RNAs não codificantes excepcionais estruturados revelados pela análise do metagenoma bacteriano

Nature 462, 656-659 (3 December 2009) | doi:10.1038/nature08586; Received 20 July 2009; Accepted 15 October 2009

Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis

Zasha Weinberg1,2, Jonathan Perreault2, Michelle M. Meyer2 & Ronald R. Breaker1,2,3

Howard Hughes Medical Institute,
Department of Molecular, Cellular and Developmental Biology,
Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, Connecticut 06520-8103, USA

Correspondence to: Ronald R. Breaker1,2,3 Correspondence and requests for materials should be addressed to R.R.B. (Email: ronald.breaker@yale.edu).

Abstract

Estimates of the total number of bacterial species1, 2, 3 indicate that existing DNA sequence databases carry only a tiny fraction of the total amount of DNA sequence space represented by this division of life. Indeed, environmental DNA samples have been shown to encode many previously unknown classes of proteins4 and RNAs5. Bioinformatics searches6, 7, 8, 9, 10 of genomic DNA from bacteria commonly identify new noncoding RNAs (ncRNAs)10, 11, 12 such as riboswitches13, 14. In rare instances, RNAs that exhibit more extensive sequence and structural conservation across a wide range of bacteria are encountered15, 16. Given that large structured RNAs are known to carry out complex biochemical functions such as protein synthesis and RNA processing reactions, identifying more RNAs of great size and intricate structure is likely to reveal additional biochemical functions that can be achieved by RNA. We applied an updated computational pipeline17 to discover ncRNAs that rival the known large ribozymes in size and structural complexity or that are among the most abundant RNAs in bacteria that encode them. These RNAs would have been difficult or impossible to detect without examining environmental DNA sequences, indicating that numerous RNAs with extraordinary size, structural complexity, or other exceptional characteristics remain to be discovered in unexplored sequence space.

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