Abstract
Bacteria can have multiple copies of a gene at separate locations on the same chromosome. Some of these gene families, including tuf (translation elongation factor EF-Tu) and rrl (ribosomal RNA), encode functions critically important for bacterial fitness. Genes within these families are known to evolve in concert using homologous recombination to transfer genetic information from one gene to another. This mechanism can counteract the detrimental effects of nucleotide sequence divergence over time. Whether such mechanisms can also protect against the potentially lethal effects of mobile genetic element insertion is not well understood. To address this we constructed two different length insertion cassettes to mimic mobile genetic elements and inserted these into various positions of the tuf and rrl genes. Wemeasured rates of recombinational repair that removed the inserted cassette and studied the underlying mechanism. Our results indicate that homologous recombination can protect the tuf and rrl genes from inactivation by mobile genetic elements, but forinsertions within shorter gene sequences the efficiency of repair is very low. Intriguingly, we found that physical distance separating genes on the chromosome directly affects the rate of recombinational repair suggesting that relative location will influence the ability of homologous recombination to maintain homogeneity.
Highlights
Gene families with multiple copies of the same gene separately located on the chromosome are a frequent feature in prokaryotic and eukaryotic genomes
Bacteria can have multiple copies of a gene at separate locations on the same chromosome. Some of these gene families, including tuf and rrl, encode functions critically important for bacterial fitness. Genes within these families are known to evolve in concert using homologous recombination to transfer genetic information from one gene to another
Our results indicate that homologous recombination can protect the tuf and rrl genes from inactivation by mobile genetic elements, but for insertions within shorter gene sequences the efficiency of repair is very low
Summary
Gene families with multiple copies of the same gene separately located on the chromosome are a frequent feature in prokaryotic and eukaryotic genomes. Despite the ancient origin of the duplication, the tuf genes of Salmonella enterica serovar Typhimurium strain LT2 differ at only 13 of 1185 nucleotides (Abdulkarim and Hughes, 1996). This high degree of nucleotide identity indicates that the tuf genes evolve in concert. It has been shown that homologous recombination between the genes leads to the exchange of genetic information, which facilitates this co-evolution (Abdulkarim and Hughes, 1996; Paulsson et al, 2017) and a similar mechanism is expected to operate in other gene families. Co-evolution by recombination can limit the divergence of sequences in gene homologs (Abdulkarim and Hughes, 1996) or of functional domains within protein paralogs (Kruithof et al, 2007)
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