The gene argR encodes a repressor that controls the synthesis of enzymes of arginine biosynthesis (Maas and Clark, 1964; Maas et al., 1964). Several symmetrical binding sites have been tentatively identified by a few mutations and sequence similarities (Cunin et al., 1983). Since some sites are adjacent, the range only covered 20 base pairs (Fig. 6). Also, we used an alignment for the ArgR sequence that was shifted one base to the left of that in Cunin et al. (1983). This is presumably a better alignment because it increased Rsequence by 1.5 bits. (It would also improve the "consensus".) Rsequence = 16.4 while Rfrequency = 18.4 bits per site.
By avoiding overlapping sites, we may have deleted part of the arginine boxes. It is possible that two neighboring sites can interpenetrate, if the recognizers bind to different faces of a DNA helix (Hochschild et al., 1983). If the sites were extended to a range -15 to +16, Rsequence becomes 18.6. In any case, the sites of the arginine regulon have not yet been characterized by DNase footprinting, chemical protection or other experiments and several more sites remain to be sequenced.
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