Kinesins in the Arabidopsis genome: a comparative analysis among eukaryotes

Abstract

Background: Kinesins constitute a superfamily of microtubule motor proteins that are found in eukaryotic organisms. Members of the kinesin superfamily perform many diverse cellular functions such as transport of vesicles and organelles, spindle formation and elongation, chromosome segregation, microtubule dynamics and morphogenesis. Only a few kinesins have been characterized in plants including Arabidopsis thaliana. Because of the diverse cellular functions in which kinesins are involved, the number, types and characteristics of kinesins present in the Arabidopsis genome would provide valuable information for many researchers.

Results: Here we have analyzed the recently completed Arabidopsis genome sequence and identified sixty-one kinesin genes in the Arabidopsis genome. Among the five completed eukaryotic genomes the Arabidopsis genome has the highest percentage of kinesin genes. Further analyses of the kinesin gene products have resulted in identification of several interesting domains in Arabidopsis kinesins that provide clues in understanding their functions. A phylogenetic analysis of all Arabidopsis kinesin motor domain sequences with 113 motor domain sequences from other organisms has revealed that Arabidopsis has seven of the nine recognized subfamilies of kinesins whereas some kinesins do not fall into any known family.

Conclusion: There are groups of Arabidopsis kinesins that are not present in yeast, Caenorhabditis elegans and Drosophila melanogaster that may, therefore, represent new subfamilies specific to plants. The domains present in different kinesins may provide clues about their functions in cellular processes. The comparative analysis presented here provides a framework for future functional studies with Arabidopsis kinesins.

Figure 1

Comparison of kinesins in completely sequenced eukaryotic genomes. A. The total number of kinesins per organism (in green) and the number of kinesins per thousand genes (in red). B. The number of kinesins per organism in each family. C.Term - C-Terminal motor, Chromo/KIF4 - chromokinesin/KIF4, U - ungrouped. At - Arabidopsis thaliana, Dm -Drosophila melanogaster, Ce - Caenorhabditis elegans,, Sc -Saccharomyces cerevisiae, Sp -Schizosaccharomyces pombe

Figure 2

Location of kinesins on the Arabidopsis chromosomes. Roman numerals represent chromosome number. Large numbers indicate chromosome length in cM. Small numbers are the kinesin numbers from Table I.

Figure 3

3 and 4 Phylogenetic tree. The tree shown above was built from a kinesin motor domain sequence alignment using the heuristic search method of PAUP v4.0b6, a maximum parsimony program, with random stepwise addition and tree bisection-reconnection (TBR). The tree is the consensus tree from 68 trees built from 100 replicates. It is arbitrarily rooted using ScSmy1 as an outgroup. Vertical dashes indicate ungrouped kinesins (light dashes - those grouped with other kinesins, bold dashes - exclusively Arabidopsis kinesins). The Arabidopsis kinesins are in bold. Kinesins from the following organisms were used: An, Aspergillus nidulans; Bm, Bombyx mori; Ce, Caenorhabditis elegans; Cf, Cylindrotheca fusiformis; Cg, Cricetulus griseus; Cr, Chlamydomonas rheinhardtii; Dd,Dictyostelium discoideum; Dm, Drosophila melanogaster; Gg, Gallus gallus; Hs, Homo sapiens; Lc, Leishmania chagasi; Lm, Leishmania major; Lp, Loligo pealii; Mm, Mus musculus; Ms, Morone saxatilis; Nc, Neurospora crassa; Nh, Nectria haematococca; N, Nicotiana tabacum; St, Solanum tuberosum; Rn, Rattus norvegicus; Sc, Saccharomyces cerevisiae; Sp, Strongylocentrotus purpuratus; Spo, Schizosaccharomyces pombe; Sr, Syncephalastrum racemosum; Um, Ustilago maydis; Xl, Xenopus laevis.

Figure 4

3 and 4 Phylogenetic tree. The tree shown above was built from a kinesin motor domain sequence alignment using the heuristic search method of PAUP v4.0b6, a maximum parsimony program, with random stepwise addition and tree bisection-reconnection (TBR). The tree is the consensus tree from 68 trees built from 100 replicates. It is arbitrarily rooted using ScSmy1 as an outgroup. Vertical dashes indicate ungrouped kinesins (light dashes - those grouped with other kinesins, bold dashes - exclusively Arabidopsis kinesins). The Arabidopsis kinesins are in bold. Kinesins from the following organisms were used: An, Aspergillus nidulans; Bm, Bombyx mori; Ce, Caenorhabditis elegans; Cf, Cylindrotheca fusiformis; Cg, Cricetulus griseus; Cr, Chlamydomonas rheinhardtii; Dd,Dictyostelium discoideum; Dm, Drosophila melanogaster; Gg, Gallus gallus; Hs, Homo sapiens; Lc, Leishmania chagasi; Lm, Leishmania major; Lp, Loligo pealii; Mm, Mus musculus; Ms, Morone saxatilis; Nc, Neurospora crassa; Nh, Nectria haematococca; N, Nicotiana tabacum; St, Solanum tuberosum; Rn, Rattus norvegicus; Sc, Saccharomyces cerevisiae; Sp, Strongylocentrotus purpuratus; Spo, Schizosaccharomyces pombe; Sr, Syncephalastrum racemosum; Um, Ustilago maydis; Xl, Xenopus laevis.

Figure 5

Alignments of neck/motor core region and kinesin light chain binding site of KHC. Alignments were done using the Clustal method in DNA STAR MEGALIGN. A. Alignment of the neck/motor core regions from the 21 kinesins falling in the C-terminal subfamily. White letters on black are identical residues, white on dark gray are strongly similar and black on light gray are weakly similar. Asterisks mark the two residues shown to confer minus end directed movement [47]. B. Alignment of the kinesin light chain binding site in KHCs. The small letters indicate the heptad positions in the heptad repeats as given by Diefenbach et al. [52]. Hs, human KHC; Hsn, human neuronal KHC; Sp, sea urchin KHC, Dm, Drosophila melanogaster KHC; Nc, Neurospora crassa KHC; Um, Ustilago maydis, At, AtMAA21.110 kinesin.

Figure 6

Schematic diagram of all Arabidopsis kinesins. Motor domain and coiled-coil domains are marked in red and green, respectively. CH, calponin homology domain; MyTH4, myosin tail homology domain; Talin-like, talin-like domain; CBD, calmodulin binding domain; ARM, armadillo/beta-catenin-like repeats; HhH1, helix-hairpin-helix domain. Bar = 100 aa.