Autophagy

Autophagy sequesters long-living miss-folded and aggregated proteins or/and damaged organelles (cargoes) into autophagosome – double-membrane vesicles, which, in turn, fuse with lysosomes to degrade the enclosed cargoes.

The latest studies showed that cells use different types of selective autophagy (e.g., autophagy selective for the degradation of specific types of cargoes (mitophagy – autophagy selective for degradation of mitochondria, aggrephagy – autophagy selective for protein aggregates, etc – Figure 1), as well as kind of nonselective autophagy, where all cellular components near the rapidly growing autophagosome are simply included. Selective autophagy assumes interplay between a few important players, linking the specific nonfunctional cellular component to the degradation machinery: First, the cargo, which frequently gets labeled for degradation by polyUbiquitin-chains. Second, autophagy receptors, which contain specific Ubiquitin-recognition domains (UBA, UBAN, etc). Additionally, the receptors possess a short semi-conserved sequence of amino acids, a so called LIR (LC3 Interaction Region) motif, to recognize the third autophagy players – Ubiquitin-like proteins of ATG8-family, called autophagy modifiers. Being represented in yeast with only one protein (ATG8), these modifiers are present in mammalian cells in several forms – LC3 (LC3A, LC3B and LC3C) and GABARAP (GABARAP, GABARAPL1 and GABARAPL2) related proteins. Similar to Ubiquitin, autophagy modifiers possess a β-sheet wrapped around a central α-helix. However, they have two additional, characteristic α-helices located N-terminally to their UBL core (Figure 2A). This N-terminal subdomain significantly varies among the different members of the LC3/GABARAP family and packs onto the UBL core to form a deep hydrophobic pocket (designated HP1). Another hydrophobic pocket (HP2) is formed by the hydrophobic residues of the central α-helix and β-strand 2 of the UBL core (Figure 2B). The two hydrophobic pockets and β-strand 2 of LC3/GABARAPs form a structural platform for recognition of various LIR motifs (Figure 3), engaging in interaction networks associated with autophagy and membrane trafficking. All three players – Ubiquitin, autophagy receptors and autophagy modifiers – are connected to each other by specific networks of protein-protein interactions (for review, see Mizushima et al., 2011; Rogov et al., 2014). These interactions are precisely regulated to provide a fast and specific answer to various cellular stresses.

In our institute we combine variety of structural (high-resolution NMR spectroscopy and X-ray analysis), biophysical (CD, ITC and SPR) and biochemical methods to understand basic molecular principles of selective autophagy on each it step: recognition of the marked for degradation cargoes by autophagy receptors, recognition of the charged autophagy receptors by autophagy modifiers, specificity and selectivity of the interactions between various LIRs (natural and artificial) and the autophagy modifiers, etc. We are investigating regulation of these specific autophagy interactions by post-translational modifications, chemical components, cellular compartmentalization, mutagenesis, etc. We are looking for physical connections between several key signaling pathways – ubiquitination, ufmylation and others – to selective autophagy.

The Institute of biophysical chemistry is a part of the several research programs aimed to investigate the autophagy and use it in therapeutic practice (SFB 1177, DKTK).

Selected publications:

Nix is a selective autophagy receptor for mitochondrial clearance. Novak I, Kirkin V, McEwan DG, Zhang J, Wild P, Rozenknop A, Rogov V, Löhr F, Popovic D, Occhipinti A, Reichert AS, Terzic J, Dötsch V, Ney PA, Dikic I. EMBO Rep. 2010 Jan;11(1):45-51. doi: 10.1038/embor.2009.256. Epub 2009 Dec 11.

Phosphorylation of the autophagy receptor optineurin restricts Salmonella growth. Wild P, Farhan H, McEwan DG, Wagner S, Rogov VV, Brady NR, Richter B, Korac J, Waidmann O, Choudhary C, Dötsch V, Bumann D, Dikic I. Science. 2011 Jul 8;333(6039):228-33. doi: 10.1126/science.1205405. Epub 2011 May 26.

Characterization of the interaction of GABARAPL-1 with the LIR motif of NBR1. Rozenknop A, Rogov VV, Rogova NY, Löhr F, Güntert P, Dikic I, Dötsch V. J Mol Biol. 2011 Jul 15;410(3):477-87. doi: 10.1016/j.jmb.2011.05.003. Epub 2011 May 18.

Structural basis for phosphorylation-triggered autophagic clearance of Salmonella. Rogov VV, Suzuki H, Fiskin E, Wild P, Kniss A, Rozenknop A, Kato R, Kawasaki M, McEwan DG, Löhr F, Güntert P, Dikic I, Wakatsuki S, Dötsch V. Biochem J. 2013 Sep 15;454(3):459-66.

Interactions between autophagy receptors and ubiquitin-like proteins form the molecular basis for selective autophagy. Rogov V, Dötsch V, Johansen T, Kirkin V. Mol Cell. 2014 Jan 23;53(2):167-78. doi: 10.1016/j.molcel.2013.12.014. Review.

CUL3-KBTBD6/KBTBD7 ubiquitin ligase cooperates with GABARAP proteins to spatially restrict TIAM1-RAC1 signaling. Genau HM, Huber J, Baschieri F, Akutsu M, Dötsch V, Farhan H, Rogov V, Behrends C. Mol Cell. 2015 Mar 19;57(6):995-1010. doi: 10.1016/j.molcel.2014.12.040. Epub 2015 Feb 12.

TECPR2 Cooperates with LC3C to Regulate COPII-Dependent ER Export. Stadel D, Millarte V, Tillmann KD, Huber J, Tamin-Yecheskel BC, Akutsu M, Demishtein A, Ben-Zeev B, Anikster Y, Perez F, Dötsch V, Elazar Z, Rogov V, Farhan H, Behrends C. Mol Cell. 2015 Oct 1;60(1):89-104. doi: 10.1016/j.molcel.2015.09.010.