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Kazuhisa Nakayama

Publications and source records attributed to Kazuhisa Nakayama.

At least 19 recordsLinked to original sources
PubMed2006

Structural basis for Rab11-dependent membrane recruitment of a family of Rab11-interacting protein 3 (FIP3)/Arfophilin-1.

Family of Rab11-interacting protein (FIP)3/Arfophlin-1 and FIP4/Arfophilin-2 are dual effectors for Rab11 and ADP ribosylation factor (ARF)5/ARF6, which are involved in membrane delivery from recycling endosomes to the plasma membrane during cytokinesis. Here, we define the distinct C-terminal binding regions of FIP3 and FIP4 for Rab11 and ARF5/ARF6. Furthermore, we determined the crystal structure of Rab11 in complex with the Rab11-binding domain (RBD) of FIP3. The long amphiphilic alpha-helix of FIP3-RBD forms a parallel coiled-coil homodimer, with two symmetric interfaces with two Rab11 molecules. The hydrophobic side of the RBD helix is involved in homodimerization and mediates the interaction with the Rab11 switch 1 region, whereas the opposite hydrophilic side interacts with the Rab11 switch 2 and is the major factor contributing to the binding specificity. The bivalent interaction of FIP3 with Rab11 at the C terminus allows FIP3 to coordinately function with other binding partners, including ARFs.

ADP-Ribosylation Factors↗
PubMed2006

Monoubiquitylation of GGA3 by hVPS18 regulates its ubiquitin-binding ability.

GGAs (Golgi-localizing, gamma-adaptin ear domain homology, ADP-ribosylation factor (ARF)-binding proteins), constitute a family of monomeric adaptor proteins and are associated with protein trafficking from the trans-Golgi network to endosomes. Here, we show that GGA3 is monoubiquitylated by a RING-H2 type-ubiquitin ligase hVPS18 (human homologue of vacuolar protein sorting 18). By in vitro ubiquitylation assays, we have identified lysine 258 in the GAT domain as a major ubiquitylation site that resides adjacent to the ubiquitin-binding site. The ubiquitylation is abolished by a mutation in either the GAT domain or ubiquitin that disrupts the GAT-ubiquitin interaction, indicating that the ubiquitin binding is a prerequisite for the ubiquitylation. Furthermore, the GAT domain ubiquitylated by hVPS18 no longer binds to ubiquitin, indicating that ubiquitylation negatively regulates the ubiquitin-binding ability of the GAT domain. These results suggest that the ubiquitin binding and ubiquitylation of GGA3-GAT domain are mutually inseparable through a ubiquitin ligase activity of hVPS18.

ADP-Ribosylation Factors↗
PubMed2006

Recruitment of clathrin onto endosomes by the Tom1-Tollip complex.

Tom1 (target of Myb 1) and its related proteins (Tom1L1/Srcasm and Tom1L2) constitute a protein family and share an N-terminal VHS (Vps27p/Hrs/Stam) domain and a following GAT (GGA and Tom1) domain, both of which are also conserved in the GGA family proteins. However, the C-terminal half is not significantly conserved between the Tom1 and GGA families or even between Tom1 and Tom1L1. We have previously shown that the GAT domain of Tom1 interacts with Tollip (Toll-interacting protein), which is associated with endosomes, to which it recruits Tom1. We here extend the previous data and show that the GAT domains of Tom1L1 and Tom1L2 also interact with Tollip, and the C-terminal regions of all the Tom1 family proteins interact with clathrin. Furthermore, when coexpressed with Tollip, all the Tom1 family proteins recruite clathrin onto endosomes. These results indicate that, in conjunction with Tollip, Tom1 family proteins play an important role in recruiting clathrin onto endosomes and suggest that they modulate endosomal functions.

Binding Sites↗
PubMed2006

AMY-1 (associate of Myc-1) localization to the trans-Golgi network through interacting with BIG2, a guanine-nucleotide exchange factor for ADP-ribosylation factors.

AMY-1 (associate of Myc-1) was originally identified as a c-Myc-binding protein that enhances the c-Myc transcription activity, and subsequently found to interact with A-kinase-anchoring proteins (AKAPs), including AKAP149, S-AKAP84 and AKAP95. We show here that, using anti-AMY-1 antibodies we raised, AMY-1 localizes to the trans-Golgi network (TGN) and the nucleus. To explore the possible function of AMY-1, we have undertaken a search for interacting partners by co-immunoprecipitation experiments using cells stably expressing FLAG-tagged AMY-1. Interestingly, we have found that AMY-1 interacts with BIG2 and BIG1, both of which are high molecular weight guanine-nucleotide exchange factors for ADP-ribosylation factors (ARFs) and mainly localize to the TGN. Furthermore, we have demonstrated that AMY-1 is associated with the TGN through interacting with BIG2 but not with BIG1 using an RNA interference approach, although AMY-1 can interact with both BIG1 and BIG2 in vitro. Taken together with the facts that BIG2 contains domains that bind to regulatory subunits of protein kinase A and that recruitment of ARF1 onto Golgi membranes is mediated, at least in part, by activation of protein kinase A, these results suggest that BIG2 alone or in concert with recruited AMY-1 coordinates ARF-mediated membrane trafficking and signaling pathways.

ADP-Ribosylation Factors↗
PubMed2005

Membrane recruitment of effector proteins by Arf and Rab GTPases.

In their GTP-bound form, Arf and Rab family GTPases associate with distinct organelle membranes, to which they recruit specific sets of effector proteins that regulate vesicular transport. The Arf GTPases are involved in the formation of coated carrier vesicles by recruiting coat proteins. On the other hand, the Rab GTPases are involved in the tethering, docking and fusion of transport vesicles with target organelles, acting in concert with the tethering and fusion machineries. Recent structural studies of the Arf1-GGA and Rab5-Rabaptin-5 complexes, as well as other effector structures in complex with the Arf and Rab GTPases, have shed light on the mechanisms underlying the GTP-dependent membrane recruitment of these effector proteins.

ADP-Ribosylation Factor 1↗
PubMed2005

Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain.

Tom1 (Target of Myb1) is suggested to be involved in the transport of ubiquitinated proteins, through the interaction of its GAT (GGA and Tom1) domain with ubiquitin. Here, we demonstrate that the three-helix bundle of Tom1-GAT has two ubiquitin-binding sites recognizing the hydrophobic Ile44 surface of ubiquitin. The complex crystal structure demonstrates that the first site is a hydrophobic patch on helices alpha1 and alpha2. NMR and biochemical data revealed that the N-terminal half of helix alpha3 of Tom1-GAT constitutes the second, stronger binding site. The double-sided ubiquitin binding enhances the efficiency of recognition of ubiquitinated proteins by Tom1.

Amino Acid Sequence↗
PubMed2005

Roles of ARFRP1 (ADP-ribosylation factor-related protein 1) in post-Golgi membrane trafficking.

ADP-ribosylation factor (ARF)-related protein 1 (ARFRP1) is a small GTPase with significant similarity to the ARF family. However, little is known about the function of ARFRP1 in mammalian cells, although knockout mice of its gene are embryonic lethal. In the present study, we demonstrate that ARFRP1 is associated mainly with the trans-Golgi compartment and the trans-Golgi network (TGN) and is an essential regulatory factor for targeting of Arl1 and GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. Furthermore, we show that, in concert with Arl1 and GRIP proteins, ARFRP1 is implicated in the Golgi-to-plasma membrane transport of the vesicular stomatitis virus G protein as well as in the retrograde transport of TGN38 and Shiga toxin from endosomes to the TGN.

ADP-Ribosylation Factors↗
PubMed2005

Structure determination of GGA-GAE and gamma1-ear in complex with peptides: crystallization of low-affinity complexes in membrane traffic.

Crystallization of protein-protein complexes is an important step in the studies of biological functions of proteins. However, weak and transient, even though specific, interactions often present difficulties in crystallization of protein complexes due to the heterogeneity of the sample mixture. For example, the gamma1-ear domain of the AP-1 complex and the GAE domain of GGA1, responsible for the interaction with accessory proteins involved in vesicular transport, are known to interact with target proteins with affinities of the order of 1-100 microM. Such low affinities have hampered crystallization trials of the complexes. To overcome this problem, the gamma1-ear and GAE domains were first co-crystallized with excess amounts of the peptides. Co-crystals of both domains were obtained and the complex structures were determined at 2.5-2.9 A resolution. Based on the crystal packing of gamma1-ear and the cognate peptide, gamma1-ear fused with a peptide tag at the N-terminus was prepared. The peptide-tagged gamma1-ear readily crystallized and the crystal diffracted far better, 1.9-2.2 A resolution, compared with the co-crystallized complex, giving significantly more details without affecting the overall complex structure.

ADP-Ribosylation Factors↗
PubMed2005

Convergence of cell cycle regulation and growth factor signals on GRASP65.

Together with other Golgi matrix components, GRASP65 contributes to the stacking of Golgi cisternae in interphase cells. During mitosis, GRASP65 is heavily phosphorylated, and in turn, cisternal stacking is inhibited leading to the breakdown of the Golgi apparatus. Here we show that GRASP65 is phosphorylated on serine 277 in interphase cells, and this is strongly enhanced in response to the addition of serum or epidermal growth factor. This is directly mediated by ERK suggesting that GRASP65 has some role in growth factor signal transduction. Phosphorylation of Ser-277 is also dramatically increased during mitosis, however this is mediated by Cdk1 and not by ERK. The microinjection of recombinant GRASP65 without N-terminal myristoylation or a peptide fragment containing Ser-277 into the cytosol of normal rat kidney cells inhibits passage through mitosis. This effect is abolished when Ser-277 is replaced with alanine suggesting the phosphorylation of Ser-277 plays an important role in cell cycle regulation. The convergence of cell cycle regulation and growth factor signals on GRASP65 Ser-277 suggests that GRASP65 may function as a signal integrator controlling the cell growth.

Amino Acid Sequence↗
PubMed2005

Expression of BIG2 and analysis of its function in mammalian cells.

BIG2 is a member of brefeldin A-inhibited guanine nucleotide exchange factors for ADP-ribosylation factors (ARFs). Although BIG2 is associated mainly with the trans-Golgi network, we have recently revealed that some population of BIG2 is associated with the recycling endosome. Moreover, we have found that expression of a catalytically inactive BIG2 mutant, E738K, selectively induces membrane tubules from this compartment. We have also demonstrated that the exchange activity of BIG2 is specific for class I ARFs (ARF1 and ARF3) in vivo and inactivation of either ARF enhances the BIG2(E738K)-induced membrane tubulation. Therefore, we have proposed that BIG2 is implicated in the structural integrity of the recycling endosome through activating class I ARFs. This article describes methods used for examining the function of BIG2 including basic protocols, which are not conventional because of cytotoxicity of BIG2 in Escherichia coli cells and its low expression efficiency in mammalian cells.

ADP-Ribosylation Factor 1↗
PubMed2005

Analysis of Arf interaction with GGAs in vitro and in vivo.

Small GTPases of the ADP-ribosylation factor (Arf) family regulate membrane traffic and dynamics in eukaryotic cells. GGAs (Golgi-localizing, gamma-adaptin ear homology domain, Arf-binding proteins) are a family of monomeric clathrin adaptor proteins that were originally identified as proteins interacting with Arfs and found to associate mainly with membranes of the trans-Golgi network (TGN). Like other adaptor and coat proteins, membrane association of GGAs is regulated by Arfs in a GTP-dependent manner. Together with or independent of the adaptor protein complex AP-1, GGAs mediate sorting of transmembrane proteins, including mannose 6-phosphate receptors, between the TGN and endosomes by clathrin-coated vesicles. This chapter describes methods to examine the interaction between Arfs and GGAs and to analyze the cellular function of GGAs regulated by Arfs.

ADP-Ribosylation Factors↗
PubMed2005

Molecular mechanism of ubiquitin recognition by GGA3 GAT domain.

GGA (Golgi-localizing, gamma-adaptin ear domain homology, ARF-binding) proteins, which constitute a family of clathrin coat adaptor proteins, have recently been shown to be involved in the ubiquitin-dependent sorting of receptors, through the interaction between the C-terminal three-helix-bundle of the GAT (GGA and Tom1) domain (C-GAT) and ubiquitin. We report here the crystal structure of human GGA3 C-GAT in complex with ubiquitin. A hydrophobic patch on C-GAT helices alpha1 and alpha2 forms a binding site for the hydrophobic Ile44 surface of ubiquitin. Two distinct orientations of ubiquitin Arg42 determine the shape and the charge distribution of ubiquitin Ile44 surface, leading to two different binding modes. Biochemical and NMR data strongly suggest another hydrophobic binding site on C-GAT helices alpha2 and alpha3, opposite to the first binding site, also binds ubiquitin although weakly. The double-sided ubiquitin binding provides the GAT domain with higher efficiency in recognizing ubiquitinated receptors for lysosomal receptor degradation.

ADP-Ribosylation Factors↗
PubMed2005

Cellular and subcellular localization of EFA6C, a third member of the EFA6 family, in adult mouse Purkinje cells.

EFA6C is a third member of the EFA6 family of guanine nucleotide exchange factors (GEFs) for ADP-ribosylation factor 6 (ARF6). In this study, we first demonstrated that EFA6C indeed activated ARF6 more selectively than ARF1 by ARF pull-down assay. In situ hybridization histochemistry revealed that EFA6C mRNA was expressed predominantly in mature Purkinje cells and the epithelial cells of the choroid plexus in contrast to the ubiquitous expression of ARF6 mRNA throughout the brain. EFA6C mRNA was already detectable in the Purkinje cells at embryonic day 13, increased progressively during post-natal development and peaked during post-natal second week. In Purkinje cells, the immunoreactivity for EFA6C was localized particularly in the post-synaptic density as well as the plasma membranes of the cell somata, dendritic shafts and spines, while the immunoreactivity in their axon terminals in the deep cerebellar nuclei was very faint. These findings suggest that EFA6C may be involved in the regulation of the membrane dynamics of the somatodendritic compartments of Purkinje cells through the activation of ARF6.

ADP-Ribosylation Factor 6↗
PubMed2004

BIG2, a guanine nucleotide exchange factor for ADP-ribosylation factors: its localization to recycling endosomes and implication in the endosome integrity.

Small GTPases of the ADP-ribosylation factor (ARF) family play a key role in membrane trafficking by regulating coated vesicle formation, and guanine nucleotide exchange is essential for the ARF function. Brefeldin A blocks the ARF-triggered coat assembly by inhibiting the guanine nucleotide exchange on ARFs and causes disintegration of the Golgi complex and tubulation of endosomal membranes. BIG2 is one of brefeldin A-inhibited guanine nucleotide exchange factors for the ARF GTPases and is associated mainly with the trans-Golgi network. In the present study, we have revealed that another population of BIG2 is associated with the recycling endosome and found that expression of a catalytically inactive BIG2 mutant, E738K, selectively induces membrane tubules from this compartment. We also have shown that BIG2 has an exchange activity toward class I ARFs (ARF1 and ARF3) in vivo and inactivation of either ARF exaggerates the BIG2(E738K)-induced tubulation of endosomal membranes. These observations together indicate that BIG2 is implicated in the structural integrity of the recycling endosome through activating class I ARFs.

ADP-Ribosylation Factors↗
PubMed2004

Stabilin-1 localizes to endosomes and the trans-Golgi network in human macrophages and interacts with GGA adaptors.

Stabilin-1 and stabilin-2 constitute a novel family of fasciclin domain-containing hyaluronan receptor homologues recently described by us. Whereas stabilin-1 is expressed in sinusoidal endothelial cells and in macrophages in vivo, stabilin-2 is absent from the latter. In the present study, we analyzed the subcellular distribution of stabilin-1 in primary human macrophages. Using flow cytometry, expression of stabilin-1 was demonstrated on the surface of interleukin-4/dexamethasone-stimulated macrophages (MPhi2). By immunofluorescence and confocal microscopy, we established that stabilin-1 is preferentially localized in early endosome antigen-1-positive early/sorting endosomes and in recycling endosomes identified by transferrin endocytosis. Association of stabilin-1 was infrequently seen with p62 lck ligand-positive late endosomes and with CD63-positive lysosomes but not in lysosome-associated membrane protein-1-positive lysosomes. Stabilin-1 was also found in the trans-Golgi network (TGN) but not in Golgi stack structures. Glutathione S-transferase pull-down assay revealed that the cytoplasmic tail of stabilin-1 but not stabilin-2 binds to recently discovered Golgi-localized, gamma-ear-containing, adenosine 5'-diphosphate-ribosylation factor-binding (GGA) adaptors GGA1, GGA2, and GGA3 long, mediating traffic between Golgi and endosomal/lysosomal compartments. Stabilin-1 did not bind to GGA3 short, which lacks a part of the Vps27p/Hrs/STAM domain. Deletion of DDSLL and LL amino acid motifs resulted in decreased binding of stabilin-1 with GGAs. A small portion of stabilin-1 colocalized with GGA2 and GGA3 in the TGN in MPhi2. Treatment with brefeldin A resulted in accumulation of stabilin-1 in the TGN. Our results suggest that stabilin-1 is involved in the GGA-mediated sorting processes at the interface of the biosynthetic and endosomal pathways; similarly to other GGA-interacting proteins, stabilin-1 may thus function in endocytic and secretory processes of human macrophages.

ADP-Ribosylation Factors↗
PubMed2004

Tollip and Tom1 form a complex and recruit ubiquitin-conjugated proteins onto early endosomes.

Tom1 (target of Myb1) is a protein of unknown function. Tom1 and its relative Tom1L1 have an N-terminal VHS (Vps27p/Hrs/Stam) domain followed by a GAT (GGA and Tom1) domain, both of which are also found in the GGA (Golgi-localizing, gamma-adaptin ear domain homology, ADP-ribosylation factor-binding protein) family of proteins. Although the VHS and GAT domains of GGA proteins bind to transmembrane cargo proteins and the small GTPase ADP-ribosylation factor, respectively, the VHS and GAT domains of Tom1 are unable to interact with these proteins. In this study, we show that the GAT domains of Tom1 and Tom1L1 interact with ubiquitin and Tollip (Toll-interacting protein). Ubiquitin bound the GAT domains of Tom1, Tom1L1, and GGA proteins, whereas Tollip interacted specifically with Tom1 and Tom1L1. Ubiquitin and Tollip bound to an overlapping region of the Tom1-GAT domain in a mutually exclusive manner. Tom1 was predominantly cytosolic when expressed in cells. On the other hand, Tollip was localized on early endosomes and recruited Tom1 and ubiquitinated proteins. These observations suggest that Tollip and Tom1 form a complex and regulate endosomal trafficking of ubiquitinated proteins.

Amino Acid Sequence↗