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The rice Os01g0367100 has been reported as PHD1 in 2011. This gene 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


  • 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]

GO assignment(s): GO:0003978, GO:0019375, GO:0009507

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]).


  • in situ hybridization performed by Chunlai Li et al. showed that the PHD1 signal was detected in the shoot apical meristem and young leaves (Figure 2B), leaf mesophyll cells around vascular bundles (Figure 2C), young inflorescences (Figure 2D), and axillary buds (Figure 2E).[1]

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


  • 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.(Figure 3)[1]

Figure 3. Phylogenetic analysis of PHD1 (from reference[1]).

Subcellular Localization

  • Confocal micrographs showing chloroplast targeting of PHD1(Figure 4A). Rice protoplasts transformed with 35S::PHD1-GFP (upper panel) and 35S::GFP (lower panel) plasmids are shown. Chlorophyll autofluorescence (middle); GFP fluorescence (left); merged images (right). Bars = 5 µm. [1]
  • PHD1 protein distribution in chloroplast subfractions. Percoll-purified intact chloroplasts were lysed and subjected to differential centrifugation fractionation into envelope, stroma, and thylakoid fractions. Proteins were separated by SDS-PAGE, and blotted against the PHD1 antibody and specific chloroplast subcompartment protein antibodies. Tic 40 is an envelope membrane protein, RbcL a stroma protein, and PsbA a thylakoid membrane protein. HSP82 was used as a cytosolic protein marker. About 15 µg of total proteins from extrachloroplast (Ep), purified chloroplast (Cp), envelope (E), stroma (S), and thylakoid (T) subfractions were loaded per line. RbcL seen in the Ep fraction is most likely due to leakage from the stroma of broken chloroplasts. (Figure 4B)[1]
  • Immunogold localization of PHD1. Thin sections of chloroplasts in leaf mesophyll cells were incubated with PHD1 antibodies (Figure 4C and Figure 4D) and preimmune serum (Figure 4E and Figure 4F). The gold label is found preferentially associated with thylakoids of the chloroplasts as seen in (Figure 4D). Chl, chloroplast; Cyt, cytosol; Mit, mitochondria; CW, cell wall. Bar = 0.5 µm.[1]

Figure 4. Subcellular localization 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


  1. 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 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.

Structured Information