Repeated extragenic sequences in prokaryotic genomes: a proposal for the origin and dynamics of the RUP element in Streptococcus pneumoniae

A survey of all Streptococcus pneumoniae GenBank/EMBL DNA sequence entries and of the public domain sequence (representing more than 90% of the genome ) of an S. pneumoniae type 4 strain allowed identification of 108 copies of a 107-bp-long highly repeated intergenic element called RUP (for repeat un it of pneumococcus), Several features of the element, revealed in this stud y, led to the proposal that RUP is an insertion sequence (IS)-derivative th at could still be mobile. Among these features are: (1) a highly significan t homology between the terminal inverted repeats (IRs) of RUPs and of IS630 -Spn1, a new putative IS of 5. pneumoniae; and (2) insertion at a TA dinucl eotide, a characteristic target of several members of the IS630 family. Tra ns-mobilization of RUP is therefore proposed to be mediated by the transpos ase of IS630-Spn1. To account for the observation that RUPs are distributed among four subtypes which exhibit different degrees of sequence homogeneit y, a scenario is invoked based on successive stages of RUP mobility and non -mobility, depending on whether an active transposase is present or absent. In the latter situation, an active transposase could be reintroduced into the species through natural transformation. Examination of sequences flanki ng RUP revealed a preferential association with ISs, It also provided evide nce that RUPs promote sequence rearrangements, thereby contributing to geno me flexibility. The possibility that RUP preferentially targets transformin g DNA of foreign origin and subsequently favours disruption/rearrangement o f exogenous sequences is discussed.