Evolution of genes and dynamic genome
Authors: Arpita Srivastava and Manisha Mangal
Division of Vegetable Science, Indian Agricultural Research Institute, Pusa Campus


Genes and genomes existing today are the cumulative result of events that have taken place in the past. The classical theory of evolution as formulated by Charles Darwin in 1859 states that (i) all living organisms today have descended from organisms living in the past; (ii) organisms that lived during earlier times differed from those living today; (iii) the changes were more or less gradual, with only small changes at a time; and (iv) the changes usually led to divergent organisms, with the number of ancestral types of organisms being smaller than the number of types today.

(i) Gene evolution by duplication

Studies of the various genomes indicate that different types of duplication must have occurred: of individual genes or parts of genes (exons), subgenomic duplications, and rarely, duplications of the whole genome. Duplication of a gene relieves the selective pressure on that gene. After a duplication event, the gene can accumulate mutations without compromising the original function, provided the duplicated gene has separate regulatory control.

(ii) Gene evolution by exon shuffling

The exon/intron structure of eukaryotic genes provides great evolutionary versatility. New genes can be created by placing parts of existing genes into a new context, using functional properties in a new combination. This is referred to as exon or domain shuffling.

(iii) Evolution of chromosomes

Evolution also occurs by structural rearrangements of the genome at the chromosomal level. Related species, e.g., mammals, differ in the number of their chromosomes and chromosomal morphology, but not in the number of genes, which often are conserved to a remarkable degree. The human chromosome 2 appears to have evolved from the fusion of two primate chromosomes. The differences in chromosome 3 are much more subtle. The orang-utan chromosome 3 differs from that of man and the other primates by a pericentric inversion. The banding patterns of all primate chromosomes are remarkably similar. This reflects their close evolutionary relationship.

(iv) Molecular phylogenetics and evolutionary tree reconstruction

In the path from an ancestral gene, two events are shown schematically. Two categories of homologs are distinguished: paralogs and orthologs. Paralogs are homologous genes that have evolved by duplication of an ancestral gene within a species. Orthologs are genes that have evolved by vertical descent from an ancestral gene between different, but related species. The human alpha- and delta-globin loci are examples of paralogs. The _-globin genes of humans and other mammals are examples of orthologs. The adjective paralogous refers to nucleotide sequence comparisons.

Further the genome is to be dynamic i.e, it is flexible and subject to changes. DNA sequences can alter their position within the genome. This unusual phenomenon was first observed in the late 1940s by Barbara McClintock while investigating the genetics of Indian corn (maize, Zea mays). She found that certain genes apparently were able to alter their position spontaneously and named them "jumping genes," later mobile genetic elements. Today they are known as transposons. Transposable genetic elements occur in large numbers in the genomes of most organisms, including man.

(i) Stable and unstable mutations

McClintock (1953) determined that certain mutations in maize are unstable. A stable mutation at the C locus causes violet corn kernels whereas unstable mutations cause fine pigment spots in individual kernels.

(ii) Effect of mutation and transposition

Normally a gene at the C locus produces a violet pigment of the aleurone in cells of Indian corn. This gene can be inactivated by insertion of a mobile element (Ds) into the gene, resulting in a colorless kernel. If Ds is removed by transposition, C-locus function is restored and small pigmented spots appear.

(iii) Insertion and removal of Ds

Activator-dissociation (Ac/Ds) is a system of controlling elements in maize. Ac is an inherently unstable autonomous element. It can activate another locus, dissociation (Ds), and cause a break in the chromosome. While Ac can move independently (autonomous transposition), Ds can move to another location in the chromosome only under the influence of Ac (non autonomous transposition). The Ac locus is a 4.6-kb transposon; Ds is defective without a transposase gene. The C locus is inactivated by the insertion of Ds. Ds can be removed under the influence of Ac. This restores normal function at the C locus. If transposition occurs early in development, the pigmented spots are relatively large; if transposition occurs late, the spots are small.

(iv) Transposons in bacteria

Transposons are classified according to their effect and molecular structure: simple insertion sequences (IS) and the more complex transposons (Tn). A transposon contains additional genes, e.g., for antibiotic resistance in bacteria. Transposition is a special type of recombination by which a DNA segment of about 750 bp to 10 kb is able to move from one position to another, either on the same or on another DNA molecule. The insertion occurs at an integration site and requires a break with subsequent integration. The sequences on either side of the integrated segment at the integration site are direct repeats. At both ends, each IS element or transposon carries inverted repeats whose lengths and base sequences are characteristic for different IS and Tn elements. One E. coli cell contains on average about ten copies of such sequences. They have also been demonstrated in yeast, Drosophila, and other eukaryotic cells.

References:
- Color Atlas of Genetics - Page 262-264 - By Eberhard Passarge

About Author / Additional Info:
I am working as a scientist at Indian Agricultural Research Institute, New Delhi with specialisation in Genetics and Plant Breeding. Basically involved in hot pepper improvement programs.