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Stutts L, Latimer S, Batyrshina Z, Dickinson G, Alborn H, Block AK, Basset GJ. The evolution of strictly monofunctional naphthoquinol C-methyltransferases is vital in cyanobacteria and plastids. THE PLANT CELL 2023; 35:3686-3696. [PMID: 37477936 PMCID: PMC10533327 DOI: 10.1093/plcell/koad202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/22/2023]
Abstract
Prenylated quinones are membrane-associated metabolites that serve as vital electron carriers for respiration and photosynthesis. The UbiE (EC 2.1.1.201)/MenG (EC 2.1.1.163) C-methyltransferases catalyze pivotal ring methylations in the biosynthetic pathways of many of these quinones. In a puzzling evolutionary pattern, prokaryotic and eukaryotic UbiE/MenG homologs segregate into 2 clades. Clade 1 members occur universally in prokaryotes and eukaryotes, excluding cyanobacteria, and include mitochondrial COQ5 enzymes required for ubiquinone biosynthesis; Clade 2 members are specific to cyanobacteria and plastids. Functional complementation of an Escherichia coli ubiE/menG mutant indicated that Clade 1 members display activity with both demethylbenzoquinols and demethylnaphthoquinols, independently of the quinone profile of their original taxa, while Clade 2 members have evolved strict substrate specificity for demethylnaphthoquinols. Expression of the gene-encoding bifunctional Arabidopsis (Arabidopsis thaliana) COQ5 in the cyanobacterium Synechocystis or its retargeting to Arabidopsis plastids resulted in synthesis of a methylated variant of plastoquinone-9 that does not occur in nature. Accumulation of methylplastoquinone-9 was acutely cytotoxic, leading to the emergence of suppressor mutations in Synechocystis and seedling lethality in Arabidopsis. These data demonstrate that in cyanobacteria and plastids, co-occurrence of phylloquinone and plastoquinone-9 has driven the evolution of monofunctional demethylnaphthoquinol methyltransferases and explains why plants cannot capture the intrinsic bifunctionality of UbiE/MenG to simultaneously synthesize their respiratory and photosynthetic quinones.
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Affiliation(s)
- Lauren Stutts
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Scott Latimer
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Zhaniya Batyrshina
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Gabriella Dickinson
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Hans Alborn
- Center for Medical, Agricultural and Veterinary Entomology, ARS, USDA, Gainesville, FL 32608, USA
| | - Anna K Block
- Center for Medical, Agricultural and Veterinary Entomology, ARS, USDA, Gainesville, FL 32608, USA
| | - Gilles J Basset
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA
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2
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Igamberdiev AU, Bykova NV. Mitochondria in photosynthetic cells: Coordinating redox control and energy balance. PLANT PHYSIOLOGY 2023; 191:2104-2119. [PMID: 36440979 PMCID: PMC10069911 DOI: 10.1093/plphys/kiac541] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 05/21/2023]
Abstract
In photosynthetic tissues in the light, the function of energy production is associated primarily with chloroplasts, while mitochondrial metabolism adjusts to balance ATP supply, regulate the reduction level of pyridine nucleotides, and optimize major metabolic fluxes. The tricarboxylic acid cycle in the light transforms into a noncyclic open structure (hemicycle) maintained primarily by the influx of malate and the export of citrate to the cytosol. The exchange of malate and citrate forms the basis of feeding redox energy from the chloroplast into the cytosolic pathways. This supports the level of NADPH in different compartments, contributes to the biosynthesis of amino acids, and drives secondary metabolism via a supply of substrates for 2-oxoglutarate-dependent dioxygenase and for cytochrome P450-catalyzed monooxygenase reactions. This results in the maintenance of redox and energy balance in photosynthetic plant cells and in the formation of numerous bioactive compounds specific to any particular plant species. The noncoupled mitochondrial respiration operates in coordination with the malate and citrate valves and supports intensive fluxes of respiration and photorespiration. The metabolic system of plants has features associated with the remarkable metabolic plasticity of mitochondria that permit the use of energy accumulated during photosynthesis in a way that all anabolic and catabolic pathways become optimized and coordinated.
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Leishmania type II dehydrogenase is essential for parasite viability irrespective of the presence of an active complex I. Proc Natl Acad Sci U S A 2021; 118:2103803118. [PMID: 34654744 DOI: 10.1073/pnas.2103803118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2021] [Indexed: 11/18/2022] Open
Abstract
Type II NADH dehydrogenases (NDH2) are monotopic enzymes present in the external or internal face of the mitochondrial inner membrane that contribute to NADH/NAD+ balance by conveying electrons from NADH to ubiquinone without coupled proton translocation. Herein, we characterize the product of a gene present in all species of the human protozoan parasite Leishmania as a bona fide, matrix-oriented, type II NADH dehydrogenase. Within mitochondria, this respiratory activity concurs with that of type I NADH dehydrogenase (complex I) in some Leishmania species but not others. To query the significance of NDH2 in parasite physiology, we attempted its genetic disruption in two parasite species, exhibiting a silent (Leishmania infantum, Li) and a fully operational (Leishmania major, Lm) complex I. Strikingly, this analysis revealed that NDH2 abrogation is not tolerated by Leishmania, not even by complex I-expressing Lm species. Conversely, complex I is dispensable in both species, provided that NDH2 is sufficiently expressed. That a type II dehydrogenase is essential even in the presence of an active complex I places Leishmania NADH metabolism into an entirely unique perspective and suggests unexplored functions for NDH2 that span beyond its complex I-overlapping activities. Notably, by showing that the essential character of NDH2 extends to the disease-causing stage of Leishmania, we genetically validate NDH2-an enzyme without a counterpart in mammals-as a candidate target for leishmanicidal drugs.
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Igamberdiev AU. Citrate valve integrates mitochondria into photosynthetic metabolism. Mitochondrion 2020; 52:218-230. [PMID: 32278088 DOI: 10.1016/j.mito.2020.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/21/2020] [Accepted: 04/07/2020] [Indexed: 12/31/2022]
Abstract
While in heterotrophic cells and in darkness mitochondria serve as main producers of energy, during photosynthesis this function is transferred to chloroplasts and the main role of mitochondria in bioenergetics turns to be the balance of the level of phosphorylation of adenylates and of reduction of pyridine nucleotides to avoid over-energization of the cell and optimize major metabolic fluxes. This is achieved via the establishment and regulation of local equilibria of the tricarboxylic acid (TCA) cycle enzymes malate dehydrogenase and fumarase in one branch and aconitase and isocitrate dehydrogenase in another branch. In the conditions of elevation of redox level, the TCA cycle is transformed into a non-cyclic open structure (hemicycle) leading to the export of the tricarboxylic acid (citrate) to the cytosol and to the accumulation of the dicarboxylic acids (malate and fumarate). While the buildup of NADPH in chloroplasts provides operation of the malate valve leading to establishment of NADH/NAD+ ratios in different cell compartments, the production of NADH by mitochondria drives citrate export by establishing conditions for the operation of the citrate valve. The latter regulates the intercompartmental NADPH/NADP+ ratio and contributes to the biosynthesis of amino acids and other metabolic products during photosynthesis.
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Affiliation(s)
- Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
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Antos-Krzeminska N, Jarmuszkiewicz W. Alternative Type II NAD(P)H Dehydrogenases in the Mitochondria of Protists and Fungi. Protist 2018; 170:21-37. [PMID: 30553126 DOI: 10.1016/j.protis.2018.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/12/2018] [Accepted: 11/04/2018] [Indexed: 01/11/2023]
Abstract
Plants, fungi, and some protists possess a more branched electron transport chain in their mitochondria compared to canonical one. In these organisms, the electron transport chain contains several rotenone-insensitive NAD(P)H dehydrogenases. Some are located on the outer surface, and others are located on the inner surface of the inner mitochondrial membrane. The putative role of these enzymes still remains elusive, but they may prevent the overreduction of the electron transport chain components and decrease the production of reaction oxygen species as a consequence. The last two decades resulted in the discovery of alternative rotenone-insensitive NAD(P)H dehydrogenases present in representatives of fungi and protozoa. The aim of this review is to gather and focus on current information concerning molecular and functional properties, regulation, and the physiological role of fungal and protozoan alternative NAD(P)H dehydrogenases.
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Affiliation(s)
- Nina Antos-Krzeminska
- Department of Bioenergetics, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland.
| | - Wieslawa Jarmuszkiewicz
- Department of Bioenergetics, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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Lee H, Golicz AA, Bayer PE, Severn-Ellis AA, Chan CKK, Batley J, Kendrick GA, Edwards D. Genomic comparison of two independent seagrass lineages reveals habitat-driven convergent evolution. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3689-3702. [PMID: 29912443 PMCID: PMC6022596 DOI: 10.1093/jxb/ery147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 04/12/2018] [Indexed: 05/06/2023]
Abstract
Seagrasses are marine angiosperms that live fully submerged in the sea. They evolved from land plant ancestors, with multiple species representing at least three independent return-to-the-sea events. This raises the question of whether these marine angiosperms followed the same adaptation pathway to allow them to live and reproduce under the hostile marine conditions. To compare the basis of marine adaptation between seagrass lineages, we generated genomic data for Halophila ovalis and compared this with recently published genomes for two members of Zosteraceae, as well as genomes of five non-marine plant species (Arabidopsis, Oryza sativa, Phoenix dactylifera, Musa acuminata, and Spirodela polyrhiza). Halophila and Zosteraceae represent two independent seagrass lineages separated by around 30 million years. Genes that were lost or conserved in both lineages were identified. All three species lost genes associated with ethylene and terpenoid biosynthesis, and retained genes related to salinity adaptation, such as those for osmoregulation. In contrast, the loss of the NADH dehydrogenase-like complex is unique to H. ovalis. Through comparison of two independent return-to-the-sea events, this study further describes marine adaptation characteristics common to seagrass families, identifies species-specific gene loss, and provides molecular evidence for convergent evolution in seagrass lineages.
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Affiliation(s)
- HueyTyng Lee
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
- School of Biological Sciences, University of Western Australia, WA, Australia
| | - Agnieszka A Golicz
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, WA, Australia
| | | | | | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, WA, Australia
| | - Gary A Kendrick
- School of Biological Sciences, University of Western Australia, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, WA, Australia
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7
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Elevation of cytosolic Ca2+ in response to energy deficiency in plants: the general mechanism of adaptation to low oxygen stress. Biochem J 2018; 475:1411-1425. [DOI: 10.1042/bcj20180169] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 03/27/2018] [Accepted: 03/29/2018] [Indexed: 02/06/2023]
Abstract
Ca2+ can be released from cell compartments to the cytosol during stress conditions. We discuss here the causes of Ca2+ release under conditions of ATP concentration decline that result in the suppression of ATPases and activation of calcium ion channels. The main signaling and metabolic consequences of Ca2+ release are considered for stressed plant cells. The signaling function includes generation and spreading of calcium waves, while the metabolic function results in the activation of particular enzymes and genes. Ca2+ is involved in the activation of glutamate decarboxylase, initiating the γ-aminobutyric acid shunt and triggering the formation of alanine, processes which play a role, in particular, in pH regulation. Ca2+ activates the transcription of several genes, e.g. of plant hemoglobin (phytoglobin, Pgb) which scavenges nitric oxide and regulates redox and energy balance through the Pgb–nitric oxide cycle. This cycle involves NADH and NADPH oxidation from the cytosolic side of mitochondria, in which Ca2+- and low pH-activated external NADH and NADPH dehydrogenases participate. Ca2+ can also activate the genes of alcohol dehydrogenase and pyruvate decarboxylase stimulating hypoxic fermentation. It is concluded that calcium is a primary factor that causes the metabolic shift under conditions of oxygen deficiency.
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Wanniarachchi VR, Dametto L, Sweetman C, Shavrukov Y, Day DA, Jenkins CLD, Soole KL. Alternative Respiratory Pathway Component Genes (AOX and ND) in Rice and Barley and Their Response to Stress. Int J Mol Sci 2018; 19:E915. [PMID: 29558397 PMCID: PMC5877776 DOI: 10.3390/ijms19030915] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 11/24/2022] Open
Abstract
Plants have a non-energy conserving bypass of the classical mitochondrial cytochrome c pathway, known as the alternative respiratory pathway (AP). This involves type II NAD(P)H dehydrogenases (NDs) on both sides of the mitochondrial inner membrane, ubiquinone, and the alternative oxidase (AOX). The AP components have been widely characterised from Arabidopsis, but little is known for monocot species. We have identified all the genes encoding components of the AP in rice and barley and found the key genes which respond to oxidative stress conditions. In both species, AOX is encoded by four genes; in rice OsAOX1a, 1c, 1d and 1e representing four clades, and in barley, HvAOX1a, 1c, 1d1 and 1d2, but no 1e. All three subfamilies of plant ND genes, NDA, NDB and NDC are present in both rice and barley, but there are fewer NDB genes compared to Arabidopsis. Cyanide treatment of both species, along with salt treatment of rice and drought treatment of barley led to enhanced expression of various AP components; there was a high level of co-expression of AOX1a and AOX1d, along with NDB3 during the stress treatments, reminiscent of the co-expression that has been well characterised in Arabidopsis for AtAOX1a and AtNDB2.
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Affiliation(s)
- Vajira R Wanniarachchi
- College of Science and Engineering, Flinders University of South Australia, GPO Box 5100, Adelaide, SA 5001, Australia.
| | - Lettee Dametto
- College of Science and Engineering, Flinders University of South Australia, GPO Box 5100, Adelaide, SA 5001, Australia.
| | - Crystal Sweetman
- College of Science and Engineering, Flinders University of South Australia, GPO Box 5100, Adelaide, SA 5001, Australia.
| | - Yuri Shavrukov
- College of Science and Engineering, Flinders University of South Australia, GPO Box 5100, Adelaide, SA 5001, Australia.
| | - David A Day
- College of Science and Engineering, Flinders University of South Australia, GPO Box 5100, Adelaide, SA 5001, Australia.
| | - Colin L D Jenkins
- College of Science and Engineering, Flinders University of South Australia, GPO Box 5100, Adelaide, SA 5001, Australia.
| | - Kathleen L Soole
- College of Science and Engineering, Flinders University of South Australia, GPO Box 5100, Adelaide, SA 5001, Australia.
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9
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Huokko T, Muth-Pawlak D, Battchikova N, Allahverdiyeva Y, Aro EM. Role of Type 2 NAD(P)H Dehydrogenase NdbC in Redox Regulation of Carbon Allocation in Synechocystis. PLANT PHYSIOLOGY 2017; 174:1863-1880. [PMID: 28533358 PMCID: PMC5490909 DOI: 10.1104/pp.17.00398] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/19/2017] [Indexed: 05/21/2023]
Abstract
NAD(P)H dehydrogenases comprise type 1 (NDH-1) and type 2 (NDH-2s) enzymes. Even though the NDH-1 complex is a well-characterized protein complex in the thylakoid membrane of Synechocystis sp. PCC 6803 (hereafter Synechocystis), the exact roles of different NDH-2s remain poorly understood. To elucidate this question, we studied the function of NdbC, one of the three NDH-2s in Synechocystis, by constructing a deletion mutant (ΔndbC) for a corresponding protein and submitting the mutant to physiological and biochemical characterization as well as to comprehensive proteomics analysis. We demonstrate that the deletion of NdbC, localized to the plasma membrane, affects several metabolic pathways in Synechocystis in autotrophic growth conditions without prominent effects on photosynthesis. Foremost, the deletion of NdbC leads, directly or indirectly, to compromised sugar catabolism, to glycogen accumulation, and to distorted cell division. Deficiencies in several sugar catabolic routes were supported by severe retardation of growth of the ΔndbC mutant under light-activated heterotrophic growth conditions but not under mixotrophy. Thus, NdbC has a significant function in regulating carbon allocation between storage and the biosynthesis pathways. In addition, the deletion of NdbC increases the amount of cyclic electron transfer, possibly via the NDH-12 complex, and decreases the expression of several transporters in ambient CO2 growth conditions.
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Affiliation(s)
- Tuomas Huokko
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku FI-20014, Finland
| | - Dorota Muth-Pawlak
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku FI-20014, Finland
| | - Natalia Battchikova
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku FI-20014, Finland
| | - Yagut Allahverdiyeva
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku FI-20014, Finland
| | - Eva-Mari Aro
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku FI-20014, Finland
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10
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Hao MS, Rasmusson AG. The evolution of substrate specificity-associated residues and Ca(2+) -binding motifs in EF-hand-containing type II NAD(P)H dehydrogenases. PHYSIOLOGIA PLANTARUM 2016; 157:338-351. [PMID: 27079180 DOI: 10.1111/ppl.12453] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 03/03/2016] [Accepted: 03/14/2016] [Indexed: 06/05/2023]
Abstract
Most eukaryotic organisms, except some animal clades, have mitochondrial alternative electron transport enzymes that allow respiration to bypass the energy coupling in oxidative phosphorylation. The energy bypass enzymes in plants include the external type II NAD(P)H dehydrogenases (DHs) of the NDB family, which are characterized by an EF-hand domain for Ca(2+) binding. Here we investigate these plant enzymes by combining molecular modeling with evolutionary analysis. Molecular modeling of the Arabidopsis thaliana AtNDB1 with the yeast ScNDI1 as template revealed distinct similarities in the core catalytic parts, and highlighted the interaction between the pyridine nucleotide and residues correlating with NAD(P)H substrate specificity. The EF-hand domain of AtNDB1 has no counterpart in ScNDI1, and was instead modeled with Ca(2+) -binding signal transducer proteins. Combined models displayed a proximity of the AtNDB1 EF-hand domain to the substrate entrance side of the catalytic part. Evolutionary analysis of the eukaryotic NDB-type proteins revealed ancient and recent reversions between the motif observed in proteins specific for NADH (acidic type) and NADPH (non-acidic type), and that the clade of enzymes with acidic motifs in angiosperms derives from non-acidic-motif NDB-type proteins present in basal plants, fungi and protists. The results suggest that Ca(2+) -dependent external NADPH oxidation is an ancient process, indicating that it has a fundamental importance for eukaryotic cellular redox metabolism. In contrast, the external NADH DHs in plants are products of a recent expansion, mirroring the expansion of the alternative oxidase family.
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Affiliation(s)
- Meng-Shu Hao
- Department of Biology, Lund University, Lund, Sweden
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11
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Jokipii-Lukkari S, Kastaniotis AJ, Parkash V, Sundström R, Leiva-Eriksson N, Nymalm Y, Blokhina O, Kukkola E, Fagerstedt KV, Salminen TA, Läärä E, Bülow L, Ohlmeier S, Hiltunen JK, Kallio PT, Häggman H. Dual targeted poplar ferredoxin NADP(+) oxidoreductase interacts with hemoglobin 1. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 247:138-149. [PMID: 27095407 DOI: 10.1016/j.plantsci.2016.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/01/2016] [Accepted: 03/25/2016] [Indexed: 06/05/2023]
Abstract
Previous reports have connected non-symbiotic and truncated hemoglobins (Hbs) to metabolism of nitric oxide (NO), an important signalling molecule involved in wood formation. We have studied the capability of poplar (Populus tremula × tremuloides) Hbs PttHb1 and PttTrHb proteins alone or with a flavin-protein reductase to relieve NO cytotoxicity in living cells. Complementation tests in a Hb-deficient, NO-sensitive yeast (Saccharomyces cerevisiae) Δyhb1 mutant showed that neither PttHb1 nor PttTrHb alone protected cells against NO. To study the ability of Hbs to interact with a reductase, ferredoxin NADP(+) oxidoreductase PtthFNR was characterized by sequencing and proteomics. To date, by far the greatest number of the known dual-targeted plant proteins are directed to chloroplasts and mitochondria. We discovered a novel variant of hFNR that lacks the plastid presequence and resides in cytosol. The coexpression of PttHb1 and PtthFNR partially restored NO resistance of the yeast Δyhb1 mutant, whereas PttTrHb coexpressed with PtthFNR failed to rescue growth. YFP fusion proteins confirmed the interaction between PttHb1 and PtthFNR in plant cells. The structural modelling results indicate that PttHb1 and PtthFNR are able to interact as NO dioxygenase. This is the first report on dual targeting of central plant enzyme FNR to plastids and cytosol.
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Affiliation(s)
- Soile Jokipii-Lukkari
- Genetics and Physiology Department, University of Oulu, P.O. Box 3000, FI-90014, Finland
| | - Alexander J Kastaniotis
- The Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, P.O. Box 5400, FI-90014, Finland
| | - Vimal Parkash
- The Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, FI-20520 Turku, Finland
| | - Robin Sundström
- The Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, FI-20520 Turku, Finland
| | - Nélida Leiva-Eriksson
- The Pure and Applied Biochemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Yvonne Nymalm
- The Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, FI-20520 Turku, Finland
| | - Olga Blokhina
- The Department of Biosciences, University of Helsinki, Viikki Biocenter 3, P.O. Box 65, FI-00014, Finland
| | - Eija Kukkola
- The Department of Biosciences, University of Helsinki, Viikki Biocenter 3, P.O. Box 65, FI-00014, Finland
| | - Kurt V Fagerstedt
- The Department of Biosciences, University of Helsinki, Viikki Biocenter 3, P.O. Box 65, FI-00014, Finland
| | - Tiina A Salminen
- The Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, FI-20520 Turku, Finland
| | - Esa Läärä
- The Department of Mathematical Sciences, University of Oulu, P.O. Box 3000, FI-90014, Finland
| | - Leif Bülow
- The Pure and Applied Biochemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Steffen Ohlmeier
- The Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, P.O. Box 5400, FI-90014, Finland
| | - J Kalervo Hiltunen
- The Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, P.O. Box 5400, FI-90014, Finland
| | - Pauli T Kallio
- The Institute of Microbiology, ETH-Zürich, CH-8093 Zürich, Switzerland
| | - Hely Häggman
- Genetics and Physiology Department, University of Oulu, P.O. Box 3000, FI-90014, Finland.
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12
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Reumann S, Chowdhary G, Lingner T. Characterization, prediction and evolution of plant peroxisomal targeting signals type 1 (PTS1s). BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1863:790-803. [PMID: 26772785 DOI: 10.1016/j.bbamcr.2016.01.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 01/01/2016] [Accepted: 01/04/2016] [Indexed: 12/22/2022]
Abstract
Our knowledge of the proteome of plant peroxisomes and their functional plasticity is far from being complete, primarily due to major technical challenges in experimental proteome research of the fragile cell organelle. Several unexpected novel plant peroxisome functions, for instance in biotin and phylloquinone biosynthesis, have been uncovered recently. Nevertheless, very few regulatory and membrane proteins of plant peroxisomes have been identified and functionally described up to now. To define the matrix proteome of plant peroxisomes, computational methods have emerged as important powerful tools. Novel prediction approaches of high sensitivity and specificity have been developed for peroxisome targeting signals type 1 (PTS1) and have been validated by in vivo subcellular targeting analyses and thermodynamic binding studies with the cytosolic receptor, PEX5. Accordingly, the algorithms allow the correct prediction of many novel peroxisome-targeted proteins from plant genome sequences and the discovery of additional organelle functions. In this review, we provide an overview of methodologies, capabilities and accuracies of available prediction algorithms for PTS1 carrying proteins. We also summarize and discuss recent quantitative, structural and mechanistic information of the interaction of PEX5 with PTS1 carrying proteins in relation to in vivo import efficiency. With this knowledge, we develop a model of how proteins likely evolved peroxisomal targeting signals in the past and still nowadays, in which order the two import pathways might have evolved in the ancient eukaryotic cell, and how the secondary loss of the PTS2 pathway probably happened in specific organismal groups.
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Affiliation(s)
- S Reumann
- Department of Plant Biochemistry and Infection Biology, Biocentre Klein Flottbek, University of Hamburg, D-22609 Hamburg, Germany; Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway.
| | - G Chowdhary
- Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway; KIIT School of Biotechnology, Campus XI, KIIT University, I-751024 Bhubaneswar, India.
| | - T Lingner
- Department of Bioinformatics, Institute for Microbiology and Genetics, D-37077 Goettingen, Germany.
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13
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Peltier G, Aro EM, Shikanai T. NDH-1 and NDH-2 Plastoquinone Reductases in Oxygenic Photosynthesis. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:55-80. [PMID: 26735062 DOI: 10.1146/annurev-arplant-043014-114752] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Oxygenic photosynthesis converts solar energy into chemical energy in the chloroplasts of plants and microalgae as well as in prokaryotic cyanobacteria using a complex machinery composed of two photosystems and both membrane-bound and soluble electron carriers. In addition to the major photosynthetic complexes photosystem II (PSII), cytochrome b6f, and photosystem I (PSI), chloroplasts also contain minor components, including a well-conserved type I NADH dehydrogenase (NDH-1) complex that functions in close relationship with photosynthesis and likewise originated from the endosymbiotic cyanobacterial ancestor. Some plants and many microalgal species have lost plastidial ndh genes and a functional NDH-1 complex during evolution, and studies have suggested that a plastidial type II NADH dehydrogenase (NDH-2) complex substitutes for the electron transport activity of NDH-1. However, although NDH-1 was initially thought to use NAD(P)H as an electron donor, recent research has demonstrated that both chloroplast and cyanobacterial NDH-1s oxidize reduced ferredoxin. We discuss more recent findings related to the biochemical composition and activity of NDH-1 and NDH-2 in relation to the physiology and regulation of photosynthesis, particularly focusing on their roles in cyclic electron flow around PSI, chlororespiration, and acclimation to changing environments.
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Affiliation(s)
- Gilles Peltier
- Institute of Environmental Biology and Biotechnology, CEA, CNRS, Aix-Marseille University, CEA Cadarache, 13018 Saint-Paul-lès-Durance, France;
| | - Eva-Mari Aro
- Department of Biochemistry, University of Turku, 20014 Turku, Finland;
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Narsai R. Databases and informatics resources for analysis of plant mitochondria. Methods Mol Biol 2016; 1305:263-79. [PMID: 25910741 DOI: 10.1007/978-1-4939-2639-8_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
As more omics data is generated from various plant species, it is becoming increasingly possible to carry out a range of in silico analyses to gain insight into mitochondrial function in plants. From the use of software tools for DNA motif analyses and transcript expression visualization to proteomic and subcellular localization resources, it is possible to carry out significant in silico analyses that are highly informative to researchers and can help to guide experimental design for further mitochondrial study. Databases specific to plant mitochondrial analyses have been developed in recent years, revealing mitochondria-specific information. This chapter outlines the databases and informatics resources that are useful for plant mitochondrial studies, with specific examples presented to indicate how these resources can be used to gain insight into plant mitochondrial function(s).
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Affiliation(s)
- Reena Narsai
- Department of Botany, Australian Research Council Centre of Excellence Plant Energy Biology, School of Life Sciences, La Trobe University, 5 Ring Road, Bundoora, VIC, 3086, Australia,
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15
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Abstract
Plant mitochondria contain at least four type II NAD(P)H dehydrogenases that link NAD(P)H oxidation to the inner membrane electron transport chain and bypass proton pumping at Complex I, hence ATP synthesis. These activities have been found in mitochondria isolated from all plant species analyzed to date. In this chapter, methods are presented to analyze the expression of genes encoding these dehydrogenases and to detect protein levels in mitochondria isolated from Arabidopsis (Arabidopsis thaliana). In addition, methods and assay conditions are presented to detect the activity of each of these four type II NAD(P)H dehydrogenases in isolated plant mitochondria.
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Affiliation(s)
- Kathleen L Soole
- School of Biological Sciences, Flinders University, Sturt Road, Bedford Park 5042, GPO Box 2100, Adelaide, 5001, SA, Australia,
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16
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Fatihi A, Latimer S, Schmollinger S, Block A, Dussault PH, Vermaas WFJ, Merchant SS, Basset GJ. A Dedicated Type II NADPH Dehydrogenase Performs the Penultimate Step in the Biosynthesis of Vitamin K1 in Synechocystis and Arabidopsis. THE PLANT CELL 2015; 27:1730-41. [PMID: 26023160 PMCID: PMC4498204 DOI: 10.1105/tpc.15.00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/07/2015] [Indexed: 05/04/2023]
Abstract
Mutation of Arabidopsis thaliana NAD(P)H DEHYDROGENASE C1 (NDC1; At5g08740) results in the accumulation of demethylphylloquinone, a late biosynthetic intermediate of vitamin K1. Gene coexpression and phylogenomics analyses showed that conserved functional associations occur between vitamin K biosynthesis and NDC1 homologs throughout the prokaryotic and eukaryotic lineages. Deletion of Synechocystis ndbB, which encodes for one such homolog, resulted in the same defects as those observed in the cyanobacterial demethylnaphthoquinone methyltransferase knockout. Chemical modeling and assay of purified demethylnaphthoquinone methyltransferase demonstrated that, by virtue of the strong electrophilic nature of S-adenosyl-l-methionine, the transmethylation of the demethylated precursor of vitamin K is strictly dependent on the reduced form of its naphthoquinone ring. NDC1 was shown to catalyze such a prerequisite reduction by using NADPH and demethylphylloquinone as substrates and flavine adenine dinucleotide as a cofactor. NDC1 displayed Michaelis-Menten kinetics and was markedly inhibited by dicumarol, a competitive inhibitor of naphthoquinone oxidoreductases. These data demonstrate that the reduction of the demethylnaphthoquinone ring represents an authentic step in the biosynthetic pathway of vitamin K, that this reaction is enzymatically driven, and that a selection pressure is operating to retain type II NAD(P)H dehydrogenases in this process.
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Affiliation(s)
- Abdelhak Fatihi
- Department of Agronomy and Horticulture, and Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Scott Latimer
- Department of Agronomy and Horticulture, and Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Stefan Schmollinger
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Anna Block
- Department of Agronomy and Horticulture, and Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Patrick H Dussault
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588
| | - Wim F J Vermaas
- School of Life Sciences and Center for the Study of Early Events in Photosynthesis, Arizona State University, Tempe, Arizona 85287
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095 Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Gilles J Basset
- Department of Agronomy and Horticulture, and Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
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17
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Bobik K, Burch-Smith TM. Chloroplast signaling within, between and beyond cells. FRONTIERS IN PLANT SCIENCE 2015; 6:781. [PMID: 26500659 PMCID: PMC4593955 DOI: 10.3389/fpls.2015.00781] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/10/2015] [Indexed: 05/18/2023]
Abstract
The most conspicuous function of plastids is the oxygenic photosynthesis of chloroplasts, yet plastids are super-factories that produce a plethora of compounds that are indispensable for proper plant physiology and development. Given their origins as free-living prokaryotes, it is not surprising that plastids possess their own genomes whose expression is essential to plastid function. This semi-autonomous character of plastids requires the existence of sophisticated regulatory mechanisms that provide reliable communication between them and other cellular compartments. Such intracellular signaling is necessary for coordinating whole-cell responses to constantly varying environmental cues and cellular metabolic needs. This is achieved by plastids acting as receivers and transmitters of specific signals that coordinate expression of the nuclear and plastid genomes according to particular needs. In this review we will consider the so-called retrograde signaling occurring between plastids and nuclei, and between plastids and other organelles. Another important role of the plastid we will discuss is the involvement of plastid signaling in biotic and abiotic stress that, in addition to influencing retrograde signaling, has direct effects on several cellular compartments including the cell wall. We will also review recent evidence pointing to an intriguing function of chloroplasts in regulating intercellular symplasmic transport. Finally, we consider an intriguing yet less widely known aspect of plant biology, chloroplast signaling from the perspective of the entire plant. Thus, accumulating evidence highlights that chloroplasts, with their complex signaling pathways, provide a mechanism for exquisite regulation of plant development, metabolism and responses to the environment. As chloroplast processes are targeted for engineering for improved productivity the effect of such modifications on chloroplast signaling will have to be carefully considered in order to avoid unintended consequences on plant growth and development.
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Affiliation(s)
| | - Tessa M. Burch-Smith
- *Correspondence: Tessa M. Burch-Smith, Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, 1414 Cumberland Avenue, M407 Walters Life Science, Knoxville, TN 37932, USA,
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Skoulding NS, Chowdhary G, Deus MJ, Baker A, Reumann S, Warriner SL. Experimental validation of plant peroxisomal targeting prediction algorithms by systematic comparison of in vivo import efficiency and in vitro PTS1 binding affinity. J Mol Biol 2014; 427:1085-101. [PMID: 25498386 DOI: 10.1016/j.jmb.2014.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/30/2014] [Accepted: 12/04/2014] [Indexed: 01/19/2023]
Abstract
Most peroxisomal matrix proteins possess a C-terminal targeting signal type 1 (PTS1). Accurate prediction of functional PTS1 sequences and their relative strength by computational methods is essential for determination of peroxisomal proteomes in silico but has proved challenging due to high levels of sequence variability of non-canonical targeting signals, particularly in higher plants, and low levels of availability of experimentally validated non-canonical examples. In this study, in silico predictions were compared with in vivo targeting analyses and in vitro thermodynamic binding of mutated variants within the context of one model targeting sequence. There was broad agreement between the methods for entire PTS1 domains and position-specific single amino acid residues, including residues upstream of the PTS1 tripeptide. The hierarchy Leu>Met>Ile>Val at the C-terminal position was determined for all methods but both experimental approaches suggest that Tyr is underweighted in the prediction algorithm due to the absence of this residue in the positive training dataset. A combination of methods better defines the score range that discriminates a functional PTS1. In vitro binding to the PEX5 receptor could discriminate among strong targeting signals while in vivo targeting assays were more sensitive, allowing detection of weak functional import signals that were below the limit of detection in the binding assay. Together, the data provide a comprehensive assessment of the factors driving PTS1 efficacy and provide a framework for the more quantitative assessment of the protein import pathway in higher plants.
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Affiliation(s)
- Nicola S Skoulding
- School of Chemistry and the Astbury Centre, University of Leeds, Leeds LS2 9JT, UK
| | - Gopal Chowdhary
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Richard Johansens Gate 4, N-4021 Stavanger, Norway; KIIT School of Biotechnology, Campus XI, KIIT University, I-751024 Bhubaneswar, India
| | - Mara J Deus
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Richard Johansens Gate 4, N-4021 Stavanger, Norway
| | - Alison Baker
- Centre for Plant Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sigrun Reumann
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Richard Johansens Gate 4, N-4021 Stavanger, Norway; Department of Biology, Biocentre Klein Flottbek, University of Hamburg, D-22609 Hamburg, Germany
| | - Stuart L Warriner
- School of Chemistry and the Astbury Centre, University of Leeds, Leeds LS2 9JT, UK.
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Wallström SV, Florez-Sarasa I, Araújo WL, Escobar MA, Geisler DA, Aidemark M, Lager I, Fernie AR, Ribas-Carbó M, Rasmusson AG. Suppression of NDA-type alternative mitochondrial NAD(P)H dehydrogenases in arabidopsis thaliana modifies growth and metabolism, but not high light stimulation of mitochondrial electron transport. PLANT & CELL PHYSIOLOGY 2014; 55:881-96. [PMID: 24486764 PMCID: PMC4016682 DOI: 10.1093/pcp/pcu021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Accepted: 01/16/2014] [Indexed: 05/18/2023]
Abstract
The plant respiratory chain contains several pathways which bypass the energy-conserving electron transport complexes I, III and IV. These energy bypasses, including type II NAD(P)H dehydrogenases and the alternative oxidase (AOX), may have a role in redox stabilization and regulation, but current evidence is inconclusive. Using RNA interference, we generated Arabidopsis thaliana plants simultaneously suppressing the type II NAD(P)H dehydrogenase genes NDA1 and NDA2. Leaf mitochondria contained substantially reduced levels of both proteins. In sterile culture in the light, the transgenic lines displayed a slow growth phenotype, which was more severe when the complex I inhibitor rotenone was present. Slower growth was also observed in soil. In rosette leaves, a higher NAD(P)H/NAD(P)⁺ ratio and elevated levels of lactate relative to sugars and citric acid cycle metabolites were observed. However, photosynthetic performance was unaffected and microarray analyses indicated few transcriptional changes. A high light treatment increased AOX1a mRNA levels, in vivo AOX and cytochrome oxidase activities, and levels of citric acid cycle intermediates and hexoses in all genotypes. However, NDA-suppressing plants deviated from the wild type merely by having higher levels of several amino acids. These results suggest that NDA suppression restricts citric acid cycle reactions, inducing a shift towards increased levels of fermentation products, but do not support a direct association between photosynthesis and NDA proteins.
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Affiliation(s)
- Sabá V. Wallström
- Department of Biology, Lund University, Biology building A, Sölvegatan 35, SE-22362 Lund, Sweden
| | - Igor Florez-Sarasa
- Grup de Recerca en Biologia de les Plantes en Condicions Mediterrànies, Universitat de les Illes Balears, Ctra Valldemossa Km. 7,5, 07122 Palma de Mallorca, Spain
- Present address: Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Wagner L. Araújo
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
- Present address: Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-000 Viçosa, Minas Gerais, Brasil
| | - Matthew A. Escobar
- Department of Biological Sciences, California State University San Marcos, 333 S. Twin Oaks Valley Road, San Marcos, CA 92096, USA
| | - Daniela A. Geisler
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mari Aidemark
- Department of Biology, Lund University, Biology building A, Sölvegatan 35, SE-22362 Lund, Sweden
| | - Ida Lager
- Department of Biology, Lund University, Biology building A, Sölvegatan 35, SE-22362 Lund, Sweden
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Miquel Ribas-Carbó
- Grup de Recerca en Biologia de les Plantes en Condicions Mediterrànies, Universitat de les Illes Balears, Ctra Valldemossa Km. 7,5, 07122 Palma de Mallorca, Spain
| | - Allan G. Rasmusson
- Department of Biology, Lund University, Biology building A, Sölvegatan 35, SE-22362 Lund, Sweden
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20
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Welchen E, García L, Mansilla N, Gonzalez DH. Coordination of plant mitochondrial biogenesis: keeping pace with cellular requirements. FRONTIERS IN PLANT SCIENCE 2014; 4:551. [PMID: 24409193 PMCID: PMC3884152 DOI: 10.3389/fpls.2013.00551] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 12/23/2013] [Indexed: 05/20/2023]
Abstract
Plant mitochondria are complex organelles that carry out numerous metabolic processes related with the generation of energy for cellular functions and the synthesis and degradation of several compounds. Mitochondria are semiautonomous and dynamic organelles changing in shape, number, and composition depending on tissue or developmental stage. The biogenesis of functional mitochondria requires the coordination of genes present both in the nucleus and the organelle. In addition, due to their central role, all processes held inside mitochondria must be finely coordinated with those in other organelles according to cellular demands. Coordination is achieved by transcriptional control of nuclear genes encoding mitochondrial proteins by specific transcription factors that recognize conserved elements in their promoter regions. In turn, the expression of most of these transcription factors is linked to developmental and environmental cues, according to the availability of nutrients, light-dark cycles, and warning signals generated in response to stress conditions. Among the signals impacting in the expression of nuclear genes, retrograde signals that originate inside mitochondria help to adjust mitochondrial biogenesis to organelle demands. Adding more complexity, several nuclear encoded proteins are dual localized to mitochondria and either chloroplasts or the nucleus. Dual targeting might establish a crosstalk between the nucleus and cell organelles to ensure a fine coordination of cellular activities. In this article, we discuss how the different levels of coordination of mitochondrial biogenesis interconnect to optimize the function of the organelle according to both internal and external demands.
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Affiliation(s)
- Elina Welchen
- Instituto de Agrobiotecnología del Litoral–Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional del LitoralSanta Fe, Argentina
- Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del LitoralSanta Fe, Argentina
- *Correspondence: Elina Welchen and Daniel H. Gonzalez, Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, CC 242 Paraje El Pozo, 3000 Santa Fe, Argentina e-mail: ;
| | - Lucila García
- Instituto de Agrobiotecnología del Litoral–Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional del LitoralSanta Fe, Argentina
- Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del LitoralSanta Fe, Argentina
| | - Natanael Mansilla
- Instituto de Agrobiotecnología del Litoral–Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional del LitoralSanta Fe, Argentina
- Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del LitoralSanta Fe, Argentina
| | - Daniel H. Gonzalez
- Instituto de Agrobiotecnología del Litoral–Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional del LitoralSanta Fe, Argentina
- Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del LitoralSanta Fe, Argentina
- *Correspondence: Elina Welchen and Daniel H. Gonzalez, Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, CC 242 Paraje El Pozo, 3000 Santa Fe, Argentina e-mail: ;
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Ge C, Spånning E, Glaser E, Wieslander A. Import determinants of organelle-specific and dual targeting peptides of mitochondria and chloroplasts in Arabidopsis thaliana. MOLECULAR PLANT 2014; 7:121-136. [PMID: 24214895 DOI: 10.1093/mp/sst148] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Most of the mitochondrial and chloroplastic proteins are synthesized in the cytosol as precursor proteins carrying an N-terminal targeting peptide (TP) directing them specifically to a correct organelle. However, there is a group of proteins that are dually targeted to mitochondria and chloroplasts using an ambiguous N-terminal dual targeting peptide (dTP). Here, we have investigated pattern properties of import determinants of organelle-specific TPs and dTPs combining mathematical multivariate data analysis (MVDA) with in vitro organellar import studies. We have used large datasets of mitochondrial and chloroplastic proteins found in organellar proteomes as well as manually selected data sets of experimentally confirmed organelle-specific TPs and dTPs from Arabidopsis thaliana. Two classes of organelle-specific TPs could be distinguished by MVDA and potential patterns or periodicity in the amino acid sequence contributing to the separation were revealed. dTPs were found to have intermediate sequence features between the organelle-specific TPs. Interestingly, introducing positively charged residues to the dTPs showed clustering towards the mitochondrial TPs in silico and resulted in inhibition of chloroplast, but not mitochondrial import in in vitro organellar import studies. These findings suggest that positive charges in the N-terminal region of TPs may function as an 'avoidance signal' for the chloroplast import.
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Affiliation(s)
- Changrong Ge
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
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Ast J, Stiebler AC, Freitag J, Bölker M. Dual targeting of peroxisomal proteins. Front Physiol 2013; 4:297. [PMID: 24151469 PMCID: PMC3798809 DOI: 10.3389/fphys.2013.00297] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 09/28/2013] [Indexed: 01/08/2023] Open
Abstract
Cellular compartmentalization into organelles serves to separate biological processes within the environment of a single cell. While some metabolic reactions are specific to a single organelle, others occur in more than one cellular compartment. Specific targeting of proteins to compartments inside of eukaryotic cells is mediated by defined sequence motifs. To achieve multiple targeting to different compartments cells use a variety of strategies. Here, we focus on mechanisms leading to dual targeting of peroxisomal proteins. In many instances, isoforms of peroxisomal proteins with distinct intracellular localization are encoded by separate genes. But also single genes can give rise to differentially localized proteins. Different isoforms can be generated by use of alternative transcriptional start sites, by differential splicing or ribosomal read-through of stop codons. In all these cases different peptide variants are produced, of which only one carries a peroxisomal targeting signal. Alternatively, peroxisomal proteins contain additional signals that compete for intracellular targeting. Dual localization of proteins residing in both the cytoplasm and in peroxisomes may also result from use of inefficient targeting signals. The recent observation that some bona fide cytoplasmic enzymes were also found in peroxisomes indicates that dual targeting of proteins to both the cytoplasm and the peroxisome might be more widespread. Although current knowledge of proteins exhibiting only partial peroxisomal targeting is far from being complete, we speculate that the metabolic capacity of peroxisomes might be larger than previously assumed.
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Affiliation(s)
- Julia Ast
- Department of Biology, Philipps University Marburg Marburg, Germany
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