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24.3Changes in the Genome

24.3.1

Vertical transmission of genome

Phenotype changes, which can be explained by mutations occurring in the genome, promote evolution. Consequently, every time the genome is inherited through generations, i.e., every time the genome is transmitted vertically through generations, there is a chance for mutations on the genome level, in other words, there is a chance for evolution.

Point mutations due to mutagens such as ultraviolet light and incorporation errors that occur during genetic replication are also examples of genomic changes. Especially in organisms that carry out sexual reproduction, gene duplication, which occurs during meiosis of gametes, and genetic recombination such as crossing over and inversion promote genomic changes in vertical transmission. For example, it is considered that chromosome 2 of humans was created by fragmentary linkage of chromosomes 12 and 13 of chimpanzees*9. This suggests that the genomic changes such as recombination of chromosomes are associated with the evolution of species (Figure 24-4).

*9 Humans have 22 pairs of autosomal chromosomes and 1 pair of sex chromosomes, whereas chimpanzees have 23 pairs of autosomal chromosomes and 1 pair of sex chromosomes.

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24.3.2

Vertical transmission and diversity of the genome

The morphology of eukaryotic multicellular organisms is very diverse, which is thought to be the result of accumulation of genetic mutations occurring during vertical transmission of the genome. On the other hand, when we look at the morphology of specific parts of the body, such as limbs, thorax and abdomen, a striking level of homology is maintained in their structures. HOM-C/Hox is known as a gene involved in such morphogenesis of organisms (see Column Selection 2 of Chapter 19). When compared among various species, the HOM-C/Hox gene was found to be very well preserved. This may be because mutation of genes related to morphogenesis can easily lead to death, and thereby mutations in those genes could not be allowed by organisms in order for them to survive. Meanwhile, the HOM-C/Hox gene has a structure in which highly similar gene sequences are repeated. This suggests that genes with slightly different functions originated from gene duplication, which led to diverse morphogenesis. In addition, as the products of the HOM-C/Hox gene are transcription factors promoting the transcription of genes by binding to DNA, it is thought that the accumulation of genomic changes, such as point mutations, duplications, and inversion of DNA sequences to which the products of the HOM-C/Hox gene bind, has enabled the diverse morphogenesis of life.

Through the HOM-C/Hox gene given as an example here, it can be seen that changes in genome sequences control evolution, that there are regions in the genome that are prone to change and those that are not, and that diversity originates from the relation between the functions of genetic products and changes in genome sequences (Figure 24-5). This is why despite the drawback that the speed of molecular evolution differs depending on the sequence, genome comparison enables tracking back the evolution of life. From this viewpoint, the concept of species is not strictly fixed but changes according to time. Even the human species changes at the genome level in the long term.

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24.3.3

Horizontal transmission of the genome

In terms of molecular phylogenetic studies, to what extent can the origin of life be traced back time? Comparisons at the genome level are gradually showing that this is not so simple. Especially with regard to bacteria, the exchange of DNA sequences between different species seemed to be carried out frequently in both eubacteria and archaebacteria. DNA such as phages*10, plasmids, and transposons*11 enables such horizontal transmission of genes. At present, as shown in Figure 24-6, concepts of phylogenetic trees are being proposed in which species have exchanged DNA sequences mutually at the genome level.

*10 Bacteriophages are viruses that infect bacteria.
*11 A piece of DNA may move from a region of the chromosomal DNA to other region. A transposon is a DNA segment that is able to insert itself into another place in the genome. It is also called mobile gene element. In 1951, an idea that “genes can change their positions and move around on chromosomes” was proposed by Barbara McClintock. At that time, this idea was more or less not accepted, as not much was even known about DNA structure. Later, it was discovered that this mobile genes were transposons, and she was awarded the Nobel Prize in Physiology or Medicine in 1983.

Figure 24-4 Genome changes and evolution of species

A) Humans and chimpanzees have about the same genome size and number of genes, but a different number of chromosomes. Consequently, the two species cannot produce offspring. B) Chromosome 2 in humans has a structure formed by a fusion of chimpanzee chromosomes 12 and 13.

Figure 24-5 Genome changes and diversity

Gene recombination such as exon shuffling may produce genes with new functions. Accumulation of mutations in genes after gene duplications may promote the production of genes with different functions. Gene mutations are accumulated not only in amino acid sequences, but also in non-translated regions such as those where gene expression is regulated. Such genome changes are thought to have given rise to the diversity of organisms.

Figure 24-6 Outline of phylogenetic trees taking into account genome changes

Schematic diagram of a phylogenetic tree taking into account genome changes through horizontal transmission. The genomes of organisms have evolved by repeating not only orderly vertical transmission, but also horizontal transmission between species. Adapted from Doolittle W.F., Scientific American, 2000, 90-95.

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