ELECTROSTATIC PROPERTIES OF PROMOTER RECOGNIZED BYE. COLIRNA POLYMERASE Eσ⁷⁰

Abstract

A comparative analysis of electrostatic patterns for 359 sigma70-specific promoters and 359 nonpromoter regions on electrostatic map of Escherichia coli genome was carried out. It was found that DNA is not a uniformly charged molecule. There are some local inhomogeneities in its electrostatic profile which correlate with promoter sequences. Electrostatic patterns of promoter DNAs can be specified due to the presence of some distinctive motifs which differ for different promoter groups and may be involved as signal elements in differential recognition of various promoters by the enzyme. Some specific electrostatic elements which are responsible for modulating promoter activities due to ADP-ribosylation of RNA polymerase alpha-subunit were found in far upstream regions of T4 phage early promoters and E. coli ribosomal promoters.

Electrostatic map of T7 DNA: comparative analysis of functional and electrostatic properties of T7 RNA polymerase-specific promoters

“…It is interesting that the most noticeable electrostatic signals involved in recognition of this enzyme were found in far upstream region of its native promoters (-70 -120 b.p.) in various templates such as DNA of E.coli and related bacteriophages T4, T7 and (Kamzolova et al, 2000(Kamzolova et al, , 2005(Kamzolova et al, , 2009Osypov et al, 2010;Sorokin et al, 2006). By contrast, there are no specific electrostatic elements in this region of T7 RNA polymerase specific promoters.…”

Deppdb — Dna Electrostatic Potential Properties Database: Electrostatic Properties of Genome Dna Elements

“…There is no text consensus in the \up-element" (though high AT content is often attributed) and functionality of this region is de¯ned by its physical properties. We have shown earlier, that electrostatics is responsible for its functioning during the global transcription switch under the T4 infection 9,11 and that strong T4, early T7-like, and E. coli ribosomal promoters with pronounced up-element have high levels of the electrostatic potential within it. 8À11 Strong lambda phage promoters also have pronounced up-element compared to the absence of it in weak promoters (Fig.…”

“…8 This matches a pronounced tendency of promoter regions to possess higher values of the electrostatic potential. 8,10 Speci¯c electrostatic elements, which are responsible for modulating promoter activities through ADP-ribosylation of the RNA polymerase alpha-subunit were identi¯ed in the far upstream regions of T4 phage early promoters 9,11 and Escherichia coli ribosomal promoters. 8,13 Electrostatic patterns of the promoter DNA can be speci¯ed due to the presence of some distinctive motifs, 12 which vary for di®erent promoter groups and may be involved as a signal element in the di®erential recognition of corresponding promoters by the enzyme.…”

System to store DNA physical properties profiles with application to the promoters of Escherichia coli

“…Для вычисления профиля электростатического потенциала выбирались фрагменты длиной 400 п. о. вокруг промоторов, входящих в компиляцию, так, чтобы точка старта транскрипции находилась в положении 271 нуклеотида. Электростатический потенциал вычисляли кулоновским методом, описанным ранее [Sorokin et al, 2006;Kamzolova et al, 2005;Kamzolova et al, 2000;Polozov et al, 1999]. Вкратце, приведем наиболее важные для дальнейшего обсуждения детали метода: рассматривается прямолинейная, но неоднородная модель геометрии ДНК, учитывающая вариации расстояния между соседними нуклеотидами в зависимости от динуклеотидного состава; профиль потенциала вычисляется простым суммированием кулоновских вкладов парциальных зарядов атомов.…”