10.6084/M9.FIGSHARE.14221726.V1
Di Peng
Di
Peng
Chen Ruan
Chen
Ruan
Shanshan Fu
Shanshan
Fu
Chengwen He
Chengwen
He
Jingzhen Song
Jingzhen
Song
Hui Li
Hui
Li
Yiran Tu
Yiran
Tu
Dachao Tang
Dachao
Tang
Lan Yao
Lan
Yao
Shaofeng Lin
Shaofeng
Lin
Ying Shi
Ying
Shi
Weizhi Zhang
Weizhi
Zhang
Hao Zhou
Hao
Zhou
Le Zhu
Le
Zhu
Cong Ma
Cong
Ma
Cheng Chang
Cheng
Chang
Jie Ma
Jie
Ma
Zhiping Xie
Zhiping
Xie
Chenwei Wang
Chenwei
Wang
Yu Xue
Yu
Xue
Atg9-centered multi-omics integration reveals new autophagy regulators in <i>Saccharomyces cerevisiae</i>
<p>In <i>Saccharomyces cerevisiae</i>, 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 <i>ATG9</i> 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 <i>ATG9</i> 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.</p> <p><b>Abbreviations:</b> 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.</p>
Biochemistry
Medicine
Cell Biology
Genetics
Molecular Biology
Biological Sciences not elsewhere classified
Developmental Biology
Taylor & Francis
2021
2021-03-16
2024-03-21
Dataset
17915403 Bytes
10.6084/m9.figshare.14221726
10.1080/15548627.2021.1898749
CC BY 4.0