Protonmotive Q cycle pathway of electron transfer and energy transduction in the three-subunit ubiquinol-cytochrome c oxidoreductase complex of Paracoccus denitrificans.

Yang, Xiaohang; Trumpower, Bernard L.

doi:10.1016/s0021-9258(18)37880-3

Cited by 53 publications

(16 citation statements)

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“…Of course, respiratory chains are, generally speaking, ancient, just not as ancient as the bioenergetic processes in acetogens and methanogens that lack cytochromes or those in sulfate reducers, in our view (see text). The scheme in ( f ) could correspond to the situation in sulfate reducers; the scheme in (g) could correspond to the situation in Paracoccus [241] or Rhodobacter [242].…”

Section: Discussionmentioning

confidence: 99%

Early bioenergetic evolution

Sousa

Thiergart

Landan

et al. 2013

Phil. Trans. R. Soc. B

233

256

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Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. This paper outlines an energetically feasible path from a particular inorganic setting for the origin of life to the first free-living cells. The sources of energy available to early organic synthesis, early evolving systems and early cells stand in the foreground, as do the possible mechanisms of their conversion into harnessable chemical energy for synthetic reactions. With regard to the possible temporal sequence of events, we focus on: (i) alkaline hydrothermal vents as the far-from-equilibrium setting, (ii) the Wood–Ljungdahl (acetyl-CoA) pathway as the route that could have underpinned carbon assimilation for these processes, (iii) biochemical divergence, within the naturally formed inorganic compartments at a hydrothermal mound, of geochemically confined replicating entities with a complexity below that of free-living prokaryotes, and (iv) acetogenesis and methanogenesis as the ancestral forms of carbon and energy metabolism in the first free-living ancestors of the eubacteria and archaebacteria, respectively. In terms of the main evolutionary transitions in early bioenergetic evolution, we focus on: (i) thioester-dependent substrate-level phosphorylations, (ii) harnessing of naturally existing proton gradients at the vent–ocean interface via the ATP synthase, (iii) harnessing of Na+ gradients generated by H+/Na+ antiporters, (iv) flavin-based bifurcation-dependent gradient generation, and finally (v) quinone-based (and Q-cycle-dependent) proton gradient generation. Of those five transitions, the first four are posited to have taken place at the vent. Ultimately, all of these bioenergetic processes depend, even today, upon CO2 reduction with low-potential ferredoxin (Fd), generated either chemosynthetically or photosynthetically, suggesting a reaction of the type ‘reduced iron → reduced carbon’ at the beginning of bioenergetic evolution.

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Section: Discussionmentioning

confidence: 99%

Early bioenergetic evolution

Sousa

Thiergart

Landan

et al. 2013

Phil. Trans. R. Soc. B

233

256

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“…After an early report on the purification and characterization of cytochrome c 1 from P. denitrificans as a polypeptide with an unusually high molecular mass (177), the bc 1 complex was isolated initially as a "supercomplex" along with cytochrome c oxidase and a membranebound cytochrome c 552 , yielding high quinol-oxidizing activity (26). Subsequently, its subunit composition was confirmed unequivocally (340), showing that only the three subunits carrying redox centers make up a complex that is also fully competent in free energy transduction (341). The cloning of the corresponding genes (162) revealed an operon structure, fbcFBC, coding for the Rieske FeS subunit, the cytochrome b, and the cytochrome c 1 subunit.…”

Section: Genes Of Oxygen Respirationmentioning

confidence: 99%

Molecular Genetics of the GenusParacoccus: Metabolically Versatile Bacteria with Bioenergetic Flexibility

Baker¹,

Ferguson

Ludwig

et al. 1998

Microbiol Mol Biol Rev

211

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SUMMARY Paracoccus denitrificans and its near relative Paracoccus versutus (formerly known as Thiobacilllus versutus) have been attracting increasing attention because the aerobic respiratory system of P. denitrificans has long been regarded as a model for that of the mitochondrion, with which there are many components (e.g., cytochrome aa3 oxidase) in common. Members of the genus exhibit a great range of metabolic flexibility, particularly with respect to processes involving respiration. Prominent examples of flexibility are the use in denitrification of nitrate, nitrite, nitrous oxide, and nitric oxide as alternative electron acceptors to oxygen and the ability to use C1 compounds (e.g., methanol and methylamine) as electron donors to the respiratory chains. The proteins required for these respiratory processes are not constitutive, and the underlying complex regulatory systems that regulate their expression are beginning to be unraveled. There has been uncertainty about whether transcription in a member of the alpha-3 Proteobacteria such as P. denitrificans involves a conventional ς70-type RNA polymerase, especially since canonical −35 and −10 DNA binding sites have not been readily identified. In this review, we argue that many genes, in particular those encoding constitutive proteins, may be under the control of a ς70 RNA polymerase very closely related to that of Rhodobacter capsulatus. While the main focus is on the structure and regulation of genes coding for products involved in respiratory processes in Paracoccus, the current state of knowledge of the components of such respiratory pathways, and their biogenesis, is also reviewed.

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“…For ferriheme complexes with (d xy ) 2 (d xz , d yz ) 3 electronic ground states (the most common electron configuration for low-spin ferrihemes in biological systems), rhombic EPR spectra have been associated with mutually parallel orientation of the axial ligand planes, and “large g max ” EPR spectra with mutually perpendicular ligand planes. , However, how perfectly perpendicular the axial ligands must be to give rise to a “large g max ” EPR spectrum, or how nearly degenerate the d xz and d yz orbitals of the heme must be, has remained a question. On the basis of their “large g max ” EPR spectra, ,,− ,, ,, the membrane-bound bis-histidine-coordinated b cytochromes − are believed to have their imidazole rings in perpendicular planes. However, when model heme complexes with perpendicular ligand planes are reduced to low-spin iron(II), the axial ligands are found to be in parallel planes and the macrocycles are not ruffled, but rather are strictly planar .…”

Section: Introductionmentioning

confidence: 99%

“…The membrane-bound bis-histidine-coordinated cytochromes of mitochondrial complexes II and III and the similar cytochromes of chloroplasts do not lose their axial ligands upon redox. − In the oxidized state, we know from the “large g max ” EPR spectra that the imidazole planes of the histidine ligands have “near-perpendicular” dihedral angles, yet we also know that low-spin Fe(II) porphyrinates prefer not to have perpendicular ligand planes with a ruffled ring conformation. , This, plus the expected rigidity of the axial ligand orientation in a membrane-bound protein, makes it unlikely that the membrane-bound cytochromes that exhibit “large g max ” EPR signals have their axial ligands lying over the meso positions in perpendicular planes. On the other hand, it has also become clear that perfect alignment of axial ligands in either strictly parallel or perpendicular planes is not required to produce normal rhombic vs “large g max ” EPR signals, respectively.…”

Section: Introductionmentioning

confidence: 99%

“…X-ray crystallographic and detailed dynamic NMR studies were carried out for this purpose. Second, OETPP is used for modeling the EPR properties of bis-histidine-ligated biological ferrihemes, − by using the cavities to orient the axial ligands in near-perpendicular planes, but not over the meso positions, where ruffling is encouraged.…”

Section: Introductionmentioning

confidence: 99%

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Molecular Structures and Magnetic Resonance Spectroscopic Investigations of Highly Distorted Six-Coordinate Low-Spin Iron(III) Porphyrinate Complexes

et al. 2001

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Three bis-axially ligated complexes of iron(III) octaethyltetraphenylporphyrin, (OETPP)Fe(III), have been prepared, which are low-spin complexes, each with two axial nitrogen-donor ligands (N-methylimidazole (N-MeIm), 4-(dimethylamino)pyridine (4-NMe(2)Py), and 2-methylimidazole (2-MeImH)). The crystal and molecular structure of the bis-(2-MeImH) complex shows the macrocycle to be in a saddled conformation, with the ligands in perpendicular planes aligned at 14 degrees to the porphyrin nitrogens so as to relieve the steric interaction between the 2-methyl groups and the porphyrin. The Fe-N(por) bond lengths are typical of nonplanar six-coordinate low-spin Fe(III) complexes, while the axial Fe-N(ax) bond lengths are substantially longer than those of [(TPP)Fe(2-MeImH)(2)](+) (2.09(2) A as compared to 2.015(4) and 2.010(4) A). The crystal and molecular structure of the bis-(4-NMe(2)Py) complex also shows the macrocycle to be in a mainly saddled conformation, but with a significant ruffled component. As a result, the average Fe-N(por) bonds are significantly shorter (1.951 A as compared to 1.974 A) than those of the bis-(2-MeImH) complex. One ligand is aligned at 9 degrees to two trans porphyrin nitrogens, while the other is at 79 degrees to the same porphyrin nitrogens, producing a dihedral angle of 70 degrees between the ligand planes. The EPR spectrum of this complex, like that of the bis-(2-MeImH) complex, is of the "large g(max)" type, with g(max) = 3.29 and 3.26, respectively. However, in frozen CD(2)Cl(2), [(OETPP)Fe(N-MeIm)(2)](+) exhibits both "large g(max)" and normal rhombic signals, suggesting the presence of both "perpendicular" and "parallel" ligand orientations. The 1- and 2D (1)H NMR spectra of each of these complexes, as well as the chloroiron(III) starting material, were investigated as a function of temperature. The COSY and NOESY/EXSY spectra of the chloride complex are consistent with the expected J-coupling and saddle inversion dynamics, respectively. Complete spectral assignments for the bis-(N-MeIm) and -(4-NMe(2)Py) complexes have been made using 2D (1)H NMR techniques. In each case, the number of resonances due to methylene (two) and phenyl protons (one each) is consistent with D(2)(d)() symmetry, and therefore an effective perpendicular orientation of the axial ligands on the time scale of the NMR experiments. The temperature dependences of the (1)H resonances of these complexes show significant deviations from Curie behavior, and also evidence of extensive ligand exchange and rotation. Spectral assignment of the eight methylene resonances of the bis-(2-MeImH) complex to the four ethyl groups was possible through the use of 2D (1)H NMR techniques. The complex is fluxional, even at -90 degrees C, and ROESY data suggest that the predominant process is saddle inversion accompanied by simultaneous rotation of the axial ligands. Saddle inversion becomes slow on the 2D NMR time scale as the temperature is lowered in the ligand order of N-MeIm > 4-NMe(2)Py > 2-MeImH, probably due mainly to progre...

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Protonmotive Q cycle pathway of electron transfer and energy transduction in the three-subunit ubiquinol-cytochrome c oxidoreductase complex of Paracoccus denitrificans.

Cited by 53 publications

References 64 publications

Early bioenergetic evolution

Early bioenergetic evolution

Molecular Genetics of the GenusParacoccus: Metabolically Versatile Bacteria with Bioenergetic Flexibility

Molecular Structures and Magnetic Resonance Spectroscopic Investigations of Highly Distorted Six-Coordinate Low-Spin Iron(III) Porphyrinate Complexes

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