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Electron paramagnetic resonance and Mössbauer spectroscopy of intact mitochondria from respiring Saccharomyces cerevisiae

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Abstract

Mitochondria from respiring cells were isolated under anaerobic conditions. Microscopic images were largely devoid of contaminants, and samples consumed O2 in an NADH-dependent manner. Protein and metal concentrations of packed mitochondria were determined, as was the percentage of external void volume. Samples were similarly packed into electron paramagnetic resonance tubes, either in the as-isolated state or after exposure to various reagents. Analyses revealed two signals originating from species that could be removed by chelation, including rhombic Fe3+ (g = 4.3) and aqueous Mn2+ ions (g = 2.00 with Mn-based hyperfine). Three S = 5/2 signals from Fe3+ hemes were observed, probably arising from cytochrome c peroxidase and the a3:Cub site of cytochrome c oxidase. Three Fe/S-based signals were observed, with averaged g values of 1.94, 1.90 and 2.01. These probably arise, respectively, from the [Fe2S2]+ cluster of succinate dehydrogenase, the [Fe2S2]+ cluster of the Rieske protein of cytochrome bc 1, and the [Fe3S4]+ cluster of aconitase, homoaconitase or succinate dehydrogenase. Also observed was a low-intensity isotropic g = 2.00 signal arising from organic-based radicals, and a broad signal with g ave = 2.02. Mössbauer spectra of intact mitochondria were dominated by signals from Fe4S4 clusters (60–85% of Fe). The major feature in as-isolated samples, and in samples treated with ethylenebis(oxyethylenenitrilo)tetraacetic acid, dithionite or O2, was a quadrupole doublet with ΔE Q = 1.15 mm/s and δ = 0.45 mm/s, assigned to [Fe4S4]2+ clusters. Substantial high-spin non-heme Fe2+ (up to 20%) and Fe3+ (up to 15%) species were observed. The distribution of Fe was qualitatively similar to that suggested by the mitochondrial proteome.

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Notes

  1. For a purified Fe4S4 ferredoxin the area under the doublet can be quantified to within 1–2%. Here, the uncertainties are considerably larger, primarily because more than one cluster contributes. The primary contributors to the doublet may be aconitase and dihydroxyacid dehydratase. Because species with slightly different but unresolved parameters contribute, lineshapes are heterogeneously broadened Lorentzians. We used both the Lorentzian and the Voight lineshape options of WMOSS. As Voight shapes are narrower at the base, this option yields, upon visual inspection, a lower estimate for the concentration.

  2. In weak applied fields, the lowest three Kramers doublets of the spin sextet are generally populated at 4.2 K, yielding three Mössbauer spectra per site. Moreover, under these conditions the magnetic splittings, like the effective g values observed by EPR, are very sensitive to the rhombicity parameter E/D. Consequently, the high-spin Fe3+ ions in our sample produce broad and barely discernible features in weak fields. However, the 8.0-T spectra are fairly insensitive to D and E/D, because the large Zeeman splitting puts essentially all Fe3+ ions into the M S  = −5/2 state, facilitating detection and quantification.

Abbreviations

CoQ:

Coenzyme Q

DTT:

Dithiothreitol

EDTA:

Ethylenediaminetetraacetic acid

EGTA:

Ethylenebis(oxyethylenenitrilo)tetraacetic acid

EPR:

Electron paramagnetic resonance

ETF:

Electron transfer flavoprotein

HEPES:

N-(2-Hydroxyethyl)piperazine-N′-ethanesulfonic acid

IM:

Inner membrane

IMS:

Intermembrane space

NHE:

Normal hydrogen electrode

OM:

Outer membrane

SH buffer:

0.6 M sorbitol/20 mM N-(2-hydroxyethyl)piperazine-N′-ethanesulfonic acid buffer pH 7.4

SP buffer:

1.2 M sorbitol/20 mM potassium phosphate buffer pH 7.4

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Acknowledgements

We thank the following people: Art Johnson and Holly Cargill (Department of Biochemistry and Biophysics, Texas A&M University) for instructions on isolating mitochondria; Rola Barhoumi (Image Analysis Laboratory, Texas A&M University) and Anne Ellis (Microscopy and Imaging Center, Texas A&M University) for collecting microscopic images; Jinny Johnson (Protein Chemistry Laboratory, Texas A&M University) for performing amino acid analyses; David P. Giedroc (Department of Biochemistry and Biophysics, Texas A&M University) for access to his atomic absorption spectrophotometer; William James (Department of Chemistry, Texas A&M University) for training on and assistance with the inductively coupled plasma mass spectrometer; Shelly Henderson Possi for help in isolating some batches and in measuring O2 consumption; Tanner Freeman for preparing one of the EPR samples; and Roland Lill for helpful discussion.

This study was supported by the Robert A. Welch Foundation (A1170) and The National Institutes of Health [GM077387 (M.P.H.), EB001475 (E.M.) and The Chemistry Biology Interface training program (B.N.H. and J.G)].

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Authors and Affiliations

  1. Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA

    Brandon N. Hudder, Jessica Garber Morales & Paul A. Lindahl

  2. Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213-2683, USA

    Audria Stubna, Eckard Münck & Michael P. Hendrich

  3. Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA

    Paul A. Lindahl

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  1. Brandon N. Hudder
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  2. Jessica Garber Morales
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  6. Paul A. Lindahl
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Correspondence to Paul A. Lindahl.

Additional information

Note added in proof: It now appears less likely that Isa1p and Isa2p contain Fe/S clusters similar to those in other Fe/S scaffold proteins.

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Hudder, B.N., Morales, J.G., Stubna, A. et al. Electron paramagnetic resonance and Mössbauer spectroscopy of intact mitochondria from respiring Saccharomyces cerevisiae . J Biol Inorg Chem 12, 1029–1053 (2007). https://doi.org/10.1007/s00775-007-0275-1

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