Multiple transcription factors of the FNR family in denitrifying Pseudomonas stutzeri : characterization of four fnr‐like genes, regulatory responses and cognate metabolic processes

Abstract

SummaryPseudomonas stutzeri is a facultative anaerobic bacterium with the capability of denitrification. In searching for regulators that control the expression of this trait in response to oxygen withdrawal, we have found an unprecedented multiplicity of four genes encoding transcription factors of the FNR family. The fnrA gene encodes a genuine FNR-type regulator, which is expressed constitutively and controls the cytochrome cbb 3 -type terminal oxidase (the cco operon), cytochrome c peroxidase (the ccp gene) and the oxygenindependent coproporphyrinogen III oxidase (the hemN gene), in addition to its previously demonstrated role in arginine catabolism (the arc operon). The fnr homologues dnrD, dnrE and dnrS encode regulators of a new subgroup within the FNR family. Their main distinctive feature is the lack of cysteine residues for complexing the [4Fe-4S] centre of redox-active FNRtype regulators. However, they form a phylogenetic lineage separate from the FixK branch of FNR proteins, which also lack this cysteine signature. We have studied the expression of the dnr genes under aerobic, oxygen-limited and denitrifying conditions. DnrD is a key regulator of denitrification by selective activation of the genes for cytochrome cd 1 nitrite reductase and NO reductase. The dnrD gene is part of the 30 kb region carrying denitrification genes of P. stutzeri. Transcrip

Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses

“…Our data show a phenotype for hemN2 alone, with w nitrate and w nitrite values of Ϫ3.2 and Ϫ3.0, respectively (Table 2). However, hemN4 has previously been reported to encode the functional HemN protein (52), based on genomic proximity to and activation by the O 2 -responsive regulator fnrA/FnrA (Psest_2538), although this was prior to the availability of the P. stutzeri genome sequence (53). We propose that HemN2, not HemN4, is the primary HemN protein in heme biosynthesis.…”

“…For nitrite reduction, we demonstrated that strain RCH2 uses the hemecontaining NirS protein rather than the copper-containing NirK protein under the conditions tested, although it appears that both forms are likely functional. In heme biosynthesis, of the four HemN homologs encoded in the RCH2 genome, HemN2, not the previously proposed HemN4 (52), is the primary heme biosynthesis version. One of three nnrS paralogs in RCH2, nnrS1, is suggested to encode a membrane-bound NO sensor that participates in regulation of NO detoxification.…”

Nitric oxide reductases of prokaryotes with emphasis on the respiratory, heme?copper oxidase type

“…Since FnrP is not involved in nor regulation but anaerobiosis is still required [201,202], it may be that Nnr has a dual function toward NO and oxygen. This may be also the case for P. stutzeri, for which so far no Fnr-type oxygen sensor-regulator has been found, although this bacterium harbors at least five Crp-Fnr regulators [111,191]. In B. japonicum the signal transduction pathway starts with the hemebased oxygen sensor-regulator system FixLJ.…”

“…The Anr regulator affected also anaerobic nitrate denitrification and the existence of recognition sequences specific for a Crp-Fnr regulator thus found its satisfactory explanation [189]. The picture, however, became more complicated when regulatory genes were found on sequencing the regions downstream of the nor operons of P. aeruginosa [190], P. stutzeri [8,191], Pseudomonas sp. G-179 [95] and Pa. denitrificans [118].…”

CooA, a paradigm for gas sensing regulatory proteins

“…10.032 structure of CO-free CooA (inactive for DNA binding) has been solved and a comparison of that structure with the active form of a close homolog, the cAMP receptor protein (termed CRP or CAP), has allowed testable hypotheses to be formed about the mechanism by which CO binding leads to a transcriptionally active form [12][13][14]. These models might also be relevant to other members of the extended CRP family of proteins [15]. (iv) Because CooA is a regulatory protein, it is technically easy to set up an assay system within the cell that allows the ready detection of CooA variants with biochemically interesting properties.…”