Bacterial adaptation of respiration from oxic to microoxic and anoxic conditions: redox control

Abstract

Under a shortage of oxygen, bacterial growth can be faced mainly by two ATP-generating mechanisms: (i) by synthesis of specific high-affinity terminal oxidases that allow bacteria to use traces of oxygen or (ii) by utilizing other substrates as final electron acceptors such as nitrate, which can be reduced to dinitrogen gas through denitrification or to ammonium. This bacterial respiratory shift from oxic to microoxic and anoxic conditions requires a regulatory strategy which ensures that cells can sense and respond to changes in oxygen tension and to the availability of other electron acceptors. Bacteria can sense oxygen by direct interaction of this molecule with a membrane protein receptor (e.g., FixL) or by interaction with a cytoplasmic transcriptional factor (e.g., Fnr). A third type of oxygen perception is based on sensing changes in redox state of molecules within the cell. Redox-responsive regulatory systems (e.g., ArcBA, RegBA/PrrBA, RoxSR, RegSR, ActSR, ResDE, and Rex) integrate the response to multiple signals (e.g., ubiquinone, menaquinone, redox active cysteine, electron transport to terminal oxidases, and NAD/NADH) and activate or repress target genes to coordinate the adaptation of bacterial respiration from oxic to anoxic conditions. Here, we provide a compilation of the current knowledge about proteins and regulatory networks involved in the redox control of the respiratory adaptation of different bacterial species to microxic and anoxic environments.

FIG. 1.

Respiratory chain(s) in mammalian mitochondrion and bacteria. (a) A summary of the topology and bioenergetics of a basic aerobic respiratory electron transport system of a mammalian mitochondrion is shown. This figure is adapted from ref. (197). (b) Schematic representation of aerobic and anaerobic nitrate respiration pathways in bacteria. MK, menaquinone; UQ, ubiquinone; Cyt, cytochrome; SDH, succinate dehydrogenase; NDH, NADH dehydrogenase; cd₁Nir, cd_1-type nitrite reductase; CuNir, Cu-type nitrite reductase; Nor, nitric oxide reductase; Nos, nitrous oxide reductase; Nar, membrane-bound nitrate reductase; Nap, periplasmic nitrate reductase; NrfA; cytochrome c nitrite reductase; UQH₂, ubihydroquinone; MKH₂, menahydroquinone.

FIG. 2.

Summary of the main types of heme–copper oxygen reductases belonging to the A, B, and C families and the bd-type quinol oxidase.

FIG. 3.

Regulation strategies of ccoNOQP gene transcription. Four regulation strategies have been described in several bacterial groups (see text for details) that involve (a) Fnr, (b) FixLJ-FixK, (c) Fnr and FixLJ-FixK, or (d) an unknown regulator. Gene transcriptional activation is indicated by arrows. Protein inactivation by O₂ is indicated by perpendicular lines. This figure is adapted from ref. (50).

FIG. 4.

Functional domains and model of Fnr and FixLJ mediated oxygen activation. (a) Fnr senses oxygen via an iron-sulfur center, which is coordinated with four cysteine residues. Under anoxic conditions, Fnr is in its active state and it promotes DNA-binding by formation of a homodimer leading to activation of gene transcription. (b) FixL is an oxygen receptor in which oxygen binds directly to a heme group that is coordinated to a histidine residue within a PAS domain. Detection of low oxygen tension changes the conformation of the input PAS domain, rendering increased autophosphorylation activity of the transmitter domain in His residue and repressing the phosphatase activity of FixL. FixL activates FixJ transcriptional activity by transferring the phosphoryl group to the N-terminal domain of FixJ (+) gene transcription activation.

FIG. 5.

Regulation of bd and bo₃ terminal oxidase expression in Escherichia coli. Fnr and ArcB provide negative or positive transcriptional control in response to oxygen availability. The genes cydAB and cyoABCDE encode bd and bo₃ oxidase polypeptides, respectively. Positive regulation (+) is denoted by arrows, and negative regulation (−) is indicated by perpendicular lines.

FIG. 6.

Functional domains and model of ArcBA-mediated redox control. (a) ArcB is attached to the membrane by two transmembrane regions (TM). A linker region containing a putative leucine-zipper and a PAS domain connects TM2 with the catalytic domains. The two cysteine-residues (Cys¹⁸⁰ and Cys²⁴¹) in the linker region are able to undergo oxidation and to form intermolecular disulfide bonds between both ArcB monomers. The transmitter domain (H1) contains the conserved His²⁹² together with the G1 and G2 nucleotide-binding motifs. The receiver domain (D1) harbors the conserved Asp⁵⁷⁶, and the histidine phosphotransfer domain (Hpt/H2) contains the conserved His⁷¹⁷. The ArcA component is represented with its N-terminal receiver domain carrying the conserved Asp⁵⁴ and its C-terminal H-T-H) domain. This figure is adapted from ref. (138). (b) MKH₂, which predominates under anaerobic conditions, would be oxidized in the presence of low levels of oxygen (∼20% aerobiosis), leading to increased levels of MKs and inactivation of ArcB kinase activity. UQH₂ predominate under microoxic conditions (∼80% aerobiosis), giving rise to activation of ArcB kinase activity. In fully aerobic conditions (100%), the UQH₂ pool is subjected to oxidation, which results in increasing levels of UQs and oxidation of the key cysteines, leading to inactivation of the ArcB kinase activity. This figure is adapted from ref. (18).

FIG. 7.

Aerobic respiratory chains in Rhodobacter capsulatus and Rhodobacter sphaeroides. The quinone-reducing (left) and quinol-oxidizing (right) branches with terminal oxidases induced under oxic conditions (gray boxes), and microoxic conditions (white boxes), are shown. Black arrows indicate the influx of reducing equivalents.

FIG. 8.

Proposed models for redox-mediated sensing by RegBA/PrrBA. (a) In Rho. capsulatus, the conserved cysteine C²⁶⁵ of RegB functions as a redox switch that controls RegB kinase activity through a metal-dependent formation of a disulfide bond in response to redox changes (235). Binding of UQ to the RegB transmembrane domain has also been proposed to inhibit RegB kinase activity, whereas UQH₂ does not affect RegB kinase activity (234). (b) In Rho. sphaeroides, the cbb₃ oxidase generates an “inhibitory” signal that can directly stimulates the phosphatase activity of PrrB. Under low oxygen conditions when the electron flow is reduced, the inhibitory signal from cbb₃ is weakened, and PrrB would retain its kinase activity (165). PrrC has been proposed as a signal mediator between the cbb₃ oxidase and the sensor kinases PrrB (7).

FIG. 9.

Regulation of bd and cbb₃ terminal oxidases expression in Rho. capsulatus (a) and Rho. sphaeroides (b). In Rho. capsulatus, RegA regulates gene transcription in response to both oxic and anoxic conditions, FnrL, HvrA, in response to anaerobiosis, and AerR and CrtJ in response to aerobiosis. In Rho. sphaeroides, FnrL, PrrA, and PspR regulate gene transcription in response to anoxic conditions. Genes cydAB and ccoNOQP encode bd and cytochrome cbb₃ oxidase polypeptides, respectively. Positive regulation (+) is denoted by arrows, and negative regulation (−) is indicated by perpendicular lines.

FIG. 10.

Aerobic respiratory chains (a) and regulation of CIO, cbb₃, and aa₃ terminal oxidase expression (b) in Pseudomonas aeruginosa. In (a), the quinone-reducing (left) and quinol-oxidizing (right) branches with terminal oxidases induced under oxic conditions (gray boxes), and microoxic conditions (white boxes), are shown. In (b), Anr and RoxSR regulators provide negative or positive transcriptional control, in response to oxygen availability. Genes cox, cioAB, and ccoNOQP encode aa₃, CIO, and cbb₃ oxidase polypeptides, respectively. Positive regulation (+) is denoted by arrows, and negative regulation (−) is indicated by perpendicular lines. CIO, cyanide insensitive oxidase.

FIG. 11.

Aerobic respiratory chains in Bradyrhizobium japonicum. The quinone-reducing (left) and quinol-oxidizing (right) branches with terminal oxidases are shown. The coxBACF-encoded cytochrome aa₃ is the predominant heme-copper oxidase for aerobic growth (gray box), and the fixNOQP-encoded cbb₃-type oxidase (white box) supports respiration under free-living microoxic and under symbiotic conditions. ^aGene number according to RhizoBase (http://genome.kazusa.or.jp/rhizobase).

FIG. 12.

Aerobic respiratory chains (a) and regulation of bd, aa₃, and caa₃ terminal oxidase expression (b) in Bacilus subtilis. In (a), the quinone-reducing and quinol-oxidizing branches with terminal oxidases induced under oxic conditions (gray boxes), and microoxic conditions (white boxes), are shown. In (b), ResDE and Fnr provide positive transcriptional control in response to oxygen availability. ResD, but not ResE, is required for transcription of cyd operon (this complex regulation is indicated with a question mark in the figure). Redox-dependent repression of cydABCD (bd oxidase) by Rex is controlled by NAD⁺/NADH ratio in the cells. Operons qox and cta encode the aerobic terminal oxidases aa₃ and caa₃. Positive regulation (+) is denoted by arrows, and negative regulation (−) is indicated by perpendicular lines.

FIG. 13.

Denitrification pathway (a) and regulation (b) in bacteria. In (a), the topological organization of denitrification enzymes is shown. The membrane-bound (NarGHI), and periplasmic, (NapABC) nitrate reductases as well as the nitrite reductases (Cu-type or cd₁-type), nitric oxide reductases (cNor, qNor, and qCu_ANor), and nitrous oxide reductase (NosZ) are shown. (b) Regulatory network of denitrification genes in response to O₂ concentration, nitrate/nitrite, and nitric oxide (NO). Positive regulation is denoted by arrows, and negative regulation is indicated by perpendicular lines. Further details are given in the text.

FIG. 14.

Schematic representation of denitrification control in Rho. sphaeroides (a) and Agrobacterium tumefaciens (b). (a) In Rho. Sphaeroides, PrrBA provides control of nirK expression in response to external redox variations, and NnrR provides control of expression of nirK and nor genes in response to NO. This figure is adapted from ref. (218). (b) In Ag. tumefaciens, ActSR provides control of nirK expression presumably in response to external redox variations, and FnrN and NnrR provide control of nirK and nor expression in response to low oxygen tension and presence of NO, respectively. Positive regulation is denoted by arrows, and negative regulation is indicated by perpendicular lines.

FIG. 15.

Schematic representation of the regulatory network of denitrification in Br. japonicum. FixLJ regulates fixK₂ gene transcription in response to a shortage of oxygen, and FixK₂ provides control of transcription on nap and nirK denitrification genes as well as the nnrR gene, whose product, in turn, activates transcription of nor genes. RegSR activates expression of fixRnifA operon presumably by sensing changes in the redox state of the cell. The NifA regulatory protein activates gene expression at very low oxygen concentrations. Control of denitrification genes by NifA has been demonstrated by our group (36). Furthermore, recent results have shown that NorC expression is significantly reduced in a Br. japonicum regR mutant (239). Sigma⁵⁴ links both regulatory cascades. Positive regulation is denoted by arrows, and negative regulation is indicated by perpendicular lines.

FIG. 16.

Schematic representation of denitrification control in Ba. subtilis. ResDE regulates gene transcription in response to both redox/oxygen changes and presence of NO, Fnr provides control in response to low oxygen concentration, NsrR in response to NO, and TnrA in response to high oxygen concentration and limited nitrogen availability. narGHJI encodes a respiratory nitrate reductase. nasBC encodes an assimilatory nitrate reductase; nasDEF, a nitrite reductase; and hmp, a flavohemoglobin. Positive regulation is denoted by arrows, and negative regulation is indicated by perpendicular lines.