A Model for Shaping Membrane Sheets by Protein Scaffolds

Membranes of peripheral endoplasmic reticulum form intricate morphologies consisting of tubules and sheets as basic elements. The physical mechanism of endoplasmic-reticulum shaping has been suggested to originate from the elastic behavior of the sheet edges formed by linear arrays of oligomeric protein scaffolds. The heart of this mechanism, lying in the relationships between the structure of the protein scaffolds and the effective intrinsic shapes and elastic properties of the sheets’ edges, has remained hypothetical. Here we provide a detailed computational analysis of these issues. By minimizing the elastic energy of membrane bending, we determine the effects of a rowlike array of semicircular arclike membrane scaffolds on generation of a membrane fold, which shapes the entire membrane surface into a flat double-membrane sheet. We show, quantitatively, that the sheet’s edge line tends to adopt a positive or negative curvature depending on the scaffold’s geometrical parameters. We compute the effective elastic properties of the sheet edge and analyze the dependence of the equilibrium distance between the scaffolds along the edge line on the scaffold geometry.     

Eating the endoplasmic reticulum: quality control by autophagy

Autophagy is connected to a surprising range of cellular processes, including the stress response, developmental remodeling, organelle homeostasis and disease pathophysiology. The inducible, predominant form of autophagy, macroautophagy, involves dynamic membrane rearrangements, culminating in the formation of a double-membrane cytosolic vesicle, an autophagosome, which sequesters cytoplasm and organelles. The signal transduction mechanisms that regulate autophagy are poorly understood and have focused on extracellular nutrient sensing. Similarly, little is known about the contribution of the endomembrane organelles to autophagy-related processes. Recent studies have provided interesting links between these topics, revealing that the secretory pathway provides membrane for autophagosome formation, and that autophagy has an important role in organelle homeostasis.     

Autophagy

Autophagy is an evolutionarily conserved cellular process through which long-lived proteins and damaged organelles are recycled to maintain energy homeostasis. These proteins and organelles are sequestered into a double-membrane structure, or autophagosome, which subsequently fuses with a lysosome in order to degrade the cargo. Although originally classified as a type of programmed cell death, autophagy is more widely viewed as a basic cell survival mechanism to combat environmental stressors. Autophagy genes were initially identified in yeast and were found to be necessary to circumvent nutrient stress and starvation. Subsequent elucidation of mammalian gene counterparts has highlighted the importance of this process to normal development. This review provides an overview of autophagy, the types of autophagy, its regulation and its known impact on development gleaned primarily from murine models.     

自噬过程的晚期阶段

自噬是高度保守的细胞内降解途径.在此过程中,部分细胞质和细胞器被双层膜的囊泡包裹形成自噬体,随后与溶酶体融合并降解被吞噬的物质.降解产物被释放到细胞质中重新用于必需的物质和能量合成.本文主要关注自噬的晚期阶段,即从自噬体合成结束到溶酶体再生过程.通过对这一过程相关基因及蛋白产物的研究,初步揭示了此过程的分子机制.     

自噬的调控通路和肿瘤

自噬是指胞浆内大分子物质和细胞器在膜包囊泡中大量降解的生物学过程,其具有独特的分子机制、形态改变和特有的调控通路,作为各种调控通路交汇点——mTOR复合体和Beclin1复合体发挥了至关重要的作用。对于人体而言,自噬具有维持细胞自我稳态,促进细胞生存的作用,然而,过度自噬则可以引起细胞死亡即＂自噬性细胞死亡＂。相关研究表明,自噬的这种特点与肿瘤的发生密切相关。对于肿瘤,自噬作用好似一把双刃剑,既促进其发生又抑制其形成。     

The emerging role of acetylation in the regulation of autophagy

Autophagy is an evolutionarily conserved catabolic process through which different components of the cells are sequestered into double-membrane cytosolic vesicles called autophagosomes, and fated to degradation through fusion with lysosomes. Autophagy plays a major function in many physiological processes including response to different stress factors, energy homeostasis, elimination of cellular organelles and tissue remodeling during development. Consequently, autophagy is strictly controlled and post-translational modifications such as phosphorylation and ubiquitination have long been associated with autophagy regulation. In contrast, the importance of acetylation in autophagy control has only emerged in the last few years. In this review, we summarize how previously identified histone acetylases and deacetylases modify key autophagic effector proteins, and discuss how this has an impact on physiological and pathological cellular processes.     

PI3K/Akt/mTOR信号通路与自噬及肿瘤的关系

自噬是一种以胞质内出现双层膜结构包裹长寿命蛋白和细胞器的自噬体为特征的细胞“自我消化”过程,在维持细胞内稳态、发育、肿瘤发生和感染中发挥重要作用。近来,诸多研究表明,自噬作为一把“双刃剑”,对肿瘤的发生发展既有促进作用,也有抑制作用。PI3K/Akt/mTOR通路由PI3激酶(PI3K)、蛋白激酶B（PKB/Akt）和哺乳动物类雷帕霉素靶蛋白（mTOR）3个作用分子组成,是一个中心的调节机构,对肿瘤细胞的生长与增殖有促进作用,同时对自噬进行抑制。本文就PI3K/Akt/mTOR通路与自噬及肿瘤发生发展的关系作一综述。     

Autophagy in organelle homeostasis: peroxisome turnover

When cells are confronted with an insufficient supply of nutrients in their extracellular fluid, they may begin to cannibalize some of their internal proteins as well as whole organelles for reuse in the synthesis of new components. This process is termed autophagy and it involves the formation of a double-membrane structure within the cell, which encloses the material to be degraded into a vesicle called an autophagosome. The autophagosome subsequently fuses with a lysosome/vacuole whose hydrolytic enzymes degrade the sequestered organelle. Degradation of peroxisomes is a specific type of autophagy, which occurs in a selective manner and has been mostly studied in yeast. Recently, it was reported that a similar selective process of autophagy occurs in mammalian cells with proliferated peroxisomes. Here we discuss characteristics of the autophagy of peroxisomes in mammalian cells and present a comprehensive model of their likely mechanism of degradation on the basis of known and common elements from other systems.     

A picky eater: exploring the mechanisms of selective autophagy in human pathologies

Autophagy is a catabolic process conserved among all eukaryotes essential for the cellular and organismal homeostasis. One of the principal roles of this pathway is to maintain an accurate balance between synthesis, degradation and subsequent recycling of cellular components. Under certain conditions, however, cells are also able to modulate autophagy and specifically remove a number of structures that are potentially harmful. Aberrant protein aggregates, damaged organelles or pathogens can be selectively incorporated into large double-membrane vesicles called autophagosomes to be delivered into lysosomes for destruction. This ability to eliminate specific structures is exploited by the cells in several physiological processes as well as in multiple pathological situations, making autophagy a precious multitask cellular degradative pathway. In this review, we will first examine what is known about the basic mechanisms of autophagy and then discuss in a second part the nature of the cargoes that are selectively sequestered into autophagosomes, what provides the specificity and the possible implications of selective types of autophagy in human pathologies.     

What to Eat: Evidence for Selective Autophagy in Plants

Autophagy is a macromolecular degradation pathway by which cells recycle their contents as a developmental process, housekeeping mechanism, and response to environmental stress. In plants, autophagy involves the sequestration of cargo to be degraded, transport to the cell vacuole in a double-membrane bound autophagosome, and subsequent degradation by lytic enzymes. Autophagy has generally been considered to be a non-selective mechanism of degradation. However, studies in yeast and animals have found numerous examples of selective autophagy, with cargo including proteins, protein aggregates, and organelles. Recent work has also provided evidence for several types of selective autophagy in plants. The degradation of protein aggregates was the first selective autophagy described in plants, and, more recently, a hybrid protein of the mammalian selective autophagy adaptors p62 and NBR1, which interacts with the autophagy machinery and may function in autophagy of protein aggregates, was described in plants. Other intracellular components have been suggested to be selectively targeted by autophagy in plants, but the current evidence is limited. Here, we discuss recent findings regarding the selective targeting of cell components by autophagy in plants.     

Transport of proteins to the yeast vacuole: autophagy, cytoplasm-to-vacuole targeting, and role of the vacuole in degradation

The vacuole/lysosome performs a central role in degradation. Proteins and organelles are transported to the vacuole by selective and non-selective pathways. Transport to the vacuole by autophagy is the primary mode for degradation of cytoplasmic constituents under starvation conditions. Autophagy overlaps mechanistically and genetically with a biosynthetic pathway termed Cvt (Cytoplasm-to-vacuole targeting) that operates under vegetative conditions to transport the resident vacuolar hydrolase aminopeptidase I (API). API import has been dissected to reveal the action of a novel mechanism that transports cargo within double-membrane vesicles. Recent work has uncovered molecular components involved in autophagy and the Cvt pathway.     

Freeze-fracture replica immunolabelling reveals human WIPI-1 and WIPI-2 as membrane proteins of autophagosomes

Autophagy defines the lifespan of eukaryotic organisms by ensuring cellular survival through regulated bulk clearance of proteins, organelles and membranes. Pathophysiological consequences of improper autophagy give rise to a variety of age-related human diseases such as cancer and neurodegeneration. Rational therapeutic implementation of autophagy modulation remains problematic, as fundamental molecular details such as the generation of autophagosomes, unique double-membrane vesicles formed to permit the process of autophagy, are insufficiently understood. Here, freeze-fracture replica immunolabelling reveals WD-repeat protein interacting with phosphoinositides 1 and 2 (WIPI-1 and WIPI-2) as membrane components of autophagosomes and the plasma membrane (PM). In addition, WIPI-1 is also present in membranes of the endoplasmic reticulum (ER) and WIPI-2 was further detected in membranes close to the Golgi cisternae. Our results identify WIPI-1 and WIPI-2 as novel protein components of autophagosomes, and of membrane sites from which autophagosomes might originate (ER, PM, Golgi area). Hence therapeutic modulation of autophagy could involve approaches that functionally target human WIPI proteins.     

The pancreatitis-induced vacuole membrane protein 1 triggers autophagy in mammalian cells

Autophagy is a degradation process of cytoplasmic cellular constituents, which serves as a survival mechanism in starving cells, and it is characterized by sequestration of bulk cytoplasm and organelles in double-membrane vesicles called autophagosomes. Autophagy has been linked to a variety of pathological processes such as neurodegenerative diseases and tumorigenesis, which highlights its biological and medical importance. We have previously characterized the vacuole membrane protein 1 (VMP1) gene, which is highly activated in acute pancreatitis, a disease associated with morphological changes resembling autophagy. Here we show that VMP1 expression triggers autophagy in mammalian cells. VMP1 expression induces the formation of ultrastructural features of autophagy and recruitment of the microtubule-associated protein 1 light-chain 3 (LC3), which is inhibited after treatment with the autophagy inhibitor 3-methiladenine. VMP1 is induced by starvation and rapamycin treatments. Its expression is necessary for autophagy, because VMP1 small interfering RNA inhibits autophagosome formation under both autophagic stimuli. VMP1 is a transmembrane protein that co-localizes with LC3, a marker of the autophagosomes. It interacts with Beclin 1, a mammalian autophagy initiator, through the VMP1-Atg domain, which is essential for autophagosome formation. VMP1 endogenous expression co-localizes with LC3 in pancreas tissue undergoing pancreatitis-induced autophagy. Finally, VMP1 stable expression targeted to pancreas acinar cell in transgenic mice induces autophagosome formation. Our results identify VMP1 as a novel autophagy-related membrane protein involved in the initial steps of the mammalian cell autophagic process.     

Autophagosome formation: core machinery and adaptations

Eukaryotic cells employ autophagy to degrade damaged or obsolete organelles and proteins. Central to this process is the formation of autophagosomes, double-membrane vesicles responsible for delivering cytoplasmic material to lysosomes. In the past decade many autophagy-related genes, ATG, have been identified that are required for selective and/or nonselective autophagic functions. In all types of autophagy, a core molecular machinery has a critical role in forming sequestering vesicles, the autophagosome, which is the hallmark morphological feature of this dynamic process. Additional components allow autophagy to adapt to the changing needs of the cell.     

Autophagy: molecular machinery for self-eating

Autophagy is a highly conserved process in eukaryotes in which the cytoplasm, including excess or aberrant organelles, is sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. This process has an important role in various biological events such as adaptation to changing environmental conditions, cellular remodeling during development and differentiation, and determination of lifespan. Auto-phagy is also involved in preventing certain types of disease, although it may contribute to some pathologies. Recent studies have identified many components that are required to drive this complicated cellular process. Auto-phagy-related genes were first identified in yeast, but homologs are found in all eukaryotes. Analyses in a range of model systems have provided huge advances toward understanding the molecular basis of autophagy. Here we review our current knowledge on the machinery and molecular mechanism of autophagy.     

Atg11 directs autophagosome cargoes to the PAS along actin cables

For more than 40 years, autophagy has been almost exclusively studied as a cellular response that allows adaptation to starvation situations. In nutrient-deprived conditions, cytoplasmic components and organelles are randomly sequestered into double-membrane vesicles called autophagosomes, creating the notion that this pathway is a nonselective process (reviewed in Refs 1, 2). Recent results, however, have demonstrated that under certain circumstances, cargoes such as protein complexes, organelles and bacteria can be selectively and exclusively incorporated into double-membrane vesicles.(1) We have recently shown that actin plays an essential role in two selective types of autophagy in the yeast Saccharomyces cerevisiae, the cytoplasm to vacuole targeting (Cvt) pathway and pexophagy, raising the possibility that the structures formed by polymers of this protein helps autophagosomes in recognizing the cargoes that must be delivered to the vacuole.(3) In this addendum, we discuss the possible central role of Atg11 as a molecule connecting cargoes, actin and pre-utophagosomal structure (PAS) elements.     

The actin cytoskeleton is required for selective types of autophagy, but not nonspecific autophagy, in the yeast Saccharomyces cerevisiae

Autophagy is a catabolic multitask transport route that takes place in all eukaryotic cells. During starvation, cytoplasmic components are randomly sequestered into huge double-membrane vesicles called autophagosomes and delivered into the lysosome/vacuole where they are destroyed. Cells are able to modulate autophagy in response to their needs, and under certain circumstances, cargoes such as aberrant protein aggregates, organelles and bacteria can be selectively and exclusively incorporated into autophagosomes. In the yeast Saccharomyces cerevisiae, for example, double-membrane vesicles are used to transport the Ape1 protease into the vacuole, or for the elimination of superfluous peroxisomes. In the present study we reveal that in this organism, actin plays a role in these two types of selective autophagy but not in the nonselective, bulk process. In particular, we show that precursor Ape1 is not correctly recruited to the PAS, the putative site of double-membrane vesicle biogenesis, and superfluous peroxisomes are not degraded in a conditional actin mutant. These phenomena correlate with a defect in Atg9 trafficking from the mitochondria to the PAS.     

Autophagy: a regulated bulk degradation process inside cells

Autophagy is a major intracellular degradation/recycling system ubiquitous in eukaryotic cells. It contributes to the turnover of cellular components by delivering portions of the cytoplasm and organelles to lysosomes, where they are digested. Autophagy is mediated by membrane trafficking of unique double-membrane structures, the so-called autophagosomes, which are formed transiently. Moreover, autophagy is dramatically induced under starvation conditions to maintain an amino acid pool so that essential proteins may be synthesized. Recent studies have revealed insights into the molecular basis of membrane dynamics and the regulation of autophagy, which had remained cryptic for a long time.     

线粒体自噬

细胞自噬(autophagy)是细胞依赖溶酶体对蛋白和细胞器进行降解的一条重要途径.目前,将通过细胞自噬降解线粒体的途径称为线粒体自噬(mitophagy).最近几年的证据表明,线粒体自噬是一个特异性的选择过程,并受到各种因子的精密调节,是细胞清除体内损伤线粒体和维持自身稳态的一种重要调节机制.自噬相关分子,如“核心”Atg 复合物,酵母线粒体外膜分子Atg32、Atg33、Uth1和Aup1,哺乳细胞线粒体外膜蛋白PINK1、NIX和胞质的Parkin等,在线粒体自噬中起关键的作用. 线粒体自噬异常与神经退行性疾病如帕金森氏病（Parkinson’s disease,PD）的发生密切相关. 本文就线粒体自噬的研究进展做简要的介绍.     

自噬过程的晚期阶段

自噬是高度保守的细胞内降解途径。在此过程中,部分细胞质和细胞器被双层膜的囊泡包裹形成自噬体,随后与溶酶体融合并降解被吞噬的物质。降解产物被释放到细胞质中重新用于必需的物质和能量合成。本文主要关注自噬的晚期阶段,即从自噬体合成结束到溶酶体再生过程。通过对这一过程相关基因及蛋白产物的研究,初步揭示了此过程的分子机制。