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Yang H, Yuan Y, Li Z. Dehydration priming remodels protein abundance and phosphorylation level regulating tolerance to subsequent dehydration or salt stress in creeping bentgrass. J Proteomics 2025; 310:105325. [PMID: 39369954 DOI: 10.1016/j.jprot.2024.105325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 09/15/2024] [Accepted: 09/30/2024] [Indexed: 10/08/2024]
Abstract
Dehydration priming (DP) induces stress memory which plays a positive role in plant adaptability, but it is not well understood how DP differentially regulates subsequent dehydration (cis priming) or salt (trans priming) tolerance at the post-translational level. Purpose of this study was to identify proteins, phosphorylation levels and sites, and relevant metabolic pathways for DP-induced dehydration or salt tolerance in Agrostis stolonifera. DP-induced differentially regulated proteins (DRPs) were mostly located in the cytoplasm, chloroplast, and cell membrane, and differentially regulated phosphoproteins (DRPPs) were mostly nuclear proteins and cytoplasmic proteins. DP regulated common phosphorylation sites ([SP] and [RxxS]) under dehydration and salt conditions and also individually affected 8 or 11 phosphorylation sites under dehydration or salt stress. DP-regulated DRPPs were mainly rich in glycolysis and glutathione metabolism pathways, RNA splicing, and dynamin family proteins under dehydration stress, whereas DP-regulated salt tolerance was mainly related to chlorophyll metabolism, photosynthesis, MAPK signaling cascade, and ABC transporter I family at the phosphorylation level. In addition, the DP also significantly up-regulated phosphorylation of histones (ATXR3 and SETD1A) in response to subsequent dehydration and salt stress as well as abundances of antioxidant enzymes, dynamin family protein, and KCS6 under dehydration stress or abundances of PETE, HMGA, XTH, and ABCI6 under salt stress, respectively. Transcriptomics analysis further indicated that DP-regulated dehydration or salt tolerance was also related to transcriptional regulation in the early stage. Current results provided better understanding of the role of stress memory in plant adaptability to repeated or crossed stress via post-translational modifications (PTMs). SIGNIFICANCE: Recurrent moderate drought may buffer drought legacies in many plant species. When plants were exposed to repeated drought stress, their adaptability to subsequent stress could be enhanced, which is known as "stress memory". Dehydration priming has been found to be an important approach to induce stress memory. Current results provided better understanding of the role of stress memory in plant adaptability to repeated or crossed stress via post-translational modifications.
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Affiliation(s)
- Huizhen Yang
- Department of Turf Science and engineering, College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Yuan
- Department of Turf Science and engineering, College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhou Li
- Department of Turf Science and engineering, College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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2
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Kar UP, Dey H, Rahaman A. Cardiolipin targets a dynamin-related protein to the nuclear membrane. eLife 2021; 10:64416. [PMID: 33661098 PMCID: PMC7946437 DOI: 10.7554/elife.64416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/03/2021] [Indexed: 12/03/2022] Open
Abstract
Dynamins are targeted to specific cellular membranes that they remodel via membrane fusion or fission. The molecular basis of conferring specificity to dynamins for their target membrane selection is not known. Here, we report a mechanism of nuclear membrane recruitment of Drp6, a dynamin member in Tetrahymena thermophila. Recruitment of Drp6 depends on a domain that binds to cardiolipin (CL)-rich bilayers. Consistent with this, nuclear localization of Drp6 was inhibited either by depleting cellular CL or by substituting a single amino acid residue that abolished Drp6 interactions with CL. Inhibition of CL synthesis, or perturbation in Drp6 recruitment to nuclear membrane, caused defects in the formation of new macronuclei post-conjugation. Taken together, our results elucidate a molecular basis of target membrane selection by a nuclear dynamin and establish the importance of a defined membrane-binding domain and its target lipid in facilitating nuclear expansion.
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Affiliation(s)
- Usha Pallabi Kar
- School of Biological Sciences, National Institute of Science Education and Research-HBNI, Bhubaneswar, India
| | - Himani Dey
- School of Biological Sciences, National Institute of Science Education and Research-HBNI, Bhubaneswar, India
| | - Abdur Rahaman
- School of Biological Sciences, National Institute of Science Education and Research-HBNI, Bhubaneswar, India
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3
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Sun B, Zhang QY, Yuan H, Gao W, Han B, Zhang M. PDV1 and PDV2 Differentially Affect Remodeling and Assembly of the Chloroplast DRP5B Ring. PLANT PHYSIOLOGY 2020; 182:1966-1978. [PMID: 32005784 PMCID: PMC7140913 DOI: 10.1104/pp.19.01490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
Chloroplasts divide by binary fission, which is driven by a ring-like multiprotein complex spanning the inner and outer envelope membranes (OEMs) at the division site. The cytosolic DYNAMIN-RELATED PROTEIN 5B (DRP5B/ARC5) is a mechanochemical GTPase involved in binary fission of the chloroplast membrane in Arabidopsis (Arabidopsis thaliana), but the dynamics of its interactions with the chloroplast membranes and their regulation by guanine nucleotides and protein effectors remain poorly characterized. Using an Arabidopsis phot2 mutant with defects in chloroplast photorelocation movement, we determined that the ring structures of DRP5B at the chloroplast division site underwent subunit exchange with a cytosolic DRP5B pool. Mutant DRP5B proteins with impaired GTPase activity retained the ability to self-assemble at the constriction sites of chloroplasts, but did not rescue the chloroplast division defects in the Arabidopsis drp5B mutant. Our in vivo kinetic measurements of the DRP5B mutant T82D suggested that turnover of the DRP5B ring at the chloroplast division site is coupled to GTP hydrolysis. Furthermore, we established that DRP5B targeting to the chloroplast surface and assembly into a ring structure at the division site are specifically determined by the chloroplast outer OEM protein PLASTID DIVISION2 (PDV2), and that DRP5B-OEM dissociation is mainly mediated by PDV1, a paralog of PDV2. Thus, this study suggests that the mechanochemical properties of DRP5B on the chloroplast surface are dynamically regulated by its GTPase activity and major binding partners.
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Affiliation(s)
- Bing Sun
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Qi-Yang Zhang
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Huan Yuan
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Wei Gao
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Bo Han
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Min Zhang
- College of Life Sciences, Capital Normal University, Beijing 100048, China
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4
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Pillai AN, Shukla S, Gautam S, Rahaman A. Small phosphatidate phosphatase (TtPAH2) of Tetrahymena complements respiratory function and not membrane biogenesis function of yeast PAH1. J Biosci 2018; 42:613-621. [PMID: 29229879 DOI: 10.1007/s12038-017-9712-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Phosphatidate phosphatases (PAH) play a central role in lipid metabolism and intracellular signaling. Herein, we report the presence of a low-molecular-weight PAH homolog in the single-celled ciliate Tetrahymena thermophila. In vitro phosphatase assay showed that TtPAH2 belongs to the magnesium-dependent phosphatidate phosphatase (PAP1) family. Loss of function of TtPAH2 did not affect the growth of Tetrahymena. Unlike other known PAH homologs, TtPAH2 did not regulate lipid droplet number and ER morphology. TtPAH2 did not rescue growth and ER/nuclear membrane defects of the pah1Δ yeast cells, suggesting that the phosphatidate phosphatase activity of the protein is not sufficient to perform these cellular functions. Surprisingly, TtPAH2 complemented the respiratory defect in the pah1Δ yeast cells indicating a specific role of TtPAH2 in respiration. Overall, our results indicate that TtPAH2 possesses the minimal function of PAH protein family in respiration. We suggest that the amino acid sequences absent from TtPAH2 but present in all other known PAH homologs are critical for lipid homeostasis and membrane biogenesis.
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Affiliation(s)
- Anoop Narayana Pillai
- National Institute of Science Education and Research (NISER), HBNI, Bhubaneswar, Khurda 752 050, India
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5
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Iwamoto M, Mori C, Osakada H, Koujin T, Hiraoka Y, Haraguchi T. Nuclear localization signal targeting to macronucleus and micronucleus in binucleated ciliate Tetrahymena thermophila. Genes Cells 2018; 23:568-579. [PMID: 29882620 DOI: 10.1111/gtc.12602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 04/27/2018] [Accepted: 05/08/2018] [Indexed: 01/25/2023]
Abstract
Ciliated protozoa possess two morphologically and functionally distinct nuclei: a macronucleus (MAC) and a micronucleus (MIC). The MAC is transcriptionally active and functions in all cellular events. The MIC is transcriptionally inactive during cell growth, but functions in meiotic events to produce progeny nuclei. Thus, these two nuclei must be distinguished by the nuclear proteins required for their distinct functions during cellular events such as cell proliferation and meiosis. To understand the mechanism of the nuclear transport specific to either MAC or MIC, we identified specific nuclear localization signals (NLSs) in two MAC- and MIC-specific nuclear proteins, macronuclear histone H1 and micronuclear linker histone-like protein (Mlh1), respectively. By expressing GFP-fused fragments of these proteins in Tetrahymena thermophila cells, two distinct regions in macronuclear histone H1 protein were assigned as independent MAC-specific NLSs and two distinct regions in Mlh1 protein were assigned as independent MIC-specific NLSs. These NLSs contain several essential lysine residues responsible for the MAC- and MIC-specific nuclear transport, but neither contains any consensus sequence with known monopartite or bipartite NLSs in other model organisms. Our findings contribute to understanding how specific nuclear targeting is achieved to perform distinct nuclear functions in binucleated ciliates.
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Affiliation(s)
- Masaaki Iwamoto
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Chie Mori
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Hiroko Osakada
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Takako Koujin
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Yasushi Hiraoka
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Tokuko Haraguchi
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
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Kar UP, Dey H, Rahaman A. Regulation of dynamin family proteins by post-translational modifications. J Biosci 2018; 42:333-344. [PMID: 28569256 DOI: 10.1007/s12038-017-9680-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Dynamin superfamily proteins comprising classical dynamins and related proteins are membrane remodelling agents involved in several biological processes such as endocytosis, maintenance of organelle morphology and viral resistance. These large GTPases couple GTP hydrolysis with membrane alterations such as fission, fusion or tubulation by undergoing repeated cycles of self-assembly/disassembly. The functions of these proteins are regulated by various post-translational modifications that affect their GTPase activity, multimerization or membrane association. Recently, several reports have demonstrated variety of such modifications providing a better understanding of the mechanisms by which dynamin proteins influence cellular responses to physiological and environmental cues. In this review, we discuss major post-translational modifications along with their roles in the mechanism of dynamin functions and implications in various cellular processes.
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Affiliation(s)
- Usha P Kar
- School of Biological Sciences, National Institute of Science Education and Research- Bhubaneswar, HBNI, 752050, Odisha, India
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7
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Kar UP, Dey H, Rahaman A. Tetrahymena dynamin-related protein 6 self-assembles independent of membrane association. J Biosci 2018; 43:139-148. [PMID: 29485122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Self-assembly on target membranes is one of the important properties of all dynamin family proteins. Drp6, a dynaminrelated protein in Tetrahymena, controls nuclear remodelling and undergoes cycles of assembly/disassembly on the nuclear envelope. To elucidate the mechanism of Drp6 function, we have characterized its biochemical and biophysical properties using size exclusion chromatography, chemical cross-linking and electron microscopy. The results demonstrate that Drp6 readily forms high-molecular-weight self-assembled structures as determined by size exclusion chromatography and chemical cross-linking. Negative stain electron microscopy revealed that Drp6 assembles into rings and spirals at physiological ionic strength. We have also shown that the recombinant Drp6 expressed in bacteria is catalytically active and its GTPase activity is not enhanced by low salt. These results suggest that, in contrast to dynamins but similar to MxA, Drp6 self-assembles in the absence of membrane templates, and its GTPase activity is not affected by ionic strength of the buffer. We discuss the self-assembly structure of Drp6 and explain the basis for lack of membrane-stimulated GTPase activity.
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Affiliation(s)
- Usha P Kar
- School of Biological Sciences, National Institute of Science Education and Research-HBNI, Bhubaneswar, India
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8
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Kar UP, Dey H, Rahaman A. Tetrahymena dynamin-related protein 6 self-assembles independent of membrane association. J Biosci 2017. [DOI: 10.1007/s12038-017-9726-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Pillai AN, Shukla S, Rahaman A. An evolutionarily conserved phosphatidate phosphatase maintains lipid droplet number and endoplasmic reticulum morphology but not nuclear morphology. Biol Open 2017; 6:1629-1643. [PMID: 28954739 PMCID: PMC5703613 DOI: 10.1242/bio.028233] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Phosphatidic acid phosphatases are involved in the biosynthesis of phospholipids and triacylglycerol, and also act as transcriptional regulators. Studies to ascertain their role in lipid metabolism and membrane biogenesis are restricted to Opisthokonta and Archaeplastida. Here, we report the role of phosphatidate phosphatase (PAH) in Tetrahymena thermophila, belonging to the Alveolata clade. We identified two PAH homologs in Tetrahymena, TtPAH1 and TtPAH2 Loss of function of TtPAH1 results in reduced lipid droplet number and an increase in endoplasmic reticulum (ER) content. It also results in more ER sheet structure as compared to wild-type Tetrahymena Surprisingly, we did not observe a visible defect in the nuclear morphology of the ΔTtpah1 mutant. TtPAH1 rescued all known defects in the yeast pah1Δ strain and is conserved functionally between Tetrahymena and yeast. The homologous gene derived from Trypanosoma also rescued the defects of the yeast pah1Δ strain. Our results indicate that PAH, previously known to be conserved among Opisthokonts, is also present in a set of distant lineages. Thus, a phosphatase cascade is evolutionarily conserved and is functionally interchangeable across eukaryotic lineages.
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Affiliation(s)
- Anoop Narayana Pillai
- School of Biological Sciences, National Institute of Science Education and Research (NISER)-Bhubaneswar, HBNI, P.O. Jatni, Khurda 752050, Odisha, India
| | - Sushmita Shukla
- School of Biological Sciences, National Institute of Science Education and Research (NISER)-Bhubaneswar, HBNI, P.O. Jatni, Khurda 752050, Odisha, India
| | - Abdur Rahaman
- School of Biological Sciences, National Institute of Science Education and Research (NISER)-Bhubaneswar, HBNI, P.O. Jatni, Khurda 752050, Odisha, India
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10
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Iwamoto M, Koujin T, Osakada H, Mori C, Kojidani T, Matsuda A, Asakawa H, Hiraoka Y, Haraguchi T. Biased assembly of the nuclear pore complex is required for somatic and germline nuclear differentiation in Tetrahymena. J Cell Sci 2015; 128:1812-23. [PMID: 25788697 PMCID: PMC4432229 DOI: 10.1242/jcs.167353] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/07/2015] [Indexed: 12/18/2022] Open
Abstract
Ciliates have two functionally distinct nuclei, a somatic macronucleus (MAC) and a germline micronucleus (MIC) that develop from daughter nuclei of the last postzygotic division (PZD) during the sexual process of conjugation. Understanding this nuclear dimorphism is a central issue in ciliate biology. We show, by live-cell imaging of Tetrahymena, that biased assembly of the nuclear pore complex (NPC) occurs immediately after the last PZD, which generates anterior-posterior polarized nuclei: MAC-specific NPCs assemble in anterior presumptive MACs but not in posterior presumptive MICs. MAC-specific NPC assembly in the anterior nuclei occurs much earlier than transport of Twi1p, which is required for MAC genome rearrangement. Correlative light-electron microscopy shows that addition of new nuclear envelope (NE) precursors occurs through the formation of domains of redundant NE, where the outer double membrane contains the newly assembled NPCs. Nocodazole inhibition of the second PZD results in assembly of MAC-specific NPCs in the division-failed zygotic nuclei, leading to failure of MIC differentiation. Our findings demonstrate that NPC type switching has a crucial role in the establishment of nuclear differentiation in ciliates.
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Affiliation(s)
- Masaaki Iwamoto
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan
| | - Takako Koujin
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan
| | - Hiroko Osakada
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan
| | - Chie Mori
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan
| | - Tomoko Kojidani
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan Japan Women's University, Tokyo 112-8681, Japan
| | - Atsushi Matsuda
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Haruhiko Asakawa
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Yasushi Hiraoka
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - Tokuko Haraguchi
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
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Kalia R, Talledge N, Frost A. Structural and functional studies of membrane remodeling machines. Methods Cell Biol 2015; 128:165-200. [PMID: 25997348 DOI: 10.1016/bs.mcb.2015.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Building cells from their component parts will hinge upon our ability to reconstitute biochemical compartmentalization and exchange between membrane-delimited organelles. By contrast with our understanding of other cellular events, the mechanisms that govern membrane trafficking has lagged because the presence of phospholipid bilayers complicates the use of standard methods. This chapter describes in vitro methods for purifying, reconstituting, and visualizing membrane remodeling activities directly by electron cryomicroscopy.
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Affiliation(s)
- Raghav Kalia
- Department of Biochemistry, University of Utah, School of Medicine, Salt Lake City, UT, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Nathaniel Talledge
- Department of Biochemistry, University of Utah, School of Medicine, Salt Lake City, UT, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Adam Frost
- Department of Biochemistry, University of Utah, School of Medicine, Salt Lake City, UT, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
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12
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Wexler-Cohen Y, Stevens GC, Barnoy E, van der Bliek AM, Johnson PJ. A dynamin-related protein contributes to Trichomonas vaginalis hydrogenosomal fission. FASEB J 2013; 28:1113-21. [PMID: 24297697 DOI: 10.1096/fj.13-235473] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Trichomonas vaginalis is a highly divergent, unicellular eukaryote of the phylum Metamonada, class Parabasalia, and the source of a common sexually transmitted infection. This parasite lacks mitochondria, but harbors an evolutionarily related organelle, the hydrogenosome. We explored the role of dynamin-related proteins (DRPs) in the division of the hydrogenosome. Eight DRP homologues [T. vaginalis DRPs (TvDRPs)], which can be grouped into 3 subclasses, are present in T. vaginalis. We examined 5 TvDRPs that are representative of each subclass, by introducing dominant negative mutations analogous to those known to interfere with mitochondrial division in yeast, worms, and mammals. Microscopic and cell fractionation analyses of parasites expressing one of the mutated TvDRPs (TVAG_350040) demonstrated that this protein localizes to hydrogenosomes. Moreover, these organelles were found to be increased in size and reduced in number in cells expressing this dominant negative protein, relative to parasites expressing the corresponding wild-type TvDRP, the other 4 mutant TvDRPs, or an empty vector control. Our data indicate a role for a TvDRP in the fission of T. vaginalis hydrogenosomes, similar to that described for peroxisomes and mitochondria. These findings reveal a conservation of core components involved in the division of diverse eukaryotic organelles across broad phylogenetic distances.
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Affiliation(s)
- Yael Wexler-Cohen
- 1University of California, 609 Charles E. Young Dr. East, 1602 Molecular Sciences Bldg. Los Angeles, CA 90024, USA.
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Mutations in Pdd1 reveal distinct requirements for its chromodomain and chromoshadow domain in directing histone methylation and heterochromatin elimination. EUKARYOTIC CELL 2013; 13:190-201. [PMID: 24297443 DOI: 10.1128/ec.00219-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Pdd1, a specialized HP1-like protein, is required for genome-wide DNA rearrangements that restructure a previously silent germ line genome into an active somatic genome during macronuclear differentiation of Tetrahymena thermophila. We deleted or otherwise mutated conserved regions of the protein to investigate how its different domains promote the excision of thousands of internal eliminated sequences (IESs). Previous studies revealed that Pdd1 contributes to recognition of IES loci after they are targeted by small-RNA-guided methylation of histone H3 on lysine 27 (H3K27), subsequently aids the establishment of H3K9 methylation, and recruits proteins that lead to excision. The phenotypes we observed for different Pdd1 alleles showed that each of the two chromodomains and the chromoshadow domain (CSD) have distinct contributions during somatic genome differentiation. Chromodomain 1 (CD1) is essential for conjugation as either its deletion or the substitution of two key aromatic amino acid residues (the W97A W100A mutant) is lethal. These mutations caused mislocalization of a cyan fluorescent protein (CFP)-tagged protein, prevented the establishment of histone H3 dimethylated on K9 (H3K9me2), and abolished IES excision. Nevertheless, the requirement for CD1 could be bypassed by recruiting Pdd1 directly to an IES by addition of a specific DNA binding domain. Chromodomain 2 (CD2) was necessary for producing viable progeny, but low levels of H3K9me2 and IES excision still occurred. A mutation in the chromoshadow domain (CSD) prevented Pdd1 focus formation but still permitted ∼17% of conjugants to produce viable progeny. However, this mutant was unable to stimulate excision when recruited to an ectopic IES, indicating that this domain is important for recruitment of excision factors.
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Poklepovich TJ, Rinaldi MA, Tomazic ML, Favale NO, Turkewitz AP, Nudel CB, Nusblat AD. The cytochrome b5 dependent C-5(6) sterol desaturase DES5A from the endoplasmic reticulum of Tetrahymena thermophila complements ergosterol biosynthesis mutants in Saccharomyces cerevisiae. Steroids 2012; 77:1313-20. [PMID: 22982564 PMCID: PMC3501532 DOI: 10.1016/j.steroids.2012.08.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 08/21/2012] [Accepted: 08/23/2012] [Indexed: 11/23/2022]
Abstract
Tetrahymena thermophila is a free-living ciliate with no exogenous sterol requirement. However, it can perform several modifications on externally added sterols including desaturation at C5(6), C7(8), and C22(23). Sterol desaturases in Tetrahymena are microsomal enzymes that require Cyt b(5), Cyt b(5) reductase, oxygen, and reduced NAD(P)H for their activity, and some of the genes encoding these functions have recently been identified. The DES5A gene encodes a C-5(6) sterol desaturase, as shown by gene knockout in Tetrahymena. To confirm and extend that result, and to develop new approaches to gene characterization in Tetrahymena, we have now, expressed DES5A in Saccharomyces cerevisiae. The DES5A gene was codon optimized and expressed in a yeast mutant, erg3Δ, which is disrupted for the gene encoding the S. cerevisiae C-5(6) sterol desaturase ERG3. The complemented strain was able to accumulate 74% of the wild type level of ergosterol, and also lost the hypersensitivity to cycloheximide associated with the lack of ERG3 function. C-5(6) sterol desaturases are expected to function at the endoplasmic reticulum. Consistent with this, a GFP-tagged copy of Des5Ap was localized to the endoplasmic reticulum in both Tetrahymena and yeast. This work shows for the first time that both function and localization are conserved for a microsomal enzyme between ciliates and fungi, notwithstanding the enormous evolutionary distance between these lineages. The results suggest that heterologous expression of ciliate genes in S. cerevisiae provides a useful tool for the characterization of genes in Tetrahymena, including genes encoding membrane protein complexes.
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Affiliation(s)
- Tomas J. Poklepovich
- Cátedra de Biotecnología y Microbiología Industrial, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, (C1113AAD) Buenos Aires, Argentina
| | - Mauro A. Rinaldi
- Cátedra de Biotecnología y Microbiología Industrial, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, (C1113AAD) Buenos Aires, Argentina
| | - Mariela L. Tomazic
- Cátedra de Biotecnología y Microbiología Industrial, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, (C1113AAD) Buenos Aires, Argentina
| | - Nicolas O. Favale
- Cátedra de Biología Celular, Departamento de Ciencias Biológicas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, (C1113AAD) Buenos Aires, Argentina
| | - Aaron P. Turkewitz
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 E. 58th Street, Chicago, IL, USA
| | - Clara B. Nudel
- Cátedra de Biotecnología y Microbiología Industrial, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, (C1113AAD) Buenos Aires, Argentina
| | - Alejandro D. Nusblat
- Cátedra de Biotecnología y Microbiología Industrial, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, (C1113AAD) Buenos Aires, Argentina
- Corresponding author at all stages of refereeing and publication, also post-publication: * Alejandro D. Nusblat, , Address: Cátedra de Biotecnología y Microbiología Industrial, Facultad de Farmacia y Bioquímica, Universidad de Buenos, Aires, Junín 956, (C1113AAD) Buenos Aires, Argentina. Phone: +54-11-4964-8270, Fax: +54-11-4964-8200
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Conservation and innovation in Tetrahymena membrane traffic: proteins, lipids, and compartments. Methods Cell Biol 2012; 109:141-75. [PMID: 22444145 DOI: 10.1016/b978-0-12-385967-9.00006-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The past decade has seen a significant expansion in our understanding of membrane traffic in Tetrahymena thermophila, facilitated by the development of new experimental tools and by the availability of the macronuclear genome sequence. Here we review studies on multiple pathways of uptake and secretion, as well as work on metabolism of membrane lipids. We discuss evidence for conservation versus innovation in the mechanisms used in ciliates compared with those in other eukaryotic lineages, and raise the possibility that existing gene expression databases can be exploited to analyze specific pathways of membrane traffic in these cells.
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16
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Comprehensive analysis reveals dynamic and evolutionary plasticity of Rab GTPases and membrane traffic in Tetrahymena thermophila. PLoS Genet 2010; 6:e1001155. [PMID: 20976245 PMCID: PMC2954822 DOI: 10.1371/journal.pgen.1001155] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2010] [Accepted: 09/10/2010] [Indexed: 12/02/2022] Open
Abstract
Cellular sophistication is not exclusive to multicellular organisms, and unicellular eukaryotes can resemble differentiated animal cells in their complex network of membrane-bound structures. These comparisons can be illuminated by genome-wide surveys of key gene families. We report a systematic analysis of Rabs in a complex unicellular Ciliate, including gene prediction and phylogenetic clustering, expression profiling based on public data, and Green Fluorescent Protein (GFP) tagging. Rabs are monomeric GTPases that regulate membrane traffic. Because Rabs act as compartment-specific determinants, the number of Rabs in an organism reflects intracellular complexity. The Tetrahymena Rab family is similar in size to that in humans and includes both expansions in conserved Rab clades as well as many divergent Rabs. Importantly, more than 90% of Rabs are expressed concurrently in growing cells, while only a small subset appears specialized for other conditions. By localizing most Rabs in living cells, we could assign the majority to specific compartments. These results validated most phylogenetic assignments, but also indicated that some sequence-conserved Rabs were co-opted for novel functions. Our survey uncovered a rare example of a nuclear Rab and substantiated the existence of a previously unrecognized core Rab clade in eukaryotes. Strikingly, several functionally conserved pathways or structures were found to be associated entirely with divergent Rabs. These pathways may have permitted rapid evolution of the associated Rabs or may have arisen independently in diverse lineages and then converged. Thus, characterizing entire gene families can provide insight into the evolutionary flexibility of fundamental cellular pathways. Single-celled organisms appear simple compared to multicellular organisms, but this may not be true at the level of the individual cell. In fact, microscopic observations suggest that protists can possess networks of organelles just as elaborate as those in animal cells. Consistent with this idea, recent analysis has identified large families of genes in protists that are predicted to act as determinants for complex membrane networks. To test these predictions and to probe relationships between cellular structures across a wide swath of evolution, we focused on one gene family in the single-celled organism Tetrahymena. These genes control the traffic between organelles, with each gene controlling a single step in this traffic. We asked three questions about each of 56 genes in the family. First, what is the gene related to in humans? Second, under what conditions is the gene being used in Tetrahymena? Third, what is the role of each gene? The results provide insights into both the dynamics and evolution of membrane traffic, including the finding that some pathways appearing both structurally and functionally similar in protists and animals are likely to have arisen independently in the two lineages.
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17
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Gotesman M, Hosein RE, Gavin RH. A FERM domain in a class XIV myosin interacts with actin and tubulin and localizes to the cytoskeleton, phagosomes, and nucleus in Tetrahymena thermophila. Cytoskeleton (Hoboken) 2010; 67:90-101. [PMID: 20169533 DOI: 10.1002/cm.20426] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Previous studies have shown that Myo1(myosin class XIV) localizes to the cytoskeleton and is involved in amitosis of the macronucleus and trafficking of phagosomes. Myo1 contains a FERM domain that could be a site for interaction between Myo1 and the cytoskeleton. Here, we explore the function of FERM by investigating its cytoskeleton binding partners and involvement in localization of Myo1. Alignment of Myo1 FERM with a talin actin-binding sequence, a MAP-2 tubulin-binding sequence, the radixin FERM dimerization motif, and the SV40 nuclear localization sequence (NLS) revealed putative actin- and tubulin-binding sequences, a putative FERM dimerization motif, and NLS-like sequences in both the N-terminal and C-terminal regions of Myo1 FERM. Alignment of Myo1 with an ERM C-terminal motif revealed a similar sequence in the Myo1 motor domain. GFP-FERM and two truncated FERM domains were separately expressed in Tetrahymena. GFP-FERM contained the entire Myo1 FERM. Truncated Myo1 FERM domains contained either the N-terminal or the C-terminal region of FERM and one putative sequence for actin-binding, one for tubulin-binding, a putative dimerization motif, and a NLS-like sequence. Actin antibody coprecipitated GFP-fusion polypeptides and tubulin from lysate of cells expressing GFP-fusions. Cosedimentation assays performed with either whole cell extracts or anti-actin immunoprecipitation pellets revealed that F-actin (independent of ATP) and microtubules cosedimented with GFP-fusion polypeptides. GFP-FERM localized to the cytoskeleton, phagosomes, and nucleus. Truncated GFP-FERM domains localized to phagosomes but not to the cytoskeleton or nucleus.
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Affiliation(s)
- Michael Gotesman
- Department of Biology, Brooklyn College of the City University of New York, 11210, USA
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18
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Cavalier-Smith T. Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution. Biol Direct 2010; 5:7. [PMID: 20132544 PMCID: PMC2837639 DOI: 10.1186/1745-6150-5-7] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 02/04/2010] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty. According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism. Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the long-standing assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex typically overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis. RESULTS I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages explicit: two initial stages (origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin) protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility. Then octagonal nuclear pore complexes (NPCs) arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange. Finally, plugging NPC lumens by an FG-nucleoporin meshwork and adopting karyopherins for nucleocytoplasmic exchange conferred compartmentation advantages. These successive changes took place in naked growing cells, probably as indirect consequences of the origin of phagotrophy. The first eukaryote had 1-2 cilia and also walled resting cysts; I outline how encystation may have promoted the origin of meiotic sex. I also explain why many alternative ideas are inadequate. CONCLUSION Nuclear pore complexes are evolutionary chimaeras of endomembrane- and mitosis-related chromatin-associated proteins. The keys to understanding eukaryogenesis are a proper phylogenetic context and understanding organelle coevolution: how innovations in one cell component caused repercussions on others.
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Identification and partial characterization of a dynamin-like protein, EhDLP1, from the protist parasite Entamoeba histolytica. EUKARYOTIC CELL 2009; 9:215-23. [PMID: 19915078 DOI: 10.1128/ec.00214-09] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The dynamin superfamily of proteins includes a large repertoire of evolutionarily conserved GTPases that interact with different subcellular organelle membranes in eukaryotes. Dynamins are thought to participate in a number of cellular processes involving membrane remodeling and scission. Dynamin-like proteins (DLPs) form a subfamily of this vast class and play important roles in cellular processes, such as mitochondrial fission, cytokinesis, and endocytosis. In the present study, a gene encoding a dynamin-like protein (EhDLP1) from the protist parasite Entamoeba histolytica was identified and the protein was partially characterized using a combination of in silico, biochemical, and imaging methods. The protein was capable of GTP binding and hydrolysis, lipid binding, and oligomerization. Immunofluorescence studies showed the protein to be associated with the nuclear membrane. A mutant of EhDLP1 lacking GTP binding and hydrolyzing activities did not associate with the nuclear membrane. The results suggest a nucleus-associated function for EhDLP1.
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20
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van Dooren GG, Reiff SB, Tomova C, Meissner M, Humbel BM, Striepen B. A novel dynamin-related protein has been recruited for apicoplast fission in Toxoplasma gondii. Curr Biol 2009; 19:267-76. [PMID: 19217294 DOI: 10.1016/j.cub.2008.12.048] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 11/18/2008] [Accepted: 12/22/2008] [Indexed: 01/06/2023]
Abstract
BACKGROUND Apicomplexan parasites cause numerous important human diseases, including malaria and toxoplasmosis. Apicomplexa belong to the Alveolata, a group that also includes ciliates and dinoflagellates. Apicomplexa retain a plastid organelle (the apicoplast) that was derived from an endosymbiotic relationship between the alveolate ancestor and a red alga. Apicoplasts are essential for parasite growth and must correctly divide and segregate into daughter cells upon cytokinesis. Apicoplast division depends on association with the mitotic spindle, although little is known about the molecular machinery involved in this process. Apicoplasts lack the conserved machinery that divides chloroplasts in plants and red algae, suggesting that these mechanisms are unique. RESULTS Here, we demonstrate that a dynamin-related protein in Toxoplasma gondii (TgDrpA) localizes to punctate regions on the apicoplast surface. We generate a conditional dominant-negative TgDrpA cell line to disrupt TgDrpA functions and demonstrate that TgDrpA is essential for parasite growth and apicoplast biogenesis. Fluorescence recovery after photobleaching and time-lapse imaging studies provide evidence for a direct role for TgDrpA in apicoplast fission. CONCLUSIONS Our data suggest that DrpA was likely recruited from the alveolate ancestor to function in fission of the symbiont and ultimately replaced the conserved division machinery of that symbiont.
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Affiliation(s)
- Giel G van Dooren
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, 30602, USA
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Ciliate biology: dynamin goes nuclear. Curr Biol 2008; 18:R923-5. [PMID: 18957241 DOI: 10.1016/j.cub.2008.07.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Dynamin and dynamin-related proteins (DRPs) mediate an array of membrane fission processes. A Tetrahymena DRP has adopted a new role, assisting in nuclear differentiation, a finding that further highlights these proteins - and this ciliate - as biological innovators.
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