RiceWiki - User contributions [en]

Os01g0253300

2014-06-06T14:35:31Z

Jianchao Zhang: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Fig1 Rice importina1 supported nuclear import of NLS-GFP in vertebratein vitroassay system.jpg|right|thumb|150px|Fig-1.Rice importina1 supported nuclear import of NLS-GFP in vertebratein vitroassay system.from ref<ref name="ref2" />]]
Os01g0253300 encodes importin subunit alpha-1a,a member of importin family, which functions a essential role in nuclear protein import by specifically and directly binding to substrates containing either a simple or bipartite NLS motif<ref name="ref1" />.In vivo assay suggests that importin alpha-1a can replace vertebrate importin a in the mediation of nuclear import of NLS substrates, implying that rice importin a1 functions as a NLS receptor in the process of nuclear import of proteins(Fig-1)<ref name="ref2" />,which indicates the importin family has a conserved transportation function both in plants and mammals.The importin alpha-1a also has a function in virus infection by interact with mungbean yellow mosaic virus capsid protein<ref name="ref3" />.

===Expression===
[[File:Fig2 Expression of importin.jpg|right|thumb|150px|Fig-2.Transcript analyses of rice importin.]]
[[File:Fig3. dark treatmeng influence the expression.jpg|middle|thumb|250px| Fig-3.An increase of importin-atranscript levels during dark-adaptation of light-grown green leaves.From ref<ref name="ref4" />]]

Transcript analyses of rice importin alpha-1a by ''Chang-Jie Jiang et al'' shows importin alpha-1a is highly expressed in callus, followed by root and etiolated leaf and lowly expressed in green leaf(Fig-2)<ref name="ref1" />.The expression level of importin alpha-1a is greatly increased after darkt treatment in green leaf[Fig-3]<ref name="ref4" /> .However it has a constitute expression pattern in non-photosynthetic tissues[Fig-4]<ref name="ref3" />.Together,it indicates a complex regulation of the importin alpha-1a transcription.

[[File:Fig4 constitue exprssion.jpg]]

Fig-4.Importin-atranscript levels in different rice tissues.(A) RNA was prepared from various tissues, roots (Root), mature leaf blades (M-Leaf), flag leaf blades (F-Leaf), stems (Stem) and suspension-cultured cells (Callus), and the transcript levels for importin-α in their tissues were examined by RNA blot analysis. Mature leaves, flag leaves and stems of field-grown plants were collected at noon on a sunny day in July. (B) The effect of illumination on the transcript levels for importin-α was examined in roots and suspension-cultured cells. Roots of water-cultured seedlings and suspension-cultured cells were exposed to white light (white fluorescent lamps; 90 μmol m−2 s−1) for 24 h (L), kept in complete darkness for 24 h (D) or kept in darkness for 24 h and then re-illuminated for 3 h (+3hL).From ref <ref name="ref3" />

===Protein structure===
1.The structure of rice importin alpha-1a comprises 10 ARM repeats (green, cartoon representation) and two NLS-like sequences from the N-terminal IBB domain(shown in yellow stick )[FIG-5]<ref name="ref5" />.
[[File:Fig5 crystal structure of importin.jpg]]

Fig-5:crystal structure of importin alpha-1a.From ref<ref name="ref5" />

2.The crystal structures of their complexes with rice importin alpha-1a show that they bind to the minor NLS binding site[Fig6A]. By contrast, the crystal structures of their complexes with mouse (Mus musculus) importin alpha-1ashow preferential binding to the major NLS binding site[Fig6B]. The results reveal the molecular basis of a number of features of the classical nuclear transport pathway specific to plants<ref name="ref5" />.

[[File:Fig 6 structure difference.jpg]]

Fig-6:Differential Binding of Plant-Specific NLSs to rImpa1a and mImpa.<ref name="ref5" />

===Evolution===
The phylogenetic tree of importin alpha shows that the rice importin alpha-1a protein is the most distant member from various organisms[Fig-7]<ref name="ref6" />.we could find another EST from Arabidopsis (accession number F15465), which has about 60% identity with #61L at the levelof both nucleotide and amino acid sequences. It might be interpreted that importin alpha-1a homologous to rice #61L(Refere to importin alpha-1a) is also present in Arabidopsis, and that the #61L protein and the homologue are functionally differentiated from the known importin alpha-1a.

[[File:Fig 7.jpg]]

Fig-7:(Phylogenetic tree of importinK. The tree was constructed by the UPGMA method using the GENETYX-MAC 7.3 software(Software Development Co., Tokyo) with default parameters. The accession number of the putative open reading frame T10M13.16 which is predicted ) From<ref name="ref6" />

===Knowledge Extension===
Rice encodes many kinds of importin proteins such as importin α1a/1b,importinβand importin α1a is the most studied gene in rice with its crystal structure complex being resolved<ref name="ref5" /><ref name="ref7" />. Importin α1a functions as another importin α protein by form a complex with importin βand NLS-containing substrate.As shown in Figure -8, a single round of importin α-mediated import can be divided into six steps: (i) formation of a ternary complex in the cytoplasm; (ii) importin β-mediated binding of the ternary complex to docking sites at the periphery of the NPC; (iii) importin β-mediated translocation through the NPC; (iv) dissociation of the ternary complex, triggered, in part, by the binding of the small nuclear GTPase Ran–GTP to importin β; (v) recycling of importin α to the cytoplasm bound to the exportin CAS–Ran–GTP; and (vi) disassembly of the export complex and release of free importin α to the cytoplasm. Disassembly is induced by the Ran–GAP-induced hydrolysis of GTP by Ran. Ran–GDP and CAS are recycled back to the nucleus for further rounds of transport. Back in the nucleus, Ran–GDP is converted to Ran–GTP by the guanine nucleotide exchange factor RCC1.<ref name="ref5" />

[[File:Fig-8 The nucleocytoplasmic shuttling cycle of importin α.png]]

Fig-8:The nucleocytoplasmic shuttling cycle of importin α. (i) Importin α (α) forms a ternary complex with importin β (β) and cargo (blue circles). (ii) The ternary complex docks at the nuclear-pore complex (NPC) and (iii)translocates into the nucleus. (iv) Binding of Ran–GTP triggers the dissociation of the ternary complex. (v)Importin α binds to the exportin CAS–Ran–GTP complex and is exported to the cytoplasm. (vi) Ran–GAP-stimulated hydrolysis of GTP by Ran triggers the dissociation of the exportin complex and releases free importin α into the cytoplasm for another transport cycle. The recycling of importin β to the cytoplasm, and of Ran–GDP to the nucleus and its conversion to Ran–GTP are not shown.

==Labs working on this gene==
*National Institute of Agrobiological Resources, Tsukuba, Ibaraki 305-8602, Japan.
*Friedrich Miescher Institute, Maulbeerstrasse 66, 4058 Basel, Switzerland.
*Central Research Institute of Electric Power Industry, Chiba, Japan.
*School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, University of Queensland, Brisbane Qld 4072, Australia.
*School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience, and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld 4072, Australia.
*The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China.
*Department of Biochemistry and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan 114, Republic of China.

==References==
<references>
<ref name="ref1">
Jiang CJ, Shoji K, Matsuki R, Baba A, Inagaki N, Ban H, Iwasaki T, Imamoto N, Yoneda Y, Deng XW, Yamamoto N. Molecular cloning of a novel importin alpha homologue from rice, by which constitutive photomorphogenic 1 (COP1) nuclear localization signal (NLS)-protein is preferentially nuclear imported. J Biol Chem. 2001 Mar 23;276(12):9322-9. Epub 2000 Dec 20.</ref>

<ref name="ref2">
Jiang CJ, Imamoto N, Matsuki R, Yoneda Y, Yamamoto N. Functional characterization of a plant importin alpha homologue. J Biol Chem. 1998 Sep 11.</ref>

<ref name="ref3">
Guerra-Peraza O, Kirk D, Seltzer V, Veluthambi K, Schmit AC, Hohn T, Herzog E. Coat proteins of Rice tungro bacilliform virus and Mungbean yellow mosaic virus contain multiple nuclear-localization signals and interact with importin alpha. J Gen Virol. 2005 Jun;86(Pt 6):1815-26.</ref>

<ref name="ref4">
Shoji K, Iwasaki T, Matsuki R, Miyao M, Yamamoto N. Cloning of a cDNA encoding an importin-alpha and down-regulation of the gene by light in rice leaves. Gene. 1998 Jun 8;212(2):279-86.</ref>
<ref name="ref5">
Chang CW1, Couñago RL, Williams SJ, Bodén M, Kobe B.Crystal structure of rice importin-α and structural basis of its interaction with plant-specific nuclear localization signals.Plant Cell. 2012 Dec;24(12):5074-88. doi: 10.1105/tpc.112.104422. Epub 2012 Dec 18.</ref>
<ref name="ref6">
Iwasaki T, Matsuki R, Shoji K, Sanmiya K, Miyao M, Yamamoto N. A novel importin alpha from rice, a component involved in the process of nuclear protein transport. FEBS Lett. 1998 May 29;428(3):259-62.</ref>
<ref name="ref7">
Goldfarb DS, Corbett AH, Mason DA, Harreman MT, Adam SA. Importin alpha: a multipurpose nuclear-transport receptor.Trends Cell Biol. 2004 Sep;14(9):505-14.</ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0253300|
Description = Importin alpha-1a subunit|
Version = NM_001049146.1 GI:115435705 GeneID:4327117|
Length = 5116 bp|
Definition = Oryza sativa Japonica Group Os01g0253300, 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 = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:8381095..8386210|
CDS = 8381261..8381470,8382333..8382429,8382526..8382617,8382709..8382840,8382955..8383140 ,8383224..8383387,8383494..8383572,8384464..8384592,8385082..8385209 ,8385328..8385691|
GCID = <gbrowseImage1>
name=NC_008394:8381095..8386210
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:8381095..8386210
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgctgcgcccgagcgagcgggtggaggtgcggcggaaccgctacaaggtggcggtggacgccgaggaggggaggcggcggcgcgaggacaacatggtggagatccgcaagagccgccgcgaggagagcctcctcaagaagcgccgcgaggggctccaggcccaggcccccgtccccgcctccgccgcaaccggcgtcgataagaagctcgaaagccttcctgctatgattggtggagtttattcggacgataacaaccttcagcttgaggccacaacacagttccgcaagttgctttctatagagaggagccctccaattgaagaggttattcaatcaggcgttgttcctagattcgtgcagtttcttaccagagaggatttcccccagctacagttcgaagctgcgtgggcacttacaaacattgcatctggcacttcggagaatacaaaggttgtcattgatcatggggctgtaccaatatttgtgaagcttcttggttcttctagtgatgatgttcgtgagcaggctgtatgggcattgggcaatgttgctggtgattcccctaagtgccgtgaccttgttcttgccaatggtgcattgctgcctctgctagcacagttgaatgagcacactaaactctctatgctaaggaatgcaacttggactttatcgaacttctgcagaggaaaaccacagccatcatttgaacagactaggcctgctcttccagcactggcacggcttattcactccaatgatgaggaagttctcactgatgcgtgctgggctctttcatatttatctgatggcactaatgacaagatccaagccgtgattgaagctggtgtttgcccccgtcttgtggagcttctcctccatccatcaccttcagtgcttatacccgcactacgaactgttggaaatattgtaactggagatgacgcgcaaactcagtgcatcattgatcatcaagccctcccttgcctcctaagtctgttgacacaaaatctcaagaaaagcatcaagaaagaggcttgctggactatttcaaatattactgctggtaacaaagatcagatacaggctgtcataaatgctggcattattggtcctctggtgaatctgctccaaacggcagagttcgatatcaagaaggaagctgcatgggccatctcaaatgctacttcaggcggtagccatgatcaaatcaagtatctggtgagcgagggctgcatcaagccattgtgtgatcttcttatttgcccagatataagaatcgttacagtttgtttggagggtctcgagaacattcttaaagtaggagaaaccgacaagaccttggctgcaggtgatgtgaatgtcttttcccagatgattgatgaagcggaaggtttggaaaagattgagaacttgcagagccatgataacaatgagatctatgaaaaagctgtgaagattcttgaggcctactggatggatgaggaggatgatacaatgggagctaccacggtagctgctccccaaggtgctacttttgactttggccaaggcggtggtgctgctcaattcaaataa</cdnaseq>|
AA = <aaseq>MSLRPSERVEVRRNRYKVAVDAEEGRRRREDNMVEIRKSRREES LLKKRREGLQAQAPVPASAATGVDKKLESLPAMIGGVYSDDNNLQLEATTQFRKLLSI ERSPPIEEVIQSGVVPRFVQFLTREDFPQLQFEAAWALTNIASGTSENTKVVIDHGAV PIFVKLLGSSSDDVREQAVWALGNVAGDSPKCRDLVLANGALLPLLAQLNEHTKLSML RNATWTLSNFCRGKPQPSFEQTRPALPALARLIHSNDEEVLTDACWALSYLSDGTNDK IQAVIEAGVCPRLVELLLHPSPSVLIPALRTVGNIVTGDDAQTQCIIDHQALPCLLSL LTQNLKKSIKKEACWTISNITAGNKDQIQAVINAGIIGPLVNLLQTAEFDIKKEAAWA ISNATSGGSHDQIKYLVSEGCIKPLCDLLICPDIRIVTVCLEGLENILKVGETDKTLA AGDVNVFSQMIDEAEGLEKIENLQSHDNNEIYEKAVKILEAYWMDEEDDTMGATTVAA PQGATFDFGQGGGAAQFK</aaseq>|
DNA = <dnaseqindica>167..376#1239..1335#1432..1523#1615..1746#1861..2046#2130..2293#2400..2478#3370..3498#3988..4115#4234..4597#gtgtgagctttaactccccccctttccccgcggccactagggtttctcctcctctttcctctcctcctccgccccgacgcctcgctagggtttttgcctctccctccgccgccgccgctgccgcgaggagaggagggggggagagcacccagccggcgagccagccatgtcgctgcgcccgagcgagcgggtggaggtgcggcggaaccgctacaaggtggcggtggacgccgaggaggggaggcggcggcgcgaggacaacatggtggagatccgcaagagccgccgcgaggagagcctcctcaagaagcgccgcgaggggctccaggcccaggcccccgtccccgcctccgccgcaaccggcgtcgataagaaggtgagtagtatactcctcgattcccccccgctcccctcccctcccctcccctgcctccgatgacgctatcccatcgtgtcctggatcccatattttaggtaggtgttggattggattgcactttttgagagggtttttgattcgtctgcggcatatttgtttaagtttgttattatacccgcatgtctactagcgtgcgggtgagggtaggttcctgctagatgtaggcaacacttagcaccacgtttcgatgcctcgattagtcacttgatttctgattctccttctgttgacaatattacaagtactgttagttggcacggttgcgaactcctagcgtttgaaatgtttccaggtacatgcctgctagctccagtgatctagttttagttttaggacatgtagattgtggtcttaggatcaaatcttccacggattcactgcggataattagttaggtgaccaggaactgtaataatgattgatcttcctgataatttttagtgtacatcttgctgttgtttcatcttatgttttgatagaagcatacaaatgagctgatgccatattatatctttatagctattttttgtgctatcttgaaattgagggtccagtgcaactttccttatgactgaaccttgtctttagtacatggaagcacataaatcatatagtagtgtttctggtcatgtttctagagacgtcctacattgataacgcatacatttatgttactgttaaactacctctggtttctgttctttgcaccacccctaaaagagaaggaaactgcttttaaaccctttttggggtttaatacgggaagttgagtatttgatatctctgttgaatgttgtagctcgaaagccttcctgctatgattggtggagtttattcggacgataacaaccttcagcttgaggccacaacacagttccgcaagttgctttctataggtacaaacctcttaaatgttttgggctgttaccttgtgaaaataatagttgaacaaaagttaattactaattacacccattacaatttttaattagagaggagccctccaattgaagaggttattcaatcaggcgttgttcctagattcgtgcagtttcttaccagagaggatttcccccagctacaggtgtgtgccaacacaatattattttcattatctggtaggttcaaataaaaatggatttattactgtggtgcttttgaattaaattttgtagttcgaagctgcgtgggcacttacaaacattgcatctggcacttcggagaatacaaaggttgtcattgatcatggggctgtaccaatatttgtgaagcttcttggttcttctagtgatgatgttcgtgagcaggtatccgatcatctcctgacttgtctttgtgctttctgtacttccttgatattattttgattgagtgcattgttggagttattaatgtttttacctcttgaaaaaaaattgaaggctgtatgggcattgggcaatgttgctggtgattcccctaagtgccgtgaccttgttcttgccaatggtgcattgctgcctctgctagcacagttgaatgagcacactaaactctctatgctaaggaatgcaacttggactttatcgaacttctgcagaggaaaaccacagccatcatttgaacaggtttggacaaagtttctttgtactctactgtagttagtagggaaagacagttccttaacatgatgtttattgggtgtcaatagactaggcctgctcttccagcactggcacggcttattcactccaatgatgaggaagttctcactgatgcgtgctgggctctttcatatttatctgatggcactaatgacaagatccaagccgtgattgaagctggtgtttgcccccgtcttgtggagcttctcctgtaagtgacaacattgcattacaattttctgccattttcctttagattcttatttgctactctcattataccctttttaatattttatactgtttacaacatgaagccatccatcaccttcagtgcttatacccgcactacgaactgttggaaatattgtaactggagatgacgcgcaaactcaggtattgtgttgattttttgcatctctatatctgacagattttgtatcaattgatatcaactactaagactcatgaatcttgagcttaatatttagaggttgtgttcatcacagttgatattaaattttaggcttgtggaaaatgtttaatatcatagttgatattaaatctagaggttgcatctaatgtggaaaatgttttgtaaaaactattgaaaaataaatgcacatatttgtcatatgtagatgcacatgtttggcaatttgacctactctttacgcccatcaattaaagatttgtctagtttgtgtcacttaaatacttgagatttgtcctctcacagtatcacttagatctatactctatactactttaaaaggtagtagtggtggtggcagtgaatctgccagcactacctctatcactaatgtatgggccctccatgttgggtgaaacccacatgctcaataaatttaaacgtcctccaaaagataatgtccatattgtttggtaagatctacagggaaggaatccataaaggggttgaaaagagccagtctacatattcttcaaatgatgagcatgcagtgtgcacagcatgatttttttttcattgcaacgcataggcaatttgctagtttgcctaaaaattcattgcctgctttgcagcaagtcatagctgctgtacttgtttcagccaaacttggcttttcttattgtattcttattattgtttgagttttaggagagctgagaatttttctgctatgctaaagctggtgttcatataatatgaaatatctactgtagatcacagcatgaaagttaattgcttttttgacatccatattgccatctcatcatctccccccaccccctttttttgtacagtgcatcattgatcatcaagccctcccttgcctcctaagtctgttgacacaaaatctcaagaaaagcatcaagaaagaggcttgctggactatttcaaatattactgctggtaacaaagatcagatacaggtatgtgtacagacttaaaaaatactgacatgctcatcattctactaagtcatgaaggatttgtgtagtgcatacttagtagttttaattgtgttccctctccaaaccataaacaccacacaatgttcatattccatgcaagctttcaggtcaacttttcctttcatgatgattacacttgttagcagactcatccttgttgtacaaagactgagaacatggtagtaacttaaagaaacccttatgtatgatttgctcgcaaagtatcaatggcagcctaatcactagtccaaatgttgctgctgggacctggggtcctagaaggggaggggatgggagcatatggatgattgattcatttacacggttgggaacttgtgcacttagctgcaatctttcgtccttaacctataatagcctatagctatagatcttgttgattgtgcatgttctgaaatgttcaacaatttgctgcattgactaccataggctgtcataaatgctggcattattggtcctctggtgaatctgctccaaacggcagagttcgatatcaagaaggaagctgcatgggccatctcaaatgctacttcaggcggtagccatgatcaaatcaagtatgtttactcaccttgcaccagttctattcagctttatgaaatgcaaatataaccgctttcatagtttcatgttaagcttcatttggatttgatattgtatggtttgttaaaataggtatctggtgagcgagggctgcatcaagccattgtgtgatcttcttatttgcccagatataagaatcgttacagtttgtttggagggtctcgagaacattcttaaagtaggagaaaccgacaagaccttggctgcaggtgatgtgaatgtcttttcccagatgattgatgaagcggaaggtttggaaaagattgagaacttgcagagccatgataacaatgagatctatgaaaaagctgtgaagattcttgaggcctactggatggatgaggaggatgatacaatgggagctaccacggtagctgctccccaaggtgctacttttgactttggccaaggcggtggtgctgctcaattcaaataaatacaggtactctcaatcctcaacatggtttgtgtttattgtgggttgtttccactcttaccataaatcctttctgttctggtatcattcacttgaggcaacaagtaatgatttcaaatttcctcgacagatttgaccagaggtggtaaattgtggccactgtgcggggtactgaattgttctggtggttcaataagctaaaggtttcaagggggccagtgttacattatttccctactggtcacggatatcatatcactacgtctgtaacagggattaaagctttgaagtctgcgtttttcatcaggctactactatgtagtgtttgcatcttttagtatggtgtgcaacattttgctacttgtatagcctgagtcgaagcttctgcaaagccgtcacaacacattcctgaacccgtctggttttgagtttcgtcaggagtgtgctgagttgcagtttgtccggacatgtaaaccattatgccttttaaattatatattgctagggtttgttcggttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001049146.1 RefSeq:Os01g0253300]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0253300

2014-06-06T14:34:41Z

Jianchao Zhang: /* Knowledge Extension */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Fig1 Rice importina1 supported nuclear import of NLS-GFP in vertebratein vitroassay system.jpg|right|thumb|150px|Fig-1.Rice importina1 supported nuclear import of NLS-GFP in vertebratein vitroassay system.from ref<ref name="ref2" />]]
Os01g0253300 encodes importin subunit alpha-1a,a member of importin family, which functions a essential role in nuclear protein import by specifically and directly binding to substrates containing either a simple or bipartite NLS motif<ref name="ref1" />.In vivo assay suggests that importin alpha-1a can replace vertebrate importin a in the mediation of nuclear import of NLS substrates, implying that rice importin a1 functions as a NLS receptor in the process of nuclear import of proteins(Fig-1)<ref name="ref2" />,which indicates the importin family has a conserved transportation function both in plants and mammals.The importin alpha-1a also has a function in virus infection by interact with mungbean yellow mosaic virus capsid protein<ref name="ref3" />.

===Expression===
[[File:Fig2 Expression of importin.jpg|right|thumb|150px|Fig-2.Transcript analyses of rice importin.]]
[[File:Fig3. dark treatmeng influence the expression.jpg|middle|thumb|250px| Fig-3.An increase of importin-atranscript levels during dark-adaptation of light-grown green leaves.From ref<ref name="ref4" />]]

Transcript analyses of rice importin alpha-1a by ''Chang-Jie Jiang et al'' shows importin alpha-1a is highly expressed in callus, followed by root and etiolated leaf and lowly expressed in green leaf(Fig-2)<ref name="ref1" />.The expression level of importin alpha-1a is greatly increased after darkt treatment in green leaf[Fig-3]<ref name="ref4" /> .However it has a constitute expression pattern in non-photosynthetic tissues[Fig-4]<ref name="ref3" />.Together,it indicates a complex regulation of the importin alpha-1a transcription.

[[File:Fig4 constitue exprssion.jpg]]

Fig-4.Importin-atranscript levels in different rice tissues.(A) RNA was prepared from various tissues, roots (Root), mature leaf blades (M-Leaf), flag leaf blades (F-Leaf), stems (Stem) and suspension-cultured cells (Callus), and the transcript levels for importin-α in their tissues were examined by RNA blot analysis. Mature leaves, flag leaves and stems of field-grown plants were collected at noon on a sunny day in July. (B) The effect of illumination on the transcript levels for importin-α was examined in roots and suspension-cultured cells. Roots of water-cultured seedlings and suspension-cultured cells were exposed to white light (white fluorescent lamps; 90 μmol m−2 s−1) for 24 h (L), kept in complete darkness for 24 h (D) or kept in darkness for 24 h and then re-illuminated for 3 h (+3hL).From ref <ref name="ref3" />

===Protein structure===
1.The structure of rice importin alpha-1a comprises 10 ARM repeats (green, cartoon representation) and two NLS-like sequences from the N-terminal IBB domain(shown in yellow stick )[FIG-5]<ref name="ref5" />.
[[File:Fig5 crystal structure of importin.jpg]]

Fig-5:crystal structure of importin alpha-1a.From ref<ref name="ref5" />

2.The crystal structures of their complexes with rice importin alpha-1a show that they bind to the minor NLS binding site[Fig6A]. By contrast, the crystal structures of their complexes with mouse (Mus musculus) importin alpha-1ashow preferential binding to the major NLS binding site[Fig6B]. The results reveal the molecular basis of a number of features of the classical nuclear transport pathway specific to plants<ref name="ref5" />.

[[File:Fig 6 structure difference.jpg]]

Fig-6:Differential Binding of Plant-Specific NLSs to rImpa1a and mImpa.<ref name="ref5" />

===Evolution===
The phylogenetic tree of importin alpha shows that the rice importin alpha-1a protein is the most distant member from various organisms[Fig-7]<ref name="ref6" />.we could find another EST from Arabidopsis (accession number F15465), which has about 60% identity with #61L at the levelof both nucleotide and amino acid sequences. It might be interpreted that importin alpha-1a homologous to rice #61L(Refere to importin alpha-1a) is also present in Arabidopsis, and that the #61L protein and the homologue are functionally differentiated from the known importin alpha-1a.

[[File:Fig 7.jpg]]

Fig-7:(Phylogenetic tree of importinK. The tree was constructed by the UPGMA method using the GENETYX-MAC 7.3 software(Software Development Co., Tokyo) with default parameters. The accession number of the putative open reading frame T10M13.16 which is predicted ) From<ref name="ref6" />

===Knowledge Extension===
Rice encodes many kinds of importin proteins such as importin α1a/1b,importinβand importin α1a is the most studied gene in rice with its crystal structure complex being resolved<ref name="ref5" /><ref name="ref7" />. Importin α1a functions as another importin α protein by form a complex with importin βand NLS-containing substrate.As shown in Figure -8, a single round of importin α-mediated import can be divided into six steps: (i) formation of a ternary complex in the cytoplasm; (ii) importin β-mediated binding of the ternary complex to docking sites at the periphery of the NPC; (iii) importin β-mediated translocation through the NPC; (iv) dissociation of the ternary complex, triggered, in part, by the binding of the small nuclear GTPase Ran–GTP to importin β; (v) recycling of importin α to the cytoplasm bound to the exportin CAS–Ran–GTP; and (vi) disassembly of the export complex and release of free importin α to the cytoplasm. Disassembly is induced by the Ran–GAP-induced hydrolysis of GTP by Ran. Ran–GDP and CAS are recycled back to the nucleus for further rounds of transport. Back in the nucleus, Ran–GDP is converted to Ran–GTP by the guanine nucleotide exchange factor RCC1.<ref name="ref5" />

[[File:Fig-8 The nucleocytoplasmic shuttling cycle of importin α.png]]

Fig-8:The nucleocytoplasmic shuttling cycle of importin α. (i) Importin α (α) forms a ternary complex with importin β (β) and cargo (blue circles). (ii) The ternary complex docks at the nuclear-pore complex (NPC) and (iii)translocates into the nucleus. (iv) Binding of Ran–GTP triggers the dissociation of the ternary complex. (v)Importin α binds to the exportin CAS–Ran–GTP complex and is exported to the cytoplasm. (vi) Ran–GAP-stimulated hydrolysis of GTP by Ran triggers the dissociation of the exportin complex and releases free importin α into the cytoplasm for another transport cycle. The recycling of importin β to the cytoplasm, and of Ran–GDP to the nucleus and its conversion to Ran–GTP are not shown.

==Labs working on this gene==
*National Institute of Agrobiological Resources, Tsukuba, Ibaraki 305-8602, Japan.
*Friedrich Miescher Institute, Maulbeerstrasse 66, 4058 Basel, Switzerland.
*Central Research Institute of Electric Power Industry, Chiba, Japan.
*School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, University of Queensland, Brisbane Qld 4072, Australia.
*School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience, and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld 4072, Australia.
*The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China.
*Department of Biochemistry and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan 114, Republic of China.

==References==
<references>
<ref name="ref1">
Jiang CJ, Shoji K, Matsuki R, Baba A, Inagaki N, Ban H, Iwasaki T, Imamoto N, Yoneda Y, Deng XW, Yamamoto N. Molecular cloning of a novel importin alpha homologue from rice, by which constitutive photomorphogenic 1 (COP1) nuclear localization signal (NLS)-protein is preferentially nuclear imported. J Biol Chem. 2001 Mar 23;276(12):9322-9. Epub 2000 Dec 20.</ref>

<ref name="ref2">
Jiang CJ, Imamoto N, Matsuki R, Yoneda Y, Yamamoto N. Functional characterization of a plant importin alpha homologue. J Biol Chem. 1998 Sep 11.</ref>

<ref name="ref3">
Guerra-Peraza O, Kirk D, Seltzer V, Veluthambi K, Schmit AC, Hohn T, Herzog E. Coat proteins of Rice tungro bacilliform virus and Mungbean yellow mosaic virus contain multiple nuclear-localization signals and interact with importin alpha. J Gen Virol. 2005 Jun;86(Pt 6):1815-26.</ref>

<ref name="ref4">
Shoji K, Iwasaki T, Matsuki R, Miyao M, Yamamoto N. Cloning of a cDNA encoding an importin-alpha and down-regulation of the gene by light in rice leaves. Gene. 1998 Jun 8;212(2):279-86.</ref>
<ref name="ref5">
Chang CW1, Couñago RL, Williams SJ, Bodén M, Kobe B.Crystal structure of rice importin-α and structural basis of its interaction with plant-specific nuclear localization signals.Plant Cell. 2012 Dec;24(12):5074-88. doi: 10.1105/tpc.112.104422. Epub 2012 Dec 18.</ref>
<ref name="ref6">
Iwasaki T, Matsuki R, Shoji K, Sanmiya K, Miyao M, Yamamoto N. A novel importin alpha from rice, a component involved in the process of nuclear protein transport. FEBS Lett. 1998 May 29;428(3):259-62.</ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0253300|
Description = Importin alpha-1a subunit|
Version = NM_001049146.1 GI:115435705 GeneID:4327117|
Length = 5116 bp|
Definition = Oryza sativa Japonica Group Os01g0253300, 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 = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:8381095..8386210|
CDS = 8381261..8381470,8382333..8382429,8382526..8382617,8382709..8382840,8382955..8383140 ,8383224..8383387,8383494..8383572,8384464..8384592,8385082..8385209 ,8385328..8385691|
GCID = <gbrowseImage1>
name=NC_008394:8381095..8386210
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:8381095..8386210
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgctgcgcccgagcgagcgggtggaggtgcggcggaaccgctacaaggtggcggtggacgccgaggaggggaggcggcggcgcgaggacaacatggtggagatccgcaagagccgccgcgaggagagcctcctcaagaagcgccgcgaggggctccaggcccaggcccccgtccccgcctccgccgcaaccggcgtcgataagaagctcgaaagccttcctgctatgattggtggagtttattcggacgataacaaccttcagcttgaggccacaacacagttccgcaagttgctttctatagagaggagccctccaattgaagaggttattcaatcaggcgttgttcctagattcgtgcagtttcttaccagagaggatttcccccagctacagttcgaagctgcgtgggcacttacaaacattgcatctggcacttcggagaatacaaaggttgtcattgatcatggggctgtaccaatatttgtgaagcttcttggttcttctagtgatgatgttcgtgagcaggctgtatgggcattgggcaatgttgctggtgattcccctaagtgccgtgaccttgttcttgccaatggtgcattgctgcctctgctagcacagttgaatgagcacactaaactctctatgctaaggaatgcaacttggactttatcgaacttctgcagaggaaaaccacagccatcatttgaacagactaggcctgctcttccagcactggcacggcttattcactccaatgatgaggaagttctcactgatgcgtgctgggctctttcatatttatctgatggcactaatgacaagatccaagccgtgattgaagctggtgtttgcccccgtcttgtggagcttctcctccatccatcaccttcagtgcttatacccgcactacgaactgttggaaatattgtaactggagatgacgcgcaaactcagtgcatcattgatcatcaagccctcccttgcctcctaagtctgttgacacaaaatctcaagaaaagcatcaagaaagaggcttgctggactatttcaaatattactgctggtaacaaagatcagatacaggctgtcataaatgctggcattattggtcctctggtgaatctgctccaaacggcagagttcgatatcaagaaggaagctgcatgggccatctcaaatgctacttcaggcggtagccatgatcaaatcaagtatctggtgagcgagggctgcatcaagccattgtgtgatcttcttatttgcccagatataagaatcgttacagtttgtttggagggtctcgagaacattcttaaagtaggagaaaccgacaagaccttggctgcaggtgatgtgaatgtcttttcccagatgattgatgaagcggaaggtttggaaaagattgagaacttgcagagccatgataacaatgagatctatgaaaaagctgtgaagattcttgaggcctactggatggatgaggaggatgatacaatgggagctaccacggtagctgctccccaaggtgctacttttgactttggccaaggcggtggtgctgctcaattcaaataa</cdnaseq>|
AA = <aaseq>MSLRPSERVEVRRNRYKVAVDAEEGRRRREDNMVEIRKSRREES LLKKRREGLQAQAPVPASAATGVDKKLESLPAMIGGVYSDDNNLQLEATTQFRKLLSI ERSPPIEEVIQSGVVPRFVQFLTREDFPQLQFEAAWALTNIASGTSENTKVVIDHGAV PIFVKLLGSSSDDVREQAVWALGNVAGDSPKCRDLVLANGALLPLLAQLNEHTKLSML RNATWTLSNFCRGKPQPSFEQTRPALPALARLIHSNDEEVLTDACWALSYLSDGTNDK IQAVIEAGVCPRLVELLLHPSPSVLIPALRTVGNIVTGDDAQTQCIIDHQALPCLLSL LTQNLKKSIKKEACWTISNITAGNKDQIQAVINAGIIGPLVNLLQTAEFDIKKEAAWA ISNATSGGSHDQIKYLVSEGCIKPLCDLLICPDIRIVTVCLEGLENILKVGETDKTLA AGDVNVFSQMIDEAEGLEKIENLQSHDNNEIYEKAVKILEAYWMDEEDDTMGATTVAA PQGATFDFGQGGGAAQFK</aaseq>|
DNA = <dnaseqindica>167..376#1239..1335#1432..1523#1615..1746#1861..2046#2130..2293#2400..2478#3370..3498#3988..4115#4234..4597#gtgtgagctttaactccccccctttccccgcggccactagggtttctcctcctctttcctctcctcctccgccccgacgcctcgctagggtttttgcctctccctccgccgccgccgctgccgcgaggagaggagggggggagagcacccagccggcgagccagccatgtcgctgcgcccgagcgagcgggtggaggtgcggcggaaccgctacaaggtggcggtggacgccgaggaggggaggcggcggcgcgaggacaacatggtggagatccgcaagagccgccgcgaggagagcctcctcaagaagcgccgcgaggggctccaggcccaggcccccgtccccgcctccgccgcaaccggcgtcgataagaaggtgagtagtatactcctcgattcccccccgctcccctcccctcccctcccctgcctccgatgacgctatcccatcgtgtcctggatcccatattttaggtaggtgttggattggattgcactttttgagagggtttttgattcgtctgcggcatatttgtttaagtttgttattatacccgcatgtctactagcgtgcgggtgagggtaggttcctgctagatgtaggcaacacttagcaccacgtttcgatgcctcgattagtcacttgatttctgattctccttctgttgacaatattacaagtactgttagttggcacggttgcgaactcctagcgtttgaaatgtttccaggtacatgcctgctagctccagtgatctagttttagttttaggacatgtagattgtggtcttaggatcaaatcttccacggattcactgcggataattagttaggtgaccaggaactgtaataatgattgatcttcctgataatttttagtgtacatcttgctgttgtttcatcttatgttttgatagaagcatacaaatgagctgatgccatattatatctttatagctattttttgtgctatcttgaaattgagggtccagtgcaactttccttatgactgaaccttgtctttagtacatggaagcacataaatcatatagtagtgtttctggtcatgtttctagagacgtcctacattgataacgcatacatttatgttactgttaaactacctctggtttctgttctttgcaccacccctaaaagagaaggaaactgcttttaaaccctttttggggtttaatacgggaagttgagtatttgatatctctgttgaatgttgtagctcgaaagccttcctgctatgattggtggagtttattcggacgataacaaccttcagcttgaggccacaacacagttccgcaagttgctttctataggtacaaacctcttaaatgttttgggctgttaccttgtgaaaataatagttgaacaaaagttaattactaattacacccattacaatttttaattagagaggagccctccaattgaagaggttattcaatcaggcgttgttcctagattcgtgcagtttcttaccagagaggatttcccccagctacaggtgtgtgccaacacaatattattttcattatctggtaggttcaaataaaaatggatttattactgtggtgcttttgaattaaattttgtagttcgaagctgcgtgggcacttacaaacattgcatctggcacttcggagaatacaaaggttgtcattgatcatggggctgtaccaatatttgtgaagcttcttggttcttctagtgatgatgttcgtgagcaggtatccgatcatctcctgacttgtctttgtgctttctgtacttccttgatattattttgattgagtgcattgttggagttattaatgtttttacctcttgaaaaaaaattgaaggctgtatgggcattgggcaatgttgctggtgattcccctaagtgccgtgaccttgttcttgccaatggtgcattgctgcctctgctagcacagttgaatgagcacactaaactctctatgctaaggaatgcaacttggactttatcgaacttctgcagaggaaaaccacagccatcatttgaacaggtttggacaaagtttctttgtactctactgtagttagtagggaaagacagttccttaacatgatgtttattgggtgtcaatagactaggcctgctcttccagcactggcacggcttattcactccaatgatgaggaagttctcactgatgcgtgctgggctctttcatatttatctgatggcactaatgacaagatccaagccgtgattgaagctggtgtttgcccccgtcttgtggagcttctcctgtaagtgacaacattgcattacaattttctgccattttcctttagattcttatttgctactctcattataccctttttaatattttatactgtttacaacatgaagccatccatcaccttcagtgcttatacccgcactacgaactgttggaaatattgtaactggagatgacgcgcaaactcaggtattgtgttgattttttgcatctctatatctgacagattttgtatcaattgatatcaactactaagactcatgaatcttgagcttaatatttagaggttgtgttcatcacagttgatattaaattttaggcttgtggaaaatgtttaatatcatagttgatattaaatctagaggttgcatctaatgtggaaaatgttttgtaaaaactattgaaaaataaatgcacatatttgtcatatgtagatgcacatgtttggcaatttgacctactctttacgcccatcaattaaagatttgtctagtttgtgtcacttaaatacttgagatttgtcctctcacagtatcacttagatctatactctatactactttaaaaggtagtagtggtggtggcagtgaatctgccagcactacctctatcactaatgtatgggccctccatgttgggtgaaacccacatgctcaataaatttaaacgtcctccaaaagataatgtccatattgtttggtaagatctacagggaaggaatccataaaggggttgaaaagagccagtctacatattcttcaaatgatgagcatgcagtgtgcacagcatgatttttttttcattgcaacgcataggcaatttgctagtttgcctaaaaattcattgcctgctttgcagcaagtcatagctgctgtacttgtttcagccaaacttggcttttcttattgtattcttattattgtttgagttttaggagagctgagaatttttctgctatgctaaagctggtgttcatataatatgaaatatctactgtagatcacagcatgaaagttaattgcttttttgacatccatattgccatctcatcatctccccccaccccctttttttgtacagtgcatcattgatcatcaagccctcccttgcctcctaagtctgttgacacaaaatctcaagaaaagcatcaagaaagaggcttgctggactatttcaaatattactgctggtaacaaagatcagatacaggtatgtgtacagacttaaaaaatactgacatgctcatcattctactaagtcatgaaggatttgtgtagtgcatacttagtagttttaattgtgttccctctccaaaccataaacaccacacaatgttcatattccatgcaagctttcaggtcaacttttcctttcatgatgattacacttgttagcagactcatccttgttgtacaaagactgagaacatggtagtaacttaaagaaacccttatgtatgatttgctcgcaaagtatcaatggcagcctaatcactagtccaaatgttgctgctgggacctggggtcctagaaggggaggggatgggagcatatggatgattgattcatttacacggttgggaacttgtgcacttagctgcaatctttcgtccttaacctataatagcctatagctatagatcttgttgattgtgcatgttctgaaatgttcaacaatttgctgcattgactaccataggctgtcataaatgctggcattattggtcctctggtgaatctgctccaaacggcagagttcgatatcaagaaggaagctgcatgggccatctcaaatgctacttcaggcggtagccatgatcaaatcaagtatgtttactcaccttgcaccagttctattcagctttatgaaatgcaaatataaccgctttcatagtttcatgttaagcttcatttggatttgatattgtatggtttgttaaaataggtatctggtgagcgagggctgcatcaagccattgtgtgatcttcttatttgcccagatataagaatcgttacagtttgtttggagggtctcgagaacattcttaaagtaggagaaaccgacaagaccttggctgcaggtgatgtgaatgtcttttcccagatgattgatgaagcggaaggtttggaaaagattgagaacttgcagagccatgataacaatgagatctatgaaaaagctgtgaagattcttgaggcctactggatggatgaggaggatgatacaatgggagctaccacggtagctgctccccaaggtgctacttttgactttggccaaggcggtggtgctgctcaattcaaataaatacaggtactctcaatcctcaacatggtttgtgtttattgtgggttgtttccactcttaccataaatcctttctgttctggtatcattcacttgaggcaacaagtaatgatttcaaatttcctcgacagatttgaccagaggtggtaaattgtggccactgtgcggggtactgaattgttctggtggttcaataagctaaaggtttcaagggggccagtgttacattatttccctactggtcacggatatcatatcactacgtctgtaacagggattaaagctttgaagtctgcgtttttcatcaggctactactatgtagtgtttgcatcttttagtatggtgtgcaacattttgctacttgtatagcctgagtcgaagcttctgcaaagccgtcacaacacattcctgaacccgtctggttttgagtttcgtcaggagtgtgctgagttgcagtttgtccggacatgtaaaccattatgccttttaaattatatattgctagggtttgttcggttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001049146.1 RefSeq:Os01g0253300]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0253300

2014-06-06T14:33:47Z

Jianchao Zhang: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Fig1 Rice importina1 supported nuclear import of NLS-GFP in vertebratein vitroassay system.jpg|right|thumb|150px|Fig-1.Rice importina1 supported nuclear import of NLS-GFP in vertebratein vitroassay system.from ref<ref name="ref2" />]]
Os01g0253300 encodes importin subunit alpha-1a,a member of importin family, which functions a essential role in nuclear protein import by specifically and directly binding to substrates containing either a simple or bipartite NLS motif<ref name="ref1" />.In vivo assay suggests that importin alpha-1a can replace vertebrate importin a in the mediation of nuclear import of NLS substrates, implying that rice importin a1 functions as a NLS receptor in the process of nuclear import of proteins(Fig-1)<ref name="ref2" />,which indicates the importin family has a conserved transportation function both in plants and mammals.The importin alpha-1a also has a function in virus infection by interact with mungbean yellow mosaic virus capsid protein<ref name="ref3" />.

===Expression===
[[File:Fig2 Expression of importin.jpg|right|thumb|150px|Fig-2.Transcript analyses of rice importin.]]
[[File:Fig3. dark treatmeng influence the expression.jpg|middle|thumb|250px| Fig-3.An increase of importin-atranscript levels during dark-adaptation of light-grown green leaves.From ref<ref name="ref4" />]]

Transcript analyses of rice importin alpha-1a by ''Chang-Jie Jiang et al'' shows importin alpha-1a is highly expressed in callus, followed by root and etiolated leaf and lowly expressed in green leaf(Fig-2)<ref name="ref1" />.The expression level of importin alpha-1a is greatly increased after darkt treatment in green leaf[Fig-3]<ref name="ref4" /> .However it has a constitute expression pattern in non-photosynthetic tissues[Fig-4]<ref name="ref3" />.Together,it indicates a complex regulation of the importin alpha-1a transcription.

[[File:Fig4 constitue exprssion.jpg]]

Fig-4.Importin-atranscript levels in different rice tissues.(A) RNA was prepared from various tissues, roots (Root), mature leaf blades (M-Leaf), flag leaf blades (F-Leaf), stems (Stem) and suspension-cultured cells (Callus), and the transcript levels for importin-α in their tissues were examined by RNA blot analysis. Mature leaves, flag leaves and stems of field-grown plants were collected at noon on a sunny day in July. (B) The effect of illumination on the transcript levels for importin-α was examined in roots and suspension-cultured cells. Roots of water-cultured seedlings and suspension-cultured cells were exposed to white light (white fluorescent lamps; 90 μmol m−2 s−1) for 24 h (L), kept in complete darkness for 24 h (D) or kept in darkness for 24 h and then re-illuminated for 3 h (+3hL).From ref <ref name="ref3" />

===Protein structure===
1.The structure of rice importin alpha-1a comprises 10 ARM repeats (green, cartoon representation) and two NLS-like sequences from the N-terminal IBB domain(shown in yellow stick )[FIG-5]<ref name="ref5" />.
[[File:Fig5 crystal structure of importin.jpg]]

Fig-5:crystal structure of importin alpha-1a.From ref<ref name="ref5" />

2.The crystal structures of their complexes with rice importin alpha-1a show that they bind to the minor NLS binding site[Fig6A]. By contrast, the crystal structures of their complexes with mouse (Mus musculus) importin alpha-1ashow preferential binding to the major NLS binding site[Fig6B]. The results reveal the molecular basis of a number of features of the classical nuclear transport pathway specific to plants<ref name="ref5" />.

[[File:Fig 6 structure difference.jpg]]

Fig-6:Differential Binding of Plant-Specific NLSs to rImpa1a and mImpa.<ref name="ref5" />

===Evolution===
The phylogenetic tree of importin alpha shows that the rice importin alpha-1a protein is the most distant member from various organisms[Fig-7]<ref name="ref6" />.we could find another EST from Arabidopsis (accession number F15465), which has about 60% identity with #61L at the levelof both nucleotide and amino acid sequences. It might be interpreted that importin alpha-1a homologous to rice #61L(Refere to importin alpha-1a) is also present in Arabidopsis, and that the #61L protein and the homologue are functionally differentiated from the known importin alpha-1a.

[[File:Fig 7.jpg]]

Fig-7:(Phylogenetic tree of importinK. The tree was constructed by the UPGMA method using the GENETYX-MAC 7.3 software(Software Development Co., Tokyo) with default parameters. The accession number of the putative open reading frame T10M13.16 which is predicted ) From<ref name="ref6" />

===Knowledge Extension===
Rice encodes many kinds of importin proteins such as importin α1a/1b,importinβand importin α1a is the most studied gene in rice with its crystal structure complex being resolved<ref name="ref5" /><ref name="ref5" />. Importin α1a functions as another importin α protein by form a complex with importin βand NLS-containing substrate.As shown in Figure -8, a single round of importin α-mediated import can be divided into six steps: (i) formation of a ternary complex in the cytoplasm; (ii) importin β-mediated binding of the ternary complex to docking sites at the periphery of the NPC; (iii) importin β-mediated translocation through the NPC; (iv) dissociation of the ternary complex, triggered, in part, by the binding of the small nuclear GTPase Ran–GTP to importin β; (v) recycling of importin α to the cytoplasm bound to the exportin CAS–Ran–GTP; and (vi) disassembly of the export complex and release of free importin α to the cytoplasm. Disassembly is induced by the Ran–GAP-induced hydrolysis of GTP by Ran. Ran–GDP and CAS are recycled back to the nucleus for further rounds of transport. Back in the nucleus, Ran–GDP is converted to Ran–GTP by the guanine nucleotide exchange factor RCC1.<ref name="ref5" />

[[File:Fig-8 The nucleocytoplasmic shuttling cycle of importin α.png]]

Fig-8:The nucleocytoplasmic shuttling cycle of importin α. (i) Importin α (α) forms a ternary complex with importin β (β) and cargo (blue circles). (ii) The ternary complex docks at the nuclear-pore complex (NPC) and (iii)translocates into the nucleus. (iv) Binding of Ran–GTP triggers the dissociation of the ternary complex. (v)Importin α binds to the exportin CAS–Ran–GTP complex and is exported to the cytoplasm. (vi) Ran–GAP-stimulated hydrolysis of GTP by Ran triggers the dissociation of the exportin complex and releases free importin α into the cytoplasm for another transport cycle. The recycling of importin β to the cytoplasm, and of Ran–GDP to the nucleus and its conversion to Ran–GTP are not shown.

==Labs working on this gene==
*National Institute of Agrobiological Resources, Tsukuba, Ibaraki 305-8602, Japan.
*Friedrich Miescher Institute, Maulbeerstrasse 66, 4058 Basel, Switzerland.
*Central Research Institute of Electric Power Industry, Chiba, Japan.
*School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, University of Queensland, Brisbane Qld 4072, Australia.
*School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience, and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld 4072, Australia.
*The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China.
*Department of Biochemistry and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan 114, Republic of China.

==References==
<references>
<ref name="ref1">
Jiang CJ, Shoji K, Matsuki R, Baba A, Inagaki N, Ban H, Iwasaki T, Imamoto N, Yoneda Y, Deng XW, Yamamoto N. Molecular cloning of a novel importin alpha homologue from rice, by which constitutive photomorphogenic 1 (COP1) nuclear localization signal (NLS)-protein is preferentially nuclear imported. J Biol Chem. 2001 Mar 23;276(12):9322-9. Epub 2000 Dec 20.</ref>

<ref name="ref2">
Jiang CJ, Imamoto N, Matsuki R, Yoneda Y, Yamamoto N. Functional characterization of a plant importin alpha homologue. J Biol Chem. 1998 Sep 11.</ref>

<ref name="ref3">
Guerra-Peraza O, Kirk D, Seltzer V, Veluthambi K, Schmit AC, Hohn T, Herzog E. Coat proteins of Rice tungro bacilliform virus and Mungbean yellow mosaic virus contain multiple nuclear-localization signals and interact with importin alpha. J Gen Virol. 2005 Jun;86(Pt 6):1815-26.</ref>

<ref name="ref4">
Shoji K, Iwasaki T, Matsuki R, Miyao M, Yamamoto N. Cloning of a cDNA encoding an importin-alpha and down-regulation of the gene by light in rice leaves. Gene. 1998 Jun 8;212(2):279-86.</ref>
<ref name="ref5">
Chang CW1, Couñago RL, Williams SJ, Bodén M, Kobe B.Crystal structure of rice importin-α and structural basis of its interaction with plant-specific nuclear localization signals.Plant Cell. 2012 Dec;24(12):5074-88. doi: 10.1105/tpc.112.104422. Epub 2012 Dec 18.</ref>
<ref name="ref6">
Iwasaki T, Matsuki R, Shoji K, Sanmiya K, Miyao M, Yamamoto N. A novel importin alpha from rice, a component involved in the process of nuclear protein transport. FEBS Lett. 1998 May 29;428(3):259-62.</ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0253300|
Description = Importin alpha-1a subunit|
Version = NM_001049146.1 GI:115435705 GeneID:4327117|
Length = 5116 bp|
Definition = Oryza sativa Japonica Group Os01g0253300, 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 = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:8381095..8386210|
CDS = 8381261..8381470,8382333..8382429,8382526..8382617,8382709..8382840,8382955..8383140 ,8383224..8383387,8383494..8383572,8384464..8384592,8385082..8385209 ,8385328..8385691|
GCID = <gbrowseImage1>
name=NC_008394:8381095..8386210
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:8381095..8386210
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgctgcgcccgagcgagcgggtggaggtgcggcggaaccgctacaaggtggcggtggacgccgaggaggggaggcggcggcgcgaggacaacatggtggagatccgcaagagccgccgcgaggagagcctcctcaagaagcgccgcgaggggctccaggcccaggcccccgtccccgcctccgccgcaaccggcgtcgataagaagctcgaaagccttcctgctatgattggtggagtttattcggacgataacaaccttcagcttgaggccacaacacagttccgcaagttgctttctatagagaggagccctccaattgaagaggttattcaatcaggcgttgttcctagattcgtgcagtttcttaccagagaggatttcccccagctacagttcgaagctgcgtgggcacttacaaacattgcatctggcacttcggagaatacaaaggttgtcattgatcatggggctgtaccaatatttgtgaagcttcttggttcttctagtgatgatgttcgtgagcaggctgtatgggcattgggcaatgttgctggtgattcccctaagtgccgtgaccttgttcttgccaatggtgcattgctgcctctgctagcacagttgaatgagcacactaaactctctatgctaaggaatgcaacttggactttatcgaacttctgcagaggaaaaccacagccatcatttgaacagactaggcctgctcttccagcactggcacggcttattcactccaatgatgaggaagttctcactgatgcgtgctgggctctttcatatttatctgatggcactaatgacaagatccaagccgtgattgaagctggtgtttgcccccgtcttgtggagcttctcctccatccatcaccttcagtgcttatacccgcactacgaactgttggaaatattgtaactggagatgacgcgcaaactcagtgcatcattgatcatcaagccctcccttgcctcctaagtctgttgacacaaaatctcaagaaaagcatcaagaaagaggcttgctggactatttcaaatattactgctggtaacaaagatcagatacaggctgtcataaatgctggcattattggtcctctggtgaatctgctccaaacggcagagttcgatatcaagaaggaagctgcatgggccatctcaaatgctacttcaggcggtagccatgatcaaatcaagtatctggtgagcgagggctgcatcaagccattgtgtgatcttcttatttgcccagatataagaatcgttacagtttgtttggagggtctcgagaacattcttaaagtaggagaaaccgacaagaccttggctgcaggtgatgtgaatgtcttttcccagatgattgatgaagcggaaggtttggaaaagattgagaacttgcagagccatgataacaatgagatctatgaaaaagctgtgaagattcttgaggcctactggatggatgaggaggatgatacaatgggagctaccacggtagctgctccccaaggtgctacttttgactttggccaaggcggtggtgctgctcaattcaaataa</cdnaseq>|
AA = <aaseq>MSLRPSERVEVRRNRYKVAVDAEEGRRRREDNMVEIRKSRREES LLKKRREGLQAQAPVPASAATGVDKKLESLPAMIGGVYSDDNNLQLEATTQFRKLLSI ERSPPIEEVIQSGVVPRFVQFLTREDFPQLQFEAAWALTNIASGTSENTKVVIDHGAV PIFVKLLGSSSDDVREQAVWALGNVAGDSPKCRDLVLANGALLPLLAQLNEHTKLSML RNATWTLSNFCRGKPQPSFEQTRPALPALARLIHSNDEEVLTDACWALSYLSDGTNDK IQAVIEAGVCPRLVELLLHPSPSVLIPALRTVGNIVTGDDAQTQCIIDHQALPCLLSL LTQNLKKSIKKEACWTISNITAGNKDQIQAVINAGIIGPLVNLLQTAEFDIKKEAAWA ISNATSGGSHDQIKYLVSEGCIKPLCDLLICPDIRIVTVCLEGLENILKVGETDKTLA AGDVNVFSQMIDEAEGLEKIENLQSHDNNEIYEKAVKILEAYWMDEEDDTMGATTVAA PQGATFDFGQGGGAAQFK</aaseq>|
DNA = <dnaseqindica>167..376#1239..1335#1432..1523#1615..1746#1861..2046#2130..2293#2400..2478#3370..3498#3988..4115#4234..4597#gtgtgagctttaactccccccctttccccgcggccactagggtttctcctcctctttcctctcctcctccgccccgacgcctcgctagggtttttgcctctccctccgccgccgccgctgccgcgaggagaggagggggggagagcacccagccggcgagccagccatgtcgctgcgcccgagcgagcgggtggaggtgcggcggaaccgctacaaggtggcggtggacgccgaggaggggaggcggcggcgcgaggacaacatggtggagatccgcaagagccgccgcgaggagagcctcctcaagaagcgccgcgaggggctccaggcccaggcccccgtccccgcctccgccgcaaccggcgtcgataagaaggtgagtagtatactcctcgattcccccccgctcccctcccctcccctcccctgcctccgatgacgctatcccatcgtgtcctggatcccatattttaggtaggtgttggattggattgcactttttgagagggtttttgattcgtctgcggcatatttgtttaagtttgttattatacccgcatgtctactagcgtgcgggtgagggtaggttcctgctagatgtaggcaacacttagcaccacgtttcgatgcctcgattagtcacttgatttctgattctccttctgttgacaatattacaagtactgttagttggcacggttgcgaactcctagcgtttgaaatgtttccaggtacatgcctgctagctccagtgatctagttttagttttaggacatgtagattgtggtcttaggatcaaatcttccacggattcactgcggataattagttaggtgaccaggaactgtaataatgattgatcttcctgataatttttagtgtacatcttgctgttgtttcatcttatgttttgatagaagcatacaaatgagctgatgccatattatatctttatagctattttttgtgctatcttgaaattgagggtccagtgcaactttccttatgactgaaccttgtctttagtacatggaagcacataaatcatatagtagtgtttctggtcatgtttctagagacgtcctacattgataacgcatacatttatgttactgttaaactacctctggtttctgttctttgcaccacccctaaaagagaaggaaactgcttttaaaccctttttggggtttaatacgggaagttgagtatttgatatctctgttgaatgttgtagctcgaaagccttcctgctatgattggtggagtttattcggacgataacaaccttcagcttgaggccacaacacagttccgcaagttgctttctataggtacaaacctcttaaatgttttgggctgttaccttgtgaaaataatagttgaacaaaagttaattactaattacacccattacaatttttaattagagaggagccctccaattgaagaggttattcaatcaggcgttgttcctagattcgtgcagtttcttaccagagaggatttcccccagctacaggtgtgtgccaacacaatattattttcattatctggtaggttcaaataaaaatggatttattactgtggtgcttttgaattaaattttgtagttcgaagctgcgtgggcacttacaaacattgcatctggcacttcggagaatacaaaggttgtcattgatcatggggctgtaccaatatttgtgaagcttcttggttcttctagtgatgatgttcgtgagcaggtatccgatcatctcctgacttgtctttgtgctttctgtacttccttgatattattttgattgagtgcattgttggagttattaatgtttttacctcttgaaaaaaaattgaaggctgtatgggcattgggcaatgttgctggtgattcccctaagtgccgtgaccttgttcttgccaatggtgcattgctgcctctgctagcacagttgaatgagcacactaaactctctatgctaaggaatgcaacttggactttatcgaacttctgcagaggaaaaccacagccatcatttgaacaggtttggacaaagtttctttgtactctactgtagttagtagggaaagacagttccttaacatgatgtttattgggtgtcaatagactaggcctgctcttccagcactggcacggcttattcactccaatgatgaggaagttctcactgatgcgtgctgggctctttcatatttatctgatggcactaatgacaagatccaagccgtgattgaagctggtgtttgcccccgtcttgtggagcttctcctgtaagtgacaacattgcattacaattttctgccattttcctttagattcttatttgctactctcattataccctttttaatattttatactgtttacaacatgaagccatccatcaccttcagtgcttatacccgcactacgaactgttggaaatattgtaactggagatgacgcgcaaactcaggtattgtgttgattttttgcatctctatatctgacagattttgtatcaattgatatcaactactaagactcatgaatcttgagcttaatatttagaggttgtgttcatcacagttgatattaaattttaggcttgtggaaaatgtttaatatcatagttgatattaaatctagaggttgcatctaatgtggaaaatgttttgtaaaaactattgaaaaataaatgcacatatttgtcatatgtagatgcacatgtttggcaatttgacctactctttacgcccatcaattaaagatttgtctagtttgtgtcacttaaatacttgagatttgtcctctcacagtatcacttagatctatactctatactactttaaaaggtagtagtggtggtggcagtgaatctgccagcactacctctatcactaatgtatgggccctccatgttgggtgaaacccacatgctcaataaatttaaacgtcctccaaaagataatgtccatattgtttggtaagatctacagggaaggaatccataaaggggttgaaaagagccagtctacatattcttcaaatgatgagcatgcagtgtgcacagcatgatttttttttcattgcaacgcataggcaatttgctagtttgcctaaaaattcattgcctgctttgcagcaagtcatagctgctgtacttgtttcagccaaacttggcttttcttattgtattcttattattgtttgagttttaggagagctgagaatttttctgctatgctaaagctggtgttcatataatatgaaatatctactgtagatcacagcatgaaagttaattgcttttttgacatccatattgccatctcatcatctccccccaccccctttttttgtacagtgcatcattgatcatcaagccctcccttgcctcctaagtctgttgacacaaaatctcaagaaaagcatcaagaaagaggcttgctggactatttcaaatattactgctggtaacaaagatcagatacaggtatgtgtacagacttaaaaaatactgacatgctcatcattctactaagtcatgaaggatttgtgtagtgcatacttagtagttttaattgtgttccctctccaaaccataaacaccacacaatgttcatattccatgcaagctttcaggtcaacttttcctttcatgatgattacacttgttagcagactcatccttgttgtacaaagactgagaacatggtagtaacttaaagaaacccttatgtatgatttgctcgcaaagtatcaatggcagcctaatcactagtccaaatgttgctgctgggacctggggtcctagaaggggaggggatgggagcatatggatgattgattcatttacacggttgggaacttgtgcacttagctgcaatctttcgtccttaacctataatagcctatagctatagatcttgttgattgtgcatgttctgaaatgttcaacaatttgctgcattgactaccataggctgtcataaatgctggcattattggtcctctggtgaatctgctccaaacggcagagttcgatatcaagaaggaagctgcatgggccatctcaaatgctacttcaggcggtagccatgatcaaatcaagtatgtttactcaccttgcaccagttctattcagctttatgaaatgcaaatataaccgctttcatagtttcatgttaagcttcatttggatttgatattgtatggtttgttaaaataggtatctggtgagcgagggctgcatcaagccattgtgtgatcttcttatttgcccagatataagaatcgttacagtttgtttggagggtctcgagaacattcttaaagtaggagaaaccgacaagaccttggctgcaggtgatgtgaatgtcttttcccagatgattgatgaagcggaaggtttggaaaagattgagaacttgcagagccatgataacaatgagatctatgaaaaagctgtgaagattcttgaggcctactggatggatgaggaggatgatacaatgggagctaccacggtagctgctccccaaggtgctacttttgactttggccaaggcggtggtgctgctcaattcaaataaatacaggtactctcaatcctcaacatggtttgtgtttattgtgggttgtttccactcttaccataaatcctttctgttctggtatcattcacttgaggcaacaagtaatgatttcaaatttcctcgacagatttgaccagaggtggtaaattgtggccactgtgcggggtactgaattgttctggtggttcaataagctaaaggtttcaagggggccagtgttacattatttccctactggtcacggatatcatatcactacgtctgtaacagggattaaagctttgaagtctgcgtttttcatcaggctactactatgtagtgtttgcatcttttagtatggtgtgcaacattttgctacttgtatagcctgagtcgaagcttctgcaaagccgtcacaacacattcctgaacccgtctggttttgagtttcgtcaggagtgtgctgagttgcagtttgtccggacatgtaaaccattatgccttttaaattatatattgctagggtttgttcggttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001049146.1 RefSeq:Os01g0253300]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

File:Fig-8 The nucleocytoplasmic shuttling cycle of importin α.png

2014-06-06T14:33:19Z

Jianchao Zhang: Fig-8:The nucleocytoplasmic shuttling cycle of importin α. (i) Importin α (α) forms a ternary complex with importin β (β) and cargo (blue circles). (ii) The ternary complex docks at the nuclear-pore complex (NPC) and (iii)translocates into the nucleu

Fig-8:The nucleocytoplasmic shuttling cycle of importin α. (i) Importin α (α) forms a ternary complex with importin β (β) and cargo (blue circles). (ii) The ternary complex docks at the nuclear-pore complex (NPC) and (iii)translocates into the nucleus. (iv) Binding of Ran–GTP triggers the dissociation of the ternary complex. (v)Importin α binds to the exportin CAS–Ran–GTP complex and is exported to the cytoplasm. (vi) Ran–GAP-stimulated hydrolysis of GTP by Ran triggers the dissociation of the exportin complex and releases free importin α into the cytoplasm for another transport cycle. The recycling of importin β to the cytoplasm, and of Ran–GDP to the nucleus and its conversion to Ran–GTP are not shown.

Os01g0678500

2014-06-06T14:27:55Z

Jianchao Zhang: /* Mutation */

Gene Os01g0678500， namely '''OsTPC1''',meaning '''rice two-pore channel 1''',can rescue the Ca2+ uptake activity and growth rate of a yeast mutant cch1

==Annotated Information==
===Function===
[[File:Expression of OsTPC1in rice tissues.jpg|right|thumb|250px|Fig-4 Expression of OsTPC1in rice tissues. First-strand cDNA was synthesized from the total RNA extracted from various tissues andamplified indicated cycles by RT-PCR. Actin cDNA was used as a control DNA. PCR products were analyzed by agarose gel electrophoresis.From<ref name="ref1" />]]
[[File:Fig-7 Intracellular localization of the GFP-OsTPC1 fusion protein.jpg|left|thumb|250px|Fig-7:Intracellular localization of the GFP-OsTPC1 fusion protein. From <ref name="ref2" />]]
'''Os01g0678500''' encodes voltage-dependent calcium channel protein TPC1(OsTCP1),which functions as major voltage-gated Ca2+ channel across the plasma membrane<ref name="ref1" /> .As cytosolic free Ca2+ serves as an important second messenger participating in signal transduction of various environmental stresses and OsTCP1 is involved in the regulation of cytosolic Ca2+ channel,the OsTCP1 plays a important role in regulating the plant growth,acts as the major ROS-responsive Ca2+ channel and is the possible target of Al-dependent inhibition<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />.Also OsTPC1 functions as one of the key regulation factor in elicitor induced disease resistance reaction, the activation of MAPK cascade and hypersensitive cell death<ref name="ref2" />. By generating Ostpc1 knock-out and apoaequorin-expressing Ostpc1 cells, ''Haruyasu Hamada et al'' indicates that OsTPC1 has a role in the regulation of TvX-induced sustained increase in cytosolic Ca2+<ref name="ref4" />.

===Mutation===
1.The OsTPC1overexpressors showed remarkably slowed growth and reduced fertility in adult plants[Fig-1 C,D].These phenotypes were exhibited in all six independent T1 transgenic lines and the expression level of the OsTPC1transcripts in the 35S::OsTPC1 plants well correlated with the severity of the phenotypes[Fig-1B,C]. OsTPC1 overexpressing lines showing severe phenotype also displayed a dwarf phenotype with dark green leaves in adult plants, and green colored roots in the seedling stage under light condition[Fig-1E] <ref name="ref1" />

[[File:Fig-1 overexpression of OsTCP1.jpg]]

Fig-1:Phenotypes of plants overexpressing OsTPC1cDNA. (A) The OsTPC1expression vector for rice transformation. 35S P, CaMV 35S promoter; OsTPC1, ORF regions (2,274 bp in size) for OsTPC1cDNA; nos T, terminator sequence of the gene for nopaline synthase. 35S::GUSwas
used as vector controls. (B) RT-PCR analysis of OsTPC1in the plants with sense OsTPC1. ActincDNA was used as a control. (C) Phenotype of overexpressing OsTPC1lines (T1) at adult stage. Plants were grown for 60 d in the greenhouse. Right: plant overexpressing OsTPC1mRNA and left: control plant overexpressing GUSgene. White bars indicate 10 cm. (D) Phenotype of overexpressing OsTPC1lines (T1) at seedling stage. Seedlings were grown for 10 d in the MS medium (16 h light/8 h darkness, 28℃). White bars indicate 10 cm. (E) Root greening observed in overexpressing OsTPC1lines (T1). Seedlings were grown for 14 d in the MS medium (continuous light, 28℃). Red bars indicate 1 mm. Control lines:C1-1 and C2-5, OsTPC1overexpressors: S2-3, S2-4 and S2-5.<ref name="ref1" />

2.By generating Tos17 insertional mutant of the OsTPC1[Fig-2A] and confirming the mutant OsTPC1 lose the complement function in yeast[Fig-2D] ,Takamitsu Kurusu et al shows adult plants of Ostpc1mutant showed slightly reduced growth rate under normal growth condition[Fig-3A] and less sensitivity to Ca2+ concentration[Fig-3B],These results suggest that OsTPC1 translocates substantial amount of Ca2+ across the plasmamembrane, and is one of the major factors affecting Ca2+ sensitivity at least in suspension-cultured cells.<ref name="ref1" />

[[File:Fig-2 mutant insertion for OsTCP1.jpg]]

Fig-2:Isolation of Tos17insertional mutant of the OsTPC1. (A) The structure of the OsTPC1gene and insertion site of Tos17in the OsTPC1 gene of the mutant line (NF1041). The exon and intron regions of OsTPC1are presented as closed and open bars, respectively. (B) A schematic representation of OsTPC1mRNA and the location of the deletion in the Ostpc1mutant. The approximate locations of primer sequences are shown by arrows. (C) PCR analysis of OsTPC1mRNA in Ostpc1and wild type. PCR products generated by using primers exon11P and P2, which amplify the mRNA region derived fromthe splicing of exon 11 to exon 21. (D) Yeast complementation analysis using Ostpc1cDNA. Square, K927 (cch1)/pYES2; circle, K927 (cch1)/pYES2-OsTPC1; triangle, K927 (cch1)/pYES2-Ostpc1. Vertical bars represent SE (n= 3) <ref name="ref1" />

===Expression===
Expression of the OsTPC1mRNA is detected at a similar level ubiquitously in calli, mature leaves and shoots except for roots where its expression was weaker.[Fig-4] <ref name="ref1" />

===Cellular localization===
To study the intracellular localization of the OsTPC1 protein, ''Takamitsu Kurusu et al'' introduced the green fluorescent protein (GFP) construct fused to the N-terminus of OsTPC1 into onion epidermal cells and examined its intracellular localization by confocal laser scanning microscopy. When GFP alone was expressed, it localized to the nucleus and the cytoplasm[Fig-7 a-c],In contrast, the GFP-OsTPC1fusion protein was specifically targeted to the plasma membrane in patches (Figure-7 d–f), suggesting that OsTPC1 functions at the plasma membrane.<ref name="ref2" />
==Labs working on this gene==
*Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588 Japan
*Medical R & D Center, The Tokyo Metropolitan Institute of Medical Science, Honkomagome 3-18-22, Bunkyo-ku, Tokyo, 113-8613 Japan
*Department of Biology, Tokyo Gakugei University, Tokyo, 184-8501 Japan
*CREST, Japan Science and Technology Agency, Saitama, 332-0012 Japan
*Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
*Department of Molecular Genetics, National Institute of Agrobiological Sciences, Kannondai, Tsukuba, Ibaraki 305-8602,Japan
*Genome & Drug Research Center, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
*Graduate School of Natural Science and Technology, Okayama University, Okayama,700-8530, Japan
*Biotechnology Research Center, University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
*Food Science Research Laboratories, Meiji Co., Ltd., 5-3-1, Chiyoda, Sakado, Saitama 350-0289, Japan
*Environmental Biology Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, 305-8506 Japan
*Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan

==References==
<references>
<ref name="ref1">
Kurusu T, Sakurai Y, Miyao A, Hirochika H, Kuchitsu K. Identification of a putative voltage-gated Ca2+ -permeable channel (OsTPC1) involved in Ca2+ influx and regulation of growth and development in rice. Plant Cell Physiol. 2004 Jun;45(6):693-702.</ref>
<ref name="ref2">
Kurusu T, Yagala T, Miyao A, Hirochika H, Kuchitsu K. Identification of a putative voltage-gated Ca2+ channel as a key regulator of elicitor-induced hypersensitive cell death and mitogen-activated protein kinase activation in rice. Plant J. 2005 Jun;42(6):798-809.</ref>
<ref name="ref3">
Hashimoto K, Saito M, Matsuoka H, Iida K, Iida H. Functional analysis of a rice putative voltage-dependent Ca2+ channel, OsTPC1, expressed in yeast cells lackingits homologous gene CCH1.Plant Cell Physiol. 2004 Apr;45(4):496-500. </ref>
<ref name="ref4">
Hamada H, Kurusu T, Okuma E, Nokajima H, Kiyoduka M, Koyano T, Sugiyama Y, Okada K, Koga J, Saji H, Miyao A, Hirochika H, Yamane H, Murata Y, Kuchitsu K. Regulation of a proteinaceous elicitor-induced Ca2+ influx and production of phytoalexins by a putative voltage-gated cation channel, OsTPC1, in cultured rice cells. J Biol Chem. 2012 Mar 23;287(13):9931-9. </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0678500|
Description = Similar to Two-pore calcium channel|
Version = NM_001050393.1 GI:115439156 GeneID:4325272|
Length = 14280 bp|
Definition = Oryza sativa Japonica Group Os01g0678500, 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 = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:29662516..29676795|
CDS = 29663493..29663580,29663659..29663699,29664261..29664332,29664532..29664618,29665072..29665162 ,29665303..29665367,29665722..29665890,29666294..29666357,29666942..29667049 ,29667712..29667769,29668401..29668544,29668895..29668960,29669815..29669887 ,29671027..29671088,29671511..29671588,29671712..29671817,29671905..29672071 ,29672549..29672609,29673792..29673901,29674421..29674516,29674942..29675049 ,29675156..29675299,29676438..29676653|
GCID = <gbrowseImage1>
name=NC_008394:29662516..29676795
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:29662516..29676795
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgagggagaggggagagatgagggaggcgaaggcgcctctgatcgcggaggcggcggagcacatatcccattcccacggctccgggtcgtccggcaccggcagccacaccagcggcggcggcggcgggtggaggggctcgaggcagtaccagcgccgctcggacgccctcgcctacggcaaccggtaccagaaggcggccgccctcgtcgacctcgcagaagatggtgtgggtatccctgaggatgtcttgaatgacacaaggtttgagagggctatgagattctattttgtgtatctccggttggattggctgtggtcacttaacctatttgctttgattcttttgaattttctcgagaagcctctctggtgccggggatattctcaacatgcttgtgatcaaagggatctttactttctggggcagttgccatacttgagcaaaactgaatctctcatatatgaggggctcacacttgttattcttgtaatggatatcttctatccactgtcctatgaaggtttaaacctattctggaagaacacaataaataaactgaaggttcttcttctcttcatcttagcatgtgacatactggtgtttgcatttagtccccaacctttcagagtagctccttacatccgtgttgcgtttctaataatgaatatcagggaactgcgaatgtgtgctgttacactggttggtatggttgggacataccttaatgttttggccctttcactattgttcctcttattcgcaagctggctagcttatgtaacatttgaggatacaccacaaggaaagactgttttctcgtcatatggtaccacgttatatcagatgtttattctcttcaccacctccaataatcctgatgtatgggttcctgcttataagagctctcgttggtcctcactattttttattgtctacgtacttttgggagtttacttcctaacaaatttaattcttgctgtcatttatgatagctttaaggagcagctagcaaagcaagtttctcaggcagactgtacaaggaaaagtatactagagaaggcatttggtatcattgatgctactggtcagggttatctcaacaaagaacagtgcctatcattactagatgagctcaacaaatacagatcgttacctaaaacctcaagggaagattttgaattaatttttgccgagcttgatcagagtggtgattttaaggttacctctgaagaatttgctacactgtgcaataccattgcaataaaattccagaaagaaccacctccatcctatctcgagaagtatccatctttctatcattcagcactgtgtgaatggttgaaatcttttgtgcggagcccactgtttgagtatattgttatttttgttcttctgatgaatctagtcgctgtcattattgaaacaacgctggatatagaaaacagctcctcgcagaaagtgtggcaagaagttgagtttgtctttggatggatttacgttatagagatggcactcaaaatattttcattaggatttggtgcctactggatggaaggtcaaaacaagtttgattttgtgcttacttggactatatttattggagagactctaacatttgccttcccatcgaagctttcttttctttcaaatggagaatggattcggtaccttcttcttggaaggatgttacgcttgacaagaattctgttgcaagttcggcgtttcagagcatttgttgcaacattctttactctgatgtctagcttgatgccatatttggggattgtattctgcaccctttgcatttactgctcccttggtttgcagatatttgggggcattgtgtatgcaggaaatccaacactagaagaaaccgatctcttcagtaacgactatcttctttttaacttcaatgactatccaagtggtatggtaactctgttcaatttgttagtgatgggcaattggcaagcttggatggagagctacaggcaattgactggaagttattggagcctgatttattttgtcagcttttacctcatttcagtattactgctgcttaatctgattgtagcatttgtgttggaggcattttttgctgagatggaactggagaaagatggcgaagctgatatccaggatcctactttggaaggaagaaacaggcggcgatctgtgcgtgtgaggacaaaggggaccatggttgatattcttcttcaccatatgttgagcaatgaacttgatggatctcaaaaccgtgaccaatag</cdnaseq>|
AA = <aaseq>MRERGEMREAKAPLIAEAAEHISHSHGSGSSGTGSHTSGGGGGW RGSRQYQRRSDALAYGNRYQKAAALVDLAEDGVGIPEDVLNDTRFERAMRFYFVYLRL DWLWSLNLFALILLNFLEKPLWCRGYSQHACDQRDLYFLGQLPYLSKTESLIYEGLTL VILVMDIFYPLSYEGLNLFWKNTINKLKVLLLFILACDILVFAFSPQPFRVAPYIRVA FLIMNIRELRMCAVTLVGMVGTYLNVLALSLLFLLFASWLAYVTFEDTPQGKTVFSSY GTTLYQMFILFTTSNNPDVWVPAYKSSRWSSLFFIVYVLLGVYFLTNLILAVIYDSFK EQLAKQVSQADCTRKSILEKAFGIIDATGQGYLNKEQCLSLLDELNKYRSLPKTSRED FELIFAELDQSGDFKVTSEEFATLCNTIAIKFQKEPPPSYLEKYPSFYHSALCEWLKS FVRSPLFEYIVIFVLLMNLVAVIIETTLDIENSSSQKVWQEVEFVFGWIYVIEMALKI FSLGFGAYWMEGQNKFDFVLTWTIFIGETLTFAFPSKLSFLSNGEWIRYLLLGRMLRL TRILLQVRRFRAFVATFFTLMSSLMPYLGIVFCTLCIYCSLGLQIFGGIVYAGNPTLE ETDLFSNDYLLFNFNDYPSGMVTLFNLLVMGNWQAWMESYRQLTGSYWSLIYFVSFYL ISVLLLLNLIVAFVLEAFFAEMELEKDGEADIQDPTLEGRNRRRSVRVRTKGTMVDIL LHHMLSNELDGSQNRDQ</aaseq>|
DNA = 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Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001050393.1 RefSeq:Os01g0678500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

File:Fig-2 mutant insertion for OsTCP1.jpg

2014-06-06T14:27:19Z

Jianchao Zhang: Fig-2:Isolation of Tos17insertional mutant of the OsTPC1. (A) The structure of the OsTPC1gene and insertion site of Tos17in the OsTPC1 gene of the mutant line (NF1041). The exon and intron regions of OsTPC1are presented as closed and open bars, respective

Fig-2:Isolation of Tos17insertional mutant of the OsTPC1. (A) The structure of the OsTPC1gene and insertion site of Tos17in the OsTPC1 gene of the mutant line (NF1041). The exon and intron regions of OsTPC1are presented as closed and open bars, respectively. (B) A schematic representation of OsTPC1mRNA and the location of the deletion in the Ostpc1mutant. The approximate locations of primer sequences are shown by arrows. (C) PCR analysis of OsTPC1mRNA in Ostpc1and wild type. PCR products generated by using primers exon11P and P2, which amplify the mRNA region derived fromthe splicing of exon 11 to exon 21. (D) Yeast complementation analysis using Ostpc1cDNA. Square, K927 (cch1)/pYES2; circle, K927 (cch1)/pYES2-OsTPC1; triangle, K927 (cch1)/pYES2-Ostpc1. Vertical bars represent SE (n= 3)

File:FigureS3.png

2014-06-05T05:00:31Z

Jianchao Zhang: Expression analysis of rice SUVH RNAi plants by real time PCR. Relative SUVH transcripts in wild type (wt) and RNAi transgenic plants were revealed by real time PCR. Actin transcripts were measured as internal controls.

Expression analysis of rice SUVH RNAi plants by real time PCR. Relative SUVH transcripts in wild type (wt) and RNAi transgenic plants were revealed by real time PCR. Actin transcripts were measured as internal controls.

File:FigureS2.png

2014-06-05T04:46:28Z

Jianchao Zhang: Expression analysis of rice SUVH over-expression plants by Northern blots. RNAs isolated from wild type and over-expression transgenic lines of 7 SUVH genes as indicated were hybridized with the corresponding cDNAs as probes. rRNA are shown as loadings co

Expression analysis of rice SUVH over-expression plants by Northern blots. RNAs isolated from wild type and over-expression transgenic lines of 7 SUVH genes as indicated were hybridized with the corresponding cDNAs as probes. rRNA are shown as loadings controls.

Os07g0182900

2014-06-04T14:40:53Z

Jianchao Zhang: /* Labs working on this gene */

Please input one-sentence summary here.

==Annotated Information==
===Function===
DNA methylation is a heritable epigenetic mark that regulates expression of genes involved in developmental processes DNA. In mammals, DNA methylation predominantly occurs in CG dinucleotides and is maintained by DNA methyltransferase1, While in plants, CG methylation
is maintained by methyltransferase1(MET1).DNA methytransferase (OsMET1) genes from rice (Oryza sativa L) have two types, OsMET1a and OsMET1b, on chromosomes 3 and 7, respectively, each encoding a cytosine-5 DNA methyltransferase (MTase), which are mainly responsible for maintaining CG dinucleotide methylation after DNA replication.OsMET1 is a plant homolog of mammalian DNA methyltransferase1(DNMT1), and MET1b plays a major role in the maintenance DNA methylation compared to MET1a, which is indispensable for the normal development of embryos in rice.

===Sequence comparison between OsMET1a and OsMET1b===
*OsMET1a has an open reading frame of 4,566 nucleotides with 12 exons and 11 introns while OsMET1b has an open reading frame of 4,491; nucleotides with 11 exons and 10 introns. Although OsMET1a and OsMET1b have high sequence similarity overall, they share only 24%; dentity in exon 1, and intron 3 of OsMET1a is absent from OsMET1b.
*A lysine–glycine repeat that is highly conserved in DNA MTases is present two-thirds of the way through the protein, separating the catalytic and regulatory domains in both OsMET1a and OsMET1b.
*The amino acid sequence downstream of the lysine–glycine repeat motif in OsMET1a showed a higher conservation (86.5%) with that of OsMET1b than did that (67.7%) for the N terminal domain (residues 1–1059). The inferred amino acid sequences of OsMET1a and OsMET1b contain several functional regions.
[[File:1.png]]

Figure 1:Proportionate diagram of OsMET1-1 showing conserved domains: S-stretch serine-rich region; E-rich region glutamic acid-rich region; BAH bromo adjacent homology domain (black boxes with white dots); IQ motif (calmodulin binding) isoleucine (I) and glutamine (Q) motif (hatched box); NLS putative nuclear localization signal (oval); KG linker the lysine-glycine repeat, KNKGKG (gray box); I to X the catalytic domain with eight highly conserved DNA MTase motifs (black bars).

===Mutation assay===
* RNAi-mediated knockdown analysis of the rice MET1 genes showed that it resulted in reactivation of a silenced β-glucuronidase (GUS) transgene in rice callus.
* A Osmet1a null mutant has no obvious phenotypes, while Osmet1b null mutant exhibited abnormal seed phenotypes, such as early embryonic lethality, decreased levels of DNA methylation at repetitive CentO sequences and at the FIEI gene locus in the embryos.
[[File:Figure 1.Phenotyes of normal type seeds and OsMET1b null mutant type(A to C) seeds.png]]

Figure 2.Phenotyes of normal type seeds and OsMET1b null mutant type(A to C) seeds

===Expression===
* Ribonuclease protection assays showed that MET1a and MET1b both express in highly replicating and dividing cells;
* MET1b is more abundantly expressed than MET1a in all of the tissues examined, like callus, root and inflorescence.
* OsMET1b does not express in differentiated tissue (10-day-old leaf), and no expression for either gene was found in mature leaves.

===Evolution===
This phylogenetic relationships between eukaryotic and prokaryotic DNA methytransferase were derived using the AlignX program of the VectorNTI suite, suggesting that the rice DNA methytransferase are related to DNA methytransferase of Dnmt1/MET1 class in diverse organisms from several kingdom.
[[File:3.jpg]]

Figure 3. Phylogenetic relationships between eukaryotic and prokaryotic DNA methytransferase
Phylogenetic relationships between eukaryotic and prokaryotic MTases were derived using the AlignX program of the VectorNTI suite with the following GenBank accessions: maize MET1 (AF063403), rice MET1-1 (OsMET1-1, AF462029), rice MET1-2 (OsMET1-2, TPA BK001405), Arabidopsis MET1(AtMET1, AT5G49160) and MET2 (MET2-type C-5 DNA MTase, AT4G08990), pea MET1 (putative C-5 DNA MTase, AF034419), carrot MET1 (carrot C-5 DNA MTase, AF007807) and MET2 (MET2-type C-5 DNA MTase, AF007808), tobacco MET1 (NtMET1, AB030726), tomato (putative C-5 DNA MTase AJ002140), rat DNMT1 (AB012214), human DNMT1 (AF180682), Xenopus DNMT1(D78638), zebra fish DNMT1 (AF483203), chicken DNMT1 (2112268A), Neurospora DIM2 (AF348971), Ascobolus DNMTase (Z96933), rice MET2a (AC069324), maize MET2a (AF243043) and Haemophilus haemolyticus M.HhaI (XYH1H1)

===Knowledge extension===
Apart from the main information listed above about function, expression and evolution about OsMET1 gene, there are also some advanced researches about this gene being conducted in the past few years. Takaki Yamauchi et al. reported in 2007 that the alternative splicing mechanisms of OsMET1a transcript and OsMET1b transcript differ, which is key to the regulation of active OsMET1 protein generation in different tissues. Daisuke Miki et al. reported in 2008 that de novo DNA methylation can be induced by siRNA targeted to endogenous transcribed sequences which is gene-specific and OsMET1-indepent in rice, which is also the first time to observe transcriptional gene silencing by siRNAs. Takaki Yamauchi et al. reported in 2009 that they successfully realized homologous recombination-promoted knock-in targeting to monitor gene expression by fusing a reporter gene named GUS codingβ-glucuronidase with its promoter in rice, in principle, this method can be applied to modify any endogenous gene which would promote basic and applied plant research.

==Labs working on this gene==
* Institute of Developmental and Molecular Biology, and Department of Biology, Texas A&M University, College Station, TX, USA
* National Institute for Basic Biology, Okazaki, Japan
* Graduate School of Science and Technology, Chiba University, Matsudo, Japan
* Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
* Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka, Japan

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os07g0182900|
Description = Similar to Cytosine-5 DNA methyltransferase MET1 (Fragment)|
Version = NM_001065587.1 GI:115470906 GeneID:4342575|
Length = 2298 bp|
Definition = Oryza sativa Japonica Group Os07g0182900, 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 = [[:category:Japonica Chromosome 7|Chromosome 7]]|
AP = Chromosome 7:4421779..4424076|
CDS = 4421780..4421864,4421955..4422066,4422154..4422301,4422417..4422614,4422710..4422988 ,4423084..4423245,4423344..4423562,4423676..4423810|
GCID = <gbrowseImage1>
name=NC_008400:4421779..4424076
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008400:4421779..4424076
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>acaaaggtgtccaaagagaaccgtcttgcaactcttgacatttttgctggctgtggaggtttatcagaaggactgcagcaagctggtgtatcgtttacaaagtgggcgattgaatatgaggaaccagctggtgaagcatttaccaaaaatcatccagaagctgcggtgtttgtggataactgcaatgtgattttgaaggcaattatggacaaatgtggagatgctgatgattgcatttcaacttctgaggctgctgaacaagcagctaaattttctcaggacaatattatgaaccttcctgtccctggtgaagtagaattcataaatggtggtcctccatgtcagggcttttctgggatgaacagatttaaccaaagcccatggagtaaagttcaatgtgagatgattttagcattcctgtcttttgctgaatatttccgccccagattctttcttttagaaaatgttaggaactttgtttcattcaacaaaggacagacatttcgactgacagttgcatcccttctggagatgggataccaggtccggtttggaattttagaggcagggacttttggtgttgctcagtccaggaaaagagcattcatttgggctgctgcacctggagagactctgcctgattggccagaaccaatgcatgtgtttgctagccctgagctgaaaataaatttgcctgatggtaaatactatgcagctgcaaaaagcactgctggtggtgctcctttccgtgcaataacagttagagatacaataggcgatttaccaaaggtggagaatggcgccagtaaactcctacttgagtacggtggcgaacccatctcctggttccagaagaagattagagggaacacgatcgcgctgaatgatcacatatctaaggagatgaatgaactgaacctcatcagatgccaacgcattccaaagcggcctggttgtgattggcatgacctaccagatgagaaggtgaaactatcatctggccaactggtggacctgatcccttggtgcctgcctaacacagctaaaaggcacaaccagtggaaagggctttatggtaggctggattgggagggcaatttccctacttctgtgacagacccccagccaatgggcaaggttggcatgtgcttccaccctgaccaggataggatcatcacagtccgtgaatgtgcgcgatctcagggctttcctgacaactaccagttcgcgggcaacatccagagcaagcacaggcagattggcaatgcggtgcctccacctcttgccttcgccctcgggaggaaactgaaggaagctgttgatgcaaagcgtcagtag</cdnaseq>|
AA = <aaseq>TKVSKENRLATLDIFAGCGGLSEGLQQAGVSFTKWAIEYEEPAG EAFTKNHPEAAVFVDNCNVILKAIMDKCGDADDCISTSEAAEQAAKFSQDNIMNLPVP GEVEFINGGPPCQGFSGMNRFNQSPWSKVQCEMILAFLSFAEYFRPRFFLLENVRNFV SFNKGQTFRLTVASLLEMGYQVRFGILEAGTFGVAQSRKRAFIWAAAPGETLPDWPEP MHVFASPELKINLPDGKYYAAAKSTAGGAPFRAITVRDTIGDLPKVENGASKLLLEYG GEPISWFQKKIRGNTIALNDHISKEMNELNLIRCQRIPKRPGCDWHDLPDEKVKLSSG QLVDLIPWCLPNTAKRHNQWKGLYGRLDWEGNFPTSVTDPQPMGKVGMCFHPDQDRII TVRECARSQGFPDNYQFAGNIQSKHRQIGNAVPPPLAFALGRKLKEAVDAKRQ</aaseq>|
DNA = <dnaseqindica>2..86#177..288#376..523#639..836#932..1210#1306..1467#1566..1784#1898..2032#tacaaaggtgtccaaagagaaccgtcttgcaactcttgacatttttgctggctgtggaggtttatcagaaggactgcagcaagctggtatgcactttccttcaataatggtgtttagctttatcatcaacatgtcggccatcagactgatattttattaccatttaaattctgtaggtgtatcgtttacaaagtgggcgattgaatatgaggaaccagctggtgaagcatttaccaaaaatcatccagaagctgcggtgtttgtggataactgcaatgtgattttgaagtaggtgcaccgtgcacttccttgattttttctgtggttttctttttacctatatagctcaatagggactgttatatgattttgcagggcaattatggacaaatgtggagatgctgatgattgcatttcaacttctgaggctgctgaacaagcagctaaattttctcaggacaatattatgaaccttcctgtccctggtgaagtagaattcataaatggtggtcctccatgtcaggtatattattttgctatacttgatggaattttctttgcacctaggcaagcaaattgtttgcacttcaatacttgtgataaatgacttcaattttgtaatttttttctcaactcagggcttttctgggatgaacagatttaaccaaagcccatggagtaaagttcaatgtgagatgattttagcattcctgtcttttgctgaatatttccgccccagattctttcttttagaaaatgttaggaactttgtttcattcaacaaaggacagacatttcgactgacagttgcatcccttctggagatgggataccaggtaattattcttctggttatacatacttaaaatgcctatgtacagcatttgttttgaatcttataataaccagaagctgtttacttgttgcttaggtccggtttggaattttagaggcagggacttttggtgttgctcagtccaggaaaagagcattcatttgggctgctgcacctggagagactctgcctgattggccagaaccaatgcatgtgtttgctagccctgagctgaaaataaatttgcctgatggtaaatactatgcagctgcaaaaagcactgctggtggtgctcctttccgtgcaataacagttagagatacaataggcgatttaccaaaggtggagaatggcgccagtaaactcctacttgaggtaaaattgcttctcctatatggctatccgctccattttatcctgtttcttctcttgatttatatgctgaatgaatcccctcttttgtaatgcagtacggtggcgaacccatctcctggttccagaagaagattagagggaacacgatcgcgctgaatgatcacatatctaaggagatgaatgaactgaacctcatcagatgccaacgcattccaaagcggcctggttgtgattggcatgacctaccagatgagaaggtaaatgccatctaccttgcggttgcattcacttccttttgtgctcttccatacattccttgcatcagcggaatgttaaccattatgagcgtgtgcaggtgaaactatcatctggccaactggtggacctgatcccttggtgcctgcctaacacagctaaaaggcacaaccagtggaaagggctttatggtaggctggattgggagggcaatttccctacttctgtgacagacccccagccaatgggcaaggttggcatgtgcttccaccctgaccaggataggatcatcacagtccgtgaatgtgcgcgatctcaggtaagctgctattgctatccatccattcaacattctcttcctgtcttctaagatattgtgaatttggaggggagtcagtactgaccgtttaactaacctattcttgtctgcagggctttcctgacaactaccagttcgcgggcaacatccagagcaagcacaggcagattggcaatgcggtgcctccacctcttgccttcgccctcgggaggaaactgaaggaagctgttgatgcaaagcgtcagtaggtgctcagagtccttctccgatgatcgagggagatgattctcccctgaaaagaaacaaacaaccaaacatatgagtgtacttattttaattgtgcgctgcatttaactttgtgtgttgattaagattttagtcatatagatccttggtaaccttgtacattttagaggttgtgttgtgattgatacccttgattcaggggtatgatttagtggctgtattcagatatttaaacaaaataatactagttagtgatggttgaattgtt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065587.1 RefSeq:Os07g0182900]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

Os07g0182900

2014-06-04T14:40:08Z

Jianchao Zhang: /* Knowledge extension */

Please input one-sentence summary here.

==Annotated Information==
===Function===
DNA methylation is a heritable epigenetic mark that regulates expression of genes involved in developmental processes DNA. In mammals, DNA methylation predominantly occurs in CG dinucleotides and is maintained by DNA methyltransferase1, While in plants, CG methylation
is maintained by methyltransferase1(MET1).DNA methytransferase (OsMET1) genes from rice (Oryza sativa L) have two types, OsMET1a and OsMET1b, on chromosomes 3 and 7, respectively, each encoding a cytosine-5 DNA methyltransferase (MTase), which are mainly responsible for maintaining CG dinucleotide methylation after DNA replication.OsMET1 is a plant homolog of mammalian DNA methyltransferase1(DNMT1), and MET1b plays a major role in the maintenance DNA methylation compared to MET1a, which is indispensable for the normal development of embryos in rice.

===Sequence comparison between OsMET1a and OsMET1b===
*OsMET1a has an open reading frame of 4,566 nucleotides with 12 exons and 11 introns while OsMET1b has an open reading frame of 4,491; nucleotides with 11 exons and 10 introns. Although OsMET1a and OsMET1b have high sequence similarity overall, they share only 24%; dentity in exon 1, and intron 3 of OsMET1a is absent from OsMET1b.
*A lysine–glycine repeat that is highly conserved in DNA MTases is present two-thirds of the way through the protein, separating the catalytic and regulatory domains in both OsMET1a and OsMET1b.
*The amino acid sequence downstream of the lysine–glycine repeat motif in OsMET1a showed a higher conservation (86.5%) with that of OsMET1b than did that (67.7%) for the N terminal domain (residues 1–1059). The inferred amino acid sequences of OsMET1a and OsMET1b contain several functional regions.
[[File:1.png]]

Figure 1:Proportionate diagram of OsMET1-1 showing conserved domains: S-stretch serine-rich region; E-rich region glutamic acid-rich region; BAH bromo adjacent homology domain (black boxes with white dots); IQ motif (calmodulin binding) isoleucine (I) and glutamine (Q) motif (hatched box); NLS putative nuclear localization signal (oval); KG linker the lysine-glycine repeat, KNKGKG (gray box); I to X the catalytic domain with eight highly conserved DNA MTase motifs (black bars).

===Mutation assay===
* RNAi-mediated knockdown analysis of the rice MET1 genes showed that it resulted in reactivation of a silenced β-glucuronidase (GUS) transgene in rice callus.
* A Osmet1a null mutant has no obvious phenotypes, while Osmet1b null mutant exhibited abnormal seed phenotypes, such as early embryonic lethality, decreased levels of DNA methylation at repetitive CentO sequences and at the FIEI gene locus in the embryos.
[[File:Figure 1.Phenotyes of normal type seeds and OsMET1b null mutant type(A to C) seeds.png]]

Figure 2.Phenotyes of normal type seeds and OsMET1b null mutant type(A to C) seeds

===Expression===
* Ribonuclease protection assays showed that MET1a and MET1b both express in highly replicating and dividing cells;
* MET1b is more abundantly expressed than MET1a in all of the tissues examined, like callus, root and inflorescence.
* OsMET1b does not express in differentiated tissue (10-day-old leaf), and no expression for either gene was found in mature leaves.

===Evolution===
This phylogenetic relationships between eukaryotic and prokaryotic DNA methytransferase were derived using the AlignX program of the VectorNTI suite, suggesting that the rice DNA methytransferase are related to DNA methytransferase of Dnmt1/MET1 class in diverse organisms from several kingdom.
[[File:3.jpg]]

Figure 3. Phylogenetic relationships between eukaryotic and prokaryotic DNA methytransferase
Phylogenetic relationships between eukaryotic and prokaryotic MTases were derived using the AlignX program of the VectorNTI suite with the following GenBank accessions: maize MET1 (AF063403), rice MET1-1 (OsMET1-1, AF462029), rice MET1-2 (OsMET1-2, TPA BK001405), Arabidopsis MET1(AtMET1, AT5G49160) and MET2 (MET2-type C-5 DNA MTase, AT4G08990), pea MET1 (putative C-5 DNA MTase, AF034419), carrot MET1 (carrot C-5 DNA MTase, AF007807) and MET2 (MET2-type C-5 DNA MTase, AF007808), tobacco MET1 (NtMET1, AB030726), tomato (putative C-5 DNA MTase AJ002140), rat DNMT1 (AB012214), human DNMT1 (AF180682), Xenopus DNMT1(D78638), zebra fish DNMT1 (AF483203), chicken DNMT1 (2112268A), Neurospora DIM2 (AF348971), Ascobolus DNMTase (Z96933), rice MET2a (AC069324), maize MET2a (AF243043) and Haemophilus haemolyticus M.HhaI (XYH1H1)

===Knowledge extension===
Apart from the main information listed above about function, expression and evolution about OsMET1 gene, there are also some advanced researches about this gene being conducted in the past few years. Takaki Yamauchi et al. reported in 2007 that the alternative splicing mechanisms of OsMET1a transcript and OsMET1b transcript differ, which is key to the regulation of active OsMET1 protein generation in different tissues. Daisuke Miki et al. reported in 2008 that de novo DNA methylation can be induced by siRNA targeted to endogenous transcribed sequences which is gene-specific and OsMET1-indepent in rice, which is also the first time to observe transcriptional gene silencing by siRNAs. Takaki Yamauchi et al. reported in 2009 that they successfully realized homologous recombination-promoted knock-in targeting to monitor gene expression by fusing a reporter gene named GUS codingβ-glucuronidase with its promoter in rice, in principle, this method can be applied to modify any endogenous gene which would promote basic and applied plant research.

==Labs working on this gene==
* Institute of Developmental and Molecular Biology, and Department of Biology, Texas A&M University, College Station, TX, USA
* National Institute for Basic Biology, Okazaki, Japan
* Graduate School of Science and Technology, Chiba University, Matsudo, Japan

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os07g0182900|
Description = Similar to Cytosine-5 DNA methyltransferase MET1 (Fragment)|
Version = NM_001065587.1 GI:115470906 GeneID:4342575|
Length = 2298 bp|
Definition = Oryza sativa Japonica Group Os07g0182900, 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 = [[:category:Japonica Chromosome 7|Chromosome 7]]|
AP = Chromosome 7:4421779..4424076|
CDS = 4421780..4421864,4421955..4422066,4422154..4422301,4422417..4422614,4422710..4422988 ,4423084..4423245,4423344..4423562,4423676..4423810|
GCID = <gbrowseImage1>
name=NC_008400:4421779..4424076
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008400:4421779..4424076
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>acaaaggtgtccaaagagaaccgtcttgcaactcttgacatttttgctggctgtggaggtttatcagaaggactgcagcaagctggtgtatcgtttacaaagtgggcgattgaatatgaggaaccagctggtgaagcatttaccaaaaatcatccagaagctgcggtgtttgtggataactgcaatgtgattttgaaggcaattatggacaaatgtggagatgctgatgattgcatttcaacttctgaggctgctgaacaagcagctaaattttctcaggacaatattatgaaccttcctgtccctggtgaagtagaattcataaatggtggtcctccatgtcagggcttttctgggatgaacagatttaaccaaagcccatggagtaaagttcaatgtgagatgattttagcattcctgtcttttgctgaatatttccgccccagattctttcttttagaaaatgttaggaactttgtttcattcaacaaaggacagacatttcgactgacagttgcatcccttctggagatgggataccaggtccggtttggaattttagaggcagggacttttggtgttgctcagtccaggaaaagagcattcatttgggctgctgcacctggagagactctgcctgattggccagaaccaatgcatgtgtttgctagccctgagctgaaaataaatttgcctgatggtaaatactatgcagctgcaaaaagcactgctggtggtgctcctttccgtgcaataacagttagagatacaataggcgatttaccaaaggtggagaatggcgccagtaaactcctacttgagtacggtggcgaacccatctcctggttccagaagaagattagagggaacacgatcgcgctgaatgatcacatatctaaggagatgaatgaactgaacctcatcagatgccaacgcattccaaagcggcctggttgtgattggcatgacctaccagatgagaaggtgaaactatcatctggccaactggtggacctgatcccttggtgcctgcctaacacagctaaaaggcacaaccagtggaaagggctttatggtaggctggattgggagggcaatttccctacttctgtgacagacccccagccaatgggcaaggttggcatgtgcttccaccctgaccaggataggatcatcacagtccgtgaatgtgcgcgatctcagggctttcctgacaactaccagttcgcgggcaacatccagagcaagcacaggcagattggcaatgcggtgcctccacctcttgccttcgccctcgggaggaaactgaaggaagctgttgatgcaaagcgtcagtag</cdnaseq>|
AA = <aaseq>TKVSKENRLATLDIFAGCGGLSEGLQQAGVSFTKWAIEYEEPAG EAFTKNHPEAAVFVDNCNVILKAIMDKCGDADDCISTSEAAEQAAKFSQDNIMNLPVP GEVEFINGGPPCQGFSGMNRFNQSPWSKVQCEMILAFLSFAEYFRPRFFLLENVRNFV SFNKGQTFRLTVASLLEMGYQVRFGILEAGTFGVAQSRKRAFIWAAAPGETLPDWPEP MHVFASPELKINLPDGKYYAAAKSTAGGAPFRAITVRDTIGDLPKVENGASKLLLEYG GEPISWFQKKIRGNTIALNDHISKEMNELNLIRCQRIPKRPGCDWHDLPDEKVKLSSG QLVDLIPWCLPNTAKRHNQWKGLYGRLDWEGNFPTSVTDPQPMGKVGMCFHPDQDRII TVRECARSQGFPDNYQFAGNIQSKHRQIGNAVPPPLAFALGRKLKEAVDAKRQ</aaseq>|
DNA = <dnaseqindica>2..86#177..288#376..523#639..836#932..1210#1306..1467#1566..1784#1898..2032#tacaaaggtgtccaaagagaaccgtcttgcaactcttgacatttttgctggctgtggaggtttatcagaaggactgcagcaagctggtatgcactttccttcaataatggtgtttagctttatcatcaacatgtcggccatcagactgatattttattaccatttaaattctgtaggtgtatcgtttacaaagtgggcgattgaatatgaggaaccagctggtgaagcatttaccaaaaatcatccagaagctgcggtgtttgtggataactgcaatgtgattttgaagtaggtgcaccgtgcacttccttgattttttctgtggttttctttttacctatatagctcaatagggactgttatatgattttgcagggcaattatggacaaatgtggagatgctgatgattgcatttcaacttctgaggctgctgaacaagcagctaaattttctcaggacaatattatgaaccttcctgtccctggtgaagtagaattcataaatggtggtcctccatgtcaggtatattattttgctatacttgatggaattttctttgcacctaggcaagcaaattgtttgcacttcaatacttgtgataaatgacttcaattttgtaatttttttctcaactcagggcttttctgggatgaacagatttaaccaaagcccatggagtaaagttcaatgtgagatgattttagcattcctgtcttttgctgaatatttccgccccagattctttcttttagaaaatgttaggaactttgtttcattcaacaaaggacagacatttcgactgacagttgcatcccttctggagatgggataccaggtaattattcttctggttatacatacttaaaatgcctatgtacagcatttgttttgaatcttataataaccagaagctgtttacttgttgcttaggtccggtttggaattttagaggcagggacttttggtgttgctcagtccaggaaaagagcattcatttgggctgctgcacctggagagactctgcctgattggccagaaccaatgcatgtgtttgctagccctgagctgaaaataaatttgcctgatggtaaatactatgcagctgcaaaaagcactgctggtggtgctcctttccgtgcaataacagttagagatacaataggcgatttaccaaaggtggagaatggcgccagtaaactcctacttgaggtaaaattgcttctcctatatggctatccgctccattttatcctgtttcttctcttgatttatatgctgaatgaatcccctcttttgtaatgcagtacggtggcgaacccatctcctggttccagaagaagattagagggaacacgatcgcgctgaatgatcacatatctaaggagatgaatgaactgaacctcatcagatgccaacgcattccaaagcggcctggttgtgattggcatgacctaccagatgagaaggtaaatgccatctaccttgcggttgcattcacttccttttgtgctcttccatacattccttgcatcagcggaatgttaaccattatgagcgtgtgcaggtgaaactatcatctggccaactggtggacctgatcccttggtgcctgcctaacacagctaaaaggcacaaccagtggaaagggctttatggtaggctggattgggagggcaatttccctacttctgtgacagacccccagccaatgggcaaggttggcatgtgcttccaccctgaccaggataggatcatcacagtccgtgaatgtgcgcgatctcaggtaagctgctattgctatccatccattcaacattctcttcctgtcttctaagatattgtgaatttggaggggagtcagtactgaccgtttaactaacctattcttgtctgcagggctttcctgacaactaccagttcgcgggcaacatccagagcaagcacaggcagattggcaatgcggtgcctccacctcttgccttcgccctcgggaggaaactgaaggaagctgttgatgcaaagcgtcagtaggtgctcagagtccttctccgatgatcgagggagatgattctcccctgaaaagaaacaaacaaccaaacatatgagtgtacttattttaattgtgcgctgcatttaactttgtgtgttgattaagattttagtcatatagatccttggtaaccttgtacattttagaggttgtgttgtgattgatacccttgattcaggggtatgatttagtggctgtattcagatatttaaacaaaataatactagttagtgatggttgaattgtt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065587.1 RefSeq:Os07g0182900]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

File:Figure 1.png

2014-06-04T14:10:18Z

Jianchao Zhang: uploaded a new version of "File:Figure 1.png": Figure 1. Phylogenetic and Expression Analysis of Rice SUVH Proteins. (A) Bootstrap tree of rice (Os) and Arabidopsis (At) SUVH proteins. Four clades are indicated. (B) Relative expression level

Awn length comparion among different plants.