Network Analysis Reveals Different Cellulose Degradation Strategies acrossTrichoderma harzianumStrains Associated with XYR1 and CRE1

Abstract

Background: Trichoderma species have attracted attention as alternative plant polysaccharide-degrading enzyme sources, among other reasons. Most Trichoderma spp., such as Trichoderma atroviride and Trichoderma harzianum, are described as mycoparasitic fungi and are widely used in agriculture as biocontrol agents. T. harzianum is also a potential candidate for hydrolytic enzyme production in which gene expression is tightly controlled. Thus, a better understanding of transcriptional regulation related to the main activator (XYR1) and repressor (CRE1) of cellulases and hemicellulases is necessary. Herein, we explore the genetic mechanisms of the key regulators of genes encoding plant cell wall-degrading enzymes by inferring a gene coexpression network for T. harzianum (IOC-3844 and CBMAI-0179) and, for comparative purposes, for T. atroviride CBMAI-0020.Results: Phylogenetic analysis indicated that both regulatory proteins are widely distributed among ascomycete fungi and suggested how T. atroviride is differentiated from T. harzianum. The coexpression network analyses separated the transcripts into several groups according to the expression profile during growth in cellulose or glucose.Groups with xyr1 or cre1 were identified, and within them, transcripts encoding carbohydrate-active enzymes (CAZymes), TFs, sugar and ion transporters, and proteins with unknown function were coexpressed. However, qualitative and quantitative differences among groups and strains were observed. Core transcripts from these groups (hubs) were identified, and they included transcripts not yet characterized or described as related to cellulose degradation. Several metabolic pathways triggered were recognized with high similarity between both regulators during cellulose degradation, but they differed according to the strains. An enrichment related to mycoparasitism in T. atroviride, especially that associated with CRE1, was observed. It was also noticed that the transcripts encoding CAZymes related to polysaccharide degradation in T.harzianum are not necessarily coexpressed with the TFs studied herein. Conclusion: Our results suggest that different strategies related to XYR1 and CRE1 are used by Trichoderma spp. during cellulose degradation and provide new insights into transcripts coexpressed with both TFs in T. harzianum. This knowledge can be exploited to improve the understanding of the genetic mechanisms involved in hydrolytic enzyme regulation, expanding the potential of T. harzianum use in several industrial applications. 3 Due to the expanding population and industrialization, the demand for energy is increasing throughout the world. Currently, the primary energy source is fossil fuels, i.e., nonrenewable sources such as natural gas, oil, and coal [1]. To reduce the dependency on these finite resources, the development of new sustainable alternatives has become critical. In this context, increasing attention has been given to the development of biofuels from biomass [2, 3]. The United States and Brazil are the world's largest bioet...

Whole-Genome Sequencing and Comparative Genomic Analysis of Potential Biotechnological Strains of Trichoderma harzianum, Trichoderma atroviride, andTrichoderma reesei

“…In this study, we detected SVs by aligning our four genomes against T. reesei QM6a (Martinez et al, 2008); although the genomes were assembled at a scaffolding level, unlike the T. reesei QM6a reference genome that was assembled at the chromosome level, we chose to proceed with this dataset because its annotation file was available . As expected, due to phylogenetic proximity to the reference genome (Rosolen et al, 2021), Tr0711 showed the lowest number of SVs compared to that of the other strains. However, although T. atroviride is phylogenetically distant from T. reesei (Rosolen et al, 2021), Ta0020 exhibited fewer SVs than that of both T. harzianum strains, and this result might be explained by the uncertain phylogenetic position of fungi in these species (Druzhinina et al, 2010).…”

“…These observations might be explained by the complex speciation process within the T. harzianum species group (Druzhinina et al, 2010); therefore, the phylogenetic position is uncertain for fungi from these species. However, the molecular identification of Th3844 and Th0179 based on the ITS and tef1 sequences has already been reported (Rosolen et al, 2021), confirming that both strains were phylogenetically close to other T. harzianum strains. Tr0711 was grouped with T. pararessei CBS 125925, and both were phylogenetically in proximity to other T. reesei strains.…”

“…However, although T. atroviride is phylogenetically distant from T. reesei (Rosolen et al, 2021), Ta0020 exhibited fewer SVs than that of both T. harzianum strains, and this result might be explained by the uncertain phylogenetic position of fungi in these species (Druzhinina et al, 2010). Although the T. harzianum strains are phylogenetically close (Rosolen et al, 2021), genetic variability across the strains is evident when comparing the SVs that were identified from mapping both genomes against T. reesei QM6a (Martinez et al, 2008). Such results are consistent with the findings of previous studies in that genetic variations between fungal strains of the same species are not uncommon (Andersen et al, 2011; de Vries et al, 2017; Thanh et al, 2019).…”

“…In addition to their mycoparasitic activities, hydrolytic enzymes from T. harzianum strains have demonstrated great potential in the conversion of lignocellulosic biomass into fermentable sugars (Almeida et al, 2021; Delabona et al, 2020b; Motta et al, 2021; Zhang et al, 2020b). Recently, different types of enzymatic profiles across Trichoderma species were reported, in which Th3844 and Th0179 presented a higher hydrolytic potential during growth on cellulose than that of Ta0020 (Almeida et al, 2021); furthermore, differences between Th3844 and Th0179 concerning the transcriptional regulation coordinated by XYR1 and CRE1 during cellulose degradation were reported (Rosolen et al, 2021). Because such diversity in enzyme response might be related to transcriptomic and genomic differences, we aimed to provide foundations for further studies that could investigate such variations at a genomic level.…”

“…Such studies have suggested the great potential of both T. harzianum strains as hydrolytic enzyme producers, and this was similar to Tr0711, while Ta0020 showed a low cellulolytic ability. Furthermore, differences in the transcription regulation within hydrolytic enzyme expression were observed for Th3844 and Th0179 (Rosolen et al, 2021), highlighting the genetic differences between such strains. Although previous studies investigated the Th3844 genomic regions, which are related to biomass degradation, through bacterial artificial chromosome (BAC) library construction (Crucello et al, 2015; Ferreira Filho et al, 2017), genomic information regarding the hydrolytic strains of T. harzianum , Th3844 and Th0179 remains unclear.…”