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Identification and phylogenetic analysis of Dictyostelium discoideum kinesin proteins.

Kollmar M, Glöckner G - BMC Genomics (2003)

Bottom Line: According to known cellular functions or strong homologies to kinesins of other organisms, four of the Dictyostelium kinesins are involved in organelle transport, six are implicated in cell division processes, two are predicted to perform multiple functions, and one kinesin may be the founder of a new subclass.According to an exhaustive phylogenetic comparison, Dictyostelium contains the same subset of kinesins that higher eukaryotes need to perform mitosis.Some of the kinesins are implicated in intracellular traffic and a small number have unpredictable functions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Abteilung NMR basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Am Fabetaberg 11, D-37077 Göttingen, Germany. mako@nmr.mpibpc.mpg.de

ABSTRACT

Background: Kinesins constitute a large superfamily of motor proteins in eukaryotic cells. They perform diverse tasks such as vesicle and organelle transport and chromosomal segregation in a microtubule- and ATP-dependent manner. In recent years, the genomes of a number of eukaryotic organisms have been completely sequenced. Subsequent studies revealed and classified the full set of members of the kinesin superfamily expressed by these organisms. For Dictyostelium discoideum, only five kinesin superfamily proteins (Kif's) have already been reported.

Results: Here, we report the identification of thirteen kinesin genes exploiting the information from the raw shotgun reads of the Dictyostelium discoideum genome project. A phylogenetic tree of 390 kinesin motor domain sequences was built, grouping the Dictyostelium kinesins into nine subfamilies. According to known cellular functions or strong homologies to kinesins of other organisms, four of the Dictyostelium kinesins are involved in organelle transport, six are implicated in cell division processes, two are predicted to perform multiple functions, and one kinesin may be the founder of a new subclass.

Conclusion: This analysis of the Dictyostelium genome led to the identification of eight new kinesin motor proteins. According to an exhaustive phylogenetic comparison, Dictyostelium contains the same subset of kinesins that higher eukaryotes need to perform mitosis. Some of the kinesins are implicated in intracellular traffic and a small number have unpredictable functions.

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Phylogenetic analysis of 390 kinesins from 50 species found in the common databases. Amino acid sequences of the motor domains were aligned by using maximum parsimony. Sequences used for alignment are available as supplemental material.
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Figure 2: Phylogenetic analysis of 390 kinesins from 50 species found in the common databases. Amino acid sequences of the motor domains were aligned by using maximum parsimony. Sequences used for alignment are available as supplemental material.

Mentions: A phylogenetic tree of the motor domains of the Dictyostelium kinesins together with 377 kinesin motor domain sequences from 50 species found in the public databases was created (Fig. 2, supplementary data [see Additional file 1]). The tree is in basic agreement with the phylogenetic results of earlier investigations that, however, only included 146 kinesins in the most extensive analysis [3]. The kinesin superfamily comprises 17 subfamilies of N-terminal motors, two subfamilies of kinesins with central motor domains, and four subfamilies with C-terminal kinesins. Subfamilies were only assigned when kinesins of different organisms contribute. The new subfamilies were designated obeying the more general nomenclature of Miki et al. [10] (N-1 to N-17, M-1 and M-2, C-1 to C-4) as well as following the old convention that new classes should be named after the first member discovered. According to this phylogenetic tree, twelve of the Dictyostelium kinesins group into nine different subfamilies, only DdKif9 might be an orphan or the founder of a new class. Based on the position of their motor domains, two of the kinesins (DdKif6 and DdKif9) are of the middle motor domain type, one (DdKif2) has the motor domain at the C-terminus and the remaining kinesins have N-terminal motor domains.


Identification and phylogenetic analysis of Dictyostelium discoideum kinesin proteins.

Kollmar M, Glöckner G - BMC Genomics (2003)

Phylogenetic analysis of 390 kinesins from 50 species found in the common databases. Amino acid sequences of the motor domains were aligned by using maximum parsimony. Sequences used for alignment are available as supplemental material.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC305348&req=5

Figure 2: Phylogenetic analysis of 390 kinesins from 50 species found in the common databases. Amino acid sequences of the motor domains were aligned by using maximum parsimony. Sequences used for alignment are available as supplemental material.
Mentions: A phylogenetic tree of the motor domains of the Dictyostelium kinesins together with 377 kinesin motor domain sequences from 50 species found in the public databases was created (Fig. 2, supplementary data [see Additional file 1]). The tree is in basic agreement with the phylogenetic results of earlier investigations that, however, only included 146 kinesins in the most extensive analysis [3]. The kinesin superfamily comprises 17 subfamilies of N-terminal motors, two subfamilies of kinesins with central motor domains, and four subfamilies with C-terminal kinesins. Subfamilies were only assigned when kinesins of different organisms contribute. The new subfamilies were designated obeying the more general nomenclature of Miki et al. [10] (N-1 to N-17, M-1 and M-2, C-1 to C-4) as well as following the old convention that new classes should be named after the first member discovered. According to this phylogenetic tree, twelve of the Dictyostelium kinesins group into nine different subfamilies, only DdKif9 might be an orphan or the founder of a new class. Based on the position of their motor domains, two of the kinesins (DdKif6 and DdKif9) are of the middle motor domain type, one (DdKif2) has the motor domain at the C-terminus and the remaining kinesins have N-terminal motor domains.

Bottom Line: According to known cellular functions or strong homologies to kinesins of other organisms, four of the Dictyostelium kinesins are involved in organelle transport, six are implicated in cell division processes, two are predicted to perform multiple functions, and one kinesin may be the founder of a new subclass.According to an exhaustive phylogenetic comparison, Dictyostelium contains the same subset of kinesins that higher eukaryotes need to perform mitosis.Some of the kinesins are implicated in intracellular traffic and a small number have unpredictable functions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Abteilung NMR basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Am Fabetaberg 11, D-37077 Göttingen, Germany. mako@nmr.mpibpc.mpg.de

ABSTRACT

Background: Kinesins constitute a large superfamily of motor proteins in eukaryotic cells. They perform diverse tasks such as vesicle and organelle transport and chromosomal segregation in a microtubule- and ATP-dependent manner. In recent years, the genomes of a number of eukaryotic organisms have been completely sequenced. Subsequent studies revealed and classified the full set of members of the kinesin superfamily expressed by these organisms. For Dictyostelium discoideum, only five kinesin superfamily proteins (Kif's) have already been reported.

Results: Here, we report the identification of thirteen kinesin genes exploiting the information from the raw shotgun reads of the Dictyostelium discoideum genome project. A phylogenetic tree of 390 kinesin motor domain sequences was built, grouping the Dictyostelium kinesins into nine subfamilies. According to known cellular functions or strong homologies to kinesins of other organisms, four of the Dictyostelium kinesins are involved in organelle transport, six are implicated in cell division processes, two are predicted to perform multiple functions, and one kinesin may be the founder of a new subclass.

Conclusion: This analysis of the Dictyostelium genome led to the identification of eight new kinesin motor proteins. According to an exhaustive phylogenetic comparison, Dictyostelium contains the same subset of kinesins that higher eukaryotes need to perform mitosis. Some of the kinesins are implicated in intracellular traffic and a small number have unpredictable functions.

Show MeSH
Related in: MedlinePlus