The evolutionary selection of DNA base pairs in gene-regulatory binding sites.

Abstract

The thereby tying together the statistics of base-pair choice, the binding strength, and the protein burden. In terms of this model, the selection pressure can be estimated from the properties of a gene-regulatory protein and its recognition sites. A key feature is the mutational randomization pressure that appears as a fundamental force shaping the optimal solutions that provide maximal growth. The model is tested on a number of gene-regulatory systems in Eseherichia coli. The same principles should hold for all proteins for which overall activity in the cell is proportional to abundance; then the selective pressure to increase the efficiency of an individual protein cannot be larger than the selective pressure to decrease the total protein burden.

Synonymous substitution-rate constants in Escherichia coli and Salmonella typhimurium and their relationship to gene expression and selection pressure

“…From this he finds that the effective population size for E. coli would be about N e = 105. This is in qualitative agreement with an estimate based on a mutationselection balance for base-pair choices in DNA recognition sites (Berg 1992).…”

Reductive evolution of proteomes and protein structures

“…The minimum length for this specificity would increase with the numbers and concentrations of competing nonspecific interactions with closely related ligands (20,28,29). As the expected numbers of competitors increase with the diversity of RNA, DNA, and protein targets, the minimum length of Fig.…”

Growth phase variation of integration host factor level in Escherichia coli

“…The abundance of IHF subunits seems high relative to that of other site-specific DNA-binding proteins (4) and to the estimated number of IHF-binding sites (19 IHF-deficient control, and much lower than those in MD96, the wild-type control (Table 4). The efficiency of plating of these phages on the same set of hosts is consistent with the E1 measurements of yields (data not shown).…”

“…To measure the abundance of IHF and its dependence on growth phase, we diluted an overnight broth culture of strain K37 2,000-fold and incubated it in LB medium for about 4 h, which allowed a 260-fold increase in mass or approximately eight doublings, before beginning sampling (Fig. 4) scanning the dried gel, was about one-third that of ribosomal protein S10, which was identified by the published coordinates (56).…”