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Homeobox genes encode transcription factors, proteins which turn on other genes. A single homeobox gene can cause a cascade of other genes to be turned on, producing an entire body segment of limb. Homeobox genes contain a stretch of DNA approximately 180 base pairs (60 amino acids) long called a homeobox which encodes a protein domain, called a homeodomain capable of binding to DNA. Single homeodomains are not usually specific enough to target the exact genes they are to turn on, so homeodomains usually work on complexes with other proteins.
HOX genes are a particular group of homeobox genes which are found in hox clusters. HOX genes pattern the body axis, determining where particular body segments and limbs grow.
HOX genes are famously found in clusters, possibly because mixing of HOX genes by crossing over would cause fatal development problems. Most animals show a similar pattern of clustering, suggesting that the clusters developed early in evolutionary history, and selection has favoured the clustering. Even more interesting than the clustering is the fact that the physical location of each gene on the chromosome usually corresponds to the location of the body part that it is in charge of.
Homeobox genes and evoluton
Because homeobox genes can turn on many other genes, and even produce entire body segments, a small mutation to a homeobox gene can produce drastic, easily visible results. Mutated HOX genes in Drosophila, the fruit fly, have been responsible for producing extra limbs or producing wings where there should be antennae. Most animals are segmented (this includes us vertebrates, with our segmented skeleton), and duplication of homeobox genes must have been important in the evolutionary history of animals with multiple segmented parts. For example, a homeotic gene duplication in a member of the Simpson family could mean that in the future all humans have five fingers.
Because small mutations to homeobox genes can have drastic effects selection makes sure that there is very little variation in homeobox genes. This means that many homeobox genes are shared by large groups of organisms who are very distantly related and share few genes. Studying which genes are shared by which groups can help in phylogenetic reconstruction.
Structural complexity is not thought of as mutations or "evolution" of the hox gene, rather, the number of hox genes dictates the structural complexity of the organism. It has been theorized that gene duplication is the major source of increasing numbers of homeobox genes.
Pax-6 is involved in development of the eye throughout most of the animal kingdom. The fact that it's shared by groups with a diverse range of eye designs suggests that there was some form of proto-eye in the common ancestor of those groups.
- Holland, P.W.H., 1999. The future of evolutionary developmental biology, in Nature 402 .
- Zhong YF, Butts T, Holland PWH, 2008. HomeoDB: a database of homeobox genes diversity
- The Hox Database
- Myers, PZ, 2004. Pharyngula: Squid HOX Genes, 
This page is part of the EvoWiki encyclopedia of genetics and molecular biology.