References
Altmann K,
Durr M and
Westermann B
(2007)
Saccharomyces cerevisiae as a model organism to study mitochondrial biology: general considerations and basic procedures.
Methods in Molecular Biology
372:
81–90.
Biederbick A,
Stehling O,
Rosser R et al.
(2006)
Role of human mitochondrial Nfs1 in cytosolic iron‐sulfur protein biogenesis and iron regulation.
Molecular and Cellular Biology
26:
5675–5687.
Boldogh IR and
Pon LA
(2007)
Purification and subfractionation of mitochondria from the yeast Saccharomyces cerevisiae.
Methods in Cell Biology
80:
45–64.
Bradley PJ,
Lahti CJ,
Plumper E and
Johnson PJ
(1997)
Targeting and translocation of proteins into the hydrogenosome of the protist Trichomonas: similarities with mitochondrial protein import.
EMBO Journal
16:
3484–3493.
Chan KW,
Slotboom DJ,
Cox S et al.
(2005)
A novel ADP/ATP transporter in the mitosome of the microaerophilic human parasite Entamoeba histolytica.
Current Biology
15:
737–742.
Chiron S,
Gaisne M,
Guillou E et al.
(2007)
Studying mitochondria in an attractive model: Schizosaccharomyces pombe.
Methods in Molecular Biology
372:
91–105.
Cox B and
Emili A
(2006)
Tissue subcellular fractionation and protein extraction for use in mass‐spectrometry‐based proteomics.
Nature Protocols
1:
1872–1878.
Daum G,
Bohni PC and
Schatz G
(1982)
Import of proteins into mitochondria. Cytochrome b2 and cytochrome c peroxidase are located in the intermembrane space of yeast mitochondria.
Journal of Biological Chemistry
257:
13028–13033.
Day DA,
Neuburger M and
Douce R
(1985)
Biochemical characterization of chlorophyll‐free mitochondria from pea leaves.
Australian Journal of Plant Physiology
12:
219–228.
Degli Esposti M
(2001)
Assessing functional integrity of mitochondria in vitro and in vivo.
Methods in Cell Biology
65:
75–96.
Diekert K,
de Kroon AI,
Kispal G and
Lill R
(2001)
Isolation and subfractionation of mitochondria from the yeast Saccharomyces cerevisiae.
Methods in Cell Biology
65:
37–51.
Distler AM,
Kerner J and
Hoppel CL
(2008)
Proteomics of mitochondrial inner and outer membranes.
Proteomics
8:
4066–4082.
Distler AM,
Kerner J,
Lee K and
Hoppel CL
(2009)
Post‐translational modifications of mitochondrial outer membrane proteins.
Methods in Enzymology
457:
97–115.
Drapier JC and
Hibbs JB Jr
(1996)
Aconitases: a class of metalloproteins highly sensitive to nitric oxide synthesis.
Methods in Enzymology
269:
26–36.
Elstner M,
Andreoli C,
Ahting U et al.
(2008)
MitoP2: an integrative tool for the analysis of the mitochondrial proteome.
Molecular Biotechnology
40:
306–315.
Embley TM and
Martin W
(2006)
Eukaryotic evolution, changes and challenges.
Nature
440:
623–630.
Eubel H,
Heazlewood JL and
Millar AH
(2007a)
Isolation and subfractionation of plant mitochondria for proteomic analysis.
Methods in Molecular Biology
355:
49–62.
Eubel H,
Lee CP,
Kuo J et al.
(2007b)
Free‐flow electrophoresis for purification of plant mitochondria by surface charge.
Plant Journal
52:
583–594.
Fang X and
Lee CS
(2009)
Proteome characterization of mouse brain mitochondria using electrospray ionization tandem mass spectrometry.
Methods in Enzymology
457:
49–62.
Fang X,
Wang W,
Yang L et al.
(2008)
Application of capillary isotachophoresis‐based multidimensional separations coupled with electrospray ionization‐tandem mass spectrometry for characterization of mouse brain mitochondrial proteome.
Electrophoresis
29:
2215–2223.
Forner F,
Foster LJ,
Campanaro S,
Valle G and
Mann M
(2006)
Quantitative proteomic comparison of rat mitochondria from muscle, heart, and liver.
Molecular & Cellular Proteomics
5:
608–619.
Gaucher SP,
Taylor SW,
Fahy E et al.
(2004)
Expanded coverage of the human heart mitochondrial proteome using multidimensional liquid chromatography coupled with tandem mass spectrometry.
Journal of Proteome Research
3:
495–505.
Gill EE,
Diaz‐Trivino S,
Barbera MJ et al.
(2007)
Novel mitochondrion‐related organelles in the anaerobic amoeba Mastigamoeba balamuthi.
Molecular Microbiology
66:
1306–1320.
Glick BS and
Pon LA
(1995)
Isolation of highly purified mitochondria from Saccharomyces cerevisiae.
Methods in Enzymology
260:
213–223.
Goldberg AV,
Molik S,
Tsaousis AD et al.
(2008)
Localization and functionality of microsporidian iron‐sulphur cluster assembly proteins.
Nature
452:
624–628.
Heazlewood JL,
Howell KA,
Whelan J and
Millar AH
(2003)
Towards an analysis of the rice mitochondrial proteome.
Plant Physiology
132:
230–242.
Herrnstadt C,
Clevenger W,
Ghosh SS et al.
(1999)
A novel mitochondrial DNA‐like sequence in the human nuclear genome.
Genomics
60:
67–77.
Ito J,
Taylor NL,
Castleden I et al.
(2009)
A survey of the Arabidopsis thaliana mitochondrial phosphoproteome.
Proteomics
9:
4229–4240.
Kapushoc ST,
Alfonzo JD,
Rubio MA and
Simpson L
(2000)
End processing precedes mitochondrial importation and editing of tRNAs in Leishmania tarentolae.
Journal of Biological Chemistry
275:
37907–37914.
Kirby DM,
Thorburn DR,
Turnbull DM and
Taylor RW
(2007)
Biochemical assays of respiratory chain complex activity.
Methods in Cell Biology
80:
93–119.
Klein M,
Binder S and
Brennicke A
(1998a)
Purification of mitochondria from Arabidopsis.
Methods in Molecular Biology
82:
49–53.
Klein M,
Hiesel R,
Andre C and
Brennicke A
(1998b)
Purification of mitochondrial DNA from green tissues of Arabidopsis.
Methods in Molecular Biology
82:
79–84.
Kobayashi T,
Sato S,
Takamiya S et al.
(2007)
Mitochondria and apicoplast of Plasmodium falciparum: behaviour on subcellular fractionation and the implication.
Mitochondrion
7:
125–132.
Lanza IR and
Nair KS
(2009)
Functional assessment of isolated mitochondria in vitro.
Methods in Enzymology
457:
349–372.
Leister D and
Herrmann JM
(2007)
Mitochondria: practical protocols.
Methods in Cell Biology,
vol. 372.
Totowa: Humana Press.
Malka F,
Aure K,
Goffart S,
Spelbrink JN and
Rojo M
(2007)
The mitochondria of cultured mammalian cells: I. Analysis by immunofluorescence microscopy, histochemistry, subcellular fractionation, and cell fusion.
Methods in Molecular Biology
372:
3–16.
Mayer A,
Driessen A,
Neupert W and
Lill R
(1995)
Purified and protein‐loaded mitochondrial outer membrane vesicles for functional analysis of preprotein transport.
Methods in Enzymology
260:
252–263.
Meisinger C,
Pfanner N and
Truscott KN
(2006)
Isolation of yeast mitochondria.
Methods in Molecular Biology
313:
33–39.
Meisinger C,
Sickmann A and
Pfanner N
(2008)
The mitochondrial proteome: from inventory to function.
Cell
134:
22–24.
Meyer EH and
Millar AH
(2008)
Isolation of mitochondria from plant cell culture.
Methods in Molecular Biology
425:
163–169.
Millar AH,
Liddell A and
Leaver CJ
(2001a)
Isolation and subfractionation of mitochondria from plants.
Methods in Cell Biology
65:
53–74.
Millar AH,
Liddell A and
Leaver CJ
(2007)
Isolation and subfractionation of mitochondria from plants.
Methods in Cell Biology
80:
65–90.
Millar AH,
Sweetlove LJ,
Giege P and
Leaver CJ
(2001b)
Analysis of the Arabidopsis mitochondrial proteome.
Plant Physiology
127:
1711–1727.
Moore AL,
Fricaud AC,
Walters AJ and
Whitehouse DG
(1993)
Isolation and purification of functionally intact mitochondria from plant cells.
Methods in Molecular Biology
19:
133–139.
Mootha VK,
Bunkenborg J,
Olsen JV et al.
(2003)
Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria.
Cell
115:
629–640.
Murayama K,
Fujimura T,
Morita M and
Shindo N
(2001)
One‐step subcellular fractionation of rat liver tissue using a Nycodenz density gradient prepared by freezing‐thawing and two‐dimensional sodium dodecyl sulfate electrophoresis profiles of the main fraction of organelles.
Electrophoresis
22:
2872–2880.
Neuburger M,
Journet EP,
Bligny R,
Carde JP and
Douce R
(1982)
Purification of plant mitochondria by isopycnic centrifugation in density gradients of Percoll.
Archives of Biochemistry and Biophysics
217:
312–323.
Pagliarini DJ,
Calvo SE,
Chang B et al.
(2008)
A mitochondrial protein compendium elucidates complex I disease biology.
Cell
134:
112–123.
Pallotti F and
Lenaz G
(2001)
Isolation and subfractionation of mitochondria from animal cells and tissue culture lines.
Methods in Cell Biology
65:
1–35.
Pallotti F and
Lenaz G
(2007)
Isolation and subfractionation of mitochondria from animal cells and tissue culture lines.
Methods in Cell Biology
80:
3–44.
Prokisch H,
Scharfe C,
Camp II DG et al.
(2004)
Integrative analysis of the mitochondrial proteome in yeast.
PLoS Biology
2:
e160.
Putz S,
Gelius‐Dietrich G,
Piotrowski M and
Henze K
(2005)
Rubrerythrin and peroxiredoxin: two novel putative peroxidases in the hydrogenosomes of the microaerophilic protozoon Trichomonas vaginalis.
Molecular and Biochemical Parasitology
142:
212–223.
Rada P,
Smid O,
Sutak R et al.
(2009)
The monothiol single‐domain glutaredoxin is conserved in the highly reduced mitochondria of Giardia intestinalis.
Eukaryotic Cell
8:
1584–1591.
Reinders J,
Zahedi RP,
Pfanner N,
Meisinger C and
Sickmann A
(2006)
Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics.
Journal of Proteome Research
5:
1543–1554.
Rieder SE and
Emr SD
(2001a)
Isolation of subcellular fractions from the yeast Saccharomyces cerevisiae. Current Protocols in Cell Biology, Chapter 3: Unit 3 8.
Rieder SE and
Emr SD
(2001b)
Overview of subcellular fractionation procedures for the yeast Saccharomyces cerevisiae. Current Protocols in Cell Biology, Chapter 3: Unit 3 7.
Rodiger A,
Baudisch B and
Klosgen RB
(2010)
Simultaneous isolation of intact mitochondria and chloroplasts from a single pulping of plant tissue.
Journal of Plant Physiology
167:
620–624.
Ryan NM
(2004)
Subecllular fractionation of animal tissues.
Methods in Molecular Biology
244:
47–52.
Sakamoto W,
Spielewoy N,
Bonnard G,
Murata M and
Wintz H
(2000)
Mitochondrial localization of AtOXA1, an Arabidopsis homologue of yeast Oxa1p involved in the insertion and assembly of protein complexes in mitochondrial inner membrane.
Plant & Cell Physiology
41:
1157–1163.
Schmitt S,
Prokisch H,
Schlunck T et al.
(2006)
Proteome analysis of mitochondrial outer membrane from Neurospora crassa.
Proteomics
6:
72–80.
Sickmann A,
Reinders J,
Wagner Y et al.
(2003)
The proteome of Saccharomyces cerevisiae mitochondria.
Proceedings of the National Academy of Sciences of the USA
100:
13207–13212.
Smith DG,
Gawryluk RM,
Spencer DF et al.
(2007)
Exploring the mitochondrial proteome of the ciliate protozoon Tetrahymena thermophila: direct analysis by tandem mass spectrometry.
Journal of Molecular Biology
374:
837–863.
Sutak R,
Dolezal P,
Fiumera HL et al.
(2004)
Mitochondrial‐type assembly of FeS centers in the hydrogenosomes of the amitochondriate eukaryote Trichomonas vaginalis.
Proceedings of the National Academy of Sciences of the USA
101:
10368–10373.
Sweetlove LJ,
Taylor NL and
Leaver CJ
(2007)
Isolation of intact, functional mitochondria from the model plant Arabidopsis thaliana.
Methods in Molecular Biology
372:
125–136.
Takashima E,
Takamiya S,
Takeo S et al.
(2001)
Isolation of mitochondria from Plasmodium falciparum showing dihydroorotate dependent respiration.
Parasitology International
50:
273–278.
Taylor SW,
Warnock DE,
Glenn GM et al.
(2002)
An alternative strategy to determine the mitochondrial proteome using sucrose gradient fractionation and 1D PAGE on highly purified human heart mitochondria.
Journal of Proteome Research
1:
451–458.
Tovar J,
Cox SS and
van der Giezen M
(2007)
A mitosome purification protocol based on percoll density gradients and its use in validating the mitosomal nature of Entamoeba histolytica mitochondrial Hsp70.
Methods in Molecular Biology
390:
167–177.
Tovar J,
Fischer A and
Clark CG
(1999)
The mitosome, a novel organelle related to mitochondria in the amitochondrial parasite Entamoeba histolytica.
Molecular Microbiology
32:
1013–1021.
Tovar J,
Leon‐Avila G,
Sanchez LB et al.
(2003)
Mitochondrial remnant organelles of Giardia function in iron‐sulphur protein maturation.
Nature
426:
172–176.
Vogtle FN,
Wortelkamp S,
Zahedi RP et al.
(2009)
Global analysis of the mitochondrial N‐proteome identifies a processing peptidase critical for protein stability.
Cell
139:
428–439.
Zischka H,
Lichtmannegger J,
Jagemann N et al.
(2008)
Isolation of highly pure rat liver mitochondria with the aid of zone‐electrophoresis in a free flow device (ZE‐FFE).
Methods in Molecular Biology
424:
333–348.
Zischka H,
Weber G,
Weber PJ et al.
(2003)
Improved proteome analysis of Saccharomyces cerevisiae mitochondria by free‐flow electrophoresis.
Proteomics
3:
906–916.
Further Reading
Allison WS and
Murphy AN
(2009)
Mitochondrial function, Part B: mitochondrial protein kinases, protein phosphatases and mitochondrial diseases.
Methods in Enzymology
457.
Allison WS and
Scheffler IE
(2009)
Mitochondrial function, Part A: mitochondrial electron transport complexes and reactive oxygen species.
Methods in Enzymology
456.
Bonifacino JS,
Dasso M,
Harford JB,
Lippincott‐Schwartz J and
Yamada KM
(2004)
Short Protocols in Cell Biology.
Hoboken: Wiley.
Davey J and
Lord M
(2003)
Essential cell biology: cell function.
Practical Approach,
vol. 263.
Oxford: IRL Press.
Day DA,
Millar AH and
Whelan J
(2004)
Plant mitochondria.
Advances in Photosynthesis and Respiration,
vol. 17.
Berlin: Springer Inc.
Graham JM and
Rickwood D
(1997)
Subcellular fractionation.
Practical Approach,
vol. 173.
Oxford: IRL Press.
Marín‐García J
(2005)
Mitochondria and the heart.
Developments in Cardiovascular Medicine,
vol. 256.
Berlin: Springer Inc.
Martínez‐Zapater JM and
Julio Salinas J
(1998)
Arabidopsis protocols.
Methods in Molecular Biology,
vol. 82.
Totowa: Humana Press.
Pon LA and
Schon EA
(2007)
Mitochondria.
In: Methods in Cell Biology, 2nd edn,
vol. 80.
San Diego: Academic Press.