The authors would like to thank Dr. G.C. Shore of McGill University, Dr. A. Strauss of the Washington School of Medicine, and Dr. M.T. Ryan of La Trobe University for the original donations of expression plasmids that were used for this research. This work was supported by funding from the Natural Sciences and Engineering Research Council of Canada (NSERC) to D. A. Hood. D. A. Hood is also the holder of a Canada Research Chair in Cell Physiology.

All animals used in these experiments are maintained in the animal care facility at York University. The experiments are conducted in accordance with the Canadian Council on Animal Care guidelines with approval from the York University Animal Care Committee (Permit: 2017-08).
1. Functional isolation of subsarcolemmal and intermyofibrillar mitochondria from skeletal muscle
<ol>
	<li>Reagent preparation:
	<ol>
		<li>Prepare all the buffers and media as mentioned in Table 1.</li>
		<li>Set the buffers to pH 7.4 and store at 4 &#176;C (up to 2 weeks), except nagrase protease.</li>
		<li>Prepare fresh nagarse protease (Table 1) each time.</li>
	</ol>
	</li>
	<li>Tissue removal and mincing 
	NOTE: A flowchart of the steps below for the isolation of mitochondria is provided in Figure 1.
	<ol>
		<li>Fill a glass scintillation vial with ~20 mL of Buffer 1 (Table 1) and place it on ice.</li>
		<li>While the mouse is under anesthetic, harvest skeletal muscles (tibialis anterior, quadriceps, gastrocnemius etc.), approximately 500-1000 mg, and place the muscles in the scintillation vial containing chilled Buffer 1. 
		NOTE: Gaseous isoflurane is used as an anesthetic at 2.5% at a flow rate of 0.4 L of O2/min. A pinch test is performed to ensure that the animal is non-responsive.</li>
		<li>Following tissue collection, euthanize the animal via cervical dislocation.</li>
		<li>Pre-chill a watch glass on ice. Remove any fat or connective tissue from the muscles and mince the tissue on the watch glass until it is a homogenous slurry.</li>
		<li>Place the minced tissue in a pre-chilled 50 mL plastic centrifugation tube (see Table of Materials) and record the exact weight.</li>
		<li>Dilute the minced tissue 10-fold with Buffer 1 + ATP (Table 1).</li>
		<li>Homogenize the muscle sample using an 8 mm twin-blade homogenizer (see Table of Materials) at a power output of 9.8 Hz for 10 s, ensuring no visible chunks of muscle are remaining.</li>
		<li>Centrifuge the samples at 800 x g for 10 min using a high-speed centrifuge (see Table of Materials). 
		NOTE: The purpose of this step is to separate SS and IMF mitochondrial fractions. The supernate contains SS mitochondria, while the pellet contains IMF mitochondria.</li>
	</ol>
	</li>
	<li>SS mitochondrial isolation
	<ol>
		<li>Filter the supernate through a single layer of cheesecloth into another set of 50 mL plastic centrifugation tubes to remove any large debris or contaminants.</li>
		<li>Centrifuge the supernate at 9,000 x g for 10 min at 4 &#176;C using a high-speed centrifuge.</li>
		<li>Discard the supernate and resuspend the pellet in 3.5 mL of Buffer 1 + ATP. 
		NOTE: Resuspend with a P1000 and do this carefully. Mitochondria are fragile organelles. Perform gently and avoid touching the pellet with the pipette tip.</li>
		<li>Centrifuge the sample at 9,000 x g for 10 min at 4 &#176;C using a high-speed centrifuge.</li>
		<li>Discard the supernate unless further processing to isolate a cytosolic fraction devoid of nuclei, mitochondria, and other organelles is desired. Resuspend the pellet carefully in roughly 95 &#181;L of the resuspension medium (Table 1) using a P200 pipette. 
		NOTE: Similar to step 1.3.3, avoid touching the pellet with the pipette tip. The volume of the resuspension medium can be altered depending on the size of the pellet. This is the SS mitochondrial fraction, which can be stored on ice until the IMF fraction is isolated. If desired, the cytosolic fraction, devoid of organelles, can be isolated by centrifuging the supernate at 100,000 x g in an ultracentrifuge (see Table of Materials) and thereafter discarding the pellet.</li>
	</ol>
	</li>
	<li>IMF mitochondrial isolation
	<ol>
		<li>Dilute the pellet from step 1.2.8 by 10-fold in Buffer 1 + ATP. Resuspend using a Teflon pestle by gently mixing the pellet and buffer together until the sample is consistent.</li>
		<li>Homogenize the sample using an 8 mm twin-blade homogenizer (see Table of Materials) at a power output of 9.8 Hz for 10 s.</li>
		<li>Centrifuge the sample at 800 x g for 10 min at 4 &#176;C using a high-speed centrifuge.</li>
		<li>Discard the supernate and dilute the IMF mitochondrial pellet 10-fold using Buffer 2 and resuspend using the Teflon pestle by gently mixing until it is homogeneous.</li>
		<li>Add 25 &#181;L/g of tissue to 10 mg/mL nagarse protease (Table 1) and place the centrifugation tube on its side on ice, gently mixing every minute by rocking the tube side to side. 
		NOTE: The addition of nagarse helps liberate IMF mitochondria by performing limited digestion of the myofibrils.</li>
		<li>After 5 min, add 20 mL of Buffer 2 (Table 1) to dilute the nagarse protease to the point of inactivity and stop the digestion.</li>
		<li>Immediately centrifuge the sample at 5,000 x g for 5 min at 4 &#176;C using a high-speed centrifuge.</li>
		<li>Discard the supernate and dilute the pellet 10-fold using Buffer 2 and resuspend using a Teflon pestle by gently mixing.</li>
		<li>Centrifuge the sample at 800 x g for 15 min at 4 &#176;C to pellet the fibrous material.</li>
		<li>Pour the supernate in a new set of 50 mL plastic centrifuge tubes, careful not to disrupt the pellet, which can be discarded.</li>
		<li>Centrifuge the sample at 9,000 x g for 10 min at 4 &#176;C as in step 1.4.7.</li>
		<li>Discard the supernate, add 3.5 mL of Buffer 2 and gently resuspend the pellet using a P1000 pipette.</li>
		<li>Centrifuge the sample at 9,000 x g for 10 min at 4 &#176;C as in step 1.4.7.</li>
		<li>Discard the supernate and resuspend the pellet gently with roughly 180 &#181;L of resuspension medium using a P200 pipette. 
		&#8203;NOTE: The volume of the resuspension medium can be altered depending on the size of the pellet. This is the IMF mitochondrial fraction, which can be stored on ice until it is to be used in the import assay.</li>
	</ol>
	</li>
</ol>
2. Mitochondrial protein import
<ol>
	<li>In vitro transcription 
	NOTE: These subsequent steps outline how to prepare a radiolabelled protein for import. The import pathway under investigation may dictate the choice of target protein, for example, to evaluate import into the mitochondrial matrix, ornithine carbamyl transferase, OCT, and malate dehydrogenase, MDH, are commonly used, while Tom40 is commonly used as an indication of import into the outer mitochondrial membrane. For the following steps, plasmid DNA encoding the protein of choice is required. The transcription of plasmid DNA can be done prior to the mitochondrial isolation on a separate day, and the mRNA collected from this experiment can be stored and used in future translation and import experiments.
	<ol>
		<li>Linearize the DNA: Combine 40 &#181;L of plasmid DNA (5 &#181;g/&#181;L), 5 &#181;L of 10x enzyme buffer and 5 &#181;L of restriction enzyme and incubate at 37 &#176;C for 30 min. 
		NOTE: The restriction enzymes utilized may vary based on the plasmid, which may require a different enzyme buffer, and experimental conditions DNA can be used in any amount/volume, as the template can be scaled up or down.</li>
		<li>Purify and precipitate the linearized DNA using phenol and ethanol. Carry out all the subsequent steps (2.1.3-2.1.15) in sterile 1.5 mL tubes, and use a tabletop centrifuge (see Table of Materials) for the centrifugation steps.</li>
		<li>Add the appropriate volume of sterile H2O so that the final volume equals 400 &#181;L. Then, add 400 &#181;L of phenol.</li>
		<li>Mix vigorously by inversion for ~10 s, and centrifuge at 17,000 x g for 1 min at 4 &#176;C. Withdraw and save the upper phase.</li>
		<li>Add 400 &#181;L of phenol:chloroform:isoamylalcohol (25:24:1, v:v:v).</li>
		<li>Mix vigorously by inversion for ~10 s, and centrifuge at 17,000 g for 1 min at 4 &#176;C. Withdraw and save the upper phase.</li>
		<li>Add 400 &#181;L of chloroform:isoamylalcohol (24:1, v:v).</li>
		<li>Mix vigorously by inversion for ~10 s, and centrifuge at 17,000 g for 1 min at 4 &#176;C. Withdraw and save the upper phase.</li>
		<li>Add 40 &#181;L of 3M sodium acetate (pH 7.0), and add 1 mL of 95% ethanol.</li>
		<li>Place sterile 1.5 mL tubes in -80 &#176;C freezer on their side for 15 min.</li>
		<li>Centrifuge the samples at 17,000 x g for 10 min at 4 &#176;C.</li>
		<li>Discard the supernate and wash the pellet with 300 &#181;L of 80% ethanol.</li>
		<li>Centrifuge the samples at 17,000 x g for 2 min at 4 &#176;C.</li>
		<li>Discard the supernate and air-dry the pellet. Once the pellet is dry, it should be clear.</li>
		<li>Resuspend the pellet in 20 &#181;L of sterile H2O</li>
		<li>Measure the DNA concentration using a spectrophotometer (see Table of Materials) and ensure that the A260:280 ratio is above 1.8.</li>
		<li>Dilute the DNA to a concentration of 0.8 &#181;g/&#181;L in sterile H2O.</li>
		<li>Transcribe the DNA: Combine plasmid (0.8 &#181;g/&#181;L, 60.8 &#181;L), sterile H2O (8.4 &#181;L), 10 mM NTP (5.2 &#181;L), 10 mM ATP ( 10.0 &#181;L), 1 mM M-7-G (11.6 &#181;L), the mix as mentioned step 2.1.19 (15.6 &#181;L), RNAsin (5.2 &#181;L) and an appropriate RNA polymerase (4.8 &#181;L) to form &#34;one reaction mix&#34; (total volume = 121.6 &#181;L) and incubate for 90 min at the optimum temperature for the polymerase (37 &#176;C for T7 polymerase; 40 &#176;C for SP6 polymerase)</li>
		<li>To prepare the mix add 200 &#181;L of 1M HEPES (pH 7.9), 100 &#181;L of 1 M MgAc2, 500 &#181;L of 4 M KAc, 100 &#181;L of 20 mM spermidine, 100 &#181;L of 0.5 M DTT, and 200 &#181;L of sterile H20. 
		NOTE: The reaction can be scaled up or down in volume as long as the provided proportions of reagents are maintained. The RNA polymerase used is dictated by the bacterial promoter sequence within the plasmid being used.</li>
		<li>Then, purify and precipitate the mRNA using phenol and ethanol as in steps 2.1.2-2.1.15. Bring the volume up to 400 &#181;L with sterile H2O (add 280 &#181;L) and proceed as described in steps 2.1.2-2.1.15. Resuspend the final pellet in 20 &#181;L of sterile H2O.</li>
		<li>Measure the concentration of mRNA using a spectrophotometer, ensure that the A260:280 ratio is ~2.0.</li>
		<li>Dilute the mRNA to 2.8 &#181;g/&#181;L in sterile H2O, and store at -20 &#176;C in 50 &#181;L aliquots.</li>
	</ol>
	</li>
	<li>In vitro translation 
	NOTE: The translation of the desired DNA must be carried out on the same day of the import experiment. This experiment requires the use of radiolabeled amino acids, and therefore the user must have a permit for the use of radioisotopes, and all handling and disposal must be in accordance with the institution&#39;s policies/requirements. Steps involving radioisotope safety measures have been omitted or described briefly, as these will likely differ based on the institution.
	<ol>
		<li>Prepare enough translation reaction mix (Table 2) to supply ~20 &#181;L per sample of mitochondria to be used in the import experiment and include the same volume for a translation lane.</li>
		<li>Incubate the reaction for 30 min at 30 &#176;C (time may vary with mRNA, 25-60 min).</li>
		<li>Record the 35S-methionine use as per the institution&#39;s radioactive safety requirements and dispose of anything that has come into contact with the radioisotope per the institution&#39;s guidelines.</li>
	</ol>
	</li>
	<li>Protein import 
	NOTE: Freshly isolated mitochondria are required for the next steps. Refer to the mitochondrial isolation protocol. Other isolation methods can be used as long as the mitochondria are viable and functional. For the subsequent steps, the mitochondrial samples utilized are resuspended in a resuspension buffer as described above (Table 1). The protein concentration of the mitochondrial sample must also be measured prior to starting the import assay.
	<ol>
		<li>Roughly 15 min following the start of the translation reaction, aliquot 90 &#181;g of mitochondria into sterile 1.5 mL tubes and pre-incubate at 30 &#176;C for ~10 min. 
		NOTE: Aliquot more mitochondria than what will actually be used in the experiment; only 75 &#181;g will be actually used. However, aliquoting in excess is not a requirement.</li>
		<li>In a fresh set of sterile 1.5 mL tubes, combine 75 &#181;g of mitochondria with 18 &#181;L of the translation reaction and incubate at 30 &#176;C for desired time.</li>
		<li>Keep the remaining volume of the translation reaction on ice; this will be utilized later. 
		NOTE: Import is a time-dependent process, so it may be prudent to start with a time-course experiment ranging in incubation times from 1-60 min. A typical reaction time is 30 min.</li>
		<li>During this time, prepare the sucrose cushion by combining 1 g of sucrose, 200 &#181;L of 2.5 M KCl, 10 &#181;L 1 M MgCl2, 100 &#181;L of 1 M HEPES (pH 7.4), and bring the volume to 5 mL using sterile H2O.</li>
		<li>Prepare a new set of sterile 1.5 mL tubes corresponding to each tube in the import reaction. Aliquot 600 &#181;L of the sucrose cushion into each tube and keep on ice until the import reaction is over.</li>
		<li>To terminate the import reaction after the appropriate incubation time, remove the tube from 30 &#176;C, place it on ice and then carefully transfer the import reaction on top of the tube with the sucrose cushion. 
		NOTE: This step needs to be done very slowly to ensure that the mitochondria are not damaged/ruptured. The sucrose cushion helps slow down the migration of the mitochondria and &#34;cushions&#34; its descent to the bottom of the tube during the subsequent centrifugation step.</li>
		<li>Centrifuge the samples + sucrose cushion at 17,000 x g for 15 min at 4 &#176;C.</li>
		<li>Prepare the breaking buffer by combining 25 mL of 2.4 M sorbitol, 2 mL of 1 M HEPES (pH 7.4), and 72 mL of double-distilled H2O.</li>
		<li>Prepare lysis buffer for SDS-PAGE gel electrophoresis: Combine 50 mL of heated glycerol, 11.5 g of SDS, 31.25 mL of 1 M Tris (pH 6.8) and bring the volume to 500 mL with double-distilled H2O.</li>
		<li>For sample preparation, mix 475 &#181;L of lysis buffer with 25 &#181;L of &#946;-mercaptoethanol to be used in a later step. 
		NOTE: Lysis buffer can be made in advance and stored at room temperature; however, the addition of &#946;-mercaptoethanol is to be done fresh.</li>
		<li>Using a P1000 pipette, carefully remove the supernate and do not disturb the pellet. Dispose of the supernate in an appropriate radioactive waste container.</li>
		<li>For import into the outer membrane, perform this using Tom40, resuspend the pellet in 50 &#181;L of freshly prepared 0.1 M sodium carbonate (pH 11.5) and incubate on ice for 30 min.</li>
		<li>Following the incubation, centrifuge the sample 14,000 x g for 5 min at 4 &#176;C. This step is only done for outer membrane import reactions.</li>
		<li>To prepare the samples for SDS-PAGE electrophoresis, add 20 &#181;L of breaking buffer, 20 &#181;L of lysis buffer, and &#946;-mercaptoethanol and resuspend well. Add 5 &#181;L of sample dye.</li>
		<li>Prepare the control/translation lane by combining 3 &#181;L of the remaining translation reaction from step 2.3.3 with 37 &#181;L of lysis buffer and 5 &#181;L of sample dye. Mix well.</li>
		<li>Boil the samples for 5 min at 95 &#176;C and spin down gently at a low speed to avoid pelleting mitochondria.</li>
		<li>Apply the samples to a SDS polyacrylamide gel. 
		NOTE: The gel percentage and subsequent run time will depend on which protein is being imported. For example, OCT is 37 kDa, and its mature processed band is slightly smaller; therefore, a 12% gel allows good separation of these bands.</li>
		<li>Once electrophoresis is complete, remove the gel and place it in double-distilled H2O.</li>
		<li>Boil the gel in 5% TCA in a fume hood for 5 min, continuously stirring/moving the gel to avoid cracking. 
		NOTE: TCA helps solidify the gel for visualization; this can be done in a metal tray over a Bunsen burner. Use enough TCA to generously cover the gel, ~&#189; full.</li>
		<li>Remove the gel and place it back in double-distilled H2O. Agitate it on a rotating plate for 1 min at ~50 rpm.</li>
		<li>Wash the gel in 10 mM Tris on a rotating plate for 5 min at ~50 rpm, again using enough to generously cover the gel, ~&#189; of the container.</li>
		<li>Precipitate the protein by washing the gel in 1 M Salicyclic acid on a rotating plate for 30 min, again using enough Salicyclic acid to generously cover the gel, ~&#189; of the container being used.</li>
		<li>Dehydrate the gel as described in steps 2.3.24-2.3.31. 
		NOTE: This can be done in a number of ways. A gel dryer (see Table of Materials) provides a time-efficient option (described below); however other commercially available methods/kits can be used that may be more cost-effective but more time-consuming. Gel drying kits can be utilized as an alternative that does not require the application of heat or suction but instead allows the gel to air-dry between cellophane sheets to prevent distortion.</li>
		<li>Place a large sheet of blotting paper down on the porous bed of the gel dryer. Place one sheet of paper towel in the area where the gel will be applied.</li>
		<li>Cut a 15 cm x 20 cm piece of blotting paper and place it on the paper towel.</li>
		<li>Scoop out the gel from the container using a second piece of 15 cm x 20 cm blotting paper and lay it down flat on top of the first piece.</li>
		<li>Cut a slightly larger piece of plastic wrap, ~20 cm x 25 cm, and place it down on gel, ensuring no creases or bubbles under the wrap. 
		NOTE: This may take a few attempts, but it is imperative that there are no trapped air pockets.</li>
		<li>Gently lay down the plastic cover of the gel dryer over top of the wrap, again ensuring that there are no bubbles or creases.</li>
		<li>Turn on the pump/vacuum and ensure that the plastic cover has formed a seal. Test the seal by lifting a corner of the plastic cover and wait for it to re-seal.</li>
		<li>Close the gel dryer and run for 90 min. Set the temperature to start at 30 &#176;C, gradually reach 80 &#176;C, and then return to 30 &#176;C at the end of the run.</li>
		<li>Once dehydrated, the gel will solidify and feel paper-thin. Wrap the gel in the plastic wrap used in the drying process.</li>
		<li>Place the dehydrated gel in a film cassette with a phosphorus film (see Table of Materials), with the white side facing the gel. Exposure times vary but can be 24-48 h for visualization of bands.</li>
		<li>Visualize using autoradiography using any suitable imager that is capable of phosphorus imaging.</li>
	</ol>
	</li>
</ol>

<ol>
	<li>Kirkwood, S. P., Munn, E. A., Brooks, G. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondrial+reticulum+in+limb+skeletal+muscle.">Mitochondrial reticulum in limb skeletal muscle.</a> The American Journal of Physiology. 251 (3), 395-402 (1986).</li><li>Glancy, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Power+grid+protection+of+the+muscle+mitochondrial+reticulum.">Power grid protection of the muscle mitochondrial reticulum.</a> Cell Reports. 19 (3), 487-496 (2017).</li><li>Vincent, A. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+3D+mapping+of+the+human+skeletal+muscle+mitochondrial+network.">Quantitative 3D mapping of the human skeletal muscle mitochondrial network.</a> Cell Reports. 26 (4), 996-1009 (2019).</li><li>Ogata, T., Yamasaki, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ultra-high-resolution+scanning+electron+microscopy+of+mitochondria+and+sarcoplasmic+reticulum+arrangement+in+human+red,+white,+and+intermediate+muscle+fibers.">Ultra-high-resolution scanning electron microscopy of mitochondria and sarcoplasmic reticulum arrangement in human red, white, and intermediate muscle fibers.</a> Anatomical Record. 248 (2), 214-223 (1997).</li><li>Hood, D. A., Tryon, L. D., Carter, H. N., Kim, Y., Chen, C. C. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Unravelling+the+mechanisms+regulating+muscle+mitochondrial+biogenesis.">Unravelling the mechanisms regulating muscle mitochondrial biogenesis.</a> Biochemical Journal. 473, 2295-2314 (2016).</li><li>Perry, C. G. R., Kane, D. A., Lanza, I. R., Neufer, P. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Methods+for+assessing+mitochondrial+function+in+diabetes.">Methods for assessing mitochondrial function in diabetes.</a> Diabetes. 62, 1032-1036 (2013).</li><li>Holloszy, J. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biochemical+adaptations+in+muscle.">Biochemical adaptations in muscle.</a> The Journal of Biological Chemistry. 242 (9), 2278-2282 (1967).</li><li>Cogswell, A. M., Stevens, R. J., Hood, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Properties+of+skeletal+muscle+mitochondria+from+subsarcolemmal+and+intermyofibrillar+isolated+regions.">Properties of skeletal muscle mitochondria from subsarcolemmal and intermyofibrillar isolated regions.</a> The American Journal of Physiology. 264, 383-389 (1993).</li><li>Koves, T. R., Noland, R. C., Bates, A. L., Henes, S. T., Muoio, D. M., Cortright, R. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Subsarcolemmal+and+intermyofibrillar+mitochondria+play+distinct+roles+in+regulating+skeletal+muscle+fatty+acid+metabolism.">Subsarcolemmal and intermyofibrillar mitochondria play distinct roles in regulating skeletal muscle fatty acid metabolism.</a> American Journal of Physiology - Cell Physiology. 288, 1074-1082 (2005).</li><li>Bizeau, M. E., Willis, W. T., Hazel, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Differential+responses+to+endurance+training+in+subsarcolemmal+and+intermyofibrillar+mitochondria.">Differential responses to endurance training in subsarcolemmal and intermyofibrillar mitochondria.</a> Journal of Applied Physiology. 85 (4), 1279-1284 (1998).</li><li>Krieger, D. A., Tate, C. A., McMillin-Wood, J., Booth, F. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Populations+of+rat+skeletal+muscle+mitochondria+after+exercise+and+immobilization.">Populations of rat skeletal muscle mitochondria after exercise and immobilization.</a> Journal of Applied Physiology: Respiratory, Environmental and Exercise Physiology. 48 (1), 23-28 (1980).</li><li>Calvo, S. E., Clauser, K. R., Mootha, V. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MitoCarta2.0:+An+updated+inventory+of+mammalian+mitochondrial+proteins.">MitoCarta2.0: An updated inventory of mammalian mitochondrial proteins.</a> Nucleic Acids Research. 44 (1), 1251-1257 (2016).</li><li>Wiedemann, N., Pfanner, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondrial+machineries+for+protein+import+and+assembly.">Mitochondrial machineries for protein import and assembly.</a> Annual Review of Biochemistry. 86 (1), 685-714 (2017).</li><li>Backes, S., Herrmann, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+translocation+into+the+intermembrane+space+and+matrix+of+mitochondria:+mechanisms+and+driving+forces.">Protein translocation into the intermembrane space and matrix of mitochondria: mechanisms and driving forces.</a> Frontiers in Molecular Biosciences. 4, 83 (2017).</li><li>Harbauer, A. B., Zahedi, R. P., Sickmann, A., Pfanner, N., Meisinger, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+protein+import+machinery+of+mitochondria+-+A+regulatory+hub+in+metabolism,+stress,+and+disease.">The protein import machinery of mitochondria - A regulatory hub in metabolism, stress, and disease.</a> Cell Metabolism. 19 (3), 357-372 (2014).</li><li>Jin, S. M., Lazarou, M., Wang, C., Kane, L. A., Narendra, D. P., Youle, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondrial+membrane+potential+regulates+PINK1+import+and+proteolytic+destabilization+by+PARL.">Mitochondrial membrane potential regulates PINK1 import and proteolytic destabilization by PARL.</a> The Journal of Cell Biology. 191 (5), 933-942 (2010).</li><li>Matsuda, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PINK1+stabilized+by+mitochondrial+depolarization+recruits+Parkin+to+damaged+mitochondria+and+activates+latent+Parkin+for+mitophagy.">PINK1 stabilized by mitochondrial depolarization recruits Parkin to damaged mitochondria and activates latent Parkin for mitophagy.</a> The Journal of Cell Biology. 189 (2), 211-221 (2010).</li><li>Fiorese, C. J., Schulz, A. M., Lin, Y. -. F., Rosin, N., Pellegrino, M. W., Haynes, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+transcription+factor+ATF5+mediates+a+mammalian+mitochondrial+UPR.">The transcription factor ATF5 mediates a mammalian mitochondrial UPR.</a> Current biology. 26 (15), 2037-2043 (2016).</li><li>Quiros, P. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multi-omics+analysis+identifies+ATF4+as+a+key+regulator+of+the+mitochondrial+stress+response+in+mammals.">Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals.</a> The Journal of Cell Biology. 216 (7), 2027-2045 (2017).</li><li>Takahashi, M., Hood, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+import+into+subsarcolemmal+and+intermyofibrillar+skeletal+muscle+mitochondria.+Differential+import+regulation+in+distinct+subcellular+regions.">Protein import into subsarcolemmal and intermyofibrillar skeletal muscle mitochondria. Differential import regulation in distinct subcellular regions.</a> The Journal of Biological Chemistry. 271 (44), 27285-27291 (1996).</li><li>Hood, D. A., Memme, J. M., Oliveira, A. N., Triolo, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Maintenance+of+skeletal+muscle+mitochondria+in+health,+exercise,+and+aging.">Maintenance of skeletal muscle mitochondria in health, exercise, and aging.</a> Annual Review of Physiology. 81, (2019).</li><li>Joseph, A., Hood, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondrion+plasticity+of+TOM+complex+assembly+in+skeletal+muscle+mitochondria+in+response+to+chronic+contractile+activity.">Mitochondrion plasticity of TOM complex assembly in skeletal muscle mitochondria in response to chronic contractile activity.</a> Mitochondrion. 12 (2), 305-312 (2012).</li><li>Singh, K., Hood, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+denervation-induced+muscle+disuse+on+mitochondrial+protein+import.">Effect of denervation-induced muscle disuse on mitochondrial protein import.</a> American Journal of Physiology-Cell Physiology. 300 (1), 138-145 (2011).</li><li>Zhang, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Altered+mitochondrial+morphology+and+defective+protein+import+reveal+novel+roles+for+Bax+and/or+Bak+in+skeletal+muscle.">Altered mitochondrial morphology and defective protein import reveal novel roles for Bax and/or Bak in skeletal muscle.</a> American Journal of Physiology. Cell Physiology. 305 (5), 502-511 (2013).</li><li>Lai, N., Kummitha, C., Rosca, M., Fujioka, H., Tandler, B., Hoppel, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+mitochondrial+subpopulations+from+skeletal+muscle:+optimizing+recovery+and+preserving+integrity.">Isolation of mitochondrial subpopulations from skeletal muscle: optimizing recovery and preserving integrity.</a> Acta Physiologica. 25 (2), 13182 (2019).</li><li>Nargund, A. M., Pellegrino, M. W., Fiorese, C. J., Baker, B. M., Haynes, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondrial+import+efficiency+of+ATFS-1+regulates+mitochondrial+UPR+activation.">Mitochondrial import efficiency of ATFS-1 regulates mitochondrial UPR activation.</a> Science. 337 (6094), 587-590 (2012).</li><li>Picard, M., Taivassalo, T., Gouspillou, G., Hepple, R. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondria:+Isolation,+structure+and+function.">Mitochondria: Isolation, structure and function.</a> Journal of Physiology. 589 (18), 4413-4421 (2011).</li><li>Kras, K. A., Willis, W. T., Barker, N., Czyzyk, T., Langlais, P. R., Katsanos, C. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Subsarcolemmal+mitochondria+isolated+with+the+proteolytic+enzyme+nagarse+exhibit+greater+protein+specific+activities+and+functional+coupling.">Subsarcolemmal mitochondria isolated with the proteolytic enzyme nagarse exhibit greater protein specific activities and functional coupling.</a> Biochemistry and Biophysics Reports. 6, 101-107 (2016).</li><li>S&#225;nchez-Duarte, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nicorandil+affects+mitochondrial+respiratory+chain+function+by+increasing+complex+III+activity+and+ROS+production+in+skeletal+muscle+mitochondria.">Nicorandil affects mitochondrial respiratory chain function by increasing complex III activity and ROS production in skeletal muscle mitochondria.</a> Journal of Membrane Biology. 253 (4), 309-318 (2020).</li><li>I&#241;igo, M. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Estrogen+receptor-&#945;+in+female+skeletal+muscle+is+not+required+for+regulation+of+muscle+insulin+sensitivity+and+mitochondrial+regulation.">Estrogen receptor-&#945; in female skeletal muscle is not required for regulation of muscle insulin sensitivity and mitochondrial regulation.</a> Molecular Metabolism. 34 (2020), 1-15 (2020).</li><li>Newsom, S. A., Stierwalt, H. D., Ehrlicher, S. E., Robinson, M. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Substrate-specific+respiration+of+isolated+skeletal+muscle+mitochondria+after+1+h+of+moderate+cycling+in+sedentary+adults.">Substrate-specific respiration of isolated skeletal muscle mitochondria after 1 h of moderate cycling in sedentary adults.</a> Medicine and Science in Sports and Exercise. 53 (7), 1375-1384 (2021).</li><li>Takahashi, M., Chesley, A., Freyssenet, D., Hood, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Contractile+activity-induced+adaptations+in+the+mitochondrial+protein+import+system.">Contractile activity-induced adaptations in the mitochondrial protein import system.</a> The American Journal of Physiology. 274 (5), 1380-1387 (1998).</li><li>Kravic, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+mammalian+skeletal+muscle,+phosphorylation+of+TOMM22+by+protein+kinase+CSNK2/CK2+controls+mitophagy.">In mammalian skeletal muscle, phosphorylation of TOMM22 by protein kinase CSNK2/CK2 controls mitophagy.</a> Autophagy. 8627, 01-65 (2017).</li><li>Opali&#324;ska, M., Meisinger, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Metabolic+control+via+the+mitochondrial+protein+import+machinery.">Metabolic control via the mitochondrial protein import machinery.</a> Current Opinion in Cell Biology. 33, 42-48 (2015).</li><li>Gerbeth, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Glucose-induced+regulation+of+protein+import+receptor+tom22+by+cytosolic+and+mitochondria-bound+kinases.">Glucose-induced regulation of protein import receptor tom22 by cytosolic and mitochondria-bound kinases.</a> Cell Metabolism. 18 (4), 578-587 (2013).</li></ol>

No conflicts of interest, financial or otherwise, are declared by the authors.

Mitochondria are uniquely dependent on the expression and coordination of both the nuclear and mitochondrial genomes for their synthesis and expansion within cells. However, the nuclear genome encodes the vast majority (99%) of the mitochondrial proteome, and this underscores the importance of the protein import machinery in supporting mitochondrial biogenesis. Import also serves as an important signaling event, as failure to import can promote the initiation of the unfolded protein response and/or mitophagy<sup class="x...

Mitochondria are organelles that exist in complex morphologies in different cell types and are recognized to possess an increasing array of functions that are critical for cellular health. As such, they can no longer be whittled down merely to energy-producing organelles. Mitochondria are key metabolic regulators, determinants of cell fate, and signaling hubs, the functions of which can serve as useful indicators of overall cellular health. In skeletal muscle cells, electron microscopy studies reveal the presence of geographically distinct subsarcolemmal (SS) and intermyofibrillar (IMF) mitochondria, which exhibit a degree of connectivity1,2,3,4 that is now recognized to be highly dynamic and adaptable to changes in skeletal muscle activity levels, as well as with age and disease. Mitochondrial content and function in muscle can be assessed in numerous ways5,6, and traditional methods of organelle isolation have been applied to better understand the respiratory and enzymatic capacities (Vmax) of mitochondria distinct from the influence of the cellular milieu7,8. In particular, these traditional methods have revealed subtle biochemical distinctions between mitochondria isolated from subsarcolemmal and intermyofibrillar regions, belying possible functional implications for metabolism in these subcellular regions8,9,10,11.
The biogenesis of mitochondria is unique in requiring the contribution of gene products from both nuclear and mitochondrial DNA. However, the vast majority of these are derived from the nucleus since mtDNA transcription only leads to the synthesis of 13 proteins. Since mitochondria normally comprise &#62;1000 proteins involved in diverse metabolic pathways, biogenesis of the organelle requires a tightly regulated means of import and assembly of precursor proteins from the cytosol into the various mitochondrial sub-compartments to maintain proper stoichiometry and function12,13. Nuclear-encoded proteins destined for mitochondria normally carry a mitochondrial targeting sequence (MTS) that targets them to the organelle and facilitates their sub-compartmental localization. Most matrix-bound proteins contain a cleavable N-terminal MTS, while those destined for the outer or inner mitochondrial membrane usually have internal targeting domains14. The import process is carried out by a set of diverse channels that provide multiple avenues for entry into the organelle13. The translocase of the outer membrane (TOM) complex shuttles precursors from the cytosol into the intermembrane space, where they are recognized by the translocase of the inner membrane (TIM) complex. This complex is responsible for importing nuclear-encoded precursors into the matrix, where proteases cleave the N-terminal targeting presequence. Proteins destined for the outer membrane can be directly inserted into this membrane through the TOM complex, while those destined for the inner membrane are inserted by a TIM protein, specifically TIM22. Following their import, proteins are further processed by resident proteases and chaperones and often combine to form larger complexes, such as those found in the electron transport chain.
Mitochondrial protein import itself also serves as a measurement of mitochondrial health, as this process relies on the presence of membrane potential and a source of energy in the form of ATP15. For example, when the membrane potential is dissipated, protein kinase PINK1 cannot be taken up by the organelle, and this leads to phosphorylation signals that trigger the onset of the degradation of the organelle through a pathway called mitophagy16,17. Under similar circumstances, when the import is impeded, the protein ATF5 cannot enter the organelle, and it subsequently translocates to the nucleus, where it serves as a transcription factor for the up-regulation of UPR gene expression18,19. Thus, measuring protein import efficiency can provide comprehensive insight into the health of the organelle, while the gene expression response can be used to indicate the degree of retrograde signaling to the nucleus.
Despite its obvious importance for the biogenesis of mitochondria and for cellular health in general, the import pathway in mammalian mitochondria is remarkably understudied. In this report, we describe the specific steps involved in measuring the import of precursor proteins into skeletal muscle mitochondria and provide data to illustrate the adaptive response of the import system to changes in muscle and disuse, illustrating the contribution of the protein import to the adaptive plasticity of skeletal muscle.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.2% BSA</td>
			<td>Sigma</td>
			<td>A2153</td>
			<td></td>
		</tr>
		<tr>
			<td>35S-methionine</td>
			<td>Perkin Elmer</td>
			<td>NEG709A500UC</td>
			<td>Purchase requires a valid radioisotope permit</td>
		</tr>
		<tr>
			<td>ATP</td>
			<td>Sigma</td>
			<td>A7699</td>
			<td></td>
		</tr>
		<tr>
			<td>Blotting paper; Whatman 3MM CHR Paper</td>
			<td>Thermo Fisher</td>
			<td>05-714-5</td>
			<td></td>
		</tr>
		<tr>
			<td>Cassette for film</td>
			<td>Kodak</td>
			<td>Kodak Xomatic</td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifugation Tube</td>
			<td>Thermo Fisher</td>
			<td>3138-0050</td>
			<td></td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>Thermo Fisher</td>
			<td>C298-4</td>
			<td></td>
		</tr>
		<tr>
			<td>DTT</td>
			<td>Sigma</td>
			<td>D9779-5G</td>
			<td></td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>BioShop</td>
			<td>EDT002</td>
			<td></td>
		</tr>
		<tr>
			<td>EGTA</td>
			<td>Sigma</td>
			<td>E4378</td>
			<td></td>
		</tr>
		<tr>
			<td>Gel Dryer</td>
			<td>BioRad</td>
			<td>Model 583</td>
			<td></td>
		</tr>
		<tr>
			<td>Gel Drying Kit</td>
			<td>Sigma or BioRad</td>
			<td>Z377570-1PAK or OW-GDF-10</td>
			<td>Various options are commercially available through many companies, these are just as few examples.</td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>Caledon Laboratory Chemicals</td>
			<td>5350-1-40</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Sigma</td>
			<td>H3375</td>
			<td></td>
		</tr>
		<tr>
			<td>High Speed Centrifuge</td>
			<td>Beckman Coulter</td>
			<td>Avanti J-25 Centrifuge</td>
			<td></td>
		</tr>
		<tr>
			<td>Homogenizer</td>
			<td>IKA</td>
			<td>T25 Digital Ultra Turrex</td>
			<td></td>
		</tr>
		<tr>
			<td>Isoamylalcohol, or 3-methylbutanol</td>
			<td>Sigma</td>
			<td>I9392</td>
			<td></td>
		</tr>
		<tr>
			<td>KAc</td>
			<td>BioShop</td>
			<td>POA301.500</td>
			<td></td>
		</tr>
		<tr>
			<td>KCl</td>
			<td>Sigma</td>
			<td>P3911</td>
			<td></td>
		</tr>
		<tr>
			<td>M7G</td>
			<td>New England Biolab</td>
			<td>S1404S</td>
			<td>Dilute with 1000ul 20mM HEPES to make 1mM stock</td>
		</tr>
		<tr>
			<td>MgCl</td>
			<td>BioShop</td>
			<td>MAG510</td>
			<td></td>
		</tr>
		<tr>
			<td>MgSO4</td>
			<td>Thermo Fisher</td>
			<td>M65-500</td>
			<td></td>
		</tr>
		<tr>
			<td>MOPS</td>
			<td>BioShop</td>
			<td>MOP001</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>BioShop</td>
			<td>SOD001</td>
			<td></td>
		</tr>
		<tr>
			<td>NTP</td>
			<td>Thermo Fisher</td>
			<td>R0191</td>
			<td></td>
		</tr>
		<tr>
			<td>OCT Plasmid</td>
			<td>-</td>
			<td>-</td>
			<td>Donated from Dr. G. C. Shore, McGill University, Montreal, Canada; alternative available through Addgene, plasmid #71877</td>
		</tr>
		<tr>
			<td>pGEM4Z/hTom40 Plasmid</td>
			<td>-</td>
			<td>-</td>
			<td>Donated from Dr. M. T. Ryan, La Trobe University, Melbourne, Australia</td>
		</tr>
		<tr>
			<td>pGMDH Plasmid</td>
			<td>-</td>
			<td>-</td>
			<td>Donated from Dr. A. Strauss, Washington University School of Medicine</td>
		</tr>
		<tr>
			<td>Phenol</td>
			<td>Sigma</td>
			<td>P4557</td>
			<td></td>
		</tr>
		<tr>
			<td>Phenol:Chloroform:Isoamyalcohol</td>
			<td>Sigma</td>
			<td>P3803</td>
			<td>Can also be made with the ratio provided</td>
		</tr>
		<tr>
			<td>Phosphorus Film</td>
			<td>Fujifilm</td>
			<td>BAS-IP MS 2025</td>
			<td></td>
		</tr>
		<tr>
			<td>Rabbit reticulocyte lysate</td>
			<td>Promega</td>
			<td>L4960</td>
			<td>Avoid freeze-thaw; aliquot lysate upon arrival; amino acids are provided in the kit as well</td>
		</tr>
		<tr>
			<td>RNAsin</td>
			<td>Promega</td>
			<td>N2311</td>
			<td></td>
		</tr>
		<tr>
			<td>Rotor for High Speed Centrifuge</td>
			<td>Beckman Coulter</td>
			<td>JA-25.50</td>
			<td></td>
		</tr>
		<tr>
			<td>SDS</td>
			<td>BioShop</td>
			<td>SDS001.500</td>
			<td>Caution: harmful if ingested or inhaled, wear a mask.</td>
		</tr>
		<tr>
			<td>Sodium acetate</td>
			<td>Bioshop</td>
			<td>SAA 304</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Carbonate</td>
			<td>VWR</td>
			<td>BDH9284</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium salicylate</td>
			<td>Millipore Sigma</td>
			<td>106601</td>
			<td></td>
		</tr>
		<tr>
			<td>Sorbitol</td>
			<td>Sigma</td>
			<td>S6021</td>
			<td></td>
		</tr>
		<tr>
			<td>SP6 RNA Polymerase</td>
			<td>Promega</td>
			<td>P1085</td>
			<td></td>
		</tr>
		<tr>
			<td>Spectrophotometer</td>
			<td>Thermo Fisher</td>
			<td>Nanodrop 2000</td>
			<td></td>
		</tr>
		<tr>
			<td>Spermidine</td>
			<td>Sigma</td>
			<td>S-2626</td>
			<td></td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>BioShop</td>
			<td>SUC507</td>
			<td></td>
		</tr>
		<tr>
			<td>T7 RNA Polymerase</td>
			<td>Promega</td>
			<td>P2075</td>
			<td></td>
		</tr>
		<tr>
			<td>Tabletop Centrifuge</td>
			<td>Thermo Fisher</td>
			<td>AccuSpin Micro 17</td>
			<td></td>
		</tr>
		<tr>
			<td>Trichloroacetic acid</td>
			<td>Thermo Fisher</td>
			<td>A322-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris</td>
			<td>BioShop</td>
			<td>TRS001</td>
			<td></td>
		</tr>
		<tr>
			<td>&#946;-mercaptoethanol</td>
			<td>Sigma</td>
			<td>M6250-100ML</td>
			<td></td>
		</tr>
	</tbody>
</table>

measurement of protein import capacity of skeletal muscle mitochondria

Mitochondria are key metabolic and regulatory organelles that determine the energy supply as well as the overall health of the cell. In skeletal muscle, mitochondria exist in a series of complex morphologies, ranging from small oval organelles to a broad, reticulum-like network. Understanding how the mitochondrial reticulum expands and develops in response to diverse stimuli such as alterations in energy demand has long been a topic of research. A key aspect of this growth, or biogenesis, is the import of precursor proteins, originally encoded by the nuclear genome, synthesized in the cytosol, and translocated into various mitochondrial sub-compartments. Mitochondria have developed a sophisticated mechanism for this import process, involving many selective inner and outer membrane channels, known as the protein import machinery (PIM). Import into the mitochondrion is dependent on viable membrane potential and the availability of organelle-derived ATP through oxidative phosphorylation. Therefore its measurement can serve as a measure of organelle health. The PIM also exhibits a high level of adaptive plasticity in skeletal muscle that is tightly coupled to the energy status of the cell. For example, exercise training has been shown to increase import capacity, while muscle disuse reduces it, coincident with changes in markers of mitochondrial content. Although protein import is a critical step in the biogenesis and expansion of mitochondria, the process is not widely studied in skeletal muscle. Thus, this paper outlines how to use isolated and fully functional mitochondria from skeletal muscle to measure protein import capacity in order to promote a greater understanding of the methods involved and an appreciation of the importance of the pathway for organelle turnover in exercise, health, and disease.

We have extensively illustrated that this protocol is a valid assay for determining the rate of import into functional and intact isolated skeletal muscle mitochondria. In comparison to untreated conditions, the import of typical precursor proteins such as malate dehydrogenase (MDH) into the matrix is sensitive to membrane potential because it can be inhibited by valinomycin, a respiratory chain uncoupler (Figure 2A). Import is also impeded when mitochondrial inner and outer...

Watch this Scientific Journal Video about Measurement of Protein Import Capacity of Skeletal Muscle Mitochondria at JoVE.com

Measurement of Protein Import Capacity of Skeletal Muscle Mitochondria

Mitochondria are key metabolic organelles that exhibit a high level of phenotypic plasticity in skeletal muscle. The import of proteins from the cytosol is a critical pathway for organelle biogenesis, essential for the expansion of the reticulum and the maintenance of mitochondrial function. Therefore, protein import serves as a barometer of cellular health.

Mitochondria are key metabolic and regulatory organelles that determine the energy supply as well as the overall health of the cell. In skeletal muscle, ...

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Unit 1

Intracellular Compartments and Protein Sorting

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2.5K Views.  York University. Mitochondria are key metabolic organelles that exhibit a high level of phenotypic plasticity in skeletal muscle. The import of proteins from the cytosol is a critical pathway for organelle biogenesis, essential for the expansion of the reticulum and the maintenance of mitochondrial function. Therefore, protein import serves as a barometer of cellular health. 

Video: Measurement of Protein Import Capacity of Skeletal Muscle Mitochondria

A Filtration-based Method of Preparing High-quality Nuclei from Cross-linked Skeletal Muscle for Chromatin Immunoprecipitation

Chromatin immunoprecipitation (ChIP) is a powerful method to determine protein binding to chromatin DNA. Fiber-rich skeletal muscle, however, has been a challenge for ChIP due to technical difficulty in isolation of high-quality nuclei with minimal contamination of myofibrils. Previous protocols have attempted to purify nuclei before cross-linking, which incurs the risk of altered DNA-protein interaction during the prolonged nuclei preparation process. In the current protocol, we first cross-linked the skeletal muscle tissue collected from mice, and the tissues were minced and sonicated. Since we found that ultracentrifugation was not able to separate nuclei from myofibrils using cross-linked muscle tissue, we devised a sequential filtration procedure to obtain high-quality nuclei devoid of significant myofibril contamination. We subsequently prepared chromatin by using an ultrasonicator, and ChIP assays with anti-BMAL1 antibody revealed robust circadian binding pattern of BMAL1 to target gene promoters. This filtration protocol constitutes an easily applicable method to isolate high-quality nuclei from cross-linked skeletal muscle tissue, allowing consistent sample processing for circadian and other time-sensitive studies. In combination with next-generation sequencing (NGS), our method can be deployed for various mechanistic and genomic studies focusing on skeletal muscle function.

We present a filtration-based protocol to isolate high-quality nuclei from cross-linked mouse skeletal muscle wherein we removed the need for ultracentrifugation, making it easily applicable. We show that chromatin prepared from the nuclei is suitable for chromatin immunoprecipitation and likely chromatin immunoprecipitation sequencing studies.

Chromatin immunoprecipitation (ChIP) is a powerful method to determine protein binding to chromatin DNA. Fiber-rich skeletal muscle, however, has been a ...

Improved Protocol for Chromatin Immunoprecipitation from Mouse Skeletal Muscle

We describe an efficient and reproducible protocol for the preparation of chromatin from adult mouse skeletal muscle, a physically resistant tissue with a high content of structural proteins. Dissected limb muscles from adult mice are physically disrupted by mechanical homogenisation, or a combination of mincing and douncing, in a hypotonic buffer before formaldehyde fixation of the cell lysate. The fixed nuclei are purified by further cycles of mechanical homogenisation or douncing and sequential filtrations to remove cell debris. The purified nuclei can be sonicated immediately or at a later stage after freezing. The chromatin can be efficiently sonicated and is suitable for chromatin immunoprecipitation experiments, as illustrated by the profiles obtained for transcription factors, RNA polymerase II, and covalent histone modifications. The binding events detected using chromatin prepared by this protocol are predominantly those taking place in the muscle fiber nuclei despite the presence of chromatin from other fiber-associated satellite and endothelial cells. This protocol is therefore adapted to study gene regulation in the adult mouse skeletal muscle.

A novel protocol for the preparation of chromatin from adult mouse skeletal muscle adapted to the study of gene regulation in muscle fibers by chromatin immunoprecipitation is presented.

We describe an efficient and reproducible protocol for the preparation of chromatin from adult mouse skeletal muscle, a physically resistant tissue with a ...

Isolation and Respiratory Measurements of Mitochondria from Arabidopsis thaliana

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.

Isolation and Respiratory Measurements of Mitochondria from Arabidopsis thaliana

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 ...

Analyses of Mitochondrial Calcium Influx in Isolated Mitochondria and Cultured Cells

Ca2+ handling by mitochondria is a critical function regulating both physiological and pathophysiological processes in a broad spectrum of cells. The ability to accurately measure the influx and efflux of Ca2+ from mitochondria is important for determining the role of mitochondrial Ca2+ handling in these processes. In this report, we present two methods for the measurement of mitochondrial Ca2+ handling in both isolated mitochondria and cultured cells. We first detail a plate reader-based platform for measuring mitochondrial Ca2+ uptake using the Ca2+ sensitive dye calcium green-5N. The plate reader-based format circumvents the need for specialized equipment, and the calcium green-5N dye is ideally suited for measuring Ca2+ from isolated tissue mitochondria. For our application, we describe the measurement of mitochondrial Ca2+ uptake in mitochondria isolated from mouse heart tissue; however, this procedure can be applied to measure mitochondrial Ca2+ uptake in mitochondria isolated from other tissues such as liver, skeletal muscle, and brain. Secondly, we describe a confocal microscopy-based assay for measurement of mitochondrial Ca2+ in permeabilized cells using the Ca2+ sensitive dye Rhod-2/AM and imaging using 2-dimensional laser-scanning microscopy. This permeabilization protocol eliminates cytosolic dye contamination, allowing for specific recording of changes in mitochondrial Ca2+. Moreover, laser-scanning microscopy allows for high frame rates to capture rapid changes in mitochondrial Ca2+ in response to various drugs or reagents applied in the external solution. This protocol can be applied to measure mitochondrial Ca2+ uptake in many cell types including primary cells such as cardiac myocytes and neurons, and immortalized cell lines.

Here, we present two protocols for the measurement of mitochondrial Ca2+ influx in isolated mitochondria and cultured cells. For isolated mitochondria, we detail a plate reader-based Ca2+ import assay using the Ca2+ sensitive dye calcium green-5N. For cultured cells, we describe a confocal microscopy method using the Ca2+ dye Rhod-2/AM.

Ca2+ handling by mitochondria is a critical function regulating both physiological and pathophysiological processes in a broad spectrum of cells. The ...

Studying Protein Import into Chloroplasts Using Protoplasts

The chloroplast is an essential organelle that is responsible for various cellular processes in plants, such as photosynthesis and the production of many secondary metabolites and lipids. Chloroplasts require a large number of proteins for these various physiological processes. Over 95% of chloroplast proteins are nucleus-encoded and imported into chloroplasts from the cytosol after translation on cytosolic ribosomes. Thus, the proper import or targeting of these nucleus-encoded chloroplast proteins to chloroplasts is essential for the proper functioning of chloroplasts as well as the plant cell. Nucleus-encoded chloroplast proteins contain signal sequences for specific targeting to chloroplasts. Molecular machinery localized to the chloroplast or cytosol recognize these signals and carry out the import process. To investigate the mechanisms of protein import or targeting to chloroplasts in vivo, we developed a rapid, efficient protoplast-based method to analyze protein import into chloroplasts of Arabidopsis. In this method, we use protoplasts isolated from leaf tissues of Arabidopsis. Here, we provide a detailed protocol for using protoplasts to investigate the mechanism by which proteins are imported into chloroplasts.

Here we describe a protocol to express proteins into protoplasts by using PEG-mediated transformation method. The method provides easy expression of proteins of interest, and efficient investigation of protein localization and the import process for various experimental conditions in vivo.

The chloroplast is an essential organelle that is responsible for various cellular processes in plants, such as photosynthesis and the production of many ...

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Accurate quantification of transcription factor (TF)-DNA interactions is essential for understanding the regulation of gene expression. Since existing approaches suffer from significant limitations, we have developed a new method for determining TF-DNA binding affinities with high sensitivity on a large scale. The assay relies on the established fluorescence anisotropy (FA) principle but introduces important technical improvements. First, we measure a full FA competitive titration curve in a single well by incorporating TF and a fluorescently labeled reference DNA in a porous agarose gel matrix. Unlabeled DNA oligomer is loaded on the top as a competitor and, through diffusion, forms a spatio-temporal gradient. The resulting FA gradient is then read out using a customized epifluorescence microscope setup. This improved setup greatly increases the sensitivity of FA signal detection, allowing both weak and strong binding to be reliably quantified, even for molecules of similar molecular weights. In this fashion, we can measure one titration curve per well of a multi-well plate, and through a fitting procedure, we can extract both the absolute dissociation constant (KD) and active protein concentration. By testing all single-point mutation variants of a given consensus binding sequence, we can survey the entire binding specificity landscape of a TF, typically on a single plate. The resulting position weight matrices (PWMs) outperform those derived from other methods in predicting in vivo TF occupancy. Here, we present a detailed guide for implementing HiP-FA on a conventional automated fluorescent microscope and the data analysis pipeline.

Here we present a novel method for determining binding affinities at equilibrium and in solution with high sensitivity on a large scale. This improves the quantitative analysis of transcription factor-DNA binding. The method is based on automated fluorescence anisotropy measurements in a controlled delivery system.

Accurate quantification of transcription factor (TF)-DNA interactions is essential for understanding the regulation of gene expression. Since existing ...

Analysis of Protein Folding, Transport, and Degradation in Living Cells by Radioactive Pulse Chase

Radioactive pulse-chase labeling is a powerful tool for studying the conformational maturation, the transport to their functional cellular location, and the degradation of target proteins in live cells. By using short (pulse) radiolabeling times (&lt;30 min) and tightly controlled chase times, it is possible to label only a small fraction of the total protein pool and follow its folding. When combined with nonreducing/reducing SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoprecipitation with (conformation-specific) antibodies, folding processes can be examined in great detail. This system has been used to analyze the folding of proteins with a huge variation in properties such as soluble proteins, single and multi-pass transmembrane proteins, heavily N- and O-glycosylated proteins, and proteins with and without extensive disulfide bonding. Pulse-chase methods are the basis of kinetic studies into a range of additional features, including co- and posttranslational modifications, oligomerization, and polymerization, essentially allowing the analysis of a protein from birth to death. Pulse-chase studies on protein folding are complementary with other biochemical and biophysical methods for studying proteins in vitro by providing increased temporal resolution and physiological information. The methods as described within this paper are adapted easily to study the folding of almost any protein that can be expressed in mammalian or insect-cell systems.

Here we describe a protocol for a general pulse-chase method that allows the kinetic analysis of folding, transport, and degradation of proteins to be followed in live cells.

Radioactive pulse-chase labeling is a powerful tool for studying the conformational maturation, the transport to their functional cellular location, and ...

Interactions with and Membrane Permeabilization of Brain Mitochondria by Amyloid Fibrils

A growing body of evidence indicates that membrane permeabilization, including internal membranes such as mitochondria, is a common feature and primary mechanism of amyloid aggregate-induced toxicity in neurodegenerative diseases. However, most reports describing the mechanisms of membrane disruption are based on phospholipid model systems, and studies directly targeting events occurring at the level of biological membranes are rare. Described here is a model for studying the mechanisms of amyloid toxicity at the membrane level. For mitochondrial isolation, density gradient medium is used to obtain preparations with minimal myelin contamination. After mitochondrial membrane integrity confirmation, the interaction of amyloid fibrils arising from &#945;-synuclein, bovine insulin, and hen egg white lysozyme (HEWL) with rat brain mitochondria, as an in vitro biological model, is investigated. The results demonstrate that treatment of brain mitochondria with fibrillar assemblies can cause different degrees of membrane permeabilization and ROS content enhancement. This indicates structure-dependent interactions between amyloid fibrils and mitochondrial membrane. It is suggested that biophysical properties of amyloid fibrils and their specific binding to mitochondrial membranes may provide explanations for some of these observations.

Provided here is a protocol for investigating the interactions between native form, prefibrillar, and mature amyloid fibrils of different peptides and proteins with mitochondria isolated from different tissues and various areas of the brain.

A growing body of evidence indicates that membrane permeabilization, including internal membranes such as mitochondria, is a common feature and primary ...

Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library

Protein dimerization events that occur only in the presence of a small-molecule ligand enable the development of small-molecule biosensors for the dissection and manipulation of biological pathways. Currently, only a limited number of chemically induced dimerization (CID) systems exist and engineering new ones with desired sensitivity and selectivity for specific small-molecule ligands remains a challenge in the field of protein engineering. We here describe a high throughput screening method, combinatorial binders-enabled selection of CID (COMBINES-CID), for the de novo engineering of CID systems applicable to a large variety of ligands. This method uses the two-step selection of a phage-displayed combinatorial nanobody library to obtain 1) &#34;anchor binders&#34; that first bind to a ligand of interest and then 2) &#34;dimerization binders&#34; that only bind to anchor binder-ligand complexes. To select anchor binders, a combinatorial library of over 109 complementarity-determining region (CDR)-randomized nanobodies is screened with a biotinylated ligand and hits are validated with the unlabeled ligand by bio-layer interferometry (BLI). To obtain dimerization binders, the nanobody library is screened with anchor binder-ligand complexes as targets for positive screening and the unbound anchor binders for negative screening. COMBINES-CID is broadly applicable to select CID binders with other immunoglobulin, non-immunoglobulin, or computationally designed scaffolds to create biosensors for in vitro and in vivo detection of drugs, metabolites, signaling molecules, etc.

Creating chemically induced protein dimerization systems with desired affinity and specificity for any given small molecule ligand would have many biological sensing and actuation applications. Here, we describe an efficient, generalizable method for de novo engineering of chemically induced dimerization systems via the stepwise selection of a phage-displayed combinatorial single-domain antibody library.

Protein dimerization events that occur only in the presence of a small-molecule ligand enable the development of small-molecule biosensors for the ...

Quantification of Subcellular Glycogen Distribution in Skeletal Muscle Fibers using Transmission Electron Microscopy

With the use of transmission electron microscopy, high-resolution images of fixed samples containing individual muscle fibers can be obtained. This enables quantifications of ultrastructural aspects such as volume fractions, surface area to volume ratios, morphometry, and physical contact sites of different subcellular structures. In the 1970s, a protocol for enhanced staining of glycogen in cells was developed and paved the way for a string of studies on the subcellular localization of glycogen and glycogen particle size using transmission electron microscopy. While most analyses interpret glycogen as if it is homogeneously distributed within the muscle fibers, providing only a single value (e.g., an average concentration), transmission electron microscopy has revealed that glycogen is stored as discrete glycogen particles located in distinct subcellular compartments. Here, the step-by-step protocol from tissue collection to the quantitative determination of the volume fraction and particle diameter of glycogen in the distinct subcellular compartments of individual skeletal muscle fibers is described. Considerations on how to 1) collect and stain tissue specimens, 2) perform image analyses and data handling, 3) evaluate the precision of estimates, 4) discriminate between muscle fiber types, and 5) methodological pitfalls and limitations are included.

A modified post-fixation procedure increases the contrast of glycogen particles in tissue. This paper provides a step-by-step protocol describing how to handle the tissue, conduct the imaging, and use stereological methods to obtain unbiased and quantitative data on fiber type-specific subcellular glycogen distribution in skeletal muscle.

With the use of transmission electron microscopy, high-resolution images of fixed samples containing individual muscle fibers can be obtained. This ...