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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.

SUBMITTER: Reddy AS

PROVIDER: S-EPMC35278 | biostudies-literature | 2001

REPOSITORIES: biostudies-literature

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Kinesins in the Arabidopsis genome: a comparative analysis among eukaryotes.

Reddy A S AS Day I S IS

BMC genomics 20010625

<h4>Background</h4>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 ...[more]

PMID: 11472632

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Project description:BackgroundKinesins, a superfamily of molecular motors, use microtubules as tracks and transport diverse cellular cargoes. All kinesins contain a highly conserved approximately 350 amino acid motor domain. Previous analysis of the completed genome sequence of one flowering plant (Arabidopsis) has resulted in identification of 61 kinesins. The recent completion of genome sequencing of several photosynthetic and non-photosynthetic eukaryotes that belong to divergent lineages offers a unique opportunity to conduct a comprehensive comparative analysis of kinesins in plant and non-plant systems and infer their evolutionary relationships.ResultsWe used the kinesin motor domain to identify kinesins in the completed genome sequences of 19 species, including 13 newly sequenced genomes. Among the newly analyzed genomes, six represent photosynthetic eukaryotes. A total of 529 kinesins was used to perform comprehensive analysis of kinesins and to construct gene trees using the Bayesian and parsimony approaches. The previously recognized 14 families of kinesins are resolved as distinct lineages in our inferred gene tree. At least three of the 14 kinesin families are not represented in flowering plants. Chlamydomonas, a green alga that is part of the lineage that includes land plants, has at least nine of the 14 known kinesin families. Seven of ten families present in flowering plants are represented in Chlamydomonas, indicating that these families were retained in both the flowering-plant and green algae lineages.ConclusionThe increase in the number of kinesins in flowering plants is due to vast expansion of the Kinesin-14 and Kinesin-7 families. The Kinesin-14 family, which typically contains a C-terminal motor, has many plant kinesins that have the motor domain at the N terminus, in the middle, or the C terminus. Several domains in kinesins are present exclusively either in plant or animal lineages. Addition of novel domains to kinesins in lineage-specific groups contributed to the functional diversification of kinesins. Results from our gene-tree analyses indicate that there was tremendous lineage-specific duplication and diversification of kinesins in eukaryotes. Since the functions of only a few plant kinesins are reported in the literature, this comprehensive comparative analysis will be useful in designing functional studies with photosynthetic eukaryotes.

Project description:BACKGROUND: Plant disease resistance (R) genes with the nucleotide binding site (NBS) play an important role in offering resistance to pathogens. The availability of complete genome sequences of Brassica oleracea and Brassica rapa provides an important opportunity for researchers to identify and characterize NBS-encoding R genes in Brassica species and to compare with analogues in Arabidopsis thaliana based on a comparative genomics approach. However, little is known about the evolutionary fate of NBS-encoding genes in the Brassica lineage after split from A. thaliana. RESULTS: Here we present genome-wide analysis of NBS-encoding genes in B. oleracea, B. rapa and A. thaliana. Through the employment of HMM search and manual curation, we identified 157, 206 and 167 NBS-encoding genes in B. oleracea, B. rapa and A. thaliana genomes, respectively. Phylogenetic analysis among 3 species classified NBS-encoding genes into 6 subgroups. Tandem duplication and whole genome triplication (WGT) analyses revealed that after WGT of the Brassica ancestor, NBS-encoding homologous gene pairs on triplicated regions in Brassica ancestor were deleted or lost quickly, but NBS-encoding genes in Brassica species experienced species-specific gene amplification by tandem duplication after divergence of B. rapa and B. oleracea. Expression profiling of NBS-encoding orthologous gene pairs indicated the differential expression pattern of retained orthologous gene copies in B. oleracea and B. rapa. Furthermore, evolutionary analysis of CNL type NBS-encoding orthologous gene pairs among 3 species suggested that orthologous genes in B. rapa species have undergone stronger negative selection than those in B .oleracea species. But for TNL type, there are no significant differences in the orthologous gene pairs between the two species. CONCLUSION: This study is first identification and characterization of NBS-encoding genes in B. rapa and B. oleracea based on whole genome sequences. Through tandem duplication and whole genome triplication analysis in B. oleracea, B. rapa and A. thaliana genomes, our study provides insight into the evolutionary history of NBS-encoding genes after divergence of A. thaliana and the Brassica lineage. These results together with expression pattern analysis of NBS-encoding orthologous genes provide useful resource for functional characterization of these genes and genetic improvement of relevant crops.

Dataset Information

Kinesins in the Arabidopsis genome: a comparative analysis among eukaryotes.

Publications

Kinesins in the Arabidopsis genome: a comparative analysis among eukaryotes.

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