Bacillus subtilis exhibits MnmC-like tRNA modification activities

References

• Boccaletto P, Machnicka MA, Purta E, et al. MODOMICS: a database of RNA modification pathways. 2017 update. Nucleic Acids Res. 2018;46:D303–d7.
   PubMed Web of Science ®Google Scholar
• Vare VY, Eruysal ER, Narendran A, et al. Chemical and conformational diversity of modified nucleosides affects tRNA structure and function. Biomolecules. 2017;7:29.
   PubMed Web of Science ®Google Scholar
• Nachtergaele S, He C. The emerging biology of RNA post-transcriptional modifications. RNA Biol. 2017;14:156–163.
   PubMed Web of Science ®Google Scholar
• Agris PF, Eruysal ER, Narendran A, et al. Celebrating wobble decoding: half a century and still much is new. RNA Biol. 2018;15:537–553.
   Web of Science ®Google Scholar
• Agris PF, Narendran A, Sarachan K, et al. The importance of being modified: the role of RNA modifications in translational fidelity. Enzymes. 2017;41:1–50.
   PubMedGoogle Scholar
• Yim L, Moukadiri I, Björk GR, et al. Further insights into the tRNA modification process controlled by proteins MnmE and GidA of Escherichia coli. Nucleic Acids Res. 2006;34:5892–5905.
   PubMed Web of Science ®Google Scholar
• Moukadiri I, Prado S, Piera J, et al. Evolutionarily conserved proteins MnmE and GidA catalyze the formation of two methyluridine derivatives at tRNA wobble positions. Nucleic Acids Res. 2009;37:7177–7193.
   PubMed Web of Science ®Google Scholar
• Armengod ME, Meseguer S, Villarroya M, et al. Modification of the wobble uridine in bacterial and mitochondrial tRNAs reading NNA/NNG triplets of 2-codon boxes. RNA Biol. 2014;11:1495–1507.
   PubMed Web of Science ®Google Scholar
• Moukadiri I, Garzón MJ, Björk GR, et al. The output of the tRNA modification pathways controlled by the Escherichia coli MnmEG and MnmC enzymes depends on the growth conditions and the tRNA species. Nucleic Acids Res. 2014;42:2602–2623.
   PubMed Web of Science ®Google Scholar
• Ikeuchi Y, Shigi N, Kato J, et al. Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol Cell. 2006;21:97–108.
   PubMed Web of Science ®Google Scholar
• Benitez-Paez A, Villarroya M, Douthwaite S, et al. YibK is the 2ʹ-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors. RNA. 2010;16:2131–2143.
   PubMed Web of Science ®Google Scholar
• Grosjean H, Breton M, Sirand-Pugnet P, et al. Predicting the minimal translation apparatus: lessons from the reductive evolution of mollicutes. PLoS Genet. 2014;10:e1004363.
   PubMed Web of Science ®Google Scholar
• Bujnicki JM, Oudjama Y, Roovers M, et al. Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA. RNA. 2004;10:1236–1242.
   PubMed Web of Science ®Google Scholar
• Kitamura A, Nishimoto M, Sengoku T, et al. Characterization and structure of the Aquifex aeolicus protein DUF752: a bacterial tRNA-methyltransferase (MnmC2) functioning without the usually fused oxidase domain (MnmC1). J Biol Chem. 2012;287:43950–43960.
   PubMed Web of Science ®Google Scholar
• Yamada Y, Murao K, Ishikura H. 5-(carboxymethylaminomethyl)-2-thiouridine, a new modified nucleoside found at the first letter position of the anticodon. Nucleic Acids Res. 1981;9:1933–1939.
   PubMed Web of Science ®Google Scholar
• Vold BS, Longmire ME, Keith DE Jr. Thiolation and 2-methylthio- modification of Bacillus subtilis transfer ribonucleic acids. J Bacteriol. 1981;148:869–876.
   PubMed Web of Science ®Google Scholar
• Andachi Y, Yamao F, Muto A, et al. Codon recognition patterns as deduced from sequences of the complete set of transfer RNA species in Mycoplasma capricolum. Resemblance to mitochondria. J Mol Biol. 1989;209:37–54.
   PubMed Web of Science ®Google Scholar
• Anton BP, Russell SP, Vertrees J, et al. Functional characterization of the YmcB and YqeV tRNA methylthiotransferases of Bacillus subtilis. Nucleic Acids Res. 2010;38:6195–6205.
   PubMed Web of Science ®Google Scholar
• Kang BI, Miyauchi K, Matuszewski M, et al. Identification of 2-methylthio cyclic N6-threonylcarbamoyladenosine (ms2ct6A) as a novel RNA modification at position 37 of tRNAs. Nucleic Acids Res. 2017;45:2124–2136.
   PubMed Web of Science ®Google Scholar
• Singhal RP, Vold B. Changes in transfer ribonucleic acids of Bacillus subtilis during different growth phases. Nucleic Acids Res. 1976;3:1249–1262.
   PubMed Web of Science ®Google Scholar
• Vold B. Modified nucleosides of Bacillus subtilis transfer ribonucleic acids. J Bacteriol. 1976;127:258–267.
   PubMed Web of Science ®Google Scholar
• Asano K, Suzuki T, Saito A, et al. Metabolic and chemical regulation of tRNA modification associated with taurine deficiency and human disease. Nucleic Acids Res. 2018;46:1565–1583.
   PubMed Web of Science ®Google Scholar
• Ruiz-Partida R, Prado S, Villarroya M, et al. An alternative homodimerization interface of MnmG reveals a conformational dynamics that is essential for its tRNA modification function. J Mol Biol. 2018;430:2822–2842.
   PubMed Web of Science ®Google Scholar
• Liu X, Speckhard DC, Shepherd TR, et al. Distinct roles for conformational dynamics in protein-ligand interactions. Structure. 2016;24:2053–2066.
   PubMed Web of Science ®Google Scholar
• Suzuki T. Chaplet column chromatography: isolation of a large set of individual RNAs in a single step. Methods Enzymol. 2007;425:231–239.
   PubMed Web of Science ®Google Scholar
• Gehrke CW, Kuo KC. Ribonucleoside analysis by reversed-phase high-performance liquid chromatography. J Chromatogr. 1989;471:3–36.
   PubMed Web of Science ®Google Scholar
• Eddy SR. Profile hidden Markov models. Bioinformatics. 1998;14:755–763.
   PubMed Web of Science ®Google Scholar
• Pruitt KD, Tatusova T, Brown GR, Maglott DR. NCBI Reference Sequences. (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 2012;40:D130–5.
   PubMed Web of Science ®Google Scholar
• Do CB, Mahabhashyam MS, Brudno M, et al. ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res. 2005;15:330–340.
   PubMed Web of Science ®Google Scholar
• Mosquera-Rendon J, Cardenas-Brito S, Pineda JD, et al. Evolutionary and sequence-based relationships in bacterial AdoMet-dependent non-coding RNA methyltransferases. BMC Res Notes. 2014;7:440.
   PubMedGoogle Scholar