Difference between revisions of "Os01g0883800"
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== Annotated Information == | == Annotated Information == | ||
=== Function === | === Function === | ||
| − | This gene is originally derived from the chinese cultivar Dee-Geo-Woo-Gen(DGWG). It encodes an oxidase enzyme involved in the biosynthesis of gibberellin, which is a plant growth hormone. The rice genome carries at least two GA20ox genes (GA20ox-1 and GA20ox-2).SD1 corresponds to GA20ox-2. Mutation of SD1 will cause a semi-dwarf phenotype of rice without seed yield being affected <ref | + | This gene is originally derived from the chinese cultivar Dee-Geo-Woo-Gen(DGWG). It encodes an oxidase enzyme involved in the biosynthesis of gibberellin, which is a plant growth hormone. The rice genome carries at least two GA20ox genes (GA20ox-1 and GA20ox-2).SD1 corresponds to GA20ox-2. Mutation of SD1 will cause a semi-dwarf phenotype of rice without seed yield being affected <ref name="ref1" />. It is not surprising that a rice semidwarfing gene encodes GA20-ox since successful production of semidwarf plants using antisense or overexpressed GA20-ox genes has been reported in Arabidopsis, Solanum dulcamara, potato, and lettuce. |
| − | It is a key enzyme in the biosynthesis of gibberellin that catalyses the three steps GA53->GA44->GA19->GA20. Impaired GA 20-oxidase activity will cause elevated content of GA53, and reduced amount of G20 | + | It is a key enzyme in the biosynthesis of gibberellin that catalyses the three steps GA53->GA44->GA19->GA20. Impaired GA 20-oxidase activity will cause elevated content of GA53, and reduced amount of G20 <ref name="ref1" />.<ref name="ref2" />. However, there is slight difference between different strains. The extent of GA1 is lower in Doongara (semi-dwarf rice strain) when compared with Kyeema (tall), while there is no significant difference between Calrose76 (semi-dwarf rice strain) and Calrose (tall). Calrose76 has lower contents of GA44 and of GA19 than Calrose, while there is no significant difference between Doongara (semi-dwarf rice strain) when compared with Kyeema (tall) <ref name="ref2" />. |
GO asignment(s): GO:0005506, GO:0016216, GO:0017000 | GO asignment(s): GO:0005506, GO:0016216, GO:0017000 | ||
=== Mutation === | === Mutation === | ||
| − | ‘dee-geo-woo-gen’ (semi-dwarf rice strain) and IR8 (semi-dwarf rice strain): A 383-base-pair deletion, which induces a frameshift that creates a stop codon in SD1 may be related with the semi-dwarf phenotype | + | ‘dee-geo-woo-gen’ (semi-dwarf rice strain) and IR8 (semi-dwarf rice strain): A 383-base-pair deletion, which induces a frameshift that creates a stop codon in SD1 may be related with the semi-dwarf phenotype <ref name="ref1" />. |
| − | Doongara (semi-dwarf rice strain): A 280-bp deletion within the coding region, which spans parts of exon 1 and exon 2, is predicted to result in a truncated, nonfunctional polypeptide containing the first 99 amino acid residues of the GA 2-oxidase, followed by an additional 3 amino acids that are in the wrong reading frame before a termination codon | + | Doongara (semi-dwarf rice strain): A 280-bp deletion within the coding region, which spans parts of exon 1 and exon 2, is predicted to result in a truncated, nonfunctional polypeptide containing the first 99 amino acid residues of the GA 2-oxidase, followed by an additional 3 amino acids that are in the wrong reading frame before a termination codon <ref name="ref2" />. |
| − | Calrose76 (semi-dwarf rice strain): The DNA sequence of Calrose76 is identical to Calrose (tall) except for a C to T transition at position 798 that resulted in a change of the predicted amino acid leucine (Leu-266) in Calrose to phenylalanine in Calrose76 | + | Calrose76 (semi-dwarf rice strain): The DNA sequence of Calrose76 is identical to Calrose (tall) except for a C to T transition at position 798 that resulted in a change of the predicted amino acid leucine (Leu-266) in Calrose to phenylalanine in Calrose76 <ref name="ref2" />. |
=== Expression === | === Expression === | ||
| − | This gene is strongly expressed in the leaf blade, stem and unopened flower, whereas GA20ox-1 is predominantly expressed in the unopened flower | + | This gene is strongly expressed in the leaf blade, stem and unopened flower, whereas GA20ox-1 is predominantly expressed in the unopened flower <ref name="ref1" />. |
| − | Primers for DNA amplication: forward primer, 5'-CAACTCACTCCCGCTCAACACAGC-3', and reverse primer, 5'-TTTGAAATGCAATGTCGTCCACC-3' were used to amplify exon 1; forward primer, 5'-GCGCCAATGGGGTAATTAAAACG-3' and reverse primer, 5'-GGCATTCCATTGTTTGTGATTGG-3' were used for exon 2; forward primer, 5'-GTTTGTCCTTGTCGCGTTGCTCAG-3' and reverse primer, 5'-TCTGTTCGTTCCGTTTCGTTCCG-3' were used for exon 3 | + | Primers for DNA amplication: forward primer, 5'-CAACTCACTCCCGCTCAACACAGC-3', and reverse primer, 5'-TTTGAAATGCAATGTCGTCCACC-3' were used to amplify exon 1; forward primer, 5'-GCGCCAATGGGGTAATTAAAACG-3' and reverse primer, 5'-GGCATTCCATTGTTTGTGATTGG-3' were used for exon 2; forward primer, 5'-GTTTGTCCTTGTCGCGTTGCTCAG-3' and reverse primer, 5'-TCTGTTCGTTCCGTTTCGTTCCG-3' were used for exon 3 <ref name="ref2" />. |
| − | Primers for RT-PCR: forward primer 5'-CAACTCACTCCCGCTCAACACAGC- 3' located 22-bp upstream from the translation start, and a reverse primer 5'-GTTCGTTCCGTTTCGGTTCCG- 3' eight-bp downstream from the TGA stop codon | + | Primers for RT-PCR: forward primer 5'-CAACTCACTCCCGCTCAACACAGC- 3' located 22-bp upstream from the translation start, and a reverse primer 5'-GTTCGTTCCGTTTCGGTTCCG- 3' eight-bp downstream from the TGA stop codon <ref name="ref2" />. |
=== Evolution === | === Evolution === | ||
This gene is conserved in ''Arabidopsis'' (47% identity) and pea(50% identity). GA20ox-2 shows 47.8% identity to | This gene is conserved in ''Arabidopsis'' (47% identity) and pea(50% identity). GA20ox-2 shows 47.8% identity to | ||
| − | GA20ox-1 in rice. There are at least three GA20-ox genes in Arabidopsis | + | GA20ox-1 in rice. There are at least three GA20-ox genes in Arabidopsis <ref name="ref1" />.<ref name="ref2" />. |
== Labs working on this gene == | == Labs working on this gene == | ||
| Line 42: | Line 42: | ||
== References == | == References == | ||
| − | <references /> | + | WHERE CITE<ref name="ref3" />? |
| − | 1. | + | <references> |
| + | <ref name="ref1">Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, et al. (2002) Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416: 701-702.</ref> | ||
| + | <ref name="ref2">Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci U S A 99: 9043-9048.</ref> | ||
| + | <ref name="ref3">Monna L, Kitazawa N, Yoshino R, Suzuki J, Masuda H, et al. (2002) Positional cloning of rice semidwarfing gene, sd-1: rice "green revolution gene" encodes a mutant enzyme involved in gibberellin synthesis. DNA Res 9: 11-17.</ref> | ||
| + | </references> | ||
| − | |||
| − | |||
| − | |||
== Structured Information == | == Structured Information == | ||
Revision as of 22:52, 12 July 2012
The rice semidwarf-1 (sd1) is well known as the "green revolution gene" and controls the plant height of rice.
Contents
Annotated Information
Function
This gene is originally derived from the chinese cultivar Dee-Geo-Woo-Gen(DGWG). It encodes an oxidase enzyme involved in the biosynthesis of gibberellin, which is a plant growth hormone. The rice genome carries at least two GA20ox genes (GA20ox-1 and GA20ox-2).SD1 corresponds to GA20ox-2. Mutation of SD1 will cause a semi-dwarf phenotype of rice without seed yield being affected [1]. It is not surprising that a rice semidwarfing gene encodes GA20-ox since successful production of semidwarf plants using antisense or overexpressed GA20-ox genes has been reported in Arabidopsis, Solanum dulcamara, potato, and lettuce.
It is a key enzyme in the biosynthesis of gibberellin that catalyses the three steps GA53->GA44->GA19->GA20. Impaired GA 20-oxidase activity will cause elevated content of GA53, and reduced amount of G20 [1].[2]. However, there is slight difference between different strains. The extent of GA1 is lower in Doongara (semi-dwarf rice strain) when compared with Kyeema (tall), while there is no significant difference between Calrose76 (semi-dwarf rice strain) and Calrose (tall). Calrose76 has lower contents of GA44 and of GA19 than Calrose, while there is no significant difference between Doongara (semi-dwarf rice strain) when compared with Kyeema (tall) [2].
GO asignment(s): GO:0005506, GO:0016216, GO:0017000
Mutation
‘dee-geo-woo-gen’ (semi-dwarf rice strain) and IR8 (semi-dwarf rice strain): A 383-base-pair deletion, which induces a frameshift that creates a stop codon in SD1 may be related with the semi-dwarf phenotype [1].
Doongara (semi-dwarf rice strain): A 280-bp deletion within the coding region, which spans parts of exon 1 and exon 2, is predicted to result in a truncated, nonfunctional polypeptide containing the first 99 amino acid residues of the GA 2-oxidase, followed by an additional 3 amino acids that are in the wrong reading frame before a termination codon [2].
Calrose76 (semi-dwarf rice strain): The DNA sequence of Calrose76 is identical to Calrose (tall) except for a C to T transition at position 798 that resulted in a change of the predicted amino acid leucine (Leu-266) in Calrose to phenylalanine in Calrose76 [2].
Expression
This gene is strongly expressed in the leaf blade, stem and unopened flower, whereas GA20ox-1 is predominantly expressed in the unopened flower [1].
Primers for DNA amplication: forward primer, 5'-CAACTCACTCCCGCTCAACACAGC-3', and reverse primer, 5'-TTTGAAATGCAATGTCGTCCACC-3' were used to amplify exon 1; forward primer, 5'-GCGCCAATGGGGTAATTAAAACG-3' and reverse primer, 5'-GGCATTCCATTGTTTGTGATTGG-3' were used for exon 2; forward primer, 5'-GTTTGTCCTTGTCGCGTTGCTCAG-3' and reverse primer, 5'-TCTGTTCGTTCCGTTTCGTTCCG-3' were used for exon 3 [2].
Primers for RT-PCR: forward primer 5'-CAACTCACTCCCGCTCAACACAGC- 3' located 22-bp upstream from the translation start, and a reverse primer 5'-GTTCGTTCCGTTTCGGTTCCG- 3' eight-bp downstream from the TGA stop codon [2].
Evolution
This gene is conserved in Arabidopsis (47% identity) and pea(50% identity). GA20ox-2 shows 47.8% identity to GA20ox-1 in rice. There are at least three GA20-ox genes in Arabidopsis [1].[2].
Labs working on this gene
Bioscience Center, and Graduate School of Bioagricultural Science, Nagoya University, Nagoya 464-8601, Japan Honda R&D, Wako Research Center, Wako 351-0193, Japan
International Rice Research Institute, Manila, DAPO Box 7777, Philippines
BioResources Center, and Plant Molecular Biology Laboratory, Riken, Tsukuba 305-0074, Japan
Division of Plant Industry, Commonwealth Scientific and Industrial Research Organization, GPO Box 1600, Canberra ACT 2601, Australia
Plant Genome Center, 1-25-2 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
References
WHERE CITE[3]?
- ↑ 1.0 1.1 1.2 1.3 1.4 Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, et al. (2002) Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416: 701-702.
- ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci U S A 99: 9043-9048.
- ↑ Monna L, Kitazawa N, Yoshino R, Suzuki J, Masuda H, et al. (2002) Positional cloning of rice semidwarfing gene, sd-1: rice "green revolution gene" encodes a mutant enzyme involved in gibberellin synthesis. DNA Res 9: 11-17.
Structured Information
| Gene Name |
Os01g0883800 |
|---|---|
| Description |
Gibberellin 20 oxidase 2 (EC 1.14.11.-) (Gibberellin C-20 oxidase 2) (GA 20-oxidase 2) (Os20ox2) (Semidwarf-1 protein) |
| Version |
NM_001051549.1 GI:115441468 GeneID:4325003 |
| Length |
2743 bp |
| Definition |
Oryza sativa Japonica Group Os01g0883800, complete gene. |
| Source |
Oryza sativa Japonica Group ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
| Chromosome | |
| Location |
Chromosome 1:40138313..40141055 |
| Sequence Coding Region |
40138313..40138869,40138972..40139293,40140765..40141055 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008394:40138313..40141055 source=RiceChromosome01 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008394:40138313..40141055 source=RiceChromosome01 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atggtggccgagcaccccacgccaccacagccgcaccaaccaccgcccatggactccaccgccggctctggcattgccgccccggcggcggcggcggtgtgcgacctgaggatggagcccaagatcccggagccattcgtgtggccgaacggcgacgcgaggccggcgtcggcggcggagctggacatgcccgtggtcgacgtgggcgtgctccgcgacggcgacgccgaggggctgcgccgcgccgcggcgcaggtggccgccgcgtgcgccacgcacgggttcttccaggtgtccgagcacggcgtcgacgccgctctggcgcgcgccgcgctcgacggcgccagcgacttcttccgcctcccgctcgccgagaagcgccgcgcgcgccgcgtcccgggcaccgtgtccggctacaccagcgcccacgccgaccgcttcgcctccaagctcccatggaaggagaccctctccttcggcttccacgaccgcgccgccgcccccgtcgtcgccgactacttctccagcaccctcggccccgacttcgcgccaatggggagggtgtaccagaagtactgcgaggagatgaaggagctgtcgctgacgatcatggaactcctggagctgagcctgggcgtggagcgaggctactacagggagttcttcgcggacagcagctcaatcatgcggtgcaactactacccgccatgcccggagccggagcggacgctcggcacgggcccgcactgcgaccccaccgccctcaccatcctcctccaggacgacgtcggcggcctcgaggtcctcgtcgacggcgaatggcgccccgtcagccccgtccccggcgccatggtcatcaacatcggcgacaccttcatggcgctgtcgaacgggaggtataagagctgcctgcacagggcggtggtgaaccagcggcgggagcggcggtcgctggcgttcttcctgtgcccgcgggaggacagggtggtgcggccgccgccgagcgccgccacgccgcagcactacccggacttcacctgggccgacctcatgcgcttcacgcagcgccactaccgcgccgacacccgcacgctcgacgccttcacgcgctggctcgcgccgccggccgccgacgccgccgcgacggcgcaggtcgaggcggccagctga</cdnaseq> |
| Protein Sequence |
<aaseq>MVAEHPTPPQPHQPPPMDSTAGSGIAAPAAAAVCDLRMEPKIPE PFVWPNGDARPASAAELDMPVVDVGVLRDGDAEGLRRAAAQVAAACATHGFFQVSEHG VDAALARAALDGASDFFRLPLAEKRRARRVPGTVSGYTSAHADRFASKLPWKETLSFG FHDRAAAPVVADYFSSTLGPDFAPMGRVYQKYCEEMKELSLTIMELLELSLGVERGYY REFFADSSSIMRCNYYPPCPEPERTLGTGPHCDPTALTILLQDDVGGLEVLVDGEWRP VSPVPGAMVINIGDTFMALSNGRYKSCLHRAVVNQRRERRSLAFFLCPREDRVVRPPP SAATPQHYPDFTWADLMRFTQRHYRADTRTLDAFTRWLAPPAADAAATAQVEAAS</aaseq> |
| Gene Sequence |
<dnaseqindica>1..557#660..981#2453..2743#atggtggccgagcaccccacgccaccacagccgcaccaaccaccgcccatggactccaccgccggctctggcattgccgccccggcggcggcggcggtgtgcgacctgaggatggagcccaagatcccggagccattcgtgtggccgaacggcgacgcgaggccggcgtcggcggcggagctggacatgcccgtggtcgacgtgggcgtgctccgcgacggcgacgccgaggggctgcgccgcgccgcggcgcaggtggccgccgcgtgcgccacgcacgggttcttccaggtgtccgagcacggcgtcgacgccgctctggcgcgcgccgcgctcgacggcgccagcgacttcttccgcctcccgctcgccgagaagcgccgcgcgcgccgcgtcccgggcaccgtgtccggctacaccagcgcccacgccgaccgcttcgcctccaagctcccatggaaggagaccctctccttcggcttccacgaccgcgccgccgcccccgtcgtcgccgactacttctccagcaccctcggccccgacttcgcgccaatggggtaattaaaacgatggtggacgacattgcatttcaaattcaaaacaaattcaaaacacaccgaccgagattatgctgaattcaaacgcgtttgtgcgcgcaggagggtgtaccagaagtactgcgaggagatgaaggagctgtcgctgacgatcatggaactcctggagctgagcctgggcgtggagcgaggctactacagggagttcttcgcggacagcagctcaatcatgcggtgcaactactacccgccatgcccggagccggagcggacgctcggcacgggcccgcactgcgaccccaccgccctcaccatcctcctccaggacgacgtcggcggcctcgaggtcctcgtcgacggcgaatggcgccccgtcagccccgtccccggcgccatggtcatcaacatcggcgacaccttcatggtaaaccatctcctattctcctctcctctgttctcctctgcttcgaagcaacagaacaagtaattcaagcttttttttctctctcgcgcgaaattgacgagaaaaataagatcgtggtaggggcggggctttcagctgaaagcgggaagaaaccgacctgacgtgatttctctgttccaatcacaaacaatggaatgccccactcctccatgtgttatgatttatctcacatcttatagttaataggagtaagtaacaagctacttttttcatattatagttcgtttgattttttttttttaaagtttttttagttttatccaaatttattgaaaaacttagcaacgtttataataccaaattagtctcatttagtttaatattgtatatattttgataatatatttatgttatattaaaaatattactatatttttctataaacattattaaaagccatttataatataaaatggaaggagtaattaatatggatctcccccgacatgagaatattttccgatggtgtgacgacgccatgtaagcttcggtgggcctggacggccagaggtgccaacagccacgtccaacaacccctgggtccccccctaacactccaaacagtagtgagtagtgtctcgtcgcgttttagtatttgatgacaaacaaagtgtgagttgagttagccaccaccaacttgcacacgagcacatacatttgtgtccattctcgccagtcacttccatctctagtcctaactcctatctagcgatgtaagcggataatttcatcatccgtatataaacctgtttgttatagttaatttcctatataatactataacagtatacattttaaaagaaaacaaaattaggataaacaggccctgctcctatccatccatggcacttggaaggaccagactcggtcatgccatgccaagccaagatatgggttatggaagagtagagaagaggagagatgagagataagcatgcgttctcctcctcgttggatgtgtattttggagggatttgtgtagtagtagcagcggcgccgcggggacggatgcggatggtggcgctttcggtggcgttttcccgggggggttttggtttggcgcttgggggggatggcatggcgcggcgtgcggctgcacgccacacacacgcgcgcgcacgcacgtacgtcgtcgtcgccgcgggcggacggtagcttagggtggtgtgttccgcgcgcgggcgcggattgttccatgccgatcgatttggcgccaccctcgccgcggctcttgtcgcgtcgtgcgcctctctcgcgcggtttgtccttgtcgcgttgctcagccggcgacgggggcacggacattggcgatgtagccctgcacgtgtcggcctctccgttgatgaatgatgatgtatgtatgtatttttttttgtctgaaggaatttgtggggaattgttgtgtgtgcaggcgctgtcgaacgggaggtataagagctgcctgcacagggcggtggtgaaccagcggcgggagcggcggtcgctggcgttcttcctgtgcccgcgggaggacagggtggtgcggccgccgccgagcgccgccacgccgcagcactacccggacttcacctgggccgacctcatgcgcttcacgcagcgccactaccgcgccgacacccgcacgctcgacgccttcacgcgctggctcgcgccgccggccgccgacgccgccgcgacggcgcaggtcgaggcggccagctga</dnaseqindica> |
| External Link(s) |
