Difference between revisions of "Os01g0367100"

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Please input one-sentence summary here.
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The rice ''Os01g0367100'' has been reported as ''PHD1'' in 2011. ''PHD1'' encodes a novel chloroplast-localized UDP-glucose epimerase (UGE) which plays an  important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity.<ref name="ref1" />
  
 
==Annotated Information==
 
==Annotated Information==
 
===Function===
 
===Function===
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Please input function information here.
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* ''PHD1'' encodes a novel chloroplast-localized UDP-glucose epimerase (UGE), which is conserved in the plant kingdom. <ref name="ref1" />
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* ''PHD1'' plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity and will be useful for improving crop yields and for bioenergy crop engineering.<ref name="ref1" />
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===Wild Type VS. Mutant===
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* ''photoassimilate defective1'' (''phd1'') with both low carbohydrate contents and stunted growth was selected from rice T-DNA insertion mutant population (Oryza sativa var. Nipponbare background).<ref name="ref1" />
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* Scanning electron micrograph of culms demonstrated that fewer starch granules were deposited in parenchyma cells of the ''phd1'' mutants.
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* During the young seedling stage, both shoots and primary roots of the mutant were shorter and lighter than those of the wild type (Figure 1A).
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* After internode elongation, the ''phd1'' mutant exhibited a semi-dwarf, less grain-filling, retarded vegetative growth, later flowering, and less tillering phenotype (Figure 1B–1E).
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* In addition, although the grain number per panicle was not altered between the mutant and wild type, the seed-setting ratio of the phd1 mutant was significantly decreased, which finally led to a significant reduction of grain yield (Figure 1F, 1G).
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* Compared to wild type, mature leaves of the mutant had somewhat reduced sucrose (Figure 1H) and rather low starch levels (Figure 1I) at all time-points taken during the light/dark cycle.<br><br>
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[[File:Phd1_mutant_phenotypes.png|center|thumb|500px|'''Figure 1.''' ''phd1 mutant phenotypes (from reference<ref name="ref1" />).'']]
  
 
===Expression===
 
===Expression===
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Please input expression information here.
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* ''in situ'' hybridization performed by ''Chunlai Li'' et al. showed that the ''PHD1'' signal was detected in the shoot apical meristem and young leaves (B), leaf mesophyll cells around vascular bundles (C), young inflorescences (D), and axillary buds (E).<ref name="ref1" /><br><br>
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[[File:Expression_analysis_of_PHD1.png|center|thumb|500px|'''Figure 2.''' ''Expression analysis of PHD1 (from reference<ref name="ref1" />).'']]
  
 
===Evolution===
 
===Evolution===
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Please input evolution information here.
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* The phylogenetic analyses between ''PHD1'' and its 16 putative homologs  made by ''Chunlai Li'' et al. in 2011 showed that ''PHD1'' is closely related to ''Sb03g014730'' from sorghum and ''LOC100193101'' from maize.<ref name="ref1" />
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[[File:Phylogenetic_analysis_of_PHD1.png|center|thumb|500px|'''Figure 3.''' ''Phylogenetic analysis of PHD1 (from reference<ref name="ref1" />).'']]
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You can also add sub-section(s) at will.
 
  
 
==Labs working on this gene==
 
==Labs working on this gene==
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Please input related labs here.
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* State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
  
 
==References==
 
==References==
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Please input cited references here.
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<references>
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<ref name="ref1">
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Li C, Wang Y, Liu L, et al. A rice plastidial nucleotide sugar epimerase is involved in galactolipid biosynthesis and improves photosynthetic efficiency[J]. PLoS genetics, 2011, 7(7): e1002196.</ref>
  
 
==Structured Information==
 
==Structured Information==

Revision as of 15:12, 7 May 2014

The rice Os01g0367100 has been reported as PHD1 in 2011. PHD1 encodes a novel chloroplast-localized UDP-glucose epimerase (UGE) which plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity.[1]

Annotated Information

Function

  • PHD1 encodes a novel chloroplast-localized UDP-glucose epimerase (UGE), which is conserved in the plant kingdom. [1]
  • PHD1 plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity and will be useful for improving crop yields and for bioenergy crop engineering.[1]

Wild Type VS. Mutant

  • photoassimilate defective1 (phd1) with both low carbohydrate contents and stunted growth was selected from rice T-DNA insertion mutant population (Oryza sativa var. Nipponbare background).[1]
  • Scanning electron micrograph of culms demonstrated that fewer starch granules were deposited in parenchyma cells of the phd1 mutants.
  • During the young seedling stage, both shoots and primary roots of the mutant were shorter and lighter than those of the wild type (Figure 1A).
  • After internode elongation, the phd1 mutant exhibited a semi-dwarf, less grain-filling, retarded vegetative growth, later flowering, and less tillering phenotype (Figure 1B–1E).
  • In addition, although the grain number per panicle was not altered between the mutant and wild type, the seed-setting ratio of the phd1 mutant was significantly decreased, which finally led to a significant reduction of grain yield (Figure 1F, 1G).
  • Compared to wild type, mature leaves of the mutant had somewhat reduced sucrose (Figure 1H) and rather low starch levels (Figure 1I) at all time-points taken during the light/dark cycle.

Figure 1. phd1 mutant phenotypes (from reference[1]).

Expression

  • in situ hybridization performed by Chunlai Li et al. showed that the PHD1 signal was detected in the shoot apical meristem and young leaves (B), leaf mesophyll cells around vascular bundles (C), young inflorescences (D), and axillary buds (E).[1]

Figure 2. Expression analysis of PHD1 (from reference[1]).

Evolution

  • The phylogenetic analyses between PHD1 and its 16 putative homologs made by Chunlai Li et al. in 2011 showed that PHD1 is closely related to Sb03g014730 from sorghum and LOC100193101 from maize.[1]
Figure 3. Phylogenetic analysis of PHD1 (from reference[1]).

Labs working on this gene

  • State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China

References

<references> [1]

Structured Information

Gene Name

Os01g0367100

Description

Conserved hypothetical protein

Version

NM_001049575.1 GI:115436563 GeneID:4325727

Length

4900 bp

Definition

Oryza sativa Japonica Group Os01g0367100, 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 1

Location

Chromosome 1:15224863..15229762

Sequence Coding Region

15225149..15225258,15225348..15225412,15225538..15225623,15227720..15227808,15227921..15228032
,15228237..15228330,15228781..15228953,15229223..15229338,15229497..15229674

Expression

GEO Profiles:Os01g0367100

Genome Context

<gbrowseImage1> name=NC_008394:15224863..15229762 source=RiceChromosome01 preset=GeneLocation </gbrowseImage1>

Gene Structure

<gbrowseImage2> name=NC_008394:15224863..15229762 source=RiceChromosome01 preset=GeneLocation </gbrowseImage2>

Coding Sequence

<cdnaseq>atgggcggcgccgccgtctccagcctgcttgccaccccaacaccgacctctcgacctcgacccgtctccaccaccaccgcccccttctccgtcaacctctccaccgcagctgcccgcgcacctcgcctcctcctcctctcgcgccgccctcgccctcgccccgccgccgcggttctcggggtgtctgatgatacaggggtcaagatggctggctccgacattgttggcaagaacgatttgctgattgttggccctggagtgcttggtcgactggtagctgagaaatggcaggaggaacatccaggatgcaaagtttttggccagaccgcaagcacagatcaccacaacgaattgtcgaatattggcatcattccctccttgaagggatccacttttcctcagaaggttccatatgttattttctgtgctcccccatctcgttcggatgattaccctggggatgtgagagtagctgcctcaaattggactggtgaaggctctttcgtttttacatcaagtactgctctgtacgattgtagtgacaacgaattgtgcaatgaggattgcccatctgtgccaattggcagaagccctcgtactgacgtccttctaaaagcagagaatgttgttcttgaggcaggaggctgtgtcctcaggctagcaggactctataaaatagatagaggtgctcattttttttggttgaggaaaggaactttggacacacgaccagatcatattatcaatcaaattcattatgaggatgctgcttcccttgcaattgccataatgaaaaagggacacaggggtcgaatctttttgggctgtgacaataagcctctttccaggcaagaaataatggactctgttaacagaagtggaaaatttgacacgaagttccaaggttttactggtacagatggtccactgggtaagaagatggagaattcgagaactcgttctgagattggttgggagcccaagtatccaagcttcacagaattccttggtcttgacagttga</cdnaseq>

Protein Sequence

<aaseq>MGGAAVSSLLATPTPTSRPRPVSTTTAPFSVNLSTAAARAPRLL LLSRRPRPRPAAAVLGVSDDTGVKMAGSDIVGKNDLLIVGPGVLGRLVAEKWQEEHPG CKVFGQTASTDHHNELSNIGIIPSLKGSTFPQKVPYVIFCAPPSRSDDYPGDVRVAAS NWTGEGSFVFTSSTALYDCSDNELCNEDCPSVPIGRSPRTDVLLKAENVVLEAGGCVL RLAGLYKIDRGAHFFWLRKGTLDTRPDHIINQIHYEDAASLAIAIMKKGHRGRIFLGC DNKPLSRQEIMDSVNRSGKFDTKFQGFTGTDGPLGKKMENSRTRSEIGWEPKYPSFTE FLGLDS</aaseq>

Gene Sequence

<dnaseqindica>4505..4614#4351..4415#4140..4225#1955..2043#1731..1842#1433..1526#810..982#425..540#89..266#ctgctccaatccactctcctccgtttgcctgatccgatcccctcacctccgtccctgcttcctcccggcgaccaccgcccgccgcgcgatgggcggcgccgccgtctccagcctgcttgccaccccaacaccgacctctcgacctcgacccgtctccaccaccaccgcccccttctccgtcaacctctccaccgcagctgcccgcgcacctcgcctcctcctcctctcgcgccgccctcgccctcgccccgccgccgcggttctcggtaaccacatctctctctttctctctccacctcggattatcttgttctcctatgtttgcggtaccatgtaccatggtgagggtgagggtgcatgggaacgagatgggcttgcaatttgatgactctttgttacttgggttttggtacttccaatccaggggtgtctgatgatacaggggtcaagatggctggctccgacattgttggcaagaacgatttgctgattgttggccctggagtgcttggtcgactggtagctgagaaatggcaggaggtattattatcagattgcccgattgttatactctatctcagttatttaccttgtgtctcctattggtttaaacttcgaaaaccatattcctctttcatcgtgtggagcataatattttttttggttcaaaatggcgtatctacttttgttgcttctgtaatactaggatttttaatatttaatcttctgattaacataaaaaaatgatgccgcactgttaattcgtttaattgagtacaataataatgtacactgtccgtactctgtaggaacatccaggatgcaaagtttttggccagaccgcaagcacagatcaccacaacgaattgtcgaatattggcatcattccctccttgaagggatccacttttcctcagaaggttccatatgttattttctgtgctcccccatctcgttcggatgattaccctggggatgtgaggtaaatgagtacgattataatgatgaatccatgattatattactgttaacagtatcatcctaccttctggtatcatgtgagttcctaatggctaaggtccattggttactcctaaacatttattttctttttaacacataaactatccaaatttgtgtttatagtgtatagtggtattttgctaatgaatatgcctctggcaacatttgcttgtgggtgtaagtttcttttttgagaggaggggtttgaattcttttccttgaaggccagaaccatgatacgcaactctcttgcgtattcaagaaaaaaagaaccattccagaacaaaatattattgaatcattgttgtaatagttccattccaatgatatgaaccattcatctatcttgcactaatcgaaacgcatacatggacatgtgatgtattcttatttcagaaaatgcgtgcagagtagctgcctcaaattggactggtgaaggctctttcgtttttacatcaagtactgctctgtacgattgtagtgacaacgaattgtgcaatgaggtatccccacaagcctgcagattgtagctgtgaagtcttccatacttttctttttggctcttttcatttatagaagttctagtgacattaaaaaaaaaacaatgtatccacaagccatattatgcaactctaaatattttttcttgacggttgaaaaactttattgtttttgttttaaccataattattcctcccattatgtaggattgcccatctgtgccaattggcagaagccctcgtactgacgtccttctaaaagcagagaatgttgttcttgaggcaggaggctgtgtcctcaggctagcaggactctatatatcctcaattgatgactatttgttgttctaaagtgcaagcaatattaacgcaagttcttttacattggtatgaagagaactgatacaacgtttccttgacttggacacacaaaatagatagaggtgctcattttttttggttgaggaaaggaactttggacacacgaccagatcatattatcaatcaaattcattatgaggtaatgagctgcaagtttatctcagttatatgtcttgttatgctgttctttctttatctgtcgtatcatttgcattgtgatcacaactgtggaacttgggtttacttaccatacatagttggtactttttataatttagatctaacttgtttgattgtataaaagcatatgcaattccattttataatttatagtgcgttgagatacattcgacagtctaaattaagttgcaatatatcttattattgtaatctaggaaagaacttttcaacctactattctgtatcttatgttttggttgctttctattgtatatttcgatctctggttttatgaactcatgaggggtttccatgaccttatatatactcctaaatatgtagttatcactacattatcctaatacaaatagctgtaaactacccaaaatatcgaagaaaagaaatactgttctcacataacattttagattatactccctccatttctaaatatttgacgccgttgacttttttaaatatgtttgactgttcgtcttattcaaaaaatttaagtaattattaattcttttcctatcatttgattcattgttaaatatgcttttatgtatacatatagttttacatatttcacaaaagtttttgaataagacgaacggtcaaatatgtgctaaaaattcaacggtgtcaagaaacggagggagtatatagtaattggatatctcccaagagtcacttgcttggtcctagaaacaagctaggcaaagagtcctacattaatcagaaataatcattatcccacattaataaaaaaaatgggaacatcgtgatattgatagtccattttttagattgcacgtgacttggaggaaggttagtttattctagggagcaaaacaacagagctggtgtggcatttcagctatatttcaagcaaaagagtcaatatgtccaatataatttagttagaaatatctattgagcatttgggttaacgtgaaaaataacaaaatgtatttttacaaacagtttccagcccatggtcattgaattaaagacacaacttgttatcttttcaatagcagttttcttttctttttttaagaaaaaactggaatgacgcaaaactgtaagcaatatttctctgcaggaaacaacagttttgcacttgttttgggagagataaaatttcaaaattcgaaggtctgatgtttatggcatatctaaagggcctagggatctgtttgaccaattgtcttctttggccccgtttggtagagctccaaactccaactccagtgggagctagctcctataggagctaaggtggttgtgaaagtgtttggctagacttgttagcttcacaccaccacgtcccctgtagtcatttcgtcgaacacttggttagcgtcgccccaccgtcagcttgtgcaccaccaccgccgacgcccgccgccggcaccgccactggtcaccccgtgcgctgccaccacccagcccatgctgctgctgcccgccgctcgtgtccaccgccgtcgacgccaccagcccgcgcgccatcgcccggcacccagcccccgcgctgtcggccagccctcgcgccgccgccgaggccgcgtgctgccgctagcccgcgtgccgccatcgaggccgtgcgccgcctccgccagcctgcccgctgccggttgccgccggatctcgctagagatgatgggaggatgggaggagagagaatgtgaggaggagtttaggggtagtttagtggcatttttttggtaatacatcaaaaaaaattaaagggtagtgggtcttttggggtggagtggagctgtggagcagcaaaaacccagctccacccccgtattacaaatttgtggagcagccttgccaactctgctccaaaaaatagagaatctgtactttggcacagctctagctctaggtaagtaggagcgggagctggagctgtgccatacggggtctttatatcatcgtgtttccccatgggctttttcatgttcattgcatggggtggctatgatggctgtttaattagctgttagtattggtgtaattctttgtggtaattatttgcaggatgctgcttcccttgcaattgccataatgaaaaagggacacaggggtcgaatctttttgggctgtgacaataagcctctttccaggtcagtgctaggctacttgttttgactaattatttgtttcctacgtccacttagctgtgtatcatgactgcactaatagctgaacgggtctgtcaactgaaacaaaatttacttcaacttttcaggcaagaaataatggactctgttaacagaagtggaaaatttgacacgaagttccaaggttttactggttagtattctacatgttcatttatgcttatattttactccacaggcattcgcatctattgcataatcttcattctgccttaactgcaggtacagatggtccactgggtaagaagatggagaattcgagaactcgttctgagattggttgggagcccaagtatccaagcttcacagaattccttggtcttgacagttgacatgcttgtgtatgcttgcaaaaatcttcaactctaaatgaacagcaacacgttgtgaaccagttattttgttttgtttccattgcgttttttttaaaagacgtaaatactgtatatcttgttctgctatgtgcttatatcagttagcgttctaagtctgaccgttgtacaatggtttcggccagagaaatatttccacccgtgtcatgttggcctcgttctggtccgtccaacatctatttgtctctttgtaaccacatttgttatgaaaacttggtttcctttc</dnaseqindica>

External Link(s)

NCBI Gene:Os01g0367100, RefSeq:Os01g0367100

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 Li C, Wang Y, Liu L, et al. A rice plastidial nucleotide sugar epimerase is involved in galactolipid biosynthesis and improves photosynthetic efficiency[J]. PLoS genetics, 2011, 7(7): e1002196.
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