Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements
نویسندگان
چکیده
منابع مشابه
Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida.
Pseudomonas putida KT2440 is a soil bacterium that effectively colonises the roots of many plants and degrades a variety of toxic aromatic compounds. Its genome has recently been sequenced. We describe that a 35 bp sequence with the structure of an imperfect palindrome, originally found repeated three times downstream of the rpoH gene terminator, is detected more than 800 times in the chromosom...
متن کاملDNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences.
A family of repetitive extragenic palindromic (REP) sequences is composed of hundreds of copies distributed throughout the chromosome. Their palindromic nature and conservation suggested that they are specifically recognized by a protein(s). We have identified DNA gyrase [DNA topoisomerase (ATP-hydrolysing), EC 5.99.1.3] as one of the REP-binding proteins. Gyrase has at least a 10-fold higher a...
متن کاملRepetitive extragenic palindromic sequences in the Pseudomonas syringae pv. tomato DC3000 genome: extragenic signals for genome reannotation.
Repetitive extragenic palindromic (REPs) sequences were first described in enterobacteriacea and later in Pseudomonas putida. We have detected a new variant (51 base pairs) of REP sequences that appears to be disseminated in more than 300 copies in the Pseudomonas syringae DC3000 genome. The finding of REP sequences in P. syringae confirms the broad presence of this type of repetitive sequence ...
متن کاملCharacterization of the Pseudomonas putida mobile genetic element ISPpu10: an occupant of repetitive extragenic palindromic sequences.
We have characterized the Pseudomonas putida KT2440 insertion element ISPpu10. This insertion sequence encodes a transposase which exhibits homology to the transposases and specific recombinases of the Piv/Moov family, and no inverted repeats are present at the borders of its left and right ends, thus constituting a new member of the atypical IS110/IS492 family. ISPpu10 was found in at least se...
متن کاملUsing Markov Models and Hidden Markov Models to Find Repetitive Extragenic Palindromic Sequences in Escherichia coli
This paper presents a technique for using simple Markov models and hidden Markov models (hmms) to search for interesting sequences in a database of DNA sequences. The models are used to create a cost map for each sequence in the database. These cost maps can be searched rapidly for subsequences that have signi cantly lower costs than a null model. Milosavljevi c's algorithmic signi cance test i...
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ژورنال
عنوان ژورنال: BMC Genomics
سال: 2006
ISSN: 1471-2164
DOI: 10.1186/1471-2164-7-62