Structure-based Analyses Reveal Distinct Binding Sites for Atg2 and Phosphoinositides in Atg18

Watanabe, Yasunori; Kobayashi, Takafumi; Yamamoto, Hayashi; Hoshida, Hisashi; Akada, Rinji; Inagaki, Fuyuhiko; Ohsumi, Yoshinori; Noda, Nobuo N.

doi:10.1074/jbc.m112.397570

Cited by 120 publications

(176 citation statements)

References 40 publications

Supporting

Mentioning

158

Contrasting

Order By: Relevance

“…The Atg18 β1-β2 loop and β2-β3 loop in blade 2 are important for PAS targeting [151]. Blade 2 is located at the opposite position to blade 5 and blade 6, and thus is not involved in membrane docking.…”

Section: Atg9 Complexmentioning

confidence: 99%

“…Blade 2 is located at the opposite position to blade 5 and blade 6, and thus is not involved in membrane docking. Additional studies indicate that the loops in blade 2 are important for Atg18-Atg2 interaction [151,154], allowing a refinement of the model for Atg18 membrane binding. While Atg18 binds to the membrane through blades 5 and 6, blade 2, which is located on the opposite side of the protein, interacts with Atg2.…”

Section: Atg9 Complexmentioning

confidence: 99%

“…Atg18, together with Atg2, helps Atg9 cycle from the PAS to peripheral sites [63]. Although the structure of Atg18 has not been solved, a paralog, Hsv2, which shares high sequence similarity with Atg18, has been studied in different yeast strains [150][151][152]. Both proteins belong to the "PROPPINs" family, which are defined by β propeller structures and the existence of phosphoinositide binding sites [152,153].…”

Section: Atg9 Complexmentioning

confidence: 99%

See 2 more Smart Citations

The machinery of macroautophagy

et al. 2013

View full text Add to dashboard Cite

Autophagy is a primarily degradative pathway that takes place in all eukaryotic cells. It is used for recycling cytoplasm to generate macromolecular building blocks and energy under stress conditions, to remove superfluous and damaged organelles to adapt to changing nutrient conditions and to maintain cellular homeostasis. In addition, autophagy plays a critical role in cytoprotection by preventing the accumulation of toxic proteins and through its action in various aspects of immunity including the elimination of invasive microbes and its participation in antigen presentation. The most prevalent form of autophagy is macroautophagy, and during this process, the cell forms a double-membrane sequestering compartment termed the phagophore, which matures into an autophagosome. Following delivery to the vacuole or lysosome, the cargo is degraded and the resulting macromolecules are released back into the cytosol for reuse. The past two decades have resulted in a tremendous increase with regard to the molecular studies of autophagy being carried out in yeast and other eukaryotes. Part of the surge in interest in this topic is due to the connection of autophagy with a wide range of human pathophysiologies including cancer, myopathies, diabetes and neurodegenerative disease. However, there are still many aspects of autophagy that remain unclear, including the process of phagophore formation, the regulatory mechanisms that control its induction and the function of most of the autophagy-related proteins. In this review, we focus on macroautophagy, briefly describing the discovery of this process in mammalian cells, discussing the current views concerning the donor membrane that forms the phagophore, and characterizing the autophagy machinery including the available structural information.

show abstract

Section: Atg9 Complexmentioning

confidence: 99%

Section: Atg9 Complexmentioning

confidence: 99%

Section: Atg9 Complexmentioning

confidence: 99%

See 1 more Smart Citation

The machinery of macroautophagy

et al. 2013

View full text Add to dashboard Cite

show abstract

“…In contrast to S. cerevisiae and K. lactis, which are widely used for molecular biology and industrial applications (Mattiazzi et al, 2012;Schaffrath and Breunig, 2000;Schwimmer et al, 2006;Smith and Snyder, 2006;van Leeuwen et al, 2012), K. marxianus has received relatively little attention, although there are an increasing number of reports describing the potential application of K. marxianus for the production of ethanol, biomass, endogenous enzymes and aromatic compounds (Bansal et al, 2008;Fonseca et al, 2008;Gao and Daugulis, 2009;Limtong et al, 2007;Nonklang et al, 2008Nonklang et al, , 2009Rodrussamee et al, 2011;Wittmann et al, 2002) and for protein structural analysis (Watanabe et al, 2012;Yamaguchi et al, 2012aYamaguchi et al, , 2012b. Thus, in the present study, we generated and characterized 79 auxotrophic mutants and identified 35 complementing genes using a novel integrative transformation approach for the development of genetic tools in K. marxianus.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, several K. marxianus proteins, including the autophagy-related proteins KmAtg7, KmAtg10 and KmHsv2, have been applied to crystal structural analysis because the formation of crystals of the orthologous S. cerevisiae proteins was difficult (Watanabe et al, 2012;Yamaguchi et al, 2012aYamaguchi et al, , 2012b. However, the genetic and functional analyses of these and other K. marxianus proteins has not been performed in K. marxianus due to the lack of genetic techniques that are commonly available for conventional yeast species.…”

Section: Introductionmentioning

confidence: 99%

Identification of auxotrophic mutants of the yeast Kluyveromyces marxianus by non‐homologous end joining‐mediated integrative transformation with genes from Saccharomyces cerevisiae

Yarimizu

Nonklang

Nakamura

et al. 2013

Yeast

Self Cite

View full text Add to dashboard Cite

The isolation and application of auxotrophic mutants for gene manipulations, such as genetic transformation, mating selection and tetrad analysis, form the basis of yeast genetics. For the development of these genetic methods in the thermotolerant fermentative yeast Kluyveromyces marxianus, we isolated a series of auxotrophic mutants with defects in amino acid or nucleic acid metabolism. To identify the mutated genes, linear DNA fragments of nutrient biosynthetic pathway genes were amplified from Saccharomyces cerevisiae chromosomal DNA and used to directly transform the K. marxianus auxotrophic mutants by random integration into chromosomes through non-homologous end joining (NHEJ). The appearance of transformant colonies indicated that the specific S. cerevisiae gene complemented the K. marxianus mutant. Using this interspecific complementation approach with linear PCR-amplified DNA, we identified auxotrophic mutations of ADE2, ADE5,7, ADE6, HIS2, HIS3, HIS4, HIS5, HIS6, HIS7, LYS1, LYS2, LYS4, LYS9, LEU1, LEU2, MET2, MET6, MET17, TRP3, TRP4 and TRP5 without the labour-intensive requirement of plasmid construction. Mating, sporulation and tetrad analysis techniques for K. marxianus were also established. With the identified auxotrophic mutant strains and S. cerevisiae genes as selective markers, NHEJ-mediated integrative transformation with PCR-amplified DNA is an attractive system for facilitating genetic analyses in the yeast K. marxianus.

show abstract

Phosphoinositide‐binding proteins in autophagy

Lystad

Simonsen

2016

FEBS Letters

View full text Add to dashboard Cite

Edited by Wilhelm JustPhosphoinositides represent a very small fraction of membrane phospholipids, having fast turnover rates and unique subcellular distributions, which make them perfect for initiating local temporal effects. Seven different phosphoinositide species are generated through reversible phosphorylation of the inositol ring of phosphatidylinositol (PtdIns). The negative charge generated by the phosphates provides specificity for interaction with various protein domains that commonly contain a cluster of basic residues. Examples of domains that bind phosphoinositides include PH domains, WD40 repeats, PX domains, and FYVE domains. Such domains often display specificity toward a certain species or subset of phosphoinositides. Here we will review the current literature of different phosphoinositide-binding proteins involved in autophagy.Keywords: autophagy; FYVE; PH; phosphoinositide; PX AutophagyAutophagy is the process by which cellular components are transported to the lysosome (or the yeast vacuole) for degradation to provide cellular homeostasis and quality control. There are three main forms of autophagy, namely microautophagy, which involves a direct engulfment of cytosolic cargo by the endosomal or lysosomal/vacuolar membrane, chaperone-mediated autophagy (CMA), involving lysosomal translocation of cytosolic protein cargo, and macroautophagy, a vesicle transport pathway where cargo is sequestered into double-membrane autophagosomes which undergo fusion with endosomes and/or the lysosome/vacuole. Autophagy is induced upon cellular stress (e.g., starvation) to facilitate cell survival by providing building blocks that can be used to produce essential molecules and generate energy. However, autophagy also serves an important quality control function under basal conditions by selective clearance of damaged or dysfunctional cellular components [1].Macroautophagy (hereafter autophagy) involves nucleation of a phagophore membrane (also called the isolation membrane) from specific phosphatidyl inositol 3-phosphate (PtdIns3P)-enriched structures, called the phagophore assembly site (PAS, a peri-vacuolar structure) in yeast and the omegasome (associated with the endoplasmic reticulum, ER) in mammals. Typically, there is only a single PAS in yeast, while several ER-associated omegasomes are detected upon Abbreviations ALFY, autophagy-linked FYVE protein; Arf6, adenosine diphosphate ribosylation factor 6; ATG, autophagy-related; BATS, biotin and thiamin synthesis-associated domain; Cvt, cytoplasm-to-vacuole; DFCP1, double FYVE-containing protein 1; ER, endoplasmic reticulum; FYCO1, FYVE and coiled-coil domain-containing 1; GRAM, glycosyltransferases Rab-like GTPase activators and myotubularins; HOPS, homotypic fusion and protein sorting; Hsv2, homologous with swollen vacuole phenotype 2; LIR, LC3-interacting region; MTMR3, myotubularin-related protein 3; mTORC1, mechanistic target of rapamycin complex 1; PA, phosphatidic acid; PAS, phagophore assembly site; PDPK1, 3-phosphoinositide-dependent protein kinase ...

show abstract

Structure-based Analyses Reveal Distinct Binding Sites for Atg2 and Phosphoinositides in Atg18

Cited by 120 publications

References 40 publications

The machinery of macroautophagy

The machinery of macroautophagy

Identification of auxotrophic mutants of the yeast Kluyveromyces marxianus by non‐homologous end joining‐mediated integrative transformation with genes from Saccharomyces cerevisiae

Phosphoinositide‐binding proteins in autophagy

Contact Info

Product

Resources

About