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Dimopoulos IS, Chan S, MacLaren RE, MacDonald IM. Pathogenic mechanisms and the prospect of gene therapy for choroideremia. Expert Opin Orphan Drugs 2015; 3:787-798. [PMID: 26251765 PMCID: PMC4522943 DOI: 10.1517/21678707.2015.1046434] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Choroideremia is a rare, X-linked disorder recognized by its specific ocular phenotype as a progressive degenerative retinopathy resulting in blindness. New therapeutic approaches, primarily based on genetic mechanisms, have emerged that aim to prevent the progressive vision loss. AREAS COVERED This article will review the research that has progressed incrementally over the past two decades from mapping to gene discovery, uncovering the presumed mechanisms triggering the retinopathy to preclinical testing of potential therapies. EXPERT OPINION While still in an evaluative phase, the introduction of gene replacement as a potential therapy has been greeted with great enthusiasm by patients, advocacy groups and the medical community.
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Affiliation(s)
- Ioannis S Dimopoulos
- University of Alberta, Department of Ophthalmology and Visual Sciences, Edmonton, Alberta, Canada
| | - Stephanie Chan
- University of Alberta, Department of Ophthalmology and Visual Sciences, Edmonton, Alberta, Canada
| | - Robert E MacLaren
- Oxford Eye Hospital and Nuffield Laboratory of Ophthalmology, John Radcliffe Hospital, Oxford, UK
- Moorfields Eye Hospital Foundation Trust, NIHR Ophthalmology Biomedical Research Centre, London, UK
| | - Ian M MacDonald
- University of Alberta, Department of Ophthalmology and Visual Sciences, Edmonton, Alberta, Canada
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52
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Satpathy S, Wagner SA, Beli P, Gupta R, Kristiansen TA, Malinova D, Francavilla C, Tolar P, Bishop GA, Hostager BS, Choudhary C. Systems-wide analysis of BCR signalosomes and downstream phosphorylation and ubiquitylation. Mol Syst Biol 2015; 11:810. [PMID: 26038114 PMCID: PMC4501846 DOI: 10.15252/msb.20145880] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 04/30/2015] [Accepted: 05/06/2015] [Indexed: 12/02/2022] Open
Abstract
B-cell receptor (BCR) signaling is essential for the development and function of B cells; however, the spectrum of proteins involved in BCR signaling is not fully known. Here we used quantitative mass spectrometry-based proteomics to monitor the dynamics of BCR signaling complexes (signalosomes) and to investigate the dynamics of downstream phosphorylation and ubiquitylation signaling. We identify most of the previously known components of BCR signaling, as well as many proteins that have not yet been implicated in this system. BCR activation leads to rapid tyrosine phosphorylation and ubiquitylation of the receptor-proximal signaling components, many of which are co-regulated by both the modifications. We illustrate the power of multilayered proteomic analyses for discovering novel BCR signaling components by demonstrating that BCR-induced phosphorylation of RAB7A at S72 prevents its association with effector proteins and with endo-lysosomal compartments. In addition, we show that BCL10 is modified by LUBAC-mediated linear ubiquitylation, and demonstrate an important function of LUBAC in BCR-induced NF-κB signaling. Our results offer a global and integrated view of BCR signaling, and the provided datasets can serve as a valuable resource for further understanding BCR signaling networks.
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Affiliation(s)
- Shankha Satpathy
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sebastian A Wagner
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Petra Beli
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rajat Gupta
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Trine A Kristiansen
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dessislava Malinova
- Division of Immune Cell Biology, MRC National Institute for Medical Research, Mill Hill, London, UK
| | - Chiara Francavilla
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pavel Tolar
- Division of Immune Cell Biology, MRC National Institute for Medical Research, Mill Hill, London, UK
| | - Gail A Bishop
- Department of Microbiology, Graduate Program in Immunology and Department of Internal Medicine, University of Iowa, Iowa City, IA, USA VAMC, Iowa City, IA, USA
| | - Bruce S Hostager
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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53
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Seitz IP, Zhour A, Kohl S, Llavona P, Peter T, Wilhelm B, Zrenner E, Ueffing M, Bartz-Schmidt KU, Fischer MD. Multimodal assessment of choroideremia patients defines pre-treatment characteristics. Graefes Arch Clin Exp Ophthalmol 2015; 253:2143-50. [PMID: 25744334 DOI: 10.1007/s00417-015-2976-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 02/05/2015] [Accepted: 02/18/2015] [Indexed: 10/23/2022] Open
Abstract
PURPOSE Choroideremia (CHM) is a X-chromosomal disorder leading to blindness by progressive degeneration of choroid, retinal pigment epithelium (RPE), and retinal neurons. A current clinical gene therapy trial (NCT01461213) showed promising safety and efficacy data in a carefully selected patient population. The present study was performed to shed light on pre-treatment characteristics of a larger cohort of CHM patients using a high resolution multi-modal approach. METHODS In a retrospective cross-sectional study, data from 58 eyes of 29 patients with clinically confirmed CHM were analysed including best-corrected visual acuity (BCVA), refractive error, spectral-domain optical coherence tomography (SD-OCT), fundus autofluorescence (FAF), perimetry, and tonometry. Residual retinal volume, area of residual RPE, and foveal thickness were quantified to further define natural disease progression and assess symmetry. RESULTS We evaluated 98 data points of BCVA [0.34 ± 0.06 (logMAR); mean ± 95 % confidence interval], 80 of IOP (14.6 ± 0.6 mmHg), and 98 of refraction (-2.16 ± 1.08 spherical equivalent). Visual fields (n = 76) demonstrated variable degrees of concentric constriction (54 % <10°, 25 % 10-30°, 21 % >30°). Mean residual RPE area on FAF (n = 64) measured 8.47 ± 1.91 mm(2) (range 0.30-38.5 mm(2)), while mean neuroretinal volume (n = 42) was found to be 1.76 ± 0.12 mm(3). Age at examination was exponentially associated with BCVA, while logarithmic functions best described progressive loss of retinal area and volume. A high degree of left to right symmetry was found in all modalities with structural markers showing the best correlation (r (2) area = 0.83; r (2) volume = 0.75). CONCLUSION Analysis of these widely available clinical data defines the natural disease characteristics of a relevant patient population eligible for gene therapeutic intervention. In the wake of preliminary reports on safety and efficacy of CHM gene therapy (NCT01461213), this multi-modal assessment of a cohort of CHM patients provides important evidence of the natural rate of disease progression and degree of symmetry between eyes.
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Affiliation(s)
- Immanuel P Seitz
- University Eye Hospital, University of Tübingen, Tübingen, Germany.,Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Ahmad Zhour
- University Eye Hospital, University of Tübingen, Tübingen, Germany
| | - Susanne Kohl
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Pablo Llavona
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Tobias Peter
- STZ Eyetrial, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Barbara Wilhelm
- STZ Eyetrial, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Eberhart Zrenner
- University Eye Hospital, University of Tübingen, Tübingen, Germany.,Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | | | - M Dominik Fischer
- University Eye Hospital, University of Tübingen, Tübingen, Germany. .,Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, UK. .,Oxford Eye Hospital, Oxford University Hospitals NHS Trust, Oxford, UK. .,Merton College, University of Oxford, Oxford, OX1 4JD, UK.
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Gutkowska M, Wnuk M, Nowakowska J, Lichocka M, Stronkowski MM, Swiezewska E. Rab geranylgeranyl transferase β subunit is essential for male fertility and tip growth in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:213-24. [PMID: 25316062 PMCID: PMC4265159 DOI: 10.1093/jxb/eru412] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Rab proteins, key players in vesicular transport in all eukaryotic cells, are post-translationally modified by lipid moieties. Two geranylgeranyl groups are attached to the Rab protein by the heterodimeric enzyme Rab geranylgeranyl transferase (RGT) αβ. Partial impairment in this enzyme activity in Arabidopsis, by disruption of the AtRGTB1 gene, is known to influence plant stature and disturb gravitropic and light responses. Here it is shown that mutations in each of the RGTB genes cause a tip growth defect, visible as root hair and pollen tube deformations. Moreover, FM 1-43 styryl dye endocytosis and recycling are affected in the mutant root hairs. Finally, it is demonstrated that the double mutant, with both AtRGTB genes disrupted, is non-viable due to absolute male sterility. Doubly mutated pollen is shrunken, has an abnormal exine structure, and shows strong disorganization of internal membranes, particularly of the endoplasmic reticulum system.
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Affiliation(s)
- Malgorzata Gutkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Marta Wnuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Julita Nowakowska
- Warsaw University, Faculty of Biology, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Malgorzata Lichocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Michal M Stronkowski
- Warsaw University of Technology, Faculty of Mathematics and Information Science, Koszykowa 75, 00-662 Warsaw, Poland
| | - Ewa Swiezewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
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55
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Stasi M, De Luca M, Bucci C. Two-hybrid-based systems: powerful tools for investigation of membrane traffic machineries. J Biotechnol 2014; 202:105-17. [PMID: 25529347 DOI: 10.1016/j.jbiotec.2014.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 12/05/2014] [Accepted: 12/11/2014] [Indexed: 01/18/2023]
Abstract
Protein-protein interactions regulate biological processes and are fundamental for cell functions. Recently, efforts have been made to define interactomes, which are maps of protein-protein interactions that are useful for understanding biological pathways and networks and for investigating how perturbations of these networks lead to diseases. Therefore, interactomes are becoming fundamental for establishing the molecular basis of human diseases and contributing to the discovery of effective therapies. Interactomes are constructed based on experimental data present in the literature and computational predictions of interactions. Several biochemical, genetic and biotechnological techniques have been used in the past to identify protein-protein interactions. The yeast two-hybrid system has beyond doubt represented a revolution in the field, being a versatile tool and allowing the immediate identification of the interacting proteins and isolation of the cDNA coding for the interacting peptide after in vivo screening. Recently, variants of the yeast two-hybrid assay have been developed, including high-throughput systems that promote the rapidly growing field of proteomics. In this review we will focus on the role of this technique in the discovery of Rab interacting proteins, highlighting the importance of high-throughput two-hybrid screening as a tool to study the complexity of membrane traffic machineries.
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Affiliation(s)
- Mariangela Stasi
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Maria De Luca
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Cecilia Bucci
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy.
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56
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Wang YC, Dozier JK, Beese LS, Distefano MD. Rapid analysis of protein farnesyltransferase substrate specificity using peptide libraries and isoprenoid diphosphate analogues. ACS Chem Biol 2014; 9:1726-35. [PMID: 24841702 PMCID: PMC4136699 DOI: 10.1021/cb5002312] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Protein farnesytransferase (PFTase)
catalyzes the farnesylation
of proteins with a carboxy-terminal tetrapeptide sequence denoted
as a Ca1a2X box. To explore the specificity
of this enzyme, an important therapeutic target, solid-phase peptide
synthesis in concert with a peptide inversion strategy was used to
prepare two libraries, each containing 380 peptides. The libraries
were screened using an alkyne-containing isoprenoid analogue followed
by click chemistry with biotin azide and subsequent visualization
with streptavidin-AP. Screening of the CVa2X and CCa2X libraries with Rattus norvegicus PFTase revealed reaction by many known recognition sequences as
well as numerous unknown ones. Some of the latter occur in the genomes
of bacteria and viruses and may be important for pathogenesis, suggesting
new targets for therapeutic intervention. Screening of the CVa2X library with alkyne-functionalized isoprenoid substrates
showed that those prepared from C10 or C15 precursors
gave similar results, whereas the analogue synthesized from a C5 unit gave a different pattern of reactivity. Lastly, the
substrate specificities of PFTases from three organisms (R. norvegicus, Saccharomyces cerevisiae, and Candida albicans) were compared
using CVa2X libraries. R. norvegicus PFTase was found to share more peptide substrates with S. cerevisiae PFTase than with C.
albicans PFTase. In general, this method is a highly
efficient strategy for rapidly probing the specificity of this important
enzyme.
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Affiliation(s)
- Yen-Chih Wang
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jonathan K. Dozier
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Lorena S. Beese
- Department
of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Mark D. Distefano
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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57
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Burke JE, Inglis AJ, Perisic O, Masson GR, McLaughlin SH, Rutaganira F, Shokat KM, Williams RL. Structures of PI4KIIIβ complexes show simultaneous recruitment of Rab11 and its effectors. Science 2014; 344:1035-8. [PMID: 24876499 DOI: 10.1126/science.1253397] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Phosphatidylinositol 4-kinases (PI4Ks) and small guanosine triphosphatases (GTPases) are essential for processes that require expansion and remodeling of phosphatidylinositol 4-phosphate (PI4P)-containing membranes, including cytokinesis, intracellular development of malarial pathogens, and replication of a wide range of RNA viruses. However, the structural basis for coordination of PI4K, GTPases, and their effectors is unknown. Here, we describe structures of PI4Kβ (PI4KIIIβ) bound to the small GTPase Rab11a without and with the Rab11 effector protein FIP3. The Rab11-PI4KIIIβ interface is distinct compared with known structures of Rab complexes and does not involve switch regions used by GTPase effectors. Our data provide a mechanism for how PI4KIIIβ coordinates Rab11 and its effectors on PI4P-enriched membranes and also provide strategies for the design of specific inhibitors that could potentially target plasmodial PI4KIIIβ to combat malaria.
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Affiliation(s)
- John E Burke
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
| | - Alison J Inglis
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Olga Perisic
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Glenn R Masson
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Stephen H McLaughlin
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Florentine Rutaganira
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco (UCSF), San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco (UCSF), San Francisco, CA 94158, USA
| | - Roger L Williams
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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58
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LI SHIQIANG, GUAN LIPING, FANG SHAOHUA, JIANG HUI, XIAO XUESHAN, YANG JIANHUA, WANG PANFENG, YIN YE, GUO XIANGMING, WANG JUN, ZHANG JIANGUO, ZHANG QINGJIONG. Exome sequencing reveals CHM mutations in six families with atypical choroideremia initially diagnosed as retinitis pigmentosa. Int J Mol Med 2014; 34:573-7. [DOI: 10.3892/ijmm.2014.1797] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 05/30/2014] [Indexed: 11/06/2022] Open
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The role of the hypervariable C-terminal domain in Rab GTPases membrane targeting. Proc Natl Acad Sci U S A 2014; 111:2572-7. [PMID: 24550285 DOI: 10.1073/pnas.1313655111] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Intracellular membrane trafficking requires correct and specific localization of Rab GTPases. The hypervariable C-terminal domain (HVD) of Rabs is posttranslationally modified by isoprenyl moieties that enable membrane association. A model asserting HVD-directed targeting has been contested in previous studies, but the role of the Rab HVD and the mechanism of Rab membrane targeting remain elusive. To elucidate the function of the HVD, we have substituted this region with an unnatural polyethylenglycol (PEG) linker by using oxime ligation. The PEGylated Rab proteins undergo normal prenylation, underlining the unique ability of the Rab prenylation machinery to process the Rab family with diverse C-terminal sequences. Through localization studies and functional analyses of semisynthetic PEGylated Rab1, Rab5, Rab7, and Rab35 proteins, we demonstrate that the role of the HVD of Rabs in membrane targeting is more complex than previously understood. The HVD of Rab1 and Rab5 is dispensable for membrane targeting and appears to function simply as a linker between the GTPase domain and the membrane. The N-terminal residues of the Rab7 HVD are important for late endosomal/lysosomal localization, apparently due to their involvement in interaction with the Rab7 effector Rab-interacting lysosomal protein. The C-terminal polybasic cluster of the Rab35 HVD is essential for plasma membrane (PM) targeting, presumably because of the electrostatic interaction with negatively charged lipids on the PM. Our findings suggest that Rab membrane targeting is dictated by a complex mechanism involving GEFs, GAPs, effectors, and C-terminal interaction with membranes to varying extents, and possibly other binding partners.
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60
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Köhnke M, Delon C, Hastie ML, Nguyen UTT, Wu YW, Waldmann H, Goody RS, Gorman JJ, Alexandrov K. Rab GTPase prenylation hierarchy and its potential role in choroideremia disease. PLoS One 2013; 8:e81758. [PMID: 24358126 PMCID: PMC3864799 DOI: 10.1371/journal.pone.0081758] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 10/16/2013] [Indexed: 11/29/2022] Open
Abstract
Protein prenylation is a widespread post-translational modification in eukaryotes that plays a crucial role in membrane targeting and signal transduction. RabGTPases is the largest group of post-translationally C-terminally geranylgeranylated. All Rabs are processed by Rab geranylgeranyl-transferase and Rab escort protein (REP). Human genetic defects resulting in the loss one of two REP isoforms REP-1, lead to underprenylation of RabGTPases that manifests in retinal degradation and blindness known as choroideremia. In this study we used a combination of microinjections and chemo-enzymatic tagging to establish whether Rab GTPases are prenylated and delivered to their target cellular membranes with the same rate. We demonstrate that although all tested Rab GTPases display the same rate of membrane delivery, the extent of Rab prenylation in 5 hour time window vary by more than an order of magnitude. We found that Rab27a, Rab27b, Rab38 and Rab42 display the slowest prenylation in vivo and in the cell. Our work points to possible contribution of Rab38 to the emergence of choroideremia in addition to Rab27a and Rab27b.
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Affiliation(s)
- Monika Köhnke
- Department of Cell and Molecular Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Christine Delon
- Department of Physical Biochemistry, Max-Planck-Institute for Molecular Physiology, Dortmund, Germany
| | - Marcus L. Hastie
- Queensland Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Herston, Queensland, Australia
| | - Uyen T. T. Nguyen
- Department of Cell and Molecular Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Yao-Wen Wu
- Department of Physical Biochemistry, Max-Planck-Institute for Molecular Physiology, Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute for Molecular Physiology, Dortmund, Germany
| | - Roger S. Goody
- Department of Physical Biochemistry, Max-Planck-Institute for Molecular Physiology, Dortmund, Germany
| | - Jeffrey J. Gorman
- Queensland Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Herston, Queensland, Australia
| | - Kirill Alexandrov
- Department of Cell and Molecular Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
- * E-mail:
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61
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Cabrera M, Ungermann C. Guanine nucleotide exchange factors (GEFs) have a critical but not exclusive role in organelle localization of Rab GTPases. J Biol Chem 2013; 288:28704-12. [PMID: 23979137 DOI: 10.1074/jbc.m113.488213] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Membrane fusion at eukaryotic organelles is initiated by Rab GTPases and tethering factors. Rabs in their GDP-bound form are kept soluble in the cytoplasm by the GDP dissociation inhibitor (GDI) chaperone. Guanine nucleotide exchange factors (GEFs) are found at organelles and are critical for Rab function. Here, we surveyed the overall role of GEFs in Rab localization. We show that GEFs, but none of the proposed GDI displacement factors, are essential for the correct membrane localization of yeast Rabs. In the absence of the GEF, Rabs lost their primary localization to the target organelle. Several Rabs, such as vacuolar Ypt7, were found at the endoplasmic reticulum and thus were still membrane-bound. Surprisingly, a Ypt7 mutant that undergoes facilitated nucleotide exchange localized to vacuoles independently of its GEF Mon1-Ccz1 and rescued vacuole morphology. In contrast, wild-type Ypt7 required its GEF for localization and to counteract the extraction by GDI. Our data agree with the emerging model that GEFs are critical for Rab localization but raise the possibility that additional factors can contribute to this process.
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Affiliation(s)
- Margarita Cabrera
- From the Biochemistry Section, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
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62
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Rab27a and melanosomes: a model to investigate the membrane targeting of Rabs. Biochem Soc Trans 2013; 40:1383-8. [PMID: 23176485 DOI: 10.1042/bst20120200] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rab proteins constitute the largest family within the Ras superfamily of small GTPases (>60 in mammals) and are essential regulators of transport between intracellular organelles. Key to this activity is their targeting to specific compartments within the cell. However, although great strides have been made over the last 25 years in assigning functions to individual Rabs and identifying their downstream effectors, the mechanism(s) regulating their targeting to specific subcellular membranes remains less well understood. In the present paper, we review the evidence supporting the proposed mechanisms of Rab targeting and highlight insights into this process provided by studies of Rab27a.
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63
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Vasireddy V, Mills JA, Gaddameedi R, Basner-Tschakarjan E, Kohnke M, Black AD, Alexandrov K, Zhou S, Maguire AM, Chung DC, Mac H, Sullivan L, Gadue P, Bennicelli JL, French DL, Bennett J. AAV-mediated gene therapy for choroideremia: preclinical studies in personalized models. PLoS One 2013; 8:e61396. [PMID: 23667438 PMCID: PMC3646845 DOI: 10.1371/journal.pone.0061396] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 03/08/2013] [Indexed: 11/19/2022] Open
Abstract
Choroideremia (CHM) is an X- linked retinal degeneration that is symptomatic in the 1st or 2nd decade of life causing nyctalopia and loss of peripheral vision. The disease progresses through mid-life, when most patients become blind. CHM is a favorable target for gene augmentation therapy, as the disease is due to loss of function of a protein necessary for retinal cell health, Rab Escort Protein 1 (REP1).The CHM cDNA can be packaged in recombinant adeno-associated virus (rAAV), which has an established track record in human gene therapy studies, and, in addition, there are sensitive and quantitative assays to document REP1 activity. An animal model that accurately reflects the human condition is not available. In this study, we tested the ability to restore REP1 function in personalized in vitro models of CHM: lymphoblasts and induced pluripotent stems cells (iPSCs) from human patients. The initial step of evaluating safety of the treatment was carried out by evaluating for acute retinal histopathologic effects in normal-sighted mice and no obvious toxicity was identified. Delivery of the CHM cDNA to affected cells restores REP1 enzymatic activity and also restores proper protein trafficking. The gene transfer is efficient and the preliminary safety data are encouraging. These studies pave the way for a human clinical trial of gene therapy for CHM.
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Affiliation(s)
- Vidyullatha Vasireddy
- F.M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jason A. Mills
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Rajashekhar Gaddameedi
- F.M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Etiena Basner-Tschakarjan
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Monika Kohnke
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia
| | - Aaron D. Black
- F.M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Krill Alexandrov
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia
| | - Shangzhen Zhou
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Albert M. Maguire
- F.M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Daniel C. Chung
- F.M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Helen Mac
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Lisa Sullivan
- Department of Anatomic Pathology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Paul Gadue
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Jeannette L. Bennicelli
- F.M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Deborah L. French
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Jean Bennett
- F.M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Sindhu M, Saini V, Piplani S, Kumar A. Molecular Dynamics of Rab7::REP1::GGTase-II Ternary Complex and Identification of Their Putative Drug Binding Sites. Indian J Pharm Sci 2013; 75:23-30. [PMID: 23901157 PMCID: PMC3719145 DOI: 10.4103/0250-474x.113534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Revised: 01/03/2013] [Accepted: 01/07/2013] [Indexed: 11/26/2022] Open
Abstract
The structure-function correlation of membrane proteins have been a difficult task, particularly in context to transient protein complexes. The molecular simulation of ternary complex of Rab7::REP1::GGTase-II was carried out to understand the basic structural events occurring during the prenylation event of Rab proteins, using the software YASARA. The study suggested that the C-terminus of Rab7 has to be in completely extended conformation during prenylation to reach the active site of RabGGTase-II. Also, attempt was made to find putative drug binding sites on the ternary complex of Rab7::REP1::GGTase-II using Q-SiteFinder programme. The comprehensive consensus probe generated by the program revealed a total of 10 major pockets as putative drug binding sites on Rab7::REP:: GGTase-II ternary complex. These pockets were found on REP protein and GGTase protein subunits. The Rab7 was found to be devoid of any putative drug binding sites in the ternary complex. The phylogenetic analysis of 60 Rab proteins of human was carried out using PHYLIP and study indicated the close phylogenetic relationship between Rab7 and Rab9 proteins of human and hence with further in silico study, the present observations can be extrapolated to Rab9 proteins. The study paves a good platform for further experimental verifications of the findings and other in silico studies like identifying the potential drug targets by searching the putative drug binding sites, generating pharmacophoric pattern, searching or constructing suitable ligand and docking studies.
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Affiliation(s)
- Meenakshi Sindhu
- Centre for Bioinformatics, M. D. University, Rohtak-124 001, India
| | - Vandana Saini
- Centre for Bioinformatics, M. D. University, Rohtak-124 001, India
| | - Sakshi Piplani
- Centre for Bioinformatics, M. D. University, Rohtak-124 001, India
| | - A. Kumar
- Centre for Bioinformatics, M. D. University, Rohtak-124 001, India
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Huang AS, Kim LA, Fawzi AA. Clinical characteristics of a large choroideremia pedigree carrying a novel CHM mutation. ACTA ACUST UNITED AC 2012; 130:1184-9. [PMID: 22965595 DOI: 10.1001/archophthalmol.2012.1117] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
OBJECTIVE To describe a large family with a novel mutation in CHM. METHODS Family members were characterized using clinical examination, wide-field fundus photography, wide-field autofluorescence, and spectral domain optical coherence tomography. The CHM mutation was identified with the National Institutes of Health-sponsored eyeGene program. RESULTS A novel nonsense CHM mutation (T1194G), resulting in a premature stop (Y398X) and loss of the final one-third C-terminal portion of the protein, was identified. A large pedigree was generated from information provided by the twice-married proband. Seven men (aged 27-39 years) and 7 women (aged 22-89 years) were evaluated. Affected men showed characteristic peripheral chorioretinal atrophy with islands of macular sparing. Female carriers exhibited a wide range of variability, from mild pigmentary alterations to significant chorioretinal atrophy with severe vision loss. Older women tended to have a more severe phenotype. Autofluorescence demonstrating subfoveal loss or absence of retinal pigment epithelium correlated with vision loss in both sexes. Spectral domain optical coherence tomography demonstrated dynamic changes and remodeling of the outer retina over time, including focal thickening, drusenlike deposits, and disruption to photoreceptor inner segment and outer segment junctions in young female carriers. CONCLUSIONS CHM (T1194G) is a novel mutation that manifests a wide range of phenotypic variability in a single family with a trend toward more severe phenotypes in older female carriers. Our findings emphasize the importance of considering X-linked diseases by carefully evaluating pedigrees in women with severe manifestations of disease. CLINICAL RELEVANCE These findings demonstrate a novel CHM mutation that emphasizes severe posterior pole carrier phenotypes, age-related changes, and early choroideremia disease.
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Affiliation(s)
- Alex S Huang
- Doheny Eye Institute, Department of Ophthalmology, Keck School of Medicine of the University of Southern California, Los Angeles, USA
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66
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Interaction between shrimp and white spot syndrome virus through PmRab7-VP28 complex: an insight using simulation and docking studies. J Mol Model 2012. [DOI: 10.1007/s00894-012-1672-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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67
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Gallegos ME, Balakrishnan S, Chandramouli P, Arora S, Azameera A, Babushekar A, Bargoma E, Bokhari A, Chava SK, Das P, Desai M, Decena D, Saramma SDD, Dey B, Doss AL, Gor N, Gudiputi L, Guo C, Hande S, Jensen M, Jones S, Jones N, Jorgens D, Karamchedu P, Kamrani K, Kolora LD, Kristensen L, Kwan K, Lau H, Maharaj P, Mander N, Mangipudi K, Menakuru H, Mody V, Mohanty S, Mukkamala S, Mundra SA, Nagaraju S, Narayanaswamy R, Ndungu-Case C, Noorbakhsh M, Patel J, Patel P, Pendem SV, Ponakala A, Rath M, Robles MC, Rokkam D, Roth C, Sasidharan P, Shah S, Tandon S, Suprai J, Truong TQN, Uthayaruban R, Varma A, Ved U, Wang Z, Yu Z. The C. elegans rab family: identification, classification and toolkit construction. PLoS One 2012; 7:e49387. [PMID: 23185324 PMCID: PMC3504004 DOI: 10.1371/journal.pone.0049387] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 10/09/2012] [Indexed: 11/29/2022] Open
Abstract
Rab monomeric GTPases regulate specific aspects of vesicle transport in eukaryotes including coat recruitment, uncoating, fission, motility, target selection and fusion. Moreover, individual Rab proteins function at specific sites within the cell, for example the ER, golgi and early endosome. Importantly, the localization and function of individual Rab subfamily members are often conserved underscoring the significant contributions that model organisms such as Caenorhabditis elegans can make towards a better understanding of human disease caused by Rab and vesicle trafficking malfunction. With this in mind, a bioinformatics approach was first taken to identify and classify the complete C. elegans Rab family placing individual Rabs into specific subfamilies based on molecular phylogenetics. For genes that were difficult to classify by sequence similarity alone, we did a comparative analysis of intron position among specific subfamilies from yeast to humans. This two-pronged approach allowed the classification of 30 out of 31 C. elegans Rab proteins identified here including Rab31/Rab50, a likely member of the last eukaryotic common ancestor (LECA). Second, a molecular toolset was created to facilitate research on biological processes that involve Rab proteins. Specifically, we used Gateway-compatible C. elegans ORFeome clones as starting material to create 44 full-length, sequence-verified, dominant-negative (DN) and constitutive active (CA) rab open reading frames (ORFs). Development of this toolset provided independent research projects for students enrolled in a research-based molecular techniques course at California State University, East Bay (CSUEB).
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Affiliation(s)
- Maria E Gallegos
- Department of Biological Sciences, California State University East Bay, Hayward, CA, USA.
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68
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Structures, mechanisms and inhibitors of undecaprenyl diphosphate synthase: A cis-prenyltransferase for bacterial peptidoglycan biosynthesis. Bioorg Chem 2012; 43:51-7. [DOI: 10.1016/j.bioorg.2011.09.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 09/13/2011] [Accepted: 09/15/2011] [Indexed: 12/20/2022]
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69
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Gutkowska M, Swiezewska E. Structure, regulation and cellular functions of Rab geranylgeranyl transferase and its cellular partner Rab Escort Protein. Mol Membr Biol 2012; 29:243-56. [DOI: 10.3109/09687688.2012.693211] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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70
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Wu YW, Goody RS, Alexandrov K. Intein-mediated construction of a library of fluorescent Rab GTPase probes. Chembiochem 2011; 12:2813-21. [PMID: 22086656 DOI: 10.1002/cbic.201100377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Indexed: 11/08/2022]
Abstract
Rab GTPases play a key role in the regulation of membrane trafficking. Post-translational geranylgeranylation is critical for their biological activity and is conferred by Rab geranylgeranyl transferease (RabGGTase), together with an accessory factor, Rab escort protein (REP). Mechanistic studies of Rab prenylation and identification of RabGGTase inhibitors require sensitive reporters of Rab prenylation. In the present work, a combination of protein engineering and expressed protein ligation was used to construct a library of semisynthetic Rab7 fluorescent conjugates. In order to avoid synthesis of a large number of fluorescently labeled peptides, we developed a strategy that combined thiol-reactive dye-labeling of cysteine with in vitro protein ligation. Application of this strategy required optimization of labeling and ligation conditions to promote thiol labeling and disfavor intramolecular cyclization. Using this approach, we constructed 46 fluorescent sensors with different spectral properties that reported on the interaction of Rab7 with RabGGTase, REP-1, and the overall prenylation reaction. Two constructs, Rab7Δ3CCK(NBD) and Rab7Δ2SCCC-dans, displayed 2.5- and 1.5-fold increase in fluorescence, respectively, upon prenylation. Moreover, dansyl-, NBD (4-nitro-benzofurazan)-, I-BA-, and I-SO-labeled Rab7 conjugates exhibited two- to tenfold change in fluorescence upon binding to REP or RabGGTase. These fluorescent sensors allowed us to monitor Rab prenylation in real time and to investigate the assembly of Rab-REP binary and Rab-REP-RabGGTase ternary complexes.
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Affiliation(s)
- Yao-Wen Wu
- Department of Physical Biochemistry, Max-Planck Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
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71
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Serum Biomarkers and Trafficking Defects in Peripheral Tissues Reflect the Severity of Retinopathy in Three Brothers Affected by Choroideremia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 723:381-7. [DOI: 10.1007/978-1-4614-0631-0_49] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Affiliation(s)
- Howard C. Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (USA)
| | - Maurine E. Linder
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853 (USA)
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73
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Esposito G, De Falco F, Tinto N, Testa F, Vitagliano L, Tandurella ICM, Iannone L, Rossi S, Rinaldi E, Simonelli F, Zagari A, Salvatore F. Comprehensive mutation analysis (20 families) of the choroideremia gene reveals a missense variant that prevents the binding of REP1 with rab geranylgeranyl transferase. Hum Mutat 2011; 32:1460-9. [DOI: 10.1002/humu.21591] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 08/11/2011] [Indexed: 12/19/2022]
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74
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Yi L, Abootorabi M, Wu YW. Semisynthesis of Prenylated Rab GTPases by Click Ligation. Chembiochem 2011; 12:2413-7. [DOI: 10.1002/cbic.201100466] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Indexed: 11/11/2022]
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75
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Chen YX, Triola G, Waldmann H. Bioorthogonal chemistry for site-specific labeling and surface immobilization of proteins. Acc Chem Res 2011; 44:762-73. [PMID: 21648407 DOI: 10.1021/ar200046h] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Understanding protein structure and function is essential for uncovering the secrets of biology, but it remains extremely challenging because of the high complexity of protein networks and their wiring. The daunting task of elucidating these interconnections requires the concerted application of methods emerging from different disciplines. Chemical biology integrates chemistry, biology, and pharmacology and has provided novel techniques and approaches to the investigation of biological processes. Among these, site-specific protein labeling with functional groups such as fluorophors, spin probes, and affinity tags has greatly facilitated both in vitro and in vivo studies of protein structure and function. Bioorthogonal chemical reactions, which enable chemo- and regioselective attachment of small-molecule probes to proteins, are particularly attractive and relevant for site-specific protein labeling. The introduction of powerful labeling techniques also has inspired the development of novel strategies for surface immobilization of proteins to create protein biochips for in vitro characterization of biochemical activities or interactions between proteins. Because this process requires the efficient immobilization of proteins on surfaces while maintaining structure and activity, tailored methods for protein immobilization based on bioorthogonal chemical reactions are in high demand. In this Account, we summarize recent developments and applications of site-specific protein labeling and surface immobilization of proteins, with a special focus on our contributions to these fields. We begin with the Staudinger ligation, which involves the formation of a stable amide bond after the reaction of a preinstalled azide with a triaryl phosphine reagent. We then examine the Diels-Alder reaction, which requires the protein of interest to be functionalized with a diene, enabling conjugation to a variety of dienophiles under physiological conditions. In the oxime ligation, an oxyamine is condensed with either an aldehyde or a ketone to form an oxime; we successfully pursued the inverse of the standard technique by attaching the oxyamine, rather than the aldehyde, to the protein. The click sulfonamide reaction, which involves the Cu(I)-catalyzed reaction of sulfonylazides with terminal alkynes, is then discussed. Finally, we consider in detail the photochemical thiol-ene reaction, in which a thiol adds to an ene group after free radical initiation. Each of these methods has been successfully developed as a bioorthogonal transformation for oriented protein immobilization on chips and for site-specific protein labeling under physiological conditions. Despite the tremendous progress in developing such transformations over the past decade, however, the demand for new bioorthogonal methods with improved kinetics and selectivities remains high.
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Affiliation(s)
- Yong-Xiang Chen
- Abteilung Chemische Biologie, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
- Fakultät Chemie, Lehrbereich Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Gemma Triola
- Abteilung Chemische Biologie, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
- Fakultät Chemie, Lehrbereich Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Herbert Waldmann
- Abteilung Chemische Biologie, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
- Fakultät Chemie, Lehrbereich Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
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76
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Yi L, Sun H, Itzen A, Triola G, Waldmann H, Goody RS, Wu YW. One-Pot Dual-Labeling of a Protein by Two Chemoselective Reactions. Angew Chem Int Ed Engl 2011; 50:8287-90. [DOI: 10.1002/anie.201100840] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 04/14/2011] [Indexed: 12/27/2022]
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77
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Yi L, Sun H, Itzen A, Triola G, Waldmann H, Goody RS, Wu YW. One-Pot Dual-Labeling of a Protein by Two Chemoselective Reactions. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100840] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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78
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Qiao Y, Gao J, Qiu Y, Wu L, Guo F, Kam-Wing Lo K, Li D. Design, synthesis, and characterization of piperazinedione-based dual protein inhibitors for both farnesyltransferase and geranylgeranyltransferase-I. Eur J Med Chem 2011; 46:2264-73. [DOI: 10.1016/j.ejmech.2011.03.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 02/25/2011] [Accepted: 03/02/2011] [Indexed: 01/13/2023]
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79
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Abstract
Intracellular membrane traffic defines a complex network of pathways that connects many of the membrane-bound organelles of eukaryotic cells. Although each pathway is governed by its own set of factors, they all contain Rab GTPases that serve as master regulators. In this review, we discuss how Rabs can regulate virtually all steps of membrane traffic from the formation of the transport vesicle at the donor membrane to its fusion at the target membrane. Some of the many regulatory functions performed by Rabs include interacting with diverse effector proteins that select cargo, promoting vesicle movement, and verifying the correct site of fusion. We describe cascade mechanisms that may define directionality in traffic and ensure that different Rabs do not overlap in the pathways that they regulate. Throughout this review we highlight how Rab dysfunction leads to a variety of disease states ranging from infectious diseases to cancer.
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Affiliation(s)
- Alex H Hutagalung
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA
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80
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Itzen A, Goody RS. GTPases involved in vesicular trafficking: Structures and mechanisms. Semin Cell Dev Biol 2011; 22:48-56. [DOI: 10.1016/j.semcdb.2010.10.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2010] [Revised: 09/09/2010] [Accepted: 10/07/2010] [Indexed: 10/18/2022]
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81
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Ghosh I, Considine N, Maunus E, Sun L, Zhang A, Buswell J, Evans TC, Xu MQ. Site-specific protein labeling by intein-mediated protein ligation. Methods Mol Biol 2011; 705:87-107. [PMID: 21125382 DOI: 10.1007/978-1-61737-967-3_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Intein-mediated protein ligation (IPL) employs an intein to create a protein possessing a C-terminal thioester that can be ligated to a protein or peptide with an amino-terminal cysteine via a native peptide bond. Here we present a procedure to conduct isolation and labeling of recombinant proteins expressed in E. coli using synthetic short peptides possessing a fluorescent moiety. This approach can be readily utilized for site-specific conjugation of a fluorophore to the C-terminus of a protein of interest, without the drawback of non-specific chemical labeling. This chapter also gives a general review of the critical parameters of intein-mediated cleavage and ligation reactions.
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Affiliation(s)
- Inca Ghosh
- New England BioLabs, Ipswich, MA 01938, USA.
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82
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Kovtun O, Mureev S, Johnston W, Alexandrov K. Towards the construction of expressed proteomes using a Leishmania tarentolae based cell-free expression system. PLoS One 2010; 5:e14388. [PMID: 21203562 PMCID: PMC3006200 DOI: 10.1371/journal.pone.0014388] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 11/25/2010] [Indexed: 11/19/2022] Open
Abstract
The adaptation of organisms to a parasitic life style is often accompanied by the emergence of novel biochemical pathways absent in free-living organisms. As a result, the genomes of specialized parasitic organisms often code for a large number (>50%) of proteins with no detectable homology or predictable function. Although understanding the biochemical properties of these proteins and their roles in parasite biogenesis is the next challenge of molecular parasitology, analysis tools developed for free-living organisms are often inadequate for this purpose. Here we attempt to solve some of these problems by developing a methodology for the rapid production of expressed proteomes in cell-free systems based on parasitic organisms. To do so we take advantage of Species Independent Translational Sequences (SITS), which can efficiently mediate translation initiation in any organism. Using these sequences we developed a single-tube in vitro translation system based on the parasitic protozoan Leishmania tarentolae. We demonstrate that the system can be primed directly with SITS containing templates constructed by overlap extension PCR. To test the systems we simultaneously amplified 31 of L. tarentolae's putative translation initiation factors and phosphatases directly from the genomic DNA and subjected them to expression, purification and activity analysis. All of the amplified products produced soluble recombinant proteins, and putative phosphatases could be purified to at least 50% purity in one step. We further compared the ability of L. tarentolae and E. coli based cell-free systems to express a set of mammalian, L. tarentolae and Plasmodium falciparum Rab GTPases in functional form. We demonstrate that the L. tarentolae cell-free system consistently produced higher quality proteins than E. coli-based system. The differences were particularly pronounced in the case of open reading frames derived from P. falciparum. The implications of these developments are discussed.
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Affiliation(s)
- Oleksiy Kovtun
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Sergey Mureev
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Wayne Johnston
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Kirill Alexandrov
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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83
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Affiliation(s)
- Jose M. Palomo
- Departamento de Biocatálisis, Instituto de Catálisis (CSIC), c/ Marie Curie 2, Cantoblanco Campus UAM, 28049 Madrid, Spain, Fax: +34‐91‐585‐4760
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84
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Brighouse A, Dacks JB, Field MC. Rab protein evolution and the history of the eukaryotic endomembrane system. Cell Mol Life Sci 2010; 67:3449-65. [PMID: 20582450 PMCID: PMC2943070 DOI: 10.1007/s00018-010-0436-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 05/28/2010] [Accepted: 06/09/2010] [Indexed: 12/20/2022]
Abstract
Spectacular increases in the quantity of sequence data genome have facilitated major advances in eukaryotic comparative genomics. By exploiting homology with classical model organisms, this makes possible predictions of pathways and cellular functions currently impossible to address in intractable organisms. Echoing realization that core metabolic processes were established very early following evolution of life on earth, it is now emerging that many eukaryotic cellular features, including the endomembrane system, are ancient and organized around near-universal principles. Rab proteins are key mediators of vesicle transport and specificity, and via the presence of multiple paralogues, alterations in interaction specificity and modification of pathways, contribute greatly to the evolution of complexity of membrane transport. Understanding system-level contributions of Rab proteins to evolutionary history provides insight into the multiple processes sculpting cellular transport pathways and the exciting challenges that we face in delving further into the origins of membrane trafficking specificity.
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Affiliation(s)
- Andrew Brighouse
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP UK
- King’s College London School of Medicine, Hodgkin Building, London, SE1 1UL UK
| | - Joel B. Dacks
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7 Canada
| | - Mark C. Field
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP UK
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85
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Nguyen UTT, Goody RS, Alexandrov K. Understanding and exploiting protein prenyltransferases. Chembiochem 2010; 11:1194-201. [PMID: 20432425 DOI: 10.1002/cbic.200900727] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Uyen T T Nguyen
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, New York, NY 10065, USA
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86
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Hála M, Soukupová H, Synek L, Zárský V. Arabidopsis RAB geranylgeranyl transferase beta-subunit mutant is constitutively photomorphogenic, and has shoot growth and gravitropic defects. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 62:615-27. [PMID: 20180921 DOI: 10.1111/j.1365-313x.2010.04172.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
RAB GTPases are important directional regulators of intracellular vesicle transport. Membrane localization of RAB GTPases is mediated by C-terminal double geranylgeranylation. This post-translational modification is catalyzed by the alpha-beta-heterodimer catalytic core of RAB geranylgeranyl transferase (RAB-GGT), which cooperates with the RAB escort protein (REP) that presents a nascent RAB. Here, we show that RAB-geranylgeranylation activity is significantly reduced in two homozygous mutants of the major Arabidopsis beta-subunit of RAB-GGT (AtRGTB1), resulting in unprenylated RAB GTPases accumulation in the cytoplasm. Both endocytosis and exocytosis are downregulated in rgtb1 homozygotes defective in shoot growth and morphogenesis. Root gravitropism is normal in rgtb1 roots, but is significantly compromised in shoots. Mutants are defective in etiolation and show constitutive photomorphogenic phenotypes that cannot be rescued by brassinosteroid treatment, similarly to the det3 mutant that is also defective in the secretory pathway. Transcriptomic analysis revealed an upregulation of specific RAB GTPases in etiolated wild-type plants. Taken together, these data suggest that the downregulation of the secretory pathway is interpreted as a photomorphogenic signal in Arabidopsis.
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Affiliation(s)
- Michal Hála
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojova 263, 165 02 Prague 6, Czech Republic
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87
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Kachalova GS, Bourenkov GP, Mengesdorf T, Schenk S, Maun HR, Burghammer M, Riekel C, Decker K, Bartunik HD. Crystal Structure Analysis of Free and Substrate-Bound 6-Hydroxy-l-Nicotine Oxidase from Arthrobacter nicotinovorans. J Mol Biol 2010; 396:785-99. [DOI: 10.1016/j.jmb.2009.12.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 12/04/2009] [Accepted: 12/07/2009] [Indexed: 10/20/2022]
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88
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McCray BA, Skordalakes E, Taylor JP. Disease mutations in Rab7 result in unregulated nucleotide exchange and inappropriate activation. Hum Mol Genet 2009; 19:1033-47. [PMID: 20028791 PMCID: PMC2830827 DOI: 10.1093/hmg/ddp567] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Rab GTPases are molecular switches that orchestrate vesicular trafficking, maturation and fusion by cycling between an active, GTP-bound form, and an inactive, GDP-bound form. The activity cycle is coupled to GTP hydrolysis and is tightly controlled by regulatory proteins. Missense mutations of the GTPase Rab7 cause a dominantly inherited axonal degeneration known as Charcot-Marie-Tooth type 2B through an unknown mechanism. We present the 2.8 Å crystal structure of GTP-bound L129F mutant Rab7 which reveals normal conformations of the effector binding regions and catalytic site, but an alteration to the nucleotide binding pocket that is predicted to alter GTP binding. Through extensive biochemical analysis, we demonstrate that disease-associated mutations in Rab7 do not lead to an intrinsic GTPase defect, but permit unregulated nucleotide exchange leading to both excessive activation and hydrolysis-independent inactivation. Consistent with augmented activity, mutant Rab7 shows significantly enhanced interaction with a subset of effector proteins. In addition, dynamic imaging demonstrates that mutant Rab7 is abnormally retained on target membranes. However, we show that the increased activation of mutant Rab7 is counterbalanced by unregulated, GTP hydrolysis-independent membrane cycling. Notably, disease mutations are able to rescue the membrane cycling of a GTPase-deficient mutant. Thus, we demonstrate that disease mutations uncouple Rab7 from the spatial and temporal control normally imposed by regulatory proteins and cause disease not by a gain of novel toxic function, but by misregulation of native Rab7 activity.
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Affiliation(s)
- Brett A McCray
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
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89
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Mureev S, Kovtun O, Nguyen UTT, Alexandrov K. Species-independent translational leaders facilitate cell-free expression. Nat Biotechnol 2009; 27:747-52. [DOI: 10.1038/nbt.1556] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 07/06/2009] [Indexed: 11/09/2022]
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90
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Abstract
The endocytosis pathway controls multiple cellular and physiological events. The lysosome is the destination of newly synthesized lysosomal hydrolytic enzymes. Internalized molecules or particles are delivered to the lysosome for degradation through sequential transport along the endocytic pathway. The endocytic pathway is also emerging as a signalling platform, in addition to the well-known role of the plasma membrane for signalling. Rab7 is a late endosome-/lysosome-associated small GTPase, perhaps the only lysosomal Rab protein identified to date. Rab7 plays critical roles in the endocytic processes. Through interaction with its partners (including upstream regulators and downstream effectors), Rab7 participates in multiple regulation mechanisms in endosomal sorting, biogenesis of lysosome [or LRO (lysosome-related organelle)] and phagocytosis. These processes are closely related to substrates degradation, antigen presentation, cell signalling, cell survival and microbial pathogen infection. Consistently, mutations or dysfunctions of Rab7 result in traffic disorders, which cause various diseases, such as neuropathy, cancer and lipid metabolism disease. Rab7 also plays important roles in microbial pathogen infection and survival, as well as in participating in the life cycle of viruses. Here, we give a brief review on the central role of Rab7 in endosomal traffic and summarize the studies focusing on the participation of Rab7 in disease pathogenesis. The underlying mechanism governed by Rab7 and its partners will also be discussed.
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91
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Chaperone-assisted production of active human Rab8A GTPase in Escherichia coli. Protein Expr Purif 2009; 65:190-5. [DOI: 10.1016/j.pep.2008.12.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Revised: 12/03/2008] [Accepted: 12/03/2008] [Indexed: 11/21/2022]
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92
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Lee MTG, Mishra A, Lambright DG. Structural mechanisms for regulation of membrane traffic by rab GTPases. Traffic 2009; 10:1377-89. [PMID: 19522756 DOI: 10.1111/j.1600-0854.2009.00942.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In all eukaryotic organisms, Rab GTPases function as critical regulators of membrane traffic, organelle biogenesis and maturation, and related cellular processes. The numerous Rab proteins have distinctive yet overlapping subcellular distributions throughout the endomembrane system. Intensive investigation has clarified the underlying molecular and structural mechanisms for several ubiquitous Rab proteins that control membrane traffic between tubular-vesicular organelles in the exocytic, endocytic and recycling pathways. In this review, we focus on structural insights that inform our current understanding of the organization of the Rab family as well as the mechanisms for membrane targeting and activation, interaction with effectors, deactivation and specificity determination.
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Affiliation(s)
- Meng-Tse Gabe Lee
- Program in Molecular Medicine and Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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93
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Mackiewicz P, Wyroba E. Phylogeny and evolution of Rab7 and Rab9 proteins. BMC Evol Biol 2009; 9:101. [PMID: 19442299 PMCID: PMC2693434 DOI: 10.1186/1471-2148-9-101] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Accepted: 05/14/2009] [Indexed: 11/14/2022] Open
Abstract
Background An important role in the evolution of intracellular trafficking machinery in eukaryotes played small GTPases belonging to the Rab family known as pivotal regulators of vesicle docking, fusion and transport. The Rab family is very diversified and divided into several specialized subfamilies. We focused on the VII functional group comprising Rab7 and Rab9, two related subfamilies, and analysed 210 sequences of these proteins. Rab7 regulates traffic from early to late endosomes and from late endosome to vacuole/lysosome, whereas Rab9 participates in transport from late endosomes to the trans-Golgi network. Results Although Rab7 and Rab9 proteins are quite small and show heterogeneous rates of substitution in different lineages, we found a phylogenetic signal and inferred evolutionary relationships between them. Rab7 proteins evolved before radiation of main eukaryotic supergroups while Rab9 GTPases diverged from Rab7 before split of choanoflagellates and metazoans. Additional duplication of Rab9 and Rab7 proteins resulting in several isoforms occurred in the early evolution of vertebrates and next in teleost fishes and tetrapods. Three Rab7 lineages emerged before divergence of monocots and eudicots and subsequent duplications of Rab7 genes occurred in particular angiosperm clades. Interestingly, several Rab7 copies were identified in some representatives of excavates, ciliates and amoebozoans. The presence of many Rab copies is correlated with significant differences in their expression level. The diversification of analysed Rab subfamilies is also manifested by non-conserved sequences and structural features, many of which are involved in the interaction with regulators and effectors. Individual sites discriminating different subgroups of Rab7 and Rab9 GTPases have been identified.
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Affiliation(s)
- Paweł Mackiewicz
- University of Wrocław, Faculty of Biotechnology, Department of Genomics, 63/77 Przybyszewskiego Street, 51-148 Wrocław, Poland.
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94
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Sergeev YV, Smaoui N, Sui R, Stiles D, Gordiyenko N, Strunnikova N, Macdonald IM. The functional effect of pathogenic mutations in Rab escort protein 1. Mutat Res 2009; 665:44-50. [PMID: 19427510 DOI: 10.1016/j.mrfmmm.2009.02.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 02/25/2009] [Accepted: 02/28/2009] [Indexed: 11/27/2022]
Abstract
Choroideremia (CHM) is a chorioretinal degeneration with an X-linked pattern of inheritance. Affected males experience progressive atrophy of the choroid, retinal pigment epithelium and retina leading to eventual blindness. The CHM gene encodes Rab escort protein 1 (REP-1). REP-1 is involved in trafficking of Rab proteins in the cell. To date, the majority of reported mutations in the CHM gene cause a complete loss of REP-1 function. Here we report pathogenic mutations: a novel missense mutation, L550P; a truncation c.1542T>A, STOP; and two deletions (c.525_526delAG and c.1646delC) in the CHM gene and their phenotypic effect. To analyze the effect of mutations, the 3D structure of human REP-1 and the proteins associated with REP-1 function were modeled using sequence homology with rat proteins. In silico analysis of the missense mutation L550P suggests that the proline residue at position 550 destabilizes the beta-structural elements, and the REP-1 tertiary structure. Truncation and deletion mutants are associated with a partial or total loss of the REP-1 essential activity and protein-protein interactions as predicted by the analysis of the structure and stability of these protein products. The presumptive loss of protein was confirmed by Western Blot analysis of protein from mononuclear cells and fibroblasts (FB) from CHM patients.
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Affiliation(s)
- Y V Sergeev
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
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95
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Wu YW, Goody RS, Abagyan R, Alexandrov K. Structure of the disordered C terminus of Rab7 GTPase induced by binding to the Rab geranylgeranyl transferase catalytic complex reveals the mechanism of Rab prenylation. J Biol Chem 2009; 284:13185-92. [PMID: 19240028 DOI: 10.1074/jbc.m900579200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Protein prenylation is a widespread process that involves the transfer of either a farnesyl or a geranylgeranyl moiety to one or more C-terminal cysteines of the target protein. Rab geranylgeranyl transferase (RabGGTase) is responsible for the largest number of individual protein prenylation events in the cell. A decade-long effort to crystallize the catalytic ternary complex of RabGGTase has remained fruitless, prompting us to use a computational approach to predict the structure of this 200-kDa assembly. On the basis of high resolution structures of two sub-complexes, we have generated a composite model where the rigid parts of the protein are represented by precomputed grid potentials, whereas the mobile parts are described in atomic details using Internal Coordinate Mechanics. Selection of the best docking solution of the flexible parts on the grid is followed by explicit atomistic refinement of the lowest energy conformations enabling realistic modeling of complex structures. Using this approach we demonstrate that the flexible C terminus of Rab7 substrate forms a series of progressively weaker and less specific interactions that channel it into the active site of RabGGTase. We have validated the computational model through biochemical experiments and demonstrated that to be prenylated RabGTPase must possess at least nine amino acids between the prenylation motif and the hydrophobic sequence anchoring the beginning of the Rab C terminus on the enzyme. This sequence, known as the C-terminal interacting motif is shown to play a dual role in Rab prenylation by contributing a significant fraction of binding energy to the catalytic complex assembly and by orienting the C terminus of RabGTPase in the vicinity of the active site of RabGGTase. This mechanism is unique to RabGGTase when compared with other prenyltransferases, which encode the specificity for their cognate substrates directly at their active site.
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Affiliation(s)
- Yao-Wen Wu
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
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96
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97
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Martín‐Belmonte F, Rodríguez‐Fraticelli AE. Chapter 3 Acquisition of Membrane Polarity in Epithelial Tube Formation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2009; 274:129-82. [DOI: 10.1016/s1937-6448(08)02003-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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98
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Chapter 5: rab proteins and their interaction partners. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2009; 274:235-74. [PMID: 19349039 DOI: 10.1016/s1937-6448(08)02005-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The Ras superfamily consists of over 150 low molecular weight proteins that cycle between an inactive guanosine diphosphate (GDP)-bound state and an active guanosine triphosphate (GTP)-bound state. They are involved in a variety of signal transduction pathways that regulate cell growth, intracellular trafficking, cell migration, and apoptosis. Several methods have been devised to detect and characterize the interacting partners of small GTPases with the aim of better understanding their physiological function in normal cells and tumor cells. The Rab (Ras analog in brain) proteins form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as membrane-associated molecular switches. The guanine nucleotide-binding status of Rab proteins is modulated by three different classes of regulatory proteins, which have been extensively studied for the Rab molecules but also for other subfamilies of the Ras superfamily. Furthermore, numerous effector molecules have been isolated especially for the Rab subfamily of proteins, which interact via a Rab-binding domain (RBD) and are recruited afterwards to specific sub-cellular compartments by the Rab proteins.
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Huizing M, Helip-Wooley A, Westbroek W, Gunay-Aygun M, Gahl WA. Disorders of lysosome-related organelle biogenesis: clinical and molecular genetics. Annu Rev Genomics Hum Genet 2008; 9:359-86. [PMID: 18544035 DOI: 10.1146/annurev.genom.9.081307.164303] [Citation(s) in RCA: 274] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Lysosome-related organelles (LROs) are a heterogeneous group of vesicles that share various features with lysosomes, but are distinct in function, morphology, and composition. The biogenesis of LROs employs a common machinery, and genetic defects in this machinery can affect all LROs or only an individual LRO, resulting in a variety of clinical features. In this review, we discuss the main components of LRO biogenesis. We also summarize the function, composition, and resident cell types of the major LROs. Finally, we describe the clinical characteristics of the major human LRO disorders.
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Affiliation(s)
- Marjan Huizing
- Cell Biology of Metabolic Disorders Unit, National Institutes of Health, Bethesda, Maryland 20892, USA.
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100
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Chavas LM, Ihara K, Kawasaki M, Torii S, Uejima T, Kato R, Izumi T, Wakatsuki S. Elucidation of Rab27 Recruitment by Its Effectors: Structure of Rab27a Bound to Exophilin4/Slp2-a. Structure 2008; 16:1468-77. [DOI: 10.1016/j.str.2008.07.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Revised: 07/18/2008] [Accepted: 07/21/2008] [Indexed: 01/03/2023]
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