MOESM1 of The transcription factor PDR-1 is a multi-functional regulator and key component of pectin deconstruction and catabolism in Neurospora crassa

Additional file 1: Figure S1. Schematic depiction of phylogeny and conserved domains/signals in the pdr-1 gene and its orthologs. The amino acid sequence of N. crassa PDR-1 (NCU09033), A. niger RhaR (An13g00910), A. nidulans RhaR (AN5673) and P. stipitis TRC1 (ABN68604) was used in a conserved domain search, as well as NLS and NES prediction. The phylogeny of these proteins was determined. B. cinerea GaaR (Bcin09g00170) constitutes the outgroup in the phylogenetic tree. GAL4 = GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain, fungal TF MHR = fungal transcription factor regulatory middle homology region, green triangle = nuclear localization signal, red triangle = nuclear export signal. Figure S2. Growth phenotypes and protein secretion of N. crassa WT, Δpdr-1 and pdr-1-comp strains. (A) Observed growth phenotypes. Strains were grown on either 2 mM l-Rha, 2 mM d-Xyl, 1% pectin or 1% xylan. The cultures were incubated for 3 days. (B) Sucrose pregrown cultures were switched to pectin medium and the concentration of secreted protein was determined. Error bars represent standard deviation (n = 3). Significance was determined by an independent two-sample t-test of WT against Δpdr-1 or pdr-1-comp with *p < 0.05. Figure S3. Venn diagrams of DEseq results and correlation studies of RNA-seq to RT-qPCR data. Strains were pregrown for 16 h on 2% sucrose and then switched to an induction medium of either 1% pectin (pec) or 2 mM l-Rha for an additional 4 h. (A) Differential expression analysis (DEseq) was performed on the RNA-seq data. Genes of the WT and the Δpdr-1 strains that were threefold upregulated (left diagram; +) or downregulated (right diagram; −) were compared. Venn diagrams were created with: http://bioinformatics.psb.ugent.be/webtools/Venn/ . WT on 1% pectin was used in biological duplicates; all other conditions were used in biological triplicates for the RNA-seq analysis. (B) Correlation analysis of RT-qPCR data to RNA-seq data. Axes are log10-scaled. The fold change expression of several key pectinase genes was determined by RT-qPCR in the WT and Δpdr-1 strain grown on 1% pectin and plotted against their respective RNA-seq data. The Pearson’s correlation coefficient (ρ) was determined. Two biological replicates were used for RT-qPCR except for ply-2, where only one was used. All biological replicates were analyzed as three technical replicates. Figure S4. Expression levels of pdr-1, gh28-1 and NCU09034 determined by RT-qPCR. (A) The strains were grown for 2 days on 1% pectin and the expression level of pdr-1 in the pdr-1-oex strain or gh28-1 in the gh28-1-oex and gh28-1-comp strain was determined. The WT strain was used as reference. (B) The WT and pdr-1-oex strain were incubated for 48 h on 1% xylan. 2 mM l-Rha was added and the strains were incubated for an additional 30 min before harvesting the RNA for RT-qPCR. Strains incubated for the same time but without l-Rha were used as controls. The expression of pdr-1 and NCU09034 was determined for both strains. Three biological replicates were used, except for pdr-1 in WT on pectin and NCU09034 in WT on xylan plus l-Rha, where only two were used. All biological replicates were analyzed as three technical replicates. Error bars represent standard deviation. Significance was determined by an independent two-sample t-test with **p < 0.01, ***p < 0.001. Figure S5. Expression profile of pdr-1 and biomass accumulation of the pdr-1-oex strain. (A) Expression profile of pdr-1. After a 16 h pre-incubation on 2% sucrose, biomass of the WT strain was washed three times with 1× Vogel’s solution and transferred to a medium of either no carbon source (NoC), 2% sucrose, 2 mM l-Rha or 1% pectin. The strain was incubated for an additional 4 h. Error bars represent standard deviation (n = 2 for 1% pectin, n = 3 for NoC, 2% sucrose and 2 mM l-Rha). (B) Determination of accumulated biomass. Strains were grown on 1% xylan with 0.5 mM l-Rha or d-GalA. A medium containing 1% xylan was used as control. Biomass was determined by dry weight. Error bars represent standard deviation (n = 3)

L'Auto-vélo : automobilisme, cyclisme, athlétisme, yachting, aérostation, escrime, hippisme / dir. Henri Desgranges

27 juin 19371937/06/27 (A38,N13339)

Additional file 2: Table S1. of Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales

Comparison of TE content estimation from REPET and Repeatexplorer. (XLSX 9 kb

Additional file 3: Figure S1. of Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales

Snapshot of synteny dot plot between C. olivacea and C. puteana. (TIFF 582 kb

Supplemental Material for Bryan et al., 2018

Supplementary data of "A variable polyglutamine repeat affects subcellular localization and regulatory activity of a <i>Populus</i> ANGUSTIFOLIA protein