Concerted folding of a Candida ribozyme into the catalytically active structure posterior to a rapid RNA compaction.
Folding of the major population of Tetrahymena intron RNA into the catalytically active structure is trapped in a slow pathway. In this report, folding of Candida albicans intron was investigated using the trans-acting Ca.L-11 ribozyme as a model. We demonstrated that both the catalytic activity (k(obs)) and compact folding equilibrium of Ca.L-11 are strongly dependent on Mg(2+) at physiological concentrations, with both showing an Mg(2+) Hill coefficient of 3. Formation of the compact structure of Ca.L-11 is shown to occur very rapidly, on a subsecond time scale similar to that of RNase T1 cleavage. Most of the ribozyme RNA population folds into the catalytically active structure with a rate constant of 2 min(-1) at 10 mM Mg(2+); neither slower kinetics nor obvious Mg(2+) inhibition is observed. These results suggest that folding of the Ca.L-11 ribozyme is initiated by a rapid magnesium-dependent RNA compaction, which is followed by a slower searching for the native contacts to form the catalytically active structure without interference from the long-lived trapped states. This model thus provides an ideal system to address a range of interesting aspects of RNA folding, such as conformational searching, ion binding and the role of productive intermediates.
Xiao
Mu
M
Department of Biotechnology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China.
Leibowitz
Michael J
MJ
Zhang
Yi
Y
D001483:Base Sequence; D002176:Candida albicans / Q000201:enzymology* / Q000235:genetics; D002384:Catalysis / Q000187:drug effects; D004305:Dose-Response Relationship, Drug; D007700:Kinetics; D008274:Magnesium / Q000494:pharmacology; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012331:RNA, Fungal / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D013379:Substrate Specificity
D016337:RNA, Catalytic; D012331:RNA, Fungal; D008274:Magnesium