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The phage Mu middle promoter Pm contains a partial UP element.

Ma J, Howe MM - G3 (Bethesda) (2015)

Bottom Line: The results demonstrated that mutations upstream of -57 had no effect on Pm activity in vivo, assayed by expression of lacZ fused downstream of a wild-type or mutant Pm.In DNase I footprinting and gel mobility shift assays, paired mutations at positions -55 and -54 did not affect Mor binding but decreased the synergistic binding of Mor with histidine tagged α (His-α), indicating that His-α binds to Pm in a sequence- and/or structure-specific manner.Taken together, these results demonstrate that Pm has a strong proximal UP element subsite, but lacks a distal subsite.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Immunology & Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163.

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UP element consensus sequences. Consensus sequences of the full UP element and both proximal and distal subsites were identified by in vitro selection (Estrem et al. 1999). A specific base is indicated when it was present in more than 70% of the sequences; R(A/G) or W(A/T) is used when those two bases were present in more than 95%; N is used when those two circumstances do not apply.
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fig1: UP element consensus sequences. Consensus sequences of the full UP element and both proximal and distal subsites were identified by in vitro selection (Estrem et al. 1999). A specific base is indicated when it was present in more than 70% of the sequences; R(A/G) or W(A/T) is used when those two bases were present in more than 95%; N is used when those two circumstances do not apply.

Mentions: The UP element, a very A/T-rich region located upstream of the −35 hexamer, is bound by the C-terminal domain of the α subunit (αCTD) of RNAP and increases rrnB P1 promoter activity up to 30-fold (Ross et al. 1993). At least one-third of stable RNA promoters and 4% of mRNA promoters may contain such UP elements (Estrem et al. 1999). In addition, the number of promoters with at least partial UP elements is even larger, because promoters with less AT-rich UP element-like sequences still exhibit UP-element function (Ross et al. 1998; Estrem et al. 1999). There are two subsites within the UP element: promoter proximal and distal; either can function independently, although the proximal subsite may exert a larger effect on promoter activity. The consensus sequence of the full UP element and its subsites (Figure 1) were identified by in vitro selection and contain mostly A and T tracts (Estrem et al. 1998, 1999). Some promoters contain another element, the extended −10 motif, which has bases TGn located immediately upstream of the −10 hexamer. This sequence is recognized by σ70 (Keilty and Rosenberg 1987; Chan and Busby 1989) and drives transcription efficiently without a −35 hexamer or activator proteins.


The phage Mu middle promoter Pm contains a partial UP element.

Ma J, Howe MM - G3 (Bethesda) (2015)

UP element consensus sequences. Consensus sequences of the full UP element and both proximal and distal subsites were identified by in vitro selection (Estrem et al. 1999). A specific base is indicated when it was present in more than 70% of the sequences; R(A/G) or W(A/T) is used when those two bases were present in more than 95%; N is used when those two circumstances do not apply.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390567&req=5

fig1: UP element consensus sequences. Consensus sequences of the full UP element and both proximal and distal subsites were identified by in vitro selection (Estrem et al. 1999). A specific base is indicated when it was present in more than 70% of the sequences; R(A/G) or W(A/T) is used when those two bases were present in more than 95%; N is used when those two circumstances do not apply.
Mentions: The UP element, a very A/T-rich region located upstream of the −35 hexamer, is bound by the C-terminal domain of the α subunit (αCTD) of RNAP and increases rrnB P1 promoter activity up to 30-fold (Ross et al. 1993). At least one-third of stable RNA promoters and 4% of mRNA promoters may contain such UP elements (Estrem et al. 1999). In addition, the number of promoters with at least partial UP elements is even larger, because promoters with less AT-rich UP element-like sequences still exhibit UP-element function (Ross et al. 1998; Estrem et al. 1999). There are two subsites within the UP element: promoter proximal and distal; either can function independently, although the proximal subsite may exert a larger effect on promoter activity. The consensus sequence of the full UP element and its subsites (Figure 1) were identified by in vitro selection and contain mostly A and T tracts (Estrem et al. 1998, 1999). Some promoters contain another element, the extended −10 motif, which has bases TGn located immediately upstream of the −10 hexamer. This sequence is recognized by σ70 (Keilty and Rosenberg 1987; Chan and Busby 1989) and drives transcription efficiently without a −35 hexamer or activator proteins.

Bottom Line: The results demonstrated that mutations upstream of -57 had no effect on Pm activity in vivo, assayed by expression of lacZ fused downstream of a wild-type or mutant Pm.In DNase I footprinting and gel mobility shift assays, paired mutations at positions -55 and -54 did not affect Mor binding but decreased the synergistic binding of Mor with histidine tagged α (His-α), indicating that His-α binds to Pm in a sequence- and/or structure-specific manner.Taken together, these results demonstrate that Pm has a strong proximal UP element subsite, but lacks a distal subsite.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Immunology & Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163.

Show MeSH
Related in: MedlinePlus