Interdependencies govern multidomain architecture in ribosomal small subunit assembly

Department of Biology, University of Rochester, Rochester, New York 14627, USA.
RNA (Impact Factor: 4.94). 02/2011; 17(2):263-77. DOI: 10.1261/rna.2332511
Source: PubMed


The 30S subunit is composed of four structural domains, the body, platform, head, and penultimate/ultimate stems. The functional integrity of the 30S subunit is dependent upon appropriate assembly and precise orientation of all four domains. We examined 16S rRNA conformational changes during in vitro assembly using directed hydroxyl radical probing mediated by Fe(II)-derivatized ribosomal protein (r-protein) S8. R-protein S8 binds the central domain of 16S rRNA directly and independently and its iron derivatized substituents have been shown to mediate cleavage in three domains of 16S rRNA, thus making it an ideal probe to monitor multidomain orientation during assembly. Cleavages in minimal ribonucleoprotein (RNP) particles formed with Fe(II)-S8 and 16S rRNA alone were compared with that in the context of the fully assembled subunit. The minimal binding site of S8 at helix 21 exists in a structure similar to that observed in the mature subunit, in the absence of other r-proteins. However, the binding site of S8 at the junction of helices 25-26a, which is transcribed after helix 21, is cleaved with differing intensities in the presence and absence of other r-proteins. Also, assembly of the body helps establish an architecture approximating, but perhaps not identical, to the 30S subunit at helix 12 and the 5' terminus. Moreover, the assembly or orientation of the neck is dependent upon assembly of both the head and the body. Thus, a complex interrelationship is observed between assembly events of independent domains and the incorporation of primary binding proteins during 30S subunit formation.

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    • "Nevertheless, the in vitro reconstitution of ribosomal subunit free of assembly factors has remained to be a classical biochemical system for decades, with a focus on studying the binding interdependence among ribosomal proteins [for examples, see (Grondek and Culver, 2004; Mizushima and Nomura, 1970; Rohl and Nierhaus, 1982)] and metastable rRNA conformational transitions [for examples, see (Calidas and Culver, 2011; Holmes and Culver, 2004, 2005; Powers et al., 1993; Ramaswamy and Woodson, 2009; Stern et al., 1989)] during the assembly process. More recently, time-resolved techniques from pulse-labeling based quantitative mass-spectrometry (QMS) (Mulder et al., 2010; Talkington et al., 2005) and synchrotron X-ray footprinting (Adilakshmi et al., 2008) have further generated a large amount of real-time data for various protein binding and rRNA folding events in the process of the in vitro 30S subunit assembly. "
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