Scientists reveal molecular and structural mechanisms of cargo recognition by autophagy receptor Nbr1
On June 25, 2021, Dr. YE Keqiong's team at the Institute of Biophysics (IBP), Chinese Academy of Sciences and Dr. DU Li-Lin's team at the National Institute of Biological Sciences (NIBS), Beijing, published a collaborative study in The EMBO Journal entitled "Molecular and structural mechanisms of ZZ domain-mediated cargo selection by Nbr1". The study discovered two new cargo proteins recognized by the autophagy receptor Nbr1 in fission yeast and revealed the structural mechanism of how a single ZZ domain of Nbr1 recognized two different proteins.
Cytoplasmic materials are transported to lysosomes or vacuoles in autophagy, which is important for cell homeostasis. Autophagy can be non-selective or selective in term of cargo specificity. In selective autophagy, cargos are specifically recognized by autophagy receptors. In 2015, Prof. DU Li-Lin's lab discovered a noncanonical selective autophagy pathway in fission yeast. The so-called Nbr1-mediated vacuolar targeting (NVT) pathway relies on the autophagy receptor Nbr1 to transport cytoplasmic hydrolases Ape2 and Lap2 from the cytosol into the vacuole. The NVT pathway relies on the endosomal sorting complexes required for transport (ESCRTs) but does not form autophagosomes as in the classic macroautophagy pathway. Several autophagy receptors have been discovered, but it is unclear how autophagy receptors specifically recognize cargos.
The newly published study found that the mannosidase Ams1 and aminopeptidase Ape4 are new cargos of the NTV pathway and they competitively bind to the first ZZ domain of Nbr1 (Nbr1-ZZ1). The researchers further determined the cryo-EM structures for Ams1 and Ape4 in complex with Nbr1-ZZ1. These structures show that Nbr1-ZZ1 not only uses a conserved acidic pocket to recognize the N-termini of Ams1 and Ape4, but also binds the cargos through cargo-specific interfaces. The two types of binding interfaces were confirmed by mutational experiments. This study unveiled a single-domain bispecific mechanism of autophagy cargo recognition and expanded the understanding of ZZ domain-mediated protein-protein interactions.
In the collaborative study, Prof. YE Keqiong at IBP and Prof. DU Li-Lin at NIBS were the corresponding authors and WANG Ying-Ying at NIBS and ZHANG Jianxiu at IBP were the co-first authors. The research was supported by National Natural Science Foundation of China, Strategic Priority Research Program of Chinese Academy of Sciences, National Key R&D Program of China, Chinese Ministry of Science and Technology and the Beijing municipal Government.
Figure. Cryo-EM structures of Ams1-Nbr1 and Ape4-Nbr1 complexes
Full text link: https://doi.org/10.15252/embj.2020107497
Contact: Ye Keqiong
Institute of Biophysics, Chinese Academy of Sciences
Beijing 100101, China
(Reported by Dr. Ye Keqiong's group)