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      Using a chimeric respiratory chain and EPR spectroscopy to determine the origin of semiquinone species previously assigned to mitochondrial complex I

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          Abstract

          Background

          For decades, semiquinone intermediates have been suggested to play an essential role in catalysis by one of the most enigmatic proton-pumping enzymes, respiratory complex I, and different mechanisms have been proposed on their basis. However, the difficulty in investigating complex I semiquinones, due to the many different enzymes embedded in the inner mitochondrial membrane, has resulted in an ambiguous picture and no consensus.

          Results

          In this paper, we re-examine the highly debated origin of semiquinone species in mitochondrial membranes using a novel approach. Our combination of a semi-artificial chimeric respiratory chain with pulse EPR spectroscopy (HYSCORE) has enabled us to conclude, unambiguously and for the first time, that the majority of the semiquinones observed in mitochondrial membranes originate from complex III. We also identify a minor contribution from complex II.

          Conclusions

          We are unable to attribute any semiquinone signals unambiguously to complex I and, reconciling our observations with much of the previous literature, conclude that they are likely to have been misattributed to it. We note that, for this earlier work, the tools we have relied on here to deconvolute overlapping EPR signals were not available. Proposals for the mechanism of complex I based on the EPR signals of semiquinone species observed in mitochondrial membranes should thus be treated with caution until future work has succeeded in isolating any complex I semiquinone EPR spectroscopic signatures present.

          Supplementary information

          Supplementary information accompanies this paper at 10.1186/s12915-020-00768-6.

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          Most cited references50

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          EasySpin, a comprehensive software package for spectral simulation and analysis in EPR.

          EasySpin, a computational package for spectral simulation and analysis in EPR, is described. It is based on Matlab, a commercial technical computation software. EasySpin provides extensive EPR-related functionality, ranging from elementary spin physics to data analysis. In addition, it provides routines for the simulation of liquid- and solid-state EPR and ENDOR spectra. These simulation functions are built on a series of novel algorithms that enhance scope, speed and accuracy of spectral simulations. Spin systems with an arbitrary number of electron and nuclear spins are supported. The structure of the toolbox as well as the theoretical background underlying its simulation functionality are presented, and some illustrative examples are given.
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            Crystal structure of the entire respiratory complex I

            Complex I is the first and largest enzyme of the respiratory chain, playing a central role in cellular energy production by coupling electron transfer between NADH and ubiquinone to proton translocation. It is implicated in many common human neurodegenerative diseases. Here we report the first crystal structure of the entire, intact complex I (from T. thermophilus) at 3.3 Å resolution. The structure of the 536 kDa complex comprises 16 different subunits with 64 transmembrane helices and 9 Fe-S clusters. The core fold of subunit Nqo8 (NuoH/ND1) is, unexpectedly, similar to a half-channel of the antiporter-like subunits. Small subunits nearby form a linked second half-channel, thus completing the fourth proton translocation pathway, in addition to the channels in three antiporter-like subunits. The quinone-binding site is unusually long, narrow and enclosed. The quinone headgroup binds at the deep end of this chamber, near cluster N2. Strikingly, the chamber is linked to the fourth channel by a “funnel” of charged residues. The link continues over the entire membrane domain as a remarkable flexible central axis of charged and polar residues. It likely plays a leading role in the propagation of conformational changes, aided by coupling elements. The structure suggests that a unique, out-of-the-membrane quinone reaction chamber allows the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle.
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              Mitochondrial complex I.

              Judy Hirst (2013)
              Complex I (NADH:ubiquinone oxidoreductase) is crucial for respiration in many aerobic organisms. In mitochondria, it oxidizes NADH from the tricarboxylic acid cycle and β-oxidation, reduces ubiquinone, and transports protons across the inner membrane, contributing to the proton-motive force. It is also a major contributor to cellular production of reactive oxygen species. The redox reaction of complex I is catalyzed in the hydrophilic domain; it comprises NADH oxidation by a flavin mononucleotide, intramolecular electron transfer along a chain of iron-sulfur clusters, and ubiquinone reduction. Redox-coupled proton translocation in the membrane domain requires long-range energy transfer through the protein complex, and the molecular mechanisms that couple the redox and proton-transfer half-reactions are currently unknown. This review evaluates extant data on the mechanisms of energy transduction and superoxide production by complex I, discusses contemporary mechanistic models, and explores how mechanistic studies may contribute to understanding the roles of complex I dysfunctions in human diseases.
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                Author and article information

                Contributors
                m.roessler@imperial.ac.uk
                Journal
                BMC Biol
                BMC Biol
                BMC Biology
                BioMed Central (London )
                1741-7007
                20 May 2020
                20 May 2020
                2020
                : 18
                Affiliations
                [1 ]GRID grid.4868.2, ISNI 0000 0001 2171 1133, School of Biological and Chemical Sciences, , Queen Mary University of London, ; Mile End Road, London, E1 4NS UK
                [2 ]GRID grid.5335.0, ISNI 0000000121885934, Medical Research Council Mitochondrial Biology Unit, , University of Cambridge, ; Cambridge, CB2 0XY UK
                [3 ]GRID grid.7445.2, ISNI 0000 0001 2113 8111, Department of Chemistry, , Imperial College London, Molecular Sciences Research Hub, ; White City Campus, Wood Lane, London, W12 0BZ UK
                Article
                768
                10.1186/s12915-020-00768-6
                7238650
                32429970
                d51d8460-f5af-4e4a-a16c-d063bb1be723
                © The Author(s) 2020

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100000265, Medical Research Council;
                Award ID: MC_U105663141
                Award ID: MC_UU_00015/2
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100000275, Leverhulme Trust;
                Award ID: RPG-2018-183
                Award Recipient :
                Funded by: The Royal Society
                Award ID: PGS-R1-191215
                Award Recipient :
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2020

                Life sciences
                nadh:ubiquinone oxidoreductase,respiratory complex i,semiquinones,electron paramagnetic resonance

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