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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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Non-synonymous versus synonymous substitutions in the depressant toxin family. dN over dS in intrafamilial comparisons of the leader and mature toxin coding domains. (A) Residue specific plot. Leader and mature residues are indicated by white and gray bars, respectively. Cysteine residues are indicated by yellow bars. (B) Matrix alignment plots were utilized to establish the correlation between the synonymous substitution rates and dN/dS ratios. Two lines distinguishes between values indicating positive (>1), neutral (0.6–1) and negative (<0.6) selections.
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Figure 4: Non-synonymous versus synonymous substitutions in the depressant toxin family. dN over dS in intrafamilial comparisons of the leader and mature toxin coding domains. (A) Residue specific plot. Leader and mature residues are indicated by white and gray bars, respectively. Cysteine residues are indicated by yellow bars. (B) Matrix alignment plots were utilized to establish the correlation between the synonymous substitution rates and dN/dS ratios. Two lines distinguishes between values indicating positive (>1), neutral (0.6–1) and negative (<0.6) selections.

Mentions: Positive selection has been suggested as playing a decisive role in the diversification of mature toxins in gene families of cone snails, snakes and scorpions [11,13,17,19,21-23]. Accordingly, it was hypothesized that in scorpions, selection could underlie both hyper-diversification of the mature toxin and conservation of the toxin leader domain. Therefore, the number of synonymous (dS) and non-synonymous (dN) substitutions per site in the toxin sequences, was assessed. Such analysis was performed on the two main toxin families identified within Boi venom gland, namely the α- and depressant toxin families. dN/dS values of 0.6 to 1.0 are indicative of neutral selection forces. Using the MEC model [24], the majority (55%) of the mature domain residues showed very strong positive selection, with 34% being under very strong negative selection and only 11% revealing a pattern interpreted as neutral selection. A similar degree of positive selection was found in both the Boi and BmK α-toxin families (not shown). Atypically, the degree of diversification within the BmK depressant toxin family was significantly low, leading to a small number of positively selected sites within the mature toxin sequence. This could be a result of a partial representation of the full variety of this specific toxin family in the databases and/or an indication of unusual evolutionary forces. Opposite to the mature toxin residues, the majority of the leader domain residues showed very strong (62%) negative selection, with only 5% being under the effect of positive selection forces and 33% being neutrally selected. The same pattern was obtained by the more promiscuous M5 and M8 models (p < 0.001) for both the depressant and α-toxin families (not shown). To establish the correlation between synonymous substitution rates and dN/dS ratios, DNAsp software was utilized. Again, the majority of the leader data points (Fig. 4B, left plot) argue in favor of a purifying selection (dN/dS < 0.6), while the majority of the mature domain data points (Fig. 4B, right plot) are indicative of diversifying selection (dN/dS>1). In addition, an apparent decrease in the synonymous mutation rate within the leader domain was observed, in comparison to the rate observed within the mature toxin (Fig. 4B) and will be discussed in the following sections.


Assembling an arsenal, the scorpion way.

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

Non-synonymous versus synonymous substitutions in the depressant toxin family. dN over dS in intrafamilial comparisons of the leader and mature toxin coding domains. (A) Residue specific plot. Leader and mature residues are indicated by white and gray bars, respectively. Cysteine residues are indicated by yellow bars. (B) Matrix alignment plots were utilized to establish the correlation between the synonymous substitution rates and dN/dS ratios. Two lines distinguishes between values indicating positive (>1), neutral (0.6–1) and negative (<0.6) selections.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Non-synonymous versus synonymous substitutions in the depressant toxin family. dN over dS in intrafamilial comparisons of the leader and mature toxin coding domains. (A) Residue specific plot. Leader and mature residues are indicated by white and gray bars, respectively. Cysteine residues are indicated by yellow bars. (B) Matrix alignment plots were utilized to establish the correlation between the synonymous substitution rates and dN/dS ratios. Two lines distinguishes between values indicating positive (>1), neutral (0.6–1) and negative (<0.6) selections.
Mentions: Positive selection has been suggested as playing a decisive role in the diversification of mature toxins in gene families of cone snails, snakes and scorpions [11,13,17,19,21-23]. Accordingly, it was hypothesized that in scorpions, selection could underlie both hyper-diversification of the mature toxin and conservation of the toxin leader domain. Therefore, the number of synonymous (dS) and non-synonymous (dN) substitutions per site in the toxin sequences, was assessed. Such analysis was performed on the two main toxin families identified within Boi venom gland, namely the α- and depressant toxin families. dN/dS values of 0.6 to 1.0 are indicative of neutral selection forces. Using the MEC model [24], the majority (55%) of the mature domain residues showed very strong positive selection, with 34% being under very strong negative selection and only 11% revealing a pattern interpreted as neutral selection. A similar degree of positive selection was found in both the Boi and BmK α-toxin families (not shown). Atypically, the degree of diversification within the BmK depressant toxin family was significantly low, leading to a small number of positively selected sites within the mature toxin sequence. This could be a result of a partial representation of the full variety of this specific toxin family in the databases and/or an indication of unusual evolutionary forces. Opposite to the mature toxin residues, the majority of the leader domain residues showed very strong (62%) negative selection, with only 5% being under the effect of positive selection forces and 33% being neutrally selected. The same pattern was obtained by the more promiscuous M5 and M8 models (p < 0.001) for both the depressant and α-toxin families (not shown). To establish the correlation between synonymous substitution rates and dN/dS ratios, DNAsp software was utilized. Again, the majority of the leader data points (Fig. 4B, left plot) argue in favor of a purifying selection (dN/dS < 0.6), while the majority of the mature domain data points (Fig. 4B, right plot) are indicative of diversifying selection (dN/dS>1). In addition, an apparent decrease in the synonymous mutation rate within the leader domain was observed, in comparison to the rate observed within the mature toxin (Fig. 4B) and will be discussed in the following sections.

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