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  • 1.
    Aigner, Harald
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wagner, Raik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sjögren, Lars
    Eubel, Holger
    Millar, Harvey
    Clarke, Adrian
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    FtsH11 protease is required for Arabidopsis thaliana to adapt to gtowth in continuous lightManuscript (preprint) (Other academic)
    Abstract [en]

    Continuous light can increase greenhouse food production; however, some of the most important greenhouse horticulture crops are not able to adapt to long photoperiods. Here, we provide evidence that knock-out of the FtsH11 protease causes molecular differences that prevent Arabidopsis thaliana to adapt to prolonged photoperiods. Previously this protease had been shown to be critical for thermotolerance (Chen et al. 2006). We demonstrate that knock-out mutants deficient of FtsH11 develop chlorosis when shifted to continuous light. When grown under normal growth conditions and short days, ftsh11 displayed changes in protein amount of chloroplast proteins involved in the photosynthetic light reaction and the Calvin cycle as well as of the FtsH12 protease. The proteomic changes are accompanied by reduced non-photochemical quenching and faster state transition. A shift to continuous light further enhanced these effects and induced morphological changes of the chloroplast and chlorosis. No changes in the mitochondrial proteome were observed between wild type and ftsh11.

  • 2.
    Angelcheva, Liudmila
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mishra, Yogesh
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Antti, Henrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kjellsen, Trygve D.
    Department of Biology, Norwegian University of Science and Technology.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Strimbeck, Richard G.
    Department of Biology, Norwegian University of Science and Technology.
    Schröder, Wolfgang P.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Metabolomic analysis of extreme freezing tolerance in Siberian spruce (Picea obovata)2014In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 204, no 3, p. 545-555Article in journal (Refereed)
    Abstract [en]

    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.

  • 3. Chen, Que
    et al.
    Arents, Jos
    Schuurmans, J. Merijn
    Ganapathy, Srividya
    de Grip, Willem J.
    Cheregi, Otilia
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    dos Santos, Filipe Branco
    Hellingwerf, Klaas J.
    Combining retinal-based and chlorophyll-based (oxygenic) photosynthesis: Proteorhodopsin expression increases growth rate and fitness of a Delta PSI strain of Synechocystis sp. PCC68032019In: Metabolic engineering, ISSN 1096-7176, E-ISSN 1096-7184, Vol. 52, p. 68-76Article in journal (Refereed)
    Abstract [en]

    To fill the "green absorption gap", a green absorbing proteorhodopsin was expressed in a PSI-deletion strain (Delta PSI) of Synechocystis sp. PCC6803. Growth-rate measurements, competition experiments and physiological characterization of the proteorhodopsin-expressing strains, relative to the Delta PSI control strain, allow us to conclude that proteorhodopsin can enhance the rate of photoheterotrophic growth of Delta PSI Synechocystis strain. The physiological characterization included measurement of the amount of residual glucose in the spent medium and analysis of oxygen uptake- and production rates. To explore the use of solar radiation beyond the PAR region, a red-shifted variant Proteorhodopsin-D212N/F234S was expressed in a retinal-deficient PSI-deletion strain (Delta PSI/Delta SynACO). Via exogenous addition of retinal analogue an infrared absorbing pigment (maximally at 740 nm) was reconstituted in vivo. However, upon illumination with 746 nm light, it did not significantly stimulate the growth (rate) of this mutant. The inability of the proteorhodopsin-expressing Delta PSI strain to grow photoautotrophically is most likely due to a kinetic rather than a thermodynamic limitation of its NADPH-dehydrogenase in NADP(+)-reduction.

  • 4. Chen, Que
    et al.
    Arents, Jos
    Schuurmans, J. Merijn
    Ganapathy, Srividya
    de Grip, Willem J.
    Cheregi, Otilia
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    dos Santos, Filipe Branco
    Hellingwerf, Klaas J.
    Functional Expression of Gloeobacter Rhodopsin in PSI-Less Synechocystis sp. PCC68032019In: Frontiers in Bioengineering and Biotechnology, E-ISSN 2296-4185, Vol. 7, article id 67Article in journal (Refereed)
    Abstract [en]

    The approach of providing an oxygenic photosynthetic organism with a cyclic electron transfer system, i.e., a far-red light-driven proton pump, is widely proposed to maximize photosynthetic efficiency via expanding the absorption spectrum of photosynthetically active radiation. As a first step in this approach, Gloeobacter rhodopsin was expressed in a PSI-deletion strain of Synechocystis sp. PCC6803. Functional expression of Gloeobacter rhodopsin, in contrast to Proteorhodopsin, did not stimulate the rate of photoheterotrophic growth of this Synechocystis strain, analyzed with growth rate measurements and competition experiments. Nevertheless, analysis of oxygen uptake and-production rates of the Gloeobacter rhodopsin-expressing strains, relative to the 1 PSI control strain, confirm that the proton-pumping Gloeobacter rhodopsin provides the cells with additional capacity to generate proton motive force. Significantly, expression of the Gloeobacter rhodopsin did modulate levels of pigment formation in the transgenic strain.

  • 5.
    Cheregi, Otilia
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Antibiotic Disc Assay for Measuring Cell Wall Function in Synechocystis sp. PCC68032016In: Bio-protocol, E-ISSN 2331-8325, Vol. 6, no 24Article in journal (Refereed)
    Abstract [en]

    This protocol describes how to investigate the integrity of the outer cell wall in thecyanobacterium Synechocystis sp. PCC6803 using antibiotics. It is adapted to the agar diffusion test(Bauer et al., 1966), in which filter paper discs impregnated with specified concentrations of antibioticswere placed on agar plates inoculated with bacteria. The antibiotics we tested, interfering with thebiosynthesis/function of bacterial cell walls, will diffuse into the agar and produce a zone ofcyanobacterial growth inhibition around the disc(s). The size of the inhibition zone reflects the sensitivityof the strain to the action of antibiotics, e.g., a mutation in a protein functioning within the cell wall or itsconstruction would render the mutant strain more sensitive to the respective antibiotic. The method hasproven to be useful for phenotyping a mutant of Synechocystis sp. PCC6803 lacking all three genesencoding Deg proteases. Deletion of these ATP-independent serine proteases was shown to haveimpact on the outer cell layers of Synechocystis cells.

  • 6.
    Cheregi, Otilia
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Regulation of the scp Genes in the Cyanobacterium Synechocystis sp PCC 6803-What is New?2015In: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 20, no 8, p. 14621-14637Article in journal (Refereed)
    Abstract [en]

    In the cyanobacterium Synechocystis sp. PCC 6803 there are five genes encoding small CAB-like (SCP) proteins, which have been shown to be up-regulated under stress. Analyses of the promoter sequences of the scp genes revealed the existence of an NtcA binding motif in two scp genes, scpB and scpE. Binding of NtcA, the key transcriptional regulator during nitrogen stress, to the promoter regions was shown by electrophoretic mobility shift assay. The metabolite 2-oxoglutarate did not increase the affinity of NtcA for binding to the promoters of scpB and scpE. A second motif, the HIP1 palindrome 5' GGCGATCGCC 3', was detected in the upstream regions of scpB and scpC. The transcription factor encoded by sll1130 has been suggested to recognize this motif to regulate heat-responsive genes. Our data suggest that HIP1 is not a regulatory element within the scp genes. Further, the presence of the high light regulatory (HLR1) motif was confirmed in scpB-E, in accordance to their induced transcriptions in cells exposed to high light. The HLR1 motif was newly discovered in eight additional genes.

  • 7.
    Cheregi, Otilia
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kotabová, Eva
    Prášil, Ondřej
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kaňa, Radek
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Presence of state transitions in the cryptophyte alga Guillardia theta2015In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 66, no 20, p. 6461-6470Article in journal (Refereed)
    Abstract [en]

    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.

  • 8.
    Cheregi, Otilia
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Miranda, Hélder
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Gröbner, Gerhard
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Inactivation of the Deg protease family in the cyanobacterium Synechocystis sp. PCC 6803 has impact on the outer cell layers2015In: Journal of Photochemistry and Photobiology. B: Biology, ISSN 1011-1344, E-ISSN 1873-2682, p. 383-394Article in journal (Refereed)
    Abstract [en]

    The serine type Deg/HtrA proteases are distributed in a wide range of organisms from Escherichia coli to humans. The cyanobacterium Synechocystis sp. PCC 6803 possesses three Deg protease orthologues: HtrA, HhoA and HhoB. Previously we compared Synechocystis 6803 wild type cells exposed to mild or severe stress conditions with a mutant lacking all three Deg proteases and demonstrated that stress had strong impact on the proteomes and metabolomes [1]. To identify the biochemical processes, which this protease family is involved in, here we compared Synechocystis sp. PCC 6803 wild type cells with a mutant lacking all three Deg proteases grown under normal growth conditions (30 °C and 40 μmol photons m−2 s−1). Deletion of the Deg proteases lead to the down-regulation of proteins related to the biosynthesis of outer cell layers (e.g. the GDP mannose 4,6-dehydratase) and affected protein secretion. During the late growth phase of the culture Deg proteases were found to be secreted to the extracellular medium of the Synechocystis sp. PCC 6803 wild type strain. While cyanobacterial Deg proteases seem to act mainly in the periplasmic space, deletion of the three proteases influences the proteome and metabolome of the whole cell. Impairments in the outer cell layers of the triple mutant might explain the higher sensitivity toward light and oxidative stress, which was observed earlier by Barker and coworkers [2].

  • 9.
    Cheregi, Otilia
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Vermaas, Wim
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    The search for new chlorophyll-binding proteins in the cyanobacterium Synechocystis sp. PCC 68032012In: Journal of Biotechnology, ISSN 0168-1656, E-ISSN 1873-4863, Vol. 162, no 1, p. 124-133Article in journal (Refereed)
    Abstract [en]

    Light harvesting provides a major challenge in the production of biofuels from microorganisms; while sunlight provides the energy necessary for biomass/biofuel production, at the same time it damages the cells. The genome of Synechocystis sp. PCC 6803 was searched for open reading frames that might code for yet unidentified chlorophyll-binding proteins with low molecular mass that could be involved in stress-adaptation. Amongst 9,167 hypothetical ORFs corresponding to potential polypeptides of 100 amino acids or less, two were identified that had the potential to be pigment-binding, because they i) encoded a potential transmembrane region, ii) showed sequence similarity with known chlorophyll-binding domains, iii) were conserved in other cyanobacterial species, and iv) their codon adaptation index indicated significant translation probability. The two ORFs were located complementary (antisense) and internal to the ferrochelatase (hemH) and the pyruvate dehydrogenase (pdh) genes and therefore were named a-fch and a-pdh, respectively. Transcription of both genes was confirmed; however, no translated proteins could be detected immunologically. Whereas mutations within a-pdh or a-fch did not lead to any obvious phenotype, it is clear that transcripts and proteins over and above the currently known set may play a role in defining the physiology of cyanobacteria and other organisms.

     

     

  • 10.
    Cheregi, Otilia
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wagner, Raik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Insights into the Cyanobacterial Deg/HtrA Proteases2016In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 7, article id 694Article in journal (Refereed)
    Abstract [en]

    Proteins are the main machinery for all living processes in a cell; they provide structural elements, regulate biochemical reactions as enzymes, and are the interface to the outside as receptors and transporters. Like any other machinery proteins have to be assembled correctly and need maintenance after damage, e.g., caused by changes in environmental conditions, genetic mutations, and limitations in the availability of cofactors. Proteases and chaperones help in repair, assembly, and folding of damaged and misfolded protein complexes cost-effective, with low energy investment compared with neo-synthesis. Despite their importance for viability, the specific biological role of most proteases in vivo is largely unknown. Deg/HtrA proteases, a family of serinetype ATP-independent proteases, have been shown in higher plants to be involved in the degradation of the Photosystem II reaction center protein D1. The objective of this review is to highlight the structure and function of their cyanobacterial orthologs. Homology modeling was used to find specific features of the SynDeg/HtrA proteases of Synechocystis sp. PCC 6803. Based on the available data concerning their location and their physiological substrates we conclude that these Deg proteases not only have important housekeeping and chaperone functions within the cell, but also are needed for remodeling the cell exterior.

  • 11. Clarke, SM
    et al.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Chemistry.
    Hendry, GS
    Shand, JA
    Wydrzynski, T
    Eaton-Rye, JJ
    Amino acid deletions in the cytosolic domains of the chlorophyll alpha-binding protein CP47 slow Q(A)(-) oxidation and/or prevent the assembly of Photosystem II2002In: PLANT MOLECULAR BIOLOGY, ISSN 0167-4412, Vol. 50, no 3, p. 563-72Article in journal (Refereed)
    Abstract [en]

    The Photosystem II (PSII) core antenna chlorophyll alpha-binding protein, CP47, contains six membrane-spanning a-helices separated by five hydrophilic loops: A-E. To identify important hydrophilic cytosolic regions, oligonucleotide-directed mutagenesis was employed to introduce short segment deletions into loops B and D, and the C-terminal domain. Four strains carrying deletions of between three and five residues were created in loop B. Two strains, with deletions adjacent to helices II and III, did not assemble PSII; however, the mutants Delta(F123-D125) and Delta(R127-S131) remained photoautotrophic with near wild-type levels of assembled reaction centers. In contrast, all deletions introduced into loop D, connecting helices IV and V, failed to assemble significant levels of PSII and were obligate photoheterotrophic mutants. However, deletions in the C-terminal domain did not prevent the assembly of PSII reaction centers although the mutant Delta(S471-T473), with a deletion adjacent to helix VI, exhibited retarded Q(A)(-) oxidation kinetics and the PSII-specific herbicide, atrazine, bound less tightly in the Delta(S471-T473) and Delta(F475-D477) strains. Deletions in the C-terminal domain also created mutants with large protein aggregates that were recognized by an antibody raised against the PSII reaction center D1 protein. Low-temperature fluorescence emission spectra of photoautotrophic strains carrying deletions in either the C-terminal domain or loop B did not provide evidence for impaired energy transfer from the phycobilisomes to the PSII reaction center. The data therefore suggest an important structural role for loop D in the assembly of PSII and a potential interaction between the C-terminal domain of CP47 and the PSII reaction center that, when perturbed, results in photoinduced protein aggregates involving the D1 protein.

  • 12. Dedic, R
    et al.
    Promnares, K
    Psencík, J
    Svoboda, A
    Korínek, M
    Tichý, M
    Komenda, J.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Chemistry.
    Hála, J
    Hole burning study of cyanobacterial Photosystem II complexes differing in the content of small putative chlorophyll-binding proteins2004In: Journal of Luminescence, ISSN 0022-2313, Vol. 107, no 1-4, p. 230-5Article in journal (Refereed)
    Abstract [en]

    This contribution presents low-temperature absorption, both broad-band and site-selective excited fluorescence, and persistent hole burning spectra of Photosystem II complexes from the Photosystem I-lacking strains of the cyanobacterium Synechocystis sp. PCC 6803 differing in the content of small putative chlorophyll-binding proteins (Scps). These proteins are homologous to light-harvesting complex of higher plants and may bind pigments. The excited state lifetimes of the complexes were determined from zero-phonon hole widths extrapolated to zero-burning dose. The area and spectral position of a phonon side-band with respect to the zero-phonon hole provided additional information concerning chlorophyll–protein coupling and the Stokes shift. Decrease of three absorption subbands at (670.0, 672.9, and 675.7 nm) in the Photosystem II isolated from the strain lacking ScpC and ScpD is in agreement with a hypothesis about the role of Scps in the chlorophyll binding. In addition, narrowing of the zero-phonon hole in Photosystem II without both Scps indicates slowering of the excitation energy transfer which may be explained by the absence of a protective excitation energy quenching related to the presence of Scps.

  • 13. Demmig-Adams, Barbara
    et al.
    Ebbert, Volker
    Mellman, David L
    Mueh, Kristine E
    Schaffer, Lisa
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Zarter, C Ryan
    Adamska, Iwona
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Adams III, William W
    Modulation of PsbS and flexible vs sustained energy dissipation by light environment in different species2006In: Physiologia Plantarum, Vol. 127, p. 670-80Article in journal (Refereed)
    Abstract [en]

    Contrasting acclimation strategies of photosynthesis and photoprotection were identified for annual mesophytes (spinach, pumpkin, and Arabidopsis) vs the tropical evergreen Monstera deliciosa. The annual species utilized full sunlight for photosynthesis to a much greater extent than the evergreen species. Conversely, the evergreen species exhibited a greater capacity for photoprotective thermal energy dissipation as well as a greater expression of the PsbS protein in full sun than the annual species. In all species, the majority of thermal energy dissipation [assessed as non-photochemical fluorescence quenching (NPQ)] was the flexible, ΔpH-dependent form of NPQ over the entire range of growth light environments. However, in response to a transfer of shade-grown plants to high light, the evergreen species exhibited a high level of sustained thermal dissipation (qI), but the annual species did not. This sustained energy dissipation in the evergreen species was not ΔpH-dependent nor did the low level of PsbS in shade leaves increase upon transfer to high light for several days. Sustained ΔpH-independent NPQ was correlated (a) initially, with sustained D1 protein phosphorylation and xanthophyll cycle arrest and (b) subsequently, with an accumulation over several days of PsbS-related one-helix proteins and newly synthesized zeaxanthin and lutein.

  • 14.
    Engelken, Johannes
    et al.
    Department of Biology, University of Konstanz, Constance, Germany .
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Adamska, Iwona
    Department of Biology, University of Konstanz, Constance, Germany.
    The extended light-harvesting complex (LHC) protein superfamily: Classification and evolutionary dynamics2012In: Functinal genomics and evolution of photosynthetic systems / [ed] Robert Burnap, Wim Vermaas, Dordrecht, Netherlands: Springer Netherlands, 2012, p. 265-284Chapter in book (Refereed)
    Abstract [en]

    The evolution of algae and land plants and their photosynthetic machineries is closely connected to the development of the extended light-harvesting complex (LHC) protein superfamily. Therefore, it is not surprising that the molecular organization, function and origin of the LHC proteins have been a central topic in plant biology and photosynthesis research during the last few years. The extended LHC protein superfamily in cyanobacteria and photosynthetic eukaryotes comprises different families, such as the LHC proteins and three groups of light stress-induced proteins, consisting of the LHC-like proteins, the red lineage CAB-like proteins and the photosystem II subunit S. This chapter provides a description of the different extended LHC superfamily members and shows their taxonomic distribution. Furthermore, an overview of scenarios suggested for the evolution of the extended LHC protein superfamily is provided and arised implications for light harvesting, stress responses and photoprotection are discussed.

  • 15. Ensminger, Ingo
    et al.
    Sveshnikov, Dmitry
    Campbell, Douglas A.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Lloyd, Jon
    Shibistova, Olga
    Öquist, Gunnar
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Intermittent low temperatures constrain spring recovery of photosynthesis in boreal Scots pine forests2004In: Global Change Biology, ISSN 1354-1013, Vol. 10, no 6, p. 995-1008Article in journal (Refereed)
    Abstract [en]

    During winter and early spring, evergreen boreal conifers are severely stressed because light energy cannot be used when photosynthesis is pre-empted by low ambient temperatures. To study photosynthetic performance dynamics in a severe boreal climate, seasonal changes in photosynthetic pigments, chloroplast proteins and photochemical efficiency were studied in a Scots pine forest near Zotino, Central Siberia. In winter, downregulation of photosynthesis involved loss of chlorophylls, a twofold increase in xanthophyll cycle pigments and sustained high levels of the light stress-induced zeaxanthin pigment. The highest levels of xanthophylls and zeaxanthin did not occur during the coldest winter period, but rather in April when light was increasing, indicating an increased capacity for thermal dissipation of excitation energy at that time. Concomitantly, in early spring the D1 protein of the photosystem II (PSII) reaction centre and the light-harvesting complex of PSII dropped to their lowest annual levels. In April and May, recovery of PSII activity, chloroplast protein synthesis and rearrangements of pigments were observed as air temperatures increased above 0°C. Nevertheless, severe intermittent low-temperature episodes during this period not only halted but actually reversed the physiological recovery. During these spring low-temperature episodes, protective processes involved a complementary function of the PsbS and early light-induced protein thylakoid proteins. Full recovery of photosynthesis did not occur until the end of May. Our results show that even after winter cold hardening, photosynthetic activity in evergreens responds opportunistically to environmental change throughout the cold season. Therefore, climate change effects potentially improve the sink capacity of boreal forests for atmospheric carbon. However, earlier photosynthesis in spring in response to warmer temperatures is strongly constrained by environmental variation, counteracting the positive effects of an early recovery process.

  • 16.
    Ferro, Lorenza
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Valladolid, Spain.
    Colombo, Michela
    Posadas, Esther
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Muñoz, Raul
    Elucidating the symbiotic interactions between a locally isolated microalga Chlorella vulgaris and its co-occurring bacterium Rhizobium sp. in synthetic municipal wastewater2019In: Journal of Applied Phycology, ISSN 0921-8971, E-ISSN 1573-5176, Vol. 31, no 4, p. 2299-2310Article in journal (Refereed)
    Abstract [en]

    Co-cultivation of microalgae and bacteria during municipal wastewater treatment can boost carbon and nutrient recovery as a result of their synergistic interactions. The symbiotic relationships between the locally isolated microalga Chlorella vulgaris and the bacterium Rhizobium sp., co-isolated from municipal wastewater, were investigated batchwise under photoautotrophic, heterotrophic, and mixotrophic conditions in a synthetic municipal wastewater medium. During photoautotrophic growth in BG11 medium, photosynthetic algal oxygenation and organic carbon production supported bacterial activity but no significant beneficial effects on microalgal growth were observed. In synthetic wastewater, a twofold higher biomass concentration was achieved in the axenic algal culture compared with the co-culture under heterotrophic conditions, suggesting a competition for nutrients. A comparable carbon removal was observed in all cultures (83–79% TOC), but a faster nitrogen consumption (59% TN) and complete phosphate assimilation (100% TP) was only achieved in the co-culture. A positive synergistic relationship was found under mixotrophic conditions, clearly supported by an in situ O2/CO2 exchange between the microorganisms. This mutualism led to a threefold higher biomass production with a 13-fold higher fatty acid content compared with the axenic algal culture, as well as a superior wastewater treatment performance (+ 58% TOC, + 41% TN and + 44% TP). The co-cultivation of C. vulgaris and Rhizobium is therefore suggested as a potential microbial consortium for a cost-efficient biomass generation during municipal wastewater reclamation, especially under mixotrophic conditions.

  • 17.
    Ferro, Lorenza
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Gentili, Francesco G.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Isolation and characterization of microalgal strains for biomass production and wastewater reclamation in Northern Sweden2018In: Algal Research, ISSN 2211-9264, Vol. 32, p. 44-53Article in journal (Refereed)
    Abstract [en]

    Microalgal strains adapted to the harsh Nordic climate were isolated from Swedish fresh- and wastewater sources and tested for their ability to grow in municipal wastewater. The 62 strains able to grow in municipal wastewater belonged to 12 different genera, of those Desmodesmus, Scenedesmus and Chlorella were most representative. Eight axenic strains were further characterized, all of which could efficiently remove nitrogen (>90%) and phosphate (>99%) from the wastewater in less than two weeks. The microalga Coelastrella sp. had the highest performance in terms of both biomass concentration and total lipid content (1.46 g/L, 30.8%) after 13 days of cultivation. This is the first report of a Coelastrella strain isolated in Sweden. Even Chlorella vulgaris performed very well with a biomass concentration and total lipid content of 1.15 g/L and 34.2%, respectively. Finally, two Desmodesmus sp. strains showed desirable traits for biofuel-feedstock, due to their fast growth rates (1.18 and 1.08 d−1) together with high oil content (29.8% and 36.7% of DW).

  • 18.
    Ferro, Lorenza
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Gorzsás, András
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Gentili, Francesco G.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Subarctic microalgal strains treat wastewater and produce biomass at low temperature and short photoperiod2018In: Algal Research, ISSN 2211-9264, Vol. 35, p. 160-167Article in journal (Refereed)
    Abstract [en]

    In Northern countries, microalgal-based processes are challenging due to low light and temperature conditions during a significant part of the year. Three natural strains from Northern Sweden (Chlorella vulgaris, Scenedesmus sp., Desmodesmus sp.) and a collection strain (Scenedesmus obliquus UTEX 417) were cultured in municipal wastewater, comparing their performances, biomass composition and nutrients removal under continuous light at standard (25 °C) and low temperature (5 °C), short photoperiod (3 h light, 25 °C), or moderate winter conditions (6 h light, 15 °C). Only the natural strains grew at low temperature, highly consuming total nitrogen and phosphate (>80% and >70%, respectively) even during cold- and dark-stress. At reduced growth rates, C. vulgaris and Scenedesmus sp. produced similar amounts of biomass (>1 g/l) as in standard conditions. Scenedesmus sp. and Desmodesmus sp. showed phenotypic plasticity and increased carbohydrate content. Short photoperiod strongly reduced growth rates, biomass and storage compounds and induced flocculation in C. vulgaris.

  • 19.
    Ferro, Lorenza
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hu, Yue
    Gentili, Francesco
    Andersson, Anders
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Microbial population dynamics in a microalgae-based municipal wastewater treatment photobioreactor located in Northern SwedenManuscript (preprint) (Other academic)
    Abstract [en]

    A pilot-scale high-rate algal pond (HRAP) located in Northern Sweden was inoculated with the collection strain S. dimorphus UTEX 417 in spring and operated until autumn. The microbial diversity of eukaryotic and prokaryotic communities and their seasonal dynamics over time were revealed by high-throughput metabarcoding of 18S and 16S rRNA genes and correlated with various environmental factors. S. dimorphus was initially stable in the culture, but other microalgae appeared later and co-dominate the system as a consequence of predation by zooplankton. Desmodesmus, Pseudocharaciopsis, Chlorella, Characium and Oocystis were the main competing algal species. Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the most abundant bacterial phyla in the HRAP. The bacterial and zooplanktonic communities changed with seasonal variation, correlation not only with changes in light and temperature, but also with abiotic factors (pH and nutrients) were observed.

  • 20.
    Ferro, Lorenza
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Miranda, Fernanda
    Gentili, Francesco
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Photosynthesis at high latitudes: adaptation of photosynthetic microorganisms to Nordic climates2019In: Biotechnological Applications of Extremophilic Microorganisms: Life in Extreme Environments, Walter de Gruyter, 2019Chapter in book (Other academic)
  • 21.
    Funk, Christiane
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Alami, Meriem
    Botany Department, University of British Columbia, Vancouver, BC, Canada.
    Tibiletti, Tania
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Green, Beverley R
    Botany Department, University of British Columbia, Vancouver, BC, Canada.
    High-light stress and the one-helix LHC-like proteins of the cryptophyte Guillardia theta2011In: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1807, no 7, p. 841-846Article in journal (Refereed)
    Abstract [en]

    Cryptophytes like the cryptomonad Guillardia theta are part of the marine phytoplankton and therefore major players in global carbon and biogeochemical cycles. Despite the importance for the cell in being able to cope with large changes in illumination on a daily basis, very little is known about photoprotection mechanisms in cryptophytes. Here we show that G. theta is able to perform non-photochemical quenching, although none of the usual xanthophyll cycle pigments (e.g. zeaxanthin, diadinoxanthin, diatoxanthin) are present at detectable levels. Instead, acclimation to high light intensity seems to involve an increase of alloxanthin. G. theta has genes for two one-helix "light-harvesting-like" proteins, related to some cyanobacterial genes which are induced in response to high light stress. Both the plastid-encoded gene (hlipP) and the nucleomorph-encoded gene (HlipNm) are expressed, but transcript levels decrease rather than increase during high light exposure, suggesting they are not involved in a high light stress response. The HlipNm protein was detected with a specific antibody; expression was constant, independent of the light exposure.

  • 22.
    Funk, Christiane
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Pruzinska, A
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Garcia-Lorenzo, M
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Degradation of the light harvesting Comple of Photosystem II2007Conference paper (Other academic)
  • 23.
    Funk, Christiane
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Wiklund, Ronney
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Chemistry.
    Jansson, Christer
    D1′ centers are less efficient than normal photosystem II centers2001In: FEBS Letters, Vol. 505, no 1, p. 113-7Article in journal (Refereed)
    Abstract [en]

    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 O2 evolution pattern was unaffected. In the F186 mutants, both the P680+/QA− recombination and O2 oscillation pattern were noticeably perturbed.

  • 24.
    Garcia Cerdan, Jose Gines
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Sveshnikov, Dmitry
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Dewez, David
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Antisense inhibition of the PsbX protein affects PSII integrity in the higher plant Arabidopsis Thaliana2009In: Plant and Cell Physiology, ISSN 0032-0781, E-ISSN 1471-9053, Vol. 50, no 2, p. 191-202Article in journal (Refereed)
    Abstract [en]

    PSII, the oxygen-evolving complex of photosynthetic organisms, contains an intriguingly large number of low molecular weight proteins. PsbX, one of these proteins, is ubiquitous in PSII complexes of cyanobacteria and plants. In previous studies, deletion of the PsbX protein in cyanobacteria has not resulted in clear phenotypic changes. Here we report the construction of an antisense (AS-PsbX) line in Arabidopsis thaliana with <10% of wild-type PsbX levels. AS-PsbX plants are capable of photoautotrophic growth, but biochemical, biophysical and immunological evidence demonstrates that reduction of PsbX contents leads to reduced levels of functional assembled PSII core complexes, while the light-harvesting antennae are not affected. In addition, levels of phosphorylation of the core proteins D1, D2 and CP43 are severely reduced in the antisense plants relative to their wild-type counterparts. We conclude that PsbX is important for accumulation of functional PSII.

  • 25.
    Garci­a-Lorenzo, Maribel
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sjödin, Andreas
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Protease gene families in Populus and Arabidopsis2006In: BMC Plant Biology, ISSN 1471-2229, E-ISSN 1471-2229, Vol. 6, no 30, p. 1-24Article in journal (Refereed)
    Abstract [en]

    Proteases play key roles in plants, maintaining strict protein quality control and degrading specific sets of proteins in response to diverse environmental and developmental stimuli. Similarities and differences between the proteases expressed in different species may give valuable insights into their physiological roles and evolution. RESULTS: We have performed a comparative analysis of protease genes in the two sequenced dicot genomes, Arabidopsis thaliana and Populus trichocarpa by using genes coding for proteases in the MEROPS database 1 for Arabidopsis to identify homologous sequences in Populus. A multigene-based phylogenetic analysis was performed. Most protease families were found to be larger in Populus than in Arabidopsis, reflecting recent genome duplication. Detailed studies on e.g. the DegP, Clp, FtsH, Lon, rhomboid and papain-Like protease families showed the pattern of gene family expansion and gene loss was complex. We finally show that different Populus tissues express unique suites of protease genes and that the mRNA levels of different classes of proteases change along a developmental gradient. CONCLUSION: Recent gene family expansion and contractions have made the Arabidopsis and Populus complements of proteases different and this, together with expression patterns, gives indications about the roles of the individual gene products or groups of proteases.

  • 26.
    García-Cerdán, José G
    et al.
    Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
    Kovács, Laszlo
    Tóth, Tünde
    Kereïche, Sami
    Aseeva, Elena
    Boekema, Egbert J
    Mamedov, Fikret
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The PsbW protein stabilizes the supramolecular organization of photosystem II in higher plants2011In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 65, no 3, p. 368-381Article in journal (Refereed)
    Abstract [en]

    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 FV/FM, 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 (FS) 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.

  • 27.
    García-Lorenzo, Maribel
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Pružinská, Adriana
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    ATP-dependent proteases in the chloroplast2008In: ATP-dependent Proteases in the Plant Chloroplast / [ed] Eva Kutejová, Kerala, India: Research Signpost , 2008, p. 145-176Chapter in book (Refereed)
    Abstract [en]

    Systematic comparative analysis of the available sequenced genomes of model organisms has led to the identification of an increasing number of protease genes. ATP-dependent proteases are one of the largest groups of proteolytic enzymes found across all kingdoms of life and are associated to several essential physiological pathways. FtsH-, Clp-, and Lon-like proteases, all derived from bacterial ancestors, also have been identified in the plant chloroplast, where they form multi-subunit complexes consisting of different gene products. Recent studies in model organisms like the annual plant Arabidopsis thaliana or the photosynthetic cyanobacterium Synechocystis sp. PCC 6803 have identified substrates and functions of these isomers. Although only a limited number of proteases has been identified by biochemical methods, novel protease homologous that are targeted to plastids have been predicted. This review covers the current knowledge on ATP-dependent proteases in the chloroplast.

  • 28.
    García-Lorenzo, Maribel
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Zelisko, Agnieszka
    Umeå University, Faculty of Science and Technology, Chemistry.
    Jackowski, Grzegorz
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Chemistry.
    Degradation of the main Photosystem II light-harvesting complex2005In: Photochemical and Photobiological Sciences, ISSN 1474-905X, E-ISSN 1474-9092, Vol. 4, p. 1065-1071Article in journal (Refereed)
    Abstract [en]

    Many factors trigger the degradation of proteins, including changes in environmental conditions, genetic mutations, and limitations in the availability of cofactors. Despite the importance for viability, still very little is known about protein degradation and its regulation. The degradation of the most abundant membrane protein on Earth, the light-harvesting complex of Photosystem II (LHC II), is highly regulated under different environmental conditions, e.g. light stress, to prevent photochemical damage of the reaction center. However, despite major effort to identify the protease/proteases involved in the degradation of the apoproteins of LHC II the molecular details of this important process remain obscure. LHC II belongs to the family of chlorophyll a/b binding proteins (CAB proteins) and is located in the thylakoid membrane of the plant chloroplast. The results of biochemical experiments to isolate and characterize the protease degrading LHC II are summarized here and compared to our own recent finding indicating that a metalloprotease of the FtsH family is involved in this process.

  • 29.
    Gojkovic, Zivan
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lindberg, Richard
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Tysklind, Mats
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Northern green algae have the capacity to remove active pharmaceutical ingredients2019In: Ecotoxicology and Environmental Safety, ISSN 0147-6513, E-ISSN 1090-2414, Vol. 170, p. 644-656Article in journal (Refereed)
    Abstract [en]

    Eight recently isolated microalgal species from Northern Sweden and the culture collection strain Scenedesmus obliquus RISE (UTEX 417) were tested for their ability to remove 19 pharmaceuticals from growth medium upon cultivation in short light path, flat panel photobioreactors. While the growth of one algal species, Chlorellasorokiniana B1-1, was completely inhibited by the addition of pharmaceuticals, and the one of Scenedesmus sp. B2-2 was strongly inhibited, the other algal strains grew well and produced biomass.

    In general, lipophilic compounds were removed highly efficient from the culture medium by the microalgae (>70% in average within 2 days). The most lipophilic compounds Biperiden, Trihexyphenidyl, Clomipramine and Amitriptyline significantly accumulated in the biomass of most algal species, with a positive correlation between accumulation and their total biomass content. More persistent in the growth medium were hydrophilic compounds like Caffeine, Fluconazole, Trimetoprim, Codeine, Carbamazepin, Oxazepam and Tramadol, which were detected in amounts of above 60% in average after algal treatment.

    While Coelastrella sp. 3–4 and Coelastrum astroideum RW10 were most efficient to accumulate certain compounds in their biomass, two algae species, Chlorella vulgaris13-1 and Chlorella saccharophila RNY, were not only highly efficient in removing all 19 pharmaceuticals from the growth medium within 12 days, at the same time only small amounts of these compounds accumulated in their biomass allowing its further use. Chlorella vulgaris 13-1 was able to remove most compounds within 6 days of growth, while Chlorella saccharophila RNY needed 8–10 days.”Wild” Nordic microalgae therefore are able to remove active pharmaceutical ingredients, equally or more efficient than the investigated culture collection strain, thereby demonstrating their possible use in sustainable wastewater reclamation in Nordic conditions.

  • 30. Gomez, Facundo M.
    et al.
    Carrion, Cristian A.
    Costa, Maria L.
    Desel, Christine
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Krupinska, Karin
    Guiamet, Juan
    Extra-plastidial degradation of chlorophyll and photosystem I in tobacco leaves involving 'senescence-associated vacuoles'2019In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 99, no 3, p. 465-477Article in journal (Refereed)
    Abstract [en]

    Chlorophyll (Chl) loss is the main visible symptom of senescence in leaves. The initial steps of Chl degradation operate within the chloroplast, but the observation that ‘senescence‐associated vacuoles’ (SAVs) contain Chl raises the question of whether SAVs might also contribute to Chl breakdown. Previous confocal microscope observations (Martínez et al., 2008) showed many SAVs containing Chl. Isolated SAVs contained Chl a and b (with a Chl a/b ratio close to 5) and lower levels of chlorophyllide a. Pheophytin a and pheophorbide a were formed after the incubation of SAVs at 30°C in darkness, suggesting the presence of Chl‐degrading activities in SAVs. Chl in SAVs was bound to a number of ‘green bands’. In the most abundant green band of SAVs, Western blot analysis showed the presence of photosystem I (PSI) Chl‐binding proteins, including the PsaA protein of the PSI reaction center and the apoproteins of the light‐harvesting complexes (Lhca 1–4). This was confirmed by: (i) measurements of 77‐K fluorescence emission spectra showing a single emission peak at around 730 nm in SAVs; (ii) mass spectrometry of the most prominent green band with the slowest electrophoretic mobility; and (iii) immunofluorescence detection of PsaA in SAVs observed through confocal microscopy. Incubation of SAVs at 30°C in darkness caused a steady decrease in PsaA levels. Overall, these results indicate that SAVs may be involved in the degradation of PSI proteins and their associated chlorophylls during the senescence of leaves.

  • 31. Gomez, Facundo M.
    et al.
    Carrion, Cristian A.
    Costa, Maria L.
    Desel, Christine
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Krupinska, Karin
    Guiamet, Juan
    Extra-plastidial degradation of chlorophyll and photosystem I in tobacco leaves involving 'senescence-associated vacuoles'2019In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 99, no 3, p. 465-477Article in journal (Refereed)
    Abstract [en]

    Chlorophyll (Chl) loss is the main visible symptom of senescence in leaves. The initial steps of Chl degradation operate within the chloroplast, but the observation that 'senescence-associated vacuoles' (SAVs) contain Chl raises the question of whether SAVs might also contribute to Chl breakdown. Previous confocal microscope observations (Martinez et al., 2008) showed many SAVs containing Chl. Isolated SAVs contained Chl a and b (with a Chl a/b ratio close to 5) and lower levels of chlorophyllide a. Pheophytin a and pheophorbide a were formed after the incubation of SAVs at 30 degrees C in darkness, suggesting the presence of Chl-degrading activities in SAVs. Chl in SAVs was bound to a number of 'green bands'. In the most abundant green band of SAVs, Western blot analysis showed the presence of photosystem I (PSI) Chl-binding proteins, including the PsaA protein of the PSI reaction center and the apoproteins of the light-harvesting complexes (Lhca 1-4). This was confirmed by: (i) measurements of 77-K fluorescence emission spectra showing a single emission peak at around 730 nm in SAVs; (ii) mass spectrometry of the most prominent green band with the slowest electrophoretic mobility; and (iii) immunofluorescence detection of PsaA in SAVs observed through confocal microscopy. Incubation of SAVs at 30 degrees C in darkness caused a steady decrease in PsaA levels. Overall, these results indicate that SAVs may be involved in the degradation of PSI proteins and their associated chlorophylls during the senescence of leaves.

  • 32.
    Granlund, Irene
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Storm, Patrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schubert, Maria
    Department of Life Sciences, Södertörns University College, SE-141 89 Huddinge, Sweden.
    García-Cerdán, José G
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The TL29 protein is lumen located, associated with PSII and not an ascorbate peroxidase2009In: Plant and Cell Physiology, ISSN 0032-0781, E-ISSN 1471-9053, Vol. 50, no 11, p. 1898-1910Article in journal (Refereed)
    Abstract [en]

    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.

  • 33.
    Granlund, Irene
    et al.
    Umeå University, Faculty of Science and Technology.
    Storm, Patrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schubert, Maria
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    The TL29 Protein is a Redox Regulated Extrinsic Protein of Photosystem II and not an Ascorbate PeroxidaseArticle in journal (Refereed)
  • 34. Hall, M.
    et al.
    Lâm, Xuân Tâm
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Persson, K.
    Structure of the HhoA protease from Synechocystis sp. PCC 6803Manuscript (preprint) (Other academic)
  • 35.
    Hall, Michael
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wagner, Raik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lam, Xuan Tam
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Persson, Karina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    The HhoA protease from Synechocystis sp. PCC 6803: novel insights into structure and activity regulation2017In: Journal of Structural Biology, ISSN 1047-8477, E-ISSN 1095-8657, Vol. 198, no 3, p. 147-153Article in journal (Refereed)
    Abstract [en]

    Proteases play a vital role in the removal of proteins, which become damaged due to temperature or oxidative stress. Important to this process in the cyanobacterium Synechocystis sp. PCC6803 is the family of Deg/HtrA proteases; HhoA (sll1679), HhoB (sll1427) and HtrA (slr1204). While previous studies have elucidated the structures of Deg/HtrA proteases from Escherichia coli and from the chloroplast of the higher plant Arabidopsis thaliana, no structural data have been available for any Deg/HtrA protease from cyanobacteria, the evolutionary ancestor of the chloroplast. To gain a deeper insight into the molecular mechanisms and regulation of these proteins we have solved the structure of the Synechocystis HhoA protease in complex with a co-purified peptide by X-ray crystallography. HhoA assembles into stable trimers, mediated by its protease domain and further into a cage-like hexamer by a novel interaction between the PDZ domains of opposing trimers. Each PDZ domain contains two loops for PDZ-PDZ formation: interaction clamp one and two (IC1, IC2). IC1 interacts with IC2 on the opposing PDZ domain and vice versa. Our structure shows a peptide bound to a conserved groove on the PDZ domain and the properties of this pocket suggest that it binds substrate proteins as well as the neo C-termini of cleaved substrates. In agreement with previous studies showing the proteolytic activity of HhoA to be activated by Ca2+ or Mg2+, binding of divalent metal ions to the central channel of the trimer by the L1 activation loop was observed.

  • 36.
    Hall, Michael
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wagner, Raik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Tam, Lam Xuan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Persson, Karina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    The HhoA protease from Synechocystis sp. PCC 6803 – Novel insights into structure and activity regulation2017In: Journal of Structural Biology, ISSN 1047-8477, E-ISSN 1095-8657, Vol. 198, no 3, p. 147-153Article in journal (Refereed)
    Abstract [en]

    Abstract Proteases play a vital role in the removal of proteins, which become damaged due to temperature or oxidative stress. Important to this process in the cyanobacterium Synechocystis sp. PCC6803 is the family of Deg/HtrA proteases; HhoA (sll1679), HhoB (sll1427) and HtrA (slr1204). While previous studies have elucidated the structures of Deg/HtrA proteases from Escherichia coli and from the chloroplast of the higher plant Arabidopsis thaliana, no structural data have been available for any Deg/HtrA protease from cyanobacteria, the evolutionary ancestor of the chloroplast. To gain a deeper insight into the molecular mechanisms and regulation of these proteins we have solved the structure of the Synechocystis HhoA protease in complex with a co-purified peptide by X-ray crystallography. HhoA assembles into stable trimers, mediated by its protease domain and further into a cage-like hexamer by a novel interaction between the PDZ domains of opposing trimers. Each PDZ domain contains two loops for PDZ-PDZ formation: interaction clamp one and two (IC1, IC2). IC1 interacts with IC2 on the opposing PDZ domain and vice versa. Our structure shows a peptide bound to a conserved groove on the PDZ domain and the properties of this pocket suggest that it binds substrate proteins as well as the neo C-termini of cleaved substrates. In agreement with previous studies showing the proteolytic activity of HhoA to be activated by Ca2+ or Mg2+, binding of divalent metal ions to the central channel of the trimer by the L1 activation loop was observed.

  • 37.
    Hernandez-Prieto, M
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Vermaas, W
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Association of the small Cab-like proteins with Photosystem II2007Conference paper (Other academic)
  • 38.
    Hernandez-Prieto, Miguel A.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Tibiletti, Tania
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Abasova, Leyla
    Institute of Plant Biology, Biological Research Center, Szeged, Hungary.
    Kirilovsky, Diana
    Commissariat à l'Energie Atomique (CEA), Institut de Biologie et Technologies de Saclay (iBiTec-S), France.
    Vass, Imre
    Institute of Plant Biology, Biological Research Center, Szeged, Hungary.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    The small CAB-like proteins of the cyanobacterium Synechocystis sp. PCC 6803: Their involvement in chlorophyll biogenesis for Photosystem II2011In: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1807, no 9, p. 1143-1151Article in journal (Refereed)
    Abstract [en]

    The five small CAB-like proteins (ScpA-E) of the cyanobacterium Synechocystis sp. PCC 6803 belong to the family of stress-induced light-harvesting-like proteins, but are constitutively expressed in a mutant deficient of Photosystem I (PSI). Using absorption, fluorescence and thermoluminescence measurements this PSI-less strain was compared with a mutant, in which all SCPs were additionally deleted. Depletion of SCPs led to structural rearrangements in Photosystem II (PSII): less photosystems were assembled; and in these, the Q(B) site was modified. Despite the lower amount of PSII, the SCP-deficient cells contained the same amount of phycobilisomes (PBS) as the control. Although, the excess PBS were functionally disconnected, their fluorescence was quenched under high irradiance by the activated Orange Carotenoid Protein (OCP). Additionally the amount of OCP, but not of the iron-stress induced protein (isiA), was higher in this SCP-depleted mutant compared with the control. As previously described, the lack of SCPs affects the chlorophyll biosynthesis (Vavilin, D., Brune, D. C., Vermaas, W. (2005) Biochim Biophys Acta 1708, 91-101). We demonstrate that chlorophyll synthesis is required for efficient PSII repair and that it is partly impaired in the absence of SCPs. At the same time, the amount of chlorophyll also seems to influence the expression of ScpC and ScpD.

  • 39. Huang, Fang
    et al.
    Hedman, Erik
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Chemistry.
    Kieselbach, Thomas
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Chemistry.
    Norling, Birgitta
    Isolation of Outer Membrane of Synechocystis sp. PCC 6803 and Its Proteomic Characterization2004In: Molecular & Cellular Proteomics, ISSN 1535-9476, Vol. 3, no 6, p. 586-95Article in journal (Refereed)
    Abstract [en]

    In this report, we describe a newly developed method for isolating outer membranes from Synechocystis sp. PCC 6803 cells. The purity of the outer membrane fraction was verified by immunoblot analysis using antibodies against membrane-specific marker proteins. We investigated the protein composition of the outer membrane using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry followed by database identification. Forty-nine proteins were identified corresponding to 29 different gene products. All of the identified proteins have a putative N-terminal signal peptide. About 40% of the proteins identified represent hypothetical proteins with unknown function. Among the proteins identified are a Toc75 homologue, a protein that was initially found in the outer envelope of chloroplasts in pea, as well as TolC, putative porins, and a pilus protein. Other proteins identified include ABC transporters and GumB, which has a suggested function in carbohydrate export. A number of proteases such as HtrA were also found in the outer membrane of Synechocystis sp. PCC 6803.

  • 40.
    Huesgen, Pitter Florian
    et al.
    Department of Biology, University of Konstanz, Germany.
    Miranda, Helder
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lam, Xuan Tam
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Perthold, Manuela
    Department of Biology, University of Konstanz, Germany.
    Schuhmann, Holger
    Department of Biology, University of Konstanz, Germany.
    Adamska, Iwona
    Department of Biology, University of Konstanz, Germany.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Recombinant Deg/HtrA proteases from Synechocystis sp. PCC 6803 differ in substrate specificity, biochemical characteristics and mechanism2011In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 435, no 3, p. 733-742Article in journal (Refereed)
    Abstract [en]

    Cyanobacteria require efficient protein quality control mechanisms to survive under dynamic, often stressful environmental conditions. It was reported that three serine proteases, HtrA, HhoA and HhoB are important for survival of Synechocystis sp. PCC 6803 under high light and temperature stresses and might have redundant physiological functions. Here we show that all three proteases can degrade unfolded model substrates, but differ in respect to cleavage sites, temperature and pH optima. For recombinant HhoA, and to a lesser extent for HtrA, we observed an interesting shift in the pH optimum from slightly acidic to alkaline in the presence of Mg2+ and Ca2+ ions. All three proteases formed different homo-oligomeric complexes with and without substrate, implying mechanistic differences in comparison to each other and to the well-studied Escherichia coli orthologues DegP and DegS. Deletion of the PDZ domain decreased, but not abolished proteolytic activity of all three proteases, and prevented substrate-induced formation of complexes higher than trimers by HtrA and HhoA. In summary, biochemical characterisation of HtrA, HhoA and HhoB lays the foundation for a better understanding of their overlapping, but not completely redundant stress resistance functions in Synechocystis sp. PCC 6803.

  • 41.
    Ishikawa, Yasuo
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Functional analysis of the PsbP-like protein (sll1418) in Synechocystis sp PCC 68032005In: Photosynthesis Research, ISSN 0166-8595, E-ISSN 1573-5079, Vol. 84, no 1-3, p. 257-262Article in journal (Refereed)
    Abstract [en]

    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.

  • 42. Karan, Hakan
    et al.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Grabert, Martin
    Oey, Melanie
    Hankamer, Ben
    Green Bioplastics as Part of a Circular Bioeconomy2019In: Trends in Plant Science, ISSN 1360-1385, E-ISSN 1878-4372, Vol. 24, no 3, p. 237-249Article, review/survey (Refereed)
    Abstract [en]

    The rapid accumulation of plastic waste is driving international demand for renewable plastics with superior qualities (e.g., full biodegradability to CO2 without harmful byproducts), as part of an expanding circular bioeconomy. Higher plants, microalgae, and cyanobacteria can drive solar-driven processes for the production of feedstocks that can be used to produce a wide variety of biodegradable plastics, as well as bioplastic-based infrastructure that can act as a long-term carbon sink. The plastic types produced, their chemical synthesis, scaled-up biorefinery concepts (e.g., plant-based methane-to-bioplastic production and co-product streams), bioplastic properties, and uses are summarized, together with the current regulatory framework and the key barriers and opportunities.

  • 43.
    Kieselbach, Thomas
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Cheregi, Otilia
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Green, Beverley R.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Proteomic analysis of the phycobiliprotein antenna of the cryptophyte alga Guillardia theta cultured under different light intensities2018In: Photosynthesis Research, ISSN 0166-8595, E-ISSN 1573-5079, Vol. 135, no 1–3, p. 149-163Article in journal (Refereed)
    Abstract [en]

    Plants and algae have developed various light-harvesting mechanisms for optimal delivery of excitation energy to the photosystems. Cryptophyte algae have evolved a novel soluble light-harvesting antenna utilizing phycobilin pigments to complement the membrane-intrinsic Chl a/c-binding LHC antenna. This new antenna consists of the plastid-encoded β-subunit, a relic of the ancestral phycobilisome, and a novel nuclear-encoded α-subunit unique to cryptophytes. Together, these proteins form the active α1β·α2β-tetramer. In all cryptophyte algae investigated so far, the α-subunits have duplicated and diversified into a large gene family. Although there is transcriptional evidence for expression of all these genes, the X-ray structures determined to date suggest that only two of the α-subunit genes might be significantly expressed at the protein level. Using proteomics, we show that in phycoerythrin 545 (PE545) of Guillardia theta, the only cryptophyte with a sequenced genome, all 20 α-subunits are expressed when the algae grow under white light. The expression level of each protein depends on the intensity of the growth light, but there is no evidence for a specific light-dependent regulation of individual members of the α-subunit family under the growth conditions applied. GtcpeA10 seems to be a special member of the α-subunit family, because it consists of two similar N- and C-terminal domains, which likely are the result of a partial tandem gene duplication. The proteomics data of this study have been deposited to the ProteomeXchange Consortium and have the dataset identifiers PXD006301 and 10.6019/PXD006301.

  • 44. Kieselbach, Thomas
    et al.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Chemistry.
    The family of Deg/HtrA proteases: from Escherichia coli to Arabidopsis2003In: Physiologia Plantarum, Vol. 119, no 3, p. 337-46Article in journal (Refereed)
    Abstract [en]

    In the genomic era, an increasing number of protease genes have been identified in various organisms. During the last few years, many of these proteases have been characterized using biochemical as well as molecular biological techniques. However, neither the precise location nor the physiological substrates of these enzymes has been identified in many cases, including the Deg/HtrA proteases, a family of serine-type ATP-independent proteases. This family has become especially interesting for many researchers following the determination of the crystal structures of an Escherichia coli and a human Deg/HtrA protease. A breakthrough in photosynthesis research has revealed that a Deg/HtrA protease of Arabidopsis thaliana is involved in the degradation of the D1 protein of photosystem II following photoinhibition. In this review, the available data on Deg/HtrAs of different organisms are compared with those from the photoautotroph cyanobacterium Synechocystis sp. PCC 6803 and the plant Arabidopsis thaliana.

  • 45.
    Klemenčič, Marina
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
    Asplund-Samuelsson, Johannes
    Dolinar, Marko
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Phylogenetic Distribution and Diversity of Bacterial Pseudo-Orthocaspases Underline Their Putative Role in Photosynthesis2019In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 10, article id 293Article in journal (Refereed)
    Abstract [en]

    Orthocaspases are prokaryotic caspase homologs – proteases, which cleave their substrates after positively charged residues using a conserved histidine – cysteine (HC) dyad situated in a catalytic p20 domain. However, in orthocaspases pseudo-variants have been identified, which instead of the catalytic HC residues contain tyrosine and serine, respectively. The presence and distribution of these presumably proteolytically inactive p20-containing enzymes has until now escaped attention. We have performed a detailed analysis of orthocaspases in all available prokaryotic genomes, focusing on pseudo-orthocaspases. Surprisingly we identified type I metacaspase homologs in filamentous cyanobacteria. While genes encoding pseudo-orthocaspases seem to be absent in Archaea, our results show conservation of these genes in organisms performing either anoxygenic photosynthesis (orders Rhizobiales, Rhodobacterales, and Rhodospirillales in Alphaproteobacteria) or oxygenic photosynthesis (all sequenced cyanobacteria, except Gloeobacter, Prochlorococcus, and Cyanobium). Contrary to earlier reports, we were able to detect pseudo-orthocaspases in all sequenced strains of the unicellular cyanobacteria Synechococcus and Synechocystis. In silico comparisons of the primary as well as tertiary structures of pseudo-p20 domains with their presumably proteolytically active homologs suggest that differences in their amino acid sequences have no influence on the overall structures. Mutations therefore affect most likely only the proteolytic activity. Our data provide an insight into diversification of pseudo-orthocaspases in Prokaryotes, their taxa-specific distribution, and allow suggestions on their taxa-specific function.

  • 46.
    Klemenčič, Marina
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Evolution and structural diversity of metacaspases2019In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 70, no 7, p. 2039-2047Article, review/survey (Refereed)
    Abstract [en]

    Caspases are metazoan proteases, best known for their involvement in programmed cell death in animals. In higher plants genetically controlled mechanisms leading to the selective death of individual cells also involve the regulated interplay of various types of proteases. Some of these enzymes are structurally homologous to caspases and have therefore been termed metacaspases. In addition to the two well-studied metacaspase variants found in higher plants, type I and type II, biochemical data have recently become available for metacaspases of type III and metacaspase-like proteases, which are present only in certain algae. Although increasing in vitro and in vivo data suggest the existence of further sub-types, a lack of structural information hampers the interpretation of their distinct functional properties. However, the identification of key amino acid residues involved in the proteolytic mechanism of metacaspases, as well as the increased availability of plant genomic and transcriptomic data, is increasingly enabling in-depth analysis of all metacaspase types found in plastid-containing organisms. Here, we review the structural distribution and diversification of metacaspases and in doing so try to provide comprehensive guidelines for further analyses of this versatile family of proteases in organisms ranging from simple unicellular species to flowering plants.

  • 47.
    Klemenčič, Marina
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Structural and functional diversity of caspase homologues in non-metazoan organisms2018In: Protoplasma, ISSN 0033-183X, E-ISSN 1615-6102, Vol. 255, no 1, p. 387-397Article, review/survey (Refereed)
    Abstract [en]

    Caspases, the proteases involved in initiation and execution of metazoan programmed cell death, are only present in animals, while their structural homologues can be found in all domains of life, spanning from simple prokaryotes (orthocaspases) to yeast and plants (metacaspases). All members of this wide protease family contain the p20 domain, which harbours the catalytic dyad formed by the two amino acid residues, histidine and cysteine. Despite the high structural similarity of the p20 domain, metacaspases and orthocaspases were found to exhibit different substrate specificities than caspases. While the former cleave their substrates after basic amino acid residues, the latter accommodate substrates with negative charge. This observation is crucial for the re-evaluation of non-metazoan caspase homologues being involved in processes of programmed cell death. In this review, we analyse the structural diversity of enzymes containing the p20 domain, with focus on the orthocaspases, and summarise recent advances in research of orthocaspases and metacaspases of cyanobacteria, algae and higher plants. Although caspase homologues were initially proposed to be involved in execution of cell death, accumulating evidence supports the role of metacaspases and orthocaspases as important contributors to cell homeostasis during normal physiological conditions or cell differentiation and ageing.

  • 48.
    Klemenčič, Marina
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, SI-1000 Ljubljana, Slovenia.
    Type III metacaspases: calcium-dependent activity proposes new function for the p10 domain2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 218, no 3 Special issue, p. 1179-1191Article in journal (Refereed)
    Abstract [en]

    Metacaspases are a subgroup of caspase homologues represented in bacteria, algae and plants. Although type I and type II metacaspases are present in plants, recently discovered and uncharacterized type III metacaspases can only be found in algae which have undergone secondary endosymbiosis. We analysed the expression levels of all 13 caspase homologues in the cryptophyte Guillardia theta in vivo and biochemically characterized its only type III metacaspase, GtMC2, in vitro. Type III metacaspase GtMC2 was shown to be an endopeptidase with a preference for basic amino acids in the P1 position, which exhibited specific N-terminal proteolytic cleavage for full catalytic efficiency. Autolytic processing, as well as the activity of the mature enzyme, required the presence of calcium ions in low millimolar concentrations. In GtMC2, two calcium-binding sites were identified, one with a dissociation constant at low and the other at high micromolar concentrations. We show high functional relatedness of type III metacaspases to type I metacaspases. Moreover, our data suggest that the low-affinity calcium-binding site is located in the p10 domain, which contains a well-conserved N-terminal region. This region can only be found in type I/II/III metacaspases, but is absent in calcium-independent caspase homologues.

  • 49. Kufryk, G
    et al.
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Vermaas, W
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Members of the ELIP-family are associated with Photosystem II in Synechocystis sp. PCC 68032007In: Photosynthesis:  Energy from the Sun / [ed] Allen J.F., Gantt E., Golbeck J.H., Osmond B. eds, Springer , 2007, p. 723-729Conference paper (Other academic)
  • 50. Kufryk, G
    et al.
    Vermaas, W
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Small chlorophyll binding proteins overexpressed in the cyanobacterium Synechocystis sp. PCC 68032007Conference paper (Other academic)
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