Autophagosomes: biogenesis from scratch?

To survive extreme environmental conditions, and in response to certain developmental and pathological situations, eukaryotic organisms employ the catabolic process of autophagy. This degradative pathway allows cells to eliminate large portions of the cytoplasm, from aberrant protein aggregates to superfluous or damaged organelles and even entire organisms such as invading bacteria. Structures targeted for destruction are sequestered into large double-membrane vesicles called autophagosomes and then delivered into the interior of the lysosome or vacuole, where they are consumed by resident hydrolases. Autophagosome formation during selective autophagy is dependent upon the cargoes, and in all cases seems to involve expansion of the sequestering membrane.

Introduction

Autophagy has been known for at least 40 years as an adaptation response to starvation and as the major factor in the turnover of long-lived proteins; however, for much of that time studies about this degradative transport route have been limited to morphological observations. These analyses were phenomenological in nature because none of the specific components making up the autophagic machinery were known. In the last decade, genetic screens in the yeast Saccharomyces cerevisiae and in other fungi have led to the isolation of ∼17 ATG (autophagy-related) genes whose products are specifically involved in this catabolic pathway [1]. Importantly, most of these genes possess clear homologues in other eukaryotic organisms and several have now been shown to function as orthologues [2, 3]. Thus, in recent years, researchers employing more complex model organisms such as Caenorhabditis elegans, Dictyostelium discoideum, Drosophila melanogaster and mice as well as mammalian cell lines have started to unveil the relevance of autophagy in several physiological processes, either by making specific knockouts of the yeast ATG homologues or alternatively by depleting the corresponding transcripts through the use of RNAi. We now know that autophagy is directly involved in eliminating aberrant protein aggregates, protecting against tumors and defending against pathogen invasions (both viral and bacterial), and that it plays an essential role in development and differentiation; autophagy may also be involved in lifespan extension and possibly in carrying out type-II programmed cell death (Figure 1) [2, 4, 5, 6].

The general mechanism of autophagy is the sequestration of the cargo material into a large double-membrane vesicle, called an autophagosome, which then fuses with the lysosome/vacuole, liberating the internal vesicle into the interior of this organelle where, together with the cargo, it is degraded by hydrolases (Figure 2). The biogenesis and consumption of this structure can be divided in four discrete morphological steps: induction, which is marked by the initiation of sequestration; the formation and completion stage, during which the cargo becomes enclosed within a completed vesicle; the docking and fusion stage, where the outer vesicle membrane tethers to and fuses with the lysosome/vacuole; and breakdown, which involves lysis of the inner vesicle and degradation of the cargo. The two latter steps have been elucidated because they use the same machinery employed by the other delivery pathways to the lysosome/vacuole [3]. By contrast, despite the advances in understanding the cellular role of autophagy and the fact that most of the identified Atg proteins participate in double membrane vesicle formation, the mechanisms underpinning the first two steps remain largely unknown. This review will focus on the recent advances in understanding these first two steps in autophagosome biogenesis.