Poster: Genomic & proteomic resources

Abs # 875: Modeling studies suggest that the accelerated sequence evolution in the alpha subunit of the Geraniaceae DNA-dependant RNA polymerase is accompanied by a high level of conservation of secondary and tertiary structure

Presenter:	Calie, Pat , pat.calie@eku.edu
Authors	Hoskins, Samantha  (A)   Hogan, Julia  (C)   Bautista, Debra  (A)   Kuhlman, Peter  (B)   Calie, Pat  (A)
Affiliations:	(A): Depts. of Biology and Chemistry, Eastern Kentucky University (B): Dept. of Chemistry, Denison University (C): Dept. of Pharmacology, University of Kentucky

Typically the genes encoding the multisubunit DNA-dependent RNA polymerase evolve at a relatively conservative rate in most lineages. By contrast, members of the Geraniaceae contain plastid-encoded RNA polymerase genes that are evolving at a much higher rate. Between the alpha subunits of distantly-related bacterial species, 30 to 50 percent of amino acids are identical, indicating a higher rate of sequence change than that observed for the catalytically-critical beta and beta' subunits. The difference between the Escherichia and Thermus alpha subunit sequences, for which crystallographic structures have been determined, is about the same as the difference between the Escherichia sequence and a typical land plant plastid sequence, at approximately 35 percent sequence identity. Remarkably, this is the same level of divergence seen between two species of the same genus, Pelargonium, in the family Geraniaceae. Moreover, the Geraniaceae alpha subunits appear to have C-terminal domains that are highly variable both in sequence and in length. To explore the possible impacts of this accelerated sequence change on the alpha subunit structure, we have constructed homology models of the alpha subunits of plastid RNA polymerases from 12 taxa spanning the diversity of plastids and bacteria, using the modeling program MOE (Molecular Operating Environment). Despite the rapid primary sequence evolution of the four representative Geraniaceae alpha subunits, the secondary and tertiary structures of these proteins are highly conserved in comparison to other plastid homologues. Our modeling efforts will be extended to the beta and beta’ subunits, with the eventual in silico construction of the core polymerase enzyme complex for all 12 taxa.