Visual Comparative Omics of Fungi for Plant Biomass Deconstruction.
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.
Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie Fongiques Marseille, France.
Shingo
S
Miyauchi
Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie FongiquesMarseille, France; CIRM-CF, UMR1163 Biodiversité et Biotechnologie FongiquesMarseille, France.
David
D
Navarro
US Department of Energy Joint Genome Institute, Walnut Creek CA, USA.
Igor V
IV
Grigoriev
US Department of Energy Joint Genome Institute, Walnut Creek CA, USA.
Anna
A
Lipzen
US Department of Energy Joint Genome Institute, Walnut Creek CA, USA.
Robert
R
Riley
Plateforme d'Analyse Protéomique de Paris Sud-Ouest, UMR1319 Micalis, INRA Jouy-en-Josas, France.
Didier
D
Chevret
Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie Fongiques Marseille, France.
Sacha
S
Grisel
Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie Fongiques Marseille, France.
Jean-Guy
JG
Berrin
Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille UniversitéMarseille, France; INRA, USC 1408 AFMBMarseille, France; Department of Biological Sciences, King Abdulaziz UniversityJeddah, Saudi Arabia.
Bernard
B
Henrissat
Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie Fongiques Marseille, France.
Marie-Noëlle
MN
Rosso
CAZymes; LPMOs; biorefinery; data visualization; lignocellulosic biomass; multi-omics integration; self-organizing maps