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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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Gene organization of Cg-defs and Cg-prp from C. gigas. a. Cg-prp genomic structures. Black boxes indicate signal peptide region; white boxes indicate anionic domain region and striped boxes indicate cationic domain region. b. Cg-defhs and Cg-defm gene structures. Black boxes indicate signal peptide region and white boxes indicate mature peptide region. Numbers indicate the length of exons and introns (bases pairs). Note the gene size is not to scale.
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Figure 2: Gene organization of Cg-defs and Cg-prp from C. gigas. a. Cg-prp genomic structures. Black boxes indicate signal peptide region; white boxes indicate anionic domain region and striped boxes indicate cationic domain region. b. Cg-defhs and Cg-defm gene structures. Black boxes indicate signal peptide region and white boxes indicate mature peptide region. Numbers indicate the length of exons and introns (bases pairs). Note the gene size is not to scale.

Mentions: Because both Cg-defs and Cg-prp AMPs are present as multigene families, we also characterized their gene structure by exhaustive gDNA sequencing from one individual. The genomic organization of Cg-prp and Cg-defs revealed two different structures for Cg-prp and one single structure for Cg-defs (Figure 2). The two structures of Cg-prp correspond either to genes with or without an intron, both arrangements coding for the long and short peptide variants. All Cg-prp genes containing the intron have the same exonic organization. Exon 1 contains the sequence encoding the signal peptide and half of the residues of the anionic domain (103 bp) while exon 2 encodes the end of the anionic domain and the cationic domain region (177-183 bp) (figure 2a). Nevertheless, we identified several indel events between introns of long and short variants. In addition, intron sequences of short Cg-prp variants showed length variations ranging from 571 to 588 bp and multiple SNPs. In contrast to Cg-prp, we found a single genomic structure for Cg-defs. Exon 1 contains the sequence encoding part of the signal peptide (43 bp) and exon 2 encodes the remaining part of the signal peptide region and the mature peptide region (149 bp), except for the last two residues encoded by exon 3 (5 bp) (figure 2b). However, no homology was found between intron sequences of Cgdefm and Cg-defhs, confirming thus the very ancient divergence time between the two lineages of these genes. Moreover, introns between Cg-defm and Cg-defhs differ by length variations. Cg-defs and Cg-prp AMP genes contain canonical GT/AG splicing recognition sequence located at the end of each intron.


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)

Gene organization of Cg-defs and Cg-prp from C. gigas. a. Cg-prp genomic structures. Black boxes indicate signal peptide region; white boxes indicate anionic domain region and striped boxes indicate cationic domain region. b. Cg-defhs and Cg-defm gene structures. Black boxes indicate signal peptide region and white boxes indicate mature peptide region. Numbers indicate the length of exons and introns (bases pairs). Note the gene size is not to scale.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Gene organization of Cg-defs and Cg-prp from C. gigas. a. Cg-prp genomic structures. Black boxes indicate signal peptide region; white boxes indicate anionic domain region and striped boxes indicate cationic domain region. b. Cg-defhs and Cg-defm gene structures. Black boxes indicate signal peptide region and white boxes indicate mature peptide region. Numbers indicate the length of exons and introns (bases pairs). Note the gene size is not to scale.
Mentions: Because both Cg-defs and Cg-prp AMPs are present as multigene families, we also characterized their gene structure by exhaustive gDNA sequencing from one individual. The genomic organization of Cg-prp and Cg-defs revealed two different structures for Cg-prp and one single structure for Cg-defs (Figure 2). The two structures of Cg-prp correspond either to genes with or without an intron, both arrangements coding for the long and short peptide variants. All Cg-prp genes containing the intron have the same exonic organization. Exon 1 contains the sequence encoding the signal peptide and half of the residues of the anionic domain (103 bp) while exon 2 encodes the end of the anionic domain and the cationic domain region (177-183 bp) (figure 2a). Nevertheless, we identified several indel events between introns of long and short variants. In addition, intron sequences of short Cg-prp variants showed length variations ranging from 571 to 588 bp and multiple SNPs. In contrast to Cg-prp, we found a single genomic structure for Cg-defs. Exon 1 contains the sequence encoding part of the signal peptide (43 bp) and exon 2 encodes the remaining part of the signal peptide region and the mature peptide region (149 bp), except for the last two residues encoded by exon 3 (5 bp) (figure 2b). However, no homology was found between intron sequences of Cgdefm and Cg-defhs, confirming thus the very ancient divergence time between the two lineages of these genes. Moreover, introns between Cg-defm and Cg-defhs differ by length variations. Cg-defs and Cg-prp AMP genes contain canonical GT/AG splicing recognition sequence located at the end of each intron.

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