Os03g0666100 - Revision history

Liman: /* References */

2016-08-08T12:18:30Z

‎References

Liman at 12:14, 8 August 2016

2016-08-08T12:14:34Z

Liman at 12:10, 8 August 2016

2016-08-08T12:10:07Z

Liman: /* Function */

2016-08-08T12:08:17Z

‎Function

Liman at 11:56, 8 August 2016

2016-08-08T11:56:30Z

Liman at 08:11, 8 August 2016

2016-08-08T08:11:18Z

Liman at 08:08, 8 August 2016

2016-08-08T08:08:37Z

Liman: /* Evolution */

2016-08-08T07:55:53Z

‎Evolution

Liman at 07:50, 8 August 2016

2016-08-08T07:50:24Z

Liman at 07:44, 8 August 2016

2016-08-08T07:44:37Z

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 Kitomi Y, Ogawa A, Kitano H, et al. CRL4 regulates crown root formation through auxin transport in rice[J]. Plant Root, 2008, 2: 19-28.
 </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.
+The rice gene Os03g0666100 was reported as CRL4 in 2008<ref name="ref1" />.
 ==Annotated Information==
 ===Function===
-* The '''''crl4''''' mutant showed several abnormalities such as loss of crown roots, aberrant gravitropic response, and increase of metaxylem-like structures in the seminal root. In addition, it could not make the transition from the vegetative to the reproductive phase. However, these abnormalities in '''''crl4''''' mutants did not seem as severe as those observed in severe alleles of '''''gnom'''''. In rice, the researchers hypothesized that a homologous gene of '''''CRL4''''', '''''CRL4-like''''', plays a redundant role with '''''CRL4''''' and can partially compensate for '''''CRL4''''' function because the expression pattern of '''''CRL4-like''''' is iden-tical to that of '''''CRL4'''''. Besides, '''''CRL4-like''''' was also considered to play a redundant role in em-bryogenesis because of the absence of abnormalities in the mature embryo of the '''''crl4''''' mutant.
+*CRL4 encodes a protein highly homologous with Arabidopsis GNOM, which mediates auxin-dependent plant growth by coordinating the polar localization of auxin efflux carrier PIN1<ref name="ref1" />.
 ===Mutation===
-* Two-week-old wild-type plants (Nipponbare) formed several crown roots in comparison to '''''crl4''''' mutants, in which crown root production was scarce at the same developmental stage (Fig. 1A). The researchers cross-sectioned the nodes in 5-day-old wild-type and '''''crl4''''' mutant seedlings to determine the cause of crown root reduc-tion in '''''crl4''''' mutants. In wild-type, several crown root primordia were formed on the outside, adjacent to the peripheral vascular cylinder (Fig. 1B). In contrast, '''''crl4''''' mutants did not produce any crown root primordia (Fig. 1C). Besides the reduced crown root number, the number of lateral roots that were obtained from a seminal root of the '''''crl4''''' mutant was clearly lower than that of the wild-type (Fig. 1D and 1E). The seminal root in the crl4 mutant was shorter than that of the wild-type (Fig. 1A), although there were no signifi-cant differences in the timing of the emergence of the seminal root. The '''''crl4''''' mutant produced the higher number of tillers (data not shown) and their growth angles were wider than those of wild-type (Fig. 1F and 1G). Some '''''crl4''''' mutants survived for more than 4 months. Four-month-old wild-type plants could reach the grain filling stage, but '''''crl4''''' mutants with tiny shoots and a single seminal root could not make the transition from the vegetative to the reproductive phase (Fig. 1F and 1G).
+* Two-week-old wild-type plants (Nipponbare) formed several crown roots in comparison to '''''crl4''''' mutants, in which crown root production was scarce at the same developmental stage (Fig. 1A). The researchers cross-sectioned the nodes in 5-day-old wild-type and '''''crl4''''' mutant seedlings to determine the cause of crown root reduc-tion in '''''crl4''''' mutants. In wild-type, several crown root primordia were formed on the outside, adjacent to the peripheral vascular cylinder (Fig. 1B). In contrast, '''''crl4''''' mutants did not produce any crown root primordia (Fig. 1C). Besides the reduced crown root number, the number of lateral roots that were obtained from a seminal root of the '''''crl4''''' mutant was clearly lower than that of the wild-type (Fig. 1D and 1E). The seminal root in the crl4 mutant was shorter than that of the wild-type (Fig. 1A), although there were no signifi-cant differences in the timing of the emergence of the seminal root. The '''''crl4''''' mutant produced the higher number of tillers (data not shown) and their growth angles were wider than those of wild-type (Fig. 1F and 1G). Some '''''crl4''''' mutants survived for more than 4 months. Four-month-old wild-type plants could reach the grain filling stage, but '''''crl4''''' mutants with tiny shoots and a single seminal root could not make the transition from the vegetative to the reproductive phase (Fig. 1F and 1G)<ref name="ref1" />.
 [[File:Os03g0666100-1.png|center|thumb|400px|'''Fig. 1 Phenotypes of crl4.''' '' <ref name="ref1" />.'']]
-* The researchers examined the root gravitropic response in '''''crl4''''' mutants by measuring the curvature after gravistimulation at 90° to the vertical. Wild-type roots responded sharply to the change in the gravity vector, whereas the response of crl4 roots was impaired (Fig. 2A). The root tip angle of wild-type and '''''crl4''''' roots was compared (θ in Fig. 2B); all wild-type roots had root tip angles of over 50°, while all '''''crl4''''' mutants had angles of below 50° (Fig. 3). The gravitropic response was therefore defective in '''''crl4''''' mutants. These results suggest that CRL4 has an auxin-related function.
+* The researchers examined the root gravitropic response in '''''crl4''''' mutants by measuring the curvature after gravistimulation at 90° to the vertical. Wild-type roots responded sharply to the change in the gravity vector, whereas the response of crl4 roots was impaired (Fig. 2A). The root tip angle of wild-type and '''''crl4''''' roots was compared (θ in Fig. 2B); all wild-type roots had root tip angles of over 50°, while all '''''crl4''''' mutants had angles of below 50° (Fig. 3). The gravitropic response was therefore defective in '''''crl4''''' mutants. These results suggest that CRL4 has an auxin-related function<ref name="ref1" />.
 [[File:Os03g0666100-2.png|center|thumb|400px|'''Fig. 2 Gravitropic response in a seminal root of crl4.''' '' <ref name="ref1" />.'']]
@@ Line 18: / Line 20: @@
 ===Expression===
-* The researchers examined the expression of CRL4 in various organs. To estimate '''''CRL4''''' transcript levels, we per-formed semi-quantitative RT-PCR analysis (Fig. 5A). '''''CRL4''''' was expressed in all the examined organs; high levels of '''''CRL4''''' transcripts were found to be accumu-lated in leaf blades and roots. CRL4-like was also expressed in all the organs and the expression pattern was similar to that of '''''CRL4''''' (Fig. 5A). The researchers also examined the '''''CRL4''''' expression pattern by in situ hybridization. In the stem, signals were ob-served at the steles of the crown root primordia (Fig. 5B and 5C), the vascular bundles and the parenchyma cells adjacent to the peripheral vascular cylinder of the stem where the crown root primordia were formed (Fig. 5D and 5E).
+* The researchers examined the expression of CRL4 in various organs. To estimate '''''CRL4''''' transcript levels, we per-formed semi-quantitative RT-PCR analysis (Fig. 5A). '''''CRL4''''' was expressed in all the examined organs; high levels of '''''CRL4''''' transcripts were found to be accumu-lated in leaf blades and roots. CRL4-like was also expressed in all the organs and the expression pattern was similar to that of '''''CRL4''''' (Fig. 5A). The researchers also examined the '''''CRL4''''' expression pattern by in situ hybridization. In the stem, signals were ob-served at the steles of the crown root primordia (Fig. 5B and 5C), the vascular bundles and the parenchyma cells adjacent to the peripheral vascular cylinder of the stem where the crown root primordia were formed (Fig. 5D and 5E)<ref name="ref1" />.
 [[File:Os03g0666100-5.png|center|thumb|400px|'''Fig. 5 Expression patterns of CRL4 and auxin distribution.''' '' <ref name="ref1" />.'']]
 ===Evolution===
-* The researchers drew dendogram of CRL4, CRL4-like and Arabidopsis '''''GNOM''''' family members; '''''GNOM''''', '''''GNOM-like1''''' (GNL1) and '''''GNOM-like2''''' (GNL2). It was constructed based on the amino acid sequence of the Sec7 domains and GBF1, which is human ARF-GEF, was used as outgroup. It therefore appears that '''''CRL4''''' is more homologous with GNOM in Arabidopsis than CRL4-like in rice (Fig. 4).
+* The researchers drew dendogram of CRL4, CRL4-like and Arabidopsis '''''GNOM''''' family members; '''''GNOM''''', '''''GNOM-like1''''' (GNL1) and '''''GNOM-like2''''' (GNL2). It was constructed based on the amino acid sequence of the Sec7 domains and GBF1, which is human ARF-GEF, was used as outgroup. It therefore appears that '''''CRL4''''' is more homologous with GNOM in Arabidopsis than CRL4-like in rice (Fig. 4)<ref name="ref1" />.
 [[File:Os03g0666100-4.png|center|thumb|400px|'''Fig. 4 Dendogram of the GNOM family proteins of Sec7 domain in Arabidopsis(GNOM, GNL1 and GNL2) and rice (CRL4 and CRL4-like).''' '' <ref name="ref1" />.'']]

@@ Line 8: / Line 8: @@
 ===Mutation===
-* Two-week-old wild-type plants (Nipponbare) formed several crown roots in comparison to crl4 mutants, in which crown root production was scarce at the same developmental stage (Fig. 1A). The researchers cross-sectioned the nodes in 5-day-old wild-type and crl4 mutant seedlings to determine the cause of crown root reduc-tion in crl4 mutants. In wild-type, several crown root primordia were formed on the outside, adjacent to the peripheral vascular cylinder (Fig. 1B). In contrast, crl4 mutants did not produce any crown root primordia (Fig. 1C). Besides the reduced crown root number, the number of lateral roots that were obtained from a seminal root of the crl4 mutant was clearly lower than that of the wild-type (Fig. 1D and 1E). The seminal root in the crl4 mutant was shorter than that of the wild-type (Fig. 1A), although there were no signifi-cant differences in the timing of the emergence of the seminal root. The crl4 mutant produced the higher number of tillers (data not shown) and their growth angles were wider than those of wild-type (Fig. 1F and 1G). Some crl4 mutants survived for more than 4 months. Four-month-old wild-type plants could reach the grain filling stage, but crl4 mutants with tiny shoots and a single seminal root could not make the transition from the vegetative to the reproductive phase (Fig. 1F and 1G).
+* Two-week-old wild-type plants (Nipponbare) formed several crown roots in comparison to '''''crl4''''' mutants, in which crown root production was scarce at the same developmental stage (Fig. 1A). The researchers cross-sectioned the nodes in 5-day-old wild-type and '''''crl4''''' mutant seedlings to determine the cause of crown root reduc-tion in '''''crl4''''' mutants. In wild-type, several crown root primordia were formed on the outside, adjacent to the peripheral vascular cylinder (Fig. 1B). In contrast, '''''crl4''''' mutants did not produce any crown root primordia (Fig. 1C). Besides the reduced crown root number, the number of lateral roots that were obtained from a seminal root of the '''''crl4''''' mutant was clearly lower than that of the wild-type (Fig. 1D and 1E). The seminal root in the crl4 mutant was shorter than that of the wild-type (Fig. 1A), although there were no signifi-cant differences in the timing of the emergence of the seminal root. The '''''crl4''''' mutant produced the higher number of tillers (data not shown) and their growth angles were wider than those of wild-type (Fig. 1F and 1G). Some '''''crl4''''' mutants survived for more than 4 months. Four-month-old wild-type plants could reach the grain filling stage, but '''''crl4''''' mutants with tiny shoots and a single seminal root could not make the transition from the vegetative to the reproductive phase (Fig. 1F and 1G).
 [[File:Os03g0666100-1.png|center|thumb|400px|'''Fig. 1 Phenotypes of crl4.''' '' <ref name="ref1" />.'']]
-* The researchers examined the root gravitropic response in crl4 mutants by measuring the curvature after gravistimulation at 90° to the vertical. Wild-type roots responded sharply to the change in the gravity vector, whereas the response of crl4 roots was impaired (Fig. 2A). The root tip angle of wild-type and crl4 roots was compared (θ in Fig. 2B); all wild-type roots had root tip angles of over 50°, while all crl4 mutants had angles of below 50° (Fig. 3). The gravitropic response was therefore defective in crl4 mutants. These results suggest that CRL4 has an auxin-related function.
+* The researchers examined the root gravitropic response in '''''crl4''''' mutants by measuring the curvature after gravistimulation at 90° to the vertical. Wild-type roots responded sharply to the change in the gravity vector, whereas the response of crl4 roots was impaired (Fig. 2A). The root tip angle of wild-type and '''''crl4''''' roots was compared (θ in Fig. 2B); all wild-type roots had root tip angles of over 50°, while all '''''crl4''''' mutants had angles of below 50° (Fig. 3). The gravitropic response was therefore defective in '''''crl4''''' mutants. These results suggest that CRL4 has an auxin-related function.
 [[File:Os03g0666100-2.png|center|thumb|400px|'''Fig. 2 Gravitropic response in a seminal root of crl4.''' '' <ref name="ref1" />.'']]
@@ Line 18: / Line 18: @@
 ===Expression===
-* The researchers examined the expression of CRL4 in various organs. To estimate CRL4 transcript levels, we per-formed semi-quantitative RT-PCR analysis (Fig. 5A). CRL4 was expressed in all the examined organs; high levels of CRL4 transcripts were found to be accumu-lated in leaf blades and roots. CRL4-like was also expressed in all the organs and the expression pattern was similar to that of CRL4 (Fig. 5A). The researchers also examined the CRL4 expression pattern by in situ hybridization. In the stem, signals were ob-served at the steles of the crown root primordia (Fig. 5B and 5C), the vascular bundles and the parenchyma cells adjacent to the peripheral vascular cylinder of the stem where the crown root primordia were formed (Fig. 5D and 5E).
+* The researchers examined the expression of CRL4 in various organs. To estimate '''''CRL4''''' transcript levels, we per-formed semi-quantitative RT-PCR analysis (Fig. 5A). '''''CRL4''''' was expressed in all the examined organs; high levels of '''''CRL4''''' transcripts were found to be accumu-lated in leaf blades and roots. CRL4-like was also expressed in all the organs and the expression pattern was similar to that of '''''CRL4''''' (Fig. 5A). The researchers also examined the '''''CRL4''''' expression pattern by in situ hybridization. In the stem, signals were ob-served at the steles of the crown root primordia (Fig. 5B and 5C), the vascular bundles and the parenchyma cells adjacent to the peripheral vascular cylinder of the stem where the crown root primordia were formed (Fig. 5D and 5E).
 [[File:Os03g0666100-5.png|center|thumb|400px|'''Fig. 5 Expression patterns of CRL4 and auxin distribution.''' '' <ref name="ref1" />.'']]
 ===Evolution===
-* The researchers drew dendogram of CRL4, CRL4-like and Arabidopsis GNOM family members; GNOM, GNOM-like1 (GNL1) and GNOM-like2 (GNL2). It was constructed based on the amino acid sequence of the Sec7 domains and GBF1, which is human ARF-GEF, was used as outgroup. It therefore appears that CRL4 is more homologous with GNOM in Arabidopsis than CRL4-like in rice (Fig. 4).
+* The researchers drew dendogram of CRL4, CRL4-like and Arabidopsis '''''GNOM''''' family members; '''''GNOM''''', '''''GNOM-like1''''' (GNL1) and '''''GNOM-like2''''' (GNL2). It was constructed based on the amino acid sequence of the Sec7 domains and GBF1, which is human ARF-GEF, was used as outgroup. It therefore appears that '''''CRL4''''' is more homologous with GNOM in Arabidopsis than CRL4-like in rice (Fig. 4).
 [[File:Os03g0666100-4.png|center|thumb|400px|'''Fig. 4 Dendogram of the GNOM family proteins of Sec7 domain in Arabidopsis(GNOM, GNL1 and GNL2) and rice (CRL4 and CRL4-like).''' '' <ref name="ref1" />.'']]

@@ Line 3: / Line 3: @@
 ==Annotated Information==
 ===Function===
 ===Mutation===

@@ Line 18: / Line 18: @@
 * The researchers examined the expression of CRL4 in various organs. To estimate CRL4 transcript levels, we per-formed semi-quantitative RT-PCR analysis (Fig. 5A). CRL4 was expressed in all the examined organs; high levels of CRL4 transcripts were found to be accumu-lated in leaf blades and roots. CRL4-like was also expressed in all the organs and the expression pattern was similar to that of CRL4 (Fig. 5A). The researchers also examined the CRL4 expression pattern by in situ hybridization. In the stem, signals were ob-served at the steles of the crown root primordia (Fig. 5B and 5C), the vascular bundles and the parenchyma cells adjacent to the peripheral vascular cylinder of the stem where the crown root primordia were formed (Fig. 5D and 5E).
-[[File:Os03g0666100-5.png|center|thumb|400px|'''Fig. 3 The crl4 mutant plant containing the empty vector(left) and the genomic DNA fragment encompassing the entire CRL4 gene (right) were shown. Bar = 1cm.''' '' <ref name="ref1" />.'']]
+[[File:Os03g0666100-5.png|center|thumb|400px|'''Fig. 5 Expression patterns of CRL4 and auxin distribution.''' '' <ref name="ref1" />.'']]
 ===Evolution===

@@ Line 19: / Line 19: @@
 ===Evolution===
-Please input evolution information here.
+* The researchers drew dendogram of CRL4, CRL4-like and Arabidopsis GNOM family members; GNOM, GNOM-like1 (GNL1) and GNOM-like2 (GNL2). It was constructed based on the amino acid sequence of the Sec7 domains and GBF1, which is human ARF-GEF, was used as outgroup. It therefore appears that CRL4 is more homologous with GNOM in Arabidopsis than CRL4-like in rice (Fig. 4).
 ==Labs working on this gene==

← Older revision		Revision as of 07:50, 8 August 2016
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	* Two-week-old wild-type plants (Nipponbare) formed several crown roots in comparison to crl4 mutants, in which crown root production was scarce at the same developmental stage (Fig. 1A). The researchers cross-sectioned the nodes in 5-day-old wild-type and crl4 mutant seedlings to determine the cause of crown root reduc-tion in crl4 mutants. In wild-type, several crown root primordia were formed on the outside, adjacent to the peripheral vascular cylinder (Fig. 1B). In contrast, crl4 mutants did not produce any crown root primordia (Fig. 1C). Besides the reduced crown root number, the number of lateral roots that were obtained from a seminal root of the crl4 mutant was clearly lower than that of the wild-type (Fig. 1D and 1E). The seminal root in the crl4 mutant was shorter than that of the wild-type (Fig. 1A), although there were no signifi-cant differences in the timing of the emergence of the seminal root. The crl4 mutant produced the higher number of tillers (data not shown) and their growth angles were wider than those of wild-type (Fig. 1F and 1G). Some crl4 mutants survived for more than 4 months. Four-month-old wild-type plants could reach the grain filling stage, but crl4 mutants with tiny shoots and a single seminal root could not make the transition from the vegetative to the reproductive phase (Fig. 1F and 1G).		* Two-week-old wild-type plants (Nipponbare) formed several crown roots in comparison to crl4 mutants, in which crown root production was scarce at the same developmental stage (Fig. 1A). The researchers cross-sectioned the nodes in 5-day-old wild-type and crl4 mutant seedlings to determine the cause of crown root reduc-tion in crl4 mutants. In wild-type, several crown root primordia were formed on the outside, adjacent to the peripheral vascular cylinder (Fig. 1B). In contrast, crl4 mutants did not produce any crown root primordia (Fig. 1C). Besides the reduced crown root number, the number of lateral roots that were obtained from a seminal root of the crl4 mutant was clearly lower than that of the wild-type (Fig. 1D and 1E). The seminal root in the crl4 mutant was shorter than that of the wild-type (Fig. 1A), although there were no signifi-cant differences in the timing of the emergence of the seminal root. The crl4 mutant produced the higher number of tillers (data not shown) and their growth angles were wider than those of wild-type (Fig. 1F and 1G). Some crl4 mutants survived for more than 4 months. Four-month-old wild-type plants could reach the grain filling stage, but crl4 mutants with tiny shoots and a single seminal root could not make the transition from the vegetative to the reproductive phase (Fig. 1F and 1G).

−	[[File:.png\|center\|thumb\|400px\|'''Fig. 1 Phenotypes of crl4.''' '' <ref name="ref1" />.'']]	+	[[File:Os03g0666100-1.png\|center\|thumb\|400px\|'''Fig. 1 Phenotypes of crl4.''' '' <ref name="ref1" />.'']]

		+	* The researchers examined the root gravitropic response in crl4 mutants by measuring the curvature after gravistimulation at 90° to the vertical. Wild-type roots responded sharply to the change in the gravity vector, whereas the response of crl4 roots was impaired (Fig. 2A). The root tip angle of wild-type and crl4 roots was compared (θ in Fig. 2B); all wild-type roots had root tip angles of over 50°, while all crl4 mutants had angles of below 50° (Fig. 3). The gravitropic response was therefore defective in crl4 mutants. These results suggest that CRL4 has an auxin-related function.
		+
		+	[[File:Os03g0666100-2.png\|center\|thumb\|400px\|'''Fig. 2 Gravitropic response in a seminal root of crl4.''' '' <ref name="ref1" />.'']]
		+	[[File:Os03g0666100-3.png\|center\|thumb\|400px\|'''Fig. 3 The crl4 mutant plant containing the empty vector(left) and the genomic DNA fragment encompassing the entire CRL4 gene (right) were shown. Bar = 1cm.''' '' <ref name="ref1" />.'']]