Biology subjects

Rosolen, R. R.

Publications and source records attributed to Rosolen, R. R..

4 recordsLinked to original sources

bioRxiv2025

Genetic response to light and carbon source variations in Trichoderma harzianum: The key regulatory roles of env1, cre1, and blr2

In filamentous fungi, light plays a key role in regulating physiological processes such as growth, conidiation, secondary metabolism, and the expression of hydrolytic enzymes. The processes that depend on light are controlled by photoreceptors, including BLR1, BLR2, and ENV1, as well as by signaling pathways involving heterotrimeric G-proteins and cyclic adenosine monophosphate (cAMP). Trichoderma harzianum is a promising candidate for biotechnological use and is able to promote hydrolytic reactions under biomass degradation conditions. However, the genetic mechanisms underlying its response to light remain poorly understood, especially under degradative conditions. This study aimed to assess the expression of carbohydrate-active enzymes (CAZymes), transcription factors (TFs), and signaling pathway proteins under different light conditions and carbon sources. The results revealed distinct patterns of relative gene expression influenced by these environmental factors, highlighting the complex regulatory mechanisms at play in T. harzianum. Moreover, our results suggested that env1, cre1, and blr2 are critical for adjusting to different light conditions and carbon sources. This highlights the importance of both factors in regulating gene expression and supporting metabolic adaptation in T. harzianum. To our knowledge, such findings have not been previously reported in the context of cellulose degradation for this species. Overall, these results offer valuable insights into how T. harzianum responds to environmental changes, revealing a complex regulatory network that is not only crucial for optimizing fungal growth in industrial applications but also deepens our understanding of its biology and ecological interactions. Highlights{blacksquare} Trichoderma harzianum is a key candidate for biotechnology applications. {blacksquare}Light and carbon control CAZymes, photoreceptors, key regulators, and signaling. {blacksquare}T. harzianum has distinct gene expression patterns under different light conditions and carbon sources. {blacksquare}env1, cre1, and blr2 regulate metabolic adaptation in T. harzianum. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=185 SRC="FIGDIR/small/657067v1_ufig1.gif" ALT="Figure 1"> View larger version (72K): org.highwire.dtl.DTLVardef@8167c7org.highwire.dtl.DTLVardef@1c46f6borg.highwire.dtl.DTLVardef@16eddc8org.highwire.dtl.DTLVardef@1a2afa6_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

Lignocellulolytic carbohydrate-active enzyme-encoding gene clusters in novel Trichoderma atroviride and Trichoderma harzianum strains: A BAC-guided transcriptome analysis

Lignocellulosic biomass is known as a challenging substrate for enzymatic hydrolysis, increasing the processing cost in biorefineries. In nature, filamentous fungi, including those of the genus Trichoderma, naturally degrade lignocellulose by using an arsenal of hydrolytic and oxidative enzymes that act synergistically with biomass degradation. This work explored the genome organization of target genes of Trichoderma atroviride and Trichoderma harzianum that are able to promote hydrolysis by identifying regions enriched in degradative enzyme-encoding genes, namely, hydrolytic clusters. We employed bacterial artificial chromosome (BAC) methodology to target specific genomic regions to explore their genetic organization, proximal gene context, and gene expression under degradative conditions. Using this tool, it was possible to inspect the linear structure and expression data of target hydrolytic-rich genomic regions. The results offered a genomic perspective of the organization of genome regions related to carbohydrate metabolism, revealing novel genome regions and genes that are positively regulated during cellulose degradation and contributing to elucidating differences in gene organization among Trichoderma species. HighlightsO_LIHigh-quality genomic regions were selected using closely related species CAZyme targets. C_LIO_LIRNA-seq data were used to quantify BAC genes expression. C_LIO_LIRelevant regions were identified by combining functional and differential expression data. C_LIO_LINovel targets for future characterization identified via differential expression. C_LI

genomics↗

bioRxiv2022

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

Trichoderma atroviride and Trichoderma harzianum are widely used as commercial biocontrol agents against plant diseases. Recently, T. harzianum IOC-3844 (Th3844) and T. harzianum CBMAI-0179 (Th0179) demonstrated great potential in the enzymatic conversion of lignocellulose into fermentable sugars. Herein, we performed whole-genome sequencing and assembly of the Th3844 and Th0179 strains. To assess the genetic diversity within the genus Trichoderma, the results of both strains were compared with strains of T. atroviride CBMAI-00020 (Ta0020) and T. reesei CBMAI-0711 (Tr0711). The sequencing coverage value of all genomes evaluated in this study was higher than that of previously reported genomes for the same species of Trichoderma. The resulting assembly revealed total lengths of 40 Mb (Th3844), 39 Mb (Th0179), 36 Mb (Ta0020), and 32 Mb (Tr0711). A genome-wide phylogenetic analysis provided details on the relationships of the newly sequenced species with other Trichoderma species. Structural variants revealed genomic rearrangements among Th3844, Th0179, Ta0020, and Tr0711 relative to the T. reesei QM6a reference genome and showed the functional effects of such variants. In conclusion, the findings presented herein allow the visualization of genetic diversity in the evaluated strains and offer opportunities to explore such fungal genomes in future biotechnological and industrial applications.

genomics↗

bioRxiv2020

Comparative gene coexpression networks analysis reveals different strategies of Trichoderma spp. associated with XYR1 and CRE1 during cellulose degradation

Trichoderma harzianum, whose gene expression is tightly controlled by the transcription factors (TFs) XYR1 and CRE1, is a potential candidate for hydrolytic enzyme production. Here, we performed a network analysis of T. harzianum IOC-3844 and T. harzianum CBMAI-0179 to explore how the regulation of these TFs varies between these strains. In addition, we explored the evolutionary relationships of XYR1 and CRE1 protein sequences among Trichoderma spp. The results of the T. harzianum strains were compared with those of Trichoderma atroviride CBMAI-0020, a mycoparasitic species. Although transcripts encoding carbohydrate-active enzymes (CAZymes), TFs, transporters, and proteins with unknown functions were coexpressed with cre1 or xyr1, other proteins indirectly related to cellulose degradation were identified. The enriched GO terms describing the transcripts of these groups differed across all strains, and several metabolic pathways with high similarity between both regulators but strain-specific differences were identified. In addition, the CRE1 and XYR1 subnetworks presented different topology profiles in each strain, likely indicating differences in the influences of these regulators according to the fungi. The hubs of the cre1 and xyr1 groups included transcripts not yet characterized or described as being related to cellulose degradation. The first-neighbor analyses confirmed the results of the profile of the coexpressed transcripts in cre1 and xyr1. The analyses of the shortest paths revealed that CAZymes upregulated under cellulose degradation conditions are most closely related to both regulators, and new targets between such signaling pathways were discovered. Although the evaluated T. harzianum strains are phylogenetically close and their amino acid sequences related to XYR1 and CRE1 are very similar, the set of transcripts related to xyr1 and cre1 differed, suggesting that each T. harzianum strain used a specific regulation strategy for cellulose degradation. More interestingly, our findings may suggest that XYR1 and CRE1 indirectly regulate genes encoding proteins related to cellulose degradation in the evaluated T. harzianum strains. An improved understanding of the basic biology of fungi during the cellulose degradation process can contribute to the use of their enzymes in several biotechnological applications and pave the way for further studies on the differences across strains of the same species.

bioinformatics↗