Bacillus subtilis exhibits MnmC-like tRNA modification activities

Abstract

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.

Survey and Validation of tRNA Modifications and Their Corresponding Genes in Bacillus subtilis sp Subtilis Strain 168

“…It is not clear if additional sulfur transfer proteins are required in B. subtilis , like they are in E. coli (CsdAE) [ 53 ]. The xm 5 U derivatives identified in the B. subtilis tRNAs ( Table 1 ) are similar to those present in E. coli, as confirmed by the Armengod laboratory [ 49 ]. The exception is cm 5 s 2 U, which might be an intermediate as the full synthesis of these complex modifications varies greatly depending on the media conditions [ 49 ].…”

“…The xm 5 U derivatives identified in the B. subtilis tRNAs (Table 1) are similar to those present in E. coli, as confirmed by the Armengod laboratory [49]. The exception is cm 5 s 2 U, which might be an intermediate as the full synthesis of these complex modifications varies greatly depending on the media conditions [49]. Orthologs of two of the three E. coli enzymes involved in synthesizing this complex modification (MnmE, MnmG) are found in B. subtilis.…”

“…Thirty-five modified ribonucleosides were identified in the bulk purified tRNA by LC-MS/MS ( Table 1 ). Of these 35, 21 had previously been mapped in B. subtilis , as listed in Modomics or in additional studies [ 49 , 50 ]. Several modifications (epoxyQ (oQ), t 6 A, mnm 5 U, and nm 5 U) are intermediates in complex modification pathways [ 51 , 52 , 53 ].…”

“…Orthologs of two of the three E. coli enzymes involved in synthesizing this complex modification (MnmE, MnmG) are found in B. subtilis. However, no MnmC ortholog is present, an observation already made by the Armengod group, who also showed that another enzyme catalyzing the same activity must be present and that it does not require S-adenosyl-L-methionine [ 49 ]. There are also differences in the thiolation enzymes which synthesize the xs 2 U34 derivatives.…”

Naturally occurring modified ribonucleosides

“…Uridines in the anticodon loop (positions 34-37) of select tRNA molecules can be modified with methyl (m) or carboxymethyl (cm) derivatives (Figure 8) (C. Chen, Huang, Anderson, & Byström, 2011). U5 in bacterial tRNA is modified by the bacterial enzymatic complex MnmE and MnmG/GidA to contain either a carboxymethylaminomethyl (cmnm) or a aminomethyl (nm) group resulting in the formation of either cmnm 5 U or nm 5 U, respectively (Ayadi, Galvanin, Pichot, Marchand, & Motorin, 2019;Mihara et al, 2002;Moukadiri et al, 2009;Moukadiri, Villarroya, Benítez-Páez, & Armengod, 2018;Sierant et al, 2018). The formation of cmnm 5 U makes use of a 5-formyluridine intermediate (J. .…”