Genomics insights into different cellobiose hydrolysis activities in two Trichoderma hamatum strains

Abstract

BackgroundEfficient biomass bioconversion is a promising solution to alternative energy resources and environmental issues associated with lignocellulosic wastes. The Trichoderma species of cellulolytic fungi have strong cellulose-degrading capability, and their cellulase systems have been extensively studied. Currently, a major limitation of Trichoderma strains is their low production of β-glucosidases.ResultsWe isolated two Trichoderma hamatum strains YYH13 and YYH16 with drastically different cellulose degrading efficiencies. YYH13 has higher cellobiose-hydrolyzing efficiency. To understand mechanisms underlying such differences, we sequenced the genomes of YYH13 and YYH16, which are essentially identical (38.93 and 38.92 Mb, respectively) and are similar to that of the T. hamatum strain GD12. Using GeneMark-ES, we annotated 11,316 and 11,755 protein-coding genes in YYH13 and YYH16, respectively. Comparative analysis identified 13 functionally important genes in YYH13 under positive selection. Through examining orthologous relationships, we identified 172,655, and 320 genome-specific genes in YYH13, YYH16, and GD12, respectively. We found 15 protease families that show differences between YYH13 and YYH16. Enzymatic tests showed that exoglucanase, endoglucanase, and β-glucosidase activities were higher in YYH13 than YYH16. Additionally, YYH13 contains 10 families of carbohydrate-active enzymes, including GH1, GH3, GH18, GH35, and GH55 families of chitinases, glucosidases, galactosidases, and glucanases, which are subject to stronger positive selection pressure. Furthermore, we found that the β-glucosidase gene (YYH1311079) and pGEX-KG/YYH1311079 bacterial expression vector may provide valuable insight for designing β-glucosidase with higher cellobiose-hydrolyzing efficiencies.ConclusionsThis study suggests that the YYH13 strain of T. hamatum has the potential to serve as a model organism for producing cellulase because of its strong ability to efficiently degrade cellulosic biomass. The genome sequences of YYH13 and YYH16 represents a valuable resource for studying efficient production of biofuels.Electronic supplementary materialThe online version of this article (doi:10.1186/s12934-017-0680-2) contains supplementary material, which is available to authorized users.

A Genomic and Transcriptomic Study on the DDT-Resistant Trichoderma hamatum FBL 587: First Genetic Data into Mycoremediation Strategies for DDT-Polluted Sites

“…Moreover, the annotated 10,994 protein-coding genes in FBL 587 fell within the known range for the genomes of the T. hamatum strains YYH13 (11,316), YYH16 (11,755) and GD12 (11,203), as reported in [13]. The 1.2% repetitive elements found in the genome of T. hamatum FBL 587 was typical among the sequenced T. hamatum strains, i.e., 1.47% repetitive elements for YYH13, 1.58% for YYH16, and 1.31% for GD12 [13]. Therefore, these NGS data indicate similar genome properties, reflecting a recent common ancestor.…”

“…This finding is also supported by further genomic analysis. In T. hamatum FBL 587 using the dbCAN CAZyme database we revealed the presence of a range of genes encoding for CAZymes that can be comparable with that of previously sequenced T. hamatum strains YYH13, YYH16 and GD12 [13][14][15], reflecting the adaption to their ecological niches as saprotrophic Trichoderma species in soil and rhizosphere, competing with other soil microorganisms. With respect to the GH class of CAZymes, the number of members of the glycoside hydrolases found in FBL 587 was similar to that harboured by other sequenced strains (YYH13, YYH16, and GD12) of T. hamatum.…”

“…The genome size of T. hamatum FBL 587 is essentially similar to that of other sequenced T. hamatum strains, namely YYH13 (38.93 Mb; [13]), YYH16 (38.92 Mb; [13]), and GD12 (38.43 Mb; [14,15]). Moreover, the annotated 10,994 protein-coding genes in FBL 587 fell within the known range for the genomes of the T. hamatum strains YYH13 (11,316), YYH16 (11,755) and GD12 (11,203), as reported in [13].…”

“…The genome size of T. hamatum FBL 587 is essentially similar to that of other sequenced T. hamatum strains, namely YYH13 (38.93 Mb; [13]), YYH16 (38.92 Mb; [13]), and GD12 (38.43 Mb; [14,15]). Moreover, the annotated 10,994 protein-coding genes in FBL 587 fell within the known range for the genomes of the T. hamatum strains YYH13 (11,316), YYH16 (11,755) and GD12 (11,203), as reported in [13]. The 1.2% repetitive elements found in the genome of T. hamatum FBL 587 was typical among the sequenced T. hamatum strains, i.e., 1.47% repetitive elements for YYH13, 1.58% for YYH16, and 1.31% for GD12 [13].…”

“…Phase I metabolizing enzymes (cytochrome P450s, and monooxygenases) catalyse xenobiotics mainly through hydroxylation/oxidation reactions, phase II conjugating enzymes (e.g., glutathione S-transferase and sulfotransferase) add polar molecules onto xenobiotics, producing water-soluble metabolites, and the phase III secretion system consists of ATP-binding cassette (ABC) and other transmembrane transporters (e.g., major facilitator superfamily (MFS) transporters) that actively export xenobiotic and/or metabolized compounds across the cell membranes [10,11]. Even though the genomic characterization of several strains of Trichoderma species [12] and of few strains of T. hamatum has been performed [13][14][15], genomic and transcriptomic studies of tolerance and degradation of DDT have not been conducted on Trichoderma species. Therefore, the identification of DDT-responsive genes encoded in the Trichoderma genome is still lacking.…”