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Abstract
Sigma(38) is a non-essential but highly homologous member of the sigma(70) family of transcription factors. In vitro mutagenesis and in vivo screening were used to identify 22 critical amino acids in the promoter interaction domain of Escherichia coli sigma(38). Electrophoretic mobility shift assay studies showed that residues involved in duplex DNA binding largely segregated into distinct regions that coincided with those of sigma(70). However, the majority of these amino acids were in non-conserved positions. Analysis indicates that this region of the two sigma(s) probably has a common overall organization but differs in how its amino acids are used to form functional open complexes. Placement of the mutations on the known sigma(70) holoenzyme structure shows two clusters; one appears to be used for duplex DNA recognition and the other for the subsequent isomerization events. Permanganate assays for DNA melting support this view.
Highlights
38 is a non-essential but highly homologous member of the 70 family of transcription factors
Placement of the mutations on the known 70 holoenzyme structure shows two clusters; one appears to be used for duplex DNA recognition and the other for the subsequent isomerization events
38 promoters generally contain only a single DNA recognition element, a Ϫ10 sequence centered between nucleotides Ϫ14 and Ϫ7 (4, 5)
Summary
The four most conserved of these nucleotides, Ϫ13C, Ϫ12T, Ϫ11A, and Ϫ7T, are involved in directing promoter selectivity and play a dominant role in setting promoter strength (4 – 6) Three of these positions, Ϫ12T, Ϫ11A, and Ϫ7T, are critical for 70 function, they are utilized at different steps during 70 transcription initiation (7). Increased concentrations of trehalose (12), as well as potassium glutamate (13), preferentially stimulate 38-dependent transcription at certain promoters The basis for these diverse properties between the two highly homologous holoenzymes have remained largely unknown. The 38 amino acids responsible for use of nucleotides Ϫ12 to Ϫ7 have not been characterized They would lie in the same part of 70 that recognizes the Ϫ10 element, conserved regions 2.3–2.5. The results will be interpreted using the known structure of the DNA interaction region of 70, and models for promoter usage by both s will be discussed
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