Abstract
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 (P1B), Ca2+-ATPases (endoplasmic reticulum-type Ca2+-ATPase and autoinhibited Ca2+-ATPase, P2A and P2B), H+-ATPases (autoinhibited H+-ATPase, P3A), 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.
Highlights
Members of the P-type ATPase ion pump superfamily are found in all three branches of life
To ensure that all possible P-type ATPase genes were identified, multiple independent sequences were searched in several different ways. We searched both the Beijing Genomics Institute (Yu et al, 2002) and Syngenta (Goff et al, 2002) rice genome sequences, in addition to the partial sequences deposited at The Institute for Genome Research
Because one additional Arabidopsis isoform was identified in subsequent releases of the “complete” Arabidopsis genome, it is possible that additional rice isoforms may be identified in future versions of the rice genome sequence
Summary
Members of the P-type ATPase ion pump superfamily are found in all three branches of life. Both Arabidopsis and rice have representative members in all five major subfamilies of P-type ATPases: heavy-metal ATPases (P1B), Ca2ϩ-ATPases (endoplasmic reticulum-type Ca2ϩ-ATPase and autoinhibited Ca2ϩATPase, P2A and P2B), Hϩ-ATPases (autoinhibited Hϩ-ATPase, P3A), putative aminophospholipid ATPases (ALA, P4), and a branch with unknown specificity (P5). Two structures of 3.1 and 2.6 Å resolution of a calcium pump (sarcoplasmic/endoplasmic reticulum [ER] calcium ATPase [SERCA]) have greatly increased the understanding of the mechanism of ion transport by P-type ATPases (Toyoshima et al, 2000; Toyoshima and Nomura, 2002). Some of the multiple isoforms may represent functionally redundant duplications
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