Characterization of the structural gene encoding a copper-containing nitrite reductase and homology of this gene to DNA of other denitrifiers

Abstract

A copper-containing nitrite reductase gene (nirU) from Pseudomonas sp. strain G-179 was found in a 1.9-kb EcoRI-BamHI DNA fragment. The coding region contained information for a polypeptide of 379 amino acids. The encoded protein had 78% identity in amino acid sequence to the nitrite reductase purified from Achromobacter cycloclastes. The ligands for type 1 copper-and type 2 copper-binding sites found in A. cycloclastes were also found in Pseudomonas sp. strain G-179, suggesting that these binding sites are conserved. Upstream from the promoter, two putativeJfr boxes were found, suggesting that an FNR-like protein may be involved in regulation of the nitrite reductase gene under anaerobic conditions. When the 1.9-kb clone was used to probe Southern blots for similar sequences in DNAs from different denitrifiers, hybridization bands were seen for 15 of 16 denitrifiers known to have nitrite reductases containing copper. Except for Pseudomonas stutzeri JM300, all denitrifiers tested that have nitrite reductases containing heme c,d, showed no or weak hybridization to this probe. Thus, this structural gene may be useful as a probe to detect denitrifiers with copper-containing nitrite reductases.

Tree species and moisture effects on soil sources of N2O: Quantifying contributions from nitrification and denitrification with 18O isotopes

“…The exchange of water oxygen with nitrite and nitric oxide has been demonstrated for some denitrifying bacteria [Garber and Hollocher, 1982;Ye et al, 1991;Shearer and Kohl, 1988], but the degree of exchange varies greatly among bacterial strains and may be related to biochemistry of nitrite reduction [Ye et al, 1991]. Bacteria possessing the heme-type nitrite reductase, as Pseudomonas chlororaphis does [Ye et al, 1993], were shown to catalyze relatively large amounts of exchange (39 -76%) [Ye et al, 1991], while Pseudomonas aureofaciens, known to possess the copper-type nitrite reductase [Glockner et al, 1993] was shown to cause relatively little incorporation of oxygen atoms from water into N 2 O (around 6%) [Ye et al, 1991]. Casciotti et al [2002] recently reported the low incorporation of oxygen isotopes of water into the N 2 O by Pseudomonas aureofaciens: While in some cases up to 10% of oxygen in N 2 O originated from water, in most cases incorporation was frequently less than 3%.…”

Reduction in denitrification activity in field soils exposed to long term contamination by 2,4,6-trinitrotoluene (TNT)

“…Denitri¢cation DNA probes were derived from plasmid pnir9 for nirS [13], plasmid pRTC19 for nirK [14] and plasmid pMW12 for nosZ [15]. Genomic DNAs from P. stutzeri ATCC 14405 (nirS) and A. cycloclastes ATCC 21921(nirK) were also used as positive controls for the colony hybridization experiments.…”

Periplasmic nitrate-reducing system of the phototrophic bacterium Rhodobacter sphaeroides DSM 158: transcriptional and mutational analysis of the napKEFDABC gene cluster

“…Hydropathy analysis ( Figure 2B) and sequence comparisons ( Figure 3A) indicate that R. sphaeroides NapE is a single transmembrane polypeptide which shows high similarity to T. pantotropha NapE (55 % identity) [5] and to the product of an ORF that is divergently transcribed from the Pseudomonas sp. nirU gene encoding the copper nitrite reductase (49 % identity) [36]. NapE and NapK do not show significant similarity to each other at the amino acid sequence level but they share some properties ( Table 2).…”