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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 (?xyr1), 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 ?xyr1. By contrast, all differentially expressed protease, lipase, chitinase, some ATP-binding cassette transporters, and heat shock protein-encoding genes were upregulated in ?xyr1. When cultured on glucose, a total of 281 genes were expressed differentially in ?xyr1, 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 ?-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.

SUBMITTER: Ma L

PROVIDER: S-EPMC5223008 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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

Ma Liang L Chen Ling L Zhang Lei L Zou Gen G Liu Rui R Jiang Yanping Y Zhou Zhihua Z

BioMed research international 20161227

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 fun ...[more]

PMID: 28116297

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Project description:Individuals of African descent in the United States suffer disproportionately from diseases with a metabolic etiology (obesity, metabolic syndrome, and diabetes), and from the pathological consequences of these disorders (hypertension and cardiovascular disease). Using a combination of genetic/genomic and bioinformatics approaches, we identified a large number of genes that were both differentially expressed between American subjects self-identified to be of either African or European ancestry and that also contained single nucleotide polymorphisms that distinguish distantly related ancestral populations. Several of these genes control the metabolism of simple carbohydrates and are direct targets for the SREBP1, a metabolic transcription factor also differentially expressed between our study populations. These data support the concept of stable patterns of gene transcription unique to a geographic ancestral lineage. The coordinated transcriptional adaptation of carbohydrate metabolism to dietary environmental pressures suggests a genetic and transcriptional mechanism for the disproportionate levels of obesity, diabetes, and cardiovascular disease observed in Americans with African ancestry. Keywords: Ancestry-dependent gene expression, functional genomics, personalized medicine, multi-factoral disease, nutrition, diabetes We utilized a “sample x reference” experimental design strategy in which RNA extracted from human peripheral blood mononuclear cells was hybridized to the microarray slide in the presence of labeled Universal Human Reference RNA (UHRR, Stratagene, LaJolla, CA). A total of 161 subjects were used in this analysis. Briefly, five hundred nanograms of total RNA were used for gene expression profiling following reverse transcription and T-7 polymerase-mediated amplification/labeling with Cyanine-5 CTP. Labeled subject cRNA was co-hybridized to Agilent G4112A Whole Human Genome 44K oligonucleotide arrays with equimolar amounts of Cyanine-3 labeled UHRR. Slides were hybridized, washed, and scanned on an Axon 4000b microarray scanner. The data were processed using GenePix Pro 6 software

Dataset Information

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

Publications

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

Similar Datasets

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