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Molecular diversity of antimicrobial effectors in the oyster Crassostrea gigas.

Schmitt P, Gueguen Y, Desmarais E, Bachère E, de Lorgeril J - BMC Evol. Biol. (2010)

Bottom Line: To gain insight into the molecular diversity of antimicrobial peptides and proteins in the oyster Crassostrea gigas, we characterized and compared the sequence polymorphism of the antimicrobial peptides (AMPs), Cg-Defensins (Cg-Defs) and Cg-Proline Rich peptide (Cg-Prp), and of the bactericidal permeability increasing protein, Cg-BPI.High diversification among the three antimicrobial effectors was evidenced by this polymorphism survey.This study shows for the first time in a mollusc that antimicrobial peptides and proteins have been subject to distinct patterns of diversification and we evidence the existence of different evolutionary routes leading to such sequence variability.

View Article: PubMed Central - HTML - PubMed

Affiliation: Ifremer, CNRS, Université de Montpellier II, IRD, UMR 5119 Ecosystèmes Lagunaires, Place Eugène Bataillon, CC80, 34095 Montpellier, France. Julien.De.Lorgeril@ifremer.fr

ABSTRACT

Background: To gain insight into the molecular diversity of antimicrobial peptides and proteins in the oyster Crassostrea gigas, we characterized and compared the sequence polymorphism of the antimicrobial peptides (AMPs), Cg-Defensins (Cg-Defs) and Cg-Proline Rich peptide (Cg-Prp), and of the bactericidal permeability increasing protein, Cg-BPI. For that, we analyzed genomic and transcript sequences obtained by specific PCR amplification and in silico searches.

Results: High diversification among the three antimicrobial effectors was evidenced by this polymorphism survey. On the basis of sequence phylogenies, each AMP aggregates into clearly defined groups of variants and is the product of a multigenic family displaying a variety of gene structures. In contrast, Cg-bpi forms a single group and is encoded by a single gene copy. Moreover, we identified for both AMPs several genetic mechanisms of diversification such as recombination, parallel mutations leading to phylogenetic homoplasy and indel events. In addition, the non synonymous to synonymous substitutions ratio by codon (dN/dS) revealed several negatively and positively selected sites for both AMPs, suggesting that directional selection pressures have shaped their sequence variations.

Conclusions: This study shows for the first time in a mollusc that antimicrobial peptides and proteins have been subject to distinct patterns of diversification and we evidence the existence of different evolutionary routes leading to such sequence variability.

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Cladograms Cg-defs and Cg-prp and schematic representation of aligned CDS with synonymous and nonsynonymous substitutions. a. Cg-defs. b. Cg-prp. Identical sequences are grouped and the number is indicated at the right of each branch of cladograms and sequence symbols are the same as in figure 1. Nonsynonymous (blue boxes) and synonymous substitutions (yellow boxes) are localized over schematic alignment. Different groups of sequences (I, II and III) and obvious recombinants (R) are boxed. Indel events are represented by dark lines (Cg-prp) and striped box (Cg-defs) and circles indicate parallel homoplasic mutations. SP: signal peptide; MP: Mature peptide; AD: Anionic Domain; CD: Cationic Domain. For accurate comparison between AMPs, cladograms were drawn in the same scale.
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Figure 3: Cladograms Cg-defs and Cg-prp and schematic representation of aligned CDS with synonymous and nonsynonymous substitutions. a. Cg-defs. b. Cg-prp. Identical sequences are grouped and the number is indicated at the right of each branch of cladograms and sequence symbols are the same as in figure 1. Nonsynonymous (blue boxes) and synonymous substitutions (yellow boxes) are localized over schematic alignment. Different groups of sequences (I, II and III) and obvious recombinants (R) are boxed. Indel events are represented by dark lines (Cg-prp) and striped box (Cg-defs) and circles indicate parallel homoplasic mutations. SP: signal peptide; MP: Mature peptide; AD: Anionic Domain; CD: Cationic Domain. For accurate comparison between AMPs, cladograms were drawn in the same scale.

Mentions: The cDNA and gDNA sequence diversity and the variable gene copy number observed between C. gigas families of antimicrobials prompted us to investigate the genetic processes that participated to the diversification. Thus, we analyzed the repartition of synonymous and non synonymous substitutions in each group from AMP phylogenies (figure 3). Each group of Cg-defs presents a specific distribution of substitutions all along the CDS (figure 3a). Thus, Cg-defh1 is the most overall conserved antimicrobial peptide, with only a few numbers of substitutions. Cg-defh2, in contrast, presents a high number of synonymous substitutions and Cg-defm presents a profile which differs from hemocyte defensins with higher number of nonsynonymous substitutions. Cg-prp shows a different profile compared to Cg-defs in terms of the distribution of substitutions. Indeed, the substitutions localized in the signal and anionic peptide region are shared by groups, while substitutions in the cationic peptide region are specific of each group (figure 3b). Altogether, these results show the existence of different constraint levels between and within the groups of AMPs (Cg-defs and Cg-prp).


Molecular diversity of antimicrobial effectors in the oyster Crassostrea gigas.

Schmitt P, Gueguen Y, Desmarais E, Bachère E, de Lorgeril J - BMC Evol. Biol. (2010)

Cladograms Cg-defs and Cg-prp and schematic representation of aligned CDS with synonymous and nonsynonymous substitutions. a. Cg-defs. b. Cg-prp. Identical sequences are grouped and the number is indicated at the right of each branch of cladograms and sequence symbols are the same as in figure 1. Nonsynonymous (blue boxes) and synonymous substitutions (yellow boxes) are localized over schematic alignment. Different groups of sequences (I, II and III) and obvious recombinants (R) are boxed. Indel events are represented by dark lines (Cg-prp) and striped box (Cg-defs) and circles indicate parallel homoplasic mutations. SP: signal peptide; MP: Mature peptide; AD: Anionic Domain; CD: Cationic Domain. For accurate comparison between AMPs, cladograms were drawn in the same scale.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2823732&req=5

Figure 3: Cladograms Cg-defs and Cg-prp and schematic representation of aligned CDS with synonymous and nonsynonymous substitutions. a. Cg-defs. b. Cg-prp. Identical sequences are grouped and the number is indicated at the right of each branch of cladograms and sequence symbols are the same as in figure 1. Nonsynonymous (blue boxes) and synonymous substitutions (yellow boxes) are localized over schematic alignment. Different groups of sequences (I, II and III) and obvious recombinants (R) are boxed. Indel events are represented by dark lines (Cg-prp) and striped box (Cg-defs) and circles indicate parallel homoplasic mutations. SP: signal peptide; MP: Mature peptide; AD: Anionic Domain; CD: Cationic Domain. For accurate comparison between AMPs, cladograms were drawn in the same scale.
Mentions: The cDNA and gDNA sequence diversity and the variable gene copy number observed between C. gigas families of antimicrobials prompted us to investigate the genetic processes that participated to the diversification. Thus, we analyzed the repartition of synonymous and non synonymous substitutions in each group from AMP phylogenies (figure 3). Each group of Cg-defs presents a specific distribution of substitutions all along the CDS (figure 3a). Thus, Cg-defh1 is the most overall conserved antimicrobial peptide, with only a few numbers of substitutions. Cg-defh2, in contrast, presents a high number of synonymous substitutions and Cg-defm presents a profile which differs from hemocyte defensins with higher number of nonsynonymous substitutions. Cg-prp shows a different profile compared to Cg-defs in terms of the distribution of substitutions. Indeed, the substitutions localized in the signal and anionic peptide region are shared by groups, while substitutions in the cationic peptide region are specific of each group (figure 3b). Altogether, these results show the existence of different constraint levels between and within the groups of AMPs (Cg-defs and Cg-prp).

Bottom Line: To gain insight into the molecular diversity of antimicrobial peptides and proteins in the oyster Crassostrea gigas, we characterized and compared the sequence polymorphism of the antimicrobial peptides (AMPs), Cg-Defensins (Cg-Defs) and Cg-Proline Rich peptide (Cg-Prp), and of the bactericidal permeability increasing protein, Cg-BPI.High diversification among the three antimicrobial effectors was evidenced by this polymorphism survey.This study shows for the first time in a mollusc that antimicrobial peptides and proteins have been subject to distinct patterns of diversification and we evidence the existence of different evolutionary routes leading to such sequence variability.

View Article: PubMed Central - HTML - PubMed

Affiliation: Ifremer, CNRS, Université de Montpellier II, IRD, UMR 5119 Ecosystèmes Lagunaires, Place Eugène Bataillon, CC80, 34095 Montpellier, France. Julien.De.Lorgeril@ifremer.fr

ABSTRACT

Background: To gain insight into the molecular diversity of antimicrobial peptides and proteins in the oyster Crassostrea gigas, we characterized and compared the sequence polymorphism of the antimicrobial peptides (AMPs), Cg-Defensins (Cg-Defs) and Cg-Proline Rich peptide (Cg-Prp), and of the bactericidal permeability increasing protein, Cg-BPI. For that, we analyzed genomic and transcript sequences obtained by specific PCR amplification and in silico searches.

Results: High diversification among the three antimicrobial effectors was evidenced by this polymorphism survey. On the basis of sequence phylogenies, each AMP aggregates into clearly defined groups of variants and is the product of a multigenic family displaying a variety of gene structures. In contrast, Cg-bpi forms a single group and is encoded by a single gene copy. Moreover, we identified for both AMPs several genetic mechanisms of diversification such as recombination, parallel mutations leading to phylogenetic homoplasy and indel events. In addition, the non synonymous to synonymous substitutions ratio by codon (dN/dS) revealed several negatively and positively selected sites for both AMPs, suggesting that directional selection pressures have shaped their sequence variations.

Conclusions: This study shows for the first time in a mollusc that antimicrobial peptides and proteins have been subject to distinct patterns of diversification and we evidence the existence of different evolutionary routes leading to such sequence variability.

Show MeSH