A SlRBP1-SlFBA7/SlGPIMT module regulates fruit size in tomato

Abstract

Fleshy fruits are vital to the human diet, providing essential nutrients, such as sugars, organic acids, and dietary fibers. RNA-binding proteins play critical functions in plant development and environment adaption, but their specific contributions to fruit development remain largely unexplored. In this study, we centered on the function of SlRBP1 in tomato fruit and reported an unexpected finding that SlRBP1 controls fruit size by regulating its targets SlFBA7 and SlGPIMT. Here, the fruit-specific silencing of SlRBP1 was achieved by artificial miRNA which subsequently led to a marked reduction of fruit size. Cytological analysis suggested that SlRBP1 silencing decreased cell division and expansion of fruit pericarp. Those key genes involved in cell development were significantly repressed in SlRBP1 knock-down mutants. Furthermore, native RNA immunoprecipitation sequencing deciphered 83 SlRBP1-binding target RNAs in fruit, including two targets that are highly expressed in fruit: SlFBA7 and SlGPIMT, which are involved in developing fruit. Indeed, silencing either SlFBA7 or SlGPIMT resulted in fruit size reduction identical to that seen with SlRBP1 silencing. These results suggest that SlRBP1 modulates fruit size through its targets SlFBA7 and SlGPIMT. Our findings provide novel perspectives on the molecular mechanisms though which RNA-binding proteins control fruit size.

Acknowledgements

This work was supported by the National Key R&D Program of China (2022YFD2100100) and the National Natural Science Foundation of China (32472803).

Author contributions

K.C. and H.Z. designed experiments. K.C. was responsible for most of the experiments and data analysis. D.L. assisted the generation of transgenic plants. L.M. helped the plasmid construct. T.L. guided the analysis of RIP-seq data. J.L., Y.L., G.Z., L.M., G.Q., D.F., and B.Z. contributed by supplying essential materials and offering intellectual insights. K.C. wrote and H.Z. revised the manuscript.

Data availability

The raw sequence data of RNA-seq and nRIP-seq reported in this paper have been deposited in the Genome Sequence Archive [58] in National Genomics Data Center [59], China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences (GSA: CRA019577 and CRA019587) that are publicly accessible at https://ngdc.cncb.ac.cn/gsa.All data generated or analyzed during this study are included in the manuscript and supporting files (Figs S1-S7; Tables S1-S5).

Conflict of interests

The authors declare that they have no conflicts of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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