Limits...
Analysis of genomic regions of Trichoderma harzianum IOC-3844 related to biomass degradation.

Crucello A, Sforça DA, Horta MA, dos Santos CA, Viana AJ, Beloti LL, de Toledo MA, Vincentz M, Kuroshu RM, de Souza AP - PLoS ONE (2015)

Bottom Line: The assembled BAC sequences revealed 232 predicted genes, 31.5% of which were related to catabolic pathways, including those involved in biomass degradation.Thus, we demonstrate a rapid and efficient tool that focuses on specific genomic regions by combining a BAC library with transcriptomic data.This is the first BAC-based structural genomic study of the cellulolytic fungus T. harzianum, and its findings provide new perspectives regarding the use of this species in biomass degradation processes.

View Article: PubMed Central - PubMed

Affiliation: Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.

ABSTRACT
Trichoderma harzianum IOC-3844 secretes high levels of cellulolytic-active enzymes and is therefore a promising strain for use in biotechnological applications in second-generation bioethanol production. However, the T. harzianum biomass degradation mechanism has not been well explored at the genetic level. The present work investigates six genomic regions (~150 kbp each) in this fungus that are enriched with genes related to biomass conversion. A BAC library consisting of 5,760 clones was constructed, with an average insert length of 90 kbp. The assembled BAC sequences revealed 232 predicted genes, 31.5% of which were related to catabolic pathways, including those involved in biomass degradation. An expression profile analysis based on RNA-Seq data demonstrated that putative regulatory elements, such as membrane transport proteins and transcription factors, are located in the same genomic regions as genes related to carbohydrate metabolism and exhibit similar expression profiles. Thus, we demonstrate a rapid and efficient tool that focuses on specific genomic regions by combining a BAC library with transcriptomic data. This is the first BAC-based structural genomic study of the cellulolytic fungus T. harzianum, and its findings provide new perspectives regarding the use of this species in biomass degradation processes.

No MeSH data available.


Related in: MedlinePlus

Schematic model of CAZy and co-regulated genes.CAZy genes are indicated with color-filled arrows. Co-regulated non-CAZy genes are indicated by white arrows with contours of the same color as those of CAZy genes with similar profiles. Similar colors indicate a similar expression profile. (A) The region of the Egl1 BAC containing Egl1 and a gene encoding a GH71 family protein, which exhibit similar expression profiles. (B) The region of the Egl2 BAC containing a GH3 family protein, an Egl2 gene, and a GH79 protein. (C) The region of the Egl3 BAC containing 5 CAZy genes: CE16, GT90, Egl3, CH37, and GT17. (D) The region of the Bgl2 BAC that contains only one CAZy, the Bgl2 gene. (E) The Cbh1 BAC, demonstrating that Cbh1 and swollenin are co-induced. Two other CAZy genes (GH92 and GCase) are also present. (F) The region of the Xyn2 BAC containing a GH27 protein and Xy2.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4383378&req=5

pone.0122122.g007: Schematic model of CAZy and co-regulated genes.CAZy genes are indicated with color-filled arrows. Co-regulated non-CAZy genes are indicated by white arrows with contours of the same color as those of CAZy genes with similar profiles. Similar colors indicate a similar expression profile. (A) The region of the Egl1 BAC containing Egl1 and a gene encoding a GH71 family protein, which exhibit similar expression profiles. (B) The region of the Egl2 BAC containing a GH3 family protein, an Egl2 gene, and a GH79 protein. (C) The region of the Egl3 BAC containing 5 CAZy genes: CE16, GT90, Egl3, CH37, and GT17. (D) The region of the Bgl2 BAC that contains only one CAZy, the Bgl2 gene. (E) The Cbh1 BAC, demonstrating that Cbh1 and swollenin are co-induced. Two other CAZy genes (GH92 and GCase) are also present. (F) The region of the Xyn2 BAC containing a GH27 protein and Xy2.

Mentions: The Egl1 BAC (165 kbp) showed 2 CAZymes: a GT from family 71 and a GH from family 7 (a predicted α-mannosyltransferase and Egl1, respectively) (Fig. 7A). Intriguingly, the two CAZymes formed a cluster, suggesting co-regulation.


Analysis of genomic regions of Trichoderma harzianum IOC-3844 related to biomass degradation.

Crucello A, Sforça DA, Horta MA, dos Santos CA, Viana AJ, Beloti LL, de Toledo MA, Vincentz M, Kuroshu RM, de Souza AP - PLoS ONE (2015)

Schematic model of CAZy and co-regulated genes.CAZy genes are indicated with color-filled arrows. Co-regulated non-CAZy genes are indicated by white arrows with contours of the same color as those of CAZy genes with similar profiles. Similar colors indicate a similar expression profile. (A) The region of the Egl1 BAC containing Egl1 and a gene encoding a GH71 family protein, which exhibit similar expression profiles. (B) The region of the Egl2 BAC containing a GH3 family protein, an Egl2 gene, and a GH79 protein. (C) The region of the Egl3 BAC containing 5 CAZy genes: CE16, GT90, Egl3, CH37, and GT17. (D) The region of the Bgl2 BAC that contains only one CAZy, the Bgl2 gene. (E) The Cbh1 BAC, demonstrating that Cbh1 and swollenin are co-induced. Two other CAZy genes (GH92 and GCase) are also present. (F) The region of the Xyn2 BAC containing a GH27 protein and Xy2.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383378&req=5

pone.0122122.g007: Schematic model of CAZy and co-regulated genes.CAZy genes are indicated with color-filled arrows. Co-regulated non-CAZy genes are indicated by white arrows with contours of the same color as those of CAZy genes with similar profiles. Similar colors indicate a similar expression profile. (A) The region of the Egl1 BAC containing Egl1 and a gene encoding a GH71 family protein, which exhibit similar expression profiles. (B) The region of the Egl2 BAC containing a GH3 family protein, an Egl2 gene, and a GH79 protein. (C) The region of the Egl3 BAC containing 5 CAZy genes: CE16, GT90, Egl3, CH37, and GT17. (D) The region of the Bgl2 BAC that contains only one CAZy, the Bgl2 gene. (E) The Cbh1 BAC, demonstrating that Cbh1 and swollenin are co-induced. Two other CAZy genes (GH92 and GCase) are also present. (F) The region of the Xyn2 BAC containing a GH27 protein and Xy2.
Mentions: The Egl1 BAC (165 kbp) showed 2 CAZymes: a GT from family 71 and a GH from family 7 (a predicted α-mannosyltransferase and Egl1, respectively) (Fig. 7A). Intriguingly, the two CAZymes formed a cluster, suggesting co-regulation.

Bottom Line: The assembled BAC sequences revealed 232 predicted genes, 31.5% of which were related to catabolic pathways, including those involved in biomass degradation.Thus, we demonstrate a rapid and efficient tool that focuses on specific genomic regions by combining a BAC library with transcriptomic data.This is the first BAC-based structural genomic study of the cellulolytic fungus T. harzianum, and its findings provide new perspectives regarding the use of this species in biomass degradation processes.

View Article: PubMed Central - PubMed

Affiliation: Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.

ABSTRACT
Trichoderma harzianum IOC-3844 secretes high levels of cellulolytic-active enzymes and is therefore a promising strain for use in biotechnological applications in second-generation bioethanol production. However, the T. harzianum biomass degradation mechanism has not been well explored at the genetic level. The present work investigates six genomic regions (~150 kbp each) in this fungus that are enriched with genes related to biomass conversion. A BAC library consisting of 5,760 clones was constructed, with an average insert length of 90 kbp. The assembled BAC sequences revealed 232 predicted genes, 31.5% of which were related to catabolic pathways, including those involved in biomass degradation. An expression profile analysis based on RNA-Seq data demonstrated that putative regulatory elements, such as membrane transport proteins and transcription factors, are located in the same genomic regions as genes related to carbohydrate metabolism and exhibit similar expression profiles. Thus, we demonstrate a rapid and efficient tool that focuses on specific genomic regions by combining a BAC library with transcriptomic data. This is the first BAC-based structural genomic study of the cellulolytic fungus T. harzianum, and its findings provide new perspectives regarding the use of this species in biomass degradation processes.

No MeSH data available.


Related in: MedlinePlus