Abstract
Autophagy is an evolutionarily conserved and highly regulated, intracellular catabolic mechanism that is important for maintaining homeostasis and coping with nutrient starvation. It is increasingly appreciated that autophagy can be highly selective, and that xenophagy, the selective autophagy of pathogens, is an important aspect of the immune response and protects against infection. This project will focus specifically on the selective autophagy of viruses.
The basis of selective autophagy is the LIR motif and interactions between this motif and Atg8-family proteins, such as LC3, contributes to the selection of specific cargoes for autophagic degradation.
An extensive literature search revealed 76 different viruses associated with selective autophagy. Using the Uniprot knowledgebase and the iLIR software, 29 viral proteins were found to contain LIR motifs. The probable functionality of these LIR motifs has been predicted, based on information provided by iLIR.
We have also hypothesised about the possible roles of the viral proteins during the autophagy process, with the aid of information gained from the literature search.
A deeper understanding of autophagy and how specific viral proteins interact with the autophagic machinery may provide therapeutic strategies and ultimately lead to the discovery of novel pharmacological agents to better treat many globally significant viral diseases.
Introduction
General background of autophagy
Autophagy is an evolutionarily conserved and highly regulated, intracellular catabolic mechanism that is important for cell survival. It enables damaged organelles, misfolded proteins and invading pathogens to be degraded; maintaining cellular homeostasis and protecting the cell from infection [1]. Most eukaryotic cells constitutively undergo autophagy at a low basal level. However, autophagy is upregulated when the cell senses stress such as nutrient starvation, ER stress or pathogen invasion. Autophagy may be thought of as a cellular ‘recycling factory’ that also promotes energy efficiency through ATP generation and mediates damage control by removing surplus or damaged proteins and organelles [2].
Autophagy has a fundamental importance in cellular homeostasis and signalling, hence it is highly relevant in a number of diseases; including neurodegenerative diseases, muscular dystrophy, cancer and processes such as development, ageing and innate immunity [3].
There are 3 defined types of autophagy – macroautophagy, microautophagy and chaperone-mediated autophagy, all of which promote proteolytic degradation of cytosolic components in lysosomes. This project will focus on macroautophagy (hereafter referred to as autophagy). Autophagy begins with the formation of the phagophore, a double-membrane structure, which elongates and closes around the cellular components to be degraded, forming the autophagosome. The autophagosome then fuses with a lysosome and resident hydrolases degrade the inner autophagosomal membrane and cellular contents. The fragments of cellular components are released and can be recycled by the cell to make other macromolecules and to replenish the cell with nutrients [4].
Much of what we know about autophagy has come from studying yeast (Saccharomyces cerevisiae). S.cerevisiae and other fungi are useful model organisms for studying autophagy because in vivo genetics work can be done quickly and easily [5]. Most of our current understanding of autophagy is due to work conducted on such organisms and multiple laboratories studying S.cerevisiae have discovered at least 36 autophagy-related (ATG) genes to date, 16 of which function in autophagy. The Atg proteins these genes encode are essential for various steps in the autophagy process and are generally classified into 6 groups:
- ULK1 kinase complex (consisting of ULK1, mAtg13, FIP200 and Atg101) which is required for induction of autophagy.
- Atg9 for membrane recycling.
- PI3K complex (Vsp34, Beclin1, Vsp15, Atg14) for vesicle nucleation.
- PI(3)P binding WIPI1/2 to aid phagophore assembly.
- Atg12-Atg5-Atg16L conjugation system for membrane expansion.
- Atg8 conjugation system involving Atg8-PE for autophagosome formation.
Mechanism of autophagy
The autophagy process is divided into distinct steps; including induction, autophagosome formation, autophagosome fusion with a lysosome, cargo breakdown, and the release of degraded cellular components back into the cytosol. (Fig. 1) Different sets of Atg proteins are involved in these steps and consist of the core autophagic machinery.
Figure 1 – Systematic diagram of autophagy. The isolation membrane/phagophore engulfs cytoplasmic components, and the resulting autophagosome fuse with a lysosome, resulting in the complete degradation of the sequestered cytoplasmic components by resident lysosomal hydrolases. http://www.med.niigata-u.ac.jp/bc1/eng/research/index.html
Autophagy induction
Autophagy occurs at a low level under normal physiological conditions, therefore, efficient induction of autophagy is required for organisms to adapt to stress and extracellular cues; including nutrient starvation, cellular stress and pathogen invasion. Signals such as nutrient limitation can induce non-selective autophagy, however the recognition of specific cargos, such as damaged organelles or invading pathogens can induce selective autophagy [6]. Insufficient autophagy can have deleterious consequences but excessive autophagy may also be harmful; therefore it needs to be tightly regulated in all eukaryotic cells [7].
Following the induction of autophagy, inhibition of mTOR leads to activation of the ULK kinase complex (UKC) at the ER membrane. The UKC then recruits the class III phosphatidylinositol 3-kinase (PI3K) complex, promoting formation of the omegasome, which appears to be the source of phagosomal membrane [8]. Atg14 directs class III PI3K, where it is phosphorylated by the UKC. The class III PI3K is activated via phosphorylation and induces the formation of phosphatidylinositol 3-phosphate (PI3P) at the ER membrane. In yeast as well as mammalian cells, autophagosomes are initiated at the phagophore assembly site (PAS); an example of a PAS in mammals is the omegasome [6]. LC3B-II produced by the Atg12-Atg5-Atg16L and the Atg8-PE conjugation systems is incorporated into the omegasome. The localization of the conjugation machinery on the isolation membrane requires UKC activity [9].
Upon mTOR inhibition by starvation, ULK1 and ULK2 become activated and phosphorylate Atg13 and FIP200, which are both important for autophagy activity. Atg101 is a newly discovered component of the ULKs-Atg13-FIP200 complex, and binds to and stabilizes Atg13, and is required for autophagy in mammalian cells [10].
Autophagosome formation
It is currently thought that double membrane autophagosomes are assembled by addition of new membrane and autophagosomal formation is considered to be the most complex step of autophagy. Multiple Atg proteins are recruited to the phagophore to participate in autophagosome formation, and this requires a highly regulated coordination between these proteins [11].
The class III phosphatidylinositol 3-kinase (PtdIns3K) complex is required for the nucleation and assembly of the initial phagophore membrane, this complex is composed of the PtdIns3K Vps34, p150, Atg14L and Beclin1. Dissociation of Beclin1 from Bcl-2 is required for autophagy induction, as Bcl-2 inhibits autophagy by binding and sequestering Beclin1. The PtdIns3K complex, together with Atg proteins, recruits two conjugation systems, Atg12-Atg5-Atg16L and Atg8-PE to the phagophore, these play a vital role in regulating the membrane elongation and expansion of the autophagosome [12] [13].
Atg8 controls the size of the autophagosome, as it determines membrane curvature of the forming autophagosome. The lipidation of Atg8 and LC3 (the mammalian Atg8 homolog) is widely used to monitor the induction of autophagy [13].
Autophagosome fusion with lysosome and cargo degradation
Once the autophagosome has formed, Atg8 which is attached to the outer membrane is cleaved from PE by Atg4 and is released back into the cytosol. In mammalian cells, the autophagosome-lysosome fusion event requires the lysosomal membrane protein LAMP-2 and Rab7 [14].
Following fusion, the cytoplasmic components are degraded inside the autolysosome by resident hydrolyses, including cathepsin B, D and L in mammalian cells. The breakdown products from the degradation, particularly amino acids, are transported back into the cytosol for protein synthesis and maintenance of cellular functions under starvation conditions [15].
Autophagy as a selective process
It was previously considered that autophagy was a largely non-selective, bulk degradation mechanism. However, the gathering body of evidence suggests that autophagy is much more selective than initially appreciated, following an array of papers describing various types of selective autophagy [16] [17] [18] [19].
Autophagy can be either non-selective or selective. Non-selective autophagy occurs when the cell is under nutrient stress and it needs to degrade surplus cellular component and recycle them. Selective autophagy occurs when there is something in particular that the cell wants to remove, specific substrates are tagged and targeting to the autophagy pathway. (Fig. 2)
Aggrephagy (selective degradation of misfolded proteins), mitophagy (selective autophagy of mitochondria), xenophagy (selective autophagy of bacteria and viruses), reticulophagy (selective autophagy of the ER), pexophagy (selective autophagy of peroxisomes) are all different types of selective autophagy. This project will focus on xenophagy, in particular the selective autophagy of viruses.
Figure 2 – Overview of selective autophagy in mammalian cells. Activation of the complex between ULK1–ULK2 and the scaffold proteins Atg13, FIP200 and Atg101 is essential for the induction of autophagy. At the nucleation step, proteins and lipids are recruited to the phagophore. The class III phosphatidylinositol 3-kinase (PI3K) complex, containing Vps34, Vps15, Beclin-1 and Atg14L, generates PtdIns(3)P at the phagophore. PtdIns(3)P is required for the recruitment of WD-repeat proteins that interact with phosphoinositides (WIPIs). Expansion of the phagophore depends on two ubiquitin-like (Ubl) conjugation systems, Atg12-Atg5-Atg16L and Atg8-PE (boxed). Conjugation of Atg5 to Atg12, which requires Atg7 and Atg10, generates an oligomeric complex between the Atg12–Atg5 conjugate and Atg16L1. Atg8/LC3 proteins are subsequently conjugated to phosphatidylethanolamine (PE) following cleavage by Atg4. The cargo for selective autophagy is recruited to the inner, concave, surface of the growing phagophore by autophagy receptors that are associated both with the cargo and with lipidated Atg8/LC3 (LC3 II). The phagophore expands and encloses its cargo to form the double-membrane autophagosome. Fusion of the autophagosome with the lysosome forms an autolysosome where the enclosed cargo is degraded by resident hydrolases [24].
LIR motif
The basis of selective autophagy is the LIR motif. The LIR motif is present in adapter molecules/cargo receptors such as p62 and NBR1; these interact with cargo proteins to be degraded, taking them to the phagophore by interacting with LC3 embedded in the phagophore membrane [20]. (Fig. 3) The interaction between the autophagic cargo receptors and Atg8-family proteins (including LC3) through LIR motifs contributes to the selection of specific cargoes for autophagic degradation.
Figure 3 – Simplistic representation of selective autophagy. An adapter molecule such as p62 or NBR1 containing an LIR motif binds to cargo protein needing to be degraded. The LIR motif interacts with LC3 on phagophore membrane and enables autophagy to be selective. (Author’s own)
In addition to cargo receptors, LIR motifs can also be found in members of the basal autophagy apparatus, proteins associated with vesicles and of their transport, Rab GTPase activating proteins (GAPs) and specific signalling proteins that are degraded by selective autophagy [21].
Studying p62 and NBR1 has provided mechanistic insight into the process of selective autophagy as both are selectively degraded and are able to act as cargo receptors for the degradation of ubiquitinated cargo proteins. The interaction between the LIR motif of cargo receptors and LC3 is essential for selective autophagy [22].
The consensus sequence of the core LIR motif is (W/F/Y)XX(L/I/V) and in all characterised LIR motifs, this linear sequence is surrounded by at least one acidic residue [13].
LIR motifs utilize two sets of hydrophobic residues (Trp/Phe/Tyr and Leu/Ile/Val) to contact two hydrophobic surfaces, the W- and L-sites on Atg8-family proteins (e.g. LC3) [23]. These are highly conserved residues among Atg8-family proteins, particularly those constructing the W- site. It is believed that these two hydrophobic pockets are a conserved feature of Atg8-family proteins [20]. All Atg8-family proteins have an exposed β-strand (β2), which is responsible for binding the LIR motif of cargo receptors through an intermolecular β-sheet. X-ray and NMR structural analysis of the LC3-p62 LIR bond revealed that the LIR motif of p62 adopts an extensive β-conformation and forms an intermolecular parallel β-sheet with β2 of LC3. (Fig. 4)
LIR-LC3 interactions are important in cargo recognition during selective autophagy but they are also required for the maturation of the autophagosome. LIR motif of factors involved in the autophagy machinery (e.g. the ULK1–ULK2 complex or ATG4) interact with Atg8 proteins, which then recruit effector proteins to the outer membrane, this is needed for the autophagosome to fuse with a lysosome so the cytosolic cargo can be degraded [24].
Figure 4 – LIR binding site of LC3. The W- and L-site of LC3 are vital in allowing the LIR motif of cargo receptors to bind. The LIR motif of cargo receptors adopts an extensive β-conformation and forms an intermolecular parallel β-sheet with β2 (in blue) of LC3. Important amino acid residues for the LIR-LC3 interaction are shown. [24]
Xenophagy
Xenophagy is the selective autophagy of invading bacteria and viruses, and is an important aspect of the hosts’ innate immune response to protect against infection. Autophagy also plays a vital role in antigen processing and presentation for CD4 and CD8 T cells, an important part of the adaptive immune response.
Selective autophagy of bacteria
Bacteria have been identified as targets for selective autophagy and this process is an important mechanism by which bacteria are removed from the body, helping to combat infection by various pathogenic bacteria [25]. However, many bacteria have developed a diverse range of strategies to avoid autophagy, by interfering with autophagy signalling or the autophagy machinery, and some bacteria can even exploit autophagy to benefit their own growth [26]. Certain bacteria can inhibit the signalling pathways that lead to the induction of autophagy, hiding themselves from autophagy recognition using host proteins or by blocking fusion of the autophagosome with the lysosome to prevent bacterial degradation.
An extracellular bacterium that invades inside a host cell is taken up into a vacuole/phagosome. Bacteria are detected inside the undamaged vacuole by toll-like receptors (TLRs) which triggers a number of pathways required to remove this invading bacteria [27].
Some bacteria remain in the phagosome, which constitutively matures, fuses with a lysosome and the bacterium is degraded. LC3 can also be conjugated onto the phagosome, which forms a LC3-decorated autophagosome around the target bacteria and delivers them to the lysosome for degradation (LC3-assisted phagocytosis). On the other hand, many bacteria have to escape the phagosome in order to migrate to the cytosol to divide. This causes massive damage to the phagosomal membrane and exposes glycans normally hidden inside the phagosome to the cytosol; these act as an ‘eat me’ signal. The exposed glycans can be bound by Gal8, which is bound by the cargo receptor NDP52. NDP52 interacts with LC3 on the phagophore membrane and the bacteria is enclosed inside the autophagosome. The bacteria are degraded when the autophagosome fuses with the lysosome (galectin-8 dependent autophagy). Conversely, cytosol-exposed glycans and bacteria can be ubiquitinated by STING and LRSAM1/PARKIN respectively which get bound by cargo receptors NDP52, Optineurin (Optn) and p62. These cargo receptors contain LIR motifs which again interact with LC3, taking the phagosome and bacteria to the phagophore to be degraded. (Fig. 5)
Salmonella enterica subsp. enterica Typhimurium
Salmonella enterica subsp. enterica Typhimurium is the Gram negative bacterium responsible for typhoid fever. This bacteria is targeted for autophagy and is taken up into a vacuole/phagosome called a Salmonella-containing vacuole (SCV). The SVC becomes decorated with ubiquitinated proteins and β-glycans which are recognised by the cargo receptors NDP52 and Optn [28]. The cargo receptors bring S. Typhimurium to the phagophore by interacting with LC3. The phagophore closes around the bacteria, forming the autophagosome, which fuses with a lysosome and the bacteria is degraded by resident hydrolases [29].
However, S. Typhimurium has evolved to inhibit autophagy induction signalling by reactivating mTOR; mTOR then relocalises to late endosomes and SCVs, thus inhibiting selective autophagy of this bacteria [6].
Figure 5 – Bacterial xenophagy: targeting intracellular bacteria for degradation. An intracellular bacterium is encapsulated in a phagosome. Top – LC3 can be conjugated to the undamaged phagosome which targets the phagosome for LC3 assisted phagocytosis (LAP). Bottom – many bacteria have to escape the phagosome in order to get into the cytosol to divide. This causes massive damage to the phagosomal membrane and exposes glycans normally hidden inside the phagosome to the cytosol, these act as an ‘eat me’ signal. The exposed glycans can be bound by Gal8, which is bound by the cargo receptor NDP52. NDP52 interacts with LC3 on the phagophore membrane and the bacteria is enclosed inside the autophagosome. The bacteria gets degraded when the autophagosome fuses with the lysosome (galectin-8 dependent autophagy). Conversely, cytosol-exposed glycans and bacteria can be ubiquitinated by STING and LRSAM1/PARKIN respectively which get bound by cargo receptors NDP52, Optn and p62. These cargo receptors again interact with LC3, taking the phagosome and bacteria to the phagophore to be degraded [27].
Mycobacterium tuberculosis
Mycobacterium tuberculosis is an obligate pathogenic bacteria responsible for most clinical cases of tuberculosis (TB). This bacteria is targeted for autophagic degradation in damaged vacuoles. During infection of macrophages, M.tuberculosis blocks phagosome maturation and replicates within the phagosome. Autophagy is thought to be triggered following damage to the phagosomes, leading to ubiquitination of host and bacterial proteins which target the phagosome down the autophagy pathway [30].
M.tuberculosis strain H37Rv produces a bacterial factor called Eis, which can inhibit autophagy activation by interfering with JNK signalling. This blocks the production of ROS, which is required to trigger autophagy, therefore the induction of autophagy is inhibited in order to benefit bacterial survival [31].
Bacillus anthracis and Vibrio cholerae
Both of these bacteria produce toxins that have been shown to inhibit autophagy induction. Oedema factor toxin from B.anthracis increases levels of intracellular cAMP, [32] which increases the negative regulation of autophagy [33]. Cholera toxin from V.cholerae can indirectly increase levels of cAMP by activating host adenylyl cyclases which inhibits autophagy induction. These bacteria have evolved this ability to block autophagy in order to aid their survival [34].
Legionella pneumophila
Legionella pneumophila is a Gram negative bacterium which is the causative agent of Legionnaires’ disease and is able to hijack autophagy to aid its own replication. L.pneumophila can actively induce autophagy using the T4SS bacterial factor, but it is able to block autophagosomal fusion with the lysosome. This bacteria uses the autophagosome as a replicative niche for its own growth [35].
Selective autophagy of viruses
As obligate, intracellular parasites, during the course of an infection, viruses encounter autophagy and interact with components of the autophagic machinery. Xenophagy is a way in which virally infected cells can be destroyed, in order to limit the viral infection and to reduce spread to other cells [36].
Once a virus has invaded into a host cell and begins to replicate, the host recognised the foreign virus and mounts an innate immune response, a component of which is selective autophagy. The cargo receptor, p62, plays a vital role in recognising and binding to viral capsid proteins and taking them to the forming autophagosome to be degraded by the autophagic pathway. (Fig. 6)
Figure 6 – Cargo receptors involved in xenophagy in mammalian cells. p62 acts as a cargo receptor and binds to viral capsid proteins, taking them to the forming autophagosome to be degraded by the autophagic pathway [22].
Evidence for the use of p62 as an adaptor for selective autophagy comes from work done by Levine et al. They studied the role of autophagy in mice who were infected with Sindbis virus (SIN) and showed that SIN capsid proteins are cleared by selective autophagy involving p62. Knockdown experiments show that p62-mediated selective autophagic degradation of the viral capsid protein reduces virally-induced cell death [37].
The replication and protein synthesis of the SIN virus within its host cell triggers autophagy via a currently unknown mechanism. (Fig. 7) It has been established that the SIN capsid protein is targeted to the autophagic machinery using the selective autophagy cargo receptor, p62. p62 interacts with LC3 on the phagophore membrane and enables the SIN capsid protein to be selectively degraded within the autolysosome. Sindbis virus is susceptible to autophagy and this process is pivotal in protecting against lethal SIN infection.
Figure 7 – Schematic model of selective viral autophagy. Once the Sindbis virus (SIN) has attached to the surface of the host cell it is taken up into the cytosol by endocytosis. The virus is uncoated and begins to replicate its genome and synthesising new viral proteins. Autophagy is triggered by an unknown sensor(s) during viral replication, and SIN capsid protein is targeted to the autophagic machinery in a process that requires the selective autophagy cargo receptor, p62. Disruption of autophagy results in the accumulation of aggregates of viral proteins and p62 within the host cell [38].
In order for a virus to be a successful pathogen and to survive within the host, it must have evolved ways of inhibiting autophagy. Virus-induced autophagy is an emerging area of investigation, and one that has been gaining momentum in recent years [39]. Although autophagy is a cellular defence mechanism, several viruses have evolved strategies to use autophagic vesicles for their own replication, using individual viral proteins to directly modulate the induction of autophagy. Two opposite outcomes of autophagy are induced by viral infections; some viruses are susceptible to autophagy and other viruses utilize the autophagy pathway to facilitate their own replication. Although autophagy has been linked to the replication of many viruses, each virus is likely to elicit different autophagic responses [38].
The HSV-1 ICP34.5 protein blocks both PKR- and Beclin 1-mediated activation of autophagy. The HIV-1 Nef protein blocks the ability of Beclin 1 to promote autophagosome maturation into autolysosomes. (Fig. 8) These strategies help to prevent viral proteins from being degraded and hence aids viral survival within the host.
Several RNA viruses including poliovirus, coxsackievirus B3, hepatitis C virus and rotavirus have been shown to induce double-membraned, autophagosome like structures in infected cells and it appears that these viruses induce autophagy in order to enhance replication. (Fig. 8)
Figure 8 – Anti-viral and pro-viral functions of autophagy. Xenophagy – autophagy may function as an anti-viral mechanism by directly capturing viral particles and/or viral components and targeting them for lysosomal degradation. The PKR-eIF2α signalling pathway and the autophagy protein Beclin 1 promote xenophagy, and some viruses have evolved to encode proteins to block the promotion of autophagy. The HSV-1 ICP34.5 protein blocks both PKR- and Beclin 1-mediated activation of autophagy. The HIV-1 Nef protein blocks the ability of Beclin 1 to promote autophagosome maturation into autolysosomes. Innate and Adaptive Immunity – autophagy genes also exert anti-viral functions by working with the innate and adaptive immune systems. Autophagy delivers viral genetic material to endosomes where the toll like receptor (TLR) 7 resides thus initiating the IFN response and aiding for formation of an anti-viral state. Autophagosomes also target viral peptides for MHC class II presentation, thereby enhancing CD4 T cell responses to these antigens. Scaffold for RNA virus genome replication and morphogenesis – some viruses use the autophagy machinery in a pro-viral capacity to aid the replication of viral genomes. Several RNA viruses including poliovirus, coxsackievirus B3, hepatitis C virus and rotavirus have been shown to induce double-membraned, autophagosome like structures in infected cells. It is thought that these viruses have evolved ways of blocking autophagosome maturation into destructive autolysosomes, thus preventing viral degradation [36].
Bioinformatics
iLIR software
The iLIR software is a freely available web resource which provides tools for assisting in the identification of novel LIR containing proteins. It provides integrated access to bioinformatics tools aiming to help researchers assess whether a protein contains a potentially functional LIR motif [40].
The iLIR software uses an amino acid sequence as an input and searches for the presence of a degenerate version of LIR, the extended LIR-motif (xLIR). Kalvari and colleagues have compiled a position-specific scoring matrix (PSSM) based on validated instances of the LIR motif. A PSSM score greater than 12 indicates that there is a greater probability that the LIR motif within the protein sequence is functional in vivo. In addition, iLIR detects LIR motifs in the disordered region of the protein sequence, these are the motifs that are more likely to be functional. Therefore, a combination of an xLIR match with a high PSSM score (>12) and/or an overlap with the disordered region is more likely to give reliable predictions that the LIR motif is functional. The iLIR software does not provide explicit predictions of functional LIR motifs but rather displays all the above information; it is up to the user to interpret the iLIR output. A limitation of the iLIR software is that it is not able to handle non-canonical LIR motifs at present [41].
hfAIM tool
The hfAIM (high fidelity Atg8-interacting motif) bioinformatics method is able to identify AIMs in proteins based on their defined degenerate consensus (W/F/Y)XX(L/I/V) sequences. However, hfAIM uses additional sequence requirements, including the presence of acidic amino acids and the absence of positively charged amino acids in certain positions. Experimental results suggest that the hfAIM tool can be used to effectively perform genome-wide in silico screens of proteins that are potentially involved in selective autophagy. Like the iLIR software, the hfAIM tool is not able to detect non-canonical sequences currently [42].
The Eukaryotic Linear Motif resource
The Eukaryotic Linear Motif (ELM) resource is used for examining functional sites within proteins in the form of short linear motifs. This resource has incorporated 4 ELM identifiers related to the LIR motif. The ELM resource displays matches to any LIR motifs but it is left to the user to determine in these motifs are functional in vivo [43].
The Human Autophagy Database
The Human Autophagy Database contains information relating to over 200 human genes/proteins that are associated with autophagy which have been collected from the biomedical literature. It characterises features that may link specific proteins to autophagic processes and provides different tools for autophagy studies [43].
The Autophagy Regulatory Network
The Autophagy Regulatory Network is an integrated systems-based resource which aims to collect and provide an interactive user interface enabling access to validated or predicted protein-protein, transcription factor-gene and miRNA-mRNA interaction related to autophagy in humans. This is the most recent addition to the web-based resources relevant to autophagy research and contains information about more than 14,000 proteins and 386 miRNAs related to autophagy [43].
This project will focus on the selective autophagy of viruses. In order to gain an appreciation for how viruses are associated with selective autophagy the literature will be searched to find associated viruses and the iLIR software will determine any putative LIR motifs within these viral proteins. Viral proteins that contain LIR motifs are thought to interact with LC3 on the phagophore membrane and be selectively degraded.
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