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Nucleic Acids Research, 1990, Vol. 18, No. 12 3597-3603
© 1990

MOLECULAR BIOLOGY

E.coli promoter spacer regions contain nonrandom sequences which correlate to spacer length

Bruce A. Beutel1 and M.Thomas Record, Jr.1,2,*

1Program in Molecular Biology, University of Wisconsin Madison, WI 53706, USA 2Departments of Chemistry and Biochemistry, University of Wisconsin Madison, WI 53706, USA

*To whom correspondence should be addressed at the Department of Chemistry, 1101 University Avenue, University of Wisconsin, Madison, WI 53706, USA

Received February 12, 1990. Revised May 10, 1990. Accepted May 10, 1990.

The –10 and –35 regions of E. coli promoter sequences are separated by a spacer region which has a consensus length of 17 base-pairs. This region is thought to contribute to promoter function by correctly positioning the two conserved regions. We have performed a statistical evaluation of 224 spacer sequences and found that spacers which deviate from the 17 base-pair consensus length have nonrandom sequences in their upstream ends. Spacer regions which are shorter than 17 base-pairs in length have a significantly higher than expected frequency of purine-purine and pyrimidine-pyrimidine homo-dinucleotides at the six upstream positions. Spacer regions which are longer than 17 base-pairs in length have a significantly higher than expected frequency of purine-pyrimidine and pyrimidine-purine hetero-dinucleotides at these positions. This suggests that the nature of the purine-pyrimidine sequence at the upstream end of spacer regions affect promoter function in a manner which is related to the spacer length. We examine the spacer sequences as a function of spacer length and discuss some possible explanations for the observed relationship between sequence and length.


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