CO₂-sensitive RNA modification Possible link between tRNA modification and mitochondrial regulation in cancer cells

A University of Tokyo research group discovered that transfer RNA modification is dynamically regulated by sensing either cellular carbon dioxide or bicarbonate concentration in human mitochondria.

N⁶-threonylcarbamoyldenosine (t⁶A) is a transfer RNA (tRNA) modification in which the amino acid L-threonine (L-Thr) is conjugated with the N⁶-amino group of the adenine base through a carbon dioxide (CO₂)-derived carbonyl group. t⁶A is present at position 37, which is 3’adjacent to the anticodon, and plays critical roles in various stages of protein synthesis. t⁶A is a highly conserved modification found in all organisms from bacteria to humans, which is required for cells to grow efficiently.

The research group led by graduate student Huan Lin and Professor Tsutomu Suzuki of the Department of Chemistry and Biotechnology at the Graduate School of Engineering, the University of Tokyo, identified two enzymes, YRDC and OSGEPL1, responsible for biogenesis of t⁶A in human mitochondrial tRNA.

In fact, the researchers found that t⁶A disappeared when the OSGEPL1 gene was knocked out, and that OSGEPL1 knockout cells showed marked reduction of protein synthesis and mitochondrial dysfunction. Then, they successfully reconstituted t⁶A formation in vitro using these recombinant proteins in the presence of four substrates including L-Thr, bicarbonate (HCO₃-), ATP and tRNA.

Kinetic measurement of t⁶A formation revealed that the Km value of HCO₃- was extremely high (31 mM). Considering that bicarbonate concentration in mitochondria ranges from 10 to 40 mM, HCO₃- is a rate-limiting factor for t⁶A formation, raising the possibility that t⁶A is dynamically regulated under physiological conditions. Consistent with this, the researchers observed a low frequency of t⁶A in mitochondrial tRNAs isolated from human cells cultured under a low bicarbonate concentration. Although tRNA modifications are generally regarded as stable and static, this result demonstrated that t⁶A is dynamically regulated by sensing bicarbonate concentration. Since low t⁶A frequency directly reduces the decoding ability of tRNA, the regulation of mitochondrial translation under some environmental or respiratory conditions is likely.

This study provides a novel concept of regulatory gene expression mediated by dynamic alteration of tRNA modification by sensing cellular metabolic status. Most cancer cells reduce mitochondrial activity and increase anaerobic glycolysis. This is called the Warburg effect. Given that most cellular CO₂ is produced during respiration, CO₂ sensitivity to t⁶A might be a key mechanism for shifting from respiration to anaerobic glycolysis by slowing down mitochondrial translation.

“I was very excited to find out that the most widely known and essential tRNA modification is regulated by a simple metabolite, CO₂ gas, challenging the conventional wisdom that tRNA modifications are stable and static,” says Dr. Lin. He continues, “This is a critical insight into the metabolic regulation of tRNA modification, which opens a new field in life science. I anticipate seeing other instances of RNA modifications dynamically regulated by sensing cellular metabolic status in the coming years.”