In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Efficient replication of hepatitis C virus (HCV) subgenomic RNA in cell culture requires the introduction of adaptive mutations. In this report we describe a system which enables efficient replication of the Con1 subgenomic replicon in Huh7 cells without the introduction of adaptive mutations. The starting hypothesis was that high amounts of the NS5A hyperphosphorylated form, p58, inhibit replication and that reduction of p58 by inhibition of specific kinase(s) below a certain threshold enables HCV replication. Upon screening of a panel of kinase inhibitors, we selected three compounds which inhibited NS5A phosphorylation in vitro and the formation of NS5A p58 in cell culture. Cells, transfected with the HCV Con1 wild-type sequence, support HCV RNA replication upon addition of any of the three compounds. The effect of the kinase inhibitors was found to be synergistic with coadaptive mutations in NS3. This is the first direct demonstration that the presence of high amounts of NS5A-p58 causes inhibition of HCV RNA replication in cell culture and that this inhibition can be relieved by kinase inhibitors.

The orphan G protein-coupled receptor 37 (GPR37) is a substrate of parkin; its insoluble aggregates accumulate in brain samples of Parkinson's disease patients. We report here that GPR37 interacts with the dopamine transporter (DAT) and modulates DAT activity. GPR37 and DAT were found colocalized in mouse striatal presynaptic membranes and in transfected cells and their interaction was confirmed by coimmunoprecipitation assays. Gpr37-null mutant mice showed enhanced DAT-mediated dopamine uptake in striatal membrane samples, with a significant increase in the number of plasma membrane DAT molecules. The null mutant mice also exhibited a decrease in cocaine-induced locomotor activity and in catalepsy induced by dopamine receptor antagonists. These results reveal the specific role of GPR37, a putative peptidergic G proteincoupled receptor, in modulating the functional expression of DAT and the behavioral responses to dopaminergic drugs.G protein-coupled receptor ͉ Parkinson's disease ͉ dopamine transporter T he orphan G protein-coupled receptor 37 (GPR37) is homologous to endothelin (ET B -R) and bombesin (GRP-R, NMB-R) receptors (1) and it is highly expressed in mammalian brain oligodendrocytes, Purkinje cells, and neurons belonging to the CA3 hippocampal region and to the substantia nigra (SN) pars compacta (2). GPR37 is a substrate of the ubiquitin-protein ligase parkin, and it has been named parkin-associated endothelin-like receptor (PAEL-R) (3). An insoluble form of GPR37 is accumulated in brain samples of Parkinson's disease (PD) patients, and the overexpression of GPR37 in cell cultures, in the absence of parkin, can lead to unfolded protein-induced cell death (3, 4). Little is known about the physiological function of the receptor in the brain and in dopaminergic neurons in particular, although it has been speculated that the aggregation of GPR37 in insoluble complexes is responsible for the preferential loss of SN neurons through the endoplasmic reticulum-specific apoptotic pathway (5, 6). Recent data reported an interaction between GPR37, the head activator neuropeptide and its binding protein (sorting protein-related receptor; SorLA), supporting the hypothesis that GPR37 is involved in neuronal cell survival (7). To investigate the receptor's function, we generated homozygous Gpr37-null mutant mice, which exhibit a reduction in striatal dopamine (DA) content, specific locomotor deficits, and enhanced sensitivity to amphetamine (8).Several binding partners for the DA transporter (DAT) have been identified, suggesting that a regulated multiprotein complex controls its synthesis, targeting, and expression at specific cellular membrane domains (9). Presynaptic DAT expression is of crucial importance in modulating the synaptic availability of DA at nigrostriatal synapses, and its regulation is dynamically controlled for the maintenance of normal dopaminergic neurotransmission. The increase or decrease of DAT expression in the presynaptic membranes results in decreased or increased synaptic DA concentration, ...

Hepatitis C virus (HCV) has been the subject of intensive studies for nearly two decades. Nevertheless, some aspects of the virus life cycle are still a mystery. The HCV nonstructural protein 5A (NS5A) has been shown to be a modulator of cellular processes possibly required for the establishment of viral persistence. NS5A is heavily phosphorylated, and a switch between a basally phosphorylated form of NS5A (p56) and a hyperphosphorylated form of NS5A (p58) seems to play a pivotal role in regulating HCV replication. Using kinase inhibitors that specifically inhibit the formation of NS5A-p58 in cells, we identified the CKI kinase family as a target. NS5A-p58 increased upon overexpression of CKI-␣, CKI-␦, and CKI-, whereas the RNA interference of only CKI-␣ reduced NS5A hyperphosphorylation. Rescue of inhibition of NS5A-p58 was achieved by CKI-␣ overexpression, and we demonstrated that the CKI-␣ isoform is targeted by NS5A hyperphosphorylation inhibitors in living cells. Finally, we showed that down-regulation of CKI-␣ attenuates HCV RNA replication.The discipline of "chemical genomics" has progressively become more and more important for the elucidation of the molecular basis of complex phenotypes. Chemical genomics implies a combination of medicinal chemistry and genetics in which small molecules are used to perturb biological pathways by modulating the activity of individual gene products. Such compounds may then assist scientists in identifying target proteins and genes. We used this combination of methodologies to better understand the mechanisms by which the hepatitis C virus (HCV) is able to replicate its genome in the host cells.The positive-sense single-stranded RNA genome of HCV encodes a single polyprotein that is co-and posttranslationally processed into at least four structural and six nonstructural (NS) proteins (22). Virus-encoded enzymes are attractive targets for the development of antiviral agents, and the HCV NS2-3 and NS3-4A proteinases, the NS3 helicase, and the RNA-dependent RNA polymerase NS5B have been investigated for many years. NS5A is a nonstructural protein without any yet-identified biochemical activity.NS5A has been described to influence many different cellular pathways involved in cell cycle control and cellular growth, apoptosis, and inflammatory and immune responses (24). In most cases, the activity of cellular kinases is directly or indirectly influenced by the presence of NS5A (24). While all this information indicates that NS5A can modulate the activity of cellular kinases, cellular kinases might also affect the function of NS5A itself. NS5A is phosphorylated in three main clusters (1), and two phosphorylated forms of NS5A, termed p56 (basally phosphorylated) and p58 (hyperphosphorylated), can be distinguished (32). The three residues S2197, S2201, and S2204 and the presence of other HCV nonstructural proteins (2, 21, 28) have been reported to be implicated in the formation of NS5A-p58.To date, the function of the differentially phosphorylated forms of NS5A in HCV genome replic...

In the developing cerebellum, the proliferation and differentiation of glial and neuronal cell types depend on the modulation of the sonic hedgehog (Shh) signaling pathway. The vertebrate Gprotein-coupled receptor 37-like 1 (GPR37L1) gene encodes a putative G-protein-coupled receptor that is expressed in newborn and adult cerebellar Bergmann glia astrocytes. This study shows that the ablation of the murine Gpr37l1 gene results in premature down-regulation of proliferation of granule neuron precursors and precocious maturation of Bergmann glia and Purkinje neurons. These alterations are accompanied by improved adult motor learning and coordination. Gpr37l1 −/− mice also exhibit specific modifications of the Shh signaling cascade. Specific assays show that in Bergmann glia cells Gpr37l1 is associated with primary cilium membranes and it specifically interacts and colocalizes with the Shh primary receptor, patched 1. These findings indicate that the patched 1-associated Gpr37l1 receptor participates in the regulation of postnatal cerebellum development by modulating the Shh pathway.mutant mouse model | mitogenic signaling