CG1603 regulation of nuclear-encoded mitochondrial gene expression

Through a genetic screen in Drosophila melanogaster, CG1603 was identified as one of the transcription factors that coordinate mitochondrial biogenesis. To investigate the role of CG1603 in regulating nuclear-encoded mitochondrial gene expression, we collected second-instar larvae from wild type and CG1603PBac mutants (a mutant allele that disrupts the translation of the full-length CG1603 protein). We purified mRNA from the samples in triplicate and compared the mRNA transcriptome profiles (RNA-seq). We found that, between wild-type and CG1603PBac larvae, more than 80% of nuclear-encoded mitochondrial genes were differentially expressed. Nearly half of the nuclear-encoded mitochondrial genes were reduced by more than twofold in CG1603PBac mutants, including many structural subunit genes of all five ETC complexes. Gene Ontology (GO) enrichment analysis of the significantly downregulated genes also revealed that the most significantly enriched biological processes were related to mitochondria, including “mitochondrial translation,” “mitochondrial gene expression,” “electron transport chain,” “aerobic respiration,” and “ATP metabolic process.” These results suggest that CG1603 is essential for nuclear mitochondrial gene expression. Overall design: Total mRNAs were extracted from second-instar larvae of wild type and CG1603PBac mutant flies in triplicate. The RNA-seq was performed with Illumina Novaseq 6000.