Recognition of promoter DNA by subdomain 4.2 of Escherichia coli sigma 70: a knowledge based model of -35 hexamer interaction with 4.2 helix-turn-helix motif.

In Escherichia coli, subdomains 2.4 and 4.2 of the primary transcription factor sigma 70 are the most highly conserved regions and are responsible for the recognition of -10 and -35 promoter elements respectively. Mutational studies provide evidence to this end and indicate that the side chains of subdomain 4.2 make specific contacts with the nucleotides at -35. Subdomain 4.2 is highly conserved among group-1 sigma factors and is strongly homologous to the classical helix-turn-helix (HTH) motif shared by bacteriophage lembda cl, Cro, the CAP protein and other homeodomain proteins, suggesting that sigma factor also belongs to the HTH class of proteins. In this study, a single point mutation of the conserved hydrophobic residue valine at position 576, in the 4.2 subdomain results in a mutant that is transcriptionally inefficient although conformationally similar to wild-type sigma. The mutant sigma, like wild-type, migrates as a 87 kDa protein on SDS gels and has 50% helicity. However, transcription at "extended -10 promoter' by RNA polymerase containing mutant sigma 70-V576G, synthesized appreciable amount of RNA product, when compared with that generated by sigma 70-W434G, a mutation in -10 DNA binding domain. A model of HTH motif for the conserved 20 residue region of 4.2 domain of E. coli sigma 70 as well as its mutant sigma 70-V576G and sigma 70-V576T were constructed based on five other homologous HTH motifs from DNA-protein complexes for which X-ray or NMR structure is available. A B-DNA structure was designed for -35 region using sequence dependent base pair parameters. The modeled HTH structure was docked into the major groove formed by the -35 hexamer DNA using the DNA-recognition rules and amino acid-nucleotide base contact information of homologous DNA-protein complexes. Analysis of the residue contact information of the model was tested and found to have good agreement with the experimental reports.