This question is aimed at those interested in sequences of bacterial genomes, particularly plasmids. It is an experiment to see if ResearchGate can help to tap into what people have noticed but not necessarily flagged up explicitly in published sequences or papers. In our paper (Thorsted et al., Journal of Molecular Biology 282: 969-90) in 1998 reporting the complete sequence IncP-1 plasmid R751 we drew attention to clusters of inverted repeats that occur at the junctions between different segments of the plasmid backbone - for example between the rep gene and the replication origin or between the two blocks of conjugative transfer genes. These inverted repeats are associated with restriction sites, for example PstI, XhoI, SalI, etc, which can occur at one or both ends and so are very obvious in restriction maps. They also appear to be hotspots for transposon insertions but this could be because they are not in essential genes and so insertions do not disrupt transcriptional units. Surprisingly they are not found in all IncP-1 plasmids-- just the IncP-1 beta plasmids. So either they have been gained or lost from this group during evolution. The question is whether others have noticed similar repeats in other genomes and whether the pattern of where they occur could help us figure out their significance.
Our plasmid (pPDL2) from sphingobium has been characterized recently and we also observed many inverted repeats. Have a look.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516476/#!po=26.9231
Thanks. After I posted the question I also did more reading and thinking. I tried putting the R751 sequence into the CRISPR finder database and it picks out the cluster of these repeats that lies between oriV (the replication origin) and trfA (the replication protein gene). I have just done the same for your plasmid pPDL2 but it comes up as negative for CRISPRs. However, for R751 I could not so far find any open reading frames in R751 that might encode Cas proteins. So the question now is, if these are really CRISPR sequences then why are they present in only a subset of the IncP-1 plasmids and what are they for. Could they be a defence against the protection that CRISPRs provide to their host? If they were transcribed in the opposite direction to chromosomal CRISPRs they might interfere with normal CRISPR function. Just an idea.
We found a very interesting cluster of inverted repeats in the genome of P. fluorscens SBW25 (there are 11 of them equidistant to the ori and the two longest are about 1500 bp long, each of them consists of tandemly repeated REP sequences with regular spacing and flanked by a terminal repeat, which is likely to be a TA system). We published the approximate positions of the repeats in Figure S8 of our 2011 paper (http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002132) unfortunately we couldn't really figure out what function they could have. But we were fascinated by the structure and organization of these repeats.
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