| 1. |
- Jansen, Willemijn J, et al.
(författare)
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Association of Cerebral Amyloid-β Aggregation With Cognitive Functioning in Persons Without Dementia.
- 2018
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Ingår i: JAMA psychiatry. - : American Medical Association (AMA). - 2168-6238 .- 2168-622X. ; 75:1, s. 84-95
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Tidskriftsartikel (refereegranskat)abstract
- Cerebral amyloid-β aggregation is an early event in Alzheimer disease (AD). Understanding the association between amyloid aggregation and cognitive manifestation in persons without dementia is important for a better understanding of the course of AD and for the design of prevention trials.To investigate whether amyloid-β aggregation is associated with cognitive functioning in persons without dementia.This cross-sectional study included 2908 participants with normal cognition and 4133 with mild cognitive impairment (MCI) from 53 studies in the multicenter Amyloid Biomarker Study. Normal cognition was defined as having no cognitive concerns for which medical help was sought and scores within the normal range on cognitive tests. Mild cognitive impairment was diagnosed according to published criteria. Study inclusion began in 2013 and is ongoing. Data analysis was performed in January 2017.Global cognitive performance as assessed by the Mini-Mental State Examination (MMSE) and episodic memory performance as assessed by a verbal word learning test. Amyloid aggregation was measured with positron emission tomography or cerebrospinal fluid biomarkers and dichotomized as negative (normal) or positive (abnormal) according to study-specific cutoffs. Generalized estimating equations were used to examine the association between amyloid aggregation and low cognitive scores (MMSE score ≤27 or memory z score≤-1.28) and to assess whether this association was moderated by age, sex, educational level, or apolipoprotein E genotype.Among 2908 persons with normal cognition (mean [SD] age, 67.4 [12.8] years), amyloid positivity was associated with low memory scores after age 70 years (mean difference in amyloid positive vs negative, 4% [95% CI, 0%-7%] at 72 years and 21% [95% CI, 10%-33%] at 90 years) but was not associated with low MMSE scores (mean difference, 3% [95% CI, -1% to 6%], P=.16). Among 4133 patients with MCI (mean [SD] age, 70.2 [8.5] years), amyloid positivity was associated with low memory (mean difference, 16% [95% CI, 12%-20%], P<.001) and low MMSE (mean difference, 14% [95% CI, 12%-17%], P<.001) scores, and this association decreased with age. Low cognitive scores had limited utility for screening of amyloid positivity in persons with normal cognition and those with MCI. In persons with normal cognition, the age-related increase in low memory score paralleled the age-related increase in amyloid positivity with an intervening period of 10 to 15 years.Although low memory scores are an early marker of amyloid positivity, their value as a screening measure for early AD among persons without dementia is limited.
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| 2. |
- Jansen, Willemijn J, et al.
(författare)
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Prevalence of cerebral amyloid pathology in persons without dementia: a meta-analysis.
- 2015
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Ingår i: JAMA. - : American Medical Association (AMA). - 1538-3598 .- 0098-7484. ; 313:19, s. 1924-38
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Tidskriftsartikel (refereegranskat)abstract
- Cerebral amyloid-β aggregation is an early pathological event in Alzheimer disease (AD), starting decades before dementia onset. Estimates of the prevalence of amyloid pathology in persons without dementia are needed to understand the development of AD and to design prevention studies.
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| 3. |
- Kieselbach, T, et al.
(författare)
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A peroxidase homologue and novel plastocyanin located by proteomics to the Arabidopsis chloroplast thylakoid lumen
- 2000
-
Ingår i: FEBS Letters. - 0014-5793 .- 1873-3468. ; 480:2-3, s. 271-276
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Tidskriftsartikel (refereegranskat)abstract
- A study by two-dimensional electrophoresis showed that the soluble, lumenal fraction of Arabidopsis thaliana thylakoids can be resolved into 300 protein spots. After subtraction of low-intensity spots and accounting for low-level stromal contamination, the number of more abundant, lumenal proteins was estimated to be between 30 and 60. Two of these proteins have been identified: a novel plastocyanin that also was the predominant component of the total plastocyanin pool, and a putative ascorbate peroxidase. Import studies shamed that these proteins are routed to the thylakoid lumen by the Sec- and delta pH-dependent translocation pathways, respectively, In addition, novel isoforms of PsbO and PsbQ were identified.
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| 4. |
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| 5. |
- Angelcheva, Liudmila, et al.
(författare)
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Metabolomic analysis of extreme freezing tolerance in Siberian spruce (Picea obovata)
- 2014
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 204:3, s. 545-555
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Tidskriftsartikel (refereegranskat)abstract
- Siberian spruce (Picea obovata) is one of several boreal conifer species that can survive at extremely low temperatures (ELTs). When fully acclimated, its tissues can survive immersion in liquid nitrogen. Relatively little is known about the biochemical and biophysical strategies of ELT survival. We profiled needle metabolites using gas chromatography coupled with mass spectrometry (GC-MS) to explore the metabolic changes that occur during cold acclimation caused by natural temperature fluctuations. In total, 223 metabolites accumulated and 52 were depleted in fully acclimated needles compared with pre-acclimation needles. The metabolite profiles were found to develop in four distinct phases, which are referred to as pre-acclimation, early acclimation, late acclimation and fully acclimated. Metabolite changes associated with carbohydrate and lipid metabolism were observed, including changes associated with increased raffinose family oligosaccharide synthesis and accumulation, accumulation of sugar acids and sugar alcohols, desaturation of fatty acids, and accumulation of digalactosylglycerol. We also observed the accumulation of protein and nonprotein amino acids and polyamines that may act as compatible solutes or cryoprotectants. These results provide new insight into the mechanisms of freezing tolerance development at the metabolite level and highlight their importance in rapid acclimation to ELT in P.obovata.
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| 6. |
- Bag, Pushan, 1993-, et al.
(författare)
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Solubilization method for isolation of photosynthetic mega- And super-complexes from conifer thylakoids
- 2021
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Ingår i: Bio-protocol. - 2331-8325. ; 11:17
-
Tidskriftsartikel (refereegranskat)abstract
- Photosynthesis is the main process by which sunlight is harvested and converted into chemical energy and has been a focal point of fundamental research in plant biology for decades. In higher plants, the process takes place in the thylakoid membranes where the two photosystems (PSI and PSII) are located. In the past few decades, the evolution of biophysical and biochemical techniques allowed detailed studies of the thylakoid organization and the interaction between protein complexes and cofactors. These studies have mainly focused on model plants, such as Arabidopsis, pea, spinach, and tobacco, which are grown in climate chambers even though significant differences between indoor and outdoor growth conditions are present. In this manuscript, we present a new mild-solubilization procedure for use with “fragile” samples such as thylakoids from conifers growing outdoors. Here, the solubilization protocol is optimized with two detergents in two species, namely Norway spruce (Picea abies) and Scots pine (Pinus sylvestris). We have optimized the isolation and characterization of PSI and PSII multimeric mega- and super-complexes in a close-to-native condition by Blue-Native gel electrophoresis. Eventually, our protocol will not only help in the characterization of photosynthetic complexes from conifers but also in understanding winter adaptation.
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| 7. |
- Chen, Yang-Er, et al.
(författare)
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Comparison of methods for extracting thylakoid membranes of Arabidopsis plants
- 2016
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Ingår i: Physiologia Plantarum. - : Wiley. - 0031-9317 .- 1399-3054. ; 156:1, s. 3-12
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Tidskriftsartikel (refereegranskat)abstract
- Robust and reproducible methods for extracting thylakoid membranes are required for the analysis of photosynthetic processes in higher plants such as Arabidopsis. Here, we compare three methods for thylakoid extraction using two different buffers. Method I involves homogenizing the plant material witha metal/glass blender; method II involves manually grinding the plant materialin ice-cold grinding buffer with a mortar and method III entails snap-freezing followed by manual grinding with a mortar, after which the frozen powder is thawed in isolation buffer. Thylakoid membrane samples extracted using each method were analyzed with respect to protein and chlorophyll content, yields relative to starting material, oxygen-evolving activity, protein complex content and phosphorylation. We also examined how the use of fresh and frozen thylakoid material affected the extracts’ contents of protein complexes. The use of different extraction buffers did not significantly alter the protein contentof the extracts in any case. Method I yielded thylakoid membranes with the highest purity and oxygen-evolving activity. Method III used low amounts of starting material and was capable of capturing rapid phosphorylation changes in the sample at the cost of higher levels of contamination. Method II yielded thylakoid membrane extracts with properties intermediate between those obtained with the other two methods. Finally, frozen and freshly isolated thylakoid membranes performed identically in blue native-polyacrylamide gel electrophoresis experiments conducted in order to separate multimeric protein supracomplexes.
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| 8. |
- Chen, Yang-Er, et al.
(författare)
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The Low Molecular Mass Photosystem II Protein PsbTn is Important for Light Acclimation
- 2019
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Ingår i: Plant Physiology. - Rockville : American Society of Plant Biologists. - 0032-0889 .- 1532-2548. ; 179:4, s. 1739-1753
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Tidskriftsartikel (refereegranskat)abstract
- Photosystem II (PSII) is a supramolecular complex containing over 30 protein subunits and a large set of cofactors including various pigments and quinones as well as Mn, Ca, Cl, and Fe ions. Eukaryotic PSII complexes contain many subunits not found in their bacterial counterparts, including the proteins PsbP, PsbQ, PsbS, and PsbW, as well as the highly homologous, low molecular mass subunits PsbTn1 and PsbTn2 whose function is currently unknown. To determine the function of PsbTn1 and PsbTn2, we generated single and double psbTn1 and psbTn2 knock-out mutants in Arabidopsis thaliana. Cross-linking and reciprocal co-immunoprecipitation experiments revealed that PsbTn is a lumenal PSII protein situated next to the cytochrome b559 subunit PsbE. The removal of the PsbTn proteins decreased the oxygen evolution rate and PSII core phosphorylation level but increased the susceptibility of PSII to photoinhibition and the production of reactive oxygen species. The assembly and stability of PSII were unaffected, indicating that the deficiencies of the psbTn1 psbTn2 double mutants are due to structural changes. Double mutants exhibited a higher rate of non-photochemical quenching of excited states than the wild type and single mutants, as well as slower state transition kinetics and a lower quantum yield of PSII when grown in the field. Based on these results, we propose that the main function of the PsbTn proteins is to enable PSII to acclimate to light shifts or intense illumination.
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| 9. |
- Cheregi, Otilia, et al.
(författare)
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Presence of state transitions in the cryptophyte alga Guillardia theta
- 2015
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Ingår i: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 66:20, s. 6461-6470
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Tidskriftsartikel (refereegranskat)abstract
- Plants and algae have developed various regulatory mechanisms for optimal delivery of excitation energy to the photosystems even during fluctuating light conditions; these include state transitions as well as non-photochemical quenching. The former process maintains the balance by redistributing antennae excitation between the photosys-tems, meanwhile the latter by dissipating excessive excitation inside the antennae. In the present study, these mecha-nisms have been analysed in the cryptophyte alga Guillardia theta. Photoprotective non-photochemical quenching was observed in cultures only after they had entered the stationary growth phase. These cells displayed a diminished overall photosynthetic efficiency, measured as CO2 assimilation rate and electron transport rate. However, in the logarithmic growth phase G. theta cells redistributed excitation energy via a mechanism similar to state transitions. These state transitions were triggered by blue light absorbed by the membrane integrated chlorophyll a/c antennae, and green light absorbed by the lumenal biliproteins was ineffective. It is proposed that state transitions in G. thetaare induced by small re-arrangements of the intrinsic antennae proteins, resulting in their coupling/uncoupling to the photosystems in state 1 or state 2, respectively. G. theta therefore represents a chromalveolate algae able to perform state transitions.
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| 10. |
- Cocco, Emma, et al.
(författare)
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The Influence of Blue and Red Light on Seed Development and Dormancy in Nicotiana tabacum L.
- 2022
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Ingår i: Seeds. - : MDPI. - 2674-1024. ; 1:3, s. 152-163
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Tidskriftsartikel (refereegranskat)abstract
- The correct development of seeds is a pivotal requirement for species preservation. This process depends on the balance between sensing the environmental stimuli/stressors and hormone-mediated transduction, which results in physiological responses. The red and blue regions of the electromagnetic spectrum are known to influence seed dormancy and germination. Here, we report on the effects induced by the blue (peak at 430 nm) and red (peak at 650 nm) regions of the electromagnetic spectrum on seeds from photo- and skotomorphogenetic capsules developed under white, blue, or red light. Regardless of exposure, seeds from skotomorphogenetic capsules showed an almost absent dormancy in association with altered germination kinetics. Conversely, in seeds from photomorphogenetic capsules, the exposure to the blue region induced skotomorphogenetic-like effects, while the exposure to the whole visible range (350–750 nm), as well as to only the red region, showed a dose-related trend. The observed differences appeared to be dependent on the wavelengths in the red and to be based on transduction mechanisms taking place in fruits. While the molecular bases of this differential effect need to be clarified, the results hint at the role played by different light wavelengths and intensities in seed development and germination. These findings may be relevant for applications in crop production and species safeguarding.
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| 11. |
- de Lichtenberg, Casper, 1989-
(författare)
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Time-resolved Structural and Mechanistic Studies of Water Oxidation in Photosystem II : water here, water there, water everywhere
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Oxygenic photosynthesis is undisputedly one of the most important chemical processes for human life on earth as it not only fills the atmosphere with the oxygen that we need to breathe, but also sustains the accumulation of biomass, which is not only used as nourishment but is also present in almost every aspect of our lives as building material, textiles in clothes and furniture, or even as living decorations to name a few.The photosynthetic water-splitting mechanism is catalyzed by a water:plastoquinone oxido-reductase by the name of photosystem II (PSII), which is embedded in the thylakoid membranes of plants, algae and cyanobacteria. As it is excited by light, charge separation occurs in the reaction center of the protein and an electron is extracted by oxidation of Mn4Ca-cluster, that constitutes the active site for the water splitting reaction in PSII. When the Mn4Ca-cluster has been oxidized 4 times, it forms an oxygen-oxygen bond between two water derived ligands bound to the Mn4Ca-cluster and returns to the lowest oxidation state of the catalytic cycle. Understanding what ligands of the cluster that are used in the water splitting reaction is the key to unlocking the underlying chemical mechanism.In this thesis I describe investigations, with room temperature X-ray diffraction (XRD) and X-ray emission spectroscopy (XES) on PSII microcrystals, of how the active site looks in all the stable intermediate oxidation states. Furthermore I describe how we uncovered the sequence of events that lead to insertion of an additional water ligand in the S2-S3 state transition of the catalytic cycle.Furthermore, through time-resolved membrane-inlet mass spectrometry (TR-MIMS) measurements of the isotopic equilibration of the substrate waters with the bulk in conditions that induce different electron magnetic resonance (EPR) spectroscopic signatures, I present evidence that the exchange of the slowly exchanging substrate water Ws is controlled by a dynamic equilibrium between conformations in the S2-state that give rise to either the low-spin multiline (LS-ML) signal or the high-spin (HS) signal. Based on the crystal structures and litterature suggestions for the conformation of the HS state different scenarios were presented for the assignment of Ws and how it exchanges. This analysis is discussed in the context of all semi-stable intermediate oxidation states in the Kok cycle.To further the understanding of this equilibrium, I also studied a selection of mutants positioned at strategic places in the vicinity of the different proposed substrates and at points that were suggested to be critical for substrate entry. With the combination of TR-MIMS and EPR, I reached the conclusion that by mutating valine 185 to asparagine, the water bound A-type conformation was stabilized, meanwhile in the mutant where aspartate 61 was mutated to alanine I observed that the barrier of the equilibrium between the exchanging conformations was so high that the interchange between them was arrested at room temperature. Additionally the retardation of the substrate exchange rates in the S3-states fit best with D61 being in the vicinity of the fast exchanging water. With this information we found the data best explained in a scenario where the water insertion of the S2-S3 transition was determining the if O-O bond formation occurred between the waters that were W2 and W3 or W2 and O5 in the S2 state. In addition, by mutation of glutamate 189 to glutamine that this residue is not important for the exchange of substrate waters in the S2 or the S3 states.Finally I use a combination of substrate labelling with TR-MIMS and time resolved labelling of the waters that ligate the Mn4Ca-cluster to show that the briding oxygen O5 is exchanging with a near identical rate to Ws, further supporting the assignment that Ws=O5.In conclusion, O-O bond formation most likely occurs between W2 (Wf) and O5 (Ws) via an oxo-oxyl radical coupling mechanism. The newly inserted water thus represents the slow exchanging water of the following S-state cycle.
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| 12. |
- Dubreuil, Carole, et al.
(författare)
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Establishment of Photosynthesis through Chloroplast Development Is Controlled by Two Distinct Regulatory Phases
- 2018
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Ingår i: Plant Physiology. - : American Society of Plant Biologists. - 0032-0889 .- 1532-2548. ; 176:2, s. 1199-1214
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Tidskriftsartikel (refereegranskat)abstract
- Chloroplasts develop from undifferentiated proplastids present in meristematic tissue. Thus, chloroplast biogenesis is closely connected to leaf development, which restricts our ability to study the process of chloroplast biogenesis per se. As a consequence, we know relatively little about the regulatory mechanisms behind the establishment of the photosynthetic reactions and how the activities of the two genomes involved are coordinated during chloroplast development. We developed a single cell-based experimental system from Arabidopsis (Arabidopsis thaliana) with high temporal resolution allowing for investigations of the transition from proplastids to functional chloroplasts. Using this unique cell line, we could show that the establishment of photosynthesis is dependent on a regulatory mechanism involving two distinct phases. The first phase is triggered by rapid light-induced changes in gene expression and the metabolome. The second phase is dependent on the activation of the chloroplast and generates massive changes in the nuclear gene expression required for the transition to photosynthetically functional chloroplasts. The second phase also is associated with a spatial transition of the chloroplasts from clusters around the nucleus to the final position at the cell cortex. Thus, the establishment of photosynthesis is a two-phase process with a clear checkpoint associated with the second regulatory phase allowing coordination of the activities of the nuclear and plastid genomes.
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| 13. |
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| 14. |
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| 15. |
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| 16. |
- Farci, Domenica, et al.
(författare)
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Isolation and characterization of a main porin from the outer membrane of Salinibacter ruber
- 2022
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Ingår i: Journal of Bioenergetics and Biomembranes. - : Springer. - 0145-479X .- 1573-6881. ; 54, s. 273-281
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Tidskriftsartikel (refereegranskat)abstract
- Salinibacter ruber is an extremophilic bacterium able to grow in high-salts environments, such as saltern crystallizer ponds. This halophilic bacterium is red-pigmented due to the production of several carotenoids and their derivatives. Two of these pigment molecules, salinixanthin and retinal, are reported to be essential cofactors of the xanthorhodopsin, a light-driven proton pump unique to this bacterium. Here, we isolate and characterize an outer membrane porin-like protein that retains salinixanthin. The characterization by mass spectrometry identified an unknown protein whose structure, predicted by AlphaFold, consists of a 8 strands beta-barrel transmembrane organization typical of porins. The protein is found to be part of a functional network clearly involved in the outer membrane trafficking. Cryo-EM micrographs showed the shape and dimensions of a particle comparable with the ones of the predicted structure. Functional implications, with respect to the high representativity of this protein in the outer membrane fraction, are discussed considering its possible role in primary functions such as the nutrients uptake and the homeostatic balance. Finally, also a possible involvement in balancing the charge perturbation associated with the xanthorhodopsin and ATP synthase activities is considered.
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| 17. |
- Funk, Christiane, et al.
(författare)
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D1' centers are less efficient than normal photosystem II centers
- 2001
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Ingår i: FEBS Letters. - 0014-5793 .- 1873-3468. ; 505:1, s. 113-117
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Tidskriftsartikel (refereegranskat)abstract
- One prominent difference between the photosystem II (PSII) reaction center protein D1 ' in Synechocystis 6803 and normal D1 is the replacement of Phe-186 in D1 with leucine in D1 '. Mutants of Synechocystis 6803 producing only D1 ', or containing engineered D1 proteins with Phe-186 substitutions, were analyzed by 77 K fluorescence emission spectra, chlorophyll a fluorescence induction yield and decay kinetics, and flash-induced oxygen evolution. Compared to D1-containing PSII centers, D1 ' centers exhibited a 50% reduction in variable chlorophyll a fluorescence yield, while the flash-induced O-2 evolution pattern was unaffected. In the F186 mutants, both the P680(+)/Q(A)(-) recombination and O-2 oscillation pattern were noticeably perturbed.
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| 18. |
- Funk, Christiane, et al.
(författare)
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From photosynthesis to industrial applications
- 2024
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Ingår i: Physiologia Plantarum. - : John Wiley & Sons. - 0031-9317 .- 1399-3054. ; 176:4
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 19. |
- Garcia-Cerdan, Jose G., et al.
(författare)
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The PsbW protein stabilizes the supramolecular organization of photosystem II in higher plants
- 2011
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Ingår i: The Plant Journal. - : Wiley-Blackwell. - 0960-7412 .- 1365-313X. ; 65:3, s. 368-381
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Tidskriftsartikel (refereegranskat)abstract
- PsbW, a 6.1-kDa low-molecular-weight protein, is exclusive to photosynthetic eukaryotes, and associates with the photosystem II (PSII) protein complex. In vivo and in vitro comparison of Arabidopsis thaliana wild-type plants with T-DNA insertion knock-out mutants completely lacking the PsbW protein, or with antisense inhibition plants exhibiting decreased levels of PsbW, demonstrated that the loss of PsbW destabilizes the supramolecular organization of PSII. No PSII-LHCII supercomplexes could be detected or isolated in the absence of the PsbW protein. These changes in macro-organization were accompanied by a minor decrease in the chlorophyll fluorescence parameter F-V/F-M, a strongly decreased PSII core protein phosphorylation and a modification of the redox state of the plastoquinone (PQ) pool in dark-adapted leaves. In addition, the absence of PsbW protein led to faster redox changes in the PQ pool, i.e. transitions from state 1 to state 2, as measured by changes in stationary fluorescence (F-S) kinetics, compared with the wild type. Despite these dramatic effects on macromolecular structure, the transgenic plants exhibited no significant phenotype under normal growth conditions. We suggest that the PsbW protein is located close to the minor antenna of the PSII complex, and is important for the contact and stability between several PSII-LHCII supercomplexes.
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| 20. |
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| 21. |
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| 22. |
- Graça, André T., et al.
(författare)
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High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction
- 2021
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the status of a model organism; nonetheless, a high-resolution structure of its Photosystem II is missing. We present the first Cryo-EM high-resolution structure of Arabidopsis PSII supercomplex with average resolution of 2.79 Å, an important model for future PSII studies. The digitonin extracted PSII complexes demonstrate the importance of: the LHG2630-lipid-headgroup in the trimerization of the light-harvesting complex II; the stabilization of the PsbJ subunit and the CP43-loop E by DGD520-lipid; the choice of detergent for the integrity of membrane protein complexes. Furthermore, our data shows at the anticipated Mn4CaO5-site a single metal ion density as a reminiscent early stage of Photosystem II photoactivation.
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| 23. |
- Graça, André T., et al.
(författare)
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Obscurity of chlorophyll tails - Is chlorophyll with farnesyl tail incorporated into PSII complexes?
- 2024
-
Ingår i: Physiologia Plantarum. - 0031-9317 .- 1399-3054. ; 176:4
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Tidskriftsartikel (refereegranskat)abstract
- Chlorophyll is essential in photosynthesis, converting sunlight into chemical energy in plants, algae, and certain bacteria. Its structure, featuring a porphyrin ring enclosing a central magnesium ion, varies in forms like chlorophyll a, b, c, d, and f, allowing light absorption at a broader spectrum. With a 20-carbon phytyl tail (except for chlorophyll c), chlorophyll is anchored to proteins. Previous findings suggested the presence of chlorophyll with a modified farnesyl tail in thermophilic cyanobacteria Thermosynechoccocus vestitus. In our Arabidopsis thaliana PSII cryo-EM map, specific chlorophylls showed incomplete phytyl tails, suggesting potential farnesyl modifications. However, further high-resolution mass spectrometry (HRMS) analysis in A. thaliana and T. vestitus did not confirm the presence of any farnesyl tails. Instead, we propose the truncated tails in PSII models may result from binding pocket flexibility rather than actual modifications.
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| 24. |
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| 25. |
- Granlund, Irene, et al.
(författare)
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Clustering of MS spectra for improved protein identification rate and screening for protein variants and modifications by MALDI-MS/MS
- 2011
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Ingår i: Journal of Proteomics. - : Elsevier BV. - 1874-3919 .- 1876-7737. ; 74:8, s. 1190-1200
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Tidskriftsartikel (refereegranskat)abstract
- It is an established fact that allelic variation and post-translational modifications create different variants of proteins, which are observed as isoelectric and size subspecies in two-dimensional gel based proteomics. Here we explore the stromal proteome of spinach and Arabidopsis chloroplast and show that clustering of mass spectra is a useful tool for investigating such variants and detecting modified peptides with amino acid substitutions or post-translational modifications. This study employs data mining by hierarchical clustering of MALDI-MS spectra, using the web version of the SPECLUST program (http://bioinfo.theplu.se/speclust.html). The tool can also be used to remove peaks of contaminating proteins and to improve protein identification, especially for species without a fully sequenced genome. Mutually exclusive peptide peaks within a cluster provide a good starting point for MS/MS investigation of modified peptides, here exemplified by the identification of an A to E substitution that accounts for the isoelectric heterogeneity in protein isoforms. (C) 2011 Elsevier B.V. All rights reserved.
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| 26. |
- Granlund, Irene, et al.
(författare)
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Difference gel electrophoresis (DIGE)
- 2010
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Ingår i: Encyclopedia of Life Sciences. - : Wiley.
-
Bokkapitel (populärvet., debatt m.m.)abstract
- One of the largest challenges in proteomics today is to be able to quantify the composition and amount of proteins found in a specific cell or tissue at a defined time point. Difference gel electrophoresis (DIGE) is a gel electrophoresis-based technique for protein quantification in complex mixtures. In DIGE the high resolution of two-dimensional gel electrophoresis is combined with the excellent dynamic range obtained by fluorescent tag labelling of protein samples. The output of DIGE experiments provides information about how many proteins display changed expression levels on a specific treatment. In addition, proteins of interest can be excised and identified with conventional mass spectrometry techniques and further analysed by other biochemical methods.
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| 27. |
- Granlund, Irene, 1961-, et al.
(författare)
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Light induced changes in protein expression and uniform regulation of transcription in the thylakoid lumen of Arabidopsis thaliana
- 2009
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 4:5, s. e5649-
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Tidskriftsartikel (refereegranskat)abstract
- In plants oxygenic photosynthesis is performed by large protein complexes found in the thylakoid membranes of chloroplasts. The soluble thylakoid lumen space is a narrow and compressed region within the thylakoid membrane which contains 80-200 proteins. Because the thylakoid lumen proteins are in close proximity to the protein complexes of photosynthesis, it is reasonable to assume that the lumen proteins are highly influenced by the presence of light. To identify light regulated proteins in the thylakoid lumen of Arabidopsis thaliana we developed a faster thylakoid preparation and combined this with difference gel electrophoresis (DIGE) of dark-adapted and light-adapted lumen proteomes. The DIGE experiments revealed that 19 lumen proteins exhibit increased relative protein levels after eight hour light exposure. Among the proteins showing increased abundance were the PsbP and PsbQ subunits of Photosystem II, major plastocyanin and several other proteins of known or unknown function. In addition, co-expression analysis of publicly available transcriptomic data showed that the co-regulation of lumen protein expression is not limited to light but rather that lumen protein genes exhibit a high uniformity of expression. The large proportion of thylakoid lumen proteins displaying increased abundance in light-adapted plants, taken together with the observed uniform regulation of transcription, implies that the majority of thylakoid lumen proteins have functions that are related to photosynthetic activity. This is the first time that an analysis of the differences in protein level during a normal day/night cycle has been performed and it shows that even a normal cycle of light significantly influences the thylakoid lumen proteome. In this study we also show for the first time, using co-expression analysis, that the prevalent lumenal chloroplast proteins are very similarly regulated at the level of transcription.
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| 28. |
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| 29. |
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| 30. |
- Granlund, Irene, et al.
(författare)
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The TL29 protein is lumen located, associated with PSII and not an ascorbate peroxidase
- 2009
-
Ingår i: Plant and Cell Physiology. - : Oxford Journals. - 0032-0781 .- 1471-9053. ; 50:11, s. 1898-1910
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Tidskriftsartikel (refereegranskat)abstract
- The TL29 protein is one of the more abundant proteins in the thylakoid lumen of plant chloroplasts. Based on its sequence homology to ascorbate peroxidases, but without any supporting biochemical evidence, TL29 was suggested to be involved in the plant defense system against reactive oxygen species and consequently renamed to APX4. Our in vivo and in vitro analyses failed to show any peroxidase activity associated with TL29; it bound neither heme nor ascorbate. Recombinant overexpressed TL29 had no ascorbate-dependent peroxidase activity, and various mutational analyses aiming to convert TL29 into an ascorbate peroxidase failed. Furthermore, in the thylakoid lumen no such activity could be associated with TL29 and, additionally, TL29 knock-out mutants did not show any decreased peroxidase activity or increased content of radical oxygen species when grown under light stress. Instead we could show that TL29 is a lumen-located component associated with PSII.
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| 31. |
- Hall, Michael, et al.
(författare)
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Preparation of stroma, thylakoid membrane, and lumen fractions from arabidopsis thaliana chloroplasts for proteomic analysis
- 2011
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Ingår i: In Chloroplast Research in Arabidopsis. - Totowa, NJ : Springer Science + Business Media, LLC 2011. - 9781617792366 ; , s. 207-222
-
Bokkapitel (refereegranskat)abstract
- For many studies regarding important chloroplast processes such as oxygenic photosynthesis, fractionation of the total chloroplast proteome is a necessary first step. Here, we describe a method for isolating the stromal, the thylakoid membrane, and the thylakoid lumen subchloroplast fractions from Arabidopsis thaliana leaf material. All three fractions can be isolated sequentially from the same plant material in a single day preparation. The isolated fractions are suitable for various proteomic analyses such as simple mapping studies or for more complex experiments such as differential expression analysis using two-dimensional difference gel electrophoresis (2D-DIGE) or mass spectrometry (MS)-based techniques. Besides this, the obtained fractions can also be used for many other purposes such as immunological assays, enzymatic activity assays, and studies of protein complexes by native-polyacrylamide gel electrophoresis (native-PAGE).
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| 32. |
- Hall, Michael, 1980-, et al.
(författare)
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Purification, crystallization and preliminary X-ray analysis of PPD6, a PsbP-domain protein from Arabidopsis thaliana
- 2012
-
Ingår i: Acta Crystallographica. Section F. - 1744-3091 .- 1744-3091. ; 68:3, s. 278-280
-
Tidskriftsartikel (refereegranskat)abstract
- The PsbP protein is an extrinsic component of photosystem II that together with PsbO and PsbQ forms the thylakoid lumenal part of the oxygen-evolving complex in higher plants. In addition to PsbP, the thylakoid lumen contains two PsbP-like proteins (PPLs) and six PsbP-domain proteins (PPDs). While the functions of the PsbP-like proteins PPL1 and PPL2 are currently under investigation, the function of the PsbP-domain proteins still remains completely unknown. PPD6 is unique among the PsbP family of proteins in that it contains a conserved disulfide bond which can be reduced in vitro by thioredoxin. The crystal structure determination of the PPD6 protein has been initiated in order to elucidate its function and to gain deeper insights into redox-regulation pathways in the thylakoid lumen. PPD6 has been expressed, purified and crystallized and preliminary X-ray diffraction data have been collected. The crystals belonged to space group P2(1), with unit-cell parameters a = 47.0, b = 64.3, c = 62.0 Å, β = 94.2°, and diffracted to a maximum d-spacing of 2.1 Å.
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| 33. |
- Hall, Michael, et al.
(författare)
-
Redox control of processes in the plant chloroplast thylakoid lumen by disulphide/dithiol exchange as studied by proteomics approaches
- 2009
-
Ingår i: 3rd EuPA Congress 2009 Stockholm. - Veszprem, Hungary : OOK-Press. - 9789638615640 ; , s. 629-631
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The chloroplasts of green plants are the site of oxygenic photosynthesis and important metabolic pathways including biosynthesis of carbohydrates, amino acids and lipids. Photosynthetic activity controls the activity of chloroplast enzymes using thioredoxin-mediated redox control. Recent proteome studies identified more than hundred potential thioredoxin targets indifferent chloroplast compartments and highlighted the impact of thioredoxin mediated redox control for chloroplast function. In this study, we addressed thioredoxin-linked redox control in the thylakoid lumen of Arabidopsis thaliana, and we showed that more than 40 percent of the known proteins of the lumen inside the photosynthetic thylakoid membrane reveal interactions with thioredoxin indicating a central function of thioredoxin control for the regulation of oxygenic photosynthesis.
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| 34. |
- Haniewicz, Patrycja, et al.
(författare)
-
Isolation of monomeric photosystem II that retains the subunit PsbS.
- 2013
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Ingår i: Photosynthesis Research. - : Springer. - 0166-8595 .- 1573-5079. ; 118:3, s. 199-207
-
Tidskriftsartikel (refereegranskat)abstract
- Photosystem II has been purified from a transplastomic strain of Nicotiana tabacum according to two different protocols. Using the procedure described in Piano et al. (Photosynth Res 106:221-226, 2010) it was possible to isolate highly active PSII composed of monomers and dimers but depleted in their PsbS protein content. A "milder" procedure than the protocol reported by Fey et al. (Biochim Biophys Acta 1777:1501-1509, 2008) led to almost exclusively monomeric PSII complexes which in part still bind the PsbS protein. This finding might support a role for PSII monomers in higher plants.
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| 35. |
- Hedman, Erik, et al.
(författare)
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Proteomic identification of glucocorticoid receptor interacting proteins
- 2006
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Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 6:10, s. 3114-26
-
Tidskriftsartikel (refereegranskat)abstract
- The glucocorticoid receptor (GR) acts as a ligand dependent transcription factor but can also cross talk with other signaling pathways via protein-protein interactions. In this paper we describe methods to study novel cytosolic GR interacting proteins, using mAb based immunoaffinity chromatography of GR from rat liver cytosol. Co-purifying proteins were identified by 2-DE in combination with MALDI-TOF-MS. Non-liganded/non-activated and in vitro liganded/activated GR, respectively, co-purifies with specific sets of proteins. Of these 34 were conclusively identified, seven have previously been reported to be part of the GR-complex, revealing 27 new possible interacting candidates for the GR-complex. Of the novel GR interacting proteins the major vault protein, TATA binding interacting protein 49a and glycoprotein PP63 were of special interest. Furthermore, using 2-D DIGE we show that the set of proteins interacting with non-liganded GR is distinctly different in protein amount compared to the proteins found with liganded/activated GR. This suggests the presence of different GR complexes in the cell, which was further substantiated by the finding of several separate GR native protein complexes, "GR-receptosomes", using blue native gel electrophoresis. Our findings suggest the existence of several new mechanisms for GR signaling and regulation.
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| 36. |
- Huesgen, Pitter F., et al.
(författare)
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Proteomic Amino-Termini Profiling Reveals Targeting Information for Protein Import into Complex Plastids
- 2013
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:9, s. e74483-
-
Tidskriftsartikel (refereegranskat)abstract
- In organisms with complex plastids acquired by secondary endosymbiosis from a photosynthetic eukaryote, the majority of plastid proteins are nuclear-encoded, translated on cytoplasmic ribosomes, and guided across four membranes by a bipartite targeting sequence. In-depth understanding of this vital import process has been impeded by a lack of information about the transit peptide part of this sequence, which mediates transport across the inner three membranes. We determined the mature N-termini of hundreds of proteins from the model diatom Thalassiosira pseudonana, revealing extensive N-terminal modification by acetylation and proteolytic processing in both cytosol and plastid. We identified 63 mature N-termini of nucleus-encoded plastid proteins, deduced their complete transit peptide sequences, determined a consensus motif for their cleavage by the stromal processing peptidase, and found evidence for subsequent processing by a plastid methionine aminopeptidase. The cleavage motif differs from that of higher plants, but is shared with other eukaryotes with complex plastids.
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| 37. |
- Hussein, Rana, et al.
(författare)
-
Cryo-electron microscopy reveals hydrogen positions and water networks in photosystem II
- 2024
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 384:6702, s. 1349-1355
-
Tidskriftsartikel (refereegranskat)abstract
- Photosystem II starts the photosynthetic electron transport chain that converts solar energy into chemical energy and thus sustains life on Earth. It catalyzes two chemical reactions: water oxidation to molecular oxygen and plastoquinone reduction. Coupling of electron and proton transfer is crucial for efficiency; however, the molecular basis of these processes remains speculative owing to uncertain water binding sites and the lack of experimentally determined hydrogen positions. We thus collected high-resolution cryo-electron microscopy data of fully hydrated photosystem II from the thermophilic cyanobacterium Thermosynechococcus vestitus to a final resolution of 1.71 angstroms. The structure reveals several previously undetected partially occupied water binding sites and more than half of the hydrogen and proton positions. This clarifies the pathways of substrate water binding and plastoquinone B protonation.
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| 38. |
- Ishikawa, Yasuo, et al.
(författare)
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Functional analysis of the PsbP-like protein (sll1418) in Synechocystis sp PCC 6803
- 2005
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Ingår i: Photosynthesis Research. - Dordrecht : Springer. - 0166-8595 .- 1573-5079. ; 84:1-3, s. 257-262
-
Tidskriftsartikel (refereegranskat)abstract
- A recent proteomic analysis of the thylakoid lumen of Arabidopsis thaliana revealed the presence of several PsbP-like proteins, and a homologue to this gene family was detected in the genome of the cyanobacterium Synechocystis sp. PCC 6803 (Schubert M, Petersson UA, Haas BJ, Funk C, Schroder WP, Kieselbach T (2002) J Biol Chem 277, 8354-8365). Using a peptide-directed antibody against this cyanobacterial PsbP-like protein (sll1418) we could show that it was localized in the thylakoid membrane and associated with Photosystem II. While salt washes did not remove the PsbP-like protein from the thylakoid membrane, it was partially lost during the detergent-based isolation of PSII membrane fractions. In total cell extracts this protein is present in the same amount as the extrinsic PsbO protein. We did not see any significant functional difference between the wild-type and a PsbP-like insertion mutant.
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| 39. |
- Johansson Jänkänpää, Hanna, et al.
(författare)
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Metabolic profiling reveals metabolic shifts in Arabidopsis plants grown under different light conditions
- 2012
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Ingår i: Plant, Cell and Environment. - : John Wiley & Sons. - 0140-7791 .- 1365-3040. ; 35:10, s. 1824-1836
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Tidskriftsartikel (refereegranskat)abstract
- Plants have tremendous capacity to adjust their morphology, physiology and metabolism in response to changes in growing conditions. Thus, analysis solely of plants grown under constant conditions may give partial or misleading indications of their responses to the fluctuating natural conditions in which they evolved. To obtain data on growth-condition dependent differences in metabolite levels we compared leaf metabolite profiles of Arabidopsis thaliana growing under three constant laboratory light conditions: 30 (LL), 300 (NL) and 600 (HL) µmol photons m(-2) s(-1) . We also shifted plants to the field and followed their metabolite composition for three days. Numerous compounds showed light-intensity dependent accumulation, including: many sugars and sugar derivatives (fructose, sucrose, glucose, galactose and raffinose); tricarboxylic acid (TCA) cycle intermediates and amino acids (ca. 30% of which were more abundant under HL and 60% under LL). However, the patterns differed after shifting NL plants to field conditions. Levels of most identified metabolites (mainly amino acids, sugars and TCA cycle intermediates) rose after 2 h and peaked after 73 h, indicative of a "biphasic response" and "circadian" effects. The results provide new insight into metabolomic level mechanisms of plant acclimation, and highlight the role of known protectants under natural conditions.
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| 40. |
- Kjellsen, Trygve D, et al.
(författare)
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Proteomics of extreme freezing tolerance in Siberian spruce (Picea obovata)
- 2010
-
Ingår i: Journal of Proteomics. - : Elsevier. - 1874-3919. ; 73:5, s. 965-975
-
Tidskriftsartikel (refereegranskat)abstract
- Differential expression of proteins in needles of the extreme freeze tolerant conifer Picea obovata during September, October and November was analyzed using DIGE technology and multivariate analysis. More than 1200 spots were detected, and the abundance of 252 of these spots was significantly altered during the course of acclimation. The 252 spots were clustered into five distinct expression profiles. Among the protein spots showing differential expression, 43 were identified by MALDI-TOF/TOF and twelve of them matched proteins associated with various biotic and abiotic stress responses in other plants. Dehydrins, Hsp70s, AAA+ ATPases, lipocalin, cyclophilins, glycine-rich protein (GNP) and several reactive oxygen intermediate scavenging proteins showed increased accumulation levels from September to November. The expression profiles and putative role of the identified proteins during acclimation and freezing tolerance are discussed.
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| 41. |
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| 42. |
- Lundberg, Erik, et al.
(författare)
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Crystal structure of the TL29 protein from Arabidopsis thaliana : An APX homolog without peroxidase activity
- 2011
-
Ingår i: Journal of Structural Biology. - : Elsevier. - 1047-8477 .- 1095-8657. ; 176:1, s. 24-31
-
Tidskriftsartikel (refereegranskat)abstract
- TL29 is a plant-specific protein found in the thylakoid lumen of chloroplasts. Despite the putative requirement in plants for a peroxidase close to the site of photosynthetic oxygen production, and the sequence homology of TL29 to ascorbate peroxidases, so far biochemical methods have not shown this enzyme to possess peroxidase activity. Here we report the three-dimensional X-ray crystal structure of recombinant TL29 from Arabidopsis thaliana at a resolution of 2.5 Å. The overall structure of TL29 is mainly alpha helical with six longer and six shorter helical segments. The TL29 structure resembles that of typical ascorbate peroxidases, however, crucial differences were found in regions that would be important for heme and ascorbate binding. Such differences suggest it to be highly unlikely that TL29 functions as a peroxidase.
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| 43. |
- Marino, Giada, et al.
(författare)
-
Family-wide characterization of Matrix Metallo-proteinases from Arabidopsis thaliana reveals their distinct proteolytic activity and cleavage site specificity.
- 2014
-
Ingår i: Biochemical Journal. - : Biochemical Journal. - 0264-6021 .- 1470-8728. ; 457:2, s. 335-346
-
Tidskriftsartikel (refereegranskat)abstract
- Matrix metalloproteases (MMPs) are a family of zinc-dependent endopeptidases widely distributed throughout all kingdoms of life. In mammals, MMPs play key roles in many physiological and pathological processes including remodeling of the extracellular matrix. In the genome of the annual plant Arabidopsis thaliana five MMP-like proteins (At-MMPs) are encoded, but their function is unknown. Previous work on these enzymes was limited to gene expression analysis, and so far proteolytic activity has been shown only for At1-MMP. We expressed and purified the catalytic domains of all five At-MMPs as His-tagged proteins in E.coli to delineate the biochemical differences and similarities among the Arabidopsis MMP family members. We demonstrate that all five recombinant At-MMPs are active proteases with distinct preferences for different protease substrates. Furthermore, we performed a family-wide characterization of their biochemical properties and highlight similarities and differences in their cleavage site specificities as well as pH- and temperature dependent activities. Detailed analysis of their sequence specificity using Proteomic Identification of protease Cleavage Sites (PICS) revealed profiles similar to human MMPs with the exception of At5-MMP; homology models of the At-MMP catalytic domains supported these results. Our results suggest that each At-MMP may be involved in different proteolytic processes during plant growth and development.
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| 44. |
- Mattsson, Niklas, et al.
(författare)
-
Prevalence of the apolipoprotein E ε4 allele in amyloid β positive subjects across the spectrum of Alzheimer's disease
- 2018
-
Ingår i: Alzheimer's and Dementia. - : Wiley. - 1552-5260 .- 1552-5279. ; 14:7, s. 913-924
-
Tidskriftsartikel (refereegranskat)abstract
- Introduction: Apolipoprotein E (APOE) ε4 is the major genetic risk factor for Alzheimer's disease (AD), but its prevalence is unclear because earlier studies did not require biomarker evidence of amyloid β (Aβ) pathology. Methods: We included 3451 Aβ+ subjects (853 AD-type dementia, 1810 mild cognitive impairment, and 788 cognitively normal). Generalized estimating equation models were used to assess APOE ε4 prevalence in relation to age, sex, education, and geographical location. Results: The APOE ε4 prevalence was 66% in AD-type dementia, 64% in mild cognitive impairment, and 51% in cognitively normal, and it decreased with advancing age in Aβ+ cognitively normal and Aβ+ mild cognitive impairment (P <.05) but not in Aβ+ AD dementia (P =.66). The prevalence was highest in Northern Europe but did not vary by sex or education. Discussion: The APOE ε4 prevalence in AD was higher than that in previous studies, which did not require presence of Aβ pathology. Furthermore, our results highlight disease heterogeneity related to age and geographical location.
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| 45. |
- Mishra, Yogesh, et al.
(författare)
-
Active-site plasticity revealed in the asymmetric dimer of AnPrx6 the 1-Cys peroxiredoxin and molecular chaperone from Anabaena sp. PCC 7120
- 2017
-
Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 7
-
Tidskriftsartikel (refereegranskat)abstract
- Peroxiredoxins (Prxs) are vital regulators of intracellular reactive oxygen species levels in all living organisms. Their activity depends on one or two catalytically active cysteine residues, the peroxidatic Cys (C-P) and, if present, the resolving Cys (C-R). A detailed catalytic cycle has been derived for typical 2-Cys Prxs, however, little is known about the catalytic cycle of 1-Cys Prxs. We have characterized Prx6 from the cyanobacterium Anabaena sp. strain PCC7120 (AnPrx6) and found that in addition to the expected peroxidase activity, AnPrx6 can act as a molecular chaperone in its dimeric state, contrary to other Prxs. The AnPrx6 crystal structure at 2.3 angstrom resolution reveals different active site conformations in each monomer of the asymmetric obligate homo-dimer. Molecular dynamic simulations support the observed structural plasticity. A FSH motif, conserved in 1-Cys Prxs, precedes the active site PxxxTxxCp signature and might contribute to the 1-Cys Prx reaction cycle.
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| 46. |
- Mishra, Yogesh, et al.
(författare)
-
Arabidopsis plants grown in the field and climate chambers significantly differ in leaf morphology and photosystem components
- 2012
-
Ingår i: BMC Plant Biology. - : BioMed Central. - 1471-2229. ; 12, s. 6-
-
Tidskriftsartikel (refereegranskat)abstract
- Background:Plants exhibit phenotypic plasticity and respond to differences in environmental conditions by acclimation. We have systematically compared leaves of Arabidopsis thaliana plants grown in the field and under controlled low, normal and high light conditions in the laboratory to determine their most prominent phenotypic differences.Results: Compared to plants grown under field conditions, the "indoor plants" had larger leaves, modified leaf shapes and longer petioles. Their pigment composition also significantly differed; indoor plants had reduced levels of xanthophyll pigments. In addition, Lhcb1 and Lhcb2 levels were up to three times higher in the indoor plants, but differences in the PSI antenna were much smaller, with only the low-abundance Lhca5 protein showing altered levels. Both isoforms of early-light-induced protein (ELIP) were absent in the indoor plants, and they had less non-photochemical quenching (NPQ). The field-grown plants had a high capacity to perform state transitions. Plants lacking ELIPs did not have reduced growth or seed set rates, but their mortality rates were sometimes higher. NPQ levels between natural accessions grown under different conditions were not correlated.Conclusion: Our results indicate that comparative analysis of field-grown plants with those grown under artificial conditions is important for a full understanding of plant plasticity and adaptation.
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| 47. |
- Mishra, Yogesh, et al.
(författare)
-
Expression, purification, crystallization and preliminary X-ray crystallographic studies of alkyl hydroperoxide reductase (AhpC) from the cyanobacterium Anabaena sp. PCC 7120
- 2011
-
Ingår i: Acta Crystallographica. Section F. - : International Union of Crystallography. - 1744-3091 .- 1744-3091. ; 67:10, s. 1203-1206
-
Tidskriftsartikel (refereegranskat)abstract
- Alkyl hydroperoxide reductase (AhpC) is a key component of a large family of thiol-specific antioxidant (TSA) proteins distributed among prokaryotes and eukaryotes. AhpC is involved in the detoxification of reactive oxygen species (ROS) and reactive sulfur species (RSS). Sequence analysis of AhpC from the cyanobacterium Anabaena sp. PCC 7120 shows that this protein belongs to the 1-Cys class of peroxiredoxins (Prxs). It has recently been reported that enhanced expression of this protein in Escherichia coli offers tolerance to multiple stresses such as heat, salt, copper, cadmium, pesticides and UV-B. However, the structural features and the mechanism behind this process remain unclear. To provide insights into its biochemical function, AhpC was expressed, purified and crystallized by the hanging-drop vapour-diffusion method. Diffraction data were collected to a maximum d-spacing of 2.5 Å using synchrotron radiation. The crystal belonged to space group P212121, with unit-cell parameters a = 80, b = 102, c = 109.6 Å. The structure of AhpC from Anabaena sp. PCC 7120 was determined by molecular-replacement methods using the human Prx enzyme hORF6 (PDB entry1prx) as the template.
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| 48. |
- Misra, Yogesh, et al.
(författare)
-
Arabidopsis Plants Grown in the Field and Climate Chambers Significantly Differ in Leaf Morphology and Photosystem Components
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Background: Plants exhibit phenotypic plasticity and respond to differences in environmental conditions by acclimation. We have systematically compared leaves of Arabidopsis thaliana plants grown in the field and under controlled low, normal and high light conditions in the laboratory to determine their most prominent phenotypic differences. Results: Compared to plants grown under field conditions, the ―indoor plants‖ had larger leaves, modified leaf shapes and longer petioles. Their pigment composition also significantly differed; indoor plants had reduced levels of xanthophyll pigments. In addition, Lhcb1 and Lhcb2 levels were up to three times higher in the indoor plants, but differences in the PSI antenna were much smaller, with only the low-abundance Lhca5 protein showing altered levels. Both isoforms of early-light-induced protein (ELIP) were absent in the indoor plants, and they had less non-photochemical quenching (NPQ). The field-grown plants had a high capacity to perform state transitions. Plants lacking ELIPs did not have reduced growth or seed set rates, but their mortality rates were sometimes higher. NPQ levels between natural ecotypes grown under different conditions were not correlated. Conclusion: Our results indicate that comparative analysis of field-grown plants with those grown under artificial conditions is important for a full understanding of plant plasticity and adaptation.
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| 49. |
- Mohammadi, Nasibeh, 1981-
(författare)
-
Determining the role of guanylate-binding proteins for host defense against Francisella tularensis
- 2022
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Francisella tularensis is a highly virulent, intracellular bacterium and the causative agent of the human disease tularemia. This is a zoonotic, often vector-borne disease. Due to its intracellular nature, F. tularensis can infect many cell types, but of special relevance is its ability to infect monocytic cells and avoid their otherwise potent antimicrobial effects. Monocytic cells can; however, control infection after activation with IFN-γ, but the molecular mechanisms behind this control are not well understood. Recently, guanylate-binding proteins (GBPs) have been identified as crucial for the control of intracellular F. tularensis and many other bacteria, viruses, and parasites. They represent a vast family of interferon-inducible proteins, but it is incompletely understood how their ubiquitous abilities to control diverse types of infections are executed. The overall aim of the thesis was to obtain a better understanding of how GBPs execute the control of infection caused by Francisella and how the bacterium counteracts the bactericidal effects of the GBPs and of other immune mediators. To this end, the responses of bone marrow-derived murine macrophages (BMDM) to Francisella was one model investigated and the other employed a co-culture system whereby BMDM were infected and to the cultures immune cells from vaccinated mice were added. To comprehensively understand the host-pathogen interaction, a variety of Francisella strains were utilized; the highly virulent SCHU S4 strain, the human live vaccine strain (LVS), and the widely used surrogate for F. tularensis, the low virulent F. novicida. All strains have similar capability of intracellular multiplication in BMDM, however, activation of the microbicidal ability of BMDM with IFN-γ, significant control of infection was observed for the LVS and F. novicida strains, whereas there was no control of the SCHU S4 infection. The control of the former strains was GBP-dependent, despite that no differences in GBP transcription or translation were observed in the infected cell cultures. Patterns of 18 cytokines very clearly discriminated the different types of infections and high levels were generally observed in F. novicida-infected cultures and very low levels in SCHU S4-infected cultures. Co-infection with F. novicida and SCHU S4 led to significant control of both strains and in these cultures, a majority of cytokines showed intermediate or high levels. A critical component in the immune recognition of Francisella is AIM2, which is a core constituent of a special form of inflammasome, a cytoplasmic multimeric complex. We determined that AIM2-deficient BMDM, despite the central role of AIM2 for immune recognition of F. novicida and LVS, still controlled infection with either of the two strains after activation with IFN-γ. Again, no control of the virulent strain SCHU S4 was observed. The co-culture system revealed further complexity beyond that of the BMDM model. Utilizing splenocytes obtained from immunized C57BL/6 mice as effectors in cultures with BMDM infected with either of the three Francisella strains, we observed that regardless of strain, significant control of replication occurred with wild-type macrophages and immune splenocytes, even for the highly virulent SCHU S4 strain, but not in cultures with immune splenocytes and GBP-deficient macrophages. Supernatants from the cultures demonstrated very distinct patterns for each of the three infections. Thus, the co-culture assay identified, as for the BMDM model, a crucial role of GBPs for the control of intracellular replication of Francisella, however, in contrast to the BMDM model, the co-culture conferred significant control of SCHU S4 infection.Collectively, our studies demonstrate a very important role of GBPs for the IFN-γ-dependent control of Francisella infection, with the notable exception of the highly virulent strain SCHU S4. A GBP-mediated control of SCHU S4 was; however, observed in the co-culture system, thereby identifying additional bactericidal mechanisms, besides those that are IFN-γ-dependent. We also demonstrate that the inflammatory potential of Francisella strains is correlated to their virulence, most notable is the almost complete lack of inflammatory response during infection with the highly virulent SCHU S4 strain, but this anti-inflammatory capacity was counteracted by the strong pro-inflammatory property of F. novicida during co-infection.
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| 50. |
- Petersson, Ulrika A., et al.
(författare)
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The Prx Q protein of Arabidopsis thaliana is a member of the luminal chloroplast proteome
- 2006
-
Ingår i: FEBS Letters. - : Wiley. - 0014-5793 .- 1873-3468. ; 580:26, s. 6055-6061
-
Tidskriftsartikel (refereegranskat)abstract
- Peroxiredoxins have been discovered in many organisms ranging from eubacteria to mammals, and their known biological functions include both oxidant defense and signal transduction. The genome of Arabidopsis thaliana encodes for ten individual peroxiredoxins, of which four are located in the chloroplast. The best-characterized member of the chloroplast peroxiredoxins is 2-Cys Prx that is associated with the stroma side of the thylakoid membrane and is considered to participate in antioxidant defense and protection of photosynthesis. This study addressed the chloroplast peroxiredoxin Prx Q and showed that its subcellular location is the lumen of the thylakoid membrane. To get insight in the biological function of the Prx Q protein of Arabidopsis, the protein levels of the Prx Q protein in thylakoid membranes were studied under different light conditions and oxidative stress. A T-DNA knockout mutant of Prx Q did not show any visible phenotype and had normal photosynthetic performance with a slightly increased oxygen evolving activity.
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