels industry. BMC Genomics , 18(179).

Authors

• Ferreira filho J.A. 556892366364
• Horta M.C.
• Beloti L.L.
• Dos santos C.A.
• De souza A.P.

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.

Keywords

Keywords: Trichoderma harzianum, CAZymes, Glycoside hydrolases, Phylogeny, RNA-Seq, Cellulases

External links

• DOI: 10.1186/s12864-017-4181-9
• Other URL: http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4181-9

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S21560
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref27612,
  	 author = {Jaire Alves Ferreira Filho and Maria Augusta  Crivelente Horta and Lilian Luzia Beloti and Clelton Aparecido dos Santos and Anete Pereira de Souza},
  	 title = {Carbohydrate-active enzymes in Trichoderma harzianum: a bioinformatic analysis bioprospecting for key enzymes for the biofuels industry},
  	 year = {2017},
  	 keywords = {Keywords: Trichoderma harzianum, CAZymes, Glycoside hydrolases, Phylogeny, RNA-Seq, Cellulases  },
  	 doi = {10.1186/s12864-017-4181-9},
  	 url = {http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4181-9},
  	 pmid = {},
  	 journal = {BMC Genomics },
  	 volume = {18},
  	 number = {179},
  	 pages = {},
  	 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.
  }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 27612
  AU  - Ferreira Filho,Jaire Alves
  AU  - Horta,Maria Augusta  Crivelente
  AU  - Beloti,Lilian Luzia
  AU  - dos Santos,Clelton Aparecido
  AU  - de Souza,Anete Pereira
  T1  - Carbohydrate-active enzymes in Trichoderma harzianum: a bioinformatic analysis bioprospecting for key enzymes for the biofuels industry
  PY  - 2017
  KW  - Keywords: Trichoderma harzianum
  KW  - CAZymes
  KW  - Glycoside hydrolases
  KW  - Phylogeny
  KW  - RNA-Seq
  KW  - Cellulases  
  UR  - http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4181-9
  N2  - 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.
  
  L3  - 10.1186/s12864-017-4181-9
  JF  - BMC Genomics 
  VL  - 18
  IS  - 179
  ER  -