Constitutive expression of <i>suf</i> genes in COP4 (CopR⁻) increases its copper tolerance.

<p>A. Northern blot analysis of <i>sufB</i> and <i>copM</i> in WT, COP4 (CopR⁻), COP20 (SufR⁻) and COP21 (CopR⁻SufR⁻) strains. Total RNA was isolated from WT, COP4, COP20 and COP21 cells grown in BG11C-Cu medium after addition of 1 µM of copper. Samples were taken at the indicated times. The filter was subsequently hybridized with <i>sufB, copM</i> and <i>rnpB</i> (as a loading control) probes. B. Growth of WT and COP20 (SufR⁻) strains in the presence of copper. Exponentially growing cells of WT and COP20 were diluted to OD₇₅₀ nm of 0.2 in BG11-Cu containing 2 µM of copper or without copper added. Growth was monitored following increase in OD_{750 nm} for 3 days. C. Growth of COP4 (CopR⁻) and COP21 (CopR⁻SufR⁻) strains in the presence of copper. Exponentially growing cells of COP4 and COP21 were diluted to OD₇₅₀ nm of 0.2 in BG11-Cu containing 1.5 µM of copper or without copper added. Growth was monitored following increase in OD_{750 nm} for 3 days. D. Growth of COP4 (SufR⁻) and COP21 (CopR⁻SufR⁻) strains in the presence of copper. Exponentially growing cells of COP4 and COP21 were diluted to OD₇₅₀ nm of 0.2 and cultured in BG11-Cu medium supplemented with the indicated copper concentration. Cultures were photographed after 3 days of growth.</p

InrS is implicated in heavy metal homeostasis.

<p>A. Phenotypic characterization of mutant strains affected in <i>inrS</i> and <i>nrsD</i> genes. Growth in presence and absence of nickel was observed in WT, NRS10 (InrS⁻) and NRS11 (NrsD⁻InrS⁻) strains. Ten fold dilutions of a 1 µg chlorophyll mL⁻¹ cell suspension were spotted onto both BG11C and BG11C supplemented with 1 µM of nickel. Plates were photographed after 5 d of growth. B. Northern blot analysis of the expression of <i>nrsD</i> in WT, NRS5 (NrsD⁻), NRS6 (NrsRS⁻), NRS10 (InrS⁻) and NRS11 (NrsD⁻InrS⁻) strains. Total RNA was isolated from WT, NRS5, NRS6, NRS10 and NRS11 strains grown in BG11C-Cu medium and exposed for 60 min to 3 µM of indicated metals ions. Control cells were not exposed to added metals (-). The filter was hybridized with <i>5′nrsD</i>, <i>copM</i>, <i>nrsB</i> and <i>rnpB</i> (as a loading control) probes. C. Phenotypic characterization of WT, NRS5 (NrsD⁻), NRS10 (InrS⁻) and NRS11 (NrsD⁻InrS⁻) mutant strains. Tolerance of WT, NRS5, NRS10 and NRS11 strains to different metals was examined. Ten fold dilutions of a 1 µg chlorophyll mL⁻¹ cell suspension cell were spotted onto BG11C, supplemented with the indicated metals ions concentrations. Plates were photographed after 5 d of growth.</p

Global responses to high copper treatment in <i>Synechocystis</i>.

<p>A. Scatter plot showing comparison between expression profiles of WT treated with copper 3 µM for 1 h (y axis) and untreated WT (x axis). Data represents the average signal of two independent hybridizations. CTR up-regulated genes are in yellow, CTR down-regulated genes in blue, <i>copMRS</i> operon in red and the genes for soluble electron carriers <i>petE</i> and <i>petJ</i> in green. B. Box plot showing ratios of gene list of treated vs. untreated samples of the categories cited in the main text that were significantly affected. C. Induction of ROS in response to copper. The determination of ROS in WT cells cultured in BG11C-Cu medium supplemented with 0.3 µM Cu (Low Cu), 3 µM Cu (High Cu) and 5 µM of methyl viologen (MV) for 1 h were determined. Untreated cells were used as control. Values are the mean of three independent experiments. Error bars represent standard error. D. Scatter plot showing comparison between expression profiles of WT treated with copper 3 µM for 1 h (y axis) and untreated WT (x axis). Data represents the average signal of two independent hybridizations. Genes related to heavy metal resistance are shown in blue.</p

Determination of the minimal inhibitory concentration for copper in <i>Synechocystis</i>.

<p>Exponentially growing cells of <i>Synechocystis</i> WT strain were diluted to OD_{750 nm} of 0.6 and cultured in BG11-Cu medium supplemented with the indicated copper concentration for 24 hours.</p

Selected genes induced in <i>Synechocystis</i> sp. PCC 6803 after the high copper treatment.

<p>Selected genes induced in <i>Synechocystis</i> sp. PCC 6803 after the high copper treatment.</p

Selected genes repressed in <i>Synechocystis</i> sp. PCC 6803 after the high copper treatment.

<p>Selected genes repressed in <i>Synechocystis</i> sp. PCC 6803 after the high copper treatment.</p

A Schematic representation depicting gene sets transcriptionally regulated by copper in <i>Synechocystis</i>.

<p>Group of up-regulated genes are shown in green and group of down-regulated genes are shown in blue. Dashed line represents a group that contains both up- and down-regulated genes.</p

<i>Synechocystis</i> strains used in this study.

<p><i>Synechocystis</i> strains used in this study.</p

The unfolded protein response and its potential role in Huntington ́s disease elucidated by a systems biology approach [v1; ref status: indexed, http://f1000r.es/59e]

Huntington ́s disease (HD) is a progressive, neurodegenerative disease with a fatal outcome. Although the disease-causing gene (huntingtin) has been known for over 20 years, the exact mechanisms leading to neuronal cell death are still controversial. One potential mechanism contributing to the massive loss of neurons observed in the brain of HD patients could be the unfolded protein response (UPR) activated by accumulation of misfolded proteins in the endoplasmic reticulum (ER). As an adaptive response to counter-balance accumulation of un- or misfolded proteins, the UPR upregulates transcription of chaperones, temporarily attenuates new translation, and activates protein degradation via the proteasome. However, persistent ER stress and an activated UPR can also cause apoptotic cell death. Although different studies have indicated a role for the UPR in HD, the evidence remains inconclusive. Here, we present extensive bioinformatic analyses that revealed UPR activation in different experimental HD models based on transcriptomic data. Accordingly, we have identified 58 genes, including RAB5A, HMGB1, CTNNB1, DNM1, TUBB, TSG101, EEF2, DYNC1H1 and SLC12A5 that provide a potential link between UPR and HD. To further elucidate the potential role of UPR as a disease-relevant process, we examined its connection to apoptosis based on molecular interaction data, and identified a set of 40 genes including ADD1, HSP90B1, IKBKB, IKBKG, RPS3A and LMNB1, which seem to be at the crossroads between these two important cellular processes

Raw data for Kalathur et al., 2015 ‘The unfolded protein response and its potential role in Huntington ́s disease elucidated by a systems biology approach’

<p>Data file 1. Legend: Lists of upregulated genes in 6 murine and 1 human (first sheet), and in at least 4 murine and 1 human HD model (second sheet).</p><p>Data file 2. Lists of downregulated genes in 5 datasets (first sheet) and in at least 4 datasets (second sheet).</p><p>Data file 3. Lists of upregulated UPR genes with stress response elements in the promoter regions (-1000bp to +500bp). Results for highly stringent gene list (UPR genes uprgulated in 6 murine and 1 human HD model) are show on sheet 1; results for less stringent gene list (upregulated in at least 4 murine and 1 human HD model) are displayed on sheet 2.</p><p>Data file 4. List of all the biological processes that are enriched amongin differentially regulated UPR genes. Results for UPR gene list of high stringency are show on sheet 1; results for gene list of lower stringency are displayed on sheet 2.</p><p>Data file 5. List of all the pathways that are enriched among upregulated UPR genes. Results for UPR gene list of high stringency are show on sheet 1; results for gene list of lower stringency are displayed on sheet 2.</p><p>Data file 6. List of components of UPR interactome shown in Figure 6</p><p>Data file 7. List of genes common between UPR and Apoptosis</p><p>Data file 8. List of proteins that interact with HTT directly or indirectly.</p><p>Data file 9. List of 53 proteins that were found in the intersection of HTT interactors, HDTT and differentially regulated UPR genes (of lower stringeny). It includes the 13 proteins from table 3 that were identified using the high stringency list of differentially regulated UPR genes. Spearman correlation coefficients and the corresponding estimated fdr for correlation or anti correlation, respectively, describe the observed correlation of gene expression and the length of polyglutamine tract in HD mice.</p