| Literature DB >> 28806134 |
Anne-Claire Jacomin1, Siva Samavedam1, Hannah Charles1, Ioannis P Nezis1.
Abstract
Macroautophagy/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.Entities:
Keywords: AIM; Atg8; LC3-interacting region motif; LIR; LIR-containing protein; LIRCP; LRS; database; prediction; virus
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Year: 2017 PMID: 28806134 PMCID: PMC5640201 DOI: 10.1080/15548627.2017.1356978
Source DB: PubMed Journal: Autophagy ISSN: 1554-8627 Impact factor: 16.016
Figure 1.Screenshot of the iLIR@Viral database ‘Classification’ menu. Example for the ICTV classification system. The genera for which no LIRCPs were found appear in red.
Figure 2.Distribution of LIR motifs in viruses. (A) Representation of the number of LIR motifs per family (bar chart, plotted on the left axis) and total number of reviewed sequences from UniProt (dot chart, plotted on the right axis). (B) Proportion of xLIR (black) and WxxL (gray) across the different families. (C) Distribution of the W-, F- and Y-type of WxxL patterns across the different families (see also Table S4). (D) Distribution of the W-, F- and Y-type of xLIR patterns across the different families (see also Table S4).