@article{gandla_overexpression_2021,
	title = {Overexpression of vesicle-associated membrane protein {PttVAP27}-17 as a tool to improve biomass production and the overall saccharification yields in {Populus} trees},
	volume = {14},
	issn = {1754-6834},
	url = {https://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/s13068-021-01895-0},
	doi = {10/gjd7kj},
	abstract = {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.},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {Biotechnology for Biofuels},
	author = {Gandla, Madhavi Latha and Mähler, Niklas and Escamez, Sacha and Skotare, Tomas and Obudulu, Ogonna and Möller, Linus and Abreu, Ilka N. and Bygdell, Joakim and Hertzberg, Magnus and Hvidsten, Torgeir R. and Moritz, Thomas and Wingsle, Gunnar and Trygg, Johan and Tuominen, Hannele and Jönsson, Leif J.},
	month = dec,
	year = {2021},
	pages = {43},
}

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.

@article{vaisanen_hunting_2020,
	title = {Hunting monolignol transporters: membrane proteomics and biochemical transport assays with membrane vesicles of {Norway} spruce},
	volume = {71},
	issn = {0022-0957, 1460-2431},
	shorttitle = {Hunting monolignol transporters},
	url = {https://academic.oup.com/jxb/article/71/20/6379/5890496},
	doi = {10.1093/jxb/eraa368},
	abstract = {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.},
	language = {en},
	number = {20},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Väisänen, Enni and Takahashi, Junko and Obudulu, Ogonna and Bygdell, Joakim and Karhunen, Pirkko and Blokhina, Olga and Laitinen, Teresa and Teeri, Teemu H and Wingsle, Gunnar and Fagerstedt, Kurt V and Kärkönen, Anna},
	editor = {Zhao, Qiao},
	month = oct,
	year = {2020},
	pages = {6379--6395},
}

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.

@article{miguel_gdsl_2020,
	title = {A {GDSL} lipase-like from {Ipomoea} batatas catalyzes efficient production of 3,5-{diCQA} when expressed in {Pichia} pastoris},
	volume = {3},
	issn = {2399-3642},
	url = {http://www.nature.com/articles/s42003-020-01387-1},
	doi = {10.1038/s42003-020-01387-1},
	abstract = {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.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Communications Biology},
	author = {Miguel, Sissi and Legrand, Guillaume and Duriot, Léonor and Delporte, Marianne and Menin, Barbara and Michel, Cindy and Olry, Alexandre and Chataigné, Gabrielle and Salwinski, Aleksander and Bygdell, Joakim and Vercaigne, Dominique and Wingsle, Gunnar and Hilbert, Jean Louis and Bourgaud, Frédéric and Hehn, Alain and Gagneul, David},
	month = dec,
	year = {2020},
	pages = {673},
}

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.

@article{arias_nuclear_2020,
	title = {Nuclear proteome analysis of {Chlamydomonas} with response to {CO2} limitation},
	volume = {46},
	issn = {22119264},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S221192641930133X},
	doi = {10/gh9mnq},
	language = {en},
	urldate = {2021-06-07},
	journal = {Algal Research},
	author = {Arias, Carolina and Obudulu, Ogonna and Zhao, Xiaoling and Ansolia, Preeti and Zhang, Xueyang and Paul, Suman and Bygdell, Joakim and Pirmoradian, Mohammad and Zubarev, Roman A. and Samuelsson, Göran and Wingsle, Gunnar and Bajhaiya, Amit K.},
	month = mar,
	year = {2020},
	pages = {101765},
}

@article{zhu_targeted_2019,
	title = {Targeted {Multiple} {Reaction} {Monitoring} {Analysis} of {CSF} {Identifies} {UCHL1} and {GPNMB} as {Candidate} {Biomarkers} for {ALS}},
	volume = {69},
	issn = {0895-8696, 1559-1166},
	url = {http://link.springer.com/10.1007/s12031-019-01411-y},
	doi = {10.1007/s12031-019-01411-y},
	abstract = {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.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Journal of Molecular Neuroscience},
	author = {Zhu, Shaochun and Wuolikainen, Anna and Wu, Junfang and Öhman, Anders and Wingsle, Gunnar and Moritz, Thomas and Andersen, Peter M. and Forsgren, Lars and Trupp, Miles},
	month = dec,
	year = {2019},
	pages = {643--657},
}

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.

@article{obudulu_multi-omics_2018,
	title = {A multi-omics approach reveals function of {Secretory} {Carrier}-{Associated} {Membrane} {Proteins} in wood formation of​ ​​{Populus}​​ ​trees},
	volume = {19},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4411-1},
	doi = {10.1186/s12864-017-4411-1},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Obudulu, Ogonna and Mähler, Niklas and Skotare, Tomas and Bygdell, Joakim and Abreu, Ilka N. and Ahnlund, Maria and Latha Gandla, Madhavi and Petterle, Anna and Moritz, Thomas and Hvidsten, Torgeir R. and Jönsson, Leif J. and Wingsle, Gunnar and Trygg, Johan and Tuominen, Hannele},
	month = dec,
	year = {2018},
	pages = {11},
}

@article{zhang_cellulose_2018,
	title = {Cellulose {Synthase} {Stoichiometry} in {Aspen} {Differs} from {Arabidopsis} and {Norway} {Spruce}},
	volume = {177},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/177/3/1096-1107/6117105},
	doi = {10.1104/pp.18.00394},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Zhang, Xueyang and Dominguez, Pia Guadalupe and Kumar, Manoj and Bygdell, Joakim and Miroshnichenko, Sergey and Sundberg, Björn and Wingsle, Gunnar and Niittylä, Totte},
	month = jul,
	year = {2018},
	pages = {1096--1107},
}

@article{bollhoner_function_2018,
	title = {The function of two type {II} metacaspases in woody tissues of \textit{{Populus}} trees},
	volume = {217},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/nph.14945},
	doi = {10/gczh42},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Bollhöner, Benjamin and Jokipii-Lukkari, Soile and Bygdell, Joakim and Stael, Simon and Adriasola, Mathilda and Muñiz, Luis and Van Breusegem, Frank and Ezcurra, Inés and Wingsle, Gunnar and Tuominen, Hannele},
	month = mar,
	year = {2018},
	pages = {1551--1565},
}

@article{bygdell_protein_2017,
	title = {Protein expression in tension wood formation monitored at high tissue resolution in {Populus}},
	volume = {68},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/68/13/3405/3867560},
	doi = {10.1093/jxb/erx186},
	language = {en},
	number = {13},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Bygdell, Joakim and Srivastava, Vaibhav and Obudulu, Ogonna and Srivastava, Manoj K and Nilsson, Robert and Sundberg, Björn and Trygg, Johan and Mellerowicz, Ewa J and Wingsle, Gunnar},
	month = jun,
	year = {2017},
	pages = {3405--3417},
}

@article{obudulu_quantitative_2016,
	title = {Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development},
	volume = {17},
	issn = {1471-2164},
	url = {http://www.biomedcentral.com/1471-2164/17/119},
	doi = {10.1186/s12864-016-2458-z},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Obudulu, Ogonna and Bygdell, Joakim and Sundberg, Björn and Moritz, Thomas and Hvidsten, Torgeir R. and Trygg, Johan and Wingsle, Gunnar},
	month = dec,
	year = {2016},
	pages = {119},
}

@article{shaikhali_redox_2016,
	title = {Redox regulation of the {MED28} and {MED32} mediator subunits is important for development and senescence},
	volume = {253},
	issn = {0033-183X, 1615-6102},
	url = {http://link.springer.com/10.1007/s00709-015-0853-y},
	doi = {10.1007/s00709-015-0853-y},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Protoplasma},
	author = {Shaikhali, Jehad and Davoine, Céline and Björklund, Stefan and Wingsle, Gunnar},
	month = may,
	year = {2016},
	pages = {957--963},
}

@article{xu_yeast_2015,
	title = {Yeast {Elongator} protein {Elp1p} does not undergo proteolytic processing in exponentially growing cells},
	volume = {4},
	issn = {2045-8827 (Electronic) 2045-8827 (Linking)},
	shorttitle = {Yeast},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26407534},
	doi = {10.1002/mbo3.285},
	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.},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Microbiologyopen},
	author = {Xu, H. and Bygdell, J. and Wingsle, G. and Bystrom, A. S.},
	month = dec,
	year = {2015},
	note = {Edition: 2015/09/27},
	keywords = {Amino Acid Sequence, Elongator complex, Elp1p, Histone Acetyltransferases/chemistry/genetics/*metabolism, Molecular Sequence Data, Peptide Elongation Factors/chemistry/genetics/*metabolism, Prb1p, Protein Structure, Tertiary, Proteolysis, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism, Saccharomyces cerevisiae/chemistry/genetics/growth \& development/*metabolism, Tandem Mass Spectrometry, tRNA modification},
	pages = {867--78},
}

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.

@article{shaikhali_biochemical_2015,
	title = {Biochemical and redox characterization of the mediator complex and its associated transcription factor {GeBPL}, a {GLABROUS1} enhancer binding protein},
	volume = {468},
	issn = {1470-8728 (Electronic) 0264-6021 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25877331},
	doi = {10.1042/BJ20150132},
	abstract = {The eukaryotic mediator integrates regulatory signals from promoter-bound transcription factors (TFs) and transmits them to RNA polymerase II (Pol II) machinery. Although redox signalling is important in adjusting plant metabolism and development, nothing is known about a possible redox regulation of mediator. In the present study, using pull-down and yeast two-hybrid assays, we demonstrate the association of mediator (MED) subunits MED10a, MED28 and MED32 with the GLABROUS1 (GL1) enhancer-binding protein-like (GeBPL), a plant-specific TF that binds a promoter containing cryptochrome 1 response element 2 (CryR2) element. All the corresponding recombinant proteins form various types of covalent oligomers linked by intermolecular disulfide bonds that are reduced in vitro by the thioredoxin (TRX) and/or glutathione/glutaredoxin (GRX) systems. The presence of recombinant MED10a, MED28 and MED32 subunits or changes of its redox state affect the DNA-binding capacity of GeBPL suggesting that redox-driven conformational changes might modulate its activity. Overall, these results advance our understanding of how redox signalling affects transcription and identify mediator as a novel actor in redox signalling pathways, relaying or integrating redox changes in combination with specific TFs as GeBPL.},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Biochem J},
	author = {Shaikhali, J. and Davoine, C. and Brannstrom, K. and Rouhier, N. and Bygdell, J. and Bjorklund, S. and Wingsle, G.},
	month = jun,
	year = {2015},
	note = {Edition: 2015/04/17},
	keywords = {Arabidopsis Proteins/genetics/*metabolism, Arabidopsis thaliana, Arabidopsis/*metabolism, CryR2, DNA-Binding Proteins/genetics/*metabolism, GLABROUS1 enhancer-binding protein (GeBP), Glutaredoxins/metabolism, Glutathione/metabolism, Mediator Complex/genetics/*metabolism, Mutagenesis, Site-Directed, Mutation, Oxidation-Reduction, Promoter Regions, Genetic, Protein Subunits/genetics/*metabolism, Recombinant Proteins/metabolism, Response Elements, Thioredoxins/metabolism, Transcription Factors, Two-Hybrid System Techniques, deoxyribonucleic acid (DNA)-binding, mediator, redox},
	pages = {385--400},
}

The eukaryotic mediator integrates regulatory signals from promoter-bound transcription factors (TFs) and transmits them to RNA polymerase II (Pol II) machinery. Although redox signalling is important in adjusting plant metabolism and development, nothing is known about a possible redox regulation of mediator. In the present study, using pull-down and yeast two-hybrid assays, we demonstrate the association of mediator (MED) subunits MED10a, MED28 and MED32 with the GLABROUS1 (GL1) enhancer-binding protein-like (GeBPL), a plant-specific TF that binds a promoter containing cryptochrome 1 response element 2 (CryR2) element. All the corresponding recombinant proteins form various types of covalent oligomers linked by intermolecular disulfide bonds that are reduced in vitro by the thioredoxin (TRX) and/or glutathione/glutaredoxin (GRX) systems. The presence of recombinant MED10a, MED28 and MED32 subunits or changes of its redox state affect the DNA-binding capacity of GeBPL suggesting that redox-driven conformational changes might modulate its activity. Overall, these results advance our understanding of how redox signalling affects transcription and identify mediator as a novel actor in redox signalling pathways, relaying or integrating redox changes in combination with specific TFs as GeBPL.

@article{businge_effect_2013,
	title = {The effect of carbohydrates and osmoticum on storage reserve accumulation and germination of {Norway} spruce somatic embryos},
	volume = {149},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12039},
	doi = {10/f2zr7w},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Businge, Edward and Bygdell, Joakim and Wingsle, Gunnar and Moritz, Thomas and Egertsdotter, Ulrika},
	month = oct,
	year = {2013},
	pages = {273--285},
}

@article{srivastava_onpls_2013,
	title = {{OnPLS} integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic {hipI}- superoxide dismutase {Populus} plants},
	volume = {14},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/1471-2164-14-893},
	doi = {10/f2zk6q},
	abstract = {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.},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Srivastava, Vaibhav and Obudulu, Ogonna and Bygdell, Joakim and Löfstedt, Tommy and Rydén, Patrik and Nilsson, Robert and Ahnlund, Maria and Johansson, Annika and Jonsson, Pär and Freyhult, Eva and Qvarnström, Johanna and Karlsson, Jan and Melzer, Michael and Moritz, Thomas and Trygg, Johan and Hvidsten, Torgeir R. and Wingsle, Gunnar},
	month = dec,
	year = {2013},
	keywords = {OnPLS, Oxidative stress, Poplar, Statistical integration, Systems biology},
	pages = {893},
}

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.

@article{chibani_atypical_2012,
	title = {Atypical {Thioredoxins} in {Poplar}: {The} {Glutathione}-{Dependent} {Thioredoxin}-{Like} 2.1 {Supports} the {Activity} of {Target} {Enzymes} {Possessing} a {Single} {Redox} {Active} {Cysteine}},
	volume = {159},
	issn = {1532-2548},
	shorttitle = {Atypical {Thioredoxins} in {Poplar}},
	url = {https://academic.oup.com/plphys/article/159/2/592/6109157},
	doi = {10/f3ptz3},
	abstract = {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.},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Chibani, Kamel and Tarrago, Lionel and Gualberto, José Manuel and Wingsle, Gunnar and Rey, Pascal and Jacquot, Jean-Pierre and Rouhier, Nicolas},
	month = jun,
	year = {2012},
	pages = {592--605},
}

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.

@article{selles_hydroperoxide_2012,
	title = {Hydroperoxide and peroxynitrite reductase activity of poplar thioredoxin-dependent glutathione peroxidase 5: kinetics, catalytic mechanism and oxidative inactivation},
	volume = {442},
	issn = {0264-6021, 1470-8728},
	shorttitle = {Hydroperoxide and peroxynitrite reductase activity of poplar thioredoxin-dependent glutathione peroxidase 5},
	url = {https://portlandpress.com/biochemj/article/442/2/369/45982/Hydroperoxide-and-peroxynitrite-reductase-activity},
	doi = {10/bqg8zt},
	abstract = {Gpxs (glutathione peroxidases) constitute a family of peroxidases, including selenocysteine- or cysteine-containing isoforms (SeCys-Gpx or Cys-Gpx), which are regenerated by glutathione or Trxs (thioredoxins) respectively. In the present paper we show new data concerning the substrates of poplar Gpx5 and the residues involved in its catalytic mechanism. The present study establishes the capacity of this Cys-Gpx to reduce peroxynitrite with a catalytic efficiency of 106 M−1·s−1. In PtGpx5 (poplar Gpx5; Pt is Populus trichocarpa), Glu79, which replaces the glutamine residue usually found in the Gpx catalytic tetrad, is likely to be involved in substrate selectivity. Although the redox midpoint potential of the Cys44–Cys92 disulfide bond and the pKa of Cys44 are not modified in the E79Q variant, it exhibited significantly improved kinetic parameters (Kperoxide and kcat) with tert-butyl hydroperoxide. The characterization of the monomeric Y151R variant demonstrated that PtGpx5 is not an obligate homodimer. Also, we show that the conserved Phe90 is important for Trx recognition and that Trx-mediated recycling of PtGpx5 occurs via the formation of a transient disulfide bond between the Trx catalytic cysteine residue and the Gpx5 resolving cysteine residue. Finally, we demonstrate that the conformational changes observed during the transition from the reduced to the oxidized form of PtGpx5 are primarily determined by the oxidation of the peroxidatic cysteine into sulfenic acid. Also, MS analysis of in-vitro-oxidized PtGpx5 demonstrated that the peroxidatic cysteine residue can be over-oxidized into sulfinic or sulfonic acids. This suggests that some isoforms could have dual functions potentially acting as hydrogen-peroxide- and peroxynitrite-scavenging systems and/or as mediators of peroxide signalling as proposed for 2-Cys peroxiredoxins.},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Biochemical Journal},
	author = {Selles, Benjamin and Hugo, Martin and Trujillo, Madia and Srivastava, Vaibhav and Wingsle, Gunnar and Jacquot, Jean-Pierre and Radi, Rafael and Rouhier, Nicolas},
	month = mar,
	year = {2012},
	pages = {369--380},
}

Gpxs (glutathione peroxidases) constitute a family of peroxidases, including selenocysteine- or cysteine-containing isoforms (SeCys-Gpx or Cys-Gpx), which are regenerated by glutathione or Trxs (thioredoxins) respectively. In the present paper we show new data concerning the substrates of poplar Gpx5 and the residues involved in its catalytic mechanism. The present study establishes the capacity of this Cys-Gpx to reduce peroxynitrite with a catalytic efficiency of 106 M−1·s−1. In PtGpx5 (poplar Gpx5; Pt is Populus trichocarpa), Glu79, which replaces the glutamine residue usually found in the Gpx catalytic tetrad, is likely to be involved in substrate selectivity. Although the redox midpoint potential of the Cys44–Cys92 disulfide bond and the pKa of Cys44 are not modified in the E79Q variant, it exhibited significantly improved kinetic parameters (Kperoxide and kcat) with tert-butyl hydroperoxide. The characterization of the monomeric Y151R variant demonstrated that PtGpx5 is not an obligate homodimer. Also, we show that the conserved Phe90 is important for Trx recognition and that Trx-mediated recycling of PtGpx5 occurs via the formation of a transient disulfide bond between the Trx catalytic cysteine residue and the Gpx5 resolving cysteine residue. Finally, we demonstrate that the conformational changes observed during the transition from the reduced to the oxidized form of PtGpx5 are primarily determined by the oxidation of the peroxidatic cysteine into sulfenic acid. Also, MS analysis of in-vitro-oxidized PtGpx5 demonstrated that the peroxidatic cysteine residue can be over-oxidized into sulfinic or sulfonic acids. This suggests that some isoforms could have dual functions potentially acting as hydrogen-peroxide- and peroxynitrite-scavenging systems and/or as mediators of peroxide signalling as proposed for 2-Cys peroxiredoxins.

@article{shaikhali_redox-mediated_2012,
	title = {Redox-mediated {Mechanisms} {Regulate} {DNA} {Binding} {Activity} of the {G}-group of {Basic} {Region} {Leucine} {Zipper} ({bZIP}) {Transcription} {Factors} in {Arabidopsis}},
	volume = {287},
	issn = {00219258},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925820477762},
	doi = {10/f22pjj},
	language = {en},
	number = {33},
	urldate = {2021-06-08},
	journal = {Journal of Biological Chemistry},
	author = {Shaikhali, Jehad and Norén, Louise and de Dios Barajas-López, Juan and Srivastava, Vaibhav and König, Janine and Sauer, Uwe H. and Wingsle, Gunnar and Dietz, Karl-Josef and Strand, Åsa},
	month = aug,
	year = {2012},
	pages = {27510--27525},
}

@article{shaikhali_cryptochrome1-dependent_2012,
	title = {The {CRYPTOCHROME1}-{Dependent} {Response} to {Excess} {Light} {Is} {Mediated} through the {Transcriptional} {Activators} {ZINC} {FINGER} {PROTEIN} {EXPRESSED} {IN} {INFLORESCENCE} {MERISTEM} {LIKE1} and {ZML2} in \textit{{Arabidopsis}}},
	volume = {24},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/24/7/3009-3025/6100855},
	doi = {10/f23c7q},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Shaikhali, Jehad and de Dios Barajas-Lopéz, Juan and Ötvös, Krisztina and Kremnev, Dmitry and Garcia, Ana Sánchez and Srivastava, Vaibhav and Wingsle, Gunnar and Bakó, Laszlo and Strand, Åsa},
	month = jul,
	year = {2012},
	pages = {3009--3025},
}

@article{palm_cisplatin_2011,
	title = {Cisplatin binds human copper chaperone {Atox1} and promotes unfolding in vitro},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1012899108},
	doi = {10/cwg7dm},
	language = {en},
	number = {17},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Palm, M. E. and Weise, C. F. and Lundin, C. and Wingsle, G. and Nygren, Y. and Bjorn, E. and Naredi, P. and Wolf-Watz, M. and Wittung-Stafshede, P.},
	month = apr,
	year = {2011},
	pages = {6951--6956},
}

@article{elfving_arabidopsis_2011,
	title = {The {Arabidopsis} thaliana {Med25} mediator subunit integrates environmental cues to control plant development},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/108/20/8245},
	doi = {10.1073/pnas.1002981108},
	abstract = {Development in plants is controlled by abiotic environmental cues such as day length, light quality, temperature, drought, and salinity. These signals are sensed by a variety of systems and transmitted by different signal transduction pathways. Ultimately, these pathways are integrated to control expression of specific target genes, which encode proteins that regulate development and differentiation. The molecular mechanisms for such integration have remained elusive. We here show that a linear 130-amino-acids-long sequence in the Med25 subunit of the Arabidopsis thaliana Mediator is a common target for the drought response element binding protein 2A, zinc finger homeodomain 1, and Myb-like transcription factors which are involved in different stress response pathways. In addition, our results show that Med25 together with drought response element binding protein 2A also function in repression of PhyB-mediated light signaling and thus integrate signals from different regulatory pathways.},
	language = {en},
	number = {20},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Elfving, Nils and Davoine, Céline and Benlloch, Reyes and Blomberg, Jeanette and Brännström, Kristoffer and Müller, Dörte and Nilsson, Anders and Ulfstedt, Mikael and Ronne, Hans and Wingsle, Gunnar and Nilsson, Ove and Björklund, Stefan},
	month = may,
	year = {2011},
	pmid = {21536906},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {RNA polymerase II, phytochrome flowering time 1, transcriptional regulation},
	pages = {8245--8250},
}

Development in plants is controlled by abiotic environmental cues such as day length, light quality, temperature, drought, and salinity. These signals are sensed by a variety of systems and transmitted by different signal transduction pathways. Ultimately, these pathways are integrated to control expression of specific target genes, which encode proteins that regulate development and differentiation. The molecular mechanisms for such integration have remained elusive. We here show that a linear 130-amino-acids-long sequence in the Med25 subunit of the Arabidopsis thaliana Mediator is a common target for the drought response element binding protein 2A, zinc finger homeodomain 1, and Myb-like transcription factors which are involved in different stress response pathways. In addition, our results show that Med25 together with drought response element binding protein 2A also function in repression of PhyB-mediated light signaling and thus integrate signals from different regulatory pathways.

@article{nilsson_proteomics_2010,
	title = {Proteomics of {Plasma} {Membranes} from {Poplar} {Trees} {Reveals} {Tissue} {Distribution} of {Transporters}, {Receptors}, and {Proteins} in {Cell} {Wall} {Formation}},
	volume = {9},
	issn = {15359476},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1535947620338068},
	doi = {10/bvk46j},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Molecular \& Cellular Proteomics},
	author = {Nilsson, Robert and Bernfur, Katja and Gustavsson, Niklas and Bygdell, Joakim and Wingsle, Gunnar and Larsson, Christer},
	month = feb,
	year = {2010},
	pages = {368--387},
}

@article{bergemalm_superoxide_2010,
	title = {Superoxide dismutase-1 and other proteins in inclusions from transgenic amyotrophic lateral sclerosis model mice: {SOD1} inclusions in {ALS} transgenic mice},
	volume = {114},
	issn = {00223042},
	shorttitle = {Superoxide dismutase-1 and other proteins in inclusions from transgenic amyotrophic lateral sclerosis model mice},
	url = {http://doi.wiley.com/10.1111/j.1471-4159.2010.06753.x},
	doi = {10/fdbwxp},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Journal of Neurochemistry},
	author = {Bergemalm, Daniel and Forsberg, Karin and Srivastava, Vaibhav and Graffmo, Karin S. and Andersen, Peter M. and Brännström, Thomas and Wingsle, Gunnar and Marklund, Stefan L.},
	month = jul,
	year = {2010},
	pages = {408--418},
}

@article{bylesjo_integrated_2009,
	title = {Integrated {Analysis} of {Transcript}, {Protein} and {Metabolite} {Data} {To} {Study} {Lignin} {Biosynthesis} in {Hybrid} {Aspen}},
	volume = {8},
	issn = {1535-3893, 1535-3907},
	url = {https://pubs.acs.org/doi/10.1021/pr800298s},
	doi = {10/ddqkpn},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Journal of Proteome Research},
	author = {Bylesjö, Max and Nilsson, Robert and Srivastava, Vaibhav and Grönlund, Andreas and Johansson, Annika I. and Jansson, Stefan and Karlsson, Jan and Moritz, Thomas and Wingsle, Gunnar and Trygg, Johan},
	month = jan,
	year = {2009},
	pages = {199--210},
}

@article{srivastava_alternative_2009,
	title = {Alternative {Splicing} {Studies} of the {Reactive} {Oxygen} {Species} {Gene} {Network} in \textit{{Populus}} {Reveal} {Two} {Isoforms} of {High}-{Isoelectric}-{Point} {Superoxide} {Dismutase}},
	volume = {149},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/149/4/1848/6107952},
	doi = {10/d5fkf9},
	abstract = {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.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Srivastava, Vaibhav and Srivastava, Manoj Kumar and Chibani, Kamel and Nilsson, Robert and Rouhier, Nicolas and Melzer, Michael and Wingsle, Gunnar},
	month = apr,
	year = {2009},
	pages = {1848--1859},
}

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.

@article{chibani_comparative_2009,
	title = {Comparative {Genomic} {Study} of the {Thioredoxin} {Family} in {Photosynthetic} {Organisms} with {Emphasis} on {Populus} trichocarpa},
	volume = {2},
	issn = {16742052},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1674205214604731},
	doi = {10/bhd78p},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Molecular Plant},
	author = {Chibani, Kamel and Wingsle, Gunnar and Jacquot, Jean-Pierre and Gelhaye, Eric and Rouhier, Nicolas},
	month = mar,
	year = {2009},
	pages = {308--322},
}

@article{yanamandra_amyloid_2009,
	title = {Amyloid {Formation} by the {Pro}-{Inflammatory} {S100A8}/{A9} {Proteins} in the {Ageing} {Prostate}},
	volume = {4},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0005562},
	doi = {10/cq9jr4},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Yanamandra, Kiran and Alexeyev, Oleg and Zamotin, Vladimir and Srivastava, Vaibhav and Shchukarev, Andrei and Brorsson, Ann-Christin and Tartaglia, Gian Gaetano and Vogl, Thomas and Kayed, Rakez and Wingsle, Gunnar and Olsson, Jan and Dobson, Christopher M. and Bergh, Anders and Elgh, Fredrik and Morozova-Roche, Ludmilla A.},
	editor = {Gazit, Ehud},
	month = may,
	year = {2009},
	pages = {e5562},
}

@article{koh_atypical_2008,
	title = {An {Atypical} {Catalytic} {Mechanism} {Involving} {Three} {Cysteines} of {Thioredoxin}},
	volume = {283},
	issn = {00219258},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925819493629},
	doi = {10/df4v82},
	language = {en},
	number = {34},
	urldate = {2021-06-10},
	journal = {Journal of Biological Chemistry},
	author = {Koh, Cha San and Navrot, Nicolas and Didierjean, Claude and Rouhier, Nicolas and Hirasawa, Masakazu and Knaff, David B. and Wingsle, Gunnar and Samian, Razip and Jacquot, Jean-Pierre and Corbier, Catherine and Gelhaye, Eric},
	month = aug,
	year = {2008},
	pages = {23062--23072},
}

@article{overmyer_complex_2008,
	title = {Complex phenotypic profiles leading to ozone sensitivity in \textit{{Arabidopsis} thaliana} mutants},
	volume = {31},
	issn = {01407791, 13653040},
	url = {http://doi.wiley.com/10.1111/j.1365-3040.2008.01837.x},
	doi = {10/bvqtdg},
	language = {en},
	number = {9},
	urldate = {2021-06-10},
	journal = {Plant, Cell \& Environment},
	author = {Overmyer, Kirk and Kollist, Hannes and Tuominen, Hannele and Betz, Christian and Langebartels, Christian and Wingsle, Gunnar and Kangasjärvi, Saijaliisa and Brader, Günter and Mullineaux, Phil and Kangasjärvi, Jaakko},
	month = sep,
	year = {2008},
	pages = {1237--1249},
}

@article{martz_effects_2007,
	title = {Effects of ultraviolet ({UV}) exclusion on the seasonal concentration of photosynthetic and {UV}-screening pigments in {Scots} pine needles},
	volume = {13},
	issn = {1354-1013, 1365-2486},
	url = {http://doi.wiley.com/10.1111/j.1365-2486.2006.01275.x},
	doi = {10/fp26ss},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Global Change Biology},
	author = {Martz, Françoise and Sutinen, Marja-Liisa and Derome, Kirsti and Wingsle, Gunnar and Julkunen-Tiitto, Riitta and Turunen, Minna},
	month = jan,
	year = {2007},
	pages = {252--265},
}

@article{backstrom_purification_2007,
	title = {Purification of a {Plant} {Mediator} from {Arabidopsis} thaliana {Identifies} {PFT1} as the {Med25} {Subunit}},
	volume = {26},
	issn = {10972765},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1097276507002882},
	doi = {10/ctkcp5},
	language = {en},
	number = {5},
	urldate = {2021-06-10},
	journal = {Molecular Cell},
	author = {Bäckström, Stefan and Elfving, Nils and Nilsson, Robert and Wingsle, Gunnar and Björklund, Stefan},
	month = jun,
	year = {2007},
	pages = {717--729},
}

@article{srivastava_downregulation_2006,
	title = {Downregulation of high-isoelectric-point extracellular superoxide dismutase mediates alterations in the metabolism of reactive oxygen species and developmental disturbances in hybrid aspen: {HipI}-{SOD} in hybrid aspen},
	volume = {49},
	issn = {09607412, 1365313X},
	shorttitle = {Downregulation of high-isoelectric-point extracellular superoxide dismutase mediates alterations in the metabolism of reactive oxygen species and developmental disturbances in hybrid aspen},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2006.02943.x},
	doi = {10/fvh67r},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {The Plant Journal},
	author = {Srivastava, Vaibhav and Schinkel, Helga and Witzell, Johanna and Hertzberg, Magnus and Torp, Mikaela and Srivastava, Manoj Kumar and Karpinska, Barbara and Melzer, Michael and Wingsle, Gunnar},
	month = dec,
	year = {2006},
	pages = {135--148},
}

@article{rouhier_engineering_2006,
	title = {Engineering functional artificial hybrid proteins between poplar peroxiredoxin {II} and glutaredoxin or thioredoxin},
	volume = {341},
	issn = {0006-291X},
	doi = {10.1016/j.bbrc.2006.01.099},
	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. (c) 2006 Elsevier Inc. All rights reserved.},
	language = {English},
	number = {4},
	journal = {Biochemical and Biophysical Research Communications},
	author = {Rouhier, N. and Gama, F. and Wingsle, G. and Gelhaye, E. and Gans, P. and Jacquot, J. P.},
	month = mar,
	year = {2006},
	note = {Place: San Diego
Publisher: Academic Press Inc Elsevier Science
WOS:000235699900056},
	keywords = {acid, cdna, dependent peroxidase, donor, expression, glutaredoxin, hydroperoxide, identification, peroxiredoxin, poplar, reductases, reduction, sequence, thioredoxin},
	pages = {1300--1308},
}

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. (c) 2006 Elsevier Inc. All rights reserved.

@article{ferreira_proteome_2006,
	title = {Proteome profiling of {Populus} euphratica {Oliv}. {Upon} heat stress},
	volume = {98},
	issn = {0305-7364},
	doi = {10.1093/aob/mcl106},
	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. 9 Methods Heat effects were evaluated through electrolyte leakage on leaf discs, and LT50 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.},
	language = {English},
	number = {2},
	journal = {Annals of Botany},
	author = {Ferreira, Silvia and Hjerno, Karin and Larsen, Martin and Wingsle, Gunnar and Larsen, Peter and Fey, Stephen and Roepstorff, Peter and Pais, Maria Salome},
	month = aug,
	year = {2006},
	note = {Place: Oxford
Publisher: Oxford Univ Press
WOS:000239630500008},
	keywords = {Populus euphratica, arabidopsis-thaliana, binding-protein, biosynthetic-pathway, carbon metabolism, escherichia-coli, gene-expression, high-temperature, mass spectrometry, mass-spectrometry, membrane-proteins, moderate heat stress, proteome   profiling, salt stress, sequence databases},
	pages = {361--377},
}

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. 9 Methods Heat effects were evaluated through electrolyte leakage on leaf discs, and LT50 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.

@article{rouhier_identification_2005,
	title = {Identification of {Plant} {Glutaredoxin} {Targets}},
	volume = {7},
	issn = {1523-0864},
	url = {https://www.liebertpub.com/doi/10.1089/ars.2005.7.919},
	doi = {10.1089/ars.2005.7.919},
	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 β-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.Antioxid. Redox Signal. 7, 919–929.},
	number = {7-8},
	urldate = {2021-06-11},
	journal = {Antioxidants \& Redox Signaling},
	author = {Rouhier, Nicolas and Villarejo, Arsenio and Srivastava, Manoj and Gelhaye, Eric and Keech, Olivier and Droux, Michel and Finkemeier, Iris and Samuelsson, Göran and Dietz, Karl Josef and Jacquot, Jean-Pierre and Wingsle, Gunnar},
	month = jul,
	year = {2005},
	note = {Publisher: Mary Ann Liebert, Inc., publishers},
	pages = {919--929},
}

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 β-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.Antioxid. Redox Signal. 7, 919–929.

@article{karlsson_hydrogen_2005,
	title = {Hydrogen peroxide and expression of {hipI}-superoxide dismutase are associated with the development of secondary cell walls in {Zinnia} elegans},
	volume = {56},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/eri207},
	doi = {10.1093/jxb/eri207},
	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.},
	number = {418},
	urldate = {2021-06-11},
	journal = {Journal of Experimental Botany},
	author = {Karlsson, Marlene and Melzer, Michael and Prokhorenko, Isabella and Johansson, Thorsten and Wingsle, Gunnar},
	month = aug,
	year = {2005},
	pages = {2085--2093},
}

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.

@article{hoglund_both_2005,
	title = {Both hypersensitive and non-hypersensitive responses are associated with resistance in {Salix} viminalis against the gall midge {Dasineura} marginemtorquens},
	volume = {56},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/eri318},
	doi = {10.1093/jxb/eri318},
	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.},
	number = {422},
	urldate = {2021-06-11},
	journal = {Journal of Experimental Botany},
	author = {Höglund, Solveig and Larsson, Stig and Wingsle, Gunnar},
	month = dec,
	year = {2005},
	pages = {3215--3222},
}

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.

@article{louis_remote_2005,
	title = {Remote sensing of sunlight-induced chlorophyll fluorescence and reflectance of {Scots} pine in the boreal forest during spring recovery},
	volume = {96},
	issn = {0034-4257},
	doi = {10.1016/j.rse.2005.01.013},
	abstract = {A measurement campaign to assess the feasibility of remote sensing of sunlight-induced chlorophyll fluorescence (ChlF) from a coniferous canopy was conducted in a boreal forest study site (Finland). A Passive Multi-wavelength Fluorescence Detector (PMFD) sensor, developed in the LURE laboratory, was used to obtain simultaneous measurements of ChlF in the oxygen absorption bands, at 687 and 760 nm, and a reflectance index, the PRI (Physiological Reflectance Index), for a month during spring recovery. When these data were compared with active fluorescence measurements performed on needles they revealed the same trend. During sunny days fluorescence and reflectance signals were found to be strongly influenced by shadows associated with the canopy structure. Moreover, chlorophyll fluorescence variations induced by rapid light changes (due to transient cloud shadows) were found to respond more quickly and with larger amplitude under summer conditions compared to those obtained under cold acclimation conditions. In addition, ChlF at 760 nm was observed to increase with the chlorophyll content. During this campaign, the CO2 assimilation was measured at the forest canopy level and was found remarkably well correlated with the PRI index. (c) 2005 Elsevier Inc. All rights reserved.},
	language = {English},
	number = {1},
	journal = {Remote Sensing of Environment},
	author = {Louis, J. and Ounis, A. and Ducruet, J. M. and Evain, S. and Laurila, T. and Thum, T. and Aurela, M. and Wingsle, G. and Alonso, L. and Pedros, R. and Moya, I.},
	month = may,
	year = {2005},
	note = {Place: New York
Publisher: Elsevier Science Inc
WOS:000229355100003},
	keywords = {CO2 flux, FLD   principle, Scots pine, airborne, boreal forest, diurnal cycle, instrument, leaves, oxygen absorption band, passive remote sensing, photoprotection, photosynthesis, photosystem-ii, pri, responses, state, sunlight-induced chlorophyll fluorescence, water-stress, xanthophyll cycle},
	pages = {37--48},
}

A measurement campaign to assess the feasibility of remote sensing of sunlight-induced chlorophyll fluorescence (ChlF) from a coniferous canopy was conducted in a boreal forest study site (Finland). A Passive Multi-wavelength Fluorescence Detector (PMFD) sensor, developed in the LURE laboratory, was used to obtain simultaneous measurements of ChlF in the oxygen absorption bands, at 687 and 760 nm, and a reflectance index, the PRI (Physiological Reflectance Index), for a month during spring recovery. When these data were compared with active fluorescence measurements performed on needles they revealed the same trend. During sunny days fluorescence and reflectance signals were found to be strongly influenced by shadows associated with the canopy structure. Moreover, chlorophyll fluorescence variations induced by rapid light changes (due to transient cloud shadows) were found to respond more quickly and with larger amplitude under summer conditions compared to those obtained under cold acclimation conditions. In addition, ChlF at 760 nm was observed to increase with the chlorophyll content. During this campaign, the CO2 assimilation was measured at the forest canopy level and was found remarkably well correlated with the PRI index. (c) 2005 Elsevier Inc. All rights reserved.

@article{gelhaye_specific_2005,
	title = {A specific form of thioredoxin h occurs in plant mitochondria and regulates the alternative oxidase (vol 101, pg 14545, 2004)},
	volume = {102},
	issn = {0027-8424},
	doi = {10/drv3tz},
	language = {English},
	number = {10},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Gelhaye, E. and Rouhier, N. and Gerard, J. and Jolivet, Y. and Gualberto, J. and Navrot, N. and Ohlsson, P. I. and Wingsle, G. and Hirasawa, M. and Knaff, D. B. and Wang, H. M. and Dizengremel, P. and Meyer, Y. and Jacquot, J. P.},
	month = mar,
	year = {2005},
	note = {Place: Washington
Publisher: Natl Acad Sciences
WOS:000227533100066},
	pages = {3886--3886},
}

@article{wiklund_new_2005,
	title = {A new metabonomic strategy for analysing the growth process of the poplar tree},
	volume = {3},
	issn = {1467-7652},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1467-7652.2005.00129.x},
	doi = {10/dhs8p7},
	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.},
	language = {en},
	number = {3},
	urldate = {2021-06-11},
	journal = {Plant Biotechnology Journal},
	author = {Wiklund, Susanne and Karlsson, Marlene and Antti, Henrik and Johnels, Dan and Sjöström, Michael and Wingsle, Gunnar and Edlund, Ulf},
	year = {2005},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1467-7652.2005.00129.x},
	keywords = {1H HR/MAS NMR, batch process, partial least squares projections to latent structures, poplar tree, principal components analysis, wood formation},
	pages = {353--362},
}

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.

@article{gelhaye_specific_2004,
	title = {A specific form of thioredoxin h occurs in plant mitochondria and regulates the alternative oxidase},
	volume = {101},
	copyright = {Copyright © 2004, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/101/40/14545},
	doi = {10/bhgv8p},
	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.},
	language = {en},
	number = {40},
	urldate = {2021-06-15},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Gelhaye, Eric and Rouhier, Nicolas and Gérard, Joelle and Jolivet, Yves and Gualberto, José and Navrot, Nicolas and Ohlsson, Per-Ingvard and Wingsle, Gunnar and Hirasawa, Masakazu and Knaff, David B. and Wang, Hongmei and Dizengremel, Pierre and Meyer, Yves and Jacquot, Jean-Pierre},
	month = oct,
	year = {2004},
	pmid = {15385674},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {glutathione peroxidase, glutathionylation, poplar, redox potential},
	pages = {14545--14550},
}

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.

@article{lovgren_prc-barrel_2004,
	title = {The {PRC}-barrel domain of the ribosome maturation protein {RimM} mediates binding to ribosomal protein {S19} in the {30S} ribosomal subunits},
	volume = {10},
	issn = {1355-8382},
	doi = {10.1261/rna.7720204},
	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--{\textgreater}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--{\textgreater}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--{\textgreater}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--{\textgreater}AA and DeltarimM mutants. However, they suppressed the 16S rRNA processing deficiency of the RimM-YY--{\textgreater}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--{\textgreater}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.},
	language = {English},
	number = {11},
	journal = {Rna},
	author = {Lovgren, J. M. and Bylund, G. O. and Srivastava, M. K. and Lundberg, L. a. C. and Persson, O. P. and Wingsle, G. and Wikstrom, P. M.},
	month = nov,
	year = {2004},
	note = {Place: Cold Spring Harbor
Publisher: Cold Spring Harbor Lab Press, Publications Dept
WOS:000224746300015},
	keywords = {16S rRNA processing, 30S maturation, RimM, dead, dnak, escherichia-coli, gene, helices 31 and 33b, mutant, mutations, rbfa, rna helicase, s13, s19, site-specific mutagenesis, temperature},
	pages = {1798--1812},
}

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–\textgreaterAA), 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–\textgreaterAA) 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–\textgreaterAA 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–\textgreaterAA and DeltarimM mutants. However, they suppressed the 16S rRNA processing deficiency of the RimM-YY–\textgreaterAA 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–\textgreaterAA) 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.

@article{karpinska_myb_2004,
	title = {{MYB} transcription factors are differentially expressed and regulated during secondary vascular tissue development in hybrid aspen},
	volume = {56},
	issn = {1573-5028},
	url = {https://doi.org/10.1007/s11103-004-3354-5},
	doi = {10/bg9dms},
	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.},
	language = {en},
	number = {2},
	urldate = {2021-06-15},
	journal = {Plant Molecular Biology},
	author = {Karpinska, Barbara and Karlsson, Marlene and Srivastava, Manoj and Stenberg, Anneli and Schrader, Jarmo and Sterky, Fredrik and Bhalerao, Rishikesh P. and Wingsle, Gunnar},
	month = sep,
	year = {2004},
	pages = {255--270},
}

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.