The nucleotide sequence of a transposable haloalkanoic acid dehalogenase regulatory gene (dehRI) fromPseudomonas putida strain PP3 and its relationship with σ54-dependent activators

The mobile genetic element,DEH found inPseudomonas putida PP3 carries a 2-haloalkanoic acid dehalogenase structural gene,dehI, and its associated regulatory gene,dehRI. The nucleotide sequence ofdehRI was determined. The gene had an open reading frame putatively encoding for a 64 kDa protein containing 571 amino acid residues. The protein was similar to previously published sequences of several other σ54-dependent activator proteins. Amino acid sequence analysis showed that the deduced DehRI protein clustered with the NifA nitrogenase regulatory activator family, and was most closely related, with 47.7% similarity, to a ‘NifA-like’ deduced partial sequence from a plasmid-encoded ORF inPseudomonas sp. strain NS671, associated with L-amino acid production. The domain structure of DehRI was analysed by alignment with other NifA-like and NtrC-like sequences and showed a highly conserved central region of approximately 230 amino acids, and a potential DNA-binding domain. No homology was detected between the deduced DehRI and other σ54-dependent activator sequences at the N-terminus, a result which was consistent with that region being the domain which recognised inducer.