PT  - JOURNAL ARTICLE
AU  - Kevin S. Franco
AU  - Zhe Sun
AU  - Yixiong Chen
AU  - Cedric Cagliero
AU  - Yuhong Zuo
AU  - Yan Ning Zhou
AU  - Mikhail Kashlev
AU  - Ding Jun Jin
AU  - Thomas D. Schneider
TI  - <em>Escherichia coli σ</em><sup>38</sup> promoters use two UP elements instead of a −35 element: resolution of a paradox and discovery that <em>σ</em><sup>38</sup> transcribes ribosomal promoters
AID  - 10.1101/2020.02.05.936344
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.02.05.936344
4099  - http://biorxiv.org/content/early/2020/02/06/2020.02.05.936344.short
4100  - http://biorxiv.org/content/early/2020/02/06/2020.02.05.936344.full
AB  - In E. coli, one RNA polymerase (RNAP) transcribes all RNA species, and different regulons are transcribed by employing different sigma (σ) factors. RNAP containing σ38 (σS) activates genes responding to stress conditions such as stationary phase. The structure of σ38 promoters has been controversial for more than two decades. To construct a model of σ38 promoters using information theory, we aligned proven transcriptional start sites to maximize the sequence information, in bits, and identified a −10 element similar to σ70 promoters. We could not align any −35 sequence logo; instead we found two patterns upstream of the −35 region. These patterns have dyad symmetry sequences and correspond to the location of UP elements in ribosomal RNA (rRNA) promoters. Additionally the UP element dyad symmetry suggests that the two polymerase α subunits, which bind to the UPs, should have two-fold dyad axis of symmetry on the polymerase and this is indeed observed in an X-ray crystal structure. Curiously the αCTDs should compete for overlapping UP elements. In vitro experiments confirm that σ38 recognizes the rrnB P1 promoter, requires a −10, UP elements and no −35. This clarifies the long-standing paradox of how σ38 promoters differ from those of σ70.