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Zhou A, Zhang W, Ge X, Liu Q, Luo F, Xu S, Hu W, Lu Y. Characterizing genetic variation on the Z chromosome in Schistosoma japonicum reveals host-parasite co-evolution. Parasit Vectors 2024; 17:207. [PMID: 38720339 PMCID: PMC11080191 DOI: 10.1186/s13071-024-06250-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/18/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Schistosomiasis is a neglected tropical disease that afflicts millions of people worldwide; it is caused by Schistosoma, the only dioecious flukes with ZW systems. Schistosoma japonicum is endemic to Asia; the Z chromosome of S. japonicum comprises one-quarter of the entire genome. Detection of positive selection using resequencing data to understand adaptive evolution has been applied to a variety of pathogens, including S. japonicum. However, the contribution of the Z chromosome to evolution and adaptation is often neglected. METHODS We obtained 1,077,526 high-quality SNPs on the Z chromosome in 72 S. japonicum using re-sequencing data publicly. To examine the faster Z effect, we compared the sequence divergence of S. japonicum with two closely related species, Schistosoma haematobium and S. mansoni. Genetic diversity was compared between the Z chromosome and autosomes in S. japonicum by calculating the nucleotide diversity (π) and Dxy values. Population structure was also assessed based on PCA and structure analysis. Besides, we employed multiple methods including Tajima's D, FST, iHS, XP-EHH, and CMS to detect positive selection signals on the Z chromosome. Further RNAi knockdown experiments were performed to investigate the potential biological functions of the candidate genes. RESULTS Our study found that the Z chromosome of S. japonicum showed faster evolution and more pronounced genetic divergence than autosomes, although the effect may be smaller than the variation among genes. Compared with autosomes, the Z chromosome in S. japonicum had a more pronounced genetic divergence of sub-populations. Notably, we identified a set of candidate genes associated with host-parasite co-evolution. In particular, LCAT exhibited significant selection signals within the Taiwan population. Further RNA interference experiments suggested that LCAT is necessary for S. japonicum survival and propagation in the definitive host. In addition, we identified several genes related to the specificity of the intermediate host in the C-M population, including Rab6 and VCP, which are involved in adaptive immune evasion to the host. CONCLUSIONS Our study provides valuable insights into the adaptive evolution of the Z chromosome in S. japonicum and further advances our understanding of the co-evolution of this medically important parasite and its hosts.
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Affiliation(s)
- An Zhou
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Wei Zhang
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xueling Ge
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qi Liu
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, 201203, China
| | - Fang Luo
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, 201203, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China
| | - Wei Hu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China.
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2
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Wehrmann M, Vilchez D. The emerging role and therapeutic implications of bacterial and parasitic deubiquitinating enzymes. Front Immunol 2023; 14:1303072. [PMID: 38077335 PMCID: PMC10703165 DOI: 10.3389/fimmu.2023.1303072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023] Open
Abstract
Deubiquitinating enzymes (DUBs) are emerging as key factors for the infection of human cells by pathogens such as bacteria and parasites. In this review, we discuss the most recent studies on the role of deubiquitinase activity in exploiting and manipulating ubiquitin (Ub)-dependent host processes during infection. The studies discussed here highlight the importance of DUB host-pathogen research and underscore the therapeutic potential of inhibiting pathogen-specific DUB activity to prevent infectious diseases.
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Affiliation(s)
- Markus Wehrmann
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
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Dimori M, Pokrovskaya ID, Liu S, Sherrill JT, Gomez-Acevedo H, Fu Q, Storrie B, Lupashin VV, Morello R. A Rab33b missense mouse model for Smith-McCort dysplasia shows bone resorption defects and altered protein glycosylation. Front Genet 2023; 14:1204296. [PMID: 37359363 PMCID: PMC10285484 DOI: 10.3389/fgene.2023.1204296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
Smith McCort (SMC) dysplasia is a rare, autosomal recessive, osteochondrodysplasia that can be caused by pathogenic variants in either RAB33B or DYM genes. These genes codes for proteins that are located at the Golgi apparatus and have a role in intracellular vesicle trafficking. We generated mice that carry a Rab33b disease-causing variant, c.136A>C (p.Lys46Gln), which is identical to that of members from a consanguineous family diagnosed with SMC. In male mice at 4 months of age, the Rab33b variant caused a mild increase in trabecular bone thickness in the spine and femur and in femoral mid-shaft cortical thickness with a concomitant reduction of the femoral medullary area, suggesting a bone resorption defect. In spite of the increase in trabecular and cortical thickness, bone histomorphometry showed a 4-fold increase in osteoclast parameters in homozygous Rab33b mice suggesting a putative impairment in osteoclast function, while dynamic parameters of bone formation were similar in mutant versus control mice. Femur biomechanical tests showed an increased in yield load and a progressive elevation, from WT to heterozygote to homozygous mutants, of bone intrinsic properties. These findings suggest an overall impact on bone material properties which may be caused by disturbed protein glycosylation in cells contributing to skeletal formation, supported by the altered and variable pattern of lectin staining in murine and human tissue cultured cells and in liver and bone murine tissues. The mouse model only reproduced some of the features of the human disease and was sex-specific, manifesting in male but not female mice. Our data reveal a potential novel role of RAB33B in osteoclast function and protein glycosylation and their dysregulation in SMC and lay the foundation for future studies.
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Affiliation(s)
- Milena Dimori
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Irina D Pokrovskaya
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Shijie Liu
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - John T Sherrill
- Department of Orthopaedic Surgery, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Horacio Gomez-Acevedo
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Qiang Fu
- Department of Internal Medicine, Division of Endocrinology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Brian Storrie
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Vladimir V Lupashin
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Roy Morello
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Department of Orthopaedic Surgery, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Division of Genetics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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Xie Y, Zhang Y, Wang Y, Feng Y. Mechanism and Modulation of SidE Family Proteins in the Pathogenesis of Legionella pneumophila. Pathogens 2023; 12:pathogens12040629. [PMID: 37111515 PMCID: PMC10143409 DOI: 10.3390/pathogens12040629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Legionella pneumophila is the causative agent of Legionnaires' disease, causing fever and lung infection, with a death rate up to 15% in severe cases. In the process of infection, Legionella pneumophila secretes over 330 effectors into host cell via the Dot/Icm type IV secretion system to modulate multiple host cellular physiological processes, thereby changing the environment of the host cell and promoting the growth and propagation of the bacterium. Among these effector proteins, SidE family proteins from Legionella pneumophila catalyze a non-canonical ubiquitination reaction, which combines mono-ADP-ribosylation and phosphodiesterase activities together to attach ubiquitin onto substrates. Meanwhile, the activity of SidE family proteins is also under multiple modulations by other effectors. Herein we summarize the key insights into recent studies in this area, emphasizing the tight link between the modular structure of SidE family proteins and the pathogen virulence as well as the fundamental mechanism and modulation network for further extensive research.
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Affiliation(s)
- Yongchao Xie
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271002, China
| | - Yi Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271002, China
| | - Yue Feng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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Lin HH, Kuo MW, Fan TC, Yu AL, Yu J. YULINK regulates vascular formation in zebrafish and HUVECs. Biol Res 2023; 56:7. [PMID: 36843032 PMCID: PMC9969694 DOI: 10.1186/s40659-023-00415-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/18/2023] [Indexed: 02/28/2023] Open
Abstract
BACKGROUND The distinct arterial and venous cell fates are dictated by a combination of various genetic factors which form diverse types of blood vessels such as arteries, veins, and capillaries. We report here that YULINK protein is involved in vasculogenesis, especially venous formation. METHODS In this manuscript, we employed gene knockdown, yeast two-hybrid, FLIM-FRET, immunoprecipitation, and various imaging technologies to investigate the role of YULINK gene in zebrafish and human umbilical vein endothelial cells (HUVECs). RESULTS Knockdown of YULINK during the arterial-venous developmental stage of zebrafish embryos led to the defective venous formation and abnormal vascular plexus formation. Knockdown of YULINK in HUVECs impaired their ability to undergo cell migration and differentiation into a capillary-like tube formation. In addition, the phosphorylated EPHB4 was decreased in YULINK knockdown HUVECs. Yeast two-hybrid, FLIM-FRET, immunoprecipitation, as well as imaging technologies showed that YULINK colocalized with endosome related proteins (EPS15, RAB33B or TICAM2) and markers (Clathrin and RHOB). VEGF-induced VEGFR2 internalization was also compromised in YULINK knockdown HUVECs, demonstrating to the involvement of YULINK. CONCLUSION This study suggests that YULINK regulates vasculogenesis, possibly through endocytosis in zebrafish and HUVECs.
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Affiliation(s)
- Hsin-Hung Lin
- grid.28665.3f0000 0001 2287 1366Chemical Biology and Molecular Biophysics Program, International Graduate Program, Academia Sinica, Taipei, Taiwan ,grid.454210.60000 0004 1756 1461Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333 Taoyuan, Taiwan
| | - Ming-Wei Kuo
- grid.454210.60000 0004 1756 1461Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333 Taoyuan, Taiwan
| | - Tan-Chi Fan
- grid.454210.60000 0004 1756 1461Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333 Taoyuan, Taiwan
| | - Alice L. Yu
- grid.454210.60000 0004 1756 1461Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333 Taoyuan, Taiwan ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California, San Diego, CA USA
| | - John Yu
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, 333, Taoyuan, Taiwan. .,Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.
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6
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Varshney K, Narayanachar SG, Girisha KM, Bhavani GS, Narayanan D, Phadke S, Nampoothiri S, Udupi GA, Raghupathy P, Nair M, Geetha TS, Bhat M. Clinical, radiological and molecular studies in 24 individuals with Dyggve-Melchior-Clausen dysplasia and Smith-McCort dysplasia from India. J Med Genet 2023; 60:204-211. [PMID: 35477554 DOI: 10.1136/jmedgenet-2021-108098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 04/10/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Dyggve-Melchior-Clausen dysplasia (DMC) and Smith-McCort dysplasia (SMC types 1 and 2) are rare spondyloepimetaphyseal dysplasias with identical radiological findings. The presence of intellectual disability in DMC and normal intellect in SMC differentiates the two. DMC and SMC1 are allelic and caused by homozygous or compound heterozygous variants in DYM. SMC2 is caused by variations in RAB33B. Both DYM and RAB33B are important in intravesicular transport and function in the Golgi apparatus. METHODS Detailed clinical phenotyping and skeletal radiography followed by molecular testing were performed in all affected individuals. Next-generation sequencing and Sanger sequencing were used to confirm DYM and RAB33B variants. Sanger sequencing of familial variants was done in all parents. RESULTS 24 affected individuals from seven centres are described. 18 had DMC and 6 had SMC2. Parental consanguinity was present in 15 of 19 (79%). Height <3 SD and gait abnormalities were seen in 20 and 14 individuals, respectively. The characteristic radiological findings of lacy iliac crests and double-humped vertebral bodies were seen in 96% and 88% of the affected. Radiological findings became attenuated with age. 23 individuals harboured biallelic variants in either DYM or RAB33B. Fourteen different variants were identified, out of which 10 were novel. The most frequently occurring variants in this group were c.719 C>A (3), c.1488_1489del (2), c.1484dup (2) and c.1563+2T>C (2) in DYM and c.400C>T (2) and c.186del (2) in RAB33B. The majority of these have not been reported previously. CONCLUSION This large cohort from India contributes to the increasing knowledge of clinical and molecular findings in these rare 'Golgipathies'.
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Affiliation(s)
- Kruti Varshney
- Department of Clinical Genetics, Centre for Human Genetics, Bangalore, Karnataka, India
| | | | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Dhanyalakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shubha Phadke
- Department of Medical Genetics, SGPGIMS, Lucknow, Uttar Pradesh, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Reseacrh Centre, Kochi, Kerala, India
| | - Gautham Arunachal Udupi
- Department of Human Genetics, National Institute of Mental Health and Neurosciences, Bangalore, Karnataka, India
| | - Palany Raghupathy
- Department of Paediatric Endocrinology, Indira Gandhi Institute of Child Health, Bangalore, Karnataka, India
| | - Mohandas Nair
- Department of Paediatrics, Government Medical College, Kozhikode, Kerala, India
| | | | - Meenakshi Bhat
- Department of Clinical Genetics, Centre for Human Genetics, Bangalore, Karnataka, India
- Department of Paediatric Genetics, Indira Gandhi Institute of Child Health, Bangalore, Karnataka, India
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Choi W, Kang S, Kim J. New insights into the role of the Golgi apparatus in the pathogenesis and therapeutics of human diseases. Arch Pharm Res 2022; 45:671-692. [PMID: 36178581 DOI: 10.1007/s12272-022-01408-z] [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: 06/22/2022] [Accepted: 09/20/2022] [Indexed: 11/24/2022]
Abstract
The Golgi apparatus is an essential cellular organelle that mediates homeostatic functions, including vesicle trafficking and the post-translational modification of macromolecules. Its unique stacked structure and dynamic functions are tightly regulated, and several Golgi proteins play key roles in the functioning of unconventional protein secretory pathways triggered by cellular stress responses. Recently, an increasing number of studies have implicated defects in Golgi functioning in human diseases such as cancer, neurodegenerative, and immunological disorders. Understanding the extraordinary characteristics of Golgi proteins is important for elucidating its associated intracellular signaling mechanisms and has important ramifications for human health. Therefore, analyzing the mechanisms by which the Golgi participates in disease pathogenesis may be useful for developing novel therapeutic strategies. This review articulates the structural features and abnormalities of the Golgi apparatus reported in various diseases and the suspected mechanisms underlying the Golgi-associated pathologies. Furthermore, we review the potential therapeutic strategies based on Golgi function.
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Affiliation(s)
- Wooseon Choi
- Department of Pharmacology, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea
| | - Shinwon Kang
- Department of Physiology, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Jiyoon Kim
- Department of Pharmacology, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea.
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Houghton FJ, Makhoul C, Cho EHJ, Williamson NA, Gleeson PA. Interacting partners of Golgi-localized small G protein Arl5b identified by a combination of in vivo proximity labelling and GFP-Trap pull down. FEBS Lett 2022; 596:2382-2399. [PMID: 35789482 DOI: 10.1002/1873-3468.14443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/10/2022] [Accepted: 06/23/2022] [Indexed: 11/09/2022]
Abstract
The small G protein Arl5b is localized on the trans-Golgi network (TGN) and regulates endosomes-to-TGN transport. Here, we combined in vivo and in vitro techniques to map the interactive partners and near neighbours of Arl5b at the TGN, using constitutively-active, membrane-bound Arl5b(Q70L)-GFP in stably expressing HeLa cells, and the proximity labelling techniques BioID and APEX2 in parallel with GFP-Trap pull-down. From mass spectrometry analysis, 22 Golgi proteins were identified; 50% were TGN-localised Rabs, Arfs and Arls. The scaffold/tethering factors ACBD3 (GCP60) and PIST (GOPC) were also identified, and we show that Arl5b is required for TGN recruitment of ACBD3. Overall, the combination of in vivo labelling and direct pull-downs indicates a highly organised complex of small G proteins on TGN membranes.
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Affiliation(s)
- Fiona J Houghton
- The Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, 3010, Australia
| | - Christian Makhoul
- The Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, 3010, Australia
| | - Ellie Hyun-Jung Cho
- The Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, 3010, Australia.,Biological Optical Microscopy Platform, The University of Melbourne, Victoria, 3010, Australia
| | - Nicholas A Williamson
- The Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, 3010, Australia
| | - Paul A Gleeson
- The Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, 3010, Australia
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Larocque G, Royle SJ. Integrating intracellular nanovesicles into integrin trafficking pathways and beyond. Cell Mol Life Sci 2022; 79:335. [PMID: 35657500 PMCID: PMC9166830 DOI: 10.1007/s00018-022-04371-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/28/2022] [Accepted: 05/11/2022] [Indexed: 12/24/2022]
Abstract
Membrane traffic controls the movement of proteins and lipids from one cellular compartment to another using a system of transport vesicles. Intracellular nanovesicles (INVs) are a newly described class of transport vesicles. These vesicles are small, carry diverse cargo, and are involved in multiple trafficking steps including anterograde traffic and endosomal recycling. An example of a biological process that they control is cell migration and invasion, due to their role in integrin recycling. In this review, we describe what is known so far about these vesicles. We discuss how INVs may integrate into established membrane trafficking pathways using integrin recycling as an example. We speculate where in the cell INVs have the potential to operate and we identify key questions for future investigation.
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Affiliation(s)
| | - Stephen J Royle
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Gibbet Hill Road, Coventry, CV4 7AL, UK.
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10
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Rab33b-exocyst interaction mediates localized secretion for focal adhesion turnover and cell migration. iScience 2022; 25:104250. [PMID: 35521520 PMCID: PMC9061791 DOI: 10.1016/j.isci.2022.104250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/17/2022] [Accepted: 04/08/2022] [Indexed: 12/19/2022] Open
Abstract
Rab proteins are well known regulators of intracellular trafficking; however, more and more studies point to their function also in other cellular processes, including cell migration. In this work, we have performed an siRNA screen to identify Rab proteins that influence cell migration. The screen revealed Rab33b as the strongest candidate that affected cell motility. Rab33b has been previously reported to localize at the Golgi apparatus to regulate Golgi-to-ER retrograde trafficking and Golgi homeostasis. We revealed that Rab33b also mediates post-Golgi transport to the plasma membrane. We further identified Exoc6, a subunit of the exocyst complex, as an interactor of Rab33b. Moreover, our data indicate that Rab33b regulates focal adhesion dynamics by modulating the delivery of cargo such as integrins to focal adhesions. Altogether, our results demonstrate a role for Rab33b in cell migration by regulating the delivery of integrins to focal adhesions through the interaction with Exoc6. RNAi screen reveals a role for Rab33b in cell migration Rab33b influences focal adhesion dynamics Rab33b interacts with the exocyst subunit Exoc6 Rab33b together with Exoc6 mediates the delivery of β1 integrin to adhesion points
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Tian Y, Parsons LM, Jankowska E, Cipollo JF. Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. Front Chem 2021; 9:767448. [PMID: 34869209 PMCID: PMC8640487 DOI: 10.3389/fchem.2021.767448] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/14/2021] [Indexed: 01/03/2023] Open
Abstract
The SARS-CoV-2 spike protein is heavily glycosylated, having 22 predicted N-glycosylation sites per monomer. It is also O-glycosylated, although the number of O-glycosites is less defined. Recent studies show that spike protein glycans play critical roles in viral entry and infection. The spike monomer has two subdomains, S1 and S2, and a receptor-binding domain (RBD) within the S1 domain. In this study, we have characterized the site-specific glycosylation patterns of the HEK293 recombinant spike RBD and S1 domains as well as the intact spike derived from the whole virus produced in Vero cells. The Vero cell-derived spike from the WA1 strain and a D614G variant was analyzed. All spike proteins, S1, and RBDs were analyzed using hydrophilic interaction chromatography (HILIC) and LC-MS/MS on an Orbitrap Eclipse Tribrid mass spectrometer. N-glycans identified in HEK293-derived S1 were structurally diverse. Those found in the HEK293-derived RBD were highly similar to those in HEK293 S1 where N-glycosites were shared. Comparison of the whole cell-derived WA1 and D614G spike proteins revealed that N-glycosites local to the mutation site appeared to be more readily detected, hinting that these sites are more exposed to glycosylation machinery. Moreover, recombinant HEK293-derived S1 was occupied almost completely with complex glycan, while both WA1 and D614G derived from the Vero E6 cell whole virus were predominantly high-mannose glycans. This stands in stark contrast to glycosylation patterns seen in both CHO- and HEK cell-derived recombinant S1, S2, and the whole spike previously reported. Concerning O-glycosylation, our analyses revealed that HEK293 recombinant proteins possessed a range of O-glycosites with compositions consistent with Core type 1 and 2 glycans. The O-glycosites shared between the S1 and RBD constructs, sites T323 and T523, were occupied by a similar range of Core 1 and 2 type O-glycans. Overall, this study reveals that the sample nature and cell substrate used for production of these proteins can have a dramatic impact on the glycosylation profile. SARS-CoV-2 spike glycans are associated with host ACE2 receptor interaction efficiency. Therefore, understanding such differences will serve to better understand these host–pathogen interactions and inform the choice of cell substrates to suite downstream investigations.
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Affiliation(s)
- Yuan Tian
- Food and Drug Administration, Center for Biologics Evaluation and Research, Division of Bacterial, Parasitic and Allergenic Products, Silver Spring, MD, United States
| | - Lisa M Parsons
- Food and Drug Administration, Center for Biologics Evaluation and Research, Division of Bacterial, Parasitic and Allergenic Products, Silver Spring, MD, United States
| | - Ewa Jankowska
- Food and Drug Administration, Center for Biologics Evaluation and Research, Division of Bacterial, Parasitic and Allergenic Products, Silver Spring, MD, United States
| | - John F Cipollo
- Food and Drug Administration, Center for Biologics Evaluation and Research, Division of Bacterial, Parasitic and Allergenic Products, Silver Spring, MD, United States
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12
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Huang Y, Qi L, Kogiso M, Du Y, Braun FK, Zhang H, Huang LF, Xiao S, Teo WY, Lindsay H, Zhao S, Baxter P, Su JMF, Adesina A, Yang J, Brabetz S, Kool M, Pfister SM, Chintagumpala M, Perlaky L, Wang Z, Zhou Y, Man TK, Li XN. Spatial Dissection of Invasive Front from Tumor Mass Enables Discovery of Novel microRNA Drivers of Glioblastoma Invasion. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2101923. [PMID: 34719887 PMCID: PMC8655179 DOI: 10.1002/advs.202101923] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Diffuse invasion is the primary cause of treatment failure of glioblastoma (GBM). Previous studies on GBM invasion have long been forced to use the resected tumor mass cells. Here, a strategy to reliably isolate matching pairs of invasive (GBMINV ) and tumor core (GBMTC ) cells from the brains of 6 highly invasive patient-derived orthotopic models is described. Direct comparison of these GBMINV and GBMTC cells reveals a significantly elevated invasion capacity in GBMINV cells, detects 23/768 miRNAs over-expressed in the GBMINV cells (miRNAINV ) and 22/768 in the GBMTC cells (miRNATC ), respectively. Silencing the top 3 miRNAsINV (miR-126, miR-369-5p, miR-487b) successfully blocks invasion of GBMINV cells in vitro and in mouse brains. Integrated analysis with mRNA expression identifies miRNAINV target genes and discovers KCNA1 as the sole common computational target gene of which 3 inhibitors significantly suppress invasion in vitro. Furthermore, in vivo treatment with 4-aminopyridine (4-AP) effectively eliminates GBM invasion and significantly prolongs animal survival times (P = 0.035). The results highlight the power of spatial dissection of functionally accurate GBMINV and GBMTC cells in identifying novel drivers of GBM invasion and provide strong rationale to support the use of biologically accurate starting materials in understanding cancer invasion and metastasis.
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Affiliation(s)
- Yulun Huang
- Department of Neurosurgery, Dushu Lake Hospital, Soochow University, Suzhou, 205124, China
- Department of Neurosurgery and Brain and Nerve Research Laboratory, the First Affiliated Hospital, Soochow University, Suzhou, 215007, China
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lin Qi
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
- Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Ann & Robert H. Lurie Children's Hospital of Chicago, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Department of Pharmacology, School of Medicine, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Mari Kogiso
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yuchen Du
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
- Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Ann & Robert H. Lurie Children's Hospital of Chicago, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Frank K Braun
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Huiyuan Zhang
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - L Frank Huang
- Department of Systems Medicine and Bioegineering, Houston Methodist Hospital Research Institute and Cancer Center, Weill Cornell Medicine, Houston, TX, 77030, USA
- Division of Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, United States, 45229, United States
| | - Sophie Xiao
- Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Ann & Robert H. Lurie Children's Hospital of Chicago, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Wan-Yee Teo
- Humphrey Oei Institute of Cancer Research, National Cancer Center Singapore, Singapore, 169610, Singapore
| | - Holly Lindsay
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sibo Zhao
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Patricia Baxter
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jack M F Su
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Adekunle Adesina
- Department of Pathology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jianhua Yang
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sebastian Brabetz
- Hopp Children's Cancer Center (KiTZ), Heidelberg, 69120, Germany
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, 69120, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, 69120, Germany
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, 69120, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, 69120, Germany
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, 69120, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, 69120, Germany
| | - Murali Chintagumpala
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Laszlo Perlaky
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhong Wang
- Department of Neurosurgery and Brain and Nerve Research Laboratory, the First Affiliated Hospital, Soochow University, Suzhou, 215007, China
| | - Youxin Zhou
- Department of Neurosurgery and Brain and Nerve Research Laboratory, the First Affiliated Hospital, Soochow University, Suzhou, 215007, China
| | - Tsz-Kwong Man
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiao-Nan Li
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
- Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Ann & Robert H. Lurie Children's Hospital of Chicago, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
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13
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Ain NU, Fatima Z, Naz S, Makitie O. RAB33B and PCNT variants in two Pakistani families with skeletal dysplasia and short stature. BMC Musculoskelet Disord 2021; 22:630. [PMID: 34284742 PMCID: PMC8293541 DOI: 10.1186/s12891-021-04503-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/01/2021] [Indexed: 11/12/2022] Open
Abstract
Background Skeletal dysplasia is a heterogeneous group of disorders resulting from different genetic variants in humans. The current study was designed to identify the genetic causes of skeletal dysplasia and short stature in two consanguineous families from Pakistan, both comprised of multiple affected individuals. Patients in one family had proportionate short stature with reduced head circumference while affected individuals in the other family had disproportionate short stature. Methods Clinical data were obtained and radiological examinations of the index patients were completed. Whole genome sequencing for probands from both families were performed followed by Sanger sequencing to confirm segregation of identified variants in the respective families. In-silico pathogenicity score prediction for identified variant and amino acid conservation analysis was completed. Results Whole Genome Sequencing identified a known biallelic variant c.6176_6189delGTCAGCTGCCGAAG; p.(Gln2060ArgfsTer48) in PCNT gene and a novel biallelic variant c.174delC; p.(Asp60ThrfsTer7) in RAB33B gene respectively in affected members of the two families. Clinical imaging revealed platyspondyly and varus deformity in the legs of the affected members in the first family. Radiographs indicated severe platyspondyly, genu valgus deformity of legs and pectus carinatum for the patients in the second family. Conclusion In this study we report the phenotypes and genetic variants in two unrelated families with two distinct forms of skeletal dysplasia. This study strengthens the previous findings that patients harboring PCNT variants are phenotypically homogeneous and also extends the genotypic spectrum of RAB33B variants. Supplementary Information The online version contains supplementary material available at 10.1186/s12891-021-04503-2.
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Affiliation(s)
- Noor Ul Ain
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, 54590, Pakistan.,Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Present address: Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
| | - Zunaira Fatima
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, 54590, Pakistan
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, 54590, Pakistan.
| | - Outi Makitie
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden. .,Folkhälsan Institute of Genetics, Helsinki, Finland. .,Children's Hospital, University of Helsinki and Helsinki University Hospital, P.O. Box 63, 00014, Helsinki, Finland.
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14
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Tüysüz B, Geyik F, Yıldırım T, Alkaya DU, Sharifova S, Kafadar A. Seven patients with Smith-McCort dysplasia 2: Four novel nonsense variants in RAB33B and follow-up findings. Eur J Med Genet 2021; 64:104248. [PMID: 34000439 DOI: 10.1016/j.ejmg.2021.104248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 12/15/2022]
Abstract
Smith-McCort dysplasia 2 (SMC2) is a rare spondylo-epiphyseal-metaphyseal dysplasia caused by biallelic RAB33B variants. Short trunk dwarfism and radiological findings including the lacy ilia appearance and double bumps of the vertebral bodies are typical features. To date, only eight patients with SMC2 had been reported. The aim of this study is to evaluate the follow-up findings of seven patients from five families with SMC2 and to present four novel variants in RAB33B. The age of diagnosis of the patients was between 4 and 18 years. All patients had variable degrees of short trunk dwarfism with barrel chest, waddling gait, hyperlordosis, genu valgum, elbow and finger joint stiffness, which became more evident with growth. Lacy iliac crest, short ilia with basilar hypoplasia, platyspondyly, dysplastic acetabulum with small and/or laterally displaced femoral heads, and small, irregular carpal bones were detected on skeletal radiographies of all patients. Typical double hump appearance of vertebral bodies was present in patients under 12 years of age, which disappeared after puberty and development of elongated vertebral bodies was also observed. At the time of diagnosis, six patients were able to walk independently; patients who were followed for five to nine years, developed severe hip pain, hip and knee joints stiffness and difficultly of walking after 10 years of age. Only two patients could walk independently during final examination. We detected four novel nonsense variants (p.Gln85Ter, p. Cys48Ter, p. Arg94Ter and p. Gln134Ter) in RAB33B. This study provides important data on long-term skeletal findings of the patients with SMC2.
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Affiliation(s)
- Beyhan Tüysüz
- Department of Pediatric Genetics, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul, Turkey.
| | - Filiz Geyik
- Department of Pediatric Genetics, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul, Turkey
| | - Timur Yıldırım
- Department of Orthopedics and Traumatology, University of Health Sciences Turkey, Baltalimani Bone Diseases Training and Research Center, Istanbul, Turkey
| | - Dilek Uludağ Alkaya
- Department of Pediatric Genetics, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul, Turkey
| | - Sabine Sharifova
- Department of Pediatric Genetics, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul, Turkey
| | - Ali Kafadar
- Department of Neurosurgery, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul, Turkey
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15
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Lu Q, Wang PS, Yang L. Golgi-associated Rab GTPases implicated in autophagy. Cell Biosci 2021; 11:35. [PMID: 33557950 PMCID: PMC7869216 DOI: 10.1186/s13578-021-00543-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/18/2021] [Indexed: 12/24/2022] Open
Abstract
Autophagy is a conserved cellular degradation process in eukaryotes that facilitates the recycling and reutilization of damaged organelles and compartments. It plays a pivotal role in cellular homeostasis, pathophysiological processes, and diverse diseases in humans. Autophagy involves dynamic crosstalk between different stages associated with intracellular vesicle trafficking. Golgi apparatus is the central organelle involved in intracellular vesicle trafficking where Golgi-associated Rab GTPases function as important mediators. This review focuses on the recent findings that highlight Golgi-associated Rab GTPases as master regulators of autophagic flux. The scope for future research in elucidating the role and mechanism of Golgi-associated Rab GTPases in autophagy and autophagy-related diseases is discussed further.
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Affiliation(s)
- Qingchun Lu
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, 3440 N Broad St, Kresge Hall, Rm. 624, Philadelphia, PA19140, USA
| | - Po-Shun Wang
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, 3440 N Broad St, Kresge Hall, Rm. 624, Philadelphia, PA19140, USA
| | - Ling Yang
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, 3440 N Broad St, Kresge Hall, Rm. 624, Philadelphia, PA19140, USA.
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16
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Kitao T, Nagai H, Kubori T. Divergence of Legionella Effectors Reversing Conventional and Unconventional Ubiquitination. Front Cell Infect Microbiol 2020; 10:448. [PMID: 32974222 PMCID: PMC7472693 DOI: 10.3389/fcimb.2020.00448] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/21/2020] [Indexed: 02/05/2023] Open
Abstract
The intracellular bacterial pathogen Legionella pneumophila employs bacteria-derived effector proteins in a variety of functions to exploit host cellular systems. The ubiquitination machinery constitutes a crucial eukaryotic system for the regulation of numerous cellular processes, and is a representative target for effector-mediated bacterial manipulation. L. pneumophila transports over 300 effector proteins into host cells through its Dot/Icm type IV secretion system. Among these, several effector proteins have been found to function as ubiquitin ligases, including unprecedented enzymes that catalyze ubiquitination through unconventional mechanisms. Recent studies have identified many L. pneumophila effector proteins that can interfere with ubiquitination. These effectors include proteins that are distantly related to the ovarian tumor protein superfamily described as deubiquitinases (DUBs), which regulate important signaling cascades in human cells. Intriguingly, L. pneumophila DUBs are not limited to enzymes that exhibit canonical DUB activity. Some L. pneumophila DUBs can catalyze the cleavage of the unconventional linkage between ubiquitin and substrates. Furthermore, novel mechanisms have been found that adversely affect the function of specific ubiquitin ligases; for instance, effector-mediated posttranslational modifications of ubiquitin ligases result in the inhibition of their activity. In the context of L. pneumophila infection, the existence of enzymes that reverse ubiquitination primarily relates to a fine tuning of biogenesis and remodeling of the Legionella-containing vacuole as a replicative niche. The complexity of the effector arrays reflects sophisticated strategies that bacteria have adopted to adapt their host environment and enable their survival in host cells. This review summarizes the current state of knowledge on the divergent mechanisms of the L. pneumophila effectors that can reverse ubiquitination, which is mediated by other effectors as well as the host ubiquitin machinery.
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Affiliation(s)
- Tomoe Kitao
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Hiroki Nagai
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Japan
- G-CHAIN, Gifu University, Gifu, Japan
| | - Tomoko Kubori
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Japan
- G-CHAIN, Gifu University, Gifu, Japan
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17
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Nielsen E. The Small GTPase Superfamily in Plants: A Conserved Regulatory Module with Novel Functions. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:247-272. [PMID: 32442390 DOI: 10.1146/annurev-arplant-112619-025827] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Small GTP-binding proteins represent a highly conserved signaling module in eukaryotes that regulates diverse cellular processes such as signal transduction, cytoskeletal organization and cell polarity, cell proliferation and differentiation, intracellular membrane trafficking and transport vesicle formation, and nucleocytoplasmic transport. These proteins function as molecular switches that cycle between active and inactive states, and this cycle is linked to GTP binding and hydrolysis. In this review, the roles of the plant complement of small GTP-binding proteins in these cellular processes are described, as well as accessory proteins that control their activity, and current understanding of the functions of individual members of these families in plants-with a focus on the model organism Arabidopsis-is presented. Some potential novel roles of these GTPases in plants, relative to their established roles in yeast and/or animal systems, are also discussed.
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Affiliation(s)
- Erik Nielsen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
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18
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Liu S, Majeed W, Grigaitis P, Betts MJ, Climer LK, Starkuviene V, Storrie B. Epistatic Analysis of the Contribution of Rabs and Kifs to CATCHR Family Dependent Golgi Organization. Front Cell Dev Biol 2019; 7:126. [PMID: 31428608 PMCID: PMC6687757 DOI: 10.3389/fcell.2019.00126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/26/2019] [Indexed: 01/05/2023] Open
Abstract
Multisubunit members of the CATCHR family: COG and NRZ complexes, mediate intra-Golgi and Golgi to ER vesicle tethering, respectively. We systematically addressed the genetic and functional interrelationships between Rabs, Kifs, and the retrograde CATCHR family proteins: COG3 and ZW10, which are necessary to maintain the organization of the Golgi complex. We scored the ability of siRNAs targeting 19 Golgi-associated Rab proteins and all 44 human Kifs, microtubule-dependent motor proteins, to suppress CATCHR-dependent Golgi fragmentation in an epistatic fluorescent microscopy-based assay. We found that co-depletion of Rab6A, Rab6A’, Rab27A, Rab39A and two minus-end Kifs, namely KIFC3 and KIF25, suppressed both COG3- and ZW10-depletion-induced Golgi fragmentation. ZW10-dependent Golgi fragmentation was suppressed selectively by a separate set of Rabs: Rab11A, Rab33B and the little characterized Rab29. 10 Kifs were identified as hits in ZW10-depletion-induced Golgi fragmentation, and, in contrast to the double suppressive Kifs, these were predominantly plus-end motors. No Rabs or Kifs selectively suppressed COG3-depletion-induced Golgi fragmentation. Protein-protein interaction network analysis indicated putative direct and indirect links between suppressive Rabs and tether function. Validation of the suppressive hits by EM confirmed a restored organization of the Golgi cisternal stack. Based on these outcomes, we propose a three-way competitive model of Golgi organization in which Rabs, Kifs and tethers modulate sequentially the balance between Golgi-derived vesicle formation, consumption, and off-Golgi transport.
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Affiliation(s)
- Shijie Liu
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Waqar Majeed
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Pranas Grigaitis
- Centre for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Heidelberg, Germany
| | - Matthew J Betts
- Centre for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Heidelberg, Germany
| | - Leslie K Climer
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Vytaute Starkuviene
- Centre for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Heidelberg, Germany.,Institute of Pharmacology and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany.,Institute of Biosciences, Vilnius University Life Sciences Centre, Vilnius, Lithuania
| | - Brian Storrie
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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19
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Morgan NE, Cutrona MB, Simpson JC. Multitasking Rab Proteins in Autophagy and Membrane Trafficking: A Focus on Rab33b. Int J Mol Sci 2019; 20:ijms20163916. [PMID: 31408960 PMCID: PMC6719199 DOI: 10.3390/ijms20163916] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 07/30/2019] [Accepted: 08/09/2019] [Indexed: 12/25/2022] Open
Abstract
Autophagy (particularly macroautophagy) is a bulk degradation process used by eukaryotic cells in order to maintain adequate energy levels and cellular homeostasis through the delivery of long-lived proteins and organelles to the lysosome, resulting in their degradation. It is becoming increasingly clear that many of the molecular requirements to fulfil autophagy intersect with those of conventional and unconventional membrane trafficking pathways. Of particular interest is the dependence of these processes on multiple members of the Rab family of small GTP binding proteins. Rab33b is a protein that localises to the Golgi apparatus and has suggested functions in both membrane trafficking and autophagic processes. Interestingly, mutations in the RAB33B gene have been reported to cause the severe skeletal disorder, Smith–McCort Dysplasia; however, the molecular basis for Rab33b in this disorder remains to be determined. In this review, we focus on the current knowledge of the participation of Rab33b and its interacting partners in membrane trafficking and macroautophagy, and speculate on how its function, and dysfunction, may contribute to human disease.
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Affiliation(s)
- Niamh E Morgan
- School of Biology and Environmental Science & Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), D04 N2E5 Dublin, Ireland
| | - Meritxell B Cutrona
- School of Biology and Environmental Science & Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), D04 N2E5 Dublin, Ireland
| | - Jeremy C Simpson
- School of Biology and Environmental Science & Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), D04 N2E5 Dublin, Ireland.
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20
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Chen YT, Wang IH, Wang YH, Chiu WY, Hu JH, Chen WH, Lee FJS. Action of Arl1 GTPase and golgin Imh1 in Ypt6-independent retrograde transport from endosomes to the trans-Golgi network. Mol Biol Cell 2019; 30:1008-1019. [PMID: 30726160 PMCID: PMC6589904 DOI: 10.1091/mbc.e18-09-0579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Arf and Rab/Ypt GTPases coordinately regulate membrane traffic and organelle structure by regulating vesicle formation and fusion. Ample evidence has indicated that proteins in these two families may function in parallel or complementarily; however, the manner in which Arf and Rab/Ypt proteins perform interchangeable functions remains unclear. In this study, we report that a Golgi-localized Arf, Arl1, could suppress Ypt6 dysfunction via its effector golgin, Imh1, but not via the lipid flippase Drs2. Ypt6 is critical for the retrograde transport of vesicles from endosomes to the trans-Golgi network (TGN), and its mutation leads to severe protein mislocalization and growth defects. We first overexpress the components of the Arl3-Syt1-Arl1-Imh1 cascade and show that only Arl1 and Imh1 can restore endosome-to-TGN trafficking in ypt6-deleted cells. Interestingly, increased abundance of Arl1 or Imh1 restores localization of the tethering factor Golgi associated retrograde–protein (GARP) complex to the TGN in the absence of Ypt6. We further show that the N-terminal domain of Imh1 is critical for restoring GARP localization and endosome-to-TGN transport in ypt6-deleted cells. Together, our results reveal the mechanism by which Arl1-Imh1 facilitates the recruitment of GARP to the TGN and compensates for the endosome-to-TGN trafficking defects in dysfunctional Ypt6 conditions.
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Affiliation(s)
- Yan-Ting Chen
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - I-Hao Wang
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Yi-Hsun Wang
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Wan-Yun Chiu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Jen-Hao Hu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Wen-Hui Chen
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Fang-Jen S Lee
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan.,Department of Medical Research, National Taiwan University Hospital, Taipei 100, Taiwan.,Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
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21
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Abstract
The Golgi apparatus is a central sorting station in the cell. It receives newly synthesized molecules from the endoplasmic reticulum and directs them to different subcellular destinations, such as the plasma membrane or the endocytic pathway. Importantly, in the last few years, it has emerged that the maintenance of Golgi structure is connected to the proper regulation of membrane trafficking. Rab proteins are small GTPases that are considered to be the master regulators of the intracellular membrane trafficking. Several of the over 60 human Rabs are involved in the regulation of transport pathways at the Golgi as well as in the maintenance of its architecture. This chapter will summarize the different roles of Rab GTPases at the Golgi, both as regulators of membrane transport, scaffold, and tethering proteins and in preserving the structure and function of this organelle.
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22
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Xiong Q, Li W, Li P, Yang M, Wu C, Eichinger L. The Role of ATG16 in Autophagy and The Ubiquitin Proteasome System. Cells 2018; 8:cells8010002. [PMID: 30577509 PMCID: PMC6356889 DOI: 10.3390/cells8010002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 02/07/2023] Open
Abstract
Autophagy and the ubiquitin proteasome system (UPS) are the two major cellular degradation pathways, which are critical for the maintenance of cell homeostasis. The two pathways differ in their mechanisms and clients. The evolutionary conserved ATG16 plays a key role in autophagy and appears to link autophagy with the UPS. Here, we review the role of ATG16 in different species. We summarize the current knowledge of its functions in autophagosome membrane expansion and autophagosome formation, in Crohn’s disease, and in bacterial sequestration. In addition, we provide information on its autophagy-independent functions and its role in the crosstalk between autophagy and the UPS.
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Affiliation(s)
- Qiuhong Xiong
- Institute of Biomedical Sciences, Shanxi University, No.92 Wucheng Road, Taiyuan 030006, China.
| | - Wenjing Li
- Institute of Biomedical Sciences, Shanxi University, No.92 Wucheng Road, Taiyuan 030006, China.
| | - Ping Li
- Institute of Biomedical Sciences, Shanxi University, No.92 Wucheng Road, Taiyuan 030006, China.
| | - Min Yang
- Institute of Biomedical Sciences, Shanxi University, No.92 Wucheng Road, Taiyuan 030006, China.
| | - Changxin Wu
- Institute of Biomedical Sciences, Shanxi University, No.92 Wucheng Road, Taiyuan 030006, China.
| | - Ludwig Eichinger
- Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany.
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Elgner F, Hildt E, Bender D. Relevance of Rab Proteins for the Life Cycle of Hepatitis C Virus. Front Cell Dev Biol 2018; 6:166. [PMID: 30564577 PMCID: PMC6288913 DOI: 10.3389/fcell.2018.00166] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/20/2018] [Indexed: 12/18/2022] Open
Abstract
Although potent direct-acting antiviral drugs for the treatment of chronic hepatitis C virus (HCV) infection are licensed, there are more than 70 million individuals suffering from chronic HCV infection. In light of the limited access to these drugs, high costs, and a lot of undiagnosed cases, it is expected that the number of HCV cases will not decrease worldwide in the next years. Therefore, and due to the paradigmatic character of HCV for deciphering the crosstalk between viral pathogens and the host cell, characterization of HCV life cycle remains a challenge. HCV belongs to the family of Flaviviridae. As an enveloped virus HCV life cycle depends in many steps on intracellular trafficking. Rab GTPases, a large family of small GTPases, play a central role in intracellular trafficking processes controlling fusion, uncoating, vesicle budding, motility by recruiting specific effector proteins. This review describes the relevance of various Rab proteins for the different steps of the HCV life cycle.
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Affiliation(s)
- Fabian Elgner
- Department of Virology, Paul-Ehrlich-Institut, Langen, Germany
| | - Eberhard Hildt
- Department of Virology, Paul-Ehrlich-Institut, Langen, Germany
| | - Daniela Bender
- Department of Virology, Paul-Ehrlich-Institut, Langen, Germany
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Zeyen L, Prange R. Host Cell Rab GTPases in Hepatitis B Virus Infection. Front Cell Dev Biol 2018; 6:154. [PMID: 30510928 PMCID: PMC6252318 DOI: 10.3389/fcell.2018.00154] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/31/2018] [Indexed: 12/15/2022] Open
Abstract
Hepatitis B virus (HBV) is a leading cause of liver disease and is presently estimated to infect more than 250 million humans. The extremely successful spread of this virus among the human population is explained by its effective transmission strategies and its manifold particle types, including virions, empty envelopes and naked capsids. Due to its tiny genome, HBV depends on cellular machineries to thrive in infected hepatocytes. To enter, traverse and exit the cell, HBV exploits host membrane trafficking pathways, including intracellular highways directed by Rab GTPases. Here, we review recent discoveries focused on how HBV co-opts and perturbs host Rab GTPase functions with an emphasis on Rab7A- and Rab33B-mediated trafficking pathways. Rab7A plays bidirectional roles in the viral life cycle, as it promotes the endocytic uptake of HBV in early stages, but restricts exocytic virion release in late stages. In intermediate stages of HBV propagation, Rab33B is needed to guide the assembly of replicative progeny nucleocapsids. Rab33B acts together with its Atg5-12/16L1 effector, a protein complex required for autophagosome formation, suggesting the concept that HBV exploits this Rab/effector complex as an assembly scaffold and machine. We also discuss whether Rab-directed trafficking pathways engaged by HBV may be applicable to other virus families. Identification of overlapping Rab functions may offer new chances to develop broad-spectrum host-targeted antiviral strategies.
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Affiliation(s)
- Lisa Zeyen
- Department of Virology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Reinhild Prange
- Department of Virology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
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25
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Wei F, Duan Y. Crosstalk between Autophagy and Nanomaterials: Internalization, Activation, Termination. ACTA ACUST UNITED AC 2018; 3:e1800259. [PMID: 32627344 DOI: 10.1002/adbi.201800259] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/02/2018] [Indexed: 12/12/2022]
Abstract
Nanomaterials (NMs) are comprehensively applied in biomedicine due to their unique physical and chemical properties. Autophagy, as an evolutionarily conserved cellular quality control process, is closely associated with the effect of NMs on cells. In this review, the recent advances in NM-induced/inhibited autophagy (NM-phagy) are summarized, with an aim to present a comprehensive description of the mechanisms of NM-phagy from the perspective of internalization, activation, and termination, thereby bridging autophagy and nanomaterials. Several possible mechanisms are extensively reviewed including the endocytosis pathway of NMs and the related cross components (clathrin and adaptor protein 2 (AP-2), adenosine diphosphate (ADP)-ribosylation factor 6 (Arf6), Rab, UV radiation resistance associated gene (UVRAG)), three main stress mechanisms (oxidative stress, damaged organelles stress, and toxicity stress), and several signal pathway-related molecules. The mechanistic insight is beneficial to understand the autophagic response to NMs or NMs' regulation of autophagy. The challenges currently encountered and research trend in the field of NM-phagy are also highlighted. It is hoped that the NM-phagy discussion in this review with the focus on the mechanistic aspects may serve as a guideline for future research in this field.
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Affiliation(s)
- Fujing Wei
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-enviroment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, P. R. China
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-enviroment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, P. R. China
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26
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Banworth MJ, Li G. Consequences of Rab GTPase dysfunction in genetic or acquired human diseases. Small GTPases 2018. [PMID: 29239692 DOI: 10.1080/215412481397833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
Rab GTPases are important regulators of intracellular membrane trafficking in eukaryotes. Both activating and inactivating mutations in Rab genes have been identified and implicated in human diseases ranging from neurological disorders to cancer. In addition, altered Rab expression is often associated with disease prognosis. As such, the study of diseases associated with Rabs or Rab-interacting proteins has shed light on the important role of intracellular membrane trafficking in disease etiology. In this review, we cover recent advances in the field with an emphasis on cellular mechanisms.
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Affiliation(s)
- Marcellus J Banworth
- a Department of Biochemistry and Molecular Biology , University of Oklahoma Health Sciences Center , Oklahoma City , OK , USA
| | - Guangpu Li
- a Department of Biochemistry and Molecular Biology , University of Oklahoma Health Sciences Center , Oklahoma City , OK , USA
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Abstract
GTP-ases of the Rab family (about 70 in human) are key regulators of intracellular transport and membrane trafficking in eukaryotic cells. Remarkably, almost one third associate with membranes of the Golgi complex and TGN (trans-Golgi network). Through interactions with a variety of effectors that include molecular motors, tethering complexes, scaffolding proteins and lipid kinases, they play an important role in maintaining Golgi architecture.
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Affiliation(s)
- Bruno Goud
- a Institut Curie, PSL Research University, CNRS, UMR 144, Molecular Mechanisms of Intracellular Transport , Paris , France
| | - Shijie Liu
- b Department of Physiology and Biophysics , University of Arkansas for Medical Sciences , Little Rock , USA
| | - Brian Storrie
- b Department of Physiology and Biophysics , University of Arkansas for Medical Sciences , Little Rock , USA
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28
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Banworth MJ, Li G. Consequences of Rab GTPase dysfunction in genetic or acquired human diseases. Small GTPases 2017; 9:158-181. [PMID: 29239692 DOI: 10.1080/21541248.2017.1397833] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Rab GTPases are important regulators of intracellular membrane trafficking in eukaryotes. Both activating and inactivating mutations in Rab genes have been identified and implicated in human diseases ranging from neurological disorders to cancer. In addition, altered Rab expression is often associated with disease prognosis. As such, the study of diseases associated with Rabs or Rab-interacting proteins has shed light on the important role of intracellular membrane trafficking in disease etiology. In this review, we cover recent advances in the field with an emphasis on cellular mechanisms.
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Affiliation(s)
- Marcellus J Banworth
- a Department of Biochemistry and Molecular Biology , University of Oklahoma Health Sciences Center , Oklahoma City , OK , USA
| | - Guangpu Li
- a Department of Biochemistry and Molecular Biology , University of Oklahoma Health Sciences Center , Oklahoma City , OK , USA
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29
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Abstract
Macroautophagy is an intracellular pathway used for targeting of cellular components to the lysosome for their degradation and involves sequestration of cytoplasmic material into autophagosomes formed from a double membrane structure called the phagophore. The nucleation and elongation of the phagophore is tightly regulated by several autophagy-related (ATG) proteins, but also involves vesicular trafficking from different subcellular compartments to the forming autophagosome. Such trafficking must be tightly regulated by various intra- and extracellular signals to respond to different cellular stressors and metabolic states, as well as the nature of the cargo to become degraded. We are only starting to understand the interconnections between different membrane trafficking pathways and macroautophagy. This review will focus on the membrane trafficking machinery found to be involved in delivery of membrane, lipids, and proteins to the forming autophagosome and in the subsequent autophagosome fusion with endolysosomal membranes. The role of RAB proteins and their regulators, as well as coat proteins, vesicle tethers, and SNARE proteins in autophagosome biogenesis and maturation will be discussed.
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Rab33B Controls Hepatitis B Virus Assembly by Regulating Core Membrane Association and Nucleocapsid Processing. Viruses 2017. [PMID: 28635671 PMCID: PMC5490832 DOI: 10.3390/v9060157] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Many viruses take advantage of cellular trafficking machineries to assemble and release new infectious particles. Using RNA interference (RNAi), we demonstrate that the Golgi/autophagosome-associated Rab33B is required for hepatitis B virus (HBV) propagation in hepatoma cell lines. While Rab33B is dispensable for the secretion of HBV subviral envelope particles, its knockdown reduced the virus yield to 20% and inhibited nucleocapsid (NC) formation and/or NC trafficking. The overexpression of a GDP-restricted Rab33B mutant phenocopied the effect of deficit Rab33B, indicating that Rab33B-specific effector proteins may be involved. Moreover, we found that HBV replication enhanced Rab33B expression. By analyzing HBV infection cycle steps, we identified a hitherto unknown membrane targeting module in the highly basic C-terminal domain of the NC-forming core protein. Rab33B inactivation reduced core membrane association, suggesting that membrane platforms participate in HBV assembly reactions. Biochemical and immunofluorescence analyses provided further hints that the viral core, rather than the envelope, is the main target for Rab33B intervention. Rab33B-deficiency reduced core protein levels without affecting viral transcription and hampered core/NC sorting to envelope-positive, intracellular compartments. Together, these results indicate that Rab33B is an important player in intracellular HBV trafficking events, guiding core transport to NC assembly sites and/or NC transport to budding sites.
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31
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Golgi trafficking defects in postnatal microcephaly: The evidence for “Golgipathies”. Prog Neurobiol 2017; 153:46-63. [DOI: 10.1016/j.pneurobio.2017.03.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/22/2017] [Accepted: 03/29/2017] [Indexed: 12/17/2022]
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Salian S, Cho TJ, Phadke SR, Gowrishankar K, Bhavani GS, Shukla A, Jagadeesh S, Kim OH, Nishimura G, Girisha KM. Additional three patients with Smith-McCort dysplasia due to novel RAB33B mutations. Am J Med Genet A 2017; 173:588-595. [PMID: 28127940 DOI: 10.1002/ajmg.a.38064] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/14/2016] [Indexed: 11/06/2022]
Abstract
Smith-McCort dysplasia (SMC OMIM 615222) and Dyggve-Melchior-Clausen dysplasia (DMC OMIM 223800) are allelic skeletal dysplasias caused by homozygous or compound heterozygous mutations in DYM (OMIM 607461). Both disorders share the same skeletal phenotypes characterized by spondylo-epi-metaphyseal dysplasia with distinctive lacy ilia. The difference rests on the presence or absence of intellectual disability, that is, intellectual disability in DMC and normal cognition in SMC. However, genetic heterogeneity was suspected in SMC. Recently, RAB33B (OMIM 605950) has been identified as the second gene for SMC. Nevertheless, only two affected families have been reported so far. Here we present three SMC patients with four novel pathogenic variants in RAB33B, including homozygosity for c.211C>T (p.R71*), homozygosity for c.365T>C (p.F122S), and compound heterozygosity for c.48delCGGGGCAG (p.G17Vfs*58) and c.490C>T (p.Q164*). We also summarize the clinical, radiological, and mutation profile of RAB33B after literature mining. This report ascertains the pathogenic relationship between RAB33B and SMC. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Smrithi Salian
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Tae-Joon Cho
- Division of Pediatric Orthopedics, Seoul National University Children's Hospital, Seoul, Korea
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Kalpana Gowrishankar
- Department of Medical Genetics, Apollo Children's Hospital, Chennai, Tamilnadu, India
| | | | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | | | - Ok-Hwa Kim
- Department of Radiology, Woorisoa Children's Hospital, Seoul, Korea
| | - Gen Nishimura
- Department of Pediatric Imaging, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
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Panarella A, Bexiga MG, Galea G, O’ Neill ED, Salvati A, Dawson KA, Simpson JC. A systematic High-Content Screening microscopy approach reveals key roles for Rab33b, OATL1 and Myo6 in nanoparticle trafficking in HeLa cells. Sci Rep 2016; 6:28865. [PMID: 27374232 PMCID: PMC4931513 DOI: 10.1038/srep28865] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 06/06/2016] [Indexed: 12/24/2022] Open
Abstract
Synthetic nanoparticles are promising tools for imaging and drug delivery; however the molecular details of cellular internalization and trafficking await full characterization. Current knowledge suggests that following endocytosis most nanoparticles pass from endosomes to lysosomes. In order to design effective drug delivery strategies that can use the endocytic pathway, or by-pass lysosomal accumulation, a comprehensive understanding of nanoparticle uptake and trafficking mechanisms is therefore fundamental. Here we describe and apply an RNA interference-based high-content screening microscopy strategy to assess the intracellular trafficking of fluorescently-labeled polystyrene nanoparticles in HeLa cells. We screened a total of 408 genes involved in cytoskeleton and membrane function, revealing roles for myosin VI, Rab33b and OATL1 in this process. This work provides the first systematic large-scale quantitative assessment of the proteins responsible for nanoparticle trafficking in cells, paving the way for subsequent genome-wide studies.
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Affiliation(s)
- Angela Panarella
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mariana G. Bexiga
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - George Galea
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Elaine D. O’ Neill
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Anna Salvati
- Centre for BioNano Interactions, School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kenneth A. Dawson
- Centre for BioNano Interactions, School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Jeremy C. Simpson
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
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34
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Cox JV, Kansal R, Whitt MA. Rab43 regulates the sorting of a subset of membrane protein cargo through the medial Golgi. Mol Biol Cell 2016; 27:1834-44. [PMID: 27053659 PMCID: PMC4884073 DOI: 10.1091/mbc.e15-03-0123] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 03/31/2016] [Indexed: 11/11/2022] Open
Abstract
To evaluate the role of cytoplasmic domains of membrane-spanning proteins in directing trafficking through the secretory pathway, we generated fluorescently tagged VSV G tsO45 with either the native G tail (G) or a cytoplasmic tail derived from the chicken AE1-4 anion exchanger (G(AE)). We previously showed that these two proteins progressed through the Golgi with distinct kinetics. To investigate the basis for the differential sorting of G and G(AE), we analyzed the role of several Golgi-associated small GTP-binding proteins and found that Rab43 differentially regulated their transport through the Golgi. We show that the expression of GFP-Rab43 arrested the anterograde transport of G(AE) in a Rab43-positive medial Golgi compartment. GFP-Rab43 expression also inhibited the acquisition of endoH-resistant sugars and the surface delivery of G(AE), as well as the surface delivery of the AE1-4 anion exchanger. In contrast, GFP-Rab43 expression did not affect the glycosylation or surface delivery of G. Unexpectedly, down-regulation of endogenous Rab43 using small interfering RNA resulted in an increase in the accumulation of G(AE) on the cell surface while having minimal effect on the surface levels of G. Our data demonstrate that Rab43 regulates the sorting of a subset of membrane-spanning cargo as they progress through the medial Golgi.
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Affiliation(s)
- John V Cox
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163
| | - Rita Kansal
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163
| | - Michael A Whitt
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163
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35
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Fisher P, Ungar D. Bridging the Gap between Glycosylation and Vesicle Traffic. Front Cell Dev Biol 2016; 4:15. [PMID: 27014691 PMCID: PMC4781848 DOI: 10.3389/fcell.2016.00015] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/22/2016] [Indexed: 11/24/2022] Open
Abstract
Glycosylation is recognized as a vitally important posttranslational modification. The structure of glycans that decorate proteins and lipids is largely dictated by biosynthetic reactions occurring in the Golgi apparatus. This biosynthesis relies on the relative distribution of glycosyltransferases and glycosidases, which is maintained by retrograde vesicle traffic between Golgi cisternae. Tethering of vesicles at the Golgi apparatus prior to fusion is regulated by Rab GTPases, coiled-coil tethers termed golgins and the multisubunit tethering complex known as the conserved oligomeric Golgi (COG) complex. In this review we discuss the mechanisms involved in vesicle tethering at the Golgi apparatus and highlight the importance of tethering in the context of glycan biosynthesis and a set of diseases known as congenital disorders of glycosylation.
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Affiliation(s)
- Peter Fisher
- Department of Biology, University of York York, UK
| | - Daniel Ungar
- Department of Biology, University of York York, UK
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36
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Elkis Y, Bel S, Rahimi R, Lerer-Goldstein T, Levin-Zaidman S, Babushkin T, Shpungin S, Nir U. TMF/ARA160 Governs the Dynamic Spatial Orientation of the Golgi Apparatus during Sperm Development. PLoS One 2015; 10:e0145277. [PMID: 26701263 PMCID: PMC4689540 DOI: 10.1371/journal.pone.0145277] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 12/02/2015] [Indexed: 12/20/2022] Open
Abstract
TMF/ARA160 is known to be a TATA element Modulatory Factor (TMF). It was initially identified as a DNA-binding factor and a coactivator of the Androgen receptor. It was also characterized as a Golgi-associated protein, which is essential for acrosome formation during functional sperm development. However, the molecular roles of TMF in this intricate process have not been revealed. Here, we show that during spermiogenesis, TMF undergoes a dynamic change of localization throughout the Golgi apparatus. Specifically, TMF translocates from the cis-Golgi to the trans-Golgi network and to the emerging vesicles surface, as the round spermatids develop. Notably, lack of TMF led to an abnormal spatial orientation of the Golgi and to the deviation of the trans-Golgi surface away from the nucleus of the developing round spermatids. Concomitantly, pro-acrosomal vesicles derived from the TMF-/- Golgi lacked targeting properties and did not tether to the spermatid nuclear membrane thereby failing to form the acrosome anchoring scaffold, the acroplaxome, around the cell-nucleus. Absence of TMF also perturbed the positioning of microtubules, which normally lie in proximity to the Golgi and are important for maintaining Golgi spatial orientation and dynamics and for chromatoid body formation, which is impaired in TMF-/- spermatids. In-silico evaluation combined with molecular and electron microscopic analyses revealed the presence of a microtubule interacting domain (MIT) in TMF, and confirmed the association of TMF with microtubules in spermatogenic cells. Furthermore, the MIT domain in TMF, along with microtubules integrity, are required for stable association of TMF with the Golgi apparatus. Collectively, we show here for the first time that a Golgi and microtubules associated protein is crucial for maintaining proper Golgi orientation during a cell developmental process.
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Affiliation(s)
- Yoav Elkis
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Shai Bel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Roni Rahimi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Tali Lerer-Goldstein
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Smadar Levin-Zaidman
- Electron Microscopy Unit, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Tatiana Babushkin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Sally Shpungin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Uri Nir
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel
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37
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Chan YS, Ng TB. Shiga toxins: from structure and mechanism to applications. Appl Microbiol Biotechnol 2015; 100:1597-1610. [PMID: 26685676 DOI: 10.1007/s00253-015-7236-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 12/03/2015] [Accepted: 12/06/2015] [Indexed: 01/03/2023]
Abstract
Shiga toxins are a group of type 2 ribosome-inactivating proteins (RIPs) produced in several types of bacteria. The toxins possess an AB5 structure, which comprises a catalytic A chain with N-glycosidase activity, and five identical B chains and recognize and bind to the target cells with specific carbohydrate moieties. In humans, the major molecular target which recognizes the Shiga toxins is the Gb3 receptor, which is mainly expressed on the cell surface of endothelial cells of the intestine, kidney, and the brain. This causes these organs to be susceptible to the toxicity of Shiga toxins. When a person is infected by Shiga toxin-producing bacteria, the toxin is produced in the gut, translocated to the circulatory system, and carried to the target cells. Toxicity of the toxin causes inflammatory responses and severe cell damages in the intestine, kidneys, and brain, bringing about the hemolytic uremic syndrome (HUS), which can be fatal. The Shiga toxin requires a couple of steps to exert its toxicity to the target cells. After binding with the target cell surface receptor, the toxin requires a complicated process to be transported into the cytosol of the cell before it can approach the ribosomes. The mechanisms for the interactions of the toxin with the cells are described in this review. The consequences of the toxin on the cells are also discussed. It gives an overview of the steps for the toxin to be produced and transported, expression of catalytic activity, and the effects of the toxin on the target cells, as well as effects on the human body.
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Affiliation(s)
- Yau Sang Chan
- School of Biomedical Sciences, Lo Kwee Seong Integrated Biomedical Sciences Building, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China.
| | - Tzi Bun Ng
- School of Biomedical Sciences, Lo Kwee Seong Integrated Biomedical Sciences Building, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China.
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38
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Amaya C, Fader CM, Colombo MI. Autophagy and proteins involved in vesicular trafficking. FEBS Lett 2015; 589:3343-53. [PMID: 26450776 DOI: 10.1016/j.febslet.2015.09.021] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/19/2015] [Accepted: 09/22/2015] [Indexed: 12/16/2022]
Abstract
Autophagy is an intracellular degradation system that, as a basic mechanism it delivers cytoplasmic components to the lysosomes in order to maintain adequate energy levels and cellular homeostasis. This complex cellular process is activated by low cellular nutrient levels and other stress situations such as low ATP levels, the accumulation of damaged proteins or organelles, or pathogen invasion. Autophagy as a multistep process involves vesicular transport events leading to tethering and fusion of autophagic vesicles with several intracellular compartments. This review summarizes our current understanding of the autophagic pathway with emphasis in the trafficking machinery (i.e. Rabs GTPases and SNAP receptors (SNAREs)) involved in specific steps of the pathway.
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Affiliation(s)
- Celina Amaya
- Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología (IHEM)-CONICET, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Casilla de Correo 56, Centro Universitario, Parque General San Martín, 5500 Mendoza, Argentina
| | - Claudio Marcelo Fader
- Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología (IHEM)-CONICET, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Casilla de Correo 56, Centro Universitario, Parque General San Martín, 5500 Mendoza, Argentina
| | - María Isabel Colombo
- Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología (IHEM)-CONICET, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Casilla de Correo 56, Centro Universitario, Parque General San Martín, 5500 Mendoza, Argentina.
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39
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Ye M, Chen Y, Zou S, Yu S, Liang Y. Ypt1 suppresses defects of vesicle trafficking and autophagy in Ypt6 related mutants. Cell Biol Int 2015; 38:663-74. [PMID: 24843892 DOI: 10.1002/cbin.10250] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Ypt/Rab GTPases coordinately regulate vesicle trafficking in yeasts. Previously, Ypt1 was shown to suppress growth defects of Ypt6 and its related mutants (ypt6ts, ric1∆, rgp1∆, ric1∆rgp1∆), but the physiological role of this suppression has not been well studied. We have investigated the effects of Ypt1 on two major trafficking pathways, vesicle trafficking and autophagy, in Ypt6 related mutants. Ypt1 restores Snc1 transport to the plasma membrane via Golgi in the exocytic pathway in Ypt6 related mutants under nutrient rich conditions. Overexpression of Ypt1 suppresses autophagic defects under nutrient starvation conditions with increased GFP-Atg8 sorting to vacuoles and GFP-Atg8 to GFP conversion in Ypt6 related mutants. However, overexpression of Ypt1 does not restore Ypt6 intracellular localisation in rgp1∆ cells. We propose that vesicle trafficking and autophagy are closely connected processes, and Ypt1 and Ypt6 have some similar functions in both cellular processes.
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Egerer J, Emmerich D, Fischer-Zirnsak B, Chan WL, Meierhofer D, Tuysuz B, Marschner K, Sauer S, Barr FA, Mundlos S, Kornak U. GORAB Missense Mutations Disrupt RAB6 and ARF5 Binding and Golgi Targeting. J Invest Dermatol 2015; 135:2368-2376. [PMID: 26000619 DOI: 10.1038/jid.2015.192] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 04/21/2015] [Accepted: 04/23/2015] [Indexed: 11/09/2022]
Abstract
Gerodermia osteodysplastica is a hereditary segmental progeroid disorder affecting skin, connective tissues, and bone that is caused by loss-of-function mutations in GORAB. The golgin, RAB6-interacting (GORAB) protein localizes to the Golgi apparatus and interacts with the small GTPase RAB6. In this study, we used different approaches to shed more light on the recruitment of GORAB to this compartment. We show that GORAB best colocalizes with trans-Golgi markers and is rapidly displaced upon Brefeldin A exposition, indicating a loose association with Golgi membranes. A yeast two-hybrid screening revealed a specific interaction with the small GTPase ADP-ribosylation factor (ARF5) in its active, GTP-bound form. ARF5 and RAB6 bind to GORAB via the same internal Golgi-targeting RAB6 and ARF5 binding (IGRAB) domain. Two GORAB missense mutations identified in gerodermia osteodysplastica patients fall within this IGRAB domain. GORAB carrying the mutation p.Ala220Pro had a cytoplasmic distribution and failed to interact with both RAB6 and ARF5. In contrast, the p.Ser175Phe mutation displaced GORAB from the Golgi compartment to vesicular structures and selectively impaired ARF5 binding. Our findings indicate that the IGRAB domain is crucial for the Golgi localization of GORAB and that loss of this localization impairs its physiological function.
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Affiliation(s)
- Johannes Egerer
- Institut fuer Medizinische Genetik und Humangenetik, Charité-Universitaetsmedizin Berlin, Berlin, Germany; Max-Planck-Institut fuer Molekulare Genetik, FG Development & Disease, Berlin, Germany
| | - Denise Emmerich
- Institut fuer Medizinische Genetik und Humangenetik, Charité-Universitaetsmedizin Berlin, Berlin, Germany; Max-Planck-Institut fuer Molekulare Genetik, FG Development & Disease, Berlin, Germany
| | - Björn Fischer-Zirnsak
- Institut fuer Medizinische Genetik und Humangenetik, Charité-Universitaetsmedizin Berlin, Berlin, Germany; Max-Planck-Institut fuer Molekulare Genetik, FG Development & Disease, Berlin, Germany
| | - Wing Lee Chan
- Institut fuer Medizinische Genetik und Humangenetik, Charité-Universitaetsmedizin Berlin, Berlin, Germany; Max-Planck-Institut fuer Molekulare Genetik, FG Development & Disease, Berlin, Germany
| | - David Meierhofer
- Max-Planck-Institut fuer Molekulare Genetik, Mass Spectrometry Facility, Berlin, Germany
| | - Beyhan Tuysuz
- Department of Pediatric Genetics, Cerrahpaşa Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Katrin Marschner
- Institut fuer Medizinische Genetik und Humangenetik, Charité-Universitaetsmedizin Berlin, Berlin, Germany
| | - Sascha Sauer
- Max-Planck-Institut fuer Molekulare Genetik, Otto-Warburg-Laboratories, Berlin, Germany
| | - Francis A Barr
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Stefan Mundlos
- Institut fuer Medizinische Genetik und Humangenetik, Charité-Universitaetsmedizin Berlin, Berlin, Germany; Max-Planck-Institut fuer Molekulare Genetik, FG Development & Disease, Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitaetsmedizin Berlin, Berlin, Germany
| | - Uwe Kornak
- Institut fuer Medizinische Genetik und Humangenetik, Charité-Universitaetsmedizin Berlin, Berlin, Germany; Max-Planck-Institut fuer Molekulare Genetik, FG Development & Disease, Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitaetsmedizin Berlin, Berlin, Germany.
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Galea G, Bexiga MG, Panarella A, O'Neill ED, Simpson JC. A high-content screening microscopy approach to dissect the role of Rab proteins in Golgi-to-ER retrograde trafficking. J Cell Sci 2015; 128:2339-49. [PMID: 25999475 DOI: 10.1242/jcs.167973] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 05/18/2015] [Indexed: 12/24/2022] Open
Abstract
Here, we describe a high-content microscopy-based screen that allowed us to systematically assess and rank proteins involved in Golgi-to-endoplasmic reticulum (ER) retrograde transport in mammalian cells. Using a cell line stably expressing a GFP-tagged Golgi enzyme, we used brefeldin A treatment to stimulate the production of Golgi-to-ER carriers and then quantitatively analysed populations of cells for changes in this trafficking event. Systematic RNA interference (RNAi)-based depletion of 58 Rab GTPase proteins and 12 Rab accessory proteins of the PRAF, YIPF and YIF protein families revealed that nine of these were strong regulators. In addition to demonstrating roles for Rab1a, Rab1b, Rab2a, and Rab6a or Rab6a' in this transport step, we also identified Rab10 and Rab11a as playing a role and being physically present on a proportion of the Golgi-to-ER tubular intermediates. Combinatorial depletions of Rab proteins also revealed previously undescribed functional co-operation and physical co-occurrence between several Rab proteins. Our approach therefore provides a novel and robust strategy for a more complete investigation of the molecular components required to regulate Golgi-to-ER transport in mammalian cells.
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Affiliation(s)
- George Galea
- School of Biology and Environmental Science and UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Mariana G Bexiga
- School of Biology and Environmental Science and UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Angela Panarella
- School of Biology and Environmental Science and UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Elaine D O'Neill
- School of Biology and Environmental Science and UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Jeremy C Simpson
- School of Biology and Environmental Science and UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
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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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Abstract
The Golgi apparatus functions as the central station of membrane traffic in cells, where newly synthesized proteins moving along the secretory pathway merge with proteins recycled from subsequent membrane organelles such as endosomes. A series of Rab GTPases act consecutively and in concert with the maturation of cis- to-trans cisternae of the Golgi apparatus. Rab GTPases control various steps in intracellular membrane traffic by recruiting downstream effector proteins. Here, we report the dynamics of Ypt6, a yeast member of the Rab GTPase family, which mediates the fusion of vesicles from endosomes at the Golgi apparatus. Ypt6 resides temporarily at the Golgi and dissociates into the cytosol upon arrival of Ypt32, another Rab GTPase functioning in the late Golgi. We found that Gyp6, a putative GTPase-activating protein (GAP) for Ypt6, specifically interacts with Ypt32, most likely as an effector. Disruption of GYP6 or introduction of a Rab-GAP activity-deficient mutation in GYP6 resulted in continual residence of Ypt6 at the Golgi. We propose that Ypt32 acts to terminate endosome-to-Golgi traffic through a Rab-GAP cascade as it does for cis-to-trans intra-Golgi traffic. Simultaneous disruption of GAP for early-acting Rab proteins in the Golgi showed appreciable defects in post-Golgi trafficking, but did not significantly affect cell growth.
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Bexiga MG, Simpson JC. Human diseases associated with form and function of the Golgi complex. Int J Mol Sci 2013; 14:18670-81. [PMID: 24025425 PMCID: PMC3794802 DOI: 10.3390/ijms140918670] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 08/09/2013] [Accepted: 09/03/2013] [Indexed: 11/16/2022] Open
Abstract
The Golgi complex lies at the heart of the secretory pathway and is responsible for modifying proteins and lipids, as well as sorting newly synthesized molecules to their correct destination. As a consequence of these important roles, any changes in its proteome can negatively affect its function and in turn lead to disease. Recently, a number of proteins have been identified, which when either depleted or mutated, result in diseases that affect various organ systems. Here we describe how these proteins have been linked to the Golgi complex, and specifically how they affect either the morphology, membrane traffic or glycosylation ability of this organelle.
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Affiliation(s)
| | - Jeremy C. Simpson
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +353-1-716-2345; Fax: +353-1-716-1153
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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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Abstract
Rab GTPases are at the central node of the machinery that regulates trafficking of organelles, including phagosomes. Thanks to the unique combination of high quality phagosome purification with highly sensitive proteomic studies, the network of Rab proteins that are dynamically associated with phagosomes during the process of maturation of this organelle is relatively well known. Whereas the phagosomal functions of many of the Rab proteins associated with phagosomes are characterized, the role(s) of most of these trafficking regulators remains to be identified. In some cases, even when the function in the context of phagosome biology is described, phagosomal Rab proteins seem to have similar roles. This review summarizes the current knowledge about the identity and function of phagosomal Rab GTPases, with a particular emphasis on new evidence that clarify these seemingly overlapping Rab functions during phagosome maturation.
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Quantitative image analysis approaches for probing Rab GTPase localization and function in mammalian cells. Biochem Soc Trans 2013; 40:1389-93. [PMID: 23176486 DOI: 10.1042/bst20120145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Membrane traffic pathways play an essential role in cells, providing a mechanism for organelles of the endomembrane system to communicate and exchange material between each other. A significant number of infections and diseases are associated with trafficking pathways, and as such gaining a greater understanding of their regulation is essential. Fluorescence-based imaging techniques are widely used to probe the trafficking machinery within cells, and many of these methods have the potential to be applied in a quantitative manner. In the present mini-review, we highlight several recent examples of how image intensity, kinetic measurements, co-localization and texture feature analysis have been used to study the function of one key family of membrane traffic regulators, the Rab GTPases. We give specific emphasis to the importance of the quantitative nature of these recent studies and comment on their potential applicability to a high-throughput format.
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Abstract
Whereas most of what we know today about the Ras-related small GTPases of the Rab family stems from observations made on Golgi complex, endosome and plasma membrane trafficking, a subset of Rabs localizes in part or predominantly to the ER (endoplasmic reticulum). Here, Rabs such as Rab1, Rab2, Rab6 and Rab33 can regulate the anterograde and retrograde trafficking of vesicles between the Golgi complex, the ERGIC (ER-Golgi intermediate compartment) and the ER itself. However, among the ER-associated Rabs, some Rabs appear to perform roles not directly related to trafficking: these Rabs (e.g. Rab32 or Rab24) could aid proteins of the atlastin and reticulon families in determining the extent and direction of ER tubulation. In so doing, these Rabs regulate not only ER contacts with other organelles such as mitochondria, but also the formation of autophagosomes.
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Abstract
Small GTPases regulate a wide range of homeostatic processes such as cytoskeletal dynamics, organelle homeostasis, cell migration and vesicle trafficking, as well as in pathologic conditions such as carcinogenesis and metastatic spreading. Therefore, it is important to understand the regulation of small GTPase signaling, but this is complicated by the fact that crosstalk exists between different GTPase families and that we have to understand how they signal in time and space. The Golgi apparatus represents a hub for several signaling molecules and its importance in this field is constantly increasing. In this review we will discuss small GTPases signaling at the Golgi apparatus. Then, we will highlight recent work that contributed to a better understanding of crosstalk between different small GTPase families, with a special emphasis on their crosstalk at the Golgi apparatus. Finally, we will give a brief overview of available methods and tools to investigate spatio-temporal small GTPase crosstalk.
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Affiliation(s)
- Francesco Baschieri
- Department of Biology, University of Konstanz, Universitätsstrasse 10, D-78457 Konstanz, Germany
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Khandelwal P, Prakasam HS, Clayton DR, Ruiz WG, Gallo LI, van Roekel D, Lukianov S, Peränen J, Goldenring JR, Apodaca G. A Rab11a-Rab8a-Myo5B network promotes stretch-regulated exocytosis in bladder umbrella cells. Mol Biol Cell 2013; 24:1007-19. [PMID: 23389633 PMCID: PMC3608489 DOI: 10.1091/mbc.e12-08-0568] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 01/29/2013] [Accepted: 01/30/2013] [Indexed: 12/03/2022] Open
Abstract
Multiple Rabs are associated with secretory granules/vesicles, but how these GTPases are coordinated to promote regulated exocytosis is not well understood. In bladder umbrella cells a subapical pool of discoidal/fusiform-shaped vesicles (DFVs) undergoes Rab11a-dependent regulated exocytosis in response to bladder filling. We show that Rab11a-associated vesicles are enmeshed in an apical cytokeratin meshwork and that Rab11a likely acts upstream of Rab8a to promote exocytosis. Surprisingly, expression of Rabin8, a previously described Rab11a effector and guanine nucleotide exchange factor for Rab8, stimulates stretch-induced exocytosis in a manner that is independent of its catalytic activity. Additional studies demonstrate that the unconventional motor protein myosin5B motor (Myo5B) works in association with the Rab8a-Rab11a module to promote exocytosis, possibly by ensuring transit of DFVs through a subapical, cortical actin cytoskeleton before fusion. Our results indicate that Rab11a, Rab8a, and Myo5B function as part of a network to promote stretch-induced exocytosis, and we predict that similarly organized Rab networks will be common to other regulated secretory pathways.
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Affiliation(s)
- Puneet Khandelwal
- Departments of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
| | | | - Dennis R. Clayton
- Departments of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
| | - Wily G. Ruiz
- Departments of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
| | - Luciana I. Gallo
- Departments of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
| | - Daniel van Roekel
- Departments of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
| | - Stefan Lukianov
- Departments of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
| | - Johan Peränen
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - James R. Goldenring
- Department of Surgery and Epithelial Biology Center, Vanderbilt University, Nashville, TN 37232
| | - Gerard Apodaca
- Departments of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
- Cell Biology, University of Pittsburgh, Pittsburgh, PA 15261
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