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

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A unique protein with an apparent molecular mass of 96 kilodaltons (p96) was detected in the murine macrophage cell line, BAC1.2F5. The murine cDNA encoding p96 was cloned and sequenced, along with cDNAs representing two alternatively spliced forms of the protein. All three proteins possessed identical amino-terminal domains with significant similarity to the amino-terminal domain of the Drosophila disabled gene product and carboxyl-terminal domains containing proline-rich sequences characteristic of src homology region (domain 3) binding regions. BAC1.2F5 cells predominantly expressed the p96 protein, although mRNA and protein corresponding to the p67 splice variant were also detected. Electrophoretic gel retardation of p96 in response to stimulation of the cells with colony-stimulating factor 1 was noticeable within 5 min after growth factor addition and reached a maximum at 60 min. Metabolic labeling experiments showed that the gel retardation of p96 was associated with increased phosphorylation of the protein exclusively on serine residues. These data identify a novel protein that is phosphorylated in response to mitogenic growth factor stimulation.

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Nedd4 E3 ligases are members of the HECT E3 ubiquitin ligase family and regulate ubiquitination-mediated protein degradation. In this report, we demonstrate that calcium releases the C2 domain-mediated auto-inhibition in both Nedd4-1 and Nedd4-2. Calcium disrupts binding of the C2 domain to the HECT domain. Consistent with this, calcium activates the E3 ubiquitin ligase activity of Nedd4. Elevation of intracellular calcium by ionomycin treatment, or activation of acetylcholine receptor or epidermal growth factor receptor by carbachol or epidermal growth factor stimulation induced activation of endogenous Nedd4 in vivo evaluated by assays of either Nedd4 E3 ligase activity or ubiquitination of Nedd4 substrate ENaC-␤. The activation effect of calcium on Nedd4 E3 ligase activity was dramatically enhanced by a membrane-rich fraction, suggesting that calcium-mediated membrane translocation through the C2 domain might be an activation mechanism of Nedd4 in vivo. Our studies have revealed an activation mechanism of Nedd4 E3 ubiquitin ligases and established a connection of intracellular calcium signaling to regulation of protein ubiquitination.Protein ubiquitination is a major intracellular signaling event. E3 ubiquitin ligase (E3), 3 including the HECT (homologous to E6-AP carboxyl terminus) domain containing and the RING (the really interesting new gene) domain containing E3 ligases, is the key enzyme that catalyzes ubiquitination and confers specificity of ubiquitination substrates (1-3). Nedd4 E3 ubiquitin ligases are members of the WW domain-containing HECT E3 ubiquitin ligase subfamily (4). There are two Nedd4 E3 ligases, Nedd4-1 and Nedd4-2, in mammalian cells (5). Human Nedd4-1 gene (Nedd4) is localized on chromosome 15, and Nedd4-2 gene (Nedd4L) is on chromosome 18 (5). Both Nedd4-1 and Nedd4-2 have the same domain structure, with the C2 domain at the N terminus, followed by four WW domains, and the HECT domain at the C terminus. The primary peptide sequences of human Nedd4-1 and Nedd4-2 are ϳ65% identical. The most unconserved regions are located between the WW1 and the WW3 domains.

Cdc42 plays an important role in intracellular signaling pathways that influence cell morphology and motility and stimulate DNA synthesis. In attempts to determine whether nonreceptor tyrosine kinases play a fundamental role in Cdc42 signaling, we have cloned and biochemically characterized a new Cdc42-associated tyrosine kinase (ACK) from bovine brain. This tyrosine kinase, named ACK-2, has a calculated molecular mass of 83 kDa and shares a number of primary structural domains with the 120-kDa ACK (ACK-1). The main differences between the primary structures of ACK-2 and ACK-1 occur in the amino-and carboxyl-terminal regions. Like ACK-1, ACK-2 binds exclusively to activated (GTP-bound) Cdc42 and does not bind to its closest homologs, e.g. activated Rac. ACK-2 could not be activated by addition of glutathione S-transferase (GST)-Cdc42(Q61L), a GTPase-defective mutant, or by GTP␥S-loaded GST-Cdc42 in in vitro kinase assays. However, ACK-2 was activated when cotransfected with wild type Cdc42 or Cdc42(Q61L) and stably associated with Cdc42(Q61L) in vivo, indicating that ACK-2 interacts with active Cdc42 in cells. Furthermore, the tyrosine kinase activity of ACK-2 was stimulated both by epidermal growth factor and bradykinin, suggesting that ACK-2 may play a role in the signaling actions of both receptor tyrosine kinases or heterotrimeric G-proteincoupled receptors.

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