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Liu Q, Tang X, Zhang X, Tong X, Sun Z, Zhang X. Mechanistic understanding of the toxicity of triphenyl phosphate (TPhP) to the marine diatom Phaeodactylum tricornutum: Targeting chloroplast and mitochondrial dysfunction. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 295:118670. [PMID: 34902529 DOI: 10.1016/j.envpol.2021.118670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Triphenyl phosphate (TPhP) has been widely detected in various environmental media, including seawater, threatening the survival of marine organisms, especially marine planktic algae that are directly exposed to contamination. However, the hazard potential of TPhP on marine algae has not been studied thoroughly and systematically. In this study, a marine diatom, Phaeodactylum tricornutum, was treated with three concentrations of TPhP (0.08, 0.4 and 0.8 mg/L), and after 24 h of exposure, population growth, ultrastructure, physiology and transcriptome changes were investigated. The results reflected that TPhP suppressed the population growth of algae in a concentration-dependent manner, and the 24-h EC50 value was 1.27 mg/L. At all test concentrations, P. tricornutum could absorb more than 70% of TPhP from seawater over 24 h. Ultrastructural observations suggested a distorted lamellar structure with higher TPhP treatments, and the contents of chlorophyll and its precursors were also altered, as were photosynthetic activities. Moreover, 0.8 mg/L TPhP decreased the mitochondrial membrane potential, induced ROS overproduction and disrupted the cell membrane permeability of algal cells. At the transcriptomic level, some differentially expressed genes were enriched in photosynthetic electron transport, carbon fixation, chlorophyll biosynthesis, the TCA cycle and mitochondrial glycolysis. Additionally, 0.8 mg/L TPhP inhibited lipid de novo biosynthesis, suggesting that it may target organelle membranes, thereby contributing to functional defects. Chloroplasts and mitochondria were interpreted to be the subcellular targets of TPhP in P. tricornutum. These data promote the understanding of the toxic action mode of TPhP toward marine diatoms.
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Affiliation(s)
- Qian Liu
- Department of Marine Ecology, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Xuexi Tang
- Department of Marine Ecology, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Xin Zhang
- Department of Marine Ecology, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Xin Tong
- Department of Marine Ecology, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Zijie Sun
- Department of Marine Ecology, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Xinxin Zhang
- Department of Marine Ecology, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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2
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Zhang K, Zhang J, Ding N, Zellmer L, Zhao Y, Liu S, Liao DJ. ACTB and GAPDH appear at multiple SDS-PAGE positions, thus not suitable as reference genes for determining protein loading in techniques like Western blotting. Open Life Sci 2021; 16:1278-1292. [PMID: 34966852 PMCID: PMC8669867 DOI: 10.1515/biol-2021-0130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/21/2021] [Accepted: 11/01/2021] [Indexed: 11/19/2022] Open
Abstract
We performed polyacrylamide gel electrophoresis of human proteins with sodium dodecyl sulfate, isolated proteins at multiple positions, and then used liquid chromatography and tandem mass spectrometry (LC-MS/MS) to determine the protein identities. Although beta-actin (ACTB) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) are 41.7 and 36 kDa proteins, respectively, LC-MS/MS identified their peptides at all the positions studied. The National Center for Biotechnology Information (USA) database lists only one ACTB mRNA but five GAPDH mRNAs and one noncoding RNA. The five GAPDH mRNAs encode three protein isoforms, while our bioinformatics analysis identified a 17.6 kDa isoform encoded by the noncoding RNA. All LC-MS/MS-identified GAPDH peptides at all positions studied are unique, but some of the identified ACTB peptides are shared by ACTC1, ACTBL2, POTEF, POTEE, POTEI, and POTEJ. ACTC1 and ACTBL2 belong to the ACT family with significant similarities to ACTB in protein sequence, whereas the four POTEs are ACTB-containing chimeric genes with the C-terminus of their proteins highly similar to the ACTB. These data lead us to conclude that GAPDH and ACTB are poor reference genes for determining the protein loading in such techniques as Western blotting, a leading role these two genes have been playing for decades in biomedical research.
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Affiliation(s)
- Keyin Zhang
- Department of Pathology, School of Clinical Medicine, Guizhou Medical University , Guiyang 550004 , Guizhou Province , People’s Republic of China
| | - Ju Zhang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University , Beijing 100015 , People’s Republic of China
| | - Nan Ding
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University , Beijing 100015 , People’s Republic of China
| | - Lucas Zellmer
- Department of Medicine, Hennepin County Medical Center , 730 South 8th St. , Minneapolis , MN 55415 , United States of America
| | - Yan Zhao
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University , Guiyang 550004 , Guizhou Province , People’s Republic of China
| | - Siqi Liu
- Beijing Genomic Institute, Building 11 of Beishan Industrial Zone, Tantian District , Shengzhen 518083 , Guangdong Province , People’s Republic of China
| | - Dezhong Joshua Liao
- Department of Pathology, School of Clinical Medicine, Guizhou Medical University , Guiyang 550004 , Guizhou Province , People’s Republic of China
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University , Guiyang 550004 , Guizhou Province , People’s Republic of China
- Department of Clinical Biochemistry, Guizhou Medical University Hospital , Guiyang 550004 , Guizhou Province , People’s Republic of China
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Villanova V, Singh D, Pagliardini J, Fell D, Le Monnier A, Finazzi G, Poolman M. Boosting Biomass Quantity and Quality by Improved Mixotrophic Culture of the Diatom Phaeodactylum tricornutum. FRONTIERS IN PLANT SCIENCE 2021; 12:642199. [PMID: 33897733 PMCID: PMC8063856 DOI: 10.3389/fpls.2021.642199] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Diatoms are photoautotrophic unicellular algae and are among the most abundant, adaptable, and diverse marine phytoplankton. They are extremely interesting not only for their ecological role but also as potential feedstocks for sustainable biofuels and high-value commodities such as omega fatty acids, because of their capacity to accumulate lipids. However, the cultivation of microalgae on an industrial scale requires higher cell densities and lipid accumulation than those found in nature to make the process economically viable. One of the known ways to induce lipid accumulation in Phaeodactylum tricornutum is nitrogen deprivation, which comes at the expense of growth inhibition and lower cell density. Thus, alternative ways need to be explored to enhance the lipid production as well as biomass density to make them sustainable at industrial scale. In this study, we have used experimental and metabolic modeling approaches to optimize the media composition, in terms of elemental composition, organic and inorganic carbon sources, and light intensity, that boost both biomass quality and quantity of P. tricornutum. Eventually, the optimized conditions were scaled-up to 2 L photobioreactors, where a better system control (temperature, pH, light, aeration/mixing) allowed a further improvement of the biomass capacity of P. tricornutum to 12 g/L.
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Affiliation(s)
- Valeria Villanova
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Commissariat á l'Énergie Atomique et aux Énergies Alternatives (CEA), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Interdisciplinary Research Institute of Grenoble, CEA Grenoble, Grenoble, France
- Fermentalg SA, Libourne, France
| | - Dipali Singh
- Microbes in the Food Chain, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- Cell System Modelling Group, Oxford Brookes University, Oxford, United Kingdom
| | | | - David Fell
- Cell System Modelling Group, Oxford Brookes University, Oxford, United Kingdom
| | | | - Giovanni Finazzi
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Commissariat á l'Énergie Atomique et aux Énergies Alternatives (CEA), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Interdisciplinary Research Institute of Grenoble, CEA Grenoble, Grenoble, France
| | - Mark Poolman
- Cell System Modelling Group, Oxford Brookes University, Oxford, United Kingdom
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4
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Zhang H, Hu Y, Yang L, Lin Z, Zhao X, Chen J, Tang X, Wang Y. Transcriptome aberration in marine microalgae Phaeodactylum tricornutum induced by commercial naphthenic acids. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115735. [PMID: 33068844 DOI: 10.1016/j.envpol.2020.115735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 09/17/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
Naphthenic acids (NAs) are cycloalkyl linear carboxylic acids primarily originating from oil sand tailings water (OSTW), and the exposure to NAs affects the photosynthesis of marine microalgaes. However, the transcriptional response upon the stress of NAs remains unclear. Herein, we investigate the transcriptome alterations of marine Phaeodactylum tricornutum induced by NAs using RNA-sequencing. In total 70 differentially expressed genes (DEGs) are enriched in seven biological process pathways, and 48 DEGs are enriched in four molecular functions. Differentially expressed genes of P. tricornutum are primarily concentrated in three photosynthesis-related pathways including the porphyrin and chlorophyll metabolism pathway, the photosynthesis pathway, and the carbon fixation pathway in photosynthetic organisms. Five DEGs such as hemE, chlM, TPI/GapC3, FbaC5, and CHLH are validated using quantitative real-time PCR assay. NAs at low concentrations affect the material energy conversion efficiency of P. tricornutum, such as chlorophyll synthesis, electron transfer efficiency, and carbon assimilation.
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Affiliation(s)
- Huanxin Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266100, China; College of Geography and Environment, Shandong Normal University, Jinan, 250000, China
| | - Yanran Hu
- School of Life Science, Central South University, Changsha, 410000, China
| | - Likun Yang
- Emory School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Zhihao Lin
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266100, China
| | - Xinyu Zhao
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266100, China
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266100, China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266100, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Ying Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266100, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
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5
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e Silva KSF, Lima RM, Baeza LC, Lima PDS, Cordeiro TDM, Charneau S, da Silva RA, Soares CMDA, Pereira M. Interactome of Glyceraldehyde-3-Phosphate Dehydrogenase Points to the Existence of Metabolons in Paracoccidioides lutzii. Front Microbiol 2019; 10:1537. [PMID: 31338083 PMCID: PMC6629890 DOI: 10.3389/fmicb.2019.01537] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/20/2019] [Indexed: 11/13/2022] Open
Abstract
Paracoccidioides is a dimorphic fungus, the causative agent of paracoccidioidomycosis. The disease is endemic within Latin America and prevalent in Brazil. The treatment is based on azoles, sulfonamides and amphotericin B. The seeking for new treatment approaches is a real necessity for neglected infections. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an essential glycolytic enzyme, well known for its multitude of functions within cells, therefore categorized as a moonlight protein. To our knowledge, this is the first approach performed on the Paracoccidioides genus regarding the description of PPIs having GAPDH as a target. Here, we show an overview of experimental GAPDH interactome in different phases of Paracoccidioides lutzii and an in silico analysis of 18 proteins partners. GAPDH interacted with 207 proteins in P. lutzii. Several proteins bound to GAPDH in mycelium, transition and yeast phases are common to important pathways such as glycolysis and TCA. We performed a co-immunoprecipitation assay to validate the complex formed by GAPDH with triose phosphate isomerase, enolase, isocitrate lyase and 2-methylcitrate synthase. We found GAPDH participating in complexes with proteins of specific pathways, indicating the existence of a glycolytic and a TCA metabolon in P. lutzii. GAPDH interacted with several proteins that undergoes regulation by nitrosylation. In addition, we modeled the GAPDH 3-D structure, performed molecular dynamics and molecular docking in order to identify the interacting interface between GAPDH and the interacting proteins. Despite the large number of interacting proteins, GAPDH has only four main regions of contact with interacting proteins, reflecting its ancestrality and conservation over evolution.
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Affiliation(s)
| | - Raisa Melo Lima
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Lilian Cristiane Baeza
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Patrícia de Sousa Lima
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Thuany de Moura Cordeiro
- Laboratório de Bioquímica e Química de Proteínas, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Sébastien Charneau
- Laboratório de Bioquímica e Química de Proteínas, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Roosevelt Alves da Silva
- Núcleo Colaborativo de Biossistemas, Instituto de Ciências Exatas, Universidade Federal de Jataí, Goiás, Brazil
| | | | - Maristela Pereira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
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6
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Chasapis CT, Makridakis M, Damdimopoulos AE, Zoidakis J, Lygirou V, Mavroidis M, Vlahou A, Miranda-Vizuete A, Spyrou G, Vlamis-Gardikas A. Implications of the mitochondrial interactome of mammalian thioredoxin 2 for normal cellular function and disease. Free Radic Biol Med 2019; 137:59-73. [PMID: 31018154 DOI: 10.1016/j.freeradbiomed.2019.04.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/15/2019] [Indexed: 12/23/2022]
Abstract
Multiple thioredoxin isoforms exist in all living cells. To explore the possible functions of mammalian mitochondrial thioredoxin 2 (Trx2), an interactome of mouse Trx2 was initially created using (i) a monothiol mouse Trx2 species for capturing protein partners from different organs and (ii) yeast two hybrid screens on human liver and rat brain cDNA libraries. The resulting interactome consisted of 195 proteins (Trx2 included) plus the mitochondrial 16S RNA. 48 of these proteins were classified as mitochondrial (MitoCarta2.0 human inventory). In a second step, the mouse interactome was combined with the current four-membered mitochondrial sub-network of human Trx2 (BioGRID) to give a 53-membered human Trx2 mitochondrial interactome (52 interactor proteins plus the mitochondrial 16S RNA). Although thioredoxins are thiol-employing disulfide oxidoreductases, approximately half of the detected interactions were not due to covalent disulfide bonds. This finding reinstates the extended role of thioredoxins as moderators of protein function by specific non-covalent, protein-protein interactions. Analysis of the mitochondrial interactome suggested that human Trx2 was involved potentially in mitochondrial integrity, formation of iron sulfur clusters, detoxification of aldehydes, mitoribosome assembly and protein synthesis, protein folding, ADP ribosylation, amino acid and lipid metabolism, glycolysis, the TCA cycle and the electron transport chain. The oxidoreductase functions of Trx2 were verified by its detected interactions with mitochondrial peroxiredoxins and methionine sulfoxide reductase. Parkinson's disease, triosephosphate isomerase deficiency, combined oxidative phosphorylation deficiency, and lactate dehydrogenase b deficiency are some of the diseases where the proposed mitochondrial network of Trx2 may be implicated.
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Affiliation(s)
- Christos T Chasapis
- Institute of Chemical Engineering Sciences (ICE-HT), Foundation for Research and Technology, Hellas (FORTH), Platani 26504, Greece
| | | | - Anastassios E Damdimopoulos
- Department of Biosciences and Nutrition, Center for Innovative Medicine (CIMED), Karolinska Institutet, Huddinge, Sweden
| | - Jerome Zoidakis
- Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | - Vasiliki Lygirou
- Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | - Manolis Mavroidis
- Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | - Antonia Vlahou
- Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | - Antonio Miranda-Vizuete
- Redox Homeostasis Group, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Sevilla, Spain
| | - Giannis Spyrou
- Department of Clinical and Experimental Medicine, Division of Clinical Chemistry, Linköping University, S-581 85 Linköping, Sweden
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Remmers IM, D'Adamo S, Martens DE, de Vos RC, Mumm R, America AH, Cordewener JH, Bakker LV, Peters SA, Wijffels RH, Lamers PP. Orchestration of transcriptome, proteome and metabolome in the diatom Phaeodactylum tricornutum during nitrogen limitation. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.08.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Río Bártulos C, Rogers MB, Williams TA, Gentekaki E, Brinkmann H, Cerff R, Liaud MF, Hehl AB, Yarlett NR, Gruber A, Kroth PG, van der Giezen M. Mitochondrial Glycolysis in a Major Lineage of Eukaryotes. Genome Biol Evol 2018; 10:2310-2325. [PMID: 30060189 PMCID: PMC6198282 DOI: 10.1093/gbe/evy164] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 12/21/2022] Open
Abstract
The establishment of the mitochondrion is seen as a transformational step in the origin of eukaryotes. With the mitochondrion came bioenergetic freedom to explore novel evolutionary space leading to the eukaryotic radiation known today. The tight integration of the bacterial endosymbiont with its archaeal host was accompanied by a massive endosymbiotic gene transfer resulting in a small mitochondrial genome which is just a ghost of the original incoming bacterial genome. This endosymbiotic gene transfer resulted in the loss of many genes, both from the bacterial symbiont as well the archaeal host. Loss of genes encoding redundant functions resulted in a replacement of the bulk of the host’s metabolism for those originating from the endosymbiont. Glycolysis is one such metabolic pathway in which the original archaeal enzymes have been replaced by bacterial enzymes from the endosymbiont. Glycolysis is a major catabolic pathway that provides cellular energy from the breakdown of glucose. The glycolytic pathway of eukaryotes appears to be bacterial in origin, and in well-studied model eukaryotes it takes place in the cytosol. In contrast, here we demonstrate that the latter stages of glycolysis take place in the mitochondria of stramenopiles, a diverse and ecologically important lineage of eukaryotes. Although our work is based on a limited sample of stramenopiles, it leaves open the possibility that the mitochondrial targeting of glycolytic enzymes in stramenopiles might represent the ancestral state for eukaryotes.
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Affiliation(s)
- Carolina Río Bártulos
- Institut für Genetik, Technische Universität Braunschweig.,Fachbereich Biologie, Universität Konstanz, Germany
| | - Matthew B Rogers
- Biosciences, University of Exeter, United Kingdom.,Rangos Research Center, University of Pittsburgh, Children's Hospital, Pittsburgh, PA
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, United Kingdom
| | - Eleni Gentekaki
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada.,School of Science and Human Gut Microbiome for Health Research Unit, Mae Fah Luang University, Chiang Rai, Thailand
| | - Henner Brinkmann
- Département de Biochimie, Université de Montréal C.P. 6128, Montréal, Quebec, Canada.,Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
| | - Rüdiger Cerff
- Institut für Genetik, Technische Universität Braunschweig
| | | | - Adrian B Hehl
- Institute of Parasitology, University of Zürich, Switzerland
| | - Nigel R Yarlett
- Department of Chemistry and Physical Sciences, Pace University
| | - Ansgar Gruber
- Fachbereich Biologie, Universität Konstanz, Germany.,Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
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9
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Ewe D, Tachibana M, Kikutani S, Gruber A, Río Bártulos C, Konert G, Kaplan A, Matsuda Y, Kroth PG. The intracellular distribution of inorganic carbon fixing enzymes does not support the presence of a C4 pathway in the diatom Phaeodactylum tricornutum. PHOTOSYNTHESIS RESEARCH 2018; 137:263-280. [PMID: 29572588 DOI: 10.1007/s11120-018-0500-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 03/18/2018] [Indexed: 05/20/2023]
Abstract
Diatoms are unicellular algae and important primary producers. The process of carbon fixation in diatoms is very efficient even though the availability of dissolved CO2 in sea water is very low. The operation of a carbon concentrating mechanism (CCM) also makes the more abundant bicarbonate accessible for photosynthetic carbon fixation. Diatoms possess carbonic anhydrases as well as metabolic enzymes potentially involved in C4 pathways; however, the question as to whether a C4 pathway plays a general role in diatoms is not yet solved. While genome analyses indicate that the diatom Phaeodactylum tricornutum possesses all the enzymes required to operate a C4 pathway, silencing of the pyruvate orthophosphate dikinase (PPDK) in a genetically transformed cell line does not lead to reduced photosynthetic carbon fixation. In this study, we have determined the intracellular location of all enzymes potentially involved in C4-like carbon fixing pathways in P. tricornutum by expression of the respective proteins fused to green fluorescent protein (GFP), followed by fluorescence microscopy. Furthermore, we compared the results to known pathways and locations of enzymes in higher plants performing C3 or C4 photosynthesis. This approach revealed that the intracellular distribution of the investigated enzymes is quite different from the one observed in higher plants. In particular, the apparent lack of a plastidic decarboxylase in P. tricornutum indicates that this diatom does not perform a C4-like CCM.
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Affiliation(s)
- Daniela Ewe
- Fachbereich Biologie, Universität Konstanz, 78457, Konstanz, Germany.
- Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic.
| | - Masaaki Tachibana
- Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, 669-1337, Japan
- Lion Corporation Pharmaceutical Laboratories No.1, Odawara, Kanagawa, 256-0811, Japan
| | - Sae Kikutani
- Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, 669-1337, Japan
- Tech Manage Corp., Tokyo, 160-0023, Japan
| | - Ansgar Gruber
- Fachbereich Biologie, Universität Konstanz, 78457, Konstanz, Germany
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czech Republic
| | | | - Grzegorz Konert
- Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus-Givat Ram, Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Yusuke Matsuda
- Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, 669-1337, Japan
| | - Peter G Kroth
- Fachbereich Biologie, Universität Konstanz, 78457, Konstanz, Germany
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10
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Abrahamian M, Kagda M, Ah-Fong AMV, Judelson HS. Rethinking the evolution of eukaryotic metabolism: novel cellular partitioning of enzymes in stramenopiles links serine biosynthesis to glycolysis in mitochondria. BMC Evol Biol 2017; 17:241. [PMID: 29202688 PMCID: PMC5715807 DOI: 10.1186/s12862-017-1087-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/21/2017] [Indexed: 12/17/2022] Open
Abstract
Background An important feature of eukaryotic evolution is metabolic compartmentalization, in which certain pathways are restricted to the cytosol or specific organelles. Glycolysis in eukaryotes is described as a cytosolic process. The universality of this canon has been challenged by recent genome data that suggest that some glycolytic enzymes made by stramenopiles bear mitochondrial targeting peptides. Results Mining of oomycete, diatom, and brown algal genomes indicates that stramenopiles encode two forms of enzymes for the second half of glycolysis, one with and the other without mitochondrial targeting peptides. The predicted mitochondrial targeting was confirmed by using fluorescent tags to localize phosphoglycerate kinase, phosphoglycerate mutase, and pyruvate kinase in Phytophthora infestans, the oomycete that causes potato blight. A genome-wide search for other enzymes with atypical mitochondrial locations identified phosphoglycerate dehydrogenase, phosphoserine aminotransferase, and phosphoserine phosphatase, which form a pathway for generating serine from the glycolytic intermediate 3-phosphoglycerate. Fluorescent tags confirmed the delivery of these serine biosynthetic enzymes to P. infestans mitochondria. A cytosolic form of this serine biosynthetic pathway, which occurs in most eukaryotes, is missing from oomycetes and most other stramenopiles. The glycolysis and serine metabolism pathways of oomycetes appear to be mosaics of enzymes with different ancestries. While some of the noncanonical oomycete mitochondrial enzymes have the closest affinity in phylogenetic analyses with proteins from other stramenopiles, others cluster with bacterial, plant, or animal proteins. The genes encoding the mitochondrial phosphoglycerate kinase and serine-forming enzymes are physically linked on oomycete chromosomes, which suggests a shared origin. Conclusions Stramenopile metabolism appears to have been shaped through the acquisition of genes by descent and lateral or endosymbiotic gene transfer, along with the targeting of the proteins to locations that are novel compared to other eukaryotes. Colocalization of the glycolytic and serine biosynthesis enzymes in mitochondria is apparently necessary since they share a common intermediate. The results indicate that descriptions of metabolism in textbooks do not cover the full diversity of eukaryotic biology. Electronic supplementary material The online version of this article (10.1186/s12862-017-1087-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Melania Abrahamian
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Meenakshi Kagda
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Audrey M V Ah-Fong
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA.
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11
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Jensen E, Clément R, Maberly SC, Gontero B. Regulation of the Calvin-Benson-Bassham cycle in the enigmatic diatoms: biochemical and evolutionary variations on an original theme. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160401. [PMID: 28717027 PMCID: PMC5516110 DOI: 10.1098/rstb.2016.0401] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2016] [Indexed: 01/19/2023] Open
Abstract
In Plantae, the Calvin-Benson-Bassham (CBB) cycle is highly regulated and most of its enzymes have been thoroughly studied. Since diatoms arose as a result of secondary endosymbiosis with one or more Plantae ancestors, their precise evolutionary history is enigmatic and complex resulting in biochemical variations on the original CBB cycle theme. The Rubisco Michaelis constant for CO2 is higher in diatoms than land plants and the nuclear-encoded Rubisco activase in Plantae is replaced by an analogous chloroplast-encoded CbbX (Calvin-Benson-Bassham protein X) in diatoms. In the CBB cycle reduction phase, phosphoglycerate kinase in diatoms is redox-regulated and similar to that in red algae; however, glyceraldehyde phosphate dehydrogenase (GAPDH) is not redox-regulated, unlike in Plantae. The phosphoribulokinase (PRK)-GAPDH-CP12 complex found in many photosynthetic organisms has not yet been found in diatoms, but a ferredoxin-NADP reductase (FNR)-GAPDH-CP12 complex has been found in one species. In the CBB cycle regeneration phase, sedoheptulose 1,7-bisphosphatase and PRK are not redox-regulated in diatoms, unlike in Plantae. Regulation at the transcriptional level seems to be important in diatoms. CBB cycle enzyme properties appear to be variable among diatoms, but this view relies on results from a few model species: a greater range of diatoms need to be studied to test this.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.
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Affiliation(s)
- Erik Jensen
- Aix Marseille Univ CNRS, BIP UMR 7281, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Romain Clément
- Aix Marseille Univ CNRS, BIP UMR 7281, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Stephen C Maberly
- Lake Ecosystems Group, Centre for Ecology and Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster LA1 4AP, UK
| | - Brigitte Gontero
- Aix Marseille Univ CNRS, BIP UMR 7281, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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12
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Heydarizadeh P, Boureba W, Zahedi M, Huang B, Moreau B, Lukomska E, Couzinet-Mossion A, Wielgosz-Collin G, Martin-Jézéquel V, Bougaran G, Marchand J, Schoefs B. Response of CO 2-starved diatom Phaeodactylum tricornutum to light intensity transition. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160396. [PMID: 28717022 PMCID: PMC5516105 DOI: 10.1098/rstb.2016.0396] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2017] [Indexed: 12/13/2022] Open
Abstract
In this study, we investigated the responses of Phaeodactylum tricornutum cells acclimated to 300 µmol m-2 s-1 photon flux density to an increase (1000 µmol m-2 s-1) or decrease (30 µmol m-2 s-1) in photon flux densities. The light shift occurred abruptly after 5 days of growth and the acclimation to new conditions was followed during the next 6 days at the physiological and molecular levels. The molecular data reflect a rearrangement of carbon metabolism towards the production of phosphoenolpyruvic acid (PEP) and/or pyruvate. These intermediates were used differently by the cell as a function of the photon flux density: under low light, photosynthesis was depressed while respiration was increased. Under high light, lipids and proteins accumulated. Of great interest, under high light, the genes coding for the synthesis of aromatic amino acids and phenolic compounds were upregulated suggesting that the shikimate pathway was activated.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.
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Affiliation(s)
- Parisa Heydarizadeh
- Metabolism, Bioengineering of Microalga Molecules and Applications (MIMMA), Mer Molécules Santé, UBL, IUML-FR 3473 CNRS, University of Le Mans, 72085 Le Mans, France
| | - Wafâa Boureba
- Metabolism, Bioengineering of Microalga Molecules and Applications (MIMMA), Mer Molécules Santé, UBL, IUML-FR 3473 CNRS, University of Le Mans, 72085 Le Mans, France
| | - Morteza Zahedi
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Bing Huang
- Metabolism, Bioengineering of Microalga Molecules and Applications (MIMMA), Mer Molécules Santé, UBL, IUML-FR 3473 CNRS, University of Le Mans, 72085 Le Mans, France
| | - Brigitte Moreau
- Metabolism, Bioengineering of Microalga Molecules and Applications (MIMMA), Mer Molécules Santé, UBL, IUML-FR 3473 CNRS, University of Le Mans, 72085 Le Mans, France
| | - Ewa Lukomska
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, BP 21105, 44311 Nantes, France
| | - Aurélie Couzinet-Mossion
- Faculté des Sciences Pharmaceutiques et Biologiques, Université de Nantes, Groupe Mer, Molécules, Santé-EA 2160, Institut Universitaire Mer et Littoral FR3473 CNRS, 9 rue Bias, BP 61112, 44035 Nantes Cedex 1, France
| | - Gaëtane Wielgosz-Collin
- Faculté des Sciences Pharmaceutiques et Biologiques, Université de Nantes, Groupe Mer, Molécules, Santé-EA 2160, Institut Universitaire Mer et Littoral FR3473 CNRS, 9 rue Bias, BP 61112, 44035 Nantes Cedex 1, France
| | | | - Gaël Bougaran
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, BP 21105, 44311 Nantes, France
| | - Justine Marchand
- Metabolism, Bioengineering of Microalga Molecules and Applications (MIMMA), Mer Molécules Santé, UBL, IUML-FR 3473 CNRS, University of Le Mans, 72085 Le Mans, France
| | - Benoît Schoefs
- Metabolism, Bioengineering of Microalga Molecules and Applications (MIMMA), Mer Molécules Santé, UBL, IUML-FR 3473 CNRS, University of Le Mans, 72085 Le Mans, France
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13
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Martin WF, Cerff R. Physiology, phylogeny, early evolution, and GAPDH. PROTOPLASMA 2017; 254:1823-1834. [PMID: 28265765 PMCID: PMC5610209 DOI: 10.1007/s00709-017-1095-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/22/2017] [Indexed: 05/23/2023]
Abstract
The chloroplast and cytosol of plant cells harbor a number of parallel biochemical reactions germane to the Calvin cycle and glycolysis, respectively. These reactions are catalyzed by nuclear encoded, compartment-specific isoenzymes that differ in their physiochemical properties. The chloroplast cytosol isoenzymes of D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) harbor evidence of major events in the history of life: the origin of the first genes, the bacterial-archaeal split, the origin of eukaryotes, the evolution of protein compartmentation during eukaryote evolution, the origin of plastids, and the secondary endosymbiosis among the algae with complex plastids. The reaction mechanism of GAPDH entails phosphorolysis of a thioester to yield an energy-rich acyl phosphate bond, a chemistry that points to primitive pathways of energy conservation that existed even before the origin of the first free-living cells. Here, we recount the main insights that chloroplast and cytosolic GAPDH provided into endosymbiosis and physiological evolution.
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Affiliation(s)
- William F. Martin
- Institute of Molecular Evolution, University of Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Rüdiger Cerff
- Institute of Genetics, Technical University of Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
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14
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Ah-Fong AMV, Kim KS, Judelson HS. RNA-seq of life stages of the oomycete Phytophthora infestans reveals dynamic changes in metabolic, signal transduction, and pathogenesis genes and a major role for calcium signaling in development. BMC Genomics 2017; 18:198. [PMID: 28228125 PMCID: PMC5322657 DOI: 10.1186/s12864-017-3585-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 02/13/2017] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The oomycete Phytophthora infestans causes the devastating late blight diseases of potato and tomato. P. infestans uses spores for dissemination and infection, like many other filamentous eukaryotic plant pathogens. The expression of a subset of its genes during spore formation and germination were studied previously, but comprehensive genome-wide data have not been available. RESULTS RNA-seq was used to profile hyphae, sporangia, sporangia undergoing zoosporogenesis, motile zoospores, and germinated cysts of P. infestans. Parallel studies of two isolates generated robust expression calls for 16,000 of 17,797 predicted genes, with about 250 transcribed in one isolate but not the other. The largest changes occurred in the transition from hyphae to sporangia, when >4200 genes were up-regulated. More than 1350 of these were induced >100-fold, accounting for 26% of total mRNA. Genes encoding calcium-binding proteins, cation channels, signaling proteins, and flagellar proteins were over-represented in genes up-regulated in sporangia. Proteins associated with pathogenicity were transcribed in waves with subclasses induced during zoosporogenesis, in zoospores, or in germinated cysts. Genes involved in most metabolic pathways were down-regulated upon sporulation and reactivated during cyst germination, although there were exceptions such as DNA replication, where transcripts peaked in zoospores. Inhibitor studies indicated that the transcription of two-thirds of genes induced during zoosporogenesis relied on calcium signaling. A sporulation-induced protein kinase was shown to bind a constitutive Gβ-like protein, which contributed to fitness based on knock-down analysis. CONCLUSIONS Spore formation and germination involves the staged expression of a large subset of the transcriptome, commensurate with the importance of spores in the life cycle. A comparison of the RNA-seq results with the older microarray data indicated that information is now available for about twice the number of genes than before. Analyses based on function revealed dynamic changes in genes involved in pathogenicity, metabolism, and signaling, with diversity in expression observed within members of multigene families and between isolates. The effects of calcium signaling, a spore-induced protein kinase, and an interacting Gβ-like protein were also demonstrated experimentally. The results reveal aspects of oomycete biology that underly their success as pathogens and potential targets for crop protection chemicals.
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Affiliation(s)
- Audrey M. V. Ah-Fong
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
| | - Kyoung Su Kim
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
- Present address: Department of Applied Biology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Korea
| | - Howard S. Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
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15
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Gawryluk RMR, Kamikawa R, Stairs CW, Silberman JD, Brown MW, Roger AJ. The Earliest Stages of Mitochondrial Adaptation to Low Oxygen Revealed in a Novel Rhizarian. Curr Biol 2016; 26:2729-2738. [PMID: 27666965 DOI: 10.1016/j.cub.2016.08.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/21/2016] [Accepted: 08/09/2016] [Indexed: 12/26/2022]
Abstract
Mitochondria exist on a functional and evolutionary continuum that includes anaerobic mitochondrion-related organelles (MROs), such as hydrogenosomes. Hydrogenosomes lack many classical mitochondrial features, including conspicuous cristae, mtDNA, the tricarboxylic acid (TCA) cycle, and ATP synthesis powered by an electron transport chain (ETC); instead, they produce ATP anaerobically, liberating H2 and CO2 gas in the process. However, our understanding of the evolutionary transformation from aerobic mitochondria to various MRO types remains incomplete. Here we describe a novel MRO from a cercomonad (Brevimastigomonas motovehiculus n. sp.; Rhizaria). We have sequenced its 30,608-bp mtDNA and characterized organelle function through a combination of transcriptomic, genomic, and cell biological approaches. B. motovehiculus MROs are metabolically versatile, retaining mitochondrial metabolic pathways, such as a TCA cycle and ETC-driven ATP synthesis, but also possessing hydrogenosomal-type pyruvate metabolism and substrate-level phosphorylation. Notably, the B. motovehiculus ETC is degenerate and appears to be losing cytochrome-based electron transport (complexes III and IV). Furthermore, the F1Fo ATP synthase (complex V) is unique, with the highly conserved Atpα subunit fragmented into four separate pieces. The B. motovehiculus MRO appears to be in the process of losing aerobic metabolic capacities. Our findings shed light on the transition between organelle types, specifically the early stages of mitochondrial adaptation to anaerobiosis.
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Affiliation(s)
- Ryan M R Gawryluk
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Ryoma Kamikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan; Graduate School of Global Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Courtney W Stairs
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Jeffrey D Silberman
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Halifax, NS B3H 4R2, Canada.
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16
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Using Proteomics to Understand How Leishmania Parasites Survive inside the Host and Establish Infection. Int J Mol Sci 2016; 17:ijms17081270. [PMID: 27548150 PMCID: PMC5000668 DOI: 10.3390/ijms17081270] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 06/21/2016] [Accepted: 07/26/2016] [Indexed: 12/15/2022] Open
Abstract
Leishmania is a protozoan parasite that causes a wide range of different clinical manifestations in mammalian hosts. It is a major public health risk on different continents and represents one of the most important neglected diseases. Due to the high toxicity of the drugs currently used, and in the light of increasing drug resistance, there is a critical need to develop new drugs and vaccines to control Leishmania infection. Over the past few years, proteomics has become an important tool to understand the underlying biology of Leishmania parasites and host interaction. The large-scale study of proteins, both in parasites and within the host in response to infection, can accelerate the discovery of new therapeutic targets. By studying the proteomes of host cells and tissues infected with Leishmania, as well as changes in protein profiles among promastigotes and amastigotes, scientists hope to better understand the biology involved in the parasite survival and the host-parasite interaction. This review demonstrates the feasibility of proteomics as an approach to identify new proteins involved in Leishmania differentiation and intracellular survival.
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17
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Levering J, Broddrick J, Dupont CL, Peers G, Beeri K, Mayers J, Gallina AA, Allen AE, Palsson BO, Zengler K. Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom. PLoS One 2016; 11:e0155038. [PMID: 27152931 PMCID: PMC4859558 DOI: 10.1371/journal.pone.0155038] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/22/2016] [Indexed: 11/18/2022] Open
Abstract
Diatoms are eukaryotic microalgae that contain genes from various sources, including bacteria and the secondary endosymbiotic host. Due to this unique combination of genes, diatoms are taxonomically and functionally distinct from other algae and vascular plants and confer novel metabolic capabilities. Based on the genome annotation, we performed a genome-scale metabolic network reconstruction for the marine diatom Phaeodactylum tricornutum. Due to their endosymbiotic origin, diatoms possess a complex chloroplast structure which complicates the prediction of subcellular protein localization. Based on previous work we implemented a pipeline that exploits a series of bioinformatics tools to predict protein localization. The manually curated reconstructed metabolic network iLB1027_lipid accounts for 1,027 genes associated with 4,456 reactions and 2,172 metabolites distributed across six compartments. To constrain the genome-scale model, we determined the organism specific biomass composition in terms of lipids, carbohydrates, and proteins using Fourier transform infrared spectrometry. Our simulations indicate the presence of a yet unknown glutamine-ornithine shunt that could be used to transfer reducing equivalents generated by photosynthesis to the mitochondria. The model reflects the known biochemical composition of P. tricornutum in defined culture conditions and enables metabolic engineering strategies to improve the use of P. tricornutum for biotechnological applications.
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Affiliation(s)
- Jennifer Levering
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Jared Broddrick
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | | | - Graham Peers
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Karen Beeri
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Joshua Mayers
- Division of Industrial Biotechnology, Department of Biology and Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Alessandra A. Gallina
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Andrew E. Allen
- J. Craig Venter Institute, La Jolla, California, United States of America
- Integrative Oceanography Division, Scripps Institute of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Karsten Zengler
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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18
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Kim J, Fabris M, Baart G, Kim MK, Goossens A, Vyverman W, Falkowski PG, Lun DS. Flux balance analysis of primary metabolism in the diatom Phaeodactylum tricornutum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:161-176. [PMID: 26590126 DOI: 10.1111/tpj.13081] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 11/04/2015] [Accepted: 11/09/2015] [Indexed: 06/05/2023]
Abstract
Diatoms (Bacillarophyceae) are photosynthetic unicellular microalgae that have risen to ecological prominence in oceans over the past 30 million years. They are of interest as potential feedstocks for sustainable biofuels. Maximizing production of these feedstocks will require genetic modifications and an understanding of algal metabolism. These processes may benefit from genome-scale models, which predict intracellular fluxes and theoretical yields, as well as the viability of knockout and knock-in transformants. Here we present a genome-scale metabolic model of a fully sequenced and transformable diatom: Phaeodactylum tricornutum. The metabolic network was constructed using the P. tricornutum genome, biochemical literature, and online bioinformatic databases. Intracellular fluxes in P. tricornutum were calculated for autotrophic, mixotrophic and heterotrophic growth conditions, as well as knockout conditions that explore the in silico role of glycolytic enzymes in the mitochondrion. The flux distribution for lower glycolysis in the mitochondrion depended on which transporters for TCA cycle metabolites were included in the model. The growth rate predictions were validated against experimental data obtained using chemostats. Two published studies on this organism were used to validate model predictions for cyclic electron flow under autotrophic conditions, and fluxes through the phosphoketolase, glycine and serine synthesis pathways under mixotrophic conditions. Several gaps in annotation were also identified. The model also explored unusual features of diatom metabolism, such as the presence of lower glycolysis pathways in the mitochondrion, as well as differences between P. tricornutum and other photosynthetic organisms.
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Affiliation(s)
- Joomi Kim
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Michele Fabris
- Plant Functional Biology and Climate Change Cluster (C3), Faculty of Science University of Technology, Sydney, New South Wales, Australia
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Gent, Belgium
- Department of Biology, Laboratory of Protistology and Aquatic Ecology, Ghent University, B-9000, Gent, Belgium
| | - Gino Baart
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Gent, Belgium
- Department of Biology, Laboratory of Protistology and Aquatic Ecology, Ghent University, B-9000, Gent, Belgium
- Centre of Microbial and Plant Genetics Lab for Genetics and Genomics and Leuven Institute for Beer Research, Leuven University, Gaston Geenslaan 1, B-3001, Leuven, Belgium
| | - Min K Kim
- Center for Computational and Integrative Biology and Department of Computer Science, Rutgers University, Camden, NJ, 08102, USA
| | - Alain Goossens
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Gent, Belgium
| | - Wim Vyverman
- Department of Biology, Laboratory of Protistology and Aquatic Ecology, Ghent University, B-9000, Gent, Belgium
| | - Paul G Falkowski
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Desmond S Lun
- Center for Computational and Integrative Biology and Department of Computer Science, Rutgers University, Camden, NJ, 08102, USA
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, 08901, USA
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, South Australia, Australia
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19
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Gruber A, Rocap G, Kroth PG, Armbrust EV, Mock T. Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:519-28. [PMID: 25438865 PMCID: PMC4329603 DOI: 10.1111/tpj.12734] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 11/19/2014] [Accepted: 11/26/2014] [Indexed: 05/19/2023]
Abstract
The plastids of ecologically and economically important algae from phyla such as stramenopiles, dinoflagellates and cryptophytes were acquired via a secondary endosymbiosis and are surrounded by three or four membranes. Nuclear-encoded plastid-localized proteins contain N-terminal bipartite targeting peptides with the conserved amino acid sequence motif 'ASAFAP'. Here we identify the plastid proteomes of two diatoms, Thalassiosira pseudonana and Phaeodactylum tricornutum, using a customized prediction tool (ASAFind) that identifies nuclear-encoded plastid proteins in algae with secondary plastids of the red lineage based on the output of SignalP and the identification of conserved 'ASAFAP' motifs and transit peptides. We tested ASAFind against a large reference dataset of diatom proteins with experimentally confirmed subcellular localization and found that the tool accurately identified plastid-localized proteins with both high sensitivity and high specificity. To identify nucleus-encoded plastid proteins of T. pseudonana and P. tricornutum we generated optimized sets of gene models for both whole genomes, to increase the percentage of full-length proteins compared with previous assembly model sets. ASAFind applied to these optimized sets revealed that about 8% of the proteins encoded in their nuclear genomes were predicted to be plastid localized and therefore represent the putative plastid proteomes of these algae.
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Affiliation(s)
- Ansgar Gruber
- Fachbereich Biologie, Universität KonstanzKonstanz, 78457, Germany
| | - Gabrielle Rocap
- School of Oceanography, Center for Environmental Genomics, University of WashingtonSeattle, WA, 98195, USA
| | - Peter G Kroth
- Fachbereich Biologie, Universität KonstanzKonstanz, 78457, Germany
| | - E Virginia Armbrust
- School of Oceanography, Center for Environmental Genomics, University of WashingtonSeattle, WA, 98195, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East AngliaNorwich Research Park, NR4 7TJ, Norwich, UK
- *
For correspondence (e-mail )
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20
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Moriyama T, Sakurai K, Sekine K, Sato N. Subcellular distribution of central carbohydrate metabolism pathways in the red alga Cyanidioschyzon merolae. PLANTA 2014; 240:585-98. [PMID: 25009310 DOI: 10.1007/s00425-014-2108-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/10/2014] [Indexed: 05/19/2023]
Abstract
Comprehensive subcellular localization analysis revealed that the subcellular distribution of carbohydrate metabolic pathways in the red alga Cyanidioschyzon is essentially identical with that in Arabidopsis , except the lack of transaldolase. In plants, the glycolysis and oxidative pentose phosphate pathways (oxPPP) are located in both cytosol and plastids. However, in algae, particularly red algae, the subcellular localization of enzymes involved in carbon metabolism is unclear. Here, we identified and examined the localization of enzymes related to glycolysis, oxPPP, and tricarboxylic acid (TCA) and Calvin-Benson cycles in the red alga Cyanidioschyzon merolae. A gene encoding transaldolase of the oxPPP was not found in the C. merolae genome, and no transaldolase activity was detected in cellular extracts. The subcellular localization of 65 carbon metabolic enzymes tagged with green fluorescent protein or hemagglutinin was examined in C. merolae cells. As expected, TCA and Calvin-Benson cycle enzymes were localized to mitochondria and plastids, respectively. The analyses also revealed that the cytosol contains the entire glycolytic pathway and partial oxPPP, whereas the plastid contains a partial glycolytic pathway and complete oxPPP, with the exception of transaldolase. Together, these results suggest that the subcellular distribution of carbohydrate metabolic pathways in C. merolae is essentially identical with that reported in the photosynthetic tissue of Arabidopsis thaliana; however, it appears that substrates typically utilized by transaldolase are consumed by glycolytic enzymes in the plastidic oxPPP of C. merolae.
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Affiliation(s)
- Takashi Moriyama
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo, 153-8902, Japan,
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Brown RWB, Collingridge PW, Gull K, Rigden DJ, Ginger ML. Evidence for loss of a partial flagellar glycolytic pathway during trypanosomatid evolution. PLoS One 2014; 9:e103026. [PMID: 25050549 PMCID: PMC4106842 DOI: 10.1371/journal.pone.0103026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 06/27/2014] [Indexed: 11/18/2022] Open
Abstract
Classically viewed as a cytosolic pathway, glycolysis is increasingly recognized as a metabolic pathway exhibiting surprisingly wide-ranging variations in compartmentalization within eukaryotic cells. Trypanosomatid parasites provide an extreme view of glycolytic enzyme compartmentalization as several glycolytic enzymes are found exclusively in peroxisomes. Here, we characterize Trypanosoma brucei flagellar proteins resembling glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoglycerate kinase (PGK): we show the latter associates with the axoneme and the former is a novel paraflagellar rod component. The paraflagellar rod is an essential extra-axonemal structure in trypanosomes and related protists, providing a platform into which metabolic activities can be built. Yet, bioinformatics interrogation and structural modelling indicate neither the trypanosome PGK-like nor the GAPDH-like protein is catalytically active. Orthologs are present in a free-living ancestor of the trypanosomatids, Bodo saltans: the PGK-like protein from B. saltans also lacks key catalytic residues, but its GAPDH-like protein is predicted to be catalytically competent. We discuss the likelihood that the trypanosome GAPDH-like and PGK-like proteins constitute molecular evidence for evolutionary loss of a flagellar glycolytic pathway, either as a consequence of niche adaptation or the re-localization of glycolytic enzymes to peroxisomes and the extensive changes to glycolytic flux regulation that accompanied this re-localization. Evidence indicating loss of localized ATP provision via glycolytic enzymes therefore provides a novel contribution to an emerging theme of hidden diversity with respect to compartmentalization of the ubiquitous glycolytic pathway in eukaryotes. A possibility that trypanosome GAPDH-like protein additionally represents a degenerate example of a moonlighting protein is also discussed.
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Affiliation(s)
- Robert W. B. Brown
- Faculty of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
| | | | - Keith Gull
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Michael L. Ginger
- Faculty of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
- * E-mail:
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Mekhalfi M, Puppo C, Avilan L, Lebrun R, Mansuelle P, Maberly SC, Gontero B. Glyceraldehyde-3-phosphate dehydrogenase is regulated by ferredoxin-NADP reductase in the diatom Asterionella formosa. THE NEW PHYTOLOGIST 2014; 203:414-423. [PMID: 24799178 DOI: 10.1111/nph.12820] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 03/22/2014] [Indexed: 05/24/2023]
Abstract
Diatoms are a widespread and ecologically important group of heterokont algae that contribute c. 20% to global productivity. Previous work has shown that regulation of their key Calvin cycle enzymes differs from that of the Plantae, and that in crude extracts, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) can be inhibited by nicotinamide adenine dinucleotide phosphate reduced (NADPH) under oxidizing conditions. The freshwater diatom, Asterionella formosa, was studied using enzyme kinetics, chromatography, surface plasmon resonance, mass spectrometry and sequence analysis to determine the mechanism behind this GAPDH inhibition. GAPDH interacted with ferredoxin-nicotinamide adenine dinucleotide phosphate (NADP) reductase (FNR) from the primary phase of photosynthesis, and the small chloroplast protein, CP12. Sequences of copurified GAPDH and FNR were highly homologous with published sequences. However, the widespread ternary complex among GAPDH, phosphoribulokinase and CP12 was absent. Activity measurements under oxidizing conditions showed that NADPH can inhibit GAPDH-CP12 in the presence of FNR, explaining the earlier observed inhibition within crude extracts. Diatom plastids have a distinctive metabolism, including the lack of the oxidative pentose phosphate pathway, and so cannot produce NADPH in the dark. The observed down-regulation of GAPDH in the dark may allow NADPH to be rerouted towards other reductive processes contributing to their ecological success.
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Affiliation(s)
- Malika Mekhalfi
- Aix-Marseille Université CNRS, BIP UMR 7281, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
| | - Carine Puppo
- Aix-Marseille Université CNRS, BIP UMR 7281, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
| | - Luisana Avilan
- Aix-Marseille Université CNRS, BIP UMR 7281, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
| | - Régine Lebrun
- Plate-forme Protéomique, FR3479, IBiSA Marseille-Protéomique IMM-CNRS, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
| | - Pascal Mansuelle
- Plate-forme Protéomique, FR3479, IBiSA Marseille-Protéomique IMM-CNRS, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
| | - Stephen C Maberly
- Centre for Ecology & Hydrology, Lake Ecosystems Group, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, UK
| | - Brigitte Gontero
- Aix-Marseille Université CNRS, BIP UMR 7281, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
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Light acclimation in diatoms: from phenomenology to mechanisms. Mar Genomics 2014; 16:5-15. [PMID: 24412570 DOI: 10.1016/j.margen.2013.12.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 11/04/2013] [Accepted: 12/12/2013] [Indexed: 01/02/2023]
Abstract
This review summarizes the current knowledge about light acclimation processes in diatoms. Against the background of the phenomenological description of the process in the 70s-80s, the recent progress in diatom genetics has generated new information about the underlying mechanisms. Although the general responses of diatoms to changes in the light climate are comparable to the green algal lineage, many differences in the underlying mechanisms have been observed in the last ten years, yielding clear evidence that the regulatory network in diatoms has unique traits that might explain their ecological success.
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24
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Gruber A, Kroth PG. Deducing intracellular distributions of metabolic pathways from genomic data. Methods Mol Biol 2014; 1083:187-211. [PMID: 24218217 DOI: 10.1007/978-1-62703-661-0_12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In the recent years, a large number of genomes from a variety of different organisms have been sequenced. Most of the sequence data has been publicly released and can be assessed by interested users. However, this wealth of information is currently underexploited by scientists not directly involved in genome annotation. This is partially because sequencing, assembly, and automated annotation can be done much faster than the identification, classification, and prediction of the intracellular localization of the gene products. This part of the annotation process still largely relies on manual curation and addition of contextual information. Users of genome databases who are unfamiliar with the types of data available from (whole) genomes might therefore find themselves either overwhelmed by the vast amount and multiple layers of data or dissatisfied with less-than-meaningful analyses of the data.In this chapter we present procedures and approaches to identify and characterize gene models of enzymes involved in metabolic pathways based on their similarity to known sequences. Furthermore we describe how to predict the subcellular location of the proteins using publicly available prediction servers and how to interpret the obtained results. The strategies we describe are generally applicable to organisms with primary plastids such as land plants or green algae. Additionally, we describe strategies suitable for those groups of algae with secondary plastids (for instance diatoms), which are characterized by a different cellular topology and a larger number of intracellular compartments compared to plants.
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Affiliation(s)
- Ansgar Gruber
- Fachbereich Biologie, Universität Konstanz, Konstanz, Germany
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25
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Michelet L, Zaffagnini M, Morisse S, Sparla F, Pérez-Pérez ME, Francia F, Danon A, Marchand CH, Fermani S, Trost P, Lemaire SD. Redox regulation of the Calvin-Benson cycle: something old, something new. FRONTIERS IN PLANT SCIENCE 2013; 4:470. [PMID: 24324475 PMCID: PMC3838966 DOI: 10.3389/fpls.2013.00470] [Citation(s) in RCA: 259] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 10/30/2013] [Indexed: 05/18/2023]
Abstract
Reversible redox post-translational modifications such as oxido-reduction of disulfide bonds, S-nitrosylation, and S-glutathionylation, play a prominent role in the regulation of cell metabolism and signaling in all organisms. These modifications are mainly controlled by members of the thioredoxin and glutaredoxin families. Early studies in photosynthetic organisms have identified the Calvin-Benson cycle, the photosynthetic pathway responsible for carbon assimilation, as a redox regulated process. Indeed, 4 out of 11 enzymes of the cycle were shown to have a low activity in the dark and to be activated in the light through thioredoxin-dependent reduction of regulatory disulfide bonds. The underlying molecular mechanisms were extensively studied at the biochemical and structural level. Unexpectedly, recent biochemical and proteomic studies have suggested that all enzymes of the cycle and several associated regulatory proteins may undergo redox regulation through multiple redox post-translational modifications including glutathionylation and nitrosylation. The aim of this review is to detail the well-established mechanisms of redox regulation of Calvin-Benson cycle enzymes as well as the most recent reports indicating that this pathway is tightly controlled by multiple interconnected redox post-translational modifications. This redox control is likely allowing fine tuning of the Calvin-Benson cycle required for adaptation to varying environmental conditions, especially during responses to biotic and abiotic stresses.
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Affiliation(s)
- Laure Michelet
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, FRE3354 Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Université Pierre et Marie CurieParis, France
| | - Mirko Zaffagnini
- Laboratory of Plant Redox Biology, Department of Pharmacy and Biotechnology (FaBiT), University of BolognaBologna, Italy
| | - Samuel Morisse
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, FRE3354 Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Université Pierre et Marie CurieParis, France
| | - Francesca Sparla
- Laboratory of Plant Redox Biology, Department of Pharmacy and Biotechnology (FaBiT), University of BolognaBologna, Italy
| | - María Esther Pérez-Pérez
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, FRE3354 Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Université Pierre et Marie CurieParis, France
| | - Francesco Francia
- Laboratory of Plant Redox Biology, Department of Pharmacy and Biotechnology (FaBiT), University of BolognaBologna, Italy
| | - Antoine Danon
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, FRE3354 Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Université Pierre et Marie CurieParis, France
| | - Christophe H. Marchand
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, FRE3354 Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Université Pierre et Marie CurieParis, France
| | - Simona Fermani
- Department of Chemistry “G. Ciamician”, University of BolognaBologna, Italy
| | - Paolo Trost
- Laboratory of Plant Redox Biology, Department of Pharmacy and Biotechnology (FaBiT), University of BolognaBologna, Italy
| | - Stéphane D. Lemaire
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, FRE3354 Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Université Pierre et Marie CurieParis, France
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Hildebrand M, Abbriano RM, Polle JEW, Traller JC, Trentacoste EM, Smith SR, Davis AK. Metabolic and cellular organization in evolutionarily diverse microalgae as related to biofuels production. Curr Opin Chem Biol 2013; 17:506-14. [PMID: 23538202 DOI: 10.1016/j.cbpa.2013.02.027] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 02/18/2013] [Accepted: 02/26/2013] [Indexed: 12/18/2022]
Abstract
Microalgae are among the most diverse organisms on the planet, and as a result of symbioses and evolutionary selection, the configuration of core metabolic networks is highly varied across distinct algal classes. The differences in photosynthesis, carbon fixation and processing, carbon storage, and the compartmentation of cellular and metabolic processes are substantial and likely to transcend into the efficiency of various steps involved in biofuel molecule production. By highlighting these differences, we hope to provide a framework for comparative analyses to determine the efficiency of the different arrangements or processes. This sets the stage for optimization on the based on information derived from evolutionary selection to diverse algal classes and to synthetic systems.
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Affiliation(s)
- Mark Hildebrand
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202, USA.
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Chauton MS, Winge P, Brembu T, Vadstein O, Bones AM. Gene regulation of carbon fixation, storage, and utilization in the diatom Phaeodactylum tricornutum acclimated to light/dark cycles. PLANT PHYSIOLOGY 2013; 161:1034-48. [PMID: 23209127 PMCID: PMC3561001 DOI: 10.1104/pp.112.206177] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The regulation of carbon metabolism in the diatom Phaeodactylum tricornutum at the cell, metabolite, and gene expression levels in exponential fed-batch cultures is reported. Transcriptional profiles and cell chemistry sampled simultaneously at all time points provide a comprehensive data set on carbon incorporation, fate, and regulation. An increase in Nile Red fluorescence (a proxy for cellular neutral lipids) was observed throughout the light period, and water-soluble glucans increased rapidly in the light period. A near-linear decline in both glucans and lipids was observed during the dark period, and transcription profile data indicated that this decline was associated with the onset of mitosis. More than 4,500 transcripts that were differentially regulated during the light/dark cycle are identified, many of which were associated with carbohydrate and lipid metabolism. Genes not previously described in algae and their regulation in response to light were integrated in this analysis together with proposed roles in metabolic processes. Some very fast light-responding genes in, for example, fatty acid biosynthesis were identified and allocated to biosynthetic processes. Transcripts and cell chemistry data reflect the link between light energy availability and light energy-consuming metabolic processes. Our data confirm the spatial localization of processes in carbon metabolism to either plastids or mitochondria or to glycolysis/gluconeogenesis, which are localized to the cytosol, chloroplast, and mitochondria. Localization and diel expression pattern may be of help to determine the roles of different isoenzymes and the mining of genes involved in light responses and circadian rhythms.
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29
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Nakayama T, Ishida KI, Archibald JM. Broad distribution of TPI-GAPDH fusion proteins among eukaryotes: evidence for glycolytic reactions in the mitochondrion? PLoS One 2012; 7:e52340. [PMID: 23284996 PMCID: PMC3527533 DOI: 10.1371/journal.pone.0052340] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 11/14/2012] [Indexed: 12/25/2022] Open
Abstract
Glycolysis is a central metabolic pathway in eukaryotic and prokaryotic cells. In eukaryotes, the textbook view is that glycolysis occurs in the cytosol. However, fusion proteins comprised of two glycolytic enzymes, triosephosphate isomerase (TPI) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), were found in members of the stramenopiles (diatoms and oomycetes) and shown to possess amino-terminal mitochondrial targeting signals. Here we show that mitochondrial TPI-GAPDH fusion protein genes are widely spread across the known diversity of stramenopiles, including non-photosynthetic species (Bicosoeca sp. and Blastocystis hominis). We also show that TPI-GAPDH fusion genes exist in three cercozoan taxa (Paulinella chromatophora, Thaumatomastix sp. and Mataza hastifera) and an apusozoan protist, Thecamonas trahens. Interestingly, subcellular localization predictions for other glycolytic enzymes in stramenopiles and a cercozoan show that a significant fraction of the glycolytic enzymes in these species have mitochondrial-targeted isoforms. These results suggest that part of the glycolytic pathway occurs inside mitochondria in these organisms, broadening our knowledge of the diversity of mitochondrial metabolism of protists.
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Affiliation(s)
- Takuro Nakayama
- Department of Biochemistry & Molecular Biology, Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ken-ichiro Ishida
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - John M. Archibald
- Department of Biochemistry & Molecular Biology, Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Dalhousie University, Halifax, Nova Scotia, Canada
- * E-mail:
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Joice AC, Lyda TL, Sayce AC, Verplaetse E, Morris MT, Michels PAM, Robinson DR, Morris JC. Extra-glycosomal localisation of Trypanosoma brucei hexokinase 2. Int J Parasitol 2012; 42:401-9. [PMID: 22619756 DOI: 10.1016/j.ijpara.2012.02.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The majority of the glycolytic enzymes in the African trypanosome are compartmentalised within peroxisome-like organelles, the glycosomes. Polypeptides harbouring peroxisomal targeting sequences (PTS type 1 or 2) are targeted to these organelles. This targeting is essential to parasite viability, as compartmentalisation of glycolytic enzymes prevents unregulated ATP-dependent phosphorylation of intermediate metabolites. Here, we report the surprising extra-glycosomal localisation of a PTS-2 bearing trypanosomal hexokinase, TbHK2. In bloodstream form parasites, the protein localises to both glycosomes and to the flagellum. Evidence for this includes fractionation and immunofluorescence studies using antisera generated against the authentic protein as well as detection of epitope-tagged recombinant versions of the protein. In the insect stage parasite, distribution is different, with the polypeptide localised to glycosomes and proximal to the basal bodies. The function of the extra-glycosomal protein remains unclear. While its association with the basal body suggests that it may have a role in locomotion in the insect stage parasite, no detectable defect in directional motility or velocity of cell movement were observed for TbHK2-deficient cells, suggesting that the protein may have a different function in the cell.
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Affiliation(s)
- April C Joice
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 39634, USA
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Ghoshroy S, Robertson DL. MOLECULAR EVOLUTION OF GLUTAMINE SYNTHETASE II AND III IN THE CHROMALVEOLATES(1). JOURNAL OF PHYCOLOGY 2012; 48:768-783. [PMID: 27011094 DOI: 10.1111/j.1529-8817.2012.01169.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Glutamine synthetase (GS) is encoded by three distinct gene families (GSI, GSII, and GSIII) that are broadly distributed among the three domains of life. Previous studies established that GSII and GSIII isoenzymes were expressed in diatoms; however, less is known about the distribution and evolution of the gene families in other chromalveolate lineages. Thus, GSII cDNA sequences were isolated from three cryptophytes (Guillardia theta D. R. A. Hill et Wetherbee, Cryptomonas phaseolus Skuja, and Pyrenomonas helgolandii Santore), and GSIII was sequenced from G. theta. Red algal GSII sequences were obtained from Bangia atropurpurea (Mertens ex Roth) C. Agardh; Compsopogon caeruleus (Balbis ex C. Agardh) Mont.; Flintiella sanguinaria F. D. Ott and Porphyridium aerugineum Geitler; Rhodella violacea (Kornmann) Wehrmeyer and Dixoniella grisea (Geitler) J. L. Scott, S. T. Broadwater, B. D. Saunders, J. P. Thomas et P. W. Gabrielson; and Stylonema alsidii (Zanardini) K. M. Drew. In Bayesian inference and maximum-likelihood (ML) phylogenetic analyses, chromalveolate GSII sequences formed a weakly supported clade that nested among sequences from glaucophytes, red algae, green algae, and plants. Red algal GSII sequences formed two distinct clades. The largest clade contained representatives from the Cyanidiophytina and Rhodophytina and grouped with plants and green algae. The smaller clade (C. caeruleus, Porphyra yezoensis, and S. alsidii) nested within the chromalveolates, although its placement was unresolved. Chromalveolate GSIII sequences formed a well-supported clade in Bayesian and ML phylogenies, and mitochondrial transit peptides were identified in many of the sequences. There was strong support for a stramenopile-haptophyte-cryptophyte GSIII clade in which the cryptophyte sequence diverged from the deepest node. Overall, the evolutionary history of the GS gene families within the algae is complex with evidence for the presence of orthologous and paralogous sequences, ancient and recent gene duplications, gene losses and replacements, and the potential for both endosymbiotic and lateral gene transfers.
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Affiliation(s)
- Sohini Ghoshroy
- Biology Department, Clark University, 950, Main Street, Worcester, MA 01610, USA
| | - Deborah L Robertson
- Biology Department, Clark University, 950, Main Street, Worcester, MA 01610, USA
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Consequences of the presence of 24-epibrassinolide, on cultures of a diatom, Asterionella formosa. Biochimie 2012; 94:1213-20. [DOI: 10.1016/j.biochi.2012.02.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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33
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Comparative analysis of diatom genomes reveals substantial differences in the organization of carbon partitioning pathways. ALGAL RES 2012. [DOI: 10.1016/j.algal.2012.04.003] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kikutani S, Tanaka R, Yamazaki Y, Hara S, Hisabori T, Kroth PG, Matsuda Y. Redox regulation of carbonic anhydrases via thioredoxin in chloroplast of the marine diatom Phaeodactylum tricornutum. J Biol Chem 2012; 287:20689-700. [PMID: 22535967 DOI: 10.1074/jbc.m111.322743] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Thioredoxins (Trxs) are important regulators of photosynthetic fixation of CO(2) and nitrogen in plant chloroplasts. To date, they have been considered to play a minor role in controlling the Calvin cycle in marine diatoms, aquatic primary producers, although diatoms possess a set of plastidic Trxs. In this study we examined the influences of the redox state and the involvement of Trxs in the enzymatic activities of pyrenoidal carbonic anhydrases, PtCA1 and PtCA2, in the marine diatom Phaeodactylum tricornutum. The recombinant mature PtCA1 and -2 (mPtCA1 and -2) were completely inactivated following oxidation by 50 μm CuCl(2), whereas DTT activated CAs in a concentration-dependent manner. The maximum activity of mPtCAs in the presence of 6 mm reduced DTT increased significantly by addition of 10 μm Trxs from Arabidopsis thaliana (AtTrx-f2 and -m2) and 5 μm Trxs from P. tricornutum (PtTrxF and -M). Analyses of mPtCA activation by Trxs in the presence of DTT revealed that the maximum mPtCA1 activity was enhanced ∼3-fold in the presence of Trx, whereas mPtCA2 was only weakly activated by Trxs, and that PtTrxs activate PtCAs more efficiently compared with AtTrxs. Site-directed mutagenesis of potential disulfide-forming cysteines in mPtCA1 and mPtCA2 resulted in a lack of oxidative inactivation of both mPtCAs. These results reveal the first direct evidence of a target of plastidic Trxs in diatoms, indicating that Trxs may participate in the redox control of inorganic carbon flow in the pyrenoid, a focal point of the CO(2)-concentrating mechanism.
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Affiliation(s)
- Sae Kikutani
- Department of Bioscience, Research Center for Environmental Bioscience, Kwansei Gakuin University, Hyogo 669-1337, Japan
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Bosco MB, Aleanzi MC, Iglesias AÁ. Plastidic phosphoglycerate kinase from Phaeodactylum tricornutum: on the critical role of cysteine residues for the enzyme function. Protist 2011; 163:188-203. [PMID: 21816671 DOI: 10.1016/j.protis.2011.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 06/23/2011] [Indexed: 11/15/2022]
Abstract
Chloroplastidic phosphoglycerate kinase (PGKase) plays a key role in photosynthetic organisms, catalyzing a key step in the Calvin cycle. We performed the molecular cloning of the gene encoding chloroplastidic PGKase-1 in the diatom Phaeodactylum tricornutum. The recombinant enzyme was expressed in Escherichia coli, purified and characterized. Afterward, it showed similar kinetic properties than the enzyme studied from other organisms, although the diatom enzyme displayed distinctive responses to sulfhydryl reagents. The activity of the enzyme was found to be dependent on the redox status in the environment, determined by different compounds, including some of physiological function. Treatment with oxidant agents, such as diamide, hydrogen peroxide, glutathione and sodium nitroprusside resulted in enzyme inhibition. Recovery of activity was possible by subsequent incubation with reducing reagents such as dithiothreitol and thioredoxins (from E. coli and P. tricornutum). We determined two midpoint potentials of different regulatory redox centers, both values indicating that PGKase-1 might be sensitive to changes in the intracellular redox environment. The role of all the six Cys residues found in the diatom enzyme was analyzed by molecular modeling and site-directed mutagenesis. Results suggest key regulatory properties for P. tricornutum PGKase-1, which could be relevant for the functioning of photosynthetic carbon metabolism in diatoms.
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Affiliation(s)
- María Belén Bosco
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (IAL, CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Paraje "El Pozo", CC 242, S3000ZAA Santa Fe, Argentina
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36
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Ginger ML, Fritz-Laylin LK, Fulton C, Cande WZ, Dawson SC. Intermediary metabolism in protists: a sequence-based view of facultative anaerobic metabolism in evolutionarily diverse eukaryotes. Protist 2010; 161:642-71. [PMID: 21036663 PMCID: PMC3021972 DOI: 10.1016/j.protis.2010.09.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Protists account for the bulk of eukaryotic diversity. Through studies of gene and especially genome sequences the molecular basis for this diversity can be determined. Evident from genome sequencing are examples of versatile metabolism that go far beyond the canonical pathways described for eukaryotes in textbooks. In the last 2-3 years, genome sequencing and transcript profiling has unveiled several examples of heterotrophic and phototrophic protists that are unexpectedly well-equipped for ATP production using a facultative anaerobic metabolism, including some protists that can (Chlamydomonas reinhardtii) or are predicted (Naegleria gruberi, Acanthamoeba castellanii, Amoebidium parasiticum) to produce H(2) in their metabolism. It is possible that some enzymes of anaerobic metabolism were acquired and distributed among eukaryotes by lateral transfer, but it is also likely that the common ancestor of eukaryotes already had far more metabolic versatility than was widely thought a few years ago. The discussion of core energy metabolism in unicellular eukaryotes is the subject of this review. Since genomic sequencing has so far only touched the surface of protist diversity, it is anticipated that sequences of additional protists may reveal an even wider range of metabolic capabilities, while simultaneously enriching our understanding of the early evolution of eukaryotes.
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Affiliation(s)
- Michael L Ginger
- School of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster LA1 4YQ, UK.
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Michel G, Tonon T, Scornet D, Cock JM, Kloareg B. Central and storage carbon metabolism of the brown alga Ectocarpus siliculosus: insights into the origin and evolution of storage carbohydrates in Eukaryotes. THE NEW PHYTOLOGIST 2010; 188:67-81. [PMID: 20618908 DOI: 10.1111/j.1469-8137.2010.03345.x] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
• Brown algae exhibit a unique carbon (C) storage metabolism. The photoassimilate D-fructose 6-phosphate is not used to produce sucrose but is converted into D-mannitol. These seaweeds also store C as β-1,3-glucan (laminarin), thus markedly departing from most living organisms, which use α-1,4-glucans (glycogen or starch). • Using a combination of bioinformatic and phylogenetic approaches, we identified the candidate genes for the enzymes involved in C storage in the genome of the brown alga Ectocarpus siliculosus and traced their evolutionary origins. • Ectocarpus possesses a complete set of enzymes for synthesis of mannitol, laminarin and trehalose. By contrast, the pathways for sucrose, starch and glycogen are completely absent. • The synthesis of β-1,3-glucans appears to be a very ancient eukaryotic pathway. Brown algae inherited the trehalose pathway from the red algal progenitor of phaeoplasts, while the mannitol pathway was acquired by lateral gene transfer from Actinobacteria. The starch metabolism of the red algal endosymbiont was entirely lost in the ancestor of Stramenopiles. In light of these novel findings we question the validity of the 'Chromalveolate hypothesis'.
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Affiliation(s)
- Gurvan Michel
- UPMC University Paris 6, UMR 7139 Marine Plants and Biomolecules, Station Biologique de Roscoff, F-29682 Roscoff, Bretagne, France.
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Marchand J, Evrard E, Guinand B, Cachot J, Quiniou L, Laroche J. Genetic polymorphism and its potential relation to environmental stress in five populations of the European flounder Platichthys flesus, along the French Atlantic coast. MARINE ENVIRONMENTAL RESEARCH 2010; 70:201-209. [PMID: 20621770 DOI: 10.1016/j.marenvres.2010.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 05/05/2010] [Accepted: 05/07/2010] [Indexed: 05/29/2023]
Abstract
In this study, new DNA markers were explored for the flounder Platichthys flesus. cDNA and genomic sequences of the genes encoding the glyceraldehyde-3-phosphate-deshydrogenase (GAPDH), the cytosolic creatine kinase (CK), the prostaglandin D synthase (PGDS) and the betaine homocysteine methyltransferase (BHMT) were characterized. The tumour suppressor p53 gene structure was already described. A PCR-SSCP (Single Strand Conformation Polymorphism) analysis was finally conducted to study the genetic polymorphism of different populations of flounders collected along the French Atlantic coast. Four highly contaminated French estuaries (Seine, Vilaine, Loire and Gironde) were sampled and compared to a reference estuary (Ster) to explore possible selective effect of the environment on specific allelic frequencies. Our results showed that two loci p53 and PGDS, could be potential markers of chemical stress: p53A allele frequency increased in contaminated systems compared to the reference system. In the Vilaine estuary, PGDS polymorphism could be related to pesticide stress.
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Affiliation(s)
- J Marchand
- Université du Maine, EA 2160 Mer, Molécule, Santé, UFR Sciences et Techniques, Le Mans F-72085, France.
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Ginger ML, McFadden GI, Michels PAM. Rewiring and regulation of cross-compartmentalized metabolism in protists. Philos Trans R Soc Lond B Biol Sci 2010; 365:831-45. [PMID: 20124348 DOI: 10.1098/rstb.2009.0259] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plastid acquisition, endosymbiotic associations, lateral gene transfer, organelle degeneracy or even organelle loss influence metabolic capabilities in many different protists. Thus, metabolic diversity is sculpted through the gain of new metabolic functions and moderation or loss of pathways that are often essential in the majority of eukaryotes. What is perhaps less apparent to the casual observer is that the sub-compartmentalization of ubiquitous pathways has been repeatedly remodelled during eukaryotic evolution, and the textbook pictures of intermediary metabolism established for animals, yeast and plants are not conserved in many protists. Moreover, metabolic remodelling can strongly influence the regulatory mechanisms that control carbon flux through the major metabolic pathways. Here, we provide an overview of how core metabolism has been reorganized in various unicellular eukaryotes, focusing in particular on one near universal catabolic pathway (glycolysis) and one ancient anabolic pathway (isoprenoid biosynthesis). For the example of isoprenoid biosynthesis, the compartmentalization of this process in protists often appears to have been influenced by plastid acquisition and loss, whereas for glycolysis several unexpected modes of compartmentalization have emerged. Significantly, the example of trypanosomatid glycolysis illustrates nicely how mathematical modelling and systems biology can be used to uncover or understand novel modes of pathway regulation.
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Affiliation(s)
- Michael L Ginger
- Division of Biomedical and Life Sciences, School of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK.
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Maberly SC, Courcelle C, Groben R, Gontero B. Phylogenetically-based variation in the regulation of the Calvin cycle enzymes, phosphoribulokinase and glyceraldehyde-3-phosphate dehydrogenase, in algae. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:735-45. [PMID: 19926682 DOI: 10.1093/jxb/erp337] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Aquatic photosynthesis is responsible for about half of the global production and is undertaken by a huge phylogenetic diversity of algae that are poorly studied. The diversity of redox-regulation of phosphoribulokinase (PRK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was investigated in a wide range of algal groups under standard conditions. Redox-regulation of PRK was greatest in chlorophytes, low or absent in a red alga and most chromalveolates, and linked to the number of amino acids between two regulatory cysteine residues. GAPDH regulation was not strongly-related to the different forms of this enzyme and was less variable than for PRK. Addition of recombinant CP12, a protein that forms a complex with PRK and GAPDH, to crude extracts inhibited GAPDH and PRK inversely in the Plantae, but in most chromalveolates had little effect on GAPDH and inhibited or stimulated PRK depending on the species. Patterns of enzyme regulation were used to produce a phylogenetic tree in which cryptophytes and haptophytes, at the base of the chromalveolates, formed a distinct clade. A second clade comprised only chromalveolates. A third clade comprised a mixture of Plantae, an excavate and three chromalveolates: a marine diatom and two others (a xanthophyte and eustigmatophyte) that are distinguished by a low content of chlorophyll c and a lack of fucoxanthin. Regulation of both enzymes was greater in freshwater than in marine taxa, possibly because most freshwaters are more dynamic than oceans. This work highlights the importance of understanding enzyme regulation in diverse algae if their ecology and productivity is to be understood.
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Affiliation(s)
- Stephen C Maberly
- Centre for Ecology and Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster LA1 4AP, UK
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Weber T, Gruber A, Kroth PG. The presence and localization of thioredoxins in diatoms, unicellular algae of secondary endosymbiotic origin. MOLECULAR PLANT 2009; 2:468-77. [PMID: 19825630 DOI: 10.1093/mp/ssp010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Diatoms are unicellular algae of great ecological importance. So far, very little is known about the regulation of carbon fixation in these algae; however, there are strong indications that in diatom plastids, the ferredoxin/thioredoxin system might play a minor role in redox regulation of the photosynthetic reactions compared to land plants. Until now, it is unknown whether there are fewer or other target enzymes of thioredoxins in diatoms. Only a single potential target enzyme for thioredoxin, the plastidic fructose-1,6-bisphosphatase, has yet been identified. Nevertheless, during the annotation of the genome of the diatom Phaeodactylum tricornutum, we identified several genes encoding different thioredoxins. Utilizing in vivo expression of GFP:presequence fusion proteins in P. tricornutum, we were able to show that these thioredoxins are targeted either into plastids, mitochondria, or remain in the cytosol. Surprisingly, two of the three usually cytosolic thioredoxin h proteins are apparently plastid associated and, together with a thioredoxin reductase, putatively located in the periplastidic compartment. This is one of the few indications for so far unknown enzymatic reactions in the space between the two pairs of diatom plastid envelope membranes.
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Affiliation(s)
- Till Weber
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
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Takishita K, Yamaguchi H, Maruyama T, Inagaki Y. A hypothesis for the evolution of nuclear-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase genes in "chromalveolate" members. PLoS One 2009; 4:e4737. [PMID: 19270733 PMCID: PMC2649427 DOI: 10.1371/journal.pone.0004737] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Accepted: 02/05/2009] [Indexed: 11/18/2022] Open
Abstract
Eukaryotes bearing red alga-derived plastids — photosynthetic alveolates (dinoflagellates plus the apicomplexan Toxoplasma gondii plus the chromerid Chromera velia), photosynthetic stramenopiles, haptophytes, and cryptophytes — possess unique plastid-targeted glyceraldehyde-3-phosphate dehydrogenases (henceforth designated as “GapC1”). Pioneering phylogenetic studies have indicated a single origin of the GapC1 enzymes in eukaryotic evolution, but there are two potential idiosyncrasies in the GapC1 phylogeny: Firstly, the GapC1 tree topology is apparently inconsistent with the organismal relationship among the “GapC1-containing” groups. Secondly, four stramenopile GapC1 homologues are consistently paraphyletic in previously published studies, although these organisms have been widely accepted as monophyletic. For a closer examination of the above issues, in this study GapC1 gene sampling was improved by determining/identifying nine stramenopile and two cryptophyte genes. Phylogenetic analyses of our GapC1 dataset, which is particularly rich in the stramenopile homologues, prompt us to propose a new scenario that assumes multiple, lateral GapC1 gene transfer events to explain the incongruity between the GapC1 phylogeny and the organismal relationships amongst the “GapC1-containing” groups. Under our new scenario, GapC1 genes uniquely found in photosynthetic alveolates, photosynthetic stramenopiles, haptophytes, and cryptopyhytes are not necessarily a character vertically inherited from a common ancestor.
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Affiliation(s)
- Kiyotaka Takishita
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan.
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Erales J, Gontero B, Maberly SC. SPECIFICITY AND FUNCTION OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE IN A FRESHWATER DIATOM, ASTERIONELLA FORMOSA (BACILLARIOPHYCEAE)(1). JOURNAL OF PHYCOLOGY 2008; 44:1455-1464. [PMID: 27039860 DOI: 10.1111/j.1529-8817.2008.00600.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The plastidic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyzes the only reductive step in the Calvin cycle and exists as different forms of which GapC1 enzyme is present in chromalveolates, such as diatoms. Biochemical studies on diatoms are still fragmentary, and, thus, in this report, GAPDH from the freshwater diatom Asterionella formosa Hassall has been purified and kinetically characterized. It is a homotetrameric enzyme with a molecular mass of ~150 ± 15 kDa. The enzyme showed Michaelis-Menten kinetics with respect to both cofactors, NADPH and NADH, with a 16-fold greater catalytic constant for NADPH. The Km for NADPH was 140 μM, the lowest affinity reported, while the catalytic constant, 815 s(-1) , is the highest reported. The Km for NADH was 93 μM, and the catalytic constant was 50 s(-1) , both are similar to reported values for other types of GAPDH. The GapC1 enzyme, like the Chlamydomonas reinhardtii A4 GAPDH, exhibits a cooperative behavior toward the substrate, 1,3-bisphosphoglyceric acid (BPGA), with both cofactors. Mass spectrometry analysis showed that when GapC1 enzyme was purified without reducing agents, it copurified with a small protein with a mass of 8.2 kDa. This protein was recognized by antibodies against CP12. When associated with this protein, GAPDH displayed a lag that disappeared upon incubation with reducing agent in the presence of either BPGA or NADPH as a consequence of dissociation of the GAPDH/CP12 complex. Thus, as in other species of algae and higher plants, regulation of GapC1 enzyme in A. formosa may occur through association-dissociation processes linked to dark-light transitions.
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Affiliation(s)
- Jenny Erales
- Laboratoire de Bioénergétique et Ingénierie des Protéines, 31 Chemin Joseph Aiguier, 13 402 Marseille Cedex 20 FranceCentre for Ecology and Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster LA1 4AP, UK
| | - Brigitte Gontero
- Laboratoire de Bioénergétique et Ingénierie des Protéines, 31 Chemin Joseph Aiguier, 13 402 Marseille Cedex 20 FranceCentre for Ecology and Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster LA1 4AP, UK
| | - Stephen C Maberly
- Laboratoire de Bioénergétique et Ingénierie des Protéines, 31 Chemin Joseph Aiguier, 13 402 Marseille Cedex 20 FranceCentre for Ecology and Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster LA1 4AP, UK
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Blair JE, Coffey MD, Park SY, Geiser DM, Kang S. A multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences. Fungal Genet Biol 2008; 45:266-77. [DOI: 10.1016/j.fgb.2007.10.010] [Citation(s) in RCA: 359] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Revised: 09/17/2007] [Accepted: 10/15/2007] [Indexed: 11/30/2022]
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Kroth PG, Chiovitti A, Gruber A, Martin-Jezequel V, Mock T, Parker MS, Stanley MS, Kaplan A, Caron L, Weber T, Maheswari U, Armbrust EV, Bowler C. A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis. PLoS One 2008; 3:e1426. [PMID: 18183306 PMCID: PMC2173943 DOI: 10.1371/journal.pone.0001426] [Citation(s) in RCA: 281] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Accepted: 12/11/2007] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Diatoms are unicellular algae responsible for approximately 20% of global carbon fixation. Their evolution by secondary endocytobiosis resulted in a complex cellular structure and metabolism compared to algae with primary plastids. METHODOLOGY/PRINCIPAL FINDINGS The whole genome sequence of the diatom Phaeodactylum tricornutum has recently been completed. We identified and annotated genes for enzymes involved in carbohydrate pathways based on extensive EST support and comparison to the whole genome sequence of a second diatom, Thalassiosira pseudonana. Protein localization to mitochondria was predicted based on identified similarities to mitochondrial localization motifs in other eukaryotes, whereas protein localization to plastids was based on the presence of signal peptide motifs in combination with plastid localization motifs previously shown to be required in diatoms. We identified genes potentially involved in a C4-like photosynthesis in P. tricornutum and, on the basis of sequence-based putative localization of relevant proteins, discuss possible differences in carbon concentrating mechanisms and CO(2) fixation between the two diatoms. We also identified genes encoding enzymes involved in photorespiration with one interesting exception: glycerate kinase was not found in either P. tricornutum or T. pseudonana. Various Calvin cycle enzymes were found in up to five different isoforms, distributed between plastids, mitochondria and the cytosol. Diatoms store energy either as lipids or as chrysolaminaran (a beta-1,3-glucan) outside of the plastids. We identified various beta-glucanases and large membrane-bound glucan synthases. Interestingly most of the glucanases appear to contain C-terminal anchor domains that may attach the enzymes to membranes. CONCLUSIONS/SIGNIFICANCE Here we present a detailed synthesis of carbohydrate metabolism in diatoms based on the genome sequences of Thalassiosira pseudonana and Phaeodactylum tricornutum. This model provides novel insights into acquisition of dissolved inorganic carbon and primary metabolic pathways of carbon in two different diatoms, which is of significance for an improved understanding of global carbon cycles.
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Affiliation(s)
- Peter G Kroth
- Fachbereich Biologie, University of Konstanz, Konstanz, Germany.
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Takishita K, Kawachi M, Noël MH, Matsumoto T, Kakizoe N, Watanabe MM, Inouye I, Ishida KI, Hashimoto T, Inagaki Y. Origins of plastids and glyceraldehyde-3-phosphate dehydrogenase genes in the green-colored dinoflagellate Lepidodinium chlorophorum. Gene 2007; 410:26-36. [PMID: 18191504 DOI: 10.1016/j.gene.2007.11.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Revised: 11/12/2007] [Accepted: 11/19/2007] [Indexed: 10/22/2022]
Abstract
The dinoflagellate Lepidodinium chlorophorum possesses "green" plastids containing chlorophylls a and b (Chl a+b), unlike most dinoflagellate plastids with Chl a+c plus a carotenoid peridinin (peridinin-containing plastids). In the present study we determined 8 plastid-encoded genes from Lepidodinium to investigate the origin of the Chl a+b-containing dinoflagellate plastids. The plastid-encoded gene phylogeny clearly showed that Lepidodinium plastids were derived from a member of Chlorophyta, consistent with pigment composition. We also isolated three different glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes from Lepidodinium-one encoding the putative cytosolic "GapC" enzyme and the remaining two showing affinities to the "plastid-targeted GapC" genes. In a GAPDH phylogeny, one of the plastid-targeted GapC-like sequences robustly grouped with those of dinoflagellates bearing peridinin-containing plastids, while the other was nested in a clade of the homologues of haptophytes and dinoflagellate genera Karenia and Karlodinium bearing "haptophyte-derived" plastids. Since neither host nor plastid phylogeny suggested an evolutionary connection between Lepidodinium and Karenia/Karlodinium, a lateral transfer of a plastid-targeted GapC gene most likely took place from a haptophyte or a dinoflagellate with haptophyte-derived plastids to Lepidodinium. The plastid-targeted GapC data can be considered as an evidence for the single origin of plastids in haptophytes, cryptophytes, stramenopiles, and alveolates. However, in the light of Lepidodinium GAPDH data, we need to closely examine whether the monophyly of the plastids in the above lineages inferred from plastid-targeted GapC genes truly reflects that of the host lineages.
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Affiliation(s)
- Kiyotaka Takishita
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
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Opii WO, Nukala VN, Sultana R, Pandya JD, Day KM, Merchant ML, Klein JB, Sullivan PG, Butterfield DA. Proteomic identification of oxidized mitochondrial proteins following experimental traumatic brain injury. J Neurotrauma 2007; 24:772-89. [PMID: 17518533 DOI: 10.1089/neu.2006.0229] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Experimental traumatic brain injury (TBI) results in a significant loss of cortical tissue at the site of injury, and in the ensuing hours and days a secondary injury exacerbates this primary injury, resulting in significant neurological dysfunction. The mechanism of the secondary injury is not well understood, but evidence implicates a critical role for mitochondria in this cascade. This mitochondrial dysfunction is believed to involve excitotoxicity, disruption of Ca(2+) homeostasis, production of reactive oxygen species (ROS), ATP depletion, oxidative damage of mitochondrial proteins, and an overall breakdown of mitochondrial bioenergetics. Although oxidative damage occurs following TBI, the identities of proteins undergoing oxidative modification after TBI have not been investigated. In the present study, we utilized the 3-h post-injury controlled cortical impact model of experimental TBI in 20 young adult male Sprague-Dawley rats, coupled with proteomics to identify specific mitochondrial fraction proteins from the cortex and hippocampus that were oxidatively modified after TBI. We identified, from the cortex, pyruvate dehydrogenase, voltage-dependent anion channel, fumarate hydratase 1, ATP synthase, and prohibitin. From the hippocampus, we identified cytochrome C oxidase Va, isovaleryl coenzyme A dehydrogenase, enolase-1, and glyceraldehyde-3-phosphate dehydrogenase as proteins that had undergone oxidative modification following TBI. In addition, we have also shown that, following TBI, there is a reduction in the activities of pyruvate dehydrogenase (PDH), complex I, and complex IV. These findings demonstrate that, following TBI, several proteins involved in mitochondrial bioenergetics are highly oxidatively modified, which may possibly underlie the massive breakdown of mitochondrial energetics and eventual cell death known to occur in this model. The identification of these proteins provides new insights into the mechanisms that take place following TBI and may provide avenues for possible therapeutic interventions after TBI.
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Affiliation(s)
- Wycliffe O Opii
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, USA
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A complex and punctate distribution of three eukaryotic genes derived by lateral gene transfer. BMC Evol Biol 2007; 7:89. [PMID: 17562012 PMCID: PMC1920508 DOI: 10.1186/1471-2148-7-89] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Accepted: 06/11/2007] [Indexed: 11/13/2022] Open
Abstract
Background Lateral gene transfer is increasingly invoked to explain phylogenetic results that conflict with our understanding of organismal relationships. In eukaryotes, the most common observation interpreted in this way is the appearance of a bacterial gene (one that is not clearly derived from the mitochondrion or plastid) in a eukaryotic nuclear genome. Ideally such an observation would involve a single eukaryote or a small group of related eukaryotes encoding a gene from a specific bacterial lineage. Results Here we show that several apparently simple cases of lateral transfer are actually more complex than they originally appeared: in these instances we find that two or more distantly related eukaryotic groups share the same bacterial gene, resulting in a punctate distribution. Specifically, we describe phylogenies of three core carbon metabolic enzymes: transketolase, glyceraldehyde-3-phosphate dehydrogenase and ribulose-5-phosphate-3-epimerase. Phylogenetic trees of each of these enzymes includes a strongly-supported clade consisting of several eukaryotes that are distantly related at the organismal level, but whose enzymes are apparently all derived from the same lateral transfer. With less sampling any one of these examples would appear to be a simple case of bacterium-to-eukaryote lateral transfer; taken together, their evolutionary histories cannot be so simple. The distributions of these genes may represent ancient paralogy events or genes that have been transferred from bacteria to an ancient ancestor of the eukaryotes that retain them. They may alternatively have been transferred laterally from a bacterium to a single eukaryotic lineage and subsequently transferred between distantly related eukaryotes. Conclusion Determining how complex the distribution of a transferred gene is depends on the sampling available. These results show that seemingly simple cases may be revealed to be more complex with greater sampling, suggesting many bacterial genes found in eukaryotic genomes may have a punctate distribution.
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Lemaire SD, Michelet L, Zaffagnini M, Massot V, Issakidis-Bourguet E. Thioredoxins in chloroplasts. Curr Genet 2007; 51:343-65. [PMID: 17431629 DOI: 10.1007/s00294-007-0128-z] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2007] [Revised: 03/05/2007] [Accepted: 03/09/2007] [Indexed: 01/03/2023]
Abstract
Thioredoxins (TRXs) are small disulfide oxidoreductases of ca. 12 kDa found in all free living organisms. In plants, two chloroplastic TRXs, named TRX f and TRX m, were originally identified as light dependent regulators of several carbon metabolism enzymes including Calvin cycle enzymes. The availability of genome sequences revealed an unsuspected multiplicity of TRXs in photosynthetic eukaryotes, including new chloroplastic TRX types. Moreover, proteomic approaches and focused studies allowed identification of 90 potential chloroplastic TRX targets. Lately, recent studies suggest the existence of a complex interplay between TRXs and other redox regulators such as glutaredoxins (GRXs) or glutathione. The latter is involved in a post-translational modification, named glutathionylation that could be controlled by GRXs. Glutathionylation appears to specifically affect the activity of TRX f and other chloroplastic enzymes and could thereby constitute a previously undescribed regulatory mechanism of photosynthetic metabolism under oxidative stress. After summarizing the initial studies on TRX f and TRX m, this review will focus on the most recent developments with special emphasis on the contributions of genomics and proteomics to the field of TRXs. Finally, new emerging interactions with other redox signaling pathways and perspectives for future studies will also be discussed.
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Affiliation(s)
- Stéphane D Lemaire
- Institut de Biotechnologie des Plantes, Unité Mixte de Recherche 8618, Centre National de la Recherche Scientifique, Univ Paris-Sud, 91405 Orsay Cedex, France.
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Zeng J, Wang Y, Shen G, Zheng X. A Phytophthora sojae gene of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) induced in host infection and its anti-oxidative function in yeast. CHINESE SCIENCE BULLETIN-CHINESE 2006. [DOI: 10.1007/s11434-006-1316-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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