Difference between revisions of "Os07g0471000"
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Figure 4 Sequence Conservation in the Dual-Catalytic Core of Ire1 | Figure 4 Sequence Conservation in the Dual-Catalytic Core of Ire1 | ||
Revision as of 14:53, 20 May 2014
OsIRE1, which is translated by Os07g0471000, is the stress sensors in the endoplasmic reticulum stress response of rice.
Contents
Annotated Information
Function
Os07g0471000 is a kind of gene which encodes endoplasmic reticulum stress sensor protein OsIRE1 in rice. OsIRE1 is not only a complex transmembrane sensor protein in endoplasmic reticulum, but a transductant in signaling transduction Endoplasmic reticulum stress. OsIRE1 is a kind of kinase, whose N-terminal portion resides are in the ER lumen, and the C-terminal portion resides in the cytosol. The N-terminal portion resides are used to recognize the unfolded or misfolded proteins overloaded in the ER, and the C-terminal portion resides contain a serine/threonine kinase domain and an endo-ribonuclease (RNase) domain [1][2]. When Endoplasmic reticulum stress is triggered by the accumulation of unfolded proteins in the ER lumen, OsIRE1 may sense accumulation of unfolded or misfolded proteins in the ER lumen and cluster, induce autophosphorylation of the kinase domain and consequent activation of the RNase domain [1]. The RNase splices OsbZIP50 which is a kind of mRNA encoding a key transcription factor in rice. The spliced form of OsbZIP50 mediates the expression of genes which encode ER quality control-related factors[3].
Expression
By using the full-length atpI protein sequence (NCBI Reference Sequence: NP_001059606.1), the primers is well-built, which could conduct gene amplication and gene analysis for further research.
Shimpei Hayashi et al.(2012) generate the transgenic plants of OsbZIP50 (OsbZIP50 KD) or rice IRE1 (OsIRE1) by RNA interference. The OsIRE1 knockdown (KD) lines showed severe defects in growth [4].
Yuhya Wakasa et al.(2013) generate the transgenic rice plants overexpressing wild-type OsIRE1 (IRE1-OE) and two disrupted-IRE1s deficient in either kinase activity (K519A-OE) or RNase activity (K833A-OE) to investigate effect of overexpression those genes on the endoplasmic reticulum stress response. Overexpression of wild-type OsIRE1 induced the ER stress response even under non-stress conditions, whereas the phenotypes of K519A-OE and K833A-OE plants are similar to that of IRE1-KD. Phenotypes of wild-type and transgenic rice plants are showed in Figure 1(cited from [5]).
The results suggest that the overexpression of K519A and K833A has an inhibitory influence on the OsIRE1/OsbZIP50 signaling and ER stress pathway. However, the mechanism of why the overexpression of K519A and K833A has an inhibitory influence on the OsIRE1/OsbZIP50 signaling and ER stress pathway isn’t clear [5].
Gene construction
Basic structure of OsIRE1 is showed in Figure 2[6].researchers described the putative domains in OsIre1p predicted from hydropathy plot and database search. SP represents signal peptide. TM represents transmembrane domain. NLS represents nuclear localization signal. Kinase represents Ser/Thr kinase domain. RNase represents ribonuclease-L like domain. Y represents location of putative N-linked glycosylation site.
Structure
The Structure of Ire1 is showed in Figure 3[7].
(A) Ribbons representation of the dimeric dualcatalytic region of Ire1 encompassing the protein kinase domain and KEN domain. The kinase N-lobe, C-lobe and the KEN domain are colored green, orange, and blue (protomer 1) and light green, yellow, and light blue (protomer 2), respectively. ADP and coordinating metal ions are shown within the kinase domain catalytic cleft. Two internal regions within the kinase domain and one internal region within the KEN domain not modeled due to disorder are shown as dashed lines.
(B) A continuous hydrophobic core connects the kinase C-lobe and the KEN domain. Residues originating from the C-lobe and KEN domain are colored in pink and green, respectively. Ribbons diagram color scheme corresponds to that of protomer 2 in (A).
(C) Detailed stereoview of the KEN domain dimer as shown in (A). Disordered regions corresponding to putative RNA specificity determinants are shown as red dashed lines.
(D and E) Dimer interface interactions involving conserved residues in the kinase domain (D) and
the KEN domain (E), respectively, viewed along the two fold axis of rotational symmetry. For clarity, only residues targeted for mutation in this study are shown in ball and stick representation. Residues colored yellow and white originate from promoter 1 and 2, respectively. Ribbons coloring scheme corresponds to that in (A).
Evolution
Ire1 is an evolutionarily conserved, ER stress sensor present in all eukaryotes with both protein kinase and ribonuclease activities[8]. Kenneth et al. (2007) conducted the structure-based sequence alignment of Ire1, especially the sequence of protein kinase domain and KEN (Kinase Extension Nuclease) domain of Ire1. The structure-based sequence alignment of Ire1 is showed in Figure 4[7]. The subjects include S. cerevisiae (yeast), H. sapiens (human), M. musculus (mouse), R. norvegicus (rat), G. gallus (chicken), X. laevis (frog), D. melanogaster (fruitfly), A. mellifera (honey bee), C. elegans (nematode), A. thaliana (mouse-ear cress), and O. sativa (rice); and RNase L sequences from H. sapiens (human), P. pygmaeus (orangutan), M. musculus (mouse), R. norvegicus (rat), and C. familiarus (dog). Residues invariant or highly conserved specifically in Ire1 are highlighted in green and yellow, respectively, while Residues invariant across the Ire1-RNaseL family of kinase-ribonucleases are colored in blue.
Figure 4 Sequence Conservation in the Dual-Catalytic Core of Ire1
Labs working on this gene
1. Genetically ModifiedOrganism Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
2. Functional Transgenic Crops Research Unit; Genetically Modified Organism Research Center; National Institute of Agrobiological Sciences; Kannondai, Tsukuba, Ibaraki, Japan
3. State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
References
- ↑ 1.0 1.1 Hetz, C. & Glimcher, L. H. Fine-tuning of the unfolded protein response: Assembling the IRE1alpha interactome. Mol. Cell 35, 551–561 (2009).
- ↑ Koizumi, N. et al. Molecular characterization of two Arabidopsis Ire1 homologs, endoplasmic reticulum-located transmembrane protein kinases. Plant Physiol. 127, 949–962 (2001).
- ↑ Yuhya Wakasa, Shimpei Hayashi, Kenjirou Ozawa & Fumio Takaiwa. Multiple roles of the ER stress sensor IRE1 demonstrated by gene targeting in rice.Scientific Reports. 2 : 944 (2012).
- ↑ Hayashi, S., Wakasa, Y., Takahashi, H., Kawakatsu, T. & Takaiwa, F. Signal transduction by IRE1-mediated splicing of bZIP50 and other stress sensors in the endoplasmic reticulum stress response of rice. Plant J. 69, 946–956 (2012).
- ↑ 5.0 5.1 Yuhya Wakasa, Shimpei Hayashi and Fumio Takaiwa. Effect of overexpression of kinase- or RNasedeficient OsIRE1 on the endoplasmic reticulum stress response in transgenic rice plants. Plant Signaling & Behavior 8:9, e25343; September 2013.
- ↑ Yoko Okushima, Nozomu Koizumi, Yube Yamaguchi, Yukio Kimata, Kenji Kohno & Hiroshi Sano. Isolation and characterization of a putative transducer of endoplasmic reticulum stress in Oryza sativa. Plant Cell physiol. 43(5): 532-539 (2002).
- ↑ 7.0 7.1 Kenneth P.K. Lee, Madhusudan Dey, Dante Neculai, Chune Cao, Thomas E. Dever, and Frank Sicheri. (2007). Structure of the Dual Enzyme Ire1 Reveals the Basis for Catalysis and Regulation in Nonconventional RNA Splicing. cell.10.057, 89-100.
- ↑ Sidrauski, C., and Walter, P. (1997). The transmembrane kinase Ire1p is a site-specific endonuclease that initiates mRNA splicing in the unfolded protein response. Cell 90, 1031–1039.
6. Shimpei Hayashi, Yuhya Wakasa & Fumio Takaiwa. Functional integration between defence and IRE1-mediated ER stress response in rice. Scientific Reports. 2 : 670 (2012).
7. Yuhya Wakasa, Youko Oono, Takayuki Yazawa, Shimpei Hayashi, Kenjirou Ozawa, Hirokazu Handa, Takashi Matsumoto and Fumio Takaiwa. RNA sequencing-mediated transcriptome analysis of rice plants in endoplasmic reticulum stress conditions. Wakasa et al. BMC Plant Biology 2014, 14:101, 1-12.
Structured Information
| Gene Name |
Os07g0471000 |
|---|---|
| Description |
Protein kinase-like domain containing protein |
| Version |
NM_001066141.1 GI:115472014 GeneID:4343198 |
| Length |
4856 bp |
| Definition |
Oryza sativa Japonica Group Os07g0471000, complete gene. |
| Source |
Oryza sativa Japonica Group ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
| Chromosome | |
| Location |
Chromosome 7:17530626..17535481 |
| Sequence Coding Region |
17530886..17531175,17531766..17531961,17532046..17533379,17533662..17533834,17533994..17534240 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008400:17530626..17535481 source=RiceChromosome07 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008400:17530626..17535481 source=RiceChromosome07 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atgaggtcgctccgccgcgtcctcctccagctcgtgctcctcgccggcgtcgccttccgcggggtccgcttcgacgacgccgccgacgccgccgccgccgcccaggggtcgtcagacctcttcgagctcccttcgccgtccccgactctcgcgctccccggcggcggggatgagggggcctcgacggagatcatcgccgcgccgtggccggggcgccacggcctgttcacgccgccgcggagcacgtcccagccggcgagagcggtggtccagccggccgccgacttcggctcccaactccagttttacgacaatggtacaattcaactagtggaccttctatcaaaattgcctcggtggcagttctccaccggaccccctctttcgaagcatatcactacttcgaaacctgatttgaactatgtcatataccttgatgggtcagaaacatcggaccttatagaagttcataatggcagtggtgtgagacttccctggaaactggaggagtttattgctgagactccatatatacgggattcttttgttacgattggatcaaaggtttcaactacttttgtggtcaatgctgatagcggtgagatcatttacaagcatagcttgccagtggccttgaacgaggtaggtggccccctggttgaggaaattccatccaagttagatgctgctagaagtggtacaagtgctaatatcatagtggttgtgagaactgattattctatcagtgcatcggatcttggggaacatttgttcaactggacaagaacttccttcactgcaaattactatgcgaggtatggccaccaagacatgcttgcccaatcgtcctgtctgcgaggaaatattccatgcattaggactgagggtccaccaattaaactttatttacctgattcaagttcagataatgcaattgtcttgagacctgtgaacgaagtttctgctgtggatgctctggaaccacttctacctccaaagaagttaccacaacctgctggcgagtctaatgtggccttggatagtgctcaaaaccagactgctgacattgccctaggtcattttgtgcctgctgacactgaattgaccaacagtgtcactaaattttcttacagatggctattccccacgtttctcatgttgttgatcatggcttgtctagtgaaattggccgatgcaagcaaatattgcaggcaatttgtgattcgatttttgaagccatttatgcgtgatgagaaattgatggacccaagaggcaaatcagagggaacatcaaaaagaaggaaggcgcggaagaaagatggacttatcaatagcactcagatcttttcagcatctgataaagaggggaatggaactggtggatcaactgaggcacaaagtaataaagcacatgattcaacaaatgtggaactccctaatggcctcaatgggcgtcagattggtaagctttgtgtttacagtaaagaaattggtaaagggagcaatggtacagttgtctttgaaggctcctatggtggtcgggaagttgctgtgaaacgtctgctgcgctctcacaatgatatagcctcgaaagagattgagaatctgattgcatctgatcaggatcctaatattgttcgaatgtatggttttgagcaggacaatgattttgtttatatctcccttgagaggtgtcgctgcagcttggctgatctaatccaactgcactcggtaccaccattttcaaatactaagggaacagacattgaactttggaggcaggatggacttccttcggcacaacttctaaagctgatgagagatgttgttgctggtattgtgcatttgcatagtttgggaattatacatcgtgatttgaagcctcagaatgttttgataagcaaggaaggacctctcagagcaaaactttcagatatgggtatcagtaagcgtttgcaggaggatatgacttctgttagtcatcatggcactggatttggaagctctggttggcaagcacctgaacagcttcgtcatggtcgtcagactcgagccatagatttatttagtttgggctgccttatattctattgcattactaaaggcaagcatccgtttggtgagtactatgaacgggacatgaaaatcataaacaatcaatttgatctcttcatagtggatcacataccagaagcagtgcatcttatttctcaactgttagatccagatccagagaagagaccaacggccgtgtatgtgatgcatcatcctttcttttggagccctgagttgtgcctttcatttctacgagataccagtgacagaattgagaaaaccagtgaaactgatctcatagatgctttggaaggcataaatgttgaagcatttggtaaaaattggggagagaaattagatgctgccctgcttgcagacatgggacgttatagaaaatatagttttgagtccactcgtgaccttctaagattgatcagaaacaaatcaggacattacagagaattttcagatgatctcaaggagctacttgggtcgctgccggagggatttgttcagtatttctcaagccgattcccaaagctgctaattaaagtctacgaggtcatgtccgagcattgcaaggacgaagaagctttcagcaaatatttccttggaagctcggcgtag</cdnaseq> |
| Protein Sequence |
<aaseq>MRSLRRVLLQLVLLAGVAFRGVRFDDAADAAAAAQGSSDLFELP SPSPTLALPGGGDEGASTEIIAAPWPGRHGLFTPPRSTSQPARAVVQPAADFGSQLQF YDNGTIQLVDLLSKLPRWQFSTGPPLSKHITTSKPDLNYVIYLDGSETSDLIEVHNGS GVRLPWKLEEFIAETPYIRDSFVTIGSKVSTTFVVNADSGEIIYKHSLPVALNEVGGP LVEEIPSKLDAARSGTSANIIVVVRTDYSISASDLGEHLFNWTRTSFTANYYARYGHQ DMLAQSSCLRGNIPCIRTEGPPIKLYLPDSSSDNAIVLRPVNEVSAVDALEPLLPPKK LPQPAGESNVALDSAQNQTADIALGHFVPADTELTNSVTKFSYRWLFPTFLMLLIMAC LVKLADASKYCRQFVIRFLKPFMRDEKLMDPRGKSEGTSKRRKARKKDGLINSTQIFS ASDKEGNGTGGSTEAQSNKAHDSTNVELPNGLNGRQIGKLCVYSKEIGKGSNGTVVFE GSYGGREVAVKRLLRSHNDIASKEIENLIASDQDPNIVRMYGFEQDNDFVYISLERCR CSLADLIQLHSVPPFSNTKGTDIELWRQDGLPSAQLLKLMRDVVAGIVHLHSLGIIHR DLKPQNVLISKEGPLRAKLSDMGISKRLQEDMTSVSHHGTGFGSSGWQAPEQLRHGRQ TRAIDLFSLGCLIFYCITKGKHPFGEYYERDMKIINNQFDLFIVDHIPEAVHLISQLL DPDPEKRPTAVYVMHHPFFWSPELCLSFLRDTSDRIEKTSETDLIDALEGINVEAFGK NWGEKLDAALLADMGRYRKYSFESTRDLLRLIRNKSGHYREFSDDLKELLGSLPEGFV QYFSSRFPKLLIKVYEVMSEHCKDEEAFSKYFLGSSA</aaseq> |
| Gene Sequence |
<dnaseqindica>261..550#1141..1336#1421..2754#3037..3209#3369..3615#3711..4005#4528..4674#ggctgtcacgcacgcacgcgtgggcgcgtagcaaagcaaagcagcgaatccggcttcactagtcttcttcccccccgccgccgcatcgatcccccttcccctcgtcttccttccctttcccccaatcagattgcttccagaagcctccttccccgcgaagcaaccaaccccttccggatcccgactccatccaaacccccatcccctcccctctcccctacgctcgaaaccctagggagatccatccacatgccgccccgatgaggtcgctccgccgcgtcctcctccagctcgtgctcctcgccggcgtcgccttccgcggggtccgcttcgacgacgccgccgacgccgccgccgccgcccaggggtcgtcagacctcttcgagctcccttcgccgtccccgactctcgcgctccccggcggcggggatgagggggcctcgacggagatcatcgccgcgccgtggccggggcgccacggcctgttcacgccgccgcggagcacgtcccagccggcgagagcggtggtccagccggccgccgacttcgggtgagcttcttggtccccctccctccgtcttcttccagttgcgatgctgttcaggaggaggctatggagtctataggaggtggatcgattggcttgtgcagcgggacagggtggggggggggggggctttgcctcctgttcttatccttggcttttggaggagcgaaatggattcccatcccgccaagtgttaaagagggtttcttgtagttagggaggcttgctatgttcctttgtcactttcttgctttcgtgctgcaatggagtggggaaatgcggggaaaagagagctctctagctgcttaggtcatgcatgatccatggttggaacagcatcttcttgctgctttggtagttctcactagcattagtaatgacatgactttgcttgattgcattgcacttcaattttagtattagttacgaattaatttatggaaatgagcagcttttgcacttactattcctagtataagaggtgctacttatgattcaaattgagctgtttggttcatttcttatgtgtgtactttccattttgtcccgccatttgaaattgcaacttatttgcttgtttttattgtgaacagctcccaactccagttttacgacaatggtacaattcaactagtggaccttctatcaaaattgcctcggtggcagttctccaccggaccccctctttcgaagcatatcactacttcgaaacctgatttgaactatgtcatataccttgatgggtcagaaacatcggaccttatagaagttcataatggcagtggtgtggtatgctttgcacaattgcgttagttctcaacatcctgtctagttttgctttgtttctcacctatcactggcttattcctgtagagacttccctggaaactggaggagtttattgctgagactccatatatacgggattcttttgttacgattggatcaaaggtttcaactacttttgtggtcaatgctgatagcggtgagatcatttacaagcatagcttgccagtggccttgaacgaggtaggtggccccctggttgaggaaattccatccaagttagatgctgctagaagtggtacaagtgctaatatcatagtggttgtgagaactgattattctatcagtgcatcggatcttggggaacatttgttcaactggacaagaacttccttcactgcaaattactatgcgaggtatggccaccaagacatgcttgcccaatcgtcctgtctgcgaggaaatattccatgcattaggactgagggtccaccaattaaactttatttacctgattcaagttcagataatgcaattgtcttgagacctgtgaacgaagtttctgctgtggatgctctggaaccacttctacctccaaagaagttaccacaacctgctggcgagtctaatgtggccttggatagtgctcaaaaccagactgctgacattgccctaggtcattttgtgcctgctgacactgaattgaccaacagtgtcactaaattttcttacagatggctattccccacgtttctcatgttgttgatcatggcttgtctagtgaaattggccgatgcaagcaaatattgcaggcaatttgtgattcgatttttgaagccatttatgcgtgatgagaaattgatggacccaagaggcaaatcagagggaacatcaaaaagaaggaaggcgcggaagaaagatggacttatcaatagcactcagatcttttcagcatctgataaagaggggaatggaactggtggatcaactgaggcacaaagtaataaagcacatgattcaacaaatgtggaactccctaatggcctcaatgggcgtcagattggtaagctttgtgtttacagtaaagaaattggtaaagggagcaatggtacagttgtctttgaaggctcctatggtggtcgggaagttgctgtgaaacgtctgctgcgctctcacaatgatatagcctcgaaagagattgagaatctgattgcatctgatcaggatcctaatattgttcgaatgtatggttttgagcaggacaatgattttgtttatatctcccttgagaggtgtcgctgcagcttggctgatctaatccaactgcactcggtaccaccattttcaaatactaagggaacagacattgaactttggaggcaggatggacttccttcggcacaacttctaaagctgatgaggtatgtgacaactggtcactggtgccctttcatgttgcacaccatgtttatcagtatatgcatgtgttgtttactttgagattaattgactaaggtcacgcttatgcatagcttaacttgatgcccttttgctaagaacactttgccaacaaccaacatccaccatttgctattacaaagttccttaatggctgatattatttgcctgcctattcttggtattgttgctagcgtgtccaccagaccaccactgatgttgcccttgtgaattttcatgtgcagagatgttgttgctggtattgtgcatttgcatagtttgggaattatacatcgtgatttgaagcctcagaatgttttgataagcaaggaaggacctctcagagcaaaactttcagatatgggtatcagtaagcgtttgcaggaggatatgacttctgttagtcatcatggcactggtaaggttcaaagttgcttgcgaatatgcaatatgagaaattactttctgtatcttttttatggtcaaggtcaactttcttaagtgcattttttagtcattgcgatgctctctctctctctctctaactagccatttcatccctgtcaacttactgcaggatttggaagctctggttggcaagcacctgaacagcttcgtcatggtcgtcagactcgagccatagatttatttagtttgggctgccttatattctattgcattactaaaggcaagcatccgtttggtgagtactatgaacgggacatgaaaatcataaacaatcaatttgatctcttcatagtggatcacataccagaagcagtgcatcttatttctcaactgttagatccagatccagagaagaggtaagaataatttggtattttgacatcgttaatgccctgaacatttaaaaaggcttcctgattttctgaatgcatttttttattaatgttaacagaccaacggccgtgtatgtgatgcatcatcctttcttttggagccctgagttgtgcctttcatttctacgagataccagtgacagaattgagaaaaccagtgaaactgatctcatagatgctttggaaggcataaatgttgaagcatttggtaaaaattggggagagaaattagatgctgccctgcttgcagacatgggacgttatagaaaatatagttttgagtccactcgtgaccttctaagattgatcagaaacaaatcaggacattacagagaattttcagatgatctcaaggtctgttgctgcatttcttgttttgtttgctttgttttagttttcctgcatacagctaaactatgggtcaaacaagaggtggtgctgtagtatgcatgaatgctgttgtgtgttcaatggatgttcatattagttgctgtgcatgaatgtagtatataggaaaagtagttagttgcagtcatgaatgttatattagttgcttctgtattatcttagatagtttcttagtttacttcttttatgtaaggttcaactaaactatgtagtgtgctagtttgtgatgattttgattctacagtcttatcttcctcacaagggtgggcactactgctgacctcctcctaggagttaggatatatctctgccttttcggttttctggagaatattaaaagtttgagatactattttatacattttcagttttctgaagaatattatcaagtttgagatactacttacagattgtgaccatgcaatcatcatcccagacgctaacatattcatgttaataaaattccaggagctacttgggtcgctgccggagggatttgttcagtatttctcaagccgattcccaaagctgctaattaaagtctacgaggtcatgtccgagcattgcaaggacgaagaagctttcagcaaatatttccttggaagctcggcgtagctgtaacctgcaggaggggtgaaggccctgccctgcctagtgtgtacactaacactcttctagcaaaaatgtatgtacatgtgatttgtaccatatatcatagggtaaagaaagttcagcctgtacattgtattccacagaattgtgtattacttatagtaaatcaaatcttttacctgact</dnaseqindica> |
| External Link(s) |
