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Article|13 Jun 2022|OPEN
Autophagy modulates the metabolism and growth of tomato fruit during development
Saleh Alseekh1,2 ,† , Feng Zhu1,3 ,† , José G. Vallarino1 , Ewelina M. Sokolowska1 , Takuya Yoshida1 , Susan Bergmann1 , Regina Wendenburg1 , Antje Bolze1 and Aleksandra Skirycz1,4 , Tamar Avin-Wittenberg1,5 , , Alisdair R. Fernie,1,2 ,
1Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
2Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
3National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070 Wuhan, China
4Boyce Thompson Institute, 14850, Ithaca, US
5Current Address: Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, 9190401
*Corresponding author. E-mail:,
Both authors contributed equally to the study.

Horticulture Research 9,
Article number: uhac129 (2022)
Views: 158

Received: 12 Jan 2022
Accepted: 29 May 2022
Published online: 13 Jun 2022


Although autophagy is a conserved mechanism operating across eukaryotes, its effects on crops and especially their metabolism has received relatively little attention. Indeed, whilst a few recent studies have used systems biology tools to look at the consequences of lack of autophagy in maize these focused on leaf tissues rather than the kernels. Here we utilized RNA interference (RNAi) to generate tomato plants that were deficient in the autophagy-regulating protease ATG4. Plants displayed an early senescence phenotype yet relatively mild changes in the foliar metabolome and were characterized by a reduced fruit yield phenotype. Metabolite profiling indicated that metabolites of ATG4-RNAi tomato leaves just exhibited minor alterations while that of fruit displayed bigger difference compared to the WT. In detail, many primary metabolites exhibited decreases in the ATG4-RNAi lines, such as proline, tryptophan and phenylalanine, while the representative secondary metabolites (quinic acid and 3-trans-caffeoylquinic acid) were present at substantially higher levels in ATG4-RNAi green fruits than in WT. Moreover, transcriptome analysis indicated that the most prominent differences were in the significant upregulation of organelle degradation genes involved in the proteasome or chloroplast vesiculation pathways, which was further confirmed by the reduced levels of chloroplastic proteins in the proteomics data. Furthermore, integration analysis of the metabolome, transcriptome and proteome data indicated that ATG4 significantly affected the lipid metabolism, chlorophyll binding proteins and chloroplast biosynthesis. These data collectively lead us to propose a more sophisticated model to explain the cellular co-ordination of the process of autophagy.