Name: phosphoproteomic strategy for profiling osmotic stress signaling in arabidopsis
Uploaded: 2020-06-25T14:00:00
Description: Watch this Scientific Journal Video about Phosphoproteomic Strategy for Profiling Osmotic Stress Signaling in Arabidopsis at JoVE.com

This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences, Grant XDB27040106.

1. Sample preparation
<ol>
	<li>Harvest the control and stress treated seedlings (1 g) in an aluminum foil and flash freeze the samples in liquid nitrogen. 
	NOTE: Higher protein concentration is usually observed from two-week-old seedlings than that from mature plants. One gram of seedlings generates approximately 10 mg of protein lysate, which is enough for the MS analysis. All centrifugation steps take place at 16,000 x g in step 1.</li>
	<li>Grind frozen seedlings into a fine powder using a mortar and...

<ol>
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J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Plant+cellular+and+molecular+responses+to+high+salinity.">Plant cellular and molecular responses to high salinity.</a> Annual Review Plant Physiology Plant Molecualr Biology. 51, 463-499 (2000).</li><li>Janmohammadi, M., Zolla, L., Rinalducci, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Low+temperature+tolerance+in+plants:+Changes+at+the+protein+level.">Low temperature tolerance in plants: Changes at the protein level.</a> Phytochemistry. 117, 76-89 (2015).</li><li>Umezawa, T., Takahashi, F., Shinozaki, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phosphorylation+networks+in+the+abscisic+acid+signaling+pathway.">Phosphorylation networks in the abscisic acid signaling pathway.</a> Enzymes. 35, 27-56 (2014).</li><li>Silva-Sanchez, C., Li, H., Chen, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recent+advances+and+challenges+in+plant+phosphoproteomics.">Recent advances and challenges in plant phosphoproteomics.</a> Proteomics. 15 (5-6), 1127-1141 (2015).</li><li>Wang, P., 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=Mapping+proteome-wide+targets+of+protein+kinases+in+plant+stress+responses.">Mapping proteome-wide targets of protein kinases in plant stress responses.</a> Proceedings of the National Academy of Sciences of the United States of America. 117 (6), 3270-3280 (2020).</li><li>Fujii, H., Verslues, P. 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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=Rapid+high-pH+reverse+phase+stageTip+for+sensitive+small-scale+membrane+proteomic+profiling.">Rapid high-pH reverse phase stageTip for sensitive small-scale membrane proteomic profiling.</a> Analytical Chemistry. 87 (24), 12016-12023 (2015).</li><li>Wang, P., 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=Reciprocal+regulation+of+the+TOR+Kinase+and+ABA+receptor+balances+plant+growth+and+stress+response.">Reciprocal regulation of the TOR Kinase and ABA receptor balances plant growth and stress response.</a> Molecular Cell. 69 (1), 100-112 (2018).</li><li>Lin, Z., 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=A+RAF-SnRK2+kinase+cascade+mediates+early+osmotic+stress+signaling+in+higher+plants.">A RAF-SnRK2 kinase cascade mediates early osmotic stress signaling in higher plants.</a> Nature Communications. 11 (1), 613 (2020).</li><li>Humphrey, S. 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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=Phosphoproteomics+of+Arabidopsis+Highly+ABA-Induced1+identifies+AT-Hook-Like10+phosphorylation+required+for+stress+growth+regulation.">Phosphoproteomics of Arabidopsis Highly ABA-Induced1 identifies AT-Hook-Like10 phosphorylation required for stress growth regulation.</a> Proceedings of the National Academy of Sciences of the United States of America. 116 (6), 2354-2363 (2019).</li><li>Yang, F., Melo-Braga, M. N., Larsen, M. R., Jorgensen, H. 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The dynamic range and complexity of plant proteome and phosphoproteome are still a limiting factor to depth of phosphoproteomics analyses. Despite the capability of single run LC-MS/MS analysis to identify 10,000 phosphorylation sites21,22, the coverage of the whole plant phosphoproteome is still limited. Therefore, a phosphoproteomic workflow that provides high sensitivity and superior separation efficiency is required in profiling the global view of plant signa...

High salinity, low temperature, and drought cause osmotic stresses, which is a major environmental factor that affects plant productivity1,2. Protein phosphorylation is one of the most significant post-translational modifications mediating signal perception and transduction in plant response to osmotic stress3,4,5. SNF1-related protein kinase 2s (SnRK2s) are involved in the osmotic stress signaling6. Nine of ten members of the SnRK2 family show significant activation in response to osmotic stress7,8. The snrk2.1/2/3/4/5/6/7/8/9/10 decuple (snrk2-dec) mutant having mutations in all ten SnRK2 displayed hypersensitivity to osmotic stress. In snrk2-dec mutant, the osmotic stress-induced accumulation of inositol 1,4,5-trisphosphate (IP3), abscisic acid (ABA) biosynthesis, and gene expressions are strongly reduced, highlighting the vital role of SnRK2s in osmotic stress responses6. However, it is still unclear how SnRK2s kinases regulate these biological processes. Profiling the phosphoproteomic changes in response to osmotic stress is an efficient way to bridge this gap and to delineate the osmotic stress-triggered defense mechanisms in plants.
Mass spectrometry (MS) is a powerful technique for mapping plant phosphoproteome9. Characterization of plant phosphoproteomics, however, remain a challenge due to the dynamic range of plant proteome and the complexity of plant lysate4. To overcome these challenges, we developed a universal plant phosphoproteomic workflow, which eliminates unwanted interferences such as from photosynthetic pigments and secondary metabolites, and enabling the deep coverage of plant phosphoproteome10. Several phosphopeptide enrichment methods such as immobilized metal ion affinity chromatography (IMAC) and metal oxide chromatography (MOC) have been developed for enriching phosphopeptides prior to MS analysis11,12,13,14,15,16. Acidic non-phosphopeptides co-purifying with phosphopeptides are the major interferences for phosphopeptide detection. Previously, we standardized the pH value and organic acid concentration of IMAC loading buffer to eliminate the binding of non-phosphopeptides, to obtain more than 90% enrichment specificity bypassing the pre-fractionation step11.
Sample loss in the multi-step process of phosphopeptide enrichment and fractionation hampers the sensitivity of phosphopeptide identification and the depth of phosphoproteomic coverage. Stop-and-go-extraction tips (stage tips) are pipette tips that contain small disks to cap the end of the tip, which can be incorporated with chromatography for peptide fractionation and cleaning17. Sample loss during the stage tip procedure can be minimized by avoiding sample transfer between the tubes. We have successfully implemented stage tip in Ga3+-IMAC and Fe3+-IMAC to separate low abundant multiple phosphorylated peptides from singly phosphorylated peptides, which improved the depth of human phosphoproteome15. In addition, the use of high pH reversed-phase (Hp-RP) stage tip has demonstrated the wider coverage of human membrane proteome compared to that of strong cation exchange (SCX) and strong anion exchange (SAX) chromatography18. Therefore, integrating IMAC and Hp-RP stage tip techniques can increase plant phosphoproteome coverage with simplicity, high specificity, and high throughput. We have demonstrated that this strategy identified more than 20,000 phosphorylation sites from Arabidopsis seedlings, representing an enhanced depth of plant phosphoproteome19.
Here, we report a stage tip-based phosphoproteomic protocol for phosphoproteomic profiling in Arabidopsis. This workflow was applied to study the phosphoproteomic perturbation of wild-type and snrk2-dec mutant seedlings in response to osmotic stress. The phosphoproteomic analysis revealed the phosphorylation sites implicated in kinase activation and early osmotic stress signaling. Comparative analysis of wild-type and snrk2-dec mutant phosphoproteome data leaded the discovery of a Raf-like kinase (RAF)-SnRK2 kinase cascade which plays a key role in osmore stress signaling in high plants.

<table>
	<tbody>
		<tr>
			<td>1.5 mL tube</td>
			<td>eppendorf</td>
			<td>22431081</td>
			<td>Protein LoBind, 1.5 mL, PCR clean, colorless, 100 tubes</td>
		</tr>
		<tr>
			<td>200 &#181;L pipet tip</td>
			<td>Gilson</td>
			<td>F1739311</td>
			<td></td>
		</tr>
		<tr>
			<td>2-chloroacetamide</td>
			<td>Sigma-Aldrich</td>
			<td>C0267</td>
			<td></td>
		</tr>
		<tr>
			<td>acetic acid</td>
			<td>Sigma-Aldrich</td>
			<td>5438080100</td>
			<td></td>
		</tr>
		<tr>
			<td>acetonitrile</td>
			<td>Sigma-Aldrich</td>
			<td>271004</td>
			<td></td>
		</tr>
		<tr>
			<td>ammonium hydroxide</td>
			<td>Sigma-Aldrich</td>
			<td>338818</td>
			<td></td>
		</tr>
		<tr>
			<td>ammonium phosphate monbasic</td>
			<td>Sigma-Aldrich</td>
			<td>216003</td>
			<td></td>
		</tr>
		<tr>
			<td>BCA Protein Assay Kit</td>
			<td>Thermo Fisher Scientific</td>
			<td>23227</td>
			<td></td>
		</tr>
		<tr>
			<td>blunt-ended needle</td>
			<td>Hamilton</td>
			<td>90516</td>
			<td>Kel-F hub (KF), point style 3, gauge 16</td>
		</tr>
		<tr>
			<td>C18-AQ beads</td>
			<td>Dr. Maisch</td>
			<td>ReproSil-Pur-C18-AQ 5 &#181;m</td>
			<td></td>
		</tr>
		<tr>
			<td>C8 Empore disk</td>
			<td>3 M</td>
			<td>2214</td>
			<td>47 mm</td>
		</tr>
		<tr>
			<td>Centrifuge</td>
			<td>eppendorf</td>
			<td>22620444</td>
			<td></td>
		</tr>
		<tr>
			<td>chloroform</td>
			<td>Sigma-Aldrich</td>
			<td>CX1058</td>
			<td></td>
		</tr>
		<tr>
			<td>data analysis software</td>
			<td></td>
			<td>Perseus 1.6.2.1</td>
			<td>https://maxquant.net/perseus/</td>
		</tr>
		<tr>
			<td>ethylenediaminetetraacetic acid (EDTA)</td>
			<td>Sigma-Aldrich</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>formic acid</td>
			<td>Sigma-Aldrich</td>
			<td>5330020050</td>
			<td></td>
		</tr>
		<tr>
			<td>Frits</td>
			<td>Agilent</td>
			<td>12131024</td>
			<td>Frits for SPE Cartridges</td>
		</tr>
		<tr>
			<td>Guanidine hydrochloride</td>
			<td>Sigma-Aldrich</td>
			<td>50933</td>
			<td></td>
		</tr>
		<tr>
			<td>H2O</td>
			<td>Sigma-Aldrich</td>
			<td>1153334000</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Sigma-Aldrich</td>
			<td>H3375</td>
			<td></td>
		</tr>
		<tr>
			<td>Iron (III) chloride</td>
			<td>Sigma-Aldrich</td>
			<td>157740</td>
			<td></td>
		</tr>
		<tr>
			<td>LTQ-orbitrap</td>
			<td>Thermo Fisher Scientific</td>
			<td>Velos Pro</td>
			<td></td>
		</tr>
		<tr>
			<td>mass spectrometer</td>
			<td>Thermo Fisher Scientific</td>
			<td>LTQ-Orbitrap Velos Pro</td>
			<td></td>
		</tr>
		<tr>
			<td>methanol</td>
			<td>Sigma-Aldrich</td>
			<td>34860</td>
			<td></td>
		</tr>
		<tr>
			<td>nano LC</td>
			<td>Thermo Fisher Scientific</td>
			<td>Easy-nLC 1000</td>
			<td></td>
		</tr>
		<tr>
			<td>Ni-NTA spin column</td>
			<td>Qiagen</td>
			<td>31014</td>
			<td></td>
		</tr>
		<tr>
			<td>N-Lauroylsarcosine sodium salt</td>
			<td>Sigma-Aldrich</td>
			<td>L9150</td>
			<td></td>
		</tr>
		<tr>
			<td>plunger</td>
			<td>Hamilton</td>
			<td>1122-01</td>
			<td>Plunger assembly N, RN, LT, LTN for model 1702 (25 &#956;l)</td>
		</tr>
		<tr>
			<td>search engine software</td>
			<td></td>
			<td>MaxQuant 1.5.4.1</td>
			<td>https://www.maxquant.org</td>
		</tr>
		<tr>
			<td>SEP-PAK Cartridge 50 mg</td>
			<td>Waters</td>
			<td>WAT054960</td>
			<td></td>
		</tr>
		<tr>
			<td>sodium deoxycholate</td>
			<td>Sigma-Aldrich</td>
			<td>D6750</td>
			<td></td>
		</tr>
		<tr>
			<td>SpeedVac</td>
			<td>Thermo Fisher Scientific</td>
			<td>SPD121P</td>
			<td></td>
		</tr>
		<tr>
			<td>TMT 6-plex</td>
			<td>Thermo Fisher Scientific</td>
			<td>90061</td>
			<td></td>
		</tr>
		<tr>
			<td>Triethylammonium bicarbonate buffer</td>
			<td>Sigma-Aldrich</td>
			<td>T7408</td>
			<td></td>
		</tr>
		<tr>
			<td>Trifluoroacetic acid</td>
			<td>Sigma-Aldrich</td>
			<td>91707</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris(2-carboxyethyl)phosphine hydrochloride</td>
			<td>Sigma-Aldrich</td>
			<td>C4706</td>
			<td></td>
		</tr>
		<tr>
			<td>Trizma hydrochloride</td>
			<td>Sigma-Aldrich</td>
			<td>T3253</td>
			<td></td>
		</tr>
	</tbody>
</table>

phosphoproteomic strategy for profiling osmotic stress signaling in arabidopsis

Protein phosphorylation is crucial for the regulation of enzyme activity and gene expression under osmotic condition. Mass spectrometry (MS)-based phosphoproteomics has transformed the way of studying plant signal transduction. However, requirement of lots of starting materials and prolonged MS measurement time to achieve the depth of coverage has been the limiting factor for the high throughput study of global phosphoproteomic changes in plants. To improve the sensitivity and throughput of plant phosphoproteomics, we have developed a stop and go extraction (stage) tip based phosphoproteomics approach coupled with Tandem Mass Tag (TMT) labeling for the rapid and comprehensive analysis of plant phosphorylation perturbation in response to osmotic stress. Leveraging the simplicity and high throughput of stage tip technique, the whole procedure takes approximately one hour using two tips to finish phosphopeptide enrichment, fractionation, and sample cleaning steps, suggesting an easy-to-use and high efficiency of the approach. This approach not only provides an in-depth plant phosphoproteomics analysis (&#62; 11,000 phosphopeptide identification) but also demonstrates the superior separation efficiency (&#60; 5% overlap) between adjacent fractions. Further, multiplexing has been achieved using TMT labeling to quantify the phosphoproteomic changes of wild-type and snrk2 decuple mutant plants. This approach has successfully been used to reveal the phosphorylation events of Raf-like kinases in response to osmotic stress, which sheds light on the understanding of early osmotic signaling in land plants.

To demonstrate the performance of this workflow, we exploited IMAC stage tip coupled with Hp-RP stage tip fractionation to measure the phosphoproteomic changes in wild-type and snrk2-dec mutant seedlings with or without mannitol treatment for 30 minutes. Each sample was performed in biological triplicates, and the experimental workflow is represented in Figure 1. The digested peptides (400 &#181;g) of each sample were labeled with one TMT-6plex channel, pooled and desalted. The phos...

Watch this Scientific Journal Video about Phosphoproteomic Strategy for Profiling Osmotic Stress Signaling in Arabidopsis at JoVE.com

Phosphoproteomic Strategy for Profiling Osmotic Stress Signaling in Arabidopsis

Presented here is a phosphoproteomic approach, namely stop and go extraction tip based phosphoproteomic, which provides high-throughput and deep coverage of Arabidopsis phosphoproteome. This approach delineates the overview of osmotic stress signaling in Arabidopsis.

Phosphoproteomic Strategy for Profiling Osmotic Stress Signaling in Arabidopsis

Protein phosphorylation is crucial for the regulation of enzyme activity and gene expression under osmotic condition. Mass spectrometry (MS)-based ...

This strategy is a powerful tool for comprehensively studying the global changes of plant phosphoproteomes, in response to biotic or abiotic stresses. This technique allows in-depth phosphoproteomics analysis, in an easy-to-use and high throughput manner. For IMAC stage tip preparation, use a 16 gauge blunt ended needle, to penetrate a propylene frit disc, and use a plunger to gently press the frit into the tip.Then, place an inverted nickel-NTA spin column, onto a 1.5 milliliter tube, and use the plunger to press the frit of nickel-NTA beads gently into the tube. For phosphopeptide enrichment, using an IMAC stage tip, add 400 microliters of loading buffer to the nickel-NTA beads, and load the entire volume of bead solution into one IMAC stage tip. Pass the solution through the tip by centrifugation and load 100 microliters of 50 millimolar EDTA, to strip the nickel ions from the tip by centrifugation.Treat the tip with 100 microliters of loading buffer by centrifugation. Next, treat the tip with 100 microliters of 50 millimolar ferric chloride in 6%acetic acid, by centrifugation. Condition the stage with 100 microliters of loading buffer, by centrifugation.Followed by centrifugation with 100 microliters of loading buffer, supplemented with the sample peptides. After centrifugation, rinse the tip two times, with 100 microliters washing buffer per wash, followed by one rinse with 100 microliters of loading buffer. At the end of of the centrifugation, use scissors to trim the front of the IMAC stage tip and place the trimmed tip inside the high pH, reversed phase tip.For phosphopeptide fractionation, using a high pH reverse phase C18 stage tip, pass 100 microliters of elution buffer through both layers of stage tips, by centrifugation. At the end of the spin, use tweezers to discard the IMAC stage tip, and add 20 microliters of Buffer A, to the high pH reverse phase stage tip. After centrifugation, add 20 microliters of Buffer 1, to the collected fraction, and collect the eluate in a new tube, by centrifugation.Repeat the process with Buffers 2 through 8, until all eight fractions have been collected. Then dry the final eluate of each fraction in a vacuum concentrator. In this representative analysis a total of 8, 107 and 7, 248 Phosphopeptides were identified from wild type, and SnRK2 decuple mutant samples respectively, illustrating the efficiency of the workflow in providing in-depth coverage for delineating the global view of signal transduction in Arabidopsis.Comparison of the number of identified phosphopeptides across eight fractions revealed the presence of few phosphopeptides in the first two fractions, but the majority of phosphopeptides were evenly distributed between the last six fractions. Suggesting this approach provides the ability, to separate complex phosphopeptides from the plant phosphoproteome. Evaluation of the overlap of phosphopeptides between two adjacent fractions, indicated that less than 5%of the phosphopeptides overlap, occurred in the adjacent fractions.After mannitol treatment, 433 phosphorylation sites were increased in the wild type sample. While, 380 sites were increased in the SnRK2 decuple mutant sample. Among these, 312 phosphosites showed induction in wild type, but not in SnRK2 dec mutant plants.It is important to use the same amount of pressure to load the frit disc into the tips, to ensure a better reproducibility of the analysis. Soon, cation exchange chromatography can be used, as an alternative measure, for fractionating the enriched phosphopeptides, to obtain a wider coverage of the plant phosphoproteome.

Research

JoVE Journal

Biochemistry

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