Os08g0137250

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Annotated Information

Function

Please input function information here. FERTILIZATION-INDEPENDENT ENDOSPERM1 (FIE1) encodes an Esc-like core component of the Polycomb repressive complex 2, which is involved in H3K27me3-mediated gene repression. Here, we identify a gain-of-function epi-allele (Epi-df) of rice (Oryza sativa) FIE1; this allele causes a dwarf stature and various floral defects that are inherited in a dominant fashion.

Expression

Please input expression information here. The rice genome contains two E(z)-like genes, OsiEZ1 and OsCLF, two homologs of Su(z)12, OsEMF2a and OsEMF2b, and two ESC-like genes, OsFIE1 and OsFIE2. OsFIE1 is expressed only in endosperm; the maternal copy is expressed while the paternal copy is not active. Other rice PcG genes are expressed in a wide range of tissues and are not imprinted in the endosperm. The two E(z)-like genes appear to have duplicated before the separation of the dicots and monocots; the two homologs of Su(z)12 possibly duplicated during the evolution of the Gramineae and the two ESC-like genes are likely to have duplicated in the ancestor of the grasses. No homologs of the Arabidopsis seed-expressed PcG genes MEA and FIS2 were identified in the rice genome.

Evolution

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You can also add sub-section(s) at will. The rice Suz(12) homologs and E(Z) homologs have patterns of expression and imprinting different from the Arabidopsis FIS2 and MEA genes. Phylogenetic tree analysis, using the E(z)-like sequences from 50 taxa shows a clear SWN clade including both dicot and monocot sequences (Figure 3). OsiEZ1 (Os03g19480) grouped with the maize proteins Mez2 and Mez3 (Supplemental Table 1) in the monocot SWN-like clade. Mez2 and Mez3 show 89% sequence identity and are likely to be genome duplicates resulting from the paleotetraploid origin of maize (Springer et al., 2002). Arabidopsis SWN groups with other dicot SWN-like proteins. The CLF-like protein clade includes proteins from spikemoss, monocots, and dicots. The separation between CLF and SWN lineages must have happened at least before the divergence of monocots and dicots. Lower plants (Physcomitrella and Selaginella) have a single CLF homolog. The rice CLF-like protein (Os06g16390) is more related to Mez1 than to CLF-like proteins from other species.

MEA was grouped with other MEA-like proteins in Arabidopsis arenosa and Brassica, forming a clade distinct from the CLF and SWN clades. No MEA-like protein has been identified from any species outside the Brassicaceae (Spillane et al., 2007).

The sequence alignment of E(z) homologs of rice, Arabidopsis, and Drosophila (Supplemental Figure 1) shows the five domains nested along the sequences: EZD1, EZD2, SANT, Cys-rich, and SET. Similar domains occur in all three maize E(z) homologs (Springer et al., 2002). The SET domain is involved in histone H3 lysine27 tri-methylation (Rea et al., 2000; Cao et al., 2002; Czermin et al., 2002; Kuzmichev et al., 2002; Müller et al., 2002). The SANT domain is often involved in nonspecific DNA binding (Aasland et al., 1996). The EZD2 mediates interaction with EMF2 class proteins (Chanvivattana et al., 2004). The functions of the other domains are not known. 

There is a major EMF2 clade occurring in lower and higher plants (Figure 4). Arabidopsis EMF2 groups with other dicot EMF2-like proteins while the two rice EMF2-like proteins group with other grass EMF2-like proteins. Amongst the higher plants, dicots and the primitive monocot groups have a single homolog of EMF2, but the grasses, rice, sorghum, maize, and barley have duplicated EMF2 proteins. VRN2-like proteins form a group within the Brassicaceae that has diverged significantly from the main EMF2 clade. FIS2 and AT4G16810 form a separate mono-clade. There are no FIS2 or VRN2 homologs outside the Brassicaceae. We have observed that the FIS2 region (Chr2 15033493–15000348 bp) has been duplicated from the VRN2 region (Chr4 9291141–9476162 bp) in the Arabidopsis genome (Supplemental Figure 4). The block duplication might have arisen 35–85 million years ago as a result of a whole-genome duplication within the Brassicaceae (Blanc et al., 2003; Simillion et al., 2002; Grant et al., 2000).

The Su(z)12 homologs of rice, Arabidopsis, and Drosophila (Supplemental Figure 2) have conserved VEFS domains (VRN2, EMF2, FIS2, and Su(z)12), and zinc finger motifs in all proteins except At4g16810, in which the zinc finger motif is lacking.

For the ESC homologs, the phylogenetic tree clearly shows two major clades that correspond to Metazoans and plants, with the exception of C. elegans, which forms a mono-clade (Figure 5). In the plant clade, the grasses, maize, Sorghum, and rice, have two copies of FIE-like genes. The dicot clade, including the anomalous position of a gymnosperm Picea sitchensis protein, includes several species, each having one copy of a FIE homolog. The rice, maize, Arabidopsis, and Drosophila ESC proteins contain seven conserved WD40 repeats (Supplemental Figure 3).

T-DNA Insertions in the PcG Genes In order to investigate the conservation of function of the PcG genes in rice development, we have isolated T-DNA mutants of three PcG genes. In the T-DNA mutants, the insertions disrupt the coding sequences in OsFIE1 and OsEMF2, and the 5′-UTR in OsCLF. There were no morphological changes in homozygotes of Osclf or Osfie1 compared to the wild-type. The T-DNA insertion in OsEMF2b caused an obvious phenotypic change. No difference was found at the seedling stage, but the homozygous mutant plants flowered earlier than wild-type in long-day conditions (16 h). At 120 d post germination, the mutant had flowered while the wild-type remained vegetative (Figure 6A). The development of some florets was arrested at a stage when anthers and pistil had differentiated and aborted (Figure 6B). Most panicles did not elongate sufficiently to be seen outside the sheath. Each panicle had 15.5 ± 4.2 non-fertile florets. The wild-type had 30.8 ± 5.3 fertile florets. In the mutant plants, each having about 10 tillers, one or two panicles protruded from the sheath with the outside florets appearing to be ‘normal’ (Figure 6C). The anthers of those florets did not release pollen (Figure 6E), in contrast to wild-type (Figure 6F). Occasionally, some florets had multiple ovaries (Figure 6D). Some florets produced pseudoseeds without fertilization (for detail, see next paragraph). In short days (8 h), the wild-type and the mutant flowered at the same time. The phenotype co-segregated with the mutation; 14 homozygous mutant plants produced abnormal early flowering panicles and 98 homozygous wild-type plants and heterozygous plants produced normal late-flowering panicles. Another allele (3A-08856, Postech) with a T-DNA insertion in the coding region at the 5’ end of OsEMF2b shows identical phenotypes. Thus, OsEMF2b is involved in repressing flowering in long days and regulating floret development.

The unfertilized ovules of OsEMF2b, OsFIE1, and OsCLF, as well as wild-type lines, produced autonomous seed-like structures similar to those in the fis mutants of Arabidopsis (Figure 6G–6L). In fertilized seeds, cellularized endosperm is surrounded by proliferated nucellar cells with a distinct border between endosperm and the nucellar cells (Figure 6G and 6I). In the autonomous pseudoseeds, there is no formation of endosperm and embryo and only proliferated nucellar cells fill the structure (Figure 6H and 6J). The frequency of pseudoseed was highly variable between and within plants, but, in general, panicles from any plant showed 0–30% of autonomous pseudoseeds.

Labs working on this gene

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References

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Structured Information

Gene Name	Os08g0137250
Description	Similar to Polycomb group protein FERTILIZATION-INDEPENDENT ENDOSPERM (Protein FERTILIZATION-INDEPENDENT SEED 3).
Version	NM_001188443.1 GI:297726016 GeneID:9271694
Length	4953 bp
Definition	Oryza sativa Japonica Group Os08g0137250, 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	Chromosome 8
Location	Chromosome 8:2094655..2099607
Sequence Coding Region	2098524..2098620,2098845..2098908,2099053..2099112,2099289..2099382
Expression	GEO Profiles:Os08g0137250
Genome Context	<gbrowseImage1> name=NC_008401:2094655..2099607 source=RiceChromosome08 preset=GeneLocation </gbrowseImage1>
Gene Structure	<gbrowseImage2> name=NC_008401:2094655..2099607 source=RiceChromosome08 preset=GeneLocation </gbrowseImage2>
Coding Sequence	<cdnaseq>ggtcacattgatgttcttcagaagtaccctgtgccagaatgtaacatctggttcatgaaattctcatgtgattttcaccacaatcagttggcaataggaaaccgtgatggtaaagtctatgtctggaaagtacagaccagccctcctgttctaattgctcggctcaataatccacaagtgaaatcagccataaggcagactgcagtgtcctttgatggaagcacaatccttgcctgcacagaggatggcaacatatggcgttgggatgaagtggatcacccaaccgccccagtcccaagcaagaaacaaaagtga</cdnaseq>
Protein Sequence	<aaseq>GHIDVLQKYPVPECNIWFMKFSCDFHHNQLAIGNRDGKVYVWKV QTSPPVLIARLNNPQVKSAIRQTAVSFDGSTILACTEDGNIWRWDEVDHPTAPVPSKK QK</aaseq>
Gene Sequence	<dnaseqindica>3870..3966#4191..4254#4399..4458#4635..4728#gcccgccgccgctccctattcctatttaatcccatctctcttcctcatcaccgctctcctctctccaggcaagaggtacgcactttttgtttcggatttgaaatctttgcttcgttttactatcattggtcataagttcttttttgaagatgtttgagaataagtttatcattgagattatcgtcacttgtgataggaagtacgcaacctcaagccggacaagacgtgagcaaagatgggccccactagtaggaaccataaatcatctcaaaaagagtaagtggtattcttatatagcacacattttttaaggatatatacatgtttcccacaaatgtttcaaacacatatagtgatatatttaaatccgacaacatttgaattgaagtgtggcaccgaatgaagccaaaccaccccgatatccacagcgcaaccgctccatcactgcctctgcctctgcctctgcctttgcctctcccgctgttgccaactccagagttgccaaggaaaggccatcttcatcaactgctggtgaaggtgaaccacaggaaacggtgctaaagcttccaagcatcccaacacttcctgcacggatggcaaagttggtgccattagaggggttgggatgcgaggcagcggtgggatcgctaacaccgagtcgggagcgagaatacaaggtgaccaacaagcacactgagggaaggcgccctgtctacgccattgtcttcaatttcctcgatgttcgctactacgacatcttcgccaccgcctgtggccctcgtgtaagatttcttacgaggcgccatattgatcttactagggaagtagtagcgcttcatgtttctataaatagatcaaaatctagtatttaccttattatcctattcgcattagatgtttttaatctgactttgtgtcacgtcccttttttcatgtttcttaatttgcctattttgaaaattcacattcgtgttcattcacctaaaatagcttaatgaaaatttcataaatatttttgtttaaaatttgactaaataaaataatcatgctgccatttattttattgtttgttaattggagttatggttttttattcgagtttggaagtggagctcaactctgtgaattattatcaatctagaaatattcctcaaaattatttttgttttatatttattaatgtaatcgtgatgtggttatgatattaccttttgttattgtgtgtgctagagttgatctgggactaacacattatacacagagggatcctagttggggtcccgacactttgcgaatgcgctttacactttaaaagtgcattaaaaaatataattttgttgaatattttgataaaaatataattaggggaaggaattataagatcatagatttcattgatcataaaattaaattttaaggatggagttatgcacatatgttattttcaatgtgtttatgctaacacgttgcgccctcgtgacctttgcagctttcaacctaccgctgcctcatgaatggcaaatttgctcttctgcaaagctatcttgatgacgatgtaagctctgccaataattttgagtgttcagtttattatctacaccctctgttccaaaataaaccaattccttgctatggatctagagatagcctatgttcagagctgtccagatccgtagtcaggaattgatttattttagatgaagaagggtttgatggcatgcctttttctaaccatggtggggtctccattgccttgcagatgaatgagtcattcttcactgtgagctgggcttgcgacattgatggcaatccattgttagtagctgcaggaagcactggaatcattcgagtcatcaactgtgccactgagaagatatataaggtctagtagtgctagtgccattttttcttctttgccactactgcaaccttggataaactttgctctgtatcagtctatatatgtttttttttcagtaatatatgccaagctatggttctgttgcttatatattggaaaataatttcttatttgatagattctgatttatctgtgttatccattccaggaggtcacatgtaattcgcttcgattaagaactatagcaatcttttgactttctatatagctactaaattgtgccttttctcttctaaacatttgtggtttcagtgggtctttagcatgtctagtcagaaaattggcatataaattatgaaccattctatatcaagtacataactgatgtgcggccagtgttttatttctgtttatgaaaaataaaataaaattacagagtcttgttggccatggtggttcagtaaacgaaataaagtctcaaccatcgaatccttcactcatcatttctgcaagcaaggttagaagattacattgcctaatctgatatctacatctatttcatttttactgatgttctttcatacggcattgtgtaggatgaatctattaagctgtggaatgtgcagacagggatcttaattttggtttttggtggagtaggaggtcaccgacacgaagtacttggtgttgtaagttgcttaagctccactgtagcattttttataaaaaaaattgtaatgctactaattaacttgaaattgtccttaaaaataggactcatccagcttctgatgtcactttttttattgagcagattcaattttattcatttcaccaggagtgaaataatccttagtcactgaaattttgcgcattctttctttacattacgagtgcaaatattaatcataattaattaatattattgcttcaggacttccacacatctgatatctaccgctttttaagttgtggaatggacaacactgtgagaatctggtcaatgaaaggttagtgaaccatctcatgataaaaagaaaaggcaattgcatgatgcttatcggtgaaagtgtgtgaatgctgtagaattctgggaatatgttgagaaatcctattcatggactgatgctacatcaaaatttccaacaaaatttgtccaatttccggtatgcttatagtatctgccaatcatatctgaatctgttctttaatctgtaatttattagtatgtataaccaatatggtatcatctctctcctttcaggtcctgtgtgctgaaatacattctaactatgtagactgtactaaatggcttggggactttgtcctgtcaaaggtaaaattgttattgctcttttgaagtcaatatttatagtgcttacaaattattatatcttggttttatcctattcataaagggctatacatactgaattactgatactgcaaatttccaggctgtaccaggaacagccttttcaatcattagattagtgttacagattggttttcccatgacaattgggttacaaaaaggacaaattcattagagtaaaatttttattactcttttgaagccaatatttctagtgcttaaaaaattattatactgtgtttttatgctagtcataaaggacaaatttattttctactgctagtgcaagttttccaatccttagactagtgctacaaattgggttttctagtgaaaattcggttatttctgaaggatgaatacatctgatgtctgctaaacttgaattttcagagtgttgaaaatgaaatcttgctgtgggaatcgatcacaaaagaagaaaaccctggcgaggtaatataatttaatttatctctagaattacaaaatcttactcgtctacttatatccaaactaatctggctatgtttattttcttaaagaaaccatgttactttctttctccatgtccctatacatactacaatacatactatgtcttcctctaaggaaaatggttcttttgatttgtagggtcacattgatgttcttcagaagtaccctgtgccagaatgtaacatctggttcatgaaattctcatgtgattttcaccacaatcagttggcaataggtaataactaatgttgcactgttctctcaagaatcattttttttgtaaggcttgacgaatcattttgttgttatcgttctaaattattacacaatatacctttttcttggaagacaatgaatatgctagtatttctttagataatggatatgcaatattgattttgatattctttaaaacaaaatgtgaagtgctgaaggataaccatgtgcttattcaaacaggaaaccgtgatggtaaagtctatgtctggaaagtacagaccagccctcctgttctaattgctcggtaatgttaacctcaagaactcaacttattaagtttcatcgtctgcatttaatttggtatataggtgttgcctgttgggtgttaatttctaccaattctcatgtcttctacatgtgtgcttatcatcatcatgatcatctacaggctcaataatccacaagtgaaatcagccataaggcagactgcagtgtcctttgatggaaggtacattactacattcatcctgttcatactataaatttatccctgcttattcattctgatggagctagcctatcatttgcactgtgtttatgcttctgttttattttttatttttgttgtttgttttcttcttggaagattaaaaaaatgttttattgtgtttccattttcttcagcacaatccttgcctgcacagaggatggcaacatatggcgttgggatgaagtggatcacccaaccgccccagtcccaagcaagaaacaaaagtgaagcaaggattatattaattgaaattaataaggctgaattggcgatttgttcttggtatactttgttatactactttgccttagcgttcatcaaaactgccatttgattttccaacattcagaaaactctatagctggatgtaagatttattatcgcaagatattcaggatgttggtcggtgacttggttttatcaataatttgctgggaatatagtacttaatct</dnaseqindica>
External Link(s)	NCBI Gene:Os08g0137250, RefSeq:Os08g0137250