Gene Amplification and Genomic Plasticity in Prokaryotes

Abstract

Gene amplification is a common feature of the genome of prokaryotic organisms. In this review, we analyze different instances of gene amplification in a variety of prokaryotes, including their mechanisms of generation and biological role. Growing evidence supports the concept that gene amplification be considered not as a mutation but rather as a dynamic genomic state related to the adaptation of bacterial populations to changing environmental conditions or biological interactions. In this context, the potentially amplifiable DNA regions impose a defined dynamic structure on the genome. If such structure has indeed been selected during evolution, it is a particularly challenging hypothesis.

Reducing the fitness cost of antibiotic resistance by amplification of initiator tRNA genes

“…Similarly, adaptive mutability in the lac system has been proposed to be mediated via selected stepwise increases in the copy number of the partly functional lac operon (26,27). Because of the high intrinsic instability of tandem amplifications, haploid segregants will rapidly appear and take over the population when the selective condition disappears (28,29). Gene amplification is also thought to be important for the creation of new genes.…”

Vertical Transmission of Biosynthetic Plasmids in Aphid Endosymbionts ( Buchnera )

“…Bacterial genomes are characterized by remarkable plasticity that allows rapid genetic adaptations to environmental changes (reviewed in references 3,33,46). Plasmids, extrachromosomal DNA molecules that replicate autonomously, contribute to this plasticity by mediating lateral gene transfer among bacterial species and genera (15,17,21,40,57,59,65) and even between kingdoms (19,24).…”

“…Plasmids, extrachromosomal DNA molecules that replicate autonomously, contribute to this plasticity by mediating lateral gene transfer among bacterial species and genera (15,17,21,40,57,59,65) and even between kingdoms (19,24). In addition to their role in lateral gene transfer, plasmids also function in gene amplification and overexpression (46,47). Just as chromosomal duplications are a common mechanism for increasing gene dosage in response to fluctuations in the environment (47,54), amplification of loci on plasmids may be adaptive when selection favors increased gene dosages (12,20).…”

The Suppressor‐mutator element and the evolutionary riddle of transposons

“…Once a duplication exists, the mechanisms that generated it also permit unequal crossing-over between identical repeats (Anderson & Roth 1977;Perelson & Bell 1977;Koch 1979). In micro-organisms, the frequency of unequal crossing-over between tandem repeats is higher than the duplication frequency (Romero & Palacios 1997). Unequal crossing-over between repeated sequences produces organisms with higher numbers of repeats, and organisms with only one remaining copy of the duplicated sequence (Perelson & Bell 1977).…”

“…Absent mechanisms to stabilize duplications or permit their asymmetric generation, organisms with many copies of a given sequence can never come to dominate a population without phenotypic selection. Prokaryotes bear out this theoretical expectation, transiently generating and readily losing large tandem duplications in response to selection (Koch 1971;Anderson & Roth 1977;Romero & Palacios 1997). The DNA segments most commonly amplified are, importantly, often bounded by transposons, which provide the dispersed homologies necessary to originate duplication (Romero & Palacios 1997).…”