A transcription network underlies the dual genomic coordination of mitochondrial biogenesis

Reviewer #1 (Public Review):

Summary:

In this manuscript, Zhang et al. report a genetic screen to identify novel transcriptional regulators that could coordinate mitochondrial biogenesis. They performed an RNAi-based modifier screen wherein they systematically knocked down all known transcription factors in the developing Drosophila eye, which was already sensitised and had decreased mitochondrial DNA content. Through this screen, they identify CG1603 as a potential regulator of mitochondrial content. They show that protein levels of mitochondrial proteins like TFAM, SDHA, and other mitochondrial proteins and mtDNA content are downregulated in CG1603 mutants. RNA-Seq and ChIP-Seq further show that CG1603 binds to the promoter regions of several known nuclear-encoded mitochondrial genes and regulates their expression. Finally, they also identified YL-1 as an upstream regulator of CG1603. Overall, it is a very important study as our understanding of the regulation of mitochondrial biogenesis remains limited across metazoans. Most studies have focused on PGC-1α as a master regulator of mitochondrial biogeneis, which seems a context-dependent regulator. Also, PGC-1α mediated regulation could not explain the regulation of 1100 genes that are required for mitochondrial biogenesis. Therefore, identifying a new regulator is crucial for understanding the overall regulation of mitochondrial biogenesis.

Reviewer #2 (Public Review):

Summary:

In this study, the authors aim to identify the nuclear genome-encoded transcription factors that regulate mtDNA maintenance and mitochondrial biogenesis. They started with an RNAi screening in developing Drosophila eyes with reduced mtDNA content and identified a number of putative candidate genes. Subsequently, using ChIP-seq data, they built a potential regulatory network that could govern mitochondrial biogenesis. Next, they focused on a candidate gene, CG1603, for further characterization. Based on the expression of different markers, such as TFAM and SDHA, in the RNAi and OE clones in the midgut cells, they argue that CG1603 promotes mitochondrial biogenesis and the expression of ETC complex genes. Then, they used a mutant of CG1603 and showed that both mtDNA levels and mitochondrial protein levels were reduced. Using clonal analyses, they further show a reduction in mitochondrial biogenesis and membrane potential upon loss of CG1603. They made a reporter line of CG1603, showed that the protein is localized to the mitochondria, and binds to polytene chromosomes in the salivary gland. Based on the RNA-seq results from the mutants and the ChIP data, the authors argue that the nucleus-encoded mitochondrial genes that are downregulated >2 folds in the CG1603 mutants and that are bound by CG1603 are related to ETC biogenesis. Finally, they show that YL-1, another candidate in the network, is an upstream regulator of CG1603.

Strengths:

This is a valuable study, which identifies a potential regulator and a network of nucleus-encoded transcription factors that regulate mitochondrial biogenesis. Through in-vivo and in-vitro experimental evidence, the authors identify the role of CG1603 in this process. The screening strategy was smart, and the follow-up experiments were nicely executed.

Weaknesses:

Some additional experiments showing the effects of CG1603 loss on ETC integrity and functionality would strengthen the work.