The Molecular History of Eukaryotic Life The Hox Genes
David Nelson Dec. 11, 2000 this section under construction Humans, worms and flies don't look very similar and they do not go through the same developmental stages. Yet the genes that control their body shape and organization are related in sequence. These genes all share a common sequence called the homeobox. This 180 nucleotide sequence codes for 60 amino acids found in these proteins. The rest of the proteins may be very different, but this 60 amino acid piece is crucial for their function. The homeodomain is a helix turn helix DNA binding domain that recognizes a specific DNA sequence. The homeodomain targets the remainder of the protein to regulate the gene expression of any genes with the appropriate recognition sequence in their control regions. There are at least 50 homeobox genes in Drosophila. They fall into two main divisions, the complex superclass and the dispersed superclass. Those in the complex group are found in clusters, the dispersed group are solo genes. One subset of these genes are called homeotic selector genes. In Drosophila, there are 8 genes arranged in a series along 650,000 base pairs of DNA. This whole region is called the HOM complex. There are two smaller subsets of these genes in the HOM complex, the antennapedia complex (5 genes) and the bithorax complex (3 genes). Other insects have these genes all in one complex, so it looks as though the HOM complex became split in Drosophila. Mutations in the 8 genes of the HOM complex cause large scale mutations in flies. A mutation in bithorax causes a fly to have an extra set of wings. Mutation in antennapedia causes a leg to grow where an antenna should be. These genes are not master switches for making wings or legs, but they specify position in the fly's body. The order of the genes on the chromosome is the same as the order of segments in the fly's body where they are expressed. The left most gene is expressed in the head, the right most gene is expressed in the abdomen. When a gene is deleted or mutated, the segment where it is normally expressed cannot tell where it is because its position clue is gone, so it behaves like the closest segment to it. That is why a bithorax mutation causes an extra set of wings. The segments adjacent to the bithorax segment dictated what should be made. These HOM genes have clear homologs in vertebrates. These are called hox gene clusters. Mice have four hox gene clusters on four different chromosomes. These are called HoxA ,B, C and D. HoxB has all the same genes as HOM plus one more. They are in exactly the same order. The other three segments are missing some of the HOM genes, but they have some extra homeobox genes not in the HOM cluster. The HOM cluster seems to have arisen by gene duplication of a single homeobox gene long ago. The ancestral cluster may have consisted of four genes that underwent a duplication to form two four gene clusters. One went on to become the Hox gene cluster and the other became what is called the Parahox cluster. The hox cluster then was duplicated in total four times in the lineage of vertebrates. This probably occurred as two rounds of complete genome duplication. Some additional gene duplication and deletion resulted in the present day set of Hox genes in mammals. These genes specify position in mouse embryos, just like they did in flies. They seem to have a similar function to the HOM cluster in flies, except it is more complicated in mammals because there are four clusters. Two sets of hox gene clusters are expressed in limb buds in perpendicular directions. The gene products from one cluster are expressed along a left to right axis in the limb bud(HoxD) and the other gene cluster is expressed top to bottom in the same bud(HoxA). This creates a checkerboard pattern that makes each position in the limb bud unique, like the elements of a mathematical array that are described by x, y and z coordinates. If a single gradient in the fly can specify the development of different symmetrical segments, like head, thorax and abdomen, then a dual gradient in the limb bud can specify the development of asymmetry in the limbs, things like the bones and muscles of the hand, the layout of nerves and blood vessels, what is to be skin and fingernails. The HoxA cluster in mouse has 11 genes, Drosophila has eight genes in the HOM cluster. HoxA has added three extra genes. Probably, if one looks back at simpler organisms there will be some that have fewer homeotic genes in these clusters, or fewer clusters. The Annual Review of Biochemistry 1994 has an article on homeodomain proteins (Vol. 63, 487-526). There, evidence is cited for one hox cluster in acorn worms (a hemichordate), two hox clusters in amphioxus (a cephalochordate) and three (or 4) in lamprey (a primitive vertebrate). More recent work shows three probable clusters in a fresh water lamprey (Sharman AC, Holland PW Estimation of Hox gene cluster number in lampreys. Int J Dev Biol 42,617-20 1998) Another paper shows one Hox cluster of at least 6 genes in ribbon worms PNAS 95, 3030 1998, that are more primitive invertebrate animals. One hox cluster is seen in sea urchins. There are also hox related genes in diploblastic animals (sponges, cnidarians) The hydra has 5 genes called cnox1-5. These do not appear to be linked in a cluster. The formation of a cluster proably came later in the triploblastic bilaterian animals. It is tempting to extrapolate that gain of hox genes in a cluster increases the complexity of an organism by allowing additional segments to be specified. Initially these would be just like adjacent segments, but there would be opportunity to evolve into more specialized functions. For example, if there are three sets of legs in insects, could another set of legs be added just by duplicating a hox gene that specified a leg segment of the body? What do the hox gene clusters of spiders, centipedes and millipedes look like? Are there dozens of duplicated hox genes that specify many identical segments? This provides the possibility of macroevolution. Duplication of hox genes, or whole hox gene clusters, followed by deletion and mutation might alter a species very dramatically in a short time period. The notion that additional body segments might arise fgrom duplicated hox genes was disproven by analyzing ther hox gene clusters of centipedes and onychophorans. The International Society of Developmental Biologists and the Society for Developmental Biology met in July 1997 at Alta, Utah. Researchers reported that centipedes and onychophorans, primitive, wormlike creatures believed to be the closest living relatives of the organisms that gave rise to the arthropods, including insects, have the same eight homeobox (Hox) genes as insects themselves. This indicates that the diverse body segments of insects did not evolve as a result of Hox gene duplication as previously thought, but may instead have arisen as a result of changes in Hox gene regulation. (Science 277, 639 1997). This is very exciting, because it offers many opportunities to evolve by changing the regulation of the hox genes and not the number of these genes. There are seven Hox clusters in zebrafish on seven different chromosomes (Science 281, 1119 1998). There are two copies of Hoxa, Hoxb and Hoxc with only one copy of Hoxd. The interpretation is that the whole fish genome duplicated to give eight Hox clusters and one Hoxd cluster was lost. In Mol Phylogenet Evol 9, 375-381 1998, Hox genes in the simplest known animal Trichoplax adhaerens are discussed. At least 5 Hox genes in sea anemone were detected by PCR. Biol Bull 193, 62-76 1997. Return to index Brooke NM, Garcia-Fernandez J, Holland PW. The ParaHox gene cluster is an evolutionary sister of the Hox gene cluster. Nature. 1998 Apr 30;392(6679):920-2. Coulier F, Burtey S, Chaffanet M, Birg F, Birnbaum D. Ancestrally-duplicated paraHOX gene clusters in humans. Int J Oncol. 2000 Sep;17(3):439-44. Kmita-Cunisse M, Loosli F, Bierne J, Gehring WJ. Homeobox genes in the ribbonworm Lineus sanguineus: evolutionary implications. Proc Natl Acad Sci U S A. 1998 Mar 17;95(6):3030-5. Garcia-Fernandez J, Holland PW. Archetypal organization of the amphioxus Hox gene cluster. Nature. 1994 Aug 18;370(6490):563-6. Popodi E, Kissinger JC, Andrews ME, Raff RA. Sea urchin Hox genes: insights into the ancestral Hox cluster. Mol Biol Evol. 1996 Oct;13(8):1078-86. Gauchat D, Mazet F, Berney C, Schummer M, Kreger S, Pawlowski J, Galliot B. Evolution of Antp-class genes and differential expression of Hydra Hox/paraHox genes in anterior patterning. Proc Natl Acad Sci U S A. 2000 Apr 25;97(9):4493-8. Pollard SL, Holland PW. Evidence for 14 homeobox gene clusters in human genome ancestry. Curr Biol. 2000 Sep 7;10(17):1059-62.