Adding Genetic Information

(C)Copyright 2011 by Carl Drews
Updated: December 10, 2011

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Contents:
The Mechanism
What Happens to the Duplicate Genes?
Pseudomonas
Conclusion

Figure 1. Duplication of the highlighted gene during replication of the genome.
http://commons.wikimedia.org/wiki/File:Gene-duplication.png

The biological process of evolution can add new (and useful) genetic information to the genome by gene duplication followed by a point mutation in one of the copies. The modified copy can perform a new biological function while the unchanged copy continues to perform the original function. This process has been observed in the Antarctic eelpout fish, which lives in very cold water. The gene that produces antifreeze protein (AFP) is thought to have evolved from a duplicate copy of the gene that produces sialic acid synthase (SAS) enzyme. AFP secretes an antifreeze protein into the eelpout's bloodstream, allowing the fish to expand its range into colder waters. The overall process is called "escape from adaptive conflict", whereby the copied gene is free to acquire a new function. The references are:

• University of Illinois (January 12, 2011):
  Researchers show how one gene becomes two (with different functions)
  http://www.news.illinois.edu/news/11/0112genes_cheng.html
  
  
• Cheng Denga, C.-H. Christina Chengc, Hua Yea, Ximiao Heb, and Liangbiao Chena, 2010. Evolution of an antifreeze protein by neofunctionalization under escape from adaptive conflict. Proceedings of the National Academy of Sciences (PNAS), 2010.
  http://www.pnas.org/content/107/50/21593.abstract?sid=c12a7d0a-07fd-4458-851d-d83bd7210112

Figure 2. The Antarctic eelpout fish (Lycodes turneri).
http://commons.wikimedia.org/wiki/File:PolarEelpout-B-Sheiko.jpg

Of course the mutated copy of the duplicate gene still has to produce a viable function in order to be useful. A mutated gene will produce a modified protein. The cell's quality control mechanism will destroy proteins that do not fold properly. However, some modified proteins do make it through the cell's filtering machinery and are expressed in the phenotype. Since altered phenotypes do arise in a population, we know that the cell's quality control mechanism does not eliminate the result of every mutation.

Jianzhi Zhang describes the evolutionary fate of duplicate genes in a scientific review article, "Evolution by gene duplication: an update ", TRENDS in Ecology and Evolution , Vol.18 No.6 June 2003:
http://www.anthro.utah.edu/~rogers/bio5410/Readings/Zhang-TRE-18-292.pdf

• Pseudogenization (dead end)
  "Gradually, the mutation-containing gene becomes a pseudogene, which is either unexpressed or functionless, an evolutionary fate that has been shown by population genetic modeling as well as by genomic analysis. After a long time evolutionarily speaking, pseudogenes will either be deleted from the genome or become so diverged from the parental genes that they are no longer identifiable." "Pseudogenization, the process by which a functional gene becomes a pseudogene, usually occurs in the first few million years after duplication if the duplicated gene is not under any selection."
  Note that: There is a substantial window of opportunity for a duplicated gene to become useful.
  
  
  

  Figure 3. The coding region in a segment of eukaryotic DNA.
  http://commons.wikimedia.org/wiki/File:Gene.png

• Conservation of gene function (more of the same is better)
  "The presence of duplicate genes is sometimes beneficial simply because extra amounts of protein or RNA products are provided."
  Note that: In this case, duplicate genetic information changes the phenotype and IS therefore new information.
  
  
• Subfunctionalization (specialization)
  "Changes of gene expression after gene duplication appear to be a general rule rather than exception and these changes often occur quickly after gene duplication. Subfunctionalization can also occur at the protein function level and can lead to functional specialization when one of the duplicate genes becomes better at performing one of the original functions of the progenitor gene."
  Note that: Here we see a splitting of formerly coupled functions, and a subsequent improvement in those functions after the separation. This improvement was made possible by decoupling the originally shorter gene sequence. The new gene sequence is longer and it's all being used to improve the reproductive chances of the organism.
  
  
• Neofunctionalization (new functions)
  "One of the most important outcomes of gene duplication is the origin of novel function. Although it seems improbable that an entirely new function could emerge in a duplicate gene, there are several examples." Zhang gives the example of the eosinophil cationic protein (ECP) gene of humans , which is toxic to bacteria because it makes their cell membranes porous . ECP is a modified duplicate of eosinophil-derived neurotoxin (EDN) , but the antibacterial activity is new. "In many cases, however, a related function, rather than an entirely new function, evolves after gene duplication. One good example is the red- and green-sensitive opsin genes of humans, which were generated by gene duplication in hominoids and Old World monkeys. After duplication, the two opsins have diverged in function, resulting in a 30-nm difference in the maximum absorption wavelength. This confers the sensitivity to a wide range of colors that humans and related primates have."
  Note that: In the opsin case the addition of new genetic information has improved our vision.

Figure 4. Scanning electron micrograph (SEM) of a number of Pseudomonas aeruginosa bacteria.
http://commons.wikimedia.org/wiki/File:Pseudomonas.jpg

The Pseudomonas bacteria has evolved the new ability to digest nylon. This process has occurred in the wild and in the laboratory. Nylon was invented and first synthesized in 1935 by Wallace Carothers at DuPont chemical. In the 1970s Japanese scientists noticed that bacterial mats were growing on nylon waste compounds. In 1984 Susumu Ohno found that the nylonase enzyme had arisen by duplicating a gene and then inserting a single extra base into the DNA code (a frame shift). In 1995 Irfan Prijambada reported that researchers at Osaka University had observed the evolution of nylon metabolism in their laboratory cultures of Pseudomonas, after carefully making sure that the original culture had no ability to digest nylon. This new and useful genetic information arose from the standard evolutionary processes of mutation, natural selection, and reproduction. Reference: Only a Theory: Evolution and the Battle for America's Soul, by Dr. Kenneth R. Miller of Brown University, 2008, pp. 79-84.

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