Genomic island

Genomic Island

A genomic island is a distinct segment of DNA within a genome that has been acquired through horizontal gene transfer. These regions are often associated with specific functions, such as pathogenicity, symbiosis, or antibiotic resistance, and can be identified by their atypical nucleotide composition compared to the rest of the genome.

Characteristics

Genomic islands are typically characterized by:

• **G+C Content**: They often have a different guanine-cytosine content compared to the host genome.
• **Flanking Direct Repeats**: Short sequences that are repeated at both ends of the island.
• **Mobile Genetic Elements**: Presence of genes related to mobility, such as integrases, transposases, or insertion sequences.
• **Functional Genes**: Genes that confer specific advantages, such as virulence factors in pathogenicity islands or nitrogen fixation genes in symbiosis islands.

Types of Genomic Islands

Genomic islands can be classified based on their function:

• Pathogenicity Islands (PAIs): These are found in pathogenic bacteria and contain genes that contribute to the bacterium's ability to cause disease. For example, the Salmonella pathogenicity island 1 (SPI-1) encodes a type III secretion system.

• Symbiosis Islands: These islands contain genes that facilitate symbiotic relationships. An example is the symbiosis island in Rhizobium species, which contains genes for nitrogen fixation.

• Antibiotic Resistance Islands: These islands carry genes that provide resistance to antibiotics, such as the SCCmec element in Staphylococcus aureus.

Detection and Analysis

The identification of genomic islands involves several bioinformatics approaches:

• **Comparative Genomics**: Comparing the genome of interest with closely related species to identify unique regions.
• **G+C Content Analysis**: Scanning the genome for regions with atypical G+C content.
• **Codon Usage Bias**: Analyzing the codon usage patterns to detect foreign DNA.
• **Presence of Mobility Genes**: Identifying genes associated with horizontal gene transfer.

Biological Significance

Genomic islands play a crucial role in the evolution and adaptation of bacteria. They allow for rapid acquisition of new traits that can enhance survival in changing environments. For instance, the acquisition of antibiotic resistance genes can enable bacteria to survive in the presence of antibiotics.

Examples

• Vibrio Pathogenicity Island (VPI): Found in Vibrio cholerae, this island contains genes for toxin production and colonization factors.
• ICEclc: An integrative and conjugative element in Pseudomonas species that carries genes for degradation of chlorinated compounds.

See Also

• Horizontal gene transfer
• Pathogenicity island
• Antibiotic resistance

References

• Hacker, J., & Kaper, J. B. (2000). Pathogenicity islands and the evolution of microbes. Annual Review of Microbiology, 54, 641-679.
• Dobrindt, U., Hochhut, B., Hentschel, U., & Hacker, J. (2004). Genomic islands in pathogenic and environmental microorganisms. Nature Reviews Microbiology, 2(5), 414-424.