Pseudogene
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A pseudogene is a nucleotide sequence that is part of the DNA or an organism that appears to have once coded a gene product (typically a protein) but no longer does so.
Pseudogenes are believed to have resulted as mutation to an original functioning coding sequence. One scenario for the evolution of a pseudogene is that the environment of an organism changes sufficiently such that the gene product is no longer necessary for the survival of that organism (for example an enzyme may not be required at a different temperature). Alternatively a gene duplication may mean that a genome has two copies of a gene when it only requires one. This means that there is then no longer selection pressure to maintain this sequence, and organisms can continue to survive even while accumulating mutations in the sequence. For example, mutations in certain nucleotide positions can result in a premature "stop" codon which leads to a shorter than normal polypeptide chain protein, which is incapable of folding into a functioning protein. Another scenario that might lead to the creation of a pseudogene is a gene duplication event. If a gene is duplicated and one copy suffers a deleterious mutation, the organism is unaffected since it has another functioning copy of the gene.
Pseudogenes can complicate molecular genetic studies. For example, a researcher who wants to amplify a gene by PCR may simultaneously amplify a pseudogene that shares similar sequences. Similarly, pseudogenes are sometimes annotated as genes in genome sequences.
In some cases, the definition of what is a pseudogene can become cloudy. For example, Hirotsune et al (2003) discovered a sequence that appeared to be a pseudogene in the sense that it did not code for a protein sequence, in contrast to a homologous gene that did code for a functional protein. However, the pseudogene is expressed and its RNA transcript regulates the activity of the homologous gene. Thus, with respect to protein-coding ability, this sequence is a pseudogene, but in a sense it is a functional non-coding RNA gene.
References
- Hirotsune S, Yoshida N, Chen A, Garrett L, Sugiyama F, Takahashi S, Yagami K, Wynshaw-Boris A, Yoshiki A. (2003), "An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene.", Nature, 423:91-96. (A functional pseudogene.) In PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12721631)