Mobile Genetic Elements 1:4, 262–268; November/December 2011; G 2011 Landes Bioscience Curiosities of REPINs and RAYTs Frederic Bertels1,* and Paul B. Rainey1,2 1New Zealand Institute for Advanced Study and Allan Wilson Centre for Molecular Ecology and Evolution; Massey University at Albany; Auckland, New Zealand; 2Max Planck Institute for Evolutionary Biology; Plön, Germany Keywords: RAYTs, REP-associated tyrosine transposase, transposase, MITE, miniature inverted-repeat transposable element, transposon, repetitive sequences Abbreviations: RAYT, REP-associated tyrosine transposase; REP, repetitive extragenic palindrome; REPIN, REP doublet forming hairpin; MITE, miniature inverted repeat transposable element © 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 c2oncern0ingREP1INdiv2ersity. We Lalso aconsidnerfactdorsaffeecting sthe evoBlution oifRoEPIN dsiversitcy,theieaesewitnhwhicche. the model organism Pseudomonas fluorescens SBW25. Here, we summarize existing knowledge and present new data REPINs might be co-opted by host genomes and the consequences of REPIN activity for the structure of bacterial genomes. of Mobile BaDcterial oDNA n oREP tsequendces (ia sREP tdourbleti) binseulectiont,beutal.so indicates that these REPINs: A New Class element.10 The element consists of two hypothesis that REP doublets are a unit of inverted orientation. Evidence supporting elements are actively moving in the Repetitive extragenic palindromic (REP) this hypothesis was derived from analysis genome. Sequence characteristics of the sequences are a common feature of of the genome of the model organism excised element also suggest a likely bacterial genomes.1-5 The possibility that Pseudomonas fluorescens SBW25 and transposition mechanism reminiscent of REPs might be selfish genetic elements includes the following: (1) demonstration the mechanism of IS605 transposition.12 was suggested on first discovery in that the distribution of REP doublets Such mechanistic similarity makes sense Escherichia coli.2,3,6 However, their short is comparable to expectations under a given the similarities between IS605 and length (~20 nucleotides), plus absence of randomly generated model (whereas RAYTs [the entities thought responsible plausible mechanism for within genome the distribution of REP singlets shows for providing transposase function to dissemination, meant this idea received a significant departure from random); REPINs (see below)].5 Given the likely limited support. Over the next 30 years (2) demonstration that REP sequences evolutionary significance of the REP the “selfish element hypothesis” further found as REP doublets show higher doublet, the entity was designated a paled, in part, thanks to numerous studies sequence conservation compared with REPIN (REP doublet forming hairpin). that provided evidence that REPs located REP sequences existing as singlets (this A schematic of the 89 bp element is shown at particular locations and in specific suggests that REP doublets are under in Figure 1. genomes perform a diverse range of selection as opposed to singlets, which While our initial analyses were based cellular processes.1,6-9 However, the fact are most likely non-functional decaying on a single (P. fluorescens SBW25) chro- that the distribution and abundance of remnants of REP doublets); and (3) identi- mosome, the study of REPINs was REPs can vary substantially among even fication of excisions of REP doublets (but extended to 18 selected bacterial genomes closely related strains4,10 suggests that the not of single REP sequences) from popula- including Escherichia coli K-12 DH10B, range of functional roles is likely to be tion sequencing data from the SBW25 Salmonella enterica serovar Paratyphi A incidental, arising from, for example, co- genome. AKU 12601, Thioalkalivibrio HL-EbGR7, option or genetic accommodation.11 The discovery of excision events— Nostoc. punctiforme PCC73102 and all fully Recently we provided evidence that events that are likely to define transposi- sequenced Pseudomonas genomes. REP REP sequences are part of a selfish genetic tion intermediates—not only supports the sequences were identified based on their *Correspondence to: Frederic Bertels; Email: f.bertels@massey.ac.nz Submitted: 09/06/11; Accepted: 10/31/11 http://dx.doi.org/10.4161/mge.18610 262 Mobile Genetic Elements Volume 1 Issue 4