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Published online 18 February 2004

Nucleic Acids Research, 2004, Vol. 32, No. 3 1166-1176
© 2004 Oxford University Press

Relevance of UP elements for three strong Bacillus subtilis phage {phi}29 promoters

Wilfried J. J. Meijer and Margarita Salas*

Instituto de Biología Molecular ‘Eladio Viñuela’ (CSIC), Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain

*To whom correspondence should be addressed. Tel: +34 91 497 8435; Fax: +34 91 497 8490; Email: msalas{at}cbm.uam.es

Various Escherichia coli promoters contain, in addition to the classical –35 and –10 hexamers, a third recognition element, named the UP element. Located upstream of the –35 box, UP elements stimulate promoter activity by forming a docking site for the C-terminal domain of the RNA polymerase {alpha} subunit ({alpha}CTD). Accumulating genetic, biochemical and structural information has provided a detailed picture on the molecular mechanism underlying UP element-dependent promoter stimulation in E.coli. However, far less is known about functional UP elements of Bacillus subtilis promoters. Here we analyse the strong early {sigma}A-RNA polymerase-dependent promoters C2, A2c and A2b of the lytic B.subtilis phage {phi}29. We demonstrate that the phage promoters contain functional UP elements although their contribution to promoter strength is very different. Moreover, we show that the UP element of the A2b promoter, being critical for its activity, is located further upstream of the –35 box than most E.coli UP elements. The importance of the UP elements for the phage promoters and how they relate to other UP elements are discussed.


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