Structure-function Analysis of an Ancient TsaD-TsaC-SUA5-TcdA Modular Enzyme Reveals a Prototype of TRNA T6A and Ct6A Synthetases

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2023 Jul 10

PMID 37427786

Authors

MengQi Jin

Zelin Zhang

Zhijiang Yu

Wei Chen

Xiaolei Wang

Dongsheng Lei

Wenhua Zhang

Affiliations

Soon will be listed here.

Abstract

N 6-threonylcarbamoyladenosine (t6A) is a post-transcriptional modification found uniquely at position 37 of tRNAs that decipher ANN-codons in the three domains of life. tRNA t6A plays a pivotal role in promoting translational fidelity and maintaining protein homeostasis. The biosynthesis of tRNA t6A requires members from two evolutionarily conserved protein families TsaC/Sua5 and TsaD/Kae1/Qri7, and a varying number of auxiliary proteins. Furthermore, tRNA t6A is modified into a cyclic hydantoin form of t6A (ct6A) by TcdA in bacteria. In this work, we have identified a TsaD-TsaC-SUA5-TcdA modular protein (TsaN) from Pandoraviruses and determined a 3.2 Å resolution cryo-EM structure of P. salinus TsaN. The four domains of TsaN share strong structural similarities with TsaD/Kae1/Qri7 proteins, TsaC/Sua5 proteins, and Escherichia coli TcdA. TsaN catalyzes the formation of threonylcarbamoyladenylate (TC-AMP) using L-threonine, HCO3- and ATP, but does not participate further in tRNA t6A biosynthesis. We report for the first time that TsaN catalyzes a tRNA-independent threonylcarbamoyl modification of adenosine phosphates, leading to t6ADP and t6ATP. Moreover, TsaN is also active in catalyzing tRNA-independent conversion of t6A nucleoside to ct6A. Our results imply that TsaN from Pandoraviruses might be a prototype of the tRNA t6A- and ct6A-modifying enzymes in some cellular organisms.

Citing Articles

Structures of KEOPS bound to tRNA reveal functional roles of the kinase Bud32.

Ona Chuquimarca S, Beenstock J, Daou S, Porat J, Keszei A, Yin J Nat Commun. 2024; 15(1):10633.

PMID: 39639027 PMC: 11621456. DOI: 10.1038/s41467-024-54787-w.

Molecular basis of A. thaliana KEOPS complex in biosynthesizing tRNA t6A.

Zheng X, Su C, Duan L, Jin M, Sun Y, Zhu L Nucleic Acids Res. 2024; 52(8):4523-4540.

PMID: 38477398 PMC: 11077089. DOI: 10.1093/nar/gkae179.

Antibacterial Activity of Rainbow Trout Plasma: In Vitro Assays and Proteomic Analysis.

Mizaeva T, Alieva K, Zulkarneev E, Kurpe S, Isakova K, Matrosova S Animals (Basel). 2023; 13(22).

PMID: 38003182 PMC: 10668809. DOI: 10.3390/ani13223565.

References

Williams C, Headd J, Moriarty N, Prisant M, Videau L, Deis L . MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci. 2017; 27(1):293-315. PMC: 5734394. DOI: 10.1002/pro.3330. View

Bolstad H, Botelho D, Wood M . Proteomic analysis of protein-protein interactions within the Cysteine Sulfinate Desulfinase Fe-S cluster biogenesis system. J Proteome Res. 2010; 9(10):5358-69. PMC: 2990340. DOI: 10.1021/pr1006087. View

Nasir A, Caetano-Anolles G . A phylogenomic data-driven exploration of viral origins and evolution. Sci Adv. 2015; 1(8):e1500527. PMC: 4643759. DOI: 10.1126/sciadv.1500527. View

Thiaville P, El Yacoubi B, Kohrer C, Thiaville J, Deutsch C, Iwata-Reuyl D . Essentiality of threonylcarbamoyladenosine (t(6)A), a universal tRNA modification, in bacteria. Mol Microbiol. 2015; 98(6):1199-221. PMC: 4963248. DOI: 10.1111/mmi.13209. View

Zhou J, Wang Y, Zeng Q, Meng S, Wang E, Zhou X . Molecular basis for t6A modification in human mitochondria. Nucleic Acids Res. 2020; 48(6):3181-3194. PMC: 7102964. DOI: 10.1093/nar/gkaa093. View

Kopina B, Missoury S, Collinet B, Fulton M, Cirio C, Van Tilbeurgh H . Structure of a reaction intermediate mimic in t6A biosynthesis bound in the active site of the TsaBD heterodimer from Escherichia coli. Nucleic Acids Res. 2021; 49(4):2141-2160. PMC: 7913687. DOI: 10.1093/nar/gkab026. View

Aravind L, Koonin E . Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J Mol Biol. 1999; 287(5):1023-40. DOI: 10.1006/jmbi.1999.2653. View

DiIorio M, Kulczyk A . A Robust Single-Particle Cryo-Electron Microscopy (cryo-EM) Processing Workflow with cryoSPARC, RELION, and Scipion. J Vis Exp. 2022; (179). DOI: 10.3791/63387. View

Murphy 4th F, Ramakrishnan V, Malkiewicz A, Agris P . The role of modifications in codon discrimination by tRNA(Lys)UUU. Nat Struct Mol Biol. 2004; 11(12):1186-91. DOI: 10.1038/nsmb861. View

10.

Tominaga T, Kobayashi K, Ishii R, Ishitani R, Nureki O . Structure of Saccharomyces cerevisiae mitochondrial Qri7 in complex with AMP. Acta Crystallogr F Struct Biol Commun. 2014; 70(Pt 8):1009-14. PMC: 4118794. DOI: 10.1107/S2053230X14014046. View

11.

Schulz F, Abergel C, Woyke T . Giant virus biology and diversity in the era of genome-resolved metagenomics. Nat Rev Microbiol. 2022; 20(12):721-736. DOI: 10.1038/s41579-022-00754-5. View

12.

Parthasarathy R, OHRT J, CHHEDA G . Conformation and possible role of hypermodified nucleosides adjacent to 3'-end of anticodon in tRNA: N-(purin-6-ylcarbamoyl)-L-threonine riboside. Biochem Biophys Res Commun. 1974; 60(1):211-8. DOI: 10.1016/0006-291x(74)90193-4. View

13.

Weiss M, Sousa F, Mrnjavac N, Neukirchen S, Roettger M, Nelson-Sathi S . The physiology and habitat of the last universal common ancestor. Nat Microbiol. 2016; 1(9):16116. DOI: 10.1038/nmicrobiol.2016.116. View

14.

Daugeron M, Missoury S, Da Cunha V, Lazar N, Collinet B, Van Tilbeurgh H . A paralog of Pcc1 is the fifth core subunit of the KEOPS tRNA-modifying complex in Archaea. Nat Commun. 2023; 14(1):526. PMC: 9889334. DOI: 10.1038/s41467-023-36210-y. View

15.

Legendre M, Fabre E, Poirot O, Jeudy S, Lartigue A, Alempic J . Diversity and evolution of the emerging Pandoraviridae family. Nat Commun. 2018; 9(1):2285. PMC: 5995976. DOI: 10.1038/s41467-018-04698-4. View

16.

Yarian C, Townsend H, Czestkowski W, Sochacka E, Malkiewicz A, Guenther R . Accurate translation of the genetic code depends on tRNA modified nucleosides. J Biol Chem. 2002; 277(19):16391-5. DOI: 10.1074/jbc.M200253200. View

17.

Luthra A, Swinehart W, Bayooz S, Phan P, Stec B, Iwata-Reuyl D . Structure and mechanism of a bacterial t6A biosynthesis system. Nucleic Acids Res. 2018; 46(3):1395-1411. PMC: 5814804. DOI: 10.1093/nar/gkx1300. View

18.

Miyauchi K, Kimura S, Suzuki T . A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification. Nat Chem Biol. 2012; 9(2):105-11. DOI: 10.1038/nchembio.1137. View

19.

El Yacoubi B, Lyons B, Cruz Y, Reddy R, Nordin B, Agnelli F . The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA. Nucleic Acids Res. 2009; 37(9):2894-909. PMC: 2685093. DOI: 10.1093/nar/gkp152. View

20.

Boccaletto P, Stefaniak F, Ray A, Cappannini A, Mukherjee S, Purta E . MODOMICS: a database of RNA modification pathways. 2021 update. Nucleic Acids Res. 2021; 50(D1):D231-D235. PMC: 8728126. DOI: 10.1093/nar/gkab1083. View