Os04g0499300

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The rice Rymv1 gene is well known as its resistence of the rice yellow mottle virus (RYMV).

Annotated Information

Function

Rymv1,rice yellow mottle virus disease resistant gene, encoding eukaryotic translation initiation factor isomer eIF (iso) 4G. Rmv1 initially located on chromosome 4 3.7cM interval SSR markers RM252 and AFLP markers E-ACG/M-ACA between the inner (Albar et al., 2003). Rymv1 located on chromosome 4, which corresponds to the position of Nipponbare sequencing atlas (5'-3 ') at 24766929 - 24761516 interval (Rice Genome Annotation Project). The isoform of the eukaryotic translation initiation factor 4G (eIF(iso)4G) plays in naturally occurring resistance in plant/virus interactions. A genetic and physical mapping approach was developed to isolate the Rymv1 locus controlling the high recessive resistance to Rice yellow mottle virus (RYMV) in the rice (Oryza sativa) variety Gigante. The locus was mapped to a 160-kb interval containing a gene from the eIF(iso)4G family. The stable transformation of a resistant line with the cDNA of this gene, derived from a susceptible variety, resulted in the loss of resistance in transgenic plants. The allelic variability of this gene was analysed in three resistant and 17 susceptible varieties from different cultivated rice species or subspecies. Compared with susceptible varieties, resistant varieties present specific alleles, characterized by either amino acid substitutions or short amino-acid deletions in the middle domain of the protein. The structure of this domain was modelled and showed that the substitutions were clustered on a small surface patch. This suggests that this domain may be involved in an interaction with the virus.

Rymv1 初步定位于水稻第4 染色体上SSR标记RM252 和AFLP标记E-ACG/M-ACA 之间的3.7cM 区间内(Albar et al.,2003)。后通过发掘新标记、构建物理图谱,将Rymv1 定位在BAC克隆OSJNBa0067K08 和OSJNBa0029H02 之间的160kb 区间内,并最终在OSJNBa0029H02 上找到Rymv1 的候选基因(Albar et al., 2006)。

Rymv1 定位在水稻第4 染色体上,对应于日本晴测序图谱的位置(5'-3')在24766929 - 24761516 区间(Rice Genome Annotation Project)。

Figure 1.Transgenic rice expressing P1 proteins displays abnormal morphology, similar to that observed in loss-of-function dcl4-1 mutants. (a) RT-PCR analysis of OsDCL4 and P1 expression level in immature inflorescences of wild-type Nipponbare (Nipp), dcl4-1 mutant and Nipponbare genotypes expressing P1Tz3 or P1Mg1 constructs (Nipp-P1Tz3 and Nipp- P1Mg1). OsEF-1a was used as an internal control. (b–e) Inflorescence phenotypes of wild-type Nipponbare (b), dcl4-1 mutant (c), and Nipp-P1Tz3 (d) and Nipp-P1Mg1 (e) transformants. (f–i) Spikelet phenotypes of wild-type Nipponbare (f), dcl4-1 mutant (g), and Nipp-P1Tz3 (h) and Nipp-P1Mg1 (i) transformants. The palea (p), the lemma (l), the keel (k) and the awn (a) are indicated

Figure 1.Transgenic rice expressing P1 proteins displays abnormal morphology, similar to that observed in loss-of-function dcl4-1 mutants.

Expression

Rymv1 contains nine exons and 8 introns, encoding eukaryotic translation initiation factor isomer eIF (iso) 4G.In the IR64 and Gigante, Rymv1 cDNA coding region of 2379bp, which encodes a protein consisting of 793 amino acids, wherein the first range of 208 ~ 435 amino acid domain corresponding MIF4G; 628 ~ 740 amino acid domain corresponding to the section MA3.Compared with the encoded products of the susceptible parent, antiviral protein MIF4G domain deleted or three single amino acid substitution of amino acids occurs, the variation of resistance at the surface of the three dimensional structure of the protein, suggesting MIF4G protein interaction domains and may be involved in virus recognition (Albar et al., 2006).EIF4E and fixed plant eIF4G eIF4F complex formation, and eIF (iso) 4E and eIF (iso) 4G formed eIF (iso) 4F complex, these two protein complexes involved in the initial steps of the translation of mRNA cap structure and recruitment of the ribosome.

Rymv1 包含9个外显子和8个内含子,编码真核翻译起始因子异构体eIF(iso)4G。在IR64和Gigante中,Rymv1 cDNA 编码区长2379bp,编码一个793氨基酸组成的蛋白,其中,第208~435 氨基酸区间对应MIF4G 功能域;第628~740 氨基酸区间对应MA3 功能域。与感病亲本的编码产物相比,抗病蛋白在MIF4G 域发生了3氨基酸的缺失或单氨基酸的置换,这些变异位于抗病蛋白三维结构的表面,暗示MIF4G 域可能参与了蛋白与病毒的交互识别作用(Albar et al., 2006)。

在植物中eIF4E 和eIF4G 形成eIF4F 复合体,而eIF(iso)4E 和eIF(iso)4G 形成eIF(iso)4F 复合体,这两个复合体参与了蛋白翻译起始步骤的mRNA 帽子结构的固定和核糖体的招募。

Figure 2. Physical and fine genetic map in the Rymv1 region. (a) A contig of eight sequenced BAC clones covering 900 kb was identified downstream from the AFLP marker E-ACG/M-ACA. The physical position of the markers defined on the BAC clones and of the candidate gene eIF(iso)4G are indicated. The marker types are abbreviated as follows: microsatellite (MS), Indel (ID) or CAPS (C). Only the most informative markers are represented here. (b) Linkage map based on 432 either F2 or F3 plants derived from the Nipponbare/Gigante cross. Distances between the markers are indicated in centimorgans.

Figure 2. Physical and fine genetic map in the Rymv1 region.

Evolution

Figure 3. Amplification profile of the AG925 marker that is able to differentiate IR64 and Gigante alleles on the candidate gene. (a) Allele-specific PG and PI primers possess G and A nucleotides, respectively, on their 3¢-extremity. PCR with the four primers generated a fragment of 269 nucleotides and fragments of either 127 or 187 nucleotides, depending on the allele amplified. (b) Amplification profiles of AG925 on DNA. Fragment sizes were determined by reference to a molecular weight marker. Gigante variety (G) amplified the 127-bp fragment, whereas IR64 (I) and Nipponbare (N) varieties amplified the 187-bp fragment. Amplification profiles were confirmed on F2 and F3 plants derived from the Nipponbare/Gigante cross, as shown here for eight plants. Genotypes with markers flanking the candidate gene are indicated with A (homozygous for Gigante allele), B (homozygous for Nipponbare allele) or H (heterozygous). (c) Amplification profile of AG925 on cDNA obtained from four T0 transgenic plants expressing a transgenic copy of the gene obtained from IR64, Nipponbare (N), Gigante (G) and Nip-R line (NR). In transgenic plants, the transgenic copy, under 35S control, is overexpressed as compared with the endogeneous copy, which enhances the detection of the 187-bp fragment.

Figure 3. Amplification profile of the AG925 marker that is able to differentiate IR64 and Gigante alleles on the candidate gene.


[Note]

Rice yellow mottle virus disease occurs mainly in more than ten countries in West and Central Africa, such as Kenya. Mainly by leaf CPI (Apophylias spp.), Jump CPI (Chaetoenema spp.), Lobular A (Sesselia passilla) and African iron beetle (Trichispa sericeas) for semi-persistent transmission, also by sap inoculation. 水稻黄斑驳病毒病,主要发生在西非和中非的十多个国家,如肯尼亚。主要由叶甲类(Apophylias spp.)、跳甲类(Chaetoenema spp.)、小叶甲(Sesselia passilla)和非洲铁甲虫(Trichispa sericeas)作半持久性传播,亦可通过汁液接种。

ONTOLOGY and related gene


Phenotypic characteristics Rice yellow mottle virus disease resistance (TO: 0000088)

Molecular function Translation initiation factor activity (GO: 0003743)

Biological processes Virus in the host body from one cell to another cell proliferation (GO: 0046740), the virus stimulation (GO: 0009615)

Cell Structure Eukaryotic translation initiation factor 4F complex (GO: 0016281)

Morphological structure In vitro culture of leaf cells (PO: 0000007), vascular leaf (PO: 0009025)

Growth Stages Vegetative stage (GRO: 0007139)

Environmental Factors Artificial climate chamber (EO: 0007269), rice yellow mottle virus (EO: 0007318)


ONTOLOGY及相关基因


表型特征 水稻黄斑驳病毒病抗性(TO:0000088)

分子功能 翻译起始因子活性(GO:0003743)

生物进程 病毒在寄主体内从一个细胞扩散到另一个细胞(GO:0046740), 对病毒刺激的反应(GO:0009615)

细胞结构 真核生物翻译起始因子4F复合物(GO:0016281)

形态构造 离体培养的叶片细胞(PO:0000007), 维管叶(PO:0009025)

生育时期 营养生长阶段(GRO:0007139)

环境因子 人工气候箱(EO:0007269), 水稻黄斑驳病毒(EO:0007318)


Labs working on this gene

1 UMR 5096, IRD/CNRS/Universite´ de Perpignan, BP 64501, 34394 Montpellier CEDEX 5, France

2 UMR 1097, IRD/CIRAD/Agro-M/INRA, BP64501, 34394 Montpellier CEDEX 5, France

3 Africa Rice Center, WARDA, 01 BP 2031, Cotonou, Benin

References

1 The rice yellow mottle virus P1 protein exhibits dual functions to suppress and activate gene silencing

 The Plant Journal, 2009, 61(3): 371-382

2 Mutations in the eIF(iso)4G translation initiation factor confer high resistance of rice to Rice yellow mottle virus

 The Plant Journal, 2006, 47(3): 417-426

3 Molecular characterization of resistance to Rice yellow mottle virus in Bekarosaka, an indica variety from Madagascar

 Rice Genetics Newsletters, 2006, 23(): 84-86

Structured Information