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ISSN: 2153-0602
Journal of Data Mining in Genomics & Proteomics
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Evolutionary Distance and Conserved Domain Analysis of Divergent Phylogenetic Lineages from Genus Naja

Sherkhane AS and Gomase VS*

The Global Open University, India

*Corresponding Author:
Gomase VS
The Global Open University
Nagaland,India
Tel: 91-998-777-0696
E-mail: [email protected]

Received date: May 21, 2014;Accepted date: August 20, 2014; Published date: August 25, 2014

Citation: Sherkhane AS, Gomase VS (2014) Evolutionary Distance and Conserved Domain Analysis of Divergent Phylogenetic Lineages from Genus Naja. J Data Mining Genomics Proteomics 5:156. doi:10.4172/2153-0602.1000156

Copyright: 2014 Sherkhane AS, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Abstract

 Naja Naja is one of the poisonous snakes in the genus Naja of Elapids family; commonly called Indian cobras and are mostly found in Asia and Africa. They are highly venomous species having a cocktail of chemicals that have different effects may be speed the heart rate, blood pressure and interfere with the normal function of the nervous system and potently block α7 homo-oligomeric neuronal AChRs causing paralysis. The aim of the present study is to identify the origin of neurotoxin, prediction of structure and function of neurotoxin by multiple sequences analysis and observing the conserved pattern of amino acid residues and to construct the phylogenetic tree for organizing evolutionary history of N. Naja of genus Naja from Elapidae family.

 

Keywords

Neurotoxins; Naja genus; Multiple sequence alignment; Conserve domain; Phylogenetic analysis

Introduction

Naja Naja is one of the poisonous snakes in the genus Naja of Elapids family and commonly called Indian cobras and are mostly found in Asia and Africa [1]. Elapidae family approximately consists of 300 venomous snakes in 62 genera [2]. The genus Naja consists of currently 26 species of cobra of which 11 inhabit Asia and 15 occur in Africa [3,4]. Proteins from Naja Naja are potent postsynaptic neurotoxins [5]. Neurotoxins that acts by binding to the nicotinic acetylcholine receptors in the postsynaptic membrane of skeletal muscles [6] causing severe local pain, swelling immediately after bite; dark discoloration, necrosis, paralysis and even death [7-10]. In this research work, we study the origin and evolution of neurotoxin from N. Naja by multiple sequence alignments that provide the functional information of conserved sequence regions of neurotoxin from Naja Naja, phylogenetic analysis shows taxonomical classification, identifying and naming new members of protein families that derived from a common ancestor [11-15].

Materials and Methods

Sources and sequence information of genus Naja neurotoxins

Thirteen sepcies has taken from genus Naja of Elapidae family, in which targeted neurotoxins protein data were used to observe molecular resemble of related protein by phylogenic analysis (Table 1) [16,17].

Multiple sequence alignment of genus Naja neurotoxins

Multiple sequence alignment [MSA] is conducted by COBALT, which aligns thirteen neurotoxin protein sequences of similar Naja genus using a combination of distance matrix and approximate parsimony methods. Numerical setting method is used to study the relative entropy threshold, in bits, that must be met for an alignment column to be displayed in red. A larger number indicates higher degree of conservation. The relative entropy is computed as: Σi fi log2 (fi / pi), where i is residue type, fi is residue frequency observed in the multiple alignment column, and pi is the background residue frequency. Identity setting used for only columns with one residue type will be colored in red [18].

Construction of a phylogenetic tree for neurotoxin from genus Naja of Elapidae family

Phylogenetic analyses were performed by fast minimum evolution algorithm and Neighbor Joining algorithms to allow the reconstruction phylogenetic tree of the molecular evolutionary history of various aligned sequences that are useful to align highly evolved gene families clearing evolutionary relationships such as multiple actin proteins [19,20]. Trees were obtained by the methods fast minimum evolution algorithm and Neighbor Joining algorithms. Evolutionary distance is studied by Grishin (protein) model [21,22] and distance between two sequences modeled as expected fraction of amino acid substitutions per site given the fraction of mismatched amino acids in the aligned region and can be computed for fraction of mismatched amino acids larger than 0.75 [23-26].

Results and Interpretation

Evolutionary distance

This study, thirteen neurotoxin protein from genus Naja is summarized to study the evolutionary distance. The identification of the origin of neurotoxin protein from genus Naja, multiple sequences analysis, observing the conserved amino acid residues and reconstruct the phylogenetic tree specify the evolutionary history, relationship of N. Naja a with different species (Table 1). Rectangle tree shows rectangular shaped rooted tree, where root is places in the longest edge. Fast minimum evolution algorithm produce un-rooted tree such as ones shown as radial or force in the tabs below. The rooted trees are created by placing a root in the middle of the longest edge (Figures 1-4). Slanted tree shows similar to rectangle, but with triangular tree shape. Neighbour Joining algorithms produce un-rooted tree such as ones shown as radial or force in the tabs below. The rooted trees are created by placing a root in the middle of the longest edge.

Accession Description Identity % E Value Total Score
P60814.1 Najanaja 100% 5e-55 176
Q9YGI4.1 Najaatra 98% 1e-52 170
O42255.1 Najasputatrix 97% 5e-52 168
P82935.2 Najakaouthia 88% 2e-40 139
Q9YGI2.1 Najanaja 72% 4e-35 125
P25679.2 Najakaouthia 85% 7e-31 114
O93422.1 Najaatra 72% 1e-27 106
P01399.1 Najaannulifera 67% 2e-24 97.8
P85520.1 Najaoxiana 69% 6e-24 96.3
P25680.1 Najanivea 68% 5e-23 94.0
P01401.1 Najahajehaje 62% 3e-21 89.4
P01400.1 Najamelanoleuca 62% 2e-20 87.0
Q9W717.1 Najanaja 54% 8e-20 86.3

Table 1: Sequences producing significant alignments

data-mining-genomics-Fast-minimum-evolution

Figure 1: Rectangle tree - Fast minimum evolution algorithm - Phylogenetic study of genus Naja with the help of rendering tree showing the evolutionary difference with N. Naja in the rectangular shaped rooted tree, root is places in the longest edge.

data-mining-genomics-Slanted-tree-Grishin

Figure 2: Slanted tree - Grishin (protein) model- Phylogenetic study of genus Naja with the help of rendering tree. Slanted tree is Similar to rectangle, but with triangular tree shape.

data-mining-genomics-unrooted-tree-shape

Figure 3: Radial tree - Grishin (protein) model- showing Phylogeny of genus Naja with the help of rendering tree. Radial tree is unrooted tree shape.

data-mining-genomics-Force-tree-Grishin

Figure 4: Force tree - Grishin (protein) model- showing Phylogeny of genus Naja with the help of rendering tree. Force tree is similar to radial, where nodes are pushed away from one another for better presentation.

MSA

Multiple sequence alignment analysis shows columns with no gaps are colored in blue or red. The red color indicates highly conserved regions and blue indicates less conserved ones. The Conservation analysis can be used to select a threshold for determining which columns are colored in red (Figure 5). Multiple sequence alignment identify conserved motifs and to predict functional role in the variable sites as well as conserved sites show the sequence divergence profile of these neurotoxin proteins, which demonstrate the sequence enrichment strategy of these sequences for adaptation to different physiological systems. Here we observed that from all sequences of neurotoxin proteins that Cys(c), Thr (T), Asn (N) (Hydrophilic amino acid) Phe(F), Gly(G), Ala(A), Pro(P) (hydrophobic amino acid), Lys (K), Arg(R), Positive charged, Asp(D), Nagative charged which is conserved in all peptides having a common ancestor. That all of these peptides share eight highly conserved cysteines which were involved in the formation of β-strands are almost conserved. Cysteine (C) is conserved in all sequences at 8 sites. Multiple sequence alignment is carried out by COBALT of Naja genus.

data-mining-genomics-Multiple-sequence-alignment

Figure 5: Multiple sequence alignment by COBALT of genus Naja. Here columns with no gaps are colored in blue or red. The red color Cys(c),Thr (T),Asn (N) hydrophilic polar, Phe(F),Gly(G),Ala(A),Pro(P) hydrophobic nonpolar,Lys (K),Arg(R), Positive charged, Asp(D),Nagative charge indicates highly conserved columns and blue indicates less conserved ones. The Conservation Setting can be used to select a threshold for determining, which columns are colored in red.

Conserved domain analysis

Molecular study of N. Naja shows conserved domains and having one of snake toxin superfamily with user query added Superfamily (Figures 6 and 7). Snake toxin domains are present in short and long neurotoxins, cytotoxins and short toxins, and in other miscellaneous venom peptides (Table 2). The toxin acts by binding to the nicotinic acetylcholine receptors in the postsynaptic membrane of skeletal muscles and preventing the binding of acetylcholine, thereby blocking the excitation of muscles. This domain contains 60-75 amino acids that are fixed by 4-5 disulfide bridges and is nearly all beta sheet; it exists as either monomers or dimers.

data-mining-genomics-Conserved-domains

Figure 6: Conserved domains on [gi|4165564|emb|CAA06888|] neurotoxin [N. Naja].

data-mining-genomics-Sequence-structure

Figure 7: Sequence structure alignment shows similarity with structure of cl11586: snake_toxin Superfamily.

Description PssmId Multi-dom E-value
snake_toxin[cd00206], Snake toxin domain, present in short and long neurotoxins, cytotoxins and short toxins, ... 119411 no 8.44e-20
Toxin_1[pfam00087], Snake toxin; A family of venomous neurotoxins and cytotoxins. Structure is small, disulfide-rich, 249576 no 5.93e-17

Table 2: List of domain hits.

Conclusion

Thirteen neurotoxin proteins of genus Naja from Elapidae family are summarized the identical regions. Using multiple sequences analysis and phylogenetic tree we observe the conserved residues to specify the evolutionary history and analysing sequence structure relationship of neurotoxin among Naja species. Efficient utilization of Polar, nonpolar, positively and negatively charged amino acids and their distribution in toxin sequence make them a killer element in snake venom. Comparative analyses specify that the neurotoxin demonstrates how proteins are generated within the nature‘s testing ground for tailormade biologic needs. Evolutionary studies of neurotoxin sequence of Naja genus found the common ancestor of all the Naja species. In future, different neurotoxin may be converted in laboratories through protein engineering to design synthetic peptide vaccine that have a much positive role.

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