Correction: The Autophagy Receptor TAX1BP1 and the Molecular Motor Myosin VI Are Required for Clearance of Salmonella Typhimurium by Autophagy

AlphaFold2-multimer guided high-accuracy prediction of typical and atypical ATG8-binding motifs

Macroautophagy/autophagy is an intracellular degradation process central to cellular homeostasis and defense against pathogens in eukaryotic cells. Regulation of autophagy relies on hierarchical binding of autophagy cargo receptors and adaptors to ATG8/LC3 protein family members. Interactions with ATG8/LC3 are typically facilitated by a conserved, short linear sequence, referred to as the ATG8/LC3 interacting motif/region (AIM/LIR), present in autophagy adaptors and receptors as well as pathogen virulence factors targeting host autophagy machinery. Since the canonical AIM/LIR sequence can be found in many proteins, identifying functional AIM/LIR motifs has proven challenging. Here, we show that protein modelling using Alphafold-Multimer (AF2-multimer) identifies both canonical and atypical AIM/LIR motifs with a high level of accuracy. AF2-multimer can be modified to detect additional functional AIM/LIR motifs by using protein sequences with mutations in primary AIM/LIR residues. By combining protein modelling data from AF2-multimer with phylogenetic analysis of protein sequences and protein-protein interaction assays, we demonstrate that AF2-multimer predicts the physiologically relevant AIM motif in the ATG8-interacting protein 2 (ATI-2) as well as the previously uncharacterized noncanonical AIM motif in ATG3 from potato (Solanum tuberosum). AF2-multimer also identified the AIM/LIR motifs in pathogen-encoded virulence factors that target ATG8 members in their plant and human hosts, revealing that cross-kingdom ATG8-LIR/AIM associations can also be predicted by AF2-multimer. We conclude that the AF2-guided discovery of autophagy adaptors/receptors will substantially accelerate our understanding of the molecular basis of autophagy in all biological kingdoms.

[Role of cytoskeleton in autophagy]

Cell autophagy plays a key role in maintaining intracellular nutritional homeostasis during starvation through elimination of aberrant or obsolete cellular structures. The cellular cytoskeleton has a crucial role in multiple processes involving membrane rearrangements and vesicle-mediated events. Autophagy is mediated by both microtubules and actin networks: microtubules promote the synthesis of autophagosome and are related to the movement of autophagosome; actin networks have been implicated in structurally supporting the expanding of phagophore, moving autophagosomes and enabling their efficient fusion with the lysosome; non-muscle myosinⅡoperates in the early stages of autophagy during the initiation and expansion of the phagophore, whereas myosinⅥ and myosin 1C are involved in the late stages of autophagosome maturation and fusion with the lysosome, respectively. This review summarizes the multiple regulation of cytoskeleton on autophagy and focuses on the regulation of autophagy by actin and myosin, providing a new approach for the study of pathogenesis and innovative therapies of autophagy related diseases.

Autophagy in Measles Virus Infection

Autophagy is a biological process that helps cells to recycle obsolete cellular components and which greatly contributes to maintaining cellular integrity in response to environmental stress factors. Autophagy is also among the first lines of cellular defense against invading microorganisms, including viruses. The autophagic destruction of invading pathogens, a process referred to as xenophagy, involves cytosolic autophagy receptors, such as p62/SQSTM1 (Sequestosome 1) or NDP52/CALCOCO2 (Nuclear Dot 52 KDa Protein/Calcium Binding And Coiled-Coil Domain 2), which bind to microbial components and target them towards growing autophagosomes for degradation. However, most, if not all, infectious viruses have evolved molecular tricks to escape from xenophagy. Many viruses even use autophagy, part of the autophagy pathway or some autophagy-associated proteins, to improve their infectious potential. In this regard, the measles virus, responsible for epidemic measles, has a unique interface with autophagy as the virus can induce multiple rounds of autophagy in the course of infection. These successive waves of autophagy result from distinct molecular pathways and seem associated with anti- and/or pro-measles virus consequences. In this review, we describe what the autophagy–measles virus interplay has taught us about both the biology of the virus and the mechanistic orchestration of autophagy.

β-catenin promotes intracellular bacterial killing via suppression of Pseudomonas aeruginosa-triggered macrophage autophagy

Objective

To investigate β-catenin-mediated bacterial elimination during Pseudomonas aeruginosa infection of macrophage-like RAW264.7 cells.

Methods

Cell viability and catenin beta 1 (CTNNB1) expression in RAW264.7 cells following P. aeruginosa infection versus uninfected cells, were detected by cell counting kit-8 assay and β-catenin Western blots. RAW264.7 cells with CTNNB1 overexpression were established with β-catenin lentivirus using flow cytometry and clonogenic limiting dilution assays. Bacterial killing was measured by plate counts; phagocytosis and nitric oxide (NO) were measured by flow cytometry; and reactive oxygen species (ROS) were measured using Griess reaction. Autophagy was determined by microtubule-associated protein 1 light chain 3 alpha-phosphatidylethanolamine conjugate (LC3-II) protein levels and formation of LC3 puncta, using Western blot and immunofluorescence staining.

Results

Following P. aeruginosa infection, RAW264.7 cell β-catenin levels were reduced in a time- and multiplicity of infection-dependent manner. CTNNB1 overexpression was associated with increased P. aeruginosa elimination, but had no effect on RAW264.7 cell phagocytosis, ROS and NO. CTNNB1 overexpression reduced LC3-II levels and formation of LC3 puncta, suggesting autophagy inhibition. Rapamycin/starvation-induced autophagy resulted in reduced bacterial killing following P. aeruginosa infection.

Conclusion

β-catenin may promote bacterial killing via suppression of P. aeruginosa-induced macrophage autophagy.