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Applied and Environmental Microbiology, April 2004, p. 2342-2348, Vol. 70, No. 4
0099-2240/04/$08.00+0     DOI: 10.1128/AEM.70.4.2342-2348.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Urease-Encoding Genes in Ammonia-Oxidizing Bacteria{dagger}

Teresa E. Koper,1 Amal F. El-Sheikh,2 Jeanette M. Norton,3* and Martin G. Klotz2

Departments of Biology,1 Plants, Soils, and Biometeorology, Utah State University, Logan, Utah 84322-4820,3 Department of Biology and Center for Genetics and Molecular Medicine, University of Louisville, Louisville, Kentucky 402922

Received 11 October 2003/ Accepted 15 December 2003

Many but not all ammonia-oxidizing bacteria (AOB) produce urease (urea amidohydrolase, EC 3.5.1.5) and are capable of using urea for chemolithotrophic growth. We sequenced the urease operons from two AOB, the ß-proteobacterium Nitrosospira sp. strain NpAV and the {gamma}-proteobacterium Nitrosococcus oceani. In both organisms, all seven urease genes were contiguous: the three structural urease genes ureABC were preceded and succeeded by the accessory genes ureD and ureEFG, respectively. Green fluorescent protein reporter gene fusions revealed that the ure genes were under control of a single operon promoter upstream of the ureD gene in Nitrosococcus oceani. Southern analyses revealed two copies of ureC in the Nitrosospira sp. strain NpAV genome, while a single copy of the ure operon was detected in the genome of Nitrosococcus oceani. The ureC gene encodes the alpha subunit protein containing the active site and conserved nickel binding ligands; these conserved regions were suitable primer targets for obtaining further ureC sequences from additional AOB. In order to develop molecular tools for detecting the ureolytic ecotype of AOB, ureC genes were sequenced from several ß-proteobacterial AOB. Pairwise identity values ranged from 80 to 90% for the UreC peptides of AOB within a subdivision. UreC sequences deduced from AOB urease genes and available UreC sequences in the public databases were used to construct alignments and make phylogenetic inferences. The UreC proteins from ß-proteobacterial AOB formed a distinct monophyletic group. Unexpectedly, the peptides from AOB did not group most closely with the UreC proteins from other ß-proteobacteria. Instead, it appears that urease in ß-proteobacterial autotrophic ammonia oxidizers is the product of divergent evolution in the common ancestor of {gamma}- and ß-proteobacteria that was initiated before their divergence during speciation. Sequence motifs conserved for the proteobacteria and variable regions possibly discriminatory for ureC from ß-proteobacterial AOB were identified for future use in environmental analysis of ureolytic AOB. These gene sequences are the first publicly available for ure genes from autotrophic AOB.

* Corresponding author. Mailing address: Department of Plants, Soils, and Biometeorology, Utah State University, Logan, UT 84322-4820. Phone: (435) 797-2166. Fax: (435) 797-3376. E-mail: jennyn{at}cc.usu.edu.

{dagger} Paper no. 7587 from the Utah Agricultural Experiment Station.

Applied and Environmental Microbiology, April 2004, p. 2342-2348, Vol. 70, No. 4
0099-2240/04/$08.00+0     DOI: 10.1128/AEM.70.4.2342-2348.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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