Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (504K) Freely available
Right arrow Supplementary Data
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (18)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Aranda-Olmedo, I.
Right arrow Articles by Marqués, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Aranda-Olmedo, I.
Right arrow Articles by Marqués, S.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2002, Vol. 30, No. 8 1826-1833
© 2002 Oxford University Press

Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida

Isabel Aranda-Olmedo, Raquel Tobes, Maximino Manzanera, Juan L. Ramos and Silvia Marqués*

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

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.

* To whom correspondence should be addressed. Tel: +34 958 121011; Fax: +34 958 129600; Email: silvia{at}eez.csic.es The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Bacteriol.Home page
P. Fonseca, R. Moreno, and F. Rojo
Genomic Analysis of the Role of RNase R in the Turnover of Pseudomonas putida mRNAs
J. Bacteriol., September 15, 2008; 190(18): 6258 - 6263.
[Abstract] [Full Text] [PDF]

Home page
 J. Immunol.Home page
M. Magnusson, R. Tobes, J. Sancho, and E. Pareja
Cutting Edge: Natural DNA Repetitive Extragenic Sequences from Gram-Negative Pathogens Strongly Stimulate TLR9
J. Immunol., July 1, 2007; 179(1): 31 - 35.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
M. I. Ramos-Gonzalez, M. J. Campos, J. L. Ramos, and M. Espinosa-Urgel
Characterization of the Pseudomonas putida Mobile Genetic Element ISPpu10: an Occupant of Repetitive Extragenic Palindromic Sequences
J. Bacteriol., January 1, 2006; 188(1): 37 - 44.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
H. Feil, W. S. Feil, P. Chain, F. Larimer, G. DiBartolo, A. Copeland, A. Lykidis, S. Trong, M. Nolan, E. Goltsman, et al.
Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000
PNAS, August 2, 2005; 102(31): 11064 - 11069.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.