IC4R009-Proteomic-2007-17385905 - Revision history

Guangyi: /* Research Findings */

2016-07-18T06:48:39Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-18T06:46:53Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-18T06:44:39Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-18T06:42:44Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-18T06:38:39Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-18T05:25:48Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-18T05:23:51Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-18T05:20:24Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-18T05:18:20Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-18T05:08:21Z

‎Research Findings

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 *Pro-Q Diamond Phosphoprotein in Gel Stain is a fluorescence dye specific for phosphoproteins. To examine the phosphoproteome and proteome in rice roots, the researchers stained proteins from 20-day-old rice roots with Pro-Q Diamond dye and SYPRO Ruby dye, respectively, following protein separation on 2-DE gels. As shown in Figure 1A, the majority of the Pro-Q Diamond dye-stained protein spots had a relatively low pI, and it was very obvious for those heavily stained protein spots. In contrast,the SYPRO Ruby stained proteins were more evenly distributed on the 2-DE gel (Figure 1B).  Many protein spots that were heavily stained with SYPRO Ruby were not stained or were weakly stained by Pro-Q Diamond dye. Conversely, many spots that were weakly stained by SYPRO Ruby were heavily stained by Pro-Q Diamond dye as revealed by comparing the spots labeled in Figure 1C and 1D.
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-[[File:IC4R009-Proteomic-2007-17385905-f1.png |center |thumb |10000px |'''''']]
+[[File:IC4R009-Proteomic-2007-17385905-f1.png |center |thumb |10000px |''''''Figure 1. 2-DE gel images of rice root proteome revealed by Pro-Q Diamond in Gel Stain and SYPRO Ruby fluorescence stain. Proteins were extracted from 20-day-old rice roots, were separated on 2-DE gels, and were stained with Pro-Q Diamond dye and SYPRO Ruby.(A) 2-DE gel image revealed by Pro-Q Diamond in Gel stain. (B) 2-DE gel image revealed by SYPRO Ruby stain. (C) An enlarged section of the image shown in A. The spot positions of several major proteins are marked and labeled for comparison. (D) An enlarged section of the image shown in B. The spot positions of several major proteins are marked and labeled for comparison.'''''']]
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 *To study how the putative phosphoproteins stained by Pro-Q Diamond dye resrpond to NaCl stress, we examined the rice root proteome with the Pro-Q Diamond dye after 10 and 24 h of 150 mM NaCl treatments.Twenty Pro-Q Diamond dye-stained protein spots displayed over 2-fold upregulation and 18 protein spots displayed over 2-fold downregulation in all three biological replicas (Figure 2 and data not shown).

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 *To study how the putative phosphoproteins stained by Pro-Q Diamond dye resrpond to NaCl stress, we examined the rice root proteome with the Pro-Q Diamond dye after 10 and 24 h of 150 mM NaCl treatments.Twenty Pro-Q Diamond dye-stained protein spots displayed over 2-fold upregulation and 18 protein spots displayed over 2-fold downregulation in all three biological replicas (Figure 2 and data not shown).
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-[[File:IC4R009-Proteomic-2007-17385905-f2a.png |center |thumb |10000px |'''''']]
+[[File:IC4R009-Proteomic-2007-17385905-f2a.png |center |thumb |10000px ]]
-[[File:IC4R009-Proteomic-2007-17385905-f2b.png |center |thumb |10000px |'''''']]
+[[File:IC4R009-Proteomic-2007-17385905-f2b.png |center |thumb |10000px ]]
-[[File:IC4R009-Proteomic-2007-17385905-f2c.png |center |thumb |10000px |'''''']]
+[[File:IC4R009-Proteomic-2007-17385905-f2c.png |center |thumb |10000px |''''''Figure 2. Protein differential regulation under salinity stress revealed by Pro-Q Diamond Phosphoprotein Gel Stain. Proteins were extracted from 20-day-old control and salt-treated rice roots,were separated on 2-DE gels, and were stained with Pro-Q Diamond dye. The cutoff of differential regulation was 2-fold of change in three biological replicas. (A) Putative phosphoproteome image of rice roots without salt stress. All protein spots subjected to upregulation under salinity stress are marked with black arrows and all protein spots subjected to downregulation are marked with white arrows. (B) Putative phosphoproteome image after 10 h of NaCl (150 mM) treatment. Proteins upregulated after 10 h of salt treatment are marked with black arrows and the proteins downregulated after 10 h of salt treatment are marked with white arrows. (C) Putative phosphoproteome image after 24 h of NaCl (150 mM) treatment. Proteins upregulated after
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 *Protein differential expression in rice roots, after 10 and 24 h of salt treatment, was also examined using SYPRO Ruby stain following 2-DE separation.Thirty-one protein spots displayed over 2-fold upregulation and 13 protein spots displayed over 2-fold downregulation in all three biological replicas (Figure 3 and data not shown).

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 *Protein differential expression in rice roots, after 10 and 24 h of salt treatment, was also examined using SYPRO Ruby stain following 2-DE separation.Thirty-one protein spots displayed over 2-fold upregulation and 13 protein spots displayed over 2-fold downregulation in all three biological replicas (Figure 3 and data not shown).
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-[[File:IC4R009-Proteomic-2007-17385905-f3a.png |center |thumb |10000px |'''''']]
+[[File:IC4R009-Proteomic-2007-17385905-f3a.png |center |thumb |10000px ]]
-[[File:IC4R009-Proteomic-2007-17385905-f3b.png |center |thumb |10000px |'''''']]
+[[File:IC4R009-Proteomic-2007-17385905-f3b.png |center |thumb |10000px ]]
-[[File:IC4R009-Proteomic-2007-17385905-f3c.png |center |thumb |10000px |'''''']]
+[[File:IC4R009-Proteomic-2007-17385905-f3c.png |center |thumb |10000px |''''''Figure 3. Protein differential expression under salinity stress revealed by SYPRO Ruby stain. Proteins were extracted from 20-day-old rice roots, were separated on 2-DE gels, and were stained with Pro-Q Diamond dye. The cutoff of differential regulation was 2-fold of change in three biological replicas. (A) Rice root proteome image without salt stress. All protein spots subjected to upregulation under salinity stress are marked with black arrows and all protein spots subjected to downregulation are marked with white arrows. (B) Rice root proteome image after
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 * After MALDI-TOF/TOF analyses, 23 of the 31 upregulated proteins and 8 of the 11 downregulated proteins had been identified

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 with high confidence as shown in Table 2.
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-[[File:IC4R009-Proteomic-2007-17385905-t2a.png |center |thumb |10000px |'''''']]
+[[File:IC4R009-Proteomic-2007-17385905-t2a.png |center |thumb |10000px ]]
-[[File:IC4R009-Proteomic-2007-17385905-t2b.png |center |thumb |10000px |'''''']]
+[[File:IC4R009-Proteomic-2007-17385905-t2b.png |center |thumb |10000px ]]
-[[File:IC4R009-Proteomic-2007-17385905-t2c.png |center |thumb |10000px |'''''']]
+[[File:IC4R009-Proteomic-2007-17385905-t2c.png |center |thumb |10000px |''''''Table 2. Differentially Expressed Proteins in the Time Course of Salt Stressa'''''']]
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 *As shown in Figure 4, seven proteins displayed differential expression whether the gel was stained by Pro-Q Diamond dye or SYPRO Ruby. The other differentially regulated proteins were specific either to Pro-Q Diamond stain or SYPRO Ruby stain.These results suggest that most proteins with quantity change during salinity stress are not phosphoproteins or have no change in phosphorylation level. On the other hand, most differentially regulated phosphoproteins have modification level change instead of quantity change during salinity stress.

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 *As shown in Figure 4, seven proteins displayed differential expression whether the gel was stained by Pro-Q Diamond dye or SYPRO Ruby. The other differentially regulated proteins were specific either to Pro-Q Diamond stain or SYPRO Ruby stain.These results suggest that most proteins with quantity change during salinity stress are not phosphoproteins or have no change in phosphorylation level. On the other hand, most differentially regulated phosphoproteins have modification level change instead of quantity change during salinity stress.
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-[[File:IC4R009-Proteomic-2007-17385905-f4.png |center |thumb |10000px |'''''']]
+[[File:IC4R009-Proteomic-2007-17385905-f4.png |center |thumb |10000px |''''''Figure 4. Venn diagram analyses of the differentially upregulated proteins under salinity stress. Differentially upregulated proteins revealed by SYPRO Ruby and Pro-Q Diamond Phosphoprotein Gel Stain were analyzed.'''''']]
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 ==Labs working on this Project==
 *Department of Biochemistry and Molecular Biology, Mississippi State University,Mail box 9650, Mississippi State, Mississippi 39762