, 1999). BIME-1 and BIME-2 correspond to SMAG TT and HH dimers. However, HH dimers are about 10 times more abundant than TT dimers. In contrast, BIME-1 (74 repeats) are three times more abundant than BIME-2 (24 repeats).

Moreover, both BIME-1 and BIME-2 are invariably comprised of elements from different subfamilies (Bachellier et al., 1999; see also http://www.pasteur.fr/recherche/unites/pmtg/repet/index.html). The predominance buy PLX3397 of TT over HH dimers, and the composite nature of dimers, is also a distinctive feature of the abundant REP families found in Pseudomonas putida (Aranda-Olmedo et al., 2002) and P. syringae (Feil et al., 2005). It has been hypothesized that REPs are mobilized by a VX 809 transposase of the IS200/IS605 family, and the corresponding genes have been shown to be flanked by REPs in many species (Nunvar et al., 2010). Four genes encoding this transposase were identified in K279a DNA (ORFs 1101,

1152, 2816 and 4509), but only ORFs 1101 and 2816 are flanked by SMAGs. We believe that REPs are an ancient component of the genomes of Proteobacteria, which have been actively mobilized by transposition only early in their history. According to this view, REPs disappeared in time from most species, their dissemination being plausibly detrimental to the cell, and have been maintained only in species in which they could no longer transpose. This hypothesis is supported by the observation that SMAG sequences were found in none of the 41 species-specific GEIs, plausibly acquired by lateral gene transfer, which account for >10% of the K279a chromosome (Rocco et al., 2009). REPs are similarly restricted to core genome regions in P. syringae (Tobes & Pareja, 2005). In contrast to what was observed for REPs in other species (Tobes & Pareja, 2006), SMAGs are not targeted by mobile DNA. However, it is worth noting that a K279a GEI encoding type 1 pili (Rocco et al., 2009) is flanked by SMAG-2 dimers. FER About 1/7 of the ORFs of the K279a strain are flanked by SMAGs in a distance range that makes the presence of promoter or terminator

sequences unlikely. It is plausible that most of these elements are transcribed into mRNA, and that their folding into RNA hairpins may influence the level of expression of flanking genes. The number of genes potentially controlled at the post-transcriptional level by SMAGs may be higher than estimated, because many repeats are inserted either upstream (17 elements) or downstream (150 elements) or within (44 elements) known or putative operons. We analyzed genes transcribed in the same direction intermingled with SMAG sequences, and found that the repeats influence the segmental mRNA stability. Both monomers and dimers function as stabilizers of upstream transcripts, and work with comparable efficiency when embedded in the same RNA context (Fig. 5).