Abstract
The domain architecture of a large RNA can help explain and/or predict folding, function, biogenesis and evolution. We offer a formal and general definition of an RNA domain and use that definition to experimentally characterize the rRNA of the ribosomal small subunit. Here the rRNA comprising a domain is compact, with a self-contained system of molecular interactions. A given rRNA helix or stem-loop must be allocated uniquely to a single domain. Local changes such as mutations can give domain-wide effects. Helices within a domain have interdependent orientations, stabilities and interactions. With these criteria we identify a core domain (domain A) of small subunit rRNA. Domain A acts as a hub, linking the four peripheral domains and imposing orientational and positional restraints on the other domains. Experimental characterization of isolated domain A, and mutations and truncations of it, by methods including selective 2′OH acylation analyzed by primer extension and circular dichroism spectroscopy are consistent with our architectural model. The results support the utility of the concept of an RNA domain. Domain A, which exhibits structural similarity to tRNA, appears to be an essential core of the small ribosomal subunit.
Highlights
The domain architecture of a large RNA can help explain and/or predict folding, function, biogenesis and evolution
Much of ribosomal function is performed by ribosomal RNAs1,2 while the ribosomal proteins act primarily as structural stabilizers[3]
The revised domain model differs from the historical domain model, in which the peripheral domains link directly to each other at a common origin and several helices participate in School of Chemistry and Biochemistry, Georgia institute of Technology, Atlanta, Georgia 30332, United States of America
Summary
The domain architecture of a large RNA can help explain and/or predict folding, function, biogenesis and evolution. We offer a formal and general definition of an RNA domain and use that definition to experimentally characterize the rRNA of the ribosomal small subunit. The rRNA comprising a domain is compact, with a self-contained system of molecular interactions. A given rRNA helix or stemloop must be allocated uniquely to a single domain Local changes such as mutations can give domainwide effects. Helices within a domain have interdependent orientations, stabilities and interactions With these criteria we identify a core domain (domain A) of small subunit rRNA. (i) The RNA comprising a domain is compact and modular, with a self-contained and integrated system of molecular interactions. (ii) Any given RNA helix or stem-loop is contained uniquely within a single domain. (iv) Molecular interactions between stem-loops within an RNA domain dictate their orientations, stabilities and interactions to be interdependent. Correspondence and requests for materials should be addressed to L.D.W. (email: loren.williams@ chemistry.gatech.edu) www.nature.com/scientificreports/
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