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Genes & Dev. 16 (13): 1696-1706

Copyright © 2002 by Cold Spring Harbor Laboratory Press.

Vol. 16, No. 13, pp. 1696-1706, July 1, 2002

Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon

Thorleif Møller, Thomas Franch, Christina Udesen, Kenn Gerdes, and Poul Valentin-Hansen1

Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark

The physiological role of Escherichia coli Spot 42 RNA has remained obscure, even though the 109-nucleotide RNA was discovered almost three decades ago. Structural features of Spot 42 RNA and previous work suggested to us that the RNA might be a regulator of discoordinate gene expression of the galactose operon, a control that is only understood at the phenomenological level. The effects of controlled expression of Spot 42 RNA or deleting the gene (spf) encoding the RNA supported this hypothesis. Down-regulation of galK expression, the third gene in the gal operon, was only observed in the presence of Spot 42 RNA and required growth conditions that caused derepression of the spf gene. Subsequent biochemical studies showed that Spot 42 RNA specifically bound at the galK Shine-Dalgarno region of the galETKM mRNA, thereby blocking ribosome binding. We conclude that Spot 42 RNA is an antisense RNA that acts to differentially regulate genes that are expressed from the same transcription unit. Our results reveal an interesting mechanism by which the expression of a promoter distal gene in an operon can be modulated and underline the importance of antisense control in bacterial gene regulation.

[Key Words: Antisense RNA; galactose operon; riboregulation; small RNAs; Spot 42 RNA; translational regulation]

1 Corresponding author.

GENES & DEVELOPMENT 16:1696-1706 © 2002 by Cold Spring Harbor Laboratory Press  ISSN 0890-9369/02 $5.00

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