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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 6s, 10s, 11s, and orphan kinesins. 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 14: Sub-region of the phylogenetic tree based on their motor domain showing kinesin 6s, 10s, 11s, and orphan kinesins. 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: The kinesin 10 family members are commonly referred as “Kid” in human (Tokai et al., 1996) and “KIF 22” in mouse (Yang et al., 1997). They have been suggested to be involved in spindle formation and chromosome movement (Miki et al., 2005). It is notable that members of the kinesin 10 family, which are present in Arabidopsis (two members) are absent in Physcomitrella (Figure 14). Although PAKRP2 has been sometimes grouped in the kinesin 10 family (Richardson et al., 2006; Zhu and Dixit, 2011a), it is more appropriate to be classified as an orphan kinesin based on our analysis (Figure 14). A detailed discussion about this classification can be found at the section for orphan kinesins below. The presence of orthologs of the Arabidopsis kinesin 10s in other basal plant species may provide clues about essential developmental processes present in a common ancestor but lost in mosses.


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 6s, 10s, 11s, and orphan kinesins. 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 14: Sub-region of the phylogenetic tree based on their motor domain showing kinesin 6s, 10s, 11s, and orphan kinesins. 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: The kinesin 10 family members are commonly referred as “Kid” in human (Tokai et al., 1996) and “KIF 22” in mouse (Yang et al., 1997). They have been suggested to be involved in spindle formation and chromosome movement (Miki et al., 2005). It is notable that members of the kinesin 10 family, which are present in Arabidopsis (two members) are absent in Physcomitrella (Figure 14). Although PAKRP2 has been sometimes grouped in the kinesin 10 family (Richardson et al., 2006; Zhu and Dixit, 2011a), it is more appropriate to be classified as an orphan kinesin based on our analysis (Figure 14). A detailed discussion about this classification can be found at the section for orphan kinesins below. The presence of orthologs of the Arabidopsis kinesin 10s in other basal plant species may provide clues about essential developmental processes present in a common ancestor but lost in mosses.

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