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Unusual location of two nearby pairs of upstream activating sequences for HbpR, the main regulatory protein for the 2-hydroxybiphenyl degradation pathway of ‘Pseudomonas azelaica’ HBP1

Process of Environmental Microbiology and Molecular Ecotoxicology, Swiss Federal Institute for Environmental Science and Technology (EAWAG), Postbox 611, CH-8600 Dübendorf, Switzerland¹

Author for correspondence: Jan Roelof van der Meer. Tel: +41 1 823 5438. Fax: +41 1 823 5547. e-mail: vdmeer{at}eawag.ch

‘Pseudomonas azelaica’ HBP1 degrades 2-hydroxybiphenyl (2-HBP) and 2,2'-diHBP by employing a meta-cleavage pathway encoded by the hbpCAD genes. The regulatory gene hbpR, located directly upstream of the hbpCAD genes and oriented in the opposite direction, encodes a transcription activator protein belonging to the so-called XylR/DmpR subclass within the NtrC family. HbpR activates transcription from two separate ⁵⁴-dependent promoters upstream of the hbpC and the hbpD genes, in the presence of the pathway substrates 2-HBP and 2,2'-diHBP. The DNA region upstream of the hbpC gene displays an unusual organization, containing two adjacent 0·3 kb regions that share 71% sequence identity. The DNA region most proximal to the hbpC promoter harbours one pair of putative upstream activating sequences (UASs C-1/C-2) and a small cryptic ORF that shows homology to hbpR itself. The second, more distal, region contains a second pair of putative UASs (UASs C-3/4) and the 5'-part of the hbpR gene. Transcriptional fusions in Escherichia coli between different deletions of the hbpR–hbpC intergenic region and the genes for bacterial luciferase revealed that most if not all of the transcriptional output from the hbpC promoter is mediated from the proximal UASs C-1/C-2. However, when the UASs C-1/C-2 were deleted and UASs C-3/C-4 were placed in an appropriate position with respect to the promoter region, the hbpC promoter was still inducible with 2-HBP, albeit at a lower level. Transcription studies in E. coli and ‘P. azelaica’ revealed that the divergently oriented hbpR gene is expressed constitutively from a ⁷⁰-dependent promoter situated within the cryptic ORF. The presence of UAS pair C-3/C-4 mediated a slightly higher promoter activity for transcription of hbpR.

Keywords: NtrC-type transcriptional activator, regulation, evolution

Abbreviations: 2-HBP, 2-hydroxybiphenyl; UAS, upstream activating sequence; RNAP, RNA polymerase; IHF, integration host factor

^a Present address: Department of Microbiology, Wageningen Agricultural University, Wageningen, The Netherlands.

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				D. Tropel and J. Roelof van der Meer Identification and Physical Characterization of the HbpR Binding Sites of the hbpC and hbpD Promoters J. Bacteriol., June 1, 2002; 184(11): 2914 - 2924. [Abstract] [Full Text] [PDF]