A long noncoding RNA promotes cellulase expression in Trichoderma reesei

Abstract

BackgroundDue to its capability to secrete large quantities of plant biomass degrading enzymes (PBDE), Trichoderma reesei is widely applied for industrial purposes. In nature, expression of PBDE is efficiently regulated in this fungus. Several factors involved in this regulatory network have been identified. However, most of them are transcription factors. Long noncoding RNAs (lncRNAs) emerged as common players acting on epigenetic or transcriptional regulation in several eukaryotic organisms. To date, no lncRNA has been described in filamentous fungi.ResultsA lncRNA termed HAX1 was identified in T. reesei QM9414. In this study, it was characterized and evidence for its regulatory impact on cellulase expression was provided. Interestingly, different versions of HAX1 were identified in different strains (namely, QM6a, QM9414, and Rut-C30), varying in terms of RNA length. Remarkably, considerable longer variants of this lncRNA are present in hypercellulolytic strains compared to the wild-type strain QM6a. Based on these results, a correlation between RNA length and the functional impact of HAX1 on PBDE expression was supposed. This assumption was verified by overexpressing the most abundant HAX1 versions identified in QM6a, QM9414, and Rut-C30. Such HAX1 overexpression on the one hand was suitable for regaining the function in hax1 disruption strains, and on the other hand resulted in notably higher cellulase activities in QM6a, especially by the expression of longer HAX1 versions.ConclusionWith HAX1, for the first time the regulatory role of a lncRNA in filamentous fungi was uncovered. Besides this, a new player involved in the complex regulation of PBDE expression in T. reesei was identified. Due to its enhancing effect on cellulase activity, HAX1 was shown to be not only interesting for basic research, but also a promising candidate for expanding the set of biotechnological tools for industrial application of T. reesei.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1081-4) contains supplementary material, which is available to authorized users.

XRN1‐associated long non‐coding RNAs may contribute to fungal virulence and sexual development in entomopathogenic fungus Cordyceps militaris

“…lncRNAs play crucial roles in epigenetic regulation and have emerged as common factors involved in a number of central cellular processes in several eukaryotes . In the past decade, studies of lncRNAs in fungi have steadily increased, such as in yeast, N. crassa , and T. reesei . However, the characteristics of lncRNAs in entomopathogenic fungi remain unclear.…”

“…34 In the past decade, studies of lncRNAs in fungi have steadily increased, such as in yeast, N. crassa, and T. reesei. 15,16,34 However, the characteristics of lncR-NAs in entomopathogenic fungi remain unclear. In this study, we evaluated lncRNAs in the entomopathogenic fungus C. militaris on a genome-wide level.…”

“…Thousands of lncRNAs that have been annotated and characterized in Neurospora crassa may use important biological functions . Recently, the lncRNA HAX1 was identified and found to promote cellulase expression in Trichoderma reesei , which is the first lncRNA identified to play a regulatory role in filamentous fungi . In Fusarium graminearum , hundreds of lncRNAs that exhibit developmental stage‐specific expression patterns during fruiting body formation were identified, and various lncRNAs were induced in parallel with their overlapping transcripts on the opposite DNA strand during sexual development, suggesting that lncRNAs play important roles in shaping fungal fruiting bodies .…”

“…15 Recently, the lncRNA HAX1 was identified and found to promote cellulase expression in Trichoderma reesei, which is the first lncRNA identified to play a regulatory role in filamentous fungi. 16 In Fusarium graminearum, hundreds of lncRNAs that exhibit developmental stage-specific expression patterns during fruiting body formation were identified, and various lncRNAs were induced in parallel with their overlapping transcripts on the opposite DNA strand during sexual development, suggesting that lncRNAs play important roles in shaping fungal fruiting bodies. 17 Transcriptional data indicated that plant pathogen Phytophthora sojae lncRNAs are transcribed in a stage-specific manner, and RNA-seq data revealed a correlation between the transcription level of lncRNAs and their neighboring genes.…”

Strategies and Challenges for the Development of Industrial Enzymes Using Fungal Cell Factories

“…Identification and manipulation of long noncoding RNAs represent another means to engineer filamentous fungi for improved heterologous protein production. Recently a long noncoding RNA, Hax1, that enhances cellulase expression was discovered in T. reesei (Till et al 2018b). With low-cost sequencing, it is possible to sequence RNA to identify possible long noncoding RNAs present under relevant fermentation conditions for production followed by functional testing to determine if they have an impact on protein production.…”