Visual Comparative Omics of Fungi for Plant Biomass Deconstruction

Abstract

Wood-decay fungi contain the cellular mechanisms to decompose such plant cell wall components as cellulose, hemicellulose, and lignin. A multi-omics approach to the comparative analysis of wood-decay fungi gives not only new insights into their strategies for decomposing recalcitrant plant biomass, but also an understanding of how to exploit these mechanisms for biotechnological applications. We have developed an analytical workflow, Applied Biomass Conversion Design for Efficient Fungal Green Technology (ABCDEFGT), to simplify the analysis and interpretation of transcriptomic and secretomic data. ABCDEFGT utilizes self-organizing maps for grouping genes with similar transcription patterns, and an overlay with secreted proteins. The key feature of ABCDEFGT is simple graphic outputs of genome-wide transcriptomic and secretomic topographies, which enables visual inspection without a priori of the omics data and facilitates discoveries of co-regulated genes and proteins. Genome-wide omics landscapes were built with the newly sequenced fungal species Pycnoporus coccineus, Pycnoporus sanguineus, and Pycnoporus cinnabarinus grown on various carbon sources. Integration of the post-genomic data revealed a global overlap, confirming the pertinence of the genome-wide approach. ABCDEFGT was evaluated by comparison with the latest clustering method for ease of output interpretation, and ABCDEFGT gave a better biological representation of fungal behaviors. The genome-wide multi-omics strategy allowed us to determine the potential synergy of particular enzymes decomposing cellulose, hemicellulose, and lignin such as Lytic Polysaccharide Monooxygenases, modular enzymes associated with a cellulose binding module1, and Class II Peroxidase isoforms co-regulated with oxido-reductases. Overall, ABCDEFGT was capable of visualizing genome-wide transcriptional and secretomic profiles for intuitive interpretations and is suitable for exploration of newly-sequenced organisms.

Broad‐specificity GH131 β‐glucanases are a hallmark of fungi and oomycetes that colonize plants

“…The ability of all tested GH131 to accommodate (β-1,3; β-1,6) bonds from laminarin suggest that GH131 enzymes could function in remodelling the fungal cell wall during plant colonization and/or nutrient extraction. This hypothesis is supported by strong transcriptional upregulation of GH16 and GH30 beta-1,6-glucanase genes during plant tissue colonization in the fungi analysed here (O'Connell et al, 2012;Gan et al, 2013;Veneault-Fourrey et al, 2014;Miyauchi et al, 2016), and the extensive fungal cell wall rearrangements generally observed during plant-fungus interactions (Balestrini and Bonfante, 2014;Geoghegan et al, 2017). This activity could also contribute to the virulence arsenal of certain mycoparasitic fungi which involves β-(1,4)-, β-(1,3)and β-(1,6)-glucanases and proteases (Benítez et al, 2004).…”

“…In C. higginsianum, genes coding for two GH5, one GH6, two GH7, and two GH12 were upregulated during that phase compared to in vitro growth (O'Connell et al, ). In a previous study on the response of the saprotrophic fungi P. sanguineus, P. coccineus and P. cinnabarinus to growth on lignocellulosic and woody substrates (Miyauchi et al, ), GH131 enzymes were shown to be co‐secreted with GH6 and GH7 cellobiohydrolases, GH5_5 and GH45 endoglucanases and AA9s. Co‐secretion of GH131 enzymes with other cellulose‐acting enzymes suggests that despite their relatively low specific activity, these enzymes could either facilitate access to the substrate for other enzymes or act in synergy with these enzymes to facilitate cellulose degradation.…”

“…Transcriptome data for the GH131‐coding genes were extracted from published studies. We compared the transcription profiles in the following conditions: (i) Biotrophic vs. necrotrophic stages of infection for C. higginsianum on Arabidopsis thaliana and C. graminicola on maize (O'Connell et al, ); (ii) Asymptomatic vs. necrotrophic stages of infection for Z. tritici on wheat leaves (Rudd et al, ; Palma‐Guerrero et al, ); (iii) free‐living mycelium vs. ectomycorrhizal stage for L. bicolor California poplar ( Populus trichocarpa ; Veneault‐Fourrey et al, ); (iv) saprotrophic growth on dead plant tissues, such as wheat straw, pine wood and aspen wood vs. maltose as a carbon source for P. sanguineus , P. cinnabarinus and P. coccineus (Miyauchi et al, ).…”

“…To investigate the biological role of GH131 enzymes in plant-colonizing fungal lifestyles, we focused on exemplar fungal species with three different lifestyles: three plant pathogens, Colletotrichum higginsianum, C. graminicola and Zymoseptoria tritici; three white-rot saprotrophic fungi, Pycnoporus sanguineus, P. coccineus and P. cinnabarinus; and one ectomycorrhizal symbiotic fungus, Laccaria bicolor, taking advantage of available genomic and transcriptomic data from different infection stages and/or substrates (Martin et al, 2008;Goodwin et al, 2011;O'Connell et al, 2012;Gan et al, 2013;Levasseur et al, 2014;Veneault-Fourrey et al, 2014;Rudd et al, 2015;Miyauchi et al, 2016;Palma-Guerrero et al, 2016) and, in the case of the plant pathogenic ones, their well-defined infection stages (Perfect et al, 1999;Duncan and Howard, 2000;O'Connell et al, 2004;Munch et al, 2008). The number of genes coding for GH131 varied among the different species, from one in L. bicolor and Z. tritici to more than seven in Colletotrichum species (Table 1).…”

An ectomycorrhizal fungus alters sensitivity to jasmonate, salicylate, gibberellin, and ethylene in host roots

“…To obtain a comprehensive view of the impact of hormone treatments on the poplar and L. bicolor transcriptomes, we constructed transcriptomic models using SHIN+GO (self-organizing map harboring informative nodes with gene ontology; Miyauchi et al, 2016Miyauchi et al, , 2017Miyauchi et al, , 2018. A self-organizing map was trained with the normalized read count of the selected replicates using Rsomoclu (Wittek et al, 2017).…”