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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

(A) Sub-region of the phylogenetic tree based on their motor domain showing kinesin 9s. 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. (B) Gene models of kinesin 9s. Schematic diagrams showing the structure and domain architecture of kinesin 9s. Domains are indicated at the bottom of the diagrams.
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Figure 9: (A) Sub-region of the phylogenetic tree based on their motor domain showing kinesin 9s. 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. (B) Gene models of kinesin 9s. Schematic diagrams showing the structure and domain architecture of kinesin 9s. Domains are indicated at the bottom of the diagrams.

Mentions: Kinesin 9s have been implicated in flagella regulation, structure, and construction (Bernstein et al., 1994; Yokoyama et al., 2004; Demonchy et al., 2009), and consistent with this function, they are absent in flowering plants, yeast, and invertebrates (Richardson et al., 2006). Our phylogenetic analysis identified three kinesin 9s in Physcomitrella (Figure 9A). Two of the three gene models found in the cosmoss.org database (Pp-Kinesin09-b and c) seem to be inaccurate because of some abnormal insertions and gaps are present when compared to other kinesin 9 sequences. The genomic sequences corresponding to the questionable regions were examined in more detailed and it was found that some exons are not present in the latest proteome version in cosmoss.org (version 1.6) and that some introns were incorrectly spliced (Figure 9B and Figure S1 in Supplementary Material). We were not able to determine if additional problems exist in the gene models of the regions after the motor domain, which due to reduced conservation are harder to identify and their detailed description is beyond the scope of this manuscript. Similarly to kinesin 2 (Sloboda and Howard, 2007), we anticipate kinesin 9s will participate in the de novo assembly of flagella during spermatogenesis in moss.


Phylogenetic analysis of the Kinesin superfamily from physcomitrella.

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

(A) Sub-region of the phylogenetic tree based on their motor domain showing kinesin 9s. 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. (B) Gene models of kinesin 9s. Schematic diagrams showing the structure and domain architecture of kinesin 9s. Domains are indicated at the bottom of the diagrams.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 9: (A) Sub-region of the phylogenetic tree based on their motor domain showing kinesin 9s. 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. (B) Gene models of kinesin 9s. Schematic diagrams showing the structure and domain architecture of kinesin 9s. Domains are indicated at the bottom of the diagrams.
Mentions: Kinesin 9s have been implicated in flagella regulation, structure, and construction (Bernstein et al., 1994; Yokoyama et al., 2004; Demonchy et al., 2009), and consistent with this function, they are absent in flowering plants, yeast, and invertebrates (Richardson et al., 2006). Our phylogenetic analysis identified three kinesin 9s in Physcomitrella (Figure 9A). Two of the three gene models found in the cosmoss.org database (Pp-Kinesin09-b and c) seem to be inaccurate because of some abnormal insertions and gaps are present when compared to other kinesin 9 sequences. The genomic sequences corresponding to the questionable regions were examined in more detailed and it was found that some exons are not present in the latest proteome version in cosmoss.org (version 1.6) and that some introns were incorrectly spliced (Figure 9B and Figure S1 in Supplementary Material). We were not able to determine if additional problems exist in the gene models of the regions after the motor domain, which due to reduced conservation are harder to identify and their detailed description is beyond the scope of this manuscript. Similarly to kinesin 2 (Sloboda and Howard, 2007), we anticipate kinesin 9s will participate in the de novo assembly of flagella during spermatogenesis in moss.

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