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Communication between RNA folding domains revealed by the tertiary folding pathway of circularly permuted ribozymes
Author(s) -
Lease Richard A.,
Adilakshmi Tadepalli,
HeilmanMiller Susan,
Woodson Sarah A.
Publication year - 2007
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.21.6.lb31-b
Subject(s) - ribozyme , rna , intron , protein tertiary structure , protein secondary structure , rnase p , chemistry , folding (dsp implementation) , group ii intron , hairpin ribozyme , group i catalytic intron , oligonucleotide , nucleic acid secondary structure , biophysics , crystallography , biology , rna splicing , biochemistry , dna , gene , electrical engineering , engineering
RNA folding is governed by a balance of long‐range and short‐range interactions. Circular permutation changes the distance between interacting residues in the primary sequence, without significantly changing the native fold of the RNA. To study the role of topology in RNA folding, we determined the equilibrium and kinetic folding pathways of two circularly permuted variants of the Tetrahymena rRNA group I intron, using time‐resolved hydroxyl radical footprinting and oligonucleotide probes. Permutation of the 5′ end to G111 in the P4 helix allowed the P4‐P6 domain to fold five times more rapidly than it does in the wild type RNA; the remainder of the intron folded five times more slowly. By contrast, permutation of the 5′ end to G303 in J8/7 allowed peripheral tertiary interactions to form more rapidly than in the wild type RNA intron but slowed the acquisition of native tertiary interactions in the catalytic center. RNase T1 digestion and FMN photocleavage structure mapping suggest that circular permutation of the intron sequence alters the initial ensemble of secondary structures, thereby changing the structure of the tertiary folding intermediates. Discontinuities in the RNA backbone disrupt folding communication between structural domains, perturbing and delaying organization of the catalytic center, implying that the 5′‐to‐3′ order of domains are subject to selective pressure during evolution. Supported by NIH GM60809 (S.W.)