Abstract
Extrachromosomal genetic elements such as bacterial endosymbionts and plasmids generally exhibit AT-contents that are increased relative to their hosts’ DNA. The AT-bias of endosymbiotic genomes is commonly explained by neutral evolutionary processes such as a mutational bias towards increased A+T. Here we show experimentally that an increased AT-content of host-dependent elements can be selectively favoured. Manipulating the nucleotide composition of bacterial cells by introducing A+T-rich or G+C-rich plasmids, we demonstrate that cells containing GC-rich plasmids are less fit than cells containing AT-rich plasmids. Moreover, the cost of GC-rich elements could be compensated by providing precursors of G+C, but not of A+T, thus linking the observed fitness effects to the cytoplasmic availability of nucleotides. Accordingly, introducing AT-rich and GC-rich plasmids into other bacterial species with different genomic GC-contents revealed that the costs of G+C-rich plasmids decreased with an increasing GC-content of their host’s genomic DNA. Taken together, our work identifies selection as a strong evolutionary force that drives the genomes of intracellular genetic elements toward higher A+T contents.
Highlights
Bacterial genomes exhibit a considerable amount of variation in their nucleotide composition (G+C versus A+T), ranging from less than 13% to more than 75% GC [1, 2]
Genomes of other intracellular elements like plasmids or bacteriophages tend to be richer in AT than the genomes of their hosts
Since A+T nucleotides are both more abundant and energetically less expensive than G+C nucleotides, an alternative explanation is that selective advantages drive the nucleotide composition of intracellular elements
Summary
Bacterial genomes exhibit a considerable amount of variation in their nucleotide composition (G+C versus A+T), ranging from less than 13% to more than 75% GC [1, 2]. A general pattern that emerged from sequencing the genomes of numerous taxa is that bacteria, whose survival obligately depends on a eukaryotic host (i.e. endosymbionts), display genomic AT-contents that are significantly increased in comparison to the genomes of their free-living relatives as well as their hosts’ genomes [4]. Intracellular genetic elements that permanently or transiently exist outside the bacterial chromosome, such as plasmids, viruses, phages, and insertion sequence (IS) elements, are usually characterized by a significantly higher AT-content than the genome of their host [5, 6]. While less attention has been paid to extrachromosomal genetic elements such as plasmids and bacteriophages, two main hypotheses have been put forward to explain the biased nucleotide composition of obligate intracellular bacteria: First, high AT-contents can result from increased levels of genetic drift and mutational bias [4, 7, 8]. Since the majority of DNA modifications caused by oxygen radicals (either from the environment or generated by endogenous cellular processes) lead to mispairing of DNA bases, which mostly results in GC!AT transitions and G/C!T/A transversions [9], in the long-run genetic drift is expected to increase the elements’ overall ATcontent
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