Proteomics Analysis Reveals the Implications of Cytoskeleton and Mitochondria in the Response of the Rat Brain to Starvation
Abstract
1. Introduction
2. Materials and Methods
2.1. Chemicals and Drugs
2.2. Animals and Experimental Design
2.3. Protein Extraction for 2-D
2.4. 2-D
2.5. Quantitative Analysis of Gel Images and Statistical Analysis
2.6. Protein Digestion and MS Analysis
2.7. Database Searching
2.8. nLC-MS Proteomics Procedure
2.8.1. Sample Preparation
2.8.2. Protein Digestion
2.8.3. nLC-MS2 Analysis
2.8.4. Data Analysis
2.8.5. Quantitative First-Mass MS1 Data Analysis in Skyline Software
3. Results
4. Discussion
Author Contributions
Acknowledgements
Conflicts of Interest
Abbreviations
2-D | two-dimensional gel electrophoresis |
MS | mass spectrometry |
MALDI-TOF/TO | Matrix-assisted laser desorption-ionization time of flight/time of flight |
nLC-MS | nanoliquid chromatography and MS analysis |
GAPDH | glyceraldehyde-3-phosphate dehydrogenase |
ATP5A1 | α subunit of ATP synthase |
ATP5B | β subunit of ATP synthase |
UQCRC1 | subunit 1 of the cytochrome b-c1 complex |
NDUFS1 | subunit of 75 kDa of NADH-ubiquinone oxidoreductase |
IMMT | MIC60 subunit of the MICOS (internal mitochondrial membrane protein) |
HSPA5 | including 78 kDa glucose-regulated protein |
CALR | calreticulin |
SPTAN1 | α-chain of non-erythrocytic spectine 1 |
GFAP | glial fibrillary acidic protein |
MAP1S | 1S microtubule-associated protein |
SCRN1 | Secernin-1 |
MAGEA11 | melanoma-associated antigen |
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BIOLOGICAL PROCESSES | |
Cytoskeleton organization | CALR, GAPDH, GFAP, MAP1S, SPTAN1 |
Organelle organization | CALR, GAPDH, GFAP, MAP1S, NDUFS1, SPTAN1 |
MOLECULAR FUNCTIONS | |
Proteins binding complex | GAPDH, GFAP, HSPA5, SPTAN1, UQCRC1 |
Transport of protons for ATP synthase activity, rotational mechanisms | ATP5A1, ATP5B |
Binding to unfolded proteins | CALR, HSPA5 |
CELLULAR COMPONENTS | |
Part of intracellular organelles | ATP5A1, ATP5B, CALR, GFAP, HSPA5, IMMT, MAP1S, NDUFS1, SCRN1, SPTAN1, UQCRC1 |
Protein complex of inner mitochondrial membrane | ATP5A1, ATP5B, NDUFS1, UQCRC1 |
Protein complex | ATP5A1, ATP5B, GAPDH, GFAP, HSPA5, MAP1S, NDUFS1, SPTAN1, UQCRC1 |
Inner mitochondrial membrane | ATP5A1, ATP5B, IMMT, NDUFS1, UQCRC1 |
Organelle membranes | ATP5A1, ATP5B, CALR, HSPA5, IMMT, NDUFS1, SCRN1,UQCRC1 |
KEGG PATHWAYS | |
Oxidative phosphorylation | ATP5A1, ATP5B, NDUFS1, UQCRC1 |
Parkinson’s disease | ATP5A1, ATP5B, NDUFS1, UQCRC1 |
Alzheimer’s disease | ATP5A1, ATP5B, NDUFS1, UQCRC1 |
Huntington’s disease | ATP5A1, ATP5B, NDUFS1, UQCRC1 |
Processing and introduction of antigens | CALR, HSPA5 |
Spot a) | Homology | Species | Mw (kDa) | pI | # Peptides b) | Access Number | MOWSE Score c) | Coverage (%) d) |
---|---|---|---|---|---|---|---|---|
501 | SCRN1 | Rattus norvegicus | 46.993 | 4.73 | 8 | sp|Q6AY84|SCRN1 | 68 | 21 |
701 | CALR | Rattus norvegicus | 48.136 | 4.37 | 16 | sp|P18418|CALR_ | 304 | 39 |
1402 | ATP5B | Oryctolagus cuniculus | 45.549 | 5.21 | 22 | tr|Q0QEN9|Q0QEN | 885 | 63 |
1404 | GFAP | Rattus norvegicus | 49.983 | 5.35 | 12 | sp|P47819|GFAP_ | 199 | 32 |
2708 | HSPA5 | Mus musculus | 72.492 | 5.01 | 34 | tr|Q9DC41|Q9DC4 | 646 | 53 |
2807 | SPTAN1 | Mus musculus | 98.016 | 5.17 | 26 | tr|Q3URW8|Q3URW | 210 | 32 |
2808 | IMMT | Rattus norvegicus | 86.689 | 5.62 | 13 | tr|A0A0G2JVH4|A | 75 | 18 |
3404 | UQCRC1 | Rattus norvegicus | 53.499 | 5.57 | 20 | sp|Q68FY0|QCR1_ | 327 | 39 |
3815 | NDUFS1 | Rattus norvegicus | 80.330 | 5.65 | 30 | sp|Q66HF1|NDUS1 | 386 | 46 |
4305 | MAP1S | Monodelphis domestica | 124.777 | 5.97 | 19 | tr|F7BK59|F7BK5 | 68 | 12 |
7506 | ATP5A1 | Rattus norvegicus | 59.889 | 9.29 | 11 | tr|F1LP05|F1LP0 | 92 | 23 |
7604 | MAGEA11 | Heterocephalus glaber | 55.034 | 5.27 | 13 | tr|G5C258|G5C25 | 66 | 19 |
8317 | GAPDH | Mus musculus | 36.072 | 8.44 | 13 | sp|P16858|G3P_M | 174 | 42 |
8319 | GAPDH | Mus musculus | 36.072 | 8.44 | 16 | sp|P16858|G3P_M | 283 | 50 |
Abbreviation | Complete name | Functions |
---|---|---|
SCRN1 | Secernine-1 | Regulates exocytosis in mastocytes |
CALR | Calreticuline | Calcium binding chaperone that promotes folding, oligomeric assembling and quality control in the endoplasmic reticulum by the calreticuline/calnexine cycle |
ATP5B | β subunit of ATP synthase, mitochondrial precursor | ATP synthase located in the mitochondrial membrane that produce ATP from ADP |
GFAP | Glial fibrillar acid protein | Specific cell target that, during development of central nervous system, distinguished astrocytes from other glia cells |
HSPA5 | Heat-shock protein family A (Hsp70) member 5 | Facilitates the assembly of multimeric protein complex in the endoplasmic reticulum |
SPTAN1 | Chain α of non-erythrocyte 1 spectrine | Interacts with calmodulin in a calcium-dependent manner and could participate in the calcium-dependent movement of cytoskeleton to membrane |
IMMT | Mic60 subunit of mitochondrial contact site and cristae organizing system MICOS complex, protein of the inner mitochondrial membrane | Maintenance of architecture of the inner mitochondrial membrane and formation of contact sites with external membrane |
UQCRC1 | Subunit 1 of mitochondrial cytochrome b-c1 | Component of the ubiquinole-cytochrome c reductase |
NDUFS1 | 75kDa subunit of NADH-mitochondrial ubiquinone oxydoreductase | Core subunit of NADH dehydrogenase |
MAP1S | Protein 1S associated to microtubule | Participate in the aggregation of mitochondria from cell death and the genomic breakdown |
ATP5A1 | ATP synthase α subunit, mitochondrial precursor | ATP synthase from mitochondrial membrane |
MAGEA11 | Antigen 11 associated to melanome | Co-regulator of androgen receptor that increases its activity. Involved in calcium homeostasis in endoplasmic reticulum |
GAPDH | Glyceraldehyde-3-phosphate dehydrogenase | Key enzyme of glycolysis |
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Cuevas-Fernández, B.; Fuentes-Almagro, C.; Peragón, J. Proteomics Analysis Reveals the Implications of Cytoskeleton and Mitochondria in the Response of the Rat Brain to Starvation. Nutrients 2019, 11, 219. https://doi.org/10.3390/nu11020219
Cuevas-Fernández B, Fuentes-Almagro C, Peragón J. Proteomics Analysis Reveals the Implications of Cytoskeleton and Mitochondria in the Response of the Rat Brain to Starvation. Nutrients. 2019; 11(2):219. https://doi.org/10.3390/nu11020219
Chicago/Turabian StyleCuevas-Fernández, Beatriz, Carlos Fuentes-Almagro, and Juan Peragón. 2019. "Proteomics Analysis Reveals the Implications of Cytoskeleton and Mitochondria in the Response of the Rat Brain to Starvation" Nutrients 11, no. 2: 219. https://doi.org/10.3390/nu11020219
APA StyleCuevas-Fernández, B., Fuentes-Almagro, C., & Peragón, J. (2019). Proteomics Analysis Reveals the Implications of Cytoskeleton and Mitochondria in the Response of the Rat Brain to Starvation. Nutrients, 11(2), 219. https://doi.org/10.3390/nu11020219