Re-adaption on Earth after Spaceflights Affects the Mouse Liver Proteome
Abstract
:1. Introduction
2. Results
3. Discussion
4. Materials and Methods
4.1. Samples
4.2. Sample Preparation
4.3. LC-MS/MS
4.4. Data Processing
4.5. Statistical Analysis
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
Abbreviations
PPAR | Peroxisome proliferator-activated receptor |
FDR | False discovery rates |
CYP | Cytochrome P450 |
FASP | Filter aided sample preparation |
LFQ | Label-free quantification |
NAFLD | Non-alcoholic fatty liver disease |
FABP | Fatty acid binding protein |
ID | Identification number |
GOCC | GeneOntology cell compartment |
GOMF | GeneOntology molecular function |
GOBP | GeneOntology biological process |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
References
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Type | Name | p-Value | Enrichment | Total | In Cluster | Cluster Size | Benj. Hoch. FDR |
---|---|---|---|---|---|---|---|
Cluster A: Significantly Higher Protein Levels in Post-flight Group | |||||||
GOCC name | Ribonucleoprotein complex | 1.62 × 10−14 | 1.92 | 55 | 52 | 218 | 1.90 × 10−12 |
KEGG name | Ribosome | 1.70 × 10−11 | 1.97 | 38 | 37 | 218 | 3.13 × 10−9 |
GOBP name | Cellular amino acid metabolic process | 2.23 × 10−12 | 1.82 | 59 | 53 | 218 | 7.79 × 10−9 |
GOBP name | Cellular nitrogen compound metabolic process | 1.07 × 10−11 | 1.54 | 116 | 88 | 218 | 1.87 × 10−8 |
GOMF name | Structural constituent of ribosome | 3.68 × 10−11 | 1.97 | 37 | 36 | 218 | 3.37 × 10−8 |
GOBP name | Nitrogen compound metabolic process | 3.29 × 10−11 | 1.52 | 119 | 89 | 218 | 3.83 × 10−8 |
GOCC name | Mitochondrial matrix | 1.69 × 10−9 | 1.91 | 36 | 34 | 218 | 9.86 × 10−8 |
GOBP name | Cellular amine metabolic process | 6.56 × 10−10 | 1.71 | 63 | 53 | 218 | 5.73 × 10−7 |
GOBP name | Translation | 1.69 × 10−9 | 1.91 | 36 | 34 | 218 | 9.81 × 10−7 |
GOBP name | Macromolecule biosynthetic process | 1.41 × 10−9 | 1.76 | 53 | 46 | 218 | 9.84 × 10−7 |
Cluster B: Significantly Lower Protein Levels in Post-flight Group | |||||||
GOCC name | Membrane part | 1.04 × 10−30 | 1.65 | 173 | 145 | 224 | 4.85 × 10−28 |
GOCC name | Intrinsic to membrane | 6.62 × 10−23 | 1.80 | 102 | 93 | 224 | 1.03 × 10−20 |
GOCC name | Integral to membrane | 6.62 × 10−23 | 1.80 | 102 | 93 | 224 | 1.55 × 10−20 |
GOCC name | Organelle membrane | 3.49 × 10−14 | 1.47 | 157 | 117 | 224 | 3.26 × 10−12 |
GOCC name | Endoplasmic reticulum part | 7.21 × 10−12 | 1.72 | 69 | 60 | 224 | 5.63 × 10−10 |
GOCC name | Endoplasmic reticulum | 5.52 × 10−11 | 1.84 | 46 | 43 | 224 | 3.69 × 10−9 |
GOCC name | Endoplasmic reticulum membrane | 2.47 × 10−9 | 1.72 | 54 | 47 | 224 | 1.28 × 10−7 |
GOCC name | Plasma membrane part | 5.85 × 10−8 | 1.67 | 52 | 44 | 224 | 2.74 × 10−6 |
GOCC name | Membrane | 4.95 × 10−7 | 1.19 | 260 | 157 | 224 | 2.10 × 10−5 |
GOMF name | Transporter activity | 1.46 × 10−6 | 1.78 | 31 | 28 | 224 | 2.67 × 10−4 |
Protein Name | Uniprot ID | Fold Change: Control/Post-flight | Fold Change: Flight/Post-flight | Student’s t-Test q-Value | ANOVA q-Value |
---|---|---|---|---|---|
Bile Secretion1 | |||||
Solute carrier organic anion transporter family member 1B2 | Q9JJL3 | - | 1.7 | 0.0187 | 0.0143 |
ATP-binding cassette sub-family G member 2 | Q7TMS5 | - | 2.7 | 0.0106 | 0.0131 |
Scavenger receptor class B member 1 | Q4FK30 | * | >0.05 | 0.0198 | |
Solute carrier family 22 member 1 | O08966 | * | >0.05 | 0.0197 | |
Sodium/potassium-transporting ATPase subunit β-1 | Q545P0 | - | 1.6 | 0.0127 | 0.0132 |
Sodium/potassium-transporting ATPase subunit beta-3 | Q544Q7 | - | 2.4 | 0.0171 | 0.0116 |
Aquaporin-1 | Q02013 | * | >0.05 | 0.0211 | |
Solute carrier organic anion transporter family member 1A1 | Q53ZW9 | - | 4.0 | 0.0293 | 0.0291 |
Sodium/potassium-transporting ATPase subunit alpha-1 | Q8VDN2 | 1.9 | 1.6 | 0.0165 | 0.0122 |
Epoxide hydrolase 1 | Q9D379 | - | 1.9 | 0.0077 | 0.0278 |
PPAR Signaling Pathway 1 | |||||
Long-chain specific acyl-CoA dehydrogenase, mitochondrial | P51174 | - | 0.6 | 0.0340 | 0.0374 |
Long-chain-fatty-acid--CoA ligase 1 | D3Z041 | - | 1.9 | 0.0052 | 0.0075 |
Very long-chain acyl-CoA synthetase | O35488 | - | 1.5 | 0.0247 | 0.0341 |
Cytochrome P450 4A10 | O88833 | * | >0.05 | 0.0154 | |
Fatty acid-binding protein, liver | Q3V2F7 | - | 3.9 | 0.0080 | 0.0187 |
Acyl-CoA-binding protein | Q548W7 | * | >0.05 | 0.0374 | |
Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | P45952 | 0.5 | 0.6 | 0.0457 | 0.0132 |
Carnitine O-palmitoyltransferase 2, mitochondrial | P52825 | - | 1.7 | 0.0110 | 0.0115 |
Carnitine O-palmitoyltransferase 1, liver isoform | Q7TQD5 | * | >0.05 | 0.0153 | |
CD36 antigen, isoform CRA_a | Q3UAI3 | - | 2.1 | 0.0044 | 0.0255 |
Cytochrome P450 4A12A | Q91WL5 | - | 5.0 | 0.0113 | 0.0128 |
Peroxisomal bifunctional enzyme | Q9DBM2 | - | 0.6 | 0.0141 | 0.0116 |
Phosphoenol pyruvate carboxy kinase, cytosolic [GTP] | Q9Z2V4 | * | >0.05 | 0.0271 | |
Retinol Metabolism 1 | |||||
Cytochrome P450 1A2 | B6VGH4 | - | 2.7 | 0.0117 | 0.0125 |
Cytochrome P450 2B10 | Q9WUD0 | * | >0.05 | 0.0120 | |
Cytochrome P450 4A10 | O88833 | * | >0.05 | 0.0154 | |
Cytochrome P450 3A11 | Q3UEN8 | - | 0.7 | 0.0198 | 0.0166 |
UDP-glucuronosyltransferase | Q3UEP4 | - | 2.1 | 0.0167 | 0.0132 |
Cytochrome P450 3A13 | Q3UW87 | - | 0.4 | 0.0121 | 0.0279 |
UDP-glucuronosyltransferase 1-1 | Q63886 | - | 1.2 | 0.0420 | 0.0185 |
UDP-glucuronosyltransferase 1-6 | Q64435 | - | 2.0 | 0.0179 | 0.0410 |
Cytochrome P450 2C54 | Q6XVG2 | * | >0.05 | 0.0476 | |
UDP-glucuronosyltransferase 2A3 | Q8BWQ1 | - | 1.9 | 0.0109 | 0.0132 |
UDP-glucuronosyltransferase | Q8K154 | - | 1.9 | 0.0172 | 0.0126 |
UDP-glucuronosyltransferase | Q8R084 | - | 3.5 | 0.0118 | 0.0119 |
Cytochrome P450 2C70 | Q91W64 | * | >0.05 | 0.0340 | |
Cytochrome P450 4A12A | Q91WL5 | - | 5.0 | 0.0113 | 0.0128 |
Dehydrogenase/reductase SDR family member 4 | Q99LB2 | - | 1.7 | 0.0108 | 0.0131 |
Cytochromes 2 | |||||
Cytochrome P450 2D26 | Q8CIM7 | 1.5 | - | 0.0474 | 0.0120 |
Cytochrome P450 4V3 | B2RSR0 | - | 2.3 | 0.0175 | 0.0176 |
Cytochrome P450 1A2 | B6VGH4 | - | 2.7 | 0.0117 | 0.0125 |
Cytochrome P450 2B10 | Q9WUD0 | * | >0.05 | 0.0120 | |
Cytochrome P450 4A10 | O88833 | * | >0.05 | 0.0154 | |
Cytochrome P450 2D9 | P11714 | - | 6.1 | 0.0117 | 0.0106 |
Cytochrome P450 2D10 | P24456 | - | 2.1 | 0.0134 | 0.0152 |
Cytochrome P450 2F2 | P33267 | - | 1.6 | 0.0264 | 0.0198 |
Cytochrome P450 3A11 | Q3UEN8 | - | 0.7 | 0.0198 | 0.0166 |
Cytochrome P450 3A13 | Q3UW87 | - | 0.4 | 0.0121 | 0.0279 |
Cytochrome P450 2C54 | Q6XVG2 | * | >0.05 | 0.0476 | |
Cytochrome P450 2C70 | Q91W64 | * | >0.05 | 0.0340 | |
Cytochrome P450 4A12A | Q91WL5 | - | 5.0 | 0.0113 | 0.0128 |
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Anselm, V.; Novikova, S.; Zgoda, V. Re-adaption on Earth after Spaceflights Affects the Mouse Liver Proteome. Int. J. Mol. Sci. 2017, 18, 1763. https://doi.org/10.3390/ijms18081763
Anselm V, Novikova S, Zgoda V. Re-adaption on Earth after Spaceflights Affects the Mouse Liver Proteome. International Journal of Molecular Sciences. 2017; 18(8):1763. https://doi.org/10.3390/ijms18081763
Chicago/Turabian StyleAnselm, Viktoria, Svetlana Novikova, and Victor Zgoda. 2017. "Re-adaption on Earth after Spaceflights Affects the Mouse Liver Proteome" International Journal of Molecular Sciences 18, no. 8: 1763. https://doi.org/10.3390/ijms18081763