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• W3136167826 abstract "In Saccharomyces cerevisiae, Atg9 is an important autophagy-related (Atg) protein, and interacts with hundreds of other proteins. How many Atg9-interacting proteins are involved in macroautophagy/autophagy is unclear. Here, we conducted a multi-omic profiling of Atg9-dependent molecular landscapes during nitrogen starvation-induced autophagy, and identified 290 and 256 genes to be markedly regulated by ATG9 in transcriptional and translational levels, respectively. Unexpectedly, we found most of known Atg proteins and autophagy regulators that interact with Atg9 were not significantly changed in the mRNA or protein level during autophagy. Based on a hypothesis that proteins with similar molecular characteristics might have similar functions, we developed a new method named inference of functional interacting partners (iFIP) to integrate the transcriptomic, proteomic and interactomic data, and predicted 42 Atg9-interacting proteins to be potentially involved in autophagy, including 15 known Atg proteins or autophagy regulators. We validated 2 Atg9-interacting partners, Glo3 and Scs7, to be functional in both bulk and selective autophagy. The mRNA and protein expressions but not subcellular localizations of Glo3 and Scs7 were affected with or without ATG9 during autophagy, whereas the colocalizations of the 2 proteins and Atg9 were markedly enhanced at early stages of the autophagic process. Further analyses demonstrated that Glo3 but not Scs7 regulates the retrograde transport of Atg9 during autophagy. A working model was illustrated to highlight the importance of the Atg9 interactome. Taken together, our study not only provided a powerful method for analyzing the multi-omics data, but also revealed 2 new players that regulate autophagy.Abbreviations: ALP: alkaline phosphatase; Arf1: ADP-ribosylation factor 1; Atg: autophagy-related; Co-IP: co-immunoprecipitation; Cvt: cytoplasm-to-vacuole targeting; DEM: differentially expressed mRNA; DEP: differentially expressed protein; DIC: differential interference contrast; E-ratio: enrichment ratio; ER: endoplasmic reticulum; ES: enrichment score; FC: fold change; FPKM: fragments per kilobase of exon per million fragments mapped; GAP: GTPase-activating protein; GFP: green fluorescent protein; GO: gene ontology; GSEA: gene set enrichment analysis; GST: glutathione S-transferase; HA: hemagglutinin; iFIP: inference of functional interacting partners; KO: knockout; LR: logistic regression; OE: over-expression; PAS: phagophore assembly site; PPI: protein-protein interaction; RFP: red fluorescence protein; RNA-seq: RNA sequencing; RT-PCR: real-time polymerase chain reaction; SCC: Spearman's correlation coefficient; SD-N: synthetic minimal medium lacking nitrogen; THANATOS: The Autophagy, Necrosis, ApopTosis OrchestratorS; Vsn: variance stabilization normalization; WT: wild-type." @default.
• W3136167826 created "2021-03-29" @default.
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• W3136167826 date "2021-03-15" @default.
• W3136167826 modified "2023-09-25" @default.
• W3136167826 title "Atg9-centered multi-omics integration reveals new autophagy regulators in<i>Saccharomyces cerevisiae</i>" @default.
• W3136167826 cites W115026104 @default.
• W3136167826 cites W1534340623 @default.
• W3136167826 cites W1534812231 @default.
• W3136167826 cites W1658504031 @default.
• W3136167826 cites W1855321011 @default.
• W3136167826 cites W1965661521 @default.
• W3136167826 cites W1967085696 @default.
• W3136167826 cites W1973268693 @default.
• W3136167826 cites W1975981696 @default.
• W3136167826 cites W1989150988 @default.
• W3136167826 cites W1990737378 @default.
• W3136167826 cites W1994423882 @default.
• W3136167826 cites W1999728854 @default.
• W3136167826 cites W2001467419 @default.
• W3136167826 cites W2001857946 @default.
• W3136167826 cites W2011580247 @default.
• W3136167826 cites W2012293083 @default.
• W3136167826 cites W2016610651 @default.
• W3136167826 cites W2017828774 @default.
• W3136167826 cites W2022829536 @default.
• W3136167826 cites W2026210863 @default.
• W3136167826 cites W2029777285 @default.
• W3136167826 cites W2029868511 @default.
• W3136167826 cites W2032700869 @default.
• W3136167826 cites W2033053971 @default.
• W3136167826 cites W2045200845 @default.
• W3136167826 cites W2056710301 @default.
• W3136167826 cites W2057764483 @default.
• W3136167826 cites W2065086182 @default.
• W3136167826 cites W2065841250 @default.
• W3136167826 cites W2066107334 @default.
• W3136167826 cites W2067490363 @default.
• W3136167826 cites W2076414670 @default.
• W3136167826 cites W2091896084 @default.
• W3136167826 cites W2096065711 @default.
• W3136167826 cites W2100305481 @default.
• W3136167826 cites W2109167860 @default.
• W3136167826 cites W2111362374 @default.
• W3136167826 cites W2112989471 @default.
• W3136167826 cites W2117513900 @default.
• W3136167826 cites W2122598723 @default.
• W3136167826 cites W2130410032 @default.
• W3136167826 cites W2131856634 @default.
• W3136167826 cites W2133922530 @default.
• W3136167826 cites W2137410525 @default.
• W3136167826 cites W2140729960 @default.
• W3136167826 cites W2140883620 @default.
• W3136167826 cites W2143013308 @default.
• W3136167826 cites W2144409921 @default.
• W3136167826 cites W2152600551 @default.
• W3136167826 cites W2152625175 @default.
• W3136167826 cites W2152719012 @default.
• W3136167826 cites W2165191318 @default.
• W3136167826 cites W2167088833 @default.
• W3136167826 cites W2170551349 @default.
• W3136167826 cites W2223119478 @default.
• W3136167826 cites W2318418872 @default.
• W3136167826 cites W2343949489 @default.
• W3136167826 cites W2524808906 @default.
• W3136167826 cites W2531883117 @default.
• W3136167826 cites W2532653761 @default.
• W3136167826 cites W2544360569 @default.
• W3136167826 cites W2575811048 @default.
• W3136167826 cites W2588205705 @default.
• W3136167826 cites W2604808360 @default.
• W3136167826 cites W2613479431 @default.
• W3136167826 cites W2621728938 @default.
• W3136167826 cites W2752326209 @default.
• W3136167826 cites W2758797028 @default.
• W3136167826 cites W2759116419 @default.
• W3136167826 cites W2768137245 @default.
• W3136167826 cites W2769700967 @default.
• W3136167826 cites W2793203740 @default.

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