1
|
Singin Ö, Astapenka A, Costina V, Kühl S, Bonekamp N, Drews O, Islinger M. Analysis of the Mouse Hepatic Peroxisome Proteome-Identification of Novel Protein Constituents Using a Semi-Quantitative SWATH-MS Approach. Cells 2024; 13:176. [PMID: 38247867 PMCID: PMC10814758 DOI: 10.3390/cells13020176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
Ongoing technical and bioinformatics improvements in mass spectrometry (MS) allow for the identifying and quantifying of the enrichment of increasingly less-abundant proteins in individual fractions. Accordingly, this study reassessed the proteome of mouse liver peroxisomes by the parallel isolation of peroxisomes from a mitochondria- and a microsome-enriched prefraction, combining density-gradient centrifugation with a semi-quantitative SWATH-MS proteomics approach to unveil novel peroxisomal or peroxisome-associated proteins. In total, 1071 proteins were identified using MS and assessed in terms of their distribution in either high-density peroxisomal or low-density gradient fractions, containing the bulk of organelle material. Combining the data from both fractionation approaches allowed for the identification of specific protein profiles characteristic of mitochondria, the ER and peroxisomes. Among the proteins significantly enriched in the peroxisomal cluster were several novel peroxisomal candidates. Five of those were validated by colocalization in peroxisomes, using confocal microscopy. The peroxisomal import of HTATIP2 and PAFAH2, which contain a peroxisome-targeting sequence 1 (PTS1), could be confirmed by overexpression in HepG2 cells. The candidates SAR1B and PDCD6, which are known ER-exit-site proteins, did not directly colocalize with peroxisomes, but resided at ER sites, which frequently surrounded peroxisomes. Hence, both proteins might concentrate at presumably co-purified peroxisome-ER membrane contacts. Intriguingly, the fifth candidate, OCIA domain-containing protein 1, was previously described as decreasing mitochondrial network formation. In this work, we confirmed its peroxisomal localization and further observed a reduction in peroxisome numbers in response to OCIAD1 overexpression. Hence, OCIAD1 appears to be a novel protein, which has an impact on both mitochondrial and peroxisomal maintenance.
Collapse
Affiliation(s)
- Öznur Singin
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
| | - Artur Astapenka
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
| | - Victor Costina
- Institute of Clinical Chemistry, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (V.C.); (O.D.)
| | - Sandra Kühl
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
| | - Nina Bonekamp
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
| | - Oliver Drews
- Institute of Clinical Chemistry, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (V.C.); (O.D.)
- Biomedical Mass Spectrometry, Center for Medical Research, Johannes Kepler University Linz, 4020 Linz, Austria
| | - Markus Islinger
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
| |
Collapse
|
2
|
López-Alcalá J, Soler-Vázquez MC, Tercero-Alcázar C, Sánchez-Ceinos J, Guzmán-Ruiz R, Malagón MM, Gordon A. Rab18 Drift in Lipid Droplet and Endoplasmic Reticulum Interactions of Adipocytes under Obesogenic Conditions. Int J Mol Sci 2023; 24:17177. [PMID: 38139006 PMCID: PMC10743551 DOI: 10.3390/ijms242417177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
The adipose tissue stores excess energy in the form of neutral lipids within adipocyte lipid droplets (LDs). The correct function of LDs requires the interaction with other organelles, such as the endoplasmic reticulum (ER) as well as with LD coat-associated proteins, including Rab18, a mediator of intracellular lipid trafficking and ER-LD interaction. Although perturbations of the inter-organelle contact sites have been linked to several diseases, such as cancer, no information regarding ER-LD contact sites in dysfunctional adipocytes from the obese adipose tissue has been published to date. Herein, the ER-LD connection and Rab18 distribution at ER-LD contact sites are examined in adipocytes challenged with fibrosis and inflammatory conditions, which represent known hallmarks of the adipose tissue in obesity. Our results show that adipocytes differentiated in fibrotic conditions caused ER fragmentation, the expansion of ER-LD contact sites, and modified Rab18 dynamics. Likewise, adipocytes exposed to inflammatory conditions favored ER-LD contact, Rab18 accumulation in the ER, and Rab18 redistribution to large LDs. Finally, our studies in human adipocytes supported the suggestion that Rab18 transitions to the LD coat from the ER. Taken together, our results suggest that obesity-related pathogenic processes alter the maintenance of ER-LD interactions and interfere with Rab18 trafficking through these contact sites.
Collapse
Affiliation(s)
- Jaime López-Alcalá
- Department of Cell Biology, Physiology, and Immunology, Adipobiology Group, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain; (J.L.-A.); (M.C.S.-V.); (C.T.-A.); (R.G.-R.)
| | - M. Carmen Soler-Vázquez
- Department of Cell Biology, Physiology, and Immunology, Adipobiology Group, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain; (J.L.-A.); (M.C.S.-V.); (C.T.-A.); (R.G.-R.)
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Instituto de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Carmen Tercero-Alcázar
- Department of Cell Biology, Physiology, and Immunology, Adipobiology Group, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain; (J.L.-A.); (M.C.S.-V.); (C.T.-A.); (R.G.-R.)
| | - Julia Sánchez-Ceinos
- Cardiology Unit, Department of Medicine-Solna, Karolinska Institute (KI), Karolinska University Hospital (NKS), 17177 Stockholm, Sweden;
| | - Rocío Guzmán-Ruiz
- Department of Cell Biology, Physiology, and Immunology, Adipobiology Group, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain; (J.L.-A.); (M.C.S.-V.); (C.T.-A.); (R.G.-R.)
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - María M. Malagón
- Department of Cell Biology, Physiology, and Immunology, Adipobiology Group, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain; (J.L.-A.); (M.C.S.-V.); (C.T.-A.); (R.G.-R.)
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ana Gordon
- Department of Cell Biology, Physiology, and Immunology, Adipobiology Group, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain; (J.L.-A.); (M.C.S.-V.); (C.T.-A.); (R.G.-R.)
| |
Collapse
|
3
|
Fine-tuning cell organelle dynamics during mitosis by small GTPases. Front Med 2022; 16:339-357. [PMID: 35759087 DOI: 10.1007/s11684-022-0926-1] [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: 10/26/2021] [Accepted: 02/24/2022] [Indexed: 11/04/2022]
Abstract
During mitosis, the allocation of genetic material concurs with organelle transformation and distribution. The coordination of genetic material inheritance with organelle dynamics directs accurate mitotic progression, cell fate determination, and organismal homeostasis. Small GTPases belonging to the Ras superfamily regulate various cell organelles during division. Being the key regulators of membrane dynamics, the dysregulation of small GTPases is widely associated with cell organelle disruption in neoplastic and non-neoplastic diseases, such as cancer and Alzheimer's disease. Recent discoveries shed light on the molecular properties of small GTPases as sophisticated modulators of a remarkably complex and perfect adaptors for rapid structure reformation. This review collects current knowledge on small GTPases in the regulation of cell organelles during mitosis and highlights the mediator role of small GTPase in transducing cell cycle signaling to organelle dynamics during mitosis.
Collapse
|
4
|
Lu J, Swearingen E, Hardy M, Collins P, Wu B, Yuan E, Lu D, Li CM, Wang S, Ollmann M. RAB18 is a key regulator of GalNAc-conjugated siRNA-induced silencing in Hep3B cells. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:423-434. [PMID: 35505960 PMCID: PMC9035644 DOI: 10.1016/j.omtn.2022.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 04/01/2022] [Indexed: 12/19/2022]
Abstract
Small interfering RNA (siRNA) therapeutics have developed rapidly in recent years, despite the challenges associated with delivery of large, highly charged nucleic acids. Delivery of siRNA therapeutics to the liver has been established, with conjugation of siRNA to N-acetylgalactosamine (GalNAc) providing durable gene knockdown in hepatocytes following subcutaneous injection. GalNAc binds the asialoglycoprotein receptor (ASGPR) that is highly expressed on hepatocytes and exploits this scavenger receptor to deliver siRNA across the plasma membrane by endocytosis. However, siRNA needs to access the RNA-induced silencing complex (RISC) in the cytoplasm to provide effective gene knockdown, and the entire siRNA delivery process is very inefficient, likely because of steps required for endosomal escape, intracellular trafficking, and stability of siRNA. To reveal the cellular factors limiting delivery of siRNA therapeutics, we performed a genome-wide pooled knockout screen on the basis of delivery of GalNAc-conjugated siRNA targeting the HPRT1 gene in the human hepatocellular carcinoma line Hep3B. Our primary genome-wide pooled knockout screen identified candidate genes that when knocked out significantly enhanced siRNA efficacy in Hep3B cells. Follow-up studies indicate that knockout of RAB18 improved the efficacy of siRNA delivered by GalNAc, cholesterol, or antibodies, but not siRNA delivered by Lipofectamine transfection, suggesting a role for RAB18 in siRNA delivery and intracellular trafficking.
Collapse
|
5
|
Miyamoto T, Hosoba K, Itabashi T, Iwane AH, Akutsu SN, Ochiai H, Saito Y, Yamamoto T, Matsuura S. Insufficiency of ciliary cholesterol in hereditary Zellweger syndrome. EMBO J 2020; 39:e103499. [PMID: 32368833 PMCID: PMC7298307 DOI: 10.15252/embj.2019103499] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 03/13/2020] [Accepted: 03/20/2020] [Indexed: 11/22/2022] Open
Abstract
Primary cilia are antenna‐like organelles on the surface of most mammalian cells that receive sonic hedgehog (Shh) signaling in embryogenesis and carcinogenesis. Cellular cholesterol functions as a direct activator of a seven‐transmembrane oncoprotein called Smoothened (Smo) and thereby induces Smo accumulation on the ciliary membrane where it transduces the Shh signal. However, how cholesterol is supplied to the ciliary membrane remains unclear. Here, we report that peroxisomes are essential for the transport of cholesterol into the ciliary membrane. Zellweger syndrome (ZS) is a peroxisome‐deficient hereditary disorder with several ciliopathy‐related features and cells from these patients showed a reduced cholesterol level in the ciliary membrane. Reverse genetics approaches revealed that the GTP exchange factor Rabin8, the Rab GTPase Rab10, and the microtubule minus‐end‐directed kinesin KIFC3 form a peroxisome‐associated complex to control the movement of peroxisomes along microtubules, enabling communication between peroxisomes and ciliary pocket membranes. Our findings suggest that insufficient ciliary cholesterol levels may underlie ciliopathies.
Collapse
Affiliation(s)
- Tatsuo Miyamoto
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Kosuke Hosoba
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan.,Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Takeshi Itabashi
- Laboratory for Cell Field Structure, RIKEN Center for Biosystems Dynamics Research, Higashi-Hiroshima, Japan
| | - Atsuko H Iwane
- Laboratory for Cell Field Structure, RIKEN Center for Biosystems Dynamics Research, Higashi-Hiroshima, Japan
| | - Silvia Natsuko Akutsu
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Hiroshi Ochiai
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yumiko Saito
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Program of Life and Environmental Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Takashi Yamamoto
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Shinya Matsuura
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| |
Collapse
|
6
|
Maharjan Y, Lee JN, Kwak SA, Dutta RK, Park C, Choe SK, Park R. TMEM135 regulates primary ciliogenesis through modulation of intracellular cholesterol distribution. EMBO Rep 2020; 21:e48901. [PMID: 32157776 PMCID: PMC7202201 DOI: 10.15252/embr.201948901] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 01/31/2020] [Accepted: 02/14/2020] [Indexed: 11/09/2022] Open
Abstract
Recent evidence has linked the lysosomal cholesterol accumulation in Niemann–Pick type C1 with anomalies associated with primary ciliogenesis. Here, we report that perturbed intracellular cholesterol distribution imposed by lysosomal cholesterol accumulation during TMEM135 depletion is closely associated with impaired ciliogenesis. TMEM135 depletion does not affect the formation of the basal body and the ciliary transition zone. TMEM135 depletion severely blunts Rab8 trafficking to the centrioles without affecting the centriolar localization of Rab11 and Rabin8, the upstream regulators of Rab8 activation. Although TMEM135 depletion prevents enhanced IFT20 localization at the centrioles, ciliary vesicle formation is not affected. Furthermore, enhanced IFT20 localization at the centrioles is dependent on Rab8 activation. Supplementation of cholesterol in complex with cyclodextrin rescues Rab8 trafficking to the centrioles and Rab8 activation, thereby recovering primary ciliogenesis in TMEM135‐depleted cells. Taken together, our data suggest that TMEM135 depletion prevents ciliary vesicle elongation, a characteristic of impaired Rab8 function. Our study thus reveals a previously uncharacterized effect of erroneous intracellular cholesterol distribution on impairing Rab8 function and primary ciliogenesis.
Collapse
Affiliation(s)
- Yunash Maharjan
- Department of Biomedical Science & Engineering, Gwangju Institute of Science & Technology, Gwangju, Korea
| | - Joon No Lee
- Department of Biomedical Science & Engineering, Gwangju Institute of Science & Technology, Gwangju, Korea
| | - Seong Ae Kwak
- Department of Microbiology and Center for Metabolic Function Regulation, Wonkwang University School of Medicine, Iksan, Korea
| | - Raghbendra Kumar Dutta
- Department of Biomedical Science & Engineering, Gwangju Institute of Science & Technology, Gwangju, Korea
| | - Channy Park
- Department of Biomedical Science & Engineering, Gwangju Institute of Science & Technology, Gwangju, Korea
| | - Seong-Kyu Choe
- Department of Microbiology and Center for Metabolic Function Regulation, Wonkwang University School of Medicine, Iksan, Korea
| | - Raekil Park
- Department of Biomedical Science & Engineering, Gwangju Institute of Science & Technology, Gwangju, Korea
| |
Collapse
|
7
|
Gao G, Sheng Y, Yang H, Chua BT, Xu L. DFCP1 associates with lipid droplets. Cell Biol Int 2019; 43:1492-1504. [PMID: 31293035 DOI: 10.1002/cbin.11199] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/07/2019] [Indexed: 01/24/2023]
Abstract
Double FYVE-containing protein 1 (DFCP1) is ubiquitously expressed, participates in intracellular membrane trafficking and labels omegasomes through specific interactions with phosphatidylinositol-3-phosphate (PI3P). Previous studies showed that subcellular DFCP1 proteins display multi-organelle localization, including in the endoplasmic reticulum (ER), Golgi apparatus and mitochondria. However, its localization and function on lipid droplets (LDs) remain unclear. Here, we demonstrate that DFCP1 localizes to the LD upon oleic acid incubation. The ER-targeted domain of DFCP1 is indispensable for its LD localization, which is further enhanced by double FYVE domains. Inhibition of PI3P binding at the FYVE domain through wortmannin treatment or double mutation at C654S and C770S have no effect on DFCP1's LD localization. These show that the mechanisms for DFCP1 targeting the omegasome and LDs are different. DFCP1 deficiency in MEF cells causes an increase in LD number and reduces LD size. Interestingly, DFCP1 interacts with GTP-bound Rab18, an LD-associated protein. Taken together, our work demonstrates the dynamic localization of DFCP1 is regulated by nutritional status in response to cellular metabolism.
Collapse
Affiliation(s)
- Guangang Gao
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Yuanyuan Sheng
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Hongyuan Yang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2052 New South Wales, Sydney, Australia
| | - Boon Tin Chua
- The Institute of Metabolism and Integrative Biology, Fudan University, 200438, Shanghai, China
| | - Li Xu
- State Key Laboratory of Membrane Biology and Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| |
Collapse
|
8
|
Cholesterol transport through the peroxisome-ER membrane contacts tethered by PI(4,5)P 2 and extended synaptotagmins. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1117-1135. [PMID: 31144242 DOI: 10.1007/s11427-019-9569-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/20/2019] [Indexed: 10/26/2022]
Abstract
Most mammalian cells take up cholesterol from low-density lipoproteins (LDLs) via receptor-mediated endocytosis. After reaching lysosomes, LDL-derived cholesterol continues to transport to downstream organelles including the ER for specific structural and functional needs. Peroxisomes are recently found to receive cholesterol from lysosomes through lysosome-peroxisome membrane contacts. However, whether and how cholesterol is conveyed from peroxisomes to the ER remain unknown. Here, by combining high-resolution microscopic analyses and in vitro reconstitution of highly purified organelles or artificial liposomes, we demonstrate that peroxisomes form membrane contacts with the ER through the interaction between peroxisomal PI(4,5)P2 and ER-resident extended synaptotagmin-1, 2 and 3 (E-Syts). Depletion of peroxisomal PI(4,5)P2 or E-Syts markedly decreases peroxisome-ER membrane contacts and induces cholesterol accumulation in lysosomes. Furthermore, we show that cholesterol is delivered from 3H-labeled peroxisomes or PI(4,5)P2-containing liposomes to the ER in vitro, and that the presence of peroxisomes augments cholesterol transfer from lysosomes to the ER. Together, our study reveals a new cholesterol transport pathway along the lysosome-peroxisome-ER membrane contacts in the cell.
Collapse
|
9
|
Huang S, Jiang L, Zhuang X. Possible Roles of Membrane Trafficking Components for Lipid Droplet Dynamics in Higher Plants and Green Algae. FRONTIERS IN PLANT SCIENCE 2019; 10:207. [PMID: 30858860 PMCID: PMC6397863 DOI: 10.3389/fpls.2019.00207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/07/2019] [Indexed: 05/04/2023]
Abstract
Lipid droplets are ubiquitous dynamic organelles that contain neutral lipids surrounded by a phospholipid monolayer. They can store and supply lipids for energy metabolism and membrane synthesis. In addition, protein transport and lipid exchange often occur between LDs and various organelles to control lipid homeostasis in response to multiple stress responses and cellular signaling. In recent years, multiple membrane trafficking proteins have been identified through LD proteomics and genetic analyses. These membrane trafficking machineries are emerging as critical regulators to function in different LD-organelle interactions, e.g., for LD dynamics, biogenesis and turnover. In this review, we will summarize recent advances in regard to LD-related membrane trafficking proteins and discuss future investigations in higher plants and green algae.
Collapse
Affiliation(s)
- Shuxian Huang
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Liwen Jiang
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Xiaohong Zhuang
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- *Correspondence: Xiaohong Zhuang,
| |
Collapse
|
10
|
Islinger M, Manner A, Völkl A. The Craft of Peroxisome Purification-A Technical Survey Through the Decades. Subcell Biochem 2018; 89:85-122. [PMID: 30378020 DOI: 10.1007/978-981-13-2233-4_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Purification technologies are one of the working horses in organelle proteomics studies as they guarantee the separation of organelle-specific proteins from the background contamination by other subcellular compartments. The development of methods for the separation of organelles was a major prerequisite for the initial detection and characterization of peroxisome as a discrete entity of the cell. Since then, isolated peroxisomes fractions have been used in numerous studies in order to characterize organelle-specific enzyme functions, to allocate the peroxisome-specific proteome or to unravel the organellar membrane composition. This review will give an overview of the fractionation methods used for the isolation of peroxisomes from animals, plants and fungi. In addition to "classic" centrifugation-based isolation methods, relying on the different densities of individual organelles, the review will also summarize work on alternative technologies like free-flow-electrophoresis or flow field fractionation which are based on distinct physicochemical parameters. A final chapter will further describe how different separation methods and quantitative mass spectrometry have been used in proteomics studies to assign the proteome of PO.
Collapse
Affiliation(s)
- Markus Islinger
- Institute for Neuroanatomy, Centre for Biomedicine and Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany.
| | - Andreas Manner
- Institute for Neuroanatomy, Centre for Biomedicine and Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Alfred Völkl
- Department of Medical Cell Biology, Institute of Anatomy, University of Heidelberg, Heidelberg, Germany
| |
Collapse
|
11
|
Kunze M. Predicting Peroxisomal Targeting Signals to Elucidate the Peroxisomal Proteome of Mammals. Subcell Biochem 2018; 89:157-199. [PMID: 30378023 DOI: 10.1007/978-981-13-2233-4_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peroxisomes harbor a plethora of proteins, but the peroxisomal proteome as the entirety of all peroxisomal proteins is still unknown for mammalian species. Computational algorithms can be used to predict the subcellular localization of proteins based on their amino acid sequence and this method has been amply used to forecast the intracellular fate of individual proteins. However, when applying such algorithms systematically to all proteins of an organism the prediction of its peroxisomal proteome in silico should be possible. Therefore, a reliable detection of peroxisomal targeting signals (PTS ) acting as postal codes for the intracellular distribution of the encoding protein is crucial. Peroxisomal proteins can utilize different routes to reach their destination depending on the type of PTS. Accordingly, independent prediction algorithms have been developed for each type of PTS, but only those for type-1 motifs (PTS1) have so far reached a satisfying predictive performance. This is partially due to the low number of peroxisomal proteins limiting the power of statistical analyses and partially due to specific properties of peroxisomal protein import, which render functional PTS motifs inactive in specific contexts. Moreover, the prediction of the peroxisomal proteome is limited by the high number of proteins encoded in mammalian genomes, which causes numerous false positive predictions even when using reliable algorithms and buries the few yet unidentified peroxisomal proteins. Thus, the application of prediction algorithms to identify all peroxisomal proteins is currently ineffective as stand-alone method, but can display its full potential when combined with other methods.
Collapse
Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
12
|
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]
|
13
|
Li C, Luo X, Zhao S, Siu GK, Liang Y, Chan HC, Satoh A, Yu SS. COPI-TRAPPII activates Rab18 and regulates its lipid droplet association. EMBO J 2016; 36:441-457. [PMID: 28003315 DOI: 10.15252/embj.201694866] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 11/11/2016] [Accepted: 11/16/2016] [Indexed: 11/09/2022] Open
Abstract
The transport protein particle (TRAPP) was initially identified as a vesicle tethering factor in yeast and as a guanine nucleotide exchange factor (GEF) for Ypt1/Rab1. In mammals, structures and functions of various TRAPP complexes are beginning to be understood. We found that mammalian TRAPPII was a GEF for both Rab18 and Rab1. Inactivation of TRAPPII-specific subunits by various methods including siRNA depletion and CRISPR-Cas9-mediated deletion reduced lipolysis and resulted in aberrantly large lipid droplets. Recruitment of Rab18 onto lipid droplet (LD) surface was defective in TRAPPII-deleted cells, but the localization of Rab1 on Golgi was not affected. COPI regulates LD homeostasis. We found that the previously documented interaction between TRAPPII and COPI was also required for the recruitment of Rab18 to the LD We hypothesize that the interaction between COPI and TRAPPII helps bring TRAPPII onto LD surface, and TRAPPII, in turn, activates Rab18 and recruits it on the LD surface to facilitate its functions in LD homeostasis.
Collapse
Affiliation(s)
- Chunman Li
- Department of Anatomy, Histology and Developmental Biology, School of Basic Medical Sciences, Health Science Centre, Shenzhen University, Shenzhen, China.,School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Xiaomin Luo
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Shan Zhao
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Gavin Ky Siu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Yongheng Liang
- Key Laboratory of Agricultural Environmental Microbiology of MOA, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Hsiao Chang Chan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Epithelial Cell Biology Research Centre, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Ayano Satoh
- The Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Sidney Sb Yu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China .,Epithelial Cell Biology Research Centre, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| |
Collapse
|
14
|
Genomics of human fatty liver disease reveal mechanistically linked lipid droplet-associated gene regulations in bland steatosis and nonalcoholic steatohepatitis. Transl Res 2016; 177:41-69. [PMID: 27376874 DOI: 10.1016/j.trsl.2016.06.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 05/13/2016] [Accepted: 06/08/2016] [Indexed: 12/11/2022]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a common disorder hallmarked by excessive lipid deposits. Based on our recent research on lipid droplet (LD) formation in hepatocytes, we investigated LD-associated gene regulations in NAFLD of different grades, that is, steatosis vs steatohepatitis by comparing liver biopsies from healthy controls (N = 13) and NAFLD patients (N = 102). On average, more than 700 differentially expressed genes (DEGs) were identified of which 146 are mechanistically linked to LD formation. We identified 51 LD-associated DEGs frequently regulated in patient samples (range ≥5 to ≤102) with the liver-receptor homolog-1(NR5A2), that is, a key regulator of cholesterol metabolism being commonly repressed among 100 patients examined. With bland steatosis, notable regulations involved hypoxia-inducible lipid droplet-associated-protein and diacylglycerol-O-acyltransferase-2 renowned for their role in LD-growth. Conversely, nonalcoholic steatohepatitis-associated DEGs coded for epidermal growth factor receptor and TLR4 signaling with decreased expression of the GTPase Rab5 and the lipid phosphohydrolase PPAP2B thus highlighting adaptive responses to inflammation, LDL-mediated endocytosis and lipogenesis, respectively. Studies with steatotic primary human hepatocyte cultures demonstrated induction of LD-associated PLIN2, CIDEC, DNAAF1, whereas repressed expression of CPT1A, ANGPTL4, and PKLR informed on burdened mitochondrial metabolism. Equally, repressed expression of the B-lymphocyte chemoattractant CXCL13 and STAT4 as well as induced FGF21 evidenced amelioration of steatosis-related inflammation. In-vitro/in-vivo patient sample comparisons confirmed C-reactive protein, SOCS3, NR5A2, and SOD2 as commonly regulated. Lastly, STRING network analysis highlighted potential "druggable" targets with PLIN2, CIDEC, and hypoxia-inducible lipid droplet-associated-protein being confirmed by immunofluorescence microscopy. In conclusion, steatosis and steatohepatitis specific gene regulations informed on the pathogenesis of NAFLD to broaden the perspective of targeted therapies.
Collapse
|
15
|
Rudashevskaya EL, Sickmann A, Markoutsa S. Global profiling of protein complexes: current approaches and their perspective in biomedical research. Expert Rev Proteomics 2016; 13:951-964. [PMID: 27602509 DOI: 10.1080/14789450.2016.1233064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Despite the rapid evolution of proteomic methods, protein interactions and their participation in protein complexes - an important aspect of their function - has rarely been investigated on the proteome-wide level. Disease states, such as muscular dystrophy or viral infection, are induced by interference in protein-protein interactions within complexes. The purpose of this review is to describe the current methods for global complexome analysis and to critically discuss the challenges and opportunities for the application of these methods in biomedical research. Areas covered: We discuss advancements in experimental techniques and computational tools that facilitate profiling of the complexome. The main focus is on the separation of native protein complexes via size exclusion chromatography and gel electrophoresis, which has recently been combined with quantitative mass spectrometry, for a global protein-complex profiling. The development of this approach has been supported by advanced bioinformatics strategies and fast and sensitive mass spectrometers that have allowed the analysis of whole cell lysates. The application of this technique to biomedical research is assessed, and future directions are anticipated. Expert commentary: The methodology is quite new, and has already shown great potential when combined with complementary methods for detection of protein complexes.
Collapse
Affiliation(s)
- Elena L Rudashevskaya
- a Department of Bioanalytics , Leibniz-Institut für Analytische Wissenschaften - ISAS eV , Dortmund , Germany
| | - Albert Sickmann
- a Department of Bioanalytics , Leibniz-Institut für Analytische Wissenschaften - ISAS eV , Dortmund , Germany.,b Medizinisches Proteom-Center , Ruhr-Universität Bochum , Bochum , Germany.,c School of Natural & Computing Sciences, Department of Chemistry , University of Aberdeen , Aberdeen , UK
| | - Stavroula Markoutsa
- a Department of Bioanalytics , Leibniz-Institut für Analytische Wissenschaften - ISAS eV , Dortmund , Germany
| |
Collapse
|
16
|
Li C, Yu SSB. Rab proteins as regulators of lipid droplet formation and lipolysis. Cell Biol Int 2016; 40:1026-32. [PMID: 27453349 DOI: 10.1002/cbin.10650] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/22/2016] [Indexed: 12/11/2022]
Abstract
Lipid droplets (LDs) are highly dynamic organelles that not only store neutral lipids but also are involved in multiple cellular processes. Dysregulation of lipogenesis or lipolysis greatly contributes to the pathogenesis of several human diseases, including obesity, diabetes, and fatty liver disease. Rab proteins have been found to be associated with LDs in proteomic studies and are also known to extensively regulate intracellular membrane traffic, suggesting that LDs actively communicate with other membrane compartments to maintain energy homeostasis. This review discusses recent studies that provide mechanistic insights into the regulation of LD formation and catabolism by Rab proteins in mammalian cells.
Collapse
Affiliation(s)
- Chunman Li
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Sidney S B Yu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China. .,Epithelial Cell Biology Research Centre, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China.
| |
Collapse
|
17
|
Small GTPases in peroxisome dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:1006-13. [PMID: 26775587 DOI: 10.1016/j.bbamcr.2016.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 01/05/2016] [Accepted: 01/07/2016] [Indexed: 12/12/2022]
Abstract
In this review article, we summarize current knowledge on peroxisome biogenesis/functions and the role that small GTPases may play in these processes. Precise intracellular distribution of cell organelles requires their regulated association to microtubules and the actin cytoskeleton. In this respect, RhoGDP/RhoGTP favor binding of peroxisomes to microtubules and actin filaments. In its GTP-bound form, RhoA activates a regulatory cascade involving Rho kinaseII and non-muscle myosinIIA. Such interactions frequently depend on phosphoinositides (PIs) of which PI4P, PI(4,5)P2, and PI(3,5)P2 were found to be present in the peroxisomal membrane. PIs are pivotal determinants of intracellular signaling and known to regulate a wide range of cellular functions. In many of these functions, small GTPases are implicated. The small GTPase ADP-ribosylation factor 1 (Arf1), for example, is known to stimulate synthesis of PI4P and PI(4,5)P2 on the Golgi to regulate protein and lipid sorting. In vitro binding assays localized Arf1 and the COPI complex to peroxisomes. In light of the recent discussion of pre-peroxisomal vesicle generation at the ER, peroxisomal Arf1-COPI vesicles may serve retrograde transport of ER-resident components. A mass spectrometric screen localized various Rab proteins to peroxisomes. Overexpression of these proteins in combination with laser-scanning fluorescence microscopy co-localized Rab6, Rab8, Rab10, Rab14, and Rab18 with peroxisomal structures. By analogy to the role these proteins play in other organelle dynamics, we may envisage what the function of these proteins may be in relation to the peroxisomal compartment.
Collapse
|
18
|
Jamdhade MD, Pawar H, Chavan S, Sathe G, Umasankar PK, Mahale KN, Dixit T, Madugundu AK, Prasad TSK, Gowda H, Pandey A, Patole MS. Comprehensive proteomics analysis of glycosomes from Leishmania donovani. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:157-70. [PMID: 25748437 DOI: 10.1089/omi.2014.0163] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Leishmania donovani is a kinetoplastid protozoan that causes a severe and fatal disease kala-azar, or visceral leishmaniasis. L. donovani infects human host after the phlebotomine sandfly takes a blood meal and resides within the phagolysosome of infected macrophages. Previous studies on host-parasite interactions have not focused on Leishmania organelles and the role that they play in the survival of this parasite within macrophages. Leishmania possess glycosomes that are unique and specialized subcellular microbody organelles. Glycosomes are known to harbor most peroxisomal enzymes and, in addition, they also possess nine glycolytic enzymes. In the present study, we have carried out proteomic profiling using high resolution mass spectrometry of a sucrose density gradient-enriched glycosomal fraction isolated from L. donovani promastigotes. This study resulted in the identification of 4022 unique peptides, leading to the identification of 1355 unique proteins from a preparation enriched in L. donovani glycosomes. Based on protein annotation, 566 (41.8%) were identified as hypothetical proteins with no known function. A majority of the identified proteins are involved in metabolic processes such as carbohydrate, lipid, and nucleic acid metabolism. Our present proteomic analysis is the most comprehensive study to date to map the proteome of L. donovani glycosomes.
Collapse
|
19
|
Mhlanga-Mutangadura T, Johnson GS, Schnabel RD, Taylor JF, Johnson GC, Katz ML, Shelton GD, Lever TE, Giuliano E, Granger N, Shomper J, O'Brien DP. A mutation in the Warburg syndrome gene, RAB3GAP1, causes a similar syndrome with polyneuropathy and neuronal vacuolation in Black Russian Terrier dogs. Neurobiol Dis 2015; 86:75-85. [PMID: 26607784 DOI: 10.1016/j.nbd.2015.11.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 11/13/2015] [Accepted: 11/18/2015] [Indexed: 11/30/2022] Open
Abstract
An autosomal recessive disease of Black Russian Terriers was previously described as a juvenile-onset, laryngeal paralysis and polyneuropathy similar to Charcot Marie Tooth disease in humans. We found that in addition to an axonal neuropathy, affected dogs exhibit microphthalmia, cataracts, and miotic pupils. On histopathology, affected dogs exhibit a spongiform encephalopathy characterized by accumulations of abnormal, membrane-bound vacuoles of various sizes in neuronal cell bodies, axons and adrenal cells. DNA from an individual dog with this polyneuropathy with ocular abnormalities and neuronal vacuolation (POANV) was used to generate a whole genome sequence which contained a homozygous RAB3GAP1:c.743delC mutation that was absent from 73 control canine whole genome sequences. An additional 12 Black Russian Terriers with POANV were RAB3GAP1:c.743delC homozygotes. DNA samples from 249 Black Russian Terriers with no known signs of POANV were either heterozygotes or homozygous for the reference allele. Mutations in human RAB3GAP1 cause Warburg micro syndrome (WARBM), a severe developmental disorder characterized by abnormalities of the eye, genitals and nervous system including a predominantly axonal peripheral neuropathy. RAB3GAP1 encodes the catalytic subunit of a GTPase activator protein and guanine exchange factor for Rab3 and Rab18 respectively. Rab proteins are involved in membrane trafficking in the endoplasmic reticulum, axonal transport, autophagy and synaptic transmission. The neuronal vacuolation and membranous inclusions and vacuoles in axons seen in this canine disorder likely reflect alterations of these processes. Thus, this canine disease could serve as a model for WARBM and provide insight into its pathogenesis and treatment.
Collapse
Affiliation(s)
| | - Gary S Johnson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, USA; Informatics Institute, University of Missouri, Columbia, USA
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, USA
| | - Gayle C Johnson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, USA
| | - Martin L Katz
- Mason Eye Institute, University of Missouri, Columbia, USA
| | - G Diane Shelton
- Department of Pathology, University of California, San Diego, La Jolla, USA
| | - Teresa E Lever
- Department of Otolaryngology, University of Missouri, Columbia, USA
| | - Elizabeth Giuliano
- Department of Veterinary Medicine & Surgery, University of Missouri, Columbia, USA
| | - Nicolas Granger
- School of Veterinary Sciences, University of Bristol, Langford House, Langford, Somerset BS40 5DU, UK
| | - Jeremy Shomper
- Department of Veterinary Medicine & Surgery, University of Missouri, Columbia, USA
| | - Dennis P O'Brien
- Department of Veterinary Medicine & Surgery, University of Missouri, Columbia, USA.
| |
Collapse
|
20
|
Acquisition of radioresistance in docetaxel-resistant human lung adenocarcinoma cells is linked with dysregulation of miR-451/c-Myc-survivin/rad-51 signaling. Oncotarget 2015; 5:6113-29. [PMID: 25026294 PMCID: PMC4171617 DOI: 10.18632/oncotarget.2176] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Chemoresistant tumors usually fail to respond to radiotherapy. However, the mechanisms involved in chemo- and radiotherapy cross resistance are not fully understood. Previously, we have identified microRNA (miR)-451 as a tumor suppressor in lung adenocarcinoma (LAD). However, whether miR-451 plays critical roles in chemo- and radiotherapy cross resistance in LAD is unclear. Here, we established two docetaxel-resistant LAD cell models (SPC-A1/DTX and H1299/DTX), and showed that miR-451 was significantly downregulated in docetaxel-resistant LAD cells. Gain - and loss - of - function assays indicated that re-expression of miR-451 could reverse radioresistance of docetaxel-resistant LAD cells both in vitro and in vivo through promoting apoptosis and DNA double-strand breaks (DSBs). The proto-oncogene c-Myc was identified as a direct target of miR-451, and re-expression of miR-451 inhibited survivin and rad-51 expression by reducing the amount of c-Myc protein binding to their promoters. Silencing of c-Myc could phenocopy the effects of miR-451 upregulation, and restoration of c-Myc could partially rescue the effect of miR-451 upregulation on radiosensitivity of docetaxel-resistant LAD cells. Therefore, dysregulation of miR-451/c-Myc-survivin/rad-51 signaling is responsible for radioresistance of docetaxel-resistant LAD cells, and targeting it will be a potential strategy for reversing chemo- and radiotherapy cross resistance of LAD patients.
Collapse
|
21
|
Golizeh M, Schneider C, Ohlund LB, Sleno L. Multidimensional LC–MS/MS analysis of liver proteins in rat, mouse and human microsomal and S9 fractions. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
22
|
Kumar R, Jain S, Kumari B, Kumar M. Protein sub-nuclear localization prediction using SVM and Pfam domain information. PLoS One 2014; 9:e98345. [PMID: 24897370 PMCID: PMC4045734 DOI: 10.1371/journal.pone.0098345] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 05/01/2014] [Indexed: 12/24/2022] Open
Abstract
The nucleus is the largest and the highly organized organelle of eukaryotic cells. Within nucleus exist a number of pseudo-compartments, which are not separated by any membrane, yet each of them contains only a specific set of proteins. Understanding protein sub-nuclear localization can hence be an important step towards understanding biological functions of the nucleus. Here we have described a method, SubNucPred developed by us for predicting the sub-nuclear localization of proteins. This method predicts protein localization for 10 different sub-nuclear locations sequentially by combining presence or absence of unique Pfam domain and amino acid composition based SVM model. The prediction accuracy during leave-one-out cross-validation for centromeric proteins was 85.05%, for chromosomal proteins 76.85%, for nuclear speckle proteins 81.27%, for nucleolar proteins 81.79%, for nuclear envelope proteins 79.37%, for nuclear matrix proteins 77.78%, for nucleoplasm proteins 76.98%, for nuclear pore complex proteins 88.89%, for PML body proteins 75.40% and for telomeric proteins it was 83.33%. Comparison with other reported methods showed that SubNucPred performs better than existing methods. A web-server for predicting protein sub-nuclear localization named SubNucPred has been established at http://14.139.227.92/mkumar/subnucpred/. Standalone version of SubNucPred can also be downloaded from the web-server.
Collapse
Affiliation(s)
- Ravindra Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Sohni Jain
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Bandana Kumari
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
- * E-mail:
| |
Collapse
|
23
|
Gerondopoulos A, Bastos RN, Yoshimura SI, Anderson R, Carpanini S, Aligianis I, Handley MT, Barr FA. Rab18 and a Rab18 GEF complex are required for normal ER structure. ACTA ACUST UNITED AC 2014; 205:707-20. [PMID: 24891604 PMCID: PMC4050724 DOI: 10.1083/jcb.201403026] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The ancestral Rab GTPase Rab18 and both subunits of the Rab3GAP complex are mutated in the human neurological and developmental disorder Warburg Micro syndrome. Here, we demonstrate that the Rab3GAP complex is a specific Rab18 guanine nucleotide exchange factor (GEF). The Rab3GAP complex localizes to the endoplasmic reticulum (ER) and is necessary for ER targeting of Rab18. It is also sufficient to promote membrane recruitment of Rab18. Disease-associated point mutations of conserved residues in either the Rab3GAP1 (T18P and E24V) or Rab3GAP2 (R426C) subunits result in loss of the Rab18 GEF and membrane-targeting activities. Supporting the view that Rab18 activity is important for ER structure, in the absence of either Rab3GAP subunit or Rab18 function, ER tubular networks marked by reticulon 4 were disrupted, and ER sheets defined by CLIMP-63 spread out into the cell periphery. Micro syndrome is therefore a disease characterized by direct loss of Rab18 function or loss of Rab18 activation at the ER by its GEF Rab3GAP.
Collapse
Affiliation(s)
| | | | - Shin-Ichiro Yoshimura
- Department of Cell Biology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Rachel Anderson
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, England, UK
| | - Sarah Carpanini
- Division of Neurobiology, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, Scotland, UK
| | - Irene Aligianis
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, Scotland, UK
| | - Mark T Handley
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, Scotland, UK
| | - Francis A Barr
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, England, UK
| |
Collapse
|
24
|
Roos J, Bejai S, Oide S, Dixelius C. RabGAP22 is required for defense to the vascular pathogen Verticillium longisporum and contributes to stomata immunity. PLoS One 2014; 9:e88187. [PMID: 24505423 PMCID: PMC3913773 DOI: 10.1371/journal.pone.0088187] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 01/03/2014] [Indexed: 02/03/2023] Open
Abstract
Verticillium longisporum is a soil-borne pathogen with a preference for plants within the family Brassicaceae. Following invasion of the roots, the fungus proliferates in the plant vascular system leading to stunted plant growth, chlorosis and premature senescence. RabGTPases have been demonstrated to play a crucial role in regulating multiple responses in plants. Here, we report on the identification and characterization of the Rab GTPase-activating protein RabGAP22 gene from Arabidopsis, as an activator of multiple components in the immune responses to V. longisporum. RabGAP22Pro :GUS transgenic lines showed GUS expression predominantly in root meristems, vascular tissues and stomata, whereas the RabGAP22 protein localized in the nucleus. Reduced RabGAP22 transcript levels in mutants of the brassinolide (BL) signaling gene BRI1-associated receptor kinase 1, together with a reduction of fungal proliferation following BL pretreatment, suggested RabGAP22 to be involved in BL-mediated responses. Pull-down assays revealed serine:glyoxylate aminotransferase (AGT1) as an interacting partner during V. longisporum infection and bimolecular fluorescence complementation (BiFC) showed the RabGAP22-AGT1 protein complex to be localized in the peroxisomes. Further, fungal-induced RabGAP22 expression was found to be associated with elevated endogenous levels of the plant hormones jasmonic acid (JA) and abscisic acid (ABA). An inadequate ABA response in rabgap22-1 mutants, coupled with a stomata-localized expression of RabGAP22 and impairment of guard cell closure in response to V. longisporum and Pseudomonas syringae, suggest that RabGAP22 has multiple roles in innate immunity.
Collapse
Affiliation(s)
- Jonas Roos
- Department of Plant Biology, Swedish University of Agricultural Sciences, Linnean Center for Plant Biology, Uppsala, Sweden
| | - Sarosh Bejai
- Department of Plant Biology, Swedish University of Agricultural Sciences, Linnean Center for Plant Biology, Uppsala, Sweden
| | - Shinichi Oide
- Molecular Microbiology and Biotechnology group, Research Institute of Innovative Technology for the Earth, Kizugawa, Kyoto, Japan
| | - Christina Dixelius
- Department of Plant Biology, Swedish University of Agricultural Sciences, Linnean Center for Plant Biology, Uppsala, Sweden
| |
Collapse
|
25
|
Quan S, Yang P, Cassin-Ross G, Kaur N, Switzenberg R, Aung K, Li J, Hu J. Proteome analysis of peroxisomes from etiolated Arabidopsis seedlings identifies a peroxisomal protease involved in β-oxidation and development. PLANT PHYSIOLOGY 2013; 163:1518-38. [PMID: 24130194 PMCID: PMC3850190 DOI: 10.1104/pp.113.223453] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plant peroxisomes are highly dynamic organelles that mediate a suite of metabolic processes crucial to development. Peroxisomes in seeds/dark-grown seedlings and in photosynthetic tissues constitute two major subtypes of plant peroxisomes, which had been postulated to contain distinct primary biochemical properties. Multiple in-depth proteomic analyses had been performed on leaf peroxisomes, yet the major makeup of peroxisomes in seeds or dark-grown seedlings remained unclear. To compare the metabolic pathways of the two dominant plant peroxisomal subtypes and discover new peroxisomal proteins that function specifically during seed germination, we performed proteomic analysis of peroxisomes from etiolated Arabidopsis (Arabidopsis thaliana) seedlings. The detection of 77 peroxisomal proteins allowed us to perform comparative analysis with the peroxisomal proteome of green leaves, which revealed a large overlap between these two primary peroxisomal variants. Subcellular targeting analysis by fluorescence microscopy validated around 10 new peroxisomal proteins in Arabidopsis. Mutant analysis suggested the role of the cysteine protease RESPONSE TO DROUGHT21A-LIKE1 in β-oxidation, seed germination, and growth. This work provides a much-needed road map of a major type of plant peroxisome and has established a basis for future investigations of peroxisomal proteolytic processes to understand their roles in development and in plant interaction with the environment.
Collapse
|