RelA-SpoT Homolog toxins pyrophosphorylate the CCA end of tRNA to inhibit protein synthesis

Tatsuaki Kurata; Tetiana Brodiazhenko; Sofia Raquel Alves Oliveira; Mohammad Roghanian; Yuriko Sakaguchi; Kathryn Jane Turnbull; Ondřej Bulvas; Hiraku Takada; Hedvig Tamman; Andres Ainelo; Radek Pohl; Dominik Rejman; Tanel Tenson; Tsutomu Suzuki; Abel Garcia-Pino; Gemma Catherine Atkinson; Vasili Hauryliuk

doi:10.1016/j.molcel.2021.06.005

RelA-SpoT Homolog toxins pyrophosphorylate the CCA end of tRNA to inhibit protein synthesis

Mol Cell. 2021 Aug 5;81(15):3160-3170.e9. doi: 10.1016/j.molcel.2021.06.005. Epub 2021 Jun 25.

Authors

Tatsuaki Kurata¹, Tetiana Brodiazhenko², Sofia Raquel Alves Oliveira², Mohammad Roghanian³, Yuriko Sakaguchi⁴, Kathryn Jane Turnbull³, Ondřej Bulvas⁵, Hiraku Takada⁶, Hedvig Tamman⁷, Andres Ainelo⁷, Radek Pohl⁵, Dominik Rejman⁵, Tanel Tenson², Tsutomu Suzuki⁴, Abel Garcia-Pino⁸, Gemma Catherine Atkinson⁹, Vasili Hauryliuk¹⁰

Affiliations

¹ Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden. Electronic address: tatsuaki.kurata@med.lu.se.
² University of Tartu, Institute of Technology, 50411 Tartu, Estonia.
³ Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden; Department of Clinical Microbiology, Rigshospitalet, 2200 Copenhagen, Denmark.
⁴ Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.
⁵ Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovonam. 2, 166 10 Prague 6, Czech Republic.
⁶ Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto 603-8555, Japan.
⁷ Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Campus La Plaine, Building BC, Room 1C4203, Boulevard du Triomphe, 1050 Brussels, Belgium.
⁸ Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Campus La Plaine, Building BC, Room 1C4203, Boulevard du Triomphe, 1050 Brussels, Belgium; WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium.
⁹ Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden. Electronic address: gemma.atkinson@med.lu.se.
¹⁰ Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden; University of Tartu, Institute of Technology, 50411 Tartu, Estonia; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden. Electronic address: vasili.hauryliuk@med.lu.se.

PMID: 34174184
DOI: 10.1016/j.molcel.2021.06.005

Abstract

RelA-SpoT Homolog (RSH) enzymes control bacterial physiology through synthesis and degradation of the nucleotide alarmone (p)ppGpp. We recently discovered multiple families of small alarmone synthetase (SAS) RSH acting as toxins of toxin-antitoxin (TA) modules, with the FaRel subfamily of toxSAS abrogating bacterial growth by producing an analog of (p)ppGpp, (pp)pApp. Here we probe the mechanism of growth arrest used by four experimentally unexplored subfamilies of toxSAS: FaRel2, PhRel, PhRel2, and CapRel. Surprisingly, all these toxins specifically inhibit protein synthesis. To do so, they transfer a pyrophosphate moiety from ATP to the tRNA 3' CCA. The modification inhibits both tRNA aminoacylation and the sensing of cellular amino acid starvation by the ribosome-associated RSH RelA. Conversely, we show that some small alarmone hydrolase (SAH) RSH enzymes can reverse the pyrophosphorylation of tRNA to counter the growth inhibition by toxSAS. Collectively, we establish RSHs as RNA-modifying enzymes.

Keywords: (p)ppApp; (p)ppGpp; RelA-SpoT Homolog; SAH; SAS; ribosome; tRNA modification; toxSAS; toxin-antitoxin; translation.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacterial Toxins / genetics
Bacterial Toxins / metabolism*
Bacterial Toxins / pharmacology
Gram-Positive Asporogenous Rods / chemistry
Gram-Positive Asporogenous Rods / metabolism
Guanosine Pentaphosphate / chemistry
Guanosine Pentaphosphate / metabolism*
Ligases / chemistry
Ligases / genetics
Ligases / metabolism*
Phosphorylation / drug effects
Protein Biosynthesis / drug effects
Protein Biosynthesis / physiology
Protein Synthesis Inhibitors / pharmacology
Pyrophosphatases
RNA, Transfer / metabolism*
Ribosomes / metabolism

Substances

Bacterial Toxins
Protein Synthesis Inhibitors
Guanosine Pentaphosphate
RNA, Transfer
guanosine-3',5'-bis(diphosphate) 3'-pyrophosphatase
Pyrophosphatases
Ligases
guanosine 3',5'-polyphosphate synthetases