RNA Sequencing Reveals Xyr1 as a Transcription Factor Regulating Gene Expression beyond Carbohydrate Metabolism

Abstract

Xyr1 has been demonstrated to be the main transcription activator of (hemi)cellulases in the well-known cellulase producer Trichoderma reesei. This study comprehensively investigates the genes regulated by Xyr1 through RNA sequencing to produce the transcription profiles of T. reesei Rut-C30 and its xyr1 deletion mutant (Δxyr1), cultured on lignocellulose or glucose. xyr1 deletion resulted in 467 differentially expressed genes on inducing medium. Almost all functional genes involved in (hemi)cellulose degradation and many transporters belonging to the sugar porter family in the major facilitator superfamily (MFS) were downregulated in Δxyr1. By contrast, all differentially expressed protease, lipase, chitinase, some ATP-binding cassette transporters, and heat shock protein-encoding genes were upregulated in Δxyr1. When cultured on glucose, a total of 281 genes were expressed differentially in Δxyr1, most of which were involved in energy, solute transport, lipid, amino acid, and monosaccharide as well as secondary metabolism. Electrophoretic mobility shift assays confirmed that the intracellular β-glucosidase bgl2, the putative nonenzymatic cellulose-attacking gene cip1, the MFS lactose transporter lp, the nmrA-like gene, endo T, the acid protease pepA, and the small heat shock protein hsp23 were probable Xyr1-targets. These results might help elucidate the regulation system for synthesis and secretion of (hemi)cellulases in T. reesei Rut-C30.

Gene Co-expression Network Reveals Potential New Genes Related to Sugarcane Bagasse Degradation in Trichoderma reesei RUT-30

“…Both proteins have a carbohydrate-binding domain that belongs to family 1 (CBM1), and one XBS was predicted in each gene promoter. Therefore, they play a role in bagasse deconstruction and are transcriptionally regulated by Xyr1, as reported previously (Reithner et al, 2014 ; Ma et al, 2016 ). In addition, 14 putative sugar transporters, three Zn2Cys6 transcriptional regulators, one putative GCN5-acetyltransferase, one methyltransferase and several other genes were also co-expressed with xyr1 and had XBS in their promoters (Figure 4A , Table S8 ).…”

The putative β-glucosidase BGL3I regulates cellulase induction in Trichoderma reesei

“…Unlike the previously reported studies [ 11 ], our recent study indicated that most of these β-glucosidase genes were upregulated by Xyr1 in the inducing medium (wheat bran and Avicel); however, a β-glucosidase gene named bgl3i ( cel3g ) was downregulated [ 12 ]. On the contrary, the expression level of bgl3i was upregulated in a xyr1 deletion strain [ 12 ]. Recently, the enzyme activities of the heterologously expressed BGL3I from Aspergillus oryzae to different substrates have been compared with other β-glucosidases of T. reesei [ 18 ].…”

“…The bgl3i gene is composed of four exons and three introns, as predicted in JGI (Transcript ID: TRIRE2_47268), and belongs to the GH3 family according to the Pfam database. It was screened using the expression profile data of our laboratory, based on the significantly increased transcription in the xyr1 disrupted strain compared with the WT under induction conditions [ 12 ]. The expression profile data and the cDNA sequence of bgl3i showed that the sites of its start codons and exon/intron junctions were not properly located on the JGI website, but were correct on NCBI (accession no.…”

“…The expression profile data and the cDNA sequence of bgl3i showed that the sites of its start codons and exon/intron junctions were not properly located on the JGI website, but were correct on NCBI (accession no. BAP59015) [ 12 ]. It is well known that the expression levels of most cellulase and hemicellulase genes are dramatically reduced in the absence of xyr1 in T. reesei [ 13 ]; thus, the increased transcription of bgl3i in xyr1 deletion strain is very distinctive.…”

“…CEL1A and CEL1B were the major intracellular β-glucosidases in T. reesei . CEL1A and CEL1B possess the highest and third highest transcription levels among the 11 annotated β-glucosidase in T. reesei , respectively [ 12 ]. CEL1A has relatively low p NPG activity, but high enzyme activities toward some oligosaccharides (Table 1 ).…”