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In vivo analysis of ribosome structure and dynamics
Author(s) -
McGinnis Jennifer,
Weeks Kevin M.
Publication year - 2009
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.23.1_supplement.847.2
Subject(s) - ribosome , ribosomal rna , rna , nucleic acid structure , translation (biology) , 5.8s ribosomal rna , primer extension , computational biology , biology , genetics , messenger rna , chemistry , gene
The ribosome catalyzes protein synthesis according to an mRNA template in a highly accurate, fast, and dynamic process called translation. Ribosomal RNA (rRNA) has been implicated in playing a crucial role in the structural, catalytic, and dynamic aspects of translation.Although rRNA appears to play a large role in ribosomal dynamics, direct in vivo measurements of RNA structure during translation have not been possible. Here, we use SHAPE (selective 2′‐hydroxylacylation analyzed by primer extension) chemistry to interrogate the local structure of 16S rRNA at single nucleotide resolution in the mid‐log phase of Escherichia coli growth. SHAPE chemistry is an effective tool for examining RNA structure in vivo and yields structural information for over 1400 16S nucleotides. In many regions, SHAPE chemistry exactly recapitulates the secondary structure derived from comparative sequence analysis. However, in several key areas, the time‐averaged rRNA structure is not consistent with the accepted static structure. Local, but highly significant, rearrangements in the RNA secondary structure thus appear tocontribute to ribosome function. A full understanding of dynamic RNA structure at nucleotide resolution will be important for complete understanding of the mechanics of translation in vivo .