Escherichia coli σ³⁸ promoters use two UP elements instead of a -35 element: resolution of a paradox and discovery that σ³⁸ transcribes ribosomal promoters
 

(citation will go here)

Franco.Schneider2022

Kevin S. Franco,
Zhe Sun,
Yixiong Chen,
Cedric Cagliero,
Yuhong Zuo,
Yan Ning Zhou,
Mikhail Kashlev,
Ding Jun Jin
and
Thomas D. Schneider

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 (σ^S) 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.

• sigma38.pdf preprint manuscript
• supplement-sigma38.zip supplementary material
• https://www.biorxiv.org/content/10.1101/2020.02.05.936344v1 preprint manuscript at bioRxiv
• https://doi.org/10.1101/2020.02.05.936344 DOI link for preprint at bioRxiv.
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Background Papers

• Sequence Logos
  • logopaper: Sequence Logos: A New Way to Display Consensus Sequences
  • schneider1986: Information Content of Binding Sites
• Sequence Walkers
  • walker: Sequence walkers
  • flexrbs: flexible ribosome binding sites
  • flexprom: flexible sigma⁷⁰ binding sites

Permanent link https://alum.mit.edu/www/toms/papers/sigma38 points to the current web location.

Schneider Lab
origin: 2020 Feb 05
updated: version = 1.03 of sigma38.html 2022 Jan 21