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Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida
Isabel Aranda-Olmedo1, Raquel Tobes, Maximino Manzanera
1Consejo 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.
Nucleic Acids Research
|April 9, 2002
Summary
Researchers discovered a novel 35 bp repetitive DNA element in Pseudomonas putida KT2440, distinct from enterobacterial repetitive extragenic palindromic (REP) sequences. This element is widespread in the P. putida genome and specific to this species.
Area of Science:
- Microbial genomics
- Bacterial genetics
- DNA sequence analysis
Background:
- Pseudomonas putida KT2440 is a soil bacterium known for plant root colonization and degradation of toxic aromatic compounds.
- The genome of P. putida KT2440 has been recently sequenced, enabling detailed genetic analysis.
- Repetitive extragenic palindromic (REP) sequences are known in Enterobacteriaceae, playing roles in genome organization.
Purpose of the Study:
- To characterize a novel 35 bp imperfect palindromic DNA sequence found repeatedly in the P. putida KT2440 chromosome.
- To investigate the distribution, location, and potential species-specificity of this novel repetitive element.
- To determine if this element represents a new class of REP sequences in non-Enterobacteriaceae.
Main Methods:
- Bioinformatic analysis of the P. putida KT2440 genome to identify and map the distribution of the 35 bp sequence.
- Analysis of the sequence's location relative to neighboring genes and its occurrence as single elements, pairs, or clusters.
- Polymerase chain reaction (PCR) scanning of various Pseudomonas species isolates using specific oligonucleotides.
Main Results:
- A 35 bp imperfect palindromic sequence is found over 800 times in the P. putida KT2440 chromosome, primarily in extragenic regions (<100 bp from genes).
- The element exists as single copies, pairs, or clusters of up to five, with alternating orientations.
- PCR analysis confirmed the sequence is present exclusively in P. putida isolates, distinguishing it from other Pseudomonas species.
Conclusions:
- The identified 35 bp element in P. putida shares structural similarities with REP sequences but has a distinct sequence.
- This study reports the first characterization of REP sequences in a non-Enterobacteriaceae bacterium.
- The P. putida 35 bp element is proposed as a distinctive REP sequence specific to the P. putida species.