The relatively small chromosomes of bacteria (~106 base pairs) utilize a simpler mechanism than eukaryotic replication. A single origin of replication initiates the duplication of the bacterial chromosome, and replication occurs simultaneously on both strands in opposite directions from the origin of replication. This efficient replication process depends on the circular topology of the bacterial genome.
Another unique feature of prokaryotic chromosomal replication is the mechanism bacteria have evolved to protect their chromosomes. The lack of a protective nuclear membrane in bacteria makes the chromosome susceptible to attack by viruses (bacteriophages). As a result, many bacteria produce restriction enzymes that degrade foreign nucleic acids. These restriction enzymes recognize specific short sequences and cleave the DNA at those sites. However, methylation of the recognition sequences in the bacterial chromosomal DNA prevents most restriction enzymes from digesting the chromosomal DNA of the bacteria. In this way, methylating enzymes add methyl groups to the replicated bacterial chromosome, preventing chromosomal degradation by its own restriction enzymes. This methylation and restriction process functions as a primitive immune system by destroying foreign bacteriophage DNA before it can usurp the bacteria's replication system. Bacterial restriction enzymes are used to specifically cleave DNA in molecular diagnostic tests and are useful for identifying genetic variations.
Additional types of replication occur in some viruses and bacteria. The rolling-circle mechanism of replication proceeds with an initial single-strand cut or nick in double-stranded circular genomes, followed by replication proceeding from the nick in a 5' to 3' direction. The new strand displaces the old strand. RNA viral genomes use the enzyme transcriptase for replication. In the case of retro-viruses, a reverse transcriptase generates an intermediate DNA molecule, which integrates into the host chromosome and then is used for generation of progeny RNA molecules. The high error rate of human immunodeficiency virus (HIV) reverse transcriptase produces numerous mutations in the viral genome.10,11 Some of these mutations confer resistance to antiretroviral therapies and can be identified by clinical molecular tests.
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