Difference between revisions of "Os04g0474800"
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==Annotated Information== | ==Annotated Information== | ||
| − | + | Function | |
This gene encodes β-glucosidases (3.2.1.21),which belongs to , β-glucosidases (3.2.1.21). It is reported that β-glucosidases (3.2.1.21) have been implicated in physiologically important processes in plants, such as response to biotic and abiotic stresses, defense against herbivores, activation of phytohormones, lignification, and cell wall remodeling. | This gene encodes β-glucosidases (3.2.1.21),which belongs to , β-glucosidases (3.2.1.21). It is reported that β-glucosidases (3.2.1.21) have been implicated in physiologically important processes in plants, such as response to biotic and abiotic stresses, defense against herbivores, activation of phytohormones, lignification, and cell wall remodeling. | ||
| − | + | Expression | |
The widely existing cell wall makes it extensively express in every cell of plant, because it is involved in the course of defense response, carbohydrate metabolism. Its encoding enzyme is found essentially in all living organisms and has been implicated in a diversity of roles, such as biomass conversion in microorganisms [1] and activation of defense compounds [2,3], phytohormones [4,5], lignin precursors [6], aromatic volatiles [7], and metabolic intermediates by releasing glucose blocking groups from the inactive glucosides in plants. | The widely existing cell wall makes it extensively express in every cell of plant, because it is involved in the course of defense response, carbohydrate metabolism. Its encoding enzyme is found essentially in all living organisms and has been implicated in a diversity of roles, such as biomass conversion in microorganisms [1] and activation of defense compounds [2,3], phytohormones [4,5], lignin precursors [6], aromatic volatiles [7], and metabolic intermediates by releasing glucose blocking groups from the inactive glucosides in plants. | ||
The enzyme can be expressed in different cells, tissues, or organs and may be expressed in response to different environmental conditions and stresses. | The enzyme can be expressed in different cells, tissues, or organs and may be expressed in response to different environmental conditions and stresses. | ||
| + | |||
| + | Reasonable Primer | ||
| + | 5' sense primer 5'-TGTCCATGGCGGCAGCAG-3' | ||
| + | 3 reversed primer 5'-AACTGGATTACTTCCATCTC-3' | ||
| + | |||
| + | Evolution | ||
Gene structural analysis of the β-glucosidases showed intron-exon boundaries and intron numbers are highly conserved among rice and other plant β-glucosidase genes.The size of rice GH1 is not unexpected, since a search of the Arabidopsis thaliana genome identified 47 glycosyl hydrolase family 1 homologues, including 8 probable. including 34 full-length genes, 2 pseudogenes, 2 gene fragments, and 2 intronless genes, were identified, as listed in Table Table1.1. Thirty-six out of 40 genes are found in both japonica and indica rice with 98–100% sequence identity. The Os11bglu35 gene was present only in japonica rice sequences, while Os11bglu37, Osbglu39 and Osbglu40 were only found in indica rice. The thirty-eight mapped GH1 genes are distributed over all chromosomes, except chromosome 2 (Table (Table1).1). The Osbglu39 and Osbglu40 sequences have not been mapped to any chromosome, and it is possible they represent contamination of endophytic genes remaining in the indica genome draft. | Gene structural analysis of the β-glucosidases showed intron-exon boundaries and intron numbers are highly conserved among rice and other plant β-glucosidase genes.The size of rice GH1 is not unexpected, since a search of the Arabidopsis thaliana genome identified 47 glycosyl hydrolase family 1 homologues, including 8 probable. including 34 full-length genes, 2 pseudogenes, 2 gene fragments, and 2 intronless genes, were identified, as listed in Table Table1.1. Thirty-six out of 40 genes are found in both japonica and indica rice with 98–100% sequence identity. The Os11bglu35 gene was present only in japonica rice sequences, while Os11bglu37, Osbglu39 and Osbglu40 were only found in indica rice. The thirty-eight mapped GH1 genes are distributed over all chromosomes, except chromosome 2 (Table (Table1).1). The Osbglu39 and Osbglu40 sequences have not been mapped to any chromosome, and it is possible they represent contamination of endophytic genes remaining in the indica genome draft. | ||
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3. Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0406, USA | 3. Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0406, USA | ||
Those main labs has done a lot about this gene | Those main labs has done a lot about this gene | ||
| − | + | 'References | |
1. Fowler T: Deletion of the Trichoderma reesei β-glucosidase gene, bgl1. In β-glucosidases: Biochemistry and Molecular Biology. Edited by Esen A. Washington DC: American Chemical Society; 1993:56-65. | 1. Fowler T: Deletion of the Trichoderma reesei β-glucosidase gene, bgl1. In β-glucosidases: Biochemistry and Molecular Biology. Edited by Esen A. Washington DC: American Chemical Society; 1993:56-65. | ||
2. Poulton JE: Cyanogenesis in plants.Plant Physiol 1990, 94:401-405. | 2. Poulton JE: Cyanogenesis in plants.Plant Physiol 1990, 94:401-405. | ||
Revision as of 04:27, 10 June 2014
Please input one-sentence summary here.
Annotated Information
Function This gene encodes β-glucosidases (3.2.1.21),which belongs to , β-glucosidases (3.2.1.21). It is reported that β-glucosidases (3.2.1.21) have been implicated in physiologically important processes in plants, such as response to biotic and abiotic stresses, defense against herbivores, activation of phytohormones, lignification, and cell wall remodeling. Expression The widely existing cell wall makes it extensively express in every cell of plant, because it is involved in the course of defense response, carbohydrate metabolism. Its encoding enzyme is found essentially in all living organisms and has been implicated in a diversity of roles, such as biomass conversion in microorganisms [1] and activation of defense compounds [2,3], phytohormones [4,5], lignin precursors [6], aromatic volatiles [7], and metabolic intermediates by releasing glucose blocking groups from the inactive glucosides in plants. The enzyme can be expressed in different cells, tissues, or organs and may be expressed in response to different environmental conditions and stresses.
Reasonable Primer 5' sense primer 5'-TGTCCATGGCGGCAGCAG-3' 3 reversed primer 5'-AACTGGATTACTTCCATCTC-3'
Evolution
Gene structural analysis of the β-glucosidases showed intron-exon boundaries and intron numbers are highly conserved among rice and other plant β-glucosidase genes.The size of rice GH1 is not unexpected, since a search of the Arabidopsis thaliana genome identified 47 glycosyl hydrolase family 1 homologues, including 8 probable. including 34 full-length genes, 2 pseudogenes, 2 gene fragments, and 2 intronless genes, were identified, as listed in Table Table1.1. Thirty-six out of 40 genes are found in both japonica and indica rice with 98–100% sequence identity. The Os11bglu35 gene was present only in japonica rice sequences, while Os11bglu37, Osbglu39 and Osbglu40 were only found in indica rice. The thirty-eight mapped GH1 genes are distributed over all chromosomes, except chromosome 2 (Table (Table1).1). The Osbglu39 and Osbglu40 sequences have not been mapped to any chromosome, and it is possible they represent contamination of endophytic genes remaining in the indica genome draft.
Phylogenetic tree of predicted protein sequences of rice and Arabidopsis Glycosyl Hydrolase Family 1 genes
Amino acid sequence alignment and phylogenetic analysis of 36 members including 34 full-length genes and 2 pseudogenes, but not including the intronless bacteria-like enzyme genes Osbglu39 and Osbglu40, and gene fragments, Os4bglu15 andOs4bglu17, showed that the sequences share a common evolutionary origin (Figure (Figure2).2). Interestingly, many members that contain closely related sequences and cluster together are located on the same chromosome, such as the members in chromosomes 1, 4, 5, 8, 9 and 11, indicating localized (intrachromosomal) duplication events. Some of the closely related GH1 members of Arabidopsis also cluster on the same chromosome [8]. Comparison between rice and ArabidopsisGH1 members revealed that 7 clearly distinct clusters of plant-like GH1 genes (marked 1 to 7 in Figure Figure2)2) contain both Arabidopsis and rice genes that are clearly more closely related to each other than to other GH1 genes within their own species. In addition, the Arabidopsis SFR2 gene (not shown) forms another interspecies cluster with its rice homologue, Os11bglu36, which is marked (8) in Figure Figure2.2. Thus, it appears the ancestor of rice and Arabidopsis had at least 8 GH1 genes. However, 22 out of 40 Arabidopsis genes group in two large clusters without rice gene members (marked AtI and AtII in Figure Figure2),2), which incorporate several of the subfamilies defined by Xu et al. [8], and appear to have diverged before the rice andArabidopsis. These include the myrosinases, which are not known to occur in rice, but also many apparent β-glucosidases. Similarly, some rice genes appear to have diverged from their cluster of Arabidopsis and rice genes before the otherArabidopsis and rice genes diverged. These include the Os3bglu7 and Os3bglu8 BMC Plant Biology
BioMed Central
Labs working on this gene
1. Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand 2. Department of Low-Temperature Science, National Agricultural Research Center for Hokkaido Region, Sapporo 062-8555, Japan 3. Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0406, USA Those main labs has done a lot about this gene 'References 1. Fowler T: Deletion of the Trichoderma reesei β-glucosidase gene, bgl1. In β-glucosidases: Biochemistry and Molecular Biology. Edited by Esen A. Washington DC: American Chemical Society; 1993:56-65. 2. Poulton JE: Cyanogenesis in plants.Plant Physiol 1990, 94:401-405. 3. Duroux L, Delmotte FM, Lancelin J-M, Keravis G, Jay-Alleand C: Insight into naphthoquinone metabolism: β-glucosidase-catalysed hydrolysis of hydrojuglone β-D-glucopyranoside.Biochem J 1998, 333:275-283. 4. Brzobohaty B, Moore I, Kristoffersen P, Bako L, Campos N, Schell J, Palme K:Release of active cytokinin by a β-glucosidase localized to the maize root meristem.Science 1993, 262:1051-1054 5. Falk A, Rask L: Expression of a zeatin-O-glucoside-degrading β-glucosidase inBrassica napus. Plant Physiol 1995, 108:1369-1377. 6. Dharmawardhana DP, Ellis BE, Carlson JE: A β-glucosidase from lodgepole pine specific for the lignin precursor coniferin.Plant Physiol 1995, 107:331-339. 7. Mizutani M, Nakanishi H, Ema J, Ma S, Noguchi E, Inohara-Ochiai M, Fukuchi-Mizutani M, Nakao M, Sakata K: Cloning of β-primeverosidase from tea leaves, a key enzyme in tea aroma formation.Plant Physiol 2002, 130:2164-2176. 8. Xu Z, Escamilla-Treviño LL, Zeng L, Lalgondar M, Bevan DR, Winkel BSJ, Mohamed A, Cheng C, Shih M, Poulton JE, Esen A: Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 1.Plant Mol Biol 2004, 55:343-367
Structured Information
| Gene Name |
Os04g0474800 |
|---|---|
| Description |
Similar to Amygdalin hydrolase isoform AH I precursor (EC 3.2.1.117) |
| Version |
NM_001059605.1 GI:115458939 GeneID:4336145 |
| Length |
3128 bp |
| Definition |
Oryza sativa Japonica Group Os04g0474800, 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 4:24146143..24149270 |
| Sequence Coding Region |
24146265..24146433,24146526..24146634,24146798..24146900,24146991..24147022,24147234..24147451 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008397:24146143..24149270 source=RiceChromosome04 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008397:24146143..24149270 source=RiceChromosome04 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>aaattcactgtcatggcagatggaagtctgaggggtggagtcaacaaagaaggcataaagtactacaataatttgatcaatgagctattatcgaaaggggtgcaaccgtttattacccttttccactgggactcacctcaggcgttggaagataaatataatggatttcttagccctaatatcataaatgactttaaggactatgctgaaatctgcttcaaggagtttggtgacagagtgaaaaattggatcaccttcaatgagccttggactttctgctctaatggctatgcaactggcctgtttgcaccaggccgttgttcgccctgggagaagggaaattgcagtgttggagattcaggaagggagccttacactgcatgccatcatcaactacttgcccacgcggaaactgttcggttgtacaaagcgaaatatcaggccttacaaaaagggaagattggaataactctggtctcgcactggtttgttcccttctcccgctccaaatccaacgatgatgctgcaaagcgtgctatagacttcatgtttggatggtttatggatcccctcattagaggcgactaccccctaagcatgagaggattggttgggaatcgcttgccacagttcactaaagaacagtctaagttggtcaagggtgcatttgactttattggacttaactactacactgcgaactatgctgataaccttcctccatcaaatggccttaacaacagctataccaccgattctcgagctaatcttaccggtgtacgaaatggcatccccataggaccgcaggctgcttcaccttggctttacgtctaccctcaaggcttccgtgacttgctactttatgttaaggagaactatggcaatcctaccgtctacatcactgaaaatggcgttgatgaattcaacaataagaccttaccactccaagaagccttgaaggatgacgctaggatagaatactaccacaagcacctcctttccctgctaagtgctataagggatggagcaaacgtgaagggatactttgcatggtcgctgcttgataacttcgagtggtcgaacggctacacagttcgatttgggataaacttcgtagattacaatgacggaaggaagagataccccaagaactctgcccattggttcaagaagttcctcctgaaatga</cdnaseq> |
| Protein Sequence |
<aaseq>KFTVMADGSLRGGVNKEGIKYYNNLINELLSKGVQPFITLFHWD SPQALEDKYNGFLSPNIINDFKDYAEICFKEFGDRVKNWITFNEPWTFCSNGYATGLF APGRCSPWEKGNCSVGDSGREPYTACHHQLLAHAETVRLYKAKYQALQKGKIGITLVS HWFVPFSRSKSNDDAAKRAIDFMFGWFMDPLIRGDYPLSMRGLVGNRLPQFTKEQSKL VKGAFDFIGLNYYTANYADNLPPSNGLNNSYTTDSRANLTGVRNGIPIGPQAASPWLY VYPQGFRDLLLYVKENYGNPTVYITENGVDEFNNKTLPLQEALKDDARIEYYHKHLLS LLSAIRDGANVKGYFAWSLLDNFEWSNGYTVRFGINFVDYNDGRKRYPKNSAHWFKKF LLK</aaseq> |
| Gene Sequence |
<dnaseqindica>2838..3006#2637..2745#2371..2473#2249..2280#1820..2037#1624..1739#751..1006#255..342#37..133#ttggtcatactccaagttgatggcaccaaacattgaaaattcactgtcatggcagatggaagtctgaggggtggagtcaacaaagaaggcataaagtactacaataatttgatcaatgagctattatcgaaaggtacgcattttccagtctacagtgtttagttccaagttcagtggctagatgcaaattagttccactccagaagtccagatattcttttattcaagatgcaaataaccttatacatttgcaggggtgcaaccgtttattacccttttccactgggactcacctcaggcgttggaagataaatataatggatttcttagccctaatatcatgtatgtcaacaattcttctgcttcaatacatcactagttataccttgataggttgaaatggaaactggtcaggttaataaacagactcagtaagataggagagtgaaatttaaactaaatgtgacaacatcaattaacctgaccatcactgtgcatacccattaaactgccgaagactcctatttcaatttcattggcttttggagctttctcctcaatttccttgtgaataacactaattgaaggtaagttgggatgtgtttttctttcgacagcattaaacccctttattggcacttacgccacccacagtagtactctcttcctatactattttcagctaaaatgtcaagagttgcctacagtgaaaattttcttatgtttactgtttgtgaaaaactgttgcagaaatgactttaaggactatgctgaaatctgcttcaaggagtttggtgacagagtgaaaaattggatcaccttcaatgagccttggactttctgctctaatggctatgcaactggcctgtttgcaccaggccgttgttcgccctgggagaagggaaattgcagtgttggagattcaggaagggagccttacactgcatgccatcatcaactacttgcccacgcggaaactgttcggttgtacaaagcgaaatatcaggtcactgaagaatccctttgagcacttgcaattcatccatgacaatgagttaaatcaaagatctgcaaatttggttttgataatccatgcttagcatttagttccagttcggtcctggtggtagaatttgttagtacatccattagcaaattactttagtaacttcagctatctgtttaaaatatcacatatcatggattggattcctatcatatcaacagacatgtgcatatactagttactttcaaaaagaatgattttactgtccttacggatcgaatactaatacatttaaaccttatcaattaaatacctgaatctgaagatgatctttgtagaaagagtgattttacagtccttgagtgatgccaggtggtaccacattttataatgtaagaggtaccaaaatttataccagaaaatgtagtacctcaggaccgtaaaaatttctcttgtagatatgtattacttgttaattatagtcctatggaacgagaaaagctctggctgcaagagaaagaaagcagaacaactagaatacattgccaaatcaaaggattggagttcagcatttacacaaccactcacttgaacaatgaaatccttcataaatgcaggccttacaaaaagggaagattggaataactctggtctcgcactggtttgttcccttctcccgctccaaatccaacgatgatgctgcaaagcgtgctatagacttcatgtttggatggtaaattctgtcacacattatttcatcattgaagttgttaaaacatgaaagaagtcttcaacaatgaatttcccttctaggtttatggatcccctcattagaggcgactaccccctaagcatgagaggattggttgggaatcgcttgccacagttcactaaagaacagtctaagttggtcaagggtgcatttgactttattggacttaactactacactgcgaactatgctgataaccttcctccatcaaatggccttaacaacagctataccaccgattctcgagctaatcttaccggtgagtcaatatgagtttatatttctattttaaattcatagtgtttgcaacattgaaatacaaagatatggcaagcttctagcatataatatccattagactgtagcatttctgataagcattttggtcagcttatgtcatagcctctgttgcacaatacctatctgtttcagacgggtcaatatatgctaacctatgctgattgtgccaggtgtacgaaatggcatccccataggaccgcaggtaactccatactttgtcctccacacaaaataaattaatagtaaatagttaaggtgagatattgaattttgtaaaatggcatgtatgtaggctgcttcaccttggctttacgtctaccctcaaggcttccgtgacttgctactttatgttaaggagaactatggcaatcctaccgtctacatcactgaaaatggtaagtctccgatactacggtaacacattctaatttttaaattaagtcagcaatgaactcctatggcataaatatttttcttctcctagcttcttgaagaaataaaatatatattctctaaaagttaatgaatctaactgattttttattgctgcatcttaaggcgttgatgaattcaacaataagaccttaccactccaagaagccttgaaggatgacgctaggatagaatactaccacaagcacctcctttccctgctaagtgctataaggtctgaactctgaactattgatcatagacccatttctgagtagggttcttcagatgctagttgacaatgcattactccatatgccttcacagggatggagcaaacgtgaagggatactttgcatggtcgctgcttgataacttcgagtggtcgaacggctacacagttcgatttgggataaacttcgtagattacaatgacggaaggaagagataccccaagaactctgcccattggttcaagaagttcctcctgaaatgataaaaaagcaccattgcactcattgcttttctcattgaataataaaagagtatatgttttgcgtgaatttggtacaagagatggaagtaatccagttaaataataaatccctctcttactgc</dnaseqindica> |
| External Link(s) |
