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Gerstner CD, Reed M, Dahl TM, Ying G, Frederick JM, Baehr W. Arf-like Protein 2 (ARL2) Controls Microtubule Neogenesis during Early Postnatal Photoreceptor Development. Cells 2022; 12:147. [PMID: 36611941 PMCID: PMC9818799 DOI: 10.3390/cells12010147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/12/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022] Open
Abstract
Arf-like protein 2 (ARL2) is a ubiquitously expressed small GTPase with multiple functions. In a cell culture, ARL2 participates with tubulin cofactor D (TBCD) in the neogenesis of tubulin αβ-heterodimers, the building blocks of microtubules. To evaluate this function in the retina, we conditionally deleted ARL2 in mouse retina at two distinct stages, either during the embryonic development (retArl2-/-) or after ciliogenesis specifically in rods (rodArl2-/-). retArl2-/- retina sections displayed distorted nuclear layers and a disrupted microtubule cytoskeleton (MTC) as early as postnatal day 6 (P6). Rod and cone outer segments (OS) did not form. By contrast, the rod ARL2 knockouts were stable at postnatal day 35 and revealed normal ERG responses. Cytoplasmic dynein is reduced in retArl2-/- inner segments (IS), suggesting that dynein may be unstable in the absence of a normal MTC. We investigated the microtubular stability in the absence of either ARL2 (retARL2-/-) or DYNC1H1 (retDync1h1-/-), the dynein heavy chain, and found that both the retArl2-/- and retDync1h1-/- retinas exhibited reduced microtubules and nuclear layer distortion. The results suggest that ARL2 and dynein depend on each other to generate a functional MTC during the early photoreceptor development.
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Affiliation(s)
- Cecilia D. Gerstner
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, UT 84132, USA
| | - Michelle Reed
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, UT 84132, USA
| | - Tiffanie M. Dahl
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, UT 84132, USA
| | - Guoxin Ying
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, UT 84132, USA
| | - Jeanne M. Frederick
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, UT 84132, USA
| | - Wolfgang Baehr
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, UT 84132, USA
- Department of Neurobiology & Anatomy, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
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2
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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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3
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Sheikh SA, Sisk RA, Schiavon CR, Waryah YM, Usmani MA, Steel DH, Sayer JA, Narsani AK, Hufnagel RB, Riazuddin S, Kahn RA, Waryah AM, Ahmed ZM. Homozygous Variant in ARL3 Causes Autosomal Recessive Cone Rod Dystrophy. Invest Ophthalmol Vis Sci 2020; 60:4811-4819. [PMID: 31743939 PMCID: PMC6944245 DOI: 10.1167/iovs.19-27263] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Purpose Cone rod dystrophy (CRD) is a group of inherited retinopathies characterized by the loss of cone and rod photoreceptor cells, which results in poor vision. This study aims to clinically and genetically characterize the segregating CRD phenotype in two large, consanguineous Pakistani families. Methods Funduscopy, optical coherence tomography (OCT), electroretinography (ERG), color vision, and visual acuity assessments were performed to evaluate the retinal structure and function of the affected individuals. Exome sequencing was performed to identify the genetic cause of CRD. Furthermore, the mutation's effect was evaluated using purified, bacterially expressed ADP-ribosylation factor-like protein 3 (ARL3) and mammalian cells. Results Fundus photography and OCT imaging demonstrated features that were consistent with CRD, including bull's eye macular lesions, macular atrophy, and central photoreceptor thinning. ERG analysis demonstrated moderate to severe reduction primarily of photopic responses in all affected individuals, and scotopic responses show reduction in two affected individuals. The exome sequencing revealed a novel homozygous variant (c.296G>T) in ARL3, which is predicted to substitute an evolutionarily conserved arginine with isoleucine within the encoded protein GTP-binding domain (R99I). The functional studies on the bacterial and heterologous mammalian cells revealed that the arginine at position 99 is essential for the stability of ARL3. Conclusions Our study uncovers an additional CRD gene and assigns the CRD phenotype to a variant of ARL3. The results imply that cargo transportation in photoreceptors as mediated by the ARL3 pathway is essential for cone and rod cell survival and vision in humans.
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Affiliation(s)
- Shakeel A Sheikh
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine University of Maryland, Baltimore, Maryland, United States.,Molecular Biology & Genetics Department, Liaquat University of Medical & Health Sciences, Jamshoro, Pakistan
| | - Robert A Sisk
- Abrahamson Pediatric Eye Institute, Cincinnati Children's Hospital, Cincinnati, Ohio, United States.,Cincinnati Eye Institute, Cincinnati, Ohio, United States
| | - Cara R Schiavon
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Yar M Waryah
- Molecular Biology & Genetics Department, Liaquat University of Medical & Health Sciences, Jamshoro, Pakistan
| | - Muhammad A Usmani
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine University of Maryland, Baltimore, Maryland, United States
| | - David H Steel
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, United Kingdom
| | - John A Sayer
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, United Kingdom
| | - Ashok K Narsani
- Institute of Ophthalmology, Liaquat University of Medical & Health Sciences, Jamshoro, Pakistan
| | - Robert B Hufnagel
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Saima Riazuddin
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine University of Maryland, Baltimore, Maryland, United States
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Ali M Waryah
- Molecular Biology & Genetics Department, Liaquat University of Medical & Health Sciences, Jamshoro, Pakistan
| | - Zubair M Ahmed
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine University of Maryland, Baltimore, Maryland, United States
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4
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Moye AR, Bedoni N, Cunningham JG, Sanzhaeva U, Tucker ES, Mathers P, Peter VG, Quinodoz M, Paris LP, Coutinho-Santos L, Camacho P, Purcell MG, Winkelmann AC, Foster JA, Pugacheva EN, Rivolta C, Ramamurthy V. Mutations in ARL2BP, a protein required for ciliary microtubule structure, cause syndromic male infertility in humans and mice. PLoS Genet 2019; 15:e1008315. [PMID: 31425546 PMCID: PMC6715254 DOI: 10.1371/journal.pgen.1008315] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 08/29/2019] [Accepted: 07/17/2019] [Indexed: 12/30/2022] Open
Abstract
Cilia are evolutionarily conserved hair-like structures with a wide spectrum of key biological roles, and their dysfunction has been linked to a growing class of genetic disorders, known collectively as ciliopathies. Many strides have been made towards deciphering the molecular causes for these diseases, which have in turn expanded the understanding of cilia and their functional roles. One recently-identified ciliary gene is ARL2BP, encoding the ADP-Ribosylation Factor Like 2 Binding Protein. In this study, we have identified multiple ciliopathy phenotypes associated with mutations in ARL2BP in human patients and in a mouse knockout model. Our research demonstrates that spermiogenesis is impaired, resulting in abnormally shaped heads, shortened and mis-assembled sperm tails, as well as in loss of axonemal doublets. Additional phenotypes in the mouse included enlarged ventricles of the brain and situs inversus. Mouse embryonic fibroblasts derived from knockout animals revealed delayed depolymerization of primary cilia. Our results suggest that ARL2BP is required for the structural maintenance of cilia as well as of the sperm flagellum, and that its deficiency leads to syndromic ciliopathy. The flagellated tails of sperm cells require a stringent developmental process that is essential for motility and fertility. The components that comprise the sperm tail assemble in regulated steps with protein processing, transport, and structural assembly dependent on each other for sperm tail maturity. In this work, we have identified ARL2BP, a previously retinal-associated protein, to be essential for sperm tail development and assembly. We show that without functional ARL2BP in humans or mice, sperm tails fail to develop, starting with the assembly of the core microtubular structure within the tail. Loss of ARL2BP also effects other ciliated cells, indicating a unique role for ARL2BP in ciliary microtubule formation. This research on ARL2BP provides further understanding on the links between vision and fertility. This work also demonstrates how genomic studies for human patients and murine models can coincide to provide greater insight into disease.
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Affiliation(s)
- Abigail R. Moye
- Department of Ophthalmology, West Virginia University, Morgantown, United States of America
- Department of Biochemistry, West Virginia University, Morgantown, United States of America
| | - Nicola Bedoni
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Jessica G. Cunningham
- Rockefeller Neurosciences Institute, West Virginia University, Morgantown, WV, United States of America
| | - Urikhan Sanzhaeva
- Department of Biochemistry, West Virginia University, Morgantown, United States of America
| | - Eric S. Tucker
- Rockefeller Neurosciences Institute, West Virginia University, Morgantown, WV, United States of America
| | - Peter Mathers
- Department of Ophthalmology, West Virginia University, Morgantown, United States of America
- Department of Biochemistry, West Virginia University, Morgantown, United States of America
- Rockefeller Neurosciences Institute, West Virginia University, Morgantown, WV, United States of America
| | - Virginie G. Peter
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Mathieu Quinodoz
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Liliana P. Paris
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto, Lisbon, Portugal
| | - Luísa Coutinho-Santos
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto, Lisbon, Portugal
| | - Pedro Camacho
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto, Lisbon, Portugal
| | - Madeleine G. Purcell
- Department of Biology, Randolph-Macon College, Ashland, VA, United States of America
| | - Abbie C. Winkelmann
- Department of Biology, Randolph-Macon College, Ashland, VA, United States of America
| | - James A. Foster
- Department of Biology, Randolph-Macon College, Ashland, VA, United States of America
| | - Elena N. Pugacheva
- Department of Biochemistry, West Virginia University, Morgantown, United States of America
| | - Carlo Rivolta
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University Hospital Basel, Switzerland
- * E-mail: (CR); (VR)
| | - Visvanathan Ramamurthy
- Department of Ophthalmology, West Virginia University, Morgantown, United States of America
- Department of Biochemistry, West Virginia University, Morgantown, United States of America
- Rockefeller Neurosciences Institute, West Virginia University, Morgantown, WV, United States of America
- * E-mail: (CR); (VR)
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5
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Sztul E, Chen PW, Casanova JE, Cherfils J, Dacks JB, Lambright DG, Lee FJS, Randazzo PA, Santy LC, Schürmann A, Wilhelmi I, Yohe ME, Kahn RA. ARF GTPases and their GEFs and GAPs: concepts and challenges. Mol Biol Cell 2019; 30:1249-1271. [PMID: 31084567 PMCID: PMC6724607 DOI: 10.1091/mbc.e18-12-0820] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/26/2019] [Accepted: 03/11/2019] [Indexed: 12/12/2022] Open
Abstract
Detailed structural, biochemical, cell biological, and genetic studies of any gene/protein are required to develop models of its actions in cells. Studying a protein family in the aggregate yields additional information, as one can include analyses of their coevolution, acquisition or loss of functionalities, structural pliability, and the emergence of shared or variations in molecular mechanisms. An even richer understanding of cell biology can be achieved through evaluating functionally linked protein families. In this review, we summarize current knowledge of three protein families: the ARF GTPases, the guanine nucleotide exchange factors (ARF GEFs) that activate them, and the GTPase-activating proteins (ARF GAPs) that have the ability to both propagate and terminate signaling. However, despite decades of scrutiny, our understanding of how these essential proteins function in cells remains fragmentary. We believe that the inherent complexity of ARF signaling and its regulation by GEFs and GAPs will require the concerted effort of many laboratories working together, ideally within a consortium to optimally pool information and resources. The collaborative study of these three functionally connected families (≥70 mammalian genes) will yield transformative insights into regulation of cell signaling.
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Affiliation(s)
- Elizabeth Sztul
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Pei-Wen Chen
- Department of Biology, Williams College, Williamstown, MA 01267
| | - James E. Casanova
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908
| | - Jacqueline Cherfils
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS and Ecole Normale Supérieure Paris-Saclay, 94235 Cachan, France
| | - Joel B. Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - David G. Lambright
- Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Amherst, MA 01605
| | - Fang-Jen S. Lee
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | | | - Lorraine C. Santy
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
| | - Annette Schürmann
- German Institute of Human Nutrition, 85764 Potsdam-Rehbrücke, Germany
| | - Ilka Wilhelmi
- German Institute of Human Nutrition, 85764 Potsdam-Rehbrücke, Germany
| | - Marielle E. Yohe
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Richard A. Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322-3050
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6
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Rafiullah R, Long AB, Ivanova AA, Ali H, Berkel S, Mustafa G, Paramasivam N, Schlesner M, Wiemann S, Wade RC, Bolthauser E, Blum M, Kahn RA, Caspary T, Rappold GA. A novel homozygous ARL13B variant in patients with Joubert syndrome impairs its guanine nucleotide-exchange factor activity. Eur J Hum Genet 2017; 25:1324-1334. [PMID: 29255182 PMCID: PMC5865152 DOI: 10.1038/s41431-017-0031-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 10/02/2017] [Accepted: 10/10/2017] [Indexed: 11/09/2022] Open
Abstract
ARL13B encodes for the ADP-ribosylation factor-like 13B GTPase, which is required for normal cilia structure and Sonic hedgehog (Shh) signaling. Disruptions in cilia structure or function lead to a class of human disorders called ciliopathies. Joubert syndrome is characterized by a wide spectrum of symptoms, including a variable degree of intellectual disability, ataxia, and ocular abnormalities. Here we report a novel homozygous missense variant c.[223G>A] (p.(Gly75Arg) in the ARL13B gene, which was identified by whole-exome sequencing of a trio from a consanguineous family with multiple-affected individuals suffering from intellectual disability, ataxia, ocular defects, and epilepsy. The same variant was also identified in a second family. We saw a striking difference in the severity of ataxia between affected male and female individuals in both families. Both ARL13B and ARL13B-c.[223G>A] (p.(Gly75Arg) expression rescued the cilia length and Shh defects displayed by Arl13b hennin (null) cells, indicating that the variant did not disrupt either ARL13B function. In contrast, ARL13B-c.[223G>A] (p.(Gly75Arg) displayed a marked loss of ARL3 guanine nucleotide-exchange factor activity, with retention of its GTPase activities, highlighting the correlation between its loss of function as an ARL3 guanine nucleotide-exchange factor and Joubert syndrome.
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Affiliation(s)
- Rafiullah Rafiullah
- Department of Human Molecular Genetics, Heidelberg University, 69120, Heidelberg, Germany
| | - Alyssa B Long
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Anna A Ivanova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Hazrat Ali
- Department of Psychiatry, Bolan Medical College, 87600, Quetta, Pakistan
| | - Simone Berkel
- Department of Human Molecular Genetics, Heidelberg University, 69120, Heidelberg, Germany
| | - Ghulam Mustafa
- Molecular and Cellular Modeling (MCM) Group, Heidelberg Institute for Theoretical Studies (HITS), 69118, Heidelberg, Germany
- Center for Molecular Biology, DKFZ-ZMBH Alliance, Heidelberg University, 69120, Heidelberg, Germany
| | - Nagarajan Paramasivam
- Computational Oncology Group, Theoretical Bioinformatics Division (B080), German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, 69120, Heidelberg, Germany
| | - Matthias Schlesner
- Computational Oncology Group, Theoretical Bioinformatics Division (B080), German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - Stefan Wiemann
- Genomic and Proteomics Core Facility, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling (MCM) Group, Heidelberg Institute for Theoretical Studies (HITS), 69118, Heidelberg, Germany
- Center for Molecular Biology, DKFZ-ZMBH Alliance, Heidelberg University, 69120, Heidelberg, Germany
| | - Eugen Bolthauser
- Division of Pediatric Neurology, University Children's Hospital, 8032, Zurich, Switzerland
| | - Martin Blum
- Institute of Zoology, University of Hohenheim, 70593, Stuttgart, Germany
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Gudrun A Rappold
- Department of Human Molecular Genetics, Heidelberg University, 69120, Heidelberg, Germany.
- Interdisciplinary Centre for Neurosciences (IZN), University of Heidelberg, 69120, Heidelberg, Germany.
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7
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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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8
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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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9
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Mariani LE, Bijlsma MF, Ivanova AA, Suciu SK, Kahn RA, Caspary T. Arl13b regulates Shh signaling from both inside and outside the cilium. Mol Biol Cell 2016; 27:mbc.E16-03-0189. [PMID: 27682584 PMCID: PMC5170560 DOI: 10.1091/mbc.e16-03-0189] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 08/16/2016] [Accepted: 09/20/2016] [Indexed: 12/21/2022] Open
Abstract
The regulatory GTPase Arl13b localizes to primary cilia, where it regulates Sonic hedgehog (Shh) signaling. Missense mutations in ARL13B can cause the ciliopathy Joubert syndrome, while the mouse null allele is embryonic lethal. We used mouse embryonic fibroblasts as a system to determine the effects of Arl13b mutations on Shh signaling. We tested a total of seven different mutants, three JS-causing variants, two point mutants predicted to alter guanine nucleotide handling, one that disrupts cilia localization, and one that prevents palmitoylation and thus membrane binding, in assays of transcriptional and non-transcriptional Shh signaling. We found that mutations disrupting Arl13b's palmitoylation site, cilia localization signal, or GTPase handling altered the Shh response in distinct assays of transcriptional or non-transcriptional signaling. In contrast, JS-causing mutations in Arl13b did not affect Shh signaling in these same assays, suggesting these mutations result in more subtle defects, likely affecting only a subset of signaling outputs. Finally, we show that restricting Arl13b from cilia interferes with its ability to regulate Shh-stimulated chemotaxis, despite previous evidence that cilia themselves are not required for this non-transcriptional Shh response. This points to a more complex relationship between the ciliary and non-ciliary roles of this regulatory GTPase than previously envisioned.
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Affiliation(s)
- Laura E Mariani
- *Department of Human Genetics, Emory University, Atlanta, GA, USA Neuroscience Graduate Program, Emory University, Atlanta, GA, USA
| | - Maarten F Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Academic Medical Center and Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Anna A Ivanova
- Department of Biochemistry, Emory University, Atlanta, GA, USA
| | - Sarah K Suciu
- *Department of Human Genetics, Emory University, Atlanta, GA, USA Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA, USA
| | - Richard A Kahn
- Department of Biochemistry, Emory University, Atlanta, GA, USA
| | - Tamara Caspary
- *Department of Human Genetics, Emory University, Atlanta, GA, USA
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10
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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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11
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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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12
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East MP, Bowzard JB, Dacks JB, Kahn RA. ELMO domains, evolutionary and functional characterization of a novel GTPase-activating protein (GAP) domain for Arf protein family GTPases. J Biol Chem 2012; 287:39538-53. [PMID: 23014990 DOI: 10.1074/jbc.m112.417477] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human family of ELMO domain-containing proteins (ELMODs) consists of six members and is defined by the presence of the ELMO domain. Within this family are two subclassifications of proteins, based on primary sequence conservation, protein size, and domain architecture, deemed ELMOD and ELMO. In this study, we used homology searching and phylogenetics to identify ELMOD family homologs in genomes from across eukaryotic diversity. This demonstrated not only that the protein family is ancient but also that ELMOs are potentially restricted to the supergroup Opisthokonta (Metazoa and Fungi), whereas proteins with the ELMOD organization are found in diverse eukaryotes and thus were likely the form present in the last eukaryotic common ancestor. The segregation of the ELMO clade from the larger ELMOD group is consistent with their contrasting functions as unconventional Rac1 guanine nucleotide exchange factors and the Arf family GTPase-activating proteins, respectively. We used unbiased, phylogenetic sorting and sequence alignments to identify the most highly conserved residues within the ELMO domain to identify a putative GAP domain within the ELMODs. Three independent but complementary assays were used to provide an initial characterization of this domain. We identified a highly conserved arginine residue critical for both the biochemical and cellular GAP activity of ELMODs. We also provide initial evidence of the function of human ELMOD1 as an Arf family GAP at the Golgi. These findings provide the basis for the future study of the ELMOD family of proteins and a new avenue for the study of Arf family GTPases.
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Affiliation(s)
- Michael P East
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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13
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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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14
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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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