A NAC transcription factor, NOR-like1, is a new positive regulator of tomato fruit ripening

Authors: GAO, YING - China Agricultural University; WEI, WEI - China Agricultural University; ZHAO, XIAODAN - China Agricultural University; TAN, XIAO-LI - China Agricultural University; FAN, ZHONGQI - South China Agricultural University; ZHANG, YIPING - China Agricultural University; JING, YUAN - China Agricultural University; MENG, LANHUAN - China Agricultural University; ZHU, BENZHONG - China Agricultural University; ZHU, HONGLIANG - China Agricultural University; CHEN, JIANYE - South China Agricultural University; Jiang, Cai-Zhong; GRIERSON, DONALD - University Of Nottingham; LUO, YUNBO - China Agricultural University; FU, DA-QI - China Agricultural University

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/11/2018
Publication Date: 12/21/2018
Citation: Gao, Y., Wei, W., Zhao, X., Tan, X., Fan, Z., Zhang, Y., Jing, Y., Meng, L., Zhu, B., Zhu, H., Chen, J., Jiang, C., Grierson, D., Luo, Y., Fu, D. 2018. A NAC transcription factor, NOR-like1, is a new positive regulator of tomato fruit ripening. Horticulture Research. 5:75. https://doi.org/10.1038/s41438-018-0111-5.
DOI: https://doi.org/10.1038/s41438-018-0111-5

Interpretive Summary: The ripening of fleshy fruits not only enhances seed dispersal and reproductive efficiency but also provides a rich source of nutrients for human and animal diets, including the essential vitamins, minerals, flavor, aroma, phytonutrients and fiber. The process of fruit ripening is precisely regulated by a transcription factor network. To understand the mechanism of fruit ripening, several important ripening-associated mutants have been identified. The characterization of NON-RIPENING (nor), COLORLESS NON-RIPENING (cnr), and RIPENING INHIBITOR (rin) has opened the door to understanding the transcriptional regulation of fruit ripening. In addition, other ripening-associated TFs have recently been studied. NAC (NAM, ATAF, and CUC) is a plant-specific gene super family, and most NAC proteins contain a highly conserved N-terminal DNA-binding domain, and a variable C-terminal domain. NAC TFs have a variety of important developmental functions, such as shoot apical meristem development, cell expansion of specific flower organs and auxin-dependent formation of the lateral root system, and also in abiotic stress responses such as pathogen attack, wounding and drought stresses. The tomato genome contains approximately 94 NAC TFs. Recently RNAi- suppression of two tomato NAC domain protein genes, SlNAC1 and SlNAC4, resulted in delayed fruit ripening, including decreasing ethylene synthesis, suppressing chlorophyll degradation, and reducing carotenoids. Apart from these two ripening-associated NAC genes, there is no information about the possible role of other members of tomato NAC family associated with tomato fruit ripening. In this study, we used TRV-mediated VIGS to screen 31 additional NAC TFs candidate genes that were highly expressed during fruit ripening and found that silencing of one of them, SlNAC3, dramatically suppressed tomato fruit ripening. Two stable knockout mutants of slnac3 obtained by CRISPR/Cas9 showed a similar phenotype to the VIGS-SlNAC3 silenced fruit. Further study showed that SlNAC3 directly binds to the promoter of several genes involved in tomato ripening processes, including ethylene biosynthesis, color production and cell wall metabolism. Our data demonstrate that SlNAC3 positively regulates tomato fruit ripening.

Technical Abstract: Fruit ripening in tomato (Solanum lycopersicum) is regulated by a network of transcription factors (TFs). The NAC TF family (containing NAM, ATAF, and CUC) is one of the largest families of plant-specific TFs, It has been reported that SlNAC1and SlNAC4 can regulate tomato fruit ripening, but we wonder if other NAC members are also involved in fruit ripening. Here, we use virus-induced gene silencing (VIGS) to screen 31 additional NAC TF candidates that are highly expressed in the fruits, and found that silencing one of them, SlNAC3, inhibits fruit ripening. To further analyze the function of SlNAC3, CRISPR/Cas9 genome-editing tool was used to generate a knock-out mutant that displayed delayed time to break by more than 14 days compared to that of wild type. The fruits of the SlNAC3 mutant showed reduced ethylene production, slowed down fruit softening and inhibited lycopene accumulation. The RNA-seq profiling and promoter analysis suggested that some genes involved in ethylene biosynthesis (SlACS2 and SlACS4), color formation (SlGGPPS2 and SlSGR1) and cell wall metabolism (SlPG2a, SlPL, SlCEL2 and SlEXP1) could be the direct targets of SlNAC3. Results of EMSA and ChIP-qPCR assay confirmed this speculation. Taken together, our data demonstrated that SlNAC3 is an important positive regulator of tomato fruit ripening.