Characterization and Structure of the Aquifex aeolicus Protein DUF752

Kitamura, Aya; Nishimoto, Madoka; Sengoku, Toru; Shibata, Rie; Jäger, Gunilla; Björk, Glenn R.; Grosjean, Henri; Yokoyama, Shigeyuki; Bessho, Yoshitaka

doi:10.1074/jbc.m112.409300

Cited by 17 publications

(20 citation statements)

References 51 publications

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“…We also reported the presence of cmnm 5 s 2 U and nm 5 s 2 U in total tRNA purified from an mnmC null mutant. However, it has been suggested that the formation of these intermediates is sensitive to growth conditions and specific strains, which might explain why they were not detected in other studies ( 23 , 26 , 41 ).…”

Section: Resultsmentioning

confidence: 83%

The output of the tRNA modification pathways controlled by theEscherichia coliMnmEG and MnmC enzymes depends on the growth conditions and the tRNA species

Moukadiri

Garzón

Björk

et al. 2013

Nucleic Acids Research

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In Escherichia coli, the MnmEG complex modifies transfer RNAs (tRNAs) decoding NNA/NNG codons. MnmEG catalyzes two different modification reactions, which add an aminomethyl (nm) or carboxymethylaminomethyl (cmnm) group to position 5 of the anticodon wobble uridine using ammonium or glycine, respectively. In and , however, cmnm5 appears as the final modification, whereas in the remaining tRNAs, the MnmEG products are converted into 5-methylaminomethyl (mnm5) through the two-domain, bi-functional enzyme MnmC. MnmC(o) transforms cmnm5 into nm5, whereas MnmC(m) converts nm5 into mnm5, thus producing an atypical network of modification pathways. We investigate the activities and tRNA specificity of MnmEG and the MnmC domains, the ability of tRNAs to follow the ammonium or glycine pathway and the effect of mnmC mutations on growth. We demonstrate that the two MnmC domains function independently of each other and that and are substrates for MnmC(m), but not MnmC(o). Synthesis of mnm5s2U by MnmEG-MnmC in vivo avoids build-up of intermediates in . We also show that MnmEG can modify all the tRNAs via the ammonium pathway. Strikingly, the net output of the MnmEG pathways in vivo depends on growth conditions and tRNA species. Loss of any MnmC activity has a biological cost under specific conditions.

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Section: Resultsmentioning

confidence: 83%

The output of the tRNA modification pathways controlled by theEscherichia coliMnmEG and MnmC enzymes depends on the growth conditions and the tRNA species

Moukadiri

Garzón

Björk

et al. 2013

Nucleic Acids Research

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“…The fact that B. subtilis MnmC-like activities reside in non MnmC homologous protein(s) calls for caution in assuming that cmnm 5 s 2 U may be the final modification in organisms lacking MnmC homologs. Moreover, the proposal that the ammonium pathway is responsible for the mnm 5 s 2 U synthesis in organisms that, like A. aeolicus [14], lack an MnmC(o) homolog, should be re-evaluated.…”

Section: Resultsmentioning

confidence: 99%

“…The ammonium pathway has been proposed to be the dominant route in Aquifex aeolicus because this species has a homolog of MnmC(m) but not of MnmC(o), and mnm 5 s 2 U, but not cmnm 5 s 2 U, has been HPLC-detected in bulk A. aeolicus tRNA hydrolysates [14]. Conversely, the glycine pathway has been considered the predominant route in Bacillus subtilis and Mycoplasma capricolum given that the genomes of both species lack the genes encoding the bifunctional MnmC protein or a monofunctional MnmC(m), and only cmnm 5 (s 2 )U(m)-type derivatives have been detected in certain MnmEG-substrate tRNAs (e.g., B. subtilis tRNA Lys UUU ) or bulk tRNA to date [14–19]. Curiously back in the mid-1970s, Vold and colleagues reported the probable presence of mnm 5 s 2 U in B. subtilis tRNA [20,21] but they did not find evidence for this nucleoside in a subsequent study [16].…”

Section: Introductionmentioning

confidence: 99%

Bacillus subtilis exhibits MnmC-like tRNA modification activities

et al. 2018

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The MnmE-MnmG complex of Escherichia coli uses either ammonium or glycine as a substrate to incorporate the 5-aminomethyl or 5-carboxymethylaminomethyl group into the wobble uridine of certain tRNAs. Both modifications can be converted into a 5-methylaminomethyl group by the independent oxidoreductase and methyltransferase activities of MnmC, which respectively reside in the MnmC(o) and MnmC(m) domains of this bifunctional enzyme. MnmE and MnmG, but not MnmC, are evolutionarily conserved. Bacillus subtilis lacks genes encoding MnmC(o) and/or MnmC(m) homologs. The glycine pathway has been considered predominant in this typical gram-positive species because only the 5-carboxymethylaminomethyl group has been detected in tRNALysUUU and bulk tRNA to date. Here, we show that the 5-methylaminomethyl modification is prevalent in B. subtilis tRNAGlnUUG and tRNAGluUUC. Our data indicate that B. subtilis has evolved MnmC(o)- and MnmC(m)-like activities that reside in non MnmC homologous protein(s), which suggests that both activities provide some sort of biological advantage.

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“…Putative orthologs of the E. coli bifunctional MnmC protein are conserved only in g-proteobacteria, but potential orthologs of a single domain have been identified in several genomes. 69,70 The phylogenetic analysis did not clear up whether the independent orthologs represent the ancestral or derived versions of the bifunctional MnmC enzyme. Nevertheless, the ability of the E. coli MnmC domains to function independently and to recognize different substrates suggests that the origin of the full MnmC protein present in g-proteobacteria likely happened by domain fusion.…”

Section: Function Of Modifications At the Wobble Uridinementioning

confidence: 99%