Abstract
BackgroundThe introduction of foreign DNA by Lateral Gene Transfer (LGT) can quickly and drastically alter genome composition. Problems can arise if the genes introduced by LGT use codons that are not suited to the host’s translational machinery. Here we investigate compensatory adaptation of E. coli in response to the introduction of large volumes of codons that are rarely used by the host genome.ResultsWe analyze genome sequences from the E. coli/Shigella complex, and find that certain tRNA genes are present in multiple copies in two pathogenic Shigella and O157:H7 subgroups of E. coli. Furthermore, we show that the codons that correspond to these multi-copy number tRNA genes are enriched in the high copy number Selfish Genetic Elements (SGE’s) in Shigella and laterally introduced genes in O157:H7. We analyze the duplicate copies and find evidence for the selective retention of tRNA genes introduced by LGT in response to the changed codon content of the genome.ConclusionThese data support a model where the relatively rapid influx of LGT genes and SGE’s introduces a large number of genes maladapted to the host’s translational machinery. Under these conditions, it becomes advantageous for the host to retain tRNA genes that are required for the incorporation of amino acids at these codons. Subsequently, the increased number of copies of these specific tRNA genes adjusts the cellular tRNA pool to the demands set by global shifts in codon usage.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0441-y) contains supplementary material, which is available to authorized users.
Highlights
The introduction of foreign DNA by Lateral Gene Transfer (LGT) can quickly and drastically alter genome composition
The most striking example from the above analysis is the multiple copies of a tRNAAGA gene, which in the type strain MG1655 is encoded by a single copy of argU, while O157:H7 Sakai has eight tRNAAGA genes
The picture of tRNA gene copy number and codon use evolution has become more sophisticated over decades of study
Summary
The introduction of foreign DNA by Lateral Gene Transfer (LGT) can quickly and drastically alter genome composition. Problems can arise if the genes introduced by LGT use codons that are not suited to the host’s translational machinery. We investigate compensatory adaptation of E. coli in response to the introduction of large volumes of codons that are rarely used by the host genome. Transferred Genes play an important role in the adaptation of bacterial pathogens [1,2,3,4,5]. SGE’s and LGT genes can contain codons that are rarely found in the host genome. It is of interest to investigate the indirect effects of introducing large numbers of these genes upon genome level traits such as codon usage and the global tRNA pool
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