An alternative possibility is that the the various components of RAYT and however is the fact that no hybrid REPINs RAYT, in addition to mobilizing REPINs, REPIN diversity, but also for the high exist in the SBW25 genome, i.e., no performs some function that not only specificity between REPIN and RAYT. REPINs where the two REP sequences benefits the REPIN, but is also important A less antagonistic model comes when that comprise a given REPIN are derived for cellular physiology. Just what this considering the possibility that REPINs, from different REP groups. function might be is currently unknown, inserted into appropriate extragenic loca- however, it is possible that the RAYT- tions, might act as binding sites for the Consequences of REPIN Activity encoded transposase physically interacts RAYT-encoded protein; that together the with REPINs at their extragenic chro- protein-DNA interaction might be readily Transposons are well known for the mosomal locations and by virtue of this co-opted by the host as a means of fine multiplicity of effects, both direct and interaction (perhaps DNA binding) plays tuning or modulating gene expression. indirect, that they reap on both genome some kind of regulatory function, possibly Coevolution under this more mutualis- architecture and evolution.21 Here we have aiding fine tuning of patterns of gene tic model is readily envisaged by virtue suggested that REPINs and their asso- expression. It is even possible that different of the fact that a RAYT / REPIN ciated RAYTs have properties that might REPs and REPIN structures may have containing population of cells is likely to be readily co-opted to perform a diverse different affinities for RAYT binding experience different environmental condi- range of cellular functions, but it is likely and thus differentially affect the levels of tions. If there is an association between that there are numerous additional con- expression of neighboring genes. Implicit REPIN and RAYT that is functionally sequences. One is the formation of long in this idea is the notion that REPINs and maintained because of benefit to the host palindromic sequences. ©intriguing their associated 2and 0notun1realistic RAYTs can 2possibilLity, be readily aSuch cell, then ninterdactionsecousld,as it is likely that this association Binthie obe The exsplainecdas SBW25 iaceonsequnence genome contains ocfREePIN a variety . co-opted for cellular function. This is an evolves with changes in environment. of long palindromic REP singlets that can especially given the convenient placement antagonistic model, account for both activity. REP sequences typically consist of protein (RAYT) binding sites in the REPIN / RAYT diversity, plus specificity; of three regions: a 5' flanking sequence (a), extragenic space of hundreds of genes the lack of conservation in the spacer a central palindrome and a 3' flanking and the known effects of REPs and region (other than to maintain hairpin sequence (b). The genome of SBW25 genes.1,6-9 Do n oneed ftor the dnature iof sinteratctionrbetiwebenseuquenctes(e20bp -.28bp) with the general REPINs on the expression of neighboring structure) could also be explained by the contains numerous long palindromic RAYT and REPIN to be tuned separately structure a-palindrome-ac (where ac is the Origins of REPIN Diversity for each locus in order to ensure that the complement of a) and b-palindrome-bc association is not costly (and perhaps even (Fig. 3A). The existence of these long As mentioned above, and described in our beneficial). palindromic REP sequences can be earlier publication,10 REPIN diversity is Under both co-evolutionary models the accounted for by REPIN excision events apparent at different organisational levels. genome is expected to harbour REPINs (Fig. 3B). For example palindromes of The existence of three different REPINs of different ages with older REPINs the structure a-palindrome-ac can be (GI, GII and GIII) and their associated showing evidence of mutational decay. formed by excision of the central RAYTs (in both the SBW25 genome and To this end we examined the average REPIN sequence—from all three REPIN other genomes investigated) points to a pairwise identity of REPs found in groups—whereas palindromes of the struc- specificity of association reminiscent of REPINs of each class with different ture b-palindrome-bc can be formed by co-evolution between the two entities. inter-REP spacers. In each instance we excision of the central REPIN sequence It is possible to envisage both antagon- found evidence of families with specific from a subset of GI REPINs only, namely, istic and mutualistic models of coevolu- spacings that have greater or lesser se- those GI REPINs that occur in the rare tion. For example, if REPINs evolved quence conservation (Table 2). This is as AA-TT orientation (Table 2 and Fig. 3). from single REP sequences that flanked expected under a co-evolutionary model. In support of this model is the fact that an ancestral IS200-like element, as pre- A distinctly different explanation for the most common long palindromic REP viously suggested10 [imperfect palindromes REPIN diversity draws on the possibility singlet is derived from the most common (similar to REPs) flanking IS200 are of interactions among different RAYTs. REPIN, whereas the long palindromic essential for transposition]—and did so For example, GI RAYTs most likely REP singlet derived from the rare AA- via a simple duplication event—then transpose GI REPINs with a 71 bp spacer TT GI REPIN is rare. Further support in little more than a single step, this (101 occurrences). GII RAYTs most comes from the discovery of a single could have resulted in enslavement of likely transpose GII REPINs with a REPIN excision event from population the transposase and generation of a non- 110 bp spacer (50 occurrences). Perhaps sequencing in which the REPIN was autonomous mobile entity. An ensuing REPINs can sometimes be substrates for excised at the 3' end of the 5' palindrome arms race between host (transposase) and more than a single RAYT, which may lead and at the 3' end of the 3' palindrome, parasite (REPIN) is thus plausible. Such to different spacer distances and thus leaving a long palindromic REP sequence processes could be responsible for both different specificities. Against this thesis behind (Fig. 4). 266 Mobile Genetic Elements Volume 1 Issue 4