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Assembling an arsenal, the scorpion way.

Kozminsky-Atias A, Bar-Shalom A, Mishmar D, Zilberberg N - BMC Evol. Biol. (2008)

Bottom Line: Upon fixation, the mature toxin-coding domain was subjected to diversifying selection resulting in a significantly higher substitution rate that can be explained solely by diversifying selection.We interpret this as resulting from purifying selection acting on both the peptide and, as reported here for the first time, the DNA sequence, to create a toxin family-specific codon bias.We thus propose that scorpion toxin genes were shaped by selective forces acting at three levels, namely (1) diversifying the mature toxin, (2) conserving the leader peptide amino acid sequence and intriguingly, (3) conserving the leader DNA sequences.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel. adiko@bgu.ac.il

ABSTRACT

Background: For survival, scorpions depend on a wide array of short neurotoxic polypeptides. The venoms of scorpions from the most studied group, the Buthida, are a rich source of small, 23-78 amino acid-long peptides, well packed by either three or four disulfide bridges that affect ion channel function in excitable and non-excitable cells.

Results: In this work, by constructing a toxin transcripts data set from the venom gland of the scorpion Buthus occitanus israelis, we were able to follow the evolutionary path leading to mature toxin diversification and suggest a mechanism for leader peptide hyper-conservation. Toxins from each family were more closely related to one another than to toxins from other species, implying that fixation of duplicated genes followed speciation, suggesting early gene conversion events. Upon fixation, the mature toxin-coding domain was subjected to diversifying selection resulting in a significantly higher substitution rate that can be explained solely by diversifying selection. In contrast to the mature peptide, the leader peptide sequence was hyper-conserved and characterized by an atypical sub-neutral synonymous substitution rate. We interpret this as resulting from purifying selection acting on both the peptide and, as reported here for the first time, the DNA sequence, to create a toxin family-specific codon bias.

Conclusion: We thus propose that scorpion toxin genes were shaped by selective forces acting at three levels, namely (1) diversifying the mature toxin, (2) conserving the leader peptide amino acid sequence and intriguingly, (3) conserving the leader DNA sequences.

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Codon usage of leucine residues at the different gene domains. The codon usage of leucine residues within the leader-coding regions of the depressant and α-toxin families is compared to that of the mature-coding domain of all toxins within the data set.
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Figure 7: Codon usage of leucine residues at the different gene domains. The codon usage of leucine residues within the leader-coding regions of the depressant and α-toxin families is compared to that of the mature-coding domain of all toxins within the data set.

Mentions: Toxin family-specific amino acid conservation within the leader peptide is apparent in the venoms of scorpions, cone snails [11,18], snakes and spiders. This is surprising as in most secreted proteins, only very basic biochemical characteristics of the leader peptide are maintained, with the amino acid sequence being variable [37]. We thus proceeded to elucidate a possible rationale for the amino acid conservation within the leader peptides of toxins. A strong negative selection was observed for most leader peptide residues within Boi toxin genes, specifically at the amino terminal (Fig. 4A). Is this the only force imposing strong nucleotide conservation in this gene domain? Examining the neutral substitution rate of the leader (within the wobble position at negatively selected sites) revealed a substantially lower rate than that of the neutral intron (Fig. 6A), implying the existence of purifying selection against synonymous sites. This is probably not the consequence of a recent exon-specific gene conversion, as certain residues within this region are relatively variable (Fig. 4A). We examined the codon usage within the leader of each of the two main toxin families (depressant and α-toxins) and identified a family-specific pattern. This pattern was unique to each family and different from that of the mature-coding domain of each family and of the combined data set of all Boi mature toxin-coding regions. This observation was statistically significant (chi square-test, p < 0.001). On the other hand, the codon usage of the mature toxin coding domain of each of the families was not significantly different than that of the entire Boi mature toxin coding regions data set. For example, the most frequently used codon for leucine, the most abundant amino acid within the leader, for α-toxin is UUG. By contrast, this codon is hardly used in the depressant toxin leader sequence (Fig. 7). The rarely used codons, CUG and CUC, are abundant within the depressant and α-toxin leader sequences, respectively (Fig. 7).


Assembling an arsenal, the scorpion way.

Kozminsky-Atias A, Bar-Shalom A, Mishmar D, Zilberberg N - BMC Evol. Biol. (2008)

Codon usage of leucine residues at the different gene domains. The codon usage of leucine residues within the leader-coding regions of the depressant and α-toxin families is compared to that of the mature-coding domain of all toxins within the data set.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651877&req=5

Figure 7: Codon usage of leucine residues at the different gene domains. The codon usage of leucine residues within the leader-coding regions of the depressant and α-toxin families is compared to that of the mature-coding domain of all toxins within the data set.
Mentions: Toxin family-specific amino acid conservation within the leader peptide is apparent in the venoms of scorpions, cone snails [11,18], snakes and spiders. This is surprising as in most secreted proteins, only very basic biochemical characteristics of the leader peptide are maintained, with the amino acid sequence being variable [37]. We thus proceeded to elucidate a possible rationale for the amino acid conservation within the leader peptides of toxins. A strong negative selection was observed for most leader peptide residues within Boi toxin genes, specifically at the amino terminal (Fig. 4A). Is this the only force imposing strong nucleotide conservation in this gene domain? Examining the neutral substitution rate of the leader (within the wobble position at negatively selected sites) revealed a substantially lower rate than that of the neutral intron (Fig. 6A), implying the existence of purifying selection against synonymous sites. This is probably not the consequence of a recent exon-specific gene conversion, as certain residues within this region are relatively variable (Fig. 4A). We examined the codon usage within the leader of each of the two main toxin families (depressant and α-toxins) and identified a family-specific pattern. This pattern was unique to each family and different from that of the mature-coding domain of each family and of the combined data set of all Boi mature toxin-coding regions. This observation was statistically significant (chi square-test, p < 0.001). On the other hand, the codon usage of the mature toxin coding domain of each of the families was not significantly different than that of the entire Boi mature toxin coding regions data set. For example, the most frequently used codon for leucine, the most abundant amino acid within the leader, for α-toxin is UUG. By contrast, this codon is hardly used in the depressant toxin leader sequence (Fig. 7). The rarely used codons, CUG and CUC, are abundant within the depressant and α-toxin leader sequences, respectively (Fig. 7).

Bottom Line: Upon fixation, the mature toxin-coding domain was subjected to diversifying selection resulting in a significantly higher substitution rate that can be explained solely by diversifying selection.We interpret this as resulting from purifying selection acting on both the peptide and, as reported here for the first time, the DNA sequence, to create a toxin family-specific codon bias.We thus propose that scorpion toxin genes were shaped by selective forces acting at three levels, namely (1) diversifying the mature toxin, (2) conserving the leader peptide amino acid sequence and intriguingly, (3) conserving the leader DNA sequences.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel. adiko@bgu.ac.il

ABSTRACT

Background: For survival, scorpions depend on a wide array of short neurotoxic polypeptides. The venoms of scorpions from the most studied group, the Buthida, are a rich source of small, 23-78 amino acid-long peptides, well packed by either three or four disulfide bridges that affect ion channel function in excitable and non-excitable cells.

Results: In this work, by constructing a toxin transcripts data set from the venom gland of the scorpion Buthus occitanus israelis, we were able to follow the evolutionary path leading to mature toxin diversification and suggest a mechanism for leader peptide hyper-conservation. Toxins from each family were more closely related to one another than to toxins from other species, implying that fixation of duplicated genes followed speciation, suggesting early gene conversion events. Upon fixation, the mature toxin-coding domain was subjected to diversifying selection resulting in a significantly higher substitution rate that can be explained solely by diversifying selection. In contrast to the mature peptide, the leader peptide sequence was hyper-conserved and characterized by an atypical sub-neutral synonymous substitution rate. We interpret this as resulting from purifying selection acting on both the peptide and, as reported here for the first time, the DNA sequence, to create a toxin family-specific codon bias.

Conclusion: We thus propose that scorpion toxin genes were shaped by selective forces acting at three levels, namely (1) diversifying the mature toxin, (2) conserving the leader peptide amino acid sequence and intriguingly, (3) conserving the leader DNA sequences.

Show MeSH
Related in: MedlinePlus