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Phylogenetic analysis of the Kinesin superfamily from physcomitrella.

Shen Z, Collatos AR, Bibeau JP, Furt F, Vidali L - Front Plant Sci (2012)

Bottom Line: We found a remarkable conservation of families and subfamily classes with Arabidopsis, which is important for future comparative analysis of function.Some of the families, such as kinesins 14s are composed of fewer members in moss, while other families, such as the kinesin 12s are greatly expanded.To improve the comparison between species, and to simplify communication between research groups, we propose a classification of subfamilies based on our phylogenetic analysis.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Biotechnology, Worcester Polytechnic Institute Worcester, MA, USA.

ABSTRACT
Kinesins are an ancient superfamily of microtubule dependent motors. They participate in an extensive and diverse list of essential cellular functions, including mitosis, cytokinesis, cell polarization, cell elongation, flagellar development, and intracellular transport. Based on phylogenetic relationships, the kinesin superfamily has been subdivided into 14 families, which are represented in most eukaryotic phyla. The functions of these families are sometimes conserved between species, but important variations in function across species have been observed. Plants possess most kinesin families including a few plant specific families. With the availability of an ever increasing number of genome sequences from plants, it is important to document the complete complement of kinesins present in a given organism. This will help develop a molecular framework to explore the function of each family using genetics, biochemistry, and cell biology. The moss Physcomitrella patens has emerged as a powerful model organism to study gene function in plants, which makes it a key candidate to explore complex gene families, such as the kinesin superfamily. Here we report a detailed phylogenetic characterization of the 71 kinesins of the kinesin superfamily in Physcomitrella. We found a remarkable conservation of families and subfamily classes with Arabidopsis, which is important for future comparative analysis of function. Some of the families, such as kinesins 14s are composed of fewer members in moss, while other families, such as the kinesin 12s are greatly expanded. To improve the comparison between species, and to simplify communication between research groups, we propose a classification of subfamilies based on our phylogenetic analysis.

No MeSH data available.


Related in: MedlinePlus

Sub-region of the phylogenetic tree based on their motor domain showing kinesin 12s. The amino acid sequences of the motor domain were aligned using ClustalW and the phylogenetic tree was constructed using the maximum likelihood method (PhyML) and a 1000 bootstrap resampling value. Numbers on the nodes show the statistical support of values above 50%. The scale shows the estimated branch length corresponding to the number of substitutions per site. The Physcomitrella numbers correspond to the Phypa number uniquely associated with each gene model (version 1.6) at cosmoss.org.
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Figure 10: Sub-region of the phylogenetic tree based on their motor domain showing kinesin 12s. The amino acid sequences of the motor domain were aligned using ClustalW and the phylogenetic tree was constructed using the maximum likelihood method (PhyML) and a 1000 bootstrap resampling value. Numbers on the nodes show the statistical support of values above 50%. The scale shows the estimated branch length corresponding to the number of substitutions per site. The Physcomitrella numbers correspond to the Phypa number uniquely associated with each gene model (version 1.6) at cosmoss.org.

Mentions: Our phylogenetic analysis shows two classes of kinesins 12s; class I kinesin 12s, which are related to the phragmoplast orienting kinesins or POKs (Muller et al., 2006), and class II kinesin 12s, which are related to the phragmoplast-associated kinesin 1s or PAKRP1s (Figure 10). We found a surprisingly large number of class I kinesin 12s in Physcomitrella: a total of 18 genes, compared with only three in Arabidopsis. Some of the gene models corresponding to regions after the motor domain seem to be incomplete, but the majority of the class I sequences show long C-terminal domains with abundant coiled coils (Figure 11). The significance of this large number of kinesins is not understood and presents a challenging problem due to the likelihood of functional redundancy between its members. Nevertheless, due to their similarity to Arabidopsis POKs, these proteins are probably important for phragmoplast orientation. In contrast to the large number of class I kinesins 12s, there are only three class II kinesin 12s in Physcomitrella, forming a monophyletic group (Figure 10). The gene models for these kinesins show very similar C-terminal structures with abundant coiled coil structures, but not of the large magnitude of the ones present in class I (Figure 11). Again, we anticipate that these kinesins will play a similar role in phragmoplast organization as that of their Arabidopsis counterparts.


Phylogenetic analysis of the Kinesin superfamily from physcomitrella.

Shen Z, Collatos AR, Bibeau JP, Furt F, Vidali L - Front Plant Sci (2012)

Sub-region of the phylogenetic tree based on their motor domain showing kinesin 12s. The amino acid sequences of the motor domain were aligned using ClustalW and the phylogenetic tree was constructed using the maximum likelihood method (PhyML) and a 1000 bootstrap resampling value. Numbers on the nodes show the statistical support of values above 50%. The scale shows the estimated branch length corresponding to the number of substitutions per site. The Physcomitrella numbers correspond to the Phypa number uniquely associated with each gene model (version 1.6) at cosmoss.org.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472504&req=5

Figure 10: Sub-region of the phylogenetic tree based on their motor domain showing kinesin 12s. The amino acid sequences of the motor domain were aligned using ClustalW and the phylogenetic tree was constructed using the maximum likelihood method (PhyML) and a 1000 bootstrap resampling value. Numbers on the nodes show the statistical support of values above 50%. The scale shows the estimated branch length corresponding to the number of substitutions per site. The Physcomitrella numbers correspond to the Phypa number uniquely associated with each gene model (version 1.6) at cosmoss.org.
Mentions: Our phylogenetic analysis shows two classes of kinesins 12s; class I kinesin 12s, which are related to the phragmoplast orienting kinesins or POKs (Muller et al., 2006), and class II kinesin 12s, which are related to the phragmoplast-associated kinesin 1s or PAKRP1s (Figure 10). We found a surprisingly large number of class I kinesin 12s in Physcomitrella: a total of 18 genes, compared with only three in Arabidopsis. Some of the gene models corresponding to regions after the motor domain seem to be incomplete, but the majority of the class I sequences show long C-terminal domains with abundant coiled coils (Figure 11). The significance of this large number of kinesins is not understood and presents a challenging problem due to the likelihood of functional redundancy between its members. Nevertheless, due to their similarity to Arabidopsis POKs, these proteins are probably important for phragmoplast orientation. In contrast to the large number of class I kinesins 12s, there are only three class II kinesin 12s in Physcomitrella, forming a monophyletic group (Figure 10). The gene models for these kinesins show very similar C-terminal structures with abundant coiled coil structures, but not of the large magnitude of the ones present in class I (Figure 11). Again, we anticipate that these kinesins will play a similar role in phragmoplast organization as that of their Arabidopsis counterparts.

Bottom Line: We found a remarkable conservation of families and subfamily classes with Arabidopsis, which is important for future comparative analysis of function.Some of the families, such as kinesins 14s are composed of fewer members in moss, while other families, such as the kinesin 12s are greatly expanded.To improve the comparison between species, and to simplify communication between research groups, we propose a classification of subfamilies based on our phylogenetic analysis.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Biotechnology, Worcester Polytechnic Institute Worcester, MA, USA.

ABSTRACT
Kinesins are an ancient superfamily of microtubule dependent motors. They participate in an extensive and diverse list of essential cellular functions, including mitosis, cytokinesis, cell polarization, cell elongation, flagellar development, and intracellular transport. Based on phylogenetic relationships, the kinesin superfamily has been subdivided into 14 families, which are represented in most eukaryotic phyla. The functions of these families are sometimes conserved between species, but important variations in function across species have been observed. Plants possess most kinesin families including a few plant specific families. With the availability of an ever increasing number of genome sequences from plants, it is important to document the complete complement of kinesins present in a given organism. This will help develop a molecular framework to explore the function of each family using genetics, biochemistry, and cell biology. The moss Physcomitrella patens has emerged as a powerful model organism to study gene function in plants, which makes it a key candidate to explore complex gene families, such as the kinesin superfamily. Here we report a detailed phylogenetic characterization of the 71 kinesins of the kinesin superfamily in Physcomitrella. We found a remarkable conservation of families and subfamily classes with Arabidopsis, which is important for future comparative analysis of function. Some of the families, such as kinesins 14s are composed of fewer members in moss, while other families, such as the kinesin 12s are greatly expanded. To improve the comparison between species, and to simplify communication between research groups, we propose a classification of subfamilies based on our phylogenetic analysis.

No MeSH data available.


Related in: MedlinePlus