Method Article
The fission yeast Schizosaccharomyces pombe is emerging as an attractive model for studying mitochondria. Here, we describe a protocol for analyzing the abundance and assembly of the mitochondrial respiratory complexes in S. pombe. This enables the characterization of conserved genes' novel functions in the mitochondrial respiratory chain.
The mitochondrial respiratory chain is crucial for cellular energy metabolism, serving as the core of oxidative phosphorylation. The mitochondrial respiratory chain comprises five enzyme complexes and their interacting supercomplexes. Analysis of the expression and complexes assembly of these proteins is vital to understanding mitochondrial function. This can be studied by combining biochemical and genetic methods in an excellent model organism fission yeast Schizosaccharomyces pombe (S. pombe), which provides a compensatory system to budding yeast for studies of mitochondrial biology. Here, we present a detailed protocol for the isolation of S. pombe mitochondria and analysis of expression levels and complexes assembly of the mitochondrial respiratory proteins by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and blue native-PAGE (BN-PAGE). Briefly, mitochondria from the wild-type and gene mutants are purified, and then their complexes are solubilized and subjected to SDS-PAGE/BN-PAGE and immunoblotting. This method enables the characterization of a gene's novel function in the mitochondrial respiratory chain.
Mitochondria play important roles in diverse biological processes, such as cellular respiration for energy, nutritional metabolism, and cell death1. The malfunction of mitochondria is related to brain, muscle, and developmental diseases2,3. Therefore, studies on mitochondria are vital to improve human aging and health.
The budding yeast Saccharomyces cerevisiae (S. cerevisiae) has long been used to study the functions of genes in mitochondria4 because yeast mutants defective in respiration can still produce energy for survival by fermentation. However, it is petite-positive and can proliferate without mitochondrial DNA (mtDNA). Consequently, the gene mutants defective in mitochondrial gene expression often lose their mtDNA, which complicates further study. In contrast, the fission yeast Schizosaccharomyces pombe (S. pombe), which is evolutionarily distant from S. cerevisiae, is a petite-negative yeast that requires mtDNA for survival. Moreover, the organization of mtDNA and mitochondrial mRNA of S. pombe is similar to those of higher eukaryotes5. Many (96) essential genes in S. pombe, compared to only six essential genes in S. cerevisiae, are required for mitochondrial gene expression6. Thus, S. pombe is emerging as an attractive model to study novel functions of genes in mitochondria. However, the number of publications studying mitochondria in S. cerevisiae is about 100-fold more than that in S. pombe, and the reported methods and protocols studying mitochondria in S. pombe are also scarce7.
The mitochondrial respiratory chain is crucial for cellular energy production and serves as a core of mitochondria8. It comprises respiratory chain complexes I-V, such as NADH-ubiquinone oxidoreductase (Complex I), succinate dehydrogenase (Complex II), ubiquinone-cytochrome c oxidoreductase or cytochrome bc1 complex (Complex III), cytochrome c oxidase (Complex IV), and ATP synthase (Complex V), together with two intermediary substrates carrying electron, ubiquinone (CoQ) and cytochrome c (Cyt c)9. They also interact and form higher-order supercomplexes, whose assembly mechanisms remain largely unclear10,11. However, S. pombe lacks complex I, which may be replaced by external NADH dehydrogenases Nde1 and internal Ndi112,13,14. The mitochondrial genome in S. pombe encodes a subunit of complex III (Cob1), three subunits of complex IV (Cox1, Cox2, Cox3), and three subunits of complex V (Atp6, Atp8, Atp9)15,16. We have recently reported that the expression and complexes assembly of these proteins are affected by the deletion of RNA helicase Mss116 (Δmss116)16 and assembly factor Shy1 (Δshy1)15 in S. pombe, respectively. To facilitate the discovery of more genes' novel functions in the mitochondrial respiratory chain using these methods, here we provide a detailed protocol for SDS-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the expression levels and blue native-PAGE (BN-PAGE) analysis of complexes assembly of the mitochondrial respiratory chain proteins in S. pombe.
The rationale behind the isolation of mitochondria from S. pombe is based on the methods established in S. cerevisiae17. The spheroplasts are first prepared by digesting yeast cell walls. They are mechanically homogenized, and the mitochondria are fractionated by differential centrifugation18. Subsequently, the mitochondrial respiratory chain proteins are solubilized and immunoblotted following SDS-PAGE and BN-PAGE. The BN-PAGE technique was originally developed for the separation of mitochondrial membrane proteins such as respiratory chain complexes19,20,21. The membrane proteins with preserved intact complexes are solubilized by mild nonionic detergents and charged by anionic dye Coomassie G-250. Thus, protein complexes are separated according to their mass in a gradient native-PAGE gel22. This method has been widely used for studying mitochondrial respiratory chain complexes in S. cerevisiae23 and mammalian cells24,25; however, it has not been extensively applied to S. pombe mitochondria.
Collectively, here we present a method in which mitochondria are isolated from S. pombe cells, and the mitochondrial respiratory chain proteins are subjected to SDS-PAGE and BN-PAGE followed by immunoblotting. The experimental flowchart is illustrated in Figure 1. With high-quality mitochondria and antibodies, this method described in S. pombe can also be applied to other organisms to identify more genes with functions in the expression and/or complexes assembly of mitochondrial respiratory chain proteins.
1. Preparation of S. pombe spheroplasts
2. Mechanical homogenization of S. pombe spheroplasts
3. Isolation of S. pombe mitochondria by centrifugation
4. SDS-PAGE and immunoblotting of mitochondrial respiratory chain proteins
5. Mitochondrial sample preparation for BN-PAGE
6. BN-PAGE and immunoblotting of mitochondrial respiratory chain complexes
We previously used this protocol to investigate the effects of the deletion of shy1, the S. pombe homolog of human SURF1, on the expression of mtDNA-encoded respiratory chain proteins and the assembly of mitochondrial respiratory chain complexes. We found that the steady-state levels of Cob1, Cox1, Cox2, Cox3, and Atp6 were significantly reduced in the Δshy1 strain (Figure 3), indicating that Shy1 is required for the expression of respiratory chain proteins encoded by mtDNA. Furthermore, the BN-PAGE analysis showed that the abundance of DG-solubilized respiratory chain supercomplexes III2IV2 and III2IV was reduced by shy1 deletion, whereas the abundance of supercomplexes III2 and V/Vn was not significantly altered in Δshy1 cells (Figure 4A). Additionally, the abundance of DDM-solubilized dimeric complex III (III2) was unchanged in the Δshy1 strain (Figure 4B). These BN-PAGE data indicate that Shy1 is also required for the formation of respiratory chain supercomplexes involving complex IV.
Figure 1: Experimental flowchart. Please click here to view a larger version of this figure.
Figure 2: Microscopic images of S. pombe cells during mitochondria isolation. (A) The normal rod shape of S. pombe cells before cell wall digestion. (B) The round shape of S. pombe spheroplasts after cell wall digestion. (C) The broken S. pombe spheroplasts after cell homogenization. Scale bars = 10 µm. Please click here to view a larger version of this figure.
Figure 3: Immunoblots of the mtDNA-encoded mitochondrial respiratory chain proteins following SDS-PAGE in S. pombe strains WT and Δshy1. The steady-state levels of mitochondrial respiratory chain proteins encoded by mtDNA were detected by SDS-PAGE and immunoblotting using the indicated antibodies against Cob1, Cox1, Cox2, Cox3, and Atp6. Hsp60 serves as a loading control. This figure has been modified from Luo et al.15. The raw blots are included in Supplementary Figure 1. Please click here to view a larger version of this figure.
Figure 4: Immunoblots of the mitochondrial respiratory chain complexes following BN-PAGE in S. pombe strains WT and Δshy1. (A) The abundance of mitochondrial respiratory chain supercomplexes solubilized by detergent DG was detected by BN-PAGE and immunoblotting using the indicated antibodies against Cob1, Cox1, and Atp6. Hsp60 serves as a loading control. (B) The abundance of mitochondrial respiratory chain dimeric complex III solubilized by detergent DDM was detected by BN-PAGE and immunoblotting using the indicated antibody against Cob1. Hsp60 serves as a loading control. This figure has been modified from Luo et al.15. The raw blots are included in Supplementary Figure 2. Please click here to view a larger version of this figure.
Reagents | Final Concentration |
Yeast extract | 0.5% |
Glucose | 3% |
Adenine | 0.02% |
Uracil | 0.02% |
Histidine | 0.02% |
Leucine | 0.02% |
Lysine | 0.02% |
Table 1: Components of YES medium for culture the S. pombe cells.
Reagents | Final Concentration |
Sorbitol | 1.4 M |
HEPES (pH 6.5, adjusted with KOH) | 40 mM |
MgCl2 | 0.5 mM |
Table 2: Components of 1x S buffer for suspending the S. pombe spheroplasts.
Reagents | Final Concentration |
Sorbitol | 600 mM |
Tris (pH 7.5, adjusted with HCl) | 10 mM |
EDTA | 1 mM |
PMSF | 1 mM |
Table 3: Components of 1x homogenization buffer for grinding the S. pombe spheroplasts.
Reagents | Final Concentration |
Sucrose | 250 mM |
MOPS (pH 7.2, adjusted with KOH) | 10 mM |
EDTA | 1 mM |
Table 4: Components of 1x SEM buffer for suspending the S. pombe mitochondria.
Reagents | Final Concentration |
6-Aminocaproice acid | 750 mM |
Bis-Tris (pH 7.0, adjusted with HCl) | 50 mM |
EDTA | 0.5 mM |
Coomassie Brilliant Blue G-250 | 5% |
Table 5: Components of 3x BN-PAGE sample buffer for preparing protein sample used in BN-PAGE. Coomassie G-250 should be completely dissolved with sonication.
Reagents | Volume | |
3% | 12% | |
40% Acrylamide/Bis (37.5 : 1) | 380 μL | 1.5 mL |
3× BN-PAGE Gel Buffer | 1.67 mL | 1.67 mL |
50% Glycerol | - | 1 mL |
10% Ammonium persulfate | 32 μL | 20 μL |
TEMED | 3.2 μL | 2 μL |
ddH2O | 2.92 mL | 810 μL |
Total Volume | 5 mL | 5 mL |
Table 6: Components of 3% and 12% BN-PAGE gel for preparing handmade BN-PAGE gradient gel.
Reagents | Final Concentration |
Tris (pH 8.0, adjusted with HCl) | 48 mM |
Glycine | 39 mM |
SDS | 0.0375% |
Methanol | 20% |
Table 7: Components of 1x BN-PAGE transfer buffer for transferring proteins in BN-PAGE gel.
Reagents | Final Concentration |
Tris (pH 8.0, adjusted with HCl) | 50 mM |
NaCl | 150 mM |
Tween-20 | 0.1% |
Table 8: Components of 1x TBST buffer for immunoblotting.
Supplementary Figure 1: Raw SDS-PAGE blots for S. pombe strains WT and Δshy1. Please click here to download this File.
Supplementary Figure 2: Raw BN-PAGE blots of S. pombe strains WT and Δshy1. Please click here to download this File.
In this study, we present a detailed protocol for isolating S. pombe mitochondria and performing SDS-PAGE and BN-PAGE to analyze the expression and complexes assembly of mitochondrial respiratory chain proteins.
Co-immunoprecipitation (co-IP) has been commonly used to detect the assembly of protein complexes; however, it is challenging for co-IP to detect the assembly of mitochondrial membrane proteins. Instead, BN-PAGE has several advantages: (i) some antibodies cannot recognize the epitopes buried in the native protein complexes during co-IP, but they work for immunoblotting upon BN-PAGE; (ii) the large membrane protein complexes tend to aggregate during co-IP, but this tendency is reduced by negatively charged Coomassie G-250 in BN-PAGE; (iii) it is difficult for co-IP to convert membrane proteins to water-soluble proteins by mild detergents NP-40 or Triton X-100 without perturbing respiratory chain complexes, but Coomassie G-250 in BN-PAGE can solubilize the membrane proteins22.
The first critical step in this protocol is the preparation of spheroplasts by digesting the cell wall, which is a key difference in isolating mitochondria between S. pombe and S. cerevisiae. To efficiently disrupt S. pombe spheroplasts and release mitochondria by mechanical homogenization, the shape of S. pombe spheroplasts should alter from rod to round in an isotonic buffer. However, the S. pombe cell walls are much more resistant to digestion than those of S. cerevisiae26. Therefore, the preparation of S. pombe spheroplasts requires more lytic enzymes and incubation time, which increases the risks of the degradation and/or disassembly of S. pombe mitochondrial respiratory chain complexes. Accordingly, high-quality lytic enzymes and proper digestion of cell walls are crucial for maintaining the integrity of mitochondrial complexes. Second, the amounts of mitochondrial proteins loaded into the BN-PAGE gel should not be fewer than 100 µg; otherwise, it is difficult to detect all the types of respiratory chain complexes23. Third, the high quality of antibodies against S. pombe mitochondrial respiratory chain proteins is important to detect the correct bands of the corresponding proteins or complexes. Thus, the careful validation of relevant antibodies is requested prior to performing this experiment, particularly for the model organisms.
The reproducibility of BN-PAGE results of mitochondrial respiratory chain proteins in S. pombe is challenging15. The quality of isolated mitochondria is the major variable. To control it, first, mitochondrial respiratory chain proteins should be reliably detected by the normal SDS-PAGE and immunoblotting. Second, the concentration and treated time of detergent DG or DDM can be adjusted according to detected types of mitochondrial respiratory chain complexes. For example, the diverse types of DG-solubilized supercomplexes formed by complex III and IV are not always detected reliably by the antibody against complex III subunit Cob1 or complex IV subunit Cox1. Given that Cob1 or Cox1 is not degraded during mitochondria isolation, the supercomplexes could be incompletely solubilized by DG from a batch of isolated mitochondria. Therefore, the concentration and treatment time of DG could be increased to troubleshoot this problem. Additionally, the DDM-solubilized individual complex could not be detected in the BN-PAGE gel, possibly due to the degradation or disassembly of complexes caused by the treatment of the aggressive detergent. Thus, the concentration and treatment time of DDM could be decreased to solve this problem.
One limitation of the method is that the quality of data heavily relies on the high quality of two reagents, lytic enzymes, and antibodies. The commercial Zymolyase-100T or Lallzyme is recommended. Another limitation is that S. pombe cells only have conserved mitochondrial respiratory chain complex II, III, IV, and V. We cannot get insight into the expression and assembly of complex I using this method in S. pombe, but the complex I can be analyzed in the filamentous fungi Podospora anserina27.
Despite these limitations, this method enables the characterization of genes' novel functions in the mitochondrial respiratory chain, which could be conserved in higher eukaryotes but is absent or different in S. cerevisiae. Our previous studies have provided such proofs-of-principle. If a gene mutation in S. pombe affects the abundance of mitochondrial respiratory chain complexes but not that of individual proteins, it is possible for the genes to function in the assembly of respiratory chain complexes. If the abundance of both complexes and individual proteins is influenced, the gene may play a role in the transcription or translation of mitochondrial respiratory chain proteins. In addition, many essential genes in S. pombe but not in S. cerevisiae play roles in mitochondria; however, their mechanisms remain largely unknown. Combined with the tools studying essential genes in S. pombe and this method, we can gain deep insights into the functions of essential genes in the mitochondrial respiratory chain, which are technically limited in mammalian cells.
We have no conflicts of interest.
We thank Dr. Ying Huang and Dr. Ying Luo for their support. This work was supported by grants (32270048 to J. S. and 31900403 to G. F.) from the National Natural Science Foundation of China.
Name | Company | Catalog Number | Comments |
6-Aminocaproice acid | Sangon | A430196 | |
Acrylamide/Bis (37.5: 1) 40% | Biolab | GS1374 | |
Ammonium persulfate | Sangon | A100486 | |
Anti-Atp6 antibody | Bioworld | in-house | IB: 1:200 |
Anti-Cob1 antibody | Bioworld | in-house | IB: 1:1000 |
Anti-Cox1 antibody | Bioworld | in-house | IB: 1:2000 |
Anti-Cox2 antibody | Bioworld | in-house | IB: 1:1000 |
Anti-Cox3 antibody | Bioworld | in-house | IB: 1:200 |
Anti-Hsp60 antibody | Bioworld | in-house | IB: 1:3000 |
BCA Protein Quantification Kit | LEAGENE | PT0001 | |
Bis-Tris | YEASEN | 60105ES25 | |
Coomassie Brilliant Blue G-250 | SERVA | 17524.01 | |
Coomassie Brilliant Blue R-250 | Sangon | A100472 | |
Digitonin | Sigma | D141 | |
D-Sorbitol | Sangon | A100691 | |
EDTA | Solarbio | E8030 | |
Gradient mixer | Millet scientific | MGM-50 | |
HEPES | Solarbio | H8090 | |
High molecular weight protein marker for native PAGE | Real Times | RTD6142 | |
IgG-Alexa Fluor Plus 800 (anti-rabbit secondary antibody) | Thermo Fisher | A32735 | IB: 1:10000 |
Immobilon-FL 0.45 μm PVDF membrane | Millipore | IPFL00005 | |
Kimble Kontes Dounce tissue grinder | Thermo Fisher | K8853000015 | |
KOH | Sangon | A610441 | |
Lallzyme MMX | Lallemand | N.A. | |
Lysing enzyme | Sigma | L3768 | |
Lyticase | Sigma | L4025 | |
MgCl2 | Sangon | A601336 | |
MOPS | Sangon | A421333 | |
Native Bis-Tris Gels (precast) | Solarbio | PG41510-N | |
PMSF | Sangon | A610425 | |
Precast Gel Running buffer for Native-PAGE | Solarbio | PG00020-N | |
Protease inhibitor cocktail for yeast extracts | Beyotime | P1020 | |
Sucrose | Sangon | A610498 | |
TEMED | Sigma | T9281 | |
Tricine | Sigma | T0377 | |
Tween-20 | Solarbio | T8220 | |
Vinotaste | Novozymes | N.A. | |
Zymolyase | MP Biomedicals | 320921 |
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