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Open Access Research article

Abundance and functional diversity of riboswitches in microbial communities

Marat D Kazanov1*, Alexey G Vitreschak1 and Mikhail S Gelfand12

Author Affiliations

1 Institute for Information Transmission Problems (the Kharkevich Institute) RAS, Bolshoi Karetnyi per. 19, Moscow, 127994, Russia

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

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BMC Genomics 2007, 8:347  doi:10.1186/1471-2164-8-347

Published: 1 October 2007

Abstract

Background

Several recently completed large-scale enviromental sequencing projects produced a large amount of genetic information about microbial communities ('metagenomes') which is not biased towards cultured organisms. It is a good source for estimation of the abundance of genes and regulatory structures in both known and unknown members of microbial communities. In this study we consider the distribution of RNA regulatory structures, riboswitches, in the Sargasso Sea, Minnesota Soil and Whale Falls metagenomes.

Results

Over three hundred riboswitches were found in about 2 Gbp metagenome DNA sequences. The abundabce of riboswitches in metagenomes was highest for the TPP, B12 and GCVT riboswitches; the S-box, RFN, YKKC/YXKD, YYBP/YKOY regulatory elements showed lower but significant abundance, while the LYS, G-box, GLMS and YKOK riboswitches were rare. Regions downstream of identified riboswitches were scanned for open reading frames. Comparative analysis of identified ORFs revealed new riboswitch-regulated functions for several classes of riboswitches. In particular, we have observed phosphoserine aminotransferase serC (COG1932) and malate synthase glcB (COG2225) to be regulated by the glycine (GCVT) riboswitch; fatty acid desaturase ole1 (COG1398), by the cobalamin (B12) riboswitch; 5-methylthioribose-1-phosphate isomerase ykrS (COG0182), by the SAM-riboswitch. We also identified conserved riboswitches upstream of genes of unknown function: thiamine (TPP), cobalamine (B12), and glycine (GCVT, upstream of genes from COG4198).

Conclusion

This study demonstrates applicability of bioinformatics to the analysis of RNA regulatory structures in metagenomes.