Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes

Research in autophagy continues to accelerate,(1) and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.(2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is 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 verify an autophagic response.     

AtVPS45 Is a Positive Regulator of the SYP41/SYP61/VTI12 SNARE Complex Involved in Trafficking of Vacuolar Cargo

We report a functional characterization of AtVPS45 (for vacuolar protein sorting 45), a protein from the Sec1/Munc18 family in Arabidopsis (Arabidopsis thaliana) that interacts at the trans-Golgi network (TGN) with the SYP41/SYP61/VTI12 SNARE complex. A null allele of AtVPS45 was male gametophytic lethal, whereas stable RNA interference lines with reduced AtVPS45 protein levels had stunted growth but were viable and fertile. In the silenced lines, we observed defects in vacuole formation that correlated with a reduction in cell expansion and with autophagy-related defects in nutrient turnover. Moreover, transport of vacuolar cargo with carboxy-terminal vacuolar sorting determinants was blocked in the silenced lines, suggesting that AtVPS45 functions in vesicle trafficking to the vacuole. These trafficking defects are similar to those observed in vti12 mutants, supporting a functional relationship between AtVPS45 and VTI12. Consistent with this, we found a decrease in SYP41 protein levels coupled to the silencing of AtVPS45, pointing to instability and malfunction of the SYP41/SYP61/VTI12 SNARE complex in the absence of its cognate Sec1/Munc18 regulator. Based on its localization on the TGN, we hypothesized that AtVPS45 could be involved in membrane fusion of retrograde vesicles recycling vacuolar trafficking machinery. Indeed, in the AtVPS45-silenced plants, we found a striking alteration in the subcellular fractionation pattern of vacuolar sorting receptors, which are required for sorting of carboxy-terminal vacuolar sorting determinant-containing cargo. We propose that AtVPS45 is essential for recycling of the vacuolar sorting receptors back to the TGN and that blocking this step underlies the defects in vacuolar cargo trafficking observed in the silenced lines.     

The syntaxin homolog AtPEP12p resides on a late post-Golgi compartment in plants.

Soluble proteins are transported to the plant vacuole through the secretory pathway via membrane-bound vesicles. Targeting of vesicles to appropriate organelles requires several membrane-bound and soluble factors that have been characterized in yeast and mammalian systems. For example, the yeast PEP12 protein is a syntaxin homolog that is involved in protein transport to the yeast vacuole. Previously, we isolated an Arabidopsis thaliana homolog of PEP12 by functional complementation of the yeast pep12 mutant. Antibodies raised against the cytoplasmic portion of AtPEP12 have been prepared and used for intracellular localization of this protein. Biochemical analysis indicates that AtPEP12 does not localize to the endoplasmic reticulum, Golgi apparatus, plasma membrane, or tonoplast in Arabidopsis plants; furthermore, based on biochemical and electron microscopy immunogold labeling analyses, AtPEP12 is likely to be localized to a post-Golgi compartment in the vacuolar pathway.     

Activation of autophagy by unfolded proteins during endoplasmic reticulum stress

Endoplasmic reticulum stress is defined as the accumulation of unfolded proteins in the endoplasmic reticulum, and is caused by conditions such as heat or agents that cause endoplasmic reticulum stress, including tunicamycin and dithiothreitol. Autophagy, a major pathway for degradation of macromolecules in the vacuole, is activated by these stress agents in a manner dependent on inositol‐requiring enzyme 1b (IRE1b), and delivers endoplasmic reticulum fragments to the vacuole for degradation. In this study, we examined the mechanism for activation of autophagy during endoplasmic reticulum stress in Arabidopsis thaliana. The chemical chaperones sodium 4–phenylbutyrate and tauroursodeoxycholic acid were found to reduce tunicamycin‐ or dithiothreitol‐induced autophagy, but not autophagy caused by unrelated stresses. Similarly, over‐expression of BINDING IMMUNOGLOBULIN PROTEIN (BIP), encoding a heat shock protein 70 (HSP70) molecular chaperone, reduced autophagy. Autophagy activated by heat stress was also found to be partially dependent on IRE1b and to be inhibited by sodium 4–phenylbutyrate, suggesting that heat‐induced autophagy is due to accumulation of unfolded proteins in the endoplasmic reticulum. Expression in Arabidopsis of the misfolded protein mimics zeolin or a mutated form of carboxypeptidase Y (CPY*) also induced autophagy in an IRE1b‐dependent manner. Moreover, zeolin and CPY* partially co‐localized with the autophagic body marker GFP–ATG8e, indicating delivery to the vacuole by autophagy. We conclude that accumulation of unfolded proteins in the endoplasmic reticulum is a trigger for autophagy under conditions that cause endoplasmic reticulum stress.     

Metabolism in normal and virus-transformed chick embryo fibroblasts as observed with glucose labeled with 14C and tritium and with tritium-labeled water.

Glucose metabolism in normal and virus-transformed chick embryo fibroblast cells in culture was observed by allowing the cells to metabolize [U-14C]glucose plus glucose labeled with tritium in the C-1, C-3, and C-6 positions. Similarities and differences between normal and transformed cells were observed and measured. Both normal and transformed cells are found to metabolize about 20% of the glucose via the oxidative pentose phosphate cycle, with the rates being about twice as much for transformed cells as for normal cells under the chosen conditions. Nevertheless, the ratio of glucose metabolized via oxidative pentose cycle to the net flow of that metabolized directly to fructose 6-phosphate is about the same in normal and transformed cells. Although the rate of flow of [14C]glucose into the tricarboxylic acid cycle intermediates and amino acids derived from them appears to be the same in normal and transformed cells, the rate of tritium incorporation from H3HO into these intermediates seems to be much higher in normal cells.     

Tritium incorporation and retention in photosynthesizing algae

The ratios of incorporation and retention of tritium compared to protium into metabolites in Chlorella pyrenoidosa and in Anacystis nidulans growing in water labeled with tritium have been determined. The algae were continuously supplied during growth with CO₂ labeled with ¹⁴CO₂, and the ¹⁴C content of metabolites were used to determined their concentrations. The tritium/protium ratios (R) of metabolites in Chlorella were determined following growth at 10 °C, 20 °C and 25 °C.As previously reported, variations in R in Chlorella, range from 0.5–0.7 for most metabolites, to values of R around 1 for metabolites of the tricarboxylic acid pathway. The R value for fumarate has now been measured. The increased R values for tricarboxylic acid cycle intermediates and related amino acids can be accounted for in terms of specific isotope effects of several enzyme-mediated steps. Very different R values for certain metabolites were found in A. nidulans. For example, R for citrate was 1.81 (the highest value observed in these studies) while aspartate was only 0.59, comparable to other metabolites in both organisms not related to the tricarboxyclic acid cycle. This lower value for aspartate is explainable in terms of the in complete tricarboxylic acid cycle in A. nidulans.No significant differences in R values for C. pyrenoidosa grown at 20 °C and 25 °C were observed, but in cells grown at 10 °C, there was a small but significant increase in R for tricarboxylic acid cycle metabolites.If the increase in R from sugar phosphates to tricarboxylic acid cycle intermediates seen in these two types of algae may be taken as an indication of likely discriminatory retention of tritium in organisms higher in the food chain, it would appear that no serious concentration of tritium due to isotopic discrimination should occur in the biosphere. However, research workers using compounds labeled with hydrogen isotopes for studies of in vivo metabolism should take into account the likelihood of such discriminatory uptake and retention during specific metabolic steps.