Analysis of Genomic Regions of Trichoderma harzianum IOC-3844 Related to Biomass Degradation

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.

Assessments on the catalytic and kinetic properties of beta-glucosidase isolated from a highly efficient antagonistic fungus Trichoderma harzianum

“…No significant difference in enzyme activity was observed in mixtures supplemented with KNO 3 (90 U/mL), NH 4 Cl (88 U/mL) and NaNO 3 (80 U/mL) ( Figure 7c) (p > 0.05). Likewise, previous researchers (GOYARI et al, 2014) have described that (NH 4 ) 2 SO 4 was an appropriate nitrogen source for cultivating fungal cultures followed by NH 4 NO 3 , KNO 3 , peptone and urea (CRUCELLO et al, 2015;GOYARI et al, 2014); hence their findings appear to be supported by the results in this study ( Figure 5c). However, using the abovementioned carbon and nitrogen sources as growth media to culture T. harzianum can be a rather costly approach to produce β-glucosidase T12, hence the use of other natural nitrogen sources i.e.…”

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

“…Horta et al (2014) [ 19 ] determined the transcriptome profile of this fungus during biomass degradation and delimited groups of overexpressed genes. Crucello et al (2015) [ 35 ] constructed the first bacterial artificial chromosome (BAC) library and found a cluster of CAZymes that were probably co-expressed, and Santos et al (2016) [ 36 ] heterologously expressed a GH1 beta-glucosidase from T. harzianum in Escherichia coli and characterized its structure and function.…”

“Integrative Genomic Analysis for the Bioprospection of Regulators and Accessory Enzymes Associated with Cellulose Degradation in a Filamentous Fungus (Trichoderma harzianum)”

“…The study of genomic regions is an important tool for providing a global view of the important genes and regulatory regions of a genome [24, 31]. The genomes of a few strains of T. harzianum are available [32, 33].…”

“…T. harzianum IOC3844 (ThIOC3844) was obtained from the Brazilian Collection of Environment and Industrial Microorganisms (CBMAI). A library of BACs consisting of 5,760 clones previously constructed for this fungus strain [24] was used to search for genomic regions. The genomic sequences of T. harzianum T6776 ( PRJNA252551 ), T. reesei QM6a ( PRJNA325840 ), T. atroviride IMI206040 ( PRJNA19867 ) and T. virens Gv29-8 ( PRJNA19983 ) were used for comparison with ThIOC3844.…”

“…The purpose of the present study was to analyze genomic regions with CAZyme genes using a bacterial artificial chromosome (BAC) library that we built [24] and to integrate these data with RNA-seq, secretome data and coregulation networks. We sequenced a massive amount of DNA and used it to integrate genomic data (genomic regions containing CAZymes), expression patterns (the transcriptome under degradation conditions), proteins (the secretome by mass spectrometry) and systems biology (with gene regulatory networks) to obtain a broad and precise overview of the CEL degradation pathways.…”