The HDC Motif
Motifs
Motifs can be used for many different endeavors including gene analysis. Sequence motifs, like the ones shown below, are short, recurring patterns in DNA that are presumed to have a biological function [1]. Structural motifs are used to convey the strength and three-dimensional structure of the DNA itself [2]. Many programs are used on the internet to predict and compare DNA and protein sequences in the motif format. Each program has it's own color legend and output information included. Here, I have used MEME or Multiple Em for Motif Elicitation [3].
MEME works by using FASTA sequences of proteins or DNA from multiple organisms. Using these sequences provided by the user, the program aligns and searches for ungapped, repeated patterns in each one. Motifs are easier to find when sequences are long and well conserved between species where as other motifs are harder to find when sequences are shorter.
HDC Motif
The histidine decarboxylase protein is highly conserved throughout the animal kingdom. Motifs are great to compare and contrast the small sequence changes within a protein between species. In coordinating Tourette syndrome from the perspective of a motif, the sequence below depicts the base pair change of G-to-A that causes symptoms of Tourette's.
ANALYSIS
In my analysis of the HDC protein motif I used four organisms for comparison, the human, chimpanzee, drosophila and zebrafish. The G-to-A mutation is prevalent in each species and has a 50/50 occurrence rate. Although the phenotypes for each organism is different, the amino acid substitution proves to knock out the HDC protein in all organisms.
REFERENCES
1 "What are DNA sequence motifs?" Nature Biotechnology 24, 423 - 425 (2006). Retrieved 26 Apr 2014.
http://www.nature.com/nbt/journal/v24/n4/full/nbt0406-423.html
2 "Sequence Motif" Wikipedia: The Free Encyclopedia. Retrieved 26 Apr 2014 http://en.wikipedia.org/wiki/Sequence_motif
3 "MEME" MEME Suite: Motif-based sequence analysis tools. Retrieved 26 Apr 2014 http://meme.nbcr.net/meme/
1 "What are DNA sequence motifs?" Nature Biotechnology 24, 423 - 425 (2006). Retrieved 26 Apr 2014.
http://www.nature.com/nbt/journal/v24/n4/full/nbt0406-423.html
2 "Sequence Motif" Wikipedia: The Free Encyclopedia. Retrieved 26 Apr 2014 http://en.wikipedia.org/wiki/Sequence_motif
3 "MEME" MEME Suite: Motif-based sequence analysis tools. Retrieved 26 Apr 2014 http://meme.nbcr.net/meme/
University of Wisconsin – Madison
Spring 2014 Genetics 564 |
|