As mitochondria are only a small percentage of the plant cell, they need to be purified for a range of studies. Mitochondria can be isolated from a variety of plant organs by homogenization, followed by differential and density gradient centrifugation to obtain a highly purified mitochondrial fraction.
Mitochondria are essential organelles involved in numerous metabolic pathways in plants, most notably the production of adenosine triphosphate (ATP) from the oxidation of reduced compounds such as nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FADH2). The complete annotation of the Arabidopsis thaliana genome has established it as the most widely used plant model system, and thus the need to purify mitochondria from a variety of organs (leaf, root, or flower) is necessary to fully utilize the tools that are now available for Arabidopsis to study mitochondrial biology. Mitochondria are isolated by homogenization of the tissue using a variety of approaches, followed by a series of differential centrifugation steps producing a crude mitochondrial pellet that is further purified using continuous colloidal density gradient centrifugation. The colloidal density material is subsequently removed by multiple centrifugation steps. Starting from 100 g of fresh leaf tissue, 2 – 3 mg of mitochondria can be routinely obtained. Respiratory experiments on these mitochondria display typical rates of 100 – 250 nmol O2 min-1 mg total mitochondrial protein-1 (NADH-dependent rate) with the ability to use various substrates and inhibitors to determine which substrates are being oxidized and the capacity of the alternative and cytochrome terminal oxidases. This protocol describes an isolation method of mitochondria from Arabidopsis thaliana leaves using continuous colloidal density gradients and an efficient respiratory measurements of purified plant mitochondria.
The history of plant mitochondrial research goes back over 100 years1. Intact mitochondria were first isolated in the early 1950s using differential centrifugation. The advent of a colloidal density gradient in the 1980s allowed mitochondria to be purified without suffering osmotic adjustment. While gradient purified mitochondria are suitable for most purposes, due to the sensitivity of mass spectrometry, even relatively minor contaminants can be detected and may be inappropriately assigned a mitochondrial location2. The use of free flow electrophoresis can remove both plastidic and peroxisome contamination3, but free flow electrophoresis is a highly specialized technique and is not required for the vast majority of studies. Furthermore, when determining the location of a protein it needs to be remembered that dual or multiple targeting of proteins occurs in cells. Over 100 dual targeted proteins are described for chloroplasts/plastids and mitochondria4, and a number of proteins targeted to mitochondria and peroxisomes are also known5. Furthermore, the re-location of proteins under specific stimuli, e.g. oxidative stress, is an emerging theme in cell biology6. Thus, the location of proteins needs to be considered in the context of the biology studied, and a variety of approaches are used to determine and verify location2.
Mitochondria are typically isolated from plant tissues by homogenization, a balance is required between breaking open the cell wall to release mitochondria, and not damaging the mitochondria. Traditionally, with potato and cauliflower, homogenization involves using household blender/juicer apparatus to make a liquid extract in a buffer with various components to maintain activity. Isolation of mitochondria from pea leaves, (a popular material for mitochondrial isolation using young seedlings (~10 days old), utilizes a blender to lyse cells as the leaf material is soft. With the availability of Arabidopsis thaliana T-DNA insertional knock-out lines, the need to be able to purify mitochondria to carry out functional studies has necessitated the development of methods to isolate mitochondria from leaf, root or flower tissue. Overall the methods developed for other plants worked well7, with the perquisite that grinding of the material needed to be optimized. For Arabidopsis this can be achieved in a variety of ways (see below), and differs between tissue types (root versus shoot). The use of the continuous gradient can also be optimized as the density of mitochondria from different organs or developmental stages means they can migrate differently. Thus, for maximum separation the density of the gradient can be refined to ensure to achieve best separation.
Once purified the mitochondria can be used for a variety of studies, including protein and tRNA uptake experiments, enzyme activity assays, respiratory chain measurements and western blot analyses. Isolated mitochondria can also be used for mass spectrometry analyses of protein abundance. Targeted multiple reaction monitoring (MRM) analyses allows for the quantification of defined proteins, but require significant assay development. In contrast, quantification by dimethyl or other isotope labels8, provides a discovery approach in identifying differences across the whole proteome that can be used to uncover novel biological insights.
This protocol is used for the isolation of intact mitochondria from Arabidopsis thaliana organs grown on soil using continuous colloidal density gradients. All procedures following the collection of the material are carried out at 4 °C.
1. Preparation of Grinding Medium, Wash Buffer, and Gradient Solutions
2. Homogenization and Mitochondrial Isolation
3. Oxygen Consumption Measurements
NOTE: Oxygen consumption by freshly isolated plant mitochondria can be analyzed with a Clark-type oxygen electrode, enabling the determination of mitochondrial intactness, cytochrome c pathway activity, and alternative pathway activity.
Using this protocol, we were able to detect different mitochondrial proteins by SDS-PAGE and immunoblotting. As shown in Figure 3A, the protein isolated from water culture tissue is sufficient to detect a faint band (2 µg). Signal intensity increases proportionately to the amounts loaded. For mitochondria isolated from tissues grown on plates (Figure 3B), the response to high light stress treatment in different genotypes can be analyzed by immunodetection with alternative oxidase antibodies.
The intactness of mitochondria, cytochrome c pathway activity and alternative pathway can be measured using freshly isolated mitochondrial samples. Mitochondrial integrity is well preserved during the described isolation procedure (Figure 4A). Adding different substrates, inhibitors and effectors to isolated mitochondria, oxygen consumption through the cytochrome c pathway and alternative oxidase pathway is influenced (Figure 4B).
Figure 1: Setup for the preparation of the gradients. Left: Centrifuge tubes (50 mL) with a slight angle placed on ice with PVC peristaltic tubing outlets taped to the inside of the tubes; Middle: Peristaltic pump; Right: Gradient pourer on top of a magnetic stirrer containing the heavy gradient (inner chamber) and light gradient (outer chamber) solutions. Please click here to view a larger version of this figure.
Figure 2: Purification of mitochondria from Arabidopsis shoots using a continuous 0 – 4.4% (w/v) PVP/28% colloidal density gradient. The dark green band is the thylakoids and other contaminations as indicated in the top of the gradient solutions. Mitochondrial fraction appeared as a white-greenish band closer to the bottom of the tube. Please click here to view a larger version of this figure.
Figure 3: Separation of mitochondrial proteins by SDS-PAGE and immunodetection using specific antibodies. (A) Mitochondria isolated from two-week-old water-cultured Arabidopsis thaliana wild type (Columbia-0, Col-0) plants were subjected to SDS-PAGE and probed with antibodies raised against NADH:ubiquinone oxidoreductase subunit S4 (Ndufs4, At5g67590). Molecular-weight unstained markers were loaded on the outer lane of the gel and the size of ten representative bands are indicated in kilo Daltons (kDa). The apparent molecular mass of the Ndufs4 protein detected is 18 kDa. Protein abundance is shown relative to the value of 2 µg total protein. (B) Two-week-old seedlings grown on Gamborg's B5 media with 3% (w/v) sucrose and 0.8% agar (w/v) were exposed to 750 µE m-2 s-1 highlight (HL) and harvested after 6 h. Mitochondria were purified and the mitochondrial proteins were separated by SDS-PAGE and probed with antibodies raised against alternative oxidase (AOX). The presence of an immunodetectable AOX protein with an apparent molecular mass of 34 kDa is indicated. Protein abundance is shown relative to the value of control (2 µg). Please click here to view a larger version of this figure.
Figure 4: Representative traces of O2 consumption by isolated plant mitochondria. (A) Mitochondria isolated from Arabidopsis thaliana wild-type plants (Col-0) as outlined above were analyzed for outer membrane integrity prior to oxygen consumption measurements. 30 µL of isolated mitochondria (150 µg total mitochondrial protein) were used. Mitochondrial integrity was determined as 90% as described above. (B) Oxygen consumption measurements were performed using 30 µL of isolated mitochondria (150 µg total mitochondrial protein) from Arabidopsis thaliana wild-type plants. Total mitochondrial respiration and the AOX pathway were determined. From these data, oxygen consumption through the cytochrome c pathway and AOX pathway can be determined. Please click here to view a larger version of this figure.
Grinding medium | |
Chemical | Concentration |
Sucrose | 0.3 M |
tetrasodium pyrophosphate (Na4P2O7 · 10 H2O) | 25 mM |
EDTA disodium salt | 2 mM |
Potassium phosphate monobasic (KH2PO4) | 10 mM |
Polyvinylpyrrolidone (PVP40) | 1% (w/v) |
Bovine serum albumin (BSA) | 1% (w/v) |
Deionized water | |
Adjust pH to 7.5 (using HCl) | |
NOTE: For 300 mL grinding medium, 1.06 g sodium ascorbate (final concentration: 17.84 mM) and 0.74 g cysteine (final concentration: 20.36 mM) are added just prior to use. Check pH after addition and adjust to 7.5 with 1 M NaOH if required. | |
2X wash buffer | |
Chemical | Concentration |
Sucrose | 0.6 M |
TES | 20 mM |
Bovine serum albumin (BSA) | 0.2% (w/v) |
Deionized water | |
Adjust pH to 7.5 (using NaOH) | |
Gradients | |
Heavy Gradient solution (4.4% (w/v) PVP) | 2 gradient tubes |
2X wash buffer | 17.5 mL |
Colloidial density gradient | 9.8 mL |
PVP-40 (20% (w/v)) | 7.7 mL |
Light Gradient Solution (0% (w/v) PVP) | 2 gradient tubes |
2X wash buffer | 17.5 mL |
Colloidial density gradient | 9.8 mL |
Deionized water | 7.7 mL |
Table 1: Composition of buffers and gradients used for mitochondria isolation.
Abbreviation | Concentration of stock solutions | Storage | Final concentration | Volume added for 1 ml reaction | |
Substrates | |||||
Cytochrome c | Cyt c | 2.5 mM (in H2O) | -20 °C | 25 μM | 10 μl |
NADH | NADH | 0.1 M (in H2O) | -20 °C | 1 mM | 10 μl |
Succinate | Succ | 500 mM (in H2O) | -20 °C | 5 mM | 10 μl |
Inhibitors | |||||
Antimycin A | AA | 1 mM (in EtOH) | -20 °C | 5 μM | 5 μl |
Cyanide | KCN | 100 mM (in H2O) | 4 °C | 1 mM | 10 μl |
Myxothiazol | Myxo | 500 μM (in EtOH) | -20 °C | 2.5 μM | 5 μl |
n-Propyl gallate | nPG | 100 mM (in EtOH) | -20 °C | 500 μM | 5 μl |
Effectors | |||||
ADP | ADP | 100 mM (in H2O) | -20 °C | 1 mM | 10 μl |
Ascorbate | Asc | 500 mM (in H2O) | Make fresh on the day of use | 10 mM | 20 μl |
ATP | ATP | 100 mM (in H2O) | -20 °C | 500 μM | 5 μl |
Dithiotreitol | DTT | 1 M (in H2O) | Make fresh on the day of use | 10 mM | 10 μl |
Pyruvate | Pyr | 1 M (in H2O) | -20 °C | 10 mM | 10 μl |
Detergent | 10% (v/v) (in H2O) | 4 °C | 0.05% (v/v) | 5 μl |
Table 2: List of substrates, inhibitors and effectors used for oxygen consumption measurements.
Typically, isolation of mitochondria from Arabidopsis leaves yields up 3 mg of mitochondria from approximately 80 – 100 3 – 4-week old plants, although yields of greater than 5 mg can often be achieved with thorough grinding. The yield varies with growth conditions and decreases dramatically as leaves senesce, although mitochondria structure seems to be well maintained during senescence9. One of the most critical features to obtain a good yield is the method of grinding to lyse cells to release mitochondria. While a number of mechanical grinding apparatus are available for purchase, for Arabidopsis grinding in a mortar and pestle achieves consistently good results in terms of yield, as it lyses the cells with little damage to organelles. While mechanical grinders are fast, they require optimization and the amount of grinding required can vary according to the tissue. With a mortar and pestle, it often convenient and more efficient if the tissue is sliced or cut with a knife or scissors before grinding. As outlined, all steps need to be carried out at 4 °C and the whole procedure from the end of grinding to obtaining a washed pellet of purified mitochondria should take approximately 4 h. As traces of detergents or other reagents on tubes or gradient pourers can dramatically reduce yield, all components used in these procedures are washed without detergent and not used in other procedures. Finally, it is important that the mitochondria are sufficiently separated from the other fractions on the gradient to allow them to be removed and washed. If they are too near the bottom of the tube, it means that the mixing of the light and heavy solutions needs to be adjusted, to allow more of the heavy solution to pour before mixing. Conversely, if the band appears diffuse and is high in the tube, mixing needs to occur a little earlier.
The method outlined here can be readily used for isolation of mitochondria from Arabidopsis flower and root tissue11,12. For roots, it is convenient to grow in hydroponic culture and need 100 g of fresh weight to obtain 2 mg amounts of mitochondria. For grinding roots should be cut into small pieces prior to grinding in a mortar and pestle, and increase yields can be obtained by re-grinding the root tissue, either in a mortar and pestle or in a blender. For floral tissue where mitochondrial function is often enhanced13, grinding with a mortar and pestle works well, but the limited amount of material means that a large amount of plants needs to be grown to harvest tissue. Mitochondria have been isolated from a variety of Arabidopsis organs using similar methods or slight modifications14,15 and from rice (Oryza sativa)16.
The limitations of the method described above are i) the large amounts of seeds required for the mitochondrial isolation, ii) only specific tissues from Arabidopsis and rice applied in this isolation method, iii) small quantities of various contaminants (such as peroxisomal proteins) still existed in the purified mitochondria. Mitochondria obtained using the methods described above are suitable for a variety of studies, ranging from oxygen uptake studies to quantitative mass spectrometry analyses of protein abundance. Gradient purified mitochondria will still contain small quantities of various contaminants, such as peroxisomal proteins3. A comparison with defined organelle lists can be used to determine changes in mitochondrial proteins, as long as the amount of contamination by non-mitochondrial proteins is small (<10%) and similar samples are compared, so the type and degree of non-mitochondrial proteins is similar. Analyses of protein abundance by SDS-PAGE or other gel-based approaches can be carried out with relatively small amounts of mitochondria (2 – 20 µg), using varying amounts of mitochondria to check the linearity of detection by antibodies (Figure 3). While porin (voltage dependent anion channel (VDAC)) is often used as a loading control for quantification, in our experience the relatively large abundance of this protein can mean that the response is often not linear if large amounts of protein are loaded on the gel, so linearity of antibody response should always be checked when using such loading controls. The significance of this approach of isolating mitochondria is that unlike gradients that use sucrose as the material to form the density gradient, colloidal density gradients do not require osmotic re-adjustment of the purified mitochondria as is required with sucrose. This means that there is less chance of rupturing the purified mitochondria and after washing to remove the colloidal density material, they can be directly used in a variety of assays or applications.
Tissue blots, where mitochondrial proteins are detected from whole leaf or tissue extracts, are an attractive approach to measure the amount of mitochondrial proteins in that tissue. Given the generally low volume of the mitochondria compared to other organelles, the detection of mitochondrial protein on whole tissue extracts needs to be interpreted with some caution, as mitochondrial protein may be beyond detection in such approaches. Careful controls, where purified mitochondria are electrophoresed along with tissue extracts to ensure identical migration and linearity of detection, need to be carried out to have confidence in such approaches.
With the help of a Clark-type oxygen electrode, changes in the oxygen partial pressure of a solution can be measured. The actual electrode consists of a platinum cathode and a silver anode, which are connected by a KCl bridge and covered by an electrolyte-moistened paper (cigarette paper) and an oxygen-permeable membrane (polytetrafluoroethylene membrane). A voltage of 600 – 700 mV leads to the reduction of oxygen, giving a linear relationship between oxygen concentration and voltage. Oxygen electrodes are available commercially from different companies. Each company will have its own instructions regarding the assembly and setup of the oxygen electrode. However, in general the silver anode and platinum cathode of the electrode disk need to be cleaned with the help of an electrode cleaning kit or an eraser pen before assembly. It is important to ensure that air bubbles do not form during assembly (e.g. between the polytetrafluoroethylene diaphragm and the cigarette paper). After assembly, the electrode disk needs to be attached to the chamber with the platinum cathode facing upwards at the base of the reaction chamber. The chamber itself is surrounded by a water jacket ensuring temperature control. It is extremely important that the chamber is always left full of water, since the membrane will dry out and crack otherwise. Likewise, the membrane must not be touched by pipettes or syringes when adding compounds to the chamber, to avoid tearing.
Prior to the assay, the respiration medium should be warmed to the same temperature as the assay chamber (in most cases 25 °C) and the membrane should be allowed to equilibrate in respiration buffer for a few min. After closing the plunger for oxygen consumption assays, the addition of effector molecules should be carried out using either non-disposable microliter syringes (e.g. micro syringes) or disposable gel loading pipette tips. If using micro syringes, it has to be ensured that the syringe is thoroughly rinsed with 100% ethanol and water between additions, to avoid contaminating stock solutions. This also applies for the washing of the chamber between measurements. Most reagents used in oxygen consumption assays are soluble in water and can easily be removed by multiple rinsing with water (approximately five times) between measurements. However, some chemicals used for assays are only soluble in organic solvents, such as antimycin A, myxothiazol, and nPG. Therefore, the chamber needs to be rinsed with an organic solvent (50% (v/v) ethanol) between assays to remove residual traces of these molecules, and then with water (approximately five times) to deplete residues.
The authors have nothing to disclose.
This study was supported by an Australian Research Council Centre of Excellence in Plant Energy Biology CE140100008, an Australian Research Council Future Fellowship (FT130100112) to MWM, and a Feodor Lynen Research Fellowship (Alexander von Humboldt Foundation, Germany) to JS.
ADP | Sigma-Aldrich | A2754 | Chemical |
Antimycin A | Sigma-Aldrich | A8674 | Chemical, dissolve in ethanol |
AOX antibody | from Tom Elthon | Elthon et al., 1989 | |
Ascorbate | Sigma-Aldrich | A0157 | Ascorbate Oxidase from Cucurbita sp. |
ATP | Sigma-Aldrich | A26209 | Chemical |
Bovine serum albumin (BSA) | Bovogen | BSAS 1.0 | Chemical |
Clarity western ECL substrate | Bio-Rad Laboratories | 1705061 | Chemical |
Criterion Stain-Free Precast Gels 8-16% 18 Wells | Bio-Rad Laboratories | 5678104 | Chemical |
Cyanide | Sigma-Aldrich | 60178 | Chemical |
Cytochrome c | Sigma-Aldrich | C3131 | Chemical |
Difco Agar, granulated | BD Biosciences | 214530 | Chemical |
Dithiotreitol | Sigma-Aldrich | D0632 | Chemical |
EDTA disodium salt | Sigma-Aldrich | E5134 | Chemical |
Gamborg B-5 Basal Medium | Austratec | G398-100L | Chemical |
Gamborg Vitamin Solution (1000x) | Austratec | G219-100ML | Chemical |
Goat Anti-Mouse IgG (H + L)-HRP Conjugate | Bio-Rad Laboratories | 1706516-2ml | Chemical |
Goat Anti-Rabbit IgG (H + L)-HRP Conjugate | Bio-Rad Laboratories | 1706515-2ml | Chemical |
L-Cysteine | Sigma | C7352-100G | Chemical |
Magnesium sulfate | Sigma-Aldrich | 230391 | Chemical |
Murashige & Skoog Basal Salt Mixture (MS) | Austratec | M524-100L | Chemical |
Myxothiazol | Sigma-Aldrich | T5580 | Chemical, dissolve in ethanol |
NADH | Sigma-Aldrich | N8129 | Chemical |
Ndufs4 antibody | from Etienne Meyer | Meyer et al., 2009 | |
n-Propyl gallate | Sigma-Aldrich | P3130 | Chemical, dissolve in ethanol |
Percoll | GE Healthcare | 17-0891-01 | Chemical, colloidal density gradient |
Polyvinylpyrrolidone (PVP40) | Sigma-Aldrich | PVP40 | Chemical |
Potassium cyanide | Sigma-Aldrich | 60178 | Chemical |
Potassium phosphate monobasic (KH2PO4) | Sigma-Aldrich | P5655 | Chemical |
Pyruvate | Sigma-Aldrich | P2256 | Chemical |
Sodium chloride | Chem-Supply | SA046 | Chemical |
Sodium dithionite | Sigma-Aldrich | 157953 | Chemical |
Sodium L-ascorbate | Sigma | A4034-100G | Chemical |
Succinate | Sigma-Aldrich | S2378 | Chemical |
Sucrose | Chem-Supply | SA030 | Chemical |
TES | Sigma-Aldrich | T1375 | Chemical |
Tetrasodium pyrophosphate (Na4P2O7 · 10H2O) | Sigma-Aldrich | 221368 | Chemical |
Trans-Blot Turbo RTA Midi Nitrocellulose Transfer Kit | Bio-Rad Laboratories | 1704271 | Chemical |
Triton-X 100 | Sigma-Aldrich | X100 | Chemical, detergent |
Western Blocking Reagent | Sigma | 11921681001 | Chemical |
Balance | Mettler Toledo | XS204 | Equipment |
Beakers | Isolab | 50 mL | |
Centrifuge | Beckman Coulter | Avanti J-26XP | Equipment |
Centrifuge tubes | Nalgene | 3117-9500 | Equipment |
Circulator | Julabo | 1124971 | Attached to oxygen electrode chamber |
Conical flask | Isolab | 500 mL | |
Dropper | 3 mL | ||
Fixed angle rotor | Beckman Coulter | JA25.5 | Equipment |
Funnel | Per Alimenti | 14 cm | For filtering |
Gradient pourer | Bio-Rad | 165-4120 | For preparation of gradients |
Magnetic Stirrer ATE | VELP Scientifica | F20300165 | Equipment |
Miracloth | VWR | EM475855-1R | Filtration material |
Mortar and pestle | Jamie Oliver | Granite, 6 Inch | Equipment |
O2view | Hansatech Instruments | Oxygen monitoring software | |
Oxygraph Plus System | Hansatech Instruments | 1187253 | Clark-type oxygen electrode |
Paintbrush | Artist first choice | 1008R-12 | |
Parafilm | Bemis | PM-996 | plastic paraffin film |
Peristaltic pump | Gilson | F155001 | For preparation of gradients |
PVC peristaltic tubing | Gilson | F117930 | For preparation of gradients |
Water bath | VELP Scientifica | OCB | Equipment |