Article

Structure and sequence conservation of hao cluster genes of autotrophic ammonia-oxidizing bacteria: evidence for their evolutionary history

University of Louisville, Department of Biology, 139 Life Science Building, Louisville, KY 40292, USA.
Applied and Environmental Microbiology (Impact Factor: 3.95). 10/2005; 71(9):5371-82. DOI: 10.1128/AEM.71.9.5371-5382.2005
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ABSTRACT Comparison of the organization and sequence of the hao (hydroxylamine oxidoreductase) gene clusters from the gammaproteobacterial autotrophic ammonia-oxidizing bacterium (aAOB) Nitrosococcus oceani and the betaproteobacterial aAOB Nitrosospira multiformis and Nitrosomonas europaea revealed a highly conserved gene cluster encoding the following proteins: hao, hydroxylamine oxidoreductase; orf2, a putative protein; cycA, cytochrome c(554); and cycB, cytochrome c(m)(552). The deduced protein sequences of HAO, c(554), and c(m)(552) were highly similar in all aAOB despite their differences in species evolution and codon usage. Phylogenetic inference revealed a broad family of multi-c-heme proteins, including HAO, the pentaheme nitrite reductase, and tetrathionate reductase. The c-hemes of this group also have a nearly identical geometry of heme orientation, which has remained conserved during divergent evolution of function. High sequence similarity is also seen within a protein family, including cytochromes c(m)(552), NrfH/B, and NapC/NirT. It is proposed that the hydroxylamine oxidation pathway evolved from a nitrite reduction pathway involved in anaerobic respiration (denitrification) during the radiation of the Proteobacteria. Conservation of the hydroxylamine oxidation module was maintained by functional pressure, and the module expanded into two separate narrow taxa after a lateral gene transfer event between gamma- and betaproteobacterial ancestors of extant aAOB. HAO-encoding genes were also found in six non-aAOB, either singly or tandemly arranged with an orf2 gene, whereas a c(554) gene was lacking. The conservation of the hao gene cluster in general and the uniqueness of the c(554) gene in particular make it a suitable target for the design of primers and probes useful for molecular ecology approaches to detect aAOB.

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Available from: Martin G Klotz, Aug 22, 2015
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    • "Earlier results indicated that the haoA and cycAB genes are under control of different promoters in N. europaea (Sayavedra-Soto et al., 1994; Arp et al., 2002; Hommes et al., 2002), however, gammaproteobacterial AOB such as N. oceani appear to produce distinct haoAB, cycAB and haoAB-cycAB transcripts indicating complex regulation similar to what was reported for the regulation of genes in the amo gene cluster (El Sheikh and Klotz, 2008; El Sheikh et al., 2008). Cytochrome c M 552 belongs to a large superfamily of membraneassociated cytochrome c proteins (NapC/NrfH) that exchange electrons with the quinone/quinol pool (Bergmann et al., 2005; Simon and Klotz, 2013). Generally in bacterial genomes, the cycB gene encoding c M 552 is clustered with other genes encoding catalytic periplasmic proteins that facilitate reduction of nitrogen oxides such as nitrate reductase (nap), nitrite reductase (nrf ), and/or homologues of cytochrome c554 that function as nitric oxide reductases (Upadhyay et al., 2006; Klotz and Stein, 2011; Simon and Klotz, 2013). "
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    • "A novel dual N assimilation and respiratory mechanism employing the reverse hydroxylamine-ubiquinone redox module (HURM; Klotz and Stein, 2008) pathway (haoA'þcycB) has been reported recently (Campbell et al., 2009). Interestingly, the nrfAH and haoA'þcycB inventories are homologues (Bergman et al., 2005; Kim et al., 2008; Klotz et al., 2008). Ammonia, whether available in the environment, obtained by nitrogen fixation or by ammonification from NOx, is another important pool of reactive nitrogen. "
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    • "Some Gamma-MOB encode haoAB genes but not the adjoining cytochromes c as in the AOB (Hou et al., 2008; Klotz et al., 2008; Nyerges and Stein, 2009; Pol et al., 2007; Poret-Peterson et al., 2008), hence ammonia oxidation is not an energy-generating pathway for these bacteria. The haoAB genes with uncharacterized function have been identified in a number of other proteobacterial genomes (Bergmann et al., 2005). Interestingly, the HAO enzyme shares an evolutionary origin with pentaheme nitrite reductase, NrfA, that is used in dissimilatory reduction of nitrite to ammonia via hydroxylamine (Einsle et al., 1999). "
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