Os01g0173100 - Revision history

192.168.72.52 at 04:34, 14 May 2015

2015-05-14T04:34:23Z

Hermione: /* Function */

2014-06-08T02:58:19Z

‎Function

Hermione: /* Labs working on this gene */

2014-06-08T02:57:17Z

‎Labs working on this gene

Hermione: /* Evolution */

2014-06-08T02:52:52Z

‎Evolution

Hermione: /* Expression */

2014-06-08T02:52:19Z

‎Expression

Hermione: /* Function */

2014-06-08T02:50:22Z

‎Function

Hermione: /* Function */

2014-06-08T02:48:45Z

‎Function

Hermione: /* Function */

2014-06-08T02:47:50Z

‎Function

Hermione: /* Function */

2014-06-08T02:41:53Z

‎Function

Hermione: /* References */

2014-06-08T02:17:32Z

‎References

← Older revision		Revision as of 04:34, 14 May 2015
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	==Structured Information==		==Structured Information==
−	~~{{JaponicaGene\|~~	+	[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]
−	~~GeneName = Os01g0173100\|~~
−	~~Description = Alba, DNA/RNA-binding protein family protein\|~~
−	~~Version = NM_001048692.1 GI:115434797 GeneID:4327120\|~~
−	~~Length = 1684 bp\|~~
−	~~Definition = Oryza sativa Japonica Group Os01g0173100, 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 1:3741778..3743461\|~~
−	~~CDS = 3741949..3742044,3742170..3742234,3742377..3742439,3743057..3743105,3743202..3743387<br>\|~~
−	~~GCID = <gbrowseImage1>~~
−	~~name=NC_008394:3741778..3743461~~
−	~~source=RiceChromosome01~~
−	~~preset=GeneLocation~~
−	~~</gbrowseImage1>\|~~
−	~~GSID = <gbrowseImage2>~~
−	~~name=NC_008394:3741778..3743461~~
−	~~source=RiceChromosome01~~
−	~~preset=GeneLocation~~
−	~~</gbrowseImage2>\|~~
−	CDNA = <cdnaseq>atggcggtggaggagatcaccgagggggtgaggaacctggccgtggagggggagcccgcggcggcggcggcggcggcgggaggtggtggtgagggggcgcagaggagggcggccgggagcagcagcaaccgcatccaggtgtccaacaccaagaagccactcttcttctatgtcaacctcgccaagaggtacatgcagcagcacggcgatgtcgagctctccgcgctcgggatggccattgcaacagttgtaactgttgcggagattcttaagaataacgggtttgctgttgaaaagaagattagaacatctacggtggaaataaacgatgaatcgagagttcgcccgctccaaaaggctaagattgagatagtgttagaaaagagcgagaaatttgatgagctgatggctgccgcagcggaagagagggaagctgcggaagctgaggagcaggcctga</cdnaseq>\|
−	AA = <aaseq>MAVEEITEGVRNLAVEGEPAAAAAAAGGGGEGAQRRAAGSSSNR IQVSNTKKPLFFYVNLAKRYMQQHGDVELSALGMAIATVVTVAEILKNNGFAVEKKIR TSTVEINDESRVRPLQKAKIEIVLEKSEKFDELMAAAAEEREAAEAEEQA</aaseq>\|
−	DNA = <dnaseqindica>1418..1513#1228..1292#1023..1085#357..405#75..260#gcacaacccaccaccaccaccaccaccgatctgcggagagcgagctaccaccaccgagcggcgtagcttgagcgatggcggtggaggagatcaccgagggggtgaggaacctggccgtggagggggagcccgcggcggcggcggcggcggcgggaggtggtggtgagggggcgcagaggagggcggccgggagcagcagcaaccgcatccaggtgtccaacaccaagaagccactcttcttctatgtcaacctcgccaaggtttgtcactctacccgcctcgcctcctctccgtgccctagccgcgagcagcagcggtttttgttgactgattggattggtttcgtttttatgcagaggtacatgcagcagcacggcgatgtcgagctctccgcgctcgggatgggtgcgtctcgctctcttctccctgttcatccctggtctcgatttggcgttaattcggggggttttagggtaataggagtgactcttgttgagttgattcgacctagaagttattaggttgtgggagaatgcgaacgatgcaagaagttactgtttgcatgtgcaattgctctgttgtttcatgattgacttctggattcccaatctatttttatcaaggtggagcatttttctgtttcgcgtttgtgtgctaggtaatcttagtattgtgttctaggatatgccattttgcgaagcagtgtatagttcaatagttggtcttgaagacttaaacgggtggtctttgtttcgtactcgcattgatatgtacataaccactcataaaatgagtcatgacaccctttcaccactcttcattacctttgcttttggtcaagtaaaactatttactgttcttaaaaaaaaaagaagctgtttataaatgtttaactcttagatgagtgctgactgtcagcccatttggttggtcggtgtagttcgatatttcctttcttcaagatgtggttttatctctactgttgaaggctgtacaaaccatattgtttgatttgtttgcagccattgcaacagttgtaactgttgcggagattcttaagaataacgggtttgctgttgaaaagagtaagaaattctttccttgcaggattgtactgcttgttttgtctcattatctgttttaacattactgttgtgggcatgcagtaatccacaatattcattgttctctactctgaattttccattttcaccttcgcttgtgtagagattagaacatctacggtggaaataaacgatgaatcgagagttcgcccgctccaaaaggctaaggtcaggctttagttgccaaagccacttatttctctcttgttaaaaaaaaaaagcctgttcttaacatgagctttctttctttctttttctaaacctgaactgattgagagctttgtttcctacagattgagatagtgttagaaaagagcgagaaatttgatgagctgatggctgccgcagcggaagagagggaagctgcggaagctgaggagcaggcctgataaggactaggagcgatgacctttgttgtgtgctttgttcctgttgtttaatactgcgtgctttagagatggcatgccttcttgtttaagttgtgtttttcttttatggcagtgtgtgtaaactcagtgactgatgataatctgtttgcaattgagttgagacagcttctc</dnaseqindica>\|
−	~~Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001048692.1 RefSeq:Os01g0173100]\|~~
−	}}
−	[[Category:Genes]]
−	~~[[Category:Japonica mRNA]]~~
−	[[Category:Oryza Sativa Japonica Group]]
−	[[Category:Japonica ~~Genes]]~~
−	~~[[Category:Japonica Chromosome 1]]~~
−	~~[[Category:~~Chromosome 1]]

@@ Line 3: / Line 3: @@
 ==Annotated Information==
 ===Function===
-[[File:hj.jpg|right|thumb|350px|Fig.1]]
+[[File:hj.jpg|right|thumb|350px|Fig.1Transcript analyses of OsAlba1 in response to different stresses and tissue-specific expression. ]]
-[[File:Exkl.jpg|right|thumb|350px|Fig.2]]
+[[File:Exkl.jpg|right|thumb|350px|Fig.2 Subcellular localization of OsAlba1-GFP fusion protein.]]
-[[File:Examplo.jpg|right|thumb|350px|Fig.3]]
+[[File:Examplo.jpg|right|thumb|350px|Fig.3 Phylogenetic relationship of OsAlba1 with its orthologs was inferred using the neighbor-joining method.]]
 Water-deficit conditions triggered OsAlba1 expression suggesting its function in dehydration stress, possibly through an ABA-dependent pathway. Functional complementation of the yeast mutant DPop6 established that OsAlba1 also functions in oxidative stress tolerance. The preferential expression of OsAlba1 in the flag leaves implies its role in grain filling. Our findings suggest that the Alba components such as OsAlba1, especially from a plant where there is no evidence for a major chromosomal role, might play important function in stress adaptation.

@@ Line 28: / Line 28: @@
 ==Labs working on this gene==
-National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
+.National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
 ==References==

@@ Line 25: / Line 25: @@
 To understand the evolutionary relationships within the Alba protein superfamily, a phylogenetic tree was constructed. The unrooted phylogram revealed presence of two separate lineages, the first group consisting of animal Alba proteins, exemplified by the human RNase/MRP subunits Rpp20/Pop7, and the second containing archaeal and plant Alba proteins. OsAlba1 (A2WL83, O. sativa ssp. indica) is identical to Q94E63 (O. sativa ssp. japonica) and I1NKP6 (O. glaberrima). It clustered together with monocot (Oryza brachyantha, Zea mays, and Hordeum vulgare) Alba proteins, suggesting a closer proximity to these as compared to dicot Alba proteins.
-Multiple sequence alignment (MSA) of OsAlba1 with other known Alba sequences from diverse sources including Archaea, Arabidopsis, yeast, human, Plasmodium and Trypanosoma revealed a high degree of conservation of amino acid in the regions of 59–72 and 101–122 in MSA, corresponding to 46–59 and 71–92, respectively, in OsAlba1. MSA showed presence of a conserved glycine residue at position 77 within Alba domain. Ten homologs of Alba protein have thus far been reported in UniProt database from indica rice, nine of which correspond to specific known genes with known locus ID on chromosomes. OsAlba1 is located on chromosome 1, albeit being a complete sequence of 152 aa in contrast to A2WL83 with 124 aa (UniProtKB/TrEMBL). The accession number of chromosome 1 of Oryza sativa ssp indica is GI 57015219 in NCBI, while that of japonica is GI 57015276. Available sequence of OsAlba1 in indica (position 4200197–4201583) corresponds to position 3805619–3807005 of japonica, indicating its different position on chromosome 1. The Alba sequences were retrieved from UniProt and a phylogenetic analysis of the Alba proteins from O. sativa ssp. indica was carried out. The phylogram appeared to be divided into two groups based on the percentage of protein sequence covered by Alba domain. The Alba domain for Group I had sequence coverage of less than 30%, while Group II comprised those with higher sequence coverage, when compared with the complete protein sequence .MSA of the phylogenetic tree is shown in Supplementary. All the ten sequences, harboring only a single domain i.e., Alba, are uncharacterized.
+Multiple sequence alignment (MSA) of OsAlba1 with other known Alba sequences from diverse sources including Archaea, Arabidopsis, yeast, human, Plasmodium and Trypanosoma revealed a high degree of conservation of amino acid in the regions of 59–72 and 101–122 in MSA, corresponding to 46–59 and 71–92, respectively, in OsAlba1. MSA showed presence of a conserved glycine residue at position 77 within Alba domain. Ten homologs of Alba protein have thus far been reported in UniProt database from indica rice, nine of which correspond to specific known genes with known locus ID on chromosomes. OsAlba1 is located on chromosome 1, albeit being a complete sequence of 152 aa in contrast to A2WL83 with 124 aa (UniProtKB/TrEMBL). The accession number of chromosome 1 of Oryza sativa ssp indica is GI 57015219 in NCBI, while that of japonica is GI 57015276. Available sequence of OsAlba1 in indica (position 4200197–4201583) corresponds to position 3805619–3807005 of japonica, indicating its different position on chromosome 1. The Alba sequences were retrieved from UniProt and a phylogenetic analysis of the Alba proteins from O. sativa ssp. indica was carried out. The phylogram appeared to be divided into two groups based on the percentage of protein sequence covered by Alba domain. The Alba domain for Group I had sequence coverage of less than 30%, while Group II comprised those with higher sequence coverage, when compared with the complete protein sequence .MSA of the phylogenetic tree is shown in Supplementary. All the ten sequences, harboring only a single domain i.e., Alba, are uncharacterized.(Fig3)
 ==Labs working on this gene==

@@ Line 16: / Line 16: @@
 hyper-osmotic stress, and this participation may, in part, depend on ABA.
-To determine the organ-specific expression of OsAlba1, we compared transcript abundance in roots, stems, leaves, flag leaves, sheaths and panicles of rice seedlings. The transcripts were abundantly and constantly transcribed in flag leaves . The expression in other major vegetative organs was substantially low. Next, we examined the protein abundance in all these tissues by immunoblot analysis. The results showed the presence of OsAlba1 in leaves and flag leaves, corroborating the mRNA profile. The predominant expression of OsAlba1 in the flag leaves seems to support the growing panicles which might be crucial during grain filling. The rice flag leaves are essential in providing photosynthates and has been reported to play an important role in grain yield and in enhancing productivity. These results may have important implications, since such organspecific gene expression is closely related to harvest yield, and perhaps crucial for driving agronomic trait/s.
+To determine the organ-specific expression of OsAlba1, we compared transcript abundance in roots, stems, leaves, flag leaves, sheaths and panicles of rice seedlings. The transcripts were abundantly and constantly transcribed in flag leaves . The expression in other major vegetative organs was substantially low. Next, we examined the protein abundance in all these tissues by immunoblot analysis. The results showed the presence of OsAlba1 in leaves and flag leaves, corroborating the mRNA profile. The predominant expression of OsAlba1 in the flag leaves seems to support the growing panicles which might be crucial during grain filling. The rice flag leaves are essential in providing photosynthates and has been reported to play an important role in grain yield and in enhancing productivity. These results may have important implications, since such organspecific gene expression is closely related to harvest yield, and perhaps crucial for driving agronomic trait/s.(Fig1)
 '''Subcellular localization of OsAlba1'''
-To verify the in silico predicted dual localization of OsAlba1, its subcellular localization was further investigated by transient expression assay using EGFP-containing vector system. The GFP expression showed accumulation of fusion protein in the nucleus, and sparsely in the cytoplasm. An increasing number of proteins, with similar and/ or distinct functions, have been reported to reside in multiple compartments. While the Alba proteins are nuclear resident and reported to play a role in tRNA processing in yeast and human, it is localized to the cytoplasm of Trupanosoma brucei in normal culture conditions but co-localizes with a subset of poly(A)-RNA in stress granules. In Plasmodium falciparum, the ring stages showed localization of Alba proteins to perinuclear foci, while in mature forms, it expanded to the cytoplasm . Thus, our results showing dual localization of Alba protein in plant is in agreement with observations made earlier.
+To verify the in silico predicted dual localization of OsAlba1, its subcellular localization was further investigated by transient expression assay using EGFP-containing vector system. The GFP expression showed accumulation of fusion protein in the nucleus, and sparsely in the cytoplasm. An increasing number of proteins, with similar and/ or distinct functions, have been reported to reside in multiple compartments. While the Alba proteins are nuclear resident and reported to play a role in tRNA processing in yeast and human, it is localized to the cytoplasm of Trupanosoma brucei in normal culture conditions but co-localizes with a subset of poly(A)-RNA in stress granules. In Plasmodium falciparum, the ring stages showed localization of Alba proteins to perinuclear foci, while in mature forms, it expanded to the cytoplasm . Thus, our results showing dual localization of Alba protein in plant is in agreement with observations made earlier.(Fig2)
 ===Evolution===

@@ Line 5: / Line 5: @@
 [[File:hj.jpg]]
 [[File:Exkl.jpg]]
 Water-deficit conditions triggered OsAlba1 expression suggesting its function in dehydration stress, possibly through an ABA-dependent pathway. Functional complementation of the yeast mutant DPop6 established that OsAlba1 also functions in oxidative stress tolerance. The preferential expression of OsAlba1 in the flag leaves implies its role in grain filling. Our findings suggest that the Alba components such as OsAlba1, especially from a plant where there is no evidence for a major chromosomal role, might play important function in stress adaptation.

@@ Line 29: / Line 29: @@
 ==References==
 .Jitendra Kumar Verma, Saurabh Gayali , Suchismita Dass , Amit Kumar , Shaista Parveen , Subhra Chakraborty, Niranjan Chakraborty, OsAlba1, a dehydration-responsive nuclear protein of rice (Oryza sativa L. ssp. indica), participates in stress adaptation, Phytochemistry 100 (2014) 16–25
 ==Structured Information==