Dataset Information

Widespread glucose-mediated repression of plant biomass utilization in the white-rot fungus Dichomitus squalens

ABSTRACT: Carbon catabolite repression (CCR) occurs in the presence of sufficient concentrations of easy metabolizable carbon sources (e.g. glucose), down-regulating the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. The extent of CCR at a global level is unknown in wood-rotting fungi – and was investigated in Dichomitus squalens with transcriptomics and exo-proteomics. Approximately 10% of expressed genes had lower expression in presence of glucose compared to Avicel or xylan alone. The glucose repressed genes included key components for utilization of plant biomass – CAZymes, sugar transporters and carbon catabolic genes. The majority of polysaccharide degrading CAZymes were repressed and included activities towards all major polymers. The repression found in the transcriptome was strongly supported by exo-proteomics – there was repression of almost all of the CAZymes whose transcripts were repressed on Avicel. The clear CCR-mediated effects indicate biotech production of CAZymes by D. squalens would benefit from de-repressed or constitutively expressing strains. The extent of CCR is surprising given that D. squalens rarely experiences high sugar concentrations in its woody environment.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Dichomitus Squalens

TISSUE(S): Cell Culture, Vegetative Cell (sensu Fungi)

SUBMITTER: Marcos Di Falco

LAB HEAD: Ronald P. de Vries

PROVIDER: PXD014774 | Pride | 2019-10-07

REPOSITORIES: Pride

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Publications

Glucose-Mediated Repression of Plant Biomass Utilization in the White-Rot Fungus <i>Dichomitus squalens</i>.

Daly Paul P Peng Mao M Di Falco Marcos M Lipzen Anna A Wang Mei M Ng Vivian V Grigoriev Igor V IV Tsang Adrian A Mäkelä Miia R MR de Vries Ronald P RP

Applied and environmental microbiology 20191114 23

The extent of carbon catabolite repression (CCR) at a global level is unknown in wood-rotting fungi, which are critical to the carbon cycle and are a source of biotechnological enzymes. CCR occurs in the presence of sufficient concentrations of easily metabolizable carbon sources (e.g., glucose) and involves downregulation of the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. We investigated this phenomenon in the white-rot fungus <i>Dichomitus squalens ...[more]

PMID: 31585998

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Project description:Hemicellulose, the second most abundant plant biomass fraction after cellulose, is widely viewed as a potential feedstock for the production of liquid fuels and other value-added materials. Degradation of hemicellulose by filamentous fungi requires production of many different enzymes, which are induced by biopolymers or its derivatives and regulated mainly at the transcriptional level through transcription factors (TFs). Neurospora crassa has been shown to express and secrete plant cell wall associated enzymes. To better understand genes specifically associated with degradation of hemicellulose, we identified 353 genes by transcriptome analysis of N. crassa wild type strain grown on beechwood xylan. Exposure to xylan induces 9 of the 19 predicted hemicellulase genes. The xylanolytic phenotype of strains with deletions in genes identified from the secretome and transcriptome analysis of wild type showed that none were essential for growth on beechwood xylan. The transcription factor XlnR/Xyr1 in Aspergillus and Trichoderma species is considered to be the major transcriptional regulator of genes encoding both cellulases and hemicellulases. We identified a xlnR/xyr1 homolog in N. crassa, NCU06971, termed xlr-1 (xylanase regulator 1). Deletion of xlr-1 in N. crassa abolishes the growth on xylan and xylose, but growth on cellulose was indistinguishable from wild type. To determine regulatory mechanisms associated with hemicellulose degradation, we explored the transcriptional regulon of XLR-1 under xylose and xylanolytic versus cellulolytic conditions. XLR-1 regulated only some predicted hemicellulase genes in N. crassa and was required for a full induction of several cellulase genes. Hemicellulase gene expression was induced by a combination of release from carbon catabolite repression (CCR) and induction. However, in N. crassa, xlr-1 is subject to non-CRE-1 mediated CCR. This systematic analysis provides the similarities and differences of hemicellulose degradation and regulation mechanisms used by N. crassa in comparison to other filamentous fungi. Four-condition experiments (minimal medium, xylan medium,xylose and Avicel medium) of mutant strain(xlr-1) compared to wild type strain; Cy3 and Cy5 dye swap

Project description:Carbon catabolite repression (CCR) is a gene regulation process that allows bacteria to use carbon-energy sources in a hierarchical manner. Thus, the presence of a preferred sugar, usually D-glucose, results in downregulation of genes participating in the transport and catabolic pathways of secondary carbon sources. Further, CCR controls the expression of global regulators that control expression of many genes involved in multiple aspects of bacterial physiology such as stress response proteins and virulence factors. The human-restricted pathogen Neisseria gonorrhoeae can rely upon a limited number of carbon-energy sources, including glucose and lactate and both are available within its infection niches. We recently reported that expression of the L-lactate permease-encoding gene lctP is subjected to glucose repression within physiological concentrations. However, the transducing mechanism or the gene that connect glucose with lctP promoter repression remained unknown. To address this issue, we performed an RNA-Seq analysis to determine the transcriptional landscape of gonococci due to changes in glucose or lactate concentrations in the growth media. Glucose was found to regulate 144 genes (5.5% of total genes in the genome) while lactate influenced the expression of 434 (16.5%) genes with an overlap of 97 genes between the two sugars. Both, glucose and lactate were found to upregulate genes involved in protein translation, a high energy consumption cellular function. Individually, glucose enhanced genes participating in glycolysis and repressed genes in the tricarboxylic acid (TCA) cycle, while lactate enhanced genes encoding respiratory enzymes and ATP synthase. Interestingly, lactate was found to repress expression of several genes encoding known gonococcal virulence factors such as tbpAB encoding the transferrin-binding proteins; the tonB and exbBD genes encoding the membrane energy transfer complex TonB-ExbB-ExbD required for many outer membrane transport systems; katA encoding an important H2O2-inducible catalase and to upregulate mtrR encoding the master repressor of the mtrCDE antimicrobial efflux pump genes. Moreover, glucose repressed mntC encoding a Zn/Mn ABC transporter and lctP, both required for resistance to killing by H2O2. These results set the framework to determine important gonococci virulent factor genes whose expression can be modulated by CCR as well as to discover the corresponding CCR regulators that control such genes.

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	Dicsqu464_BSA_May292018.fasta	Fasta
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	PD10.raw	Raw
	PD11.raw	Raw