AUTHOR=Aklilu Behailu B. , Culligan Kevin M. 

TITLE=Molecular Evolution and Functional Diversification of Replication Protein A1 in Plants

JOURNAL=Frontiers in Plant Science

VOLUME=7

YEAR=2016

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2016.00033

DOI=10.3389/fpls.2016.00033

ISSN=1664-462X

ABSTRACT=<p>Replication protein A (RPA) is a heterotrimeric, single-stranded DNA binding complex required for eukaryotic DNA replication, repair, and recombination. RPA is composed of three subunits, RPA1, RPA2, and RPA3. In contrast to single RPA subunit genes generally found in animals and yeast, plants encode multiple paralogs of RPA subunits, suggesting subfunctionalization. Genetic analysis demonstrates that five <italic>Arabidopsis thaliana</italic> RPA1 paralogs (RPA1A to RPA1E) have unique and overlapping functions in DNA replication, repair, and meiosis. We hypothesize here that RPA1 subfunctionalities will be reflected in major structural and sequence differences among the paralogs. To address this, we analyzed amino acid and nucleotide sequences of <italic>RPA1</italic> paralogs from 25 complete genomes representing a wide spectrum of plants and unicellular green algae. We find here that the plant <italic>RPA1</italic> gene family is divided into three general groups termed <italic>RPA1A, RPA1B</italic>, and <italic>RPA1C</italic>, which likely arose from two progenitor groups in unicellular green algae. In the family <italic>Brassicaceae</italic> the <italic>RPA1B</italic> and <italic>RPA1C</italic> groups have further expanded to include two unique sub-functional paralogs <italic>RPA1D</italic> and <italic>RPA1E</italic>, respectively. In addition, <italic>RPA1</italic> groups have unique domains, motifs, <italic>cis</italic>-elements, gene expression profiles, and pattern of conservation that are consistent with proposed functions in monocot and dicot species, including a novel C-terminal zinc-finger domain found only in plant RPA1C-like sequences. These results allow for improved prediction of RPA1 subunit functions in newly sequenced plant genomes, and potentially provide a unique molecular tool to improve classification of <italic>Brassicaceae</italic> species.</p>