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Calcareous sponge genomes reveal complex evolution of α-carbonic anhydrases and two key biomineralization enzymes.

Voigt O, Adamski M, Sluzek K, Adamska M - BMC Evol. Biol. (2014)

Bottom Line: We found that the CA repertoires of two calcareous sponge species are strikingly more complex than those of other sponges.The complex evolutionary history of the CA family is driven by frequent gene diversification and losses.These evolutionary patterns likely facilitated the numerous events of independent recruitment of CAs into biomineralization within Metazoa.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Calcium carbonate biominerals form often complex and beautiful skeletal elements, including coral exoskeletons and mollusc shells. Although the ability to generate these carbonate structures was apparently gained independently during animal evolution, it sometimes involves the same gene families. One of the best-studied of these gene families comprises the α- carbonic anhydrases (CAs), which catalyse the reversible transformation of CO2 to HCO3 - and fulfill many physiological functions. Among Porifera -the oldest animal phylum with the ability to produce skeletal elements- only the class of calcareous sponges can build calcitic spicules, which are the extracellular products of specialized cells, the sclerocytes. Little is known about the molecular mechanisms of their synthesis, but inhibition studies suggest an essential role of CAs. In order to gain insight into the evolution and function of CAs in biomineralization of a basal metazoan species, we determined the diversity and expression of CAs in the calcareous sponges Sycon ciliatum and Leucosolenia complicata by means of genomic screening, RNA-Seq and RNA in situ hybridization expression analysis. Active biomineralization was located with calcein-staining.

Results: We found that the CA repertoires of two calcareous sponge species are strikingly more complex than those of other sponges. By characterizing their expression patterns, we could link two CAs (one intracellular and one extracellular) to the process of calcite spicule formation in both studied species. The extracellular biomineralizing CAs seem to be of paralogous origin, a finding that advises caution against assuming functional conservation of biomineralizing genes based upon orthology assessment alone. Additionally, calcareous sponges possess acatalytic CAs related to human CAs X and XI, suggesting an ancient origin of these proteins. Phylogenetic analyses including CAs from genomes of all non-bilaterian phyla suggest multiple gene losses and duplications and presence of several CAs in the last common ancestor of metazoans.

Conclusions: We identified two key biomineralization enzymes from the CA-family in calcareous sponges and propose their possible interaction in spicule formation. The complex evolutionary history of the CA family is driven by frequent gene diversification and losses. These evolutionary patterns likely facilitated the numerous events of independent recruitment of CAs into biomineralization within Metazoa.

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CA evolution reconciled with three phylogentic hypotheses. (a) Three different phylogentic hypotheses for the relationships of non-bilaterian phyla used for tree-reconcilation. The number of inferred ortholog origins (corresponds to ‘co-speciation’ in the JANE software), gene duplications and gene losses are presented for each evolutionary scenario. Note that the numbers are similar regardless the underliyng phylogeny of phyla. (b) CA-evolution in Porifera as obtained under all three phylogenetic hypotheses presented in (a). Accordingly, eight CAs occurred in the last common ancestor of Porifera, of which several were lost in the different sponge lineages, followed by lineage-specific duplications. Three CA forms are in the last common ancestor gave rise to the three CA clades of Calcarea (CAL1-III, Figure 2). sclCA1 and L-CAs are recovered as orthologs in S. cilatum and L. complicata. A possible origin of ancestral scl-CA2 is indicated (orange). The monophyletic clades of demosponge and hexactinellid CAs (clade DEM and HEX, repectively in Figure 2) appears to be the result of substantial gene loss, followed by several duplications.
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Fig5: CA evolution reconciled with three phylogentic hypotheses. (a) Three different phylogentic hypotheses for the relationships of non-bilaterian phyla used for tree-reconcilation. The number of inferred ortholog origins (corresponds to ‘co-speciation’ in the JANE software), gene duplications and gene losses are presented for each evolutionary scenario. Note that the numbers are similar regardless the underliyng phylogeny of phyla. (b) CA-evolution in Porifera as obtained under all three phylogenetic hypotheses presented in (a). Accordingly, eight CAs occurred in the last common ancestor of Porifera, of which several were lost in the different sponge lineages, followed by lineage-specific duplications. Three CA forms are in the last common ancestor gave rise to the three CA clades of Calcarea (CAL1-III, Figure 2). sclCA1 and L-CAs are recovered as orthologs in S. cilatum and L. complicata. A possible origin of ancestral scl-CA2 is indicated (orange). The monophyletic clades of demosponge and hexactinellid CAs (clade DEM and HEX, repectively in Figure 2) appears to be the result of substantial gene loss, followed by several duplications.

Mentions: With the exceptions of Demospongiae and Hexactinellida, all included taxa possess more than one clade of CA, which must have arisen by CA duplications in early animal evolution. Also, species-specific or group-specific clades of CAs occur for all included taxa, suggesting a very frequent lineage-specific diversification of CA genes in animals. To gain further insight in CA evolution, we reconciled our CA phylogeny with two more recent hypotheses [41,42] and a more classical hypothesis about the relationships of non-bilaterian animals with methods provided in Jane 4 [43]. For each of the three phylogenetic hypotheses we visualized the potential CA gene histories, and found that in all cases frequent duplications and losses of CA genes can be observed (Figure 5a and Additional file 7). The reconstructions suggest that the last common ancestor of metazoans already possessed multiple CA genes, but the number of genes differs between the phylogenetic hypotheses (Additional file 7). Despite the underlying phyla-phylogeny, the presence of eight CAs in the common ancestor of sponges is reconstructed and identical gene histories within sponges are observed (Figure 5b). In each sponge class different ancestral CAs were lost, followed by a radiation from the remaining CA(s). At least three versions of CAs were present in the common ancestor of Calcarea, which were ancestral to L-CAs, scl-CA1 and to the CAs of clade CAL II, respectively. Clade CAL II includes scl-CA2, but within this gene lineage duplications and losses occurred after the common ancestor of S. ciliatum and L. complicata (Figure 5), which complicates ortholog assignment. According to our phylogenetic analyses and the tree reconciliation, scl-CA2 of S. ciliatum (SciCA2) and L. complicata (LcoCA3) are not of ortholog origin but instead might be out-paralogs, originating from a gene duplication that predated the speciation event (Figure 5b). The low support values and the differing topology of the Bayesian analyses, however, make unambiguous interpretations difficult. S. ciliatum scl-CA2 (SciCA2) and SciCA3 are in-paralogs, diverging from a lineage-specific duplication of an ancestral gene, and both are co-orthologs to LcoCA2 (Figure 5).Figure 5


Calcareous sponge genomes reveal complex evolution of α-carbonic anhydrases and two key biomineralization enzymes.

Voigt O, Adamski M, Sluzek K, Adamska M - BMC Evol. Biol. (2014)

CA evolution reconciled with three phylogentic hypotheses. (a) Three different phylogentic hypotheses for the relationships of non-bilaterian phyla used for tree-reconcilation. The number of inferred ortholog origins (corresponds to ‘co-speciation’ in the JANE software), gene duplications and gene losses are presented for each evolutionary scenario. Note that the numbers are similar regardless the underliyng phylogeny of phyla. (b) CA-evolution in Porifera as obtained under all three phylogenetic hypotheses presented in (a). Accordingly, eight CAs occurred in the last common ancestor of Porifera, of which several were lost in the different sponge lineages, followed by lineage-specific duplications. Three CA forms are in the last common ancestor gave rise to the three CA clades of Calcarea (CAL1-III, Figure 2). sclCA1 and L-CAs are recovered as orthologs in S. cilatum and L. complicata. A possible origin of ancestral scl-CA2 is indicated (orange). The monophyletic clades of demosponge and hexactinellid CAs (clade DEM and HEX, repectively in Figure 2) appears to be the result of substantial gene loss, followed by several duplications.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4265532&req=5

Fig5: CA evolution reconciled with three phylogentic hypotheses. (a) Three different phylogentic hypotheses for the relationships of non-bilaterian phyla used for tree-reconcilation. The number of inferred ortholog origins (corresponds to ‘co-speciation’ in the JANE software), gene duplications and gene losses are presented for each evolutionary scenario. Note that the numbers are similar regardless the underliyng phylogeny of phyla. (b) CA-evolution in Porifera as obtained under all three phylogenetic hypotheses presented in (a). Accordingly, eight CAs occurred in the last common ancestor of Porifera, of which several were lost in the different sponge lineages, followed by lineage-specific duplications. Three CA forms are in the last common ancestor gave rise to the three CA clades of Calcarea (CAL1-III, Figure 2). sclCA1 and L-CAs are recovered as orthologs in S. cilatum and L. complicata. A possible origin of ancestral scl-CA2 is indicated (orange). The monophyletic clades of demosponge and hexactinellid CAs (clade DEM and HEX, repectively in Figure 2) appears to be the result of substantial gene loss, followed by several duplications.
Mentions: With the exceptions of Demospongiae and Hexactinellida, all included taxa possess more than one clade of CA, which must have arisen by CA duplications in early animal evolution. Also, species-specific or group-specific clades of CAs occur for all included taxa, suggesting a very frequent lineage-specific diversification of CA genes in animals. To gain further insight in CA evolution, we reconciled our CA phylogeny with two more recent hypotheses [41,42] and a more classical hypothesis about the relationships of non-bilaterian animals with methods provided in Jane 4 [43]. For each of the three phylogenetic hypotheses we visualized the potential CA gene histories, and found that in all cases frequent duplications and losses of CA genes can be observed (Figure 5a and Additional file 7). The reconstructions suggest that the last common ancestor of metazoans already possessed multiple CA genes, but the number of genes differs between the phylogenetic hypotheses (Additional file 7). Despite the underlying phyla-phylogeny, the presence of eight CAs in the common ancestor of sponges is reconstructed and identical gene histories within sponges are observed (Figure 5b). In each sponge class different ancestral CAs were lost, followed by a radiation from the remaining CA(s). At least three versions of CAs were present in the common ancestor of Calcarea, which were ancestral to L-CAs, scl-CA1 and to the CAs of clade CAL II, respectively. Clade CAL II includes scl-CA2, but within this gene lineage duplications and losses occurred after the common ancestor of S. ciliatum and L. complicata (Figure 5), which complicates ortholog assignment. According to our phylogenetic analyses and the tree reconciliation, scl-CA2 of S. ciliatum (SciCA2) and L. complicata (LcoCA3) are not of ortholog origin but instead might be out-paralogs, originating from a gene duplication that predated the speciation event (Figure 5b). The low support values and the differing topology of the Bayesian analyses, however, make unambiguous interpretations difficult. S. ciliatum scl-CA2 (SciCA2) and SciCA3 are in-paralogs, diverging from a lineage-specific duplication of an ancestral gene, and both are co-orthologs to LcoCA2 (Figure 5).Figure 5

Bottom Line: We found that the CA repertoires of two calcareous sponge species are strikingly more complex than those of other sponges.The complex evolutionary history of the CA family is driven by frequent gene diversification and losses.These evolutionary patterns likely facilitated the numerous events of independent recruitment of CAs into biomineralization within Metazoa.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Calcium carbonate biominerals form often complex and beautiful skeletal elements, including coral exoskeletons and mollusc shells. Although the ability to generate these carbonate structures was apparently gained independently during animal evolution, it sometimes involves the same gene families. One of the best-studied of these gene families comprises the α- carbonic anhydrases (CAs), which catalyse the reversible transformation of CO2 to HCO3 - and fulfill many physiological functions. Among Porifera -the oldest animal phylum with the ability to produce skeletal elements- only the class of calcareous sponges can build calcitic spicules, which are the extracellular products of specialized cells, the sclerocytes. Little is known about the molecular mechanisms of their synthesis, but inhibition studies suggest an essential role of CAs. In order to gain insight into the evolution and function of CAs in biomineralization of a basal metazoan species, we determined the diversity and expression of CAs in the calcareous sponges Sycon ciliatum and Leucosolenia complicata by means of genomic screening, RNA-Seq and RNA in situ hybridization expression analysis. Active biomineralization was located with calcein-staining.

Results: We found that the CA repertoires of two calcareous sponge species are strikingly more complex than those of other sponges. By characterizing their expression patterns, we could link two CAs (one intracellular and one extracellular) to the process of calcite spicule formation in both studied species. The extracellular biomineralizing CAs seem to be of paralogous origin, a finding that advises caution against assuming functional conservation of biomineralizing genes based upon orthology assessment alone. Additionally, calcareous sponges possess acatalytic CAs related to human CAs X and XI, suggesting an ancient origin of these proteins. Phylogenetic analyses including CAs from genomes of all non-bilaterian phyla suggest multiple gene losses and duplications and presence of several CAs in the last common ancestor of metazoans.

Conclusions: We identified two key biomineralization enzymes from the CA-family in calcareous sponges and propose their possible interaction in spicule formation. The complex evolutionary history of the CA family is driven by frequent gene diversification and losses. These evolutionary patterns likely facilitated the numerous events of independent recruitment of CAs into biomineralization within Metazoa.

Show MeSH
Related in: MedlinePlus