Y. Agari, S. Sato, T. Wakamatsu, Y. Bessho, A. Ebihara et al., X-ray crystal structure of a hypothetical Sua5 protein from Sulfolobus tokodaii strain 7, Proteins, vol.70, pp.1108-1111, 2008.

P. F. Agris, Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications, EMBO Rep, vol.9, pp.629-635, 2008.

H. Ashkenazy, S. Abadi, E. Martz, O. Chay, I. Mayrose et al., ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules, Nucleic Acids Res, vol.44, pp.344-350, 2016.

R. T. Batey and J. S. Kieft, Improved native affinity purification of RNA, RNA, vol.13, pp.1384-1389, 2007.

P. Boccaletto, M. A. Machnicka, E. Purta, P. Piatkowski, B. Baginski et al., MODOMICS: a database of RNA modification pathways, update. Nucleic Acids Res, vol.46, pp.303-307, 2017.

D. A. Braun, J. Rao, G. Mollet, D. Schapiro, M. Daugeron et al., Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly, Nat Genet, vol.49, pp.1529-1538, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02187752

G. B. Chheda, R. H. Hall, J. Mozejko, D. I. Magrath, M. P. Schweizer et al., Aminoacyl nucleosides. VI. Isolation and preliminary characterization of threonyladenine derivatives from transfer ribonucleic acid, Biochemistry, vol.8, pp.3278-3282, 1969.

G. E. Crooks, G. Hon, J. Chandonia, and S. E. Brenner, WebLogo: a sequence logo generator, Genome Res, vol.14, pp.1188-1190, 2004.

M. Daugeron, T. L. Lenstra, M. Frizzarin, B. El-yacoubi, X. Liu et al., Gcn4 misregulation reveals a direct role for the evolutionary conserved EKC/KEOPS in the t 6 A modification of tRNAs, Nucleic Acids Res, vol.39, pp.6148-6160, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-01404019

C. Deutsch, B. El-yacoubi, V. De-crécy-lagard, and D. Iwata-reuyl, Biosynthesis of threonylcarbamoyl adenosine (t 6 A), a universal tRNA nucleoside, J Biol Chem, vol.287, pp.13666-13673, 2012.

M. Downey, R. Houlsworth, L. Maringele, A. Rollie, M. Brehme et al., A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator, Cell, vol.124, pp.1155-1168, 2006.

S. Edvardson, L. Prunetti, A. Arraf, D. Haas, J. M. Bacusmo et al., tRNA N 6 -adenosine threonylcarbamoyltransferase defect due to KAE1/ TCS3 (OSGEP) mutation manifest by neurodegeneration and renal tubulopathy, Eur J Hum Genet, vol.25, pp.545-551, 2017.

B. El-yacoubi, B. Lyons, Y. Cruz, R. Reddy, B. Nordin et al., The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA, Nucleic Acids Res, vol.37, pp.2894-2909, 2009.

B. El-yacoubi, I. Hatin, C. Deutsch, T. Kahveci, J. Rousset et al., A role for the universal Kae1/ Qri7/YgjD (COG0533) family in tRNA modification, EMBO J, vol.30, pp.882-893, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00593551

P. Emsley and K. Cowtan, Coot: model-building tools for molecular graphics, Acta Crystallogr D Biol Crystallogr, vol.60, pp.2126-2132, 2004.

T. M. Fu, X. Liu, L. Li, and X. D. Su, The structure of the hypothetical protein smu.1377c from Streptococcus mutans suggests a role in tRNA modification, Acta Crystallogr Sect F Struct Biol Cryst Commun, vol.66, pp.771-775, 2010.

R. D. Gietz and R. H. Schiestl, Large-scale high-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method, Nat Protoc, vol.2, pp.38-41, 2007.

J. Grodberg and J. J. Dunn, ompT encodes the Escherichia coli outer membrane protease that cleaves T7 RNA polymerase during purification, J Bacteriol, vol.170, pp.1245-1253, 1988.

H. Grosjean, M. Sprinzl, and S. Steinberg, Posttranscriptionally modified nucleosides in transfer RNA: their locations and frequencies, Biochimie, vol.77, pp.139-141, 1995.

K. A. Harris, V. Jones, Y. Bilbille, M. A. Swairjo, and P. F. Agris, YrdC exhibits properties expected of a subunit for a tRNA threonylcarbamoyl transferase, RNA, vol.17, pp.1678-1687, 2011.

K. A. Harris, A. Shekhtman, and P. F. Agris, Specific RNA-protein interactions detected with saturation transfer difference NMR, RNA Biol, vol.10, pp.1307-1311, 2013.

K. A. Harris, B. G. Bobay, K. L. Sarachan, A. F. Sims, Y. Bilbille et al., NMR-based structural analysis of threonylcarbamoyl-AMP synthase and its substrate interactions, J Biol Chem, vol.290, pp.20032-20043, 2015.

W. Kabsch, XDS. Acta Crystallogr D Biol Crystallogr, vol.66, pp.125-132, 2010.

E. Kisseleva-romanova, R. Lopreiato, A. Baudin-baillieu, J. Rousselle, L. Ilan et al., Yeast homolog of a cancer-testis antigen defines a new transcription complex, EMBO J, vol.25, pp.3576-3585, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00133495

M. Kuratani, T. Kasai, R. Akasaka, K. Higashijima, T. Terada et al., Crystal structure of Sulfolobus tokodaii Sua5 complexed with L-threonine and AMPPNP, Proteins, vol.79, pp.2065-2075, 2011.

V. V. Kushnirov, Rapid and reliable protein extraction from yeast, Yeast, vol.16, pp.857-860, 2000.

R. A. Laskowski and M. B. Swindells, LigPlot+: multiple ligand-protein interaction diagrams for drug discovery, J Chem Inf Model, vol.51, pp.2778-2786, 2011.

C. T. Lauhon, Mechanism of N 6 -threonylcarbamoyladenonsine, 2012.

, A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP, Biochemistry, vol.51, pp.8950-8963

E. Lescrinier, K. Nauwelaerts, K. Zanier, K. Poesen, M. Sattler et al., The naturally occurring N 6 -threonyl adenine in anticodon loop of Schizosaccharomyces pombe tRNAi causes formation of a unique U-turn motif, Nucleic Acids Res, vol.34, pp.2878-2886, 2006.

D. Liger, L. Mora, N. Lazar, S. Figaro, J. Henri et al., Mechanism of activation of methyltransferases involved in translation by the Trm112 "hub" protein, Nucleic Acids Res, vol.39, pp.6249-6259, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00624935

C. A. Lin, S. R. Ellis, and H. L. True, The Sua5 protein is essential for normal translational regulation in yeast, Mol Cell Biol, vol.30, pp.354-363, 2010.

M. A. Machnicka, K. Milanowska, O. Oglou, O. Purta, E. Kurkowska et al., MODOMICS: a database of RNA modification pathways-2013 update, Nucleic Acids Res, vol.41, pp.262-267, 2013.

D. Mao, D. Neculai, M. Downey, S. Orlicky, Y. Z. Haffani et al., Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine, Mol Cell, vol.32, pp.259-275, 2008.

F. V. Murphy, V. Ramakrishnan, A. Malkiewicz, and P. F. Agris, The role of modifications in codon discrimination by tRNA Lys UUU, Nat Struct Mol Biol, vol.11, pp.1186-1191, 2004.

C. E. Nichols, H. K. Lamb, P. Thompson, E. Omari, K. Lockyer et al., Crystal structure of the dimer of two essential Salmonella typhimurium proteins, YgjD & YeaZ and calorimetric evidence for the formation of a ternary YgjD-YeaZ-YjeE complex, Protein Sci, vol.22, pp.628-640, 2013.

C. Parthier, S. Görlich, F. Jaenecke, C. Breithaupt, U. Bräuer et al., The O-carbamoyltransferase TobZ catalyzes an ancient enzymatic reaction, Angew Chem Int Ed Engl, vol.51, pp.4046-4052, 2012.

L. Perrochia, E. Crozat, A. Hecker, W. Zhang, J. Bareille et al., In vitro biosynthesis of a universal t 6 A tRNA modification in Archaea and Eukarya, Nucleic Acids Res, vol.41, pp.1953-1964, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00822760

L. Perrochia, D. Guetta, A. Hecker, P. Forterre, and T. Basta, Functional assignment of KEOPS/EKC complex subunits in the biosynthesis of the universal t 6 A tRNA modification, Nucleic Acids Res, vol.41, pp.9484-9499, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00881058

S. Petkun, R. Shi, Y. Li, A. Asinas, C. Munger et al., Structure of hydrogenase maturation protein HypF with reaction intermediates shows two active sites, Structure, vol.19, pp.1773-1783, 2011.

E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt et al., UCSF Chimera-a visualization system for exploratory research and analysis, J Comput Chem, vol.25, pp.1605-1612, 2004.

D. M. Powers and A. Peterkofsky, Biosynthesis and specific labeling of N-(purin-6-ylcarbamoyl)threonine of Escherichia coli transfer RNA, Biochem Biophys Res Commun, vol.46, pp.831-838, 1972.

S. R. Price, N. Ito, C. Oubridge, J. M. Avis, and K. Nagai, Crystallization of RNA-protein complexes. I. Methods for the large-scale preparation of RNA suitable for crystallographic studies, J Mol Biol, vol.249, pp.398-408, 1995.

K. D. Sonawane and S. B. Sambhare, The influence of hypermodified nucleosides lysidine and t 6 A to recognize the AUA codon instead of AUG: a molecular dynamics simulation study, Integr Biol (Camb), vol.7, pp.1387-1395, 2015.

M. Srinivasan, P. Mehta, Y. Yu, E. Prugar, E. V. Koonin et al., The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t 6 A, EMBO J, vol.30, pp.873-881, 2011.

J. W. Stuart, Z. Gdaniec, R. Guenther, M. Marszalek, E. Sochacka et al., Functional anticodon architecture of human tRNA Lys3 includes disruption of intraloop hydrogen bonding by the naturally occurring amino acid modification, t 6 A, Biochemistry, vol.39, pp.13396-13404, 2000.

S. Takemura, M. Murakami, and M. Miyazaki, Nucleotide sequence of isoleucine transfer RNA from Torulopsis utilis, J Biochem, vol.65, pp.489-491, 1969.

M. Teplova, V. Tereshko, R. Sanishvili, A. Joachimiak, T. Bushueva et al., The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding, Protein Sci, vol.9, pp.2557-2566, 2000.

P. C. Thiaville, B. El-yacoubi, L. Perrochia, A. Hecker, M. Prigent et al., Cross kingdom functional conservation of the core universally conserved threonylcarbamoyladenosine tRNA synthesis enzymes, Eukaryot Cell, vol.13, pp.1222-1231, 2014.

P. C. Thiaville, B. El-yacoubi, C. Köhrer, J. J. Thiaville, C. Deutsch et al., Essentiality of threonylcarbamoyladenosine (t 6 A), a universal tRNA modification, in bacteria, Mol Microbiol, vol.98, pp.1199-1221, 2015.

P. C. Thiaville, D. Iwata-reuyl, and V. De-crécy-lagard, Diversity of the biosynthesis pathway for threonylcarbamoyladenosine (t 6 A), a universal modification of tRNA, RNA Biol, vol.11, pp.1529-1539, 2015.

P. C. Thiaville, R. Legendre, D. Rojas-benítez, A. Baudin-baillieu, I. Hatin et al., Global translational impacts of the loss of the tRNA modification t 6 A in yeast, Microb Cell, vol.3, pp.29-45, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01412631

S. Unni, Y. Huang, R. M. Hanson, M. Tobias, S. Krishnan et al., Web servers and services for electrostatics calculations with APBS and PDB2PQR, J Comput Chem, vol.32, pp.1488-1491, 2011.

L. Wan, D. Mao, D. Neculai, J. Strecker, D. Chiovitti et al., Reconstitution and characterization of eukaryotic N 6 -threonylcarbamoylation of tRNA using a minimal enzyme system, Nucleic Acids Res, vol.41, pp.6332-6346, 2013.

L. Wan, M. C. Pillon, N. Thevakumaran, Y. Sun, A. Chakrabartty et al., Structural and functional characterization of KEOPS dimerization by Pcc1 and its role in t 6 A biosynthesis, Nucleic Acids Res, vol.44, pp.6971-6980, 2016.

J. Weissenbach and H. Grosjean, Effect of threonylcarbamoyl modification, 1981.

, A) in yeast tRNA Arg III on codon-anticodon and anticodon-anticodon interactions. A thermodynamic and kinetic evaluation, Eur J Biochem, vol.116, pp.207-213

M. D. Winn, G. N. Murshudov, and M. Z. Papiz, Macromolecular TLS refinement in REFMAC at moderate resolutions, Methods Enzymol, vol.374, pp.300-321, 2003.

M. D. Winn, C. C. Ballard, K. D. Cowtan, E. J. Dodson, P. Emsley et al., Overview of the CCP4 suite and current developments, Acta Crystallogr D Biol Crystallogr, vol.67, pp.235-242, 2011.

C. Yarian, H. Townsend, W. Czestkowski, E. Sochacka, A. J. Malkiewicz et al., Accurate translation of the genetic code depends on tRNA modified nucleosides, J Biol Chem, vol.277, pp.16391-16395, 2002.

W. Zhang, B. Collinet, M. Graille, M. C. Daugeron, N. Lazar et al., Crystal structures of the Gon7/Pcc1 and Bud32/Cgi121 complexes provide a model for the complete yeast KEOPS complex, Nucleic Acids Res, vol.43, pp.3358-3372, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01220993

W. Zhang, B. Collinet, L. Perrochia, D. Durand, and H. Van-tilbeurgh, The ATP-mediated formation of the YgjD-YeaZ-YjeE complex is required for the biosynthesis of tRNA t 6 A in Escherichia coli, Nucleic Acids Res, vol.43, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01277988

, Access the most recent version at doi, RNA References, vol.24, pp.926-938, 2018.

, This article cites 60 articles, 13 of which can be accessed free at