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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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Abstract

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 tumefaciens). 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 element. 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.

Item Type:Thesis (PhD)
Date of Award:1993
Refereed:No
Supervisor(s):O'Connell, Michael
Uncontrolled Keywords:Genetic sequencing
Subjects:Biological Sciences > Biochemistry
DCU Faculties and Centres:DCU Faculties and Schools > Faculty of Science and Health > School of Biotechnology
Use License:This item is licensed under a Creative Commons Attribution-NonCommercial-No Derivative Works 3.0 License. View License
ID Code:19145
Deposited On:04 Sep 2013 14:36 by Celine Campbell. Last Modified 04 Sep 2013 14:36

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