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Kaksonen GroupPublications

RNA Clamping by Vasa Assembles a piRNA Amplifier Complex on Transposon Transcripts.
Xiol, J., Spinelli, P., Laussmann, M.A., Homolka, D., Yang, Z., Cora, E., Coute, Y., Conn, S., Kadlec, J., Sachidanandam, R., Kaksonen, M., Cusack, S., Ephrussi, A. & Pillai, R.S.
Cell. 2014 Jun 4. pii: S0092-8674(14)00660-6. doi: 10.1016/j.cell.2014.05.018.
Germline-specific Piwi-interacting RNAs (piRNAs) protect animal genomes against transposons and are essential for fertility. piRNAs targeting active transposons are amplified by the ping-pong cycle, which couples Piwi endonucleolytic slicing of target RNAs to biogenesis of new piRNAs. Here, we describe the identification of a transient Amplifier complex that mediates biogenesis of secondary piRNAs in insect cells. Amplifier is nucleated by the DEAD box RNA helicase Vasa and contains the two Piwi proteins participating in the ping-pong loop, the Tudor protein Qin/Kumo and antisense piRNA guides. These components assemble on the surface of Vasa's helicase domain, which functions as an RNA clamp to anchor Amplifier onto transposon transcripts. We show that ATP-dependent RNP remodeling by Vasa facilitates transfer of 5' sliced piRNA precursors between ping-pong partners, and loss of this activity causes sterility in Drosophila. Our results reveal the molecular basis for the small RNA amplification that confers adaptive immunity against transposons.
Europe PMC

The initiation of clathrin-mediated endocytosis is mechanistically highly flexible.
Brach, T., Godlee, C., Moeller-Hansen, I., Boeke, D. & Kaksonen, M.
Curr Biol. 2014 Mar 3;24(5):548-54. doi: 10.1016/j.cub.2014.01.048. Epub 2014 Feb13.
Clathrin-mediated endocytosis is driven by a complex machinery of proteins, which assemble in a regular order at the plasma membrane [1-3]. The assembly of the endocytic machinery is conventionally thought to be a continuous process of mechanistically dependent steps, starting from a defined initiation step. Indeed, several initiation mechanisms involving single proteins have been proposed in mammalian cells [4, 5]. Here, we demonstrate that the initiation mechanism of endocytosis is highly flexible. We disrupted the long early phase of endocytosis in yeast by deleting seven genes encoding early endocytic proteins. Surprisingly, membrane uptake and vesicle budding dynamics were largely normal in these mutant cells. Regulated cargo recruitment was, however, defective. In addition, different early endocytic proteins were able to initiate vesicle budding when anchored to a plasma membrane domain where endocytosis does not normally take place. Our results suggest that the cargo-recruiting early phase is not mechanistically required for vesicle budding, but early-arriving proteins can recruit the budding machinery into position at the plasma membrane. Separable early and late phases allow for a robust process of vesicle budding to follow from variable initiation mechanisms. Such a modular design could easily adapt and evolve to respond to different cellular requirements.
Europe PMC

Review series: From uncertain beginnings: initiation mechanisms of clathrin-mediated endocytosis.
Godlee, C. & Kaksonen, M.
J Cell Biol. 2013 Dec 9;203(5):717-25. doi: 10.1083/jcb.201307100.
Clathrin-mediated endocytosis is a central and well-studied trafficking process in eukaryotic cells. How this process is initiated is likely to be a critical point in regulating endocytic activity spatially and temporally, but the underlying mechanisms are poorly understood. During the early stages of endocytosis three components-adaptor and accessory proteins, cargo, and lipids-come together at the plasma membrane to begin the formation of clathrin-coated vesicles. Although different models have been proposed, there is still no clear picture of how these three components cooperate to initiate endocytosis, which may indicate that there is some flexibility underlying this important event.
Europe PMC

Interactome map uncovers phosphatidylserine transport by oxysterol-binding proteins.
Maeda, K., Anand, K., Chiapparino, A., Kumar, A., Poletto, M., Kaksonen, M. & Gavin, A.C.
Nature. 2013 Sep 12;501(7466):257-61. doi: 10.1038/nature12430. Epub 2013 Aug 11.
The internal organization of eukaryotic cells into functionally specialized, membrane-delimited organelles of unique composition implies a need for active, regulated lipid transport. Phosphatidylserine (PS), for example, is synthesized in the endoplasmic reticulum and then preferentially associates--through mechanisms not fully elucidated--with the inner leaflet of the plasma membrane. Lipids can travel via transport vesicles. Alternatively, several protein families known as lipid-transfer proteins (LTPs) can extract a variety of specific lipids from biological membranes and transport them, within a hydrophobic pocket, through aqueous phases. Here we report the development of an integrated approach that combines protein fractionation and lipidomics to characterize the LTP-lipid complexes formed in vivo. We applied the procedure to 13 LTPs in the yeast Saccharomyces cerevisiae: the six Sec14 homology (Sfh) proteins and the seven oxysterol-binding homology (Osh) proteins. We found that Osh6 and Osh7 have an unexpected specificity for PS. In vivo, they participate in PS homeostasis and the transport of this lipid to the plasma membrane. The structure of Osh6 bound to PS reveals unique features that are conserved among other metazoan oxysterol-binding proteins (OSBPs) and are required for PS recognition. Our findings represent the first direct evidence, to our knowledge, for the non-vesicular transfer of PS from its site of biosynthesis (the endoplasmic reticulum) to its site of biological activity (the plasma membrane). We describe a new subfamily of OSBPs, including human ORP5 and ORP10, that transfer PS and propose new mechanisms of action for a protein family that is involved in several human pathologies such as cancer, dyslipidaemia and metabolic syndrome.
Europe PMC

Detection and characterization of protein interactions in vivo by a simple live-cell imaging method.
Gallego, O., Specht, T., Brach, T., Kumar, A., Gavin, A.C. & Kaksonen, M.
PLoS One. 2013 May 1;8(5):e62195. doi: 10.1371/journal.pone.0062195. Print 2013.
Over the last decades there has been an explosion of new methodologies to study protein complexes. However, most of the approaches currently used are based on in vitro assays (e.g. nuclear magnetic resonance, X-ray, electron microscopy, isothermal titration calorimetry etc). The accurate measurement of parameters that define protein complexes in a physiological context has been largely limited due to technical constrains. Here, we present PICT (Protein interactions from Imaging of Complexes after Translocation), a new method that provides a simple fluorescence microscopy readout for the study of protein complexes in living cells. We take advantage of the inducible dimerization of FK506-binding protein (FKBP) and FKBP-rapamycin binding (FRB) domain to translocate protein assemblies to membrane associated anchoring platforms in yeast. In this assay, GFP-tagged prey proteins interacting with the FRB-tagged bait will co-translocate to the FKBP-tagged anchor sites upon addition of rapamycin. The interactions are thus encoded into localization changes and can be detected by fluorescence live-cell imaging under different physiological conditions or upon perturbations. PICT can be automated for high-throughput studies and can be used to quantify dissociation rates of protein complexes in vivo. In this work we have used PICT to analyze protein-protein interactions from three biological pathways in the yeast Saccharomyces cerevisiae: Mitogen-activated protein kinase cascade (Ste5-Ste11-Ste50), exocytosis (exocyst complex) and endocytosis (Ede1-Syp1).
Europe PMC

Molecular basis for coupling the plasma membrane to the actin cytoskeleton during clathrin-mediated endocytosis.
Skruzny, M., Brach, T., Ciuffa, R., Rybina, S., Wachsmuth, M. & Kaksonen, M.
Proc Natl Acad Sci U S A. 2012 Sep 18;109(38):E2533-42. Epub 2012 Aug 27.
Dynamic actin filaments are a crucial component of clathrin-mediated endocytosis when endocytic proteins cannot supply enough energy for vesicle budding. Actin cytoskeleton is thought to provide force for membrane invagination or vesicle scission, but how this force is transmitted to the plasma membrane is not understood. Here we describe the molecular mechanism of plasma membrane-actin cytoskeleton coupling mediated by cooperative action of epsin Ent1 and the HIP1R homolog Sla2 in yeast Saccharomyces cerevisiae. Sla2 anchors Ent1 to a stable endocytic coat by an unforeseen interaction between Sla2's ANTH and Ent1's ENTH lipid-binding domains. The ANTH and ENTH domains bind each other in a ligand-dependent manner to provide critical anchoring of both proteins to the membrane. The C-terminal parts of Ent1 and Sla2 bind redundantly to actin filaments via a previously unknown phospho-regulated actin-binding domain in Ent1 and the THATCH domain in Sla2. By the synergistic binding to the membrane and redundant interaction with actin, Ent1 and Sla2 form an essential molecular linker that transmits the force generated by the actin cytoskeleton to the plasma membrane, leading to membrane invagination and vesicle budding.
Europe PMC

Plasma membrane reshaping during endocytosis is revealed by time-resolved electron tomography.
Kukulski, W., Schorb, M., Kaksonen, M. & Briggs, J.A.
Cell. 2012 Aug 3;150(3):508-20. doi: 10.1016/j.cell.2012.05.046.
Endocytosis, like many dynamic cellular processes, requires precise temporal and spatial orchestration of complex protein machinery to mediate membrane budding. To understand how this machinery works, we directly correlated fluorescence microscopy of key protein pairs with electron tomography. We systematically located 211 endocytic intermediates, assigned each to a specific time window in endocytosis, and reconstructed their ultrastructure in 3D. The resulting virtual ultrastructural movie defines the protein-mediated membrane shape changes during endocytosis in budding yeast. It reveals that clathrin is recruited to flat membranes and does not initiate curvature. Instead, membrane invagination begins upon actin network assembly followed by amphiphysin binding to parallel membrane segments, which promotes elongation of the invagination into a tubule. Scission occurs on average 9 s after initial bending when invaginations are approximately 100 nm deep, releasing nonspherical vesicles with 6,400 nm2 mean surface area. Direct correlation of protein dynamics with ultrastructure provides a quantitative 4D resource.
Europe PMC

Precise, correlated fluorescence microscopy and electron tomography of lowicryl sections using fluorescent fiducial markers.
Kukulski, W., Schorb, M., Welsch, S., Picco, A., Kaksonen, M. & Briggs, J.A.
Methods Cell Biol. 2012;111:235-57. doi: 10.1016/B978-0-12-416026-2.00013-3.
The application of fluorescence and electron microscopy to the same specimen allows the study of dynamic and rare cellular events at ultrastructural detail. Here, we present a correlative microscopy approach, which combines high accuracy of correlation, high sensitivity for detecting faint fluorescent signals, as well as robustness and reproducibility to permit large dataset collections. We provide a step-by-step protocol that allows direct mapping of fluorescent protein signals into electron tomograms. A localization precision of <100 nm is achieved by using fluorescent fiducial markers which are visible both in fluorescence images and in electron tomograms. We explain the critical details of the procedure, give background information on the individual steps, present results from test experiments carried out during establishment of the method, as well as information about possible modifications to the protocol, such as its application to 2D electron micrographs. This simple, robust, and flexible method can be applied to a large variety of cellular systems, such as yeast cell pellets and mammalian cell monolayers, to answer a broad spectrum of structure-function related questions.
Europe PMC

Reassessment of the role of plasma membrane domains in the regulation of vesicular traffic in yeast.
Brach, T., Specht, T. & Kaksonen, M.
J Cell Sci. 2011 Feb 1;124(Pt 3):328-37. Epub 2011 Jan 11.
The Saccharomyces cerevisiae plasma membrane has been proposed to contain two stably distributed domains. One of these domains, known as MCC (membrane compartment of Can1) or eisosomes, consists of furrow-like membrane invaginations and associated proteins. The other domain, called MCP (membrane compartment of Pma1), consists of the rest of the membrane area surrounding the MCC patches. The role of this plasma membrane domain organization in endocytosis is under debate. Here we show by live-cell imaging that vesicular traffic is restricted to the MCP and the distribution of endocytic and exocytic sites within the MCP is independent of the MCC patch positions. Photobleaching experiments indicated that Can1 and Tat2, two MCC-enriched permeases, exchange quickly between the two domains. Total internal reflection fluorescence and epi-fluorescence microscopy showed that the enrichment of Can1 at the MCC persisted after addition of its substrate, whereas the enrichment of Tat2 disappeared within 90 seconds. The rates of stimulated endocytosis of Can1 as well as Tat2 were similar in both wild-type cells and pil1Delta cells, which lack the MCC. Thus, our data suggest that the enrichment of certain plasma membrane proteins in the MCC does not regulate the rate of their endocytosis.
Europe PMC

Correlated fluorescence and 3D electron microscopy with high sensitivity and spatial precision.
Kukulski, W., Schorb, M., Welsch, S., Picco, A., Kaksonen, M. & Briggs, J.A.
J Cell Biol. 2011 Jan 10;192(1):111-9. doi: 10.1083/jcb.201009037. Epub 2011 Jan3.
Correlative electron and fluorescence microscopy has the potential to elucidate the ultrastructural details of dynamic and rare cellular events, but has been limited by low precision and sensitivity. Here we present a method for direct mapping of signals originating from approximately 20 fluorescent protein molecules to 3D electron tomograms with a precision of less than 100 nm. We demonstrate that this method can be used to identify individual HIV particles bound to mammalian cell surfaces. We also apply the method to image microtubule end structures bound to mal3p in fission yeast, and demonstrate that growing microtubule plus-ends are flared in vivo. We localize Rvs167 to endocytic sites in budding yeast, and show that scission takes place halfway through a 10-s time period during which amphiphysins are bound to the vesicle neck. This new technique opens the door for direct correlation of fluorescence and electron microscopy to visualize cellular processes at the ultrastructural scale.
Europe PMC

A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae.
Gallego, O., Betts, M.J., Gvozdenovic-Jeremic, J., Maeda, K., Matetzki, C., Aguilar-Gurrieri, C., Beltran-Alvarez, P., Bonn, S., Fernandez-Tornero, C., Jensen, L.J., Kuhn, M., Trott, J., Rybin, V., Muller, C.W., Bork, P., Kaksonen, M., Russell, R.B. & Gavin, A.C.
Mol Syst Biol. 2010 Nov 30;6:430. doi: 10.1038/msb.2010.87.
Protein-metabolite networks are central to biological systems, but are incompletely understood. Here, we report a screen to catalog protein-lipid interactions in yeast. We used arrays of 56 metabolites to measure lipid-binding fingerprints of 172 proteins, including 91 with predicted lipid-binding domains. We identified 530 protein-lipid associations, the majority of which are novel. To show the data set's biological value, we studied further several novel interactions with sphingolipids, a class of conserved bioactive lipids with an elusive mode of action. Integration of live-cell imaging suggests new cellular targets for these molecules, including several with pleckstrin homology (PH) domains. Validated interactions with Slm1, a regulator of actin polarization, show that PH domains can have unexpected lipid-binding specificities and can act as coincidence sensors for both phosphatidylinositol phosphates and phosphorylated sphingolipids.
Europe PMC

Taking apart the endocytic machinery.
Kaksonen, M.
J Cell Biol. 2008 Mar 24;180(6):1059-60.
The formation of clathrin-coated endocytic vesicles is driven by a complex and highly dynamic molecular machinery. In this issue, Idrissi et al. (Idrissi, F.-Z., H. Grotsch, I.M. Fernandez-Golbano, C. Presciatto-Baschong, H. Riezman, and M.-I. Geli. 2008. J. Cell Biol. 180:1219-1232) reveal some of the secrets of this machinery by analyzing the localizations of nine endocytic proteins during vesicle budding in yeast using quantitative immunoelectron microscopy.
Europe PMC

Endocytic vesicle scission by lipid phase boundary forces.
Liu, J., Kaksonen, M., Drubin, D.G. & Oster, G.
Proc Natl Acad Sci U S A. 2006 Jul 5;103(27):10277-82. Epub 2006 Jun 26.
Endocytosis in budding yeast is thought to occur in several phases. First, the membrane invaginates and then elongates into a tube. A vesicle forms at the end of the tube, eventually pinching off to form a "free" vesicle. Experiments show that actin polymerization is an active participant in the endocytic process, along with a number of membrane-associated proteins. Here we investigate the possible roles of these components in driving vesiculation by constructing a quantitative model of the process beginning at the stage where the membrane invagination has elongated into a tube encased in a sheath of membrane-associated protein. This protein sheath brings about the scission step where the vesicle separates from the tube. When the protein sheath is dynamin, it is commonly assumed that scission is brought about by the constriction of the sheath. Here, we show that an alternative scenario can work as well: The protein sheath acts as a "filter" to effect a phase separation of lipid species. The resulting line tension tends to minimize the interface between the tube region and the vesicle region. Interestingly, large vesicle size can further facilitate the reduction of the interfacial diameter down to a few nanometers, small enough so that thermal fluctuations can fuse the membrane and pinch off the vesicle. To deform the membrane into the tubular vesicle shape, the membrane elastic resistance forces must be balanced by some additional forces that we show can be generated by actin polymerization and/or myosin I. These active forces are shown to be important in successful scission processes as well.
Europe PMC

Harnessing actin dynamics for clathrin-mediated endocytosis.
Kaksonen, M., Toret, C.P. & Drubin, D.G.
Nat Rev Mol Cell Biol. 2006 Jun;7(6):404-14.
Actin polymerization often occurs at the plasma membrane to drive the protrusion of lamellipodia and filopodia at the leading edge of migrating cells. A role for actin polymerization in another cellular process that involves the reshaping of the plasma membrane--namely endocytosis--has recently been established. Live-cell imaging studies are shedding light on the order and timing of the molecular events and mechanisms of actin function during endocytosis.
Europe PMC

A modular design for the clathrin- and actin-mediated endocytosis machinery.
Kaksonen, M., Toret, C.P. & Drubin, D.G.
Cell. 2005 Oct 21;123(2):305-20.
Endocytosis depends on an extensive network of interacting proteins that execute a series of distinct subprocesses. Previously, we used live-cell imaging of six budding-yeast proteins to define a pathway for association of receptors, adaptors, and actin during endocytic internalization. Here, we analyzed the effects of 61 deletion mutants on the dynamics of this pathway, revealing functions for 15 proteins, and we analyzed the dynamics of 8 of these proteins. Our studies provide evidence for four protein modules that cooperate to drive coat formation, membrane invagination, actin-meshwork assembly, and vesicle scission during clathrin/actin-mediated endocytosis. We found that clathrin facilitates the initiation of endocytic-site assembly but is not needed for membrane invagination or vesicle formation. Finally, we present evidence that the actin-meshwork assembly that drives membrane invagination is nucleated proximally to the plasma membrane, opposite to the orientation observed for previously studied actin-assembly-driven motility processes.
Europe PMC

A pathway for association of receptors, adaptors, and actin during endocytic internalization.
Kaksonen, M., Sun, Y. & Drubin, D.G.
Cell. 2003 Nov 14;115(4):475-87.
In budding yeast, many proteins involved in endocytic internalization, including adaptors and actin cytoskeletal proteins, are localized to cortical patches of differing protein composition. Using multicolor real-time fluorescence microscopy and particle tracking algorithms, we define an early endocytic pathway wherein an invariant sequence of changes in cortical patch protein composition correlates with changes in patch motility. Three Arp2/3 activators each showed a distinct behavior, suggesting distinct patch-related endocytic functions. Actin polymerization occurs late in the endocytic pathway and is required both for endocytic internalization and for patch disassembly. In cells lacking the highly conserved endocytic protein Sla2p, patch motility was arrested and actin comet tails associated with endocytic patch complexes. Fluorescence recovery after photobleaching of the actin comet tails revealed that endocytic complexes are nucleation sites for rapid actin polymerization. Attention is now focused on the mechanisms by which the order and timing of events in this endocytic pathway are achieved.
Europe PMC