Homeotic Genes and Body Patterns
Every organism has a unique body pattern. Although specialized body structures, such as arms and legs, may be similar in makeup (for example, both are made of muscle and bone), their shapes and details are different. During growth of the embryo, arms and legs develop differently due to the actions of special genes, called homeotic genes, which specify how structures develop in different segments of the body.
How did scientists discover genes that determine body pattern?
Scientists discovered these genes by studying bizarre mutations in fruit flies. They correlated mutations in different genes with transformations in the flies' body patterns. These types of mutations, called homeotic mutations, cause structures in one body segment to be replaced by structures normally found in another segment.
Antenna to leg
One research group, led by biologist Ed Lewis, studied fruit flies that had legs growing out of their heads in place of antennae! They found that a mutation in a single gene, called Antennapedia, made this transformation happen. Scientists believe that this mutation changes not only the antennal structure, but makes that entire segment of the fruit fly's body develop as if it were a different segment.
Dr. Lewis's work demonstrated that antennal cells carry all of the information necessary to become leg cells. This is a general principle: every cell in an organism carries, within its DNA, all of the information necessary to build the entire organism.
Common sequence characteristics
While studying the DNA sequences of many genes that control body pattern, researchers found that each contains a similar stretch of about 180 nucleotides within its sequence. They named this stretch a homeobox, and classified all genes containing it as homeotic genes. The homeobox is only a portion of each gene. For example, if the words below were homeotic genes, the capital letters would represent the homeobox:
Shown below is the homeotic gene expression seen in the fruit fly. As you mouse over the different genes in the homeotic complexes, you can observe that each gene is responsible for controlling body pattern in a particular region. Also notice that the genes are arranged on the chromosome in an order corresponding to the order they appear on the body.
Many organisms have similar sets of homeotic genes
Researchers were curious to know whether organisms other than fruit flies also had homeotic genes that regulated body patterning. Several research groups, led by Bill McGinnis, Michael Levine and Walter Gehring, examined this question.
First, they looked through the DNA from a variety of animals for sequences similar to the homeobox. They took advantage of the fact that DNA is double stranded, meaning that DNA is composed of two separable strands, connected by A-T and C-G base pairs.
How did they do this?
The two strands in DNA can be melted apart at high temperatures. Once separated, the strands are free to pair with other DNA molecules in the same mixture. If the two original strands are the only molecules in the mixture, then they will re-pair with each other, reforming the original double-stranded DNA molecule. If other DNA molecules with similar sequences are present in the mixture, then new double-stranded DNA molecules will be formed using different combinations of single strands.
To see whether other animals contain homeobox sequences in their DNA, the researchers mixed fruit fly homeobox DNA sequences with DNA from other animals, such as frogs. They heated the mixture to separate the DNA strands, then allowed the mixture to cool slowly. The slow cooling process allows DNA molecules with complementary sequences to find each other and pair together. Then they observed whether double stranded DNA sequences had formed between the fruit fly and frog DNA. Finally, they isolated the frog sequences that had base paired with the fruit fly homeobox DNA and determined the frog DNA sequence.
What did they find?
Every animal tested had homeobox sequences in its DNA.
Homeobox sequences found in most mammalian genes are very similar to those in fruit flies. These sequences have been conserved throughout evolution without much change.
Gene sequences maintained over evolutionary time are thought to be especially important to the basic development of even distantly related organisms. For example, flour beetles and fruit flies share a cluster of homeobox genes, called the homeotic complex or HOM-C, that are very similar in sequence and function.
Genes in different organisms that share similar sequence and function are called homologous. The insect HOM-C gene cluster also shares homology with Hox gene complexes in mammals.
Homeotic gene organization is conserved through evolution
The extent to which gene sequence and organization are conserved between organisms gives us clues about the amount of evolutionary time that has passed since the two organisms diverged from one another. For example, the homeotic gene clusters in the flour beetle (Tribolium) and the fruit fly (Drosophila) are very similar. In contrast, the homeotic gene clusters in these two insects differ greatly from those in the mouse. The presence of homeotic gene sequences in animals as different as insects and mammals suggests that this type of gene has a crucial function in many, and perhaps all, animals.
This figure shows the organization of homeotic gene clusters in the flour beetle, the fruit fly and the mouse. The colored boxes represent different homeotic genes as they are laid out on a chromosome (signified by the blue line).
The squiggle in the middle of the Drosophila chromosome represents the space on the chromosome between the two homeotic gene clusters, ANT-C and BX-C. Each of the four homeotic gene clusters in the mouse (inside the pink box) resides on a different chromosome.
The mouse, fruit fly and flour beetle have similar homeobox genes. What can gene organization tell us about evolutionary relationships between these organisms?
One way scientists study this type of problem is to compare the chromosomal arrangement of homologous genes in different organisms. The homeotic genes of the flour beetles cluster tightly on one chromosome - scientists refer to this clustering as tight linkage. Genes that are closer together on a chromosome are more likely to be inherited by the next generation as a linked group.
Homeotic genes in the fruit fly are broken into two clusters on the same chromosome and separated by a long stretch of DNA (blue line). The five genes shown at left (blue and pink boxes) represent the Antennapedia complex (ANT-C). The three genes shown at right (yellow boxes) are part of the Bithorax complex (BX-C).
The mouse has four homeotic gene clusters. All four are similar, but they are located on different chromosomes. Scientists believe that this sort of gene arrangement results from the duplication of a chromosomal region. The homeotic gene cluster in mammals has apparently been duplicated four times. Each cluster is somewhat different. Most are incomplete, missing some fraction of the genes that are present in the ancestral gene cluster.
Mutations in mammalian homeotic genes
Homeotic genes in mammalian genomes appear to have been duplicated over evolutionary time. If you line them up using DNA sequence as a guide, you can see that the genes' organization is conserved.
In each case, the corresponding genes between each cluster (for example, A4, B4, C4, D4) are more closely related to each other than to the genes within a cluster (for example, A4, A5, A6). Some clusters have lost genes. Other genes are retained in all four clusters.
Genes that correspond to each other in each duplicated cluster (i.e. A4, B4, C4, D4) are called paralogs. Studies have shown that paralogs have similar, and often overlapping, functions in the animal. For this reason, it is difficult to study the function of a homeotic gene by making a mutation in the gene and studying its effects - in many cases, the effects are hidden by the normal functions of other genes in the same paralogous group.
To remove the function provided by a group of paralogs, a mutation must be made in every gene in the group. If the function is removed in this way, dramatic effects can be observed.
Mice with mutations in paralogous genes
This picture, provided by Mario Capecchi's research group at the University of Utah, shows the effects of mutating two of the three genes in one paralogous group in the mouse HOX cluster. These are the forelimb bones from mice with mutations in two genes from the Hox-11 group.
The capital letters A and D represent the normal HOX A-11 or HOX D-11 genes. The small letters a and d represent mutated genes. For each picture, the genotype of the animal at these two genes is shown. For example, "aa; DD" represents a mouse carrying two mutated copies of the HOX A-11 gene and two normal copies of the HOX D-11 gene.
- (a) is a normal forelimb. The letters h, r, and u indicate the three main bones of the forelimb: r=radius, u=ulna, h=humerus.
- (b) shows the forelimb from a mouse carrying two mutated copies of HOX A-11 and two normal copies of HOX D-11.
- (c) shows the forelimb from a mouse carrying two mutated copies of HOX D-11 and two normal copies of HOX A-11. Note that the structure and arrangement of the bones in (b) and (c) are both approximately normal. Therefore, mutation of a single gene in this paralogous group has only a mild effect on the animal.
- (d) shows the forelimb from a mouse carrying mutations in both copies of both genes. Note that two of the forelimb bones, the radius and ulna, are almost completely missing. The mutations in both genes have produced a striking change in body shape.
In insects, the phenotypes of mutations in homeotic genes are much easier to observe, since only one copy of each homeotic gene exists. If this single gene is mutated, no other normal gene can mask the effects of the mutation.
Homeotic gene mutations may play a role in evolutionary change
Organisms can survive and reproduce even with homeotic gene mutations that produce differences in body shape. This means that homeotic mutations can be an effective means for evolutionary change.
For example, in a mammal, a single homeotic mutation might produce an arm that is shorter, or longer, or broader. Regardless, it will probably still look and work like an arm.
A change in body shape might lead to an advantage for an organism. For example, the mutation may allow it to capture food more effectively or be more attractive in some way. If this is the case, then the mutant organism may have greater reproductive fitness. Its genes may be preferentially passed along to the next generation, thus influencing the course of evolution.