Ere is a frequent occurrence of GC pairs at each end
Ere is a frequent occurrence of GC pairs at each end of the Direct Repeats [33,34]. The insertion sites that we have detected for ISRm22 fulfill both requirements (Figure 2). Another proposed characteristic of Tn5 transposition is the preferable integration in actively transcribing or highly super-coiled DNA regions [33]. In this sense, REP sequences are frequently located in regions between convergent genes. These DNA fragments are especially prone to be highly supercoiled since simultaneous transcription of both convergent genes can generate increased positive supercoiling at the end of the genes [3]. Through testing the frequency of Tn5 insertion into specifically designed synthetic target sequences, it has been found that IS50 recognizes a preferred 9-bp sequence as its target. Moreover, sequences resembling this consensus target function optimally when embedded in a cluster of overlapping similar sequences [33]. In accordance with these Tn5 data, we have found that the majority of ISRm22 copies are inserted into a cluster of REP sequences. In the type 1 association cases (ISPa11, ISPpu9, ISPpu10, ISRm22 and ISRm19) the conserved sequence encompasses almost the complete REP sequence (Figure 2). All consensus sequences share a high percentage of GCs, a greater conservation in GCs than in ATs, a palindromic structure, and a similar length (with the exception of ISPsy8 which displays a shorter consensus). In spite of the differences in their corresponding transposase sequences, ISPpu9 and ISPpu10 show the same point of insertion within the consensus sequence. REP-recognizer ISs could share some features in their target recognition PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26577270 domains. The determination of the transposases belonging to this subset could provide new clues to search for a common mechanism of recognizing the DNA target.Page 8 of(page number not for citation purposes)BMC Genomics 2006, 7:http://www.biomedcentral.com/1471-2164/7/Target selectivity differs significantly between different ISs. While some ISs display high target specificity, other elements exhibit regional preferences that could reflect more global parameters such as local DNA structure [16]. Thus, regional specificity has been related with GC or AT abundance, degree of supercoiling, DNA bending, replication related factors, and transcription related factors [16]. Transposition activity is frequently modulated by various host factors. The list of such factors includes the histonelike protein IHF, which has been experimentally proved to bind REP sequences. Another two REP-binder proteins, DNA polymerase I [35,36] and DNA gyrase [37-39] have also been implicated in transposition activity. Clusters of REP sequences could provide an appropriate context to recruit all the elements playing a role in transposition. The detected type 2 associations could reflect a favourable context for transposition provided by REP sequence clusters in Lixisenatide site combination with a minor stringency for the DNA target. REP elements have also been related to recombination events. Thus, REP sequences have been found at the recombination junctions of lambda bio transducing PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26024392 phages [13] and it has been experimentally detected that amplification of plasmid F_128 is initiated by REP-REP recombination [14]. REP elements are DNA points especially suitable for undergoing transposition or recombination events, because they are frequently placed at extragenic spaces limited by convergent genes [5]. Their extragenic location would warrant that transposit.
