Corrigendum: Systems survey of endocytosis by multiparametric image analysis (original) (raw)
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Systems survey of endocytosis by multiparametric image analysis
Nature, 2010
Endocytosis is a complex process fulfilling many cellular and developmental functions. Understanding how it is regulated and integrated with other cellular processes requires a comprehensive analysis of its molecular constituents and general design principles. Here, we developed a new strategy to phenotypically profile the human genome with respect to transferrin (TF) and epidermal growth factor (EGF) endocytosis by combining RNA interference, automated high-resolution confocal microscopy, quantitative multiparametric image analysis and high-performance computing. We identified several novel components of endocytic trafficking, including genes implicated in human diseases. We found that signalling pathways such as Wnt, integrin/cell adhesion, transforming growth factor (TGF)-b and Notch regulate the endocytic system, and identified new genes involved in cargo sorting to a subset of signalling endosomes. A systems analysis by Bayesian networks further showed that the number, size, concentration of cargo and intracellular position of endosomes are not determined randomly but are subject to specific regulation, thus uncovering novel properties of the endocytic system.
proteins physically moves from the cis position (nearest the ER) to the trans position (farthest from the ER), successively becoming first a medial-Golgi cisterna and then a trans-Golgi cisterna. This process, known as cisternal progression, does not involve the budding off and fusion of anterograde transport vesicles. During cisternal progression, enzymes and other Golgi-resident proteins are constantly being retrieved from later to earlier Golgi cisternae by retrograde transport vesicles, thereby remaining localized to the cis-, medial-, or trans-Golgi cisternae.
Prospective isolation and global gene expression analysis of definitive and visceral endoderm
Developmental Biology, 2007
In spite of the therapeutic importance of endoderm derivatives such as the pancreas, liver, lung, and intestine, there are few molecular markers specific for early endoderm. In order to identify endoderm-specific genes as well as to define transcriptional differences between definitive and visceral endoderm, we performed microarray analysis on E8.25 definitive and visceral endoderm. We have developed an early endoderm gene expression signature, and clarified the transcriptional similarities and differences between definitive and visceral endoderm. Additionally, we have developed methods for flow cytometric isolation of definitive and visceral endoderm. These results shed light on the mechanism of endoderm formation and should facilitate investigation of endoderm formation from embryonic stem cells.
Cell, 2003
and Genetics proteins. Indeed, Robinson presented evidence that Pfotenhauerstrasse 108 AP-2 is required for endocytosis of membrane proteins D-01307 Dresden whose cytoplasmic tails contain the endocytosis signal Germany YXXφ (where X is any amino acid and φ is a bulky 2 The Norwegian Radium Hospital hydrophobic amino acid). This signal is found in a num-Department of Biochemistry ber of membrane proteins, including the transferrin re-Montebello ceptor, TGN38, and the cation-independent mannose N-0310 Oslo 6-phosphate receptor. Using the RNAi knockdown ap-Norway proach, Robinson showed that proteins with clathrin endocytosis signals different from YXXφ, such as FXNPXY, are endocytosed by AP-2-independent pathways (Fig-The ability to internalize macromolecules by endocyure 1). Which, then, are the clathrin adaptors for these tosis is a property of all eukaryotic cells. Frontline proteins? Robinson suggested that a group of clathrinresearch on endocytosis has been presented in a sucand cargo-associated proteins that have so far been cessful series of biannual meetings in Europe. This regarded as accessory proteins for clathrin and AP-2 year's meeting on "Membrane Dynamics in Endocytocould be good candidates. These proteins include Epsis" was held September 13-18 in Acquafredda di Masin, Hip1, Dab2, AP180, -arrestin, and ARH (Motley et ratea, on the coast of southern Italy. Four key quesal., 2003; Conner and Schmid, 2003a). This imposes a tions were addressed: What are the molecular novel level of diversity on endocytic routes and mechamechanisms of endocytic membrane trafficking? How nisms: even the mechanisms of cargo recruitment during does endocytosis modulate receptor signaling and the clathrin pathway involve different types of adaptors. vice versa? What is the importance of endocytosis When AP-2 is involved, how is cargo recognition acduring development? How do endocytic organelles complished, and how is the cargo targeted specifically contribute to immunity or susceptibility to pathogens?
Eisosomes mark static sites of endocytosis
2006
Abstract Endocytosis functions to recycle plasma membrane components, to regulate cell-surface expression of signalling receptors and to internalize nutrients in all eukaryotic cells. Internalization of proteins, lipids and other cargo can occur by one of several pathways that have different, but often overlapping, molecular requirements 1, 2, 3, 4, 5.
Proceedings of The National Academy of Sciences, 2006
The FYVE domain binds with high specificity and avidity to phosphatidylinositol 3-phosphate. It is present in Ϸ30 proteins in humans, some of which have been implicated in functions ranging from early endosome fusion to signal transduction through the TGF- receptor. To develop a further understanding of the biological roles of this protein family, we turned to the nematode Caenorhabditis elegans, which contains only 12 genes predicted to encode for phosphatidylinositol 3-phosphate binding, FYVE domain-containing proteins, all of which have homologs in the human genome. Each of these proteins was targeted individually by RNA interference. One protein, WDFY2, produced a strong inhibition of endocytosis when silenced. WDFY2 contains WD40 motifs and a FYVE domain, is highly conserved between species, and localizes to a set of small endosomes that reside within 100 nm from the plasma membrane. These endosomes are involved in transferrin uptake but lack the classical endosomal markers Rab5 and EEA1. Silencing of WDFY2 by siRNA in mammalian cells impaired transferrin endocytosis. These studies reveal the important, conserved role of WDFY2 in endocytosis, and the existence of a subset of early endosomes, closely associated with the plasma membrane, that may constitute the first stage of endocytic processing of internalized cargo.
Plant Signaling & Behavior, 2008
Endocytosis regulates many important and diverse processes in eukaryotic life. EH domain containing proteins function as regulators of endocytosis through protein-protein interactions. Several interactors of mammalian EHDs were identified, including clathrin machinery components. The four human EHD proteins share high homology at the protein level and possess similar domains, but appear to be involved in different stages of intracellular trafficking. EHD1 regulates recycling through the endocytic recycling compartment (ERC). EHD2 has been found to inhibit internalization in mammalians when overexpressed.