Autophagy is a catabolic membrane-trafficking process that occurs in all eukaryotic cells and leads to the hydrolytic degradation of cytosolic material in the vacuolar or lysosomal lumen. Mitophagy, a selective form of autophagy targeting mitochondria, is poorly understood at present. Several recent reports suggest that mitophagy is a selective process that targets damaged mitochondria, whereas other studies imply a role for mitophagy in cell death processes. In a screen for protein phosphatase homologs that functionally interact with the autophagy-dedicated protein kinase Atg1p in yeast, we have identified Aup1p, encoded by Saccharomyces cerevisiae reading frame YCR079w. Aup1p is highly similar to a family of protein phosphatase homologs in animal cells that are predicted to localize to mitochondria based on sequence analysis. Interestingly, we found that Aup1p localizes to the mitochondrial intermembrane space and is required for efficient mitophagy in stationary phase cells. Viability studies demonstrate that Aup1p is required for efficient survival of cells in prolonged stationary phase cultures, implying a pro-survival role for mitophagy under our working conditions. Our data suggest that Aup1p may be part of a signal transduction mechanism that marks mitochondria for sequestration into autophagosomes.Mitochondria perform numerous essential physiological functions in all eukaryotic cells. Apart from their role in oxidative phosphorylation and fatty acid oxidation, they are also essential for biosynthesis of central building blocks such as amino acids and nucleotides. At the same time, mitochondria are a threat to cellular well-being. Mitochondria are a major source of reactive oxygen species in cells. In addition, disruption of mitochondrial compartmentalization results in leakage of cytochrome c and other cytotoxic factors, and mitochondria with defective chemiosmotic coupling can cause an energy drain on the cell. Accumulation of mitochondrial genetic variation and mitochondrial damage are widely considered to underlie many age-related metabolic diseases and late-onset genetic disorders (1, 2). It is commonly postulated that in normal cells defective mitochondria are broken down in the lysosomal compartment through autophagy, and inability to clear defective mitochondria is thought to underlie numerous pathological conditions (3, 4).Autophagy is a set of catabolic membrane trafficking mechanisms that allow import of cytosolic material into the vacuole/ lysosome. The best understood form of autophagy is macroautophagy, in which intracellular membranes of undetermined origin engulf cytosolic material to form a double or multi-bilayer membrane bound intermediate called the autophagosome (reviewed in Refs. 3 and 5-8). This intermediate then goes on to fuse with the vacuole/lysosome, releasing a single-bilayer bound vesicle called an autophagic body into the lumen of the lytic compartment where it is broken down, releasing the cytosol-derived material for further degradation to biosynthetic building blocks. Cl...

Gut microbiome diversity has been strongly associated with mood-relating behaviours, including major depressive disorder (MDD). This association stems from the recently characterised bi-directional communication system between the gut and the brain, mediated by neuroimmune, neuroendocrine and sensory neural pathways. While the link between gut microbiome and depression is well supported by research, a major question needing to be addressed is the causality in the connection between the two, which will support the understanding of the role that the gut microbiota play in depression. In this article, we address this question by examining a theoretical 'chronology', reviewing the evidence supporting two possible sequences of events. First, we discuss that alterations in the gut microbiota populations of specific species might contribute to depression, and secondly, that depressive states might induce modification of specific gut microbiota species and eventually contribute to more severe depression. The feasibility of both sequences is supported by pre-clinical trials. For instance, research in rodents has shown an onset of depressive behaviour following faecal transplantations from patients with MDD. On the other hand, mental induction of stress and depressive behaviour in rodents resulted in reduced gut microbiota richness and diversity. Synthesis of these chronology dynamics raises important research directions to further understand the role that gut microbiota play in mood-relating behaviours, which holds substantial potential clinical outcomes for persons who experience MDD or related depressive disorders.

No abstract

Here we outline the principles of the different approaches and their relative advantages. We demonstrate the unique contribution of flux analysis for phenotype elucidation using a thoroughly studied metabolic reaction as a case study, the microbial aerobic/anaerobic shift, highlighting the importance of flux analysis as a single layer of data as well as interlaced in multi-omics studies.