Evolution: Difference between revisions
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'''Fig. 1:''' '''Amino Acid Sequence (260 aa)''' of N-acetylneuraminic Acid (2gfh) protein from ''Mus musculus'' (House Mouse) | '''Fig. 1:''' '''Amino Acid Sequence (260 aa)''' of N-acetylneuraminic Acid (2gfh) protein from ''Mus musculus'' (House Mouse) | ||
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The bacteria sequence matches used for multiple sequence analysis and phylogenetic tree mapping were representative of the other baterial sequences not selected. These selected sequences had the highest bit scores and E-values. | The bacteria sequence matches used for multiple sequence analysis and phylogenetic tree mapping were representative of the other baterial sequences not selected. These selected sequences had the highest bit scores and E-values. | ||
=='''Multiple Sequence Alignments (msa)'''== | =='''Multiple Sequence Alignments (msa)'''== | ||
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The topmost sequence belongs to the query protein. | '''The topmost sequence belongs to the query protein'''. | ||
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# '''''Bacillus licheniformis'''' | # '''''Bacillus licheniformis''''' | ||
# '''''Bacillus subtilis''''' | # '''''Bacillus subtilis''''' | ||
# '''''Bacillus halodurans''''' | # '''''Bacillus halodurans''''' | ||
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All five sequences belong to bacteria. With the exception of '''''Symbiobacterium thermophilum''''', the rest are '''''Bacillus''''' '''sp.''' | |||
'''''Symbiobacterium''''' are an uncultivable thermophiles isolated from compost. Their survival based mainly on microbial commensalism. This bacteria can only grow ''in vitro'', if it is '''co-cultured with''' '''''Bacillus''''' '''sp'''. bacteria. This could therefore explain its '''genetic association with''' '''''Bacillus''''', as observed from the sequence alignment. | |||
However, interestingly, '''''Bacillus''''' is classified as '''Gram-positive''', while '''''Symbiobacterium''''' is a '''Gram-negative''' bacterium. As observed from the sequence alignment, '''other Gram-negative''' bacterium protein sequences ('''''Vibrio''''' '''Sp.''') '''do not''' contain the '''large gap insertion''' at the '''91 to 114 amino acid positions''', with the exception of ''Symbiobacterium''. Hence, more genetic (and even functional) analysis might be necessary to determine the hydrolase protein relationship between the Gram-positive ''Bacillus'' with the Gram-negative ''Symbiobacterium''. | |||
A '''highly conserved''' (with invariant) section of amino acids '''(LV)–(LVA)–(LIV)–(LIV)-T-N-G''' was observed in all the sequences from amino acid '''211 to 217''' in the alignment. Downstream of this conserved portion of genes are 5 more invariant positions (1 or 2 amino acids in length). | |||
From these short conservation regions, the functions or even structure of the encoded proteins could have significance in its evolutionary pattern. | |||
=='''Phylogenetic Map (Tree)'''== | =='''Phylogenetic Map (Tree)'''== | ||
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[[Image:phylo_radial1a.png|Radial View]] | [[Image:phylo_radial1a.png|Radial View]] | ||
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[[Image:untitled.png|Strapboot Tree]] | |||
From the Rectangular Cladogram view, it could be observed that there are '''four distinct separate groups'''. | |||
From the Rectangular Cladogram view of the tree, it was observed that there were two main Domains — Procaryotes and Eucaryotes. This would also be the root and first branching point of the phylogenetic tree. | |||
In the Eucaryotic part of the tree, the protein could first be observed in [http://www.tolweb.org/Bilateria/2459 '''Deuterostomia'''] phylum. From there, it was branched off to both [http://www.tolweb.org/Deuterostomia/2466 '''Chordata''' and '''Echinodermata'''] phyla. | |||
''[http://images.google.com.au/imgres?imgurl=http://www.goldenstateimages.com/sql_images/thumbs/SUR-009c.jpg&imgrefurl=http://www.goldenstateimages.com/GSI_search.php%3Fsrch%3Dpurple%2520sea%2520urchin%26op%3Dex&h=153&w=230&sz=30&tbnid=oLd2P1ry-oZ1_M:&tbnh=72&tbnw=108&prev=/images%3Fq%3Dstrongylocentrotus%2Bpurpuratus%26um%3D1&start=3&sa=X&oi=images&ct=image&cd=3 Strongylocentrotus purpuratus]'' (Purple Sea Urchin), forms part of the '''Echinodermata''' phylum. | |||
The phylum '''Chordata''' would then be further branched into ''[http://en.wikipedia.org/wiki/Image:African_Clawed_Frog_bw.jpg Xenopus laevis]'' (African Clawed Frog) in '''Amphibia'''; in ''[http://animaldiversity.ummz.umich.edu/site/resources/david_blank/gallus3.jpg/view.html Gallus gallus]'' (Red Junglefowl) in '''Aves'''; and ''[http://animaldiversity.ummz.umich.edu/site/resources/susan_hoffman/mus1_small.jpg/view.html Mus musculus]'' (House Mouse) in '''Mammalia''' classes, respectively. | |||
The '''Arthropoda''' phylum, branched off from '''Deuterostomia''', would be further branched into '''Hexapoda''' class, consisting winged insects ''[http://www.ento.csiro.au/aicn/name_s/b_4116.htm Tribolium castaneum]'' (Rust-red Flour Beetle), ''[http://en.wikipedia.org/wiki/Image:Aedes_aegypti_biting_human.jpg Aedes aegypti]'' (''Aedes'' mosquito) and ''[http://en.wikipedia.org/wiki/Image:Drosophila_melanogaster_-_side_%28aka%29.jpg Drosophila melanogaster]'' (Fruit Fly). | |||
For the Procaryotic domain, branching mainly occurs between '''Gram-positive''' (''Bacillus'' Sp.) and '''Gram-negative''' (''Vibrio'' Sp.) bacteria. | |||
Hence, it can be generally deduced that the N-acetylneuraminic acid (hydrolase) protein is non-evolutionary specific, as it is observed to be present in almost all main phyla and classes of organisms from the two main Procaryotic and Eucaryotic Domains. Its functional significance would therefore be a general one. | |||
=='''Bootstrapping'''== | |||
See '''[[Materials and Methods]]''' | |||
Bootstrapping values obtained were analysed. Branch values occurring below 75% (<75%) are indicated by an asterisk (*) [Fig. 4]. | |||
[[Image:bootstrap1.png|Bootstrap Values]] | |||
Fig. 4: Branch bootstrap values in Rectangular Cladogram view. Branches with strap values <75% were indicated with asterisks (*) | |||
Tree bootstrapping is necessary to test for the reliability of the branching patterns and distances formed on the phylogenetic tree. This was done by making “pseudoreplicates” of multiple sequence alignments of up to 100 sets. The distance matrices were recalculated using these duplicate alignment values to generate a bootstrap tree, which can be used to compare the branching patterns and distances with the original phylogenetic tree. | |||
The bootstrap values (in percentage) obtained on each branch, signify branching confidence. Bootstrap values of 95% equate to full branching confidence; 75% value equates to 95% branching confidence; 60% value equates to much lowered branching confidence; while 50% value would render no branching confidence. | |||
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Proceed to '''[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Function Function]''' | |||
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[http:// | Back to '''[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/N-acetylneuraminic_acid_phosphatase Home Page]''' |
Latest revision as of 05:49, 21 May 2008
Sequence Homology
The following query protein sequence of N-acetylneuraminic Acid was obtained from GenBank: