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Direct target network of the Neurospora crassa plant cell wall deconstruction regulators CLR-1, CLR-2, and XLR-1.

Craig JP, Coradetti ST, Starr TL, Glass NL - MBio (2015)

Bottom Line: The XLR-1 regulon was defined using a constitutively active mutant allele, resulting in hemicellulase gene expression and secretion under noninducing conditions.CLR-1 bound to its regulon under noninducing conditions; however, this binding alone did not translate into gene expression and enzyme secretion.Coordinated optimization of these regulatory networks is likely required for optimal microbial enzyme production.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA Energy Biosciences Institute, University of California, Berkeley, Berkeley, California, USA Chan Soon-Shiong Institute of Molecular Medicine, Windber, Pennsylvania, USA.

No MeSH data available.


Related in: MedlinePlus

Identification of XLR-1 regulon, direct targets, and XLR-1 binding site. (A) RNAseq analyses of the most highly expressed hemicellulase genes in the xlr-1A828V strain relative to the WT strain and a Δxlr-1 mutant shifted to sucrose (sucr), no-carbon (nc), or xylan medium conditions. (B) Hierarchical clustering of gene expression of the strains shown shifted to sucrose, no-carbon, or xylan conditions. Genes within cluster 1 are dependent upon XLR-1 for expression. (C) Venn diagram depicting overlap of genes that show differential expression (DE), genes that have similar expression patterns through hierarchical clustering (HC) in the WT strain versus the xlr-1A828V strain under no-carbon conditions (Cuffdiff; Padj = <0.05; 4-fold), and genes that showed significant binding of XLR-1 in their promoter regions (XLR-1 ChIP). (D) Consensus binding sequence for XLR-1 based on promoter regions bound by XLR-1 in the ChIPseq data.
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fig6: Identification of XLR-1 regulon, direct targets, and XLR-1 binding site. (A) RNAseq analyses of the most highly expressed hemicellulase genes in the xlr-1A828V strain relative to the WT strain and a Δxlr-1 mutant shifted to sucrose (sucr), no-carbon (nc), or xylan medium conditions. (B) Hierarchical clustering of gene expression of the strains shown shifted to sucrose, no-carbon, or xylan conditions. Genes within cluster 1 are dependent upon XLR-1 for expression. (C) Venn diagram depicting overlap of genes that show differential expression (DE), genes that have similar expression patterns through hierarchical clustering (HC) in the WT strain versus the xlr-1A828V strain under no-carbon conditions (Cuffdiff; Padj = <0.05; 4-fold), and genes that showed significant binding of XLR-1 in their promoter regions (XLR-1 ChIP). (D) Consensus binding sequence for XLR-1 based on promoter regions bound by XLR-1 in the ChIPseq data.

Mentions: RNAseq analyses of the xlr-1A828V mutant, the Δxlr-1 mutant, and the WT strain revealed the presence of both xlr-1-dependent and xlr-1-independent xylan-induced genes. As shown in Fig. 6A, the pattern of induction and expression of the dominant hemicellulase genes in the xlr-1A828V mutant under no-carbon conditions was remarkably similar to that of a WT strain exposed to xylan (see Dataset S3 in the supplemental material). A cluster of 50 xylan-inducible genes were responsive to the xlr-1A828V mutant and the WT strain under xylan conditions (Fig. 6B; cluster 1) and were dominated by xylanases and xylose-utilization genes. XLR-1-independent, xylan-induced genes in a second cluster (100 genes) were dominated by pectinases (Fig. 6B; cluster 2). These genes were induced in strains switched to pectin media (7), suggesting that this large cluster of genes is induced by pectin contamination of the xylan substrate and not by xylan per se.


Direct target network of the Neurospora crassa plant cell wall deconstruction regulators CLR-1, CLR-2, and XLR-1.

Craig JP, Coradetti ST, Starr TL, Glass NL - MBio (2015)

Identification of XLR-1 regulon, direct targets, and XLR-1 binding site. (A) RNAseq analyses of the most highly expressed hemicellulase genes in the xlr-1A828V strain relative to the WT strain and a Δxlr-1 mutant shifted to sucrose (sucr), no-carbon (nc), or xylan medium conditions. (B) Hierarchical clustering of gene expression of the strains shown shifted to sucrose, no-carbon, or xylan conditions. Genes within cluster 1 are dependent upon XLR-1 for expression. (C) Venn diagram depicting overlap of genes that show differential expression (DE), genes that have similar expression patterns through hierarchical clustering (HC) in the WT strain versus the xlr-1A828V strain under no-carbon conditions (Cuffdiff; Padj = <0.05; 4-fold), and genes that showed significant binding of XLR-1 in their promoter regions (XLR-1 ChIP). (D) Consensus binding sequence for XLR-1 based on promoter regions bound by XLR-1 in the ChIPseq data.
© Copyright Policy - open-access
Related In: Results  -  Collection

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fig6: Identification of XLR-1 regulon, direct targets, and XLR-1 binding site. (A) RNAseq analyses of the most highly expressed hemicellulase genes in the xlr-1A828V strain relative to the WT strain and a Δxlr-1 mutant shifted to sucrose (sucr), no-carbon (nc), or xylan medium conditions. (B) Hierarchical clustering of gene expression of the strains shown shifted to sucrose, no-carbon, or xylan conditions. Genes within cluster 1 are dependent upon XLR-1 for expression. (C) Venn diagram depicting overlap of genes that show differential expression (DE), genes that have similar expression patterns through hierarchical clustering (HC) in the WT strain versus the xlr-1A828V strain under no-carbon conditions (Cuffdiff; Padj = <0.05; 4-fold), and genes that showed significant binding of XLR-1 in their promoter regions (XLR-1 ChIP). (D) Consensus binding sequence for XLR-1 based on promoter regions bound by XLR-1 in the ChIPseq data.
Mentions: RNAseq analyses of the xlr-1A828V mutant, the Δxlr-1 mutant, and the WT strain revealed the presence of both xlr-1-dependent and xlr-1-independent xylan-induced genes. As shown in Fig. 6A, the pattern of induction and expression of the dominant hemicellulase genes in the xlr-1A828V mutant under no-carbon conditions was remarkably similar to that of a WT strain exposed to xylan (see Dataset S3 in the supplemental material). A cluster of 50 xylan-inducible genes were responsive to the xlr-1A828V mutant and the WT strain under xylan conditions (Fig. 6B; cluster 1) and were dominated by xylanases and xylose-utilization genes. XLR-1-independent, xylan-induced genes in a second cluster (100 genes) were dominated by pectinases (Fig. 6B; cluster 2). These genes were induced in strains switched to pectin media (7), suggesting that this large cluster of genes is induced by pectin contamination of the xylan substrate and not by xylan per se.

Bottom Line: The XLR-1 regulon was defined using a constitutively active mutant allele, resulting in hemicellulase gene expression and secretion under noninducing conditions.CLR-1 bound to its regulon under noninducing conditions; however, this binding alone did not translate into gene expression and enzyme secretion.Coordinated optimization of these regulatory networks is likely required for optimal microbial enzyme production.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA Energy Biosciences Institute, University of California, Berkeley, Berkeley, California, USA Chan Soon-Shiong Institute of Molecular Medicine, Windber, Pennsylvania, USA.

No MeSH data available.


Related in: MedlinePlus