Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance

Takayuki Ohira (), Keiichi Minowa, Kei Sugiyama, Seisuke Yamashita, Yuriko Sakaguchi, Kenjyo Miyauchi, Ryo Noguchi, Akira Kaneko, Izumi Orita, Toshiaki Fukui, Kozo Tomita () and Tsutomu Suzuki ()
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Takayuki Ohira: The University of Tokyo
Keiichi Minowa: The University of Tokyo
Kei Sugiyama: The University of Tokyo
Seisuke Yamashita: Graduate School of Frontier Sciences, The University of Tokyo
Yuriko Sakaguchi: The University of Tokyo
Kenjyo Miyauchi: The University of Tokyo
Ryo Noguchi: The University of Tokyo
Akira Kaneko: Tokyo Institute of Technology
Izumi Orita: Tokyo Institute of Technology
Toshiaki Fukui: Tokyo Institute of Technology
Kozo Tomita: Graduate School of Frontier Sciences, The University of Tokyo
Tsutomu Suzuki: The University of Tokyo

Nature, 2022, vol. 605, issue 7909, 372-379

Abstract: Abstract Post-transcriptional modifications have critical roles in tRNA stability and function1–4. In thermophiles, tRNAs are heavily modified to maintain their thermal stability under extreme growth temperatures5,6. Here we identified 2′-phosphouridine (Up) at position 47 of tRNAs from thermophilic archaea. Up47 confers thermal stability and nuclease resistance to tRNAs. Atomic structures of native archaeal tRNA showed a unique metastable core structure stabilized by Up47. The 2′-phosphate of Up47 protrudes from the tRNA core and prevents backbone rotation during thermal denaturation. In addition, we identified the arkI gene, which encodes an archaeal RNA kinase responsible for Up47 formation. Structural studies showed that ArkI has a non-canonical kinase motif surrounded by a positively charged patch for tRNA binding. A knockout strain of arkI grew slowly at high temperatures and exhibited a synthetic growth defect when a second tRNA-modifying enzyme was depleted. We also identified an archaeal homologue of KptA as an eraser that efficiently dephosphorylates Up47 in vitro and in vivo. Taken together, our findings show that Up47 is a reversible RNA modification mediated by ArkI and KptA that fine-tunes the structural rigidity of tRNAs under extreme environmental conditions.

Date: 2022
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DOI: 10.1038/s41586-022-04677-2

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