Abstract
BackgroundResearch on filamentous fungi emphasized the remarkable redundancy in genes encoding hydrolytic enzymes, the similarities but also the large differences in their expression, especially through the role of the XlnR/XYR1 transcriptional activator. The purpose of this study was to evaluate the specificities of the industrial fungus Talaromyces versatilis, getting clues into the role of XlnR and the importance of glucose repression at the transcriptional level, to provide further levers for cocktail production.ResultsBy studying a set of 62 redundant genes representative of several categories of enzymes, our results underlined the huge plasticity of transcriptional responses when changing nutritional status. As a general trend, the more heterogeneous the substrate, the more efficient to trigger activation. Genetic modifications of xlnR led to significant reorganisation of transcriptional patterns. Just a minimal set of genes actually fitted in a simplistic model of regulation by a transcriptional activator, and this under specific substrates. On the contrary, the diversity of xlnR+ versus ΔxlnR responses illustrated the existence of complex and unpredicted patterns of co-regulated genes that were highly dependent on the culture condition, even between genes that encode members of a functional category of enzymes. They notably revealed a dual, substrate-dependant repressor-activator role of XlnR, with counter-intuitive transcripts regulations that targeted specific genes. About glucose, it appeared as a formal repressive sugar as we observed a massive repression of most genes upon glucose addition to the mycelium grown on wheat straw. However, we also noticed a positive role of this sugar on the basal expression of a few genes, (notably those encoding cellulases), showing again the strong dependence of these regulatory mechanisms upon promoter and nutritional contexts.ConclusionsThe diversity of transcriptional patterns appeared to be the rule, while common and stable behaviour, both within gene families and with fungal literature, the exception. The setup of a new biotechnological process to reach optimized, if not customized expression patterns of enzymes, hence appeared tricky just relying on published data that can lead, in the best scenario, to approximate trends. We instead encourage preliminary experimental assays, carried out in the context of interest to reassess gene responses, as a mandatory step before thinking in (genetic) strategies for the improvement of enzyme production in fungi.
Highlights
Research on filamentous fungi emphasized the remarkable redundancy in genes encoding hydrolytic enzymes, the similarities and the large differences in their expression, especially through the role of the XlnR/XYR1 transcriptional activator
Balanced choice of Gene Of Interest (GOI) to consider redundancy in the genes coding for similar hydrolytic activities in T. versatilis To better understand the transcriptional network that governs gene expression in the filamentous fungus Talaromyces versatilis, we selected a set of 62 representative genes of interest (GOIs) encoding hydrolytic and auxiliary enzymes in plant biomass degradation (Table 1 and more detailed information in the Additional file 1)
A preliminary list of GOIs was selected based on expressed candidates in a whole cell RNA sequencing (RNA-seq) study carried out during cultures on glucose and wheat straw [59], and from a proteomic analysis of the Rovabio® cocktail [37]
Summary
Research on filamentous fungi emphasized the remarkable redundancy in genes encoding hydrolytic enzymes, the similarities and the large differences in their expression, especially through the role of the XlnR/XYR1 transcriptional activator. Biomass degradation is an essential yet complex process in nature, for degrading the plant cell wall [1] This structure is a highly heterogeneous material mainly composed of cellulose, hemicellulose, lignin and pectin, whose degradation is achieved through multiple means, including the use of enzymes with different and complementary activities [2,3,4]. They are assigned into five enzyme classes, including Glycoside Hydrolases (GH) and Auxiliary Activities (AA) This classification relies on amino acids sequence similarity, secondary and tertiary fold conservation, and stereochemical architecture of catalytic mechanisms. This classification, does not preclude functional redundancy between families, as for instance enzymes bearing xylanase activity that belong to GH10, GH11, GH5, GH7, GH8 and GH43 families [10]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
