Escherichia coli sigma38 promoters use two UP elements instead of a -35

Wednesday, September 24, 2014 — Poster Session IV
10:00 a.m. –12:00 p.m.	FAES Academic Center	NCI	COMPBIO-5

* FARE Award Winner

Authors

• K.S. Franco
• C.N.L Cagliero
• Y.N. Zhou
• D.J. Jin
• T.D. Schneider

Abstract

In E. coli, one RNA polymerase (RNAP) is responsible for transcription of all RNA species; however, different regulons are recognized by RNAP containing different sigma factors. RNAP containing sigmaS (sigma38) is responsible for the expression of genes responding to stress conditions such as stationary phase or osmotic shock. In order to begin construction of a model of sigma38 promoters, we aligned proven transcriptional starts recorded in RegulonDB. We then shuffled the sequences to maximize the information upstream of the start and identified a -10 similar to that in sigma70 promoters. Because activators can replace the -35, alignment of the -35 region of sigma70 promoters is difficult, but in the case of sigma38 promoters we could not identify any -35 pattern at all. However, we found two patterns upstream of the -35 region. These patterns are complementary and correspond to the location of UP elements bound by the polymerase alphaCTD in ribosomal promoters. Essentially all sigma38 promoters can be characterized this way. We propose that sigma38promoters do not use a -35 but use two UP elements instead. We are planning experiments to test this model.

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