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Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction
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Edité par CCSD ; BioMed Central -
International audience. AbstractBackground: The hydrolysis of biomass to simple sugars used for the production of biofuels in biorefneries requiresthe action of cellulolytic enzyme mixtures. During the last 50 years, the ascomycete Trichoderma reesei, the mainsource of industrial cellulase and hemicellulase cocktails, has been subjected to several rounds of classical mutagenesiswith the aim to obtain higher production levels. During these random genetic events, strains unable to producecellulases were generated. Here, whole genome sequencing and transcriptomic analyses of the cellulase-negativestrain QM9978 were used for the identifcation of mutations underlying this cellulase-negative phenotype.Results: Sequence comparison of the cellulase-negative strain QM9978 to the reference strain QM6a identifed atotal of 43 mutations, of which 33 were located either close to or in coding regions. From those, we identifed 23 single-nucleotidevariants, nine InDels, and one translocation. The translocation occurred between chromosomes V andVII, is located upstream of the putative transcription factor vib1, and abolishes its expression in QM9978 as detectedduring the transcriptomic analyses. Ectopic expression of vib1 under the control of its native promoter as well as overexpressionof vib1 under the control of a strong constitutive promoter restored cellulase expression in QM9978, thusconfrming that the translocation event is the reason for the cellulase-negative phenotype. Gene deletion of vib1 inthe moderate producer strain QM9414 and in the high producer strain Rut-C30 reduced cellulase expression in bothcases. Overexpression of vib1 in QM9414 and Rut-C30 had no efect on cellulase production, most likely because vib1is already expressed at an optimal level under normal conditions.Conclusion: We were able to establish a link between a chromosomal translocation in QM9978 and the cellulasenegativephenotype of the strain. We identifed the transcription factor vib1 as a key regulator of cellulases in T. reeseiwhose expression is absent in QM9978. We propose that in T. reesei, as in Neurospora crassa, vib1 is involved in cellulaseinduction, although the exact mechanism remains to be elucidated. The data presented here show an example ofa combined genome sequencing and transcriptomic approach to explain a specifc trait, in this case the QM9978cellulase-negative phenotype, and how it helps to better understand the mechanisms during cellulase gene regulation.When focusing on mutations on the single base-pair level, changes on the chromosome level can be easily
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