LETTER TO THE EDITOR Figure 1. Secondary structure predicted for spacer sequence between the individual a GI REPIN. The secondary structure shows the REP units, but also with respect to the adlomuobslettp.eBrlufeecbtohxaiirnpdi nicafotermstehde bpyosaitiGoInRoEfPthe specific sequence of the spacer region. short imperfect palindromes (REPs). In terms of the diversity in spacer Secondary structure predicted by the mfold length, GI REPINs in SBW25 show 11 web server (http://mfold.rna.albany.edu/? different inter-REP spacings; five different q=mfold/DNA-Folding-Form).22 spacings are found within GII REPINs and eight within GIII REPINs (Table 2). Perhaps more surprising—given that there proximal association with REP-associated are hundreds of REPINs in the SBW25 tyrosine transposases (RAYTs),10 which genome—is the fact that no two REPINs are implicated in REPIN dispersal. In are identical at the level of the DNA these 18 genomes, REP sequences adja- sequence that comprises the spacer region. cent to RAYTs were found to exist as Nonetheless, the spacer region of all doublets with specific features character- REPINs is organized so as to form a istic of REPINs. REPINs therefore appear hairpin structure. to be widely distributed elements. In addition to the diversity of inter- REP spacings and diversity of the spacer REPIN Diversity within sequence, GI REPINs also exist in two © 2012 L aCompnarisons the dof SBW25 the efrequsency Genome of Bthemoist omotif different s(the orientations cpreseince eof as enither evident tcheAeAor by the . arrangement of the central AA or TT abundant 16-mers from SBW25, with TT motif (in all SBW25 REP sequences) randomly assembled genomes, and with ensures that each REP palindrome is the closely related genome of P. fluorescens imperfect). Since REPINs consist of two Pf0–1, revealed at least 96 different over- inverted REP sequences, there are two Do n oalgoritthm, thdese96 idifsferent t16-mrersiwebreTuT-AA t(coemmon.)(as in most GI, all represented 16-mers. Using a grouping possible doublet configurations: either found to belong to just three distinct GII and GIII doublets) or AA-TT (rare) groups, termed GI, GII and GIII (as found in a minority of GI doublets) (Table 1). The three groups were named (Fig. 2A and B). Interestingly, GI doub- in order of their abundance in the SBW25 lets in the TT-AA configuration are genome, with GI being the most abundant flanked by multiple conserved ‘A’s and (618 occurrences). All three sequence ‘T’s at the 5' and 3' end, respectively, groups occur predominantly in extragenic which may reflect co-option of the REP space and contain an imperfect palindro- doublet for transcription attenuation.8 mic core, thus possessing all features of The region flanking GI doublets in the repetitive extragenic palindromic sequences AA-TT orientation are devoid of runs (REPs). of ‘A’s or ‘T’s, however, runs of ‘A’ and Since REPINs are exclusively formed ‘T’ nucleotides directly flanking REP by REP sequences of the same group, sequences are observed inside the doublet they can also be categorized into GI, GII (Fig. 2A and B). This suggests that the and GIII REPINs. Nevertheless, REPINs AA-TT configuration evolved from the 3' show considerable within group diversity, and 5' REP sequences of two co-localized both with regard to the length of the TT-AA GI doublets (Fig. 2C). Table 1. Short repetitive sequence groups in the SBW25 genome Groupa I II III Sequenceb GTGGGAGGGGGCTTGC GTGAGCGGGCTTGCCC GAGGGAGCTTGCTCCC Occurrences 618 241 208 Palindromic corec GGGGGCTTGCCCCC GCGGGCTTGCCCCGC GGGAGCTTGCTCCC a16-mers were assigned to one of three groups (GI, GII and GIII) using a grouping algorithm. bSequence of the most common 16-mer from each group. cEach GI, GII and GIII sequence either contains or overlaps an imperfect palindrome (the palindromic core). Table reproduced from Bertels and Rainey.10 www.landesbioscience.com Mobile Genetic Elements 263