Identification of the methyltransferase targeting C2499 in Deinococcus radiodurans 23S ribosomal RNA

Abstract

The bacterium Deinococcus radiodurans—like all other organisms—introduces nucleotide modifications into its ribosomal RNA. We have previously found that the bacterium contains a Carbon-5 methylation on cytidine 2499 of its 23S ribosomal RNA, which is so far the only modified version of cytidine 2499 reported. Using homology search, we identified the open reading frame DR_0049 as the primary candidate gene for the methyltransferase that modifies cytidine 2499. Mass spectrometric analysis demonstrated that recombinantly expressed DR0049 protein methylates E. coli cytidine 2499 both in vitro and in vivo. We also inactivated the DR_0049 gene in D. radiodurans through insertion of a chloramphenicol resistance cassette. This resulted in complete absence of the cytidine 2499 methylation, which all together demonstrates that DR_0049 encodes the methyltransferase producing m5C2499 in D. radiodurans 23S rRNA. Growth experiments disclosed that inactivation of DR_0049 is associated with a severe growth defect, but available ribosome structures show that cytidine 2499 is positioned very similar in D. radiodurans harbouring the modification and E. coli without the modification. Hence there is no obvious structure-based explanation for the requirement for the C2499 posttranscriptional modification in D. radiodurans.Electronic supplementary materialThe online version of this article (doi:10.1007/s00792-015-0800-z) contains supplementary material, which is available to authorised users.

Complete list of canonical post-transcriptional modifications in theBacillus subtilisribosome and their link to RbgA driven large subunit assembly

“…Significant number of residues were discovered in rRNA of C. sporogenes (14), in P. aeruginosa (15), S. aureus (16), and in B. subtilis, where a total of ten rRNA methylations and pseudouridines were experimentally confirmed (17)(18)(19)(20)(21)(22). In addition, many experimentally verified rRNA modification sites remain uncatalogued in RNA modification databases like Modomix (23) due to the fact that only a few were found per species (24)(25)(26)(27).…”