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Jermusek FA, Webb LJ. Electrostatic Impact of Brefeldin A on Thiocyanate Probes Surrounding the Interface of Arf1-BFA-ARNO4M, a Protein-Drug-Protein Complex. Biochemistry 2024; 63:27-41. [PMID: 38078826 DOI: 10.1021/acs.biochem.3c00366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Protein-protein interactions regulate many cellular processes, making them ideal drug candidates. Design of such drugs, however, is hindered by a lack of understanding of the factors that contribute to the interaction specificity. Specific protein-protein complexes possess both structural and electrostatic complementarity, and while structural complementarity of protein complexes has been extensively investigated, fundamental understanding of the complicated networks of electrostatic interactions at these interfaces is lacking, thus hindering the rational design of orthosterically binding small molecules. To better understand the electrostatic interactions at protein interfaces and how a small molecule could contribute to and fit within that environment, we used a model protein-drug-protein system, Arf1-BFA-ARNO4M, to investigate how small molecule brefeldin A (BFA) perturbs the Arf1-ARNO4M interface. By using nitrile probe labeled Arf1 sites and measuring vibrational Stark effects as well as temperature dependent infrared shifts, we measured changes in the electric field and hydrogen bonding at this interface upon BFA binding. At all five probe locations of Arf1, we found that the vibrational shifts resulting from BFA binding corroborate trends found in Poisson-Boltzmann calculations of surface potentials of Arf1-ARNO4M and Arf1-BFA-ARNO4M, where BFA contributes negative electrostatic potential to the protein interface. The data also corroborate previous hypotheses about the mechanism of interfacial binding and confirm that alternating patches of hydrophobic and polar interactions lead to BFA binding specificity. These findings demonstrate the impact of BFA on this protein-protein interface and have implications for the design of other interfacial drug candidates.
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Affiliation(s)
- Frank A Jermusek
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Lauren J Webb
- Department of Chemistry and Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
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2
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Viktorova EG, Gabaglio S, Moghimi S, Zimina A, Wynn BG, Sztul E, Belov GA. The development of resistance to an inhibitor of a cellular protein reveals a critical interaction between the enterovirus protein 2C and a small GTPase Arf1. PLoS Pathog 2023; 19:e1011673. [PMID: 37721955 PMCID: PMC10538752 DOI: 10.1371/journal.ppat.1011673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/28/2023] [Accepted: 09/08/2023] [Indexed: 09/20/2023] Open
Abstract
The cellular protein GBF1, an activator of Arf GTPases (ArfGEF: Arf guanine nucleotide exchange factor), is recruited to the replication organelles of enteroviruses through interaction with the viral protein 3A, and its ArfGEF activity is required for viral replication, however how GBF1-dependent Arf activation supports the infection remains enigmatic. Here, we investigated the development of resistance of poliovirus, a prototype enterovirus, to increasing concentrations of brefeldin A (BFA), an inhibitor of GBF1. High level of resistance required a gradual accumulation of multiple mutations in the viral protein 2C. The 2C mutations conferred BFA resistance even in the context of a 3A mutant previously shown to be defective in the recruitment of GBF1 to replication organelles, and in cells depleted of GBF1, suggesting a GBF1-independent replication mechanism. Still, activated Arfs accumulated on the replication organelles of this mutant even in the presence of BFA, its replication was inhibited by a pan-ArfGEF inhibitor LM11, and the BFA-resistant phenotype was compromised in Arf1-knockout cells. Importantly, the mutations strongly increased the interaction of 2C with the activated form of Arf1. Analysis of other enteroviruses revealed a particularly strong interaction of 2C of human rhinovirus 1A with activated Arf1. Accordingly, the replication of this virus was significantly less sensitive to BFA than that of poliovirus. Thus, our data demonstrate that enterovirus 2Cs may behave like Arf1 effector proteins and that GBF1 but not Arf activation can be dispensable for enterovirus replication. These findings have important implications for the development of host-targeted anti-viral therapeutics.
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Affiliation(s)
- Ekaterina G. Viktorova
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Samuel Gabaglio
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Seyedehmahsa Moghimi
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Anna Zimina
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Bridge G. Wynn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham; Birmingham, Alabama, United States of America
| | - Elizabeth Sztul
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham; Birmingham, Alabama, United States of America
| | - George A. Belov
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
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3
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Functional diversity in the RAS subfamily of small GTPases. Biochem Soc Trans 2022; 50:921-933. [PMID: 35356965 DOI: 10.1042/bst20211166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/15/2022] [Accepted: 03/21/2022] [Indexed: 12/12/2022]
Abstract
RAS small GTPases regulate important signalling pathways and are notorious drivers of cancer development and progression. While most research to date has focused on understanding and addressing the oncogenic potential of three RAS oncogenes: HRAS, KRAS, and NRAS; the full RAS subfamily is composed of 35 related GTPases with diverse cellular functions. Most remain deeply understudied despite strong evolutionary conservation. Here, we highlight a group of 17 poorly characterized RAS GTPases that are frequently down-regulated in cancer and evidence suggests may function not as oncogenes, but as tumour suppressors. These GTPases remain largely enigmatic in terms of their cellular function, regulation, and interaction with effector proteins. They cluster within two families we designate as 'distal-RAS' (D-RAS; comprised of DIRAS, RASD, and RASL10) and 'CaaX-Less RAS' (CL-RAS; comprised of RGK, NKIRAS, RERG, and RASL11/12 GTPases). Evidence of a tumour suppressive role for many of these GTPases supports the premise that RAS subfamily proteins may collectively regulate cellular proliferation.
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4
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Wu Y, Bai Y, McEwan DG, Bentley L, Aravani D, Cox RD. Palmitoylated small GTPase ARL15 is translocated within Golgi network during adipogenesis. Biol Open 2021; 10:273707. [PMID: 34779483 PMCID: PMC8689486 DOI: 10.1242/bio.058420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 11/10/2021] [Indexed: 11/20/2022] Open
Abstract
The small GTPase ARF family member ARL15 gene locus is associated in population studies with increased risk of type 2 diabetes, lower adiponectin and higher fasting insulin levels. Previously, loss of ARL15 was shown to reduce insulin secretion in a human β-cell line and loss-of-function mutations are found in some lipodystrophy patients. We set out to understand the role of ARL15 in adipogenesis and showed that endogenous ARL15 palmitoylated and localised in the Golgi of mouse liver. Adipocyte overexpression of palmitoylation-deficient ARL15 resulted in redistribution to the cytoplasm and a mild reduction in expression of some adipogenesis-related genes. Further investigation of the localisation of ARL15 during differentiation of a human white adipocyte cell line showed that ARL15 was predominantly co-localised with a marker of the cis face of Golgi at the preadipocyte stage and then translocated to other Golgi compartments after differentiation was induced. Finally, co-immunoprecipitation and mass spectrometry identified potential interacting partners of ARL15, including the ER-localised protein ARL6IP5. Together, these results suggest a palmitoylation dependent trafficking-related role of ARL15 as a regulator of adipocyte differentiation via ARL6IP5 interaction. This article has an associated First Person interview with the first author of the paper. Summary: ARL15 (GTPase ARF family) is associated with adipose traits. ARL15 is palmitoylated, localised to Golgi in preadipocytes and translocated to other Golgi compartments during differentiation. ARL15 interacts with ER-localised ARL6IP5.
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Affiliation(s)
- Yixing Wu
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Oxford, Oxfordshire, OX11 0RD, UK
| | - Ying Bai
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Oxford, Oxfordshire, OX11 0RD, UK
| | - David G McEwan
- Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee, UK.,Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Liz Bentley
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Oxford, Oxfordshire, OX11 0RD, UK
| | - Dimitra Aravani
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Oxford, Oxfordshire, OX11 0RD, UK
| | - Roger D Cox
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Oxford, Oxfordshire, OX11 0RD, UK
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5
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Li M, Zhao R, Du Y, Shen X, Ning Q, Li Y, Liu D, Xiong Q, Zhang Z. The Coordinated KNR6-AGAP-ARF1 Complex Modulates Vegetative and Reproductive Traits by Participating in Vesicle Trafficking in Maize. Cells 2021; 10:cells10102601. [PMID: 34685581 PMCID: PMC8533723 DOI: 10.3390/cells10102601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 02/07/2023] Open
Abstract
The KERNEL NUMBER PER ROW6 (KNR6)-mediated phosphorylation of an adenosine diphosphate ribosylation factor (Arf) GTPase-activating protein (AGAP) forms a key regulatory module for the numbers of spikelets and kernels in the ear inflorescences of maize (Zea mays L.). However, the action mechanism of the KNR6–AGAP module remains poorly understood. Here, we characterized the AGAP-recruited complex and its roles in maize cellular physiology and agronomically important traits. AGAP and its two interacting Arf GTPase1 (ARF1) members preferentially localized to the Golgi apparatus. The loss-of-function AGAP mutant produced by CRISPR/Cas9 resulted in defective Golgi apparatus with thin and compact cisternae, together with delayed internalization and repressed vesicle agglomeration, leading to defective inflorescences and roots, and dwarfed plants with small leaves. The weak agap mutant was phenotypically similar to knr6, showing short ears with fewer kernels. AGAP interacted with KNR6, and a double mutant produced shorter inflorescence meristems and mature ears than the single agap and knr6 mutants. We hypothesized that the coordinated KNR6–AGAP–ARF1 complex modulates vegetative and reproductive traits by participating in vesicle trafficking in maize. Our findings provide a novel mechanistic insight into the regulation of inflorescence development, and ear length and kernel number, in maize.
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Affiliation(s)
- Manfei Li
- College of Life Science, Yangtze University, Jingzhou 434025, China;
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; (R.Z.); (Y.D.); (X.S.); (Q.N.); (Y.L.); (D.L.); (Q.X.)
| | - Ran Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; (R.Z.); (Y.D.); (X.S.); (Q.N.); (Y.L.); (D.L.); (Q.X.)
| | - Yanfang Du
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; (R.Z.); (Y.D.); (X.S.); (Q.N.); (Y.L.); (D.L.); (Q.X.)
| | - Xiaomeng Shen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; (R.Z.); (Y.D.); (X.S.); (Q.N.); (Y.L.); (D.L.); (Q.X.)
| | - Qiang Ning
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; (R.Z.); (Y.D.); (X.S.); (Q.N.); (Y.L.); (D.L.); (Q.X.)
| | - Yunfu Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; (R.Z.); (Y.D.); (X.S.); (Q.N.); (Y.L.); (D.L.); (Q.X.)
| | - Dan Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; (R.Z.); (Y.D.); (X.S.); (Q.N.); (Y.L.); (D.L.); (Q.X.)
| | - Qing Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; (R.Z.); (Y.D.); (X.S.); (Q.N.); (Y.L.); (D.L.); (Q.X.)
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; (R.Z.); (Y.D.); (X.S.); (Q.N.); (Y.L.); (D.L.); (Q.X.)
- Correspondence:
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6
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Regulation of the Small GTPase Ras and Its Relevance to Human Disease. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2262:19-43. [PMID: 33977469 DOI: 10.1007/978-1-0716-1190-6_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ras research has experienced a considerable boost in recent years, not least prompted by the Ras initiative launched by the NCI in 2013 ( https://www.cancer.gov/research/key-initiatives/ras ), accompanied and conditioned by a strongly reinvigorated determination within the Ras community to develop therapeutics attacking directly the Ras oncoproteins. As a member of the small G-protein superfamily, function and transforming activity of Ras all revolve about its GDP/GTP loading status. For one thing, the extent of GTP loading will determine the proportion of active Ras in the cell, with implications for intensity and quality of downstream signaling. But also the rate of nucleotide exchange, i.e., the Ras-GDP/GTP cycling rate, can have a major impact on Ras function, as illustrated perhaps most impressively by newly discovered fast-cycling oncogenic mutants of the Ras-related GTPase Rac1. Thus, while the last years have witnessed memorable new findings and technical developments in the Ras field, leading to an improved insight into many aspects of Ras biology, they have not jolted at the basics, but rather deepened our view of the fundamental regulatory principles of Ras activity control. In this brief review, we revisit the role and mechanisms of Ras nucleotide loading and its implications for cancer in the light of recent findings.
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7
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The Golgin Protein RUD3 Regulates Fusarium graminearum Growth and Virulence. Appl Environ Microbiol 2021; 87:AEM.02522-20. [PMID: 33452023 DOI: 10.1128/aem.02522-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/07/2021] [Indexed: 12/11/2022] Open
Abstract
Golgins are coiled-coil proteins that play prominent roles in maintaining the structure and function of the Golgi complex. However, the role of golgin proteins in phytopathogenic fungi remains poorly understood. In this study, we functionally characterized the Fusarium graminearum golgin protein RUD3, a homolog of ScRUD3/GMAP-210 in Saccharomyces cerevisiae and mammalian cells. Cellular localization observation revealed that RUD3 is located in the cis-Golgi. Deletion of RUD3 caused defects in vegetative growth, ascospore discharge, deoxynivalenol (DON) production, and virulence. Moreover, the Δrud3 mutant showed reduced expression of tri genes and impairment of the formation of toxisomes, both of which play essential roles in DON biosynthesis. We further used green fluorescent protein (GFP)-tagged SNARE protein SEC22 (SEC22-GFP) as a tool to study the transport between the endoplasmic reticulum (ER) and Golgi and observed that SEC22-GFP was retained in the cis-Golgi in the Δrud3 mutant. RUD3 contains the coiled coil (CC), GRAB-associated 2 (GA2), GRIP-related Arf binding (GRAB), and GRAB-associated 1 (GA1) domains, which except for GA1, are indispensable for normal localization and function of RUD3, whereas only CC is essential for normal RUD3-RUD3 interaction. Together, these results demonstrate how the golgin protein RUD3 mediates retrograde trafficking in the ER-to-Golgi pathway and is necessary for growth, ascospore discharge, DON biosynthesis, and pathogenicity in F. graminearum IMPORTANCE Fusarium head blight (FHB) caused by the fungal pathogen Fusarium graminearum is an economically important disease of wheat and other small grain cereal crops worldwide, and limited effective control strategies are available. A better understanding of the regulation mechanisms of F. graminearum development, deoxynivalenol (DON) biosynthesis, and pathogenicity is therefore important for the development of effective control management of this disease. Golgins are attached via their extreme carboxy terminus to the Golgi membrane and are involved in vesicle trafficking and organelle maintenance in eukaryotic cells. In this study, we systematically characterized a highly conserved Golgin protein, RUD3, and found that it is required for vegetative growth, ascospore discharge, DON production, and pathogenicity in F. graminearum Our findings provide a comprehensive characterization of the golgin family protein RUD3 in plant-pathogenic fungus, which could help to identify a new potential target for effective control of this devastating disease.
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8
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Turn RE, Linnert J, Gigante ED, Wolfrum U, Caspary T, Kahn RA. Roles for ELMOD2 and Rootletin in ciliogenesis. Mol Biol Cell 2021; 32:800-822. [PMID: 33596093 PMCID: PMC8108518 DOI: 10.1091/mbc.e20-10-0635] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
ELMOD2 is a GTPase-activating protein with uniquely broad specificity for ARF family GTPases. We previously showed that it acts with ARL2 in mitochondrial fusion and microtubule stability and with ARF6 during cytokinesis. Mouse embryonic fibroblasts deleted for ELMOD2 also displayed changes in cilia-related processes including increased ciliation, multiciliation, ciliary morphology, ciliary signaling, centrin accumulation inside cilia, and loss of rootlets at centrosomes with loss of centrosome cohesion. Increasing ARL2 activity or overexpressing Rootletin reversed these defects, revealing close functional links between the three proteins. This was further supported by the findings that deletion of Rootletin yielded similar phenotypes, which were rescued upon increasing ARL2 activity but not ELMOD2 overexpression. Thus, we propose that ARL2, ELMOD2, and Rootletin all act in a common pathway that suppresses spurious ciliation and maintains centrosome cohesion. Screening a number of markers of steps in the ciliation pathway supports a model in which ELMOD2, Rootletin, and ARL2 act downstream of TTBK2 and upstream of CP110 to prevent spurious release of CP110 and to regulate ciliary vesicle docking. These data thus provide evidence supporting roles for ELMOD2, Rootletin, and ARL2 in the regulation of ciliary licensing.
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Affiliation(s)
- Rachel E Turn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322.,Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322
| | - Joshua Linnert
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität, Mainz 655099, Germany
| | - Eduardo D Gigante
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322.,Neuroscience Graduate Program, Emory University, Atlanta, GA 30322
| | - Uwe Wolfrum
- Institut für Molekulare Physiologie, Johannes Gutenberg-Universität, Mainz 655099, Germany
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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9
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Deretic D, Lorentzen E, Fresquez T. The ins and outs of the Arf4-based ciliary membrane-targeting complex. Small GTPases 2021; 12:1-12. [PMID: 31068062 PMCID: PMC7781591 DOI: 10.1080/21541248.2019.1616355] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/09/2019] [Accepted: 05/02/2019] [Indexed: 10/26/2022] Open
Abstract
The small GTPase Arf4-based ciliary membrane-targeting complex recognizes specific targeting signals within sensory receptors and regulates their directed movement to primary cilia. Activated Arf4 directly binds the VxPx ciliary-targeting signal (CTS) of the light-sensing receptor rhodopsin. Recent findings revealed that at the trans-Golgi, marked by the small GTPase Rab6, activated Arf4 forms a functional complex with rhodopsin and the Arf guanine nucleotide exchange factor (GEF) GBF1, providing positive feedback that drives further Arf4 activation in ciliary trafficking. Arf4 function is conserved across diverse cell types; however, it appears that not all its aspects are conserved across species, as mouse Arf4 is a natural mutant in the conserved α3 helix, which is essential for its interaction with rhodopsin. Generally, activated Arf4 regulates the assembly of the targeting nexus containing the Arf GAP ASAP1 and the Rab11a-FIP3-Rabin8 dual effector complex, which controls the assembly of the highly conserved Rab11a-Rabin8-Rab8 ciliary-targeting module. It was recently found that this module interacts with the R-SNARE VAMP7, likely in its activated, c-Src-phosphorylated form. Rab11 and Rab8 bind VAMP7 regulatory longin domain (LD), whereas Rabin8 interacts with the SNARE domain, capturing VAMP7 for delivery to the ciliary base and subsequent pairing with the cognate SNAREs syntaxin 3 and SNAP-25. This review will focus on the implications of these novel findings that further illuminate the role of well-ordered Arf and Rab interaction networks in targeting of sensory receptors to primary cilia. Abbreviations: CTS: Ciliary-Targeting Signal; GAP: GTPase Activating Protein; GEF: Guanine Nucleotide Exchange Factor; RTC(s), Rhodopsin Transport Carrier(s); SNARE: Soluble N-ethylmaleimide-sensitive Factor Attachment Protein Receptor; TGN: Trans-Golgi Network.
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Affiliation(s)
- Dusanka Deretic
- Departments of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, NM, USA
- Cell Biology and Physiology, University of New Mexico, Albuquerque, NM, USA
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Theresa Fresquez
- Departments of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, NM, USA
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10
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Enterovirus Infection Induces Massive Recruitment of All Isoforms of Small Cellular Arf GTPases to the Replication Organelles. J Virol 2020; 95:JVI.01629-20. [PMID: 33087467 DOI: 10.1128/jvi.01629-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/18/2020] [Indexed: 12/12/2022] Open
Abstract
Enterovirus replication requires the cellular protein GBF1, a guanine nucleotide exchange factor for small Arf GTPases. When activated, Arfs associate with membranes, where they regulate numerous steps of membrane homeostasis. The requirement for GBF1 implies that Arfs are important for replication, but which of the different Arfs function(s) during replication remains poorly understood. Here, we established cell lines expressing each of the human Arfs fused to a fluorescent tag and investigated their behavior during enterovirus infection. Arf1 was the first to be recruited to the replication organelles, where it strongly colocalized with the viral antigen 2B and mature virions but not double-stranded RNA. By the end of the infectious cycle, Arf3, Arf4, Arf5, and Arf6 were also concentrated on the replication organelles. Once on the replication membranes, all Arfs except Arf3 were no longer sensitive to inhibition of GBF1, suggesting that in infected cells they do not actively cycle between GTP- and GDP-bound states. Only the depletion of Arf1, but not other class 1 and 2 Arfs, significantly increased the sensitivity of replication to GBF1 inhibition. Surprisingly, depletion of Arf6, a class 3 Arf, normally implicated in plasma membrane events, also increased the sensitivity to GBF1 inhibition. Together, our results suggest that GBF1-dependent Arf1 activation directly supports the development and/or functioning of the replication complexes and that Arf6 plays a previously unappreciated role in viral replication. Our data reveal a complex pattern of Arf activation in enterovirus-infected cells that may contribute to the resilience of viral replication in different cellular environments.IMPORTANCE Enteroviruses include many known and emerging pathogens, such as poliovirus, enteroviruses 71 and D68, and others. However, licensed vaccines are available only against poliovirus and enterovirus 71, and specific anti-enterovirus therapeutics are lacking. Enterovirus infection induces the massive remodeling of intracellular membranes and the development of specialized domains harboring viral replication complexes, replication organelles. Here, we investigated the roles of small Arf GTPases during enterovirus infection. Arfs control distinct steps in intracellular membrane traffic, and one of the Arf-activating proteins, GBF1, is a cellular factor required for enterovirus replication. We found that all Arfs expressed in human cells, including Arf6, normally associated with the plasma membrane, are recruited to the replication organelles and that Arf1 appears to be the most important Arf for enterovirus replication. These results document the rewiring of the cellular membrane pathways in infected cells and may provide new ways of controlling enterovirus infections.
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11
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Fisher S, Kuna D, Caspary T, Kahn RA, Sztul E. ARF family GTPases with links to cilia. Am J Physiol Cell Physiol 2020; 319:C404-C418. [PMID: 32520609 PMCID: PMC7500214 DOI: 10.1152/ajpcell.00188.2020] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The ADP-ribosylation factor (ARF) superfamily of regulatory GTPases, including both the ARF and ARF-like (ARL) proteins, control a multitude of cellular functions, including aspects of vesicular traffic, lipid metabolism, mitochondrial architecture, the assembly and dynamics of the microtubule and actin cytoskeletons, and other pathways in cell biology. Considering their general utility, it is perhaps not surprising that increasingly ARF/ARLs have been found in connection to primary cilia. Here, we critically evaluate the current knowledge of the roles four ARF/ARLs (ARF4, ARL3, ARL6, ARL13B) play in cilia and highlight key missing information that would help move our understanding forward. Importantly, these GTPases are themselves regulated by guanine nucleotide exchange factors (GEFs) that activate them and by GTPase-activating proteins (GAPs) that act as both effectors and terminators of signaling. We believe that the identification of the GEFs and GAPs and better models of the actions of these GTPases and their regulators will provide a much deeper understanding and appreciation of the mechanisms that underly ciliary functions and the causes of a number of human ciliopathies.
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Affiliation(s)
- Skylar Fisher
- 1Department of Biochemistry, Emory University
School of Medicine, Atlanta,
Georgia
| | - Damian Kuna
- 2Department of Cell, Developmental and Integrative
Biology, University of Alabama at Birmingham,
Birmingham, Alabama
| | - Tamara Caspary
- 3Department of Human Genetics, Emory
University School of Medicine, Atlanta,
Georgia
| | - Richard A. Kahn
- 1Department of Biochemistry, Emory University
School of Medicine, Atlanta,
Georgia
| | - Elizabeth Sztul
- 2Department of Cell, Developmental and Integrative
Biology, University of Alabama at Birmingham,
Birmingham, Alabama
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12
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Turn RE, East MP, Prekeris R, Kahn RA. The ARF GAP ELMOD2 acts with different GTPases to regulate centrosomal microtubule nucleation and cytokinesis. Mol Biol Cell 2020; 31:2070-2091. [PMID: 32614697 PMCID: PMC7543072 DOI: 10.1091/mbc.e20-01-0012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
ELMOD2 is a ∼32 kDa protein first purified by its GTPase-activating protein (GAP) activity toward ARL2 and later shown to have uniquely broad specificity toward ARF family GTPases in in vitro assays. To begin the task of defining its functions in cells, we deleted ELMOD2 in immortalized mouse embryonic fibroblasts and discovered a number of cellular defects, which are reversed upon expression of ELMOD2-myc. We show that these defects, resulting from the loss of ELMOD2, are linked to two different pathways and two different GTPases: with ARL2 and TBCD to support microtubule nucleation from centrosomes and with ARF6 in cytokinesis. These data highlight key aspects of signaling by ARF family GAPs that contribute to previously underappreciated sources of complexity, including GAPs acting from multiple sites in cells, working with multiple GTPases, and contributing to the spatial and temporal control of regulatory GTPases by serving as both GAPs and effectors.
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Affiliation(s)
- Rachel E Turn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322.,Biochemistry, Cell & Developmental Biology Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30307
| | - Michael P East
- Department of Pharmacology, University of North Carolina Chapel Hill, Chapel Hill, NC 27599
| | - Rytis Prekeris
- Department of Cell and Developmental Biology, University of Colorado, Aurora, CO 80045
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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A Redundant Mechanism of Recruitment Underlies the Remarkable Plasticity of the Requirement of Poliovirus Replication for the Cellular ArfGEF GBF1. J Virol 2019; 93:JVI.00856-19. [PMID: 31375590 DOI: 10.1128/jvi.00856-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/26/2019] [Indexed: 12/24/2022] Open
Abstract
The replication of many positive-strand RNA viruses [(+)RNA viruses] depends on the cellular protein GBF1, but its role in the replication process is not clear. In uninfected cells, GBF1 activates small GTPases of the Arf family and coordinates multiple steps of membrane metabolism, including functioning of the cellular secretory pathway. The nonstructural protein 3A of poliovirus and related viruses has been shown to directly interact with GBF1, likely mediating its recruitment to the replication complexes. Surprisingly, viral mutants with a severely reduced level of 3A-GBF1 interaction demonstrate minimal replication defects in cell culture. Here, we systematically investigated the conserved elements of GBF1 to understand which determinants are important to support poliovirus replication. We demonstrate that multiple GBF1 mutants inactive in cellular metabolism could still be fully functional in the replication complexes. Our results show that the Arf-activating property, but not the primary structure of the Sec7 domain, is indispensable for viral replication. They also suggest a redundant mechanism of recruitment of GBF1 to the replication sites, which is dependent not only on direct interaction of the protein with the viral protein 3A but also on determinants located in the noncatalytic C-terminal domains of GBF1. Such a double-targeting mechanism explains the previous observations of the remarkable tolerance of different levels of GBF1-3A interaction by the virus and likely constitutes an important element of the resilience of viral replication.IMPORTANCE Enteroviruses are a vast group of viruses associated with diverse human diseases, but only two of them could be controlled with vaccines, and effective antiviral therapeutics are lacking. Here, we investigated in detail the contribution of a cellular protein, GBF1, in the replication of poliovirus, a representative enterovirus. GBF1 supports the functioning of cellular membrane metabolism and is recruited to viral replication complexes upon infection. Our results demonstrate that the virus requires a limited subset of the normal GBF1 functions and reveal the elements of GBF1 essential to support viral replication under different conditions. Since diverse viruses often rely on the same cellular proteins for replication, understanding the mechanisms by which these proteins support infection is essential for the development of broad-spectrum antiviral therapeutics.
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Dejgaard SY, Presley JF. Rab18 regulates lipolysis via Arf/GBF1 and adipose triglyceride lipase. Biochem Biophys Res Commun 2019; 520:526-531. [PMID: 31610914 DOI: 10.1016/j.bbrc.2019.10.069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/06/2019] [Indexed: 01/09/2023]
Abstract
Rab18 is a small GTPase associated with lipid droplets and other membranes. While it likely has multiple functions on lipid droplets, one proposed function is regulation of lipolysis. Previous work has concentrated on regulation of autophagy; however, in this study, we provide evidence that Rab18 plays a role upstream of the cytosolic lipolytic enzyme adipose triglyceride lipase (ATGL) and that recruitment of ATGL by Rab18 is mediated by elements of the Arf/GBF1 machinery. We find that Arf4-GFP is accumulated on the subset of lipid droplets associated with Rab18, and that this association is lost within 5 min upon treatment with 5 μg/ml of the drug brefeldin A, which targets GBF1 and other Sec7-domain containing Arf exchange factors. ATGL-GFP is also recruited to lipid droplets, but is lost more slowly after treatment with 5 μg/ml brefeldin A, with significant loss from lipid droplets after 1 h treatment, and almost complete loss from lipid droplets 4 h after brefeldin A treatment. Upon overexpression of the dominant negative GDP-locked cerulean-Rab18-S22 N, GFP-ATGL and Arf4 are lost from the surface of lipid droplets similarly to BFA treatment. This study establishes, for the first time, an essential role for Rab18 in recruiting ATGL to lipid droplets.
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Affiliation(s)
- Selma Yilmaz Dejgaard
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada; Department of Medical Biology, Near East University, Nicosia, Cyprus
| | - John F Presley
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada.
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15
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Structural Organization and Dynamics of Homodimeric Cytohesin Family Arf GTPase Exchange Factors in Solution and on Membranes. Structure 2019; 27:1782-1797.e7. [PMID: 31601460 PMCID: PMC6948192 DOI: 10.1016/j.str.2019.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/03/2019] [Accepted: 09/16/2019] [Indexed: 12/30/2022]
Abstract
Membrane dynamic processes require Arf GTPase activation by guanine nucleotide exchange factors (GEFs) with a Sec7 domain. Cytohesin family Arf GEFs function in signaling and cell migration through Arf GTPase activation on the plasma membrane and endosomes. In this study, the structural organization of two cytohesins (Grp1 and ARNO) was investigated in solution by size exclusion-small angle X-ray scattering and negative stain-electron microscopy and on membranes by dynamic light scattering, hydrogen-deuterium exchange-mass spectrometry and guanosine diphosphate (GDP)/guanosine triphosphate (GTP) exchange assays. The results suggest that cytohesins form elongated dimers with a central coiled coil and membrane-binding pleckstrin-homology (PH) domains at opposite ends. The dimers display significant conformational heterogeneity, with a preference for compact to intermediate conformations. Phosphoinositide-dependent membrane recruitment is mediated by one PH domain at a time and alters the conformational dynamics to prime allosteric activation by Arf-GTP. A structural model for membrane targeting and allosteric activation of full-length cytohesin dimers is discussed.
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16
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Gangopadhyay A, Chakraborty HJ, Datta A. Employing virtual screening and molecular dynamics simulations for identifying hits against the active cholera toxin. Toxicon 2019; 170:1-9. [PMID: 31494206 DOI: 10.1016/j.toxicon.2019.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/22/2019] [Accepted: 09/01/2019] [Indexed: 12/24/2022]
Abstract
Cholera is a major global threat, affecting millions each year. The ADP ribosyltransferase activity of the active cholera toxin catalyses the massive loss of water and electrolytes during cholera infections. The active toxin heterodimer comprises the A1 subunit from Vibrio cholerae and ARF (ADP Ribosylation Factor) from the human host. Although the active toxin is a potential target for drug discovery against cholera, it has been scarcely targeted to date. The A1-ARF interface contains a potential druggable site for small molecule inhibitors. By combining a sequential docking and scoring strategy with molecular dynamics (MD) simulations, this study identified hits against the protein-protein interface (PPI) of the active cholera toxin from an in-house library of 9,175 ADMET-screened alkaloids. The docking algorithms and scoring functions of Glide SP, Glide XP, and AutoDock were employed for initial library screening. Three alkaloids were initially selected by docking-based virtual screening. The stability of the hit-toxin complexes was validated by MD simulations. Two of the three hits, namely, A6225 (7-formyldehydrothalicsimidine) and A16503 (1,2,7,8-tetrahydroxy dibenz[cd,f]indol-4(5H)-one), formed stable complexes with the toxin. Analyses of the hydrogen bond occupancies revealed that the hits formed stable hydrogen bonds with the toxin PPI. The hits identified herein can serve as reference compounds for drug discovery against cholera in the future.
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Affiliation(s)
- Aditi Gangopadhyay
- Department of Chemical Technology, University of Calcutta, 92, APC Road, Kolkata 700009, West Bengal, India; DBT Centre for Bioinformatics, Presidency University, Kolkata 700073, West Bengal, India.
| | - Hirak Jyoti Chakraborty
- DBT Centre for Bioinformatics, Presidency University, Kolkata 700073, West Bengal, India; Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, West Bengal, India
| | - Abhijit Datta
- DBT Centre for Bioinformatics, Presidency University, Kolkata 700073, West Bengal, India; Department of Botany, Jhargram Raj College, Jhargram 721507, Paschim Medinipur, India
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17
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Wang H, Liu Y, Zhang L, Kundu JK, Liu W, Wang X. ADP ribosylation factor 1 facilitates spread of wheat dwarf virus in its insect vector. Cell Microbiol 2019; 21:e13047. [DOI: 10.1111/cmi.13047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/01/2019] [Accepted: 05/13/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Hui Wang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing China
| | - Yan Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing China
| | - Lu Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing China
| | - Jiban Kumar Kundu
- Division of Crop Protection and Plant HealthCrop Research Institute Praha 6 Czech Republic
| | - Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing China
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18
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Comparative Genomic Analysis of Trichinella spiralis Reveals Potential Mechanisms of Adaptive Evolution. BIOMED RESEARCH INTERNATIONAL 2019; 2019:2948973. [PMID: 31240209 PMCID: PMC6556364 DOI: 10.1155/2019/2948973] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 04/10/2019] [Indexed: 12/20/2022]
Abstract
Trichinellosis caused by parasitic nematodes of the genus Trichinella may result in human morbidity and mortality worldwide. Deciphering processes that drive species diversity and adaptation are key to understanding parasitism and developing effective control strategies. Our goal was to identify genes that are under positive selection and possible mechanisms of adaptive evolution of Trichinella spiralis genes using a comparative genomic analysis with the genomes of Brugia malayi, Trichuris suis, Ancylostoma ceylanicum, and Caenorhabditis elegans. The CODEML program derived from the PAML package was used to deduce the most probable dN/dS ratio, a measurement to detect genes/proteins undergoing adaptation. For each pair of sequences, those with a dN/dS ratio > 1 were considered positively selected genes (PSGs). Altogether, 986 genes were positively selected (p-value < 0.01). Genes involved in metabolic pathways, signaling pathways, and cytosolic DNA-sensing pathways were significantly enriched among the PSGs. Several PSGs are associated with exploitation of the host: modification of the host's metabolism, creation of new parasite-specific morphological structures between T. spiralis and the host interface, xenobiotic metabolism to combat low oxygen concentrations and host toxicity, muscle cell transformation, cell cycle arrest, DNA repair processes during nurse cell formation, antiapoptotic factors, immunomodulation, and regulation of epigenetic processes. Some of the T. spiralis PSGs have C. elegans orthologs that confer severe or lethal RNAi phenotypes. Fifty-seven PSGs in T. spiralis were analyzed to encode differentially expressed proteins. The present study utilized an overall comparative genomic analysis to discover PSGs within T. spiralis and their relationships with biological function and organism fitness. This analysis adds to our understanding of the possible mechanism that contributes to T. spiralis parasitism and biological adaptation within the host, and thus these identified genes may be potential targets for drug and vaccine development.
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19
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Uchida R, Egawa T, Fujita Y, Furuta K, Taguchi H, Tanaka S, Nishida K. Identification of the minimal region of peptide derived from ADP-ribosylation factor1 (ARF1) that inhibits IgE-mediated mast cell activation. Mol Immunol 2019; 105:32-37. [DOI: 10.1016/j.molimm.2018.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 10/23/2018] [Accepted: 11/08/2018] [Indexed: 10/27/2022]
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20
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Malaby AW, Das S, Chakravarthy S, Irving TC, Bilsel O, Lambright DG. Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors. Structure 2017; 26:106-117.e6. [PMID: 29276036 PMCID: PMC5752578 DOI: 10.1016/j.str.2017.11.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 10/22/2017] [Accepted: 11/27/2017] [Indexed: 11/16/2022]
Abstract
Membrane dynamic processes including vesicle biogenesis depend on Arf
GTPase activation by guanine nucleotide exchange factors (GEFs) containing a
catalytic Sec7 domain and a membrane targeting module such as a PH domain. The
catalytic output of cytohesin family Arf GEFs is controlled by autoinhibitory
interactions that impede accessibility of the exchange site in the Sec7 domain.
These restraints can be relieved through activator Arf-GTP binding to an
allosteric site comprising the PH domain and proximal autoinhibitory elements
(Sec7-PH linker and C-terminal helix). Small angle X-ray scattering and
negative-stain electron microscopy were used to investigate the structural
organization and conformational dynamics of Cytohesin-3 (Grp1) in autoinhibited
and active states. The results support a model in which hinge dynamics in the
autoinhibited state expose the activator site for Arf-GTP binding, while
subsequent C-terminal helix unlatching and repositioning unleash conformational
entropy in the Sec7-PH linker to drive exposure of the exchange site.
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Affiliation(s)
- Andrew W Malaby
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Sanchaita Das
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Thomas C Irving
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Osman Bilsel
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - David G Lambright
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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21
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Gao H, Sun W, Song Z, Yu Y, Wang L, Chen X, Zhang Q. A Method to Generate and Analyze Modified Myristoylated Proteins. Chembiochem 2017; 18:324-330. [PMID: 27925692 DOI: 10.1002/cbic.201600608] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Indexed: 11/07/2022]
Abstract
Covalent lipid modification of proteins is essential to their cellular localizations and functions. Engineered lipid motifs, coupled with bio-orthogonal chemistry, have been utilized to identify myristoylated or palmitoylated proteins in cells. However, whether modified proteins have similar properties as endogenous ones has not been well investigated mainly due to lack of methods to generate and analyze purified proteins. We have developed a method that utilizes metabolic interference and mass spectrometry to produce and analyze modified, myristoylated small GTPase ADP-ribosylation factor 1 (Arf1). The capacities of these recombinant proteins to bind liposomes and load and hydrolyze GTP were measured and compared with the unmodified myristoylated Arf1. The ketone-modified myristoylated Arf1 could be further labeled by fluorophore-coupled hydrazine and subsequently visualized through fluorescence imaging. This methodology provides an effective model system to characterize lipid-modified proteins with additional functions before applying them to cellular systems.
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Affiliation(s)
- Huanyao Gao
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Wei Sun
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Zhiquan Song
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Yanbao Yu
- Department of Biochemistry and Biophysics, School of Medicine, The University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Li Wang
- Department of Biochemistry and Biophysics, School of Medicine, The University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Xian Chen
- Department of Biochemistry and Biophysics, School of Medicine, The University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Qisheng Zhang
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, NC, 27599, USA
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22
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Humphreys D, Singh V, Koronakis V. Inhibition of WAVE Regulatory Complex Activation by a Bacterial Virulence Effector Counteracts Pathogen Phagocytosis. Cell Rep 2016; 17:697-707. [PMID: 27732847 PMCID: PMC5081413 DOI: 10.1016/j.celrep.2016.09.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 06/24/2016] [Accepted: 09/14/2016] [Indexed: 02/05/2023] Open
Abstract
To establish pathogenicity, bacteria must evade phagocytosis directed by remodeling of the actin cytoskeleton. We show that macrophages facilitate pathogen phagocytosis through actin polymerization mediated by the WAVE regulatory complex (WRC), small GTPases Arf and Rac1, and the Arf1 activator ARNO. To establish extracellular infections, enteropathogenic (EPEC) and enterohaemorrhagic (EHEC) Escherichia coli hijack the actin cytoskeleton by injecting virulence effectors into the host cell. Here, we find that the virulence effector EspG counteracts WRC-dependent phagocytosis, enabling EPEC and EHEC to remain extracellular. By reconstituting membrane-associated actin polymerization, we find that EspG disabled WRC activation through two mechanisms: EspG interaction with Arf6 blocked signaling to ARNO while EspG binding of Arf1 impeded collaboration with Rac1, thereby inhibiting WRC recruitment and activation. Investigating the mode of EspG interference revealed sites in Arf1 required for WRC activation and a mechanism facilitating pathogen evasion of innate host defenses.
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Affiliation(s)
- Daniel Humphreys
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK.
| | - Vikash Singh
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Vassilis Koronakis
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK.
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23
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Gadahi JA, Wang S, Bo G, Ehsan M, Yan R, Song X, Xu L, Li X. Proteomic Analysis of the Excretory and Secretory Proteins of Haemonchus contortus (HcESP) Binding to Goat PBMCs In Vivo Revealed Stage-Specific Binding Profiles. PLoS One 2016; 11:e0159796. [PMID: 27467391 PMCID: PMC4965049 DOI: 10.1371/journal.pone.0159796] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 07/09/2016] [Indexed: 02/06/2023] Open
Abstract
Haemonchus contortus is a parasitic gastrointestinal nematode, and its excretory and secretory products (HcESPs) interact extensively with the host cells. In this study, we report the interaction of proteins from HcESPs at different developmental stages to goat peripheral blood mononuclear cells (PBMCs) in vivo using liquid chromatography-tandem mass spectrometry. A total of 407 HcESPs that interacted with goat PBMCs at different time points were identified from a H. contortus protein database using SEQUEST searches. The L4 and L5 stages of H. contortus represented a higher proportion of the identified proteins compared with the early and late adult stages. Both stage-specific interacting proteins and proteins that were common to multiple stages were identified. Forty-seven interacting proteins were shared among all stages. The gene ontology (GO) distributions of the identified goat PBMC-interacting proteins were nearly identical among all developmental stages, with high representation of binding and catalytic activity. Cellular, metabolic and single-organism processes were also annotated as major biological processes, but interestingly, more proteins were annotated as localization processes at the L5 stage than at the L4 and adult stages. Based on the clustering of homologous proteins, we improved the functional annotations of un-annotated proteins identified at different developmental stages. Some unnamed H. contortus ATP-binding cassette proteins, including ADP-ribosylation factor and P-glycoprotein-9, were identified by STRING protein clustering analysis.
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Affiliation(s)
- Javaid Ali Gadahi
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Shuai Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Gao Bo
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Muhammad Ehsan
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - RuoFeng Yan
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - XiaoKai Song
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - LiXin Xu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - XiangRui Li
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
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24
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Naramoto S, Dainobu T, Tokunaga H, Kyozuka J, Fukuda H. Cellular and developmental function of ACAP type ARF-GAP proteins are diverged in plant cells. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2016; 33:309-314. [PMID: 31274992 PMCID: PMC6565945 DOI: 10.5511/plantbiotechnology.16.0309a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 03/09/2016] [Indexed: 05/29/2023]
Abstract
Vesicle transport is crucial for various cellular functions and development of multicellular organisms. ARF-GAP is one of the key regulators of vesicle transport and is diverse family of proteins. Arabidopsis has 15 ARF-GAP proteins and four members are classified as ACAP type ARF-GAP proteins. Our previous study identified that VASCULAR NETWORK DEFECTIVE3 (VAN3), an ACAP ARF-GAP, played crucial roles in leaf vascular formation. However, it remains question how other members of plant ACAP ARF-GAPs function in cellular and developmental processes. To characterize these, we analyzed spatial expression pattern and subcellular localization of VAN3 and three other ACAPs, so called VAN3-like proteins (VALs). Expression pattern analysis revealed that they were expressed in distinctive developmental processes. Subcellular localization analysis in protoplast cells indicated that in contrast to VAN3, which localizes on trans-Golgi networks/early endosomes (TGNs/EEs), VAL1 and VAL2 were localized on ARA6-labelled endosomes, and VAL3 resided mainly in the cytoplasm. These results indicated that VAN3 and VALs are differently expressed in a tissue level and function in different intracellular compartments, in spite of their significant sequence similarities. These findings suggested functional divergence among plant ACAPs. Cellular localizations of all members of animal ACAP proteins are identical. Therefore our findings also suggested that plant evolved ACAP proteins in plant specific manner.
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Affiliation(s)
- Satoshi Naramoto
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Tomoko Dainobu
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Hiroki Tokunaga
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Junko Kyozuka
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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25
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Regulators and Effectors of Arf GTPases in Neutrophils. J Immunol Res 2015; 2015:235170. [PMID: 26609537 PMCID: PMC4644846 DOI: 10.1155/2015/235170] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 09/30/2015] [Indexed: 12/22/2022] Open
Abstract
Polymorphonuclear neutrophils (PMNs) are key innate immune cells that represent the first line of defence against infection. They are the first leukocytes to migrate from the blood to injured or infected sites. This process involves molecular mechanisms that coordinate cell polarization, delivery of receptors, and activation of integrins at the leading edge of migrating PMNs. These phagocytes actively engulf microorganisms or form neutrophil extracellular traps (NETs) to trap and kill pathogens with bactericidal compounds. Association of the NADPH oxidase complex at the phagosomal membrane for production of reactive oxygen species (ROS) and delivery of proteolytic enzymes into the phagosome initiate pathogen killing and removal. G protein-dependent signalling pathways tightly control PMN functions. In this review, we will focus on the small monomeric GTPases of the Arf family and their guanine exchange factors (GEFs) and GTPase activating proteins (GAPs) as components of signalling cascades regulating PMN responses. GEFs and GAPs are multidomain proteins that control cellular events in time and space through interaction with other proteins and lipids inside the cells. The number of Arf GAPs identified in PMNs is expanding, and dissecting their functions will provide important insights into the role of these proteins in PMN physiology.
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26
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Dümmer M, Forreiter C, Galland P. Gravitropism in Arabidopsis thaliana: Root-specific action of the EHB gene and violation of the resultant law. JOURNAL OF PLANT PHYSIOLOGY 2015; 189:24-33. [PMID: 26496692 DOI: 10.1016/j.jplph.2015.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 09/06/2015] [Accepted: 09/09/2015] [Indexed: 06/05/2023]
Abstract
Gravitropic bending of seedlings of Arabidopsis thaliana in response to centrifugal accelerations was determined in a range between 0.0025 and 4×g to revisit and validate the so-called resultant law, which claims that centrifugation causes gravitropic organs to orient parallel to the resultant stimulus vector. We show here for seedlings of A. thaliana that this empirical law holds for hypocotyls but surprisingly fails for roots. While the behavior of hypocotyls could be modeled by an arc tangent function predicted by the resultant law, roots displayed a sharp maximum at 1.8×g that substantially overshoots the predicted value and that represents a novel phenomenon, diagravitropism elicited by centrifugal acceleration. The gravitropic bending critically depended on the orientation of the seedling relative to the centrifugal acceleration. If the centrifugal vector pointed toward the cotyledons, gravitropic bending of hypocotyls and roots was substantially enhanced. The complex behavior of Arabidopsis seedlings provides strong evidence that gravitropic bending entails a cosine component (longitudinal stimulus) to which the seedlings were more sensitive than to the classical sine component. The absolute gravitropic thresholds of hypocotyls and roots were determined in a clinostat-centrifuge and found to be below 0.015×g. A tropism mutant lacking the EHB1 protein, which interacts with ARF-GAP (ARF GTPase-activating protein) and thus indirectly with a small ARF-type G protein, displayed a lower gravitropic threshold for roots and also enhanced bending, while the responses of the hypocotyls remained nearly unaffected.
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Affiliation(s)
- Michaela Dümmer
- Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, D-35032 Marburg, Germany
| | - Christoph Forreiter
- Abteilung für Biologie, Naturwissenschaftlich-Technische Fakultät, Universität Siegen, Adolf Reichwein Str. 2, D-57068 Siegen, Germany
| | - Paul Galland
- Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, D-35032 Marburg, Germany.
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Abstract
Mutant genes that underlie Mendelian forms of amyotrophic lateral sclerosis (ALS) and biochemical investigations of genetic disease models point to potential driver pathophysiological events involving endoplasmic reticulum (ER) stress and autophagy. Several steps in these cell biological processes are known to be controlled physiologically by small ADP-ribosylation factor (ARF) signaling. Here, we investigated the role of ARF guanine nucleotide exchange factors (GEFs), cytohesins, in models of ALS. Genetic or pharmacological inhibition of cytohesins protects motor neurons in vitro from proteotoxic insults and rescues locomotor defects in a Caenorhabditis elegans model of disease. Cytohesins form a complex with mutant superoxide dismutase 1 (SOD1), a known cause of familial ALS, but this is not associated with a change in GEF activity or ARF activation. ER stress evoked by mutant SOD1 expression is alleviated by antagonism of cytohesin activity. In the setting of mutant SOD1 toxicity, inhibition of cytohesin activity enhances autophagic flux and reduces the burden of misfolded SOD1. These observations suggest that targeting cytohesins may have potential benefits for the treatment of ALS.
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Ding ZF, Ren J, Tan JM, Wang Z, Yin SW, Huang Y, Huang X, Wang W, Lan JF, Ren Q. Characterization of two novel ADP ribosylation factors from giant freshwater prawn Macrobrachium rosenbergii and their responses to WSSV challenge. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 48:204-209. [PMID: 25451300 PMCID: PMC7124501 DOI: 10.1016/j.dci.2014.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 10/10/2014] [Accepted: 10/13/2014] [Indexed: 06/04/2023]
Abstract
ADP-ribosylation factors (Arfs) are small GTP-binding proteins that have an essential function in intracellular trafficking and organelle structure. To date, little information is available on the Arfs in the economically important giant freshwater prawn Macrobrachium rosenbergii and their relationship to viral infection. Here we identified two Arf genes from M. rosenbergii (MrArf1 and MrArf2) for the first time. Phylogenetic analysis showed that MrArf1, together with MjArf1 from shrimp Marsupenaeus japonicus belonged to Class I Arfs. By contrast, MrArf2 didn't not match any of the Arfs classes of I/II/III, although it could be clustered with an Arf protein from M. japonicas called MjArfn, which may represent an analog of the Arf. MrArf1 was ubiquitously expressed in all the examined tissues, with the highest transcription level in the hepatopancreas, whereas MrArf2 was only highly expressed in the hepatopancreas and exhibited very low levels in the heart, stomach, gills and intestine. The expression level of MrArf1 in the gills was down-regulated post 24 h WSSV challenge, and reached the maximal level at 48 h. MrArf1 in the hepatopancreas went up from 24 to 48 h WSSV challenge. MrArf2 transcript in the gill also went down at 24 h and then was upregulated at 48 h WSSV challenge. MrArf2 increased significantly in the hepatopancreas 24 h after infection and then went down at 48 h WSSV challenge. RNAi results showed that knockdown of MrArf1 or MrArf2 could inhibit the expression of the envelope protein gene vp28 of the WSSV. So, it could be speculated that MrArf1 and MrArf2 might play important roles in the innate immune system against WSSV infection.
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Affiliation(s)
- Zheng-Feng Ding
- Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China; Freshwater Fisheries Research Institute of Jiangsu Province, 79 Chating East Street, Nanjing 210017, China
| | - Jie Ren
- Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Jing-Min Tan
- Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Zheng Wang
- Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Shao-Wu Yin
- Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Ying Huang
- Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Xin Huang
- Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Wen Wang
- Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Jiang-Feng Lan
- College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Qian Ren
- Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China.
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Ranjan P, Kashyap RS, Goel M, Veetil SK, Kateriya S. Cellular organelles facilitate dimerization of a newly identified Arf from Chlamydomonas reinhardtii. JOURNAL OF PHYCOLOGY 2014; 50:1137-1145. [PMID: 26988793 DOI: 10.1111/jpy.12245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 08/22/2014] [Indexed: 06/05/2023]
Abstract
GTPases of the Ras superfamily regulate a wide variety of cellular processes including vesicular transport and various secretory pathways of the cell. ADP - ribosylation factor (ARF) belongs to one of the five major families of the Ras superfamily and serves as an important component of vesicle formation and transport machinery of the cells. The binding of GTP to these Arfs and its subsequent hydrolysis, induces conformational changes in these proteins leading to their enzymatic activities. The dimeric form of Arf is associated with membrane pinch-off during vesicle formation. In this report, we have identified an arf gene from the unicellular green alga Chlamydomonas reinhardtii, CrArf, and showed that the oligomeric state of the protein in C. renhardtii is modulated by the cellular membrane environment of the organism. Protein cross-linking experiments showed that the purified recombinant CrArf has the ability to form a dimer. Both the 20-kDa monomeric and 40-kDa dimeric forms of CrArf were recognized from Chlamydomonas total cell lysate (CrTLC) and purified recombinant CrArf by the CrArf specific antibody. The membranous environment of the cell appeared to facilitate dimerization of the CrArf, as dimeric form was found exclusively associated with the membrane bound organelles. The subcellular localization studies in Chlamydomonas suggested that CrArf mainly localized in the cytosol and was mislocalized in vesicle transport machinery inhibitor treated cells. This research sheds light on the importance of the cellular membrane environment for regulating the oligomeric state of CrArf protein in this organism and associated functional role.
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Affiliation(s)
- Peeyush Ranjan
- Department of Biochemistry, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Rudra Shankar Kashyap
- Department of Biochemistry, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Manisha Goel
- Department of Biophysics, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Sindhu Kandoth Veetil
- Department of Biochemistry, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Suneel Kateriya
- Department of Biochemistry, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India
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Kawada D, Kobayashi H, Tomita T, Nakata E, Nagano M, Siekhaus DE, Toshima JY, Toshima J. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:144-56. [PMID: 25409928 DOI: 10.1016/j.bbamcr.2014.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 10/09/2014] [Accepted: 10/10/2014] [Indexed: 11/26/2022]
Abstract
Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular trafficking. Among them, the Rab, Arf, and Rho families function in successive steps of vesicle transport, in forming vesicles from donor membranes, directing vesicle trafficking toward target membranes and docking vesicles onto target membranes. These proteins act as molecular switches that are controlled by a cycle of GTP binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs in the regulation of the endocytic pathway using fluorescently labeled yeast mating pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells show defective α-factor binding to the cell surface. Interestingly, Ste2p, the α-factor receptor, was mis-localized from the plasma membrane to the vacuole in glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent function, as well as the GAP activity, of Glo3p is important for both α-factor binding and Ste2p localization at the cell surface. Additionally, we found that deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi compartments and causes a defect in transport from the TGN to the plasma membrane. Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN transport pathway, but not in the early endosome-to-TGN transport pathway. These findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell surface proteins.
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Affiliation(s)
- Daiki Kawada
- Department of Biological Science and Technology, Tokyo University of Science, Niijuku 6-3-1, Katsushika-ku, Tokyo 125-8585, Japan
| | - Hiromu Kobayashi
- Department of Biological Science and Technology, Tokyo University of Science, Niijuku 6-3-1, Katsushika-ku, Tokyo 125-8585, Japan
| | - Tsuyoshi Tomita
- Department of Biological Science and Technology, Tokyo University of Science, Niijuku 6-3-1, Katsushika-ku, Tokyo 125-8585, Japan
| | - Eisuke Nakata
- Department of Biological Science and Technology, Tokyo University of Science, Niijuku 6-3-1, Katsushika-ku, Tokyo 125-8585, Japan
| | - Makoto Nagano
- Department of Biological Science and Technology, Tokyo University of Science, Niijuku 6-3-1, Katsushika-ku, Tokyo 125-8585, Japan; Research Center for RNA Science, RIST, Tokyo University of Science, Niijuku 6-3-1, Katsushika-ku, Tokyo 125-8585, Japan
| | | | - Junko Y Toshima
- Research Center for RNA Science, RIST, Tokyo University of Science, Niijuku 6-3-1, Katsushika-ku, Tokyo 125-8585, Japan; Faculty of Science and Engineering, Waseda University, Wakamatsu-cho 2-2, Shinjuku-ku, Tokyo 162-8480, Japan.
| | - Jiro Toshima
- Department of Biological Science and Technology, Tokyo University of Science, Niijuku 6-3-1, Katsushika-ku, Tokyo 125-8585, Japan; Research Center for RNA Science, RIST, Tokyo University of Science, Niijuku 6-3-1, Katsushika-ku, Tokyo 125-8585, Japan.
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31
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The ADP-ribosylation factor 1 gene is indispensable for mouse embryonic development after implantation. Biochem Biophys Res Commun 2014; 453:748-53. [DOI: 10.1016/j.bbrc.2014.10.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 10/03/2014] [Indexed: 11/24/2022]
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32
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Queiroz RML, Charneau S, Mandacaru SC, Schwämmle V, Lima BD, Roepstorff P, Ricart CAO. Quantitative proteomic and phosphoproteomic analysis of Trypanosoma cruzi amastigogenesis. Mol Cell Proteomics 2014; 13:3457-72. [PMID: 25225356 DOI: 10.1074/mcp.m114.040329] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Chagas disease is a tropical neglected disease endemic in Latin America caused by the protozoan Trypanosoma cruzi. The parasite has four major life stages: epimastigote, metacyclic trypomastigote, bloodstream trypomastigote, and amastigote. The differentiation from infective trypomastigotes into replicative amastigotes, called amastigogenesis, takes place in vivo inside mammalian host cells after a period of incubation in an acidic phagolysosome. This differentiation process can be mimicked in vitro by incubating tissue-culture-derived trypomastigotes in acidic DMEM. Here we used this well-established differentiation protocol to perform a comprehensive quantitative proteomic and phosphoproteomic analysis of T. cruzi amastigogenesis. Samples from fully differentiated forms and two biologically relevant intermediate time points were Lys-C/trypsin digested, iTRAQ-labeled, and multiplexed. Subsequently, phosphopeptides were enriched using a TiO2 matrix. Non-phosphorylated peptides were fractionated via hydrophilic interaction liquid chromatography prior to LC-MS/MS analysis. LC-MS/MS and bioinformatics procedures were used for protein and phosphopeptide quantitation, identification, and phosphorylation site assignment. We were able to identify regulated proteins and pathways involved in coordinating amastigogenesis. We also observed that a significant proportion of the regulated proteins were membrane proteins. Modulated phosphorylation events coordinated by protein kinases and phosphatases that are part of the signaling cascade induced by incubation in acidic medium were also evinced. To our knowledge, this work is the most comprehensive quantitative proteomics study of T. cruzi amastigogenesis, and these data will serve as a trustworthy basis for future studies, and possibly for new potential drug targets.
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Affiliation(s)
- Rayner M L Queiroz
- From the ‡Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, 70910-900 Brazil; §Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Sébastien Charneau
- From the ‡Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, 70910-900 Brazil
| | - Samuel C Mandacaru
- From the ‡Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, 70910-900 Brazil
| | - Veit Schwämmle
- §Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Beatriz D Lima
- From the ‡Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, 70910-900 Brazil
| | - Peter Roepstorff
- §Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Carlos A O Ricart
- From the ‡Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, 70910-900 Brazil;
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33
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Asymmetric neuroblast divisions producing apoptotic cells require the cytohesin GRP-1 in Caenorhabditis elegans. Genetics 2014; 198:229-47. [PMID: 25053664 DOI: 10.1534/genetics.114.167189] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cytohesins are Arf guanine nucleotide exchange factors (GEFs) that regulate membrane trafficking and actin cytoskeletal dynamics. We report here that GRP-1, the sole Caenorhabditis elegans cytohesin, controls the asymmetric divisions of certain neuroblasts that divide to produce a larger neuronal precursor or neuron and a smaller cell fated to die. In the Q neuroblast lineage, loss of GRP-1 led to the production of daughter cells that are more similar in size and to the transformation of the normally apoptotic daughter into its sister, resulting in the production of extra neurons. Genetic interactions suggest that GRP-1 functions with the previously described Arf GAP CNT-2 and two other Arf GEFs, EFA-6 and BRIS-1, to regulate the activity of Arf GTPases. In agreement with this model, we show that GRP-1's GEF activity, mediated by its SEC7 domain, is necessary for the posterior Q cell (Q.p) neuroblast division and that both GRP-1 and CNT-2 function in the Q.posterior Q daughter cell (Q.p) to promote its asymmetry. Although functional GFP-tagged GRP-1 proteins localized to the nucleus, the extra cell defects were rescued by targeting the Arf GEF activity of GRP-1 to the plasma membrane, suggesting that GRP-1 acts at the plasma membrane. The detection of endogenous GRP-1 protein at cytokinesis remnants, or midbodies, is consistent with GRP-1 functioning at the plasma membrane and perhaps at the cytokinetic furrow to promote the asymmetry of the divisions that require its function.
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34
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Selyunin AS, Reddick LE, Weigele BA, Alto NM. Selective protection of an ARF1-GTP signaling axis by a bacterial scaffold induces bidirectional trafficking arrest. Cell Rep 2014; 6:878-91. [PMID: 24582959 PMCID: PMC4017587 DOI: 10.1016/j.celrep.2014.01.040] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 12/24/2013] [Accepted: 01/28/2014] [Indexed: 10/25/2022] Open
Abstract
Bidirectional vesicular transport between the endoplasmic reticulum (ER) and Golgi is mediated largely by ARF and Rab GTPases, which orchestrate vesicle fission and fusion, respectively. How their activities are coordinated in order to define the successive steps of the secretory pathway and preserve traffic directionality is not well understood in part due to the scarcity of molecular tools that simultaneously target ARF and Rab signaling. Here, we take advantage of the unique scaffolding properties of E. coli secreted protein G (EspG) to describe the critical role of ARF1/Rab1 spatiotemporal coordination in vesicular transport at the ER-Golgi intermediate compartment. Structural modeling and cellular studies show that EspG induces bidirectional traffic arrest by tethering vesicles through select ARF1-GTP/effector complexes and local inactivation of Rab1. The mechanistic insights presented here establish the effectiveness of a small bacterial catalytic scaffold for studying complex processes and reveal an alternative mechanism of immune regulation by an important human pathogen.
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Affiliation(s)
- Andrey S Selyunin
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Lovett Evan Reddick
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Bethany A Weigele
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Neal M Alto
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA.
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35
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Rouhana J, Hoh F, Estaran S, Henriquet C, Boublik Y, Kerkour A, Trouillard R, Martinez J, Pugnière M, Padilla A, Chavanieu A. Fragment-based identification of a locus in the Sec7 domain of Arno for the design of protein-protein interaction inhibitors. J Med Chem 2013; 56:8497-511. [PMID: 24112024 DOI: 10.1021/jm4009357] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
By virtual screening using a fragment-based drug design (FBDD) approach, 33 fragments were selected within small pockets around interaction hot spots on the Sec7 surface of the nucleotide exchange factor Arno, and then their ability to interfere with the Arno-catalyzed nucleotide exchange on the G-protein Arf1 was evaluated. By use of SPR, NMR, and fluorescence assays, the direct binding of three of the identified fragments to Arno Sec7 domain was demonstrated and the promiscuous aggregate behavior evaluated. Then the binding mode of one fragment and of a more active analogue was solved by X-ray crystallography. This highlighted the role of stable and transient pockets at the Sec7 domain surface in the discovery and binding of interfering compounds. These results provide structural information on how small organic compounds can interfere with the Arf1-Arno Sec7 domain interaction and may guide the rational drug design of competitive inhibitors of Arno enzymatic activity.
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Affiliation(s)
- Jad Rouhana
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Universités Montpellier 1 et 2, Faculté de Pharmacie, 15 Avenue Charles Flahault BP14491, 34093 Montpellier Cedex 5, France
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36
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Rocca DL, Amici M, Antoniou A, Blanco Suarez E, Halemani N, Murk K, McGarvey J, Jaafari N, Mellor JR, Collingridge GL, Hanley JG. The small GTPase Arf1 modulates Arp2/3-mediated actin polymerization via PICK1 to regulate synaptic plasticity. Neuron 2013; 79:293-307. [PMID: 23889934 PMCID: PMC3725416 DOI: 10.1016/j.neuron.2013.05.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2013] [Indexed: 11/17/2022]
Abstract
Inhibition of Arp2/3-mediated actin polymerization by PICK1 is a central mechanism to AMPA receptor (AMPAR) internalization and long-term depression (LTD), although the signaling pathways that modulate this process in response to NMDA receptor (NMDAR) activation are unknown. Here, we define a function for the GTPase Arf1 in this process. We show that Arf1-GTP binds PICK1 to limit PICK1-mediated inhibition of Arp2/3 activity. Expression of mutant Arf1 that does not bind PICK1 leads to reduced surface levels of GluA2-containing AMPARs and smaller spines in hippocampal neurons, which occludes subsequent NMDA-induced AMPAR internalization and spine shrinkage. In organotypic slices, NMDAR-dependent LTD of AMPAR excitatory postsynaptic currents is abolished in neurons expressing mutant Arf1. Furthermore, NMDAR stimulation downregulates Arf1 activation and binding to PICK1 via the Arf-GAP GIT1. This study defines Arf1 as a critical regulator of actin dynamics and synaptic function via modulation of PICK1. The Arf1-PICK1-Arp2/3 pathway regulates actin polymerization NMDAR activation activates the Arf-GAP GIT1 to deactivate Arf1 Arf1 controls NMDAR-dependent, PICK1-mediated AMPAR trafficking and LTD A noncanonical role is described for Arf1 in vesicle traffic, distinct from COPI regulation
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Affiliation(s)
- Daniel L Rocca
- School of Biochemistry, Centre for Synaptic Plasticity, Medical Sciences Building and Dorothy Hodgkin Building, University of Bristol, University Walk, Bristol BS8 1TD, UK
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Zheng P, Gao F, Deng K, Gong W, Sun Z. Expression, purification and preliminary X-ray crystallographic analysis of Arf1-GDP in complex with dimeric p23 peptide. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1155-8. [PMID: 24100571 PMCID: PMC3792679 DOI: 10.1107/s1744309113024330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 08/31/2013] [Indexed: 05/19/2024]
Abstract
Arf1 is a member of the Ras superfamily and is involved in COPI vesicle formation. Arf1-GDP can interact with dimeric p23. Here, human Arf1 (residues 18-181) was cloned, expressed and purified in Escherichia coli. For crystallization, Arf1-GDP was mixed with dimeric p23 peptide in a 1:5 molar ratio. Crystals were obtained which diffracted to 2.7 Å resolution. The crystals belonged to space group P6₁22, with unit-cell parameters a=b=80.6, c=336.0 Å, α=β=90, γ=120°. The asymmetric unit of the crystals contained two molecules, with a Matthews coefficient of 3.2 Å3 Da(-1) and a solvent content of 61.9%.
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Affiliation(s)
- Peng Zheng
- Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100039, People’s Republic of China
| | - Feng Gao
- Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, People’s Republic of China
| | - Kai Deng
- Reproductive Medicine Research Center, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, People’s Republic of China
| | - Weimin Gong
- Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, People’s Republic of China
| | - Zhe Sun
- Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, People’s Republic of China
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Structural basis for membrane recruitment and allosteric activation of cytohesin family Arf GTPase exchange factors. Proc Natl Acad Sci U S A 2013; 110:14213-8. [PMID: 23940353 PMCID: PMC3761562 DOI: 10.1073/pnas.1301883110] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
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.
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Paul D, Bartenschlager R. Architecture and biogenesis of plus-strand RNA virus replication factories. World J Virol 2013; 2:32-48. [PMID: 24175228 PMCID: PMC3785047 DOI: 10.5501/wjv.v2.i2.32] [Citation(s) in RCA: 208] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 01/18/2013] [Accepted: 01/24/2013] [Indexed: 02/05/2023] Open
Abstract
Plus-strand RNA virus replication occurs in tight association with cytoplasmic host cell membranes. Both, viral and cellular factors cooperatively generate distinct organelle-like structures, designated viral replication factories. This compartmentalization allows coordination of the different steps of the viral replication cycle, highly efficient genome replication and protection of the viral RNA from cellular defense mechanisms. Electron tomography studies conducted during the last couple of years revealed the three dimensional structure of numerous plus-strand RNA virus replication compartments and highlight morphological analogies between different virus families. Based on the morphology of virus-induced membrane rearrangements, we propose two separate subclasses: the invaginated vesicle/spherule type and the double membrane vesicle type. This review discusses common themes and distinct differences in the architecture of plus-strand RNA virus-induced membrane alterations and summarizes recent progress that has been made in understanding the complex interplay between viral and co-opted cellular factors in biogenesis and maintenance of plus-strand RNA virus replication factories.
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Affiliation(s)
| | - William T. Jackson
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- * E-mail:
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Garcia R, Nguyen L, Brazill D. Dictyostelium discoideum SecG interprets cAMP-mediated chemotactic signals to influence actin organization. Cytoskeleton (Hoboken) 2013; 70:269-80. [PMID: 23564751 PMCID: PMC3693759 DOI: 10.1002/cm.21107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 03/04/2013] [Accepted: 03/05/2013] [Indexed: 11/12/2022]
Abstract
Tight control of actin cytoskeletal dynamics is essential for proper cell function and survival. Arf nucleotide binding-site opener (ARNO), a mammalian guanine nucleotide exchange factor for Arf, has been implicated in actin cytoskeletal regulation but its exact role is still unknown. To explore the role of ARNO in this regulation as well as in actin-mediated processes, the Dictyostelium discoideum homolog, SecG, was examined. SecG peaks during aggregation and mound formation. The overexpression of SecG arrests development at the mound stage. SecG overexpressing (SecG OE) cells fail to stream during aggregation. Although carA is expressed, SecG OE cells do not chemotax toward cAMP, indicating SecG is involved in the cellular response to cAMP. This chemotactic defect is specific to cAMP-directed chemotaxis, as SecG OE cells chemotax to folate without impairment and exhibit normal cell motility. The chemotactic defects of the SecG mutants may be due to an impaired cAMP response as evidenced by altered cell polarity and F-actin polymerization after cAMP stimulation. Cells overexpressing SecG have increased filopodia compared to wild type cells, implying that excess SecG causes abnormal organization of F-actin. The general function of the cytoskeleton, however, is not disrupted as the SecG OE cells exhibit proper cell-substrate adhesion. Taken together, the results suggest proper SecG levels are needed for appropriate response to cAMP signaling in order to coordinate F-actin organization during development.
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Affiliation(s)
- Rebecca Garcia
- Department of Biological Sciences, Center for the Study of Gene Structure and Function, Hunter College and the Graduate Center of the City University of New York, New York, NY 10065
| | - Liem Nguyen
- Department of Biological Sciences, Center for the Study of Gene Structure and Function, Hunter College and the Graduate Center of the City University of New York, New York, NY 10065
| | - Derrick Brazill
- Department of Biological Sciences, Center for the Study of Gene Structure and Function, Hunter College and the Graduate Center of the City University of New York, New York, NY 10065
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Abstract
Small GTPases are versatile temporal and spatial regulators of virtually all cellular processes including signal transduction, cytoskeleton dynamics and membrane trafficking. They function as molecular switches, aided by a multitude of regulatory and effector proteins that link them into functional networks. A picture is beginning to emerge whereupon scaffold proteins with many functional domains perform the regulatory and effector functions, thus allowing the ordered recruitment and activation of small GTPases. This leads to the formation of scaffolding patches that coordinate cargo concentration and capture, with the recruitment and activation of the membrane tethering complexes and fusion regulators. This review will focus on the crosstalk of Arf and Rab GTPases at the Golgi complex and the scaffolds that facilitate their activation during trafficking of sensory receptors to primary cilia. The evolutionary conservation of the GTPase cascades in ciliogenesis and yeast budding will be discussed.
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Affiliation(s)
- Dusanka Deretic
- Department of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, NM, USA.
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Braun R, Finney R, Yan C, Chen QR, Hu Y, Edmonson M, Meerzaman D, Buetow K. Discovery analysis of TCGA data reveals association between germline genotype and survival in ovarian cancer patients. PLoS One 2013; 8:e55037. [PMID: 23555554 PMCID: PMC3605427 DOI: 10.1371/journal.pone.0055037] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 12/21/2012] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Ovarian cancer remains a significant public health burden, with the highest mortality rate of all the gynecological cancers. This is attributable to the late stage at which the majority of ovarian cancers are diagnosed, coupled with the low and variable response of advanced tumors to standard chemotherapies. To date, clinically useful predictors of treatment response remain lacking. Identifying the genetic determinants of ovarian cancer survival and treatment response is crucial to the development of prognostic biomarkers and personalized therapies that may improve outcomes for the late-stage patients who comprise the majority of cases. METHODS To identify constitutional genetic variations contributing to ovarian cancer mortality, we systematically investigated associations between germline polymorphisms and ovarian cancer survival using data from The Cancer Genome Atlas Project (TCGA). Using stage-stratified Cox proportional hazards regression, we examined >650,000 SNP loci for association with survival. We additionally examined whether the association of significant SNPs with survival was modified by somatic alterations. RESULTS Germline polymorphisms at rs4934282 (AGAP11/C10orf116) and rs1857623 (DNAH14) were associated with stage-adjusted survival (p= 1.12e-07 and 1.80e-07, FDR q= 1.2e-04 and 2.4e-04, respectively). A third SNP, rs4869 (C10orf116), was additionally identified as significant in the exome sequencing data; it is in near-perfect LD with rs4934282. The associations with survival remained significant when somatic alterations. CONCLUSIONS Discovery analysis of TCGA data reveals germline genetic variations that may play a role in ovarian cancer survival even among late-stage cases. The significant loci are located near genes previously reported as having a possible relationship to platinum and taxol response. Because the variant alleles at the significant loci are common (frequencies for rs4934282 A/C alleles = 0.54/0.46, respectively; rs1857623 A/G alleles = 0.55/0.45, respectively) and germline variants can be assayed noninvasively, our findings provide potential targets for further exploration as prognostic biomarkers and individualized therapies.
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Affiliation(s)
- Rosemary Braun
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA.
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Wang TZ, Xia XZ, Zhao MG, Tian QY, Zhang WH. Expression of a Medicago falcata small GTPase gene, MfARL1 enhanced tolerance to salt stress in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 63:227-235. [PMID: 23298681 DOI: 10.1016/j.plaphy.2012.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 12/17/2012] [Indexed: 06/01/2023]
Abstract
To understand the role of small GTPases in response to abiotic stress, we isolated a gene encoding a small GTPase, designated MfARL1, from a subtracted cDNA library in Medicago falcata, a native legume species in semi-arid grassland in northern China. The function of MfARL1 in response to salt stress was studied by expressing MfARL1 in Arabidopsis. Wild-type (WT) and transgenic plants constitutively expressing MfARL1 showed comparable phenotype when grown under control conditions. Germination of seeds expressing MfARL1 was less suppressed by salt stress than that of WT seeds. Transgenic seedlings had higher survival rate than WT seedlings under salt stress, suggesting that expression of MfARL1 confers tolerance to salt stress. The physiological and molecular mechanisms underlying these phenomena were elucidated. Salt stress led to a significant decrease in chlorophyll contents in WT plants, but not in transgenic plants. Transgenic plants accumulated less amounts of H(2)O(2) and malondialdehyde than their WT counterparts under salt stress, which can be accounted for by the higher catalase activities, lower activities of superoxide dismutase, and peroxidase in transgenic plants than in WT plants. Transgenic plants displayed lower Na(+)/K(+) ratio due to less accumulation of Na(+) than wild-type under salt stress conditions. The lower Na(+)/K(+) ratio may result from less accumulation of Na(+) due to reduced expression of AtHKT1 that encodes Na(+) transporter in transgenic plants under salt stress. These findings demonstrate that MfARL1 encodes a novel stress-responsive small GTPase that is involved in tolerance to salt stress.
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Affiliation(s)
- Tian-Zuo Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, PR China.
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Distinct synaptic localization patterns of brefeldin A-resistant guanine nucleotide exchange factors BRAG2 and BRAG3 in the mouse retina. J Comp Neurol 2013; 521:860-76. [DOI: 10.1002/cne.23206] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Revised: 05/11/2012] [Accepted: 07/27/2012] [Indexed: 11/07/2022]
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46
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Khan AR. Oligomerization of rab/effector complexes in the regulation of vesicle trafficking. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:579-614. [PMID: 23663983 DOI: 10.1016/b978-0-12-386931-9.00021-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Rabs comprise the largest member of the Ras superfamily of small GTPases with over 60 proteins in mammals and 11 proteins in yeast. Like all small GTPases, Rabs oscillate between an inactive GDP-bound conformation and an active GTP-bound state that is tethered to lipid membranes via a C-terminal prenylation site on conserved cysteine residues. In their active state, Rabs regulate various aspects of membrane trafficking, including vesicle formation, transport, docking, and fusion. The critical element of biological activity is the recruitment of cytosolic effector proteins to specific endomembranes by active Rabs. The importance of Rabs in cellular processes is apparent from their links to genetic disorders, immunodeficiency, cancer, and pathogen invasion. During the last decade, numerous structures of complexes have shed light on the molecular basis for Rab/effector specificity and their topological organization on subcellular membranes. Here, I review the known structures of Rab/effector complexes and their modes of oligomerization. This is followed by a brief discussion on the thermodynamics of effector recruitment, which has not been documented sufficiently in previous reviews. A summary of diseases associated with Rab/effector trafficking pathways concludes this chapter.
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Affiliation(s)
- Amir R Khan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
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Rouhana J, Padilla A, Estaran S, Bakari S, Delbecq S, Boublik Y, Chopineau J, Pugnière M, Chavanieu A. Kinetics of interaction between ADP-ribosylation factor-1 (Arf1) and the Sec7 domain of Arno guanine nucleotide exchange factor, modulation by allosteric factors, and the uncompetitive inhibitor brefeldin A. J Biol Chem 2012; 288:4659-72. [PMID: 23255605 DOI: 10.1074/jbc.m112.391748] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The GDP/GTP nucleotide exchange of Arf1 is catalyzed by nucleotide exchange factors (GEF), such as Arno, which act through their catalytic Sec7 domain. This exchange is a complex mechanism that undergoes conformational changes and intermediate complex species involving several allosteric partners such as nucleotides, Mg(2+), and Sec7 domains. Using a surface plasmon resonance approach, we characterized the kinetic binding parameters for various intermediate complexes. We first confirmed that both GDP and GTP counteract equivalently to the free-nucleotide binary Arf1-Arno complex stability and revealed that Mg(2+) potentiates by a factor of 2 the allosteric effect of GDP. Then we explored the uncompetitive inhibitory mechanism of brefeldin A (BFA) that conducts to an abortive pentameric Arf1-Mg(2+)-GDP-BFA-Sec7 complex. With BFA, the association rate of the abortive complex is drastically reduced by a factor of 42, and by contrast, the 15-fold decrease of the dissociation rate concurs to stabilize the pentameric complex. These specific kinetic signatures have allowed distinguishing the level and nature as well as the fate in real time of formed complexes according to experimental conditions. Thus, we showed that in the presence of GDP, the BFA-resistant Sec7 domain of Arno can also associate to form a pentameric complex, which suggests that the uncompetitive inhibition by BFA and the nucleotide allosteric effect combine to stabilize such abortive complex.
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Affiliation(s)
- Jad Rouhana
- Institut des Biomolécules Max Mousseron, IBMM, UMR 5247 CNRS-Universités Montpellier 1 et 2 Faculté de Pharmacie, 15 avenue Charles Flahault BP14491, 34093 Montpellier cedex 5, France
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The capping domain in RalF regulates effector functions. PLoS Pathog 2012; 8:e1003012. [PMID: 23166491 PMCID: PMC3499574 DOI: 10.1371/journal.ppat.1003012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 09/18/2012] [Indexed: 12/24/2022] Open
Abstract
The Legionella pneumophila effector protein RalF functions as a guanine nucleotide exchange factor (GEF) that activates the host small GTPase protein ADP-ribosylation factor (Arf), and recruits this host protein to the vacuoles in which this pathogen resides. GEF activity is conferred by the Sec7 domain located in the N-terminal region of RalF. Structural studies indicate that the C-terminal region of RalF makes contacts with residues in the Sec7 domain important for Arf interactions. Theoretically, the C-terminal region of RalF could prevent nucleotide exchange activity by blocking the ability of Arf to interact with the Sec7 domain. For this reason, the C-terminal region of RalF has been termed a capping domain. Here, the role of the RalF capping domain was investigated by comparing biochemical and effector activities mediated by this domain in both the Legionella RalF protein (LpRalF) and in a RalF ortholog isolated from the unrelated intracellular pathogen Rickettsia prowazekii (RpRalF). These data indicate that both RalF proteins contain a functional Sec7 domain and that the capping domain regulates RalF GEF activity. The capping domain has intrinsic determinants that mediate localization of the RalF protein inside of host cells and confer distinct effector activities. Localization mediated by the capping domain of LpRalF enables the GEF to modulate membrane transport in the secretory pathway, whereas, the capping domain of RpRalF enables this bacterial GEF to modulate actin dynamics occurring near the plasma membrane. Thus, these data reveal that divergence in the function of the C-terminal capping domain alters the in vivo functions of the RalF proteins. Legionella pneumophila and Rickettsia prowazekii are two pathogenic intracellular bacteria, phylogenetically distant and presenting different intracellular lifestyles. Interestingly, both organisms encode a protein called RalF, which in Legionella has been shown to be an effector protein that functions as a guanine nucleotide exchange factor (GEF) for the Arf family of eukaryotic GTPases. We show that the Sec7 domains in both proteins have a similar enzymatic ability to activate Arf1, however, the two proteins differ in their effector functions inside mammalian cells. The Legionella RalF protein targets secretory transport functions, whereas, the Rickettsia RalF protein modulates actin dynamics at the plasma membrane. These differences in RalF effector activities are mediated by a C-terminal domain that directs localization and interaction with host cell determinants. These data reveal important properties of the RalF protein that provide insight into differential roles for Arf during infection by Legionella and Rickettsia, and also provide a model for investigating how intracellular localization of structurally similar Arf GEFs enables a protein to regulate functionally distinct host cell processes.
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Saito Y, Inoue T, Zhu G, Kimura N, Okada M, Nishimura M, Kimura N, Murayama S, Kaneko S, Shigemoto R, Imoto K, Suzuki T. Hyperpolarization-activated cyclic nucleotide gated channels: a potential molecular link between epileptic seizures and Aβ generation in Alzheimer's disease. Mol Neurodegener 2012; 7:50. [PMID: 23034178 PMCID: PMC3524764 DOI: 10.1186/1750-1326-7-50] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 09/27/2012] [Indexed: 12/20/2022] Open
Abstract
Background One of the best-characterized causative factors of Alzheimer’s disease (AD) is the generation of amyloid-β peptide (Aβ). AD subjects are at high risk of epileptic seizures accompanied by aberrant neuronal excitability, which in itself enhances Aβ generation. However, the molecular linkage between epileptic seizures and Aβ generation in AD remains unclear. Results X11 and X11-like (X11L) gene knockout mice suffered from epileptic seizures, along with a malfunction of hyperpolarization-activated cyclic nucleotide gated (HCN) channels. Genetic ablation of HCN1 in mice and HCN1 channel blockage in cultured Neuro2a (N2a) cells enhanced Aβ generation. Interestingly, HCN1 levels dramatically decreased in the temporal lobe of cynomolgus monkeys (Macaca fascicularis) during aging and were significantly diminished in the temporal lobe of sporadic AD patients. Conclusion Because HCN1 associates with amyloid-β precursor protein (APP) and X11/X11L in the brain, genetic deficiency of X11/X11L may induce aberrant HCN1 distribution along with epilepsy. Moreover, the reduction in HCN1 levels in aged primates may contribute to augmented Aβ generation. Taken together, HCN1 is proposed to play an important role in the molecular linkage between epileptic seizures and Aβ generation, and in the aggravation of sporadic AD.
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Affiliation(s)
- Yuhki Saito
- Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita12-Nishi6, Kita-ku, Sapporo, 060-0812, Japan
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Secretion of soluble vascular endothelial growth factor receptor 1 (sVEGFR1/sFlt1) requires Arf1, Arf6, and Rab11 GTPases. PLoS One 2012; 7:e44572. [PMID: 22962618 PMCID: PMC3433446 DOI: 10.1371/journal.pone.0044572] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 08/09/2012] [Indexed: 11/19/2022] Open
Abstract
The soluble form of vascular endothelial growth factor receptor 1 (sVEGFR-1/sFlt1) is generated by alternative splicing of the FLT1 gene. Secretion of sFlt1 from endothelial cells plays an important role in blood vessel sprouting and morphogenesis. However, excess sFlt1 secretion is associated with diseases such as preeclampsia and chronic kidney disease. To date, the secretory transport process involved in the secretion of sFlt1 is poorly understood. In the present study, we investigated the itinerary of sFlt1 trafficking along the secretory pathway. To understand the timecourse of sFlt1 secretion, endothelial cells stably expressing sFlt1 were metabolically radiolabeled with [(35)S]-methionine and cysteine. Our results indicate that after initial synthesis the levels of secreted [(35)S]-sFlt1 in the extracellular medium peaks at 8 hours. Treatment with brefeldin A (BFA), a drug which blocks trafficking between the endoplasmic reticulum (ER) and the Golgi complex, inhibited extracellular release of sFlt1 suggesting that ER to Golgi and intra-Golgi trafficking of sFlt1 are essential for its secretion. Furthermore, we show that ectopic expression of dominant-negative mutant forms of Arf1, Arf6, and Rab11 as well as siRNA-mediated knockdown of these GTPases block secretion of sFlt1 during normoxic and hypoxic conditions suggesting role for these small GTPases. This work is the first to report role of regulatory proteins involved in sFlt1 trafficking along the secretory pathway and may provide insights and new molecular targets for the modulation of sFlt-1 release during physiological and pathological conditions.
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