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

@article{citeulike:2658552, 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.}, address = {University of Louisville, Department of Biology, 139 Life Science Building, Louisville, KY 40292, USA.}, author = {Bergmann, D. J. and Hooper, A. B. and Klotz, M. G.}, citeulike-article-id = {2658552}, citeulike-linkout-0 = {http://dx.doi.org/10.1128/AEM.71.9.5371-5382.2005}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/16151127}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=16151127}, doi = {10.1128/AEM.71.9.5371-5382.2005}, issn = {0099-2240}, journal = {Applied and environmental microbiology}, keywords = {ammonium, gene, hao, hydroxylamine, nitrifcation, sequence}, month = {September}, number = {9}, pages = {5371--5382}, posted-at = {2008-04-11 19:16:56}, priority = {0}, title = {Structure and sequence conservation of hao cluster genes of autotrophic ammonia-oxidizing bacteria: evidence for their evolutionary history.}, url = {http://dx.doi.org/10.1128/AEM.71.9.5371-5382.2005}, volume = {71}, year = {2005} }

TY - JOUR ID - citeulike:2658552 L3 - citeulike-article-id:2658552 N2 - 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. IS - 9 JF - Applied and environmental microbiology SN - 0099-2240 AD - University of Louisville, Department of Biology, 139 Life Science Building, Louisville, KY 40292, USA. EP - 5382 TI - Structure and sequence conservation of hao cluster genes of autotrophic ammonia-oxidizing bacteria: evidence for their evolutionary history. VL - 71 SP - 5371 KW - ammonium KW - gene KW - hao KW - hydroxylamine KW - nitrifcation KW - sequence AU - Bergmann, DJ AU - Hooper, AB AU - Klotz, MG PY - 2005/09// UR - http://dx.doi.org/10.1128/AEM.71.9.5371-5382.2005 ER -