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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 1s and armadillo repeat containing kinesins (ARKs). 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 1s and ARKs. Schematic diagrams showing the structure and domain architecture of kinesin 1s and armadillo repeat containing kinesins (ARKs). Domains are indicated at the bottom of the diagrams. Armadillo repeats are comprised of a repeating sequence of forty-two amino acids that can form helices which upon repetition form a right handed super helix.
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Figure 1: (A) Sub-region of the phylogenetic tree based on their motor domain showing kinesin 1s and armadillo repeat containing kinesins (ARKs). 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 1s and ARKs. Schematic diagrams showing the structure and domain architecture of kinesin 1s and armadillo repeat containing kinesins (ARKs). Domains are indicated at the bottom of the diagrams. Armadillo repeats are comprised of a repeating sequence of forty-two amino acids that can form helices which upon repetition form a right handed super helix.

Mentions: Phylogenetic analysis based on the motor domain indicates that there are five sequences in Physcomitrella related to the Arabidopsis ARK (Figure 1A). Four of these sequences are closely related to each other, forming a monophyletic group and their gene models show the presence of armadillo repeats (Figure 1B); we classified these as class I. The gene model for the fifth sequence is lacking the armadillo repeats that would confirm its identity as an armadillo repeat containing kinesin (Figure 1B); we tentatively classified this single kinesin as ARK-Like since the tree topology fails to confirm this kinesins as an ortholog of the lone At-kinesin 01. But it is intriguing that a very short gene model is also a landmark of this Arabidopsis kinesin 1 (Richardson et al., 2006).


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 1s and armadillo repeat containing kinesins (ARKs). 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 1s and ARKs. Schematic diagrams showing the structure and domain architecture of kinesin 1s and armadillo repeat containing kinesins (ARKs). Domains are indicated at the bottom of the diagrams. Armadillo repeats are comprised of a repeating sequence of forty-two amino acids that can form helices which upon repetition form a right handed super helix.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: (A) Sub-region of the phylogenetic tree based on their motor domain showing kinesin 1s and armadillo repeat containing kinesins (ARKs). 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 1s and ARKs. Schematic diagrams showing the structure and domain architecture of kinesin 1s and armadillo repeat containing kinesins (ARKs). Domains are indicated at the bottom of the diagrams. Armadillo repeats are comprised of a repeating sequence of forty-two amino acids that can form helices which upon repetition form a right handed super helix.
Mentions: Phylogenetic analysis based on the motor domain indicates that there are five sequences in Physcomitrella related to the Arabidopsis ARK (Figure 1A). Four of these sequences are closely related to each other, forming a monophyletic group and their gene models show the presence of armadillo repeats (Figure 1B); we classified these as class I. The gene model for the fifth sequence is lacking the armadillo repeats that would confirm its identity as an armadillo repeat containing kinesin (Figure 1B); we tentatively classified this single kinesin as ARK-Like since the tree topology fails to confirm this kinesins as an ortholog of the lone At-kinesin 01. But it is intriguing that a very short gene model is also a landmark of this Arabidopsis kinesin 1 (Richardson et al., 2006).

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