Os02g0811000

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Annotated Information

Os02g0811000(LOC_Os02g56610) was first identified as the TH1 gene which encoded an unknown functional protein contained 248 amino acids and a DUF640 domain by Li et al., 2012. Several studies suggest that TH1 was an important gene controlling the lemma and palea development in rice. The later researchers by Ma et al., 2013 and Yan et al., 2013 also found the mutants of Os02g0811000 (LOC_Os02g56610) gene, and named them as BLS1( beak like spikelet1) and BSG1(beak-shaped grain1).

Function

The TH1 gene controls the grain shape and development of lemma and palea through regulating the cell division and extension. Loss-function or down regulation of the TH1 gene caused tortuous and slender lemma/palea and the decrease of grain weight[1].

BLS1 is required for lateral development of the lemma and palea and does not function at stages of floral-organ initiation and patterning. The bls1 mutants display altered shapes of lemmas and paleas and show abnormal lateral development of lemma and palea. [2]

BSG1 determines grain shape and size probably by modifying cell division and expansion in the grain hull. Map-based cloning revealed that BSG1 encoded a DUF640 domain protein, TRIANGULAR HULL 1, of unknown function. The BSG1 mutation affected the expression of genes potentially involved in the cell cycle and GW2, an important regulator of grain size in rice[3].

Expression

RT-PCR analysis and GUS staining showed that the transcripts of TH1 mainly accumulated in young inflorescence, lemma and palea of spikelet [1].

Fig. 1 The expression pattern of the TH1 gene (Li et al., 2012) .

BLS1 is expressed strongly in young inflorescence, specifically the young lemmas and paleas of spikelets. Subcellular localization analysis showed that BLS1 is localized in the nucleus[2].

Fig. 2 Expression pattern of BLS1(Ma et al., 2013).

Fig. 3 Subcellular localization of BLS1(Ma et al., 2013).

Quantitative PCR and GUS fusion reporter assays showed that BSG1 was expressed mainly in the young panicle and elongating stem[3].

Fig.4 Expression pattern of BSG1(Yan et al., 2013).

Mutations

The th1-1 mutant exhibited obviously triangular hull with tortuous and slender lemma/palea. Observation of the lemma and palea of th1-1 using scanning electron microscopy (SEM) revealed that the th1-1 had narrower lemma and palea. Just before heading, we viewed the epidermis of lemma and palea using SEM, and found that the bulges in the th1-1 mutant were more than that of wild type. Further examination on transverse sections of lemma and palea showed that the number of fibrous sclerenchyma cells was increased in the th1-1 mutant [1]. Using a map-based cloning strategy, the TH1 gene was narrowed down to a 60-kb region on the long arm of chromosome 2. Sequence verification revealed that the th1-1 mutant harbored 1-bp deletion in exon 2 of LOC_Os02g56610 which resulted in a frame-shift mutation [1].

Fig. 5 Phenotypes of the th1-1 mutant (Li et al., 2012).

Fig. 6 Map-based cloning of TH1 (Li et al., 2012).

In bls1 mutant, floral-organ identity and floral-organ patterningare normal, and the defects occur at the stage of the lemma and palea expansion, whereas the other aspects of floral architecture and form are not affected[2].

Fig. 7 Phenotypes of wild type (WT) and bls1 mutant spikelets(Ma et al., 2013).

The bls1 mutant was controlled by a single recessive gene locus in a region of about 65 kb region between markers M14 and M10 on chromosome 2[2].

Fig. 8 Map-based cloning and confirmation of the BLS1 gene(Ma et al., 2013).

The BSG1 gene Produced beak-shaped grains of decreased width, thickness and weight with a loosely interlocked lemma and palea that were unable toclose tightly. Starch granules were also irregularly packaged in the bsg1 grains. Consistent with the lemma and palea shapes, the outer parenchyma cell layers of these bsg1 tissues developed fewer cells with decreased size[3].

Fig. 9 Characterization of the bsg1-1 mutant(Yan et al., 2013).

The deletion in bsg1-1 and amino acid transition in bsg1-2 both occurred in the DUF640 coding sequence. A 5-bp deletion in the genomic sequence of the predicted gene Os02g0811000 was identified in bsg1-1. In bsg1-2, a transition from A to T in the exon of the same Os02g0811000 gene, resulting in a change of amino acid from Asp to Val[3].

Fig. 10 Map-based cloning of BSG1(Yan et al., 2013).

phylogenetic analyses

Bioinformatic analysis revealed that BLS1 encodes a protein with a conserved domain of unknown function. In the rice database, this domain is called ALOG. Ma et al. construct a phylogenetic tree (Fig. 11) which shows the relationship between BLS1 and other proteins with ALOG domains. Among the 23 BLS1 homologs, only three genes have been reported so far: LIGHTDEPENDENT SHORT HYPOCOTYLS1 (LSH1)/ ORGAN BOUNDARY1 (OBO2), LSH3/ OBO1 , and ELONGATED EMPTY GLUME (ELE) /G1 . And the phylogenetic analysis showed that the BLS1 gene is in a distinct clade, including four putative homologs, Grmzm2g168371, Sb04g036620, Bradi3g54800, and Grmzm2g027302 from the genomes of maize, sorghum and Brachypodium , which shared around 80 % amino acid sequence identity with the BLS1 protein[2].

Fig. 11 Phylogenetic tree of proteins containing the ALOG domain.

Primers

HX1 (5’-gtactggcaaagcaagatgg-3;5’-atcgggaagcagattcatcc-3’) were used to amplify the ORF sequence of LOC_Os02g56610 from th1-1;HX2 (5’-catgtgtgtggcactgttgc-3; 5’-cactctagctacatagtgtgc-3’) were used to amplify the genomic sequence of LOC_Os02g56610 from th1-2 [1].

Labs working on this gene

1. State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China. 2. National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China. 3. National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China. 4. State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.

References

[1] Xiaojiao Li,Lianjun Sun;Lubin Tan,Fengxia Liu,Zuofeng Zhu,Yongcai Fu,Xianyou Sun,Xuewen Sun,Daoxin Xie,Chuanqing Sun,2012. TH1, a DUF640 domain-like gene controls lemma and palea development in rice. Plant Molecular Biology, 78(4-5): 351-359. [2] Xiaoding Ma,Zhijun Cheng,Fuqing Wu,Mingna Jin,Liguo Zhang,Feng Zhou,Jiulin Wang,Kunneng Zhou,Jian Ma,Qibing Lin,Cailin Lei,Jianmin Wan,2013. BEAK LIKE SPIKELET1 is Required for Lateral Development of Lemma and Palea in Rice. Plant Molecular Biology Reporter, 31(1): 98-108. [3] Yan D W, Zhou Y, Ye S H, et al. , 2013. BEAK-SHAPED GRAIN1/TRIANGULAR HULL 1, a DUF640 gene, is associated with grain shape, size and weight in rice. Sci China Life Sci, 56: 275–283.

Structured Information

Gene Name	Os02g0811000
Description	Protein of unknown function DUF640 domain containing protein
Version	NM_001055008.1 GI:115449464 GeneID:4331099
Length	2100 bp
Definition	Oryza sativa Japonica Group Os02g0811000, 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 2
Location	Chromosome 2:35574485..35576584
Sequence Coding Region	35575238..35575984
Expression	GEO Profiles:Os02g0811000
Genome Context	<gbrowseImage1> name=NC_008395:35574485..35576584 source=RiceChromosome02 preset=GeneLocation </gbrowseImage1>
Gene Structure	<gbrowseImage2> name=NC_008395:35574485..35576584 source=RiceChromosome02 preset=GeneLocation </gbrowseImage2>
Coding Sequence	<cdnaseq>atggatcgtcaccatcaccaccaccaccaccaccaccatcacatgatgtcgggcggcgggcaagacccggcggcgggggacggcggcgccggcggcgccacgcaggacagcttcttcctcggcccggccgcggccgccatgttctccggcgccgggtcgtcgtcgtcgggcgcggggacgtcggcgggaggcggcggcggcgggccatcgccgtccagctcgtcgccgtcgctgagccggtacgagtcgcagaagcggcgggactggaacacgttcgggcagtacctgcggaaccaccggccgccgctgtccctgtcgcggtgcagcggcgcgcacgtgctggagttcctcaagtacatggaccagttcgggaagacgaaggtgcacacgccggtgtgccccttctacggccaccccaacccgccggcgccatgcccgtgcccgctccgccaagcctggggctccctcgacgcgctcatcggccgcctccgcgccgcctacgaggagaacggcggcacgccggagatgaaccccttcggcgcccgcgccgtccgcctctacctgcgcgaggtgcgcgagacgcaggccagggcgagggggatcagctacgagaagaagaagcgcaagaagccctcgtccgccggcgccggagccgggccctcgtccgaggggagcccgccgccacccggcggctcggccagcggcggcggcgacacgtcggcgtcgccgcagttcatcatcccgtga</cdnaseq>
Protein Sequence	<aaseq>MDRHHHHHHHHHHHMMSGGGQDPAAGDGGAGGATQDSFFLGPAA AAMFSGAGSSSSGAGTSAGGGGGGPSPSSSSPSLSRYESQKRRDWNTFGQYLRNHRPP LSLSRCSGAHVLEFLKYMDQFGKTKVHTPVCPFYGHPNPPAPCPCPLRQAWGSLDALI GRLRAAYEENGGTPEMNPFGARAVRLYLREVRETQARARGISYEKKKRKKPSSAGAGA GPSSEGSPPPPGGSASGGGDTSASPQFIIP</aaseq>
Gene Sequence	<dnaseqindica>601..1347#atttctacctcacacacctagctagcaagtaggctctctcactccacacccacactactcctcccaggctgcctgcctaaaaggctagacctatccatctcttccccccactcctccagcatcgccatcatccactgttcatccactccatctctctctctctctctctctctctctctctccatcgatccctgcaggttcttgctgctgctgctgctgccttgcttgctgtcaagcatggcttgaccacctgagagcgaggagagcatagcgtagtacttggctagctgctgttcaattcctcatggatgattggaggatcgctagctaggtcgcccggatccacggacacctctcctcgtctcgtgctcgtgcatgccaagatcgatcgatcccagctgctgctgcgagtggagcagtggaggaggagatcggctgctacctgacctagatcgggaagcagattcatccggtacatgttatatatagatatagatcgttgcttaggttcttctcttcttgtttgatttcgtcggagcaagaaatgatgcttgcttcttgtgattcaggttgcattacggcggcgaggcgagggcgaggatggatcgtcaccatcaccaccaccaccaccaccaccatcacatgatgtcgggcggcgggcaagacccggcggcgggggacggcggcgccggcggcgccacgcaggacagcttcttcctcggcccggccgcggccgccatgttctccggcgccgggtcgtcgtcgtcgggcgcggggacgtcggcgggaggcggcggcggcgggccatcgccgtccagctcgtcgccgtcgctgagccggtacgagtcgcagaagcggcgggactggaacacgttcgggcagtacctgcggaaccaccggccgccgctgtccctgtcgcggtgcagcggcgcgcacgtgctggagttcctcaagtacatggaccagttcgggaagacgaaggtgcacacgccggtgtgccccttctacggccaccccaacccgccggcgccatgcccgtgcccgctccgccaagcctggggctccctcgacgcgctcatcggccgcctccgcgccgcctacgaggagaacggcggcacgccggagatgaaccccttcggcgcccgcgccgtccgcctctacctgcgcgaggtgcgcgagacgcaggccagggcgagggggatcagctacgagaagaagaagcgcaagaagccctcgtccgccggcgccggagccgggccctcgtccgaggggagcccgccgccacccggcggctcggccagcggcggcggcgacacgtcggcgtcgccgcagttcatcatcccgtgagttcttctcgatccccatcgccatctccgcatctccattgatcgatcgagcctcgcagcaagaaattccaatctccttggcagaaatgccatcttgctttgccagtacaaggcatcatatctcttctttcctcctgaattggtttcgatctctcccattttgcaaaaaaagatttctcctctttttaatttcatctctgtctcgctttctaagctaggacgaaggtcatgcatgagtgagtacttagtttaattcttgtttttttccttagctttgggacgtcaattaattggtagctgctgtcttcgatcgatctcgtcccgtttggtttaattattttgatgcaagaactggagtaaatttgatgagaatctcaagctagctagcctaattaggagttgtaatatttgttttagtctgggggatttgcaagaacaaaagtagcagaagctgtaggcatagcaagctagctagtgttagtatctgtagaatttgttcttgtaatagcttgtcgccaagctagccaagtgcagtggcgtcagcaatgcttccttctatctatcatgtactagtgatgatgtcttggtcttcctttcttggttgagcaaaagggcaaaaagggagagatcgactagctgatgagatgatgagtgatttcaattggtagcttaattaagacagaaacaacatgtgttatgtgtacttgtcctgggaacagattccatatatatgccaaatgctttaatttgggct</dnaseqindica>
External Link(s)	NCBI Gene:Os02g0811000, RefSeq:Os02g0811000