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Neumann N, Jeffares DC, Poole AM. Outsourcing the Nucleus: Nuclear Pore Complex Genes are no Longer Encoded in Nucleomorph Genomes. Evol Bioinform Online 2017. [DOI: 10.1177/117693430600200023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The nuclear pore complex (NPC) facilitates transport between nucleus and cytoplasm. The protein constituents of the NPC, termed nucleoporins (Nups), are conserved across a wide diversity of eukaryotes. In apparent exception to this, no nucleoporin genes have been identified in nucleomorph genomes. Nucleomorphs, nuclear remnants of once free-living eukaryotes, took up residence as secondary endosymbionts in cryptomonad and chlorarachniophyte algae. As these genomes are highly reduced, Nup genes may have been lost, or relocated to the host nucleus. However, Nup genes are often poorly conserved between species, so absence may be an artifact of low sequence similarity. We therefore constructed an evolutionary bioinformatic screen to establish whether the apparent absence of Nup genes in nucleomorph genomes is due to genuine absence or the inability of current methods to detect homologues. We searched green plant ( Arabidopsis and rice), green alga ( Chlamydomonas reinhardtii) and red alga ( Cyanidioschyzon merolae) genomes, plus two nucleomorph genomes ( Bigelowiella natans and Guillardia theta) with profile hidden Markov models (HMMs) from curated alignments of known vertebrate/yeast Nups. Since the plant, algal and nucleomorph genomes all belong to the kingdom Plantae, and are evolutionarily distant from the outgroup (vertebrate/yeast) training set, we use the plant and algal genomes as internal positive controls for the sensitivity of the searches in nucleomorph genomes. We find numerous Nup homologues in all plant and free-living algal species, but none in either nucleomorph genome. BLAST searches using identified plant and algal Nups also failed to detect nucleomorph homologues. We conclude that nucleomorph Nup genes have either been lost, being replaced by host Nup genes, or, that nucleomorph Nup genes have been transferred to the host nucleus twice independently; once in the evolution of the red algal nucleomorph and once in the green algal nucleomorph.
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Affiliation(s)
- Nadja Neumann
- Department of Molecular Biology and Functional Genomics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Daniel C. Jeffares
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, U.K
| | - Anthony M. Poole
- Department of Molecular Biology and Functional Genomics, Stockholm University, SE-106 91 Stockholm, Sweden
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Batzenschlager M, Masoud K, Janski N, Houlné G, Herzog E, Evrard JL, Baumberger N, Erhardt M, Nominé Y, Kieffer B, Schmit AC, Chabouté ME. The GIP gamma-tubulin complex-associated proteins are involved in nuclear architecture in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2013; 4:480. [PMID: 24348487 PMCID: PMC3842039 DOI: 10.3389/fpls.2013.00480] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 11/05/2013] [Indexed: 05/08/2023]
Abstract
During interphase, the microtubular cytoskeleton of cycling plant cells is organized in both cortical and perinuclear arrays. Perinuclear microtubules (MTs) are nucleated from γ-Tubulin Complexes (γ-TuCs) located at the surface of the nucleus. The molecular mechanisms of γ-TuC association to the nuclear envelope (NE) are currently unknown. The γ-TuC Protein 3 (GCP3)-Interacting Protein 1 (GIP1) is the smallest γ-TuC component identified so far. AtGIP1 and its homologous protein AtGIP2 participate in the localization of active γ-TuCs at interphasic and mitotic MT nucleation sites. Arabidopsis gip1gip2 mutants are impaired in establishing a fully functional mitotic spindle and exhibit severe developmental defects. In this study, gip1gip2 knock down mutants were further characterized at the cellular level. In addition to defects in both the localization of γ-TuC core proteins and MT fiber robustness, gip1gip2 mutants exhibited a severe alteration of the nuclear shape associated with an abnormal distribution of the nuclear pore complexes. Simultaneously, they showed a misorganization of the inner nuclear membrane protein AtSUN1. Furthermore, AtGIP1 was identified as an interacting partner of AtTSA1 which was detected, like the AtGIP proteins, at the NE. These results provide the first evidence for the involvement of a γ-TuC component in both nuclear shaping and NE organization. Functional hypotheses are discussed in order to propose a model for a GIP-dependent nucleo-cytoplasmic continuum.
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Affiliation(s)
- Morgane Batzenschlager
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, UPR 2357, Conventionné avec l'Université de StrasbourgStrasbourg, France
| | - Kinda Masoud
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, UPR 2357, Conventionné avec l'Université de StrasbourgStrasbourg, France
| | - Natacha Janski
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, UPR 2357, Conventionné avec l'Université de StrasbourgStrasbourg, France
| | - Guy Houlné
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, UPR 2357, Conventionné avec l'Université de StrasbourgStrasbourg, France
| | - Etienne Herzog
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, UPR 2357, Conventionné avec l'Université de StrasbourgStrasbourg, France
| | - Jean-Luc Evrard
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, UPR 2357, Conventionné avec l'Université de StrasbourgStrasbourg, France
| | - Nicolas Baumberger
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, UPR 2357, Conventionné avec l'Université de StrasbourgStrasbourg, France
| | - Mathieu Erhardt
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, UPR 2357, Conventionné avec l'Université de StrasbourgStrasbourg, France
| | - Yves Nominé
- Biotechnologie et Signalisation cellulaire, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, UMR 7242, Université de StrasbourgIllkirch, France
| | - Bruno Kieffer
- Institut de Génétique et Biologie Moléculaire et Cellulaire, Ecole Supérieure de Biotechnologie de StrasbourgIllkirch, France
| | - Anne-Catherine Schmit
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, UPR 2357, Conventionné avec l'Université de StrasbourgStrasbourg, France
- *Correspondence: Anne-Catherine Schmit, Institut de Biologie Moléculaire des Plantes, UPR2357 du CNRS, 12, rue du Gl Zimmer, 67084 Strasbourg-Cedex, France e-mail:
| | - Marie-Edith Chabouté
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, UPR 2357, Conventionné avec l'Université de StrasbourgStrasbourg, France
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Li F, Zhai YP, Tang YM, Wang LP, Wan PJ. Identification of a novel partner gene, TPR, fused to FGFR1 in 8p11 myeloproliferative syndrome. Genes Chromosomes Cancer 2012; 51:890-7. [DOI: 10.1002/gcc.21973] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 04/21/2012] [Indexed: 11/09/2022] Open
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Evans DE, Shvedunova M, Graumann K. The nuclear envelope in the plant cell cycle: structure, function and regulation. ANNALS OF BOTANY 2011; 107:1111-8. [PMID: 21239406 PMCID: PMC3091801 DOI: 10.1093/aob/mcq268] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 11/30/2010] [Accepted: 12/03/2010] [Indexed: 05/03/2023]
Abstract
BACKGROUND Higher plants are, like animals, organisms in which successful completion of the cell cycle requires the breakdown and reformation of the nuclear envelope in a highly controlled manner. Interestingly, however, while the structures and processes appear similar, there are remarkable differences in protein composition and function between plants and animals. SCOPE Recent characterization of integral and associated components of the plant nuclear envelope has been instrumental in understanding its functions and behaviour. It is clear that protein interactions at the nuclear envelope are central to many processes in interphase and dividing cells and that the nuclear envelope has a key role in structural and regulatory events. CONCLUSION Dissecting the mechanisms of nuclear envelope breakdown and reformation in plants is necessary before a better understanding of the functions of nuclear envelope components during the cell cycle can be gained.
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Affiliation(s)
| | | | - K. Graumann
- School of Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
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Murphy SP, Simmons CR, Bass HW. Structure and expression of the maize (Zea mays L.) SUN-domain protein gene family: evidence for the existence of two divergent classes of SUN proteins in plants. BMC PLANT BIOLOGY 2010; 10:269. [PMID: 21143845 PMCID: PMC3017857 DOI: 10.1186/1471-2229-10-269] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 12/08/2010] [Indexed: 05/03/2023]
Abstract
BACKGROUND The nuclear envelope that separates the contents of the nucleus from the cytoplasm provides a surface for chromatin attachment and organization of the cortical nucleoplasm. Proteins associated with it have been well characterized in many eukaryotes but not in plants. SUN (Sad1p/Unc-84) domain proteins reside in the inner nuclear membrane and function with other proteins to form a physical link between the nucleoskeleton and the cytoskeleton. These bridges transfer forces across the nuclear envelope and are increasingly recognized to play roles in nuclear positioning, nuclear migration, cell cycle-dependent breakdown and reformation of the nuclear envelope, telomere-led nuclear reorganization during meiosis, and karyogamy. RESULTS We found and characterized a family of maize SUN-domain proteins, starting with a screen of maize genomic sequence data. We characterized five different maize ZmSUN genes (ZmSUN1-5), which fell into two classes (probably of ancient origin, as they are also found in other monocots, eudicots, and even mosses). The first (ZmSUN1, 2), here designated canonical C-terminal SUN-domain (CCSD), includes structural homologs of the animal and fungal SUN-domain protein genes. The second (ZmSUN3, 4, 5), here designated plant-prevalent mid-SUN 3 transmembrane (PM3), includes a novel but conserved structural variant SUN-domain protein gene class. Mircroarray-based expression analyses revealed an intriguing pollen-preferred expression for ZmSUN5 mRNA but low-level expression (50-200 parts per ten million) in multiple tissues for all the others. Cloning and characterization of a full-length cDNA for a PM3-type maize gene, ZmSUN4, is described. Peptide antibodies to ZmSUN3, 4 were used in western-blot and cell-staining assays to show that they are expressed and show concentrated staining at the nuclear periphery. CONCLUSIONS The maize genome encodes and expresses at least five different SUN-domain proteins, of which the PM3 subfamily may represent a novel class of proteins with possible new and intriguing roles within the plant nuclear envelope. Expression levels for ZmSUN1-4 are consistent with basic cellular functions, whereas ZmSUN5 expression levels indicate a role in pollen. Models for possible topological arrangements of the CCSD-type and PM3-type SUN-domain proteins are presented.
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Affiliation(s)
- Shaun P Murphy
- Institute of Molecular Biophysics, The Florida State University, Tallahassee, FL, USA 32306-4370
| | | | - Hank W Bass
- Institute of Molecular Biophysics, The Florida State University, Tallahassee, FL, USA 32306-4370
- Department of Biological Science, The Florida State University, Tallahassee, FL, USA 32306-4370
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Nuclear envelope proteins and their role in nuclear positioning and replication. Biochem Soc Trans 2010; 38:741-6. [DOI: 10.1042/bst0380741] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Controlled movement of the nucleus is important in a wide variety of plant cellular events. Positioning involving intact nuclei occurs in cell division, development, tip growing systems such as the root hair and in response to stimuli, including light, touch and infection. Positioning is also essential in the division and replication of nuclear components, ranging from chromosome attachment to the breakdown and reformation of the nuclear envelope. Although description and understanding of the processes involved have advanced rapidly in recent years, significant gaps remain in our knowledge, especially concerning nuclear proteins involved in anchoring and interacting with cytoskeletal and nucleoskeletal elements involved in movement. In the present review, processes involving the movement and positioning of nuclei and nuclear components are described together with novel proteins implicated in nucleoskeletal and cytoskeletal interactions.
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Abstract
Recent progress in understanding the plant NE (nuclear envelope) has resulted from significant advances in identifying and characterizing the protein constituents of the membranes and nuclear pores. Here, we review recent findings on the membrane integral and membrane-associated proteins of the key domains of the NE, the pore domain and inner and outer NEs, together with information on protein targeting and NE function.
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Ben-Efraim I, Frosst PD, Gerace L. Karyopherin binding interactions and nuclear import mechanism of nuclear pore complex protein Tpr. BMC Cell Biol 2009; 10:74. [PMID: 19835572 PMCID: PMC2770460 DOI: 10.1186/1471-2121-10-74] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 10/16/2009] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Tpr is a large protein with an extended coiled-coil domain that is localized within the nuclear basket of the nuclear pore complex. Previous studies 1 involving antibody microinjection into mammalian cells suggested a role for Tpr in nuclear export of proteins via the CRM1 export receptor. In addition, Tpr was found to co-immunoprecipitate with importins alpha and beta from Xenopus laevis egg extracts 2, although the function of this is unresolved. Yeast Mlp1p and Mlp2p, which are homologous to vertebrate Tpr, have been implicated in mRNA surveillance to retain unspliced mRNAs in the nucleus34. To augment an understanding of the role of Tpr in nucleocytoplasmic trafficking, we explored the interactions of recombinant Tpr with the karyopherins CRM1, importin beta and importin alpha by solid phase binding assays. We also investigated the conditions required for nuclear import of Tpr using an in vitro assay. RESULTS We found that Tpr binds strongly and specifically to importin alpha, importin beta, and a CRM1 containing trimeric export complex, and that the binding sites for importins alpha and beta are distinct. We also determined that the nuclear import of Tpr is dependent on cytosolic factors and energy and is efficiently mediated by the importin alpha/beta import pathway. CONCLUSION Based on the binding and nuclear import assays, we propose that Tpr is imported into the nucleus by the importin alpha/beta heterodimer. In addition, we suggest that Tpr can serve as a nucleoporin binding site for importin beta during import of importin beta cargo complexes and/or importin beta recycling. Our finding that Tpr bound preferentially to CRM1 in an export complex strengthens the notion that Tpr is involved in protein export.
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Affiliation(s)
- Iris Ben-Efraim
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Phyllis D Frosst
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- National Human Genome Research Institute, National Institutes of Health Bethesda, Maryland 20892, USA
| | - Larry Gerace
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Fiserova J, Kiseleva E, Goldberg MW. Nuclear envelope and nuclear pore complex structure and organization in tobacco BY-2 cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 59:243-55. [PMID: 19392704 DOI: 10.1111/j.1365-313x.2009.03865.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The nuclear envelope (NE) is a fundamental structure of eukaryotic cells with a dual role: it separates two distinct compartments, and enables communication between them via nuclear pore complexes (NPCs). Little is known about NPCs and NE structural organization in plants. We investigated the structure of NPCs from both sides of the NE in tobacco BY-2 cells. We detected structural differences between the NPCs of dividing and quiescent nuclei. Importantly, we also traced the organizational pattern of the NPCs, and observed non-random NPC distribution over the nuclear surface. Lastly, we observed an organized filamentous protein structure that underlies the inner nuclear membrane, and interconnects NPCs. The results are discussed within the context of the current understanding of NE structure and function in higher eukaryotes.
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Affiliation(s)
- Jindriska Fiserova
- Department of Biological and Biomedical Sciences, Durham University, South Road, Durham DH13LE, UK
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Vuosku J, Sarjala T, Jokela A, Sutela S, Sääskilahti M, Suorsa M, Läärä E, Häggman H. One tissue, two fates: different roles of megagametophyte cells during Scots pine embryogenesis. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:1375-86. [PMID: 19246593 PMCID: PMC2657542 DOI: 10.1093/jxb/erp020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
In the Scots pine (Pinus sylvestris L.) seed, embryos grow and develop within the corrosion cavity of the megagametophyte, a maternally derived haploid tissue, which houses the majority of the storage reserves of the seed. In the present study, histochemical methods and quantification of the expression levels of the programmed cell death (PCD) and DNA repair processes related genes (MCA, TAT-D, RAD51, KU80, and LIG) were used to investigate the physiological events occurring in the megagametophyte tissue during embryo development. It was found that the megagametophyte was viable from the early phases of embryo development until the early germination of mature seeds. However, the megagametophyte cells in the narrow embryo surrounding region (ESR) were destroyed by cell death with morphologically necrotic features. Their cell wall, plasma membrane, and nuclear envelope broke down with the release of cell debris and nucleic acids into the corrosion cavity. The occurrence of necrotic-like cell death in gymnosperm embryogenesis provides a favourable model for the study of developmental cell death with necrotic-like morphology and suggests that the mechanism underlying necrotic cell death is evolutionary conserved.
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Affiliation(s)
- Jaana Vuosku
- Department of Biology, University of Oulu, PO Box 3000, 90014 Oulu, Finland.
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Dittmer TA, Richards EJ. Role of LINC proteins in plant nuclear morphology. PLANT SIGNALING & BEHAVIOR 2008; 3:485-7. [PMID: 19704494 PMCID: PMC2634438 DOI: 10.4161/psb.3.7.5682] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Accepted: 01/31/2008] [Indexed: 05/05/2023]
Abstract
A common fate of post-mitotic interphase plant nuclei is morphological differentiation into an array of shapes and sizes. Development of nuclear morphology occurs in a cell-specific manner and is influenced by cell shape and nuclear DNA content. The LINC (LITTLE NUCLEI) proteins are plant-specific nuclear coiled-coil proteins that appear to couple nuclear development to cellular (shape) and nuclear (DNA content) cues. linc mutations cause a variety of defects, including smaller more spherical nuclei and whole-plant dwarfing. Supplementing our previous results, we constructed transgenic plants expressing LINC1-GFP from the native promoter and found that LINC1 is predominantly expressed in proliferating tissues. Moreover, LINC1-GFP signal was found to be concentrated at the nuclear periphery. These results suggest that LINC1 plays an important structural role at an early stage in nuclear development.
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Affiliation(s)
- Travis A Dittmer
- Department of Biology; Washington University; St. Louis, Missouri USA
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Graumann K, Irons SL, Runions J, Evans DE. Retention and mobility of the mammalian lamin B receptor in the plant nuclear envelope. Biol Cell 2007; 99:553-62. [PMID: 17868028 DOI: 10.1042/bc20070033] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND INFORMATION In a previous study, we showed that GFP (green fluorescent protein) fused to the N-terminal 238 amino acids of the mammalian LBR (lamin B receptor) localized to the NE (nuclear envelope) when expressed in the plant Nicotiana tabacum. The protein was located in the NE during interphase and migrated with nuclear membranes during cell division. Targeting and retention of inner NE proteins requires several mechanisms: signals that direct movement through the nuclear pore complex, presence of a transmembrane domain or domains and retention by interaction with nuclear or nuclear-membrane constituents. RESULTS Binding mutants of LBR-GFP were produced to investigate the mechanisms for the retention of LBR in the NE. FRAP (fluorescence recovery after photobleaching) analysis of mutant and wild-type constructs was employed to examine the retention of LBR-GFP in the plant NE. wtLBR-GFP (wild-type LBR-GFP) was shown to have significantly lower mobility in the NE than the lamin-binding domain deletion mutant, which showed increased mobility in the NE and was also localized to the endoplasmic reticulum and punctate structures in some cells. Modification of the chromatin-binding domain resulted in the localization of the protein in nuclear inclusions, in which it was immobile. CONCLUSIONS As expression of truncated LBR-GFP in plant cells results in altered targeting and retention compared with wtLBR-GFP, we conclude that plant cells can recognize the INE (inner NE)-targeting motif of LBR. The altered mobility of the truncated protein suggests that not only do plant cells recognize this signal, but also have nuclear proteins that interact weakly with LBR.
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Affiliation(s)
- Katja Graumann
- Research School of Life Sciences, Oxford Brookes University, Gipsy Lane, Oxford OX3 0BP, UK
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Wiermer M, Palma K, Zhang Y, Li X. Should I stay or should I go? Nucleocytoplasmic trafficking in plant innate immunity. Cell Microbiol 2007; 9:1880-90. [PMID: 17506817 DOI: 10.1111/j.1462-5822.2007.00962.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Communication between the cytoplasm and the nucleus is a fundamental feature of eukaryotic cells. Bidirectional transport of macromolecules across the nuclear envelope is typically mediated by receptors and occurs exclusively through nuclear pore complexes (NPCs). The components and molecular mechanisms regulating nucleocytoplasmic trafficking and signalling processes are well studied in animals and yeast but are poorly understood in plants. Current work shows that components of the NPC and the nuclear import and export machinery play essential roles in plant innate immunity. Translocation of defence regulators and Resistance (R) proteins between the cytoplasm and the nucleus are recently uncovered aspects of plant defence responses against pathogens. Future studies will reveal more details on the spatial and temporal dynamics and regulation of this process.
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Affiliation(s)
- Marcel Wiermer
- Michael Smith Laboratories, Room 301, 2185 East Mall, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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van Ooijen G, van den Burg HA, Cornelissen BJC, Takken FLW. Structure and function of resistance proteins in solanaceous plants. ANNUAL REVIEW OF PHYTOPATHOLOGY 2007; 45:43-72. [PMID: 17367271 DOI: 10.1146/annurev.phyto.45.062806.094430] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Gene-for-gene resistance in plants is based on the presence of a resistance (R) gene in the host and a matching Avirulence (Avr) gene in the pathogen. Many R genes have been cloned over the past two decades, mostly from the Solanaceae. The gene products, called R proteins, display modular domain structures. R protein function has recently been shown to require dynamic interactions between the various domains. In addition to these intramolecular interactions, R proteins interact with other proteins to form signaling complexes that are able to activate an innate immune response that arrests proliferation of the invading pathogen, thereby conferring disease resistance. In this review, we summarize current understanding of R protein structure and function, as well as the molecular mechanisms underlying the activation of defense signaling processes. As well as being a rich source for R genes, Solanaceae are a leading model system in which to study inter- and intramolecular interactions of R proteins.
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Affiliation(s)
- Gerben van Ooijen
- Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GB Amsterdam, The Netherlands.
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15
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Domínguez F, Cejudo F. Identification of a nuclear-localized nuclease from wheat cells undergoing programmed cell death that is able to trigger DNA fragmentation and apoptotic morphology on nuclei from human cells. Biochem J 2006; 397:529-36. [PMID: 16613587 PMCID: PMC1533310 DOI: 10.1042/bj20051809] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PCD (programmed cell death) in plants presents important morphological and biochemical differences compared with apoptosis in animal cells. This raises the question of whether PCD arose independently or from a common ancestor in plants and animals. In the present study we describe a cell-free system, using wheat grain nucellar cells undergoing PCD, to analyse nucleus dismantling, the final stage of PCD. We have identified a Ca2+/Mg2+ nuclease and a serine protease localized to the nucleus of dying nucellar cells. Nuclear extracts from nucellar cells undergoing PCD triggered DNA fragmentation and other apoptotic morphology in nuclei from different plant tissues. Inhibition of the serine protease did not affect DNA laddering. Furthermore, we show that the nuclear extracts from plant cells triggered DNA fragmentation and apoptotic morphology in nuclei from human cells. The inhibition of the nucleolytic activity with Zn2+ or EDTA blocked the morphological changes of the nucleus. Moreover, nuclear extracts from apoptotic human cells triggered DNA fragmentation and apoptotic morphology in nuclei from plant cells. These results show that degradation of the nucleus is morphologically and biochemically similar in plant and animal cells. The implication of this finding on the origin of PCD in plants and animals is discussed.
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Affiliation(s)
- Fernando Domínguez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla-CSIC, 41092-Sevilla, Spain
| | - Francisco J. Cejudo
- Instituto de Bioquímica Vegetal y Fotosíntesis, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla-CSIC, 41092-Sevilla, Spain
- To whom correspondence should be addressed (email )
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Kanamori N, Madsen LH, Radutoiu S, Frantescu M, Quistgaard EMH, Miwa H, Downie JA, James EK, Felle HH, Haaning LL, Jensen TH, Sato S, Nakamura Y, Tabata S, Sandal N, Stougaard J. A nucleoporin is required for induction of Ca2+ spiking in legume nodule development and essential for rhizobial and fungal symbiosis. Proc Natl Acad Sci U S A 2006; 103:359-64. [PMID: 16407163 PMCID: PMC1326171 DOI: 10.1073/pnas.0508883103] [Citation(s) in RCA: 301] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nuclear-cytoplasmic partitioning and traffic between cytoplasmic and nuclear compartments are fundamental processes in eukaryotic cells. Nuclear pore complexes mediate transport of proteins, RNAs and ribonucleoprotein particles in and out of the nucleus. Here we present positional cloning of a plant nucleoporin gene, Nup133, essential for a symbiotic signal transduction pathway shared by Rhizobium bacteria and mycorrhizal fungi. Mutation of Nup133 results in a temperature sensitive nodulation deficient phenotype and absence of mycorrhizal colonization. Root nodules developing with reduced frequency at permissive temperatures are ineffective and electron microscopy show that Rhizobium bacteria are not released from infection threads. Measurement of ion fluxes using a calcium-sensitive dye show that Nup133 is required for the Ca2+ spiking normally detectable within minutes after application of purified rhizobial Nod-factor signal molecules to root hairs. Localization of NUP133 in the nuclear envelope of root cells and root hair cells shown with enhanced yellow fluorescent protein fusion proteins suggests a novel role for NUP133 nucleoporins in a rapid nuclear-cytoplasmic communication after host-plant recognition of symbiotic microbes. Our results identify a component of an intriguing signal process requiring interaction at the cell plasma membrane and at intracellular nuclear and plastid organelle-membranes to induce a second messenger.
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Affiliation(s)
- Norihito Kanamori
- Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10 and C.F. Møllers Vej Bldg 130, 8000 Aarhus C, Denmark
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18
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Fang Y, Spector DL. Centromere positioning and dynamics in living Arabidopsis plants. Mol Biol Cell 2005; 16:5710-8. [PMID: 16195344 PMCID: PMC1289415 DOI: 10.1091/mbc.e05-08-0706] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2005] [Revised: 09/13/2005] [Accepted: 09/15/2005] [Indexed: 11/11/2022] Open
Abstract
The organization and dynamics of the genome have been shown to influence gene expression in many organisms. Data from mammalian tissue culture cells have provided conflicting conclusions with regard to the extent to which chromatin organization is inherited from mother to daughter nuclei. To gain insight into chromatin organization and dynamics, we developed transgenic Arabidopsis lines in which centromeres were tagged with a green fluorescent protein fusion of the centromere-specific histone H3. Using four-dimensional (4-D) live cell imaging, we show that Arabidopsis centromeres are constrained at the nuclear periphery during interphase and that the organization of endoreduplicated sister centromeres is cell type dependent with predominant clustering in root epidermal cells and dispersion in leaf epidermal cells. 4-D tracking of the entire set of centromeres through mitosis, in growing root meristematic cells, demonstrated that global centromere position is not precisely transmitted from the mother cell to daughter cells. These results provide important insight into our understanding of chromatin organization among different cells of a living organism.
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Affiliation(s)
- Yuda Fang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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19
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Rose A, Schraegle SJ, Stahlberg EA, Meier I. Coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control. BMC Evol Biol 2005; 5:66. [PMID: 16288662 PMCID: PMC1322226 DOI: 10.1186/1471-2148-5-66] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2005] [Accepted: 11/16/2005] [Indexed: 11/16/2022] Open
Abstract
Background Long alpha-helical coiled-coil proteins are involved in diverse organizational and regulatory processes in eukaryotic cells. They provide cables and networks in the cyto- and nucleoskeleton, molecular scaffolds that organize membrane systems and tissues, motors, levers, rotating arms, and possibly springs. Mutations in long coiled-coil proteins have been implemented in a growing number of human diseases. Using the coiled-coil prediction program MultiCoil, we have previously identified all long coiled-coil proteins from the model plant Arabidopsis thaliana and have established a searchable Arabidopsis coiled-coil protein database. Results Here, we have identified all proteins with long coiled-coil domains from 21 additional fully sequenced genomes. Because regions predicted to form coiled-coils interfere with sequence homology determination, we have developed a sequence comparison and clustering strategy based on masking predicted coiled-coil domains. Comparing and grouping all long coiled-coil proteins from 22 genomes, the kingdom-specificity of coiled-coil protein families was determined. At the same time, a number of proteins with unknown function could be grouped with already characterized proteins from other organisms. Conclusion MultiCoil predicts proteins with extended coiled-coil domains (more than 250 amino acids) to be largely absent from bacterial genomes, but present in archaea and eukaryotes. The structural maintenance of chromosomes proteins and their relatives are the only long coiled-coil protein family clearly conserved throughout all kingdoms, indicating their ancient nature. Motor proteins, membrane tethering and vesicle transport proteins are the dominant eukaryote-specific long coiled-coil proteins, suggesting that coiled-coil proteins have gained functions in the increasingly complex processes of subcellular infrastructure maintenance and trafficking control of the eukaryotic cell.
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Affiliation(s)
- Annkatrin Rose
- Department of Plant Cellular and Molecular Biology, Plant Biotechnology Center, Ohio State University, 1060 Carmack Road, Columbus, OH 43210, USA
| | | | - Eric A Stahlberg
- Ohio Super Computer Center, 1224 Kinnear Road, Columbus, OH 43212, USA
| | - Iris Meier
- Department of Plant Cellular and Molecular Biology, Plant Biotechnology Center, Ohio State University, 1060 Carmack Road, Columbus, OH 43210, USA
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Bozhkov PV, Suarez MF, Filonova LH, Daniel G, Zamyatnin AA, Rodriguez-Nieto S, Zhivotovsky B, Smertenko A. Cysteine protease mcII-Pa executes programmed cell death during plant embryogenesis. Proc Natl Acad Sci U S A 2005; 102:14463-8. [PMID: 16183741 PMCID: PMC1242326 DOI: 10.1073/pnas.0506948102] [Citation(s) in RCA: 195] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2005] [Indexed: 01/26/2023] Open
Abstract
Programmed cell death (PCD) is indispensable for eukaryotic development. In animals, PCD is executed by the caspase family of cysteine proteases. Plants do not have close homologues of caspases but possess a phylogenetically distant family of cysteine proteases named metacaspases. The cellular function of metacaspases in PCD is unknown. Here we show that during plant embryogenesis, metacaspase mcII-Pa translocates from the cytoplasm to nuclei in terminally differentiated cells that are destined for elimination, where it colocalizes with the nuclear pore complex and chromatin, causing nuclear envelope disassembly and DNA fragmentation. The cell-death function of mcII-Pa relies on its cysteine-dependent arginine-specific proteolytic activity. Accordingly, mutation of catalytic cysteine abrogates the proteolytic activity of mcII-Pa and blocks nuclear degradation. These results establish metacaspase as an executioner of PCD during embryo patterning and provide a functional link between PCD and embryogenesis in plants. Although mcII-Pa and metazoan caspases have different substrate specificity, they serve a common function during development, demonstrating the evolutionary parallelism of PCD pathways in plants and animals.
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Affiliation(s)
- Peter V Bozhkov
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, Box 7080, SE-75007 Uppsala, Sweden.
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Abstract
In a eukaryotic cell, the nuclear envelope (NE) separates genetic information from the environment of biosynthesis and metabolism. Transfer of macromolecules across the NE involves the nuclear pores--large multisubunit protein complexes--and machinery that facilitates rapid, directional, and selective transport. While core elements of the transport process are conserved between kingdoms, different solutions to similar problems have also evolved. Although the structure and composition of the yeast and mammalian nuclear pore have been unraveled recently, the plant nuclear pore remains largely enigmatic. Like any other process, nucleocytoplasmic transport can be regulated. Several examples from plants are discussed that promise insights into the regulation of signaling pathways. While controlling the partitioning of cellular components, the nuclear envelope also presents an obstacle to viruses and transforming agents that need access to the genome, and different mechanisms have evolved to overcome this obstacle. Finally, the recent recognition of the importance of small RNAs for gene regulation emphasizes the need to understand small RNA nuclear export and the levels of its regulation. This review attempts to wed our molecular-mechanistic understanding of nucleocytoplasmic trafficking drawn from all model systems with the intriguing examples of regulated nucleocytoplasmic partitioning in plants.
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Affiliation(s)
- Iris Meier
- Plant Biotechnology Center and Department of Plant Cellular and Molecular Biology, The Ohio State University, Columbus, Ohio 43210, USA
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22
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Patel S, Rose A, Meulia T, Dixit R, Cyr RJ, Meier I. Arabidopsis WPP-domain proteins are developmentally associated with the nuclear envelope and promote cell division. THE PLANT CELL 2004; 16:3260-73. [PMID: 15548735 PMCID: PMC535872 DOI: 10.1105/tpc.104.026740] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2004] [Accepted: 10/04/2004] [Indexed: 05/20/2023]
Abstract
The nuclear envelope (NE) acts as a selective barrier to macromolecule trafficking between the nucleus and the cytoplasm and undergoes a complex reorganization during mitosis. Different eukaryotic kingdoms show specializations in NE function and composition. In contrast with vertebrates, the protein composition of the NE and the function of NE proteins are barely understood in plants. MFP1 attachment factor 1 (MAF1) is a plant-specific NE-associated protein first identified in tomato (Lycopersicon esculentum). Here, we demonstrate that two Arabidopsis thaliana MAF1 homologs, WPP1 and WPP2, are associated with the NE specifically in undifferentiated cells of the root tip. Reentry into cell cycle after callus induction from differentiated root segments reprograms their NE association. Based on green fluorescent protein fusions and immunogold labeling data, the proteins are associated with the outer NE and the nuclear pores in interphase cells and with the immature cell plate during cytokinesis. RNA interference-based suppression of the Arabidopsis WPP family causes shorter primary roots, a reduced number of lateral roots, and reduced mitotic activity of the root meristem. Together, these data demonstrate the existence of regulated NE targeting in plants and identify a class of plant-specific NE proteins involved in mitotic activity.
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Affiliation(s)
- Shalaka Patel
- Plant Biotechnology Center and Department of Plant Molecular and Cellular Biology, The Ohio State University, Columbus, Ohio 43210, USA
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23
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Abstract
Eukaryotic genomes are distributed on linear chromosomes that are grouped together in the nucleus, an organelle separated from the cytoplasm by a characteristic double membrane studded with large proteinaceous pores. The chromatin within chromosomes has an as yet poorly characterized higher-order structure, but in addition to this, chromosomes and specific subchromosomal domains are nonrandomly positioned in nuclei. This review examines functional implications of the long-range organization of the genome in interphase nuclei. A rigorous test of the physiological importance of nuclear architecture is achieved by introducing mutations that compromise both structure and function. Focussing on such genetic approaches, we address general concepts of interphase nuclear order, the role of the nuclear envelope (NE) and lamins, and finally the importance of spatial organization for DNA replication and heritable gene expression.
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Affiliation(s)
- Angela Taddei
- University of Geneva, Department of Molecular Biology, CH-1211 Geneva 4, Switzerland
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Oka M, Yanagawa Y, Asada T, Yoneda A, Hasezawa S, Sato T, Nakagawa H. Inhibition of proteasome by MG-132 treatment causes extra phragmoplast formation and cortical microtubule disorganization during M/G1 transition in synchronized tobacco cells. PLANT & CELL PHYSIOLOGY 2004; 45:1623-32. [PMID: 15574838 DOI: 10.1093/pcp/pch183] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The 26S proteasome plays essential roles in cell cycle progression in various types of cell. We previously reported that the inhibition of 26S proteasome activities by a proteasome inhibitor, MG-132, exclusively caused cell cycle arrest in synchronized tobacco BY-2 cells. Here we report a further observation of 26S proteasome involvement during M/G1 transition utilizing a transgenetic BY-2 cell line that stably expresses a GFP-alpha-tubulin fusion protein (BY-GT16). Interestingly, MG-132 treatment caused the arrest of cell cycle progression prior to entering the G1 phase. Indeed, phragmoplast-like structures were formed and cortical microtubules were not organized after the collapse of the original phragmoplasts. Additionally, actin microfilaments showed irregular rearrangements when further incubated with MG-132 and as the phragmoplast-like structures developed. Since these phragmoplast-like structures had a similar configuration and ability to form cell plates to that of the original phragmoplasts, we designated these phragmoplast-like structures as extra phragmoplasts. Furthermore, we showed that a tobacco kinesin-related polypeptide of 125 kDa (TKRP125) localized in the extra phragmoplasts and that its protein level remained unchanged during MG-132 treatment. We propose that TKRP125 might be one of the possible targets of the ubiquitin-proteasome degradation pathway during M/G1 transition.
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Affiliation(s)
- Masayoshi Oka
- Department of Bioproduction Science, Faculty of Horticulture, Chiba University, Matsudo, Chiba, 271-8510 Japan
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Brandizzi F, Irons SL, Evans DE. The plant nuclear envelope: new prospects for a poorly understood structure. THE NEW PHYTOLOGIST 2004; 163:227-246. [PMID: 33873618 DOI: 10.1111/j.1469-8137.2004.01118.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The nuclear envelope (NE) is one of the least characterized cellular structures in plant cells. In particular, knowledge of its dynamic behaviour during the cell cycle and of its protein composition is limited. This review summarizes current views on the plant NE and highlights fundamental differences with other organisms. We also introduce the power of new technology available to investigate the NE and how this has already begun to revolutionize our knowledge of the biology of the plant NE. Contents Summary 227 I. Introduction 227 II. The membranes of the nuclear envelope 228 III. Functions of the nuclear envelope 231 IV. Proteins associated with the nuclear envelope 236 V. New tools for studying the nuclear envelope 239 VI. Conclusions and future prospects 241 Acknowledgements 242 References 242.
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Affiliation(s)
- Federica Brandizzi
- Biology Department, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5E2
| | - Sarah L Irons
- Research School of Biological and Molecular Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - David E Evans
- Research School of Biological and Molecular Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
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Lemaire SD, Guillon B, Le Maréchal P, Keryer E, Miginiac-Maslow M, Decottignies P. New thioredoxin targets in the unicellular photosynthetic eukaryote Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 2004; 101:7475-80. [PMID: 15123830 PMCID: PMC409943 DOI: 10.1073/pnas.0402221101] [Citation(s) in RCA: 183] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2004] [Indexed: 01/25/2023] Open
Abstract
Proteomics were used to identify the proteins from the eukaryotic unicellular green alga Chlamydomonas reinhardtii that can be reduced by thioredoxin. These proteins were retained specifically on a thioredoxin affinity column made of a monocysteinic thioredoxin mutant able to form mixed disulfides with its targets. Of a total of 55 identified targets, 29 had been found previously in higher plants or Synechocystis, but 26 were new targets. Biochemical tests were performed on three of them, showing a thioredoxin-dependent activation of isocitrate lyase and isopropylmalate dehydrogenase and a thioredoxin-dependent deactivation of catalase that is redox insensitive in Arabidopsis. In addition, we identified a Ran protein, a previously uncharacterized nuclear target in a photosynthetic organism. The metabolic and evolutionary implications of these findings are discussed.
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Affiliation(s)
- Stéphane D Lemaire
- Institut de Biotechnologie des Plantes, Bâtiment 630, Unité Mixte de Recherche 8618, Centre National de la Recherche Scientifique/Université Paris-Sud, F-91405 Orsay-Cedex, France.
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