PT  - JOURNAL ARTICLE
AU  - Jaire A. Ferreira Filho
AU  - Maria Augusta C. Horta
AU  - Clelton A. dos Santos
AU  - Deborah A. Almeida
AU  - Natália F. Murad
AU  - Juliano S. Mendes
AU  - Danilo A. Sforça
AU  - Claudio Benício C. Silva
AU  - Aline Crucello
AU  - Anete P. de Souza
TI  - “Integrative Genomic Analysis for the Bioprospection of Regulators and Accessory Enzymes Associated with Cellulose Degradation in a Filamentous Fungus (<em>Trichoderma harzianum</em>)”
AID  - 10.1101/731323
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 731323
4099  - http://biorxiv.org/content/early/2019/08/21/731323.short
4100  - http://biorxiv.org/content/early/2019/08/21/731323.full
AB  - Background Unveiling fungal genome structure and function reveals the potential biotechnological use of fungi. Trichoderma harzianum is a powerful CAZyme-producing fungus. We studied the genomic regions in T. harzianum IOC3844 containing CAZyme genes, transcription factors and transporters.Results We used bioinformatics tools to mine the T. harzianum genome for potential genomics, transcriptomics, and exoproteomics data and coexpression networks. The DNA was sequenced by PacBio SMRT technology for multi-omics data analysis and integration. In total, 1676 genes were annotated in the genomic regions analyzed; 222 were identified as CAZymes in T. harzianum IOC3844. When comparing transcriptome data under cellulose or glucose conditions, 114 genes were differentially expressed in cellulose, with 51 CAZymes. CLR2, a transcription factor physically and phylogenetically conserved in T. harzianum spp., was differentially expressed under cellulose conditions. The genes induced/repressed under cellulose conditions included those important for plant biomass degradation, including CIP2 of the CE15 family and a copper-dependent LPMO of the AA9 family.Conclusions Our results provide new insights into the relationship between genomic organization and hydrolytic enzyme expression and regulation in T. harzianum IOC3844. Our results can improve plant biomass degradation, which is fundamental for developing more efficient strains and/or enzymatic cocktails for the production of hydrolytic enzymes.AAAuxiliary enzymes;Bburied;BACbacterial artificial chromosome;BLASTBasic local alignment search tool;bpBase pair;BRENDABraunschweig Enzyme Database;Cloop;CAZymesCarbohydrate-active enzymes;CBMAIBrazilian Collection of Environment and Industrial Microorganisms;CBMCarbohydrate-binding module;CECarbohydrate esterases;CELCellulose;CIP1cellulose-induced protein 1;CIP2cellulose-induced protein 2;CLR2cellulose degradation regulator 2;DNADeoxyribonucleic acid;Ebeta-sheet;ECEnzyme commission number;Exexposed;FCfold change;GHGlycoside hydrolases;GLUGlucose;GOgene ontologies;GTGlycosyltransferases;Hhelix;JTTJones-Taylor-Thornton;kbKilobases;LPMOLytic polysaccharides monooxygenase;Mmedium;MbMegabase;MEGAMolecular evolutionary genetics analysis;MFSmajor facilitator superfamily permease;MLmaximum likelihood;PacBioPacific Biosciences;PBcRPacBio Corrected Reads;PCRPolymerase chain reaction;PLPolysaccharide lyases;RNARibonucleic acid;RNA-SeqRNA sequencing;RPKMReads per kilobase of exon model per million mapped reads;SMRTSingle-Molecule Real-Time;TaIMI206040T. atroviride IMI206040;TFstranscription factors;ThB97T. harzianum B97;ThIOC3844Trichoderma harzianum IOC-3844;ThTR274T. harzianum TR274;Th6766T. harzianum;TPMTranscripts per million;TrQM6aT. reesei QM6a;TvGv29-8T. virens Gv29-8