Transcriptome analysis of chloride intracellular channel knockdown in Drosophila identifies oxidation-reduction function as possible mechanism of altered sensitivity to ethanol sedation

• Published in: PloS one 2021-07, Vol.16 (7), p.e0246224
• Main Authors: Weston, Rory M, Schmitt, Rebecca E, Grotewiel, Mike, Miles, Michael F
• Format: Article
• Language: English
• Subjects: Alcohol; Alcohol, Denatured; Amino acids; Analysis; Animals; Apoptosis; Bioinformatics; Biological activity; Biology and Life Sciences; Channel gating; Chloride; Chloride channels; Chloride Channels - genetics; Chloride Channels - metabolism; Chlorides; Drosophila; Drosophila melanogaster - genetics; Drosophila melanogaster - metabolism; Drosophila Proteins - genetics; Drosophila Proteins - metabolism; Enrichment; Ethanol; Ethanol - pharmacology; Exposure; Fruit flies; Gene expression; Gene Expression Profiling; Gene Knockdown Techniques; Genes; Genetics; Heme; Hyperoxia; Hypnotics and Sedatives - pharmacology; Insects; Intracellular; Invertebrates; Ion channels; Lipids; Medicine and Health Sciences; Membrane trafficking; Membranes; Messenger RNA; Metabolism; Molecular modelling; Neurosciences; Nucleoli; Oxidation; Oxidation-Reduction - drug effects; Oxidation-reduction potential; Oxidation-reduction reaction; Oxidative stress; Oxidoreductase; Physical Sciences; Principal components analysis; Properties; Protein turnover; Proteins; Redox reactions; Research and Analysis Methods; RNA Interference; RNA-mediated interference; Sensitivity analysis; Toxicology; Transcription; Transcriptomes; Translation; Vertebrates
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0246224

Chloride intracellular channels (CLICs) are a unique family of evolutionarily conserved metamorphic proteins, switching between stable conformations based on redox conditions. CLICs have been implicated in a wide variety biological processes including ion channel activity, apoptosis, membrane trafficking, and enzymatic oxidoreductase activity. Understanding the molecular mechanisms by which CLICs engage in these activities is an area of active research. Here, the sole Drosophila melanogaster ortholog, Clic, was targeted for RNAi knockdown to identify genes and biological processes associated with Clic expression. Clic knockdown had a substantial impact on global transcription, altering expression of over 7% of transcribed Drosophila genes. Overrepresentation analysis of differentially expressed genes identified enrichment of Gene Ontology terms including Cytoplasmic Translation, Oxidation-Reduction Process, Heme Binding, Membrane, Cell Junction, and Nucleolus. The top term, Cytoplasmic Translation, was enriched almost exclusively with downregulated genes. Drosophila Clic and vertebrate ortholog Clic4 have previously been tied to ethanol sensitivity and ethanol-regulated expression. Clic knockdown-responsive genes from the present study were found to overlap significantly with gene sets from 4 independently published studies related to ethanol exposure and sensitivity in Drosophila. Bioinformatic analysis of genes shared between these studies revealed an enrichment of genes related to amino acid metabolism, protein processing, oxidation-reduction processes, and lipid particles among others. To determine whether the modulation of ethanol sensitivity by Clic may be related to co-regulated oxidation-reduction processes, we evaluated the effect of hyperoxia on ethanol sedation in Clic knockdown flies. Consistent with previous findings, Clic knockdown reduced acute ethanol sedation sensitivity in flies housed under normoxia. However, this effect was reversed by exposure to hyperoxia, suggesting a common set of molecular-genetic mechanism may modulate each of these processes. This study suggests that Drosophila Clic has a major influence on regulation of oxidative stress signaling and that this function overlaps with the molecular mechanisms of acute ethanol sensitivity in the fly.