Bioinformatics studies and tools

Viruses

Hulo, C., et al. (2011). "ViralZone: a knowledge resource to understand virus diversity." Nucleic Acids Res 39(Database issue): D576-582.

International Committee on Taxonomy of Viruses. and A. M. Q. King (2012). Virus taxonomy : classification and nomenclature of viruses : ninth report of the International Committee on Taxonomy of Viruses. London ; Waltham, MA, Academic Press.

LIR motifs

Behrends, C., et al. (2010). "Network organization of the human autophagy system." Nature 466(7302): 68-76.

Jacomin, A. C., et al. (2016). "iLIR database: A web resource for LIR motif-containing proteins in eukaryotes." Autophagy: 1-9.

Kalvari, I., et al. (2014). "iLIR: A web resource for prediction of Atg8-family interacting proteins." Autophagy 10(5): 913-925.

Popelka, H. and D. J. Klionsky (2015). "Analysis of the native conformation of the LIR/AIM motif in the Atg8/LC3/GABARAP-binding proteins." Autophagy 11(12): 2153-2159.

Xie, Q., et al. (2016). "hfAIM: A reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated Atg8-interacting motifs in various organisms." Autophagy 12(5): 876-887.

Reviews – Cellular self-defenses against invading pathogens and evading strategies

Deretic, V., et al. (2013). "Autophagy in infection, inflammation and immunity." Nat Rev Immunol 13(10): 722-737.

Randow, F. and P. J. Lehner (2009). "Viral avoidance and exploitation of the ubiquitin system." Nat Cell Biol 11(5): 527-534.

Randow, F., et al. (2013). "Cellular self-defense: how cell-autonomous immunity protects against pathogens." Science 340(6133): 701-706.

Reviews – Pro-/Anti-viral autophagy

Beljanski, V., et al. (2015). "The intersection between viral oncolysis, drug resistance, and autophagy." Biol Chem 396(12): 1269-1280.

Chiramel, A. I., et al. (2013). "Divergent roles of autophagy in virus infection." Cells 2(1): 83-104.

Dong, X. and B. Levine (2013). "Autophagy and viruses: adversaries or allies?" J Innate Immun 5(5): 480-493.

Jackson, W. T. (2015). "Viruses and the autophagy pathway." Virology 479-480: 450-456.

Lamiable, O. and J. L. Imler (2014). "Induced antiviral innate immunity in Drosophila." Curr Opin Microbiol 20: 62-68.

Lennemann, N. J. and C. B. Coyne (2015). "Catch me if you can: the link between autophagy and viruses." PLoS Pathog 11(3): e1004685.

Rey-Jurado, E., et al. (2015). "Contribution of autophagy to antiviral immunity." FEBS Lett 589(22): 3461-3470.

Richetta, C. and M. Faure (2013). "Autophagy in antiviral innate immunity." Cell Microbiol 15(3): 368-376.

Yordy, B., et al. (2013). "Autophagy and selective deployment of Atg proteins in antiviral defense." Int Immunol 25(1): 1-10.

Viruses inhibiting autophagy

Influenza virus:

Beale, R., et al. (2014). "A LC3-interacting motif in the influenza A virus M2 protein is required to subvert autophagy and maintain virion stability." Cell Host Microbe 15(2): 239-247.

Gannage, M., et al. (2009). "Matrix protein 2 of influenza A virus blocks autophagosome fusion with lysosomes." Cell Host Microbe 6(4): 367-380.

HIV-1

Borel, S., et al. (2015). "HIV-1 viral infectivity factor interacts with microtubule-associated protein light chain 3 and inhibits autophagy." AIDS 29(3): 275-286.

Campbell, G. R., et al. (2015). "Human Immunodeficiency Virus Type 1 Nef Inhibits Autophagy through Transcription Factor EB Sequestration." PLoS Pathog 11(6): e1005018.

Human cytomegalovirus

Chaumorcel, M., et al. (2012). "The human cytomegalovirus protein TRS1 inhibits autophagy via its interaction with Beclin 1." J Virol 86(5): 2571-2584.

Mouna, L., et al. (2016). "Analysis of the role of autophagy inhibition by two complementary human cytomegalovirus BECN1/Beclin 1-binding proteins." Autophagy 12(2): 327-342.

Murine cytomegalovirus

Fliss, P. M., et al. (2012). "Viral mediated redirection of NEMO/IKKgamma to autophagosomes curtails the inflammatory cascade." PLoS Pathog 8(2): e1002517.

Viruses activating autophagy

Review enteroviruses

Lai, J. K., et al. (2016). "The Autophagic Machinery in Enterovirus Infection." Viruses 8(2).

Coxsackievirus

Shi, X., et al. (2016). "Coxsackievirus B3 infection induces autophagic flux, and autophagosomes are critical for efficient viral replication." Arch Virol 161(8): 2197-2205.

Wong, J., et al. (2008). "Autophagosome supports coxsackievirus B3 replication in host cells." J Virol 82(18): 9143-9153.

Wu, H., et al. (2016). "Protein 2B of Coxsackievirus B3 Induces Autophagy Relying on Its Transmembrane Hydrophobic Sequences." Viruses 8(5).

Human rhinovirus

Klein, K. A. and W. T. Jackson (2011). "Human rhinovirus 2 induces the autophagic pathway and replicates more efficiently in autophagic cells." J Virol 85(18): 9651-9654.

Poliovirus

Taylor, M. P. and K. Kirkegaard (2007). "Modification of cellular autophagy protein LC3 by poliovirus." J Virol 81(22): 12543-12553.

Dengue virus

Panyasrivanit, M., et al. (2009). "Co-localization of constituents of the dengue virus translation and replication machinery with amphisomes." J Gen Virol 90(Pt 2): 448-456.

Hepatitis C virus

Quan, M., et al. (2014). "A functional role for NS5ATP9 in the induction of HCV NS5A-mediated autophagy." J Viral Hepat 21(6): 405-415.

Sir, D., et al. (2012). "Replication of hepatitis C virus RNA on autophagosomal membranes." J Biol Chem 287(22): 18036-18043.

Japanese encephalitis virus

Wang, X., et al. (2015). "Capsid, membrane and NS3 are the major viral proteins involved in autophagy induced by Japanese encephalitis virus." Vet Microbiol 178(3-4): 217-229.

Yellow fever virus

Ravindran, R., et al. (2014). "Vaccine activation of the nutrient sensor GCN2 in dendritic cells enhances antigen presentation." Science 343(6168): 313-317.

Zika virus

Hamel, R., et al. (2015). "Biology of Zika Virus Infection in Human Skin Cells." J Virol 89(17): 8880-8896.

Liang, Q., et al. (2016). "Zika Virus NS4A and NS4B Proteins Deregulate Akt-mTOR Signaling in Human Fetal Neural Stem Cells to Inhibit Neurogenesis and Induce Autophagy." Cell Stem Cell 19(5): 663-671.