Studies on a novel insertion sequence, ISR11, isolated from rhizobium leguminosarum biovar viciae
O'Brien, John (1993) Studies on a novel insertion sequence, ISR11, isolated from rhizobium leguminosarum biovar viciae. PhD thesis, Dublin City University.
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An insertion sequence, ISRll, isolated from Rhizobium
leguminosarum biovar viciae was studied in detail. Both
strands of the entire element were sequenced. The inverted
repeats (13bp) and target duplications (8bp) of the element
had features in common with three other IS elements, I S R m 2 , IS66 and IS866 (from Rhizobium meliloti and Agrobacterium
The GENBANK and PIR sequence databases were searched
for similarities to ISRll. The homologies found were to
other insertion sequences, unidentified open reading frames
and to several genes. All these sequences were from species
of Rhizobiaceae and all mapped to four small regions of the
Two approaches were taken to identifying coding regions
within ISRll. Gene search by signal identified twenty
two open reading frames. The sequence of all these ORFs was
translated to protein sequences and compared to the sequence
databases. Four ORFs showed significant homology to five
sequences from Rhizobiaceae none of which were insertion
sequences. The second approach, gene search by content, was
a statistical method based on an assumed codon bias in the
element and was unsuccessful.
Five frameshifting motifs were found in ISRll , four of
which were in frame with the ORFs in which they were located. Four binding sites for DnaA protein, one for integration host factor (IHF) and a potential promoter (which may be associated with one of the ORFs) were also found.
The distribution of ISRll throughout the Rhizobiaceae
was examined by Southern hybridization. The element was
found to be widespread but not ubiquitous in these species.
The banding patterns observed were not sufficiently different for IS Rll to be used as a DNA fingerprinting probe on its own. No homologous sequences were detected outside the Rhizobiaceae.
Using the element's inverted repeats as primers for
polymerase chain reaction experiments, a family of related
insertion sequences was discovered in the Rhizobiaceae. The
elements ranged in size from c. 5 - 0-7kb and were present
in some strains which showed no homology to ISRll in the
Southern blots and absent from some strains which did.
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