title: Characterization of early autophagy signaling by quantitative phosphoproteomics.
abstract: Under conditions of nutrient shortage autophagy is the primary cellular mechanism ensuring availability of substrates for continuous biosynthesis. Subjecting cells to starvation or rapamycin efficiently induces autophagy by inhibiting the MTOR signaling pathway triggering increased autophagic flux. To elucidate the regulation of early signaling events upon autophagy induction, we applied quantitative phosphoproteomics characterizing the temporal phosphorylation dynamics after starvation and rapamycin treatment. We obtained a comprehensive atlas of phosphorylation kinetics within the first 30 min upon induction of autophagy with both treatments affecting widely different cellular processes. The identification of dynamic phosphorylation already after 2 min demonstrates that the earliest events in autophagy signaling occur rapidly after induction. The data was subjected to extensive bioinformatics analysis revealing regulated phosphorylation sites on proteins involved in a wide range of cellular processes and an impact of the treatments on the kinome. To approach the potential function of the identified phosphorylation sites we performed a screen for MAP1LC3-interacting proteins and identified a group of binding partners exhibiting dynamic phosphorylation patterns. The data presented here provide a valuable resource on phosphorylation events underlying early autophagy induction.
authors.affiliation: Freiburg Institute for Advanced Studies (FRIAS); School of Life Sciences-LifeNet; Freiburg, Germany; ZBSA Center for Biological Systems Analysis; University of Freiburg; Freiburg, Germany.
authors.forename: Kristoffer Tg
authors.initials: KT
authors.lastname: Rigbolt
authors.affiliation: Freiburg Institute for Advanced Studies (FRIAS); School of Life Sciences-LifeNet; Freiburg, Germany; ZBSA Center for Biological Systems Analysis; University of Freiburg; Freiburg, Germany.
authors.forename: Mostafa
authors.initials: M
authors.lastname: Zarei
authors.affiliation: Freiburg Institute for Advanced Studies (FRIAS); School of Life Sciences-LifeNet; Freiburg, Germany; ZBSA Center for Biological Systems Analysis; University of Freiburg; Freiburg, Germany; Department of Dermatology; University Freiburg Medical Center; Freiburg, Germany.
authors.forename: Adrian
authors.initials: A
authors.lastname: Sprenger
authors.affiliation: Freiburg Institute for Advanced Studies (FRIAS); School of Life Sciences-LifeNet; Freiburg, Germany; ZBSA Center for Biological Systems Analysis; University of Freiburg; Freiburg, Germany.
authors.forename: Andrea C
authors.initials: AC
authors.lastname: Becker
authors.affiliation: Freiburg Institute for Advanced Studies (FRIAS); School of Life Sciences-LifeNet; Freiburg, Germany; ZBSA Center for Biological Systems Analysis; University of Freiburg; Freiburg, Germany.
authors.forename: Britta
authors.initials: B
authors.lastname: Diedrich
authors.affiliation: BIOSS Centre for Biological Signaling Studies; University of Freiburg; Freiburg, Germany.
authors.forename: Xun
authors.initials: X
authors.lastname: Huang
authors.affiliation: Freiburg Institute for Advanced Studies (FRIAS); School of Life Sciences-LifeNet; Freiburg, Germany; ZBSA Center for Biological Systems Analysis; University of Freiburg; Freiburg, Germany; BIOSS Centre for Biological Signaling Studies; University of Freiburg; Freiburg, Germany.
authors.forename: Sven
authors.initials: S
authors.lastname: Eiselein
authors.affiliation: Centre for High-throughput Biology; Department of Biochemistry and Molecular Biology; University of British Columbia; Vancouver, BC CA.
authors.forename: Anders R
authors.initials: AR
authors.lastname: Kristensen
authors.affiliation: Freiburg Institute for Advanced Studies (FRIAS); School of Life Sciences-LifeNet; Freiburg, Germany; ZBSA Center for Biological Systems Analysis; University of Freiburg; Freiburg, Germany.
authors.forename: Christine
authors.initials: C
authors.lastname: Gretzmeier
authors.affiliation: Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense, Denmark.
authors.forename: Jens S
authors.initials: JS
authors.lastname: Andersen
authors.affiliation: BIOSS Centre for Biological Signaling Studies; University of Freiburg; Freiburg, Germany.
authors.forename: Zhike
authors.initials: Z
authors.lastname: Zi
authors.affiliation: Freiburg Institute for Advanced Studies (FRIAS); School of Life Sciences-LifeNet; Freiburg, Germany; ZBSA Center for Biological Systems Analysis; University of Freiburg; Freiburg, Germany; Department of Dermatology; University Freiburg Medical Center; Freiburg, Germany; BIOSS Centre for Biological Signaling Studies; University of Freiburg; Freiburg, Germany.
authors.forename: Jörn
authors.initials: J
authors.lastname: Dengjel
mesh_terms: D001343:Autophagy / Q000187:drug effects*; D045744:Cell Line, Tumor; D006801:Humans; D010750:Phosphoproteins / Q000378:metabolism; D010766:Phosphorylation / Q000187:drug effects; D040901:Proteomics; D015398:Signal Transduction / Q000187:drug effects*; D020123:Sirolimus / Q000494:pharmacology*; D013217:Starvation / Q000378:metabolism; D013997:Time Factors
chemical_list: D010750:Phosphoproteins; D020123:Sirolimus
keywords: autophagy; bioinformatics; mass spectrometry; phosphoproteomics; phosphorylation; proteomics; signal transduction