Cooperative DNA Binding by Xenopus Transcription Factor IIIA

Resolving the contributions of two cooperative mechanisms to the DNA binding of AGT

The O(6)-alkylguanine DNA alkyltransferase (AGT) is a DNA repair enzyme that binds DNA with moderate cooperativity. This cooperativity is important for its search for alkylated bases. A structural model of the cooperative complex of AGT with DNA predicts short-range interactions between nearest protein neighbors and long-range interactions between proteins separated in the array. DNA substrates ranging from 11bp to 30bp allowed us to use differences in binding stoichiometry to resolve short- and long-range protein contributions to the stability of AGT complexes. We found that the short-range component of ΔG°(coop) was nearly independent of DNA length and protein packing density. In contrast the long-range component oscillated with DNA length, with a period equal to the occluded binding site size (4bp). The amplitude of the long-range component decayed from ∼-4 kcal/mole of interaction to ∼-1.2 kcal/mol of interaction as the size of cooperative unit increased from 4 to 7 proteins, suggesting a mechanism to limit the size of cooperative clusters. These features allow us to make testable predictions about AGT distributions and interactions with chromatin structures in vivo.

Use of DNA length variation to detect periodicities in positively cooperative, nonspecific binding

The experiments described here demonstrate ways in which DNA length can be used as an experimental variable for the characterization of positively cooperative, sequence nonspecific DNA binding. Examples are drawn from recent studies of the interactions of O(6)-alkylguanine DNA alkyltransferase (AGT) with duplex DNAs (Melikishvili et al. (2008). Interactions of human O(6)-alkylguanine-DNA alkyltransferase (AGT) with short double-stranded DNAs. Biochemistry 47, 13754-13763). Oscillations in binding density and apparent binding site size (S(app)) are predicted by models in which a single cooperative assembly forms on each DNA molecule and in which enzyme molecules bind full-length binding sites, but not partial ones. These oscillations provide an accurate, DNA-length independent measure of the occluded binding site size (the length of DNA that one protein molecule occupies to the exclusion of others). In addition, length-dependent oscillations in association constant (K) and cooperativity (ω) reveal the degree to which substrate length can influence these parameters.

The interaction of TFIIIA with specific RNA-DNA heteroduplexes

We examine the association of transcription factor TFIIIA with RNA-DNA heteroduplexes containing sequences from the Xenopus borealis 5 S rRNA gene. Under conditions where TFIIIA selectively binds to 5 S rRNA or the internal control region of the 5 S rRNA gene, no specific association of TFIIIA with DNA-RNA heteroduplexes containing either strand of 5 S DNA could be detected. We discuss our results with respect to specific models of TFIIIA recognition of the internal control region and of DNA-RNA hybrids by zinc finger proteins.

Xenopus transcription factor IIIA (XTFIIIA): after a decade of research

Xenopus transcription factor IIIA (XTFIIIA) is the first eukaryotic transcription factor purified to homogeneity and is specifically required for the 5S RNA gene transcription. It contains two structural domains and nine zinc finger motifs through which it recognizes the promoter region of the 5S RNA gene. It also binds to 5S RNA and serves to store 5S RNA in the form of 7S ribonucleoprotein particles in oocytes. Additionally, it forms a metastable complex with 5S DNA and promotes the formation of stable and competent transcription complexes. Its expression is developmentally controlled at the level of transcription and translation. Moreover, it participates in the assembly of active chromatin templates and at least, in part, is responsible for the developmental regulation of two kinds of 5S RNA genes in Xenopus.