Tuesday, April 14, 2009
Genetic exceptions
One of Caroll's core arguments for evolutionary theory is the universality of genetic code, that the same sequences are used to code for proteins in every species. But as he mentions on page 75, there are a few exceptions to this rule. Find examples of those exceptions and explain why they might read genetic code differently than other cells/organisms. What clues does this give us to the nature of LUCA?
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Tuesday, April 14, 2009
ReplyDeleteGenetic exceptions
One of Caroll's core arguments for evolutionary theory is the universality of genetic code, that the same sequences are used to code for proteins in every species. But as he mentions on page 75, there are a few exceptions to this rule. Find examples of those exceptions and explain why they might read genetic code differently than other cells/organisms. What clues does this give us to the nature of LUCA?
Answer: The exceptions to this rule of the same sequences coding for protein in every species include the fact that a large portion of DNA is "noncoding". Scientists have difficulty trying to figure out where “coded” messages begin and end. In some species such as microbes, genes are very closely packed with small spaces of noncoding DNA between thousands of genes. In humans, genes occupy only a small portion of the entire DNA. We have long fragments of noncoding DNA. Some of this noncoding DNA control how genes are used but a lot of it is just “junk”. This junk accumulates and is often very repetitive. It can be looked at as remnants from before changes took place and before the genes were fossilized. But also, this “junk” can be used to make new changes.
Because of this “junk”, the genetic code might be read differently. Alternative splicing can occur between different introns and exons which will eventually translate into new protein. Organisms without a lot of introns have fewer chances to promote diversity and have less choices of genetic material to use for making proteins.
This tells us that LUCA probably had very few junk DNA in its genome. It probably had the minimum number of genes required to just survive, but nothing more: not a lot of diversity. But as time passed, more and more “junk” accumulated and created changes and new genes and proteins that now are evident in the thousands of different species of organisms in the world today.
On page 75, when Carroll mentions that there are a few exceptions to the universal code, he is referring to the idea that some codons are read differently in certain organisms, not that in the universal code there are exceptions to identical sequences that code for identical proteins in each species. This is found with the example of the four different amino acid sequences for a neurotoxin that functions through the blocking of potassium channels. Despite the extreme differences between the amino acid sequences, sea anemones (cnidarian), scorpions (arthropod), cone shell (mollusk), and the black mamba snake (vertebrate) all have developed the code for a different protein that functions similarity. It is more of an example of convergent evolution than an example of how same sequences are read to code for same proteins (The question was probably worded a little confusingly and the implied meaning was not what the author had intend).
ReplyDeleteInstead, the exceptions to the universal code is how different codons are read in different organisms. For example, while normally there are three different combinations of bases that code for a stop codon in protein translation or transcription, in other organisms the some of these stop codons are assigned to different amino acids. An example of this is the microorganism Mycoplasma capricolum. UGA is not a stop codon as it normally is in the majority of organisms including humans, but instead in Mycoplasma capricolum, it codes for tryptophan. As well, it seems that many of the exceptions to the universal code is found in the genetic code of mitochondrial genome. The mitochondrion was theorized to have developed from and endosymbiotic bacterium near the time eukaryotes arose. As well a few protozoan species have a differential interpretation of genetic sequences for certain amino acids. Some of the exceptions to the universal code are listed in the following table from: http://www.answers.com/topic/genetic-code.
EXCEPTIONS TO THE UNIVERSAL GENETIC CODE
Organism Normal codon Usual meaning New meaning
Mammalian AGA, AGG Arginine Stop codon
mitochondria AUA Isoleucine Methionine
UGA Stop codon Tryptophan
Drosophila AGA, AGG Arginine Serine
mitochondria AUA Isoleucine Methionine
UGA Stop codon Tryptophan
Yeast AUA Isoleucine Methionine
mitochondria UGA Stop codon Tryptophan
CUA, CUC, CUG, CUU Leucine Threonine
Higher plant UGA Stop codon Tryptophan
mitochondria CGG Arginine Tryptophan
Protozoan nuclei UAA, UAG Stop codons Glutamine
Mycoplasma capricolum bacteria UGA Stop codon Tryptophan
Another phenomenon that occurs with the exceptions to the universal genetic code is the pair of different amino acids from the standard 20. This includes selenocysteine an amino acid that is encoded by UGA which is usually a codon signaling a stop to transcription. But in certain organisms, translational machinery is able to discriminate between a UGA codon that signals a stop and a UGA codon that codes for selenocysteine. This specific codon usage has been found in different species of archea, eubacteria, and animals. Another one of these nonstandard amino acids is pyrrolysine, which is coded by the codon UAG and is found in species of archea and bacteria. It is relatively unknown how the translationary mechanisms differentiate between identical codons coding for one of the nonstandard amino acids.
It seems that most of these exceptions are found in the mitochondrial genome of different species. While the mitochondria most likely evolved with Endosymbiosis of a separate organism that was incorporated in the metabolic processes of eukaryotic cells, this may contain a clue about the universality of the genetic code. This process happened many years ago, when the genetic code should have been extremely similar to its original form, if it had descended from a universal ancestor. The different interpretation of codons, and the small number of exceptions in the face of a vast amount of different organisms points to a couple of different possible happenings in my opinion. Either, the redundancy of the genetic code and the idea of wobble in pairing base pairs contributed to the formation of different interpretation of codons or that there had been more than one universal ancestor, where one entire branch generally died out with a small remainder that demonstrates the exceptions to the universal genetic code. Another possibility is that there was a division of the genealogical tree early in organismal history, where consequently one branching form the universal ancestor were less suited to survival. While these hypotheses are not backed by any hard evidence, and are totally my opinion, these are my takes to the exceptions to the supposed universal genetic code. The first hypothesis with the relaxation of the interpretation of codons from the inclusion of the redundancy notion is most likely.
http://www.answers.com/topic/genetic-code
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html
http://www.arn.org/docs/pbsevolution/pbsfalseclaim091001.htm
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Endosymbiosis.html
http://en.wikipedia.org/wiki/Human_mitochondrial_genetics