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.

Saleh Alseekh;Feng Zhu;José G.Vallarino;Ewelina M.Sokolowska;Takuya Yoshida;Susan Bergmann;Regina Wendenburg;Antje Bolze;Aleksandra Skirycz;Tamar Avin-Wittenberg;Alisdair R.Fernie

Max-Planck-Institute of Molecular Plant Physiology,14476 Potsdam-Golm,Germany;Center of Plant Systems Biology and Biotechnology,4000 Plovdiv,Bulgaria;National R&D Center for Citrus Preservation,Key Laboratory of Horticultural Plant Biology,Ministry of Education,Huazhong Agricultural University,430070 Wuhan,China;Boyce Thompson Institute,14850,Ithaca,US;Current Address:Department of Plant and Environmental Sciences,Alexander Silberman Institute of Life Sciences,The Hebrew University of Jerusalem,Givat Ram,Jerusalem,9190401

园艺研究（英文）

[1]Saleh Alseekh;Feng Zhu;José G.Vallarino;Ewelina M.Sokolowska;Takuya Yoshida;Susan Bergmann;Regina Wendenburg;Antje Bolze;Aleksandra Skirycz;Tamar Avin-Wittenberg;Alisdair R.Fernie-.Autophagy modulates the metabolism and growth of tomato fruit during development)[J].园艺研究（英文）,2022(01):352-365

ATG4,quinic,caffeoylquinic,vesiculation

Autophagy,modulates,metabolism,growth,tomato,during,development,Although,autophagy,conserved,mechanism,operating,across,eukaryotes,effects,crops,especially,their,has,received,relatively,little,attention,Indeed,whilst,few,recent,studies,have,systems,biology,tools,look,consequences,lack,maize,these,focused,leaf,tissues,rather,than,kernels,Here,utilized,interference,RNAi,generate,plants,that,were,deficient,regulating,protease,Plants,displayed,early,senescence,phenotype,yet,mild,changes,foliar,metabolome,characterized,by,reduced,yield,Metabolite,profiling,indicated,metabolites,leaves,just,exhibited,minor,alterations,while,bigger,compared,WT,detail,many,primary,decreases,lines,such,proline,tryptophan,phenylalanine,representative,secondary,acid,substantially,higher,levels,green,fruits,Moreover,transcriptome,analysis,most,prominent,differences,upregulation,organelle,degradation,genes,involved,proteasome,pathways,which,was,further,confirmed,chloroplastic,proteins,proteomics,data,Furthermore,integration,proteome,significantly,affected,lipid,chlorophyll,binding,biosynthesis,These,collectively,lead,propose,sophisticated,model,explain,cellular,ordination,process

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