An
analysis of the
Arabidopsis actin-related
proteins (ARPs) in a sequence phylogram reveals ancient & divergent
classes that predate the split among the four eukaryotic kingdoms.
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The ARPs are highly divergent as revealed by the length of branches in this phylogram relative to the brancing among the conventional actins from four kingdoms (left). For comparison see how closely related conventional Arabidopsis actin AtACT2 is to conventional actins from human (HsACTB) and yeast (ScACT1) . Six of the Arabidopsis ARPs (AtARP4, 4a, 5, 6, 7, and 8) are expressed in all plant organs and based on their positions in the tree relatively to partially characterized fungal, protist, and animal ARPs they are nuclear ARPs. This nuclear localization has been confirmed for AtARP4, 6, and 7. ARP4a is a pseudogene. AtARP2 and 3 and cytoplasmic proteins and expressed at very low levels in plants. In animals they control nucleation and initiate actin filament branching. Little is known about the plant AtARP2 & AtARP3 homologues. Higher plants lack a homologue to ARP1 the ARP which takes part in the centractin/ flagellar complex. This is consistant with the loss of motile sperm in angiosperms since their divergence with a common ancestor of the gymnosperms. Figure Legend. Phylogenetic relationships of actin and actin-related proteins. Arabidopsis (At), rice (Os), human (Hs) and yeast (Sc) ARP sequences are compared in a neighbor-joining (NBJ) tree. Clades of ARP sequences are named based primarily on the nomenclature of yeast ARPs or distinct plant ARPs. The tree is rooted to highly conserved conventional actins. Because branch length is sensitive to the degree of sequence divergence in the NBJ tree, the accelerated rate of divergence among ARPs relative to actins is supported by the long horizontal distances among ARPs compared with the short distances among actins. The tree shows that Arabidopsis and rice contain eight ancient and highly divergent classes of ARPs, six classes that have homologs in yeast and human (ARP2–ARP6 and ARP9), and two classes that are specific to plants (ARP7 and ARP8). The accession numbers for the protein sequences used in the tree are as follows. Human: HsACTB, P02570; HsARP1, S29089; HsARP2A, AB64187; HsARP3, P32391; HsBAF53A, 096019; HsARP5, CAD37358; HsARP6X, Q9GZN1; HsARP8, Q9H981; HsARP11, Q9NZ32. Yeast: ScACT1, P02579; ScARP1, P38696; ScARP2, P32381; ScARP3, P47117; ScARP4, P80428; ScARP5, P53946; ScARP6, Q12509; ScARP7, Q12406; ScARP8, Q12386; ScARP9, Q055123; ScARP10, Q04549. Arabidopsis: AtACT2, Q96292 (for ARPs, see Table 2). Rice: OsRAC1, AA038821 (for ARPs, see Table 2). The various yeast, human and plant ARPs and actin are shown in black, purple and green, respectively. The major ARP classes are indicated adjacent to each clade of ARPs; the two novel plant-specific ARP classes are in green.
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