Flexible open conformation of the AP-3 complex explains its role in cargo recruitment at the Golgi

Schoppe, Jannis; Schubert, Evelyn; Apelbaum, Amir; Yavavli, Erdal; Birkholz, Oliver; Stephanowitz, Heike; Han, Yaping; Perz, Angela; Hofnagel, Oliver; Liu, Fan; Piehler, Jacob; Raunser, Stefan; Ungermann, Christian

doi:10.1016/j.jbc.2021.101334

Cited by 14 publications

(16 citation statements)

References 81 publications

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“…The effects of SYD-2 on APB-3 may be explained in two ways. AP-3 recruitment to membrane surfaces depends on binding to cargo proteins [ 82 ]. Therefore, after AP-3 has sorted cargo, SYD-2 may facilitate UNC-104 clustering, and thereby permit sufficient force generation to enable the exit of cargo proteins from an endosomal compartment.…”

Section: Discussionmentioning

confidence: 99%

LRK-1/LRRK2 and AP-3 regulate trafficking of synaptic vesicle precursors through active zone protein SYD-2/Liprin-α

Nadiminti,

Dixit,

Ratnakaran

et al. 2024

PLoS Genet

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Synaptic vesicle proteins (SVps) are transported by the motor UNC-104/KIF1A. We show that SVps travel in heterogeneous carriers in C. elegans neuronal processes, with some SVp carriers co-transporting lysosomal proteins (SV-lysosomes). LRK-1/LRRK2 and the clathrin adaptor protein complex AP-3 play a critical role in the sorting of SVps and lysosomal proteins away from each other at the SV-lysosomal intermediate trafficking compartment. Both SVp carriers lacking lysosomal proteins and SV-lysosomes are dependent on the motor UNC-104/KIF1A for their transport. In lrk-1 mutants, both SVp carriers and SV-lysosomes can travel in axons in the absence of UNC-104, suggesting that LRK-1 plays an important role to enable UNC-104 dependent transport of synaptic vesicle proteins. Additionally, LRK-1 acts upstream of the AP-3 complex and regulates its membrane localization. In the absence of the AP-3 complex, the SV-lysosomes become more dependent on the UNC-104-SYD-2/Liprin-α complex for their transport. Therefore, SYD-2 acts to link upstream trafficking events with the transport of SVps likely through its interaction with the motor UNC-104. We further show that the mistrafficking of SVps into the dendrite in lrk-1 and apb-3 mutants depends on SYD-2, likely by regulating the recruitment of the AP-1/UNC-101. SYD-2 acts in concert with AP complexes to ensure polarized trafficking & transport of SVps.

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Section: Discussionmentioning

confidence: 99%

LRK-1/LRRK2 and AP-3 regulate trafficking of synaptic vesicle precursors through active zone protein SYD-2/Liprin-α

Nadiminti,

Dixit,

Ratnakaran

et al. 2024

PLoS Genet

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“…The effects of SYD-2 on APB-3 may be explained in two ways. AP-3 recruitment to membrane surfaces depends on binding to cargo proteins (Schoppe et al ., 2021). Therefore, after AP-3 has sorted cargo, SYD-2 may facilitate UNC-104 clustering, and thereby permit sufficient force generation to enable exit of cargo proteins from an endosomal compartment.…”

Section: Discussionmentioning

confidence: 99%

Active zone protein SYD-2/Liprin-α acts downstream of LRK-1/LRRK2 to regulate polarized trafficking of synaptic vesicle precursors through clathrin adaptor protein complexes

Nadiminti

Dixit

Ratnakaran

et al. 2023

Preprint

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Synaptic vesicle proteins (SVps) are thought to travel in heterogeneous carriers dependent on the motor UNC-104/KIF1A. In C. elegans neurons, we found that some SVps are transported along with lysosomal proteins by the motor UNC-104/KIF1A. LRK-1/LRRK2 and the clathrin adaptor protein complex AP-3 are critical for the separation of lysosomal proteins from SVp transport carriers. In lrk-1 mutants, both SVp carriers and SVp carriers containing lysosomal proteins are independent of UNC-104, suggesting that LRK-1 plays a key role in ensuring UNC-104-dependent transport of SVps. Additionally, LRK-1 likely acts upstream of the AP-3 complex and regulates the membrane localization of AP-3. The action of AP-3 is necessary for the active zone protein SYD-2/Liprin-α to facilitate the transport of SVp carriers. In the absence of the AP-3 complex, SYD-2/Liprin-α acts with UNC-104 to instead facilitate the transport of SVp carriers containing lysosomal proteins. We further show that the mistrafficking of SVps into the dendrite in lrk-1 and apb-3 mutants depends on SYD-2, likely by regulating the recruitment of the AP-1/UNC-101. We propose that SYD-2 acts in concert with both the AP-1 and AP-3 complexes to ensure polarized trafficking of SVps.

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“…Considering the lengths of the cross-linker spacer and lysine side chains as well as a certain degree of in-solution flexibility not captured in the analyzed crystallographic or cryoEM structural snapshots, we set a maximum distance constraint of up to 35Å between Cα atoms of cross-linked residues. For structural mapping of the cross-links, we used the structures of the HOPS tethering complex (Shvarev et al, 2022), the AP-3 vesicle-forming complex (Schoppe et al, 2021), the PI3K complex II (Rostislavleva et al, 2015), and the EGO, SEA and TORC1 complexes , involved in signaling (Zhang et al, 2019;Tafur et al, 2022;Prouteau et al, 2023) (Figure 1C, Figure 1-S1 B). We excluded the V-ATPase in this analysis due to the co-existence of many conformational and rotational states.…”

Section: A Cross-linking Mass Spectrometry Map Of Vacuolar Protein In...mentioning

confidence: 99%

Yeast TLDc domain-containing proteins control assembly and subcellular localization of the V-ATPase

Klössel,

Zhu,

Amado

et al. 2023

Preprint

Self Cite

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Yeast vacuoles, equivalent to lysosomes in other eukaryotes, are important acidic degradative organelles as well as storage compartments and signaling hubs. To perform these functions, they rely on important protein complexes, including the V-ATPase, responsible for organelle acidification. In this study, we used cross-linking mass spectrometry to characterize the protein complexes of isolated vacuoles. We were able to detect many known protein-protein interactions, including known protein complexes, as well as undescribed ones. Among these, we identified the uncharacterized TLDc domain-containing protein Rtc5 as a novel interactor of the V-ATPase. We show that Rtc5 localizes to the vacuole membrane depending on N-myristoylation and on its interactions with the V-ATPase. We further analyzed the influence of this protein, and the second yeast TLDc domain-containing protein, Oxr1, on V-ATPase function. We find that both Rtc5 and Oxr1 promote the disassembly of the vacuolar V-ATPasein vivo, counteracting the role of the assembly chaperone, the RAVE complex. Finally, Oxr1 is necessary for the retention in the late Golgi complex of an organelle-specific subunit of the V-ATPase. Collectively, our results shed light on thein vivoroles of yeast TLDc domain-containing proteins in relation to the V-ATPase, highlighting the multifaceted regulation of this crucial protein complex.

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Flexible open conformation of the AP-3 complex explains its role in cargo recruitment at the Golgi

Cited by 14 publications

References 81 publications

LRK-1/LRRK2 and AP-3 regulate trafficking of synaptic vesicle precursors through active zone protein SYD-2/Liprin-α

LRK-1/LRRK2 and AP-3 regulate trafficking of synaptic vesicle precursors through active zone protein SYD-2/Liprin-α

Active zone protein SYD-2/Liprin-α acts downstream of LRK-1/LRRK2 to regulate polarized trafficking of synaptic vesicle precursors through clathrin adaptor protein complexes

Yeast TLDc domain-containing proteins control assembly and subcellular localization of the V-ATPase

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