Abstract
ABSTRACTMacroautophagy/autophagy has been shown to mediate the selective lysosomal degradation of pathogenic bacteria and viruses (xenophagy), and to contribute to the activation of innate and adaptative immune responses. Autophagy can serve as an antiviral defense mechanism but also as a proviral process during infection. Atg8-family proteins play a central role in the autophagy process due to their ability to interact with components of the autophagy machinery as well as selective autophagy receptors and adaptor proteins. Such interactions are usually mediated through LC3-interacting region (LIR) motifs. So far, only one viral protein has been experimentally shown to have a functional LIR motif, leaving open a vast field for investigation. Here, we have developed the iLIR@viral database (http://ilir.uk/virus/) as a freely accessible web resource listing all the putative canonical LIR motifs identified in viral proteins. Additionally, we used a curated text-mining analysis of the literature to identify novel putative LIR motif-containing proteins (LIRCPs) in viruses. We anticipate that iLIR@viral will assist with elucidating the full complement of LIRCPs in viruses.
Highlights
Autophagy is a multistep process that consists of the isolation of cytoplasmic components into double-membrane vesicles, called autophagosomes, that shuttle to lysosomes, which serve as end-point degradative organelles
Two virus taxonomic systems have been used: the nomenclature used by the International Committee on Taxonomy of Viruses (ICTV) to name the species, genus and families of each of the viruses cited in the database, and the Baltimore classification system that groups viruses depending on their genome and kind of replication.[63,64]
For each specific family or group of viruses, the data are presented in a table containing (i) the clickable UniProtKB accession number of the protein, (ii) the information related to the LC3-interacting region (LIR)-motif (position, sequence, PSSM score, if the pattern is recognized as an xLIR or WxxL motif and the presence of the motif in an intrinsically disordered region (ANCHOR)), (iii) the name of the protein and (iv) the name of the species
Summary
Autophagy is a multistep process that consists of the isolation of cytoplasmic components into double-membrane vesicles, called autophagosomes, that shuttle to lysosomes, which serve as end-point degradative organelles. It is a catabolic mechanism that enables the removal of damaged or excess cellular organelles and proteins, thereby contributing to the maintenance of cell homeostasis and survival.[1]. The autophagic machinery is highly conserved from unicellular eukaryotes to metazoans. Among the proteins that take part in this process, the Atg8-family proteins play a central role.[2] these proteins are involved in the elongation and maturation of the autophagosome and its fusion with lysosomes.[1,3] Phosphatidylethanolamine-conjugated Atg8-family proteins reside on autophagosomal membranes where they can contribute to the recruitment of other core autophagy machinery proteins essential for the effective course of the autophagy process.[1,4,5,6,7]
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