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

Abstract

BackgroundThe hydrolysis of biomass to simple sugars used for the production of biofuels in biorefineries requires the action of cellulolytic enzyme mixtures. During the last 50 years, the ascomycete Trichoderma reesei, the main source of industrial cellulase and hemicellulase cocktails, has been subjected to several rounds of classical mutagenesis with the aim to obtain higher production levels. During these random genetic events, strains unable to produce cellulases were generated. Here, whole genome sequencing and transcriptomic analyses of the cellulase-negative strain QM9978 were used for the identification of mutations underlying this cellulase-negative phenotype.ResultsSequence comparison of the cellulase-negative strain QM9978 to the reference strain QM6a identified a total of 43 mutations, of which 33 were located either close to or in coding regions. From those, we identified 23 single-nucleotide variants, nine InDels, and one translocation. The translocation occurred between chromosomes V and VII, is located upstream of the putative transcription factor vib1, and abolishes its expression in QM9978 as detected during the transcriptomic analyses. Ectopic expression of vib1 under the control of its native promoter as well as overexpression of vib1 under the control of a strong constitutive promoter restored cellulase expression in QM9978, thus confirming that the translocation event is the reason for the cellulase-negative phenotype. Gene deletion of vib1 in the moderate producer strain QM9414 and in the high producer strain Rut-C30 reduced cellulase expression in both cases. Overexpression of vib1 in QM9414 and Rut-C30 had no effect on cellulase production, most likely because vib1 is already expressed at an optimal level under normal conditions.ConclusionWe were able to establish a link between a chromosomal translocation in QM9978 and the cellulase-negative phenotype of the strain. We identified the transcription factor vib1 as a key regulator of cellulases in T. reesei whose expression is absent in QM9978. We propose that in T. reesei, as in Neurospora crassa, vib1 is involved in cellulase induction, although the exact mechanism remains to be elucidated. The data presented here show an example of a combined genome sequencing and transcriptomic approach to explain a specific trait, in this case the QM9978 cellulase-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 overlooked and through this work we provide an example that stresses the importance of the big picture of the genomic landscape during analysis of sequencing data.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-017-0897-7) contains supplementary material, which is available to authorized users.

“Integrative Genomic Analysis for the Bioprospection of Regulators and Accessory Enzymes Associated with Cellulose Degradation in a Filamentous Fungus (Trichoderma harzianum)”

“…In the genome of ThIOC3844, we found a cluster with the CLR2 TF in association with other putative transcription factors, CAZymes, transporters and MFS permease. The same behavior was found for the T. reesei CLR2 TF, which has physical proximity and coexpression with a sugar transporter [29, 41]. These results indicate that there may be a mechanism for the joint regulation and expression of this TF with transporters related to biomass degradation.…”

“Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)”

“…In the ThIOC3844 genome, we found a cluster with the CLR2 TF in association with other putative TFs, CAZymes, transporters and MFS permease. The same behavior was found for the T. reesei CLR2 TF, which has physical proximity and is coexpressed with a sugar transporter [ 32 , 45 ]. These results indicate a mechanism for joint regulation and expression of this TF with transporters related to biomass degradation.…”

Regulation of plant cell wall degradation by light in Trichoderma

“…Later on, investigation of the genome of QM9978 and comparison to that of QM6a recently led to the finding that the PhoG homologue VIB1 is responsible for the defect in cellulase induction of this strain. A translocation of the gene abolished expression of vib1 in QM9978 [ 68 ]. Interestingly, vib1 is strongly down-regulated in light upon growth on cellulose in the wild-type strain QM6a (Stappler and Schmoll, unpublished).…”