title: Substitution of uridine in vivo by the intrinsic photoactivable probe 4-thiouridine in Escherichia coli RNA. Its use for E. coli ribosome structural analysis.
abstract: In vivo incorporation of the uridine-photoactivable analogue, 4-thiouridine, into the ribosomal RNA of an Escherichia coli pyrD strain has been demonstrated. It is highly dependent on the exogenous uridine and 4-thiouridine concentrations as well as on temperature. We have defined conditions allowing the substitution of 13 +/- 2% of the uridine residues in bulk RNA by 4-thiouridine. On a high-Mg2+ sucrose gradient, 33 +/- 3% of ribonucleic particles sediment as 70S ribosomes, the remaining being in the form of non-associated 50S and 30S particles containing immature rRNA. The thiolated 70S ribosomes tolerate a 4-5% substitution level (40 thiouridine molecules/particle). Surprisingly, 3-4% of ribosomal proteins, about two protein molecules/particle, were spontaneously covalently bound to 4-thiouridine-substituted rRNA. Specific 366-nm photoactivation increased this proportion to 10-12%, i.e. up to six or seven ribosomal protein molecules/particle. The photochemical cross-linking proceeds with apparent first-order kinetics with a quantum yield close to 5 X 10(-3). Although extensive photodynamic breakage of rRNA occurs under aerobic conditions, both the kinetics and yield of ribosomal protein cross-linking were independent of oxygenation conditions. The thiolated (4.5%) 70S ribosomes allowed the poly(U)-directed poly(Phe)synthesis at 48% the control rate. Photoactivation decreased this activity to 28% and 10% when performed under nitrogen and in aerated conditions, respectively.
mesh_terms: D004926:Escherichia coli / Q000187:drug effects / Q000254:growth & development / Q000378:metabolism*; D007700:Kinetics; D010777:Photochemistry; D012329:RNA, Bacterial / Q000096:biosynthesis; D012335:RNA, Ribosomal / Q000096:biosynthesis*; D012270:Ribosomes / Q000378:metabolism*; D013056:Spectrophotometry, Ultraviolet; D013891:Thiouridine / Q000378:metabolism* / Q000494:pharmacology; D014529:Uridine / Q000378:metabolism
chemical_list: D012329:RNA, Bacterial; D012335:RNA, Ribosomal; D013891:Thiouridine; D014529:Uridine