Selection of Random RNA Fragments as Method for Searching for a Site of Regulation of Translation of E. coli Streptomycin mRNA by Ribosomal Protein S7

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A. V. Surdina¹, T. I. Rassokhin¹, A. V. Golovin², V. A. Spiridonova¹, B. Kraal³, and A. M. Kopylov^1,4*

¹Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; fax: (9495) 939-3181; E-mail: kopylov@rnp-group.genebee.msu.su

²Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia

³Leiden Institute of Chemistry, Leiden University, 2300RA Leiden, The Netherlands

⁴Chemical Faculty, Lomonosov Moscow State University, 119992 Moscow, Russia

^* To whom correspondence should be addressed.

Received October 18, 2007; Revision received December 19, 2007

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In E. coli cells ribosomal small subunit biogenesis is regulated by RNA-protein interactions involving protein S7. S7 initiates the subunit assembly interacting with 16S rRNA. During shift-down of rRNA synthesis level, free S7 inhibits self-translation by interacting with 96 nucleotides long specific region of streptomycin (str) mRNA between cistrons S12 and S7 (intercistron). Many bacteria do not have the extended intercistron challenging development of specific approaches for searching putative mRNA regulatory regions, which are able to interact with proteins. The paper describes application of SERF approach (Selection of Random RNA Fragments) to reveal regulatory regions of str mRNA. Set of random DNA fragments has been generated from str operon by random hydrolysis and then transcribed into RNA; the fragments being able to bind protein S7 (serfamers) have been selected by iterative rounds. S7 binds to single serfamer, 109 nucleotide long (RNA109), derived from the intercistron. After multiple copying and selection, the intercistronic mutant (RNA109) has been isolated; it has enhanced affinity to S7. RNA109 binds to the protein better than authentic intercistronic str mRNA; apparent dissociation constants are 26 ± 5 and 60 ± 8 nM, respectively. Location of S7 binding site on the mRNA, as well as putative mode of regulation of coupled translation of S12 and S7 cistrons have been hypothesized.

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KEY WORDS: ribosome biogenesis, S7 protein, streptomycin operon, bacteria, translation regulation, SELEX, SERF

DOI: 10.1134/S0006297908060047

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