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Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?

Dmitry Rodionov Alexey Vitreschak 1 Andrey Mironov Mikhail Gelfand
1 ADAGE - Applying discrete algorithms to genomics
INRIA Lorraine, LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications
Abstract : Comparative analysis of genes, operons and regulatory elements was applied to analysis of the lysine biosynthetic pathway in available bacterial genomes. We report identification of a lysine-specific RNA element, named the LYS element, in the regulatory regions of bacterial genes involved in biosynthesis and transport of lysine. Similarly to the previously described RNA regulatory elements for three vitamins (riboflavin, thiamin and cobalamin), purine and methionine regulons, this regulatory RNA structure is highly conserved on the sequence and structural levels. The LYS element includes regions of lysine-constitutive mutations previously identified in E. coli and B. subtilis. A possible mechanism of the lysine-specific riboswitch is similar to the previously defined mechanisms for the other metabolite-specific riboswitches and involves either transcriptional or translational attenuation in various groups of bacteria. Identification of LYS elements in Gram-negative gamma-proteobacteria, Gram-positive bacteria from the Bacillus/Clostridium group, and Thermotogales resulted in description of the previously uncharacterized lysine regulon in these bacterial species. Positional analysis of LYS elements lead to identification of a number of new candidate lysine transporters, namely LysW, YvsH and LysXY. Finally, the most likely candidates for genes of lysine biosynthesis missing in Gram-positive bacteria were identified using the genome context analysis.
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https://hal.inria.fr/inria-00099648
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Submitted on : Tuesday, September 26, 2006 - 9:39:45 AM
Last modification on : Friday, February 26, 2021 - 3:28:02 PM

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Dmitry Rodionov, Alexey Vitreschak, Andrey Mironov, Mikhail Gelfand. Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?. Nucleic Acids Research, Oxford University Press, 2003, 31 (23), pp.1-10. ⟨inria-00099648⟩

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