Self-digestion as a means of survival

February 27, 2009

How cells recognize and deal with protein waste

In times of starvation, cells tighten their belts: they start to digest their own proteins and cellular organs. The process - known as autophagy - takes place in special organelles called autophagosomes. It is a strategy that simple yeast cells have developed as a means of survival when times get tough, and in the course of evolution, it has become a kind of self-cleaning process. In mammalian cells, autophagosomes are also responsible for getting rid of misfolded proteins, damaged organelles or disease-causing bacteria.

If this process malfunctions, it can result in infectious diseases, as well as cancer, Parkinson's or Alzheimer's disease. Biochemists at Frankfurt's Goethe University, working together with scientists from the University of Tromsø in Norway, the Weizmann Institute in Israel and the Tokyo Metropolitan Institute in Japan have just come up with an explanation as to how autophagosomes know exactly which proteins and organelles they should degrade.

"Although autophagy has been known for more than 30 years, it is astonishing that no-one thought of looking for the receptors that make this process so selective" explains Prof. Ivan Dikic from the Institute of Biochemistry II and the Cluster of Excellence 'Macromolecular Complexes' in Frankfurt. He had a head start in this field, since over several years, he and his group have researched and now published their work on another self-cleaning process in the cell: the degradation of small proteins in the proteasome, which acts as a kind of molecular shredder.

"We know that the molecules which are destined to be discarded are marked with the small protein ubiquitin and this is recognised by a receptor located at the gateway to the proteasome. It was natural to suggest a similar recognition mechanism for protein degradation by autophagosomes", says Dikic.

Unlike the proteasome, which is a complex molecular machine, autophagosomes simply consist of a double membrane that floats around in the cytoplasm. Not unlike white blood cells, they can engulf larger proteins or even whole cell organelles. But since they have no enzymes with which they can digest their own cargo, they fuse with lysosomes. When a Yoshinori Ohsumi's group in Japan reported that they had discovered ubiquitin-like proteins (ATG8) on the outer surface of the autophagosome and gone on to prove that they were specific for autophagy, Dikic and his colleague Dr. Vladimir Kirkin immediately began their search for potential autophagy receptors that might bind to the family of ATG8 proteins.

The team of international scientists report in the current issue of the renowned journal "Molecular Cell", that by employing methods from cell biology, biochemistry and mouse genetics, they have been able to identify a further protein, in addition to the known p62/SQSTM1 protein, that may act as a receptor. This is the protein NBR1, which has long been associated with cancer. Both proteins have a similar chain-like structure. At one end they bind to the ubiquitin that marks the protein aggregates and organelles that are to be degraded. Next to the ubiquitin-binding site is a domain that binds to the ATG8 proteins found at the autophagosomal membrane. Here, the protein waste can dock onto the autophagosome and can then be wrapped up in the membrane.

Vladimir Kirkin, who is now at Merck Serono in Darmstadt, is continuing these investigations with the long-term aim of developing new drugs. Dikic and his group are now concentrating on mitochondria - which are implicated in oxidative stress in cells - hoping to locate the receptors for autophagy on these important organelles.

Goethe University Frankfurt

Autophagosome and Phagosome (Methods in Molecular Biology)
by Vojo Deretic (Editor)

Autophagy and phagocytosis are distinct yet partially morphologically similar processes. Understanding them is vital for the studies of cancer, aging, neurodegeneration, immunology, and infectious diseases. This book presents autophagosome and phagosome methods for novices and advanced researchers alike. Comprehensive and forward-thinking, the book offers a valuable guide to both cellular processes while inciting researchers to explore their potentially important connections.

The function and trafficking of Atg8 during autophagosome formation.
by Zhiping Xie (Author)

Eukaryotic cells rely on autophagy to remove excess or damaged organelles and proteins. In this pathway, cytoplasmic materials are delivered to the lysosomes via double-membrane vesicles, the autophagosomes. The formation of autophagosomes, which involves the expansion and deformation of the precursor membrane sac, the phagophore, is catalyzed by the core autophagy machinery proteins at the phagophore assembly site (PAS). Previous studies have gradually discovered the order of assembly of the core autophagy machinery proteins at the PAS. In contrast, we know little about what these proteins do after PAS assembly. In this study, I first focused on how Atg8, one of the core machinery proteins, functions in autophagosome formation and demonstrated that (1) the amount of Atg8 at the PAS...

Analysis of the molecular mechanism of autophagosome formation in yeast and zebrafish models.
by Congcong He (Author)

Autophagy is a conserved intracellular degradative pathway induced by various stress or developmental signals in eukaryotes, and its malfunction contributes to a variety of diseases. During autophagy, cargos such as cytosolic proteins, damaged organelles and invasive pathogens are engulfed into double-membrane autophagosomes, transported to, and degraded in the lysosome/vacuole. Over 30 ATG (autopha gy-related) genes have been identified in the budding yeast S. cerevisiae. To understand the molecular mechanism controlling membrane delivery during autophagy, I studied protein interactions involving Atg9, the only known transmembrane protein required for autophagosome formation. In yeast, Atg9 cycles between peripheral sites and the phagophore assembly site (PAS), suggesting its role in...

Analysis of the molecular mechanism of autophagosome formation in Saccharomyces cerevisiae.
by Wei-Lien Yen (Author)

Autophagy is an evolutionarily conserved catabolic pathway in eukaryotic cells, which is involved in the degradation of long-lived proteins, organelles, and a large portion of the cytoplasm in response to internal and external stresses, such as nutrient starvation. In addition, autophagy is involved in development, and cellular remodeling, and plays a cytoprotective role by removing protein aggregates, and damaged or superfluous organelles, which may contribute to a role in life span extension. Defects in autophagy are associated with various diseases, such as cancer, gastrointestinal disorders and neurodegeneration. During autophagy, the cargos that are targeted for degradation are sequestered into double-membrane vesicles. However, the mechanisms of vesicle formation and completion as...

Autophagosome and phagosome. (Methods in molecular biology; 445)
by Ed. by Vojo Deretic. (Author)

Autophagy in Immunity and Infection
by Vojo Deretic (Editor)

This first book to cover this new topic at the interface of cell biology, immunology and infection biology offers a unique insight as to how the innate and possibly the adaptive immune system are shaped by cellular mechanisms. Following a comprehensive introduction to autophagy, the work features cellular mechanisms and medical implications, structured according to all major pathogens, while also covering emerging infectious diseases, such as tuberculosis. Edited by one of the authors of a groundbreaking paper on this topic.

Autophagy in Infection and Immunity (Current Topics in Microbiology and Immunology)
by Beth Levine (Editor), Tamotsu Yoshimori (Editor), Vojo Deretic (Editor)

Autophagy is a fundamental biological process that enables cells to autodigest their own cytosol during starvation and other forms of stress. It has a growing spectrum of acknowledged roles in immunity, aging, development, neurodegeneration, and cancer biology. An immunological role of autophagy was first recognized with the discovery of autophagy’s ability to sanitize the cellular interior by killing intracellular microbes. Since then, the repertoire of autophagy’s roles in immunity has been vastly expanded to include a diverse but interconnected portfolio of regulatory and effector functions. Autophagy is an effector of Th1/Th2 polarization; it fuels MHC II presentation of cytosolic (self and microbial) antigens; it shapes central tolerance; it affects B and T cell homeostasis; it...

Autophagy in Disease and Clinical Applications, Volume 453: Part C (Methods in Enzymology)
by Daniel Klionsky (Editor)

The third and final installment of Daniel J. Klionsky's new three-volume treatment of autophagy, this volume focuses on monitoring autophagy with regard to disease connections, and presents methods that can be used to analyze autophagy in clinical samples. Edited by one of the leading authorities in the field, this volume and its companion volumes, Autophagy: Lower Eukaryotes and Autophagy in Mammalian Systems, provide a comprehensive overview of the techniques involved in studying autophagy in eukaryotes and simple animal systems, mammalian cells and non-human animals, and humans.

Particularly in times of stress, like starvation and disease, higher organisms have an internal mechanism in their cells for chewing up and recycling parts of themselves. The process of internal "house...

Autophagy in Mammalian Systems, Volume 452: Part B (Methods in Enzymology)
by Daniel Klionsky (Editor)

Particularly in times of stress, like starvation and disease, higher organisms have an internal mechanism in their cells for chewing up and recycling parts of themselves. The process of internal "house-cleaning” in the cell is called autophagy - literally self-eating. Breakthroughs in understanding the molecular basis of autophagy came after the cloning of ATG1 in yeast. These ATG genes in yeast were the stepping stones to the explosion of research into the molecular analysis of autophagy in higher eukaryotes. In the future, this research will help to design clinical approaches that can turn on autophagy and halt tumor growth.

In this volume, a robust slate of methods for conducting research are presented, establishing a consensus of appropriate criteria for monitoring...