IRC3 Regulates Mitochondrial Translation in Response to Metabolic Cues in Saccharomyces cerevisiae

ABSTRACT

Mitochondrial oxidative phosphorylation (OXPHOS) enzymes have a dual genetic origin. Mechanisms regulating the expression of nucleus-encoded OXPHOS subunits in response to metabolic cues (glucose versus glycerol) are well understood, while the regulation of mitochondrially encoded OXPHOS subunits is poorly defined. Here, we show that IRC3, a DEAD/H box helicase gene, previously implicated in mitochondrial DNA maintenance, is central to integrating metabolic cues with mitochondrial translation. Irc3 associates with mitochondrial small ribosomal subunits in cells consistent with its role in regulating translation elongation based on the Arg8^m reporter system. IRC3-deleted cells retained mitochondrial DNA despite a growth defect on glycerol plates. Glucose-grown Δirc3ρ⁺ and irc3 temperature-sensitive cells at 37°C have reduced translation rates from the majority of mRNAs. In contrast, when galactose was the carbon source, a reduction in mitochondrial translation was observed predominantly from Cox1 mRNA in Δirc3ρ⁺ cells but no defect was observed in irc3 temperature-sensitive cells, at 37°C. In support of a model whereby IRC3 responds to metabolic cues to regulate mitochondrial translation, Δirc3 suppressor strains isolated for restoration of growth on glycerol medium restore mitochondrial protein synthesis differentially in the presence of glucose versus glycerol.

KEYWORDS:

• mitochondria
• OXPHOS
• RNA helicase
• metabolic cues
• translation

SUPPLEMENTAL MATERIAL

Supplemental material is available online only.

ACKNOWLEDGMENTS

We are extremely grateful to Janine R. Maddock for strains, plasmids, and antibodies, Thomas D. Fox for antibodies to Arg8, Xochitl Pérez Martínez for strains YC162, RGV139, RGV140, and XPM78a, and Antoni Barrientos for strains XPM171a and W303I⁰. We also thank Jagreet Kaur and Suman Dhar for critically reading the manuscript and Shahnaz Ansari for technical assistance. We are grateful for the instrumentation facilities at CIF, UDSC, and DST-FIST/UGC-SAP-supported CIF, Genetics.

This work was supported by grants from the Department of Biotechnology (grant no. BT/PR14740/BRB/10/875/2010 and BT/PR15104/GBD/27315/2011), SERB (grant no. EMR/2015/000650), and CSIR [grant no. 27(0324)/EMR-II] and by an R&D grant from Delhi University to K.D. and DU-IOE. J.K. acknowledges UGC, BSR, SERB, and ICMR for junior research fellowships and senior research fellowships.

J.K. performed experiments and analyzed data. K.D. and J.K. conceived the project, designed experiments, analyzed the data, and wrote the paper. K.D. was responsible for securing funding for this work.