Structural and biochemical advances on the recruitment of the autophagy-initiating ULK and TBK1 complexes by autophagy receptor NDP52

The recruitment of Unc-51-like kinase and TANK-binding kinase 1 complexes is essential for Nuclear dot protein 52-mediated selective autophagy and relies on the specific association of NDP52, RB1-inducible coiled-coil protein 1, and Nak-associated protein 1 (5-azacytidine-induced protein 2, AZI2). However, the underlying molecular mechanism remains elusive. Here, we find that except for the NDP52 SKIP carboxyl homology (SKICH)/RB1CC1 coiled-coil interaction, the LC3-interacting region of NDP52 can directly interact with the RB1CC1 Claw domain, as that of NAP1 FIP200-binding region (FIR). The determined crystal structures of NDP52 SKICH/RB1CC1 complex, NAP1 FIR/RB1CC1 complex, and the related NAP1 FIR/Gamma-aminobutyric acid receptor-associated protein complex not only elucidate the molecular bases underpinning the interactions of RB1CC1 with NDP52 and NAP1 but also reveal that RB1CC1 Claw and Autophagy-related protein 8 family proteins are competitive in binding to NAP1 and NDP52. Overall, our findings provide mechanistic insights into the interactions of NDP52, NAP1 with RB1CC1 and ATG8 family proteins.

Download Full-text

Development of new tools to study lipidated mammalian ATG8

10.21203/rs.3.rs-221701/v1 ◽

2021 ◽

Author(s):

Sang-Won Park ◽

Pureum Jeon ◽

Akinori Yamasaki ◽

Hye Eun Lee ◽

Ji Young Mun ◽

...

Keyword(s):

Amyotrophic Lateral Sclerosis ◽

Light Chain ◽

Functional Significance ◽

Aminobutyric Acid ◽

Acid Receptor ◽

Receptor Associated Protein ◽

Selective Autophagy ◽

Selective Interaction ◽

Available Information ◽

Lateral Sclerosis

Abstract Mammals conserve multiple mammalian ATG8 proteins (mATG8s) consisting of γ-aminobutyric acid receptor-associated protein (GABARAP) and microtubule-associated protein 1 light-chain 3 (LC3) subfamilies that tightly bind to the autophagic membranes in a lipidated form. They are crucial in selective autophagy and recruit proteins bearing LC3-interacting region (LIR) motifs. However, because limited research tools are available, information about the specific roles of each lipidated mATG8 in selective autophagy is scarce. Here, we identified LIR motifs specific to the lipidated form of each mATG8 and characterized the residues critical for their selective interaction using cell-based assays and structural analyses. Then, we used these selective LIR motifs to develop probes and irreversible deconjugases that targeted selective lipidated mATG8s in the autophagic membrane, revealing that lipidated GABARAP subfamily proteins regulate aggrephagy of amyotrophic lateral sclerosis-linked protein aggregates. Our tools will be useful in elucidating the functional significance of each mATG8 protein in autophagy research.

Download Full-text

Role of gamma aminobutyric acid A receptor associated protein (GABARAP) in the podocytes of GABARAP Tg mice

Juntendo Medical Journal ◽

10.14789/pjmj.57.488 ◽

2011 ◽

Vol 57 (5) ◽

pp. 488-493

Author(s):

MIYUKI TAKAGI ◽

KATSUHIKO ASANUMA ◽

ISEI TANIDA ◽

YASUHIKO TOMINO

Keyword(s):

Aminobutyric Acid ◽

Gamma Aminobutyric Acid ◽

Receptor Associated Protein

Download Full-text

The gamma -aminobutyric acid type A (GABAA) receptor-associated protein (GABARAP) promotes GABAA receptor clustering and modulates the channel kinetics

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.190133497 ◽

2000 ◽

Vol 97 (21) ◽

pp. 11557-11562 ◽

Cited By ~ 142

Author(s):

L. Chen ◽

H. Wang ◽

S. Vicini ◽

R. W. Olsen

Keyword(s):

Gabaa Receptor ◽

Type A ◽

Aminobutyric Acid ◽

Gamma Aminobutyric Acid ◽

Channel Kinetics ◽

Receptor Clustering ◽

Receptor Associated Protein ◽

Acid Type

Download Full-text

Peroxisomal Atg37 binds Atg30 or palmitoyl-CoA to regulate phagophore formation during pexophagy

The Journal of Cell Biology ◽

10.1083/jcb.201307050 ◽

2014 ◽

Vol 204 (4) ◽

pp. 541-557 ◽

Cited By ~ 69

Author(s):

Taras Y. Nazarko ◽

Katharine Ozeki ◽

Andreas Till ◽

Geetha Ramakrishnan ◽

Pouya Lotfi ◽

...

Keyword(s):

Pichia Pastoris ◽

Membrane Protein ◽

Membrane Trafficking ◽

Protein Complex ◽

Receptor Protein ◽

Related Protein ◽

Peroxisomal Membrane ◽

Selective Autophagy ◽

Trafficking Pathway ◽

Human Orthologue

Autophagy is a membrane trafficking pathway that sequesters proteins and organelles into autophagosomes. The selectivity of this pathway is determined by autophagy receptors, such as the Pichia pastoris autophagy-related protein 30 (Atg30), which controls the selective autophagy of peroxisomes (pexophagy) through the assembly of a receptor protein complex (RPC). However, how the pexophagic RPC is regulated for efficient formation of the phagophore, an isolation membrane that sequesters the peroxisome from the cytosol, is unknown. Here we describe a new, conserved acyl-CoA–binding protein, Atg37, that is an integral peroxisomal membrane protein required specifically for pexophagy at the stage of phagophore formation. Atg30 recruits Atg37 to the pexophagic RPC, where Atg37 regulates the recruitment of the scaffold protein, Atg11. Palmitoyl-CoA competes with Atg30 for Atg37 binding. The human orthologue of Atg37, acyl-CoA–binding domain containing protein 5 (ACBD5), is also peroxisomal and is required specifically for pexophagy. We suggest that Atg37/ACBD5 is a new component and positive regulator of the pexophagic RPC.

Download Full-text

Cellular Sequences in Pestivirus Genomes Encoding Gamma-Aminobutyric Acid (A) Receptor-Associated Protein and Golgi-Associated ATPase Enhancer of 16 Kilodaltons

Journal of Virology ◽

10.1128/jvi.76.24.13069-13076.2002 ◽

2002 ◽

Vol 76 (24) ◽

pp. 13069-13076 ◽

Cited By ~ 29

Author(s):

Paul Becher ◽

Heinz-Jürgen Thiel ◽

Margaret Collins ◽

Joe Brownlie ◽

Michaela Orlich

Keyword(s):

Nonstructural Protein ◽

Cellular Protein ◽

Genomic Region ◽

Aminobutyric Acid ◽

Covalent Attachment ◽

Gamma Aminobutyric Acid ◽

Gaba A ◽

Receptor Associated Protein ◽

Diarrhea Virus ◽

Viral Sequences

ABSTRACT The presence of cellular protein coding sequences within viral RNA genomes is a unique and particularly interesting feature of cytopathogenic (cp) pestiviruses. Here we report the identification and characterization of two novel cellular sequences in the genomes of cp bovine viral diarrhea virus (BVDV) strains. In BVDV strain CP X604, we detected a duplication of the genomic region encoding NS3, NS4A, and part of NS4B, together with an insertion of sequences that code for cellular gamma-aminobutyric acid (A) receptor-associated protein [GABA(A)-RAP]. Transient-expression studies showed that the GABA(A)-RAP sequence leads to additional processing of the viral polyprotein and thereby to the expression of nonstructural protein NS3. Transfection of bovine cells with RNA transcribed from an infectious cDNA clone revealed that the GABA(A)-RAP-encoding insertion together with the duplicated viral sequences constitutes the genetic basis for the cytopathogenicity of strain CP X604. Surprisingly, molecular analysis of another cp BVDV strain (CP 721) resulted in the identification of a cellular Golgi-associated ATPase enhancer of 16 kDa (GATE-16)-encoding insertion together with duplicated viral sequences. To our knowledge, the genomes of CP X604 and CP 721 are the first viral RNAs found with cellular sequences encoding GABA(A)-RAP and GATE-16, respectively. Interestingly, the two cellular proteins belong to a family of eukaryotic proteins involved in various intracellular trafficking processes. Processing after the C-terminal glycine residue of GABA(A)-RAP and GATE-16 by cellular proteases is essential for covalent attachment to target molecules. Accordingly, it can be assumed that these cellular proteases also recognize the cleavage sites in the context of the respective viral polyproteins and thereby lead to the generation of NS3, the marker protein of cp BVDV.

Download Full-text

Borna Disease Virus P Protein Affects Neural Transmission through Interactions with Gamma-Aminobutyric Acid Receptor-Associated Protein

Journal of Virology ◽

10.1128/jvi.00877-08 ◽

2008 ◽

Vol 82 (24) ◽

pp. 12487-12497 ◽

Cited By ~ 22

Author(s):

Guiqing Peng ◽

Yan Yan ◽

Chengliang Zhu ◽

Shiqun Wang ◽

Xiaohong Yan ◽

...

Keyword(s):

Disease Virus ◽

Aminobutyric Acid ◽

Gamma Aminobutyric Acid ◽

Borna Disease Virus ◽

Acid Receptor ◽

Receptor Associated Protein ◽

P Gene ◽

P Protein ◽

Neural Transmission ◽

Borna Disease

ABSTRACT Borna disease virus (BDV) is one of the infectious agents that causes diseases of the central nervous system in a wide range of vertebrate species and, perhaps, in humans. The phosphoprotein (P) of BDV, an essential cofactor of virus RNA-dependent RNA polymerase, is required for virus replication. In this study, we identified the gamma-aminobutyric acid receptor-associated protein (GABARAP) with functions in neurobiology as one of the viral P protein-interacting cellular factors by using an approach of phage display-based protein-protein interaction analysis. Direct binding between GABARAP and P protein was confirmed by coimmunoprecipitation, protein pull-down, and mammalian two-hybrid analyses. GABARAP originally was identified as a linker between the gamma-aminobutyric acid receptor (GABAR) and the microtubule to regulate receptor trafficking and plays important roles in the regulation of the inhibitory neural transmitter gamma-aminobutyric acid (GABA). We showed that GABARAP colocalizes with P protein in the cells infected with BDV or transfected with the P gene, which resulted in shifting the localization of GABARAP from the cytosol to the nucleus. We further demonstrated that P protein blocks the trafficking of GABAR, a principal GABA-gated ion channel that plays important roles in neural transmission, to the surface of cells infected with BDV or transfected with the P gene. We proposed that during BDV infection, P protein binds to GABARAP, shifts the distribution of GABARAP from the cytoplasm to the nucleus, and disrupts the trafficking of GABARs to the cell membranes, which may result in the inhibition of GABA-induced currents and in the enhancement of hyperactivity and anxiety.

Download Full-text