haloferax volcanii strain ds2  (ATCC)

Journal: bioRxiv

Article Title: Rapid rewiring of an archaeal transcription factor function via flexible cis-trans interactions

doi: 10.1101/2024.11.20.624553

Figure Lengend Snippet: Haloarchaeal species exhibit differential susceptibility to oxidative stress conditions. Growth is plotted as the log10 optical density at 600 nm (OD600) over time (hours). Each curve represents the generalized additive model (GAM) fit to the raw data from at least 3 biological replicate experiments (seeded from starter cultures inoculated with separate colonies), each with 3 technical replicates (aliquots from the same starter culture). Shaded grey ribbons indicate the standard error. Error is low where ribbons are not visible. Concentrations are written above the corresponding growth curve in each panel. Concentrations surrounded by a box is that condition chosen for testing Δ rosR growth in subsequent experiments. (A) Hfx. volcanii growth under a titration of peroxide (H 2 O 2 ) concentrations. (B) Hfx. mediterranei growth under H 2 O 2 . (C) Hfx. volcanii growth under varying paraquat (PQ) concentrations. (D) Hfx. mediterranei growth under PQ.

Article Snippet: Wild-type strains Halobacterium salinarum NRC-1 ( Hs) , Haloferax volcanii strain DS2 ( Hv) , and Haloferax mediterranei ( Hm) ATCC 33500 were used in this study.

Techniques: Titration

Journal: bioRxiv

Article Title: Rapid rewiring of an archaeal transcription factor function via flexible cis-trans interactions

doi: 10.1101/2024.11.20.624553

Figure Lengend Snippet: hv RosR activates arlA1 and arlA2 , encoding structural components of the archaellum in Hfx. volcanii . (A) Top, genomic region encoding the archaellum and related motility functions; middle, ChIP-seq data for the region highlighted in teal (read depth y-axis is shown at right); bottom, chromosomal coordinates for genes in the zoomed region, with genes on the forward strand depicted on top of the line and reverse strand below the line. (B) Scatterplot of normalized counts from RNA-seq data, with parental control strain counts on the X-axis and hv Δ rosR counts on the y-axis. Genes passing the significance threshold of p < 0.05 and log2 fold change >= |1| are shown in blue, those significant genes also bound in ChIP-seq data in pink (see legend). (C) ChIP-qPCR validation of ChIP-seq data. Bar height represents the mean enrichment of hv RosR binding each site relative to a control region. Error bars represent the standard deviation from the mean of triplicate samples. hv RosR-HA enrichment is shown in salmon and PyrE2-HA parent strain control in grey. Amplicons tested are shown in orange below the bar graph (“peak 1, peak 2, peak 3”) and are set relative to chromosomal position of the corresponding genes. Asterisks indicate the statistical significance of enrichment for each peak (salmon bars) relative to the parent control (grey bars) by two-sided unpaired Student’s t-test, * p < 1.02 x 10 -3 , ** p < 4.71 x 10 -4 , *** p < 6.31 x 10 -5 . (D) Logo of the consensus binding motif detected computationally from hv RosR ChIP-seq binding site sequences. Motif position in nucleotides is given on the x-axis and bit score of per-base representation in the position weight matrix is given on the y-axis. See also Supplementary Table S4 for detailed RNA-seq, ChIP-seq, and motif data.

Article Snippet: Wild-type strains Halobacterium salinarum NRC-1 ( Hs) , Haloferax volcanii strain DS2 ( Hv) , and Haloferax mediterranei ( Hm) ATCC 33500 were used in this study.

Techniques: ChIP-sequencing, RNA Sequencing, Control, ChIP-qPCR, Biomarker Discovery, Binding Assay, Standard Deviation