Proteomic evidence for genetic epistasis: ClpR4 mutations switch leaf variegation to virescence in Arabidopsis

Authors

  • Wenjuan Wu,

    1. 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
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    • These authors contributed equally to this work.
  • Ying Zhu,

    1. 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
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    • These authors contributed equally to this work.
  • Zhaoxue Ma,

    1. 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
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  • Yi Sun,

    1. 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
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  • Quan Quan,

    1. Department of Chemistry, The University of Hong Kong, Hong Kong, China
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  • Peng Li,

    1. Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, , East China Normal University, Shanghai 200241, China
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  • Pengzhan Hu,

    1. Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, , East China Normal University, Shanghai 200241, China
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  • Tieliu Shi,

    1. Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, , East China Normal University, Shanghai 200241, China
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  • Clive Lo,

    1. School of Biological Sciences, The University of Hong Kong, Hong Kong, China
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  • Ivan K. Chu,

    1. Department of Chemistry, The University of Hong Kong, Hong Kong, China
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  • Jirong Huang

    Corresponding author
    1. 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
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Summary

Chloroplast development in plants is regulated by a series of coordinated biological processes. In this work, a genetic suppressor screen for the leaf variegation phenotype of the thylakoid formation 1 (thf1) mutant combined with a proteomic assay was employed to elucidate this complicated network. We identified a mutation in ClpR4, named clpR4-3, which leads to leaf virescence and also rescues the var2 variegation. Proteomic analysis showed that the chloroplast proteome of clpR4-3 thf1 is dominantly controlled by clpR4-3, providing molecular mechanisms that cause genetic epistasis of clpR4-3 to thf1. Classification of the proteins significantly mis-regulated in the mutants revealed that those functioning in the expression of plastid genes are oppositely regulated while proteins functioning in antioxidative stress, protein folding, and starch metabolism are changed in the same direction between thf1 and clpR4-3. The levels of FtsHs including FtsH2/VAR2, FtsH8, and FtsH5/VAR1 are greatly reduced in thf1 compared with those in the wild type, but are higher in clpR4-3 thf1 than in thf1. Quantitative PCR analysis revealed that FtsH expression in clpR4-3 thf1 is regulated post-transcriptionally. In addition, a number of ribosomal proteins are less expressed in the clpR4-3 proteome, which is in line with the reduced levels of rRNAs in clpR4-3. Furthermore, knocking out PRPL11, one of the most downregulated proteins in the clpR4-3 thf1 proteome, rescues the leaf variegation phenotype of the thf1 and var2 mutants. These results provide insights into molecular mechanisms by which the virescent clpR4-3 mutation suppresses leaf variegation of thf1 and var2.

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