title: A complex ligase ribozyme evolved in vitro from a group I ribozyme domain.
abstract: Like most proteins, complex RNA molecules often are modular objects made up of distinct structural and functional domains. The component domains of a protein can associate in alternative combinations to form molecules with different functions. These observations raise the possibility that complex RNAs also can be assembled from preexisting structural and functional domains. To test this hypothesis, an in vitro evolution procedure was used to isolate a previously undescribed class of complex ligase ribozymes, starting from a pool of 10(16) different RNA molecules that contained a constant region derived from a large structural domain that occurs within self-splicing group I ribozymes. Attached to this constant region were three hypervariable regions, totaling 85 nucleotides, that gave rise to the catalytic motif within the evolved catalysts. The ligase ribozymes catalyze formation of a 3',5'-phosphodiester linkage between adjacent template-bound oligonucleotides, one bearing a 3' hydroxyl and the other a 5' triphosphate. Ligation occurs in the context of a Watson-Crick duplex, with a catalytic rate of 0.26 min(-1) under optimal conditions. The constant region is essential for catalytic activity and appears to retain the tertiary structure of the group I ribozyme. This work demonstrates that complex RNA molecules, like their protein counterparts, can share common structural domains while exhibiting distinct catalytic functions.
authors.affiliation: Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, 15 rue Descartes, 67084 Strasbourg, France. gjoyce@scripps.edu
authors.forename: L
authors.initials: L
authors.lastname: Jaeger
authors.forename: M C
authors.initials: MC
authors.lastname: Wright
authors.forename: G F
authors.initials: GF
authors.lastname: Joyce
mesh_terms: D000818:Animals; D001483:Base Sequence; D002384:Catalysis; D020134:Catalytic Domain; D019020:Directed Molecular Evolution; D015723:Gene Library; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011118:Polynucleotide Ligases / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D016337:RNA, Catalytic / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D013768:Tetrahymena / Q000201:enzymology
chemical_list: D016337:RNA, Catalytic; D011118:Polynucleotide Ligases