Structural Basis of the Autophagy-Related LC3/Atg13 LIR Complex: Recognition and Interaction Mechanism

Suzuki, Hisao; Tabata, Keisuke; Morita, Eiji; Kawasaki, Masato; Kato, Ryuichi; Dobson, Renwick C. J.; Yoshimori, Tamotsu; Wakatsuki, Soichi

doi:10.1016/j.str.2013.09.023

Cited by 99 publications

(113 citation statements)

References 50 publications

(55 reference statements)

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“…[46][47][48] Other core members of the autophagy machinery, Atg3, Atg32 in yeast or ATG4B, ATG7, and ATG13 in mammals, undergo LIR-dependent interactions with LC3 that potentially contribute to autophagy regulation. 17,21,22,[49][50][51] Moreover, some vesicle trafficking proteins, such as the RAB7-interacting protein FYCO1 or the GAP TBC1D5, interact with LC3 and play critical roles in intracellular trafficking of autophagosomes in a LIR-dependent manner. 52,53 Based on our data, interaction between PEBP1 and LC3 via the LIR motif might regulate the accessibility of free LC3 proteins for conjugation to PE, which is a critical step necessary for autophagosome biogenesis (depicted in Fig.…”

Section: Discussionmentioning

confidence: 99%

PEBP1, a RAF kinase inhibitory protein, negatively regulates starvation-induced autophagy by direct interaction with LC3

et al. 2016

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Autophagy plays a critical role in maintaining cell homeostasis in response to various stressors through protein conjugation and activation of lysosome-dependent degradation. MAP1LC3B/LC3B (microtubuleassociated protein 1 light chain 3 b) is conjugated with phosphatidylethanolamine (PE) in the membranes and regulates initiation of autophagy through interaction with many autophagy-related proteins possessing an LC3-interacting region (LIR) motif, which is composed of 2 hydrophobic amino acids (tryptophan and leucine) separated by 2 non-conserved amino acids (WXXL). In this study, we identified a new putative LIR motif in PEBP1/RKIP (phosphatidylethanolamine binding protein 1) that was originally isolated as a PE-binding protein and also a cellular inhibitor of MAPK/ERK signaling. PEBP1 was specifically bound to PE-unconjugated LC3 in cells, and mutation (WXXL mutated to AXXA) of this LIR motif disrupted its interaction with LC3 proteins. Interestingly, overexpression of PEBP1 significantly inhibited starvationinduced autophagy by activating the AKT and MTORC1 (mechanistic target of rapamycin [serine/ threonine kinase] complex 1) signaling pathway and consequently suppressing the ULK1 (unc-51 like autophagy activating kinase 1) activity. In contrast, ablation of PEBP1 expression dramatically promoted the autophagic process under starvation conditions. Furthermore, PEBP1 lacking the LIR motif highly stimulated starvation-induced autophagy through the AKT-MTORC1-dependent pathway. PEBP1 phosphorylation at Ser153 caused dissociation of LC3 from the PEBP1-LC3 complex for autophagy induction. PEBP1-dependent suppression of autophagy was not associated with the MAPK pathway. These findings suggest that PEBP1 can act as a negative mediator in autophagy through stimulation of the AKT-MTORC1 pathway and direct interaction with LC3.

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Section: Discussionmentioning

confidence: 99%

PEBP1, a RAF kinase inhibitory protein, negatively regulates starvation-induced autophagy by direct interaction with LC3

et al. 2016

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“…The five genes were then digested with SacI and HindIII (New England Biolabs) restriction enzymes and subcloned into the pET30⌬S.E. expression vector (28), purified using an agarose DNA extraction kit (Roche Applied Science), and ligated with T4 DNA ligase at 20°C for 30 min.…”

Section: Methodsmentioning

confidence: 99%

Conformational Dynamics and Allostery in Pyruvate Kinase

Donovan

Zhu

Liuni

et al. 2016

Journal of Biological Chemistry

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Pyruvate kinase catalyzes the final step in glycolysis and is allosterically regulated to control flux through the pathway. Two models are proposed to explain how Escherichia coli pyruvate kinase type 1 is allosterically regulated: the "domain rotation model" suggests that both the domains within the monomer and the monomers within the tetramer reorient with respect to one another; the "rigid body reorientation model" proposes only a reorientation of the monomers within the tetramer causing rigidification of the active site. To test these hypotheses and elucidate the conformational and dynamic changes that drive allostery, we performed time-resolved electrospray ionization mass spectrometry coupled to hydrogendeuterium exchange studies followed by mutagenic analysis to test the activation mechanism. Global exchange experiments, supported by thermostability studies, demonstrate that fructose 1,6-bisphosphate binding to the allosteric domain causes a shift toward a globally more dynamic ensemble of conformations. Mapping deuterium exchange to peptides within the enzyme highlight site-specific regions with altered conformational dynamics, many of which increase in conformational flexibility. Based upon these and mutagenic studies, we propose an allosteric mechanism whereby the binding of fructose 1,6-bisphosphate destabilizes an ␣-helix that bridges the allosteric and active site domains within the monomeric unit. This destabilizes the ␤-strands within the (␤/␣) 8 -barrel domain and the linked active site loops that are responsible for substrate binding. Our data are consistent with the domain rotation model but inconsistent with the rigid body reorientation model given the increased flexibility at the interdomain interface, and we can for the first time explain how fructose 1,6-bisphosphate affects the active site.

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“…Human ATG13 also contains a LIR motif [55]. The crystal structures of the ATG13 LIR bound to LC3A, B, and C have recently been determined [56]. The structure showed that the FVMI peptide sequence of ATG13 binds in an essentially identical manner to the corresponding WTHL peptide of p62.…”

Section: Structural Aspects Of Ulk1 Complex Componentsmentioning

confidence: 99%

Structure and function of the ULK1 complex in autophagy

Lin

Hurley

2016

Current Opinion in Cell Biology

207

159

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The ULK1 complex initiates autophagosome formation, linking cellular nutrient status to downstream events in autophagy. Recent work suggests that the ULK1 complex might also be activated in selective autophagy independent of nutrient or energy status. In this review we will discuss our current understanding of how the ULK1 complex is regulated by different signals, as well as how this complex then regulates other components of the autophagy machinery. Recently obtained structural data both on ULK1 and the orthologous yeast Atg1 complex are beginning to shed light on the higher-order organization of ULK1 complex. Ultimately, these insights might make it possible to understand how cargo organization and structure recruits and regulates ULK1 in selective autophagy initiation.

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Structural Basis of the Autophagy-Related LC3/Atg13 LIR Complex: Recognition and Interaction Mechanism

Cited by 99 publications

References 50 publications

PEBP1, a RAF kinase inhibitory protein, negatively regulates starvation-induced autophagy by direct interaction with LC3

PEBP1, a RAF kinase inhibitory protein, negatively regulates starvation-induced autophagy by direct interaction with LC3

Conformational Dynamics and Allostery in Pyruvate Kinase

Structure and function of the ULK1 complex in autophagy

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