Association of a multi-synthetase complex with translating ribosomes in the archaeon Thermococcus kodakarensis

Abstract

AbstractIn archaea and eukaryotes aminoacyl-tRNA synthetases (aaRSs) associate in multi-synthetase complexes (MSCs), however the role of such MSCs in translation is unknown. MSC function was investigated in vivo in the archaeon Thermococcus kodakarensis, wherein six aaRSs were affinity co-purified together with several other factors involved in protein synthesis, suggesting that MSCs may interact directly with translating ribosomes. In support of this hypothesis, the aminoacyl-tRNA synthetase (aaRS) activities of the MSC were enriched in isolated T. kodakarensis polysome fractions. These data indicate that components of the archaeal protein synthesis machinery associate into macromolecular assemblies in vivo and provide the potential to increase translation efficiency by limiting substrate diffusion away from the ribosome, thus facilitating rapid recycling of tRNAs.Structured summary of protein interactionsLeuRS physically interacts with DNA methylase 115, flagellin 118, acetylpolyamine aminohydrolase 140, Pyruvoyl-dependent arginine decarboxylase 154, RecJ-like exonuclease 476, acetyl-CoA acetyltransferase (mevanolate Pathway) 110, glutamine amidotransferase, class I 437, GMP synthase subunit B 184, pyridoxine biosynthesis protein 1183, quinolinate synthetase 206, L-aspartate oxidase 322, uridylate kinase 164, putative molybdenum cofactor biosynthesis protein C 127, bifunctional carboxypeptidase/aminoacylase 214, aspartate racemase 166, serine/threonine protein kinase 111, SAM-dependent methyltransferase 144, GTP cyclohydrolase 398, DNA topoisomerase VI subunit A 209, DNA topoisomerase VI subunit B 192, Type A Flavoprotein 911, NAD(P)H:rubredoxin oxidoreductase (Fatty acid metabolism) 120, NAD(P)H:rubredoxin oxidoreductase 120, cofactor-independent phosphoglycerate mutase 909, bis(5’-adenosyl)-triphosphatase 205, thiamine monophosphate kinase 179, pyruvate formate lyase family activating protein 298, 3-hydroxy-3-methylglutaryl-CoA reductase (mevanolate), N(2), N(2)-dimethylguanosine tRNA methyltransferase 145, N2, N2-dimethylguanosine tRNA methyltransferase 170, putative 5-methylcytosine restriction system, GTPase subunit 947, D-aminopeptidase 540, calcineurin superfamily metallophosphoesterase 118, rubrerythrin-related protein 317, 30S ribosomal protein S12P 161, DNA-directed RNA polymerase subunit beta 373, protein disulfide oxidoreductase 139, 30S ribosomal protein S27e 178, ribonuclease Z 122, 2-oxoglutarate ferredoxin oxidoreductase subunit gamma 352, 2-oxoglutarate ferredoxin oxidoreductase subunit alpha 407, methylmalonyl-CoA mutase, N-terminus of large subunit 172, AP endonuclease (base excision repair pathway) 365, CTP synthetase 105, PBP family phospholipid-binding protein 272, lipoate-protein ligase A, C-terminal section 234, peptide chain release factor 1 331, 30S ribosomal protein S15P 143, NADH oxidase 432, Putative oxidoreductase 538, NAD(P)H-flavin oxidoreductase 471, ferredoxin--NADP(+) reductase subunit alpha 471, Lrp/AsnC family transcriptional regulator 378, glycine dehydrogenase subunit 2 255, glycerol kinase 257, phosphomannomutase-related protein 321, ribose-5-phosphate isomerase A 107, phosphate transport regulator 193, isopentenyl pyrophosphate isomerase (mevanolate Pathway) 500, amino acid kinase 203, NADH:polysulfide oxidoreductase 203, 5’-methylthioadenosine phosphorylase 158, 30S ribosomal protein S9P 171, DNA-directed RNA polymerase subunit D 302, cytidylate kinase 305, adenylate kinase 109, 30S ribosomal protein S8P 180, 30S ribosomal protein S17P 131, serine--glyoxylate aminotransferase, class V (transferasetransaminase), predicetd ATPase 204, metallo-beta-lactamase superfamily hydrolase 134, metallo-beta-lactamase superfamily hydrolase 134, metal-dependent hydrolase 253, putative RNA-associated protein 167, proteasome subunit alpha 174, tRNA-modifying enzyme 172, sugar-phosphate nucleotydyltransferase 108, cytidylyltransferase 128, N-acetylchitobiose deacetylase 124, transcriptional regulator 364, glutamine synthetase 120, N6-adenine-specific DNA methylase 194, ArsR family transcriptional regulator 113, 5’-methylthioadenosine phosphorylase II 280, DNA repair and recombination protein RadA 323, 30S ribosomal protein S6e 106, pyruvate ferredoxin oxidoreductase subunit beta 282, cysteine desulfurase 521, hydrogenase maturation protein HypF 235, iron-molybdenum cofactor-binding protein 192, ATPase 260, 4Fe-4S cluster-binding protein 254, phosphopyruvate hydratase 650, fructose-1,6-bisphosphatase 140, aspartate carbamoyltransferase catalytic subunit 158, Bipolar DNA helicase 448, bipolar DNA helicase 448, molybdenum cofactor biosynthesis protein A 182, proteasome-activating nucleotidase 474, deoxycytidylate deaminase 163, cell division protein FtsZ 821, ribulose bisophosphate carboxylase 1767, chaperonin beta subunit 460, DEAD/DEAH box RNA helicase 175, 30S ribosomal protein S10P, elongation factor 1A, elongation factor 2, cysteinyl-tRNA synthetase, translation-associated GTPase, prolyl-tRNA synthetase, translation initiation factor 2B subunit beta, tyrosyl-tRNA synthetase, glycyl-tRNA synthetase, methionyl-tRNA synthetase, 30S ribosomal protein S3Ae, 30S ribosomal protein S19e, translation initiation factor 2, 30S ribosomal protein S2, 30S ribosomal protein S11P, 30S ribosomal protein S4, 30S ribosomal protein S5P, 30S ribosomal protein S4e and 30S ribosomal protein S19P by pull down (View interaction)