The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria

Abstract

Perfect short inverted repeats (IRs) are known to be enriched in a variety of bacterial and eukaryotic genomes. Currently, it is unclear whether perfect IRs are conserved over evolutionary time scales. In this study, we aimed to characterize the prevalence and evolutionary conservation of IRs across 20 proteobacterial strains. We first identified IRs in Escherichia coli K-12 substr MG1655 and showed that they are overabundant. We next aimed to test whether this overabundance is reflected in the conservation of IRs over evolutionary time scales. To this end, for each perfect IR identified in E. coli MG1655, we collected orthologous sequences from related proteobacterial genomes. We next quantified the evolutionary conservation of these IRs, that is, the presence of the exact same IR across orthologous regions. We observed high conservation of perfect IRs: out of the 234 examined orthologous regions, 145 were more conserved than expected, which is statistically significant even after correcting for multiple testing. Our results together with previous experimental findings support a model in which imperfect IRs are corrected to perfect IRs in a preferential manner via a template switching mechanism.

Coding palindromes in mitochondrial genes of Nematomorpha

“…What could be the mechanism for the formation and stability of palindromes in the mitochondrial genomes of Nematomorpha? Active maintenance of inverted repeat structures has been documented previously in the bacterial genomes (65), in the human X and Y chromosomes (66,67) and in the genomes of Caenorhabditis species (68). One possible mechanism for palindrome formation and concerted evolution of its complementary arms is the template switching mechanism (69).…”

Template switching in DNA replication can create and maintain RNA hairpins

“…We showed earlier that DNA replication-related template switch mutations (TSMs) can produce reverse-complement repeats needed for perfect DNA hairpins and fix the basepairing of existing stems (7). The mechanism has been most thoroughly studied in microbes (5,6,15,16) and been aware of in eukaryotic research (17), but few studies have looked at the role of the resulting mutations in genes (though see (18)).…”

PCIR: a database of Plant Chloroplast Inverted Repeats

“…Inverted repeats (IRs) are DNA secondary structures that consist of six or more nucleotides in reverse complementary sequence orientation (1,2). Shortly after the β-helix structure of DNA was proposed by Watson and Crick (3), the existence of IRs was recognized to account for some biological processes of cells (4,5).…”

“…Shortly after the β-helix structure of DNA was proposed by Watson and Crick (3), the existence of IRs was recognized to account for some biological processes of cells (4,5). IRs are distributed abundantly in a variety of eukaryote and prokaryote plastids (2). When the transcription or replication processes occurring, two strands separating and IRs might produce with nucleotides transiting from inter-strand to intra-strand base pairing.…”