Supplementary MaterialsAdditional file 1 Nucleotide sequences of unannotated genes (arrows) are

Supplementary MaterialsAdditional file 1 Nucleotide sequences of unannotated genes (arrows) are denoted with the same color. genes, twenty-two and thirteen exclusive REP classes had been established in fluorescent pseudomonads and stenotrophomonads, respectively. In stenotrophomonads, REP components were typically within tens or a couple of hundred copies per genome. REPs of fluorescent pseudomonads had been generally more many, happening in hundreds or also over one thousand ideal copies of particular REP course per genome. REP sequences showed extremely heterogeneous distribution. The abundances of REP classes approximately followed host strains phylogeny, differing markedly among individual clades. High abundances of particular REP classes appeared to depend on the presence of the cognate RAYT gene, and deviations from this state could be attributed to recent or ancient mutations of and related bacteria [3]. Similarly, Chi sequences, which serve as sites of recombination initiation, are overrepresented in host genomes [4]. Repeated elements are part of sophisticated CRISPR systems, which provide defense against invading mobile elements [5]. Finally, various types of MITEs (miniature inverted repeats transposable elements), which are predicted to be derived from autonomous transposable elements, are implicated in transcription regulation and other processes [6,7]. REP (repetitive extragenic palindrome) elements have now been known for over 30?years [8], originally from and related enterobacteria [9]. They were later identified in other species, belonging predominantly to gammaproteobacteria C and others [14], each species possessing different types of REP sequences. REPs are typically highly numerous and occur almost exclusively in intergenic regions. The definition of REP elements was recently refined [14] to reflect their common features on sequence level: a 5-terminal conserved tetranucleotide (GTA/GG) and downstream complementary (palindromic) region with variable base composition. REP elements are mostly arranged into repeats of higher order. REPINs (REP doublet forming hairpin) are composed of two closely spaced REPs in inverted orientation [15] and were found to represent the predominant REP form in insertion sequence family [21,22], RAYTs carry conserved residues to perform DNA cleavage C the catalytic tyrosine and two metal-coordinating histidines. Since REP elements were found flanking RAYT genes in almost all species where they have been previously recorded, REPs were the likely substrates to be cleaved by RAYTs. The predicted REP-specific nuclease activity of RAYT was recently confirmed experimentally [23], and the crystal structure of REP/RAYT complex was solved [24]. The structure helped to elucidate the role of conserved tetranucleotide and palindrome (two defining features of REP elements) in REP recognition by RAYTs. Owing to rapid expansion of Next-generation DNA sequencing methods, increasing numbers of new genomic sequences are reported each year. These provide great opportunity to conduct comparative analyses. We explored the distribution of REP elements and their associated RAYTs in sequenced genomes of sixty-three fluorescent TP-434 distributor pseudomonads and ten stenotrophomonads, two groups of omnipresent environmental bacteria with biotechnological and biocontrol applications [12,25]. Our results indicate quick diversification Tcf4 and proliferation of REPs in both studied groups. Furthermore, RAYTs appear to play a principal role in REP dissemination, as RAYT presence correlates with REP abundance. Our results provide support for the hypothesis that REP/RAYT system is an example of mobile element domestication. Outcomes and debate Phylogenetic romantic relationships of studied bacterias Our preliminary evaluation of offered TP-434 distributor genomes uncovered that the best intraspecific diversity of REP components and their linked RAYTs existed in bacterias of the complicated and in sp. (data not really shown). In depth mining TP-434 distributor of bacterial genomic databases recovered 63 genomes affiliated to (fluorescent pseudomonads) and 10 genomes affiliated to (stenotrophomonads). Among fluorescent pseudomonads, species of and complicated [26], had been included, in addition to numerous was been shown to be naturally proficient for transformation [28], whereas organic competence is unidentified in and genes. Resulting clades are marked with vertical lines to the proper of corresponding strains and labeled with letters A C I. Open in another window Figure 2 Neighbor-Signing up for phylogram of 10 stenotrophomonads. The tree was made of TP-434 distributor concatenated comprehensive nucleotide sequences of and genes. Resulting clades are marked with vertical lines to the proper of corresponding strains and labeled with letters A C C. Diversity of REP sequences and RAYTs Within the next.