Reprogramming of G protein-coupled receptor recycling and signaling by a kinase switch

The postendocytic recycling of signaling receptors is subject to multiple requirements. Why this is so, considering that many other proteins can recycle without apparent requirements, is a fundamental question. Here we show that cells can leverage these requirements to switch the recycling of the beta-2 adrenergic receptor (B2AR), a prototypic signaling receptor, between sequence-dependent and bulk recycling pathways, based on extracellular signals. This switch is determined by protein kinase A-mediated phosphorylation of B2AR on the cytoplasmic tail. The phosphorylation state of B2AR dictates its partitioning into spatially and functionally distinct endosomal microdomains mediating bulk and sequence-dependent recycling, and also regulates the rate of B2AR recycling and resensitization. Our results demonstrate that G protein-coupled receptor recycling is not always restricted to the sequence-dependent pathway, but may be reprogrammed as needed by physiological signals. Such flexible reprogramming might provide a versatile method for rapidly modulating cellular responses to extracellular signaling.How proteins are sorted in the endocytic pathway is a fundamental question in cell biology. This is especially relevant for signaling receptors, given that relatively small changes in rates of receptor sorting into the recycling pathway can cause significant changes in surface receptors, and hence in cellular sensitivity (1–3). Our knowledge of receptor signaling and trafficking comes mainly from studying examples such as the beta-2 adrenergic receptor (B2AR), a prototypical member of G protein-coupled receptor (GPCR) family, the largest family of signaling receptors (2–5). B2AR activation initiates surface receptor removal and transport to endosomes, causing cellular desensitization (6, 7). The rate and extent of resensitization is then determined by B2AR surface recycling (1–3, 8, 9).Interestingly, the recycling of signaling receptors is functionally distinct from the recycling of constitutively cycling proteins like the transferrin receptor (TfR) (1, 6, 10, 11). TfR recycles by “bulk” geometric sorting, largely independent of specific cytoplasmic sequences (12, 13). B2AR recycling, in contrast, requires a specific PSD95-Dlg1-zo-1 domain (PDZ)-ligand sequence on its C-terminal tail, which links the receptor to the actin cytoskeleton (14, 15). Recent work has identified physically and biochemically distinct microdomains on early endosomes that mediate B2AR recycling independent of TfR (14–16). Although the exact mechanisms of B2AR sorting into these domains remain under investigation, this sorting clearly requires specific sequence elements on B2AR (1, 10, 11, 17). Importantly, why signaling receptor sorting is subject to such specialized requirements, considering that cargo like TfR apparently can recycle without specific sequence requirements, is not clear (1, 12–16). One possibility is that these requirements allow signaling pathways to regulate and redirect receptor trafficking between different pathways as needed (17–19). Although this is an attractive idea, whether and how physiological signals regulate receptor sorting remain poorly understood (7, 19).Here we show that adrenergic signaling can switch B2AR recycling between the sequence-dependent and bulk recycling pathways. Adrenergic activation, via protein kinase A (PKA)-mediated B2AR phosphorylation on the cytoplasmic tail, restricts B2AR to spatially defined PDZ- and actin-dependent endosomal microdomains. Dephosphorylation of B2AR switches B2AR to the bulk (PDZ-independent) recycling pathway, causing faster recycling of B2AR and increased cellular sensitivity. Our results suggest that cells may leverage sequence requirements for rapid adaptive reprogramming of signaling receptor trafficking and cellular sensitivity.     

Variable priming of a docked synaptic vesicle

The priming of a docked synaptic vesicle determines the probability of its membrane (VM) fusing with the presynaptic membrane (PM) when a nerve impulse arrives. To gain insight into the nature of priming, we searched by electron tomography for structural relationships correlated with fusion probability at active zones of axon terminals at frog neuromuscular junctions. For terminals fixed at rest, the contact area between the VM of docked vesicles and PM varied >10-fold with a normal distribution. There was no merging of the membranes. For terminals fixed during repetitive evoked synaptic transmission, the normal distribution of contact areas was shifted to the left, due in part to a decreased number of large contact areas, and there was a subpopulation of large contact areas where the membranes were hemifused, an intermediate preceding complete fusion. Thus, fusion probability of a docked vesicle is related to the extent of its VM–PM contact area. For terminals fixed 1 h after activity, the distribution of contact areas recovered to that at rest, indicating the extent of a VM–PM contact area is dynamic and in equilibrium. The extent of VM–PM contact areas in resting terminals correlated with eccentricity in vesicle shape caused by force toward the PM and with shortness of active zone material macromolecules linking vesicles to PM components, some thought to include Ca²⁺ channels. We propose that priming is a variable continuum of events imposing variable fusion probability on each vesicle and is regulated by force-generating shortening of active zone material macromolecules in dynamic equilibrium.Synaptic vesicles (SVs) move toward and dock on (are held in contact with) the presynaptic plasma membrane (PM) of a neuron’s axon terminal before fusing with the PM and releasing their neurotransmitter into the synaptic cleft to mediate synaptic transmission (1, 2). Docking is achieved by force-generating interactions of the vesicle membrane (VM) protein synaptobrevin with the PM proteins syntaxin and SNAP25 (3, 4). These interactions, which produce force by forming a coiled coil called the SNARE core complex, are regulated by auxiliary proteins (1, 5–7). Such force on the VM–PM contact site may also play a role in their fusion (8). At typical synapses, docking and fusion take place at structurally specialized regions along the PM called active zones (9, 10). Several lines of evidence suggest that the formation of the SNARE core complex occurs in the macromolecules composing the common active zone organelle, active zone material (AZM) (2, 11–14), which is positioned near Ca²⁺ channels concentrated in the PM at active zones (15–17). Influx of Ca²⁺ through the channels after the arrival of a nerve impulse triggers fusion of the VM of docked SVs with the PM.Priming is a step in synaptic transmission between the docking of an SV on, and fusion with, the PM and accounts for the observation that relatively few docked SVs fuse with the PM after the arrival of a nerve impulse (18). It has been suggested that priming transitions docked SVs from fusion-incompetent (i.e., having 0% fusion probability) to fusion-competent (i.e., having 100% fusion probability), in a binary way (reviewed in ref. 19). However, as described for frog neuromuscular junctions (20–23), the number of SVs that can fuse with the PM after arrival of an impulse varies greatly with differing concentrations of cytosolic Ca²⁺, indicating that priming is more complex than a simple binary transition. Biochemical and electrophysiological approaches have provided evidence that priming is mediated by interactions between the SNARE proteins and their regulators (7, 12–14, 24) and can involve differences in positioning of docked SVs relative to Ca²⁺ channels (25). Biochemistry has also led to the suggestion that primed SVs may become deprimed (26).We have previously shown by electron tomography on frog neuromuscular junctions (NMJs) fixed at rest that there are, for docked SVs, variations in the extent of the VM–PM contact area and in the length of the several AZM macromolecules linking the VM to the PM, the so-called ribs, pegs, and pins (2, 27). Here, we examined these, and other, structural variations in the same axon terminals fixed at rest, during repetitive evoked synaptic activity, or after recovery from such activity, with a view toward testing and extending our understanding of the processes that regulate priming. Our findings suggest a model in which all docked SVs are primed to varying degrees by a reversible continuum of AZM-mediated forces on them, and it is the degree of priming at any moment that determines the probability of a docked SV fusing with the PM upon arrival of a nerve impulse.     

Lysine 63-linked polyubiquitination is required for EGF receptor degradation

Ubiquitination mediates endocytosis and endosomal sorting of various signaling receptors, transporters, and channels. However, the relative importance of mono- versus polyubiquitination and the role of specific types of polyubiquitin linkages in endocytic trafficking remain controversial. We used mass spectrometry-based targeted proteomics to show that activated epidermal growth factor receptor (EGFR) is ubiquitinated by one to two short (two to three ubiquitins) polyubiquitin chains mainly linked via lysine 63 (K63) or conjugated with a single monoubiquitin. Multimonoubiquitinated EGFR species were not found. To directly test whether K63 polyubiquitination is necessary for endocytosis and post-endocytic sorting of EGFR, a chimeric protein, in which the K63 linkage-specific deubiquitination enzyme AMSH [associated molecule with the Src homology 3 domain of signal transducing adaptor molecule (STAM)] was fused to the carboxyl terminus of EGFR, was generated. MS analysis of EGFR-AMSH ubiquitination demonstrated that the fraction of K63 linkages was substantially reduced, whereas relative amounts of monoubiquitin and K48 linkages increased, compared with that of wild-type EGFR. EGFR-AMSH was efficiently internalized into early endosomes, but, importantly, the rates of ligand-induced sorting to late endosomes and degradation of EGFR-AMSH were dramatically decreased. The slow degradation of EGFR-AMSH resulted in the sustained signaling activity of this chimeric receptor. Ubiquitination patterns, rate of endosomal sorting, and signaling kinetics of EGFR fused with the catalytically inactive mutant of AMSH were reversed to normal. Altogether, the data are consistent with the model whereby short K63-linked polyubiquitin chains but not multimonoubiquitin provide an increased avidity for EGFR interactions with ubiquitin adaptors, thus allowing rapid sorting of activated EGFR to the lysosomal degradation pathway.Ubiquitination, a posttranslational modification of proteins by attachment of the ubiquitin (Ub) polypeptide, is an important molecular signal that regulates endocytosis and post-endocytic sorting of membrane proteins (1–3). Ubiquitination is carried out by the sequential activity of E1, E2, and E3 enzymes; the latter, E3 ligases, typically determine the substrate specificity of Ub conjugation (4). Deubiquitinating enzymes (DUBs), a group of proteases capable of cleaving Ub from conjugates with target proteins, counteract the activity of the ubiquitination system (5). Ub is predominantly conjugated to lysine residues and much more rarely to the amino-terminal methionine or other amino acids in the substrate. Lysines and the amino-terminal methionine in the Ub molecule can also be conjugated to another molecule of Ub, leading to the formation of polyUb chains (6). Depending on the specific residue that links Ubs into a chain, polyUb chains have different molecular folding, are recognized by specific Ub-binding domains (UBDs) and have distinct functions (7). The structure and interaction mechanisms of lysine 48 (K48)- and K63-linked chains are most well-characterized (8–12). Crystal and NMR structures of K63 di-Ubs revealed extended, open conformation of two Ubs with high conformational freedom, as opposed to closed conformation of K48-polyUb linkages (reviewed in ref. 11). Therefore, ubiquitination substrates including endocytic cargo can be mono- and polyubiquitinated by different chains, but the role of these diverse types of ubiquitination in the regulation of endocytic trafficking remains incompletely understood.Epidermal growth factor (EGF) receptor (EGFR) was one of the first endocytic cargos in mammalian cells that were found to be ubiquitinated (13). This receptor has the profound role in eukaryotic development, regulation of various tissues in adult organisms, and pathogenesis of cancer (14). Therefore, EGFR has been a prototypic model for studying the mechanisms of endocytosis and endocytosis-relevant ubiquitination. EGFR is ubiquitinated by Cbl E3 ligases at the cell surface and after internalization in endosomes (15–17). The internalization step of EGFR trafficking is regulated by multiple redundant mechanisms, including ubiquitination, and is not significantly inhibited in the absence of receptor ubiquitination (18). By contrast, sorting of the internalized receptor in multivesicular bodies (MVBs), which leads to its incorporation into intraluminal vesicles of MVB and degradation in lysosomes, is highly sensitive to the extent of EGFR ubiquitination (15, 19).Based on differential recognition by Ub antibodies, EGFR was proposed to be conjugated with multiple monoUbs (20). Moreover, replacement of the cytoplasmic domain of EGFR with the Ub mutant incapable of polyubiquitination resulted in EGF-independent endocytosis and degradation of such chimeric receptor, thus suggesting that monoubiquitination is sufficient for EGFR endocytosis and MVB sorting (20). Subsequently, mass spectrometric (MS) analysis demonstrated a significant amount of EGFR polyubiquitination, mainly by K63-linked chains (19, 21, 22). However, whether K63 polyubiquitination is necessary for EGFR endocytic trafficking remains unknown.The role of cargo ubiquitination by K63-linked chains has been proposed in studies of endocytosis and MVB sorting of yeast permeases (23–27). These studies, however, used an approach of global elimination of K63 polyubiquitination in the cell to demonstrate the importance of these chains in endocytic trafficking. Because numerous proteins, including ESCRT components mediating MVB sorting are polyubiquitinated with K63 linkages, the inhibitory effects of the blockade of K63-linked polyubiquitination on endocytosis and MVB sorting observed in these studies may be indirect [e.g., not related to cargo ubiquitination (25)]. By contrast, an alternative approach based on the analysis of genetically engineered chimeric cargo molecules fused to Ub or a DUB demonstrated that monoubiquitination is fully sufficient for endocytosis and sorting of several membrane proteins to the vacuole in yeast (28).A number of mammalian endocytic cargo is polyubiquitinated by K63-linked chains (29–31) and, to a lesser extent, with K48 linkages (32–35). Similarly to studies in yeast, the role of these Ub linkages in mammalian cells was mainly examined by overexpressing K63R or K48R Ub mutants incapable of forming corresponding polyUb chains, leading to inhibition of K63 or K48 polyubiquitination of all cellular substrates (31–33). To test whether K63 polyubiquitination is required for EGFR endocytosis and endosomal sorting, we analyzed the stoichiometry of EGFR ubiquitination by MS and generated a chimeric EGFR fused at the carboxyl terminus to a DUB with the specificity toward K63 linkages. Analysis of the internalization and post-endocytic sorting of this chimeric receptor showed that K63 polyUb chains are necessary for the efficient EGF-induced down-regulation of EGFR.     

Overlapping functions of stonin 2 and SV2 in sorting of the calcium sensor synaptotagmin 1 to synaptic vesicles

Neurotransmission involves the calcium-regulated exocytic fusion of synaptic vesicles (SVs) and the subsequent retrieval of SV membranes followed by reformation of properly sized and shaped SVs. An unresolved question is whether each SV protein is sorted by its own dedicated adaptor or whether sorting is facilitated by association between different SV proteins. We demonstrate that endocytic sorting of the calcium sensor synaptotagmin 1 (Syt1) is mediated by the overlapping activities of the Syt1-associated SV glycoprotein SV2A/B and the endocytic Syt1-adaptor stonin 2 (Stn2). Deletion or knockdown of either SV2A/B or Stn2 results in partial Syt1 loss and missorting of Syt1 to the neuronal surface, whereas deletion of both SV2A/B and Stn2 dramatically exacerbates this phenotype. Selective missorting and degradation of Syt1 in the absence of SV2A/B and Stn2 impairs the efficacy of neurotransmission at hippocampal synapses. These results indicate that endocytic sorting of Syt1 to SVs is mediated by the overlapping activities of SV2A/B and Stn2 and favor a model according to which SV protein sorting is guarded by both cargo-specific mechanisms as well as association between SV proteins.Neurotransmission is based on the calcium-triggered fusion of neurotransmitter-filled synaptic vesicles (SVs) with the presynaptic plasma membrane. To sustain neurotransmitter release, neurons have evolved mechanisms to retrieve SV membranes and to reform SVs locally within presynaptic nerve terminals. How SVs are reformed and maintain their compositional identity (1, 2) is controversial (3–5). One possibility is that upon fusion SV proteins remain clustered at the active zone—that is, by association between SV proteins—and are retrieved via “kiss-and-run” or ultrafast endocytosis (6), thereby alleviating the need for specific sorting of individual SV proteins. Alternatively, if SVs lose their identity during multiple rounds of exo-/endocytosis (7, 8), specific mechanisms exist to orchestrate high-fidelity SV protein sorting, either directly at the plasma membrane via slow clathrin-mediated endocytosis (CME) or at endosome-like vacuoles generated by fast clathrin-independent membrane retrieval (5, 9). Endocytic adaptors for SV protein sorting include the heterotetrameric adaptor protein complex 2 (AP-2) (9), the synaptobrevin 2/VAMP2 adaptor AP180 (10), and the AP-2μ–related protein stonin 2 (Stn2), a specific sorting adaptor for the SV calcium sensor synaptotagmin 1 (Syt1) (8, 11). Although genetic inactivation of the Stn2 orthologs Stoned B and Unc41 in flies and worms is lethal due to defective neurotransmission caused by degradation and missorting of Syt1 (12, 13), Stn2 knockout (KO) mice are viable and able to internalize Syt1, albeit with reduced fidelity of sorting (14). Thus, mammalian synapses, in contrast to invertebrates, have evolved mechanisms to sort Syt1 in the absence of its specific sorting adaptor Stn2. One possibility is that Syt1 sorting in addition to its direct recognition by Stn2 is facilitated by complex formation with other SV proteins. Likely candidates for such a piggyback mechanism are the SV2 family of transmembrane SV glycoproteins (15, 16), which might regulate Syt1 function either via direct interaction (17, 18) or by facilitating its binding to AP-2 (19). Apart from the distantly related SVOP protein (20), no close SV2 homologs exist in invertebrates, suggesting that SV2 fulfills a unique function at mammalian synapses. KO of SV2A or combined loss of its major A and B isoforms in mice causes early postnatal lethality due to epileptic seizures (21, 22), impaired neurotransmission (23, 24), and defects in Syt1 trafficking (25), whereas SV2B KO mice are phenotypically normal (17). Given that SV2A in addition to its association with Syt1 binds to endocytic proteins including AP-2 and Eps15 (25), SV2 would be a likely candidate for mediating Syt1 sorting to SVs.Here we demonstrate that endocytic sorting of Syt1 is mediated by the overlapping activities of SV2A/B and Stn2. Deletion or knockdown of either SV2A/B or Stn2 results in partial Syt1 loss and missorting of Syt1 to the neuronal surface, whereas deletion of both SV2A/B and Stn2 dramatically exacerbates this phenotype, resulting in severely impaired basal neurotransmission. Our results favor a model according to which SV protein sorting is guarded by both cargo-specific mechanisms as well as association between SV proteins.     

Actomyosin dynamics drive local membrane component organization in an in vitro active composite layer

The surface of a living cell provides a platform for receptor signaling, protein sorting, transport, and endocytosis, whose regulation requires the local control of membrane organization. Previous work has revealed a role for dynamic actomyosin in membrane protein and lipid organization, suggesting that the cell surface behaves as an active composite composed of a fluid bilayer and a thin film of active actomyosin. We reconstitute an analogous system in vitro that consists of a fluid lipid bilayer coupled via membrane-associated actin-binding proteins to dynamic actin filaments and myosin motors. Upon complete consumption of ATP, this system settles into distinct phases of actin organization, namely bundled filaments, linked apolar asters, and a lattice of polar asters. These depend on actin concentration, filament length, and actin/myosin ratio. During formation of the polar aster phase, advection of the self-organizing actomyosin network drives transient clustering of actin-associated membrane components. Regeneration of ATP supports a constitutively remodeling actomyosin state, which in turn drives active fluctuations of coupled membrane components, resembling those observed at the cell surface. In a multicomponent membrane bilayer, this remodeling actomyosin layer contributes to changes in the extent and dynamics of phase-segregating domains. These results show how local membrane composition can be driven by active processes arising from actomyosin, highlighting the fundamental basis of the active composite model of the cell surface, and indicate its relevance to the study of membrane organization.The cell surface mediates interactions between the cell and the outside world by serving as the site for signal transduction. It also facilitates the uptake and release of cargo and supports adhesion to substrates. These diverse roles require that the cell surface components involved in each function are spatially and temporally organized into domains spanning a few nanometers (nanoclusters) to several micrometers (microdomains). The cell surface itself may be considered as a fluid–lipid bilayer wherein proteins are embedded (1). In the living cell, this multicomponent system is supported by an actin cortex, composed of a branched network of actin and a collection of filaments (2–4).Current models of membrane organization fall into three categories: those invoking lipid–lipid and lipid–protein interactions in the plasma membrane [e.g., the fluid mosaic model (1, 5) and the lipid raft hypothesis (6)], or those that appeal to the membrane-associated actin cortex (e.g., the picket fence model) (7), or a combination of these (8, 9). Although these models based on thermodynamic equilibrium principles have successfully explained the organization and dynamics of a range of membrane components and molecules, there is a growing class of phenomena that appears inconsistent with chemical and thermal equilibrium, which might warrant a different explanation. These include aspects of the organization and dynamics of outer leaflet glycosyl-phosphatidylinositol-anchored proteins (GPI-anchored proteins) (10–13), inner leaflet Ras proteins (14), and actin-binding transmembrane proteins (13, 15, 16).Recent experimental and theoretical work has shown that these features can be explained by taking into account that many cortical and membrane proteins are driven by ATP-consuming processes that drive the system out of equilibrium (13, 15, 17). The membrane models mentioned above have by-and-large neglected this active nature of the actin cortex where actin filaments are being continuously polymerized and depolymerized (18–21), in addition to being persistently acted upon by a variety of myosin motors (22–24) that consume ATP and exert contractile stresses on cortical actin filaments, continually remodeling the architecture of the cortex (4, 21, 25). These active processes in turn can generate tangential stresses and currents on the cell surface, which could drive the dynamics and local composition of membrane components at different scales (22, 26–29).Actin polymerization is proposed to be driven at the membrane by two nucleators, the Arp2/3 complex, which creates a densely branched network, as well as formins that nucleate filaments (18, 21, 30). A number of myosin motors are also associated with the juxtamembranous actin cortex, of which nonmuscle myosin II is the major component in remodeling the cortex and creating actin flows (4, 23, 25, 26, 31, 32). Based on our observations that the clustering of cell surface components that couple directly or indirectly to cortical actin [e.g., GPI-anchored proteins, proteins of the Ezrin, Radaxin, or Moesin (ERM) family (13, 15)] depends on myosin activity, we proposed that this clustering arises from the coupling to contractile actomyosin platforms (called “actin asters”) produced at the cortex (15, 33).A coarse-grained theory describing this idea has been put forward and corroborated by the verification of its key predictions in live cells (15, 33), but a systematic identification of the underlying microscopic processes is lacking. Given the complexity of numerous processes acting at the membrane of a living cell, we use an in vitro approach to study the effect of an energy-consuming actomyosin network on the dynamics of membrane molecules that directly interact with filamentous actin.A series of in vitro studies have explored the organization of confined, dynamic filaments (both actin and microtubules) (34–39) or the role of actin architecture on membrane organization (40–46). Indeed, these studies have yielded insights into the nontrivial emergent configurations that mixtures of polar filaments and motors can adopt when fueled by ATP (34–37), in particular constitutively remodeling steady states that display characteristics of active mechanics (38, 39, 47). However, the effect of linking these mechanics to the confining lipid bilayer and its organization has not been studied.The consequences of actin polymerization on membrane organization, in particular on giant unilamellar vesicles (GUVs), have been addressed in a number of studies on the propulsion of GUVs by an actin comet tail (40, 45, 46). In those experiments, the apparent advection of membrane bound ActA or WASP toward the site of actin polymerization is mainly due to the change in binding affinity of WASP to actin through Arp2/3 (44) and the spherical geometry resulting in the drag of actin to one pole of the vesicle after symmetry break of the actin shell. That this dynamic process changes the bulk properties of the bilayer, namely the critical temperature of a phase-separating lipid bilayer, was shown by Liu and Fletcher (40) when the actin nucleator N-WASP was connected to a lipid species (PIP₂) that was capable of partitioning into one of the two phases.Besides these pioneering studies on the effects of active processes on membrane organization, little was done to directly test the effect of active lateral stresses as well as actomyosin remodeling at the membrane, particularly on the dynamics and organization of membrane-associated components.To this end, we build an active composite in vitro by stepwise addition of components: a supported lipid bilayer with an actin-binding component, actin filaments, and myosin motors. By systematically varying the concentrations of actin and myosin as well as the average actin filament length, we find distinct states of actomyosin organization at the membrane surface upon complete ATP consumption. More importantly, we find that the ATP-fueled contractile actomyosin currents induce the transient accumulation of actin-binding membrane components. As predicted, the active mechanics of actin and myosin at physiologically relevant ATP concentrations drives the system into a nonequilibrium steady state with anomalous density fluctuations and the transient clustering of actin-binding components of the lipid bilayer (15, 33). Finally, connection of this active layer of actomyosin to a phase-segregating bilayer, influences its phase behavior and coarsening dynamics.     

Retro-translocation of mitochondrial intermembrane space proteins

The content of mitochondrial proteome is maintained through two highly dynamic processes, the influx of newly synthesized proteins from the cytosol and the protein degradation. Mitochondrial proteins are targeted to the intermembrane space by the mitochondrial intermembrane space assembly pathway that couples their import and oxidative folding. The folding trap was proposed to be a driving mechanism for the mitochondrial accumulation of these proteins. Whether the reverse movement of unfolded proteins to the cytosol occurs across the intact outer membrane is unknown. We found that reduced, conformationally destabilized proteins are released from mitochondria in a size-limited manner. We identified the general import pore protein Tom40 as an escape gate. We propose that the mitochondrial proteome is not only regulated by the import and degradation of proteins but also by their retro-translocation to the external cytosolic location. Thus, protein release is a mechanism that contributes to the mitochondrial proteome surveillance.Mitochondrial biogenesis is essential for eukaryotic cells. Because most mitochondrial proteins originate in the cytosol, mitochondria had to develop a protein import system. Given the complex architecture of these organelles, with two membranes and two aqueous compartments, protein import and sorting require the cooperation of several pathways. The main entry gate for precursor proteins is the translocase of the outer mitochondrial membrane (TOM) complex. Upon entering mitochondria, proteins are routed to different sorting machineries (1–5).Reaching the final location is one step in the maturation of mitochondrial proteins that must be accompanied by their proper folding. The mitochondrial intermembrane space assembly (MIA) pathway for intermembrane space (IMS) proteins illustrates the importance of coupling these processes because this pathway links protein import with oxidative folding (6–10). Upon protein synthesis in the cytosol, the cysteine residues of IMS proteins remain in a reduced state, owing to the reducing properties of the cytosolic environment (11, 12). After entering the TOM channel, precursor proteins are specifically recognized by Mia40 protein, and their cysteine residues are oxidized through the cooperative action of Mia40 and Erv1 proteins (7, 13–17). Mia40 is a receptor, folding catalyst, and disulfide carrier, and the Erv1 protein serves as a sulfhydryl oxidase. The oxidative folding is believed to provide a trapping mechanism that prevents the escape of proteins from the IMS back to the cytosol (10, 13, 18). Our initial result raised a possibility that the reverse process can also occur, as we observed the relocation of in vitro imported Tim8 from mitochondria to the incubation buffer (13). Thus, we sought to establish whether and how this process can proceed in the presence of the intact outer membrane (OM). Our study provides, to our knowledge, the first characterization of the mitochondrial protein retro-translocation. The protein retro-translocation serves as a regulatory and quality control mechanism for the mitochondrial IMS proteome.     

ECHIDNA-mediated post-Golgi trafficking of auxin carriers for differential cell elongation

The plant hormone indole-acetic acid (auxin) is essential for many aspects of plant development. Auxin-mediated growth regulation typically involves the establishment of an auxin concentration gradient mediated by polarly localized auxin transporters. The localization of auxin carriers and their amount at the plasma membrane are controlled by membrane trafficking processes such as secretion, endocytosis, and recycling. In contrast to endocytosis or recycling, how the secretory pathway mediates the localization of auxin carriers is not well understood. In this study we have used the differential cell elongation process during apical hook development to elucidate the mechanisms underlying the post-Golgi trafficking of auxin carriers in Arabidopsis. We show that differential cell elongation during apical hook development is defective in Arabidopsis mutant echidna (ech). ECH protein is required for the trans-Golgi network (TGN)–mediated trafficking of the auxin influx carrier AUX1 to the plasma membrane. In contrast, ech mutation only marginally perturbs the trafficking of the highly related auxin influx carrier LIKE-AUX1-3 or the auxin efflux carrier PIN-FORMED-3, both also involved in hook development. Electron tomography reveals that the trafficking defects in ech mutant are associated with the perturbation of secretory vesicle genesis from the TGN. Our results identify differential mechanisms for the post-Golgi trafficking of de novo-synthesized auxin carriers to plasma membrane from the TGN and reveal how trafficking of auxin influx carriers mediates the control of differential cell elongation in apical hook development.Polar auxin transport (PAT) plays a key role in plant development (1–5). PAT is mediated by plasma membrane localized auxin influx and efflux carriers of the auxin-resistant (AUX)/like-AUX (LAX), pin-formed (PIN), and ABCB families (6–12). Highly regulated tissue, cellular localization, and amount of auxin carriers at the plasma membrane (PM) provide directionality to the auxin transport and underlies the creation of auxin concentration gradient that is essential for controlling several aspects of plant development (13–18). One of the developmental programs in which auxin concentration gradient plays a central role is the formation of apical hook, a bending in the embryonic stem during early seedling germination (19). Hook formation involves differential elongation of cells on the two opposite sides of the hypocotyl. This process is mediated by the formation of an auxin maximum at the concave side of the hook, leading to the inhibition of cell elongation (20–25). A model based on mutational analysis shows that auxin carriers including polarly localized auxin efflux and influx facilitators PIN3 and AUX1/LAX3, respectively, are important for hook development (23, 24). The amount of auxin carriers at the PM is important for the regulation of auxin concentration, and this depends on the balance between secretion, endocytosis, and recycling. The analysis of PIN efflux carriers has revealed how cell wall anchoring, endocytosis, targeted degradation, and also posttranslational modifications strongly influence the location and amount of these carriers at the PM (15, 17, 26–29). In contrast, little is known about the mechanisms and molecular components underlying the deposition of auxin carriers at the PM. Post-Golgi secretion to the PM occurs via the trans-Golgi network (TGN), a post-Golgi compartment (30). The TGN is a complex tubulo-vesicular membrane network maturing from the trans-most cisternae of the Golgi apparatus to become a highly dynamic independent structure from which secretory vesicles (SVs) and CLATHRIN-coated vesicles (CCVs) originate (31–34). Although auxin carriers traffic via TGN, components and mechanisms specifically involved in trafficking to the PM of de novo-synthesized auxin carriers remain largely undefined (35, 36). Importantly, it is not known whether auxin carriers traffic through SV or CCV sites of the TGN on their way to the PM. We have used apical hook development as a model system to investigate the mechanisms that link post-Golgi trafficking of auxin carriers to the PM with control of differential cell elongation. We previously identified the transmembrane TGN-localized protein ECHIDNA (ECH) that is required for cell elongation (37). We discovered that the ech mutant is defective in hook development and is insensitive to ethylene like the aux1 mutant. These data prompted us to investigate the role of ECH and the TGN in post-Golgi trafficking of auxin carriers during hook development. Using genetic, pharmacological, and cell biological approaches, we show that distinct mechanisms/components underlie post-Golgi trafficking of influx and efflux carriers. We show that post-Golgi trafficking of de novo-synthesized AUX1 occurs via an ECH-dependent SV-based pathway, whereas that of PIN3 and LAX3 are largely independent of ECH at the TGN. Thus, these results reveal the complexity of trafficking from the TGN to PM as shown by the differential trafficking of influx carriers AUX1 versus LAX3 and the efflux carrier PIN3. Hence, our results reveal an additional layer of regulatory control to auxin transport.     

Self-assembly of alkynylplatinum(II) terpyridine amphiphiles into nanostructures via steric control and metal–metal interactions

A series of mono- and dinuclear alkynylplatinum(II) terpyridine complexes containing the hydrophilic oligo(para-phenylene ethynylene) with two 3,6,9-trioxadec-1-yloxy chains was designed and synthesized. The mononuclear alkynylplatinum(II) terpyridine complex was found to display a very strong tendency toward the formation of supramolecular structures. Interestingly, additional end-capping with another platinum(II) terpyridine moiety of various steric bulk at the terminal alkyne would lead to the formation of nanotubes or helical ribbons. These desirable nanostructures were found to be governed by the steric bulk on the platinum(II) terpyridine moieties, which modulates the directional metal−metal interactions and controls the formation of nanotubes or helical ribbons. Detailed analysis of temperature-dependent UV-visible absorption spectra of the nanostructured tubular aggregates also provided insights into the assembly mechanism and showed the role of metal−metal interactions in the cooperative supramolecular polymerization of the amphiphilic platinum(II) complexes.Square-planar d⁸ platinum(II) polypyridine complexes have long been known to exhibit intriguing spectroscopic and luminescence properties (1–54) as well as interesting solid-state polymorphism associated with metal−metal and π−π stacking interactions (1–14, 25). Earlier work by our group showed the first example, to our knowledge, of an alkynylplatinum(II) terpyridine system [Pt(tpy)(C ≡ CR)]⁺ that incorporates σ-donating and solubilizing alkynyl ligands together with the formation of Pt···Pt interactions to exhibit notable color changes and luminescence enhancements on solvent composition change (25) and polyelectrolyte addition (26). This approach has provided access to the alkynylplatinum(II) terpyridine and other related cyclometalated platinum(II) complexes, with functionalities that can self-assemble into metallogels (27–31), liquid crystals (32, 33), and other different molecular architectures, such as hairpin conformation (34), helices (35–38), nanostructures (39–45), and molecular tweezers (46, 47), as well as having a wide range of applications in molecular recognition (48–52), biomolecular labeling (48–52), and materials science (53, 54). Recently, metal-containing amphiphiles have also emerged as a building block for supramolecular architectures (42–44, 55–59). Their self-assembly has always been found to yield different molecular architectures with unprecedented complexity through the multiple noncovalent interactions on the introduction of external stimuli (42–44, 55–59).Helical architecture is one of the most exciting self-assembled morphologies because of the uniqueness for the functional and topological properties (60–69). Helical ribbons composed of amphiphiles, such as diacetylenic lipids, glutamates, and peptide-based amphiphiles, are often precursors for the growth of tubular structures on an increase in the width or the merging of the edges of ribbons (64, 65). Recently, the optimization of nanotube formation vs. helical nanostructures has aroused considerable interests and can be achieved through a fine interplay of the influence on the amphiphilic property of molecules (66), choice of counteranions (67, 68), or pH values of the media (69), which would govern the self-assembly of molecules into desirable aggregates of helical ribbons or nanotube scaffolds. However, a precise control of supramolecular morphology between helical ribbons and nanotubes remains challenging, particularly for the polycyclic aromatics in the field of molecular assembly (64–69). Oligo(para-phenylene ethynylene)s (OPEs) with solely π−π stacking interactions are well-recognized to self-assemble into supramolecular system of various nanostructures but rarely result in the formation of tubular scaffolds (70–73). In view of the rich photophysical properties of square-planar d⁸ platinum(II) systems and their propensity toward formation of directional Pt···Pt interactions in distinctive morphologies (27–31, 39–45), it is anticipated that such directional and noncovalent metal−metal interactions might be capable of directing or dictating molecular ordering and alignment to give desirable nanostructures of helical ribbons or nanotubes in a precise and controllable manner.Herein, we report the design and synthesis of mono- and dinuclear alkynylplatinum(II) terpyridine complexes containing hydrophilic OPEs with two 3,6,9-trioxadec-1-yloxy chains. The mononuclear alkynylplatinum(II) terpyridine complex with amphiphilic property is found to show a strong tendency toward the formation of supramolecular structures on diffusion of diethyl ether in dichloromethane or dimethyl sulfoxide (DMSO) solution. Interestingly, additional end-capping with another platinum(II) terpyridine moiety of various steric bulk at the terminal alkyne would result in nanotubes or helical ribbons in the self-assembly process. To the best of our knowledge, this finding represents the first example of the utilization of the steric bulk of the moieties, which modulates the formation of directional metal−metal interactions to precisely control the formation of nanotubes or helical ribbons in the self-assembly process. Application of the nucleation–elongation model into this assembly process by UV-visible (UV-vis) absorption spectroscopic studies has elucidated the nature of the molecular self-assembly, and more importantly, it has revealed the role of metal−metal interactions in the formation of these two types of nanostructures.     

Transition paths,diffusive processes,and preequilibria of protein folding

Fundamental relationships between the thermodynamics and kinetics of protein folding were investigated using chain models of natural proteins with diverse folding rates by extensive comparisons between the distribution of conformations in thermodynamic equilibrium and the distribution of conformations sampled along folding trajectories. Consistent with theory and single-molecule experiment, duration of the folding transition paths exhibits only a weak correlation with overall folding time. Conformational distributions of folding trajectories near the overall thermodynamic folding/unfolding barrier show significant deviations from preequilibrium. These deviations, the distribution of transition path times, and the variation of mean transition path time for different proteins can all be rationalized by a diffusive process that we modeled using simple Monte Carlo algorithms with an effective coordinate-independent diffusion coefficient. Conformations in the initial stages of transition paths tend to form more nonlocal contacts than typical conformations with the same number of native contacts. This statistical bias, which is indicative of preferred folding pathways, should be amenable to future single-molecule measurements. We found that the preexponential factor defined in the transition state theory of folding varies from protein to protein and that this variation can be rationalized by our Monte Carlo diffusion model. Thus, protein folding physics is different in certain fundamental respects from the physics envisioned by a simple transition-state picture. Nonetheless, transition state theory can be a useful approximate predictor of cooperative folding speed, because the height of the overall folding barrier is apparently a proxy for related rate-determining physical properties.Protein folding is an intriguing phenomenon at the interface of physics and biology. In the early days of folding kinetics studies, folding was formulated almost exclusively in terms of mass-action rate equations connecting the folded, unfolded, and possibly, one or a few intermediate states (1, 2). With the advent of site-directed mutagenesis, the concept of free energy barriers from transition state theory (TST) (3) was introduced to interpret mutational data (4), and subsequently, it was adopted for the Φ-value analysis (5). Since the 1990s, the availability of more detailed experimental data (6), in conjunction with computational development of coarse-grained chain models, has led to an energy landscape picture of folding (7–15). This perspective emphasizes the diversity of microscopic folding trajectories, and it conceptualizes folding as a diffusive process (16–25) akin to the theory of Kramers (26).For two-state-like folding, the transition path (TP), i.e., the sequence of kinetic events that leads directly from the unfolded state to the folded state (27, 28), constitutes only a tiny fraction of a folding trajectory that spends most of the time diffusing, seemingly unproductively, in the vicinity of the free energy minimum of the unfolded state. The development of ultrafast laser spectroscopy (29, 30) and single-molecule (27, 28, 31) techniques have made it possible to establish upper bounds on the transition path time (t_TP) ranging from <200 and <10 μs by earlier (27) and more recent (28), respectively, direct single-molecule FRET to <2 μs (30) by bulk relaxation measurements. Consistent with these observations, recent extensive atomic simulations have also provided estimated t_TP values of the order of ∼1 μs (32, 33). These advances offer exciting prospects of characterizing the productive events along folding TPs.It is timely, therefore, to further the theoretical investigation of TP-related questions (19). To this end, we used coarse-grained C_α models (14) to perform extensive simulations of the folding trajectories of small proteins with 56- to 86-aa residues. These tractable models are useful, because despite significant progress, current atomic models cannot provide the same degree of sampling coverage for proteins of comparable sizes (32, 33). In addition to structural insights, this study provides previously unexplored vantage points to compare the diffusion and TST pictures of folding. Deviations of folding behaviors from TST predictions are not unexpected, because TST is mostly applicable to simple gas reactions; however, the nature and extent of the deviations have not been much explored. Our explicit-chain simulation data conform well to the diffusion picture but not as well to TST. In particular, the preexponential factors of the simulated folding rates exhibit a small but appreciable variation that depends on native topology. These findings and others reported below underscore the importance of single-molecule measurements (13, 27, 28, 31, 34, 35) in assessing the merits of proposed scenarios and organizing principles of folding (7–25, 36, 37).     

Four-dimensional live imaging of apical biosynthetic trafficking reveals a post-Golgi sorting role of apical endosomal intermediates

Emerging data suggest that in polarized epithelial cells newly synthesized apical and basolateral plasma membrane proteins traffic through different endosomal compartments en route to the respective cell surface. However, direct evidence for trans-endosomal pathways of plasma membrane proteins is still missing and the mechanisms involved are poorly understood. Here, we imaged the entire biosynthetic route of rhodopsin-GFP, an apical marker in epithelial cells, synchronized through recombinant conditional aggregation domains, in live Madin-Darby canine kidney cells using spinning disk confocal microscopy. Our experiments directly demonstrate that rhodopsin-GFP traffics through apical recycling endosomes (AREs) that bear the small GTPase Rab11a before arriving at the apical membrane. Expression of dominant-negative Rab11a drastically reduced apical delivery of rhodopsin-GFP and caused its missorting to the basolateral membrane. Surprisingly, functional inhibition of dynamin-2 trapped rhodopsin-GFP at AREs and caused aberrant accumulation of coated vesicles on AREs, suggesting a previously unrecognized role for dynamin-2 in the scission of apical carrier vesicles from AREs. A second set of experiments, using a unique method to carry out total internal reflection fluorescence microscopy (TIRFM) from the apical side, allowed us to visualize the fusion of rhodopsin-GFP carrier vesicles, which occurred randomly all over the apical plasma membrane. Furthermore, two-color TIRFM showed that Rab11a-mCherry was present in rhodopsin-GFP carrier vesicles and was rapidly released upon fusion onset. Our results provide direct evidence for a role of AREs as a post-Golgi sorting hub in the biosynthetic route of polarized epithelia, with Rab11a regulating cargo sorting at AREs and carrier vesicle docking at the apical membrane.Polarized epithelial cells maintain separate apical and basolateral plasma membrane (PM) domains to carry out essential vectorial absorptive and secretory functions. Tightly regulated vesicular trafficking is required to sort and target distinct sets of proteins to their respective membranes (1). Studies performed with the epithelial model cell line Madin-Darby canine kidney (MDCK) indicate that newly synthesized membrane proteins take an indirect route to the PM. After leaving the trans-Golgi network (TGN), PM proteins first traverse endosomal compartments before reaching apical or basolateral cell surfaces (2–4). Some basolateral PM proteins traverse common recycling endosomes (CREs) where they are sorted into carrier vesicles directed toward the basolateral PM by clathrin and the clathrin adaptor AP-1B (5, 6). Alternatively, basolateral proteins can be sorted at the TGN by the clathrin adaptor AP-1A (7–9). Along the apical route it has been shown that nonraft-associated apical proteins traverse Rab11-positive apical recycling endosomes (AREs) en route to the apical PM (10). Trans-endosomal trafficking is likely to play important roles in cell physiology; for example, endosomal compartments may function as common regulatory hubs for newly synthesized and recycling PM proteins. In particular, recent data show that the small GTPase Rab11 is an important regulator of biological processes that require apical trafficking, e.g., lumen formation during epithelial tubulogenesis (11), apical secretion of discoidal/fusiform vesicles in bladder umbrella cells (12), and apical microvillus morphogenesis and rhodopsin localization in fly photoreceptors (13). However, despite the physiological importance of trans-endosomal trafficking, the underlying mechanisms remain largely unclear.Previous studies on trans-endosomal trafficking in polarized epithelial cells have relied on pulse chase/cell fractionation protocols (3, 4) or on monitoring how ablation of an endosomal compartment affects surface arrival of a given cargo protein (4, 6, 10). These approaches, although valuable, provide limited resolution on the types of endosomes involved and on the kinetics of trans-endosomal trafficking. Elucidating the mechanisms of trans-endosomal trafficking in fully polarized epithelial cells will benefit from new methods that allow direct imaging and quantification of the transit through specific endosomal intermediates along the biosynthetic transport routes. Here, we report experiments in which we studied the biosynthetic trans-endosomal trafficking of an apical reporter, rhodopsin-GFP (14, 15), synchronized by reversible aggregation at the endoplasmic reticulum (ER) through recombinant tagging with conditional aggregation domains (CADs) (16). Post-Golgi trafficking through endosomal compartments of rhodopsin-GFP, freed from the CADs through a furin-cleavage site, was traced and quantified by spinning disk confocal microscopy and its surface delivery was analyzed using a unique total internal reflection fluorescence microscopy (TIRFM) protocol that allows live imaging of the apical PM (17).These experiments show that rhodopsin-GFP traverses AREs during apical transport and is delivered to the apical PM by carrier vesicles that fuse randomly with the cell surface. Our data also demonstrate that the GTPases Rab11a and dynamin-2 (dyn2) play active regulatory roles in trans-ARE trafficking and apical delivery and suggest that AREs are sorting-competent organelles. To our knowledge, this is a unique direct visualization of trans-endosomal trafficking in polarized epithelial cells by live imaging.     

Structural basis for membrane recruitment and allosteric activation of cytohesin family Arf GTPase exchange factors

Membrane recruitment of cytohesin family Arf guanine nucleotide exchange factors depends on interactions with phosphoinositides and active Arf GTPases that, in turn, relieve autoinhibition of the catalytic Sec7 domain through an unknown structural mechanism. Here, we show that Arf6-GTP relieves autoinhibition by binding to an allosteric site that includes the autoinhibitory elements in addition to the PH domain. The crystal structure of a cytohesin-3 construct encompassing the allosteric site in complex with the head group of phosphatidyl inositol 3,4,5-trisphosphate and N-terminally truncated Arf6-GTP reveals a large conformational rearrangement, whereby autoinhibition can be relieved by competitive sequestration of the autoinhibitory elements in grooves at the Arf6/PH domain interface. Disposition of the known membrane targeting determinants on a common surface is compatible with multivalent membrane docking and subsequent activation of Arf substrates, suggesting a plausible model through which membrane recruitment and allosteric activation could be structurally integrated.Guanine nucleotide exchange factors (GEFs) activate GTPases by catalyzing exchange of GDP for GTP (1). Because many GEFs are recruited to membranes through interactions with phospholipids, active GTPases, or other membrane-associated proteins (1–5), GTPase activation can be restricted or amplified by spatial–temporal overlap of GEFs with binding partners. GEF activity can also be controlled by autoregulatory mechanisms, which may depend on membrane recruitment (6–11). Structural relationships between these mechanisms are poorly understood.Arf GTPases function in trafficking and cytoskeletal dynamics (5, 12, 13). Membrane partitioning of a myristoylated (myr) N-terminal amphipathic helix primes Arfs for activation by Sec7 domain GEFs (14–17). Cytohesins comprise a metazoan Arf GEF family that includes the mammalian proteins cytohesin-1 (Cyth1), ARNO (Cyth2), and Grp1 (Cyth3). The Drosophila homolog steppke functions in insulin-like growth factor signaling, whereas Cyth1 and Grp1 have been implicated in insulin signaling and Glut4 trafficking, respectively (18–20). Cytohesins share a modular architecture consisting of heptad repeats, a Sec7 domain with exchange activity for Arf1 and Arf6, a PH domain that binds phosphatidyl inositol (PI) polyphosphates, and a C-terminal helix (CtH) that overlaps with a polybasic region (PBR) (21–28). The overlapping CtH and PBR will be referred to as the CtH/PBR. The phosphoinositide specificity of the PH domain is influenced by alternative splicing, which generates diglycine (2G) and triglycine (3G) variants differing by insertion of a glycine residue in the β1/β2 loop (29). Despite similar PI(4,5)P₂ (PIP₂) affinities, the 2G variant has 30-fold higher affinity for PI(3,4,5)P₃ (PIP₃) (30). In both cases, PIP₃ is required for plasma membrane (PM) recruitment (23, 26, 31–33), which is promoted by expression of constitutively active Arf6 or Arl4d and impaired by PH domain mutations that disrupt PIP₃ or Arf6 binding, or by CtH/PBR mutations (8, 34–36).Cytohesins are autoinhibited by the Sec7-PH linker and CtH/PBR, which obstruct substrate binding (8). Autoinhibition can be relieved by Arf6-GTP binding in the presence of the PIP₃ head group (8). Active myr-Arf1 and myr-Arf6 also stimulate exchange activity on PIP₂-containing liposomes (37). Whether this effect is due to relief of autoinhibition per se or enhanced membrane recruitment is not yet clear. Phosphoinositide recognition by PH domains, catalysis of nucleotide exchange by Sec7 domains, and autoinhibition in cytohesins are well characterized (8, 16, 17, 30, 38–43). How Arf-GTP binding relieves autoinhibition and promotes membrane recruitment is unknown. Here, we determine the structural basis for relief of autoinhibition and investigate potential mechanistic relationships between allosteric regulation, phosphoinositide binding, and membrane targeting.     

Visualization of the type III secretion sorting platform of Shigella flexneri

Bacterial type III secretion machines are widely used to inject virulence proteins into eukaryotic host cells. These secretion machines are evolutionarily related to bacterial flagella and consist of a large cytoplasmic complex, a transmembrane basal body, and an extracellular needle. The cytoplasmic complex forms a sorting platform essential for effector selection and needle assembly, but it remains largely uncharacterized. Here we use high-throughput cryoelectron tomography (cryo-ET) to visualize intact machines in a virulent Shigella flexneri strain genetically modified to produce minicells capable of interaction with host cells. A high-resolution in situ structure of the intact machine determined by subtomogram averaging reveals the cytoplasmic sorting platform, which consists of a central hub and six spokes, with a pod-like structure at the terminus of each spoke. Molecular modeling of wild-type and mutant machines allowed us to propose a model of the sorting platform in which the hub consists mainly of a hexamer of the Spa47 ATPase, whereas the MxiN protein comprises the spokes and the Spa33 protein forms the pods. Multiple contacts among those components are essential to align the Spa47 ATPase with the central channel of the MxiA protein export gate to form a unique nanomachine. The molecular architecture of the Shigella type III secretion machine and its sorting platform provide the structural foundation for further dissecting the mechanisms underlying type III secretion and pathogenesis and also highlight the major structural distinctions from bacterial flagella.Type III secretion systems (T3SSs) are essential virulence determinants for many Gram-negative pathogens. The injectisome, also known as the needle complex, is the central T3SS machine required to inject effector proteins from the bacterium into eukaryotic host cells (1, 2). The injectisome has three major components: an extracellular needle, a basal body, and a cytoplasmic complex (3). Contact with a host cell membrane triggers activation of the injectisome and the insertion of a translocon pore into the target cell membrane. The entire complex then serves as a conduit for direct translocation of effectors (1, 2). Assembly of a functional T3SS requires recognition and sorting of specific secretion substrates in a well-defined order by the cytoplasmic complex (4, 5). Furthermore, genes encoding the cytoplasmic complex are regulated by physical and environmental signals (6), providing temporal control of the injection of effector proteins and thereby optimizing invasion and virulence.Significant progress has been made in elucidating T3SS structures from many different bacteria (7, 8). 3D reconstructions of purified injectisomes from Salmonella and Shigella, together with the atomic structures of major basal body proteins, have provided a detailed view of basal body architecture (9, 10). Recent in situ structures of injectisomes from Shigella flexneri, Salmonella enterica, and Yersinia enterocolitica revealed an export gate and the structural flexibility of the basal body (11, 12). Unfortunately, these in situ structures from intact bacteria (11, 12) did not reveal any evident densities related to the proposed model of the cytoplasmic complex (8, 13).The flagellar C ring is the cytoplasmic complex in evolutionarily related flagellar systems. It is composed of flagellar proteins FliG, FliM, and FliN and plays an essential role in flagellar assembly, rotation, and switching (14). Large drum-shaped structures of the flagellar C ring have been determined in both purified basal bodies (15, 16) and in situ motors (17–19). Similarly, electron microscopy analysis in Shigella indicated that the Spa33 protein (a homolog of the flagellar proteins FliN and FliM) is localized beneath the basal body via interactions with MxiG and MxiJ and is an essential component of the putative C ring (20). Recent experimental evidence suggests that the putative C ring provides a sorting platform for the recognition and secretion of the substrates in S. enterica (5). This sorting platform consists of three proteins, SpaO, OrgA, and OrgB, which are highly conserved among other T3SSs (21) (SI Appendix, Table S1). Despite its critical roles, little is still known about the structure and assembly of the cytoplasmic sorting platform in T3SS. In this study, we choose S. flexneri as a model system to study the intact T3SS machine and its cytoplasmic complex, mainly because a wealth of structural, biochemical, and functional information is available for the S. flexneri T3SS (22).     

Structural interactions of a voltage sensor toxin with lipid membranes

Protein toxins from tarantula venom alter the activity of diverse ion channel proteins, including voltage, stretch, and ligand-activated cation channels. Although tarantula toxins have been shown to partition into membranes, and the membrane is thought to play an important role in their activity, the structural interactions between these toxins and lipid membranes are poorly understood. Here, we use solid-state NMR and neutron diffraction to investigate the interactions between a voltage sensor toxin (VSTx1) and lipid membranes, with the goal of localizing the toxin in the membrane and determining its influence on membrane structure. Our results demonstrate that VSTx1 localizes to the headgroup region of lipid membranes and produces a thinning of the bilayer. The toxin orients such that many basic residues are in the aqueous phase, all three Trp residues adopt interfacial positions, and several hydrophobic residues are within the membrane interior. One remarkable feature of this preferred orientation is that the surface of the toxin that mediates binding to voltage sensors is ideally positioned within the lipid bilayer to favor complex formation between the toxin and the voltage sensor.Protein toxins from venomous organisms have been invaluable tools for studying the ion channel proteins they target. For example, in the case of voltage-activated potassium (Kv) channels, pore-blocking scorpion toxins were used to identify the pore-forming region of the channel (1, 2), and gating modifier tarantula toxins that bind to S1–S4 voltage-sensing domains have helped to identify structural motifs that move at the protein–lipid interface (3–5). In many instances, these toxin–channel interactions are highly specific, allowing them to be used in target validation and drug development (6–8).Tarantula toxins are a particularly interesting class of protein toxins that have been found to target all three families of voltage-activated cation channels (3, 9–12), stretch-activated cation channels (13–15), as well as ligand-gated ion channels as diverse as acid-sensing ion channels (ASIC) (16–21) and transient receptor potential (TRP) channels (22, 23). The tarantula toxins targeting these ion channels belong to the inhibitor cystine knot (ICK) family of venom toxins that are stabilized by three disulfide bonds at the core of the molecule (16, 17, 24–31). Although conventional tarantula toxins vary in length from 30 to 40 aa and contain one ICK motif, the recently discovered double-knot toxin (DkTx) that specifically targets TRPV1 channels contains two separable lobes, each containing its own ICK motif (22, 23).One unifying feature of all tarantula toxins studied thus far is that they act on ion channels by modifying the gating properties of the channel. The best studied of these are the tarantula toxins targeting voltage-activated cation channels, where the toxins bind to the S3b–S4 voltage sensor paddle motif (5, 32–36), a helix-turn-helix motif within S1–S4 voltage-sensing domains that moves in response to changes in membrane voltage (37–41). Toxins binding to S3b–S4 motifs can influence voltage sensor activation, opening and closing of the pore, or the process of inactivation (4, 5, 36, 42–46). The tarantula toxin PcTx1 can promote opening of ASIC channels at neutral pH (16, 18), and DkTx opens TRPV1 in the absence of other stimuli (22, 23), suggesting that these toxin stabilize open states of their target channels.For many of these tarantula toxins, the lipid membrane plays a key role in the mechanism of inhibition. Strong membrane partitioning has been demonstrated for a range of toxins targeting S1–S4 domains in voltage-activated channels (27, 44, 47–50), and for GsMTx4 (14, 50), a tarantula toxin that inhibits opening of stretch-activated cation channels in astrocytes, as well as the cloned stretch-activated Piezo1 channel (13, 15). In experiments on stretch-activated channels, both the d- and l-enantiomers of GsMTx4 are active (14, 50), implying that the toxin may not bind directly to the channel. In addition, both forms of the toxin alter the conductance and lifetimes of gramicidin channels (14), suggesting that the toxin inhibits stretch-activated channels by perturbing the interface between the membrane and the channel. In the case of Kv channels, the S1–S4 domains are embedded in the lipid bilayer and interact intimately with lipids (48, 51, 52) and modification in the lipid composition can dramatically alter gating of the channel (48, 53–56). In one study on the gating of the Kv2.1/Kv1.2 paddle chimera (53), the tarantula toxin VSTx1 was proposed to inhibit Kv channels by modifying the forces acting between the channel and the membrane. Although these studies implicate a key role for the membrane in the activity of Kv and stretch-activated channels, and for the action of tarantula toxins, the influence of the toxin on membrane structure and dynamics have not been directly examined. The goal of the present study was to localize a tarantula toxin in membranes using structural approaches and to investigate the influence of the toxin on the structure of the lipid bilayer.     

Sorting Nexin 27 regulates basal and activity-dependent trafficking of AMPARs

Activity-dependent changes in synaptic strength have long been postulated as cellular correlates of learning and memory. Long-term potentiation (LTP), a well characterized form of synaptic plasticity, is often expressed as an increase in the number of postsynaptic AMPA-type glutamate receptors (AMPARs). Although the precise molecular mechanisms governing LTP remain elusive, this study identifies one member of the sorting nexin family, Sorting Nexin 27 (SNX27), as a critical component in this process. The ability of sorting nexins to bind specific phospholipids as well as their propensity to form protein–protein complexes, points to a role for these proteins in membrane trafficking and protein sorting. Here, we demonstrate that SNX27 binds to AMPARs, and that this interaction is regulated in an activity-dependent manner. Furthermore, we provide evidence that SNX27 is synaptically enriched and its level of expression regulates targeting of AMPARs to the neuronal surface. Loss of SNX27 abolishes recruitment of surface AMPARs during chemical LTP. Collectively, our data suggest a role for SNX27 in modulating synaptic plasticity through regulated interaction with AMPARs.Modulation of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) activity, whether through changes in surface expression or conductance, contributes significantly to the dynamic nature of neuronal networks. During long-term potentiation (LTP), AMPARs are delivered to the plasma membrane to induce an early burst and for long-term maintenance of synaptic potentiation (1). Importantly, aberrant AMPAR trafficking has been found to contribute to impaired synaptic plasticity and deficits in learning and memory (2–4) for review see (5). AMPAR trafficking, which contributes to changes in synaptic strength, is facilitated through a complex and fluidic endosomal recycling network (6, 7). Beneath the plasma membrane, the endosomal network comprises a series of interconnected membranous compartments responsible for recycling proteins. Internalized receptors enter the early endosome to be sorted for lysosomal and proteasomal degradation, or are recycled back to the plasma membrane (6, 7). Although a great deal is known about the mechanisms for protein sorting along the degradative pathway, a comprehensive delineation of how cargo is selectively reinserted into the neuronal surface remains to be determined. Studies have shown that protein complexes can regulate AMPAR trafficking from early endosomes back to the plasma membrane (8–10). Recycling of AMPAR-containing endosomes to the plasma membrane is critical for AMPAR localization, particularly after LTP induction; knockdown or mutation of proteins associated with the recycling machinery redistributes AMPARs from the spine surface to internal endosomes (8–10). Thus, recycling endosomes and their trafficking may provide a mechanistic link between synaptic potentiation and AMPAR insertion.Further insight into the mechanisms of sorting at the level of endosomes comes from the characterization of protein–protein interactions. Several proteins have been identified that can promote or destabilize AMPA receptor surface expression/targeting through direct interaction with AMPARs (1, 6, 7). Much focus has been directed at identifying molecules that specifically interact with the C-terminal domains of AMPAR subunits as they are accessible to the intracellular milieu of the cell. Using this approach here we identified sorting nexin 27 (SNX27) as an AMPAR binding partner.SNX27 is a member of the sorting nexin family of proteins. Sorting nexins (SNXs) are a diverse group of cytoplasmic and membrane-associated proteins implicated in endocytosis and protein trafficking. They have been identified across phyla, from yeast to mammals, and their essential role in many endosomal recycling pathways is evolutionarily conserved (11). The hallmark of the sorting nexin family is the presence of a phox-homology domain (PX), a 100- to 140-aa sequence shown to interact with phosphatidylinositol phosphate (PIP) of structural membrane lipids (12). This protein–lipid interaction serves as a mechanism by which sorting nexin proteins can dock at the plasma membrane or endosomes, as these membranes are enriched in various PIPs (11).Outside of their PX domain, SNXs are a structurally diverse group of proteins. Several members contain other important functional domains, including those capable of mediating protein–protein interaction. Current literature suggests duality to SNXs function in endosomal trafficking: They use their membrane association domains to localize to endosomes while using their protein–protein interaction domains to promote protein complex formation (11). Thus, SNXs act as critical adaptor molecules; orchestrating protein recycling through recognition and concentration of specific cargo, driving membrane remodeling and eliciting scission to form a cargo-enriched carrier (11, 13).SNX27 is of particular interest for synaptic protein recycling, as it is the only sorting nexin to contain a postsynaptic density 95/discs large/zona occludens (PDZ) domain, and is implicated in mediating PDZ-directed sorting from endosomes to the plasma membrane (14–18). The PDZ domain is a protein interaction module recognizing short amino acid motifs found at the C termini of several synaptic targets. Importantly, the PDZ ligand sequence is found on AMPAR intracellular domains, and are heavily involved mediating the assembly of multiprotein complexes, and expression of surface AMPARs (19, 20). We demonstrate that SNX27 is enriched at synapses, and that SNX27 protein level critically regulates surface AMPAR expression. We determined that the PX as well as the PDZ domain is indispensable for SNX27-mediated regulation of AMPAR surface targeting. Moreover, the interaction between SNX27 and AMPARs is regulated by neuronal activity, and SNX27 is required for chemical LTP-elicited surface AMPAR expression. Together, these findings offer a SNX-mediated mechanism for AMPAR sorting and recruitment to the plasma membrane during LTP.     

Heteromerization of PIP aquaporins affects their intrinsic permeability

The plant aquaporin plasma membrane intrinsic proteins (PIP) subfamily represents one of the main gateways for water exchange at the plasma membrane (PM). A fraction of this subfamily, known as PIP1, does not reach the PM unless they are coexpressed with a PIP2 aquaporin. Although ubiquitous and abundantly expressed, the role and properties of PIP1 aquaporins have therefore remained masked. Here, we unravel how FaPIP1;1, a fruit-specific PIP1 aquaporin from Fragaria x ananassa, contributes to the modulation of membrane water permeability (P_f) and pH aquaporin regulation. Our approach was to combine an experimental and mathematical model design to test its activity without affecting its trafficking dynamics. We demonstrate that FaPIP1;1 has a high water channel activity when coexpressed as well as how PIP1–PIP2 affects gating sensitivity in terms of cytosolic acidification. PIP1–PIP2 random heterotetramerization not only allows FaPIP1;1 to arrive at the PM but also produces an enhancement of FaPIP2;1 activity. In this context, we propose that FaPIP1;1 is a key participant in the regulation of water movement across the membranes of cells expressing both aquaporins.The plasma membrane (PM) is the first barrier that limits water exchange in plant cells. The rate of its water transport capacity is mainly associated with aquaporins. Among the seven aquaporin subfamilies described in the plant kingdom, only plasma membrane intrinsic proteins (PIP) and some members of the nodulin-26–like intrinsic proteins (NIP) and X intrinsic proteins (XIP) subfamilies have been shown to be preferentially localized at the PM (1, 2). Of these, PIP aquaporins appear to have a large role in controlling membrane water permeability, whereas NIP and XIP have been mainly described as solute transporters (2–4). Plant PIP aquaporins represent a conserved subfamily that has been historically divided into two subgroups due to their differences in primary structure, PIP1 and PIP2. Interestingly, PIP aquaporins compose ∼40% of the total aquaporin set, and the PIP1 and PIP2 ratio among different species is relatively constant (5–12). Fig. S1 shows the distribution of all aquaporin genes present in plants whose genome has been completely sequenced and analyzed. Antisense inhibition experiments on Arabidopsis thaliana PIP1 and PIP2 have suggested that the two subgroups of aquaporins contribute to root or leaf hydraulic conductivity in the same way (13). In several plant species, members of the PIP1 and PIP2 subgroups were shown to be coexpressed in the same cell type (14–17).Although PIP1 are as ubiquitous as PIP2, the functional properties of each type of channel are different. PIP2 are very well described as a homotetramer with high water transport activity (18, 19) and a gating mechanism unequivocally associated with specific and conserved amino acid motifs triggered by cytosolic acidification (20–22), phosphorylation (23, 24), or divalent cation concentration (22). In contrast, PIP1 have shown complex heterogeneity in water and solute transport and posttranslational regulation. Many reports show that some PIP1 are nonfunctional in regard to water transport (6, 25), whereas other PIP1 act as low-efficiency water channels (26–28), and a minority group shows activity comparable to that of PIP2 (20, 29) or, in contrast, serves as solute channels (25, 30).In addition to their transport properties, many PIP1 show membrane relocalization as a regulatory mechanism, a feature that clearly distinguishes them from any PIP2. These PIP1 fail to reach the PM when expressed alone, but they can succeed if they are coexpressed with PIP2. It has been proposed that this process is a consequence of a physical interaction between PIP1 and PIP2, as reported in both homologous (31) and heterologous systems (14, 32). Although there are some PIP1 with the ability to reach the PM on their own (20, 27, 29), this PIP1–PIP2 interaction seems to be present for several pairs of PIP among different species with functional consequences (14, 21, 28, 33–35).Although the molecular basis of this interaction is still not clear, some data support a model in which the aquaporins of the two subgroups physically interact—very likely by heterooligomerization—to facilitate PIP1 trafficking (31). Recently, it was shown that the first extracellular loop of PIP2 (loop A in BvPIP2;1) could be relevant to the formation of heterotetramers with PIP1 (32). The modification of cytosolic pH sensing, reflected by a shift in the EC₅₀ of oocytes coexpressing BvPIP2;2 and BvPIP1;1 compared with BvPIP2;2 expressed alone, favors the heterooligomerization hypothesis (21).The aim of this work is to contribute to the understating of the PIP1 and PIP2 interaction and to elucidate the functional properties of PIP1 and the role it plays in defining overall membrane permeability.     

Cellular heterogeneity profiling by hyaluronan probes reveals an invasive but slow-growing breast tumor subset

Tumor heterogeneity confounds cancer diagnosis and the outcome of therapy, necessitating analysis of tumor cell subsets within the tumor mass. Elevated expression of hyaluronan (HA) and HA receptors, receptor for HA-mediated motility (RHAMM)/HA-mediated motility receptor and cluster designation 44 (CD44), in breast tumors correlates with poor outcome. We hypothesized that a probe for detecting HA–HA receptor interactions may reveal breast cancer (BCa) cell heterogeneity relevant to tumor progression. A fluorescent HA (F-HA) probe containing a mixture of polymer sizes typical of tumor microenvironments (10–480 kDa), multiplexed profiling, and flow cytometry were used to monitor HA binding to BCa cell lines of different molecular subtypes. Formulae were developed to quantify binding heterogeneity and to measure invasion in vivo. Two subsets exhibiting differential binding (HA^−/low vs. HA^high) were isolated and characterized for morphology, growth, and invasion in culture and as xenografts in vivo. F-HA–binding amounts and degree of heterogeneity varied with BCa subtype, were highest in the malignant basal-like cell lines, and decreased upon reversion to a nonmalignant phenotype. Binding amounts correlated with CD44 and RHAMM displayed but binding heterogeneity appeared to arise from a differential ability of HA receptor-positive subpopulations to interact with F-HA. HA^high subpopulations exhibited significantly higher local invasion and lung micrometastases but, unexpectedly, lower proliferation than either unsorted parental cells or the HA^−/low subpopulation. Querying F-HA binding to aggressive tumor cells reveals a previously undetected form of heterogeneity that predicts invasive/metastatic behavior and that may aid both early identification of cancer patients susceptible to metastasis, and detection/therapy of invasive BCa subpopulations.Breast tumors display substantial heterogeneity driven by genetic and epigenetic mechanisms (1–3). These processes select and support tumor cell subpopulations with distinct phenotypes in proliferation, metastatic/invasive proclivity, and treatment susceptibility that contribute to clinical outcomes. Currently, there is a paucity of biomarkers to identify these subpopulations (3–12). Although detection of genetic heterogeneity may itself be a breast cancer (BCa) prognostic marker (3, 13–15), the phenotypes manifested from this diversity are context-dependent. Therefore, phenotypic markers provide additional powerful tools for biological information required to design diagnostics and therapeutics. Glycomic approaches have enormous potential for revealing tumor cell phenotypic heterogeneity because glycans are themselves highly heterogeneous and their complexity reflects the nutritional, microenvironmental, and genetic dynamics of the tumors (16–18).We used hyaluronan (HA) as a model carbohydrate ligand for probing heterogeneity in glycosaminoglycan–BCa cell receptor interactions. We reasoned this approach would reveal previously undetected cellular and functional heterogeneity linked to malignant progression because the diversity of cell glycosylation patterns, which can occur as covalent and noncovalent modifications of proteins and lipids as well as different sizes of such polysaccharides as HA, is unrivaled (16, 17, 19). In particular, tumor and wound microenvironments contain different sizes of HA polymers that bind differentially to cell receptors to activate signaling pathways regulating cell migration, invasion, survival, and proliferation (19–22).More than other related glycosaminoglycans, HA accumulation within BCa tumor cells and peritumor stroma is a predictor of poor outcome (23) and of the conversion of the preinvasive form of BCa, ductal carcinoma in situ, to an early invasive form of BCa (24). HA is a nonantigenic and large, relatively simple, unbranched polymer, but the manner in which it is metabolized is highly complex (19, 25). There are literally thousands of different HA sizes in remodeling microenvironments, including tumors. HA polymers bind to cells via at least six known receptors (16, 19, 20, 26–32). Two of these, cluster designation 44 (CD44) and receptor for HA-mediated motility/HA-mediated motility receptor (RHAMM/HMMR), form multivalent complexes with different ranges of HA sizes (19, 29, 33), and both receptors are implicated in BCa progression (19–21, 23, 29, 30, 33–36). Elevated CD44 expression in the peritumor stroma is associated with increased relapse (37), and in primary BCa cell subsets may contribute to tumor initiation and progression (38–40). Elevated RHAMM expression in BCa tumor subsets is a prognostic indicator of poor outcome and increased metastasis (22, 33, 41). RHAMM polymorphisms may also be a factor in BCa susceptibility (42, 43).We postulated that multivalent interactions resulting from mixture of a polydisperse population of fluorescent HA (F-HA) sizes, typical of those found in remodeling microenvironments of wounds and tumors (19, 20, 29), with cellular HA receptors would uncover a heterogeneous binding pattern useful for sorting tumor cells into distinct subsets. We interrogated the binding of F-HA to BCa lines of different molecular subtypes, and related binding/uptake patterns to CD44 and RHAMM display, and to tumor cell growth, invasion, and metastasis.     

Reconstitution of long and short patch mismatch repair reactions using Saccharomyces cerevisiae proteins

A problem in understanding eukaryotic DNA mismatch repair (MMR) mechanisms is linking insights into MMR mechanisms from genetics and cell-biology studies with those from biochemical studies of MMR proteins and reconstituted MMR reactions. This type of analysis has proven difficult because reconstitution approaches have been most successful for human MMR whereas analysis of MMR in vivo has been most advanced in the yeast Saccharomyces cerevisiae. Here, we describe the reconstitution of MMR reactions using purified S. cerevisiae proteins and mispair-containing DNA substrates. A mixture of MutS homolog 2 (Msh2)–MutS homolog 6, Exonuclease 1, replication protein A, replication factor C-Δ1N, proliferating cell nuclear antigen and DNA polymerase δ was found to repair substrates containing TG, CC, +1 (+T), +2 (+GC), and +4 (+ACGA) mispairs and either a 5′ or 3′ strand interruption with different efficiencies. The Msh2–MutS homolog 3 mispair recognition protein could substitute for the Msh2–Msh6 mispair recognition protein and showed a different specificity of repair of the different mispairs whereas addition of MutL homolog 1–postmeiotic segregation 1 had no affect on MMR. Repair was catalytic, with as many as 11 substrates repaired per molecule of Exo1. Repair of the substrates containing either a 5′ or 3′ strand interruption occurred by mispair binding-dependent 5′ excision and subsequent resynthesis with excision tracts of up to ∼2.9 kb occurring during the repair of the substrate with a 3′ strand interruption. The availability of this reconstituted MMR reaction now makes possible detailed biochemical studies of the wealth of mutations identified that affect S. cerevisiae MMR.DNA mismatch repair (MMR) is a critical DNA repair pathway that is coupled to DNA replication in eukaryotes where it corrects misincorporation errors made during DNA replication (1–9). This pathway prevents mutations and acts to prevent the development of cancer (10, 11). MMR also contributes to gene conversion by repairing mispaired bases that occur during the formation of recombination intermediates (3, 4, 12). Finally, MMR acts to suppress recombination between divergent but homologous DNA sequences, thereby preventing the formation of genome rearrangements that can result from nonallelic homologous recombination (4, 13–15).Our knowledge of the mechanism of eukaryotic MMR comes from several general lines of investigation (3–9). Studies of bacterial MMR have provided a basic mechanistic framework for comparative studies (5). Genetic and cell-biology studies, primarily in Saccharomyces cerevisiae, have identified eukaryotic MMR genes, provided models for how their gene products define MMR pathways, and elucidated some of the details of how MMR pathways interact with replication (1–4). Reconstitution studies, primarily in human systems, have identified some of the catalytic features of eukaryotic MMR (7–9, 16, 17). Biochemical and structural studies of S. cerevisiae and human MMR proteins have provided information about the function of individual MMR proteins (6–9).In eukaryotic MMR, mispairs are bound by MutS homolog 2 (Msh2)–MutS homolog 6 (Msh6) and Msh2–MutS homolog 3 (Msh3), two partially redundant complexes of MutS-related proteins (3, 4, 18, 19). These complexes recruit a MutL-related complex, called MutL homoloh 1 (Mlh1)–postmeiotic segregation 1 (Pms1) in S. cerevisiae and Mlh1–postmeiotic segregation 2 (Pms2) in human and mouse (3, 4, 20–23). The Mlh1–Pms1/Pms2 complex has an endonuclease activity suggested to play a role in the initiation of the excision step of MMR (24, 25). Downstream of mismatch recognition is a mispair excision step that can be catalyzed by Exonuclease 1 (Exo1) (26–28); however, defects in both S. cerevisiae and mouse Exo1 result in only a partial MMR deficiency, suggesting the existence of additional excision mechanisms (26, 27, 29). DNA polymerase δ, the single-strand DNA binding protein replication protein A (RPA), the sliding clamp proliferating cell nuclear antigen (PCNA), and the clamp loader replication factor C (RFC) are also required for MMR at different steps, including activation of Mlh1–Pms1/Pms2, stimulation of Exo1, potentially in Exo1-independent mispair excision, and in the gap-filling resynthesis steps of MMR (3, 16, 17, 24, 27, 30–36). Although much is known about these core MMR proteins, it is not well understood how eukaryotic MMR is coupled to DNA replication (1, 2), how excision is targeted to the newly replicated strand (1, 25, 37–39), or how different MMR mechanisms such as Exo1-dependent and -independent subpathways are selected or how many such subpathways exist (1, 24, 27, 29).S. cerevisiae has provided a number of tools for studying MMR, including forward genetic screens for mutations affecting MMR, including dominant and separation-of-function mutations, the ability to evaluate structure-based mutations in vivo, cell biological tools for visualizing and analyzing MMR proteins in vivo, and overproduction of individual MMR proteins for biochemical analysis. However, linking these tools with biochemical systems that catalyze MMR reactions in vitro for mechanistic studies has not yet been possible. Here, we describe the development of MMR reactions reconstituted using purified proteins for the analysis of MMR mechanisms.