||RNA modifications were reconstructed from several sources:
36 rRNA modifications catalyzed by the M. genitalium enzyme complement were first compiled for E. coli [PUB_0105, PUB_0119, PUB_0120]. Of these modifications 11 were of motifs conserved in M. genitalium as determined by sequence alignment.
tRNA Modifications were similarly compiled from [PUB_0045, PUB_0055, PUB_0056, PUB_0064, PUB_0065, PUB_0560, PUB_0651] with the following notes:
tRNA containing U35 reading codons ending in A are not thiolated in Mycoplasmas [PUB_0055]. In other organisms tRNAs with U35 in their anticodon interact poorly with A-rich codons, and require modification to improve the efficiency of codon reading [PUB_0055].
No hypermodification of U34 observed in mycoplasmas [PUB_0055, PUB_0056]. No TrmE or TrmU activity [PUB_0055, PUB_0056].
s2U34 not modified in Mycoplasma tRNAs [PUB_0055].
TrmE catalyzes second step in hypermodification of uridine to mnm5s2U at wobble position (34) [PUB_0045]. hypermodification increases efficiency of wobble recognition for Lys, Gln, Glu.
TrmU catalyzes first step in hypermodification of uridine to mnm5s2U at wobble position (34) [PUB_0045]. hypermodification increases efficiency of wobble recognition for Lys, Gln, Glu.
U8 is involved in a reverse Hoogsteen base pair with A14 [PUB_0064]. 2'-hydroxyl of U8 is hydrogen-bonded to A21 [PUB_0064].
ThiI U8 4 carbon thiolation not required [PUB_0065].
RNA modifications – reconstructed for E. coli and mapped to M. genitalium by sequence alignment
Kinetics – modification kinetics were compiled from the primary literature
m6A1518, m62A1518 [PUB_0296]
m6A1519, m62A1519 [PUB_0296]
?U955, ?U1911, ?U1917, ?U2504, ?U2580 [PUB_0125]
s2U33, cmnm5s2U33 [PUB_0216]
No degradation pathways have been found for modified nucleosides. Modified nucleosides are believed to accumulate in the cytoplasm or be excreted into media. In multicellular organisms modified nucleosides are excreted into urine. Modified nucleosides are not incorporated into growing transcripts. Modified nucleosides are not believed to have any additional functions. Sources: [PUB_0269, PUB_0663, PUB_0664, PUB_0665, PUB_0666, PUB_0667, PUB_0668, PUB_0669, PUB_0670, PUB_0671].
Eds Schomburg D, Schomburg I, Chang A. tRNA Sulfurtransferase. Springer Berlin, Heidelberg 218-22 (2008). WholeCell: PUB_0309, ISBN: 9783540715245
Basturea GN, Deutscher MP. Substrate specificity and properties of the Escherichia coli 16S rRNA methyltransferase, RsmE. RNA 13, 1969-76 (2007). WholeCell: PUB_0295, PubMed: 17872509
Björk GR, Ericson JU, Gustafsson CE, Hagervall TG, Jönsson YH, Wikström PM. Transfer RNA modification. Annu Rev Biochem 56, 263-87 (1987). WholeCell: PUB_0065, PubMed: 3304135
Björk GR, Huang B, Persson OP, Byström AS. A conserved modified wobble nucleoside (mcm5s2U) in lysyl-tRNA is required for viability in yeast. RNA 13, 1245-55 (2007). WholeCell: PUB_0055, PubMed: 17592039
Bullinger D, Neubauer H, Fehm T, Laufer S, Gleiter CH, Kammerer B. Metabolic signature of breast cancer cell line MCF-7: profiling of modified nucleosides via LC-IT MS coupling. BMC Biochem 8, 25 (2007). WholeCell: PUB_0666, PubMed: 18047657
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