Oxygen as Acceptor

Abstract

Like most bacteria, Escherichia coli has a flexible and branched respiratory chain that enables the prokaryote to live under a variety of environmental conditions, from highly aerobic to completely anaerobic. In general, the bacterial respiratory chain is composed of dehydrogenases, a quinone pool, and reductases. Substrate-specific dehydrogenases transfer reducing equivalents from various donor substrates (NADH, succinate, glycerophosphate, formate, hydrogen, pyruvate, and lactate) to a quinone pool (menaquinone, ubiquinone, and dimethylmenoquinone). Then electrons from reduced quinones (quinols) are transferred by terminal reductases to different electron acceptors. Under aerobic growth conditions, the terminal electron acceptor is molecular oxygen. A transfer of electrons from quinol to O₂ is served by two major oxidoreductases (oxidases), cytochrome bo₃ encoded by cyoABCDE and cytochrome bd encoded by cydABX. Terminal oxidases of aerobic respiratory chains of bacteria, which use O₂ as the final electron acceptor, can oxidize one of two alternative electron donors, either cytochrome c or quinol. This review compares the effects of different inhibitors on the respiratory activities of cytochrome bo₃ and cytochrome bd in E. coli. It also presents a discussion on the genetics and the prosthetic groups of cytochrome bo₃ and cytochrome bd. The E. coli membrane contains three types of quinones that all have an octaprenyl side chain (C₄₀). It has been proposed that the bo₃ oxidase can have two ubiquinone-binding sites with different affinities. "WHAT'S NEW" IN THE REVISED ARTICLE: The revised article comprises additional information about subunit composition of cytochrome bd and its role in bacterial resistance to nitrosative and oxidative stresses. Also, we present the novel data on the electrogenic function of appBCX-encoded cytochrome bd-II, a second bd-type oxidase that had been thought not to contribute to generation of a proton motive force in E. coli, although its spectral properties closely resemble those of cydABX-encoded cytochrome bd.

Figure 1

Simplified view of the E. coli respiratory chain under aerobic and microaerobic conditions. The two NADH-quinone oxidoreductases called NDH-I and NDH-II and succinate-quinone oxidoreductase (SQR) transfer reducing equivalents to ubiquinone-8 (UQ-8) to yield reduced UQ-8, ubiquinol-8. Three quinol-oxygen oxidoreductases, cytochrome bo₃ (CyoABCD), cytochrome bd (CydABX), and cytochrome bd-II (AppBCX), oxidize ubiquinol-8 and reduce O₂ to 2H₂O. CydABX and possibly AppBCX oxidize menaquinol-8. NDH-I, CyoABCD, CydABX, and AppBCX are coupled (Δμ_H⁺ generators); NDH-II and SQR are uncoupled (no Δμ_H⁺ generation). The energetic efficiency of each enzyme is indicated as the number of protons delivered to the periplasmic side of the membrane per electron (H⁺/e⁻ ratio). doi:10.1128/ecosalplus.ESP-0012-2015.f1

Figure 2

Structures of ubiquinone-8, the reduced ubiquinone-8 (ubiquinol-8), menaquinone-8, and the reduced menaquinone-8 (menaquinol-8). doi:10.1128/ecosalplus.ESP-0012-2015.f2

Figure 3

Structures of heme B (protoheme IX), heme O, and heme D (chlorin), which are redox cofactors of cytochrome bo₃ and/or cytochrome bd from E. coli. doi:10.1128/ecosalplus.ESP-0012-2015.f3

Figure 4

Structure of cytochrome bo₃ from E. coli. Only two main subunits are shown: subunit I in gray and subunit II in yellow. Hemes are shown in red (heme o₃ on the right and heme b on the left). The cyan sphere near heme o₃ represents the Cu_B center. The amino acid residues of possible proton-conducting pathways, the D (red-tag) and K (blue-tag) channels, in subunit I are shown. The most likely position of the membrane is depicted by the gray background. doi:10.1128/ecosalplus.ESP-0012-2015.f4

Figure 5

Proposed topology of the CydA and CydB subunits of cytochrome bd from E. coli. The axial ligands of heme b₅₉₅ (H19) and heme b₅₅₈ (H186 and M393) in the CydA subunit are shown in purple and red, respectively. The protein sequence data have been taken from information available at http://genolist.pasteur.fr/Colibri/. The alignment has been made by using the TOPO2 program available at http://www.sacs.ucsf.edu/TOPO2. The model is very similar to that reported in reference . doi:10.1128/ecosalplus.ESP-0012-2015.f5

Figure 6

Schematic model of electron and proton transfer pathways in cytochrome bd from E. coli. There are two protonatable groups, X_P and X_N, redox coupled to the heme b₅₉₅-heme d active site. A highly conserved residue, E445, was proposed to be either the X_P group or the gateway in a channel that connects X_P with the cytoplasm or the periplasm (52). A strictly conserved E107 residue is a part of the channel mediating proton transfer to X_N from the cytoplasm (54). X_b, a group at the periplasmic side of the membrane that picks up and releases a proton as heme b₅₅₈, is reduced and oxidized. doi:10.1128/ecosalplus.ESP-0012-2015.f6

Figure 7

Cytochrome bd reaction scheme. The three rhombuses represent hemes b₅₅₈, b₅₉₅, and d, respectively. The minus signs and red backgrounds in the rhombuses denote that the heme is in the ferrous state. R-CO, R, A_R, P, F, O are fully ferrous CO bound, fully ferrous unligated, fully ferrous O₂ bound, peroxy, oxoferryl, and fully ferric species, respectively. Transient peroxy species (P) discovered by Belevich et al. (53) is shown as a true peroxy complex of ferric heme d. It is possible, however, that P is an oxoferryl form with a π-cation radical on the porphyrin ring of heme d (285, 286). doi:10.1128/ecosalplus.ESP-0012-2015.f7