1
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Li FL, Guan KL. The Arf family GTPases: Regulation of vesicle biogenesis and beyond. Bioessays 2023; 45:e2200214. [PMID: 36998106 PMCID: PMC10282109 DOI: 10.1002/bies.202200214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 04/01/2023]
Abstract
The Arf family proteins are best known for their roles in the vesicle biogenesis. However, they also play fundamental roles in a wide range of cellular regulation besides vesicular trafficking, such as modulation of lipid metabolic enzymes, cytoskeleton remodeling, ciliogenesis, lysosomal, and mitochondrial morphology and functions. Growing studies continue to expand the downstream effector landscape of Arf proteins, especially for the less-studied members, revealing new biological functions, such as amino acid sensing. Experiments with cutting-edge technologies and in vivo functional studies in the last decade help to provide a more comprehensive view of Arf family functions. In this review, we summarize the cellular functions that are regulated by at least two different Arf members with an emphasis on those beyond vesicle biogenesis.
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Affiliation(s)
- Fu-Long Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kun-Liang Guan
- Department of Pharmacology and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
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2
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Nolasco S, Bellido J, Serna M, Carmona B, Soares H, Zabala JC. Colchicine Blocks Tubulin Heterodimer Recycling by Tubulin Cofactors TBCA, TBCB, and TBCE. Front Cell Dev Biol 2021; 9:656273. [PMID: 33968934 PMCID: PMC8100514 DOI: 10.3389/fcell.2021.656273] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/29/2021] [Indexed: 11/17/2022] Open
Abstract
Colchicine has been used to treat gout and, more recently, to effectively prevent autoinflammatory diseases and both primary and recurrent episodes of pericarditis. The anti-inflammatory action of colchicine seems to result from irreversible inhibition of tubulin polymerization and microtubule (MT) assembly by binding to the tubulin heterodimer, avoiding the signal transduction required to the activation of the entire NLRP3 inflammasome. Emerging results show that the MT network is a potential regulator of cardiac mechanics. Here, we investigated how colchicine impacts in tubulin folding cofactors TBCA, TBCB, and TBCE activities. We show that TBCA is abundant in mouse heart insoluble protein extracts. Also, a decrease of the TBCA/β-tubulin complex followed by an increase of free TBCA is observed in human cells treated with colchicine. The presence of free TBCA is not observed in cells treated with other anti-mitotic agents such as nocodazole or cold shock, neither after translation inhibition by cycloheximide. In vitro assays show that colchicine inhibits tubulin heterodimer dissociation by TBCE/TBCB, probably by interfering with interactions of TBCE with tubulin dimers, leading to free TBCA. Manipulation of TBCA levels, either by RNAi or overexpression results in decreased levels of tubulin heterodimers. Together, these data strongly suggest that TBCA is mainly receiving β-tubulin from the dissociation of pre-existing heterodimers instead of newly synthesized tubulins. The TBCE/TBCB+TBCA system is crucial for controlling the critical concentration of free tubulin heterodimers and MT dynamics in the cells by recycling the tubulin heterodimers. It is conceivable that colchicine affects tubulin heterodimer recycling through the TBCE/TBCB+TBCA system producing the known benefits in the treatment of pericardium inflammation.
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Affiliation(s)
- Sofia Nolasco
- Faculdade de Medicina Veterinária, CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Universidade de Lisboa, Lisbon, Portugal.,Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal
| | - Javier Bellido
- Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, Santander, Spain
| | - Marina Serna
- Spanish National Cancer Research Center, CNIO, Madrid, Spain
| | - Bruno Carmona
- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal.,Centro de Química Estrutural - Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Helena Soares
- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal.,Centro de Química Estrutural - Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Juan Carlos Zabala
- Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, Santander, Spain
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3
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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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4
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Schiavon CR, Griffin ME, Pirozzi M, Parashuraman R, Zhou W, Jinnah HA, Reines D, Kahn RA. Compositional complexity of rods and rings. Mol Biol Cell 2018; 29:2303-2316. [PMID: 30024290 PMCID: PMC6249804 DOI: 10.1091/mbc.e18-05-0274] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Rods and rings (RRs) are large linear- or circular-shaped structures typically described as polymers of IMPDH (inosine monophosphate dehydrogenase). They have been observed across a wide variety of cell types and species and can be induced to form by inhibitors of IMPDH. RRs are thought to play a role in the regulation of de novo guanine nucleotide synthesis; however, the function and regulation of RRs is poorly understood. Here we show that the regulatory GTPase, ARL2, a subset of its binding partners, and several resident proteins at the endoplasmic reticulum (ER) also localize to RRs. We also have identified two new inducers of RR formation: AICAR and glucose deprivation. We demonstrate that RRs can be disassembled if guanine nucleotides can be generated by salvage synthesis regardless of the inducer. Finally, we show that there is an ordered addition of components as RRs mature, with IMPDH first forming aggregates, followed by ARL2, and only later calnexin, a marker of the ER. These findings suggest that RRs are considerably more complex than previously thought and that the function(s) of RRs may include involvement of a regulatory GTPase, its effectors, and potentially contacts with intracellular membranes.
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Affiliation(s)
- Cara R Schiavon
- Cancer Biology Graduate Program, Graduate Division of Biomedical and Biological Sciences, Laney Graduate School, Atlanta, GA 30307
| | - Maxwell E Griffin
- Cancer Biology Graduate Program, Graduate Division of Biomedical and Biological Sciences, Laney Graduate School, Atlanta, GA 30307
| | - Marinella Pirozzi
- EuroBioImaging Facility, Institute of Protein Biochemistry, 80131 Naples, Italy
| | - Raman Parashuraman
- EuroBioImaging Facility, Institute of Protein Biochemistry, 80131 Naples, Italy
| | - Wei Zhou
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322
| | - H A Jinnah
- Department of Neurology and Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Daniel Reines
- Department of Biochemistry, 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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5
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Francis JW, Goswami D, Novick SJ, Pascal BD, Weikum ER, Ortlund EA, Griffin PR, Kahn RA. Nucleotide Binding to ARL2 in the TBCD∙ARL2∙β-Tubulin Complex Drives Conformational Changes in β-Tubulin. J Mol Biol 2017; 429:3696-3716. [PMID: 28970104 DOI: 10.1016/j.jmb.2017.09.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/31/2017] [Accepted: 09/26/2017] [Indexed: 11/25/2022]
Abstract
Microtubules are highly dynamic tubulin polymers that are required for a variety of cellular functions. Despite the importance of a cellular population of tubulin dimers, we have incomplete information about the mechanisms involved in the biogenesis of αβ-tubulin heterodimers. In addition to prefoldin and the TCP-1 Ring Complex, five tubulin-specific chaperones, termed cofactors A-E (TBCA-E), and GTP are required for the folding of α- and β-tubulin subunits and assembly into heterodimers. We recently described the purification of a novel trimer, TBCD•ARL2•β-tubulin. Here, we employed hydrogen/deuterium exchange coupled with mass spectrometry to explore the dynamics of each of the proteins in the trimer. Addition of guanine nucleotides resulted in changes in the solvent accessibility of regions of each protein that led to predictions about each's role in tubulin folding. Initial testing of that model confirmed that it is ARL2, and not β-tubulin, that exchanges GTP in the trimer. Comparisons of the dynamics of ARL2 monomer to ARL2 in the trimer suggested that its protein interactions were comparable to those of a canonical GTPase with an effector. This was supported by the use of nucleotide-binding assays that revealed an increase in the affinity for GTP by ARL2 in the trimer. We conclude that the TBCD•ARL2•β-tubulin complex represents a functional intermediate in the β-tubulin folding pathway whose activity is regulated by the cycling of nucleotides on ARL2. The co-purification of guanine nucleotide on the β-tubulin in the trimer is also shown, with implications to modeling the pathway.
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Affiliation(s)
- Joshua W Francis
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Devrishi Goswami
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, United States
| | - Scott J Novick
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, United States
| | - Bruce D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, United States
| | - Emily R Weikum
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, United States
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States.
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6
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Ivanova AA, Caspary T, Seyfried NT, Duong DM, West AB, Liu Z, Kahn RA. Biochemical characterization of purified mammalian ARL13B protein indicates that it is an atypical GTPase and ARL3 guanine nucleotide exchange factor (GEF). J Biol Chem 2017; 292:11091-11108. [PMID: 28487361 PMCID: PMC5491791 DOI: 10.1074/jbc.m117.784025] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 05/02/2017] [Indexed: 12/11/2022] Open
Abstract
Primary cilia play central roles in signaling during metazoan development. Several key regulators of ciliogenesis and ciliary signaling are mutated in humans, resulting in a number of ciliopathies, including Joubert syndrome (JS). ARL13B is a ciliary GTPase with at least three missense mutations identified in JS patients. ARL13B is a member of the ADP ribosylation factor family of regulatory GTPases, but is atypical in having a non-homologous, C-terminal domain of ∼20 kDa and at least one key residue difference in the consensus GTP-binding motifs. For these reasons, and to establish a solid biochemical basis on which to begin to model its actions in cells and animals, we developed preparations of purified, recombinant, murine Arl13b protein. We report results from assays for solution-based nucleotide binding, intrinsic and GTPase-activating protein-stimulated GTPase, and ARL3 guanine nucleotide exchange factor activities. Biochemical analyses of three human missense mutations found in JS and of two consensus GTPase motifs reinforce the atypical properties of this regulatory GTPase. We also discovered that murine Arl13b is a substrate for casein kinase 2, a contaminant in our preparation from human embryonic kidney cells. This activity, and the ability of casein kinase 2 to use GTP as a phosphate donor, may be a source of differences between our data and previously published results. These results provide a solid framework for further research into ARL13B on which to develop models for the actions of this clinically important cell regulator.
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Affiliation(s)
| | - Tamara Caspary
- Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322 and
| | | | | | - Andrew B West
- the Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Zhiyong Liu
- the Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, Alabama 35294
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7
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Newman LE, Schiavon CR, Turn RE, Kahn RA. The ARL2 GTPase regulates mitochondrial fusion from the intermembrane space. CELLULAR LOGISTICS 2017; 7:e1340104. [PMID: 28944094 PMCID: PMC5602422 DOI: 10.1080/21592799.2017.1340104] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 06/05/2017] [Indexed: 01/11/2023]
Abstract
Mitochondria are essential, dynamic organelles that regularly undergo both fusion and fission in response to cellular conditions, though mechanisms of the regulation of their dynamics are incompletely understood. We provide evidence that increased activity of the small GTPase ARL2 is strongly correlated with an increase in fusion, while loss of ARL2 activity results in a decreased rate of mitochondrial fusion. Strikingly, expression of activated ARL2 can partially restore the loss of fusion resulting from deletion of either mitofusin 1 (MFN1) or mitofusin 2 (MFN2), but not deletion of both. We only observe the full effects of ARL2 on mitochondrial fusion when it is present in the intermembrane space (IMS), as constructs driven to the matrix or prevented from entering mitochondria are essentially inactive in promoting fusion. Thus, ARL2 is the first regulatory (small) GTPase shown to act inside mitochondria or in the fusion pathway. Finally, using high-resolution, structured illumination microscopy (SIM), we find that ARL2 and mitofusin immunoreactivities present as punctate staining along mitochondria that share a spatial convergence in fluorescence signals. Thus, we propose that ARL2 plays a regulatory role in mitochondrial fusion, acting from the IMS and requiring at least one of the mitofusins in their canonical role in fusion of the outer membranes.
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Affiliation(s)
- Laura E. Newman
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Cara R. Schiavon
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Rachel E. Turn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Richard A. Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
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8
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Francis JW, Newman LE, Cunningham LA, Kahn RA. A Trimer Consisting of the Tubulin-specific Chaperone D (TBCD), Regulatory GTPase ARL2, and β-Tubulin Is Required for Maintaining the Microtubule Network. J Biol Chem 2017; 292:4336-4349. [PMID: 28126905 DOI: 10.1074/jbc.m116.770909] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/24/2017] [Indexed: 11/06/2022] Open
Abstract
Microtubule dynamics involves the polymerization and depolymerization of tubulin dimers and is an essential and highly regulated process required for cell viability, architecture, and division. The regulation of the microtubule network also depends on the maintenance of a pool of αβ-tubulin heterodimers. These dimers are the end result of complex folding and assembly events, requiring the TCP1 Ring Complex (TriC or CCT) chaperonin and five tubulin-specific chaperones, tubulin binding cofactors A-E (TBCA-TBCE). However, models of the actions of these chaperones are incomplete or inconsistent. We previously purified TBCD from bovine tissues and showed that it tightly binds the small GTPase ARL2 but appears to be inactive. Here, in an effort to identify the functional form of TBCD and using non-denaturing gels and immunoblotting, we analyzed lysates from a number of mouse tissues and cell lines to identify the quaternary state(s) of TBCD and ARL2. We found that both proteins co-migrated in native gels in a complex of ∼200 kDa that also contained β-tubulin. Using human embryonic kidney cells enabled the purification of the TBCD·ARL2·β-tubulin trimer found in cell and tissue lysates as well as two other novel TBCD complexes. Characterization of ARL2 point mutants that disrupt binding to TBCD suggested that the ARL2-TBCD interaction is critical for proper maintenance of microtubule densities in cells. We conclude that the TBCD·ARL2·β-tubulin trimer represents a functional complex whose activity is fundamental to microtubule dynamics.
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Affiliation(s)
- Joshua W Francis
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Laura E Newman
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Leslie A Cunningham
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Richard A Kahn
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
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9
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Matsumoto S, Fujii S, Kikuchi A. Arl4c is a key regulator of tubulogenesis and tumourigenesis as a target gene of Wnt-β-catenin and growth factor-Ras signalling. J Biochem 2016; 161:27-35. [PMID: 28053143 DOI: 10.1093/jb/mvw069] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/13/2016] [Indexed: 12/19/2022] Open
Abstract
Epithelial tubular morphogenesis (tubulogenesis) is a fundamental morphogenetic process of many epithelial organs. In this developmental process, epithelial cells migrate, proliferate, polarize and differentiate towards surrounding mesenchymal tissue to form tubule structures. Although epithelial tissue structures are basically stable in the postnatal period, epithelial cells regain highly proliferative and invasive potentials within mesenchymal tissue during tumour formation (tumourigenesis). Therefore, there must be a common molecular basis orchestrating the cellular behaviours involved in both tubulogenesis and tumourigenesis. ADP-ribosylation factor (Arf)-like protein 4c (Arl4c), which belongs to the small GTP-binding protein family, is expressed by the simultaneous activation of Wnt-β-catenin and growth factor-Ras-mitogen-activated protein kinase signalling, was identified as an essential regulator of tubulogenesis. Arl4c expression was also involved in the tumour formation of colorectal and lung cancers. In this review, we focus on Arl4c as a novel Wnt signal target molecule that links epithelial tubulogenesis to tumourigenesis.
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Affiliation(s)
- Shinji Matsumoto
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shinsuke Fujii
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan.,Laboratory of Oral Pathology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Akira Kikuchi
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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10
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Edvardson S, Tian G, Cullen H, Vanyai H, Ngo L, Bhat S, Aran A, Daana M, Da’amseh N, Abu-Libdeh B, Cowan NJ, Heng JIT, Elpeleg O. Infantile neurodegenerative disorder associated with mutations in TBCD, an essential gene in the tubulin heterodimer assembly pathway. Hum Mol Genet 2016; 25:4635-4648. [PMID: 28158450 PMCID: PMC6459059 DOI: 10.1093/hmg/ddw292] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/05/2016] [Accepted: 08/25/2016] [Indexed: 02/07/2023] Open
Abstract
Mutation in a growing spectrum of genes is known to either cause or contribute to primary or secondary microcephaly. In primary microcephaly the genetic determinants frequently involve mutations that contribute to or modulate the microtubule cytoskeleton by causing perturbations of neuronal proliferation and migration. Here we describe four patients from two unrelated families each with an infantile neurodegenerative disorder characterized by loss of developmental milestones at 9–24 months of age followed by seizures, dystonia and acquired microcephaly. The patients harboured homozygous missense mutations (A475T and A586V) in TBCD, a gene encoding one of five tubulin-specific chaperones (termed TBCA-E) that function in concert as a nanomachine required for the de novo assembly of the α/β tubulin heterodimer. The latter is the subunit from which microtubule polymers are assembled. We found a reduced intracellular abundance of TBCD in patient fibroblasts to about 10% (in the case of A475T) or 40% (in the case of A586V) compared to age-matched wild type controls. Functional analyses of the mutant proteins revealed a partially compromised ability to participate in the heterodimer assembly pathway. We show via in utero shRNA-mediated suppression that a balanced supply of tbcd is critical for cortical cell proliferation and radial migration in the developing mouse brain. We conclude that TBCD is a novel functional contributor to the mammalian cerebral cortex development, and that the pathological mechanism resulting from the mutations we describe is likely to involve compromised interactions with one or more TBCD-interacting effectors that influence the dynamics and behaviour of the neuronal cytoskeleton.
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Affiliation(s)
- Shimon Edvardson
- Monique and Jacques Roboh Department of Genetic Research, Hadassah, Hebrew University Medical Center Jerusalem, Jerusalem, Israel
- Neuropediatric Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Guoling Tian
- Department of Biochemistry & Molecular Pharmacology, NYU Langone Medical Center, New York, NY, USA
| | - Hayley Cullen
- The Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia, Australia
| | - Hannah Vanyai
- The Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia, Australia
| | - Linh Ngo
- The Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia, Australia
| | - Saiuj Bhat
- The Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia, Australia
| | - Adi Aran
- Neuropediatric Unit, Shaare Zedek Medical Center; Hebrew University-Hadassah School of Medicine, Jerusalem, Israel
| | - Muhannad Daana
- Neuropediatric Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Naderah Da’amseh
- Department of Pediatrics and Genetics, Makassed Hospital, Al-Quds Medical School, Jerusalem
| | - Bassam Abu-Libdeh
- Department of Pediatrics and Genetics, Makassed Hospital, Al-Quds Medical School, Jerusalem
| | - Nicholas J. Cowan
- Department of Biochemistry & Molecular Pharmacology, NYU Langone Medical Center, New York, NY, USA
| | - Julian Ik-Tsen Heng
- The Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia, Australia
| | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah, Hebrew University Medical Center Jerusalem, Jerusalem, Israel
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11
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Francis JW, Turn RE, Newman LE, Schiavon C, Kahn RA. Higher order signaling: ARL2 as regulator of both mitochondrial fusion and microtubule dynamics allows integration of 2 essential cell functions. Small GTPases 2016; 7:188-196. [PMID: 27400436 PMCID: PMC5129891 DOI: 10.1080/21541248.2016.1211069] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 07/05/2016] [Accepted: 07/06/2016] [Indexed: 10/21/2022] Open
Abstract
ARL2 is among the most highly conserved proteins, predicted to be present in the last eukaryotic common ancestor, and ubiquitously expressed. Genetic screens in multiple model organisms identified ARL2, and its cytosolic binding partner cofactor D (TBCD), as important in tubulin folding and microtubule dynamics. Both ARL2 and TBCD also localize to centrosomes, making it difficult to dissect these effects. A growing body of evidence also has found roles for ARL2 inside mitochondria, as a regulator of mitochondrial fusion. Other studies have revealed roles for ARL2, in concert with its closest paralog ARL3, in the traffic of farnesylated cargos between membranes and specifically to cilia and photoreceptor cells. Details of each of these signaling processes continue to emerge. We summarize those data here and speculate about the potential for cross-talk or coordination of cell regulation, termed higher order signaling, based upon the use of a common GTPase in disparate cell functions.
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Affiliation(s)
- Joshua W. Francis
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Rachel E. Turn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Laura E. Newman
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Cara Schiavon
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Richard A. Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
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12
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Li R, Jin Z, Gao L, Liu P, Yang Z, Zhang D. Effective protein inhibition in intact mouse oocytes through peptide nanoparticle-mediated antibody transfection. PeerJ 2016; 4:e1849. [PMID: 27114861 PMCID: PMC4841238 DOI: 10.7717/peerj.1849] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/06/2016] [Indexed: 11/20/2022] Open
Abstract
Female meiosis is a fundamental area of study in reproductive medicine, and the mouse oocyte model of in vitro maturation (IVM) is most widely used to study female meiosis. To investigate the probable role(s) of an unknown protein in female meiosis, the method traditionally used involves microinjecting a specific antibody into mouse oocytes. Recently, in studies on somatic cells, peptide nanoparticle-mediated antibody transfection has become a popular tool because of its high efficiency, low toxicity, good stability, and strong serum compatibility. However, untill now no researchers have tried using this technique on mouse oocytes because the zona pellucida surrounding the oocyte membrane (vitelline membrane) is usually thought or proved to be a tough barrier to macromolecules such as antibodies and proteins. Therefore, we attempted to introduce an antibody into mouse oocytes using a peptide nanoparticle. Here we show for the first time that with our optimized method, an antibody can be effectively delivered into mouse oocytes and inhibit its target protein with high specificity. We obtained significant results using small GTPase Arl2 as a test subject protein. We propose peptide nanoparticle-mediated antibody transfection to be a superior alternative to antibody microinjection for preliminary functional studies of unknown proteins in mouse oocytes.
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Affiliation(s)
- Ruichao Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University , Nanjing, Jiangsu , China
| | - Zhen Jin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University , Nanjing, Jiangsu , China
| | - Leilei Gao
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University , Nanjing, Jiangsu , China
| | - Peng Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University , Nanjing, Jiangsu , China
| | - Zhixia Yang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University , Nanjing, Jiangsu , China
| | - Dong Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University , Nanjing, Jiangsu , China
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13
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Chen K, Koe CT, Xing ZB, Tian X, Rossi F, Wang C, Tang Q, Zong W, Hong WJ, Taneja R, Yu F, Gonzalez C, Wu C, Endow S, Wang H. Arl2- and Msps-dependent microtubule growth governs asymmetric division. J Cell Biol 2016; 212:661-76. [PMID: 26953351 PMCID: PMC4792071 DOI: 10.1083/jcb.201503047] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 02/10/2016] [Indexed: 12/18/2022] Open
Abstract
Drosophila Arl2 governs neuroblast asymmetric cell division through regulation of microtubule growth and localization of Msps to centrosomes. Asymmetric division of neural stem cells is a fundamental strategy to balance their self-renewal and differentiation. It is long thought that microtubules are not essential for cell polarity in asymmetrically dividing Drosophila melanogaster neuroblasts (NBs; neural stem cells). Here, we show that Drosophila ADP ribosylation factor like-2 (Arl2) and Msps, a known microtubule-binding protein, control cell polarity and spindle orientation of NBs. Upon arl2 RNA intereference, Arl2-GDP expression, or arl2 deletions, microtubule abnormalities and asymmetric division defects were observed. Conversely, overactivation of Arl2 leads to microtubule overgrowth and depletion of NBs. Arl2 regulates microtubule growth and asymmetric division through localizing Msps to the centrosomes in NBs. Moreover, Arl2 regulates dynein function and in turn centrosomal localization of D-TACC and Msps. Arl2 physically associates with tubulin cofactors C, D, and E. Arl2 functions together with tubulin-binding cofactor D to control microtubule growth, Msps localization, and NB self-renewal. Therefore, Arl2- and Msps-dependent microtubule growth is a new paradigm regulating asymmetric division of neural stem cells.
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Affiliation(s)
- Keng Chen
- Neuroscience and Behavioral Disorders Program, Duke-National University of Singapore Graduate Medical School, Singapore 169857 National University of Singapore Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456
| | - Chwee Tat Koe
- Neuroscience and Behavioral Disorders Program, Duke-National University of Singapore Graduate Medical School, Singapore 169857 National University of Singapore Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456
| | - Zhanyuan Benny Xing
- Department of Cell Biology, Duke University, Duke University Medical Center, Durham, NC 27710
| | - Xiaolin Tian
- Neuroscience Center of Excellence, Department of Cell Biology and Anatomy, Louisiana State University Health Sciences Center, New Orleans, LA 70112
| | - Fabrizio Rossi
- Institute for Research in Biomedicine Barcelona, 08028 Barcelona, Spain
| | - Cheng Wang
- Neuroscience and Behavioral Disorders Program, Duke-National University of Singapore Graduate Medical School, Singapore 169857
| | - Quan Tang
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604 Department of Biological Sciences, National University of Singapore, Singapore 117604
| | - Wenhui Zong
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604 Department of Biological Sciences, National University of Singapore, Singapore 117604
| | - Wan Jin Hong
- Institute of Molecular and Cell Biology, Singapore 138673
| | - Reshma Taneja
- National University of Singapore Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456 Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
| | - Fengwei Yu
- Neuroscience and Behavioral Disorders Program, Duke-National University of Singapore Graduate Medical School, Singapore 169857 National University of Singapore Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456 Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604 Department of Biological Sciences, National University of Singapore, Singapore 117604
| | - Cayetano Gonzalez
- Institute for Research in Biomedicine Barcelona, 08028 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Chunlai Wu
- Neuroscience Center of Excellence, Department of Cell Biology and Anatomy, Louisiana State University Health Sciences Center, New Orleans, LA 70112
| | - Sharyn Endow
- Neuroscience and Behavioral Disorders Program, Duke-National University of Singapore Graduate Medical School, Singapore 169857 Department of Cell Biology, Duke University, Duke University Medical Center, Durham, NC 27710
| | - Hongyan Wang
- Neuroscience and Behavioral Disorders Program, Duke-National University of Singapore Graduate Medical School, Singapore 169857 National University of Singapore Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456 Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
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14
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Abstract
Protein phosphatase 2A (PP2A) plays a critical multi-faceted role in the regulation of the cell cycle. It is known to dephosphorylate over 300 substrates involved in the cell cycle, regulating almost all major pathways and cell cycle checkpoints. PP2A is involved in such diverse processes by the formation of structurally distinct families of holoenzymes, which are regulated spatially and temporally by specific regulators. Here, we review the involvement of PP2A in the regulation of three cell signaling pathways: wnt, mTOR and MAP kinase, as well as the G1→S transition, DNA synthesis and mitotic initiation. These processes are all crucial for proper cell survival and proliferation and are often deregulated in cancer and other diseases.
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Affiliation(s)
- Nathan Wlodarchak
- a McArdle Laboratory for Cancer Research, University of Wisconsin-Madison , Madison , WI , USA
| | - Yongna Xing
- a McArdle Laboratory for Cancer Research, University of Wisconsin-Madison , Madison , WI , USA
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15
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The Function of Arf-like Proteins ARL2 and ARL3 in Photoreceptors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 854:655-61. [PMID: 26427472 DOI: 10.1007/978-3-319-17121-0_87] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Arf-like proteins (ARLs) are ubiquitously expressed small G proteins of the RAS superfamily. In photoreceptors, ARL2 and ARL3 participate in the trafficking of lipidated membrane-associated proteins and colocalize in the inner segment with UNC119A and PDEδ. UNC119A and PDEδ are acyl- and prenyl-binding proteins, respectively, involved in trafficking of acylated (transducin-α subunit, nephrocystin NPHP3) and prenylated proteins (GRK1, PDE6). Germline Arl3 knockout mice do not survive beyond postnatal day 21 and display ciliary defects in multiple organs (kidney, liver and pancreas) as well as retinal degeneration. Conditional knockouts will be necessary to delineate mechanisms of protein transport in retina disease.
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16
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Lokaj M, Kösling SK, Koerner C, Lange SM, van Beersum SEC, van Reeuwijk J, Roepman R, Horn N, Ueffing M, Boldt K, Wittinghofer A. The Interaction of CCDC104/BARTL1 with Arl3 and Implications for Ciliary Function. Structure 2015; 23:2122-32. [PMID: 26455799 PMCID: PMC4635315 DOI: 10.1016/j.str.2015.08.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/26/2015] [Accepted: 08/29/2015] [Indexed: 01/23/2023]
Abstract
Cilia are small antenna-like cellular protrusions critical for many developmental signaling pathways. The ciliary protein Arl3 has been shown to act as a specific release factor for myristoylated and farnesylated ciliary cargo molecules by binding to the effectors Unc119 and PDE6δ. Here we describe a newly identified Arl3 binding partner, CCDC104/CFAP36. Biochemical and structural analyses reveal that the protein contains a BART-like domain and is called BARTL1. It recognizes an LLxILxxL motif at the N-terminal amphipathic helix of Arl3, which is crucial for the interaction with the BART-like domain but also for the ciliary localization of Arl3 itself. These results seem to suggest a ciliary role of BARTL1, and possibly link it to the Arl3 transport network. We thus speculate on a regulatory mechanism whereby BARTL1 aids the presentation of active Arl3 to its GTPase-activating protein RP2 or hinders Arl3 membrane binding in the area of the transition zone.
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Affiliation(s)
- Mandy Lokaj
- Max-Planck-Institute of Molecular Physiology, Emeritus Group, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Stefanie K Kösling
- Max-Planck-Institute of Molecular Physiology, Emeritus Group, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Carolin Koerner
- Max-Planck-Institute of Molecular Physiology, Emeritus Group, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Sven M Lange
- Max-Planck-Institute of Molecular Physiology, Emeritus Group, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Sylvia E C van Beersum
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Jeroen van Reeuwijk
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Ronald Roepman
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Nicola Horn
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tübingen, Nägelestrasse 5, 72074 Tübingen, Germany
| | - Marius Ueffing
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tübingen, Nägelestrasse 5, 72074 Tübingen, Germany
| | - Karsten Boldt
- Medical Proteome Center, Institute for Ophthalmic Research, University of Tübingen, Nägelestrasse 5, 72074 Tübingen, Germany
| | - Alfred Wittinghofer
- Max-Planck-Institute of Molecular Physiology, Emeritus Group, Otto-Hahn-Straße 15, 44227 Dortmund, Germany.
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17
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Gonçalves J, Tavares A, Carvalhal S, Soares H. Revisiting the tubulin folding pathway: new roles in centrosomes and cilia. Biomol Concepts 2015; 1:423-34. [PMID: 25962015 DOI: 10.1515/bmc.2010.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Centrosomes and cilia are critical eukaryotic organelles which have been in the spotlight in recent years given their implication in a myriad of cellular and developmental processes. Despite their recognized importance and intense study, there are still many open questions about their biogenesis and function. In the present article, we review the existing data concerning members of the tubulin folding pathway and related proteins, which have been identified at centrosomes and cilia and were shown to have unexpected roles in these structures.
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18
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Newman LE, Zhou CJ, Mudigonda S, Mattheyses AL, Paradies E, Marobbio CMT, Kahn RA. The ARL2 GTPase is required for mitochondrial morphology, motility, and maintenance of ATP levels. PLoS One 2014; 9:e99270. [PMID: 24911211 PMCID: PMC4050054 DOI: 10.1371/journal.pone.0099270] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/13/2014] [Indexed: 02/06/2023] Open
Abstract
ARF-like 2 (ARL2) is a member of the ARF family and RAS superfamily of regulatory GTPases, predicted to be present in the last eukaryotic common ancestor, and essential in a number of model genetic systems. Though best studied as a regulator of tubulin folding, we previously demonstrated that ARL2 partially localizes to mitochondria. Here, we show that ARL2 is essential to a number of mitochondrial functions, including mitochondrial morphology, motility, and maintenance of ATP levels. We compare phenotypes resulting from ARL2 depletion and expression of dominant negative mutants and use these to demonstrate that the mitochondrial roles of ARL2 are distinct from its roles in tubulin folding. Testing of current models for ARL2 actions at mitochondria failed to support them. Rather, we found that knockdown of the ARL2 GTPase activating protein (GAP) ELMOD2 phenocopies two of three phenotypes of ARL2 siRNA, making it a likely effector for these actions. These results add new layers of complexity to ARL2 signaling, highlighting the need to deconvolve these different cell functions. We hypothesize that ARL2 plays essential roles inside mitochondria along with other cellular functions, at least in part to provide coupling of regulation between these essential cell processes.
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Affiliation(s)
- Laura E. Newman
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Cheng-jing Zhou
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Samatha Mudigonda
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Alexa L. Mattheyses
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Eleonora Paradies
- Consiglio Nazionale delle Ricerche Institute of Biomembranes and Bioenergetics, Bari, Italy
| | | | - Richard A. Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
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19
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Ivanova AA, East MP, Yi SL, Kahn RA. Characterization of recombinant ELMOD (cell engulfment and motility domain) proteins as GTPase-activating proteins (GAPs) for ARF family GTPases. J Biol Chem 2014; 289:11111-11121. [PMID: 24616099 PMCID: PMC4036250 DOI: 10.1074/jbc.m114.548529] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/05/2014] [Indexed: 11/06/2022] Open
Abstract
The ARF family of regulatory GTPases, within the RAS superfamily, is composed of ~30 members in mammals, including up to six ARF and at least 18 ARF-like (ARL) proteins. They exhibit significant structural and biochemical conservation and regulate a variety of essential cellular processes, including membrane traffic, cell division, and energy metabolism; each with links to human diseases. We previously identified members of the ELMOD family as GTPase-activating proteins (GAPs) for ARL2 that displayed crossover activity for ARFs as well. To further characterize the GAP activities of the three human ELMODs as GAPs we developed new preparations of each after overexpression in human embryonic kidney (HEK293T) cells. This allowed much higher specific activities and enhanced stability and solubility of the purified proteins. The specificities of ELMOD1-3 as GAPs for six different members of the ARF family were determined and found to display wide variations, which we believe will reveal differences in cellular functions of family members. The non-opioid sigma-1 receptor (S1R) was identified as a novel effector of GAP activity of ELMOD1-3 proteins as its direct binding to either ELMOD1 or ELMOD2 resulted in loss of GAP activity. These findings are critical to understand the roles of ELMOD proteins in cell signaling in general and in the inner ear specifically, and open the door to exploration of the regulation of their GAP activities via agonists or antagonists of the S1R.
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Affiliation(s)
- Anna A Ivanova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Michael P East
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Slee L Yi
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322.
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20
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Abstract
The ARF-like (ARL) proteins, within the ARF family, are a collection of functionally diverse GTPases that share extensive (>40 %) identity with the ARFs and each other and are assumed to share basic mechanisms of regulation and a very incompletely documented degree of overlapping regulators. At least four ARLs were already present in the last eukaryotic common ancestor, along with one ARF, and these have been expanded to >20 members in mammals. We know little about the majority of these proteins so our review will focus on those about which the most is known, including ARL1, ARL2, ARL3, ARL4s, ARL6, ARL13s, and ARFRP1. From this fragmentary information we extract some generalizations and conclusions regarding the sources and extent of specificity and functions of the ARLs.
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Affiliation(s)
- Alfred Wittinghofer
- Max-Planck-Institute of Molecular Physiology, Dortmund, Nordrhein-Westfalen Germany
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21
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MicroRNA-195 targets ADP-ribosylation factor-like protein 2 to induce apoptosis in human embryonic stem cell-derived neural progenitor cells. Cell Death Dis 2013; 4:e695. [PMID: 23807224 PMCID: PMC3702293 DOI: 10.1038/cddis.2013.195] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Neural progenitor cells (NPCs) derived from human embryonic stem cells (hESCs) have great potential in cell therapy, drug screening and toxicity testing of neural degenerative diseases. However, the molecular regulation of their proliferation and apoptosis, which needs to be revealed before clinical application, is largely unknown. MicroRNA miR-195 is known to be expressed in the brain and is involved in a variety of proapoptosis or antiapoptosis processes in cancer cells. Here, we defined the proapoptotic role of miR-195 in NPCs derived from two independent hESC lines (human embryonic stem cell-derived neural progenitor cells, hESC-NPCs). Overexpression of miR-195 in hESC-NPCs induced extensive apoptotic cell death. Consistently, global transcriptional microarray analyses indicated that miR-195 primarily regulated genes associated with apoptosis in hESC-NPCs. Mechanistically, a small GTP-binding protein ADP-ribosylation factor-like protein 2 (ARL2) was identified as a direct target of miR-195. Silencing ARL2 in hESC-NPCs provoked an apoptotic phenotype resembling that of miR-195 overexpression, revealing for the first time an essential role of ARL2 for the survival of human NPCs. Moreover, forced expression of ALR2 could abolish the cell number reduction caused by miR-195 overexpression. Interestingly, we found that paraquat, a neurotoxin, not only induced apoptosis but also increased miR-195 and reduced ARL2 expression in hESC-NPCs, indicating the possible involvement of miR-195 and ARL2 in neurotoxin-induced NPC apoptosis. Notably, inhibition of miR-195 family members could block neurotoxin-induced NPC apoptosis. Collectively, miR-195 regulates cell apoptosis in a context-dependent manner through directly targeting ARL2. The finding of the critical role of ARL2 for the survival of human NPCs and association of miR-195 and ARL2 with neurotoxin-induced apoptosis have important implications for understanding molecular mechanisms that control NPC survival and would facilitate our manipulation of the neurological pathogenesis.
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22
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Mori R, Toda T. The dual role of fission yeast Tbc1/cofactor C orchestrates microtubule homeostasis in tubulin folding and acts as a GAP for GTPase Alp41/Arl2. Mol Biol Cell 2013; 24:1713-24, S1-8. [PMID: 23576550 PMCID: PMC3667724 DOI: 10.1091/mbc.e12-11-0792] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 02/22/2013] [Accepted: 03/29/2013] [Indexed: 11/11/2022] Open
Abstract
Supplying the appropriate amount of correctly folded α/β-tubulin heterodimers is critical for microtubule dynamics. Formation of assembly-competent heterodimers is remarkably elaborate at the molecular level, in which the α- and β-tubulins are separately processed in a chaperone-dependent manner. This sequential step is performed by the tubulin-folding cofactor pathway, comprising a specific set of regulatory proteins: cofactors A-E. We identified the fission yeast cofactor: the orthologue of cofactor C, Tbc1. In addition to its roles in tubulin folding, Tbc1 acts as a GAP in regulating Alp41/Arl2, a highly conserved small GTPase. Of interest, the expression of GDP- or GTP-bound Alp41 showed the identical microtubule loss phenotype, suggesting that continuous cycling between these forms is important for its functions. In addition, we found that Alp41 interacts with Alp1(D), the orthologue of cofactor D, specifically when in the GDP-bound form. Intriguingly, Alp1(D) colocalizes with microtubules when in excess, eventually leading to depolymerization, which is sequestered by co-overproducing GDP-bound Alp41. We present a model of the final stages of the tubulin cofactor pathway that includes a dual role for both Tbc1 and Alp1(D) in opposing regulation of the microtubule.
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Affiliation(s)
- Risa Mori
- Cell Regulation Laboratory, Cancer Research UK, London Research Institute, Lincoln's Inn Fields Laboratories, London WC2A 3LY, United Kingdom
| | - Takashi Toda
- Cell Regulation Laboratory, Cancer Research UK, London Research Institute, Lincoln's Inn Fields Laboratories, London WC2A 3LY, United Kingdom
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23
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Price HP, Hodgkinson MR, Wright MH, Tate EW, Smith BA, Carrington M, Stark M, Smith DF. A role for the vesicle-associated tubulin binding protein ARL6 (BBS3) in flagellum extension in Trypanosoma brucei. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1823:1178-91. [PMID: 22609302 PMCID: PMC3793860 DOI: 10.1016/j.bbamcr.2012.05.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 04/23/2012] [Accepted: 05/05/2012] [Indexed: 11/17/2022]
Abstract
The small GTPase Arl6 is implicated in the ciliopathic human genetic disorder Bardet-Biedl syndrome, acting at primary cilia in recruitment of the octomeric BBSome complex, which is required for specific trafficking events to and from the cilium in eukaryotes. Here we describe functional characterisation of Arl6 in the flagellated model eukaryote Trypanosoma brucei, which requires motility for viability. Unlike human Arl6 which has a ciliary localisation, TbARL6 is associated with electron-dense vesicles throughout the cell body following co-translational modification by N-myristoylation. Similar to the related protein ARL-3A in T. brucei, modulation of expression of ARL6 by RNA interference does not prevent motility but causes a significant reduction in flagellum length. Tubulin is identified as an ARL6 interacting partner, suggesting that ARL6 may act as an anchor between vesicles and cytoplasmic microtubules. We provide evidence that the interaction between ARL6 and the BBSome is conserved in unicellular eukaryotes. Overexpression of BBS1 leads to translocation of endogenous ARL6 to the site of exogenous BBS1 at the flagellar pocket. Furthermore, a combination of BBS1 overexpression and ARL6 RNAi has a synergistic inhibitory effect on cell growth. Our findings indicate that ARL6 in trypanosomes contributes to flagellum biogenesis, most likely through an interaction with the BBSome.
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Key Words
- arf, adp-ribosylation factor
- arl, adp-ribosylation factor-like
- arl6ip, arl6 interacting protein
- bbs, bardet–biedl syndrome
- bbs1, bardet–biedl syndrome 1 protein
- bsf, bloodstream form
- cona, concanavalin a
- gef, guanine nucleotide exchange factor
- gpcr, g-protein coupled receptor
- hrg4, human retinal gene 4
- ift, intraflagellar transport
- itc, isothermal titration calorimetry
- mant, n-methylanthraniloyl
- map2, microtubule associated protein 2
- nes, nuclear export signal
- nls, nuclear localisation signal
- nmt, myristoyl-coa:protein n-myristoyltransferase
- pcf, procyclic form
- pcm1, pericentriolar material 1
- pfr, paraflagellar rod
- pm, plasma membrane
- rnai, rna interference
- rp2, retinitis pigmentosa protein 2
- tap, tandem affinity purification
- tiem, transmission immuno-electron microscopy
- trypanosoma brucei
- arl6
- bbsome
- bbs1
- flagellum
- tubulin
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Affiliation(s)
- Helen P Price
- Centre for Immunology and Infection, Department of Biology, University of York, Heslington, York YO10 5YW, UK.
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24
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Tian G, Thomas S, Cowan NJ. Effect of TBCD and its regulatory interactor Arl2 on tubulin and microtubule integrity. Cytoskeleton (Hoboken) 2011; 67:706-14. [PMID: 20740604 DOI: 10.1002/cm.20480] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Assembly of the α/β tubulin heterodimer requires the participation of a series of chaperone proteins (TBCA-E) that function downstream of the cytosolic chaperonin (CCT) as a heterodimer assembly machine. TBCD and TBCE are also capable of acting in a reverse reaction in which they disrupt native heterodimers. Homologs of TBCA-E exist in all eukaryotes, and the amino acid sequences of α- and β-tubulin isotypes are rigidly conserved among vertebrates. However, the efficiency with which TBCD effects tubulin disruption in vivo depends on its origin: bovine (but not human) TBCD efficiently destroys tubulin and microtubules upon overexpression in cultured cells. Here we show that recombinant bovine TBCD is produced in HeLa cells as a stoichiometric cocomplex with β-tubulin, consistent with its behavior in vitro and in vivo. In contrast, expression of human TBCD using the same host/vector system results in the generation of TBCD that is not complexed with β-tubulin. We show that recombinant human TBCD functions indistinguishably from its nonrecombinant bovine counterpart in in vitro CCT-driven folding reactions, in tubulin disruption reactions, and in tubulin GTPase activating protein assays in which TBCD and TBCC stimulate GTP hydrolysis by β-tubulin at a heterodimer concentration far below that required for polymerization into microtubules. We conclude that bovine and human TBCD have functionally identical roles in de novo tubulin heterodimer assembly, and show that the inability of human TBCD to disrupt microtubule integrity upon overexpression in vivo can be overcome by siRNA-mediated suppression of expression of the TBCD regulator Arl2 (ADP ribosylation factor-like protein).
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Affiliation(s)
- Guoling Tian
- Department of Biochemistry, NYU Langone Medical Center, 550 First Avenue, New York, New York 10016, USA
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25
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Wang K, Li P, Dong Y, Cai X, Hou D, Guo J, Yin Y, Zhang Y, Li J, Liang H, Yu B, Chen J, Zen K, Zhang J, Zhang CY, Chen X. A microarray-based approach identifies ADP ribosylation factor-like protein 2 as a target of microRNA-16. J Biol Chem 2011; 286:9468-76. [PMID: 21199864 DOI: 10.1074/jbc.m110.178335] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
microRNAs (miRNAs) are generally thought to negatively regulate the expression of their target genes by mRNA degradation or by translation repression. Here we show an efficient way to identify miRNA target genes by screening alterations in global mRNA levels following changes in miRNA levels. In this study, we used mRNA microarrays to measure global mRNA expression in three cell lines with increased or decreased levels of miR-16 and performed bioinformatics analysis based on multiple target prediction algorithms. For further investigation among the predicted miR-16 target genes, we selected genes that show an expression pattern opposite to that of miR-16. One of the candidate target genes that may interact with miR-16, ADP-ribosylation factor-like protein 2 (ARL2), was further investigated. First, ARL2 was deduced to be an ideal miR-16 target by computational predictions. Second, ARL2 mRNA and protein levels were significantly abolished by treatment with miR-16 precursors, whereas a miR-16 inhibitor increased ARL2 mRNA and protein levels. Third, a luciferase reporter assay confirmed that miR-16 directly recognizes the 3'-untranslated region (3'-UTR) of ARL2. Finally, we showed that miR-16 could regulate proliferation and induce a significant G0/G1 cell cycle arrest, which was due at least in part, to the down-regulation of ARL2. In summary, the present study suggests that integrating global mRNA profiling and bioinformatics tools may provide the basis for further investigation of the potential targets of a given miRNA. These results also illustrate a novel function of miR-16 targeting ARL2 in modulating proliferation and cell cycle progression.
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Affiliation(s)
- Kehui Wang
- Jiangsu Diabetes Center, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210093, China
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26
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Abstract
The Arf-like (Arl) small GTPases have a diverse range of functions in the eukaryotic cell. Metazoan Arl2 acts as a regulator of microtubule biogenesis, binding to the tubulin-specific chaperone cofactor D. Arl2 also has a mitochondrial function through its interactions with BART and ANT-1, the only member of the Ras superfamily to be found in this organelle to date. In the present study, we describe characterization of the Arl2 orthologue in the protozoan parasite Trypanosoma brucei. Modulation of TbARL2 expression in bloodstream form parasites by RNA interference (RNAi) causes inhibition of cleavage furrow formation, resulting in a severe defect in cytokinesis and the accumulation of multinucleated cells. RNAi of TbARL2 also results in loss of acetylated alpha-tubulin but not of total -tubulin from cellular microtubules. While overexpression of TbARL2(myc) also leads to a defect in cytokinesis, an excess of untagged protein has no effect on cell division, demonstrating the importance of the extreme C-terminus in correct function. TbARL2 overexpressing cells (either myc-tagged or untagged) have an increase in acetylated -tubulin. Our data indicate that Arl2 has a fundamentally conserved role in trypanosome microtubule biogenesis that correlates with -tubulin acetylation.
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27
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Beghin A, Belin S, Sleiman RH, Brunet Manquat S, Goddard S, Tabone E, Jordheim LP, Treilleux I, Poupon MF, Diaz JJ, Dumontet C. ADP ribosylation factor like 2 (Arl2) regulates breast tumor aggressivity in immunodeficient mice. PLoS One 2009; 4:e7478. [PMID: 19829707 PMCID: PMC2759505 DOI: 10.1371/journal.pone.0007478] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Accepted: 09/02/2009] [Indexed: 11/19/2022] Open
Abstract
We have previously reported that ADP ribosylation factor like 2 (Arl2), a small GTPase, content influences microtubule dynamics and cell cycle distribution in breast tumor cells, as well as the degree and distribution of phosphorylated P53. Here we show, in two different human breast adenocarcinoma models, that Arl2 content has a major impact on breast tumor cell aggressivity both in vitro and in vivo. Cells with reduced content of Arl2 displayed reduced contact inhibition, increased clonogenic or cluster formation as well as a proliferative advantage over control cells in an in vitro competition assay. These cells also caused larger tumors in SCID mice, a phenotype which was mimicked by the in vivo administration of siRNA directed against Arl2. Cells with increased Arl2 content displayed reduced aggressivity, both in vitro and in vivo, with enhanced necrosis and were also found to contain increased PP2A phosphatase activity. A rt-PCR analysis of fresh human tumor breast samples suggested that low Arl2 expression was associated with larger tumor size and greater risk of lymph node involvement at diagnosis. These data underline the role of Arl2, a small GTPase, as an important regulator of breast tumor cell aggressivity, both in vitro and in vivo.
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Affiliation(s)
- Anne Beghin
- Inserm, U590, Lyon, France
- Université Lyon 1, ISPB, Lyon, France
| | - Stéphane Belin
- CNRS, Centre de Génétique Moléculaire et Cellulaire, UMR 5534, Villeurbanne, France
| | | | | | - Sophie Goddard
- Centre Léon Bérard, Service Anatomie-Cytologie Pathologiques, Lyon, France
| | - Eric Tabone
- Centre Léon Bérard, Service Anatomie-Cytologie Pathologiques, Lyon, France
| | | | - Isabelle Treilleux
- Centre Léon Bérard, Service Anatomie-Cytologie Pathologiques, Lyon, France
| | | | - Jean-Jacques Diaz
- CNRS, Centre de Génétique Moléculaire et Cellulaire, UMR 5534, Villeurbanne, France
| | - Charles Dumontet
- Inserm, U590, Lyon, France
- Université Lyon 1, ISPB, Lyon, France
- * E-mail:
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28
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Zhang T, Li S, Zhang Y, Zhong C, Lai Z, Ding J. Crystal structure of the ARL2-GTP-BART complex reveals a novel recognition and binding mode of small GTPase with effector. Structure 2009; 17:602-10. [PMID: 19368893 DOI: 10.1016/j.str.2009.01.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 01/02/2009] [Accepted: 01/16/2009] [Indexed: 11/17/2022]
Abstract
ARL2 is a member of the ADP-ribosylation factor family but has unique biochemical features. BART is an effector of ARL2 that is essential for nuclear retention of STAT3 and may also be involved in mitochondria transport and apoptosis. Here we report the crystal structure and biochemical characterization of human ARL2-GTP-BART complex. ARL2-GTP assumes a typical small GTPase fold with a unique N-terminal alpha helix conformation. BART consists of a six alpha helix bundle. The interactions between ARL2 and BART involve two interfaces: a conserved N-terminal LLXIL motif of ARL2 is embedded in a hydrophobic cleft of BART and the switch regions of ARL2 interact with helix alpha3 of BART. Both interfaces are essential for the binding as verified by mutagenesis study. This novel recognition and binding mode is different from that of other small GTPase-effector interactions and provides molecular basis for the high specificity of ARL2 for BART.
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Affiliation(s)
- Tianlong Zhang
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Shanghai 200031, China
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29
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Bailey LK, Campbell LJ, Evetts KA, Littlefield K, Rajendra E, Nietlispach D, Owen D, Mott HR. The structure of binder of Arl2 (BART) reveals a novel G protein binding domain: implications for function. J Biol Chem 2008; 284:992-9. [PMID: 18981177 DOI: 10.1074/jbc.m806167200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ADP-ribosylation factor-like (Arl) family of small G proteins are involved in the regulation of diverse cellular processes. Arl2 does not appear to be membrane localized and has been implicated as a regulator of microtubule dynamics. The downstream effector for Arl2, Binder of Arl 2 (BART) has no known function but, together with Arl2, can enter mitochondria and bind the adenine nucleotide transporter. We have solved the solution structure of BART and show that it forms a novel fold composed of six alpha-helices that form three interlocking "L" shapes. Analysis of the backbone dynamics reveals that the protein is highly anisotropic and that the loops between the central helices are dynamic. The regions involved in the binding of Arl2 were mapped onto the surface of BART and are found to localize to these loop regions. BART has faces of differing charge and structural elements, which may explain how it can interact with other proteins.
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Affiliation(s)
- Laura K Bailey
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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30
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Eichhorn PJA, Creyghton MP, Bernards R. Protein phosphatase 2A regulatory subunits and cancer. Biochim Biophys Acta Rev Cancer 2008; 1795:1-15. [PMID: 18588945 DOI: 10.1016/j.bbcan.2008.05.005] [Citation(s) in RCA: 273] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Revised: 05/20/2008] [Accepted: 05/21/2008] [Indexed: 01/06/2023]
Abstract
The serine/threonine protein phosphatase (PP2A) is a trimeric holoenzyme that plays an integral role in the regulation of a number of major signaling pathways whose deregulation can contribute to cancer. The specificity and activity of PP2A are highly regulated through the interaction of a family of regulatory B subunits with the substrates. Accumulating evidence indicates that PP2A acts as a tumor suppressor. In this review we summarize the known effects of specific PP2A holoenzymes and their roles in cancer relevant pathways. In particular we highlight PP2A function in the regulation of MAPK and Wnt signaling.
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Affiliation(s)
- Pieter J A Eichhorn
- Division of Molecular Carcinogenesis, Center for Cancer Genomics and Center for Biomedical Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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31
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Kosmaoglou M, Schwarz N, Bett JS, Cheetham ME. Molecular chaperones and photoreceptor function. Prog Retin Eye Res 2008; 27:434-49. [PMID: 18490186 PMCID: PMC2568879 DOI: 10.1016/j.preteyeres.2008.03.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Molecular chaperones facilitate and regulate protein conformational
change within cells. This encompasses many fundamental cellular processes:
including the correct folding of nascent chains; protein transport and
translocation; signal transduction and protein quality control. Chaperones are,
therefore, important in several forms of human disease, including
neurodegeneration. Within the retina, the highly specialized photoreceptor cell
presents a fascinating paradigm to investigate the specialization of molecular
chaperone function and reveals unique chaperone requirements essential to
photoreceptor function. Mutations in several photoreceptor proteins lead to
protein misfolding mediated neurodegeneration. The best characterized of these
are mutations in the molecular light sensor, rhodopsin, which cause autosomal
dominant retinitis pigmentosa. Rhodopsin biogenesis is likely to require
chaperones, while rhodopsin misfolding involves molecular chaperones in quality
control and the cellular response to protein aggregation. Furthermore, the
specialization of components of the chaperone machinery to photoreceptor
specific roles has been revealed by the identification of mutations in molecular
chaperones that cause inherited retinal dysfunction and degeneration. These
chaperones are involved in several important cellular pathways and further
illuminate the essential and diverse roles of molecular
chaperones.
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Affiliation(s)
- Maria Kosmaoglou
- Division of Molecular and Cellular Neuroscience, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1 V 9EL, UK
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32
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Cunningham LA, Kahn RA. Cofactor D functions as a centrosomal protein and is required for the recruitment of the gamma-tubulin ring complex at centrosomes and organization of the mitotic spindle. J Biol Chem 2008; 283:7155-65. [PMID: 18171676 DOI: 10.1074/jbc.m706753200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microtubules are highly dynamic structures, composed of alpha/beta-tubulin heterodimers. Biosynthesis of the functional dimer involves the participation of several chaperones, termed cofactors A-E, that act on folding intermediates downstream of the cytosolic chaperonin CCT (1, 2). We show that cofactor D is also a centrosomal protein and that overexpression of either the full-length protein or either of two centrosome localization domains leads to the loss of anchoring of the gamma-tubulin ring complex and of nucleation of microtubule growth at centrosomes. In contrast, depletion of cofactor D by short interfering RNA results in mitotic spindle defects. Because none of these changes in cofactor D activity produced a change in the levels of alpha-or beta-tubulin, we conclude that these newly discovered functions for cofactor D are distinct from its previously described role in tubulin folding. Thus, we describe a new role for cofactor D at centrosomes that is important to its function in polymerization of tubulin and organization of the mitotic spindle.
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Affiliation(s)
- Leslie A Cunningham
- Department of Biochemistry and the Biochemistry, Cell, and Developmental Biology Program, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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33
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Prigione A, Cortopassi G. Mitochondrial DNA deletions induce the adenosine monophosphate-activated protein kinase energy stress pathway and result in decreased secretion of some proteins. Aging Cell 2007; 6:619-30. [PMID: 17651460 DOI: 10.1111/j.1474-9726.2007.00323.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial DNA (mtDNA) deletions occur sporadically in zygotic and somatic tissues and reach their highest concentration in substantia nigra. Previously, we noted the increase of the adenosine monophosphate (AMP)-activated protein kinase (AMPK) transcript by microarray in multiple cells and tissues bearing deletions. In this work, we demonstrate that the induction of AMPK transcript is dependent on deletions by quantitative polymerase chain reaction, and also demonstrate a deficiency in adenosine triphosphate (ATP) synthesis in the same cells. Consistent with AMPK induction, its known targets SREBF1 (sterol regulatory element binding protein-1) and ATG12 were inhibited and induced, respectively. AMPK induction is known to decrease secretory processes in some cells, and the secretion of both osteoprotegerin (OPG) and fibronectin (FN) proteins to the extracellular space was significantly deficient. Deletions caused a defect in the adenosine diphosphate (ADP)-ribosylation factor-like 2 (ARL2) transcript, which is known to be important in secretion and interacts with protein phosphatase 2A (PP2A) and thus AMPK. The deletion-dependent dysfunctions occurred even in cells bearing less than 30% deletions, suggesting that the concept of a high biological 'threshold' for deletions should be further revised downward. The defects in ATP synthesis, induction of the AMPK and SREBF1 transcripts, and decreased expression of ARL2 and secretion of OPG and FN were recapitulated by low doses of rotenone, demonstrating that they were a specific consequence of electron transport chain inhibition. Thus, mtDNA deletions result in cellular energy depletion, which causes the induction of AMPK and its regulated targets, and inhibit secretion of some proteins. We integrate these observations into a pathophysiological model for how mitochondrial deletions cause disease.
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Affiliation(s)
- Alessandro Prigione
- Department of Neuroscience and Biomedical Technologies, University of Milan-Bicocca, Monza, Italy
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34
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Shultz T, Shmuel M, Hyman T, Altschuler Y. Beta-tubulin cofactor D and ARL2 take part in apical junctional complex disassembly and abrogate epithelial structure. FASEB J 2007; 22:168-82. [PMID: 17704193 DOI: 10.1096/fj.06-7786com] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In epithelial cells, the apical junctional complex (AJC), composed of tight junctions (TJs) and adherens junctions (AJs), maintains cell-surface polarity by forming a fence that prevents lateral movement and diffusion of proteins and lipids between the apical and basolateral PM and holds the epithelial monolayer intact through cell-cell contacts. Disassembly of this complex is a prime event in development and cell transformation. Maintenance of the AJC has been shown to involve mainly the actin cytoskeleton. Recent findings also point to the involvement of the microtubule (MT) system. Here we show the first evidence that in polarized epithelial MDCK cells, ARF-like protein 2 (ARL2) and beta-tubulin cofactor D, known to be involved in MT dynamics, have a role in disassembly of the AJC followed by cell dissociation from the epithelial monolayer, which is not dependent on MT depolymerization. In addition, we show that beta-tubulin cofactor D is partially localized to the lateral PM through its 15 C-terminal amino acids and intact MTs. ARL2 inhibited beta-tubulin cofactor D-dependent cell dissociation from the monolayer and AJC disassembly. To our knowledge, this is the first evidence that beta-tubulin cofactor D plays a role in cells independent of its presumed role in folding tubulin heterodimers. We conclude that ARL2 and beta-tubulin cofactor D participate in AJC disassembly and epithelial depolarization.
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Affiliation(s)
- Tamar Shultz
- Department of Pharmacology, School of Pharmacy, Faculty of Medicine, Hebrew University of Jerusalem, Israel
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35
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Bowzard JB, Cheng D, Peng J, Kahn RA. ELMOD2 is an Arl2 GTPase-activating protein that also acts on Arfs. J Biol Chem 2007; 282:17568-80. [PMID: 17452337 DOI: 10.1074/jbc.m701347200] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Regulatory GTPases in the Ras superfamily employ a cycle of alternating GTP binding and hydrolysis, controlled by guanine nucleotide exchange factors and GTPase-activating proteins (GAPs), as essential features of their actions in cells. Studies of these GAPs and guanine nucleotide exchange factors have provided important insights into our understanding of GTPase signaling and biology. Within the Ras superfamily, the Arf family is composed of 30 members in mammals, including 22 Arf-like (Arl) proteins. Much less is known about the mechanisms of cell regulation by Arls than by Arfs. We report the purification from bovine testis of an Arl2 GAP and its identity as ELMOD2, a protein with no previously described function. ELMOD2 is one of six human proteins that contain an ELMO domain, and a second member, ELMOD1, was also found to have Arl2 GAP activity. Surprisingly, ELMOD2 also exhibited GAP activity against Arf proteins even though it does not contain the canonical Arf GAP sequence signature. The broader specificity of ELMOD2, as well as the previously described role for ELMO1 and ELMO2 in linking Arf6 and Rac1 signaling, suggests that ELMO family members may play a more general role in integrating signaling pathways controlled by Arls and other GTPases.
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Affiliation(s)
- J Bradford Bowzard
- Department of Biochemistry, Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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36
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Beghin A, Honore S, Messana C, Matera EL, Aim J, Burlinchon S, Braguer D, Dumontet C. ADP ribosylation factor like 2 (Arl2) protein influences microtubule dynamics in breast cancer cells. Exp Cell Res 2006; 313:473-85. [PMID: 17188265 DOI: 10.1016/j.yexcr.2006.10.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 10/16/2006] [Accepted: 10/24/2006] [Indexed: 11/22/2022]
Abstract
ADP ribosylation factor like 2 (Arl2) protein is involved in the folding of tubulin peptides. Variants of the human adenocarcinoma line MCF7 cells with increased or reduced content of Arl2 protein were produced and characterized. Western blot analysis performed after separation of the different fractions of tubulins showed that the content in polymerizable soluble heterodimers was significantly increased in cells with the highest Arl2 expression level (MA+) and reduced in cells with the lowest Arl2 expression level (MA-) in comparison to control cells (MP). Microtubule dynamic instability, measured after microinjection of rhodamine-labelled tubulin in living cells, was significantly enhanced in MA+ cells and reduced in MA- cells. These alterations involved modifications of the microtubule growth and shortening rates, duration of attenuation phases, percentage of time spent in each phase (growth, shortening and attenuation) and catastrophe frequency. We also observed modifications in the expression level of the tumor suppressor protein phosphatase 2Ac, which has been shown to form a complex with Arl2. Finally, cell cycle progression was modified in these cells, particularly in regard to duration of telophase. In summary, alterations in Arl2 protein content were found to be associated with modifications in tubulin pools, microtubule dynamics as well as cell cycle progression.
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Affiliation(s)
- Anne Beghin
- Laboratoire de Cytologie Analytique, UMR INSERM 590; Université de Lyon FR69008, Lyon, France.
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37
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Fedyanina OS, Mardanov PV, Tokareva EM, McIntosh JR, Grishchuk EL. Chromosome segregation in fission yeast with mutations in the tubulin folding cofactor D. Curr Genet 2006; 50:281-94. [PMID: 17004072 DOI: 10.1007/s00294-006-0095-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2006] [Revised: 07/19/2006] [Accepted: 07/19/2006] [Indexed: 10/24/2022]
Abstract
Faithful chromosome segregation requires the combined activities of the microtubule-based mitotic spindle and the multiple proteins that form mitotic kinetochores. Here, we show that the fission yeast mitotic mutant, tsm1-512, is an allele of the tubulin folding chaperone, cofactor D. Chromosome segregation in this and in an additional cofactor D mutant depends on growth conditions that are monitored specifically by the mitotic checkpoint proteins Mad1, 2, 3 and Bub3. The temperature-sensitive mutants we have used disrupt the function of cofactor D to different extents, but both strains form a mitotic spindle in which the poles separate in anaphase. However, chromosome segregation is often unequal, apparently due to a defect in kinetochore-microtubule interactions. Mutations in cofactor D render cells particularly sensitive to the expression levels of a CENP-B-like protein, Abp1p, which works as an allele-specific, high-copy suppressor of cofactor D. This and other genetic interactions between cofactor D mutants and specific kinetochore and spindle components suggest their critical role in establishing the normal kinetochore-microtubule interface.
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38
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Evans RJ, Chapple JP, Grayson C, Hardcastle AJ, Cheetham ME. Assay and functional analysis of the ARL3 effector RP2 involved in X-linked retinitis pigmentosa. Methods Enzymol 2006; 404:468-80. [PMID: 16413292 DOI: 10.1016/s0076-6879(05)04041-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Mutations in RP2 cause X-linked retinitis pigmentosa and also macular and peripapillary atrophy. RP2 is a functional homologue of the tubulin folding cofactor, cofactor C, as it can replace the beta tubulin GTPase stimulating activity of cofactor C in an in vitro assay. An important difference between RP2 and cofactor C is their subcellular localization. RP2 is targeted to the cytoplasmic face of the plasma membrane by dual N-terminal acylation, and this post-translational modification is important for protein function. The activity of tubulin folding cofactors is modulated by certain ADP ribosylation factor-like (Arl) proteins. It has been shown that RP2 can interact directly with Arl3. Here we describe the methodologies that we have developed to analyze the interaction of RP2 with Arl3 and to investigate the effect of RP2 post-translational modifications on its subcellular and tissue localization.
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Affiliation(s)
- R Jane Evans
- Institute of Ophthalmology, University College London, United Kingdom
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39
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Zhou C, Cunningham L, Marcus AI, Li Y, Kahn RA. Arl2 and Arl3 regulate different microtubule-dependent processes. Mol Biol Cell 2006; 17:2476-87. [PMID: 16525022 PMCID: PMC1446103 DOI: 10.1091/mbc.e05-10-0929] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Arl2 and Arl3 are closely related members of the Arf family of regulatory GTPases that arose from a common ancestor early in eukaryotic evolution yet retain extensive structural, biochemical, and functional features. The presence of Arl3 in centrosomes, mitotic spindles, midzones, midbodies, and cilia are all supportive of roles in microtubule-dependent processes. Knockdown of Arl3 by siRNA resulted in changes in cell morphology, increased acetylation of alpha-tubulin, failure of cytokinesis, and increased number of binucleated cells. We conclude that Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis. In contrast, an excess of Arl2 activity, achieved by expression of the [Q70L]Arl2 mutant, caused the loss of microtubules and cell cycle arrest in M phase. Initial characterization of the underlying defects suggests a defect in the ability to polymerize tubulin in the presence of excess Arl2 activity. We also show that Arl2 is present in centrosomes and propose that its action in regulating tubulin polymerization is mediated at centrosomes. Somewhat paradoxically, no phenotypes were observed Arl2 expression was knocked down or Arl3 activity was increased in HeLa cells. We conclude that Arl2 and Arl3 have related but distinct roles at centrosomes and in regulating microtubule-dependent processes.
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Affiliation(s)
- Chengjing Zhou
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322-3050, USA
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40
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Kühnel K, Veltel S, Schlichting I, Wittinghofer A. Crystal Structure of the Human Retinitis Pigmentosa 2 Protein and Its Interaction with Arl3. Structure 2006; 14:367-78. [PMID: 16472755 DOI: 10.1016/j.str.2005.11.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 10/24/2005] [Accepted: 11/01/2005] [Indexed: 11/29/2022]
Abstract
The crystal structure of human retinitis pigmentosa 2 protein (RP2) was solved to 2.1 angstroms resolution. It consists of an N-terminal beta helix and a C-terminal ferredoxin-like alpha/beta domain. RP2 is functionally and structurally related to the tubulin-specific chaperone cofactor C. Seven of nine known RP2 missense mutations identified in patients are located in the beta helix domain, and most of them cluster to the hydrophobic core and are likely to destabilize the protein. Two residues, Glu138 and the catalytically important Arg118, are solvent-exposed and form a salt bridge, indicating that Glu138 might be critical for positioning Arg118 for catalysis. RP2 is a specific effector protein of Arl3. The N-terminal 34 residues and beta helix domain of RP2 are required for this interaction. The abilitities of RP2 to bind Arl3 and cause retinitis pigmentosa seem to be correlated, since both the R118H and E138G mutants show a drastically reduced affinity to Arl3.
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Affiliation(s)
- Karin Kühnel
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Strukturelle Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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41
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Abstract
Database mining and phylogenetic analysis of the Arf (ADP-ribosylation factor) superfamily revealed the presence in mammals of at least 22 members, including the six Arfs, two Sars and 14 Arl (Arf-like) proteins. At least six Arf family members were found in very early eukaryotes, including orthologues of Arf, Sar, Arl2, Arl3, Arl6 and Arl8. While roles for Arfs in membrane traffic are well known, those for most of the Arls remain unknown. Depletion in cells of the most closely related human Arf proteins, Arf1-Arf5, reveals specificities among their cellular roles and suggests that they may function in pairs at different steps in endocytic and secretory membrane traffic. In addition, recent results from a number of laboratories suggest that several of the Arl proteins may be involved in different aspects of microtubule-dependent functions. Thus, a second major role for Arf family GTPases, that of regulating microtubules, is emerging. Because membrane traffic is often dependent upon movement of vesicles along microtubules this raises the possibility that these two fundamental functions of Arf family members, regulation of vesicle traffic and microtubule dynamics, diverged from one function of Arfs in the earliest cells that has continued to branch and allow additional levels of regulation.
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Hanzal-Bayer M, Linari M, Wittinghofer A. Properties of the interaction of Arf-like protein 2 with PDEdelta. J Mol Biol 2005; 350:1074-82. [PMID: 15979089 DOI: 10.1016/j.jmb.2005.05.036] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2005] [Revised: 05/04/2005] [Accepted: 05/18/2005] [Indexed: 02/06/2023]
Abstract
Arf-like proteins (Arl) share certain characteristic features with the Arf subfamily of Ras superfamily proteins, but their function is unknown. Here, we show by a variety of spectroscopic techniques that Arl2, unlike most other Ras-related proteins, has micromolar rather than picomolar affinity for nucleotides. As a consequence of low affinity, nucleotide dissociation rates are rather fast, arguing that it is not regulated by guanine nucleotide exchange factors. Arl2 is isolated as prey in a yeast double hybrid screen using phosphodiesterase 6delta (PDEdelta) as bait. This interaction is dependent on GTP, and the binding of PDEdelta substantially stabilizes GTP binding, increasing affinity and decreasing dissociation rates by a similar factor. Among all Arl proteins tested, PDEdelta only interacted with the closely related proteins Arl2 and Arl3, strongly suggesting that Arl2/3 are specific regulators of PDEdelta.
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Affiliation(s)
- Michael Hanzal-Bayer
- Max-Planck-Institute for Molecular Physiology, Department of Structural Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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Short B, Haas A, Barr FA. Golgins and GTPases, giving identity and structure to the Golgi apparatus. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1744:383-95. [PMID: 15979508 DOI: 10.1016/j.bbamcr.2005.02.001] [Citation(s) in RCA: 194] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2004] [Revised: 02/09/2005] [Accepted: 02/09/2005] [Indexed: 12/22/2022]
Abstract
In this review we will focus on the recent advances in how coiled-coil proteins of the golgin family give identity and structure to the Golgi apparatus in animal cells. A number of recent studies reveal a common theme for the targeting of golgins containing the ARL-binding GRIP domain, and the related ARF-binding GRAB domain. Similarly, other golgins such as the vesicle tethering factor p115 and Bicaudal-D are targeted by the Rab GTPases, Rab1 and Rab6, respectively. Together golgins and their regulatory GTPases form a complex network, commonly known as the Golgi matrix, which organizes Golgi membranes and regulates membrane trafficking.
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Affiliation(s)
- Benjamin Short
- Intracellular Protein Transport, Independent Junior Research Group, Max-Planck-Institute of Biochemistry, Martinsried, 82152, Germany
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Li Y, Kelly WG, Logsdon JM, Schurko AM, Harfe BD, Hill-Harfe KL, Kahn RA. Functional genomic analysis of the ADP-ribosylation factor family of GTPases: phylogeny among diverse eukaryotes and function in C. elegans. FASEB J 2005; 18:1834-50. [PMID: 15576487 DOI: 10.1096/fj.04-2273com] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
ADP-ribosylation factor (Arf) and Arf-like (Arl) proteins are a family of highly conserved 21 kDa GTPases that emerged early in the evolution of eukaryotes. These proteins serve regulatory roles in vesicular traffic, lipid metabolism, microtubule dynamics, development, and likely other cellular processes. We found evidence for the presence of 6 Arf family members in the protist Giardia lamblia and 22 members in mammals. A phylogenetic analysis was performed to delineate the evolutionary relationships among Arf family members and to attempt to organize them by both their evolutionary origins and functions in cells and/or organisms. The approximately 100 protein sequences analyzed from animals, fungi, plants, and protists clustered into 11 groups, including Arfs, nine Arls, and Sar proteins. To begin functional analyses of the family in a metazoan model organism, we examined roles for all three C. elegans Arfs (Arf-1, Arf-3, and Arf-6) and three Arls (Arl-1, Arl-2, and Arl-3) by use of RNA-mediated interference (RNAi). Injection of double-stranded RNA (dsRNA) encoding Arf-1 or Arf-3 into N2 hermaphrodites produced embryonic lethality in their offspring and, later, sterility in the injected animals themselves. Injection of Arl-2 dsRNA resulted in a disorganized germline and sterility in early offspring, with later offspring exhibiting an early embryonic arrest. Thus, of the six Arf family members examined in C. elegans, at least three are required for embryogenesis. These data represent the first analysis of the role(s) of multiple members of this family in the development of a multicellular organism.
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Affiliation(s)
- Yawei Li
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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Sahin A, Lemercier G, Tetaud E, Espiau B, Myler P, Stuart K, Bakalara N, Merlin G. Trypanosomatid flagellum biogenesis: ARL-3A is involved in several species. Exp Parasitol 2005; 108:126-33. [PMID: 15582509 DOI: 10.1016/j.exppara.2004.07.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2004] [Revised: 06/25/2004] [Accepted: 07/21/2004] [Indexed: 11/22/2022]
Abstract
Overexpression in Leishmania amazonensis promastigotes of the GTPase-deficient small G protein LdARL-3A-Q70L specifically provokes the loss of the flagella without affecting cell viability and body size. However, motility is lost and, remarkably, cells do not survive in the insect vector Lutzomyia longipalpis gut, leading to interruption of parasite transmission. We report here that overexpression of the same protein in Leishmania major, Leishmania donovani, and Crithidia fasciculata also led to significant alterations of the flagella. Surprisingly, ablation of TbARL-3A expression by RNAi in Trypanosoma brucei brucei also provoked flagella shortening, revealing that overexpression of the GTPase-deficient protein seems functionally equivalent to a drastic reduction in its native counterpart abundance. This renders possible complementary studies of an essential pathway in related organisms. Potential significance for the protein function is discussed as well as future strategies for stopping the transmission of several neglected parasitic diseases.
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Affiliation(s)
- Annelise Sahin
- Laboratoire de Génomique Fonctionnelle des Trypanosomatides, UMR CNRS 5162, Université Bordeaux 2, 146 Rue Léo Saignat, 33000 Bordeaux, France
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Abstract
Arl2 is a approximately 20 kDa GTPase in the ADP-ribosylation factor (Arf) family within the Ras superfamily with roles in microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis. Arl2 has been implicated as a regulator of the pathway responsible for formation of properly folded tubulin heterodimers and in adenine nucleotide transport in mitochondria. The identification and characterization of Arl2 binding partners and regulators of Arl2 activities are critical steps in the further dissection of these and likely other Arl2-dependent functions. This chapter describes methods for preparing recombinant Arl2, loading different radiolabeled guanine nucleotides onto the GTPase, identifying high-affinity Arl2 binding proteins, and assaying Arl2 GTPase activating proteins (GAPs). These methods may also prove useful for studies of other Arls or other GTPases.
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Affiliation(s)
- J Bradford Bowzard
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
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Abstract
ADP-ribosylation factor (Arf) GTP-binding proteins are among the best-characterized members of the Ras superfamily of GTPases, with well-established functions in membrane-trafficking pathways. A recent watershed of genomic and structural information has identified a family of conserved related proteins: the Arf-like (Arl) GTPases. The best-characterized Arl protein, Arl2, regulates the folding of beta tubulin, and recent data suggest that Arl1 and Arf-related protein 1 (ARFRP1) are localized to the trans-Golgi network (TGN), where they function, in part, to regulate the tethering of endosome-derived transport vesicles. Other Arl proteins are localized to the cytosol, nucleus, cytoskeleton and mitochondria, which indicates that Arl proteins have diverse roles that are distinct from the known functions of traditional Arf GTPases.
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Affiliation(s)
- Christopher G Burd
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6058, USA.
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