Membrane Protein Families - The P-Type ATPases


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Genomic Comparison of P-type ATPase Ion Pumps in Arabidopsis and Rice.

Members of the P-type ATPase ion pump superfamily (TC# 3.A.3) are found in all three branches of life. Forty-six P-type ATPase genes were identified in Arabidopsis thaliana, 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 (HMA, P1B), calcium ATPases (ECA and ACA, P2A and P2B), H+-ATPases (AHA, P3A), putative amino-phospholipid 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. While 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.

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Phylogenetic Tree of P-type ATPases from Arabidopsis and Rice

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	Supplemental Information		Reference
	Alignments for Arabidopsis and Rice Subgroup 1B (HMA) Alignments for Arabidopsis and Rice Subgroup 2A (ECA) Alignments for Arabidopsis and Rice Subgroup 2B (ACA) Alignments for Arabidopsis and Rice Subgroup 3A (AHA) Alignments for Arabidopsis and Rice Subgroup 4 (ALA) Alignments for Arabidopsis and Rice Subgroup 5 (Unknown)		Baxter, I, Tchieu, J., Sussman, M.R., Boutry, M., Palmgren, M.G., Gribskov, M., Harper, J.F. and Axelsen, K.B. Genomic Comparison of P-type ATPase Ion Pumps in Arabidopsis and Rice. Plant Physiol. June 2003, Vol. 132, pp. 618-628 PMID: 12805592

	Family Descriptions
	Heavy Metal Transporting ATPases There are eight P1B ATPases in rice just like in Arabidopsis. The P1B ATPases are divided into six clusters, based on sequence alignments and intron positions. Seven Arabidopsis P1B ATPases were previously identified (Axelsen and Palmgren, 2001), but the completion of the Arabidopsis sequencing revealed an eighth gene, AtHMA8, which is most identical (43%) to PAA1/AtHMA6. It was previously observed that Arabidopsis underwent a expansion in numbers of P1B ATPases compared to other eukaryotic organisms, which only have one or two (Axelsen and Palmgren, 2001). The parallel discovery of eight P1B ATPases in rice suggests that this expansion was important for the evolution of angiosperms (for a recent review of heavy metal transport in plants, see (Williams et al., 2000)).		ER Calcium ATPase Transport Family The P2A ATPases include the well-characterized mammalian sarcoplasmic/endoplasmic reticulum calcium ATPase (SERCA) Ca2+-ATPases (Carafoli and Brini, 2000; Geisler et al., 2000; Sze et al., 2000). Three members of this subfamily are found in the rice genome, compared to four in Arabidopsis. The P2A ATPases are divided into two clusters, based on sequence alignments and intron positions. Within cluster 1, AtECA2 may be special, as it has lost three of seven introns and has diverged from the other pumps in its cluster. Experiments in yeast suggest that ECAs can transport Ca2+, Mn2+, and Zn2+ (Wu et al., 2002).
	Aminophospholipid ATPase Transporter Family This large subfamily of divergent ATPases, which is only found in eukaryotes, includes 12 and 10 genes in Arabidopsis and rice, respectively. The P4 ATPases are divided into five clusters, based on sequence alignments and intron positions. The previously reported gene model for AtALA3 has been changed based on the similarity with its ortholog, OsALA8. The donor site of the second-to-last exon has been moved four nucleotides upstream, resulting in the last exon being read in another frame and making the protein 90 amino acids longer. The P4 ATPases have been implicated in aminophospholipid flipping. However, it is not clear if the flipase activity is the primary function of P4 ATPases or an indirect effect of its activity.		H+ Transporting ATPase Family The P3A H+-ATPases are not found in animal systems. Arabidopsis has 11 while rice has 10. Of the six subfamilies of P-type ATPases, the P3A branch shows the least divergence. The P3A ATPases are divided into five clusters, based on sequence alignments and intron positions. While the bootstrap values that delineate clusters 2 and 4 are quite low, this branch is further supported by a similar clustering analysis that included additional tobacco genes (Arango et al., 2003).
	Calcium Transporting ATPase Family The plant P2B ATPases are related to the mammalian plasma membrane calmodulin-stimulated ATPases, but differ in having an N-terminal rather than a C-terminal autoinhibitor (Carafoli and Brini, 2000; Geisler et al., 2000; Sze et al., 2000). There are 10 P2B ATPases in Arabidopsis and 11 in rice. The P2B ATPases are divided into four clusters, based on sequence alignments and intron positions. Cluster 3 is special because it is the only cluster of P-type ATPases that harbors intron-less genes. In contrast, genes in cluster 4 have as many as 33 introns.		Unknown ATPase Transporter Family There is a single member of the P5 ATPases in each organism; the proteins are 77% identical (Fig. 8). The P5 ATPases are the least studied of the P-type ATPase subfamilies. The only protein to have been studied in some detail is SPF1/COD1, one of two members in S. cerevisiae (Cronin et al., 2002; Vashist et al., 2002). The studies have given no clear idea of ion specificity, but do suggest a functional connection to lipid biogenesis and pathogen response.

A distributed project investigating gene networks that control uptake and accumulation of plant nutrients and toxic metals. Funded by the plant genome program of the National Science Foundation (DBI-0077378). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.

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