Lignin-degrading peroxidases in white-rot fungus Trametes hirsuta 072. Absolute expression quantification of full multigene family

Abstract

Ligninolytic heme peroxidases comprise an extensive family of enzymes, which production is characteristic for white-rot Basidiomycota. The majority of fungal heme peroxidases are encoded by multigene families that differentially express closely related proteins. Currently, there were very few attempts to characterize the complete multigene family of heme peroxidases in a single fungus. Here we are focusing on identification and characterization of peroxidase genes, which are transcribed and secreted by basidiomycete Trametes hirsuta 072, an efficient lignin degrader. The T. hirsuta genome contains 18 ligninolytic peroxidase genes encoding 9 putative lignin peroxidases (LiP), 7 putative short manganese peroxidases (MnP) and 2 putative versatile peroxidases (VP). Using ddPCR method we have quantified the absolute expression of the 18 peroxidase genes under different culture conditions and on different growth stages of basidiomycete. It was shown that only two genes (one MnP and one VP) were prevalently expressed as well as secreted into cultural broth under all conditions investigated. However their transcriptome and protein profiles differed in time depending on the effector used. The expression of other peroxidase genes revealed a significant variability, so one can propose the specific roles of these enzymes in fungal development and lifestyle.

Effects of organic matter and low oxygen on the mycobenthos in a coastal lagoon

“…B). The ‘brown rot’ fungus Postia and the ‘white rot’ fungus Trametes (Vasina et al ., ) also exhibited a relatively higher gene expression in the lignocellulose treatments – suggesting that their activity was stimulated by this substrate. Most of the genes expressed encode hypothetical proteins with as‐of‐yet no biochemically determined function (Fig.…”

“…6B). High relative expression genes encoding hypothetical proteins from the basidiomycete genera Wallemia, the 'brown rot' fungus Postia, and the 'white rot' fungus Trametes (Vasina et al, 2017) were detected ( Fig. 6B).…”

“…A higher relative expression of genes in the presence of lignocellulose from the basidiomycete genera Trametes (a 'white rot' fungus) (Vasina et al, 2017) and Postia ('brown rot' Fungi) (Rytioja et al, 2014) is likely due to their specialized traits geared towards degrading lignin. Several species of Trametes produce lignin degrading peroxidases (Vasina et al, 2017) and Postia also produce enzymes that contribute to lignocellulose degradation (Martinez et al, 2009). Basidiomycete Fungi are typically less abundant in the marine environment relative to Ascomycota and Chytrid Fungi (Richards et al, 2012).…”

White-rot basidiomycetes Junghuhnia nitida and Steccherinum bourdotii: Oxidative potential and laccase properties in comparison with Trametes hirsuta and Coriolopsis caperata

“…In contrast, during cultivation of T . hirsuta on various media, secretion of peroxidases was shown to precede laccase secretion [ 22 , 48 ]. Such a difference in the secretion profiles of ligninolytic enzymes may be due to the fact that J .…”

Selection and Evaluation of Reference Genes for ddPCR-Based Transcript Abundance Studies in Oidiodendron Maius Across Varying Carbon Sources

“…Increasingly, however, it is becoming an indispensable tool in transcript abundance analysis as it exhibits greater sensitivity than qPCR when examining subtle fold-differences and has bene ts when mRNA is in low abundance (7). Additionally, ddPCR allows for reliable and reproducible measurements when anticipating closely related gene sequences or in the examination of highly similar mRNAs, such as those in multigene families (8). Due to the capacity of ddPCR to absolutely quantify the number of copies of the target in a given sample, normalization, such as the use of a reference gene, is not considered obligatory.…”