Analysis of Pseudomonas putida alkane-degradation gene clusters and flanking insertion sequences: evolution and regulation of the alk genes

Institute of Biotechnology, Swiss Federal Institute of Technology (ETH), ETH-Hönggerberg, CH-8093 Zürich, Switzerland 1 Author for correspondence: Jan B. van Beilen. Tel: +41 1 6333444. Fax: +41 1 6331051. e-mail: vanbeilen{at}biotech.biol.ethz.ch The Pseudomonas putida GPo1 (commonly known as Pseudomonas oleovorans GPo1) alkBFGHJKL and alkST gene clusters, which encode proteins involved in the conversion of n-alkanes to fatty acids, are located end to end on the OCT plasmid, separated by 9·7 kb of DNA. This DNA segment encodes, amongst others, a methyl-accepting transducer protein (AlkN) that may be involved in chemotaxis to alkanes. In P. putida P1, the alkBFGHJKL and alkST gene clusters are flanked by almost identical copies of the insertion sequence IS Ppu4 , constituting a class 1 transposon. Other insertion sequences flank and interrupt the alk genes in both strains. Apart from the coding regions of the GPo1 and P1 alk genes (80–92% sequence identity), only the alkB and alkS promoter regions are conserved. Competition experiments suggest that highly conserved inverted repeats in the alkB and alkS promoter regions bind AlkS. Keywords: alkane degradation, insertion sequence, chemotaxis, regulation The EMBL accession numbers for the sequences reported in this paper are AJ245436 [ P. putida ( oleovorans ) GPo1 alk gene clusters and flanking DNA], AJ233397 ( P. putida P1 alk gene clusters and flanking DNA), AJ249793 ( P. putida P1 nahKJ genes), AJ249825 [ P. putida ( oleovorans ) GPo1 16S RNA gene] and AJ271219 ( P. putida P1 16S RNA gene). a Present address: DSM Research, Postbus 18, 6160 MD Geleen, The Netherlands. b Present address: Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK.