Identification of 5-Hydroxycytidine at Position 2501 Concludes Characterization of Modified Nucleotides in E. coli 23S rRNA

Distinction between the Cfr Methyltransferase Conferring Antibiotic Resistance and the Housekeeping RlmN Methyltransferase

“…A similar protein from the clinical Staphylococcus aureus strain Newman exhibits 36% sequence identity to E. coli protein RlmN, and a primer extension stop at A2503 of 23S rRNA from this strain (E. coli numbering used for all organisms) is absent when the corresponding gene is inactivated (2), suggesting that it is also an RlmN. More recently, Deinococcus radiodurans has also been shown to have the m 2 A2503 modification (35). T. thermophilus was reported to have methylation at A2503 in 23S RNA (36), knockout of the rlmN-like gene abolishes A2503 methylation (A. Rasmussen, H. Park, and F. Kirpekar, unpublished data), and Bacillus species are also methylated at A2503 (B. T. Porse, and F. Kirpekar, unpublished data).…”

The last rRNA methyltransferase of E. coli revealed: The yhiR gene encodes adenine-N6 methyltransferase specific for modification of A2030 of 23S ribosomal RNA

“…However, several rRNA modification enzymes remained undiscovered. It is still unknown which genes are responsible for the formation of D2449 and oh 5 C2501 (Havelund et al 2011). Also, it is likely that some yet-unknown modification sites, perhaps active only under certain conditions, still could be found in the ribosome ).…”

Mass spectrometry in the biology of RNA and its modifications

“…Evidently, little information about the precise nature of modifications is obtained, except for ribose methylations that give distinct backbone fragmentation [57] and a diagnostic ribose derivative [23], and the dynamic range in MALDI MS often limits the use to RNAs smaller thañ 500 nt. However, these issues can be tackled by applying further LC-MS n analyses to identify the modifications, if required in combination with a sub-fractioning of the RNA (see [136] for an example). The MALDI-MS based approach has been used in a series of biological issues by our lab and others in screening for endogenous [123,127] and antibiotic resistance-conferring [23,[137][138][139] rRNA modifications.…”