title: Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida.
abstract: 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 chromosome of this strain. The structure of this DNA segment is analogous to that of the so-called enterobacteriaceae repetitive extragenic palindromic (REP) sequences, although its sequence is different. Computer-assisted analysis of the presence and distribution of this repeated sequence in the P.putida chromosome revealed that in at least 80% of the cases the sequence is extragenic, and in 82% of the cases the distance of this extragenic element to the end of one of the neighbouring genes was <100 bp. This 35 bp element can be found either as a single element, as pairs of elements, or sometimes forming clusters of up to five elements in which they alternate orientation. PCR scanning of chromosomes from different isolates of Pseudomonas sp. strains using oligonucleotides complementary to the most conserved region of this sequence shows that it is only present in isolates of the species P.putida. For this reason we suggest that the P.putida 35 bp element is a distinctive REP sequence in P.putida. This is the first time that REP sequences have been described and characterised in a group of non-enterobacteriaceae.
authors.affiliation: Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Departamento de Bioquímica y Biología Molecular y Celular de Plantas, Apdo. de correos 419, E-18080 Granada, Spain.
authors.forename: Isabel
authors.initials: I
authors.lastname: Aranda-Olmedo
authors.forename: Raquel
authors.initials: R
authors.lastname: Tobes
authors.forename: Maximino
authors.initials: M
authors.lastname: Manzanera
authors.forename: Juan L
authors.initials: JL
authors.lastname: Ramos
authors.forename: Silvia
authors.initials: S
authors.lastname: Marqués
mesh_terms: D001483:Base Sequence; D002876:Chromosomes, Bacterial; D004269:DNA, Bacterial / Q000235:genetics*; D021901:DNA, Intergenic; D005798:Genes, Bacterial; D008969:Molecular Sequence Data; D016958:Pseudomonas putida / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid; D016415:Sequence Alignment; D013045:Species Specificity; D013728:Terminator Regions, Genetic
chemical_list: D004269:DNA, Bacterial; D021901:DNA, Intergenic