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Choura M, Ebel C, Hanin M. Genomic analysis of intrinsically disordered proteins in cereals: From mining to meaning. Gene 2019; 714:143984. [DOI: 10.1016/j.gene.2019.143984] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 06/21/2019] [Accepted: 07/15/2019] [Indexed: 12/29/2022]
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Pagani TD, Guimarães ACR, Waghabi MC, Corrêa PR, Kalume DE, Berrêdo-Pinho M, Degrave WM, Mendonça-Lima L. Exploring the Potential Role of Moonlighting Function of the Surface-Associated Proteins From Mycobacterium bovis BCG Moreau and Pasteur by Comparative Proteomic. Front Immunol 2019; 10:716. [PMID: 31080447 PMCID: PMC6497762 DOI: 10.3389/fimmu.2019.00716] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/18/2019] [Indexed: 12/14/2022] Open
Abstract
Surface-associated proteins from Mycobacterium bovis BCG Moreau RDJ are important components of the live Brazilian vaccine against tuberculosis. They are important targets during initial BCG vaccine stimulation and modulation of the host's immune response, especially in the bacterial-host interaction. These proteins might also be involved in cellular communication, chemical response to the environment, pathogenesis processes through mobility, colonization, and adherence to the host cell, therefore performing multiple functions. In this study, the proteomic profile of the surface-associated proteins from M. bovis BCG Moreau was compared to the BCG Pasteur reference strain. The methodology used was 2DE gel electrophoresis combined with mass spectrometry techniques (MALDI-TOF/TOF), leading to the identification of 115 proteins. Of these, 24 proteins showed differential expression between the two BCG strains. Furthermore, 27 proteins previously described as displaying moonlighting function were identified, 8 of these proteins showed variation in abundance comparing BCG Moreau to Pasteur and 2 of them presented two different domain hits. Moonlighting proteins are multifunctional proteins in which two or more biological functions are fulfilled by a single polypeptide chain. Therefore, the identification of such proteins with moonlighting predicted functions can contribute to a better understanding of the molecular mechanisms unleashed by live BCG Moreau RDJ vaccine components.
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Affiliation(s)
- Talita Duarte Pagani
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ana Carolina R Guimarães
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Mariana C Waghabi
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Paloma Rezende Corrêa
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Dário Eluan Kalume
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil.,Unidade de Espectrometria de Massas e Proteômica, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcia Berrêdo-Pinho
- Laboratório de Microbiologia Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Wim Maurits Degrave
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Leila Mendonça-Lima
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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Haimovich G, Cohen-Zontag O, Gerst JE. A role for mRNA trafficking and localized translation in peroxisome biogenesis and function? BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:911-21. [PMID: 26367800 DOI: 10.1016/j.bbamcr.2015.09.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/08/2015] [Accepted: 09/09/2015] [Indexed: 02/03/2023]
Abstract
Peroxisomes are distinct membrane-enclosed organelles involved in the β-oxidation of fatty acids and synthesis of ether phospholipids (e.g. plasmalogens), as well as cholesterol and its derivatives (e.g. bile acids). Peroxisomes comprise a distinct and highly segregated subset of cellular proteins, including those of the peroxisome membrane and the interior matrix, and while the mechanisms of protein import into peroxisomes have been extensively studied, they are not fully understood. Here we will examine the potential role of RNA trafficking and localized translation on protein import into peroxisomes and its role in peroxisome biogenesis and function. Given that RNAs encoding peroxisome biogenesis (PEX) and matrix proteins have been found in association with the endoplasmic reticulum and peroxisomes, it suggests that localized translation may play a significant role in the import pathways of these different peroxisomal constituents.
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Affiliation(s)
- Gal Haimovich
- Dept. of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Osnat Cohen-Zontag
- Dept. of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jeffrey E Gerst
- Dept. of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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Intrinsic acyl-CoA thioesterase activity of a peroxisomal ATP binding cassette transporter is required for transport and metabolism of fatty acids. Proc Natl Acad Sci U S A 2013; 110:1279-84. [PMID: 23288899 DOI: 10.1073/pnas.1218034110] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Peroxisomes are organelles that perform diverse metabolic functions in different organisms, but a common function is β-oxidation of a variety of long chain aliphatic, branched, and aromatic carboxylic acids. Import of substrates into peroxisomes for β-oxidation is mediated by ATP binding cassette (ABC) transporter proteins of subfamily D, which includes the human adrenoleukodystropy protein (ALDP) defective in X-linked adrenoleukodystrophy (X-ALD). Whether substrates are transported as CoA esters or free acids has been a matter of debate. Using COMATOSE (CTS), a plant representative of the ABCD family, we demonstrate that there is a functional and physical interaction between the ABC transporter and the peroxisomal long chain acyl-CoA synthetases (LACS)6 and -7. We expressed recombinant CTS in insect cells and showed that membranes from infected cells possess fatty acyl-CoA thioesterase activity, which is stimulated by ATP. A mutant, in which Serine 810 is replaced by asparagine (S810N) is defective in fatty acid degradation in vivo, retains ATPase activity but has strongly reduced thioesterase activity, providing strong evidence for the biological relevance of this activity. Thus, CTS, and most likely the other ABCD family members, represent rare examples of polytopic membrane proteins with an intrinsic additional enzymatic function that may regulate the entry of substrates into the β-oxidation pathway. The cleavage of CoA raises questions about the side of the membrane where this occurs and this is discussed in the context of the peroxisomal coenzyme A (CoA) budget.
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Completion of the core β-oxidative pathway of benzoic acid biosynthesis in plants. Proc Natl Acad Sci U S A 2012; 109:16383-8. [PMID: 22988098 DOI: 10.1073/pnas.1211001109] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Despite the importance of benzoic acid (BA) as a precursor for a wide array of primary and secondary metabolites, its biosynthesis in plants has not been fully elucidated. BA formation from phenylalanine requires shortening of the C(3) side chain by two carbon units, which can occur by a non-β-oxidative route and/or a β-oxidative pathway analogous to the catabolism of fatty acids. Enzymes responsible for the first and last reactions of the core BA β-oxidative pathway (cinnamic acid → cinnamoyl-CoA → 3-hydroxy-3-phenylpropanoyl-CoA → 3-oxo-3-phenylpropanoyl-CoA → BA-CoA) have previously been characterized in petunia, a plant with flowers rich in phenylpropanoid/benzenoid volatile compounds. Using a functional genomics approach, we have identified a petunia gene encoding cinnamoyl-CoA hydratase-dehydrogenase (PhCHD), a bifunctional peroxisomal enzyme responsible for two consecutively occurring unexplored intermediate steps in the core BA β-oxidative pathway. PhCHD spatially, developmentally, and temporally coexpresses with known genes in the BA β-oxidative pathway, and correlates with emission of benzenoid volatiles. Kinetic analysis of recombinant PhCHD revealed it most efficiently converts cinnamoyl-CoA to 3-oxo-3-phenylpropanoyl-CoA, thus forming the substrate for the final step in the pathway. Down-regulation of PhCHD expression in petunia flowers resulted in reduced CHD enzyme activity, as well as decreased formation of BA-CoA, BA and their derived volatiles. Moreover, transgenic lines accumulated the PhCHD substrate cinnamoyl-CoA and the upstream pathway intermediate cinnamic acid. Discovery of PhCHD completes the elucidation of the core BA β-oxidative route in plants, and together with the previously characterized CoA-ligase and thiolase enzymes, provides evidence that the whole pathway occurs in peroxisomes.
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Hamada T, Tominaga M, Fukaya T, Nakamura M, Nakano A, Watanabe Y, Hashimoto T, Baskin TI. RNA Processing Bodies, Peroxisomes, Golgi Bodies, Mitochondria, and Endoplasmic Reticulum Tubule Junctions Frequently Pause at Cortical Microtubules. ACTA ACUST UNITED AC 2012; 53:699-708. [DOI: 10.1093/pcp/pcs025] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Ching SLK, Gidda SK, Rochon A, van Cauwenberghe OR, Shelp BJ, Mullen RT. Glyoxylate reductase isoform 1 is localized in the cytosol and not peroxisomes in plant cells. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2012; 54:152-68. [PMID: 22309191 DOI: 10.1111/j.1744-7909.2012.01103.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Glyoxylate reductase (GLYR) is a key enzyme in plant metabolism which catalyzes the detoxification of both photorespiratory glyoxylate and succinic semialdehdye, an intermediate of the γ-aminobutyrate (GABA) pathway. Two isoforms of GLYR exist in plants, GLYR1 and GLYR2, and while GLYR2 is known to be localized in plastids, GLYR1 has been reported to be localized in either peroxisomes or the cytosol. Here, we reappraised the intracellular localization of GLYR1 in Arabidopsis thaliana L. Heynh (ecotype Lansberg erecta) using both transiently-transformed suspension cells and stably-transformed plants, in combination with fluorescence microscopy. The results indicate that GLYR1 is localized exclusively to the cytosol regardless of the species, tissue and/or cell type, or exposure of plants to environmental stresses that would increase flux through the GABA pathway. Moreover, the C-terminal tripeptide sequence of GLYR1, -SRE, despite its resemblance to a type 1 peroxisomal targeting signal, is not sufficient for targeting to peroxisomes. Collectively, these results define the cytosol as the intracellular location of GLYR1 and provide not only important insight to the metabolic roles of GLYR1 and the compartmentation of the GABA and photorespiratory pathways in plant cells, but also serve as a useful reference for future studies of proteins proposed to be localized to peroxisomes and/or the cytosol.
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Affiliation(s)
- Steven L K Ching
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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Muench DG, Zhang C, Dahodwala M. Control of cytoplasmic translation in plants. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:178-94. [DOI: 10.1002/wrna.1104] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Radulovic M, Godovac-Zimmermann J. Proteomic approaches to understanding the role of the cytoskeleton in host-defense mechanisms. Expert Rev Proteomics 2011; 8:117-26. [PMID: 21329431 DOI: 10.1586/epr.10.91] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The cytoskeleton is a cellular scaffolding system whose functions include maintenance of cellular shape, enabling cellular migration, division, intracellular transport, signaling and membrane organization. In addition, in immune cells, the cytoskeleton is essential for phagocytosis. Following the advances in proteomics technology over the past two decades, cytoskeleton proteome analysis in resting and activated immune cells has emerged as a possible powerful approach to expand our understanding of cytoskeletal composition and function. However, so far there have only been a handful of studies of the cytoskeleton proteome in immune cells. This article considers promising proteomics strategies that could augment our understanding of the role of the cytoskeleton in host-defense mechanisms.
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Affiliation(s)
- Marko Radulovic
- Division of Medicine, University College London, 5 University Street, London WC1E 6JF, UK.
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Crofts AJ, Crofts N, Whitelegge JP, Okita TW. Isolation and identification of cytoskeleton-associated prolamine mRNA binding proteins from developing rice seeds. PLANTA 2010; 231:1261-76. [PMID: 20217123 DOI: 10.1007/s00425-010-1125-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 02/10/2010] [Indexed: 05/08/2023]
Abstract
The messenger RNA of the rice seed storage protein prolamine is targeted to the endoplasmic reticulum (ER) membranes surrounding prolamine protein bodies via a mechanism, which is dependent upon both RNA sorting signals and the actin cytoskeleton. In this study we have used an RNA bait corresponding to the previously characterized 5'CDS prolamine cis-localization sequence for the capture of RNA binding proteins (RBPs) from cytoskeleton-enriched fractions of developing rice seed. In comparison to a control RNA, the cis-localization RNA bait sequence led to the capture of a much larger number of proteins, 18 of which have been identified by tandem mass spectrometry. Western blots demonstrate that several of the candidate proteins analyzed to date show good to excellent specificity for binding to cis-localization sequences over the control RNA bait. Temporal expression studies showed that steady state protein levels for one RNA binding protein, RBP-A, paralleled prolamine gene expression. Immunoprecipitation studies showed that RBP-A is bound to prolamine and glutelin RNAs in vivo, supporting a direct role in storage protein gene expression. Using confocal immunofluorescence microscopy, RBP-A was found to be distributed to multiple compartments in the cell. In addition to the nucleus, RBP-A co-localizes with microtubules and is associated with cortical ER membranes. Collectively, these results indicate that employing a combination of in vitro binding and in vivo binding and localization studies is a valid strategy for the identification of putative prolamine mRNA binding proteins, such as RBP-A, which play a role in controlling expression of storage protein mRNAs in the cytoplasm.
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Affiliation(s)
- Andrew J Crofts
- Institute of Biological Chemistry, Washington State University, Clark Hall, Room #299, 100 Dairy Road, Pullman, WA 99164-6340, USA.
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Doroshenk KA, Crofts AJ, Morris RT, Wyrick JJ, Okita TW. Proteomic Analysis of Cytoskeleton-Associated RNA Binding Proteins in Developing Rice Seed. J Proteome Res 2009; 8:4641-53. [DOI: 10.1021/pr900537p] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kelly A. Doroshenk
- Institute of Biological Chemistry, School of Molecular Biosciences, Washington State University, Pullman, Washington 99164 and Department of Natural Sciences, Akita International University, 193-2 Okutsubakidai, Tsubakigawa, Yuwa Akita-city, Akita 010-1211, Japan
| | - Andrew J. Crofts
- Institute of Biological Chemistry, School of Molecular Biosciences, Washington State University, Pullman, Washington 99164 and Department of Natural Sciences, Akita International University, 193-2 Okutsubakidai, Tsubakigawa, Yuwa Akita-city, Akita 010-1211, Japan
| | - Robert T. Morris
- Institute of Biological Chemistry, School of Molecular Biosciences, Washington State University, Pullman, Washington 99164 and Department of Natural Sciences, Akita International University, 193-2 Okutsubakidai, Tsubakigawa, Yuwa Akita-city, Akita 010-1211, Japan
| | - John J. Wyrick
- Institute of Biological Chemistry, School of Molecular Biosciences, Washington State University, Pullman, Washington 99164 and Department of Natural Sciences, Akita International University, 193-2 Okutsubakidai, Tsubakigawa, Yuwa Akita-city, Akita 010-1211, Japan
| | - Thomas W. Okita
- Institute of Biological Chemistry, School of Molecular Biosciences, Washington State University, Pullman, Washington 99164 and Department of Natural Sciences, Akita International University, 193-2 Okutsubakidai, Tsubakigawa, Yuwa Akita-city, Akita 010-1211, Japan
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Hwang YT, McCartney AW, Gidda SK, Mullen RT. Localization of the Carnation Italian ringspot virus replication protein p36 to the mitochondrial outer membrane is mediated by an internal targeting signal and the TOM complex. BMC Cell Biol 2008; 9:54. [PMID: 18811953 PMCID: PMC2573885 DOI: 10.1186/1471-2121-9-54] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Accepted: 09/23/2008] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Carnation Italian ringspot virus (CIRV) is a positive-strand RNA virus that causes massive structural alterations of mitochondria in infected host cells, the most conspicuous being the formation of numerous internal vesicles/spherules that are derived from the mitochondrial outer membrane and serve as the sites for viral RNA replication. While the membrane-bound components of the CIRV replication complex, including a 36-kD RNA-binding protein (p36), are known to be essential for these changes in mitochondrial morphology and are relatively well characterized in terms of their roles in nascent viral RNA synthesis, how these proteins are specifically targeted and inserted into mitochondria is poorly defined. RESULTS Here we report on the molecular signal responsible for sorting p36 to the mitochondrial outer membrane. Using a combination of gain-of-function assays with portions of p36 fused to reporter proteins and domain-swapping assays with p36 and another closely-related viral RNA-binding protein, p33, that sorts specifically to the peroxisomal boundary membrane, we show that the mitochondrial targeting information in p36 resides within its two transmembrane domains (TMDs) and intervening hydrophilic loop sequence. Comprehensive mutational analysis of these regions in p36 revealed that the primary targeting determinants are the moderate hydrophobicity of both TMDs and the positively-charged face of an amphipathic helix within the intervening loop sequence. We show also using bimolecular fluorescence complementation (BiFC) that p36 interacts with certain components of the translocase complex in the mitochondrial outer membrane (TOM), but not with the sorting and assembly machinery (SAM). CONCLUSION Our results provide insight to how viruses, such as CIRV, exploit specific host-cell protein sorting pathways to facilitate their replication. The characterization of the targeting and insertion of p36 into the mitochondrial outer membrane also sheds light on the mechanisms involved in sorting of host-cell membrane proteins to mitochondria, a process that has been largely unexplored in plants.
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Affiliation(s)
- Yeen Ting Hwang
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Andrew W McCartney
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
- JD Irving, Limited, Woodlands Division, 1350 Regent Street, Fredericton, New Brunswick, E3C 2G6, Canada
| | - Satinder K Gidda
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Lingard MJ, Gidda SK, Bingham S, Rothstein SJ, Mullen RT, Trelease RN. Arabidopsis PEROXIN11c-e, FISSION1b, and DYNAMIN-RELATED PROTEIN3A cooperate in cell cycle-associated replication of peroxisomes. THE PLANT CELL 2008; 20:1567-85. [PMID: 18539750 PMCID: PMC2483373 DOI: 10.1105/tpc.107.057679] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Although participation of PEROXIN11 (PEX11), FISSION1 (FISl), and DYNAMIN-RELATED PROTEIN (DRP) has been well established during induced peroxisome proliferation in response to external stimuli, their roles in cell cycle-associated constitutive replication/duplication have not been fully explored. Herein, bimolecular fluorescence complementation experiments with Arabidopsis thaliana suspension cells revealed homooligomerization of all five PEX11 isoforms (PEX11a-e) and heterooligomerizations of all five PEX11 isoforms with FIS1b, but not FIS1a nor DRP3A. Intracellular protein targeting experiments demonstrated that FIS1b, but not FIS1a nor DRP3A, targeted to peroxisomes only when coexpressed with PEX11d or PEX11e. Simultaneous silencing of PEX11c-e or individual silencing of DRP3A, but not FIS1a nor FIS1b, resulted in approximately 40% reductions in peroxisome number. During G2 in synchronized cell cultures, peroxisomes sequentially enlarged, elongated, and then doubled in number, which correlated with peaks in PEX11, FIS1, and DRP3A expression. Overall, these data support a model for the replication of preexisting peroxisomes wherein PEX11c, PEX11d, and PEX11e act cooperatively during G2 to promote peroxisome elongation and recruitment of FIS1b to the peroxisome membrane, where DRP3A stimulates fission of elongated peroxisomes into daughter peroxisomes, which are then distributed between daughter cells.
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Affiliation(s)
- Matthew J Lingard
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501, USA
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Abe M, Fujiwara M, Kurotani KI, Yokoi S, Shimamoto K. Identification of dynamin as an interactor of rice GIGANTEA by tandem affinity purification (TAP). PLANT & CELL PHYSIOLOGY 2008; 49:420-32. [PMID: 18296724 DOI: 10.1093/pcp/pcn019] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
GIGANTEA (GI), CONSTANS (CO) and FLOWERING LOCUS T (FT) regulate photoperiodic flowering in Arabidopsis. In rice, OsGI, Hd1 and Hd3a were identified as orthologs of GI, CO and FT, respectively, and are also important regulators of flowering. Although GI has roles in both flowering and the circadian clock, our understanding of its biochemical functions is still limited. In this study, we purified novel OsGI-interacting proteins by using the tandem affinity purification (TAP) method. The TAP method has been used effectively in a number of model species to isolate proteins that interact with proteins of interest. However, in plants, the TAP method has been used in only a few studies, and no novel proteins have previously been isolated by this method. We generated transgenic rice plants and cell cultures expressing a TAP-tagged version of OsGI. After a two-step purification procedure, the interacting proteins were analyzed by mass spectrometry. Seven proteins, including dynamin, were identified as OsGI-interacting proteins. The interaction of OsGI with dynamin was verified by co-immunoprecipitation using a myc-tagged version of OsGI. Moreover, an analysis of Arabidopsis dynamin mutants indicated that although the flowering times of the mutants were not different from those of wild-type plants, an aerial rosette phenotype was observed in the mutants. We also found that OsGI is present in both the nucleus and the cytosol by Western blot analysis and by transient assays. These results indicate that the TAP method is effective for the isolation of novel proteins that interact with target proteins in plants.
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Affiliation(s)
- Makoto Abe
- Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0101, Japan
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Guo F, Yu L, Watkins S, Han Y. Orientation of microtubules suggests a role in mRNA transportation in fertilized eggs of Chinese pine (Pinus tabulaeformis). PROTOPLASMA 2007; 231:239-243. [PMID: 17922266 DOI: 10.1007/s00709-007-0266-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Accepted: 02/03/2007] [Indexed: 05/25/2023]
Abstract
Polysomes become associated with microtubules (MTs) in egg cells of Chinese pine upon fertilization, providing direct evidence for MT-based intracellular mRNA and polysome localization. We have investigated by immunoelectron microscopy the orientation and spatial distribution of MTs and their association with polysomes in the fertilized egg cells. There is a perinuclear accumulation of MTs and polysomes in the zygote soon after fertilization. At this time, some of the MTs are perpendicular to the nuclear envelope and directly connected to the outer membrane or nuclear-pore complexes (NPC) at one end, and the other ends reach to the outer tier or cortical MTs that are parallel to the long axis of the zygote. The polysomes in the perinuclear region show the same spatial and temporal pattern as the MTs. Immunolocalization of the mRNA-binding protein hnRNP indicates that the mRNAs are loaded onto the nucleus-associated MTs immediately after their export from the nuclear-pore complexes. The polysomes and mRNAs are then transported from these MTs to the outer tier and/or cortical MTs, where they further localize to the polar region of the cell.
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Affiliation(s)
- Fengli Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Science, China Agricultural University, Beijing, China.
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Hamada T. Microtubule-associated proteins in higher plants. JOURNAL OF PLANT RESEARCH 2007; 120:79-98. [PMID: 17285404 DOI: 10.1007/s10265-006-0057-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Accepted: 11/09/2006] [Indexed: 05/09/2023]
Abstract
A variety of microtubule-associated proteins (MAPs) have been reported in higher plants. Microtubule (MT) polymerization starts from the gamma-tubulin complex (gammaTuC), a component of the MT nucleation site. MAP200/MOR1 and katanin regulate the length of the MT by promoting the dynamic instability of MTs and cutting MTs, respectively. In construction of different MT structures, MTs are bundled or are associated with other components--actin filaments, the plasma membrane, and organelles. The MAP65 family and some of kinesin family are important in bundling MTs. MT plus-end-tracking proteins (+TIPs) including end-binding protein 1 (EB1), Arabidopsis thaliana kinesin 5 (ATK5), and SPIRAL 1 (SPR1) localize to the plus end of MTs. It has been suggested that +TIPs are involved in binding of MT to other structures. Phospholipase D (PLD) is a possible candidate responsible for binding of MTs to the plasma membrane. Many candidates have been reported as actin-binding MAPs, for example calponin-homology domain (KCH) family kinesin, kinesin-like calmodulin-binding protein (KCBP), and MAP190. RNA distribution and translation depends on MT structures, and several RNA-related MAPs have been reported. This article gives an overview of predicted roles of these MAPs in higher plants.
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Affiliation(s)
- Takahiro Hamada
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan.
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Makkar RS, Contreras MA, Paintlia AS, Smith BT, Haq E, Singh I. Molecular organization of peroxisomal enzymes: protein-protein interactions in the membrane and in the matrix. Arch Biochem Biophys 2006; 451:128-40. [PMID: 16781659 DOI: 10.1016/j.abb.2006.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Revised: 05/03/2006] [Accepted: 05/04/2006] [Indexed: 11/30/2022]
Abstract
The beta-oxidation of fatty acids in peroxisomes produces hydrogen peroxide (H2O2), a toxic metabolite, as a bi-product. Fatty acids beta-oxidation activity is deficient in X-linked adrenoleukodystrophy (X-ALD) because of mutation in ALD-gene resulting in loss of very long chain acyl-CoA synthetase (VLCS) activity. It is also affected in disease with catalase negative peroxisomes as a result of inactivation by H2O2. Therefore, the following studies were undertaken to delineate the molecular interactions between both the ALD-gene product (adrenoleukodystrophy protein, ALDP) and VLCS as well as H2O2 degrading enzyme catalase and proteins of peroxisomal beta-oxidation. Studies using a yeast two hybrid system and surface plasmon resonance techniques indicate that ALDP, a peroxisomal membrane protein, physically interacts with VLCS. Loss of these interactions in X-ALD cells may result in a deficiency in VLCS activity. The yeast two-hybrid system studies also indicated that catalase physically interacts with L-bifunctional enzyme (L-BFE). Interactions between catalase and L-BFE were further supported by affinity purification, using a catalase-linked resin. The affinity bound 74-kDa protein, was identified as L-BFE by Western blot with specific antibodies and by proteomic analysis. Additional support for their interaction comes from immunoprecipitation of L-BFE with antibodies against catalase as a catalase- L-BFE complex. siRNA for L-BFE decreased the specific activity and protein levels of catalase without changing its subcellular distribution. These observations indicate that L-BFE might help in oligomerization and possibly in the localization of catalase at the site of H2O2 production in the peroxisomal beta-oxidation pathway.
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Affiliation(s)
- Randhir S Makkar
- The Charles Darby Children's Research Institute, Department of Pediatrics, Medical University of South Carolina, Charleston, SC 29425, USA
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Muench DG, Park NI. Messages on the move: the role of the cytoskeleton in mRNA localization and translation in plant cellsThis review is one of a selection of papers published in the Special Issue on Plant Cell Biology. ACTA ACUST UNITED AC 2006. [DOI: 10.1139/b05-167] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The cytoskeleton plays an important role in numerous cellular processes, including subcellular mRNA localization and translation. Several examples of mRNA localization have emerged in plant cells, and these appear to function in protein targeting, the establishment of polarity, and cell-to-cell trafficking. The identification of several cytoskeleton-associated RNA-binding proteins in plant cells has made available candidate proteins that mediate the interaction between mRNA and the cytoskeleton, and possibly play a role in mRNA localization and translational control. We propose a model that links mRNA–microtubule interactions to translational autoregulation, a process that may assist in the efficient and regulated binding of proteins to microtubules.
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Affiliation(s)
- Douglas G. Muench
- Department of Biological Sciences, University of Calgary, 2500 University Dr. N.W, Calgary, AB T2N 1N4, Canada
| | - Nam-Il Park
- Department of Biological Sciences, University of Calgary, 2500 University Dr. N.W, Calgary, AB T2N 1N4, Canada
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Mullen RT, McCartney AW, Flynn CR, Smith GS. Peroxisome biogenesis and the formation of multivesicular peroxisomes during tombusvirus infection: a role for ESCRT?This review is one of a selection of papers published in the Special Issue on Plant Cell Biology. ACTA ACUST UNITED AC 2006. [DOI: 10.1139/b06-005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peroxisomes are highly dynamic organelles with regard to their metabolic functions, shapes, distribution, movements, and biogenesis. They are also important as sites for the development of some viral pathogens. It has long been known that certain members of the tombusvirus family recruit peroxisomes for viral RNA replication and that this process is accompanied by dramatic changes in peroxisome morphology, the most remarkable of which is the extensive inward vesiculation of the peroxisomal boundary membrane leading to the formation of a peroxisomal multivesicular body (pMVB). While it is unclear how the internal vesicles of a pMVB form, they appear to serve in effectively concentrating viral membrane-bound replication complexes and protecting nascent viral RNAs from host-cell defences. Here, we review briefly the biogenesis of peroxisomes and pMVBs and discuss recent studies that have begun to shed light on how components of the tombusvirus replicase exploit the molecular mechanisms involved in peroxisome membrane protein sorting. We also address the question of what controls invagination and vesicle formation at the peroxisomal membrane during pMVB biogenesis. We propose that tombusviruses exploit protein constituents of the class E vacuolar protein-sorting pathway referred to as ESCRT (endosomal sorting complex required for transport) in the formation of pMVBs. This new pMVB–ESCRT hypothesis reconciles current paradigms of pMVB biogenesis with the role of ESCRT in endosomal multivesicular body formation and the ability of enveloped RNA viruses, including HIV, to appropriate the ESCRT machinery to execute their budding programme from cells.
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Affiliation(s)
- Robert T. Mullen
- Department of Molecular and Cellular Biology, The University of Guelph, Guelph, ON N1G 2W1, Canada
- Harrington Department of Bioengineering, Arizona State University, Tempe, AZ 85287-9709, USA
| | - Andrew W. McCartney
- Department of Molecular and Cellular Biology, The University of Guelph, Guelph, ON N1G 2W1, Canada
- Harrington Department of Bioengineering, Arizona State University, Tempe, AZ 85287-9709, USA
| | - C. Robb Flynn
- Department of Molecular and Cellular Biology, The University of Guelph, Guelph, ON N1G 2W1, Canada
- Harrington Department of Bioengineering, Arizona State University, Tempe, AZ 85287-9709, USA
| | - Graham S.T. Smith
- Department of Molecular and Cellular Biology, The University of Guelph, Guelph, ON N1G 2W1, Canada
- Harrington Department of Bioengineering, Arizona State University, Tempe, AZ 85287-9709, USA
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Chuong SDX, Park NI, Freeman MC, Mullen RT, Muench DG. The peroxisomal multifunctional protein interacts with cortical microtubules in plant cells. BMC Cell Biol 2005; 6:40. [PMID: 16313672 PMCID: PMC1325227 DOI: 10.1186/1471-2121-6-40] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Accepted: 11/28/2005] [Indexed: 12/25/2022] Open
Abstract
Background The plant peroxisomal multifunctional protein (MFP) possesses up to four enzymatic activities that are involved in catalyzing different reactions of fatty acid β-oxidation in the peroxisome matrix. In addition to these peroxisomal activities, in vitro assays revealed that rice MFP possesses microtubule- and RNA-binding activities suggesting that this protein also has important functions in the cytosol. Results We demonstrate that MFP is an authentic microtubule-binding protein, as it localized to the cortical microtubule array in vivo, in addition to its expected targeting to the peroxisome matrix. MFP does not, however, interact with the three mitotic microtubule arrays. Microtubule co-sedimentation assays of truncated versions of MFP revealed that multiple microtubule-binding domains are present on the MFP polypeptide. This indicates that these regions function together to achieve high-affinity binding of the full-length protein. Real-time imaging of a transiently expressed green fluorescent protein-MFP chimera in living plant cells illustrated that a dynamic, spatial interaction exits between peroxisomes and cortical microtubules as peroxisomes move along actin filaments or oscillate at fixed locations. Conclusion Plant MFP is associated with the cortical microtubule array, in addition to its expected localization in the peroxisome. This observation, coupled with apparent interactions that frequently occur between microtubules and peroxisomes in the cell cortex, supports the hypothesis that MFP is concentrated on microtubules in order to facilitate the regulated import of MFP into peroxisomes.
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Affiliation(s)
- Simon DX Chuong
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, Canada T2N 1N4, Canada
| | - Nam-Il Park
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, Canada T2N 1N4, Canada
| | - Michelle C Freeman
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, Canada T2N 1N4, Canada
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada N1G 2W1, Canada
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, Canada T2N 1N4, Canada
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Chuong SDX, Good AG, Taylor GJ, Freeman MC, Moorhead GBG, Muench DG. Large-scale identification of tubulin-binding proteins provides insight on subcellular trafficking, metabolic channeling, and signaling in plant cells. Mol Cell Proteomics 2004; 3:970-83. [PMID: 15249590 DOI: 10.1074/mcp.m400053-mcp200] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microtubules play an essential role in the growth and development of plants and are known to be involved in regulating many cellular processes ranging from translation to signaling. In this article, we describe the proteomic characterization of Arabidopsis tubulin-binding proteins that were purified using tubulin affinity chromatography. Microtubule co-sedimentation assays indicated that most, if not all, of the proteins in the tubulin-binding protein fraction possessed microtubule-binding activity. Two-dimensional gel electrophoresis of the tubulin-binding protein fraction was performed, and 86 protein spots were excised and analyzed for protein identification. A total of 122 proteins were identified with high confidence using LC-MS/MS. These proteins were grouped into six categories based on their predicted functions: microtubule-associated proteins, translation factors, RNA-binding proteins, signaling proteins, metabolic enzymes, and proteins with other functions. Almost one-half of the proteins identified in this fraction were related to proteins that have previously been reported to interact with microtubules. This study represents the first large-scale proteomic identification of eukaryotic cytoskeleton-binding proteins, and provides insight on subcellular trafficking, metabolic channeling, and signaling in plant cells.
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Affiliation(s)
- Simon D X Chuong
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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Moore BD. Bifunctional and moonlighting enzymes: lighting the way to regulatory control. TRENDS IN PLANT SCIENCE 2004; 9:221-8. [PMID: 15130547 DOI: 10.1016/j.tplants.2004.03.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Affiliation(s)
- Brandon d Moore
- Department of Genetics, Biochemistry, and Life Science Studies, Clemson University, Clemson, SC 29634, USA.
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Harper JD, Weerakoon ND, Gardiner JC, Blackman LM, Marc J. A 75-kDa plant protein isolated by tubulin-affinity chromatography is a peroxisomal matrix enzyme. ACTA ACUST UNITED AC 2002. [DOI: 10.1139/b02-088] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The function of microtubules in plant cells relies on their interactions with various, largely unidentified, proteins. A 75-kDa polypeptide (p75) was isolated previously by tubulin affinity chromatography of tobacco BY-2 proteins and is further characterized here. We have obtained two peptide sequences of 13 and 8 amino acid residues from the p75, which have 77% and 87% similarity to two putative dTDP-glucose 4,6-dehydratase proteins of 74.9 and 75.3 kDa in Arabidopsis. The proteins contain a peroxisomal matrix targeting signal SKL or AKL near their carboxyl terminus, an epimerase-dehydratase motif, and a region of 321 amino acid residues sharing 41% similarity with a dTDP-glucose 4,6-dehydratase from Aneurinibacillus thermoaerophilus. A monoclonal antibody 4B9 against the tobacco p75 reacted with a 75-kDa polypeptide on immunoblots of tobacco BY-2 and Arabidopsis protein extracts, and in immunofluorescence microscopy it revealed small organelle-like structures in tobacco BY-2 and Arabidopsis root-tip cells. Double labelling with an antibody against the peroxisomal marker enzyme, catalase, showed that the organelles are indeed peroxisomes. The peroxisomes were in closer association with actin filaments than microtubules. This observation supports recent findings that plant peroxisomes move on actin filaments. We propose that the peroxisomal dTDP-glucose 4,6-dehydratases may be involved in plant defence responses to oxidative stress.Key words: actin, antibodies, microtubules.
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Collings DA, Harper JDI, Marc J, Overall RL, Mullen RT. Life in the fast lane: actin-based motility of plant peroxisomes. ACTA ACUST UNITED AC 2002. [DOI: 10.1139/b02-036] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peroxisomal shape, distribution, motility, and interactions with cytoskeletal elements were examined during interphase in living leek (Allium porrum L.) epidermal cells transiently transformed with a construct encoding the green fluorescent protein bearing a carboxy-terminal type 1 peroxisomal targeting signal. Confocal laser scanning microscopy and time-course analysis revealed that labeled peroxisomes were either spherical or rod-shaped and possessed several types of motility including random oscillations, slow and fast directional and bidirectional movements, and stop-and-go movements. Co-localization studies indicated that most peroxisomes were in close association with actin filaments, while treatment of cells with the actin-disrupting drug cytochalasin D blocked all types of peroxisomal movements. In contrast, the overall spatial organization of peroxisomes and the microtubule cytoskeleton were different, and the microtubule-destabilizing agent oryzalin had no obvious effect on peroxisomal motility. These data indicate that the peroxisome in plant cells is a highly dynamic compartment that is dependent upon the actin cytoskeleton, not microtubules, for its subcellular distribution and movements.Key words: actin filaments, cytoskeleton, green fluorescent protein, leek, microtubules, peroxisomes.
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