Ivy Mead 24 March 2011 Bioinformatics Lab report 4 Three-finger toxins (3FTx) have been found in several different groups of vertebrates, including snakes (elapidae) as well as mammals (Naimuddin et al., 2011). In some venomous snakes 3FTx proteins have been found in the venom as widely effective neurotoxins transmitted by bite. As well as wide ranging neurological effects, 3FTx proteins have also been known to have cytotoxic and platelet inhibition effects (Jiang et al., 2011). 3FTx proteins in general have been found to imitate interleukins and targets for ion channels and receptors in the body, which is made possible by it’s molecular structure. The 3FTx proteins are characterized by a highly conserved cysteine structure and a highly diverse series of loop regions. The variation in the loop regions is thought to aid in molecular mimicry (Naimuddin et al., 2011). Thus eleven sequences of distinct 3FTx proteins isolated from snake venom were aligned and a set of analyses was carried out in order to answer several interesting questions. An evolutionary tree of the sequences was produced, providing a general structure to the data (Figure 1). Interestingly enough, one species (Ophiophagus Hannah) had two different types of 3FTx proteins and they were placed on different branches of the tree. Literature sources state that evolution of the toxin family 3FTx is driven by positive selection, which makes sense to a certain extent (Jiang et al., 2011). Toxic venom can aid a snake in two ways, by allowing them to disable prey more easily and by aiding in protection against potential predators. The more effective the venom is at doing those things, likely the better the snake is expected to adapt. However, the positive selection pressures only seem to be affecting the second region of the protein, as seen by looking at the mRNA sequence. When aligned, the first half of the sequence is highly conserved and the second half is very diverse. The sequence diversity caused by positive selection in that second half is likely the key to the success of the protein because it allows a wide range of harmful effects to the prey and/or predator of the snake. However, as with everything in evolutionary biology, there could always be other factors playing a part that could be obscuring the true causes in this case. To explore the possibility of forces of selection shaping the evolution of the 3FTx toxic protein family, codon-based tests of neutral, positive, and purifying selection were carried out in MEGA using the Nei-Gojobori method on the data collected. The results of the codon-based tests of neutrality carried out showed a very small number of statistically significant probabilities (P < 0.05) indicating neutral selection acting on the protein family, thus it is unclear if that force is acting on the family. The results of the codon-based tests of positive selection showed also a small number of statistically significant probabilities (P < 0.05) indicating that neutral selection could possibly be acting on the protein family but not for certain. The results of the codon-based tests of purifying selection showed no statistically significant probabilities (P < 0.05) indicating that it is unlikely that purifying selection has been a driving force for the evolution of the protein family (Tamura et al, 2007) (Nei and Gojobori, 1986). Part of what seems to make the 3FTx toxins so effective as a part of venom is their ability to bind to many different receptors and neurons by being able to mimic the binding site. The first half of nucleotide sequence coding for the protein was found to be highly conserved, likely a remnant of the family’s pre-venom structure, which allows it to bind to many different sites in the prey’s body. The part that seems to distinguish the protein from related proteins, is the second half of the sequence, which as mentioned earlier is highly variable and most likely ultimately allows the protein to be toxic. Figure 1. An evolutionary relationship tree of the studied 3FTx sequences from different types of snakes. Units of tree are in number of base substitutions per site. This figure was compiled using UPGMA method, with distances calculated using the Juke-Cantor method using the program MEGA5 (Sneath and Sokal, 1973)(Jukes and Cantor, 1969). Works Cited: Jiang, Y. et al., Venom gland transcriptomes of two elapid snake (Bungarus multicinctus and Naja atra) and evolution of toxin genes. 2011. BMC Genomics. 12: 1. Accessed on Mar 17, 2011 from http://www.biomedcentral.com/1471-2164/12/1. Jukes, T. and C. Cantor. Evolution of protein molecules. In Munto, H., editor. Mammalian Protein Metabolism. Academic Press: New York. 1969. Nei, M. and T. Gojobori. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. 1986. Molecular Biology and Evolution, 3:418426. Naimuddin, M., et al. Directed evolution of a three-finger neurotoxin by using cDNA display yields antagonists as well as agonists of interleukin-6 receptor signaling. 2011. Molecular Brain. 4: 2. Accessed Mar 17, 2011 from http://www.molecularbrain.com/content/4/1/2. Sneath, P. and R. Sokal. Numerical Taxonomy. Freeman: San Francisco. 1973. Tamura K. et al., MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. 2007. Molecular Biology and Evolution 24:1596-1599.