Os10g0573900 - Revision history

Rice2012: /* References */

2015-06-13T08:59:10Z

‎References

Lmw2015: /* Structured Information */

2015-06-12T04:17:55Z

‎Structured Information

Shijc: /* Evolution */

2014-12-24T01:09:22Z

‎Evolution

Shijc at 18:20, 23 December 2014

2014-12-23T18:20:52Z

Shijc: /* References */

2014-12-23T18:17:48Z

‎References

Shijc at 18:15, 23 December 2014

2014-12-23T18:15:07Z

124.16.129.48 at 21:13, 22 July 2012

2012-07-22T21:13:30Z

127.0.0.1: Created page with "{{JaponicaGene| GeneName = Os10g0573900| Description = NMD3 family protein| Version = NM_001072005.1 GI:115483605 GeneID:4349477| Length = 2005 bp| Definition = Oryza sat..."

2012-06-21T08:49:44Z

Created page with "{{JaponicaGene| GeneName = Os10g0573900| Description = NMD3 family protein| Version = NM_001072005.1 GI:115483605 GeneID:4349477| Length = 2005 bp| Definition = Oryza sat..."

New page

{{JaponicaGene|
GeneName = Os10g0573900|
Description = NMD3 family protein|
Version = NM_001072005.1 GI:115483605 GeneID:4349477|
Length = 2005 bp|
Definition = Oryza sativa Japonica Group Os10g0573900, 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 10|Chromosome 10]]|
AP = Chromosome 10:23237629..23239633|
CDS = 23238015..23239586|
GCID = <gbrowseImage1>
name=NC_008403:23237629..23239633
source=RiceChromosome10
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008403:23237629..23239633
source=RiceChromosome10
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgctgccggggtcggcggcgccggcggctgggagcggcatgttcgtgccaacgcagacggtgggcacggtgctgtgctgcatctgcggcgtggcgatgcagcccaacccggccaacatgtgcgcgcgctgcatccgcgcccgcgtcgacatcaccgagggcgtcccgcgccacgccgccgtcgtctactgccccgactgcacctcctacctccagccgccgcgctcctggctccgcgccggcccggagtcccccgagctcatgcagatcctcctccgccgcctcaaccgccccctcgcccgcctccgcgtctccctctccgccgccgagttcgtcttctccgagccccactccaagcgcctccgcctcaagctccgcctccgccgcgaggtcttcaacgccgtcgtcctcgagcagacccaccccgtcgagttcaccgtccacgatcgcctctgcgatgcctgcgcccgcgcccagtccaaccccgaccagtgggtcgccgtcgtccagctccgccagcacgtcccgcaccgccgcaccttcctctacctcgagcagctcctcctcaagcacggccaggcctccctcgccctccgcgtcgccgccgcccccggcggcctcgacttcttcttcggctcccgctcgcacgccgcccgcctcgtcgacttcctcgccaccgtcgcccccgtccagacccagaccgccaagcagctcgtctcccacgacaccaagagcaacgtctacaactacaagcacaccttctccgtcgagatctgccccatctgccgggaggacctcatcgcccttagccctcaggtgtcccgcgatcttggaggccttggacctatcgtcctctgcatcaaggtcaccaatgccatcgctctgcttgaccccctcaccctgcgtgtgcaccacctcgaggaaaagaagtacagggtctacaacttcaaggctgctctcaccagcaagcagctcgtcgagtacatcgtgctagacatcgagcacgagtcaccagagattaccattgacggatctcgctaccagttggcttatgcccaggtcgcccgggtctccgactttgggaaaaacgacaccatgttcaccgtgcggactcatcttggccacctgctgaatcctggagaccttgcccttgggtatgatctttatggtgccaacttgaatgatgatgacatggacacagctatgatgcgccacagtctgcctgaagtcattcttgttaagaagagcttcgccaagaggccacgcacacgccgatggaagctgaagaggcttccaatggaggaagatgctgtaaataaggccaagggggagctagagaagagggctgatgagtatgaggagtttctcagggacttggagcacaactctgatattagattccagattgatctatacaaggatgaggactacaggtcggagatggcatctactattggtgatgatgttcccactgtgccgattgaggaactaattgaggacctaagtcttggtgatgatgaggaggaggatgaaggtggggaaggcaaccaacatgctgttatggtgggatga</cdnaseq>|
AA = <aaseq>MLPGSAAPAAGSGMFVPTQTVGTVLCCICGVAMQPNPANMCARC IRARVDITEGVPRHAAVVYCPDCTSYLQPPRSWLRAGPESPELMQILLRRLNRPLARL RVSLSAAEFVFSEPHSKRLRLKLRLRREVFNAVVLEQTHPVEFTVHDRLCDACARAQS NPDQWVAVVQLRQHVPHRRTFLYLEQLLLKHGQASLALRVAAAPGGLDFFFGSRSHAA RLVDFLATVAPVQTQTAKQLVSHDTKSNVYNYKHTFSVEICPICREDLIALSPQVSRD LGGLGPIVLCIKVTNAIALLDPLTLRVHHLEEKKYRVYNFKAALTSKQLVEYIVLDIE HESPEITIDGSRYQLAYAQVARVSDFGKNDTMFTVRTHLGHLLNPGDLALGYDLYGAN LNDDDMDTAMMRHSLPEVILVKKSFAKRPRTRRWKLKRLPMEEDAVNKAKGELEKRAD EYEEFLRDLEHNSDIRFQIDLYKDEDYRSEMASTIGDDVPTVPIEELIEDLSLGDDEE EDEGGEGNQHAVMVG</aaseq>|
DNA = <dnaseqindica>48..1619#gagatcccccaatccactcgattcgatccaatccggcgaggtacaggatgctgccggggtcggcggcgccggcggctgggagcggcatgttcgtgccaacgcagacggtgggcacggtgctgtgctgcatctgcggcgtggcgatgcagcccaacccggccaacatgtgcgcgcgctgcatccgcgcccgcgtcgacatcaccgagggcgtcccgcgccacgccgccgtcgtctactgccccgactgcacctcctacctccagccgccgcgctcctggctccgcgccggcccggagtcccccgagctcatgcagatcctcctccgccgcctcaaccgccccctcgcccgcctccgcgtctccctctccgccgccgagttcgtcttctccgagccccactccaagcgcctccgcctcaagctccgcctccgccgcgaggtcttcaacgccgtcgtcctcgagcagacccaccccgtcgagttcaccgtccacgatcgcctctgcgatgcctgcgcccgcgcccagtccaaccccgaccagtgggtcgccgtcgtccagctccgccagcacgtcccgcaccgccgcaccttcctctacctcgagcagctcctcctcaagcacggccaggcctccctcgccctccgcgtcgccgccgcccccggcggcctcgacttcttcttcggctcccgctcgcacgccgcccgcctcgtcgacttcctcgccaccgtcgcccccgtccagacccagaccgccaagcagctcgtctcccacgacaccaagagcaacgtctacaactacaagcacaccttctccgtcgagatctgccccatctgccgggaggacctcatcgcccttagccctcaggtgtcccgcgatcttggaggccttggacctatcgtcctctgcatcaaggtcaccaatgccatcgctctgcttgaccccctcaccctgcgtgtgcaccacctcgaggaaaagaagtacagggtctacaacttcaaggctgctctcaccagcaagcagctcgtcgagtacatcgtgctagacatcgagcacgagtcaccagagattaccattgacggatctcgctaccagttggcttatgcccaggtcgcccgggtctccgactttgggaaaaacgacaccatgttcaccgtgcggactcatcttggccacctgctgaatcctggagaccttgcccttgggtatgatctttatggtgccaacttgaatgatgatgacatggacacagctatgatgcgccacagtctgcctgaagtcattcttgttaagaagagcttcgccaagaggccacgcacacgccgatggaagctgaagaggcttccaatggaggaagatgctgtaaataaggccaagggggagctagagaagagggctgatgagtatgaggagtttctcagggacttggagcacaactctgatattagattccagattgatctatacaaggatgaggactacaggtcggagatggcatctactattggtgatgatgttcccactgtgccgattgaggaactaattgaggacctaagtcttggtgatgatgaggaggaggatgaaggtggggaaggcaaccaacatgctgttatggtgggatgagttaatatgtttacctgtgctgtgcttctgccttctggtgatggttgctgccaaccgcagatcataggtctgaactgcatctgtttaatccgtataagttttgttctcccctttacttctataagttataagttttgttgctaaattgtttcaacttttgctgtttctcatgatagatgttgtatcaccttatcctgtatctggtgttgcagcttggcttaaattatatttctctattcttattgtctgtgatatgttgttttcttgccatagtgtggctgatcacaacatatcttaaaatagatgcattgtttgatttccaaaacatctagtttggtgtttagattgtgccagattcatatttttactatatgtttttagtcccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001072005.1 RefSeq:Os10g0573900]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 10]]
[[Category:Chromosome 10]]

← Older revision		Revision as of 08:59, 13 June 2015
Line 46:		Line 46:
	[[Category:Japonica Chromosome 10]]		[[Category:Japonica Chromosome 10]]
	[[Category:Chromosome 10]]		[[Category:Chromosome 10]]
		+	==Structured Information==

@@ Line 16: / Line 16: @@
 ===Evolution===
-NMD3 is one of the highly conserved trans-acting factors and mediates the nuclear export of the 60S ribosomal subunit from yeast to plants <ref name="ref14" /><ref name="ref15" /><ref name="ref4" />. Through a BlastP search of the rice genome, the current work identified only one annotated NMD3 sequence with an open reading frame located at the locus LOC_Os10g42320 (Rice Genome Annotation Project, http://rice.plantbiology.msu.edu/) or Os10g0573900 (National Center for Biotechnology Information, http:// www.ncbi.nlm.nih.gov/). An unrooted phylogenetic tree was further constructed including the NMD3 from 18 representative species of bacteria, animals, and plants using the neighbour-joining method. OsNMD3 was clustered with sorghum NMD3 (SbNMD3) into a monophyletic clade that arose before the divergence of monocot and dicot phyla. Despite different evolutionary scenarios, OsNMD3 is conserved among the examined species. Within the length of 523 amino acids, OsNMD3 has four cysteine repeat motifs (Cx2C) at the N-terminus with an NLS (414–430 aa) and a leucine-rich NES (494–503 aa) at the C-terminus. These motifs are highly conserved among all eukaryotic cells, indicating that OsNMD3 may play roles in 60S ribosome dynamics that are similar to those reported in other species.
+NMD3 is one of the highly conserved trans-acting factors and mediates the nuclear export of the 60S ribosomal subunit from yeast to plants <ref name="ref14" /><ref name="ref15" /><ref name="ref4" />. Through a BlastP search of the rice genome, the current work identified only one annotated NMD3 sequence with an open reading frame located at the locus LOC_Os10g42320 (Rice Genome Annotation Project, http://rice.plantbiology.msu.edu/) or Os10g0573900 (National Center for Biotechnology Information, http://www.ncbi.nlm.nih.gov/). An unrooted phylogenetic tree was further constructed including the NMD3 from 18 representative species of bacteria, animals, and plants using the neighbour-joining method. OsNMD3 was clustered with sorghum NMD3 (SbNMD3) into a monophyletic clade that arose before the divergence of monocot and dicot phyla. Despite different evolutionary scenarios, OsNMD3 is conserved among the examined species. Within the length of 523 amino acids, OsNMD3 has four cysteine repeat motifs (Cx2C) at the N-terminus with an NLS (414–430 aa) and a leucine-rich NES (494–503 aa) at the C-terminus. These motifs are highly conserved among all eukaryotic cells, indicating that OsNMD3 may play roles in 60S ribosome dynamics that are similar to those reported in other species.
 ==Labs working on this gene==

@@ Line 6: / Line 6: @@
 In plants, the process of ribosome biogenesis has remained largely unknown; thus, the exploration of a conserved protein that has been well studied in other organisms is an optimal way to gain insight into ribosomal dynamics. NMD3 is such a protein due to its importance and conservation throughout eukaryotic species <ref name="ref2" /> <ref name="ref3" /> <ref name="ref4" />. Rice possesses one annotated NMD3 sequence with all representative motifs, including Cx2C repeats at the N-terminus as well as an NLS and NES at the C-terminus. Transient expression assays in rice protoplasts revealed that OsNMD3 shuttles between the nucleus and cytoplasm via CRM1/XPO1, demonstrating its conserved behaviour as a pre-60S nuclear export adaptor, as reported in other species. OsNMD3 was further found to interact with the 60S subunit via OsRPL10Ac1, and it co-sedimented with 60S and 80S ribosome components in ribosome profile analysis.
 [[File:Shijc-Os10g0573900-Fig2.jpeg|right|thumb|200px|'' OsNMD3 is nucleocytoplasmically localized. (from reference <ref name="ref1" />).'']]
-After being transported from the nucleus, NMD3 must be released from pre-60S particles. This process occurs in the cytoplasm and is an important step toward 60S ribosome maturation <ref name="ref5" /> <ref name="ref6" />. In eukaryotes, the conserved trans-factor NMD3 and eIF6/Tif6 bind to the joining interface with 40S subunit, which blocks premature translation. Release of NMD3 from pre-60S particles can trigger the following events: joining with 40S subunits, processing precursor rRNAs, and forming fully functional ribosomes. Therefore, this step is critical for controlling ribosomal quality for translation <ref name="ref7" /> <ref name="ref8" /> <ref name="ref9" />. RPL10 and the GTPase LSG1 have been implicated in the release of NMD3 <ref name="ref9" />. However, nothing thus far is known about how cytoplasmic maturation of 60S pre-particles occurs in plants. The current work found that OsNMD3ΔNLS was trapped in the cytoplasm. Therefore, truncated OsNMD3 disturbs the cytoplasmic maturation process of 60S particles and affects translational efficiency, which could be further supported by the following findings: (1) both OsNMD3 and OsNMD3ΔNLS bound to OsRPL10Ac1; surplus cytoplasmic OsNMD3ΔNLS may therefore bind to OsRPL10Ac1 and disturb its normal interaction with endogenous OsNMD3; (2) overexpression of OsNMD3 ΔNLS altered the ribosomal structure and interfered with the release of endogenous OsNMD3 from 60S subunits; the presence of OsNMD3ΔNLS in polysomes indicated that cytoplasmic OsNMD3ΔNLS might be loaded onto the ribosome by an unknown mechanism; and (3) transgenic plants showed a reduction in translational efficiency and altered ribosomal structure based on transactivation assays and pharmaceutical treatments with several antibiotics. The protein abundance of CESAs, which participate in cellulose biosynthesis, was significantly low in the OsNMD3ΔNLS transgenic lines, providing solid evidence that OsNMD3ΔNLS decreased the efficiency of protein synthesis. The observation of reduced cellulose content and altered sugar composition was similar to that reported in Arabidopsis plants overexpressing AtNMD3 ΔNES <ref name="ref4" />. However, the underlying mechanism differs because the latter was due to the obstruction of AtNMD3 nuclear export. Cell-wall biosynthesis is sensitive to the functionality of nascent ribosomes because these processes are likely to require rapid, abundant protein synthesis. Moreover, RNA sequencing was used to perform a genome-wide examination of the pathways affected by the aberrant 60S particles. The expression level of many factors involved in ribosomal biogenesis was significantly altered in the transgenic plants.
+After being transported from the nucleus, NMD3 must be released from pre-60S particles. This process occurs in the cytoplasm and is an important step toward 60S ribosome maturation <ref name="ref5" /> <ref name="ref6" />. In eukaryotes, the conserved trans-factor NMD3 and eIF6/Tif6 bind to the joining interface with 40S subunit, which blocks premature translation. Release of NMD3 from pre-60S particles can trigger the following events: joining with 40S subunits, processing precursor rRNAs, and forming fully functional ribosomes. Therefore, this step is critical for controlling ribosomal quality for translation <ref name="ref7" /> <ref name="ref8" /> <ref name="ref9" />. RPL10 and the GTPase LSG1 have been implicated in the release of NMD3 <ref name="ref9" />. However, nothing thus far is known about how cytoplasmic maturation of 60S pre-particles occurs in plants. The current work found that OsNMD3ΔNLS was trapped in the cytoplasm. Therefore, truncated OsNMD3 disturbs the cytoplasmic maturation process of 60S particles and affects translational efficiency, which could be further supported by the following findings: (1) both OsNMD3 and OsNMD3ΔNLS bound to OsRPL10Ac1; surplus cytoplasmic OsNMD3ΔNLS may therefore bind to OsRPL10Ac1 and disturb its normal interaction with endogenous OsNMD3; (2) overexpression of OsNMD3 ΔNLS altered the ribosomal structure and interfered with the release of endogenous OsNMD3 from 60S subunits; the presence of OsNMD3ΔNLS in polysomes indicated that cytoplasmic OsNMD3ΔNLS might be loaded onto the ribosome by an unknown mechanism; and (3) transgenic plants showed a reduction in translational efficiency and altered ribosomal structure based on transactivation assays and pharmaceutical treatments with several antibiotics. The protein abundance of CESAs, which participate in cellulose biosynthesis, was significantly low in the OsNMD3ΔNLS transgenic lines, providing solid evidence that OsNMD3ΔNLS decreased the efficiency of protein synthesis. The observation of reduced cellulose content and altered sugar composition was similar to that reported in Arabidopsis plants overexpressing AtNMD3 ΔNES <ref name="ref4" />. However, the underlying mechanism differs because the latter was due to the obstruction of AtNMD3 nuclear export. Cell-wall biosynthesis is sensitive to the functionality of nascent ribosomes because these processes are likely to require rapid, abundant protein synthesis. Moreover, RNA sequencing was used to perform a genome-wide examination of the pathways affected by the aberrant 60S particles<ref name="ref10" />. The expression level of many factors involved in ribosomal biogenesis was significantly altered in the transgenic plants.
 ===Transgenic Types===

@@ Line 22: / Line 22: @@
 ==References==
 <ref name="ref1"> Shi Y, Liu X, Li R, Gao Y, Xu Z, Zhang B, Zhou Y. Retention of OsNMD3 in the cytoplasm disturbs protein synthesis efficiency and affects plant development in rice. Journal of Experimental Botany, 2014, 65(12): 3055-3069. </ref>
 <ref name="ref2"> Johnson AW, Lund E, Dahlberg J. 2002. Nuclear export of ribosomal subunits.Trends in Biochemical Science 27, 580–585. </ref>
@@ Line 37: / Line 38: @@
 <ref name="ref14"> Ho JH, Johnson AW. 1999. NMD3 encodes an essential cytoplasmic protein required for stable 60S ribosomal subunits in Saccharomyces cerevisiae . Molecular Cell Biology 19, 2389–2399. </ref>
 <ref name="ref15">Thomas F, Kutay U. 2003. Biogenesis and nuclear export of ribosomal subunits in higher eukaryotes depend on the CRM1 export pathway. Journal of Cell Science 116, 2409–2419. </ref>
 ==Structured Information==

@@ Line 1: / Line 1: @@
-Please input one-sentence summary here.
+“OsNMD3”, a highly conserved trans-factor, the 60S ribosomal subunit nuclear export adaptor NMD3. <ref name="ref1" />
 ==Annotated Information==
 ===Function===
-Please input function information here.
+[[File:Shijc-Os10g0573900-Fig1.jpeg|right|thumb|200px|'' Expression of OsNMD3 ΔNLS GFP affects plant growth. (from reference <ref name="ref1" />).'']]
 ===Expression===
-Please input expression information here.
+The presence of NES and NLS motifs indicates that OsNMD3 is nucleocytoplasmically localized. This work therefore fused the green fluorescent protein (GFP) to the C-terminus of full-length OsNMD3 (OsNMD3GFP) and to the C-terminus of truncated OsNMD3 lacking either the NES (OsNMD3ΔNESGFP) or NLS (OsNMD3ΔNLSGFP) and transiently expressed the resulting constructs in rice protoplasts. Fluorescent signals of OsNMD3GFP were observed in both the nucleus and cytoplasm, whereas those of OsNMD3ΔNESGFP and OsNMD3ΔNLSGFP were trapped in the nucleus and cytoplasm, respectively. It has been reported that yeast NMD3 (ScNMD3) acts as a bridge between pre-60S subunits and the nuclear export factor CRM1/XPO1, and leptomycin B (LMB) could block this process <ref name="ref11" /><ref name="ref12" /><ref name="ref13" />. To investigate whether OsNMD3 shares a similar export pathway with ScNMD3, the current work treated rice protoplasts transiently expressing OsNMD3GFP with LMB and examined the distribution of GFP signals. In contrast to the control cells expressing GFP only, which showed GFP signals in both the nucleus and cytoplasm, the OsNMD3GFP signals were retained in the nucleus after treatment. Taken together, these data indicate that OsNMD3 shuttles between the nucleus and cytoplasm via CRM1/XPO1 and functions as a nuclear export adaptor for 60S ribosomal subunits.
 ===Evolution===
-Please input evolution information here.
+NMD3 is one of the highly conserved trans-acting factors and mediates the nuclear export of the 60S ribosomal subunit from yeast to plants <ref name="ref14" /><ref name="ref15" /><ref name="ref4" />. Through a BlastP search of the rice genome, the current work identified only one annotated NMD3 sequence with an open reading frame located at the locus LOC_Os10g42320 (Rice Genome Annotation Project, http://rice.plantbiology.msu.edu/) or Os10g0573900 (National Center for Biotechnology Information, http:// www.ncbi.nlm.nih.gov/). An unrooted phylogenetic tree was further constructed including the NMD3 from 18 representative species of bacteria, animals, and plants using the neighbour-joining method. OsNMD3 was clustered with sorghum NMD3 (SbNMD3) into a monophyletic clade that arose before the divergence of monocot and dicot phyla. Despite different evolutionary scenarios, OsNMD3 is conserved among the examined species. Within the length of 523 amino acids, OsNMD3 has four cysteine repeat motifs (Cx2C) at the N-terminus with an NLS (414–430 aa) and a leucine-rich NES (494–503 aa) at the C-terminus. These motifs are highly conserved among all eukaryotic cells, indicating that OsNMD3 may play roles in 60S ribosome dynamics that are similar to those reported in other species.
 ==Labs working on this gene==
-Please input related labs here.
+. State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
 ==References==
-Please input cited references here.
+<ref name="ref1"> Shi Y, Liu X, Li R, Gao Y, Xu Z, Zhang B, Zhou Y. Retention of OsNMD3 in the cytoplasm disturbs protein synthesis efficiency and affects plant development in rice. Journal of Experimental Botany, 2014, 65(12): 3055-3069. </ref>
 ==Structured Information==

@@ Line 40: / Line 40: @@
 </references>
 [[Category:Genes]]
 [[Category:Japonica mRNA]]

← Older revision		Revision as of 21:13, 22 July 2012
Line 1:		Line 1:
		+	Please input one-sentence summary here.
		+
		+	==Annotated Information==
		+	===Function===
		+	Please input function information here.
		+
		+	===Expression===
		+	Please input expression information here.
		+
		+	===Evolution===
		+	Please input evolution information here.
		+
		+	You can also add sub-section(s) at will.
		+
		+	==Labs working on this gene==
		+	Please input related labs here.
		+
		+	==References==
		+	Please input cited references here.
		+
		+	==Structured Information==
	{{JaponicaGene\|		{{JaponicaGene\|
	GeneName = Os10g0573900\|		GeneName = Os10g0573900\|