Curiosities of REPINs and RAYTs

Abstract

Repetitive extragenic palindromic (REP) sequences are a ubiquitous feature of bacterial genomes. Recent work shows that REPs are remnants of a larger mobile genetic element termed a REPIN. REPINs consists of two REP sequences in inverted orientation separated by a spacer region and are thought to be non-autonomous mobile genetic elements that exploit the transposase encoded by REP-Associated tYrosine Transposases (RAYTs). Complimentarity between the two ends of the REPIN suggests that the element forms hairpin structures in single stranded DNA or RNA. In addition to REPINs, other more complex arrangements of REPs have been identified in bacterial genomes, including the genome of the model organism Pseudomonas fluorescens SBW25. Here, we summarize existing knowledge and present new data concerning REPIN diversity. We also consider factors affecting the evolution of REPIN diversity, the ease with which REPINs might be co-opted by host genomes and the consequences of REPIN activity for the structure of bacterial genomes.

Conformational diversity of single‐stranded DNA from bacterial repetitive extragenic palindromes: Implications for the DNA recognition elements of transposases

“…REP elements are abundant2 and mobile4 segments of bacterial genomes, with the latter characteristic possibly due to their association with transposase RAYT,10 which has been postulated to serve as their mobilizer. The CD, UV melting, and DSC data presented here reveal complex conformational behavior of single stranded repetitive extragenic DNA elements (REPs), which we judge to be important in differential recognition and regulation.…”

“…REP-dependent regulation of transcription and mRNA turnover has been recorded in E. coli and several other gamma proteobacteria 7–9. REP elements were hypothesized to be mobile, which was confirmed in Pseudomonas fluorescens , where excisions of REPINs were detected 4. A class of transposase-related nucleases, termed REP-associated tyrosine transposases (RAYTs), recently were discovered and proposed to function as primary mobilizers of REP elements 10.…”

“…First discovered in Escherichia coli ,1 these imperfect palindromic elements are numerous in the genome 2. REPs occur predominantly in intergenic regions, where they are mostly found in clusters called REPINs (REP doublet forming hairpins),3,4 and BIMEs (bacterial interspersed mosaic elements) 5. REPs and their clusters serve as binding sites for several proteins in E. coli 6.…”

“…[7][8][9] REP elements were hypothesized to be mobile, which was confirmed in Pseudomonas fluorescens, where excisions of REPINs were detected. 4 A class of transposase-related nucleases, termed REP-associated tyrosine transposases (RAYTs), recently were discovered and proposed to function as primary mobilizers of REP elements. 10 RAYTs belong to the HUH superfamily of nucleases whose members promote replication or mobilization of various mobile genetic elements (viruses, plasmids and insertion sequences).…”

Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea

“…We predict that, as in VNG_R0052 case, PATEs might also be functionally transcribed in other organisms. Moreover, since PATEs have counterparts in bacteria (REPINS, found for example in Pseudomonas fluorescens 30 ), we extend this prediction to bacteria.…”