Homeotic genes

SIGNIFICANCE: Embryonic development and organogenesis proceed by way of a complex series of cascaded gene activities that culminate in the activation of the homeotic genes to specify the final identities of body parts and shapes. The discovery of homeotic genes has provided the key to understanding these patterns of development in multicellular organisms. Study of homeotic genes is not only helping scientists understand the variety and evolution of body shapes (morphology) but also providing new insights into genetic diseases and cancer.

The Discovery of Homeotic Genes

One of the most powerful tools in genetic research is the application of mutagenic agents, such as x-rays or certain chemicals, that cause base changes in the DNA of genes to create mutant organisms. These mutants display altered appearances, or phenotypes, that give geneticists clues about how the normal genes function. Few geneticists have used this powerful research tool as well as Christiane Nüsslein-Volhard, who shared the 1995 Nobel Prize in Physiology or Medicine with Edward B. Lewis and Eric Wieschaus. Nüsslein-Volhard and her colleagues analyzed thousands of mutant Drosophila melanogaster fruit flies and discovered many of the genes that function early in embryogenesis.

Among the many mutant Drosophila flies studied by these and other investigators, two were particularly striking. One mutant had two sets of fully normal wings; the second set of wings, just behind the first set, displaced the normal halteres (flight balancers). The other mutant had a pair of legs protruding from its head in place of its antennae. These mutants were termed “homeotic” because major body parts were displaced to other regions. Using such mutants, Lewis was able to identify a clustered set of three genes responsible for the extra wings and map or locate them on the third chromosome of Drosophila. He called this gene cluster the bithorax complex (BX-C). The second mutation was called antennapedia, and its complex, with five genes, was called ANT-C. If all the BX-C genes were removed, the fly larvae had normal head structures, partially normal middle or thoracic structures (where wings and halteres are located), and very abnormal abdominal structures that appeared to be nothing more than the last thoracic structure repeated several times. From these genetic studies, it was concluded that the BX-C genes control the development of parts of the thorax and the entire abdomen and that the ANT-C genes control the rest of the thorax and most of the head.

The BX-C and ANT-C genes were called homeotic selector genes—“selector” because they act as major switch points to select or activate whole groups of other genes for one developmental pathway or another (for example, formation of legs, antennae, or wings from small groups of larval cells in special compartments called imaginal disks). Although geneticists knew that these homeotic selector genes are arranged tandemly in two clusters on the third Drosophila chromosome, they did not know the molecular details of these genes or understand how they functioned to cause such massive disruptions in the Drosophila body parts.

The Molecular Properties of Homeotic Genes

With so many mutant embryos and adult flies available, and with precise knowledge about the locations of the homeotic genes on the third chromosome, the stage was set for an intensive molecular analysis of the genes in each complex. In 1983, William Bender’s laboratory used new, powerful molecular methods to isolate and thoroughly characterize the molecular details of Drosophila homeotic genes. He showed that the three bithorax genes constituted only 10 percent of the whole BX-C cluster. What was the function of the other 90 percent if it did not contain genes? Then William McGinnis’s and J. Weiner’s laboratories made another startling discovery: the base sequences (the order of the nucleotides in the DNA) of the homeotic genes they examined contained nearly the same sequence in the terminal 180 bases. This conserved 180-base sequence was termed the “homeobox.” What was the function of this odd but commonly found DNA sequence? What kind of protein did this homeobox-containing gene make?

Soon it was discovered that homeotic genes and homeoboxes are not confined to Drosophila. All animals have them, both vertebrates, such as mice and humans, and invertebrates, such as worms and even sea sponges. The sequence is conserved not only within homeotic and other developmental genes but also throughout the entire animal kingdom. All animals seem to possess versions of an ancestral homeobox gene that has duplicated and diverged over evolutionary time.

New discoveries about homeobox genes flowed out of laboratories all over the world in the late twentieth and early twenty-first centuries. It was discovered that the order of the homeobox genes in the gene clusters from all animals is roughly the same as the order of the eight genes found in the original BX-C and ANT-C homeotic clusters of Drosophila. In more complex animals such as mice and humans, the two Drosophila-type clusters are duplicated on four chromosomes instead of just one. Mice have thirty-two homeotic genes, plus a few extra not found in Drosophila. Frank Ruddle hypothesized that the more anatomically complex the animal, the more homeotic genes it will have in its chromosomes. Experimental evidence from several laboratories has supported Ruddle’s hypothesis.

The questions posed earlier about the functions of extra DNA in the homeotic clusters and the role of the homeobox in gene function were finally answered. It seems that all homeotic genes code for transcription factors, or proteins that control the activity or expression of other genes. The homeobox portion codes for a section of protein, the homeodomain, that binds to base sequences in the promoters of other genes. This can lead to either activation (turning on) or repression (turning off) of expression of target genes. In addition to the conserved homeodomain, the transcription factors encoded by homeobox genes contain additional domains that interact with the transcriptional machinery. For activation of target gene expression, a protein-protein interaction domain called an activation domain must be present within the protein to recruit the preinitiation complex factors to the promoter. The preinitiation complex positions the II over the gene transcription start site for transcription. A secondary role of homeotic genes is the repression of inappropriate gene expression. Target gene repression is mediated via a repression domain that recruits repressors to the homeodomain protein anchored to a site via its homeodomain. This leads to the additional recruitment of a repression complex, which causes the conformation of the DNA to change so that RNA polymerase II cannot bind.

The clustered organization of homeobox genes along the chromosome is conserved between flies and mice and corresponds to the segmental organization of the embryo along the anterior-posterior body axis. Thus, earlier idea of homeotic genes as selector genes makes sense.

The vertebrate homologues of the Antennapedia type homeobox genes are called Hox genes. In addition to these genes, a number of independent homeobox genes have been identified that are involved in either organ or tissue specification. These include the NK (for "natural killer") genes.

Impact and Applications

In a 1997 episode of the television series The X-Files, a scientist creates a living being using a similar method as the modern scientific experiments on the Drosophila fruit flies. The creature, which seems to have two heads, is seen as a monster by the townspeople. Federal Bureau of Investigation (FBI) agent Dana Scully patiently explains to her partner, Fox Mulder, that the scientist altered the being's homeobox genes, causing the mutant phenotype. The scenario was science fiction, but with the successful cloning of Dolly the sheep in 1997, the prospect of manipulating homeobox genes in embryos was no longer far-fetched.

The first concern of scientists is to elucidate more molecular details about the actual processes by which discrete genes transform an undifferentiated egg cell into a body with perfectly formed, bilateral limbs. Sometimes mutations in homeobox genes cause malformed limbs, extra digits on the hands or feet, or fingers fused together, conditions known as synpolydactyly; often limb and hand deformities are accompanied by genital abnormalities. Several reports in 1997 provided experimental evidence for mutated homeobox genes in certain types of leukemia and cancerous tumors. Beginning in 1996, the number of reports describing correlations between mutated homeobox genes and specific cancers and other developmental abnormalities increased dramatically. During the 2010s, scientists confirmed a link between mutated homeobox genes did lead to an increased possibility of cancer. By 2023, scientists had made progress in establishing this link. From their research, they theorized that homeobox D10 (HOXD 10), which controls cell differentiation and morphogenesis, contributes to the metastatic development of cancer. Researchers were optimistic that future studies would likely lead to new treatments for limb deformities and certain cancers.

Key Terms

• promoterthe control region in genes where transcription factors bind to activate or repress
• transcription factora protein with specialized structures that binds specifically to the promoters in genes and controls the gene’s activity

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