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Characterization of the definitive classical calpain family of vertebrates using phylogenetic, evolutionary and expression analyses.

Macqueen DJ, Wilcox AH - Open Biol (2014)

Bottom Line: We reveal that while all vertebrate classical calpains have been subject to persistent purifying selection during evolution, the degree and nature of selective pressure has often been lineage-dependent.This highlighted systematic divergence in expression across vertebrate taxa, with most classic calpain genes from fish and amphibians having more extensive tissue distribution than in amniotes.Our data suggest that classical calpain functions have frequently diverged during vertebrate evolution and challenge the ongoing value of the established system of classifying calpains by expression.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen AB24 2TZ, UK.

ABSTRACT
The calpains are a superfamily of proteases with extensive relevance to human health and welfare. Vast research attention is given to the vertebrate 'classical' subfamily, making it surprising that the evolutionary origins, distribution and relationships of these genes is poorly characterized. Consequently, there exists uncertainty about the conservation of gene family structure, function and expression that has been principally defined from work with mammals. Here, more than 200 vertebrate classical calpains were incorporated in phylogenetic analyses spanning an unprecedented range of taxa, including jawless and cartilaginous fish. We demonstrate that the common vertebrate ancestor had at least six classical calpains, including a single gene that gave rise to CAPN11, 1, 2 and 8 in the early jawed fish lineage, plus CAPN3, 9, 12, 13 and a novel calpain gene, hereafter named CAPN17. We reveal that while all vertebrate classical calpains have been subject to persistent purifying selection during evolution, the degree and nature of selective pressure has often been lineage-dependent. The tissue expression of the complete classic calpain family was assessed in representative teleost fish, amphibians, reptiles and mammals. This highlighted systematic divergence in expression across vertebrate taxa, with most classic calpain genes from fish and amphibians having more extensive tissue distribution than in amniotes. Our data suggest that classical calpain functions have frequently diverged during vertebrate evolution and challenge the ongoing value of the established system of classifying calpains by expression.

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EST profiles approximating the mRNA transcript levels of classical calpain family members in human tissues. The size of each dot represents the number of ESTs representing separate family members divided by the total number of ESTs for each tissue. Phylogenetic relationships of different classical calpains are shown.
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RSOB130219F6: EST profiles approximating the mRNA transcript levels of classical calpain family members in human tissues. The size of each dot represents the number of ESTs representing separate family members divided by the total number of ESTs for each tissue. Phylogenetic relationships of different classical calpains are shown.

Mentions: Next, we explored classical calpain gene tissue expression in humans exploiting EST profiles (figure 6). While this approach suffers from potential biases, it is reliable in a global sense, considering that 45 human tissues are represented by more than 100 000 ESTs on average. Two included control housekeeping genes had ubiquitous expression profiles, and all classical calpain genes were expressed in multiple tissues, with considerable variation in expression breadth (figure 6). As shown independently [10], CAPN1 and 2 mRNA was not ubiquitous, being absent in a limited number of tissues, but nevertheless, it was considerably broader than the other classical calpains (figure 6). CAPN3 was expressed in 26 of 45 tissues, inconsistent with a ‘muscle-specific’ classification [1,2] (figure 6). Interestingly, human CAPN3 is more highly represented in skin than muscle ESTs (figure 6). While CAPN8 and CAPN9, as expected, were expressed in tissues of the gastrointestinal tract [1,2], there was also expression outside this system (figure 6). CAPN11 mRNA was not restricted to testis [1,2] (figure 6). CAPN12 was expressed in 16 of 45 tissues, again inconsistent with its classification [1,2]. CAPN13 and 14 were expressed in 16 and five of 45 tissues, respectively (figure 6).Figure 6.


Characterization of the definitive classical calpain family of vertebrates using phylogenetic, evolutionary and expression analyses.

Macqueen DJ, Wilcox AH - Open Biol (2014)

EST profiles approximating the mRNA transcript levels of classical calpain family members in human tissues. The size of each dot represents the number of ESTs representing separate family members divided by the total number of ESTs for each tissue. Phylogenetic relationships of different classical calpains are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4043111&req=5

RSOB130219F6: EST profiles approximating the mRNA transcript levels of classical calpain family members in human tissues. The size of each dot represents the number of ESTs representing separate family members divided by the total number of ESTs for each tissue. Phylogenetic relationships of different classical calpains are shown.
Mentions: Next, we explored classical calpain gene tissue expression in humans exploiting EST profiles (figure 6). While this approach suffers from potential biases, it is reliable in a global sense, considering that 45 human tissues are represented by more than 100 000 ESTs on average. Two included control housekeeping genes had ubiquitous expression profiles, and all classical calpain genes were expressed in multiple tissues, with considerable variation in expression breadth (figure 6). As shown independently [10], CAPN1 and 2 mRNA was not ubiquitous, being absent in a limited number of tissues, but nevertheless, it was considerably broader than the other classical calpains (figure 6). CAPN3 was expressed in 26 of 45 tissues, inconsistent with a ‘muscle-specific’ classification [1,2] (figure 6). Interestingly, human CAPN3 is more highly represented in skin than muscle ESTs (figure 6). While CAPN8 and CAPN9, as expected, were expressed in tissues of the gastrointestinal tract [1,2], there was also expression outside this system (figure 6). CAPN11 mRNA was not restricted to testis [1,2] (figure 6). CAPN12 was expressed in 16 of 45 tissues, again inconsistent with its classification [1,2]. CAPN13 and 14 were expressed in 16 and five of 45 tissues, respectively (figure 6).Figure 6.

Bottom Line: We reveal that while all vertebrate classical calpains have been subject to persistent purifying selection during evolution, the degree and nature of selective pressure has often been lineage-dependent.This highlighted systematic divergence in expression across vertebrate taxa, with most classic calpain genes from fish and amphibians having more extensive tissue distribution than in amniotes.Our data suggest that classical calpain functions have frequently diverged during vertebrate evolution and challenge the ongoing value of the established system of classifying calpains by expression.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen AB24 2TZ, UK.

ABSTRACT
The calpains are a superfamily of proteases with extensive relevance to human health and welfare. Vast research attention is given to the vertebrate 'classical' subfamily, making it surprising that the evolutionary origins, distribution and relationships of these genes is poorly characterized. Consequently, there exists uncertainty about the conservation of gene family structure, function and expression that has been principally defined from work with mammals. Here, more than 200 vertebrate classical calpains were incorporated in phylogenetic analyses spanning an unprecedented range of taxa, including jawless and cartilaginous fish. We demonstrate that the common vertebrate ancestor had at least six classical calpains, including a single gene that gave rise to CAPN11, 1, 2 and 8 in the early jawed fish lineage, plus CAPN3, 9, 12, 13 and a novel calpain gene, hereafter named CAPN17. We reveal that while all vertebrate classical calpains have been subject to persistent purifying selection during evolution, the degree and nature of selective pressure has often been lineage-dependent. The tissue expression of the complete classic calpain family was assessed in representative teleost fish, amphibians, reptiles and mammals. This highlighted systematic divergence in expression across vertebrate taxa, with most classic calpain genes from fish and amphibians having more extensive tissue distribution than in amniotes. Our data suggest that classical calpain functions have frequently diverged during vertebrate evolution and challenge the ongoing value of the established system of classifying calpains by expression.

Show MeSH