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.     

Arf6 coordinates actin assembly through the WAVE complex,a mechanism usurped by Salmonella to invade host cells

ADP ribosylation factor (Arf) 6 anchors to the plasma membrane, where it coordinates membrane trafficking and cytoskeleton remodelling, but how it assembles actin filaments is unknown. By reconstituting membrane-associated actin assembly mediated by the WASP family veroprolin homolog (WAVE) regulatory complex (WRC), we recapitulated an Arf6-driven actin polymerization pathway. We show that Arf6 is divergent from other Arf members, as it was incapable of directly recruiting WRC. We demonstrate that Arf6 triggers actin assembly at the membrane indirectly by recruiting the Arf guanine nucleotide exchange factor (GEF) ARNO that activates Arf1 to enable WRC-dependent actin assembly. The pathogen Salmonella usurped Arf6 for host cell invasion by recruiting its canonical GEFs EFA6 and BRAG2. Arf6 and its GEFs facilitated membrane ruffling and pathogen invasion via ARNO, and triggered actin assembly by generating an Arf1–WRC signaling hub at the membrane in vitro and in cells. This study reconstitutes Arf6-dependent actin assembly to reveal a mechanism by which related Arf GTPases orchestrate distinct steps in the WRC cytoskeleton remodelling pathway.ADP ribosylation factor (Arf) GTPases are best known for their roles in vesicle and organelle trafficking (1). Class I and II Arfs (Arf1, Arf3, Arf4, and Arf5) are found predominantly in and around the Golgi apparatus. In contrast, the more divergent Class III Arf (Arf6) operates almost exclusively at the plasma membrane (2). Consistent with its localization, Arf6 has been heavily implicated in trafficking events at the cell surface, including the regulation of endocytosis and exocytosis (1). In particular, Arf6 and its guanine nucleotide exchange factors (GEFs) are believed to be pivotal to the recycling of endosomes and receptors to and from the plasma membrane (3, 4). Arf6 also has a clear role in cortical cytoskeleton rearrangement (5). This is strongly supported by evidence of Arf6 and Rac1 (Ras-related C3 botulinum toxin substrate) interplay (6), exemplified by Arf6 recruitment of the Rac1 GEF Kalirin, Arf6 promotion of Rac1 activation, and lamellipodia formation (7–9).Rac1 is required for generation of lamellipodia that lead to membrane ruffles and macropinocytosis (10). Rac1 is thought to achieve this by activating the WRC, which comprises WAVE (WASP family veroprolin homolog), Abi (abl-interactor 1), Cyfip (cytoplasmic FMR1 interacting protein), Nap1 (NCK-associated protein 1), HSPC300 (heat shock protein C300), or their homologs (10–12). We recently established that Rac1 was not sufficient for WRC recruitment to the membrane and its activation, which instead requires direct binding by Rac1 and an Arf GTPase (13). This in vitro Arf activity could be supplied by multiple isoforms including Arf1 and Arf5, but only Arf1 facilitated WRC-dependent lamellipodia formation and macropinocytosis of the bacterial pathogen Salmonella into human host cells (13–15). Intriguingly, Arf6 also promoted Salmonella invasion (14), and, given the capability of Arfs to modulate WRC, it seems likely that Arf6 also recruits and activates the WRC at the plasma membrane. However, despite mounting evidence that Arf6 remodels the cytoskeleton, a molecular mechanism by which Arf6 drives Arp2/3-dependent actin assembly has not been resolved.     

Reduction of toxic RNAs in myotonic dystrophies type 1 and type 2 by the RNA helicase p68/DDX5

Myotonic dystrophies type 1 (DM1) and type 2 (DM2) are neuromuscular diseases, caused by accumulation of CUG and CCUG RNAs in toxic aggregates. Here we report that the increased stability of the mutant RNAs in both types of DM is caused by deficiency of RNA helicase p68. We have identified p68 by studying CCUG-binding proteins associated with degradation of the mutant CCUG repeats. Protein levels of p68 are reduced in DM1 and DM2 biopsied skeletal muscle. Delivery of p68 in DM1/2 cells causes degradation of the mutant RNAs, whereas delivery of p68 in skeletal muscle of DM1 mouse model reduces skeletal muscle myopathy and atrophy. Our study shows that correction of p68 may reduce toxicity of the mutant RNAs in DM1 and in DM2.Myotonic dystrophy type 1 (DM1) is a neuromuscular disease characterized by myotonia, distal muscle weakness, heart conduction defects, and, in the congenital form, a delay in myogenesis and severe cognitive abnormalities (1). DM1 is caused by expanded CTG repeats within the 3′ untranslated region of the DMPK gene (2). Myotonic dystrophy type 2 (DM2) is a late-onset disease that is caused by expanded CCTG repeats in intron 1 of the ZNF9/CNBP gene (3). Development of therapeutic approaches for DM1 or DM2 is an urgent need. Numerous data suggest that DM1 and DM2 are caused by RNA gain-of-function mechanisms (4–6). Initial studies showed that mutant RNAs mainly affect two RNA-binding proteins, CUG-binding protein 1 (CUGBP1) and muscleblind-like protein 1 (MBNL1) (7–9). CUG repeats elevate protein levels of CUGBP1 by increasing its stability (5). In addition, CUG repeats change signal transduction pathways, such as the glycogen synthase kinase 3β (GSK3β)–cyclin D3 pathway, regulating CUGBP1 activity (5, 10). CUG and CCUG repeats form double-stranded hairpin structures and sequester MBNL1 (9, 11, 12). Several other RNA-binding proteins, such as Staufen1 and two members of the DEAD-box RNA helicases family, DDX5/p68 and DDX6, are also involved in DM1 (13–15).We showed that the mutant CUG and CCUG RNAs are very stable (16), suggesting that the activity of RNA-binding proteins regulating RNA decay is reduced in DM1 and in DM2. In this study, we tested this hypothesis by isolation and analysis of several CCUG-binding proteins. We found that the levels of one of these proteins, p68, are reduced in DM1 and DM2 biopsied muscle and that correction of p68 leads to degradation of the mutant CUG and CCUG RNAs, disintegration of RNA foci, and reduction of DM muscle pathology.     

EFA6 controls Arf1 and Arf6 activation through a negative feedback loop

Guanine nucleotide exchange factors (GEFs) of the exchange factor for Arf6 (EFA6), brefeldin A-resistant Arf guanine nucleotide exchange factor (BRAG), and cytohesin subfamilies activate small GTPases of the Arf family in endocytic events. These ArfGEFs carry a pleckstrin homology (PH) domain in tandem with their catalytic Sec7 domain, which is autoinhibitory and supports a positive feedback loop in cytohesins but not in BRAGs, and has an as-yet unknown role in EFA6 regulation. In this study, we analyzed how EFA6A is regulated by its PH and C terminus (Ct) domains by reconstituting its GDP/GTP exchange activity on membranes. We found that EFA6 has a previously unappreciated high efficiency toward Arf1 on membranes and that, similar to BRAGs, its PH domain is not autoinhibitory and strongly potentiates nucleotide exchange on anionic liposomes. However, in striking contrast to both cytohesins and BRAGs, EFA6 is regulated by a negative feedback loop, which is mediated by an allosteric interaction of Arf6-GTP with the PH-Ct domain of EFA6 and monitors the activation of Arf1 and Arf6 differentially. These observations reveal that EFA6, BRAG, and cytohesins have unanticipated commonalities associated with divergent regulatory regimes. An important implication is that EFA6 and cytohesins may combine in a mixed negative-positive feedback loop. By allowing EFA6 to sustain a pool of dormant Arf6-GTP, such a circuit would fulfill the absolute requirement of cytohesins for activation by Arf-GTP before amplification of their GEF activity by their positive feedback loop.Guanine nucleotide exchange factors (GEFs), which activate small GTPases by stimulating their intrinsically very slow GDP/GTP exchange, are key players in the extraordinary diversity of small GTPases pathways (reviewed in ref. 1). Small GTPases carry little specificity determinants on their own to determine when and where they should be turned on and which pathway they should activate (2), which are instead largely monitored by their GEFs. Thus, understanding how different members of a GEF family activate an individual small GTPase in distinct patterns is a major issue in small GTPase biology in normal cells and in diseases.An important contribution to the functional specificity of GEFs is how they themselves are regulated. Crystallographic studies combined with biochemical studies that reconstituted GEF-stimulated GDP/GTP nucleotide exchange have been instrumental in uncovering a growing complexity of regulatory mechanisms (reviewed in ref. 1). These include autoinhibitory elements outside the catalytic GEF domain that block access to the active site (3–7), large conformational changes that release autoinhibition in response to various stimuli (8–11), positive feedback loops in which freshly produced GTP-bound GTPases stimulate GDP/GTP exchange (10, 12–15), and potentiation of nucleotide exchange by colocalization on membranes (11, 13, 16, 17).These previous studies demonstrated that a wide range of regulatory regimes can be achieved even at the scale of a single GEF family by regulatory mechanisms that combine in multiple ways. GEFs that activate small GTPases of the Arf family (ArfGEFs), which are major regulators of many aspects of membrane traffic and organelle structure in eukaryotic cells (reviewed in refs. 18 and 19), form one of the best-characterized GEF families to date (reviewed in ref. 1), making a comprehensive view of their regulatory repertoire within reach. ArfGEFs comprise two major groups: the BIG/GBF1 group, which functions at the Golgi, and a group composed of the exchange factor for Arf6 (EFA6), brefeldin A-resistant Arf guanine nucleotide exchange factor (BRAG), and cytohesin subfamilies, which activate Arf GTPases at the cell periphery and function in various aspects of endocytosis (reviewed in ref. 20). The actual substrates of these ArfGEFs have been difficult to establish, notably because the most abundant Arf isoform, Arf1, was long believed to be excluded from the plasma membrane where the Arf6 isoform is located. Accordingly, cytohesins and BRAGs have been described as Arf6-specific GEFs in cells but are now recognized as active Arf1-GEFs (16, 21, 22), whereas EFA6 remains the sole ArfGEF considered to be strictly Arf6-specific (23, 24).Members of the EFA6, BRAG, and cytohesin subfamilies have divergent N-terminal domains but a related domain organization in their C terminus comprising a Sec7 domain, which stimulates GDP/GTP exchange, followed by a pleckstrin homology (PH) domain, which has multiple regulatory functions. In cytohesins, the PH domain recognizes signaling phosphoinositides by its canonical lipid-binding site (25), autoinhibits the Sec7 domain by obstructing its Arf-binding site (4), and amplifies nucleotide exchange by a positive feedback loop involving its direct interaction with Arf1-GTP or Arf6-GTP (10, 13, 21). In contrast, the PH domain of BRAG is not autoinhibitory and is not involved in a feedback loop, but instead strongly potentiates nucleotide exchange by binding to polyanionic membranes without marked phosphoinositides preference (16).How members of the EFA6 subfamily are regulated is currently unknown. These ArfGEFs are found predominantly (although not exclusively) in the brain and function in the coordination of endocytosis and actin dynamics (23, 26, 27), in the maintenance of tight junctions (28), in microtubule dynamics in Caenorhabditis elegans embryos (29), and in the formation and maintenance of dendrites (30), although the molecular details of these functions remain largely unknown. Consistent with an important role in the brain, defects in EFA6 functions have been found in neurologic disorders (31) and in human gliomas (32). The PH domain of EFA6 subfamily members drives the localization of EFA6 members to the plasma membrane (26) and it binds to PIP₂ lipids (33). It is followed by a 150-residue C-terminal (Ct) domain predicted to form a coiled coil, which massively induces actin-rich membrane protrusions when expressed with the PH domain (26). The divergence of regulatory mechanisms between Sec7-PH–containing cytohesins and BRAGs prompted us to undertake a quantitative biochemical investigation of EFA6 nucleotide exchange regulation. Our findings reveal an overlooked dual specificity of EFA6 for Arf1 and Arf6 and an unprecedented regulation by a negative feedback loop, with important potential implications for the activation of Arf GTPases in endocytic events.     

N terminus of ASPP2 binds to Ras and enhances Ras/Raf/MEK/ERK activation to promote oncogene-induced senescence

The ASPP2 (also known as 53BP2L) tumor suppressor is a proapoptotic member of a family of p53 binding proteins that functions in part by enhancing p53-dependent apoptosis via its C-terminal p53-binding domain. Mounting evidence also suggests that ASPP2 harbors important nonapoptotic p53-independent functions. Structural studies identify a small G protein Ras-association domain in the ASPP2 N terminus. Because Ras-induced senescence is a barrier to tumor formation in normal cells, we investigated whether ASPP2 could bind Ras and stimulate the protein kinase Raf/MEK/ERK signaling cascade. We now show that ASPP2 binds to Ras–GTP at the plasma membrane and stimulates Ras-induced signaling and pERK1/2 levels via promoting Ras–GTP loading, B-Raf/C-Raf dimerization, and C-Raf phosphorylation. These functions require the ASPP2 N terminus because BBP (also known as 53BP2S), an alternatively spliced ASPP2 isoform lacking the N terminus, was defective in binding Ras–GTP and stimulating Raf/MEK/ERK signaling. Decreased ASPP2 levels attenuated H-RasV12–induced senescence in normal human fibroblasts and neonatal human epidermal keratinocytes. Together, our results reveal a mechanism for ASPP2 tumor suppressor function via direct interaction with Ras–GTP to stimulate Ras-induced senescence in nontransformed human cells.ASPP2, also known as 53BP2L, is a tumor suppressor whose expression is altered in human cancers (1). Importantly, targeting of the ASPP2 allele in two different mouse models reveals that ASPP2 heterozygous mice are prone to spontaneous and γ-irradiation–induced tumors, which rigorously demonstrates the role of ASPP2 as a tumor suppressor (2, 3). ASPP2 binds p53 via the C-terminal ankyrin-repeat and SH3 domain (4–6), is damage-inducible, and can enhance damage-induced apoptosis in part through a p53-mediated pathway (1, 2, 7–10). However, it remains unclear what biologic pathways and mechanisms mediate ASPP2 tumor suppressor function (1). Indeed, accumulating evidence demonstrates that ASPP2 also mediates nonapoptotic p53-independent pathways (1, 3, 11–15).The induction of cellular senescence forms an important barrier to tumorigenesis in vivo (16–21). It is well known that oncogenic Ras signaling induces senescence in normal nontransformed cells to prevent tumor initiation and maintain complex growth arrest pathways (16, 18, 21–24). The level of oncogenic Ras activation influences its capacity to activate senescence; high levels of oncogenic H-RasV12 signaling leads to low grade tumors with senescence markers, which progress to invasive cancers upon senescence inactivation (25). Thus, tight control of Ras signaling is critical to ensure the proper biologic outcome in the correct cellular context (26–28).The ASPP2 C terminus is important for promoting p53-dependent apoptosis (7). The ASPP2 N terminus may also suppress cell growth (1, 7, 29–33). Alternative splicing can generate the ASPP2 N-terminal truncated protein BBP (also known as 53BP2S) that is less potent in suppressing cell growth (7, 34, 35). Although the ASPP2 C terminus mediates nuclear localization, full-length ASPP2 also localizes to the cytoplasm and plasma membrane to mediate extranuclear functions (7, 11, 12, 36). Structural studies of the ASPP2 N terminus reveal a β–Grasp ubiquitin-like fold as well as a potential Ras-binding (RB)/Ras-association (RA) domain (32). Moreover, ASPP2 can promote H-RasV12–induced senescence (13, 15). However, the molecular mechanism(s) of how ASPP2 directly promotes Ras signaling are complex and remain to be completely elucidated.Here, we explore the molecular mechanisms of how Ras-signaling is enhanced by ASPP2. We demonstrate that ASPP2: (i) binds Ras-GTP and stimulates Ras-induced ERK signaling via its N-terminal domain at the plasma membrane; (ii) enhances Ras-GTP loading and B-Raf/C-Raf dimerization and forms a ASPP2/Raf complex; (iii) stimulates Ras-induced C-Raf phosphorylation and activation; and (iv) potentiates H-RasV12–induced senescence in both primary human fibroblasts and neonatal human epidermal keratinocytes. These data provide mechanistic insight into ASPP2 function(s) and opens important avenues for investigation into its role as a tumor suppressor in human cancer.     

Altered cofactor regulation with disease-associated p97/VCP mutations

Dominant mutations in p97/VCP (valosin-containing protein) cause a rare multisystem degenerative disease with varied phenotypes that include inclusion body myopathy, Paget’s disease of bone, frontotemporal dementia, and amyotrophic lateral sclerosis. p97 disease mutants have altered N-domain conformations, elevated ATPase activity, and altered cofactor association. We have now discovered a previously unidentified disease-relevant functional property of p97 by identifying how the cofactors p37 and p47 regulate p97 ATPase activity. We define p37 as, to our knowledge, the first known p97-activating cofactor, which enhances the catalytic efficiency (k_cat/K_m) of p97 by 11-fold. Whereas both p37 and p47 decrease the K_m of ATP in p97, p37 increases the k_cat of p97. In contrast, regulation by p47 is biphasic, with decreased k_cat at low levels but increased k_cat at higher levels. By deleting a region of p47 that lacks homology to p37 (amino acids 69–92), we changed p47 from an inhibitory cofactor to an activating cofactor, similar to p37. Our data suggest that cofactors regulate p97 ATPase activity by binding to the N domain. Induced conformation changes affect ADP/ATP binding at the D1 domain, which in turn controls ATPase cycling. Most importantly, we found that the D2 domain of disease mutants failed to be activated by p37 or p47. Our results show that cofactors play a critical role in controlling p97 ATPase activity, and suggest that lack of cofactor-regulated communication may contribute to p97-associated disease pathogenesis.The p97 AAA [ATPase associated with diverse cellular activities; also called VCP (valosin-containing protein)] participates in key steps in ubiquitin-dependent protein quality control (1), autophagy (2, 3), membrane remodeling (4, 5), and numerous other fundamentally important cellular functions. p97 directs proteins to two major degradation systems: the proteasome and autophagy pathways. This key role of p97 underscores its importance in protein homeostasis and strongly implicates p97 in neurodegenerative diseases (6). Dominantly inherited missense mutations in p97 were initially associated with a rare degenerative disorder termed inclusion body myopathy with Paget’s disease of bone and frontotemporal dementia (IBMPFD) (7, 8). Subsequently, it has been found that mutations in p97 cause a wider spectrum of degenerative diseases that includes amyotrophic lateral sclerosis (9–12) and parkinsonism (13). Thus, the acronym IBMPFD is insufficient. Moreover, mutations in the heterogeneous nuclear ribonucleoproteins hnRNPA2B1 and hnRNPA1 also cause a syndrome similar to conditions associated with VCP mutations (14). To account for the varied phenotypes and genetic etiologies of IBMPFD, it has been suggested that the term multisystem proteinopathy type 1 (MSP1) (14) be used to describe the phenotypic syndrome associated with mutations in p97. Disease mutants of p97 contribute to pathology by disrupting autophagosome (2, 3) and endosome maturation, which leads to vacuolation, weakness, and muscle atrophy (15, 16). However, the molecular disease mechanisms associated with mutant p97 are still being investigated, with the eventual hope of developing therapeutic agents for these serious illnesses.p97 assembles into a homohexamer, as revealed by X-ray crystallography (17, 18). A single monomer is composed of an N domain, which interacts with p97 cofactor proteins, and two ATPase domains, D1 and D2. The D1 and D2 domains form stacked hexameric rings, whereas the N domains extend outward, coplanar with the D1 ring. Most of the disease mutations occur in the N domain, whereas some occur in the D1 or the N–D1 linker region (see SI Appendix, Fig. S1A for examples). All p97 disease mutants tested thus far can form stable hexamers (19, 20) and exhibit increased D2 ATPase activity (19–23). Disease mutations lead to increased proteolytic susceptibility of the D2 ring (19). Structural and biochemical studies suggest that disease mutations alter N-domain and D1 conformations (20, 23, 24) and cause defects in interdomain communication between neighboring subunits.A major role of the N domain is to recruit cofactors (25, 26), such as the Npl4 (nuclear protein localization homolog 4) and Ufd1 (ubiquitin fusion degradation 1) heterodimers (27), and an array of 13 UBX (ubiquitin regulatory X) domain cofactors (28). By recruiting certain cofactor proteins, the N domain may link the mechanochemical activity of ATP hydrolysis to the unfolding or disassembly of substrate proteins. p47, the first p97 UBX cofactor discovered, is required for p97-mediated membrane fusion (29). Binding of p47 (also called NSFL1 cofactor p47 or UBX domain-containing protein 2C) to the N domain of p97 significantly reduces the diameter of the p97 ring (29) and inhibits wild-type p97 ATPase activity (30). Although actively studied, the physiological functions of p97–cofactor complexes and their mechanisms are largely unknown.X-ray crystallography of p97 has revealed that the N domain of p97 is conformationally flexible (17, 18), adopting two primary conformations. In the up conformation, the N domain extends above the D1 ring, whereas in the down conformation, the N domain lies coplanar with the D1 ring. The conformation is nucleotide-dependent, that is, determined by the binding state of the D1 domain (17). It has been proposed that the flexibility of the N domain is crucial to ATP hydrolysis, because modifying the N domain reduces ATPase activity. Specifically, reducing N-domain mobility inhibits wild-type p97 ATPase activity (20). Moreover, removing the N domain (1∼209) altogether was shown to block the enhanced ATPase activity of a disease mutant (20).In wild-type p97, the N domains exist in a tightly regulated, heterogeneous arrangement of up and down conformations. In contrast, disease mutants exhibit dysregulated N-domain conformations (12, 17, 24). Crystal structures of two disease mutants showed all six N domains of the complex in the up conformation, a behavior that has been observed in only disease mutants (23). A recent study found that this uniform arrangement is a secondary effect of reduced ADP binding by the D1 domain, whose state controls N-domain conformation (23).Altered conformation of the N domain in p97 disease mutants is further supported by atypical p97 cofactor binding in cells (31–33). Decreased binding to a UBX cofactor, UBXD1, is observed in 293T cells expressing p97 disease mutants and leads to a blockade of caveolin 1 trafficking (33). Intriguingly, disease mutants can coimmunoprecipitate more p47 and Npl4/Ufd1 heterodimers than WT p97, suggesting elevated binding affinities for p47 and Npl4/Ufd1 in mutant cells (31, 33). However, the consequences of altered binding to cofactors in cells that express mutant p97 have not been investigated biochemically. To provide a mechanistic understanding of cofactor-regulated ATPase activity, we analyzed the effect of p37 and p47 on the ATPase activity of WT and disease mutants of p97 in this study.     

DNA damage in stem cells activates p21, inhibits p53, and induces symmetric self-renewing divisions

DNA damage leads to a halt in proliferation owing to apoptosis or senescence, which prevents transmission of DNA alterations. This cellular response depends on the tumor suppressor p53 and functions as a powerful barrier to tumor development. Adult stem cells are resistant to DNA damage-induced apoptosis or senescence, however, and how they execute this response and suppress tumorigenesis is unknown. We show that irradiation of hematopoietic and mammary stem cells up-regulates the cell cycle inhibitor p21, a known target of p53, which prevents p53 activation and inhibits p53 basal activity, impeding apoptosis and leading to cell cycle entry and symmetric self-renewing divisions. p21 also activates DNA repair, limiting DNA damage accumulation and self-renewal exhaustion. Stem cells with moderate DNA damage and diminished self-renewal persist after irradiation, however. These findings suggest that stem cells have evolved a unique, p21-dependent response to DNA damage that leads to their immediate expansion and limits their long-term survival.Adult stem cells (SCs) are thought to be resistant to DNA damage (DD)-induced apoptosis or senescence owing to the activation of unique pro-survival and DD repair (DDR) responses (1–3). Genetic alterations that decrease DNA repair activities lead to increased DD and reduced self-renewal in SCs, suggesting that DDR is critical to preservation of SC function (1, 4, 5). DDR decreases during physiological aging, a phenomenon correlated with the accumulation of endogenous DD and decreased self-renewal in aged SCs (6–9).In differentiated cells, DD triggers a checkpoint response that leads to apoptosis or senescence and depends on activation of the tumor suppressor p53 (10). This is considered a powerful tumor-suppressor mechanism, as demonstrated by the finding that p53 is invariably inactivated in spontaneous tumors (11). After irradiation, p53 is up-regulated in populations enriched for hematopoietic, hair follicle bulge, and colon SCs (5, 12–15). Whether this is critical for activation of the DDR response and maintenance of self-renewal, why p53 induction does not result in SC apoptosis or senescence, and how tumor suppression is executed in SCs remain unclear, however. Indirect evidence indicates that the cell cycle inhibitor p21, a downstream effector of p53, might be involved in DD processing in SCs. In the absence of p21, SCs exhaust prematurely (16) and after a low radiation dose display reduced reconstitution capacity (17). Here we report our studies on the role of p53 and p21 in DD processing of highly purified hematopoietic SCs (HSCs) and mammary SCs (MaSCs).     

From the Cover: Feature Article: mTOR complex 2-Akt signaling at mitochondria-associated endoplasmic reticulum membranes (MAM) regulates mitochondrial physiology

The target of rapamycin (TOR) is a highly conserved protein kinase and a central controller of growth. Mammalian TOR complex 2 (mTORC2) regulates AGC kinase family members and is implicated in various disorders, including cancer and diabetes. Here we report that mTORC2 is localized to the endoplasmic reticulum (ER) subcompartment termed mitochondria-associated ER membrane (MAM). mTORC2 localization to MAM was growth factor-stimulated, and mTORC2 at MAM interacted with the IP₃ receptor (IP3R)-Grp75–voltage-dependent anion-selective channel 1 ER-mitochondrial tethering complex. mTORC2 deficiency disrupted MAM, causing mitochondrial defects including increases in mitochondrial membrane potential, ATP production, and calcium uptake. mTORC2 controlled MAM integrity and mitochondrial function via Akt mediated phosphorylation of the MAM associated proteins IP3R, Hexokinase 2, and phosphofurin acidic cluster sorting protein 2. Thus, mTORC2 is at the core of a MAM signaling hub that controls growth and metabolism.Mitochondria-associated endoplasmic reticulum (ER) membrane (MAM) is a subcompartment of the ER that forms a quasisynaptic structure with mitochondria. The main function of this membrane is to facilitate the transfer of lipids and calcium between the two organelles. MAM thereby controls mitochondrial physiology and apoptosis (1, 2). MAM also mediates ER homeostasis and lipid biosynthesis by harboring chaperones and several key lipid synthesis enzymes (3–6). In mammalian MAM, the ER and mitochondria are physically tethered to each other by the IP₃ receptor (IP3R)-Grp75-VDAC1 (voltage-dependent anion-selective channel 1) trimeric complex (7) and by dimers of the mitofusin (Mfn) proteins Mfn1 and Mfn2 (8) (Fig. S1H). The σ-1 receptor also stabilizes MAM by interacting with IP3R and VDAC (9). MAM formation is regulated by multiple signaling inputs, including calcium and possibly growth factors (10–12). However, the mechanism(s) that controls MAM formation is largely unknown other than it involves recruitment of MAM components by the MAM resident proteins phosphofurin acidic cluster sorting protein 2 (PACS2) and Rab32 (13–15). Akt, an AGC family kinase that is also found at MAM (16), phosphorylates PACS2 (17), but it remains to be determined whether Akt is involved in mediating MAM integrity.Akt, often up-regulated in cancer, also phosphorylates hexokinase 2 (HK2) to promote association of HK2 with the MAM protein VDAC1 (18, 19). This association, possibly at MAM (20, 21), enables HK2, using ATP exiting mitochondria through VDAC1, to phosphorylate glucose and thereby stimulate glycolysis (22). Conversely, upon inhibition of Akt, HK2 dissociates from VDAC1, causing VDAC1 closure and increased mitochondrial membrane potential (19). This regulation of HK2 by Akt has been proposed to account for enhanced glycolysis in cancer cells, also known as the Warburg effect (23). Furthermore, Akt regulates calcium release from MAM by phosphorylating IP3R, thereby controlling apoptosis (24–26). Thus, MAM is increasingly recognized as a signaling hub controlling cell physiology (15), and is implicated in a wide spectrum of diseases, including cancer, neurodegenerative disorders, inflammation, and infection (27).The target of rapamycin (TOR) pathway is a cellular signaling cascade that, like mitochondria, is present in all eukaryotes (28, 29). TOR integrates and relays signals from both extra- and intracellular sources (e.g., growth factors, nutrients, and cellular energy levels), and thereby instructs the cell to grow. TOR is found in two structurally and functionally distinct protein complexes that in mammalian cells are termed mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2) (30). mTORC2 comprises mTOR, rictor, mammalian lethal with SEC13 protein 8 (mLST8), stress-activated protein kinase (SAPK)-interacting protein (Sin1), and protor [also known as proline-rich protein 5 (PRR5)] (31), and phosphorylates AGC kinases, such as Akt, serum/glucocorticoid-regulated kinase 1 (SGK1), and PKC, all of which are linked to cancer and diabetes (32). Growth factors activate mTORC2 by promoting mTORC2-ribosome association in a PI3K-dependent manner (33, 34). mTORC2 is antiapoptotic, presumably via its role in phosphorylating and activating Akt (34–38).Various observations indicate that mTORC2 is linked to both the ER and mitochondria. Recent findings suggest that mTORC2 is at the ER, possibly through interaction with ER-bound ribosomes (34, 39). mTORC2 phosphorylates Akt at the ER (39, 40), and mTORC2 signaling is sensitive to ER stress (41, 42). In Chlamydomonas, TOR associates with membranes from the ER (43). With regard to mitochondria, mTOR has been observed in close proximity to the outer mitochondrial membrane (44), and mTOR and mLST8 interact with the mitochondrial outer-membrane protein VDAC1 (45) and the mitochondria-associated protein Grp75 (46), respectively. mTORC2 regulates the cellular distribution of mitochondria (47), and mTORC2-activated Akt is associated with mitochondria (18, 48, 49). Pink1, a regulator of mitochondrial function, has been implicated in mTORC2 activation (50). mTORC2-addicted cancer cells exhibit enhanced dependence on mitochondria, Rab32 and HK2 (51). Finally, Barquilla et al. reported that TORC2 in trypanosomes is localized to both ER and mitochondria (52). Thus, mTORC2 has been physically and functionally linked to both the ER and mitochondria.Here we investigate the localization of mTORC2. We show that ribosome-bound mTORC2 is at MAM. Localization to MAM is growth factor-dependent. MAM-associated mTORC2 activates Akt and thereby controls MAM integrity, mitochondrial metabolism, and cell survival. Thus, our findings describe a critical role for mTORC2 in a MAM signaling hub.     

From the Cover: PNAS Plus: Cell-cycle regulation of formin-mediated actin cable assembly

Assembly of appropriately oriented actin cables nucleated by formin proteins is necessary for many biological processes in diverse eukaryotes. However, compared with knowledge of how nucleation of dendritic actin filament arrays by the actin-related protein-2/3 complex is regulated, the in vivo regulatory mechanisms for actin cable formation are less clear. To gain insights into mechanisms for regulating actin cable assembly, we reconstituted the assembly process in vitro by introducing microspheres functionalized with the C terminus of the budding yeast formin Bni1 into extracts prepared from yeast cells at different cell-cycle stages. EM studies showed that unbranched actin filament bundles were reconstituted successfully in the yeast extracts. Only extracts enriched in the mitotic cyclin Clb2 were competent for actin cable assembly, and cyclin-dependent kinase 1 activity was indispensible. Cyclin-dependent kinase 1 activity also was found to regulate cable assembly in vivo. Here we present evidence that formin cell-cycle regulation is conserved in vertebrates. The use of the cable-reconstitution system to test roles for the key actin-binding proteins tropomyosin, capping protein, and cofilin provided important insights into assembly regulation. Furthermore, using mass spectrometry, we identified components of the actin cables formed in yeast extracts, providing the basis for comprehensive understanding of cable assembly and regulation.Eukaryotic cells contain populations of actin structures with distinct architectures and protein compositions, which mediate varied cellular processes (1). Understanding how F-actin polymerization is regulated in time and space is critical to understanding how actin structures provide mechanical forces for corresponding biological processes. Branched actin filament arrays, which concentrate at sites of clathrin-mediated endocytosis (2, 3) and at the leading edge of motile cells (4), are nucleated by the actin-related protein-2/3 (Arp2/3) complex. In contrast, bundles of unbranched actin filaments, which sometimes mediate vesicle trafficking or form myosin-containing contractile bundles, often are nucleated by formin proteins (5–14).Much has been learned about how branched actin filaments are polymerized by the Arp2/3 complex and how these filaments function in processes such as endocytosis (2, 15). In contrast, relatively little is known about how actin cables are assembled under physiological conditions. In previous studies, branched actin filaments derived from the Arp2/3 complex have been reconstituted using purified proteins (16–19) or cellular extracts (20–25). When microbeads were coated with nucleation-promoting factors for the Arp2/3 complex and then were incubated in cell extracts, actin comet tails were formed by sequential actin nucleation, symmetry breaking, and tail elongation. Importantly, the motility behavior of F-actin assembled by the Arp2/3 complex using defined, purified proteins differs from that of F-actin assembled by the Arp2/3 complex in the full complexity of cytoplasmic extracts (19, 26–28).Formin-based actin filament assembly using purified proteins also has been reported (29, 30). However, reconstitution of formin-derived actin cables under the more physiological conditions represented by cell extracts has not yet been reported.The actin nucleation activity of formin proteins is regulated by an inhibitory interaction between the N- and C-terminal domains, which can be released when GTP-bound Rho protein binds to the formin N-terminal domain, allowing access of the C terminus (FH1-COOH) to actin filament barbed ends (31–40). In yeast, the formin Bni1 N terminus also has an inhibitory effect on actin nucleation through binding to the C terminus (41).Interestingly, several recent reports provided evidence for cell-cycle regulation of F-actin dynamics in oocytes and early embryos (42–45). However, which specific types of actin structures are regulated by the cell cycle and what kind of nucleation factors and actin interacting-proteins are involved remain to be determined.Here, we report a reconstitution of actin cables in yeast extracts from microbeads derivatized with Bni1 FH1-COOH, identifying the proteins involved, increasing the inventory of the proteins that regulate actin cable dynamics and establishing that the actin cable reconstitution in cytoplasmic extracts is cell-cycle regulated.     

TIPE2 protein serves as a negative regulator of phagocytosis and oxidative burst during infection

Phagocytosis and oxidative burst are two major effector arms of innate immunity. Although it is known that both are activated by Toll-like receptors (TLRs) and Rac GTPases, how their strengths are controlled in quiescent and TLR-activated cells is not clear. We report here that TIPE2 (TNFAIP8L2) serves as a negative regulator of innate immunity by linking TLRs to Rac. TLRs control the expression levels of TIPE2, which in turn dictates the strengths of phagocytosis and oxidative burst by binding to and blocking Rac GTPases. Consequently, TIPE2 knockout cells have enhanced phagocytic and bactericidal activities and TIPE2 knockout mice are resistant to bacterial infection. Thus, TIPE2 sets the strengths of phagocytosis and oxidative burst and may be targeted to effectively control infections.Phagocytosis and oxidative burst (or respiratory burst) are two fundamental effector mechanisms of innate immunity that work in concert to eliminate infectious microbes (1, 2). Phagocytosis allows the phagocytes of the immune system (monocytes and granulocytes) to engulf infectious microbes and to contain them in a special vacuole called a phagosome. Oxidative burst in turn injects into the vacuole reactive oxygen species (ROS) (e.g., superoxide radical and hydrogen peroxide) that kill the microbes. Deficiency in either of these innate immune mechanisms leads to immune deficiency and uncontrolled infections (3–6).Both phagocytosis and oxidative burst are controlled by the Rac proteins of the Ras small GTPase superfamily (1–4). There are three mammalian Rac GTPases, which are designated as Rac1, Rac2, and Rac3. Small GTPases are enzymes that hydrolyze GTP. They are active when bound to GTP and inactive when bound to GDP and serve as molecular “on-and-off” switches of signaling pathways that control a wide variety of cellular processes including growth, motility, vesicle trafficking, and death (7). Rac GTPases control phagocytosis by promoting actin polymerization through their effector proteins such as p21-activated kinases (PAKs), WASP family Verprolin homology domain-containing protein (WAVE), and IQ motif containing GTPase-activating protein-1 (IQGAP1) (1). Rac GTPases also mediate ROS production by binding and activating the NADPH oxidase complex through the p67(Phox) protein (1). Rac GTPase deficiency in mice and humans leads to an immune-deficient syndrome, which is characterized by defective phagocytosis and oxidative burst, recurrent infection, and granulomas (3–6).Although quiescent phagocytes are capable of phagocytosis and ROS production, their levels are low. Toll-like receptor (TLR) activation or microbial infection significantly up-regulates these innate immune processes (8–11). However, the mechanisms whereby microbes promote them are not well understood. TIPE2, or tumor necrosis factor-α–induced protein 8 (TNFAIP8)-like 2 (TNFAIP8L2), is a member of the TNFAIP8 family, which is preferentially expressed in hematopoietic cells (12–18). It is significantly down-regulated in patients with infectious or autoimmune disorders (15, 19). The mammalian TNFAIP8 family consists of four members: TNFAIP8, TIPE1, TIPE2, and TIPE3, whose functions are largely unknown (14, 20). We recently generated TIPE2-deficient mice and discovered that TIPE2 plays a crucial role in immune homeostasis (14). We report here that TIPE2 controls innate immunity by targeting the Rac GTPases.