Difference between revisions of "Os01g0928000"
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| − | + | The rice gene Os01g0928000 was reported as '''''OsICE2''''' in 2011<ref name="ref1"/>, '''''OsbHLH001/OsICE2''''' in 2013<ref name="ref2"/>, respectively. | |
==Annotated Information== | ==Annotated Information== | ||
===Function=== | ===Function=== | ||
| − | + | ''OsICE'' '''homologs''' ''OsbHLH001/OsICE2'' and ''OsbHLH002/OsICE1'' function in '''regulating ''OsDREB1B'' and ''OsHsfA3''''' involved in '''cold acclimation''' and '''trehalose synthesis'''<ref name="ref1"/><ref name="ref2"/>. | |
| + | |||
| + | '''GO assignment(s):''' GO:0005634, [http://amigo.geneontology.org/amigo/term/GO:0030528 GO:0030528], GO:0045449 | ||
===Expression=== | ===Expression=== | ||
| − | + | *Chilling stress on rice seedlings induced '''two ICE-related proteins''' with molecular masses of approximately 55 and 40 kDa. These sizes are consistent with those predicted for ''OsICE1'' and ''OsICE2'', respectively. In contrast to the proteins, cold stress had little or no effect on the expression of ''OsICE1'' and ''OsICE2''<ref name="ref1"/>. | |
| + | |||
| + | *'''Salt stress upregulated''' levels of ''OsICE2'' '''protein''' but had '''no effect''' on OsICE2 '''mRNA''' levels. RT-PCR revealed that '''cold stress increased''' the levels of ''OsICE1'' and ''OsICE2'' proteins but did not enhance the expression of their genes. ''OsICE1'' and ''OsICE2'' are regulated mainly '''by post-translational mechanisms''', in a manner similar to that of ''Arabidopsis'' ICE1<ref name="ref1"/>. | ||
===Evolution=== | ===Evolution=== | ||
| − | + | [[File: OsICE2 phylogenic1.jpg|right|thumb|250px|'''Figure 1.''' ''Phylogenic tree of ICE (Inducer of CBF Expression) homologs.(from reference <ref name="ref1"/>).'']] | |
| + | *A '''phylogenetic tree''' of '''ICE homologs''' in '''dicots''' and '''monocots''', using ''Arabidopsis'' PIF3 and human c-myc as outgroups, showed that ICE-related genes can be classified into '''monocot and dicot subfamilies''' (Figure 1). | ||
| + | |||
| + | *''OsICE1'' and ''OsICE2'' share '''very similar sets of motifs''', notably '''an acidic domain''', '''a Ser-rich domain''', '''a bHLH domain''', and '''a possible zipper region''', with ''Arabidopsis'' ''ICE1'', although ''OsICE2'' has a shorter junction region between the acidic region and the Ser-rich region in the amino terminus than ''OsICE1'' and ''Arabidopsis ICE1''<ref name="ref1"/>. | ||
| − | + | *Although ''OsICE1'' and ''OsICE2'' have '''different predicted molecular masses''', they share '''48% similarity''' at the '''amino acid level'''. They also have '''similarities''' of '''39%''' and '''45%''', respectively, to ''Arabidopsis''<ref name="ref1"/>. | |
==Labs working on this gene== | ==Labs working on this gene== | ||
| − | + | *Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 812-8581, Japan | |
| + | *Department of Bioresource Sciences, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan | ||
| + | *School of Agriculture, Kyushu University, Fukuoka 812-8581, Japan | ||
==References== | ==References== | ||
| − | + | <references> | |
| + | * <ref name="ref1"> | ||
| + | Nakamura J, Yuasa T, Huong T T, et al. Rice homologs of inducer of CBF expression (OsICE) are involved in cold acclimation[J]. Plant biotechnology, 2011, 28(3): 303-309. | ||
| + | </ref> | ||
| + | * <ref name="ref2"> | ||
| + | Chen Y, Li F, Ma Y, et al. Overexpression of OrbHLH001, a putative helix–loop–helix transcription factor, causes increased expression of AKT1 and maintains ionic balance under salt stress in rice[J]. Journal of plant physiology, 2013, 170(1): 93-100. | ||
| + | </ref> | ||
| + | </references> | ||
==Structured Information== | ==Structured Information== | ||
Revision as of 02:27, 12 March 2015
The rice gene Os01g0928000 was reported as OsICE2 in 2011[1], OsbHLH001/OsICE2 in 2013[2], respectively.
Contents
Annotated Information
Function
OsICE homologs OsbHLH001/OsICE2 and OsbHLH002/OsICE1 function in regulating OsDREB1B and OsHsfA3 involved in cold acclimation and trehalose synthesis[1][2].
GO assignment(s): GO:0005634, GO:0030528, GO:0045449
Expression
- Chilling stress on rice seedlings induced two ICE-related proteins with molecular masses of approximately 55 and 40 kDa. These sizes are consistent with those predicted for OsICE1 and OsICE2, respectively. In contrast to the proteins, cold stress had little or no effect on the expression of OsICE1 and OsICE2[1].
- Salt stress upregulated levels of OsICE2 protein but had no effect on OsICE2 mRNA levels. RT-PCR revealed that cold stress increased the levels of OsICE1 and OsICE2 proteins but did not enhance the expression of their genes. OsICE1 and OsICE2 are regulated mainly by post-translational mechanisms, in a manner similar to that of Arabidopsis ICE1[1].
Evolution
- A phylogenetic tree of ICE homologs in dicots and monocots, using Arabidopsis PIF3 and human c-myc as outgroups, showed that ICE-related genes can be classified into monocot and dicot subfamilies (Figure 1).
- OsICE1 and OsICE2 share very similar sets of motifs, notably an acidic domain, a Ser-rich domain, a bHLH domain, and a possible zipper region, with Arabidopsis ICE1, although OsICE2 has a shorter junction region between the acidic region and the Ser-rich region in the amino terminus than OsICE1 and Arabidopsis ICE1[1].
- Although OsICE1 and OsICE2 have different predicted molecular masses, they share 48% similarity at the amino acid level. They also have similarities of 39% and 45%, respectively, to Arabidopsis[1].
Labs working on this gene
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 812-8581, Japan
- Department of Bioresource Sciences, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan
- School of Agriculture, Kyushu University, Fukuoka 812-8581, Japan
References
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 Nakamura J, Yuasa T, Huong T T, et al. Rice homologs of inducer of CBF expression (OsICE) are involved in cold acclimation[J]. Plant biotechnology, 2011, 28(3): 303-309.
- ↑ 2.0 2.1 Chen Y, Li F, Ma Y, et al. Overexpression of OrbHLH001, a putative helix–loop–helix transcription factor, causes increased expression of AKT1 and maintains ionic balance under salt stress in rice[J]. Journal of plant physiology, 2013, 170(1): 93-100.
Structured Information
| Gene Name |
Os01g0928000 |
|---|---|
| Description |
Similar to Transcription factor ICE1 (Inducer of CBF expression 1) (Basic helix- loop-helix protein 116) (bHLH116) (AtbHLH116) |
| Version |
NM_001051807.1 GI:115441984 GeneID:4326959 |
| Length |
2897 bp |
| Definition |
Oryza sativa Japonica Group Os01g0928000, 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 1:42509063..42511959 |
| Sequence Coding Region |
42509361..42509444,42509571..42509741,42510073..42510300,42511286..42511948 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008394:42509063..42511959 source=RiceChromosome01 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008394:42509063..42511959 source=RiceChromosome01 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atggacgaggcggaggcggcggcggcggcggcgaagatggacgagctggcgggaggaggaggaggaggcggcggcgactggtcgtacctcgcggcggacgcgctggcggcggcgtcgttcacggcgttcccgttccaccaccaccaccaccaccaccaccgcgacgtgctctcggcgtcgaccccgtcgtcgctgctcctcaacatggacgcggccaccgccgcggccatgttcgacttccaggcggccttcccgtcgtcctccgtcccgccgccgccgcccacgacgacggcggcgctcccgccgttccacgacttcgcctcctccaacccgttcgacgacgcgccgcccccgttcctcgcgccgccggggcagaagctcgggttcctggggccccccggcggcgcgttcggcggcgggatggggtgggacgacgacgacgagatcgagcagagcgtggacgcctcgtccatgggtgtctcggcctcgctggagaatgccgcgcccgtggcggccggaggaggcggcggcggtggcggcggcggtgggaggggcaagaagaaggggatgccggccaagaacctcatggcggagcggcggcgcaggaagaagctcaacgaccgcctctacatgctgcgctccgtggtgcccaagatcagcaagatggacagagcttctatccttggtgatgcaattgagtacttgaaggagctcctgcagaggattaacgatcttcacaatgaacttgagtctgctcctagctcttcgcttactggaccatcatcggctagcttccacccatcaacacccacattgcagacgtttcctggccgcgttaaggaggaactttgcccaacctcatttccaagccctagtggtcaacaagccacggtcgaagttaggatgagggaaggtcatgcagtcaatatccacatgttctgcgcacgcaggcccggcattctgatgtccacattgagggctctcgacagccttggcctcgggatcgagcaggcggtcatcagctgtttcaatgggtttgcaatggatgttttccgcgccgagcaatgcagggatggtcctggactcgggcctgaagaaattaagaccgtgctcctgcactctgctggccttcagaacgcaatgtaa</cdnaseq> |
| Protein Sequence |
<aaseq>MDEAEAAAAAAKMDELAGGGGGGGGDWSYLAADALAAASFTAFP FHHHHHHHHRDVLSASTPSSLLLNMDAATAAAMFDFQAAFPSSSVPPPPPTTTAALPP FHDFASSNPFDDAPPPFLAPPGQKLGFLGPPGGAFGGGMGWDDDDEIEQSVDASSMGV SASLENAAPVAAGGGGGGGGGGGRGKKKGMPAKNLMAERRRRKKLNDRLYMLRSVVPK ISKMDRASILGDAIEYLKELLQRINDLHNELESAPSSSLTGPSSASFHPSTPTLQTFP GRVKEELCPTSFPSPSGQQATVEVRMREGHAVNIHMFCARRPGILMSTLRALDSLGLG IEQAVISCFNGFAMDVFRAEQCRDGPGLGPEEIKTVLLHSAGLQNAM</aaseq> |
| Gene Sequence |
<dnaseqindica>2516..2599#2219..2389#1660..1887#12..674#gcgaggttgccatggacgaggcggaggcggcggcggcggcggcgaagatggacgagctggcgggaggaggaggaggaggcggcggcgactggtcgtacctcgcggcggacgcgctggcggcggcgtcgttcacggcgttcccgttccaccaccaccaccaccaccaccaccgcgacgtgctctcggcgtcgaccccgtcgtcgctgctcctcaacatggacgcggccaccgccgcggccatgttcgacttccaggcggccttcccgtcgtcctccgtcccgccgccgccgcccacgacgacggcggcgctcccgccgttccacgacttcgcctcctccaacccgttcgacgacgcgccgcccccgttcctcgcgccgccggggcagaagctcgggttcctggggccccccggcggcgcgttcggcggcgggatggggtgggacgacgacgacgagatcgagcagagcgtggacgcctcgtccatgggtgtctcggcctcgctggagaatgccgcgcccgtggcggccggaggaggcggcggcggtggcggcggcggtgggaggggcaagaagaaggggatgccggccaagaacctcatggcggagcggcggcgcaggaagaagctcaacgaccgcctctacatgctgcgctccgtggtgcccaagatcagcaaggtgattaatgacctcatttctattttttcactgttcattgctaattatttaattaatcagcagctccagtttctactagactgtatcttattaattaaattaatcagcattttctatttctacttttctaatttcagttttggcaacatgtttcagttcttgagtgatgtatactggtgtaggtcctgtaggagtgtgtttgtcatgatatttgtcactgaaattggttccaattttggtgctgaattcttgaattggctccacttcagatccaaaaaaacatccttttttcattagatctatgtcataccttgtcatgttcacatggtaacatgaggagttcctattcagcttgctggatggttgttttacagttcagttatggtaatttcagttctgaaattatacttcaatgtcttttttctaggactttataatttgtcgtagcttgagattacacatattatggggaactttgattctgatccatggccagatttagtgatgcatgattaacacagtgccatgcacaagatgtagttgaaagtgaccagataccagataactcacaaattcttttcccccttttctttctgttttttttttgtagttcttcgtgttggatgttttgtctttaacttttgttggtttccttgaaaaaagtcgttcactttggaagtttcggcatgcgaagtgcatattcagttctctgcagtcctttcgtgtgaagaacttactactttccttcacagcgatcaagatggttttgaacaataaagaaagacctgatgtactacagttcttgggatattatgacaagttgcagtctaacaattcagcgccatgtacgatgtgccgttttttagtgtagcagtacaaaacaatttatgtcaaagtgttcttaatgccaactatgtctgactcgtttcatgttaatatctatagtttatcatctcattaccagttttcttctcctttgtgacagatggacagagcttctatccttggtgatgcaattgagtacttgaaggagctcctgcagaggattaacgatcttcacaatgaacttgagtctgctcctagctcttcgcttactggaccatcatcggctagcttccacccatcaacacccacattgcagacgtttcctggccgcgttaaggaggaactttgcccaacctcatttccaagccctagtggtcaacaagccacggttagtcaaattttgaccatgattgttaagcctttgcactagtggcaattatgcaattggcccttgatacttatatgcttaagcatgctttagtgctcaagattaacgcacttgggagctactccttttgtttcaaaatataagcaattcttgctatgtatctggacaagaaatgcttatattttggaacggagggaatattacttatttcgcggtacttgcactttgcagtctgcacaagtacttgatcattcaggccttgttgattcatgtagcggtaacaatatggtgtatagcaaccaagtgacattcacctctcttgtttgttcaggtcgaagttaggatgagggaaggtcatgcagtcaatatccacatgttctgcgcacgcaggcccggcattctgatgtccacattgagggctctcgacagccttggcctcgggatcgagcaggcggtcatcagctgtttcaatgggtttgcaatggatgttttccgcgccgaggtttgcattctccacatcataatatttttctcctccagctgagggttttttttcagttgtgttcgatctgatcctaccgttgttgttcactctcttaatgcttgctctgtacttctgttttgccagcaatgcagggatggtcctggactcgggcctgaagaaattaagaccgtgctcctgcactctgctggccttcagaacgcaatgtaatcagcaagtcagaaagcagtcaagaccaatgcactgggatttgatcagtgatcatttgcatcagatgatctggtttatcaaaaagttatagtaagtatggcatatatgctgtttatctaggagaactgatgagatgaggctcgccatctagagacatgtgtgatgatgatgatgtaactgggtttctttctttctgttgtcgtttttttttctgaatgttgtttgtgatgtaataggatctttgtccattgaaaccatgtccattatcatgatgagaatatgaacccagtgtcttttg</dnaseqindica> |
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