1
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Kashif M, Alsaiari AA, Kumar B, Asalam M, Khan MI, Ahmad A, Lone RA, Almehmadi M, Zamzami MA, Akhtar MS. Recombinant expression and preliminary characterization of Peptidyl-prolyl cis/trans-isomerase Rrd1 from Saccharomyces cerevisiae. PLoS One 2023; 18:e0282749. [PMID: 37310980 DOI: 10.1371/journal.pone.0282749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/22/2023] [Indexed: 06/15/2023] Open
Abstract
Sacchromycescerevisiae Peptidyl-prolylcis/trans-isomerase Rrd1 has been linked to DNA repair, bud morphogenesis, advancement of the G1 phase, DNA replication stress, microtubule dynamics and is also necessary for the quick decrease in Sgs1p levels in response to rapamycin. In present study, Rrd1 gene was amplified by standard PCR and subsequently cloned downstream to bacteriophage T7 inducible promoter and lac operator of expression vector pET21d(+). Additionally, immobilized metal affinity chromatography (IMAC) was used to purify the protein upto its homogeneity, and its homogeneous purity was further confirmed through western blotting. Size exclusion chromatography implies that Rrd1 is existing as monomer in its natural state. Foldwise Rrd1 protein belongs to PTPA-like protein superfamily. Rrd1 showed characteristic negative minima at 222 and 208 nm represent protein typically acquired α helix in the far-UV CD spectra. Fluorescence spectra showed properly folded tertiary structures of Rrd1 at physiological conditions. Rrd1protein can be identified from different species using a fingerprint created by PIPSA analysis. The protein's abundance could aid in its crystallization, biophysical characterization and identification of other-interacting partners of Rrd1 protein.
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Affiliation(s)
- Mohd Kashif
- Center for Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Bhupendra Kumar
- Center for Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Mohd Asalam
- CSIR-Central Drug Research Institute Sector 10, Jankipuram Extension, Lucknow, Uttar Pradesh, India
| | | | - Abrar Ahmad
- Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rayees Ahmad Lone
- Center for Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Mazen Almehmadi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohd Sohail Akhtar
- CSIR-Central Drug Research Institute Sector 10, Jankipuram Extension, Lucknow, Uttar Pradesh, India
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2
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Wu S, Fan J, Tang F, Chen L, Zhang X, Xiao D, Li X. The role of RIM in neurotransmitter release: promotion of synaptic vesicle docking, priming, and fusion. Front Neurosci 2023; 17:1123561. [PMID: 37179554 PMCID: PMC10169678 DOI: 10.3389/fnins.2023.1123561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/06/2023] [Indexed: 05/15/2023] Open
Abstract
There are many special sites at the end of a synapse called active zones (AZs). Synaptic vesicles (SVs) fuse with presynaptic membranes at these sites, and this fusion is an important step in neurotransmitter release. The cytomatrix in the active zone (CAZ) is made up of proteins such as the regulating synaptic membrane exocytosis protein (RIM), RIM-binding proteins (RIM-BPs), ELKS/CAST, Bassoon/Piccolo, Liprin-α, and Munc13-1. RIM is a scaffold protein that interacts with CAZ proteins and presynaptic functional components to affect the docking, priming, and fusion of SVs. RIM is believed to play an important role in regulating the release of neurotransmitters (NTs). In addition, abnormal expression of RIM has been detected in many diseases, such as retinal diseases, Asperger's syndrome (AS), and degenerative scoliosis. Therefore, we believe that studying the molecular structure of RIM and its role in neurotransmitter release will help to clarify the molecular mechanism of neurotransmitter release and identify targets for the diagnosis and treatment of the aforementioned diseases.
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Affiliation(s)
- Shanshan Wu
- Emergency Department, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Jiali Fan
- Emergency Department, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Fajuan Tang
- Emergency Department, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Lin Chen
- Emergency Department, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xiaoyan Zhang
- Emergency Department, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Dongqiong Xiao
- Emergency Department, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xihong Li
- Emergency Department, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
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3
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Domínguez Cadena LC, Schultz TE, Zamoshnikova A, Donovan ML, Mathmann CD, Yu CH, Mori G, Stow JL, Blumenthal A. Rab6b localizes to the Golgi complex in murine macrophages and promotes tumor necrosis factor release in response to mycobacterial infection. Immunol Cell Biol 2021; 99:1067-1076. [PMID: 34555867 DOI: 10.1111/imcb.12503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/27/2021] [Accepted: 09/21/2021] [Indexed: 11/30/2022]
Abstract
The proinflammatory cytokine tumor necrosis factor (TNF) plays a central role in the host control of mycobacterial infections. Expression and release of TNF are tightly regulated, yet the molecular mechanisms that control the release of TNF by mycobacteria-infected host cells, in particular macrophages, are incompletely understood. Rab GTPases direct the transport of intracellular membrane-enclosed vesicles and are important regulators of macrophage cytokine secretion. Rab6b is known to be predominantly expressed in the brain where it functions in retrograde transport and anterograde vesicle transport for exocytosis. Whether it executes similar functions in the context of immune responses is unknown. Here we show that Rab6b is expressed by primary mouse macrophages, where it localized to the Golgi complex. Infection with Mycobacterium bovis bacille Calmette-Guérin (BCG) resulted in dynamic changes in Rab6b expression in primary mouse macrophages in vitro as well as in organs from infected mice in vivo. We further show that Rab6b facilitated TNF release by M. bovis BCG-infected macrophages, in the absence of discernible impact on Tnf messenger RNA and intracellular TNF protein expression. Our observations identify Rab6b as a positive regulator of M. bovis BCG-induced TNF trafficking and secretion by macrophages and positions Rab6b among the molecular machinery that orchestrates inflammatory cytokine responses by macrophages.
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Affiliation(s)
- Leslie C Domínguez Cadena
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Thomas E Schultz
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Alina Zamoshnikova
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Meg L Donovan
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Carmen D Mathmann
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Chien-Hsiung Yu
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Giorgia Mori
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Jennifer L Stow
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Antje Blumenthal
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
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4
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Liu BHM, Tey SK, Mao X, Ma APY, Yeung CLS, Wong SWK, Ng TH, Xu Y, Yao Y, Fung EYM, Tan KV, Khong P, Ho DW, Ng IO, Tang AHN, Cai SH, Yun JP, Yam JWP. TPI1-reduced extracellular vesicles mediated by Rab20 downregulation promotes aerobic glycolysis to drive hepatocarcinogenesis. J Extracell Vesicles 2021; 10:e12135. [PMID: 34401050 PMCID: PMC8357635 DOI: 10.1002/jev2.12135] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 06/30/2021] [Accepted: 07/30/2021] [Indexed: 12/24/2022] Open
Abstract
Rab GTPases are major mediators that ensure the proper spatiotemporal regulation of intracellular trafficking. Functional impairment and altered expression of Rab proteins have been revealed in various human cancers. There is an emerging evidence about the role of Rab proteins in the biogenesis of extracellular vesicles (EVs). In hepatocellular carcinoma (HCC), using RNA sequencing comparing expression profiles of adjacent non-tumorous tissues and HCC, Rab20 is identified to be the most frequently downregulated Rab member in HCC. Functionally, restoration of Rab20 in metastatic HCC cells results in the release of EVs with a diminished activity to promote cell growth, motility and metastasis. Conversely, EVs released from normal liver cells with Rab20 knockdown loses suppressive effect on HCC cell growth and motility. Proteomic profiling revealed the level of triosephosphate isomerase 1 (TPI1), a glycolytic enzyme, in EVs to be positively associated with Rab20 expression of the releasing cells. TPI1 targeted to be expressed in EVs released by Rab20 knockdown cells compromises the oncogenic activity of EVs. Besides, EVs released by TPI1 knockdown cells recapitulates the promoting effect of EVs derived from HCC cells with Rab20 underexpression. Aerobic glycolysis is beneficial to the survival and proliferation of tumour cells. Here, we observed that the enhanced cell growth and motility are driven by the enhanced aerobic glycolysis induced by EVs with reduced TPI1. The addition of glycolytic inhibitor blocks the promoting effect of EVs with reduced TPI1. Taken together, our study provides a mechanistic link among tumour cell-derived EVs and glucose metabolism in HCC with Rab20 deregulation.
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Affiliation(s)
- Bonnie Hei Man Liu
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Sze Keong Tey
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Xiaowen Mao
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Angel Po Yee Ma
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Cherlie Lot Sum Yeung
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Samuel Wan Ki Wong
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Tung Him Ng
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Yi Xu
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
- Department of Hepatopancreatobiliary SurgerySecond Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Yue Yao
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
- Department of EndocrinologySecond Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Eva Yi Man Fung
- Department of ChemistryState Key Laboratory of Synthetic ChemistryThe University of Hong KongHong KongChina
| | - Kel Vin Tan
- Department of Diagnostic RadiologyQueen Mary Hospitalthe University of Hong KongHong KongChina
| | - Pek‐Lan Khong
- Department of Diagnostic RadiologyQueen Mary Hospitalthe University of Hong KongHong KongChina
| | - Daniel Wai‐Hung Ho
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
- State Key Laboratory of Liver Research (The University of Hong Kong)Hong KongChina
| | - Irene Oi‐Lin Ng
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
- State Key Laboratory of Liver Research (The University of Hong Kong)Hong KongChina
| | - Alexander Hin Ning Tang
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Shao Hang Cai
- Department of Infectious DiseasesNanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Jing Ping Yun
- Department of PathologySun Yat‐sen University Cancer CentreGuangzhouChina
| | - Judy Wai Ping Yam
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
- State Key Laboratory of Liver Research (The University of Hong Kong)Hong KongChina
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5
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Kumar AP, Verma CS, Lukman S. Structural dynamics and allostery of Rab proteins: strategies for drug discovery and design. Brief Bioinform 2020; 22:270-287. [PMID: 31950981 DOI: 10.1093/bib/bbz161] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/29/2019] [Accepted: 11/15/2019] [Indexed: 01/09/2023] Open
Abstract
Rab proteins represent the largest family of the Rab superfamily guanosine triphosphatase (GTPase). Aberrant human Rab proteins are associated with multiple diseases, including cancers and neurological disorders. Rab subfamily members display subtle conformational variations that render specificity in their physiological functions and can be targeted for subfamily-specific drug design. However, drug discovery efforts have not focused much on targeting Rab allosteric non-nucleotide binding sites which are subjected to less evolutionary pressures to be conserved, hence are likely to offer subfamily specificity and may be less prone to undesirable off-target interactions and side effects. To discover druggable allosteric binding sites, Rab structural dynamics need to be first incorporated using multiple experimentally and computationally obtained structures. The high-dimensional structural data may necessitate feature extraction methods to identify manageable representative structures for subsequent analyses. We have detailed state-of-the-art computational methods to (i) identify binding sites using data on sequence, shape, energy, etc., (ii) determine the allosteric nature of these binding sites based on structural ensembles, residue networks and correlated motions and (iii) identify small molecule binders through structure- and ligand-based virtual screening. To benefit future studies for targeting Rab allosteric sites, we herein detail a refined workflow comprising multiple available computational methods, which have been successfully used alone or in combinations. This workflow is also applicable for drug discovery efforts targeting other medically important proteins. Depending on the structural dynamics of proteins of interest, researchers can select suitable strategies for allosteric drug discovery and design, from the resources of computational methods and tools enlisted in the workflow.
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Affiliation(s)
- Ammu Prasanna Kumar
- Department of Chemistry, College of Arts and Sciences, Khalifa University, Abu Dhabi, United Arab Emirates.,Research Unit in Bioinformatics, Department of Biochemistry and Microbiology, Rhodes University, South Africa
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore
| | - Suryani Lukman
- Department of Chemistry, College of Arts and Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
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6
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Nehammer C, Ejlerskov P, Gopal S, Handley A, Ng L, Moreira P, Lee H, Issazadeh-Navikas S, Rubinsztein DC, Pocock R. Interferon-β-induced miR-1 alleviates toxic protein accumulation by controlling autophagy. eLife 2019; 8:49930. [PMID: 31799933 PMCID: PMC6914338 DOI: 10.7554/elife.49930] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/03/2019] [Indexed: 12/22/2022] Open
Abstract
Appropriate regulation of autophagy is crucial for clearing toxic proteins from cells. Defective autophagy results in accumulation of toxic protein aggregates that detrimentally affect cellular function and organismal survival. Here, we report that the microRNA miR-1 regulates the autophagy pathway through conserved targeting of the orthologous Tre-2/Bub2/CDC16 (TBC) Rab GTPase-activating proteins TBC-7 and TBC1D15 in Caenorhabditis elegans and mammalian cells, respectively. Loss of miR-1 causes TBC-7/TBC1D15 overexpression, leading to a block on autophagy. Further, we found that the cytokine interferon-β (IFN-β) can induce miR-1 expression in mammalian cells, reducing TBC1D15 levels, and safeguarding against proteotoxic challenges. Therefore, this work provides a potential therapeutic strategy for protein aggregation disorders.
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Affiliation(s)
- Camilla Nehammer
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Patrick Ejlerskov
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, United Kingdom
| | - Sandeep Gopal
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia
| | - Ava Handley
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia
| | - Leelee Ng
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia
| | - Pedro Moreira
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia
| | - Huikyong Lee
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, United Kingdom
| | - Shohreh Issazadeh-Navikas
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David C Rubinsztein
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, United Kingdom.,UK Dementia Research Institute, University of Cambridge, Cambridge, United Kingdom
| | - Roger Pocock
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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7
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Chichger H, Rounds S, Harrington EO. Endosomes and Autophagy: Regulators of Pulmonary Endothelial Cell Homeostasis in Health and Disease. Antioxid Redox Signal 2019; 31:994-1008. [PMID: 31190562 PMCID: PMC6765061 DOI: 10.1089/ars.2019.7817] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 06/07/2019] [Indexed: 12/12/2022]
Abstract
Significance: Alterations in oxidant/antioxidant balance injure pulmonary endothelial cells and are important in the pathogenesis of lung diseases, such as Acute Respiratory Distress Syndrome (ARDS), ischemia/reperfusion injury, pulmonary arterial hypertension (PAH), and emphysema. Recent Advances: The endosomal and autophagic pathways regulate cell homeostasis. Both pathways support recycling or degradation of macromolecules or organelles, targeted to endosomes or lysosomes, respectively. Thus, both processes promote cell survival. However, with environmental stress or injury, imbalance in endosomal and autophagic pathways may enhance macromolecular or organelle degradation, diminish biosynthetic processes, and cause cell death. Critical Issues: While the role of autophagy in cellular homeostasis in pulmonary disease has been investigated, the role of the endosome in the lung vasculature is less known. Furthermore, autophagy can either decrease or exacerbate endothelial injury, depending upon inciting insult and disease process. Future Directions: Diseases affecting the pulmonary endothelium, such as emphysema, ARDS, and PAH, are linked to altered endosomal or autophagic processing, leading to enhanced degradation of macromolecules and potential cell death. Efforts to target this imbalance have yielded limited success as treatments for lung injuries, which may be due to the complexity of both processes. It is possible that endosomal trafficking proteins, such as Rab GTPases and late endosomal/lysosomal adaptor, MAPK and MTOR activator 1, may be novel therapeutic targets. While endocytosis or autophagy have been linked to improved function of the pulmonary endothelium in vitro and in vivo, further studies are needed to identify targets for modulating cellular homeostasis in the lung.
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Affiliation(s)
- Havovi Chichger
- Biomedical Research Group, Department of Biomedical and Forensic Sciences, Anglia Ruskin University, Cambridge, United Kingdom
| | - Sharon Rounds
- Vascular Research Laboratory, Providence Veterans Affairs Medical Center, Providence, Rhode Island
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Alpert Medical School of Brown University, Providence, Rhode Island
| | - Elizabeth O. Harrington
- Vascular Research Laboratory, Providence Veterans Affairs Medical Center, Providence, Rhode Island
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Alpert Medical School of Brown University, Providence, Rhode Island
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8
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Münzberg E, Stein M. Structure and Dynamics of Mono- vs. Doubly Lipidated Rab5 in Membranes. Int J Mol Sci 2019; 20:ijms20194773. [PMID: 31561436 PMCID: PMC6801778 DOI: 10.3390/ijms20194773] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/25/2019] [Accepted: 09/25/2019] [Indexed: 01/13/2023] Open
Abstract
The Rab5 small GTPase is a regulator of endosomal trafficking and vesicle fusion. It possesses two adjacent cysteine residues for post-translational geranylgeranylation at its C-terminus for the protein to associate with the early endosome membrane. We compare the effect of mono-lipidification of only one cysteine residue with the doubly modified, fully functional Rab protein in both guanosine diphosphate (GDP)- and guanosine triphosphate (GTP)-bound states and in different membranes (one, three, and six-component membranes). Molecular simulations show that the mono-geranylgeranylated protein is less strongly associated with the membranes and diffuses faster than the doubly lipidated protein. The geranylgeranyl anchor membrane insertion depth is smaller and the protein–membrane distance distribution is broad and uncharacteristic for the membrane composition. The mono-geranylgeranylated protein reveals an unspecific association with the membrane and an orientation at the membrane that does not allow a nucleotide-specific recruitment of further effector proteins. This work shows that double-lipidification is critical for Rab5 to perform its physiological function and mono-geranylgeranylation renders it membrane-associated but non-functional.
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Affiliation(s)
- Eileen Münzberg
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, Sandtorstrasse 1, 39106 Magdeburg, Germany.
| | - Matthias Stein
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, Sandtorstrasse 1, 39106 Magdeburg, Germany.
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9
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Edler E, Stein M. Recognition and stabilization of geranylgeranylated human Rab5 by the GDP Dissociation Inhibitor (GDI). Small GTPases 2019; 10:227-242. [PMID: 29065764 PMCID: PMC6548291 DOI: 10.1080/21541248.2017.1371268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/18/2017] [Accepted: 08/18/2017] [Indexed: 01/13/2023] Open
Abstract
The small GTPase Rab5 is the key regulator of early endosomal fusion. It is post-translationally modified by covalent attachment of two geranylgeranyl (GG) chains to adjacent cysteine residues of the C-terminal hypervariable region (HVR). The GDP dissociation inhibitor (GDI) recognizes membrane-associated Rab5(GDP) and serves to release it into the cytoplasm where it is kept in a soluble state. A detailed new structural and dynamic model for human Rab5(GDP) recognition and binding with human GDI at the early endosome membrane and in its dissociated state is presented. In the cytoplasm, the GDI protein accommodates the GG chains in a transient hydrophobic binding pocket. In solution, two different binding modes of the isoprenoid chains inserted into the hydrophobic pocket of the Rab5(GDP):GDI complex can be identified. This equilibrium between the two states helps to stabilize the protein-protein complex in solution. Interprotein contacts between the Rab5 switch regions and characteristic patches of GDI residues from the Rab binding platform (RBP) and the C-terminus coordinating region (CCR) reveal insight on the formation of such a stable complex. GDI binding to membrane-anchored Rab5(GDP) is initially mediated by the solvent accessible switch regions of the Rab-specific RBP. Formation of the membrane-associated Rab5(GDP):GDI complex induces a GDI reorientation to establish additional interactions with the Rab5 HVR. These results allow to devise a detailed structural model for the process of extraction of GG-Rab5(GDP) by GDI from the membrane and the dissociation from targeting factors and effector proteins prior to GDI binding.
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Affiliation(s)
- Eileen Edler
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Matthias Stein
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
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10
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Kumar AP, Lukman S. Allosteric binding sites in Rab11 for potential drug candidates. PLoS One 2018; 13:e0198632. [PMID: 29874286 PMCID: PMC5991966 DOI: 10.1371/journal.pone.0198632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/22/2018] [Indexed: 12/19/2022] Open
Abstract
Rab11 is an important protein subfamily in the RabGTPase family. These proteins physiologically function as key regulators of intracellular membrane trafficking processes. Pathologically, Rab11 proteins are implicated in many diseases including cancers, neurodegenerative diseases and type 2 diabetes. Although they are medically important, no previous study has found Rab11 allosteric binding sites where potential drug candidates can bind to. In this study, by employing multiple clustering approaches integrating principal component analysis, independent component analysis and locally linear embedding, we performed structural analyses of Rab11 and identified eight representative structures. Using these representatives to perform binding site mapping and virtual screening, we identified two novel binding sites in Rab11 and small molecules that can preferentially bind to different conformations of these sites with high affinities. After identifying the binding sites and the residue interaction networks in the representatives, we computationally showed that these binding sites may allosterically regulate Rab11, as these sites communicate with switch 2 region that binds to GTP/GDP. These two allosteric binding sites in Rab11 are also similar to two allosteric pockets in Ras that we discovered previously.
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Affiliation(s)
- Ammu Prasanna Kumar
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Suryani Lukman
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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11
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Makaraci P, Kim K. trans-Golgi network-bound cargo traffic. Eur J Cell Biol 2018; 97:137-149. [PMID: 29398202 DOI: 10.1016/j.ejcb.2018.01.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/15/2017] [Accepted: 01/16/2018] [Indexed: 12/19/2022] Open
Abstract
Cargo following the retrograde trafficking are sorted at endosomes to be targeted the trans-Golgi network (TGN), a central receiving organelle. Though molecular requirements and their interaction networks have been somewhat established, the complete understanding of the intricate nature of their action mechanisms in every step of the retrograde traffic pathway remains unachieved. This review focuses on elucidating known functions of key regulators, including scission factors at the endosome and tethering/fusion mediators at the receiving dock, TGN, as well as a diverse range of cargo.
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Affiliation(s)
- Pelin Makaraci
- Department of Biology, Missouri State University, 901 S National Ave., Springfield, MO 65807, USA
| | - Kyoungtae Kim
- Department of Biology, Missouri State University, 901 S National Ave., Springfield, MO 65807, USA.
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12
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Inoshita M, Mima J. Human Rab small GTPase- and class V myosin-mediated membrane tethering in a chemically defined reconstitution system. J Biol Chem 2017; 292:18500-18517. [PMID: 28939769 DOI: 10.1074/jbc.m117.811356] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/21/2017] [Indexed: 12/13/2022] Open
Abstract
Membrane tethering is a fundamental process essential for the compartmental specificity of intracellular membrane trafficking in eukaryotic cells. Rab-family small GTPases and specific sets of Rab-interacting effector proteins, including coiled-coil tethering proteins and multisubunit tethering complexes, are reported to be responsible for membrane tethering. However, whether and how these key components directly and specifically tether subcellular membranes remains enigmatic. Using chemically defined proteoliposomal systems reconstituted with purified human Rab proteins and synthetic liposomal membranes to study the molecular basis of membrane tethering, we established here that Rab-family GTPases have a highly conserved function to directly mediate membrane tethering, even in the absence of any types of Rab effectors such as the so-called tethering proteins. Moreover, we demonstrate that membrane tethering mediated by endosomal Rab11a is drastically and selectively stimulated by its cognate Rab effectors, class V myosins (Myo5A and Myo5B), in a GTP-dependent manner. Of note, Myo5A and Myo5B exclusively recognized and cooperated with the membrane-anchored form of their cognate Rab11a to support membrane tethering mediated by trans-Rab assemblies on opposing membranes. Our findings support the novel concept that Rab-family proteins provide a bona fide membrane tether to physically and specifically link two distinct lipid bilayers of subcellular membranes. They further indicate that Rab-interacting effector proteins, including class V myosins, can regulate these Rab-mediated membrane-tethering reactions.
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Affiliation(s)
- Motoki Inoshita
- From the Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Joji Mima
- From the Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
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13
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Edler E, Schulze E, Stein M. Membrane localization and dynamics of geranylgeranylated Rab5 hypervariable region. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1335-1349. [PMID: 28455099 DOI: 10.1016/j.bbamem.2017.04.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/18/2017] [Accepted: 04/23/2017] [Indexed: 12/11/2022]
Abstract
The small GTPase Rab5 is a key regulator of endosomal trafficking processes and a marker for the early endosome. The C-terminal hypervariable region (HVR) of Rab5 is post-translationally modified at residues Cys212 and Cys213 to accommodate two geranylgeranyl anchors (C20 carbon chain length) in order to associate Rab5 with the membrane. The structural role of the HVR regarding protein-early endosome membrane recruitment is not resolved due to its high degree of flexibility and lack of crystallographic information. Here, full-atomistic and coarse-grained molecular dynamics simulations of the truncated Rab5 HVR206-215 in three model membranes of increasing complexity (pure phospholipid bilayer, ternary membrane with cholesterol, six-component early endosome) were performed. Specific electrostatic interactions between the HVR206-215 Arg209 residue and the phosphate group of the inositol ring of PI(3)P were detected. This shows that PI(3)P acts as a first contact site of protein recruitment to the early endosome. The free energy change of HVR206-215 extraction from the bilayer was largest for the physiological negatively charged membrane. 5μs coarse-grained simulations revealed an active recruitment of PI(3)P to the HVR206-215 supporting the formation of Rab5- and PI(3)P enriched signaling platforms.
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Affiliation(s)
- Eileen Edler
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Eric Schulze
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany; International Max Planck Research School (IMPRS) for Advanced Methods in Process and Systems Engineering, Magdeburg, Germany
| | - Matthias Stein
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany.
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14
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Pérez-Montesinos G, López-Ortega O, Piedra-Reyes J, Bonifaz LC, Moreno J. Dynamic Changes in the Intracellular Association of Selected Rab Small GTPases with MHC Class II and DM during Dendritic Cell Maturation. Front Immunol 2017; 8:340. [PMID: 28396666 PMCID: PMC5367080 DOI: 10.3389/fimmu.2017.00340] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/09/2017] [Indexed: 01/13/2023] Open
Abstract
Antigen processing for presentation by major histocompatibility complex class II (MHCII) molecules requires the latter to travel through the endocytic pathway together with its chaperons: the invariant chain (Ii) and DM. Nevertheless, the nature of the compartments where MHCII molecules travel to acquire peptides lacks definition regarding molecules involved in intracellular vesicular trafficking, such as Rab small GTPases. We aimed to define which Rab proteins are present during the intracellular transport of MHCII, DM, and Ii through the endocytic pathway on their route to the cell surface during dendritic cell (DC) maturation. We examined, by means of three-color confocal microscopy, the association of MHCII, DM, and Ii with Rab5, Rab7, Rab9, and Rab11 during the maturation of bone marrow-derived or spleen DC in response to LPS as an inflammatory stimulus. Prior to the stage of immature DC, MHCII migrated from diffuse small cytoplasmic vesicles, predominantly Rab5+Rab7- and Rab5+Rab7+ into a pericentriolar Rab5+Rab7+Rab9+ cluster, with Rab11+ areas. As DC reached the mature phenotype, MHCII left the pericentriolar endocytic compartments toward the cell surface in Rab11+ and Rab9+Rab11+ vesicles. The invariant chain and MHCII transport pathways were not identical. DM and MHCII appeared to arrive to pericentriolar endocytic compartments of immature DC through partially different routes. The association of MHCII molecules with distinct Rab GTPases during DC maturation suggests that after leaving the biosynthetic pathway, MHCII sequentially traffic from typical early endosomes to multivesicular late endosomes to finally arrive at the cell surface in Rab11+ recycling-type endosomes. In immature DCs, DM encounters transiently MHCII in the Rab5+Rab7+Rab9+ compartments, to remain there in mature DC.
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Affiliation(s)
- Gibrán Pérez-Montesinos
- Research Unit on Autoimmune Diseases, Research Unit on Immunochemistry, Centro México Nacional Siglo XXI, IMSS, Instituto Mexicano del Seguro Social, Mexico City, Distrito Federal, Mexico
- Centro Dermatológico “Dr. Ladislao de la Pascua”, Secretaría de Salud del Distrito Federal, Mexico City, Distrito Federal, Mexico
| | - Orestes López-Ortega
- Hospital Juárez de México, Secretaría de Salud, Mexico City, Distrito Federal, Mexico
| | - Jessica Piedra-Reyes
- Hospital Juárez de México, Secretaría de Salud, Mexico City, Distrito Federal, Mexico
| | - Laura C. Bonifaz
- Research Unit on Autoimmune Diseases, Research Unit on Immunochemistry, Centro México Nacional Siglo XXI, IMSS, Instituto Mexicano del Seguro Social, Mexico City, Distrito Federal, Mexico
| | - José Moreno
- Research Unit on Autoimmune Diseases, Research Unit on Immunochemistry, Centro México Nacional Siglo XXI, IMSS, Instituto Mexicano del Seguro Social, Mexico City, Distrito Federal, Mexico
- Hospital Juárez de México, Secretaría de Salud, Mexico City, Distrito Federal, Mexico
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15
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Bright LJ, Gout JF, Lynch M. Early stages of functional diversification in the Rab GTPase gene family revealed by genomic and localization studies in Paramecium species. Mol Biol Cell 2017; 28:1101-1110. [PMID: 28251922 PMCID: PMC5391186 DOI: 10.1091/mbc.e16-06-0361] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 02/21/2017] [Accepted: 02/22/2017] [Indexed: 01/08/2023] Open
Abstract
Rab GTPase family members in Paramecium have higher retention rates and more-divergent expression levels than other genes after whole-genome duplications, consistent with early steps in functional diversification. Localization analysis also uncovers functionally diversifying Rab11 genes. New gene functions arise within existing gene families as a result of gene duplication and subsequent diversification. To gain insight into the steps that led to the functional diversification of paralogues, we tracked duplicate retention patterns, expression-level divergence, and subcellular markers of functional diversification in the Rab GTPase gene family in three Paramecium aurelia species. After whole-genome duplication, Rab GTPase duplicates are more highly retained than other genes in the genome but appear to be diverging more rapidly in expression levels, consistent with early steps in functional diversification. However, by localizing specific Rab proteins in Paramecium cells, we found that paralogues from the two most recent whole-genome duplications had virtually identical localization patterns, and that less closely related paralogues showed evidence of both conservation and diversification. The functionally conserved paralogues appear to target to compartments associated with both endocytic and phagocytic recycling functions, confirming evolutionary and functional links between the two pathways in a divergent eukaryotic lineage. Because the functionally diversifying paralogues are still closely related to and derived from a clade of functionally conserved Rab11 genes, we were able to pinpoint three specific amino acid residues that may be driving the change in the localization and thus the function in these proteins.
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Affiliation(s)
- Lydia J Bright
- Department of Biology, Indiana University, Bloomington, IN 47405 .,Department of Biology, State University of New York at New Paltz, New Paltz, NY 12561
| | | | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN 47405
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16
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Edler E, Stein M. Probing the druggability of membrane-bound Rab5 by molecular dynamics simulations. J Enzyme Inhib Med Chem 2017; 32:434-443. [PMID: 28090783 PMCID: PMC6010109 DOI: 10.1080/14756366.2016.1260564] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Rab5 is a small GTPase and a key regulator in early endosomal trafficking. Rab5 and its effectors are involved in a large number of infectious diseases and certain types of cancer. We performed µs atomistic molecular dynamics simulations of inactive and active full-length Rab5 anchored to a complex model bilayer with composition of the early endosome membrane. Direct interactions between the Rab5 G domain and the bilayer were observed. We found two dominant nucleotide-dependent orientations characterised by a different accessibility of the switch regions. The “buried switch” orientation was mainly associated with inactive Rab5 accompanied with a rather extended structure of the hypervariable C-terminal region. Active Rab5 preferred an orientation in which the switch regions are accessible to effector proteins. These structural differences may provide an opportunity to selectively target one Rab5 state and lead to new approaches in the development of Rab5-specific therapies.
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Affiliation(s)
- Eileen Edler
- a Molecular Simulations and Design Group , Max Planck Institute for Dynamics of Complex Technical Systems , Magdeburg , Germany
| | - Matthias Stein
- a Molecular Simulations and Design Group , Max Planck Institute for Dynamics of Complex Technical Systems , Magdeburg , Germany
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17
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Lukman S, Nguyen MN, Sim K, Teo JCM. Discovery of Rab1 binding sites using an ensemble of clustering methods. Proteins 2017; 85:859-871. [PMID: 28120477 DOI: 10.1002/prot.25254] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/28/2016] [Accepted: 01/19/2017] [Indexed: 12/29/2022]
Abstract
Targeting non-native-ligand binding sites for potential investigative and therapeutic applications is an attractive strategy in proteins that share common native ligands, as in Rab1 protein. Rab1 is a subfamily member of Rab proteins, which are members of Ras GTPase superfamily. All Ras GTPase superfamily members bind to native ligands GTP and GDP, that switch on and off the proteins, respectively. Rab1 is physiologically essential for autophagy and transport between endoplasmic reticulum and Golgi apparatus. Pathologically, Rab1 is implicated in human cancers, a neurodegenerative disease, cardiomyopathy, and bacteria-caused infectious diseases. We have performed structural analyses on Rab1 protein using a unique ensemble of clustering methods, including multi-step principal component analysis, non-negative matrix factorization, and independent component analysis, to better identify representative Rab1 proteins than the application of a single clustering method alone does. We then used the identified representative Rab1 structures, resolved in multiple ligand states, to map their known and novel binding sites. We report here at least a novel binding site on Rab1, involving Rab1-specific residues that could be further explored for the rational design and development of investigative probes and/or therapeutic small molecules against the Rab1 protein. Proteins 2017; 85:859-871. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Suryani Lukman
- Khalifa University, Abu Dhabi Campus, PO Box, 127788, Abu Dhabi, United Arab Emirates
| | - Minh N Nguyen
- Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Kelvin Sim
- OneAnalytix Pte Ltd, Onn Wah Building #04-01, 11 Changi South Lane Singapore, 486154, Singapore
| | - Jeremy C M Teo
- Khalifa University, Abu Dhabi Campus, PO Box, 127788, Abu Dhabi, United Arab Emirates
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18
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Jacob A, Linklater E, Bayless BA, Lyons T, Prekeris R. The role and regulation of Rab40b-Tks5 complex during invadopodia formation and cancer cell invasion. J Cell Sci 2016; 129:4341-4353. [PMID: 27789576 PMCID: PMC5201011 DOI: 10.1242/jcs.193904] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/30/2016] [Indexed: 12/12/2022] Open
Abstract
Invadopodia formation and extracellular matrix degradation are key events during cancer cell invasion, yet little is known about mechanisms mediating these processes. Here, we report that Rab40b plays a key role in mediating invadopodia function during breast cancer cell invasion. We also identify Tks5 (also known as SH3PXD2A), a known Src kinase substrate, as a new Rab40b effector protein and show that Tks5 functions as a tether that mediates Rab40b-dependent targeting of transport vesicles containing MMP2 and MMP9 to the extending invadopodia. Importantly, we also demonstrate that Rab40b and Tks5 levels are regulated by known tumor suppressor microRNA miR-204. This is the first study that identifies a new Rab40b–Tks5- and miR-204-dependent invadopodia transport pathway that regulates MMP2 and MMP9 secretion, and extracellular matrix remodeling during cancer progression. Highlighted Article: Rab40b plays a key role in mediating invadopodia function during breast cancer cell invasion by binding to Tks5 and functioning as a tether mediating MMP2 and MMP9 targeting to the extending invadopodia.
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Affiliation(s)
- Abitha Jacob
- Department of Cell and Developmental Biology, School of Medicine, Anschutz Medical Campus, University of Colorado Denver, Aurora, CO 80045, USA
| | - Erik Linklater
- Department of Cell and Developmental Biology, School of Medicine, Anschutz Medical Campus, University of Colorado Denver, Aurora, CO 80045, USA
| | - Brian A Bayless
- Department of Cell and Developmental Biology, School of Medicine, Anschutz Medical Campus, University of Colorado Denver, Aurora, CO 80045, USA
| | - Traci Lyons
- Department of Medicine/Division of Medical Oncology, School of Medicine, Anschutz Medical Campus, University of Colorado Denver, Aurora, CO 80045, USA
| | - Rytis Prekeris
- Department of Cell and Developmental Biology, School of Medicine, Anschutz Medical Campus, University of Colorado Denver, Aurora, CO 80045, USA
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19
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Tong R, Wade RC, Bruce NJ. Comparative electrostatic analysis of adenylyl cyclase for isoform dependent regulation properties. Proteins 2016; 84:1844-1858. [PMID: 27667304 DOI: 10.1002/prot.25167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/29/2016] [Accepted: 09/06/2016] [Indexed: 01/26/2023]
Abstract
The enzyme adenylyl cyclase (AC) plays a pivotal role in a variety of signal transduction pathways inside the cell, where it catalyzes the cyclization of adenosine triphosphate (ATP) into the second-messenger cyclic adenosine monophosphate (cAMP). Among other roles, AC regulates processes involved in neural plasticity, innervation of smooth muscles of the heart and the endocrine system of the pancreas. The functional diversity of AC is manifested in its different isoforms, each having a specific regulation pattern. There is an increasing amount of data available concerning the regulatory properties of AC isoforms, however little is known about the interactions on a structural level. Here, we conducted a comparative electrostatic analysis of the catalytic domains of all nine transmembrane AC isoforms with the aim of detecting, verifying and predicting the binding sites of molecular regulators on AC. The results provide support for the positioning of the binding site of the inhibitory protein Gi α at a pseudo-symmetric position to the stimulatory Gs α binding site. They also provide a structural interpretation of the Gβγ interaction with ACs 2, 4, and 7 and suggest a new binding site for RGS2. Comparison of the small molecule binding sites on AC shows that overall they have high electrostatic similarity, but regions of electrostatic differences are identified. These could provide a basis for the development of novel compounds with isoform-specific modulatory effects on AC. Proteins 2016; 84:1844-1858. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Rudi Tong
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.,Institute of Pharmacy and Molecular Biotechnology (IPMB) Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR) Heidelberg University, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany
| | - Neil J Bruce
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
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20
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Sakane A, Yoshizawa S, Nishimura M, Tsuchiya Y, Matsushita N, Miyake K, Horikawa K, Imoto I, Mizuguchi C, Saito H, Ueno T, Matsushita S, Haga H, Deguchi S, Mizuguchi K, Yokota H, Sasaki T. Conformational plasticity of JRAB/MICAL-L2 provides "law and order" in collective cell migration. Mol Biol Cell 2016; 27:3095-3108. [PMID: 27582384 PMCID: PMC5063617 DOI: 10.1091/mbc.e16-05-0332] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/23/2016] [Indexed: 01/23/2023] Open
Abstract
In fundamental biological processes, cells often move in groups, a process termed collective cell migration. Collectively migrating cells are much better organized than a random assemblage of individual cells. Many molecules have been identified as factors involved in collective cell migration, and no one molecule is adequate to explain the whole picture. Here we show that JRAB/MICAL-L2, an effector protein of Rab13 GTPase, provides the "law and order" allowing myriad cells to behave as a single unit just by changing its conformation. First, we generated a structural model of JRAB/MICAL-L2 by a combination of bioinformatic and biochemical analyses and showed how JRAB/MICAL-L2 interacts with Rab13 and how its conformational change occurs. We combined cell biology, live imaging, computational biology, and biomechanics to show that impairment of conformational plasticity in JRAB/MICAL-L2 causes excessive rigidity and loss of directionality, leading to imbalance in cell group behavior. This multidisciplinary approach supports the concept that the conformational plasticity of a single molecule provides "law and order" in collective cell migration.
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Affiliation(s)
- Ayuko Sakane
- Department of Biochemistry, Tokushima University, Tokushima 770-8503, Japan
| | - Shin Yoshizawa
- Image Processing Research Team, RIKEN Center for Advanced Photonics, RIKEN, Wako 351-0198, Japan
| | - Masaomi Nishimura
- Image Processing Research Team, RIKEN Center for Advanced Photonics, RIKEN, Wako 351-0198, Japan
| | - Yuko Tsuchiya
- National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki 567-0085, Japan
| | - Natsuki Matsushita
- Translational Research Center, Ehime University Hospital, Ehime 791-0295, Japan
| | - Kazuhisa Miyake
- Department of Biochemistry, Tokushima University, Tokushima 770-8503, Japan
| | - Kazuki Horikawa
- Department of Optical Imaging, Tokushima University, Tokushima 770-8503, Japan
| | - Issei Imoto
- Department of Human Genetics, Graduate School of Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Chiharu Mizuguchi
- Institute of Biomedical Sciences, Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Hiroyuki Saito
- Institute of Biomedical Sciences, Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Takato Ueno
- Transdisciplinary Life Science Course, Faculty of Advanced Life Science, Hokkaido University, Sapporo 770-8503, Japan
| | - Sachi Matsushita
- Translational Research Center, Ehime University Hospital, Ehime 791-0295, Japan
| | - Hisashi Haga
- Transdisciplinary Life Science Course, Faculty of Advanced Life Science, Hokkaido University, Sapporo 770-8503, Japan
| | - Shinji Deguchi
- Laboratory for Mechanobiology and Bioengineering, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Kenji Mizuguchi
- National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki 567-0085, Japan
| | - Hideo Yokota
- Image Processing Research Team, RIKEN Center for Advanced Photonics, RIKEN, Wako 351-0198, Japan
| | - Takuya Sasaki
- Department of Biochemistry, Tokushima University, Tokushima 770-8503, Japan
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21
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Liu S, Majeed W, Kudlyk T, Lupashin V, Storrie B. Identification of Rab41/6d Effectors Provides an Explanation for the Differential Effects of Rab41/6d and Rab6a/a' on Golgi Organization. Front Cell Dev Biol 2016; 4:13. [PMID: 26973836 PMCID: PMC4771738 DOI: 10.3389/fcell.2016.00013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 02/09/2016] [Indexed: 11/24/2022] Open
Abstract
Unexpectedly, members of the Rab VI subfamily exhibit considerable variation in their effects on Golgi organization and trafficking. By fluorescence microscopy, neither depletion nor overexpression of the GDP-locked form of Rab6a/a', the first trans Golgi-associated Rab protein discovered, affects Golgi ribbon organization while, on the other hand, both Rab41/6d depletion and overexpression of GDP-locked form cause Golgi fragmentation into a cluster of punctate elements, suggesting that Rab41/6d has an active role in maintenance of Golgi ribbon organization. To establish a molecular basis for these differences, we screened for Rab41/6d interacting proteins by yeast two-hybrid assay. 155 non-repetitive hits were isolated and sequenced, and after searching in NCBI database, 102 different proteins and protein fragments were identified. None of these hits overlapped with any published Rab6a/a' effector. Eight putative Rab41 interactors involved in membrane trafficking were found. Significantly, these exhibited a preferential interaction with GTP- vs. GDP-locked Rab41/6d. Of the 8 hits, the dynactin 6, syntaxin 8, and Kif18A plasmids were the only ones expressing the full-length protein. Hence, these 3 proteins were selected for further study. We found that depletion of dynactin 6 or syntaxin 8, but not Kif18A, resulted in a fragmented Golgi apparatus that displayed a Rab41/6d knockdown phenotype, i.e., the Golgi apparatus was disrupted into a cluster of punctate Golgi elements. Co-immunoprecipation experiments verified that the interaction of dynactin 6 and syntaxin 8 with GTP-locked Rab41/6d was stronger than that with wild type Rab41/6d and least with the GDP-locked form. In contrast, co-immunoprecipitation interaction with Rab6a was greatest with the GDP-locked Rab6a, suggestive of a non-physiological interaction. In conclusion, we suggest that dynactin 6, a subunit of dynactin complex, the minus-end-directed, dynein motor, provides a sufficient molecular basis to explain the active role of Rab41/6d in maintaining Golgi ribbon organization while syntaxin 8 contributes more indirectly to Golgi positioning.
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Affiliation(s)
- Shijie Liu
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences Little Rock, AR, USA
| | - Waqar Majeed
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences Little Rock, AR, USA
| | - Tetyana Kudlyk
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences Little Rock, AR, USA
| | - Vladimir Lupashin
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences Little Rock, AR, USA
| | - Brian Storrie
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences Little Rock, AR, USA
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22
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Alterations in late endocytic trafficking related to the pathobiology of LRRK2-linked Parkinson's disease. Biochem Soc Trans 2016; 43:390-5. [PMID: 26009181 DOI: 10.1042/bst20140301] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene comprise the most common cause of familial Parkinson's disease (PD), and variants increase the risk for sporadic PD. LRRK2 displays kinase and GTPase activity, and altered catalytic activity correlates with neurotoxicity, making LRRK2 a promising therapeutic target. Despite the importance of LRRK2 for disease pathogenesis, its normal cellular function, and the mechanism(s) by which pathogenic mutations cause neurodegeneration remain unclear. LRRK2 seems to regulate a variety of intracellular vesicular trafficking events to and from the late endosome in a manner dependent on various Rab proteins. At least some of those events are further regulated by LRRK2 in a manner dependent on two-pore channels (TPCs). TPCs are ionic channels localized to distinct endosomal structures and can cause localized calcium release from those acidic stores, with downstream effects on vesicular trafficking. Here, we review current knowledge about the link between LRRK2, TPC- and Rab-mediated vesicular trafficking to and from the late endosome, highlighting a possible cross-talk between endolysosomal calcium stores and Rab proteins underlying pathomechanism(s) in LRRK2-related PD.
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23
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Garg D, Skouloubris S, Briffotaux J, Myllykallio H, Wade RC. Conservation and Role of Electrostatics in Thymidylate Synthase. Sci Rep 2015; 5:17356. [PMID: 26612036 PMCID: PMC4661567 DOI: 10.1038/srep17356] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 10/28/2015] [Indexed: 11/17/2022] Open
Abstract
Conservation of function across families of orthologous enzymes is generally accompanied by conservation of their active site electrostatic potentials. To study the electrostatic conservation in the highly conserved essential enzyme, thymidylate synthase (TS), we conducted a systematic species-based comparison of the electrostatic potential in the vicinity of its active site. Whereas the electrostatics of the active site of TS are generally well conserved, the TSs from minimal organisms do not conform to the overall trend. Since the genomes of minimal organisms have a high thymidine content compared to other organisms, the observation of non-conserved electrostatics was surprising. Analysis of the symbiotic relationship between minimal organisms and their hosts, and the genetic completeness of the thymidine synthesis pathway suggested that TS from the minimal organism Wigglesworthia glossinidia (W.g.b.) must be active. Four residues in the vicinity of the active site of Escherichia coli TS were mutated individually and simultaneously to mimic the electrostatics of W.g.b TS. The measured activities of the E. coli TS mutants imply that conservation of electrostatics in the region of the active site is important for the activity of TS, and suggest that the W.g.b. TS has the minimal activity necessary to support replication of its reduced genome.
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Affiliation(s)
- Divita Garg
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.,Munich Center for Integrated Protein Science, Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Stephane Skouloubris
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645, INSERM U1182, Université Paris-Saclay, 91128, Palaiseau, France.,Université Paris-Sud, 91405, Orsay, France
| | - Julien Briffotaux
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645, INSERM U1182, Université Paris-Saclay, 91128, Palaiseau, France
| | - Hannu Myllykallio
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645, INSERM U1182, Université Paris-Saclay, 91128, Palaiseau, France
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Baden-Württemberg, Germany
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24
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Soltan Ghoraie L, Burkowski F, Zhu M. Using kernelized partial canonical correlation analysis to study directly coupled side chains and allostery in small G proteins. Bioinformatics 2015; 31:i124-32. [PMID: 26072474 PMCID: PMC4765857 DOI: 10.1093/bioinformatics/btv241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Motivation: Inferring structural dependencies among a protein’s side chains helps us understand their coupled motions. It is known that coupled fluctuations can reveal pathways of communication used for information propagation in a molecule. Side-chain conformations are commonly represented by multivariate angular variables, but existing partial correlation methods that can be applied to this inference task are not capable of handling multivariate angular data. We propose a novel method to infer direct couplings from this type of data, and show that this method is useful for identifying functional regions and their interactions in allosteric proteins. Results: We developed a novel extension of canonical correlation analysis (CCA), which we call ‘kernelized partial CCA’ (or simply KPCCA), and used it to infer direct couplings between side chains, while disentangling these couplings from indirect ones. Using the conformational information and fluctuations of the inactive structure alone for allosteric proteins in the Ras and other Ras-like families, our method identified allosterically important residues not only as strongly coupled ones but also in densely connected regions of the interaction graph formed by the inferred couplings. Our results were in good agreement with other empirical findings. By studying distinct members of the Ras, Rho and Rab sub-families, we show further that KPCCA was capable of inferring common allosteric characteristics in the small G protein super-family. Availability and implementation:https://github.com/lsgh/ismb15 Contact:lsoltang@uwaterloo.ca
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Affiliation(s)
- Laleh Soltan Ghoraie
- Department of Computer Science and Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON, Canada
| | - Forbes Burkowski
- Department of Computer Science and Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON, Canada
| | - Mu Zhu
- Department of Computer Science and Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON, Canada
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25
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Sohn YS, Shin HC, Park WS, Ge J, Kim CH, Lee BL, Do Heo W, Jung JU, Rigden DJ, Oh BH. Lpg0393 of Legionella pneumophila is a guanine-nucleotide exchange factor for Rab5, Rab21 and Rab22. PLoS One 2015; 10:e0118683. [PMID: 25821953 PMCID: PMC4379102 DOI: 10.1371/journal.pone.0118683] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/22/2015] [Indexed: 11/18/2022] Open
Abstract
Legionella pneumophila, a human intracellular pathogen, encodes about 290 effector proteins that are translocated into host cells through a secretion machinery. Some of these proteins have been shown to manipulate or subvert cellular processes during infection, but functional roles of a majority of them remain unknown. Lpg0393 is a newly identified Legionella effector classified as a hypothetical protein. Through X-ray crystallographic analysis, we show that Lpg0393 contains a Vps9-like domain, which is structurally most similar to the catalytic core of human Rabex-5 that activates the endosomal Rab proteins Rab5, Rab21 and Rab22. Consistently, Lpg0393 exhibited a guanine-nucleotide exchange factor activity toward the endosomal Rabs. This work identifies the first example of a bacterial guanine-nucleotide exchange factor that is active towards the Rab5 sub-cluster members, implying that the activation of these Rab proteins might be advantageous for the intracellular survival of Legionella.
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Affiliation(s)
- Young-Sik Sohn
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Korea
| | - Ho-Chul Shin
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Korea
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-600, Korea
| | - Wei Sun Park
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Korea
| | - Jianning Ge
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Chan-Hee Kim
- Global Research Laboratory of Insect Symbiosis, College of Pharmacy, Pusan National University, Jangjeon Dong, Kumjeong Ku, Busan, 609-735, Korea
| | - Bok Luel Lee
- Global Research Laboratory of Insect Symbiosis, College of Pharmacy, Pusan National University, Jangjeon Dong, Kumjeong Ku, Busan, 609-735, Korea
| | - Won Do Heo
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Korea
| | - Jae U. Jung
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Daniel John Rigden
- Institute of Integrative Biology, University of Liverpool, Crown St., Liverpool, L69 7ZB, United Kingdom
- * E-mail: (BHO); (DJR)
| | - Byung-Ha Oh
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Korea
- * E-mail: (BHO); (DJR)
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26
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Liu S, Storrie B. How Rab proteins determine Golgi structure. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:1-22. [PMID: 25708460 DOI: 10.1016/bs.ircmb.2014.12.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rab proteins, small GTPases, are key regulators of mammalian Golgi apparatus organization. Based on the effect of Rab activation state, Rab proteins fall into two functional classes. In Class1, inactivation induces Golgi ribbon fragmentation and/or redistribution of Golgi enzymes to the Endoplasmic Reticulum, while overexpression of wild type or activation has little, if any, effect on Golgi ribbon organization. In Class 2, the reverse is true. We give emphasis to Rab6, the most abundant Golgi-associated Rab protein. Rab6 depletion in HeLa cells causes an increase in Golgi cisternal number, longer, more continuous cisternae, and a pronounced accumulation of vesicles; the effect of Rab6 on Golgi ribbon organization is probably through regulation of vesicle transport. In effector studies, motor proteins and their regulators are found to be key Rab6 effectors. A related Rab, Rab41, affects Golgi ribbon organization in a contrasting manner. The balance between minus- and plus-end directed motor recruitment may well be the major Rab-dependent factor in Golgi ribbon organization.
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Affiliation(s)
- Shijie Liu
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Brian Storrie
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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27
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Wandinger-Ness A, Zerial M. Rab proteins and the compartmentalization of the endosomal system. Cold Spring Harb Perspect Biol 2014; 6:a022616. [PMID: 25341920 PMCID: PMC4413231 DOI: 10.1101/cshperspect.a022616;] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Of the approximately 70 human Rab GTPases, nearly three-quarters are involved in endocytic trafficking. Significant plasticity in endosomal membrane transport pathways is closely coupled to receptor signaling and Rab GTPase-regulated scaffolds. Here we review current literature pertaining to endocytic Rab GTPase localizations, functions, and coordination with regulatory proteins and effectors. The roles of Rab GTPases in (1) compartmentalization of the endocytic pathway into early, recycling, late, and lysosomal routes; (2) coordination of individual transport steps from vesicle budding to fusion; (3) effector interactomes; and (4) integration of GTPase and signaling cascades are discussed.
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Affiliation(s)
- Angela Wandinger-Ness
- Department of Pathology MSC08 4640, University of New Mexico HSC, Albuquerque, New Mexico 87131
| | - Marino Zerial
- Max Planck Institute of Molecular and Cell Biology and Genetics, 01307 Dresden, Germany
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28
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Wandinger-Ness A, Zerial M. Rab proteins and the compartmentalization of the endosomal system. Cold Spring Harb Perspect Biol 2014; 6:a022616. [PMID: 25341920 DOI: 10.1101/cshperspect.a022616] [Citation(s) in RCA: 414] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Of the approximately 70 human Rab GTPases, nearly three-quarters are involved in endocytic trafficking. Significant plasticity in endosomal membrane transport pathways is closely coupled to receptor signaling and Rab GTPase-regulated scaffolds. Here we review current literature pertaining to endocytic Rab GTPase localizations, functions, and coordination with regulatory proteins and effectors. The roles of Rab GTPases in (1) compartmentalization of the endocytic pathway into early, recycling, late, and lysosomal routes; (2) coordination of individual transport steps from vesicle budding to fusion; (3) effector interactomes; and (4) integration of GTPase and signaling cascades are discussed.
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Affiliation(s)
- Angela Wandinger-Ness
- Department of Pathology MSC08 4640, University of New Mexico HSC, Albuquerque, New Mexico 87131
| | - Marino Zerial
- Max Planck Institute of Molecular and Cell Biology and Genetics, 01307 Dresden, Germany
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29
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Kiss RS, Nilsson T. Rab proteins implicated in lipid storage and mobilization. J Biomed Res 2014; 28:169-77. [PMID: 25013400 PMCID: PMC4085554 DOI: 10.7555/jbr.28.20140029] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 02/28/2014] [Indexed: 12/28/2022] Open
Abstract
Abnormal intracellular accumulation or transport of lipids contributes greatly to the pathogenesis of human diseases. In the liver, excess accumulation of triacylglycerol (TG) leads to fatty liver disease encompassing steatosis, steatohepatitis and fibrosis. This places individuals at risk of developing cirrhosis, hepatocellular carcinoma or hepatic decompensation and also contributes to the emergence of insulin resistance and dyslipidemias affecting many other organs. Excessive accumulation of TG in adipose tissue contributes to insulin resistance as well as to the release of cytokines attracting leucocytes leading to a pro-inflammatory state. Pathological accumulation of cholesteryl ester (CE) in macrophages in the arterial wall is the progenitor of atherosclerotic plaques and heart disease. Overconsumption of dietary fat, cholesterol and carbohydrates explains why these diseases are on the increase yet offers few clues for how to prevent or treat individuals. Dietary regimes have proven futile and barring surgery, no realistic alternatives are at hand as effective drugs are few and not without side effects. Overweight and obesity-related diseases are no longer restricted to the developed world and as such, constitute a global problem. Development of new drugs and treatment strategies are a priority yet requires as a first step, elucidation of the molecular pathophysiology underlying each associated disease state. The lipid droplet (LD), an up to now overlooked intracellular organelle, appears at the heart of each pathophysiology linking key regulatory and metabolic processes as well as constituting the site of storage of both TGs and CEs. As the molecular machinery and mechanisms of LDs of each cell type are being elucidated, regulatory proteins used to control various cellular processes are emerging. Of these and the subject of this review, small GTPases belonging to the Rab protein family appear as important molecular switches used in the regulation of the intracellular trafficking and storage of lipids.
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Affiliation(s)
- Robert Scott Kiss
- Department of Medicine, McGill University, Montreal, Canada; ; Research Institute of McGill University Health Centre, Montreal, Canada
| | - Tommy Nilsson
- Department of Medicine, McGill University, Montreal, Canada; ; Research Institute of McGill University Health Centre, Montreal, Canada
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30
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Rab41 is a novel regulator of Golgi apparatus organization that is needed for ER-to-Golgi trafficking and cell growth. PLoS One 2013; 8:e71886. [PMID: 23936529 PMCID: PMC3735572 DOI: 10.1371/journal.pone.0071886] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 07/03/2013] [Indexed: 12/13/2022] Open
Abstract
Background The 60+ members of the mammalian Rab protein family group into subfamilies postulated to share common functionality. The Rab VI subfamily contains 5 Rab proteins, Rab6a/a’, Rab6b, Rab6c and Rab41. High-level knockdown of Rab6a/a’ has little effect on the tightly organized Golgi ribbon in HeLa cells as seen by fluorescence microscopy. In striking contrast, we found Rab41 was strongly required for normal Golgi ribbon organization. Methods/Results Treatment of HeLa cells with Rab41 siRNAs scattered the Golgi ribbon into clustered, punctate Golgi elements. Overexpression of GDP-locked Rab41, but not wild type or GTP-locked Rab41, produced a similar Golgi phenotype. By electron microscopy, Rab41 depletion produced short, isolated Golgi stacks. Golgi-associated vesicles accumulated. At low expression levels, wild type and GTP-locked Rab41 showed little concentration in the Golgi region, but puncta were observed and most were in ruffled regions at the cell periphery. There was 25% co-localization of GTP-locked Rab41 with the ER marker, Sec61p. GDP-locked Rab41, as expected, displayed an entirely diffuse cytoplasmic distribution. Depletion of Rab41 or overexpression of GDP-locked Rab41 partially inhibited ER-to-Golgi transport of VSV-G protein. However, Rab41 knockdown had little, if any, effect on endosome-to-Golgi transport of SLTB. Additionally, after a 2-day delay, treatment with Rab41 siRNA inhibited cell growth, while overexpression of GDP-locked Rab41, but not wild type or GTP-locked Rab41, produced a rapid, progressive cell loss. In double knockdown experiments with Rab6, the Golgi ribbon was fragmented, a result consistent with Rab41 and Rab6 acting in parallel. Conclusion We provide the first evidence for distinctive Rab41 effects on Golgi organization, ER-to-Golgi trafficking and cell growth. When combined with the evidence that Rab6a/a’ and Rab6b have diverse roles in Golgi function, while Rab6c regulates mitotic function, our data indicate that Rab VI subfamily members, although related by homology and structure, share limited functional conservation.
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31
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Jacob A, Jing J, Lee J, Schedin P, Gilbert SM, Peden AA, Junutula JR, Prekeris R. Rab40b regulates trafficking of MMP2 and MMP9 during invadopodia formation and invasion of breast cancer cells. J Cell Sci 2013; 126:4647-58. [PMID: 23902685 DOI: 10.1242/jcs.126573] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Invadopodia-dependent degradation of the basement membrane plays a major role during metastasis of breast cancer cells. Basement membrane degradation is mediated by targeted secretion of various matrix metalloproteinases (MMPs). Specifically, MMP2 and MMP9 (MMP2/9) possess the ability to hydrolyze components of the basement membrane and regulate various aspects of tumor growth and metastasis. However, the membrane transport machinery that mediates targeting of MMP2/9 to the invadopodia during cancer cell invasion remains to be defined. Because Rab GTPases are key regulators of membrane transport, we screened a human Rab siRNA library and identified Rab40b GTPase as a protein required for secretion of MMP2/9. We also have shown that Rab40b functions during at least two distinct steps of MMP2/9 transport. Here, we demonstrate that Rab40b is required for MMP2/9 sorting into VAMP4-containing secretory vesicles. We also show that Rab40b regulates transport of MMP2/9 secretory vesicles during invadopodia formation and is required for invadopodia-dependent extracellular matrix degradation. Finally, we demonstrate that Rab40b is also required for breast cancer cell invasion in vitro. On the basis of these findings, we propose that Rab40b mediates trafficking of MMP2/9 during invadopodia formation and metastasis of breast cancer cells.
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Affiliation(s)
- Abitha Jacob
- Department of Cell and Developmental Biology, School of Medicine, Anschutz Medical Campus, University of Colorado Denver, Aurora, CO 80045, USA
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32
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Pfeffer SR. Rab GTPase regulation of membrane identity. Curr Opin Cell Biol 2013; 25:414-9. [PMID: 23639309 DOI: 10.1016/j.ceb.2013.04.002] [Citation(s) in RCA: 259] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 03/25/2013] [Accepted: 04/05/2013] [Indexed: 11/15/2022]
Abstract
A fundamental question in cell biology is how cells determine membrane compartment identity and the directionality with which cargoes pass through the secretory and endocytic pathways. The discovery of so-called 'Rab cascades' provides a satisfying molecular mechanism that helps to resolve this paradox. One Rab GTPase has the ability to template the localization of the subsequent acting Rab GTPase along a given transport pathway. Thus, in addition to determining compartment identity and functionality, Rab GTPases are likely able to order the events of membrane trafficking. This review will highlight recent advances in our understanding of Rabs and Rab cascades.
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Affiliation(s)
- Suzanne R Pfeffer
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive B400, Stanford, CA 94305-5307, USA.
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Abstract
Two key questions in the autophagy field are the mechanisms that underlie the signals for autophagy initiation and the source of membrane for expansion of the nascent membrane, the phagophore. In this review, we discuss recent findings highlighting the role of the classical endosomal pathway, from plasma membrane to lysosome, in the formation and expansion of the phagophore and subsequent degradation of the autophagosome contents. We also highlight the striking conservation of regulatory factors between the two pathways, including those regulating membrane budding and fusion, and the role of the lysosome in sensing the nutrient status of the cell, regulating mTORC1 activity, and ultimately the initiation of autophagy. Editor's suggested further reading in BioEssays The evolution of dynamin to regulate clathrin-mediated endocytosis Abstract.
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