1
|
Nickolov K, Gauthier A, Hashimoto K, Laitinen T, Väisänen E, Paasela T, Soliymani R, Kurusu T, Himanen K, Blokhina O, Fagerstedt KV, Jokipii-Lukkari S, Tuominen H, Häggman H, Wingsle G, Teeri TH, Kuchitsu K, Kärkönen A. Regulation of PaRBOH1-mediated ROS production in Norway spruce by Ca 2+ binding and phosphorylation. Front Plant Sci 2022; 13:978586. [PMID: 36311083 PMCID: PMC9608432 DOI: 10.3389/fpls.2022.978586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Plant respiratory burst oxidase homologs (RBOHs) are plasma membrane-localized NADPH oxidases that generate superoxide anion radicals, which then dismutate to H2O2, into the apoplast using cytoplasmic NADPH as an electron donor. PaRBOH1 is the most highly expressed RBOH gene in developing xylem as well as in a lignin-forming cell culture of Norway spruce (Picea abies L. Karst.). Since no previous information about regulation of gymnosperm RBOHs exist, our aim was to resolve how PaRBOH1 is regulated with a focus on phosphorylation. The N-terminal part of PaRBOH1 was found to contain several putative phosphorylation sites and a four-times repeated motif with similarities to the Botrytis-induced kinase 1 target site in Arabidopsis AtRBOHD. Phosphorylation was indicated for six of the sites in in vitro kinase assays using 15 amino-acid-long peptides for each of the predicted phosphotarget site in the presence of protein extracts of developing xylem. Serine and threonine residues showing positive response in the peptide assays were individually mutated to alanine (kinase-inactive) or to aspartate (phosphomimic), and the wild type PaRBOH1 and the mutated constructs transfected to human kidney embryogenic (HEK293T) cells with a low endogenous level of extracellular ROS production. ROS-producing assays with HEK cells showed that Ca2+ and phosphorylation synergistically activate the enzyme and identified several serine and threonine residues that are likely to be phosphorylated including a novel phosphorylation site not characterized in other plant species. These were further investigated with a phosphoproteomic study. Results of Norway spruce, the first gymnosperm species studied in relation to RBOH regulation, show that regulation of RBOH activity is conserved among seed plants.
Collapse
Affiliation(s)
- Kaloian Nickolov
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Adrien Gauthier
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- UniLaSalle, Agro-Ecology, Hydrogeochemistry, Environments & Resources, UP 2018.C101 of the Ministry in Charge of Agriculture (AGHYLE) Research Unit CS UP 2018.C101, Mont-Saint-Aignan, France
| | - Kenji Hashimoto
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Teresa Laitinen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Enni Väisänen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Tanja Paasela
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Natural Resources Institute Finland (Luke), Production Systems, Helsinki, Finland
| | - Rabah Soliymani
- Meilahti Clinical Proteomics Core Facility, Biochemistry & Dev. Biology, University of Helsinki, Biomedicum-Helsinki, Helsinki, Finland
| | - Takamitsu Kurusu
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Kristiina Himanen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Olga Blokhina
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Kurt V. Fagerstedt
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Soile Jokipii-Lukkari
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Hannele Tuominen
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Hely Häggman
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Gunnar Wingsle
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Teemu H. Teeri
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Kazuyuki Kuchitsu
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Anna Kärkönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Natural Resources Institute Finland (Luke), Production Systems, Helsinki, Finland
| |
Collapse
|
2
|
Nibbering P, Castilleux R, Wingsle G, Niittylä T. CAGEs are Golgi-localized GT31 enzymes involved in cellulose biosynthesis in Arabidopsis. Plant J 2022; 110:1271-1285. [PMID: 35289007 PMCID: PMC9321575 DOI: 10.1111/tpj.15734] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 05/31/2023]
Abstract
Cellulose is the main structural component in the plant cell walls. We show that two glycosyltransferase family 31 (GT31) enzymes of Arabidopsis thaliana, here named cellulose synthesis associated glycosyltransferases 1 and 2 (CAGE1 and 2), influence both primary and secondary cell wall cellulose biosynthesis. cage1cage2 mutants show primary cell wall defects manifesting as impaired growth and cell expansion in seedlings and etiolated hypocotyls, along with secondary cell wall defects, apparent as collapsed xylem vessels and reduced xylem wall thickness in the inflorescence stem. Single and double cage mutants also show increased sensitivity to the cellulose biosynthesis inhibitor isoxaben. The cage1cage2 phenotypes were associated with an approximately 30% reduction in cellulose content, an approximately 50% reduction in secondary cell wall CELLULOSE SYNTHASE (CESA) protein levels in stems and reduced cellulose biosynthesis rate in seedlings. CESA transcript levels were not significantly altered in cage1cage2 mutants, suggesting that the reduction in CESA levels was caused by a post-transcriptional mechanism. Both CAGE1 and 2 localize to the Golgi apparatus and are predicted to synthesize β-1,3-galactans on arabinogalactan proteins. In line with this, the cage1cage2 mutants exhibit reduced levels of β-Yariv binding to arabinogalactan protein linked β-1,3-galactan. This leads us to hypothesize that defects in arabinogalactan biosynthesis underlie the cellulose deficiency of the mutants.
Collapse
Affiliation(s)
- Pieter Nibbering
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science Centre, Swedish University of Agricultural Sciences901 83UmeåSweden
| | - Romain Castilleux
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science Centre, Swedish University of Agricultural Sciences901 83UmeåSweden
| | - Gunnar Wingsle
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science Centre, Swedish University of Agricultural Sciences901 83UmeåSweden
| | - Totte Niittylä
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science Centre, Swedish University of Agricultural Sciences901 83UmeåSweden
| |
Collapse
|
3
|
Gandla ML, Mähler N, Escamez S, Skotare T, Obudulu O, Möller L, Abreu IN, Bygdell J, Hertzberg M, Hvidsten TR, Moritz T, Wingsle G, Trygg J, Tuominen H, Jönsson LJ. Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees. Biotechnol Biofuels 2021; 14:43. [PMID: 33593413 PMCID: PMC7885582 DOI: 10.1186/s13068-021-01895-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/04/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Bioconversion of wood into bioproducts and biofuels is hindered by the recalcitrance of woody raw material to bioprocesses such as enzymatic saccharification. Targeted modification of the chemical composition of the feedstock can improve saccharification but this gain is often abrogated by concomitant reduction in tree growth. RESULTS In this study, we report on transgenic hybrid aspen (Populus tremula × tremuloides) lines that showed potential to increase biomass production both in the greenhouse and after 5 years of growth in the field. The transgenic lines carried an overexpression construct for Populus tremula × tremuloides vesicle-associated membrane protein (VAMP)-associated protein PttVAP27-17 that was selected from a gene-mining program for novel regulators of wood formation. Analytical-scale enzymatic saccharification without any pretreatment revealed for all greenhouse-grown transgenic lines, compared to the wild type, a 20-44% increase in the glucose yield per dry weight after enzymatic saccharification, even though it was statistically significant only for one line. The glucose yield after enzymatic saccharification with a prior hydrothermal pretreatment step with sulfuric acid was not increased in the greenhouse-grown transgenic trees on a dry-weight basis, but increased by 26-50% when calculated on a whole biomass basis in comparison to the wild-type control. Tendencies to increased glucose yields by up to 24% were present on a whole tree biomass basis after acidic pretreatment and enzymatic saccharification also in the transgenic trees grown for 5 years on the field when compared to the wild-type control. CONCLUSIONS The results demonstrate the usefulness of gene-mining programs to identify novel genes with the potential to improve biofuel production in tree biotechnology programs. Furthermore, multi-omic analyses, including transcriptomic, proteomic and metabolomic analyses, performed here provide a toolbox for future studies on the function of VAP27 proteins in plants.
Collapse
Affiliation(s)
| | - Niklas Mähler
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden
| | - Sacha Escamez
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Tomas Skotare
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
- Computational Life Science Cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden
| | - Ogonna Obudulu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Linus Möller
- SweTree Technologies, PO Box 7981, 907 19, Umeå, Sweden
| | - Ilka N Abreu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Joakim Bygdell
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | | | - Torgeir R Hvidsten
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Thomas Moritz
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Gunnar Wingsle
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Johan Trygg
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
- Computational Life Science Cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden
| | - Hannele Tuominen
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden.
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden.
| | - Leif J Jönsson
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| |
Collapse
|
4
|
Miguel S, Legrand G, Duriot L, Delporte M, Menin B, Michel C, Olry A, Chataigné G, Salwinski A, Bygdell J, Vercaigne D, Wingsle G, Hilbert JL, Bourgaud F, Hehn A, Gagneul D. A GDSL lipase-like from Ipomoea batatas catalyzes efficient production of 3,5-diCQA when expressed in Pichia pastoris. Commun Biol 2020; 3:673. [PMID: 33188250 PMCID: PMC7666189 DOI: 10.1038/s42003-020-01387-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 10/09/2020] [Indexed: 12/18/2022] Open
Abstract
The synthesis of 3,5-dicaffeoylquinic acid (3,5-DiCQA) has attracted the interest of many researchers for more than 30 years. Recently, enzymes belonging to the BAHD acyltransferase family were shown to mediate its synthesis, albeit with notably low efficiency. In this study, a new enzyme belonging to the GDSL lipase-like family was identified and proven to be able to transform chlorogenic acid (5-O-caffeoylquinic acid, 5-CQA, CGA) in 3,5-DiCQA with a conversion rate of more than 60%. The enzyme has been produced in different expression systems but has only been shown to be active when transiently synthesized in Nicotiana benthamiana or stably expressed in Pichia pastoris. The synthesis of the molecule could be performed in vitro but also by a bioconversion approach beginning from pure 5-CQA or from green coffee bean extract, thereby paving the road for producing it on an industrial scale. Miguel et al. identify a new enzyme belonging to the GDSL lipase-like family that is involved in the final stage of transformation of 5-CQA into 3,5-diCQA. This enzyme is able to realize an efficient transformation by over 60%, making the transformation process a valuable technological tool that can be easily transferred on an industrial scale.
Collapse
Affiliation(s)
- Sissi Miguel
- Plant Advanced Technologies, Vandœuvre-lès-Nancy, France
| | - Guillaume Legrand
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV - Institut Charles Viollette, 59000, Lille, France
| | - Léonor Duriot
- Plant Advanced Technologies, Vandœuvre-lès-Nancy, France
| | - Marianne Delporte
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV - Institut Charles Viollette, 59000, Lille, France
| | - Barbara Menin
- Université de Lorraine-INRAE, LAE, 54000, Nancy, France
| | - Cindy Michel
- Plant Advanced Technologies, Vandœuvre-lès-Nancy, France
| | | | - Gabrielle Chataigné
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV - Institut Charles Viollette, 59000, Lille, France
| | | | - Joakim Bygdell
- Chemistry Department, Umeå University, 90183, Umeå, Sweden
| | - Dominique Vercaigne
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV - Institut Charles Viollette, 59000, Lille, France
| | - Gunnar Wingsle
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Jean Louis Hilbert
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV - Institut Charles Viollette, 59000, Lille, France
| | | | - Alain Hehn
- Université de Lorraine-INRAE, LAE, 54000, Nancy, France.
| | - David Gagneul
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV - Institut Charles Viollette, 59000, Lille, France.
| |
Collapse
|
5
|
Väisänen E, Takahashi J, Obudulu O, Bygdell J, Karhunen P, Blokhina O, Laitinen T, Teeri TH, Wingsle G, Fagerstedt KV, Kärkönen A. Hunting monolignol transporters: membrane proteomics and biochemical transport assays with membrane vesicles of Norway spruce. J Exp Bot 2020; 71:6379-6395. [PMID: 32777074 PMCID: PMC7586744 DOI: 10.1093/jxb/eraa368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/02/2020] [Indexed: 05/02/2023]
Abstract
Both the mechanisms of monolignol transport and the transported form of monolignols in developing xylem of trees are unknown. We tested the hypothesis of an active, plasma membrane-localized transport of monolignol monomers, dimers, and/or glucosidic forms with membrane vesicles prepared from developing xylem and lignin-forming tissue-cultured cells of Norway spruce (Picea abies L. Karst.), as well as from control materials, comprising non-lignifying Norway spruce phloem and tobacco (Nicotiana tabacum L.) BY-2 cells. Xylem and BY-2 vesicles transported both coniferin and p-coumaryl alcohol glucoside, but inhibitor assays suggested that this transport was through the tonoplast. Membrane vesicles prepared from lignin-forming spruce cells showed coniferin transport, but the Km value for coniferin was much higher than those of xylem and BY-2 cells. Liquid chromatography-mass spectrometry analysis of membrane proteins isolated from spruce developing xylem, phloem, and lignin-forming cultured cells revealed multiple transporters. These were compared with a transporter gene set obtained by a correlation analysis with a selected set of spruce monolignol biosynthesis genes. Biochemical membrane vesicle assays showed no support for ABC-transporter-mediated monolignol transport but point to a role for secondary active transporters (such as MFS or MATE transporters). In contrast, proteomic and co-expression analyses suggested a role for ABC transporters and MFS transporters.
Collapse
Affiliation(s)
- Enni Väisänen
- Viikki Plant Science Centre, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Junko Takahashi
- Viikki Plant Science Centre, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Ogonna Obudulu
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, Umeå, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Joakim Bygdell
- Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Pirkko Karhunen
- Department of Chemistry, University of Helsinki, Helsinki, Finland
| | - Olga Blokhina
- Viikki Plant Science Centre, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Teresa Laitinen
- Viikki Plant Science Centre, Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Teemu H Teeri
- Viikki Plant Science Centre, Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Gunnar Wingsle
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Kurt V Fagerstedt
- Viikki Plant Science Centre, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Anna Kärkönen
- Viikki Plant Science Centre, Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Natural Resources Institute Finland (Luke), Production Systems, Plant Genetics, Helsinki, Finland
| |
Collapse
|
6
|
Zhu S, Wuolikainen A, Wu J, Öhman A, Wingsle G, Moritz T, Andersen PM, Forsgren L, Trupp M. Targeted Multiple Reaction Monitoring Analysis of CSF Identifies UCHL1 and GPNMB as Candidate Biomarkers for ALS. J Mol Neurosci 2019; 69:643-657. [PMID: 31721001 PMCID: PMC6858390 DOI: 10.1007/s12031-019-01411-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 09/26/2019] [Indexed: 02/06/2023]
Abstract
The neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and Parkinson’s disease (PD) share some common molecular deficits including disruption of protein homeostasis leading to disease-specific protein aggregation. While insoluble protein aggregates are the defining pathological confirmation of diagnosis, patient stratification based on early molecular etiologies may identify distinct subgroups within a clinical diagnosis that would respond differently in therapeutic development programs. We are developing targeted multiple reaction monitoring (MRM) mass spectrometry methods to rigorously quantify CSF proteins from known disease genes involved in lysosomal, ubiquitin-proteasomal, and autophagy pathways. Analysis of CSF from 21 PD, 21 ALS, and 25 control patients, rigorously matched for gender, age, and age of sample, revealed significant changes in peptide levels between PD, ALS, and control. In patients with PD, levels of two peptides for chromogranin B (CHGB, secretogranin 1) were significantly reduced. In CSF of patients with ALS, levels of two peptides from ubiquitin carboxy-terminal hydrolase like protein 1 (UCHL1) and one peptide each for glycoprotein non-metastatic melanoma protein B (GPNMB) and cathepsin D (CTSD) were all increased. Analysis of patients with ALS separated into two groups based on length of survival after CSF sampling revealed that the increases in GPNMB and UCHL1 were specific for short-lived ALS patients. While analysis of additional cohorts is required to validate these candidate biomarkers, this study suggests methods for stratification of ALS patients for clinical trials and identifies targets for drug efficacy measurements during therapeutic development.
Collapse
Affiliation(s)
- Shaochun Zhu
- Department of Clinical Science, Neurosciences, Umeå University, Building 10, NUS, Umeå, Sweden
| | | | - Junfang Wu
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Anders Öhman
- Department of Clinical Science, Neurosciences, Umeå University, Building 10, NUS, Umeå, Sweden
| | - Gunnar Wingsle
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Thomas Moritz
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Peter M Andersen
- Department of Clinical Science, Neurosciences, Umeå University, Building 10, NUS, Umeå, Sweden
| | - Lars Forsgren
- Department of Clinical Science, Neurosciences, Umeå University, Building 10, NUS, Umeå, Sweden
| | - Miles Trupp
- Department of Clinical Science, Neurosciences, Umeå University, Building 10, NUS, Umeå, Sweden.
| |
Collapse
|
7
|
Zhang X, Dominguez PG, Kumar M, Bygdell J, Miroshnichenko S, Sundberg B, Wingsle G, Niittylä T. Cellulose Synthase Stoichiometry in Aspen Differs from Arabidopsis and Norway Spruce. Plant Physiol 2018; 177:1096-1107. [PMID: 29760198 PMCID: PMC6053019 DOI: 10.1104/pp.18.00394] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 05/03/2018] [Indexed: 05/02/2023]
Abstract
Cellulose is synthesized at the plasma membrane by cellulose synthase complexes (CSCs) containing cellulose synthases (CESAs). Genetic analysis and CESA isoform quantification indicate that cellulose in the secondary cell walls of Arabidopsis (Arabidopsis thaliana) is synthesized by isoforms CESA4, CESA7, and CESA8 in equimolar amounts. Here, we used quantitative proteomics to investigate whether the CSC model based on Arabidopsis secondary cell wall CESA stoichiometry can be applied to the angiosperm tree aspen (Populus tremula) and the gymnosperm tree Norway spruce (Picea abies). In the developing xylem of aspen, the secondary cell wall CESA stoichiometry was 3:2:1 for PtCESA8a/b:PtCESA4:PtCESA7a/b, while in Norway spruce, the stoichiometry was 1:1:1, as observed previously in Arabidopsis. Furthermore, in aspen tension wood, the secondary cell wall CESA stoichiometry changed to 8:3:1 for PtCESA8a/b:PtCESA4:PtCESA7a/b. PtCESA8b represented 73% of the total secondary cell wall CESA pool, and quantitative polymerase chain reaction analysis of CESA transcripts in cryosectioned tension wood revealed increased PtCESA8b expression during the formation of the cellulose-enriched gelatinous layer, while the transcripts of PtCESA4, PtCESA7a/b, and PtCESA8a decreased. A wide-angle x-ray scattering analysis showed that the shift in CESA stoichiometry in tension wood coincided with an increase in crystalline cellulose microfibril diameter, suggesting that the CSC CESA composition influences microfibril properties. The aspen CESA stoichiometry results raise the possibility of alternative CSC models and suggest that homomeric PtCESA8b complexes are responsible for cellulose biosynthesis in the gelatinous layer in tension wood.
Collapse
Affiliation(s)
- Xueyang Zhang
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE 901 83 Umea, Sweden
| | - Pia Guadalupe Dominguez
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE 901 83 Umea, Sweden
| | - Manoj Kumar
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE 901 83 Umea, Sweden
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Joakim Bygdell
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE 901 83 Umea, Sweden
| | - Sergey Miroshnichenko
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE 901 83 Umea, Sweden
| | - Björn Sundberg
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE 901 83 Umea, Sweden
| | - Gunnar Wingsle
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE 901 83 Umea, Sweden
| | - Totte Niittylä
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE 901 83 Umea, Sweden
| |
Collapse
|
8
|
Bollhöner B, Jokipii-Lukkari S, Bygdell J, Stael S, Adriasola M, Muñiz L, Van Breusegem F, Ezcurra I, Wingsle G, Tuominen H. The function of two type II metacaspases in woody tissues of Populus trees. New Phytol 2018; 217:1551-1565. [PMID: 29243818 DOI: 10.1111/nph.14945] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 11/07/2017] [Indexed: 05/03/2023]
Abstract
Metacaspases (MCs) are cysteine proteases that are implicated in programmed cell death of plants. AtMC9 (Arabidopsis thaliana Metacaspase9) is a member of the Arabidopsis MC family that controls the rapid autolysis of the xylem vessel elements, but its downstream targets in xylem remain uncharacterized. PttMC13 and PttMC14 were identified as AtMC9 homologs in hybrid aspen (Populus tremula × tremuloides). A proteomic analysis was conducted in xylem tissues of transgenic hybrid aspen trees which carried either an overexpression or an RNA interference construct for PttMC13 and PttMC14. The proteomic analysis revealed modulation of levels of both previously known targets of metacaspases, such as Tudor staphylococcal nuclease, heat shock proteins and 14-3-3 proteins, as well as novel proteins, such as homologs of the PUTATIVE ASPARTIC PROTEASE3 (PASPA3) and the cysteine protease RD21 by PttMC13 and PttMC14. We identified here the pathways and processes that are modulated by PttMC13 and PttMC14 in xylem tissues. In particular, the results indicate involvement of PttMC13 and/or PttMC14 in downstream proteolytic processes and cell death of xylem elements. This work provides a valuable reference dataset on xylem-specific metacaspase functions for future functional and biochemical analyses.
Collapse
Affiliation(s)
- Benjamin Bollhöner
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90187, Umeå, Sweden
| | - Soile Jokipii-Lukkari
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90187, Umeå, Sweden
| | - Joakim Bygdell
- Department of Chemistry, Umeå University, 90187, Umeå, Sweden
| | - Simon Stael
- VIB-Ugent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium
| | - Mathilda Adriasola
- School of Biotechnology, Royal Institute of Technology (KTH), 10691, Stockholm, Sweden
| | - Luis Muñiz
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90187, Umeå, Sweden
| | - Frank Van Breusegem
- VIB-Ugent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Gent, Belgium
| | - Inés Ezcurra
- School of Biotechnology, Royal Institute of Technology (KTH), 10691, Stockholm, Sweden
| | - Gunnar Wingsle
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Hannele Tuominen
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90187, Umeå, Sweden
| |
Collapse
|
9
|
Obudulu O, Mähler N, Skotare T, Bygdell J, Abreu IN, Ahnlund M, Latha Gandla M, Petterle A, Moritz T, Hvidsten TR, Jönsson LJ, Wingsle G, Trygg J, Tuominen H. A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of Populus trees. BMC Genomics 2018; 19:11. [PMID: 29298676 PMCID: PMC5753437 DOI: 10.1186/s12864-017-4411-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/21/2017] [Indexed: 01/03/2023] Open
Abstract
Background Secretory Carrier-Associated Membrane Proteins (SCAMPs) are highly conserved 32–38 kDa proteins that are involved in membrane trafficking. A systems approach was taken to elucidate function of SCAMPs in wood formation of Populus trees. Phenotypic and multi-omics analyses were performed in woody tissues of transgenic Populus trees carrying an RNAi construct for Populus tremula x tremuloides SCAMP3 (PttSCAMP3; Potri.019G104000). Results The woody tissues of the transgenic trees displayed increased amounts of both polysaccharides and lignin oligomers, indicating increased deposition of both the carbohydrate and lignin components of the secondary cell walls. This coincided with a tendency towards increased wood density as well as significantly increased thickness of the suberized cork in the transgenic lines. Multivariate OnPLS (orthogonal projections to latent structures) modeling of five different omics datasets (the transcriptome, proteome, GC-MS metabolome, LC-MS metabolome and pyrolysis-GC/MS metabolome) collected from the secondary xylem tissues of the stem revealed systemic variation in the different variables in the transgenic lines, including changes that correlated with the changes in the secondary cell wall composition. The OnPLS model also identified a rather large number of proteins that were more abundant in the transgenic lines than in the wild type. Several of these were related to secretion and/or endocytosis as well as both primary and secondary cell wall biosynthesis. Conclusions Populus SCAMP proteins were shown to influence accumulation of secondary cell wall components, including polysaccharides and phenolic compounds, in the woody tissues of Populus tree stems. Our multi-omics analyses combined with the OnPLS modelling suggest that this function is mediated by changes in membrane trafficking to fine-tune the abundance of cell wall precursors and/or proteins involved in cell wall biosynthesis and transport. The data provides a multi-level source of information for future studies on the function of the SCAMP proteins in plant stem tissues. Electronic supplementary material The online version of this article (10.1186/s12864-017-4411-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ogonna Obudulu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden.,Computational life science cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden.,Present address: Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Niklas Mähler
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187, Umeå, Sweden.,Faculty of Chemistry, Biotechnology and Food Science, Norwegian, University of Life Sciences, 1432, Ås, Norway
| | - Tomas Skotare
- Department of Chemistry, Umeå University, 90187, Umeå, Sweden.,Computational life science cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden
| | - Joakim Bygdell
- Department of Chemistry, Umeå University, 90187, Umeå, Sweden.,Computational life science cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden
| | - Ilka N Abreu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Maria Ahnlund
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | | | - Anna Petterle
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187, Umeå, Sweden
| | - Thomas Moritz
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Torgeir R Hvidsten
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187, Umeå, Sweden.,Faculty of Chemistry, Biotechnology and Food Science, Norwegian, University of Life Sciences, 1432, Ås, Norway
| | - Leif J Jönsson
- Department of Chemistry, Umeå University, 90187, Umeå, Sweden
| | - Gunnar Wingsle
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Johan Trygg
- Department of Chemistry, Umeå University, 90187, Umeå, Sweden.,Computational life science cluster (CLiC), Department of Chemistry, Umeå University, Umeå, Sweden
| | - Hannele Tuominen
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 90187, Umeå, Sweden.
| |
Collapse
|
10
|
Bygdell J, Srivastava V, Obudulu O, Srivastava MK, Nilsson R, Sundberg B, Trygg J, Mellerowicz EJ, Wingsle G. Protein expression in tension wood formation monitored at high tissue resolution in Populus. J Exp Bot 2017; 68:3405-3417. [PMID: 28633298 PMCID: PMC5853651 DOI: 10.1093/jxb/erx186] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 05/30/2017] [Indexed: 05/18/2023]
Abstract
Tension wood (TW) is a specialized tissue with contractile properties that is formed by the vascular cambium in response to gravitational stimuli. We quantitatively analysed the proteomes of Populus tremula cambium and its xylem cell derivatives in stems forming normal wood (NW) and TW to reveal the mechanisms underlying TW formation. Phloem-, cambium-, and wood-forming tissues were sampled by tangential cryosectioning and pooled into nine independent samples. The proteomes of TW and NW samples were similar in the phloem and cambium samples, but diverged early during xylogenesis, demonstrating that reprogramming is an integral part of TW formation. For example, 14-3-3, reactive oxygen species, ribosomal and ATPase complex proteins were found to be up-regulated at early stages of xylem differentiation during TW formation. At later stages of xylem differentiation, proteins involved in the biosynthesis of cellulose and enzymes involved in the biosynthesis of rhamnogalacturonan-I, rhamnogalacturonan-II, arabinogalactan-II and fasciclin-like arabinogalactan proteins were up-regulated in TW. Surprisingly, two isoforms of exostosin family proteins with putative xylan xylosyl transferase function and several lignin biosynthesis proteins were also up-regulated, even though xylan and lignin are known to be less abundant in TW than in NW. These data provided new insight into the processes behind TW formation.
Collapse
Affiliation(s)
- Joakim Bygdell
- Department of Chemistry, Umeå University, Umeå, Sweden
- Computational life science cluster (CLiC), Umeå University, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Ogonna Obudulu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Manoj K Srivastava
- Crop Improvement Division, Indian Grassland and Fodder Research Institute, Jhansi, UP, India
| | - Robert Nilsson
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Björn Sundberg
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Johan Trygg
- Department of Chemistry, Umeå University, Umeå, Sweden
- Computational life science cluster (CLiC), Umeå University, Sweden
| | - Ewa J Mellerowicz
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Gunnar Wingsle
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| |
Collapse
|
11
|
|
12
|
Obudulu O, Bygdell J, Sundberg B, Moritz T, Hvidsten TR, Trygg J, Wingsle G. Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development. BMC Genomics 2016; 17:119. [PMID: 26887814 PMCID: PMC4758094 DOI: 10.1186/s12864-016-2458-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 02/09/2016] [Indexed: 01/08/2023] Open
Abstract
Background Wood development is of outstanding interest both to basic research and industry due to the associated cellulose and lignin biomass production. Efforts to elucidate wood formation (which is essential for numerous aspects of both pure and applied plant science) have been made using transcriptomic analyses and/or low-resolution sampling. However, transcriptomic data do not correlate perfectly with levels of expressed proteins due to effects of post-translational modifications and variations in turnover rates. In addition, high-resolution analysis is needed to characterize key transitions. In order to identify protein profiles across the developmental region of wood formation, an in-depth and tissue specific sampling was performed. Results We examined protein profiles, using an ultra-performance liquid chromatography/quadrupole time of flight mass spectrometry system, in high-resolution tangential sections spanning all wood development zones in Populus tremula from undifferentiated cambium to mature phloem and xylem, including cell expansion and cell death zones. In total, we analyzed 482 sections, 20–160 μm thick, from four 47-year-old trees growing wild in Sweden. We obtained high quality expression profiles for 3,082 proteins exhibiting consistency across the replicates, considering that the trees were growing in an uncontrolled environment. A combination of Principal Component Analysis (PCA), Orthogonal Projections to Latent Structures (OPLS) modeling and an enhanced stepwise linear modeling approach identified several major transitions in global protein expression profiles, pinpointing (for example) locations of the cambial division leading to phloem and xylem cells, and secondary cell wall formation zones. We also identified key proteins and associated pathways underlying these developmental landmarks. For example, many of the lignocellulosic related proteins were upregulated in the expansion to the early developmental xylem zone, and for laccases with a rapid decrease in early xylem zones. We observed upregulation of two forms of xylem cysteine protease (Potri.002G005700.1 and Potri.005G256000.2; Pt-XCP2.1) in early xylem and their downregulation in late maturing xylem. Our data also show that Pt-KOR1.3 (Potri.003G151700.2) exhibits an expression pattern that supports the hypothesis put forward in previous studies that this is a key xyloglucanase involved in cellulose biosynthesis in primary cell walls and reduction of cellulose crystallinity in secondary walls. Conclusion Our novel multivariate approach highlights important processes and provides confirmatory insights into the molecular foundations of wood development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2458-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ogonna Obudulu
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden. .,Computational life science cluster (CLiC), Umeå University, Umeå, Sweden.
| | - Joakim Bygdell
- Department of Chemistry, Umeå University, SE-90187, Umeå, Sweden. .,Computational life science cluster (CLiC), Umeå University, Umeå, Sweden.
| | - Björn Sundberg
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden.
| | - Thomas Moritz
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden.
| | - Torgeir R Hvidsten
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, SE-90187, Umeå, Sweden. .,Computational life science cluster (CLiC), Umeå University, Umeå, Sweden. .,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway.
| | - Johan Trygg
- Department of Chemistry, Umeå University, SE-90187, Umeå, Sweden. .,Computational life science cluster (CLiC), Umeå University, Umeå, Sweden.
| | - Gunnar Wingsle
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden.
| |
Collapse
|
13
|
Xu H, Bygdell J, Wingsle G, Byström AS. Yeast Elongator protein Elp1p does not undergo proteolytic processing in exponentially growing cells. Microbiologyopen 2015; 4:867-78. [PMID: 26407534 PMCID: PMC4694139 DOI: 10.1002/mbo3.285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/27/2015] [Accepted: 07/30/2015] [Indexed: 01/09/2023] Open
Abstract
In eukaryotic organisms, Elongator is a six-subunit protein complex required for the formation of 5-carbamoylmethyl (ncm(5) ) and 5-methylcarboxymethyl (mcm(5) ) side chains on uridines present at the wobble position (U34 ) of tRNA. The open reading frame encoding the largest Elongator subunit Elp1p has two in-frame 5' AUG methionine codons separated by 48 nucleotides. Here, we show that the second AUG acts as the start codon of translation. Furthermore, Elp1p was previously shown to exist in two major forms of which one was generated by proteolysis of full-length Elp1p and this proteolytic cleavage was suggested to regulate Elongator complex activity. In this study, we found that the vacuolar protease Prb1p was responsible for the cleavage of Elp1p. The cleavage occurs between residues 203 (Lys) and 204 (Ala) as shown by amine reactive Tandem Mass Tag followed by LC-MS/MS (liquid chromatography mass spectrometry) analysis. However, using a modified protein extraction procedure, including trichloroacetic acid, only full-length Elp1p was observed, showing that truncation of Elp1p is an artifact occurring during protein extraction. Consequently, our results indicate that N-terminal truncation of Elp1p is not likely to regulate Elongator complex activity.
Collapse
Affiliation(s)
- Hao Xu
- Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
| | - Joakim Bygdell
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 87, Umeå, Sweden
| | - Gunnar Wingsle
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 87, Umeå, Sweden
| | - Anders S Byström
- Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
| |
Collapse
|
14
|
Srivastava V, Obudulu O, Bygdell J, Löfstedt T, Rydén P, Nilsson R, Ahnlund M, Johansson A, Jonsson P, Freyhult E, Qvarnström J, Karlsson J, Melzer M, Moritz T, Trygg J, Hvidsten TR, Wingsle G. OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants. BMC Genomics 2013; 14:893. [PMID: 24341908 PMCID: PMC3878592 DOI: 10.1186/1471-2164-14-893] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 11/27/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reactive oxygen species (ROS) are involved in the regulation of diverse physiological processes in plants, including various biotic and abiotic stress responses. Thus, oxidative stress tolerance mechanisms in plants are complex, and diverse responses at multiple levels need to be characterized in order to understand them. Here we present system responses to oxidative stress in Populus by integrating data from analyses of the cambial region of wild-type controls and plants expressing high-isoelectric-point superoxide dismutase (hipI-SOD) transcripts in antisense orientation showing a higher production of superoxide. The cambium, a thin cell layer, generates cells that differentiate to form either phloem or xylem and is hypothesized to be a major reason for phenotypic perturbations in the transgenic plants. Data from multiple platforms including transcriptomics (microarray analysis), proteomics (UPLC/QTOF-MS), and metabolomics (GC-TOF/MS, UPLC/MS, and UHPLC-LTQ/MS) were integrated using the most recent development of orthogonal projections to latent structures called OnPLS. OnPLS is a symmetrical multi-block method that does not depend on the order of analysis when more than two blocks are analysed. Significantly affected genes, proteins and metabolites were then visualized in painted pathway diagrams. RESULTS The main categories that appear to be significantly influenced in the transgenic plants were pathways related to redox regulation, carbon metabolism and protein degradation, e.g. the glycolysis and pentose phosphate pathways (PPP). The results provide system-level information on ROS metabolism and responses to oxidative stress, and indicate that some initial responses to oxidative stress may share common pathways. CONCLUSION The proposed data evaluation strategy shows an efficient way of compiling complex, multi-platform datasets to obtain significant biological information.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gunnar Wingsle
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden.
| |
Collapse
|
15
|
Businge E, Bygdell J, Wingsle G, Moritz T, Egertsdotter U. The effect of carbohydrates and osmoticum on storage reserve accumulation and germination of Norway spruce somatic embryos. Physiol Plant 2013; 149:273-85. [PMID: 23421376 DOI: 10.1111/ppl.12039] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 01/22/2013] [Accepted: 01/27/2013] [Indexed: 05/22/2023]
Abstract
Somatic embryogenesis (SE) represents a useful experimental system for studying the regulatory mechanisms of embryo development. In this study, the effect of carbohydrates and osmoticum on storage reserve accumulation and germination of Norway spruce [Picea abies (L.) Karst] somatic embryos were investigated. Using time lapse photography, we monitored development from proliferation of proembryogenic masses (PEMs) to maturation of somatic embryos in two P. abies cell lines cultured on two maturation treatments. A combination of sugar assays, metabolic and proteomic analyses were used to quantify storage reserves in the mature somatic embryos. The maturation treatment containing a nonpermeating osmoticum, polyethylene glycol (PEG, 7.5%) and maltose (3%) as the carbohydrate gave significantly high maturation and low germination frequencies of somatic embryos compared to the treatment with only 3% sucrose. Somatic embryos treated with 3% sucrose contained high levels of sucrose, raffinose and late embryogenesis abundant (LEA) proteins. These compounds are known to be involved in the acquisition of desiccation tolerance during seed development and maturation. In addition the sucrose treatment significantly increased the content of starch in the somatic embryos while the maltose and PEG treatment resulted in somatic embryos with a high content of storage proteins. The high levels of sucrose, raffinose and LEA proteins in the embryos treated with 3% sucrose suggest that sucrose may improve the germination of somatic embryos by promoting the acquisition of desiccation tolerance.
Collapse
Affiliation(s)
- Edward Businge
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | | | | | | | | |
Collapse
|
16
|
Shaikhali J, de Dios Barajas-Lopéz J, Ötvös K, Kremnev D, Garcia AS, Srivastava V, Wingsle G, Bako L, Strand Å. The CRYPTOCHROME1-dependent response to excess light is mediated through the transcriptional activators ZINC FINGER PROTEIN EXPRESSED IN INFLORESCENCE MERISTEM LIKE1 and ZML2 in Arabidopsis. Plant Cell 2012; 24:3009-25. [PMID: 22786870 PMCID: PMC3426129 DOI: 10.1105/tpc.112.100099] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 06/05/2012] [Accepted: 06/19/2012] [Indexed: 05/19/2023]
Abstract
Exposure of plants to light intensities that exceed the electron utilization capacity of the chloroplast has a dramatic impact on nuclear gene expression. The photoreceptor Cryptochrome 1 (cry1) is essential to the induction of genes encoding photoprotective components in Arabidopsis thaliana. Bioinformatic analysis of the cry1 regulon revealed the putative cis-element CryR1 (GnTCKAG), and here we demonstrate an interaction between CryR1 and the zinc finger GATA-type transcription factors ZINC FINGER PROTEIN EXPRESSED IN INFLORESCENCE MERISTEM LIKE1 (ZML1) and ZML2. The ZML proteins specifically bind to the CryR1 cis-element as demonstrated in vitro and in vivo, and TCTAG was shown to constitute the core sequence required for ZML2 binding. In addition, ZML2 activated transcription of the yellow fluorescent protein reporter gene driven by the CryR1 cis-element in Arabidopsis leaf protoplasts. T-DNA insertion lines for ZML2 and its homolog ZML1 demonstrated misregulation of several cry1-dependent genes in response to excess light. Furthermore, the zml1 and zml2 T-DNA insertion lines displayed a high irradiance-sensitive phenotype with significant photoinactivation of photosystem II (PSII), indicated by reduced maximum quantum efficiency of PSII, and severe photobleaching. Thus, we identified the ZML2 and ZML1 GATA transcription factors as two essential components of the cry1-mediated photoprotective response.
Collapse
Affiliation(s)
- Jehad Shaikhali
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-901 87 Umea, Sweden
| | | | - Krisztina Ötvös
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-901 87 Umea, Sweden
- Institute of Plant Biology, Biological Research Center, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
| | - Dmitry Kremnev
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-901 87 Umea, Sweden
| | - Ana Sánchez Garcia
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-901 87 Umea, Sweden
| | - Vaibhav Srivastava
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, S-901 87 Umea, Sweden
| | - Gunnar Wingsle
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, S-901 87 Umea, Sweden
| | - Laszlo Bako
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-901 87 Umea, Sweden
| | - Åsa Strand
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-901 87 Umea, Sweden
- Address correspondence to
| |
Collapse
|
17
|
Shaikhali J, Norén L, de Dios Barajas-López J, Srivastava V, König J, Sauer UH, Wingsle G, Dietz KJ, Strand Å. Redox-mediated mechanisms regulate DNA binding activity of the G-group of basic region leucine zipper (bZIP) transcription factors in Arabidopsis. J Biol Chem 2012; 287:27510-25. [PMID: 22718771 DOI: 10.1074/jbc.m112.361394] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plant genes that contain the G-box in their promoters are responsive to a variety of environmental stimuli. Bioinformatics analysis of transcriptome data revealed that the G-box element is significantly enriched in promoters of high light-responsive genes. From nuclear extracts of high light-treated Arabidopsis plants, we identified the AtbZIP16 transcription factor as a component binding to the G-box-containing promoter fragment of light-harvesting chlorophyll a/b-binding protein2.4 (LHCB2.4). AtbZIP16 belongs to the G-group of Arabidopsis basic region leucine zipper (bZIP) type transcription factors. Although AtbZIP16 and its close homologues AtbZIP68 and AtGBF1 bind the G-box, they do not bind the mutated half-sites of the G-box palindrome. In addition, AtbZIP16 interacts with AtbZIP68 and AtGBF1 in the yeast two-hybrid system. A conserved Cys residue was shown to be necessary for redox regulation and enhancement of DNA binding activity in all three proteins. Furthermore, transgenic Arabidopsis lines overexpressing the wild type version of bZIP16 and T-DNA insertion mutants for bZIP68 and GBF1 demonstrated impaired regulation of LHCB2.4 expression. Finally, overexpression lines for the mutated Cys variant of bZIP16 provided support for the biological significance of Cys(330) in redox regulation of gene expression. Thus, our results suggest that environmentally induced changes in the redox state regulate the activity of members of the G-group of bZIP transcription factors.
Collapse
Affiliation(s)
- Jehad Shaikhali
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Chibani K, Tarrago L, Gualberto JM, Wingsle G, Rey P, Jacquot JP, Rouhier N. Atypical thioredoxins in poplar: the glutathione-dependent thioredoxin-like 2.1 supports the activity of target enzymes possessing a single redox active cysteine. Plant Physiol 2012; 159:592-605. [PMID: 22523226 PMCID: PMC3375927 DOI: 10.1104/pp.112.197723] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 04/19/2012] [Indexed: 05/20/2023]
Abstract
Plant thioredoxins (Trxs) constitute a complex family of thiol oxidoreductases generally sharing a WCGPC active site sequence. Some recently identified plant Trxs (Clot, Trx-like1 and -2, Trx-lilium1, -2, and -3) display atypical active site sequences with altered residues between the two conserved cysteines. The transcript expression patterns, subcellular localizations, and biochemical properties of some representative poplar (Populus spp.) isoforms were investigated. Measurements of transcript levels for the 10 members in poplar organs indicate that most genes are constitutively expressed. Using transient expression of green fluorescent protein fusions, Clot and Trx-like1 were found to be mainly cytosolic, whereas Trx-like2.1 was located in plastids. All soluble recombinant proteins, except Clot, exhibited insulin reductase activity, although with variable efficiencies. Whereas Trx-like2.1 and Trx-lilium2.2 were efficiently regenerated both by NADPH-Trx reductase and glutathione, none of the proteins were reduced by the ferredoxin-Trx reductase. Only Trx-like2.1 supports the activity of plastidial thiol peroxidases and methionine sulfoxide reductases employing a single cysteine residue for catalysis and using a glutathione recycling system. The second active site cysteine of Trx-like2.1 is dispensable for this reaction, indicating that the protein possesses a glutaredoxin-like activity. Interestingly, the Trx-like2.1 active site replacement, from WCRKC to WCGPC, suppresses its capacity to use glutathione as a reductant but is sufficient to allow the regeneration of target proteins employing two cysteines for catalysis, indicating that the nature of the residues composing the active site sequence is crucial for substrate selectivity/recognition. This study provides another example of the cross talk existing between the glutathione/glutaredoxin and Trx-dependent pathways.
Collapse
|
19
|
Ekström JO, Habayeb MS, Srivastava V, Kieselbach T, Wingsle G, Hultmark D. Drosophila Nora virus capsid proteins differ from those of other picorna-like viruses. Virus Res 2011; 160:51-8. [PMID: 21605604 DOI: 10.1016/j.virusres.2011.05.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 05/03/2011] [Accepted: 05/06/2011] [Indexed: 01/29/2023]
Abstract
The recently discovered Nora virus from Drosophila melanogaster is a single-stranded RNA virus. Its published genomic sequence encodes a typical picorna-like cassette of replicative enzymes, but no capsid proteins similar to those in other picorna-like viruses. We have now done additional sequencing at the termini of the viral genome, extending it by 455 nucleotides at the 5' end, but no more coding sequence was found. The completeness of the final 12,333-nucleotide sequence was verified by the production of infectious virus from the cloned genome. To identify the capsid proteins, we purified Nora virus particles and analyzed their proteins by mass spectrometry. Our results show that the capsid is built from three major proteins, VP4A, B and C, encoded in the fourth open reading frame of the viral genome. The viral particles also contain traces of a protein from the third open reading frame, VP3. VP4A and B are not closely related to other picorna-like virus capsid proteins in sequence, but may form similar jelly roll folds. VP4C differs from the others and is predicted to have an essentially α-helical conformation. In a related virus, identified from EST database sequences from Nasonia parasitoid wasps, VP4C is encoded in a separate open reading frame, separated from VP4A and B by a frame-shift. This opens a possibility that VP4C is produced in non-equimolar quantities. Altogether, our results suggest that the Nora virus capsid has a different protein organization compared to the order Picornavirales.
Collapse
Affiliation(s)
- Jens-Ola Ekström
- Department of Molecular Biology, Umeå University, S-901 87 Umeå, Sweden.
| | | | | | | | | | | |
Collapse
|
20
|
Bergemalm D, Forsberg K, Srivastava V, Graffmo KS, Andersen PM, Brännström T, Wingsle G, Marklund SL. Superoxide dismutase-1 and other proteins in inclusions from transgenic amyotrophic lateral sclerosis model mice. J Neurochem 2010; 114:408-18. [DOI: 10.1111/j.1471-4159.2010.06753.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
21
|
Nilsson R, Bernfur K, Gustavsson N, Bygdell J, Wingsle G, Larsson C. Proteomics of plasma membranes from poplar trees reveals tissue distribution of transporters, receptors, and proteins in cell wall formation. Mol Cell Proteomics 2009; 9:368-87. [PMID: 19955078 PMCID: PMC2830847 DOI: 10.1074/mcp.m900289-mcp200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
By exploiting the abundant tissues available from Populus trees, 3-4 m high, we have been able to isolate plasma membranes of high purity from leaves, xylem, and cambium/phloem at a time (4 weeks after bud break) when photosynthesis in the leaves and wood formation in the xylem should have reached a steady state. More than 40% of the 956 proteins identified were found in the plasma membranes of all three tissues and may be classified as "housekeeping" proteins, a typical example being P-type H(+)-ATPases. Among the 213 proteins predicted to be integral membrane proteins, transporters constitute the largest class (41%) followed by receptors (14%) and proteins involved in cell wall and carbohydrate metabolism (8%) and membrane trafficking (8%). ATP-binding cassette transporters (all members of subfamilies B, C, and G) and receptor-like kinases (four subfamilies) were two of the largest protein families found, and the members of these two families showed pronounced tissue distribution. Leaf plasma membranes were characterized by a very high proportion of transporters, constituting almost half of the integral proteins. Proteins involved in cell wall synthesis (such as cellulose and sucrose synthases) and membrane trafficking were most abundant in xylem plasma membranes in agreement with the role of the xylem in wood formation. Twenty-five integral proteins and 83 soluble proteins were exclusively found in xylem plasma membranes, which identifies new candidates associated with cell wall synthesis and wood formation. Among the proteins uniquely found in xylem plasma membranes were most of the enzymes involved in lignin biosynthesis, which suggests that they may exist as a complex linked to the plasma membrane.
Collapse
Affiliation(s)
- Robert Nilsson
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå Plant Science Centre, SE-90183 Umeå, Sweden.
| | | | | | | | | | | |
Collapse
|
22
|
Srivastava V, Srivastava MK, Chibani K, Nilsson R, Rouhier N, Melzer M, Wingsle G. Alternative splicing studies of the reactive oxygen species gene network in Populus reveal two isoforms of high-isoelectric-point superoxide dismutase. Plant Physiol 2009; 149:1848-1859. [PMID: 19176719 PMCID: PMC2663752 DOI: 10.1104/pp.108.133371] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Accepted: 01/26/2009] [Indexed: 05/27/2023]
Abstract
Recent evidence has shown that alternative splicing (AS) is widely involved in the regulation of gene expression, substantially extending the diversity of numerous proteins. In this study, a subset of expressed sequence tags representing members of the reactive oxygen species gene network was selected from the PopulusDB database to investigate AS mechanisms in Populus. Examples of all known types of AS were detected, but intron retention was the most common. Interestingly, the closest Arabidopsis (Arabidopsis thaliana) homologs of half of the AS genes identified in Populus are not reportedly alternatively spliced. Two genes encoding the protein of most interest in our study (high-isoelectric-point superoxide dismutase [hipI-SOD]) have been found in black cottonwood (Populus trichocarpa), designated PthipI-SODC1 and PthipI-SODC2. Analysis of the expressed sequence tag libraries has indicated the presence of two transcripts of PthipI-SODC1 (hipI-SODC1b and hipI-SODC1s). Alignment of these sequences with the PthipI-SODC1 gene showed that hipI-SODC1b was 69 bp longer than hipI-SODC1s due to an AS event involving the use of an alternative donor splice site in the sixth intron. Transcript analysis showed that the splice variant hipI-SODC1b was differentially expressed, being clearly expressed in cambial and xylem, but not phloem, regions. In addition, immunolocalization and mass spectrometric data confirmed the presence of hipI-SOD proteins in vascular tissue. The functionalities of the spliced gene products were assessed by expressing recombinant hipI-SOD proteins and in vitro SOD activity assays.
Collapse
Affiliation(s)
- Vaibhav Srivastava
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
| | | | | | | | | | | | | |
Collapse
|
23
|
Chibani K, Wingsle G, Jacquot JP, Gelhaye E, Rouhier N. Comparative genomic study of the thioredoxin family in photosynthetic organisms with emphasis on Populus trichocarpa. Mol Plant 2009; 2:308-22. [PMID: 19825616 DOI: 10.1093/mp/ssn076] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The recent genome sequencing of Populus trichocarpa and Vitis vinifera, two models of woody plants, of Sorghum bicolor, a model of monocot using C4 metabolism, and of the moss Physcomitrella patens, together with the availability of photosynthetic organism genomes allows performance of a comparative genomic study with organisms having different ways of life, reproduction modes, biological traits, and physiologies. Thioredoxins (Trxs) are small ubiquitous proteins involved in the reduction of disulfide bridges in a variety of target enzymes present in all sub-cellular compartments and involved in many biochemical reactions. The genes coding for these enzymes have been identified in these newly sequenced genomes and annotated. The gene content, organization and distribution were compared to other photosynthetic organisms, leading to a refined classification. This analysis revealed that higher plants and bryophytes have a more complex family compared to algae and cyanobacteria and to non-photosynthetic organisms, since poplar exhibits 49 genes coding for typical and atypical thioredoxins and thioredoxin reductases, namely one-third more than monocots such as Oryza sativa and S. bicolor. The higher number of Trxs in poplar is partially explained by gene duplication in the Trx m, h, and nucleoredoxin classes. Particular attention was paid to poplar genes with emphasis on Trx-like classes called Clot, thioredoxin-like, thioredoxins of the lilium type and nucleoredoxins, which were not described in depth in previous genomic studies.
Collapse
Affiliation(s)
- Kamel Chibani
- UMR 1136 Nancy University-INRA, Interactions Arbres Microorganismes, IFR 110 GEEF, Faculté des Sciences, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France
| | | | | | | | | |
Collapse
|
24
|
Bylesjö M, Nilsson R, Srivastava V, Grönlund A, Johansson AI, Jansson S, Karlsson J, Moritz T, Wingsle G, Trygg J. Integrated analysis of transcript, protein and metabolite data to study lignin biosynthesis in hybrid aspen. J Proteome Res 2009; 8:199-210. [PMID: 19053836 DOI: 10.1021/pr800298s] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tree biotechnology will soon reach a mature state where it will influence the overall supply of fiber, energy and wood products. We are now ready to make the transition from identifying candidate genes, controlling important biological processes, to discovering the detailed molecular function of these genes on a broader, more holistic, systems biology level. In this paper, a strategy is outlined for informative data generation and integrated modeling of systematic changes in transcript, protein and metabolite profiles measured from hybrid aspen samples. The aim is to study characteristics of common changes in relation to genotype-specific perturbations affecting the lignin biosynthesis and growth. We show that a considerable part of the systematic effects in the system can be tracked across all platforms and that the approach has a high potential value in functional characterization of candidate genes.
Collapse
Affiliation(s)
- Max Bylesjö
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Overmyer K, Kollist H, Tuominen H, Betz C, Langebartels C, Wingsle G, Kangasjärvi S, Brader G, Mullineaux P, Kangasjärvi J. Complex phenotypic profiles leading to ozone sensitivity in Arabidopsis thaliana mutants. Plant Cell Environ 2008; 31:1237-1249. [PMID: 18518918 DOI: 10.1111/j.1365-3040.2008.01837.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Genetically tractable model plants offer the possibility of defining the plant O(3) response at the molecular level. To this end, we have isolated a collection of ozone (O(3))-sensitive mutants of Arabidopsis thaliana. Mutant phenotypes and genetics were characterized. Additionally, parameters associated with O(3) sensitivity were analysed, including stomatal conductance, sensitivity to and accumulation of reactive oxygen species, antioxidants, stress gene-expression and the accumulation of stress hormones. Each mutant has a unique phenotypic profile, with O(3) sensitivity caused by a unique set of alterations in these systems. O(3) sensitivity in these mutants is not caused by gross deficiencies in the antioxidant pathways tested here. The rcd3 mutant exhibits misregulated stomata. All mutants exhibited changes in stress hormones consistent with the known hormonal roles in defence and cell death regulation. One mutant, dubbed re-8, is an allele of the classic leaf development mutant reticulata and exhibits phenotypes dependent on light conditions. This study shows that O(3) sensitivity can be determined by deficiencies in multiple interacting plant systems and provides genetic evidence linking these systems.
Collapse
Affiliation(s)
- Kirk Overmyer
- Department of Biological and Environmental Sciences, Plant Biology, University of Helsinki, Helsinki, Finland.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Koh CS, Navrot N, Didierjean C, Rouhier N, Hirasawa M, Knaff DB, Wingsle G, Samian R, Jacquot JP, Corbier C, Gelhaye E. An atypical catalytic mechanism involving three cysteines of thioredoxin. J Biol Chem 2008; 283:23062-72. [PMID: 18552403 DOI: 10.1074/jbc.m802093200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Unlike other thioredoxins h characterized so far, a poplar thioredoxin of the h type, PtTrxh4, is reduced by glutathione and glutaredoxin (Grx) but not NADPH:thioredoxin reductase (NTR). PtTrxh4 contains three cysteines: one localized in an N-terminal extension (Cys(4)) and two (Cys(58) and Cys(61)) in the classical thioredoxin active site ((57)WCGPC(61)). The property of a mutant in which Cys(58) was replaced by serine demonstrates that it is responsible for the initial nucleophilic attack during the catalytic cycle. The observation that the C4S mutant is inactive in the presence of Grx but fully active when dithiothreitol is used as a reductant indicates that Cys(4) is required for the regeneration of PtTrxh4 by Grx. Biochemical and x-ray crystallographic studies indicate that two intramolecular disulfide bonds involving Cys(58) can be formed, linking it to either Cys(61) or Cys(4). We propose thus a four-step disulfide cascade mechanism involving the transient glutathionylation of Cys(4) to convert this atypical thioredoxin h back to its active reduced form.
Collapse
Affiliation(s)
- Cha San Koh
- Equipe Biocristallographie, UMR 7036 CNRS-Université Henri Poincaré, URAFPA, Equipe PB2P, Faculté des Sciences et Techniques, Nancy Université, BP 239, 54506 Vandoeuvre Cedex France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Bäckström S, Elfving N, Nilsson R, Wingsle G, Björklund S. Purification of a plant mediator from Arabidopsis thaliana identifies PFT1 as the Med25 subunit. Mol Cell 2007; 26:717-29. [PMID: 17560376 DOI: 10.1016/j.molcel.2007.05.007] [Citation(s) in RCA: 196] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Revised: 04/04/2007] [Accepted: 05/07/2007] [Indexed: 11/26/2022]
Abstract
Mediator, a central coregulator of transcription, has been identified as a large protein complex in eukaryotes ranging from yeast to man. It is therefore remarkable that Mediator has not yet been identified within the plant kingdom. Here we identify Mediator in a plant, Arabidopsis thaliana. The plant Mediator subunits typically show very low homology to other species, but our biochemical purification identifies 21 conserved and six A. thaliana-specific Mediator subunits. Most notably, we identify the A. thaliana proteins STRUWWELPETER (SWP) and PHYTOCHROME AND FLOWERING TIME 1 (PFT1) as the Med14 and Med25 subunits, respectively. These findings show that specific plant Mediator subunits are linked to the regulation of specialized processes such as the control of cell proliferation and the regulation of flowering time in response to light quality. The identification of the plant Mediator will provide new tools and insights into the regulation of transcription in plants.
Collapse
Affiliation(s)
- Stefan Bäckström
- Department of Medical Biochemistry and Biophysics, KBC, Umeå University, SE-901 87 Umeå, Sweden.
| | | | | | | | | |
Collapse
|
28
|
Srivastava V, Schinkel H, Witzell J, Hertzberg M, Torp M, Srivastava MK, Karpinska B, Melzer M, Wingsle G. Downregulation of high-isoelectric-point extracellular superoxide dismutase mediates alterations in the metabolism of reactive oxygen species and developmental disturbances in hybrid aspen. Plant J 2007; 49:135-48. [PMID: 17233796 DOI: 10.1111/j.1365-313x.2006.02943.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Transgenic hybrid aspen (Populus tremula L. x P. tremuloides Michx.) plants expressing a high-isoelectric-point superoxide dismutase (hipI-SOD) gene in antisense orientation were generated to investigate its function. Immunolocalization studies showed the enzyme to be localized extracellularly, in the secondary cell wall of xylem vessels and phloem fibers. The antisense lines of hipI-SOD exhibited a distinct phenotype; growth rate was reduced, stems were thinner and leaves smaller than in wild-type (WT) plants. The abundance of hipI-SOD was reduced in the bark and xylem of plants from these antisense lines. The vascular tissue of transgenic lines became lignified earlier than in WT plants and also showed an increased accumulation of reactive oxygen species (ROS). Xylem fibers and vessels were shorter and thinner in the transgenic lines than in WT plants. The total phenolic content was enhanced in the antisense lines. Furthermore, microarray analysis indicated that several enzymes involved in cell signaling, lignin biosynthesis and stress responses were upregulated in apical vascular tissues of transgenic plants. The upregulation of selected genes involved in lignin biosynthesis was also verified by real-time PCR. The results suggest that, in the transgenic plants, a premature transition into maturation occurs and the process is discussed in terms of the effects of increased accumulation of ROS due to reduced expression of hipI-SOD during development and differentiation.
Collapse
Affiliation(s)
- Vaibhav Srivastava
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
| | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Ferreira S, Hjernø K, Larsen M, Wingsle G, Larsen P, Fey S, Roepstorff P, Salomé Pais M. Proteome profiling of Populus euphratica Oliv. upon heat stress. Ann Bot 2006; 98:361-77. [PMID: 16740589 PMCID: PMC2803470 DOI: 10.1093/aob/mcl106] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Populus euphratica is a light-demanding species ecologically characterized as a pioneer. It grows in shelter belts along riversides, being part of the natural desert forest ecosystems in China and Middle Eastern countries. It is able to survive extreme temperatures, drought and salt stress, marking itself out as an important plant species to study the mechanisms responsible for survival of woody plants under heat stress. METHODS Heat effects were evaluated through electrolyte leakage on leaf discs, and LT(50) was determined to occur above 50 degrees C. Protein accumulation profiles of leaves from young plants submitted to 42/37 degrees C for 3 d in a phytotron were determined through 2D-PAGE, and a total of 45 % of up- and downregulated proteins were detected. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF)/TOF analysis, combined with searches in different databases, enabled the identification of 82 % of the selected spots. KEY RESULTS Short-term upregulated proteins are related to membrane destabilization and cytoskeleton restructuring, sulfur assimilation, thiamine and hydrophobic amino acid biosynthesis, and protein stability. Long-term upregulated proteins are involved in redox homeostasis and photosynthesis. Late downregulated proteins are involved mainly in carbon metabolism. CONCLUSIONS Moderate heat response involves proteins related to lipid biogenesis, cytoskeleton structure, sulfate assimilation, thiamine and hydrophobic amino acid biosynthesis, and nuclear transport. Photostasis is achieved through carbon metabolism adjustment, a decrease of photosystem II (PSII) abundance and an increase of PSI contribution to photosynthetic linear electron flow. Thioredoxin h may have a special role in this process in P. euphratica upon moderate heat exposure.
Collapse
Affiliation(s)
- Sílvia Ferreira
- Unit of Molecular Biology and Plant Biotechnology, Institute of Applied Science and Technology, Science Faculty of Lisbon University, Campo Grande, 1749-016 Lisbon, Portugal.
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Rouhier N, Gama F, Wingsle G, Gelhaye E, Gans P, Jacquot JP. Engineering functional artificial hybrid proteins between poplar peroxiredoxin II and glutaredoxin or thioredoxin. Biochem Biophys Res Commun 2006; 341:1300-8. [PMID: 16476584 DOI: 10.1016/j.bbrc.2006.01.099] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Accepted: 01/21/2006] [Indexed: 11/21/2022]
Abstract
The existence of natural peroxiredoxin-glutaredoxin hybrid enzymes in several bacteria is in line with previous findings indicating that poplar peroxiredoxin II can use glutaredoxin as an electron donor. This peroxiredoxin remains however unique since it also uses thioredoxin with a quite good efficiency. Based on the existing fusions, we have created artificial enzymes containing a poplar peroxiredoxin module linked to glutaredoxin or thioredoxin modules. The recombinant fusion enzymes folded properly into non-covalently bound homodimers or homotetramers. Two of the three protein constructs exhibit peroxidase activity, a reaction where the two modules need to function together, but they also display enzymatic activities specific of each module. In addition, mass spectrometry analyses indicate that the Prx module can be both glutathiolated or overoxidized in vitro. This is discussed in the light of the Prx reactivity.
Collapse
Affiliation(s)
- Nicholas Rouhier
- UMR 1136 Interactions Arbres Mircoorganismes INRA-UHP, IFR 110 GEEF, Faculté des Sciences, 54506 Vandouevre-les-Nancy Cedex, France.
| | | | | | | | | | | |
Collapse
|
31
|
Höglund S, Larsson S, Wingsle G. Both hypersensitive and non-hypersensitive responses are associated with resistance in Salix viminalis against the gall midge Dasineura marginemtorquens. J Exp Bot 2005; 56:3215-22. [PMID: 16263902 DOI: 10.1093/jxb/eri318] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Hypersensitivity responses (HR) play a major role in plant resistance to pathogens. It is often claimed that HR is also important in plant resistance to insects, although there is little unambiguous documentation. Large genotypic variation in resistance against the gall midge Dasineura marginemtorquens is found in Salix viminalis. Variation in larval performance and induced responses within a full-sib S. viminalis family is reported here; 36 sibling plants were completely resistant (larvae died within 48 h after egg hatch, no gall induction), 11 plants were totally susceptible, 25 plants were variable (living and dead larvae present on the same plant). Resistance was associated with HR, but to different degrees; 21 totally resistant genotypes showed typical HR symptoms (many distinct necrotic spots) whereas the remaining 15 genotypes showed no, or very few, such symptoms. Hydrogen peroxide, used as a marker for HR, was induced in genotypes expressing HR symptoms but not in resistant genotypes without symptoms, or in susceptible genotypes. These data suggest that production of hydrogen peroxide, and accompanying cell death, cannot explain larval mortality in the symptomless reaction. Another, as yet unknown, mechanism of resistance may be present. If so, then it is possible that this unknown mechanism also contributes to resistance in plants displaying HR. The apparent complexity observed in this interaction, with both visible and invisible plant responses associated with resistance against an adapted insect species, may have implications for the study of resistance factors in other plant-insect interactions.
Collapse
Affiliation(s)
- Solveig Höglund
- Department of Entomology, Swedish University of Agricultural Sciences, Box 7044, SE-750 07 Uppsala, Sweden.
| | | | | |
Collapse
|
32
|
Karlsson M, Melzer M, Prokhorenko I, Johansson T, Wingsle G. Hydrogen peroxide and expression of hipI-superoxide dismutase are associated with the development of secondary cell walls in Zinnia elegans. J Exp Bot 2005; 56:2085-93. [PMID: 15955789 DOI: 10.1093/jxb/eri207] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A special form of a CuZn-superoxide dismutase with a high isoelectric point (hipI-SOD; EC 1.15.1.1) and hydrogen peroxide (H2O2) production were studied during the secondary cell wall formation of the inducible tracheary element cell-culture system of Zinnia elegans L. Confocal microscopy after labelling with 2',7'-dichlorofluorescin diacetate showed H2O2 to be located largely in the secondary cell walls in developing tracheary elements. Fluorescence-activated cell sorting analysis showed there were lower levels of H2O2 in the population containing tracheary elements when H2O2 scavengers such as ascorbate, catalase, and reduced glutathione were applied to the cell culture. Inhibitors of NADPH oxidase and SOD also reduced the amount of H2O2 in the tracheary elements. Furthermore, addition of these compounds to cell cultures at the time of tracheary element initiation reduced the amount of lignin and the development of the secondary cell walls. Analysis of UV excitation under a confocal laser scanning microscope confirmed these results. The expression of hipI-SOD increased as the number of tracheary elements in the cell culture increased and developed. Additionally, immunolocalization of a hipI-SOD isoform during the tracheary element differentiation showed a developmental build-up of the protein in the Golgi apparatus and the secondary cell wall. These findings suggest a novel hipI-SOD could be involved in the regulation of H2O2 required for the development of the secondary cell walls of tracheary elements.
Collapse
Affiliation(s)
- Marlene Karlsson
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå Plant Science Centre, 90183 Umeå, Sweden
| | | | | | | | | |
Collapse
|
33
|
Rouhier N, Villarejo A, Srivastava M, Gelhaye E, Keech O, Droux M, Finkemeier I, Samuelsson G, Dietz KJ, Jacquot JP, Wingsle G. Identification of plant glutaredoxin targets. Antioxid Redox Signal 2005; 7:919-29. [PMID: 15998247 DOI: 10.1089/ars.2005.7.919] [Citation(s) in RCA: 145] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Glutaredoxins (Grxs) are small ubiquitous proteins of the thioredoxin (Trx) family, which catalyze dithiol-disulfide exchange reactions or reduce protein-mixed glutathione disulfides. In plants, several Trx-interacting proteins have been isolated from different compartments, whereas very few Grx-interacting proteins are known. We describe here the determination of Grx target proteins using a mutated poplar Grx, various tissular and subcellular plant extracts, and liquid chromatography coupled to tandem mass spectrometry detection. We have identified 94 putative targets, involved in many processes, including oxidative stress response [peroxiredoxins (Prxs), ascorbate peroxidase, catalase], nitrogen, sulfur, and carbon metabolisms (methionine synthase, alanine aminotransferase, phosphoglycerate kinase), translation (elongation factors E and Tu), or protein folding (heat shock protein 70). Some of these proteins were previously found to interact with Trx or to be glutathiolated in other organisms, but others could be more specific partners of Grx. To substantiate further these data, Grx was shown to support catalysis of the stroma beta-type carbonic anhydrase and Prx IIF of Arabidopsis thaliana, but not of poplar 2-Cys Prx. Overall, these data suggest that the interaction could occur randomly either with exposed cysteinyl disulfide bonds formed within or between target proteins or with mixed disulfides between a protein thiol and glutathione.
Collapse
Affiliation(s)
- Nicolas Rouhier
- Unité Mixte de Recherches 1136 INRA UHP (Interaction Arbres Microorganismes), IFR 110 Génomique Ecophysiologie et Ecologie Fonctionnelles, Université Henri Poincaré, Vandoeuvre, France.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Wiklund S, Karlsson M, Antti H, Johnels D, Sjöström M, Wingsle G, Edlund U. A new metabonomic strategy for analysing the growth process of the poplar tree. Plant Biotechnol J 2005; 3:353-62. [PMID: 17129317 DOI: 10.1111/j.1467-7652.2005.00129.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
High-resolution, magic angle spinning, proton nuclear magnetic resonance (1H HR/MAS NMR) spectroscopy and multivariate data analysis using batch processing (BP) were applied to the analysis of two different genotypes of poplar tree (Populus tremula L. x tremuloides Michx.) containing an antisense construct of PttMYB76 and control (wild-type). A gene encoding a MYB transcription factor, with unknown function, PttMYB76, was selected from a cambial expressed sequence tag (EST) library of poplar tree (Populus tremula L. x tremuloides Michx.) for metabonomic characterization. The PttMYB76 gene is believed to affect different paths in the phenyl propanoid synthetic pathway. This pathway leads to the formation of S- and G-lignin, flavonoids and sinapate esters. Milled poplar samples collected at the internodes of the tree were analysed using 1H HR/MAS NMR spectroscopy. The application of multivariate BP of the NMR results revealed a growth-related gradient in the plant internode direction, as well as the discrimination between the trees with down-regulated PttMYB76 expression and wild-type populations. This paper focuses on the potential of a new analytical multivariate approach for analysing time-related plant metabonomic data. The techniques used could, with the aid of suitable model compounds, be of high relevance to the detection and understanding of the different lignification processes within the two types of poplar tree. Additionally, the findings highlight the importance of applying robust and organized multivariate data analysis approaches to facilitate the modelling and interpretation of complex biological data sets.
Collapse
Affiliation(s)
- Susanne Wiklund
- Department of Chemistry, Organic Chemistry, Umeå University, S-901 87 Umeå, Sweden.
| | | | | | | | | | | | | |
Collapse
|
35
|
Lövgren JM, Bylund GO, Srivastava MK, Lundberg LAC, Persson OP, Wingsle G, Wikström PM. The PRC-barrel domain of the ribosome maturation protein RimM mediates binding to ribosomal protein S19 in the 30S ribosomal subunits. RNA 2004; 10:1798-812. [PMID: 15496525 PMCID: PMC1370667 DOI: 10.1261/rna.7720204] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The RimM protein in Escherichia coli is associated with free 30S ribosomal subunits but not with 70S ribosomes. A DeltarimM mutant is defective in 30S maturation and accumulates 17S rRNA. To study the interaction of RimM with the 30S and its involvement in 30S maturation, RimM amino acid substitution mutants were constructed. A mutant RimM (RimM-YY-->AA), containing alanine substitutions for two adjacent tyrosines within the PRC beta-barrel domain, showed a reduced binding to 30S and an accumulation of 17S rRNA compared to wild-type RimM. The (RimM-YY-->AA) and DeltarimM mutants had significantly lower amounts of polysomes and also reduced levels of 30S relative to 50S compared to a wild-type strain. A mutation in rpsS, which encodes r-protein S19, suppressed the polysome- and 16S rRNA processing deficiencies of the RimM-YY-->AA but not that of the DeltarimM mutant. A mutation in rpsM, which encodes r-protein S13, suppressed the polysome deficiency of both rimM mutants. Suppressor mutations, found in either helices 31 or 33b of 16S rRNA, improved growth of both the RimM-YY-->AA and DeltarimM mutants. However, they suppressed the 16S rRNA processing deficiency of the RimM-YY-->AA mutant more efficiently than that of the DeltarimM mutant. Helices 31 and 33b are known to interact with S13 and S19, respectively, and S13 is known to interact with S19. A GST-RimM but not a GST-RimM(YY-->AA) protein bound strongly to S19 in 30S. Thus, RimM likely facilitates maturation of the region of the head of 30S that contains S13 and S19 as well as helices 31 and 33b.
Collapse
MESH Headings
- Alanine/metabolism
- Amino Acid Sequence
- Amino Acid Substitution
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Gene Expression Regulation, Bacterial
- Glutathione Transferase/metabolism
- Models, Molecular
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Mutation
- Protein Structure, Tertiary
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA-Binding Proteins
- Recombinant Proteins/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomes/metabolism
- Sequence Homology, Amino Acid
- Tyrosine/metabolism
Collapse
Affiliation(s)
- J Mattias Lövgren
- Department of Molecular Biology, Umeå University, SE-90187 Umeå, Sweden
| | | | | | | | | | | | | |
Collapse
|
36
|
Gelhaye E, Rouhier N, Gérard J, Jolivet Y, Gualberto J, Navrot N, Ohlsson PI, Wingsle G, Hirasawa M, Knaff DB, Wang H, Dizengremel P, Meyer Y, Jacquot JP. A specific form of thioredoxin h occurs in plant mitochondria and regulates the alternative oxidase. Proc Natl Acad Sci U S A 2004; 101:14545-50. [PMID: 15385674 PMCID: PMC521959 DOI: 10.1073/pnas.0405282101] [Citation(s) in RCA: 172] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The plant mitochondrial thioredoxin (Trx) system has been described as containing an NADPH-dependent Trx reductase and Trx o. In addition to the mitochondrial isoform, Trx o, plants are known to contain several chloroplastic Trx isoforms and the cytosolic Trx h isoforms. We report here the presence in plant mitochondria of a Trx isoform (PtTrxh2) belonging to the Trx h group. Western blot analyses with mitochondrial proteins isolated from both poplar and GFP fusion constructs indicate that PtTrxh2 is targeted to plant mitochondria. The recombinant protein, PtTrxh2, has been shown to be reduced efficiently by the mitochondrial Trx reductase AtNTRA. PtTrxh2 is also able to reduce alternative oxidase homodimers and to allow its activation by pyruvate. In contrast, neither PtTrxh2 nor AtTrxo1 exhibits activity with several poplar glutathione peroxidases and especially a putative mitochondrial isoform. Incubation of PtTrxh2 with glutathione disulfide led to the formation of glutathionylated Trx, identified by mass spectrometry. The formation of a glutathione adduct increases the redox potential of PtTrxh2 from -290 to -225 mV. In addition to Trx o, this study shows that Trx h could also be present in mitochondria. This previously unrecognized complexity is not unexpected, considering the multiple redox-regulated processes found in plant mitochondria.
Collapse
Affiliation(s)
- Eric Gelhaye
- Unité Mixte de Recherche, Institut National de la Recherche Agronomique 1136, Interactions Arbres/Micro-organismes, Université Henri Poincaré, Faculté des Sciences et Techniques, BP 239 54506 Vandoeuvre Cedex, France.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Karpinska B, Karlsson M, Srivastava M, Stenberg A, Schrader J, Sterky F, Bhalerao R, Wingsle G. MYB transcription factors are differentially expressed and regulated during secondary vascular tissue development in hybrid aspen. Plant Mol Biol 2004; 56:255-70. [PMID: 15604742 DOI: 10.1007/s11103-004-3354-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
More than 120,000 poplar ESTs have been sequenced from 20 different cDNA libraries by the Swedish Centre for Tree Functional Genomics. We screened this EST collection for MYB transcription factors involved in secondary vascular tissue formation, and genes assigned as PttMYB3Ra, PttMYB4a and PttMYB21a were selected for further characterisation. Three MYB genes showed different expression patterns in various organs, tissues and stem sub-sections representing different developmental stages of vascular tissue formation. Furthermore, the analysis showed that PttMYB21a expression was much higher in secondary cell wall formation zone of xylem and phloem fibers than in other developmental zones. Transgenic hybrid aspen plants, expressing the 3'-part of the PttMYB21a gene in antisense orientation were generated to assess the function of PttMYB21a gene in vascular tissue formation and lignification. All transgenic lines showed reduced growth and had fewer internodes compared to the wild-type. The analysis of selected lines showed that acid soluble lignin present in the bark was higher in transgenic lines as compared to wild-type plants. Moreover a higher transcript level of caffeoyl-CoA 3-O-methyltransferase [CCoAOMT]; EC 2.1.1.104) was found in the phloem of the transgenic plants, suggesting that PttMYB21a might function as a transcriptional repressor.
Collapse
Affiliation(s)
- Barbara Karpinska
- Department of Botany, Stockholm University, Lilla Frescativ. 5, Stockholm, SE-10691, Sweden
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Karpinska B, Karlsson M, Schinkel H, Streller S, Süss KH, Melzer M, Wingsle G. A novel superoxide dismutase with a high isoelectric point in higher plants. expression, regulation, and protein localization. Plant Physiol 2001; 126:1668-77. [PMID: 11500564 PMCID: PMC117165 DOI: 10.1104/pp.126.4.1668] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2000] [Revised: 02/08/2001] [Accepted: 04/19/2001] [Indexed: 05/18/2023]
Abstract
Several isoforms of superoxide dismutase (SOD) with a high isoelectric point (pI) have been identified by isoelectric focusing chromatography in protein extracts from Scots pine (Pinus sylvestris) needles. One of these isoforms, a CuZn-SOD with a pI of about 10 and thus denoted hipI-SOD, has been isolated and purified to apparent homogeneity. A cDNA encoding the hipI-SOD protein was cloned and sequenced. Northern hybridization of mRNA isolated from different organs and tissues showed that hipI-SOD has a markedly different pattern of expression compared with chloroplastic and cytosolic SOD. Furthermore, the transcript levels of hipI-SOD and cytosolic SOD were found to respond differently to mechanical wounding, treatment with oxidized glutathione, paraquat, and ozone. Immunogold electron microscopy localized the hipI-SOD in the plasma membrane of sieve cells and the Golgi apparatus of albuminous cells. Moreover, high protein density was also detected in extracellular spaces such as secondary cell wall thickenings of the xylem and sclerenchyma and in intercellular spaces of parenchyma cells.
Collapse
Affiliation(s)
- B Karpinska
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Faculty of Forestry, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
| | | | | | | | | | | | | |
Collapse
|
39
|
Abstract
Several CuZn-superoxide dismutases (SODs; EC 1.15.1.1) were cloned from hybrid aspen (Populus tremula L. x tremuloides Michx.). Two of the cloned genes encode representatives of a novel type of CuZn-SOD and we named it HipI-SOD because of its high isoelectric point (> or =9). The SODs were cloned by screening a cDNA library with a probe based on a Scots pine (Pinus sylvestris L.) CuZn-SOD that is predominantly located extracellularly. The expression pattern of HipI-SOD was examined using a Northern blot technique and compared with the expression patterns of cytosolic and chloroplastic SODs. Distinct expression patterns were observed for the three types of CuZn-SOD, with HipI-SODs showing strong expression in apical tissues. Southern blots as well as protein analysis suggest that these novel HipI-SODs belong to a small gene family, one member of which might be monomeric.
Collapse
Affiliation(s)
- H Schinkel
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå
| | | | | |
Collapse
|
40
|
Karpinska B, Wingsle G, Karpinski S. Antagonistic effects of hydrogen peroxide and glutathione on acclimation to excess excitation energy in Arabidopsis. IUBMB Life 2000; 50:21-6. [PMID: 11087116 DOI: 10.1080/15216540050176548] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The redox status of the quinone B (Q(B)) and plastoquinone (PQ) pools plays a key role in the cellular and systemic signalling processes that control acclimatory responses in plants. In this study, we demonstrate the effects of hydrogen peroxide and glutathione on acclimatory responses controlled by redox events in the proximity of the Q(B)-PQ pools. Our results suggest that the chloroplast is a sink for H2O2 and that, paradoxically, high concentrations of H2O2 in the chloroplast protect the photosynthetic apparatus and the plant cell from photoinhibition and photooxidative damage. Excess glutathione, however, caused an effect antagonistic to that observed for high H2O2. An explanation of this apparent paradox and a hypothetical redox-signalling model are suggested.
Collapse
Affiliation(s)
- B Karpinska
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Faculty of Forestry, Swedish University of Agricultural Sciences
| | | | | |
Collapse
|
41
|
Karpinski S, Reynolds H, Karpinska B, Wingsle G, Creissen G, Mullineaux P. Systemic signaling and acclimation in response to excess excitation energy in Arabidopsis. Science 1999; 284:654-7. [PMID: 10213690 DOI: 10.1126/science.284.5414.654] [Citation(s) in RCA: 493] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Land plants are sessile and have developed sophisticated mechanisms that allow for both immediate and acclimatory responses to changing environments. Partial exposure of low light-adapted Arabidopsis plants to excess light results in a systemic acclimation to excess excitation energy and consequent photooxidative stress in unexposed leaves. Thus, plants possess a mechanism to communicate excess excitation energy systemically, allowing them to mount a defense against further episodes of such stress. Systemic redox changes in the proximity of photosystem II, hydrogen peroxide, and the induction of antioxidant defenses are key determinants of this mechanism of systemic acquired acclimation.
Collapse
Affiliation(s)
- S Karpinski
- Department of Forest Genetics and Plant Physiology, Faculty of Forestry, Swedish University of Agricultural Sciences, SE-901 83 Umeâ, Sweden.
| | | | | | | | | | | |
Collapse
|
42
|
Abstract
Freezing injury of plants may be caused by the deleterious reactions of active oxygen species, and free-radical scavenging systems may be important in the alleviation of freezing stress. To test the feasibility of this hypothesis, enzymes and metabolites that cooperatively scavenge O2 and H2O2 were analyzed in Scots pine (Pinus sylvestris L.) seedlings during a stepwise cold acclimation procedure. Elevated levels of enzymatic scavengers such as ascorbate peroxidase, glutathione reductase, monodehydroascorbate reductase, and dehydroascorbate reductase were found, along with increased freezing tolerance during cold acclimation, supporting the hypothesis. Induction of the scavenging systems during acclimation is discussed in relation to freezing tolerance.
Collapse
Affiliation(s)
- D L Tao
- Institute of Applied Ecology, Academia Sinica, Shenyang, 110015, China
| | | | | |
Collapse
|
43
|
Wingsle G, Karpinski S. Differential redox regulation by glutathione of glutathione reductase and CuZn-superoxide dismutase gene expression in Pinus sylvestris L. needles. Planta 1996; 198:151-7. [PMID: 8580767 DOI: 10.1007/bf00197598] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Glutathione reductase (GR; EC 1.6.4.2) and superoxide dismutase (SOD; EC 1.15.1.1) are two well-known enzymes involved in the scavenging of reactive oxygen intermediates. However, little is known about the regulation of Gor and Sod genes in plant cells. To obtain information about hypothetical redox regulatory mechanisms controlling Gor and Sod gene expression we artificially enhanced the levels of reduced and oxidized forms of glutathione (GSH and GSSG) in Pinus sylvestris L. needles. Scots pine shoots were placed for 12 h in beakers containing 5 mM GSH, 5 mM GSSG or water. Increased levels of both GSSG and GSH were observed in the GSSG-treated needles after 3 h. In contrast, only the GSH level was increased by the GSH treatment. Thus, the GSH/GSSG ratio increased up to 15-fold during the GSH treatment and decreased approximately two-fold during the GSSG treatment. The GR activity was significantly higher (60%) when GSSG was applied, without any apparent change in the amount and isoform population of GR or accumulation of Gor gene transcripts. This indicates that the GR activity increased per se in the GSSG treatment. The level of cytosolic CuZn-Sod transcripts was decreased significantly by the GSH treatment without any change in enzyme activity. The chloroplastic CuZn-Sod gene generally showed a more stable transcript level in the different treatments. However, a similarity between the cytosolic and chloroplastic levels of CuZn-Sod transcripts could be observed in different treatments. This suggests that the redox state of glutathione plays an important role in the in vivo regulation of CuZn-Sod gene expression in plants.
Collapse
Affiliation(s)
- G Wingsle
- Department of Forest Genetics and Plant Physiology, Faculty of Forestry, Swedish University of Agricultural Sciences, Umeå, Sweden.
| | | |
Collapse
|
44
|
Streller S, Krömer S, Wingsle G. Isolation and purification of mitochondrial Mn-superoxide dismutase from the gymnosperm Pinus sylvestris L. Plant Cell Physiol 1994; 35:859-867. [PMID: 7981961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Manganese superoxide dismutase (Mn-SOD; EC 1.15.1.1) was purified from germinating seeds of Scots pine (Pinus sylvestris L.) 3 days after the start of imbibition. The purification schedule included (NH4)2SO4 fractionation, anion-exchange and hydrophobic-interaction chromatographies and chromatofocusing. Purified Mn-SOD had an apparent specific activity of 4,130 McCord-Fridovich units (mg protein)-1. The molecular mass of the holoenzyme was estimated to be 91 kDa by size-exclusion chromatography, and a molecular mass of 23 kDa was determined by SDS-PAGE. However, isoelectric focusing demonstrated that the purified enzyme consisted of three similarly migrating isoforms, with isoelectric points of approximately 6.5. NH2-terminal amino acid sequencing of purified Mn-SOD revealed no differences among the three isoforms. The comparison of the first 32 NH2-terminal amino acids with sequences of NH2-terminal amino acids of Mn-SODs from angiosperms reflected the phylogenetic distances between Scots pine, which is a gymnosperm, and angiospermic species. Cell fractionation suggested the mitochondrial localization of Mn-SODs and no evidence for glyoxysomal localization was found. Mn-SOD activity was absent from dry seeds. It was detectable at a considerable level after imbibition for 24 h, and it was again absent from 3-week-old seedlings.
Collapse
Affiliation(s)
- S Streller
- Department of Forest Genetics and Plant Physiology, Faculty of Forestry, Swedish University of Agricultural Sciences, Umeå
| | | | | |
Collapse
|
45
|
Abstract
Four new isoforms of superoxide dismutase (SOD; superoxide: superoxide oxidoreductase, EC 1.15.1.1.) were identified in extracellular washing fluid from Scots pine (Pinus sylvestris L.) needles. The isoforms had an apparent molecular mass of 33 kDa. No neutral carbohydrates were present in the enzymes. The enzymatic activities were inhibited by 3 mM NaCN. One of the putative extracellular SOD isoforms was purified and NH2-terminal-sequenced. The sequence contained the domain KAVAVL. The domains VEG and V(K/S)G, present in chloroplastic and cytosolic CuZn SODs of plants, respectively, were not detected. The enzyme was composed of two subunits of 17.8 kDa each. The isoelectric point was determined to be 6.5. The results suggest the existence of an extracellular SOD in Scots pine.
Collapse
Affiliation(s)
- S Streller
- Department of Forest Genetics and Plant Physiology, Faculty of Forestry, Swedish University of Agricultural Sciences, Umeå
| | | |
Collapse
|
46
|
Karpinski S, Wingsle G, Karpinska B, Hallgren JE. Molecular Responses to Photooxidative Stress in Pinus sylvestris (L.) (II. Differential Expression of CuZn-Superoxide Dismutases and Glutathione Reductase. Plant Physiol 1993; 103:1385-1391. [PMID: 12232032 PMCID: PMC159130 DOI: 10.1104/pp.103.4.1385] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The influence of photooxidative stress on genes expressing superoxide dismutase (Sod) and glutathione reductase (Gor) was analyzed in needles of top and side shoots of 3-year-old Pinus sylvestris (L.) seedlings. The study was carried out in the field during spring recovery. From mid-April the top shoots of seedlings protruded above the snow and thus were exposed to sunlight, whereas the side shoots were covered with snow until May 4. Needles were sampled from top and side shoots on five different occasions. At the beginning of May the mRNA levels for cytosolic CuZn-Sod were significantly higher in top-shoot needles than in side-shoot needles. Similar results were obtained for chloroplastic CuZn-Sod mRNA. After May 6 we could not detect any significant differences between top- and side-shoot needles for either CuZn-Sod mRNA level. Transcript accumulation for the chloroplastic CuZn-Sod was up to 4-fold higher than for cytosolic CuZn-Sod in both types of shoots. On June 1 minimum transcript levels were observed for both CuZn-SOD isoforms. Protein activity analysis for CuZn-SOD isozymes did not reveal any significant differences between top- and side-shoot needles during the whole period of measurements. The mRNA level for chloroplastic Gor was similar in both types of shoots. However, the total GR activity was significantly higher in top-shoot needles than in side-shoot needles at the beginning of May. The analysis of mRNA accumulation for chloroplastic CuZn-Sod and Gor indicates that transcript levels were at least 5- to 20-fold higher for CuZn-Sod than for chloroplastic Gor. The differential expressions of Sod and Gor genes are discussed in relation to regulation of the enzymic scavenging system during photooxidative stress conditions.
Collapse
Affiliation(s)
- S. Karpinski
- Department of Forest Genetics and Plant Physiology, Faculty of Forestry, Swedish University of Agricultural Science, S-901 83 Umea, Sweden
| | | | | | | |
Collapse
|
47
|
Wingsle G, Gardeström P, Hällgren JE, Karpinski S. Isolation, Purification, and Subcellular Localization of Isozymes of Superoxide Dismutase from Scots Pine (Pinus sylvestris L.) Needles. Plant Physiol 1991; 95:21-8. [PMID: 16667953 PMCID: PMC1077479 DOI: 10.1104/pp.95.1.21] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Two of four isozymes of superoxide dismutase (SOD) (EC 1.15.1.1) were purified from Scots pine (Pinus sylvestris L.) needles. One form was cytosolic (SOD-1) and the other was associated with chloroplasts (SOD-3). The holoenzyme molecular masses was estimated at approximately 35 kilodaltons by gel filtration. The subunit molecular weight of the dimeric enzymes was estimated to 16.5 kilodaltons (SOD-1) and 20.4 kilodaltons (SOD-3) on sodium dodecyl sulfatepolyacrylamide gels. The NH(2)-terminal sequence of the pine enzymes showed similarities to other purified superoxide dismutases located in the corresponding compartment. The cytosolic form revealed two additional amino acids at position 1 and 2 at the NH(2)-terminal. Both forms were cyanide- and hydrogenperoxide-sensitive and SOD-3 was found to contain approximately one copper atom per subunit, indicating that they belong to the cupro-zinc SODs. The isoelectric point was 4.9 and 4.5 for SOD-1 and SOD-3, respectively.
Collapse
Affiliation(s)
- G Wingsle
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, S-901 83 Umeå, Sweden
| | | | | | | |
Collapse
|
48
|
Palmqvist K, Sundblad LG, Wingsle G, Samuelsson G. Acclimation of Photosynthetic Light Reactions during Induction of Inorganic Carbon Accumulation in the Green Alga Chlamydomonas reinhardtii. Plant Physiol 1990; 94:357-66. [PMID: 16667710 PMCID: PMC1077232 DOI: 10.1104/pp.94.1.357] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Cells of the unicellular green algae Chlamydomonas reinhardtii were grown in high dissolved inorganic carbon (DIC) concentrations (supplied with 50 milliliters per liter CO(2)[g]) and transferred to low DIC concentrations (supplied with </= 100 microliters per liter CO(2)[g]). Immediately after transfer from high to low DIC the emission of photosystem II related chlorophyll a fluorescence was substantially quenched. It is hypothesized that the suddenly induced inorganic carbon limitation of photosynthesis resulted in a phosphorylation of LHCII, leading to the subsequent state 1 to state 2 transition. After 2 hours of low-DIC acclimation, 77 K fluorescence measurements revealed an increase in the fluorescence emitted from photosystem I, due to direct excitation, suggesting a change in photosystem II/photosystem I stoichiometry or an increased light harvesting capacity of photosystem I. After 5 to 6 hours of acclimation a considerable increase in spillover from photosystem II to photosystem I was observed. These adjustments of the photosynthetic light reactions reached steady-state after about 12 hours of low DIC treatment. The quencher of fluorescence could be removed by 5 minutes of dark treatment followed by 5 minutes of weak light treatment, of any of four different light qualities. It is hypothesized that this restoration of fluorescence was due to a state 2 to state 1 transition in low-DIC acclimated cells. A decreased ratio of violaxanthin to zeaxanthin was also observed in 12 hour low DIC treated cells, compared with high DIC grown cells. This ratio was not coupled to the level of fluorescence quenching. The role of different processes during the induction of a DIC accumulating mechanism is discussed.
Collapse
Affiliation(s)
- K Palmqvist
- Department of Plant Physiology, University of Umeå, S-901 87 Umeå, Sweden
| | | | | | | |
Collapse
|