Abstract
Ribosomal phosphoprotein P1 (RPP1) is an integral component of the P-protein stalk in the 60S subunit of eukaryotic ribosomes and is required for the efficient elongation of translation. Previously, Arabidopsis RPP1A was revealed to be involved in the regulation of seed size and seed storage protein accumulation. In this work, the seedling growth analysis shows that the knockout mutation of Arabidopsis RPP1A significantly promoted seedling growth, particularly in the shoots. The label-free quantitative proteomic analysis demonstrated that a total of 593 proteins were differentially accumulated between the germinating seeds of the wild-type Col-0 and rpp1a mutant. And these proteins were significantly enriched in the intracellular transport, nitrogen compound transport, protein transport, and organophosphate metabolic process. The abundance of proteins involved in the RNA and protein processing processes, including ncRNA processing and protein folding, were significantly increased in the rpp1a mutant. Mutation in RPP1A highlighted the effects on the ribosome, energy metabolism, and nitrogen metabolism. The abundance of enzymes involved in glycolysis and pyruvate mechanism was decreased in the germinating seeds of the rpp1a mutant. Whereas the processes of amino acid biosynthesis, protein processing in endoplasmic reticulum, and biosynthesis of cofactors were enhanced in the germinating seeds of the rpp1a mutant. Taken together, the lack of RPP1A triggered changes in other ribosomal proteins, and the higher amino acid contents in the seedlings of the rpp1a mutant probably contributed to enhanced biosynthesis, processing, and transport of proteins, resulting in accelerated growth. Our results show the novel role of a P-protein and shed new light on the regulatory mechanism of seedling growth.
Key message
Knockout mutation of Arabidopsis RPP1A leads to more amino acid supply to support enhanced seedling growth.
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The datasets generated or analysed during the current study are available in the supplementary information files.
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Acknowledgements
The authors thank Ruonan Wang, Yuchen Fei, Caiwen Xue, Xin Zhang, Mingke Yan, and Yi Xiong for their help and discussion of the experiments.
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This work was supported by the National Natural Science Foundation of China (32070279, 31370280, 41401284), the Natural Science Foundation of Jiangsu Province (BK20221560), and the Project of Priority and Key Areas, Institute of Soil Science, Chinese Academy of Sciences (ISSASIP2206).
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PL contributed to the conception and design of this study. Material preparation, data collection, and bioinformatics analysis were performed by PL, LZ, PZ, YP, and BL. The first draft of the manuscript was written by LZ. All authors commented and modified the manuscript. All authors read and approved the final manuscript.
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Supplementary file1 Representative images showing the hypocotyl and root phenotypes of the wild-type Col-0, rpp1a-1, and rpp1a-2 mutants grown on ES agar medium. Photographs were taken 4, 6, and 8 days after germination (bar, 1 cm) (PDF 7611 KB)
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Supplementary file2 Comparison of proteomic profiles between the germinating seeds and young siliques. Venn diagram showing the intersection between total proteins (a), differentially accumulated proteins (DAPs) (b), and DAPs in the ribosome (c) identified between the wild-type Col-0 and rpp1a mutant in the germinating seeds and young siliques (PDF 405 KB)
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Supplementary file3 Total high-confidence proteins detected in the germinating seeds of the wild-type Col-0 and rpp1a mutant. (XLSX 2404 KB)
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Supplementary file4 Differentially accumulated proteins identified between the germinating seeds of the wild-type Col-0 and rpp1a mutant. (XLSX 32 KB)
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Supplementary file5 Gene ontology enrichment results of the differentially accumulated proteins, increased proteins, and decreased proteins identified between the germinating seeds of the wild-type Col-0 and rpp1a mutant (XLSX 26 KB)
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Zheng, L., Zhou, P., Pan, Y. et al. Proteomic profile of the germinating seeds reveals enhanced seedling growth in Arabidopsis rpp1a mutant. Plant Mol Biol 113, 105–120 (2023). https://doi.org/10.1007/s11103-023-01378-w
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DOI: https://doi.org/10.1007/s11103-023-01378-w