Os03g0427300 - Revision history

Liman: /* Annotated Information */

2016-08-05T04:00:42Z

‎Annotated Information

Liman at 03:55, 5 August 2016

2016-08-05T03:55:44Z

Liman: /* Mutation */

2016-08-05T03:50:52Z

‎Mutation

Liman: /* Mutation */

2016-08-05T03:48:01Z

‎Mutation

Liman: /* Mutation */

2016-08-05T03:45:03Z

‎Mutation

Liman: /* References */

2016-08-05T03:44:29Z

‎References

Liman: /* Mutation */

2016-08-05T03:44:08Z

‎Mutation

Liman: /* Mutation */

2016-08-05T03:25:42Z

‎Mutation

Liman: /* Mutation */

2016-08-05T03:25:01Z

‎Mutation

Liman at 03:17, 5 August 2016

2016-08-05T03:17:56Z

@@ Line 4: / Line 4: @@
 ===Function===
 * From this and other studies, it is apparent that the small GTPase Rab5 plays a role in both storage protein mRNA and protein sorting.
 * The results of the microarray and 2D-DIGE analyses of glup4 may be a reflection of Rab5’s role in RNA and protein
-sorting. Over 50 genes were identified whose transcript or protein expression was affected in the glup4 mutant by at least 2-fold (Table 1–Table 4).
+* The results of the microarray and 2D-DIGE analyses of '''''glup4''''' may be a reflection of Rab5’s role in RNA and protein sorting. Over 50 genes were identified whose transcript or protein expression was affected in the glup4 mutant by at least 2-fold (Table 1–Table 4).
 ===Mutation===
-* Using RT-PCR in the presence of dUTPOregon Green to label RNAs and rhodamine B hexyl ester to stain prolamine protein bodies, glutelin RNAs are found to be preferentially transported to the cisternal-ER (Cis-ER) in wildtype endosperm (Fig. 1). Prolamine RNAs, on the other hand, are targeted to ER that delimits the spherical prolamine protein bodies (PB-ER). In the glup4 mutant, however, glutelin RNAs are partially misdirected from the Cis-ER to the PB-ER (Fig. 1), as well as to large dilated multivesicular body-like structures located near the plasma membrane (data not shown). The glutelin RNA mistargeting was not only observed in one gene (Gt-2), but also in others (GluA-1, GluA- 3 and GluB-1, data not shown). Prolamine RNA localization to the PB-ER is unaffected (Fig. 1), suggesting that Rab5 is involved in glutelin RNA sorting only<ref name="ref1" />.
+* Using RT-PCR in the presence of dUTPOregon Green to label RNAs and rhodamine B hexyl ester to stain prolamine protein bodies, glutelin RNAs are found to be preferentially transported to the cisternal-ER (Cis-ER) in wildtype endosperm (Fig. 1). Prolamine RNAs, on the other hand, are targeted to ER that delimits the spherical prolamine protein bodies (PB-ER). In the '''''glup4''''' mutant, however, glutelin RNAs are partially misdirected from the Cis-ER to the PB-ER (Fig. 1), as well as to large dilated multivesicular body-like structures located near the plasma membrane (data not shown). The glutelin RNA mistargeting was not only observed in one gene (Gt-2), but also in others (GluA-1, GluA- 3 and GluB-1, data not shown). Prolamine RNA localization to the PB-ER is unaffected (Fig. 1), suggesting that Rab5 is involved in glutelin RNA sorting only<ref name="ref1" />.
 [[File:Os03g0427300-1.png|center|thumb|400px|'''Fig. 1. Localization of prolamine and glutelin mRNAs in wildtype and glup4 developing rice endosperm.''' '' <ref name="ref1" />.'']]
-* Microarray analysis of transcripts isolated from glup4 and wildtype developing seeds identified 35 transcripts that were upregulated and 10 that were downregulated by at least 2-fold in the glup4 mutant using a stringent P value (<0.001) to avoid false positives (Table 1 and Table 2)<ref name="ref1" />.
+* Microarray analysis of transcripts isolated from '''''glup4''''' and wildtype developing seeds identified 35 transcripts that were upregulated and 10 that were downregulated by at least 2-fold in the '''''glup4''''' mutant using a stringent P value (<0.001) to avoid false positives (Table 1 and Table 2)<ref name="ref1" />.
-[[File:Os03g0427300-2.png|center|thumb|400px|'''Table 1. Transcripts upregulated in the glup4 mutant compared to wildtype (P < 0.001)''' '' <ref name="ref1" />.'']]
+[[File:Os03g0427300-2.png|center|thumb|400px|'''Table 1. Transcripts upregulated in the '''''glup4''''' mutant compared to wildtype (P < 0.001)''' '' <ref name="ref1" />.'']]
-[[File:Os03g0427300-3.png|center|thumb|400px|'''Table 2. Transcripts downregulated in the glup4 mutant compared to
+[[File:Os03g0427300-3.png|center|thumb|400px|'''Table 2. Transcripts downregulated in the '''''glup4''''' mutant compared to
 wildtype (P < 0.001)''' '' <ref name="ref1" />.'']]
-* The researchers utilized 2D-DIGE to analyze the protein expression profiles of soluble extracts from 12–14 DAF wildtype and glup4 rice seeds (Fig. 3). Twenty-one protein spots were found to be differentially expressed (P < 0.05) with at least a 2-fold change in expression when analyzed on pH 3–10 non-linear immobilized pH gradient strips. Only two proteins were found to have at least a 2-fold increase in expression in the glup4 mutant (Table 3). One of these proteins, annotated as a glycosyl hydrolase, has similarity to xylanase inhibitor (XI) proteins, which function in cell wall restructuring<ref name="ref3" />. Although not the same protein, xylanase inhibitor TAXI-VI mRNA was also found to be upregulated in the mutant (Table 1).
+* The researchers utilized 2D-DIGE to analyze the protein expression profiles of soluble extracts from 12–14 DAF wildtype and '''''glup4''''' rice seeds (Fig. 3). Twenty-one protein spots were found to be differentially expressed (P < 0.05) with at least a 2-fold change in expression when analyzed on pH 3–10 non-linear immobilized pH gradient strips. Only two proteins were found to have at least a 2-fold increase in expression in the glup4 mutant (Table 3). One of these proteins, annotated as a glycosyl hydrolase, has similarity to xylanase inhibitor (XI) proteins, which function in cell wall restructuring<ref name="ref3" />. Although not the same protein, xylanase inhibitor TAXI-VI mRNA was also found to be upregulated in the mutant (Table 1)<ref name="ref1" />.
-[[File:Os03g0427300-4.png|center|thumb|400px|'''Fig. 3. Two-dimensional difference in gel electrophoresis (2D-DIGE) analysis comparing the soluble protein fraction from glup4 and wildtype developing rice seeds using pH 3-10 nonlinear immobilized pH gradient strips.''' '' <ref name="ref1" />.'']]
+[[File:Os03g0427300-4.png|center|thumb|400px|'''Fig. 3. Two-dimensional difference in gel electrophoresis (2D-DIGE) analysis comparing the soluble protein fraction from '''''glup4''''' and wildtype developing rice seeds using pH 3-10 nonlinear immobilized pH gradient strips.''' '' <ref name="ref1" />.'']]
 [[File:Os03g0427300-5.png|center|thumb|400px|'''Table 3. Proteins upregulated in the glup4 mutant compared to wildtype (P < 0.05)''' '' <ref name="ref1" />.'']]
-* A number of proteins involved in other aspects of carbon
+* A number of proteins involved in other aspects of carbon metabolism were found to be downregulated in '''''glup4''''',
-metabolism were found to be downregulated in glup4,
+including glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and pyruvate, orthophosphate dikinase (PPDK, Table 4)<ref name="ref1" />.
 ==Labs working on this gene==

@@ Line 3: / Line 3: @@
 ==Annotated Information==
 ===Function===
 ===Mutation===
 * Using RT-PCR in the presence of dUTPOregon Green to label RNAs and rhodamine B hexyl ester to stain prolamine protein bodies, glutelin RNAs are found to be preferentially transported to the cisternal-ER (Cis-ER) in wildtype endosperm (Fig. 1). Prolamine RNAs, on the other hand, are targeted to ER that delimits the spherical prolamine protein bodies (PB-ER). In the glup4 mutant, however, glutelin RNAs are partially misdirected from the Cis-ER to the PB-ER (Fig. 1), as well as to large dilated multivesicular body-like structures located near the plasma membrane (data not shown). The glutelin RNA mistargeting was not only observed in one gene (Gt-2), but also in others (GluA-1, GluA- 3 and GluB-1, data not shown). Prolamine RNA localization to the PB-ER is unaffected (Fig. 1), suggesting that Rab5 is involved in glutelin RNA sorting only<ref name="ref1" />.
@@ Line 29: / Line 33: @@
 [[File:Os03g0427300-6.png|center|thumb|400px|'''Table 4. Proteins downregulated in the glup4 mutant compared to wildtype (P < 0.05)''' '' <ref name="ref1" />.'']]
 ==Labs working on this gene==

← Older revision		Revision as of 03:50, 5 August 2016
Line 20:		Line 20:

	[[File:Os03g0427300-5.png\|center\|thumb\|400px\|'''Table 3. Proteins upregulated in the glup4 mutant compared to wildtype (P < 0.05)''' '' <ref name="ref1" />.'']]		[[File:Os03g0427300-5.png\|center\|thumb\|400px\|'''Table 3. Proteins upregulated in the glup4 mutant compared to wildtype (P < 0.05)''' '' <ref name="ref1" />.'']]
		+
		+	* A number of proteins involved in other aspects of carbon
		+	metabolism were found to be downregulated in glup4,
		+	including glyceraldehyde 3-phosphate dehydrogenase
		+	(GAPDH) and pyruvate, orthophosphate dikinase (PPDK,
		+	Table 4).
		+
		+	[[File:Os03g0427300-6.png\|center\|thumb\|400px\|'''Table 4. Proteins downregulated in the glup4 mutant compared to wildtype (P < 0.05)''' '' <ref name="ref1" />.'']]

	===Expression Pattern===		===Expression Pattern===

@@ Line 8: / Line 8: @@
 [[File:Os03g0427300-1.png|center|thumb|400px|'''Fig. 1. Localization of prolamine and glutelin mRNAs in wildtype and glup4 developing rice endosperm.''' '' <ref name="ref1" />.'']]
-* Microarray analysis of transcripts isolated from glup4 and wildtype developing seeds identified 35 transcripts that
+* Microarray analysis of transcripts isolated from glup4 and wildtype developing seeds identified 35 transcripts that were upregulated and 10 that were downregulated by at least 2-fold in the glup4 mutant using a stringent P value (<0.001) to avoid false positives (Table 1 and Table 2)<ref name="ref1" />.
 [[File:Os03g0427300-2.png|center|thumb|400px|'''Table 1. Transcripts upregulated in the glup4 mutant compared to wildtype (P < 0.001)''' '' <ref name="ref1" />.'']]
@@ Line 17: / Line 16: @@
 * The researchers utilized 2D-DIGE to analyze the protein expression profiles of soluble extracts from 12–14 DAF wildtype and glup4 rice seeds (Fig. 3). Twenty-one protein spots were found to be differentially expressed (P < 0.05) with at least a 2-fold change in expression when analyzed on pH 3–10 non-linear immobilized pH gradient strips. Only two proteins were found to have at least a 2-fold increase in expression in the glup4 mutant (Table 3). One of these proteins, annotated as a glycosyl hydrolase, has similarity to xylanase inhibitor (XI) proteins, which function in cell wall restructuring<ref name="ref3" />. Although not the same protein, xylanase inhibitor TAXI-VI mRNA was also found to be upregulated in the mutant (Table 1).
 ===Expression Pattern===

@@ Line 16: / Line 16: @@
 wildtype (P < 0.001)''' '' <ref name="ref1" />.'']]
-* The researchers utilized
+* The researchers utilized 2D-DIGE to analyze the protein expression profiles of soluble extracts from 12–14 DAF wildtype and glup4 rice seeds (Fig. 3). Twenty-one protein spots were found to be differentially expressed (P < 0.05) with at least a 2-fold change in expression when analyzed on pH 3–10 non-linear immobilized pH gradient strips. Only two proteins were found to have at least a 2-fold increase in expression in the glup4 mutant (Table 3). One of these proteins, annotated as a glycosyl hydrolase, has similarity to xylanase inhibitor (XI) proteins, which function in cell wall restructuring<ref name="ref3" />. Although not the same protein, xylanase inhibitor TAXI-VI mRNA was also found to be upregulated in the mutant (Table 1).
 ===Expression Pattern===

@@ Line 50: / Line 50: @@
 </ref>
 * <ref name="ref3">
+Simpson, D.J., G.B. Fincher, A.H.C. Huang and V. Cameron-Mills (2003) Structure and function of cereal and related higher plant (1→4)-beta-xylan endohydrolases. J. Cereal Sci. 37: 111–127.
 </ref>
 </references>
 ==Structured Information==
       [[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 3]]

@@ Line 1: / Line 1: @@
-Please input one-sentence summary here.
+'''''Glup4''''' gene encodes small GTPase, Rab5a in rice<ref name="ref2" />.
 ==Annotated Information==
@@ Line 22: / Line 22: @@
 </ref>
 * <ref name="ref2">
+Satoh-Cruz M, Fukuda M, Ogawa M, et al. Glup4 gene encodes small GTPase, Rab5a in rice[J]. Rice Genet Newsl, 2010, 25: 48-49.
 </ref>
 * <ref name="ref3">