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An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.

ABSTRACT: The thermophilic fungus Chaetomium thermophilum holds great promise for structural biology. To increase the efficiency of its biochemical and structural characterization and to explore its thermophilic properties beyond those of individual proteins, we obtained transcriptomics and proteomics data, and integrated them with computational annotation methods and a multitude of biochemical experiments conducted by the structural biology community. We considerably improved the genome annotation of Chaetomium thermophilum and characterized the transcripts and expression of thousands of genes. We furthermore show that the composition and structure of the expressed proteome of Chaetomium thermophilum is similar to its mesophilic relatives. Data were deposited in a publicly available repository and provide a rich source to the structural biology community.

SUBMITTER: Bock T

PROVIDER: S-EPMC4267624 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

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An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.

Bock Thomas T Chen Wei-Hua WH Ori Alessandro A Malik Nayab N Silva-Martin Noella N Huerta-Cepas Jaime J Powell Sean T ST Kastritis Panagiotis L PL Smyshlyaev Georgy G Vonkova Ivana I Kirkpatrick Joanna J Doerks Tobias T Nesme Leo L Baßler Jochen J Kos Martin M Hurt Ed E Carlomagno Teresa T Gavin Anne-Claude AC Barabas Orsolya O Müller Christoph W CW van Noort Vera V Beck Martin M Bork Peer P

Nucleic acids research 20141114 22

The thermophilic fungus Chaetomium thermophilum holds great promise for structural biology. To increase the efficiency of its biochemical and structural characterization and to explore its thermophilic properties beyond those of individual proteins, we obtained transcriptomics and proteomics data, and integrated them with computational annotation methods and a multitude of biochemical experiments conducted by the structural biology community. We considerably improved the genome annotation of Cha ...[more]

PMID: 25398899

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Project description:BackgroundLignocellulose is the most abundant and renewable biomass resource on the planet. Lignocellulose can be converted into biofuels and high-value compounds; however, its recalcitrance makes its breakdown a challenge. Lytic polysaccharide monooxygenases (LPMOs) offer tremendous promise for the degradation of recalcitrant polysaccharides. Chaetomium thermophilum, having many LPMO-coding genes, is a dominant thermophilic fungus in cellulose-rich and self-heating habitats. This study explores the genome, secretomes and transcript levels of specific genes of C. thermophilum.ResultsThe genome of C. thermophilum encoded a comprehensive set of cellulose- and xylan-degrading enzymes, especially 18 AA9 LPMOs that belonged to different subfamilies. Extracellular secretomes showed that arabinose and microcrystalline cellulose (MCC) could specifically induce the secretion of carbohydrate-active enzymes (CAZymes), especially AA9 LPMOs, by C. thermophilum under different carbon sources. Temporal analyses of secretomes and transcripts revealed that arabinose induced the secretion of xylanases by C. thermophilum, which was obviously different from other common filamentous fungi. MCC could efficiently induce the specific secretion of LPMO2s, possibly because the insert in loop3 on the substrate-binding surface of LPMO2s strengthened its binding capacity to cellulose. LPMO2s, cellobio hydrolases (CBHs) and cellobiose dehydrogenases (CDHs) were cosecreted, forming an efficient cellulose degradation system of oxidases and hydrolases under thermophilic conditions.ConclusionsThe specific expression of LPMO2s and cosecretion of hydrolases and oxidases by the thermophilic fungus C. thermophilum play an important role in cellulose degradation. This insight increases our understanding of the cellulose degradation under thermophilic conditions and may inspire the design of the optimal enzyme cocktails for more efficient exploration of biomass resources in industrial applications.

Dataset Information

An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.

Publications

An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.

Similar Datasets

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