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Evolutionary analysis of WD40 super family proteins involved in spindle checkpoint and RNA export: molecular evolution of spindle checkpoint.

Reddy DM, Aspatwar A, Dholakia BB, Gupta VS - Bioinformation (2008)

Bottom Line: Amino acid sequences of BUB3 and Rae1 homologs were retrieved from various databases and phylogenetic analysis was performed with the MEGA program.Multiple sequence alignments of these two protein homologues with the ClustalX software revealed specific amino acid signatures corresponding to the protein function and also few amino acids, which are conserved in BUB3 and Rae1 indicating some common overlapping function.Data indicated a common ancestral origin of these two important proteins and further suggest that, BUB3 mediated cell cycle checkpoint might have evolved with compartmentalization of genetic material into the nucleus in eukaryotes.

View Article: PubMed Central - PubMed

Affiliation: Plant Molecular Biology Unit, Division of Biochemical Sciences, National Chemical Laboratory, Pune 411008, India.

ABSTRACT
The spindle checkpoint delays sister chromatid separation until all chromosomes have undergone bipolar spindle attachment. Previous studies have revealed BUB3, as an essential spindle checkpoint protein and its extensive sequence similarity with Rae1 (Gle2), a highly conserved member of WD40 repeat protein family throughout their length which was first shown to be involved in mRNA export. However, the recent discovery of Rae1 as an essential mitotic checkpoint protein, based on the studies from mouse and drosophila, has renewed the interest in its function during cell division. Study of evolution of proteins involved in checkpoint might throw light on evolution of eukaryotic cell cycle regulation. Here we report the evolutionary relationships between these two WD40 repeat family proteins. Amino acid sequences of BUB3 and Rae1 homologs were retrieved from various databases and phylogenetic analysis was performed with the MEGA program. Multiple sequence alignments of these two protein homologues with the ClustalX software revealed specific amino acid signatures corresponding to the protein function and also few amino acids, which are conserved in BUB3 and Rae1 indicating some common overlapping function. Data indicated a common ancestral origin of these two important proteins and further suggest that, BUB3 mediated cell cycle checkpoint might have evolved with compartmentalization of genetic material into the nucleus in eukaryotes.

No MeSH data available.


Related in: MedlinePlus

Domain analysis with different BUB3 proteins from various organisms. Filled boxes with blue color represent WD40 domains. Domains with red line represent BUB3 like proteins while Rae1 like proteins with green lines. The proteins having both the activity are in brown lines.
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Related In: Results  -  Collection


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Figure 1: Domain analysis with different BUB3 proteins from various organisms. Filled boxes with blue color represent WD40 domains. Domains with red line represent BUB3 like proteins while Rae1 like proteins with green lines. The proteins having both the activity are in brown lines.

Mentions: We also carried out domain analysis of BUB3 and Rae1 proteins from various organisms from fungi, yeast, plants, vertebrates, invertebrates and archaea bacteria. Figure 1 gives the representative organization and number of WD40 repeats in various proteins from different taxa. Result showed that, archaea bacteria had only a single copy of WD40 protein with sixteen WD40 domains that might be involved in different cellular functions. Later on the number of WD40 repeat domain reduced down to three/four in BUB3/Rae1 in fungi. There after the number increased to four/five in BUB3 of plants and humans. But in Rae1 the number of WD40 repeats in plants was five and in humans it was four. However, in C. elegans the BUB3 protein had five WD40 repeats and Rae1 had only four. The probable reason for decrease in the number of WD40 repeats, compared to archaea in eukaryotes could be their specialization in specific cellular processes. In the two microsporidial proteins, one protein had only two and the other was having the three WD40 domains while the protein of T. curvata seven WD40 repeat domains. It is central assumption of evolution that gene duplications provide the genetic raw material to create proteins with new functions. As these homologs evolved in higher eukaryotes, they acquired some additional domains such as C-terminal carboxidase and PPAT domains, which might have specific function. We had eliminated four such proteins from final phylogenetic analysis as they were forming a separate cluster in the cladogram assuming that these proteins, which are hypothetical and do not have any functional characterization except the homology prediction. Compilation and analysis of amino acid sequences of a particular protein from a variety of biological sources can provide us with the amino acid sequence signatures that are important for the function of that protein. Keeping this in view a closer examination of aligned amino acid sequence alignments was performed. In agreement with the earlier studies the sequence homology extended over the entire protein length with semi-conserved substitutions and was especially high in the segment that links WD40 repeats 3 and 4 (Figure 2) between the two groups of proteins. This analysis revealed specific amino acid signatures in terms of conserved amino acids at specific sites in the given groups of proteins. As shown in Figure 2 the entire Rae1 group proteins had phenylalanine (F) (marked with ↓ in Figure 2) while BUB3 proteins had mainly leucine (L) and isoleucine (I). Similarly tyrosine (Y) was identified in all Rae1 like proteins, with alanine (A) on either side. In case of BUB3 proteins, this tyrosine was replaced with either isoleucine (I), valine (V) or leucine (L) at the same position (marked with * in Figure 2). In earlier analysis, glycine (G) had been shown as conserved amino acid in all Rae1 homologs and this was not conserved in the BUB3 proteins [12]. Our analysis with the homologues from Rae1 and BUB3 also showed the same conservation for glycine in all the Rae1 proteins. Probably this glycine might have active site role in Rae1, as the change of glycine to glutamic acid in Rae1-1 mutant of S. pombe resulted in loss of function [7]. Additionally, we identified phenylalanine (an aromatic amino acid) in all the BUB3 proteins and even in E. cuniculi Rae1 (data not shown) protein. This result indicated that E. cuniculi Rae1 protein (Q8SRM6) might have role in cell division activity (see phylogenetic analysis for more supporting evidence) and further it might have evolved with more specific activity such as mitotic spindle checkpoint protein in eukaryotes.


Evolutionary analysis of WD40 super family proteins involved in spindle checkpoint and RNA export: molecular evolution of spindle checkpoint.

Reddy DM, Aspatwar A, Dholakia BB, Gupta VS - Bioinformation (2008)

Domain analysis with different BUB3 proteins from various organisms. Filled boxes with blue color represent WD40 domains. Domains with red line represent BUB3 like proteins while Rae1 like proteins with green lines. The proteins having both the activity are in brown lines.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2561167&req=5

Figure 1: Domain analysis with different BUB3 proteins from various organisms. Filled boxes with blue color represent WD40 domains. Domains with red line represent BUB3 like proteins while Rae1 like proteins with green lines. The proteins having both the activity are in brown lines.
Mentions: We also carried out domain analysis of BUB3 and Rae1 proteins from various organisms from fungi, yeast, plants, vertebrates, invertebrates and archaea bacteria. Figure 1 gives the representative organization and number of WD40 repeats in various proteins from different taxa. Result showed that, archaea bacteria had only a single copy of WD40 protein with sixteen WD40 domains that might be involved in different cellular functions. Later on the number of WD40 repeat domain reduced down to three/four in BUB3/Rae1 in fungi. There after the number increased to four/five in BUB3 of plants and humans. But in Rae1 the number of WD40 repeats in plants was five and in humans it was four. However, in C. elegans the BUB3 protein had five WD40 repeats and Rae1 had only four. The probable reason for decrease in the number of WD40 repeats, compared to archaea in eukaryotes could be their specialization in specific cellular processes. In the two microsporidial proteins, one protein had only two and the other was having the three WD40 domains while the protein of T. curvata seven WD40 repeat domains. It is central assumption of evolution that gene duplications provide the genetic raw material to create proteins with new functions. As these homologs evolved in higher eukaryotes, they acquired some additional domains such as C-terminal carboxidase and PPAT domains, which might have specific function. We had eliminated four such proteins from final phylogenetic analysis as they were forming a separate cluster in the cladogram assuming that these proteins, which are hypothetical and do not have any functional characterization except the homology prediction. Compilation and analysis of amino acid sequences of a particular protein from a variety of biological sources can provide us with the amino acid sequence signatures that are important for the function of that protein. Keeping this in view a closer examination of aligned amino acid sequence alignments was performed. In agreement with the earlier studies the sequence homology extended over the entire protein length with semi-conserved substitutions and was especially high in the segment that links WD40 repeats 3 and 4 (Figure 2) between the two groups of proteins. This analysis revealed specific amino acid signatures in terms of conserved amino acids at specific sites in the given groups of proteins. As shown in Figure 2 the entire Rae1 group proteins had phenylalanine (F) (marked with ↓ in Figure 2) while BUB3 proteins had mainly leucine (L) and isoleucine (I). Similarly tyrosine (Y) was identified in all Rae1 like proteins, with alanine (A) on either side. In case of BUB3 proteins, this tyrosine was replaced with either isoleucine (I), valine (V) or leucine (L) at the same position (marked with * in Figure 2). In earlier analysis, glycine (G) had been shown as conserved amino acid in all Rae1 homologs and this was not conserved in the BUB3 proteins [12]. Our analysis with the homologues from Rae1 and BUB3 also showed the same conservation for glycine in all the Rae1 proteins. Probably this glycine might have active site role in Rae1, as the change of glycine to glutamic acid in Rae1-1 mutant of S. pombe resulted in loss of function [7]. Additionally, we identified phenylalanine (an aromatic amino acid) in all the BUB3 proteins and even in E. cuniculi Rae1 (data not shown) protein. This result indicated that E. cuniculi Rae1 protein (Q8SRM6) might have role in cell division activity (see phylogenetic analysis for more supporting evidence) and further it might have evolved with more specific activity such as mitotic spindle checkpoint protein in eukaryotes.

Bottom Line: Amino acid sequences of BUB3 and Rae1 homologs were retrieved from various databases and phylogenetic analysis was performed with the MEGA program.Multiple sequence alignments of these two protein homologues with the ClustalX software revealed specific amino acid signatures corresponding to the protein function and also few amino acids, which are conserved in BUB3 and Rae1 indicating some common overlapping function.Data indicated a common ancestral origin of these two important proteins and further suggest that, BUB3 mediated cell cycle checkpoint might have evolved with compartmentalization of genetic material into the nucleus in eukaryotes.

View Article: PubMed Central - PubMed

Affiliation: Plant Molecular Biology Unit, Division of Biochemical Sciences, National Chemical Laboratory, Pune 411008, India.

ABSTRACT
The spindle checkpoint delays sister chromatid separation until all chromosomes have undergone bipolar spindle attachment. Previous studies have revealed BUB3, as an essential spindle checkpoint protein and its extensive sequence similarity with Rae1 (Gle2), a highly conserved member of WD40 repeat protein family throughout their length which was first shown to be involved in mRNA export. However, the recent discovery of Rae1 as an essential mitotic checkpoint protein, based on the studies from mouse and drosophila, has renewed the interest in its function during cell division. Study of evolution of proteins involved in checkpoint might throw light on evolution of eukaryotic cell cycle regulation. Here we report the evolutionary relationships between these two WD40 repeat family proteins. Amino acid sequences of BUB3 and Rae1 homologs were retrieved from various databases and phylogenetic analysis was performed with the MEGA program. Multiple sequence alignments of these two protein homologues with the ClustalX software revealed specific amino acid signatures corresponding to the protein function and also few amino acids, which are conserved in BUB3 and Rae1 indicating some common overlapping function. Data indicated a common ancestral origin of these two important proteins and further suggest that, BUB3 mediated cell cycle checkpoint might have evolved with compartmentalization of genetic material into the nucleus in eukaryotes.

No MeSH data available.


Related in: MedlinePlus