Macroautophagy (hereafter referred to as autophagy) is the bulk degradation and recycling of cytoplasmic materials by forming a double membrane vesicle called the autophagosome. Autophagosome formation is regulated by the coordinated action of a set of proteins. ATG9A is the only multispanning transmembrane protein that plays an essential role in autophagosome formation, yet its function is largely elusive. Previous studies have shown that the C-terminus of ATG9A plays an important role in regulating its trafficking and proper function in autophagy. In line with that idea, we previously identified an AMPK- and ULK1- mediated phosphorylation on the C terminus of ATG9A at S761, which is required for proper ATG9A trafficking and autophagic flux. In our current study, we employed a BioID-based proteomics approach and identified a network of ATG9A C terminal interactors that include members of the ULK1 complex, ATG13, and ATG101, as well as protein complexes within the ER, Golgi, and endosomal trafficking pathways, many of which provide new insight into ATG9A trafficking mechanisms. We discovered that ATG9A exists with ATG13 and ATG101 in a separate subcomplex outside the canonical ULK1 complex. We show that the ATG13-ATG101 subcomplex regulates ATG9A trafficking and basal P62 degradation.

Autophagy, as the name suggests, is a cellular process of self-eating in which cytoplasmic debris is engulfed by a double membrane vesicle dubbed the autophagosome and is ultimately degraded and recycled by proteases in the lysosome. The process is initiated by a group of core ATG proteins, including a multi-pass transmembrane protein called ATG9A. Although ATG9A has been shown to be essential for both stress induced and basal autophagy, its mechanism and interaction network remain largely illusive. Our current study employs BioID proteomics to identify a network of interactors, including regulators of membrane fusion and vesicle trafficking, such as TRAPP, EARP, GARP, exocyst, AP-1 and AP-4 complexes, as well as members of the ULK1 autophagy kinase complex. Further investigations confirm that two components of the ULK1 complex, ATG13 and ATG101, directly interact with ATG9A. Using CRISPR, we show that deletion of ATG13 or ATG101 disrupts ATG9A trafficking and causes an accumulation of ATG9A at p62/SQSTM1-positive ubiquitin clusters. Lentivirus reconstitution and split-mVenus approaches using an ULK1 binding deficient mutant of ATG13 reveal that ATG9A interacts with ATG13 and ATG101 in an ULK1-independent manner. Together, these data reveal ATG9A interactions in vesicle trafficking and autophagy pathways, including a role for an ULK1- independent ATG13 complex in regulating ATG9A.

Paralogs are present during ribosome biogenesis as well as in mature ribosomes in form of ribosomal proteins, and are commonly believed to play redundant functions within the cell. Two previously identified paralogs are the protein pair Ssf1 and Ssf2 (94% homologous). Ssf2 is believed to replace Ssf1 in case of its absence from cells, and depletion of both proteins leads to severely impaired cell growth. Results reveal that, under normal conditions, the Ssf paralogs associate with similar sets of proteins but with varying stabilities. Moreover, disruption of their pre-rRNP particles using high stringency buffers revealed that at least three proteins, possibly Dbp9, Drs1 and Nog1, are strongly associated with each Ssf protein under these conditions, and most likely represent a distinct subcomplex. In this study, depletion phenotypes obtained upon altering Nop7, Ssf1 and/or Ssf2 protein levels revealed that the Ssf paralogs cannot fully compensate for the depletion of one another because they are both, independently, required along parallel pathways that are dependent on the levels of availability of specific ribosome biogenesis proteins. Finally, this work provides evidence that, in yeast, Nop7 is genetically linked with both Ssf proteins. / Les paralogues sont présents lors de la biogenèse des ribosomes ainsi que dans les ribosomes matures sous forme de protéines ribosomiques, et sont généralement censées jouer des fonctions redondantes dans la cellule. Deux paralogues précédemment identifiées sont la paire de protéines Ssf1 et Ssf2 (94 % d'homologie). Ssf2 remplacerait Ssf1 en cas d’absence du dernier dans la cellule, et l’absence des deux protéines diminue la croissance cellulaire. Nos résultats révèlent que, dans des conditions normales, les paralogues Ssf s’associent à des ensembles de protéines similaires, mais avec différentes stabilités. De plus, la perturbation de leurs particules pré-rRNP à l’aide de tampons de haute stringence a révélé qu'au moins trois protéines, probablement Dbp9, Drs1 et Nog1, sont fortement associées à chaque protéine Ssf dans ces conditions, et très probablement représentent des sous-complexes distincts. Dans cette étude, les phénotypes cellulaires observés lors de la déplétion des protéines Nop7, Ssf1 et/ou Ssf2 ont révélé que les paralogues Ssf ne peuvent pas compenser entièrement pour la diminution de l'autre, car ils sont, indépendamment l’un de l’autre, nécessaires le long de voies de biogénèse ribosomale parallèles qui dépendent des niveaux de protéines impliqués dans la biogénèse des ribosomes disponibles. Enfin, ce travail fournit des preuves que, dans la levure, Nop7 est génétiquement lié aux deux protéines Ssf.

[pt] Constatou-se que os atos piratas no Golfo da Guiné, especialmente em Nigéria, estão fortemente associados ao roubo de cargas de petróleo e à pilhagem das instalações de exploração do produto. As ações dos perpetradores de tais atos, como é o caso da Nigéria que se debruçou mais, visam atingir o Estado Federal e as multinacionais exploradoras do petróleo bruto nacional. Com base na Teoria dos Complexos Regionais de Segurança e nos conceitos teóricos sobre a securitização, procurou-se analisar a pirataria na região estudada como uma ameaça existencial socialmente construída e como um objeto securitizado por uma variedade de atores políticos (regionais e internacionais). O objetivo cabal é mostrar que, no atual contexto da corrida pelo petróleo no Golfo da Guiné, a securitização da pirataria provoca a despolitização de questões econômicas e sociais inerentes aos Estados locais e a ameaça suas soberanias e integridades territoriais. / [en] It was found that pirates acts in the Gulf of Guinea, especially in Nigeria, are strongly associated with the theft of oil cargo and the pillaging of the product exploration installations. The actions of the perpetrators of such acts, as is the case of Nigeria which leaned more, aim to achieve the Federal State and the multinationals exploiting the national crude oil. Based on the Theory of Regional Security Complex and on the theoretical concepts of securitization, we tried to analyze piracy in the region studied as a socially constructed existential threat and a securitized object by a variety of political actors (regional and international). The full goal is to show that, in the current context of the race for oil in the Gulf of Guinea, the securitization of piracy causes the depoliticization of economic and social issues related to local states and threatens their sovereignty and territorial integrity.