Putative Insertion Sequence

Paul N Hengen pnh at fcsparc6.ncifcrf.gov
Wed Jun 23 11:11:58 EST 1993

In article <1993Jun23.120415.1 at sara.cc.utu.fi> metzler at sara.cc.utu.fi writes:

>	The bacteria that I work with (Clavibacter xyli subsp. cynodontis)
>contains a cryptic plasmid. A small region of this plasmid is repeated
>many times (more than 50) on the chromosome. This suggests that it is
>an insertion sequence, although probably not a transposon, given the
>high copy number.

I'm confused about this. Why do you determine that it is not a
transposon based on the number of copies in the chromosome?

>Searching databases comes up with no matches. These two sequences are 
>99% identical for most of their lengths. At the ends where they diverge,
>they each contain different, direct tandem repeats (one is 7 bp, the other
>is 15 bp, but not perfect, 12 bp match exactly). Nothing I have read in 
>the literature describes anything like this. The direct repeats that are
>seen normally at insertion sites are at opposite ends of the insertion sequence
>not tandemly at one end as these are. Has anyone ever seen or read about
>anything like this? Of course, I need to continue sequencing, but with
>no matches to anything in the database, I would like to have some evidence 
>that what I am pursuing is actually likely to lead somewhere interesting.

How much more interesting does it have to be? :-)

You are right about the repeats seen on the opposite ends of the insertion
site. Transposons characteristically duplicate segments of the bacterial
chromosome upon transposition. The transposable element you have found may
have some preference for where it will transpose. For example, Tn7 is a site
specific transposon. Some of the more "random" transposons like Tn5 do prefer
certain strings of bases as well, but not to the extent as site-specific ones.

Paul N. Hengen
National Cancer Institute
Frederick Cancer Research and Development Center
Frederick, Maryland 21702-1201 USA

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