Identification of Reference and Biomarker Proteins in Chlamydomonas reinhardtii Cultured under Different Stress Conditions
Abstract
:1. Introduction
2. Results and Discussion
2.1. Growth of C. reinhardtii Cells under Stress
2.2. Total Protein Alteration of C. reinhardtii Cells under Stress
2.3. Recombinant Protein Expression, Antibody Generation, and Specificity Validation
2.4. Expression Profiling of Candidate Proteins
2.5. Identification of Reference Proteins under Abiotic Stresses
2.6. Identification of Biomarkers under Abiotic Stresses
3. Materials and Methods
3.1. C. reinhardtii Strain and Culture
3.2. Abiotic Stress Treatments
3.3. Detection of Cell Density and Cell Number
3.4. Candidate Proteins
3.5. Recombinant Protein Expression and Antibody Generation
3.6. C. reinhardtii Protein Extraction and Quantification
3.7. Western Blot Analyses
3.8. Pearson’s Correlation Coefficient (PCC) Analysis
3.9. Average Relative Fold Change (ARF) Calculation and Biomarker Selection
4. Conclusions
Supplementary Materials
Supplementary File 1Acknowledgments
Author Contributions
Conflicts of Interest
References
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CK | Dark | 5 °C | 40 °C | NaCl | Glucose | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
OD750 | TP | OD750 | TP | OD750 | TP | OD750 | TP | OD750 | TP | OD750 | TP | TP with * | |
OD750 | 1.000 | 0.988 ** | 1.000 | 0.781 | 1.000 | 0.626 | 1.000 | 0.890 * | 1.000 | 0.844 | 1.000 | 0.935 * | |
FAP127 | 0.913 * | 0.862 | 0.949 * | 0.921 * | 0.634 | 0.905 * | 0.133 | 0.434 | 0.948 * | 0.633 | 0.999 ** | 0.933 * | 3 |
Histone H3 | 0.957 * | 0.950 * | 0.685 | 0.827 | 0.697 | 0.937 * | 0.722 | 0.916 * | 0.963 ** | 0.949 * | 0.879 * | 0.713 | 4 |
TUB-1 | 0.953 * | 0.949 * | 0.787 | 0.769 | 0.480 | 0.956 * | 0.819 | 0.982 ** | 0.903 * | 0.986 ** | 0.930 * | 0.765 | 4 |
RCK1 | 0.945 * | 0.944 * | 0.996 ** | 0.808 | 0.491 | 0.868 | −0.870 | −0.849 | 0.948 * | 0.769 | 0.994 ** | 0.899 * | 2 |
D1 | 0.977 ** | 0.946 * | −0.541 | −0.336 | 0.208 | 0.650 | 0.812 | 0.974 ** | 0.997 ** | 0.804 | 0.968 ** | 0.865 | 2 |
OEE2 | 0.974 ** | 0.969 ** | 0.937 * | 0.866 | 0.439 | 0.742 | 0.737 | 0.952 * | 0.944 * | 0.963 ** | 0.984 ** | 0.868 | 3 |
RBCL | 0.929 * | 0.895 * | 0.862 | 0.919 * | 0.800 | 0.881 * | 0.914 * | 0.921 * | 0.938 * | 0.771 | 0.984 ** | 0.879 * | 5 |
RBCS2 | 0.883 * | 0.862 | 0.856 | 0.896 * | 0.747 | 0.978 ** | 0.449 | 0.778 | 0.914 * | 0.615 | 0.795 | 0.876 | 2 |
RMT1 | 0.819 | 0.787 | −0.678 | −0.491 | 0.912 * | 0.799 | 0.901 * | 0.954 * | 0.938 * | 0.637 | 0.975 ** | 0.959 ** | 2 |
ATPs-6 | 0.939 * | 0.918 * | 0.920 * | 0.958 * | −0.666 | −0.944 * | 0.920 * | 0.996 ** | 0.959 ** | 0.782 | 0.962 ** | 0.994 ** | 5 |
ATPs-A | 0.384 | 0.279 | 0.986 ** | 0.818 | 0.523 | 0.917 * | 0.964 ** | 0.889 * | 0.932 * | 0.919 * | 0.778 | 0.592 | 3 |
BCR1 | 0.961 ** | 0.982 ** | −0.125 | −0.002 | 0.745 | 0.836 | - | - | 0.884 * | 0.681 | 0.929 * | 0.790 | 1 |
FAB2 | 0.915 * | 0.914 * | −0.286 | 0.207 | 0.668 | 0.973 ** | 0.958 * | 0.982 ** | 0.915 * | 0.774 | −0.815 | −0.851 | 3 |
GAP2 | 0.903 * | 0.957 * | 0.893 * | 0.824 | 0.701 | 0.991 ** | −0.275 | 0.071 | 0.798 | 0.577 | 0.973 ** | 0.963 ** | 3 |
MPC1 | 0.762 | 0.708 | 0.930 * | 0.944 * | 0.854 | 0.899 * | 0.000 | 0.315 | 0.831 | 0.431 | 0.804 | 0.836 | 2 |
HSP70A | 0.900 * | 0.848 | 0.951 * | 0.920 * | 0.515 | 0.764 | −0.045 | 0.287 | 0.844 | 0.922 * | 0.985 ** | 0.901 * | 3 |
HSP90B | 0.531 | 0.457 | 0.827 | 0.668 | 0.860 | 0.838 | 0.149 | 0.361 | 0.778 | 0.427 | 0.770 | 0.804 | 0 |
Protein with * | 13(11)11 | 8(4)6 | 1(0)10 | 5(5)9 | 13(4)5 | 12(7)7 |
No. | Gene Name | Au10_Locus/ID | Category | Subcellular Localization | Annotation | MW (kD) | Antigen Sequence | References |
---|---|---|---|---|---|---|---|---|
1 | FAP127 | Cre17.g737100 | Structure | Motile cilium | Flagellar associated protein | 51 | YSEGLQEDKKIRN | |
2 | Histone H3 | Cre06.g268350 | Structure | Nucleus | Histone H3 | 15 | TELLIRKLPFQRLV | [28] |
3 | IC2 | Cre12.g506000 | Structure | Flagella | Flagellar outer dynein arm Intermediate chain 2 | 64 | WDLRKMNECVENMPL | [33,42] |
4 | TUB-1 | Cre12.g542250 | Structure | Cytoskeleton | Beta tubulin 1 | 50 | QYQDATADEEGEYEDEEQQ | |
5 | FKBP12 | Cre13.g586300 | Signaling | Endoplasmic reticulum | Peptidyl-prolyl cis-trans isomerase FKBP-type | 12 | Expressed protein (Full length) | [43] |
6 | RCK1 | Cre06.g278222 | Signaling | Whole cell | Receptor of activated protein kinase C1 | 35 | Expressed protein (Full length) | [44] |
7 | D1 | NP_958377.1 | Photosynthesis | Chloroplast | Photosystem II protein D1 | 39 | IRETTENESANE | [26] |
8 | OEE2 | Cre12.g550850 | Photosynthesis | Chloroplast | Oxygen-evolving enhancer protein 2 of photosystem II | 30 | Expressed protein (Full length) | [45] |
9 | RBCL | NP_958405.1 | Photosynthesis | Chloroplast | Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (chloroplast) | 53 | MRDDYVEKDRSR | [46] |
10 | RBCS2 | Cre02.g120150 | Photosynthesis | Chloroplast | Ribulose-15-bisphosphate carboxylase/oxygenase small subunit 2 | 21 | QRPKSARDWQPA | |
11 | RMT1 | Cre16.g661350 | Photosynthesis | Chloroplast | Rubisco large subunit N-methyltransferase | 52 | LRPSMTYSITPDQQ | |
12 | ATPs-6 | Cre01.g018800 | Metabolism | Mitochondria | Mitochondrial F1F0 ATP synthase subunit 6 | 35 | NMMAGHSSVKILSG | |
13 | ATPs-A | ACS16334 | Metabolism | Mitochondria | ATP synthase CF0 A subunit, partial (chloroplast) | 13 | AGLSKKGLSYFEKY | |
14 | ATPs-β | Cre17.g698000 | Metabolism | Mitochondria | ATP synthase CF1 beta subunit | 53 | FAGVGERTREGNDL | [22] |
15 | BCR1 | Cre08.g359350 | Metabolism | Chloroplast | Biotin carboxylase (ACCase complex) | 56 | EFVEICTDHGLEFIG | [47] |
16 | FAB2 | Cre17.g701700 | Metabolism | Chloroplast | Plastid acyl-ACP desaturase, d-9 stearate desaturase | 45 | DEGRHEIAYCKIMDG | [47] |
17 | GAP2 | Cre07.g354200 | Metabolism | Whole cell | Glyceraldehyde 3-phosphate dehydrogenase | 40 | DLVSTDFQGDNRSSIFDAKAGI | [48] |
18 | MPC1 | Cre03.g172300 | Metabolism | Integral component of membrane | Mitochondrial phosphate carrier protein | 37 | DVAKKTDSTKYAMP | |
19 | HSP70A | Cre08.g372100 | HSP | Whole cell | Heat shock protein 70A | 71 | EQVFSTYSDNQPGV/Expressed protein (N-terminal) | [19] |
20 | HSP90B | Cre17.g730950 | HSP | Whole cell | Heat shock protein 90B | 87 | GKDSKLKDLKESFK |
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Shi, J.; Huang, T.; Chai, S.; Guo, Y.; Wei, J.; Dou, S.; Li, L.; Liu, G. Identification of Reference and Biomarker Proteins in Chlamydomonas reinhardtii Cultured under Different Stress Conditions. Int. J. Mol. Sci. 2017, 18, 1822. https://doi.org/10.3390/ijms18081822
Shi J, Huang T, Chai S, Guo Y, Wei J, Dou S, Li L, Liu G. Identification of Reference and Biomarker Proteins in Chlamydomonas reinhardtii Cultured under Different Stress Conditions. International Journal of Molecular Sciences. 2017; 18(8):1822. https://doi.org/10.3390/ijms18081822
Chicago/Turabian StyleShi, Jianan, Teng Huang, Shuaijie Chai, Yalu Guo, Jian Wei, Shijuan Dou, Liyun Li, and Guozhen Liu. 2017. "Identification of Reference and Biomarker Proteins in Chlamydomonas reinhardtii Cultured under Different Stress Conditions" International Journal of Molecular Sciences 18, no. 8: 1822. https://doi.org/10.3390/ijms18081822