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RESEARCH PAPERS ON SYSTEMS BIOLOGY/GENOMICS/BIOINFORMATICS

Genomic Comparison of P-Type ATPase Ion Pumps in Arabidopsis and Rice¹

Department of Cell Biology, Plant Division, The Scripps Research Institute, La Jolla, California 92037 (I.B., J.F.H.); Department of Biology, University of California, San Diego, La Jolla, California 92093 (J.T., M.G.); Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706 (M.R.S.); Unite de Biochemie Physiologique, Institut des Sciences de la Vie, Universite Catholique de Louvain, Louvain-La-Neuve, Belgium (M.B.); Plant Physiology and Anatomy Laboratory, Department of Plant Biology, The Royal Veterinary and Agricultural University, Copenhagen, Denmark (M.G.P., K.B.A.); and SWISS-PROT group, Swiss Institute of Bioinformatics, Geneva, Switzerland (K.B.A.)

Members of the P-type ATPase ion pump superfamily are found in all three branches of life. Forty-six P-type ATPase genes were identified in Arabidopsis, the largest number yet identified in any organism. The recent completion of two draft sequences of the rice (Oryza sativa) genome allows for comparison of the full complement of P-type ATPases in two different plant species. Here, we identify a similar number (43) in rice, despite the rice genome being more than three times the size of Arabidopsis. The similarly large families suggest that both dicots and monocots have evolved with a large preexisting repertoire of P-type ATPases. Both Arabidopsis and rice have representative members in all five major subfamilies of P-type ATPases: heavy-metal ATPases (P_1B), Ca²⁺-ATPases (endoplasmic reticulum-type Ca²⁺-ATPase and autoinhibited Ca²⁺-ATPase, P_2A and P_2B), H⁺-ATPases (autoinhibited H⁺-ATPase, P_3A), putative aminophospholipid ATPases (ALA, P₄), and a branch with unknown specificity (P₅). The close pairing of similar isoforms in rice and Arabidopsis suggests potential orthologous relationships for all 43 rice P-type ATPases. A phylogenetic comparison of protein sequences and intron positions indicates that the common angiosperm ancestor had at least 23 P-type ATPases. Although little is known about unique and common features of related pumps, clear differences between some members of the calcium pumps indicate that evolutionarily conserved clusters may distinguish pumps with either different subcellular locations or biochemical functions.

¹ Work is supported in part by the Department of Energy (grant no. DOE DE–FG03–94ER20152 to J.F.H.), Syngenta (grant to J.F.H.), by the National Science Foundation (grant no. DBI 0077378 to J.F.H. and M.G.), and by Human Frontiers Science Program (grant no. RG0268 to J.F.H., M.R.S., M.B., and M.G.P.).

^* Corresponding author; e-mail harper{at}scripps.edu; fax 858–784–9840.

Received February 9, 2003; returned for revision February 25, 2003; accepted February 25, 2003.

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