Comparison of insert positions and sequence conservation within the C-terminal linker region demonstrated that mutants harbouring inserts at positions of overall conservation showed loss of transport activity, whereas insertion into heterogeneous sequence parts was, in general, compatible with autotransport activity (Fig. 5B).
This indicates that the SMI-049 lineage is genetically very stable both with respect to point mutations and to transpositional activity of insertion sequences, in contrast with reports of other M. tuberculosis lineages e.g. the Beijing lineage.
This suggests that the SPV/SPD are promoting SPC activity upon insertion.
Any such genetic variations can be the result of TE activity, involving insertion, excision, or ectopic recombination [ 42, 43].
In addition to this effect of endonuclease activity, the insertion of TEs is thought to be important for the molecular evolution of R genes.
Whilst the piperidine analogue 8v retained activity, the insertion of an additional oxygen atom, in the case of the morpholine analogue 8vi, caused a significant decrease in activity (see also analogue S8xxx in the Supporting Information 11).
The hydrophobic domain of D-Phe-L-Leu (polymyxin B) or D-Leu-L-Leu (polymyxin E) can also affect its antibacterial activity through insertion with bacterial OM [ 26].
Even if the intein or intron has optimized its splicing activity, the insertion sequence still bears with it the burden of replicating, transcribing and in the case of inteins also translating, hundreds of superfluous nucleotides.
To analyze BRAMI-1's transposition activity and insertion time, we designed 50 MIP primers, 25 for B. rapa and 25 for B. oleracea, from the flanking regions of the BRAMI-1 insertions, especially insertions in genic regions (Additional file 2).
Due to diverse genetic effects associated with the activity of insertion elements, developing tools to identify and map the location of these DNA sequences in bacterial genomes is essential to advance our understanding of the role IS elements play in gene regulation and genome plasticity.
