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  • 1. Abraham, Edit
    et al.
    Miskolczi, Pal
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ayaydin, Ferhan
    Yu, Ping
    Kotogany, Edit
    Bako, Laszlo
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Oetvoes, Krisztina
    Horvath, Gabor V.
    Dudits, Denes
    Immunodetection of retinoblastoma-related protein and its phosphorylated form in interphase and mitotic alfalfa cells2011In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 62, no 6, p. 2155-2168Article in journal (Refereed)
    Abstract [en]

    Plant retinoblastoma-related (RBR) proteins are primarily considered as key regulators of G(1)/S phase transition, with functional roles in a variety of cellular events during plant growth and organ development. Polyclonal antibody against the C-terminal region of the Arabidopsis RBR1 protein also specifically recognizes the alfalfa 115 kDa MsRBR protein, as shown by the antigen competition assay. The MsRBR protein was detected in all cell cycle phases, with a moderate increase in samples representing G(2)/M cells. Antibody against the human phospho-pRb peptide (Ser807/811) cross-reacted with the same 115 kDa MsRBR protein and with the in vitro phosphorylated MsRBR protein C-terminal fragment. Phospho-MsRBR protein was low in G(1) cells. Its amount increased upon entry into the S phase and remained high during the G(2)/M phases. Roscovitine treatment abolished the activity of alfalfa MsCDKA1;1 and MsCDKB2;1, and the phospho-MsRBR protein level was significantly decreased in the treated cells. Colchicine block increased the detected levels of both forms of MsRBR protein. Reduced levels of the MsRBR protein in cells at stationary phase or grown in hormone-free medium can be a sign of the division-dependent presence of plant RBR proteins. Immunolocalization of the phospho-MsRBR protein indicated spots of variable number and size in the labelled interphase nuclei and high signal intensity of nuclear granules in prophase. Structures similar to phospho-MsRBR proteins cannot be recognized in later mitotic phases. Based on the presented western blot and immunolocalization data, the possible involvement of RBR proteins in G(2)/M phase regulation in plant cells is discussed.

  • 2.
    Andersson, Inger
    Department of Molecular Biology, Swedish University of Agricultural Sciences.
    Catalysis and regulation in Rubisco.2008In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 59, no 7, p. 1555-1568Article in journal (Refereed)
    Abstract [en]

    Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the incorporation of inorganic CO(2) into the organic molecules of life. Rubisco is extremely inefficient as a catalyst and its carboxylase activity is compromised by numerous side-reactions including oxygenation of its sugar phosphate substrate by atmospheric O(2). The reduction in the catalytic efficiency as a result of these processes has implications for crop yield, nitrogen and water usage, and for the global carbon cycle. Several aspects of Rubisco including its complex biosynthesis and multi-step catalytic reaction are subject to tight control involving light, cellular metabolites, and molecular chaperones. Numerous high-resolution crystal structures of different forms of Rubisco are now available, including structures of mutant enzymes. These provide a molecular framework for the understanding of these processes at the molecular level.

  • 3. Betti, Marco
    et al.
    Bauwe, Hermann
    Busch, Florian A.
    Fernie, Alisdair R.
    Keech, Olivier
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Levey, Myles
    Ort, Donald R.
    Parry, Martin A. J.
    Sage, Rowan
    Timm, Stefan
    Walker, Berkley
    Weber, Andreas P. M.
    Manipulating photorespiration to increase plant productivity: recent advances and perspectives for crop improvement2016In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 67, no 10, p. 2977-2988Article, review/survey (Refereed)
    Abstract [en]

    Recycling of the 2-phosphoglycolate generated by the oxygenase reaction of Rubisco requires a complex and energy-consuming set of reactions collectively known as the photorespiratory cycle. Several approaches aimed at reducing the rates of photorespiratory energy or carbon loss have been proposed, based either on screening for natural variation or by means of genetic engineering. Recent work indicates that plant yield can be substantially improved by the alteration of photorespiratory fluxes or by engineering artificial bypasses to photorespiration. However, there is also evidence indicating that, under certain environmental and/or nutritional conditions, reduced photorespiratory capacity may be detrimental to plant performance. Here we summarize recent advances obtained in photorespiratory engineering and discuss prospects for these advances to be transferred to major crops to help address the globally increasing demand for food and biomass production.

  • 4.
    Blanco, Nicolas E.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario (CEFOBI-CONICET/UNR), Rosario, Argentina.
    Liebsch, Daniela
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina.
    Guinea Diaz, Manuel
    Strand, Åsa
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Whelan, James
    Dual and dynamic intracellular localization of Arabidopsis thaliana SnRK1.12019In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 70, no 8, p. 2325-2338Article in journal (Refereed)
    Abstract [en]

    Sucrose non-fermenting 1 (SNF1)-related protein kinase 1.1 (SnRK1.1; also known as KIN10 or SnRK1 alpha) has been identified as the catalytic subunit of the complex SnRK1, the Arabidopsis thaliana homologue of a central integrator of energy and stress signalling in eukaryotes dubbed AMPK/Snf1/SnRK1. A nuclear localization of SnRK1.1 has been previously described and is in line with its function as an integrator of energy and stress signals. Here, using two biological models (Nicotiana benthamiana and Arabidopsis thaliana), native regulatory sequences, different microscopy techniques, and manipulations of cellular energy status, it was found that SnRK1.1 is localized dynamically between the nucleus and endoplasmic reticulum (ER). This distribution was confirmed at a spatial and temporal level by co-localization studies with two different fluorescent ER markers, one of them being the SnRK1.1 phosphorylation target HMGR. The ER and nuclear localization displayed a dynamic behaviour in response to perturbations of the plastidic electron transport chain. These results suggest that an ER-associated SnRK1.1 fraction might be sensing the cellular energy status, being a point of crosstalk with other ER stress regulatory pathways.

  • 5.
    Bollhoner, Benjamin
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Prestele, Jakob
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Tuominen, Hannele
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Xylem cell death: emerging understanding of regulation and function2012In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 63, no 3, p. 1081-1094Article, review/survey (Refereed)
    Abstract [en]

    Evolutionary, as well as genetic, evidence suggests that vascular development evolved originally as a cell death programme that allowed enhanced movement of water in the extinct protracheophytes, and that secondary wall formation in the water-conducting cells evolved afterwards, providing mechanical support for effective long-distance transport of water. The extant vascular plants possess a common regulatory network to coordinate the different phases of xylem maturation, including secondary wall formation, cell death, and finally autolysis of the cell contents, by the action of recently identified NAC domain transcription factors. Consequently, xylem cell death is an inseparable part of the xylem maturation programme, making it difficult to uncouple cell death mechanistically from secondary wall formation, and thus identify the key factors specifically involved in regulation of cell death. Current knowledge suggests that the necessary components for xylem cell death are produced early during xylem differentiation, and cell death is prevented through the action of inhibitors and storage of hydrolytic enzymes in inactive forms in compartments such as the vacuole. Bursting of the central vacuole triggers autolytic hydrolysis of the cell contents, which ultimately leads to cell death. This cascade of events varies between the different xylem cell types. The water-transporting tracheary elements rely on a rapid cell death programme, with hydrolysis of cell contents taking place for the most part, if not entirely, after vacuolar bursting, while the xylem fibres disintegrate cellular contents at a slower pace, well before cell death. This review includes a detailed description of cell morphology, function of plant growth regulators, such as ethylene and thermospermine, and the action of hydrolytic nucleases and proteases during cell death of the different xylem cell types.

  • 6.
    Brouwer, Bastiaan
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Gardeström, Per
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Keech, Olivier
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    In response to partial plant shading, the lack of phytochrome A does not directly induce leaf senescence but alters the fine-tuning of chlorophyll biosynthesis2014In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 65, no 14, p. 4037-4049Article in journal (Refereed)
    Abstract [en]

    Phytochrome is thought to control the induction of leaf senescence directly, however, the signalling and molecular mechanisms remain unclear. In the present study, an ecophysiological approach was used to establish a functional connection between phytochrome signalling and the physiological processes underlying the induction of leaf senescence in response to shade. With shade it is important to distinguish between complete and partial shading, during which either the whole or only a part of the plant is shaded, respectively. It is first shown here that, while PHYB is required to maintain chlorophyll content in a completely shaded plant, only PHYA is involved in maintaining the leaf chlorophyll content in response to partial plant shading. Second, it is shown that leaf yellowing associated with strong partial shading in phyA-mutant plants actually correlates to a decreased biosynthesis of chlorophyll rather than to an increase of its degradation. Third, it is shown that the physiological impact of this decreased biosynthesis of chlorophyll in strongly shaded phyA-mutant leaves is accompanied by a decreased capacity to adjust the Light Compensation Point. However, the increased leaf yellowing in phyA-mutant plants is not accompanied by an increase of senescence-specific molecular markers, which argues against a direct role of PHYA in inducing leaf senescence in response to partial shade. In conclusion, it is proposed that PHYA, but not PHYB, is essential for fine-tuning the chlorophyll biosynthetic pathway in response to partial shading. In turn, this mechanism allows the shaded leaf to adjust its photosynthetic machinery to very low irradiances, thus maintaining a positive carbon balance and repressing the induction of leaf senescence, which can occur under prolonged periods of shade.

  • 7. Bygdell, Joakim
    et al.
    Srivastava, Vaibhav
    KTH, School of Biotechnology (BIO), Glycoscience.
    Obudulu, Ogonna
    Srivastava, Manoj K.
    Nilsson, Robert
    Sundberg, Bjorn
    Trygg, Johan
    Mellerowicz, Ewa J.
    Wingsle, Gunnar
    Protein expression in tension wood formation monitored at high tissue resolution in Populus2017In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, no 13, p. 3405-3417Article in journal (Refereed)
    Abstract [en]

    Tension wood (TW) is a specialized tissue with contractile properties that is formed by the vascular cambium in response to gravitational stimuli. We quantitatively analysed the proteomes of Populus tremula cambium and its xylem cell derivatives in stems forming normal wood (NW) and TW to reveal the mechanisms underlying TW formation. Phloem-, cambium-, and wood-forming tissues were sampled by tangential cryosectioning and pooled into nine independent samples. The proteomes of TW and NW samples were similar in the phloem and cambium samples, but diverged early during xylogenesis, demonstrating that reprogramming is an integral part of TW formation. For example, 14-3-3, reactive oxygen species, ribosomal and ATPase complex proteins were found to be up-regulated at early stages of xylem differentiation during TW formation. At later stages of xylem differentiation, proteins involved in the biosynthesis of cellulose and enzymes involved in the biosynthesis of rhamnogalacturonan-I, rhamnogalacturonan-II, arabinogalactan-II and fasciclin-like arabinogalactan proteins were up-regulated in TW. Surprisingly, two isoforms of exostosin family proteins with putative xylan xylosyl transferase function and several lignin biosynthesis proteins were also up-regulated, even though xylan and lignin are known to be less abundant in TW than in NW. These data provided new insight into the processes behind TW formation.

  • 8.
    Bygdell, Joakim
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Srivastava, Vaibhav
    Obudulu, Ogonna
    Srivastava, Manoj K.
    Nilsson, Robert
    Sundberg, Björn
    Trygg, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mellerowicz, Ewa J.
    Wingsle, Gunnar
    Protein expression in tension wood formation monitored at high tissue resolution in Populus2017In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, no 13, p. 3405-3417Article in journal (Refereed)
    Abstract [en]

    Tension wood (TW) is a specialized tissue with contractile properties that is formed by the vascular cambium in response to gravitational stimuli. We quantitatively analysed the proteomes of Populus tremula cambium and its xylem cell derivatives in stems forming normal wood (NW) and TW to reveal the mechanisms underlying TW formation. Phloem-, cambium-, and wood-forming tissues were sampled by tangential cryosectioning and pooled into nine independent samples. The proteomes of TW and NW samples were similar in the phloem and cambium samples, but diverged early during xylogenesis, demonstrating that reprogramming is an integral part of TW formation. For example, 14-3-3, reactive oxygen species, ribosomal and ATPase complex proteins were found to be up-regulated at early stages of xylem differentiation during TW formation. At later stages of xylem differentiation, proteins involved in the biosynthesis of cellulose and enzymes involved in the biosynthesis of rhamnogalacturonan-I, rhamnogalacturonan-II, arabinogalactan-II and fasciclin-like arabinogalactan proteins were up-regulated in TW. Surprisingly, two isoforms of exostosin family proteins with putative xylan xylosyl transferase function and several lignin biosynthesis proteins were also up-regulated, even though xylan and lignin are known to be less abundant in TW than in NW. These data provided new insight into the processes behind TW formation.

  • 9. Capovilla, Giovanna
    et al.
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tübingen, Germany.
    Posé, David
    Control of flowering by ambient temperature2015In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 66, no 1, p. 59-69Article in journal (Refereed)
    Abstract [en]

    The timing of flowering is a crucial decision in the life cycle of plants since favourable conditions are needed to maximize reproductive success and, hence, the survival of the species. It is therefore not surprising that plants constantly monitor endogenous and environmental signals, such as day length (photoperiod) and temperature, to adjust the timing of the floral transition. Temperature in particular has been shown to have a tremendous effect on the timing of flowering: the effect of prolonged periods of cold, called the vernalization response, has been extensively studied and the underlying epigenetic mechanisms are reasonably well understood in Arabidopsis thaliana. In contrast, the effect of moderate changes in ambient growth temperature on the progression of flowering, the thermosensory pathway, is only starting to be understood on the molecular level. Several genes and molecular mechanisms underlying the thermosensory pathway have already been identified and characterized in detail. At a time when global temperature is rising due to climate change, this knowledge will be pivotal to ensure crop production in the future.

  • 10. Capovilla, Giovanna
    et al.
    Symeonidi, Efthymia
    Wu, Rui
    Schmid, Markus
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstr. 35, 72076 Tübingen, Germany.
    Contribution of major FLM isoforms to temperature-dependent flowering in Arabidopsis thaliana2017In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, no 18, p. 5117-5127Article in journal (Refereed)
    Abstract [en]

    FLOWERING LOCUS M (FLM), a component of the thermosensory flowering time pathway in Arabidopsis thaliana, is regulated by temperature-dependent alternative splicing (AS). The main splicing variant, FLM-beta, is a well-documented floral repressor that is down-regulated in response to increasing ambient growth temperature. Two hypotheses have been formulated to explain how flowering time is modulated by AS of FLM. In the first model a second splice variant, FLM-delta, acts as a dominant negative isoform that competes with FLM-beta at elevated ambient temperatures, thereby indirectly promoting flowering. Alternatively, it has been suggested that the induction of flowering at elevated temperatures is caused only by reduced FLM-beta expression. To better understand the role of the two FLM splice forms, we employed CRISPR/Cas9 technology to specifically delete the exons that characterize each splice variant. Lines that produced repressive FLM-beta but were incapable of producing FLM-delta were late flowering. In contrast, FLM-beta knockout lines that still produced FLM-delta flowered early, but not earlier than the flm-3 loss of function mutant, as would be expected if FLM-delta had a dominant-negative effect on flowering. Our data support the role of FLM-beta as a flower repressor and provide evidence that a contribution of FLM-delta to the regulation of flowering time in wild-type A. thaliana seems unlikely.

  • 11.
    Carlsson, Gunilla H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Cardinale, Francesca
    Univ Turin, Dept Agr Forestry & Food Sci, Largo Paolo Braccini 2, I-10095 Grugliasco 2, Italy.
    Prandi, Cristina
    Univ Turin, Dept Chem, Via P Giuria 7, I-10125 Turin, Italy.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    The elusive ligand complexes of the DWARF14 strigolactone receptor2018In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 69, no 9, p. 2345-2354Article in journal (Refereed)
    Abstract [en]

    Strigolactones, a group of terpenoid lactones, control many aspects of plant growth and development, but the active forms of these plant hormones and their mode of action at the molecular level are still unknown. The strigolactone protein receptor is unusual because it has been shown to cleave the hormone and supposedly forms a covalent bond with the cleaved hormone fragment. This interaction is suggested to induce a conformational change in the receptor that primes it for subsequent interaction with partners in the signalling pathway. Substantial efforts have been invested into describing the interaction of synthetic strigolactone analogues with the receptor, resulting in a number of crystal structures. This investigation combines a re-evaluation of models in the Protein Data Bank with a search for new conditions that may permit the capture of a receptor-ligand complex. While weak difference density is frequently observed in the binding cavity, possibly due to a low-occupancy compound, the models often contain features not supported by the X-ray data. Thus, at this stage, we do not believe that any detailed deductions about the nature, conformation, or binding mode of the ligand can be made with any confidence.

  • 12.
    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.

  • 13.
    Crawford, Tim
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Lehotai, Nóra
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Strand, Åsa
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The role of retrograde signals during plant stress responses2018In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 69, no 11, p. 2783-2795Article, review/survey (Refereed)
    Abstract [en]

    Chloroplast and mitochondria not only provide the energy to the plant cell but due to the sensitivity of organellar processes to perturbations caused by abiotic stress, they are also key cellular sensors of environmental fluctuations. Abiotic stresses result in reduced photosynthetic efficiency and thereby reduced energy supply for cellular processes. Thus, in order to acclimate to stress, plants must re-program gene expression and cellular metabolism to divert energy from growth and developmental processes to stress responses. To restore cellular energy homeostasis following exposure to stress, the activities of the organelles must be tightly co-ordinated with the transcriptional re-programming in the nucleus. Thus, communication between the organelles and the nucleus, so-called retrograde signalling, is essential to direct the energy use correctly during stress exposure. Stress-triggered retrograde signals are mediated by reactive oxygen species and metabolites including beta-cyclocitral, MEcPP (2-C-methyl-D-erythritol 2,4-cyclodiphosphate), PAP (3'-phosphoadenosine 5'-phosphate), and intermediates of the tetrapyrrole biosynthesis pathway. However, for the plant cell to respond optimally to environmental stress, these stress-triggered retrograde signalling pathways must be integrated with the cytosolic stress signalling network. We hypothesize that the Mediator transcriptional co-activator complex may play a key role as a regulatory hub in the nucleus, integrating the complex stress signalling networks originating in different cellular compartments.

  • 14. DELUCIA, EH
    et al.
    DAY, TA
    Oquist, Gunnar
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    THE POTENTIAL FOR PHOTOINHIBITION OF PINUS-SYLVESTRIS L SEEDLINGS EXPOSED TO HIGH LIGHT AND LOW SOIL-TEMPERATURE1991In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 42, no 238, p. 611-617Article in journal (Refereed)
    Abstract [en]

    The effect of high light and root chilling on gas exchange, chlorophyll fluorescence, and bulk shoot water potential (PSI-shoot) was examined for Pinus sylvestris seedlings. Transferring plants from low light (200-mu-mol m-2 s-1, PAR) and a soil temperature of 15-degrees-C to high light (850-mu-mol m-2 S-1) and 1-degrees-C caused > 90% decrease in net photosynthesis and leaf conductance measured at 350 mm3 dm-3 CO2, and a decrease in the ratio of variable to maximum fluorescence (F(v)/F(m)) from 0.83 to 0.63. The decrease in F(v)/F(m) was, however, only marginally greater than when seedlings were transferred from low to high light but kept at a soil temperature of 15-degrees-C. Thus, photoinhibition was a minor component of the substantial decrease observed for net photosynthesis at 1-degrees-C soil temperature. The decrease in net photosynthesis and PSI-shoot at 1-degrees-C was associated with an increased in calculated intracellular CO2 concentration, suggesting that non-stomatal factors related to water stress were involved in inhibiting carbon assimilation. Measurements at saturating external CO2 concentration, however, indicate that stomatal closure was the dominant factor limiting net photosynthesis at low soil temperature. This interpretation was confirmed with additional experiments using Pinus taeda and Picea engelmannii seedlings. Decreases in gas-exchange variables at 5-degrees-C soil temperature were not associated with changes in PSI-shoot. Thus, hormonal factors, localized decreases in PSI-needle, or changes in xylem flux may mediate the response to moderate root chilling.

  • 15. Dinant, S.
    et al.
    Wolff, N.
    De Marco, F.
    Vilaine, F.
    Gissot, L.
    Aubry, E.
    Sandt, C.
    Bellini, C.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.
    Le Hir, R.
    Synchrotron FTIR and Raman spectroscopy provide unique spectral fingerprints for Arabidopsis floral stem vascular tissues2019In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 70, no 3, p. 871-883Article in journal (Refereed)
    Abstract [en]

    Cell walls are highly complex structures that are modified during plant growth and development. For example, the development of phloem and xylem vascular cells, which participate in the transport of sugars and water as well as providing support, can be influenced by cell-specific wall composition. Here, we used synchrotron radiation-based Fourier-transform infrared (SR-FTIR) and Raman spectroscopy to analyse the cell wall composition of floral stem vascular tissues of wild-type Arabidopsis and the double-mutant sweet11-1 sweet12-1, which has impaired sugar transport. The SR-FTIR spectra showed that in addition to modified xylem cell wall composition, phloem cell walls in the double-mutant line were characterized by modified hemicellulose composition. Combining Raman spectroscopy with a classification and regression tree (CART) method identified combinations of Raman shifts that could distinguish xylem vessels and fibers. In addition, the disruption of the SWEET11 and SWEET12 genes impacted on xylem wall composition in a cell-specific manner, with changes in hemicelluloses and cellulose observed at the xylem vessel interface. These results suggest that the facilitated transport of sugars by transporters that exist between vascular parenchyma cells and conducting cells is important in ensuring correct phloem and xylem cell wall composition.

  • 16. Eklund, D. Magnus
    et al.
    Svensson, Emma M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Kost, Benedikt
    Physcomitrella patens: a model to investigate the role of RAC/ROP GTPase signalling in tip growth2010In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 61, no 7, p. 1917-1937Article, review/survey (Refereed)
    Abstract [en]

    Polarized cell expansion plays an important role in plant morphogenesis. Tip growth is a dramatic form of this process, which is widely used as a model to study its regulation by RAC/ROP GTPase signalling. During the dominant haploid phase of its life cycle, the moss Physcomitrella patens contains different types of cells that expand by tip growth. Physcomitrella is a highly attractive experimental system because its genome has been sequenced, and transgene integration by homologous recombination occurs in this plant at frequencies allowing effective gene targeting. Furthermore, together with the vascular spikemoss Selaginella moellendorffii, whose genome has also been sequenced, the non-vascular moss Physcomitrella provides an evolutionary link between green algae and angiosperms. BLAST searches established that the Physcomitrella and Selaginella genomes encode not only putative RAC/ROP GTPases, but also homologues of all known regulators of polarized RAC/ROP signalling, as well as of key effectors acting in signalling cascades downstream of RAC/ROP activity. Nucleotide sequence relationships within seven different families of Physcomitrella, Selaginella, Arabidopsis thaliana and Nicotiana tabacum (tobacco) genes with distinct functions in RAC/ROP signalling were characterized based on extensive maximum likelihood and Neighbor-Joining analyses. The results of these analyses are interpreted in the light of current knowledge concerning expression patterns and molecular functions of RAC/ROP signalling proteins in angiosperms. A key aim of this study is to facilitate the use of Physcomitrella as a model to investigate the molecular control of tip growth in plants.

  • 17.
    Escamez, Sacha
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Stael, Simon
    Vainonen, Julia P.
    Willems, Patrick
    Jin, Huiting
    Kimura, Sachie
    Van Breusegem, Frank
    Gevaert, Kris
    Wrzaczek, Michael
    Tuominen, Hannele
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Extracellular peptide Kratos restricts cell death during vascular development and stress in Arabidopsis2019In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 70, no 7, p. 2199-2210Article in journal (Refereed)
    Abstract [en]

    During plant vascular development, xylem tracheary elements (TEs) form water-conducting, empty pipes by genetically regulated cell death. Cell death is prevented from spreading to non-TEs by unidentified intercellular mechanisms, downstream of METACASPASE9 (MC9)-mediated regulation of autophagy in TEs. Here, we identified differentially abundant extracellular peptides in vascular-differentiating wild-type and MC9-down-regulated Arabidopsis cell suspensions. A peptide named Kratos rescued the abnormally high ectopic non-TE death resulting from either MC9 knockout or TE-specific overexpression of the ATG5 autophagy protein during experimentally induced vascular differentiation in Arabidopsis cotyledons. Kratos also reduced cell death following mechanical damage and extracellular ROS production in Arabidopsis leaves. Stress-induced but not vascular non-TE cell death was enhanced by another identified peptide, named Bia. Bia is therefore reminiscent of several known plant cell death-inducing peptides acting as damage-associated molecular patterns. In contrast, Kratos plays a novel extracellular cell survival role in the context of development and during stress response.

  • 18.
    Escamez, Sacha
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Tuominen, Hannele
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Programmes of cell death and autolysis in tracheary elements: when a suicidal cell arranges its own corpse removal2014In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 65, no 5, p. 1313-1321Article, review/survey (Refereed)
    Abstract [en]

    Differentiation of tracheary elements (TEs) is finalized by programmed cell death (PCD) and autolysis. This review integrates TE differentiation, PCD, and autolysis in a biological and evolutionary context.Tracheary element (TE) differentiation represents a unique system to study plant developmental programmed cell death (PCD). TE PCD occurs after deposition of the secondary cell walls when an unknown signal induces tonoplast rupture and the arrest of cytoplasmic streaming. TE PCD is tightly followed by autolysis of the protoplast and partial hydrolysis of the primary cell walls. This review integrates TE differentiation, programmed cell death (PCD), and autolysis in a biological and evolutionary context. The collective evidence from the evolutionary and molecular studies suggests that TE differentiation consists primarily of a programme for cell death and autolysis under the direct control of the transcriptional master switches VASCULAR NAC DOMAIN 6 (VND6) and VND7. In this scenario, secondary cell walls represent a later innovation to improve the water transport capacity of TEs which necessitates transcriptional regulators downstream of VND6 and VND7. One of the most fascinating features of TEs is that they need to prepare their own corpse removal by expression and accumulation of hydrolases that are released from the vacuole after TE cell death. Therefore, TE differentiation involves, in addition to PCD, a programmed autolysis which is initiated before cell death and executed post-mortem. It has recently become clear that TE PCD and autolysis are separate processes with separate molecular regulation. Therefore, the importance of distinguishing between the cell death programme per se and autolysis in all plant PCD research and of careful description of the morphological, biochemical, and molecular sequences in each of these processes, is advocated.

  • 19.
    Forsberg, Simon K. G.
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Carlborg, Örjan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    On the relationship between epistasis and genetic variance heterogeneity.2017In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, no 20, p. 5431-5438Article in journal (Refereed)
    Abstract [en]

    Epistasis and genetic variance heterogeneity are two non-additive genetic inheritance patterns that are often, but not always, related. Here we use theoretical examples and empirical results from earlier analyses of experimental data to illustrate the connection between the two. This includes an introduction to the relationship between epistatic gene action, statistical epistasis, and genetic variance heterogeneity, and a brief discussion about how genetic processes other than epistasis can also give rise to genetic variance heterogeneity.

  • 20.
    Fritioff, Åsa
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Greger, Maria
    Stockholm University, Faculty of Science, Department of Botany.
    Fate of Cadmium in Elodea canadensis2007In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 67, no 2, p. 365-375Article in journal (Refereed)
    Abstract [en]

    Elodea canadensis is a submersed macrophytes, widely distributed in stormwater treatment ponds and able to remove heavy metals from water. This study examines the Cd uptake, translocation, and efflux patterns in Elodea. Several experiments were set up in a climate chamber. To study the root and shoot Cd uptake, living and dead roots and shoots were treated with 109Cd in one- and two-compartment systems. Furthermore, to examine Cd translocation and distribution, either roots or shoots were treated with 109Cd. Finally, the efflux of Cd from roots and shoots, respectively, to the external solution was studied after loading whole plants with 109Cd. Results from the two compartment studies show that Cd is accumulated via direct uptake by both roots and shoots of Elodea. The Cd accumulation proved not to be metabolically dependent in Elodea, and the apoplastic uptake in particular was decreased by Cd pretreatment. In one week, up to 23% of the root uptake was translocated to the shoots, while about 2% of the Cd accumulated by shoots was translocated to the roots. Thus, slight dispersion of Cd is possible, while metal immobilization will not be directly mediated via the Elodea plant. The efflux experiment proved that both shoots of dead plants and roots of living plants had a faster efflux than did shoots of living plants. This information is relevant for an understanding of the fate of Cd in stormwater treatment ponds with Elodea

    .

  • 21.
    Giummarella, Nicola
    Wallenberg Wood Science Center.
    Koutaniemi, Sanna (Contributor)
    Kärkönen, Anna (Contributor)
    Lawoko, Martin
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Wood Chemistry and Pulp Technology. Wallenberg Wood Science Center.
    Nativity of lignin carbohydrate bonds substantiated by biomimetic synthesis2019In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431Article in journal (Refereed)
    Abstract [en]

    The question of whether lignin is covalently linked to carbohydrates in native wood, forming what is referred to as lignin–carbohydrate complexes (LCCs), still lacks unequivocal proof. This is mainly due to the need to isolate lignin from woody materials prior to analysis, under conditions leading to partial chemical modification of the native wood polymers. Thus, the correlation between the structure of the isolated LCCs and LCCs in situ remains open. As a way to circumvent the problematic isolation, biomimicking lignin polymerization in vivo and in vitro is an interesting option. Herein, we report the detection of lignin–carbohydrate bonds in the extracellular lignin formed by tissue-cultured Norway spruce cells, and in modified biomimetic lignin synthesis (dehydrogenation polymers). Semi-quantitative 2D heteronuclear singular quantum coherence (HSQC)-, 31P -, and 13C-NMR spectroscopy were applied as analytical tools. Combining results from these systems, four types of lignin–carbohydrate bonds were detected; benzyl ether, benzyl ester, γ-ester, and phenyl glycoside linkages, providing direct evidence of lignin–carbohydrate bond formation in biomimicked lignin polymerization. Based on our findings, we propose a sequence for lignin–carbohydrate bond formation in plant cell walls.

  • 22. Guenin, Stephanie
    et al.
    Mauriat, Melanie
    Pelloux, Jerome
    Van Wuytswinkel, Olivier
    Bellini, Catherine
    Gutierrez, Laurent
    Normalization of qRT-PCR data: the necessity of adopting a systematic, experimental conditions-specific, validation of references2009In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 60, no 2, p. 487-493Article in journal (Refereed)
    Abstract [en]

    Quantitative RT-PCR (reverse transcription polymerase chain reaction, also known as qRT-PCR or real-time RT-PCR) has been used in large proportions of transcriptome analyses published to date. The accuracy of the results obtained by this method strongly depends on accurate transcript normalization using stably expressed genes, known as references. Statistical algorithms have been developed recently to help validate reference genes but, surprisingly, this robust approach is under-utilized in plants. Instead, putative ’housekeeping’ genes tend to be used as references without any proper validation. The concept of normalization in transcript quantification is introduced here and the factors affecting its reliability in qRT-PCR are discussed in an attempt to convince molecular biologists, and non-specialists, that systematic validation of reference genes is essential for producing accurate, reliable data in qRT-PCR analyses, and thus should be an integral component of them.

  • 23. Guerriero, Gea
    et al.
    Spadiut, Oliver
    Kerschbamer, Christine
    Giorno, Filomena
    Baric, Sanja
    Ezcurra, Ines
    KTH, School of Biotechnology (BIO), Glycoscience.
    Analysis of cellulose synthase genes from domesticated apple identifies collinear genes WDR53 and CesA8A: Partial co-expression, bicistronic mRNA, and alternative splicing of CESA8A2012In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 63, no 16, p. 6045-6056Article in journal (Refereed)
    Abstract [en]

    Cellulose synthase (CesA) genes constitute a complex multigene family with six major phylogenetic clades in angiosperms. The recently sequenced genome of domestic apple, Malus-domestica was mined for CesA genes, by blasting full-length cellulose synthase protein (CESA) sequences annotated in the apple genome against protein databases from the plant models Arabidopsis thaliana and Populus trichocarpa. Thirteen genes belonging to the six angiosperm CesA clades and coding for proteins with conserved residues typical of processive glycosyltransferases from family 2 were detected. Based on their phylogenetic relationship to Arabidopsis CESAs, as well as expression patterns, a nomenclature is proposed to facilitate further studies. Examination of their genomic organization revealed that MdCesA8-A is closely linked and co-oriented with WDR53, a gene coding for a WD40 repeat protein. The WDR53 and CesA8 genes display conserved collinearity in dicots and are partially co-expressed in the apple xylem. Interestingly, the presence of a bicistronic WDR53-CesA8A transcript was detected in phytoplasma-infected phloem tissues of apple. The bicistronic transcript contains a spliced intergenic sequence that is predicted to fold into hairpin structures typical of internal ribosome entry sites, suggesting its potential cap-independent translation. Surprisingly, the CesA8A cistron is alternatively spliced and lacks the zinc-binding domain. The possible roles of WDR53 and the alternatively spliced CESA8 variant during cellulose biosynthesis in M.-xdomestica are discussed.

  • 24. Guo, Qianqian
    et al.
    Turnbull, Matthew Hamish
    Song, Jiancheng
    Roche, Jessica
    Novak, Ondrej
    Späth, Jana
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Jameson, Paula Elizabeth
    Love, Jonathan
    Depletion of carbohydrate reserves limits nitrate uptake during early regrowth in Lolium perenne L.2017In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, no 7, p. 1569-1583Article in journal (Refereed)
    Abstract [en]

    The mechanisms linking C/N balance to N uptake and assimilation are central to plant responses to changing soil nutrient levels. Defoliation and subsequent regrowth of grasses both impact C partitioning, thereby creating a significant point of interaction with soil N availability. Using defoliation as an experimental treatment, we investigated the dynamic relationships between plant carbohydrate status and NO3--responsive uptake systems, transporter gene expression, and nitrate assimilation in Lolium perenne L. High- and low-affinity NO3- uptake was reduced in an N-dependent manner in response to a rapid and large shift in carbohydrate remobilization triggered by defoliation. This reduction in NO3- uptake was rescued by an exogenous glucose supplement, confirming the carbohydrate dependence of NO3- uptake. The regulation of NO3- uptake in response to the perturbation of the plant C/N ratio was associated with changes in expression of putative high- and low-affinity NO3- transporters. Furthermore, NO3- assimilation appears to be regulated by the C-N status of the plant, implying a mechanism that signals the availability of C metabolites for NO3- uptake and assimilation at the whole-plant level. We also show that cytokinins may be involved in the regulation of N acquisition and assimilation in response to the changing plant C/N ratio.

  • 25. Hodges, Michael
    et al.
    Dellero, Younes
    Keech, Olivier
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Betti, Marco
    Raghavendra, Agepati S.
    Sage, Rowan
    Zhu, Xin-Guang
    Allen, Doug K.
    Weber, Andreas P. M.
    Perspectives for a better understanding of the metabolic integration of photorespiration within a complex plant primary metabolism network2016In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 67, no 10, p. 3015-3026Article, review/survey (Refereed)
    Abstract [en]

    Recent advances in photorespiration research are described and future priorities to better understand the metabolic integration of the photorespiratory cycle within the complex network of plant primary metabolism are discussed.Photorespiration is an essential high flux metabolic pathway that is found in all oxygen-producing photosynthetic organisms. It is often viewed as a closed metabolic repair pathway that serves to detoxify 2-phosphoglycolic acid and to recycle carbon to fuel the Calvin-Benson cycle. However, this view is too simplistic since the photorespiratory cycle is known to interact with several primary metabolic pathways, including photosynthesis, nitrate assimilation, amino acid metabolism, C-1 metabolism and the Krebs (TCA) cycle. Here we will review recent advances in photorespiration research and discuss future priorities to better understand (i) the metabolic integration of the photorespiratory cycle within the complex network of plant primary metabolism and (ii) the importance of photorespiration in response to abiotic and biotic stresses.

  • 26. HUSSDANELL, K
    et al.
    Sellstedt, Anita
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    NITROGENASE ACTIVITY IN RESPONSE TO DARKENING AND DEFOLIATION OF ALNUS-INCANA1985In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 36, no 170, p. 1352-1358Article in journal (Refereed)
  • 27. Jahan, Sultana N.
    et al.
    Asman, Anna K. M.
    Corcoran, Padraic
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Fogelqvist, Johan
    Vetukuri, Ramesh R.
    Dixelius, Christina
    Plant-mediated gene silencing restricts growth of the potato late blight pathogen Phytophthora infestans2015In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 66, no 9, p. 2785-2794Article in journal (Refereed)
    Abstract [en]

    A host-induced gene-silencing strategy for controlling potato late blight is presented, a plant disease that conventionally requires regular application of fungicides at high rates.Phytophthora infestans is an oomycete that causes severe damage to potato, and is well known for its ability to evolve rapidly in order to overcome resistant potato varieties. An RNA silencing strategy was evaluated here to clarify if small interfering RNA homologous to selected genes in P. infestans could be targeted from the plant host to reduce the magnitude of the infection. As a proof-of-concept, a hairpin RNA (hp-RNA) construct using the GFP marker gene was designed and introduced in potato. At 72 hpi, a 55-fold reduction of the signal intensity of a corresponding GFP expressing P. infestans strain on leaf samples of transgenic plants, compared with wild-type potato, was detected. This suggests that an RNA interference construct in the potato host could be processed and target a transcript of the pathogen. Three genes important in the infection process of P. infestans, PiGPB1, PiCESA2, and PiPEC, together with PiGAPDH taking part in basic cell maintenance were subsequently tested using an analogous transgenic strategy. Out of these gene candidates, the hp-PiGPB1 targeting the G protein beta-subunit (PiGPB1) important for pathogenicity resulted in most restricted disease progress. Further, Illumina sequencing of inoculated transgenic potato leaves revealed sRNAs of 24/25 nt size homologous to the PiGPB1 gene in the transgenic plants indicating post-transcriptional silencing of the target gene. The work demonstrates that a host-induced gene-silencing approach is functional against P. infestans but is highly dependent on target gene for a successful outcome. This finding broadens the arsenal of control strategies to this important plant disease.

  • 28.
    Janasch, Markus
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Asplund-Samuelsson, Johannes
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Steuer, R.
    Hudson, Elton P.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Kinetic modeling of the Calvin cycle identifies flux control and stable metabolomes in Synechocystis carbon fixation2019In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 70, no 3, p. 973-983Article in journal (Refereed)
    Abstract [en]

    Biological fixation of atmospheric CO2 via the Calvin-Benson-Bassham cycle has massive ecological impact and offers potential for industrial exploitation, either by improving carbon fixation in plants and autotrophic bacteria, or by installation into new hosts. A kinetic model of the Calvin-Benson-Bassham cycle embedded in the central carbon metabolism of the cyanobacterium Synechocystis sp. PCC 6803 was developed to investigate its stability and underlying control mechanisms. To reduce the uncertainty associated with a single parameter set, random sampling of the steady-state metabolite concentrations and the enzyme kinetic parameters was employed, resulting in millions of parameterized models which were analyzed for flux control and stability against perturbation. Our results show that the Calvin cycle had an overall high intrinsic stability, but a high concentration of ribulose 1,5-bisphosphate was associated with unstable states. Low substrate saturation and high product saturation of enzymes involved in highly interconnected reactions correlated with increased network stability. Flux control, that is the effect that a change in one reaction rate has on the other reactions in the network, was distributed and mostly exerted by energy supply (ATP), but also by cofactor supply (NADPH). Sedoheptulose 1,7-bisphosphatase/fructose 1,6-bisphosphatase, fructose-bisphosphate aldolase, and transketolase had a weak but positive effect on overall network flux, in agreement with published observations. The identified flux control and relationships between metabolite concentrations and system stability can guide metabolic engineering. The kinetic model structure and parameterizing framework can be expanded for analysis of metabolic systems beyond the Calvin cycle.

  • 29.
    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.

  • 30.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    At the end of the day: a common molecular mechanism for photoperiod responses in plants?2009In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 60, no 9, p. 2501-2515Article, review/survey (Refereed)
    Abstract [en]

    Photoperiod or daylength affects a diverse set of traits in plants, including flowering and tuberization in annuals, as well as growth cessation and bud set in perennials. During the last 10-15 years, great progress has been made in the understanding of molecular mechanisms controlling photoperiodic induction of flowering, in particular in the model species Arabidopsis thaliana. An obvious question is to what extent the molecular mechanisms revealed in A. thaliana are also shared by other species and other traits controlled by photoperiod. The purpose of this review is to summarize data on the molecular mechanisms of photoperiod control in plants with a focus of annual growth rhythm in perennial plants.

  • 31.
    Larsson, Anna M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Valegård, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Crystal structures of β-carboxysome shell protein CcmP: ligand binding correlates with the closed or open central pore2017In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, no 14, p. 3857-3867Article in journal (Refereed)
    Abstract [en]

    Cyanobacterial CO2 fixation is promoted by encapsulating and co-localizing the CO2-fixing enzymes within a protein shell, the carboxysome. A key feature of the carboxysome is its ability to control selectively the flux of metabolites in and out of the shell. The beta-carboxysome shell protein CcmP has been shown to form a double layer of pseudohexamers with a relatively large central pore (similar to 13 angstrom diameter), which may allow passage of larger metabolites such as the substrate for CO2 fixation, ribulose 1,5-bisphosphate, through the shell. Here we describe two crystal structures, at 1.45 angstrom and 1.65 angstrom resolution, of CcmP from Synechococcus elongatus PCC7942 (SeCcmP). The central pore of CcmP is open or closed at its ends, depending on the conformation of two conserved residues, Glu69 and Arg70. The presence of glycerol resulted in a pore that is open at one end and closed at the opposite end. When glycerol was omitted, both ends of the barrel became closed. A binding pocket at the interior of the barrel featured residual density with distinct differences in size and shape depending on the conformation, open or closed, of the central pore of SeCcmP, suggestive of a metabolite-driven mechanism for the gating of the pore.

  • 32.
    Lastdrager, Jeroen
    et al.
    Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands .
    Hanson, Johannes
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
    Smeekens, Sjef
    Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
    Sugar signals and the control of plant growth and development2014In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 65, no 3, p. 799-807Article, review/survey (Refereed)
    Abstract [en]

    Sugars are key regulators that control plant growth and development, including biomass accumulation. Major sugar-responsive signalling systems are reviewed, with emphasis on trehalose 6-phosphate, TOR kinase, SnRK1, and the C/S1-bZIP network.Sugars have a central regulatory function in steering plant growth. This review focuses on information presented in the past 2 years on key players in sugar-mediated plant growth regulation, with emphasis on trehalose 6-phosphate, target of rapamycin kinase, and Snf1-related kinase 1 regulatory systems. The regulation of protein synthesis by sugars is fundamental to plant growth control, and recent advances in our understanding of the regulation of translation by sugars will be discussed.

  • 33.
    Li, Muyang
    et al.
    DOE-Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan State University, Department of Biosystems & Agricultural Engineering, Michigan State University, East Lansing.
    Heckwolf, Marlies
    DOE-Great Lakes Bioenergy Research Center, Michigan State University, East Lansing.
    Crowe, Jacob D.
    Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing.
    Williams, Daniel L.
    Michigan State University, DOE-Great Lakes Bioenergy Research Center, Michigan State University, East Lansing.
    Magee, Timothy D.
    Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing.
    Kaeppler, Shawn M.
    DOE-Great Lakes Bioenergy Research Center, Michigan State University, East Lansing.
    Lion, Natalia de
    DOE-Great Lakes Bioenergy Research Center, Michigan State University, East Lansing.
    Hodge, David
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Sustainable Process Engineering.
    Cell-wall properties contributing to improved deconstruction by alkaline pre-treatment and enzymatic hydrolysis in diverse maize (Zea mays L.) lines2015In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 66, no 14, p. 4305-4315Article in journal (Refereed)
    Abstract [en]

    A maize (Zea mays L. subsp. mays) diversity panel consisting of 26 maize lines exhibiting a wide range of cell-wall properties and responses to hydrolysis by cellulolytic enzymes was employed to investigate the relationship between cell-wall properties, cell-wall responses to mild NaOH pre-treatment, and enzymatic hydrolysis yields. Enzymatic hydrolysis of the cellulose in the untreated maize was found to be positively correlated with the water retention value, which is a measure of cell-wall susceptibility to swelling. It was also positively correlated with the lignin syringyl/guaiacyl ratio and negatively correlated with the initial cell-wall lignin, xylan, acetate, and p-coumaric acid (pCA) content, as well as pCA released from the cell wall by pre-treatment. The hydrolysis yield following pre-treatment exhibited statistically significant negative correlations to the lignin content after pre-treatment and positive correlations to the solubilized ferulic acid and pCA. Several unanticipated results were observed, including a positive correlation between initial lignin and acetate content, lack of correlation between acetate content and initial xylan content, and negative correlation between each of these three variables to the hydrolysis yields for untreated maize. Another surprising result was that pCA release was negatively correlated with hydrolysis yields for untreated maize and, along with ferulic acid release, was positively correlated with the pre-treated maize hydrolysis yields. This indicates that these properties that may negatively contribute to the recalcitrance in untreated cell walls may positively contribute to their deconstruction by alkaline pre-treatment.

  • 34. Lindén, Pernilla
    et al.
    Keech, Olivier
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Stenlund, Hans
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Gardeström, Per
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Moritz, Thomas
    Reduced mitochondrial malate dehydrogenase activity has a strong effect on photorespiratory metabolism as revealed by 13C labelling2016In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 67, no 10, p. 3123-3135Article in journal (Refereed)
    Abstract [en]

    Mitochondrial malate dehydrogenase (mMDH) catalyses the interconversion of malate and oxaloacetate (OAA) in the tricarboxylic acid (TCA) cycle. Its activity is important for redox control of the mitochondrial matrix, through which it may participate in regulation of TCA cycle turnover. In Arabidopsis, there are two isoforms of mMDH. Here, we investigated to which extent the lack of the major isoform, mMDH1 accounting for about 60% of the activity, affected leaf metabolism. In air, rosettes of mmdh1 plants were only slightly smaller than wild type plants although the fresh weight was decreased by about 50%. In low CO2 the difference was much bigger, with mutant plants accumulating only 14% of fresh weight as compared to wild type. To investigate the metabolic background to the differences in growth, we developed a 13CO2 labelling method, using a custom-built chamber that enabled simultaneous treatment of sets of plants under controlled conditions. The metabolic profiles were analysed by gas- and liquid- chromatography coupled to mass spectrometry to investigate the metabolic adjustments between wild type and mmdh1. The genotypes responded similarly to high CO2 treatment both with respect to metabolite pools and 13C incorporation during a 2-h treatment. However, under low CO2 several metabolites differed between the two genotypes and, interestingly most of these were closely associated with photorespiration. We found that while the glycine/serine ratio increased, a concomitant altered glutamine/glutamate/α-ketoglutarate relation occurred. Taken together, our results indicate that adequate mMDH activity is essential to shuttle reductants out from the mitochondria to support the photorespiratory flux, and strengthen the idea that photorespiration is tightly intertwined with peripheral metabolic reactions.

  • 35.
    Lundmark, Maria
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hurry, Vaughan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Lapointe, Line
    Département de biologie and Centre d’étude de la forêt, Université Laval, Québec City, Québec, Canada G1V 0A6.
    Low temperature maximizes growth of Crocus vernus (L.) Hill via changes in carbon partitioning and corm development.2009In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 60, no 7, p. 2203-2213Article in journal (Refereed)
    Abstract [en]

    In Crocus vernus, a spring bulbous species, prolonged growth at low temperatures results in the development of larger perennial organs and delayed foliar senescence. Because corm growth is known to stop before the first visual sign of leaf senescence, it is clear that factors other than leaf duration alone determine final corm size. The aim of this study was to determine whether reduced growth at higher temperatures was due to decreased carbon import to the corm or to changes in the partitioning of this carbon once it had reached the corm. Plants were grown under two temperature regimes and the amount of carbon fixed, transported, and converted into a storable form in the corm, as well as the partitioning into soluble carbohydrates, starch, and the cell wall, were monitored during the growth cycle. The reduced growth at higher temperature could not be explained by a restriction in carbon supply or by a reduced ability to convert the carbon into starch. However, under the higher temperature regime, the plant allocated more carbon to cell wall material, and the amount of glucose within the corm declined earlier in the season. Hexose to sucrose ratios might control the duration of corm growth in C. vernus by influencing the timing of the cell division, elongation, and maturation phases. It is suggested that it is this shift in carbon partitioning, not limited carbon supply or leaf duration, which is responsible for the smaller final biomass of the corm at higher temperatures.

  • 36. Maris, An
    et al.
    Kaewthai, Nomchit
    KTH, School of Biotechnology (BIO), Glycoscience.
    Eklöf, Jens
    KTH, School of Biotechnology (BIO), Glycoscience.
    Miller, Janice G.
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Glycoscience.
    Fry, Stephen C.
    Verbelen, Jean-Pierre
    Vissenberg, Kris
    Differences in enzymic properties of five recombinant xyloglucan endotransglucosylase/hydrolase (XTH) proteins of Arabidopsis thaliana2011In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 62, no 1, p. 261-271Article in journal (Refereed)
    Abstract [en]

    Xyloglucan endotransglucosylase/hydrolases (XTHs) are cell wall enzymes that are able to graft xyloglucan chains to oligosaccharides or to other available xyloglucan chains and/or to hydrolyse xyloglucan chains. As they are involved in the modification of the load-bearing cell-wall components, they are believed to be very important in the regulation of growth and development. Given the large number (33) of XTH genes in Arabidopsis and the overlapping expression patterns, specific enzymic properties may be expected. Five predominantly root-expressed Arabidopsis thaliana XTHs belonging to subgroup I/II were analysed here. These represent two sets of closely related genes: AtXTH12 and 13 on the one hand (trichoblast-enriched) and AtXTH17, 18, and 19 on the other (expressed in nearly all cell types in the root). They were all recombinantly produced in the yeast Pichia pastoris and partially purified by ammonium sulphate precipitation before they were subsequently all subjected to a series of identical in vitro tests. The kinetic properties of purified AtXTH13 were investigated in greater detail to rule out interference with the assays by contaminating yeast proteins. All five proteins were found to exhibit only the endotransglucosylase (XET; EC 2.4.1.207) activity towards xyloglucan and non-detectable endohydrolytic (XEH; EC 3.2.1.151) activity. Their endotransglucosylase activity was preferentially directed towards xyloglucan and, in some cases, water-soluble cellulose acetate, rather than to mixed-linkage beta-glucan. Isoforms differed in optimum pH (5.0-7.5), in temperature dependence and in acceptor substrate preferences.

  • 37. Mateo, Alfonso
    et al.
    Funck, Dietmar
    Mühlenbock, Per
    Kular, Baldeep
    Mullineaux, Philip M
    Karpinski, Stanislaw
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Controlled levels of salicylic acid are required for optimal photosynthesis and redox homeostasis.2006In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 57, no 8, p. 1795-807Article in journal (Refereed)
    Abstract [en]

    Sudden exposure of plants to high light (HL) leads to metabolic and physiological disruption of the photosynthetic cells. Changes in ROS content, adjustment of photosynthetic processes and the antioxidant pools and, ultimately, gene induction are essential components for a successful acclimation to the new light conditions. The influence of salicylic acid (SA) on plant growth, short-term acclimation to HL, and on the redox homeostasis of Arabidopsis thaliana leaves was assessed here. The dwarf phenotype displayed by mutants with high SA content (cpr1-1, cpr5-1, cpr6-1, and dnd1-1) was less pronounced when these plants were grown in HL, suggesting that the inhibitory effect of SA on growth was partly overcome at higher light intensities. Moreover, higher SA content affected energy conversion processes in low light, but did not impair short-term acclimation to HL. On the other hand, mutants with low foliar SA content (NahG and sid2-2) were impaired in acclimation to transient exposure to HL and thus predisposed to oxidative stress. Low and high SA levels were strictly correlated to a lower and higher foliar H(2)O(2) content, respectively. Furthermore high SA was also associated with higher GSH contents, suggesting a tight correlation between SA, H(2)O(2) and GSH contents in plants. These observations implied an essential role of SA in the acclimation processes and in regulating the redox homeostasis of the cell. Implications for the role of SA in pathogen defence signalling are also discussed.

  • 38.
    Mateo, Alfonso
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Funck, Dietmar
    Mühlenbock, Per
    Stockholm University, Faculty of Science, Department of Botany.
    Mullineaux, Philip M.
    Karpinski, Stanislaw
    Stockholm University, Faculty of Science, Department of Botany.
    Controlled levels of salicylic acid are required for optimal photosynthesis and redox homeostasis2006In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 57, no 8, p. 1795-1807Article in journal (Refereed)
    Abstract [en]

    Sudden exposure of plants to high light (HL) leads to metabolic and physiological disruption of the photosynthetic cells. Changes in ROS content, adjustment of photosynthetic processes and the antioxidant pools and, ultimately, gene induction are essential components for a successful acclimation to the new light conditions. The influence of salicylic acid (SA) on plant growth, short-term acclimation to HL, and on the redox homeostasis of Arabidopsis thaliana leaves was assessed here. The dwarf phenotype displayed by mutants with high SA content (cpr1-1, cpr5-1, cpr6-1, and dnd1-1) was less pronounced when these plants were grown in HL, suggesting that the inhibitory effect of SA on growth was partly overcome at higher light intensities. Moreover, higher SA content affected energy conversion processes in low light, but did not impair short-term acclimation to HL. On the other hand, mutants with low foliar SA content (NahG and sid2-2) were impaired in acclimation to transient exposure to HL and thus predisposed to oxidative stress. Low and high SA levels were strictly correlated to a lower and higher foliar H2O2 content, respectively. Furthermore high SA was also associated with higher GSH contents, suggesting a tight correlation between SA, H2O2 and GSH contents in plants. These observations implied an essential role of SA in the acclimation processes and in regulating the redox homeostasis of the cell. Implications for the role of SA in pathogen defence signalling are also discussed.

  • 39. Miguel, Andreia
    et al.
    Milhinhos, Ana
    Novak, Ondrej
    Jones, Brian
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Faculty of Agriculture, Food and Natural Resources, University of Sydney, Sydney, Australia.
    Miguel, Celia M.
    The SHORT-ROOT-like gene PtSHR2B is involved in Populus phellogen activity2016In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 67, no 5, p. 1545-1555Article in journal (Refereed)
    Abstract [en]

    SHORT-ROOT (SHR) is a GRAS transcription factor first characterized for its role in the specification of the stem cell niche and radial patterning in Arabidopsis thaliana (At) roots. Three SHR-like genes have been identified in Populus trichocarpa (Pt). PtSHR1 shares high similarity with AtSHR over the entire length of the coding sequence. The two other Populus SHR-like genes, PtSHR2A and PtSHR2B, are shorter in their 5' ends when compared with AtSHR. Unlike PtSHR1, that is expressed throughout the cambial zone of greenhouse-grown Populus trees, PtSHR2Bprom:uidA expression was detected in the phellogen. Additionally, PtSHR1 and PtSHR2B expression patterns markedly differ in the shoot apex and roots of in vitro plants. Transgenic hybrid aspen expressing PtSHR2B under the 35S constitutive promoter showed overall reduced tree growth while the proportion of bark increased relative to the wood. Reverse transcription-quantitative PCR (RT-qPCR) revealed increased transcript levels of cytokinin metabolism and response-related genes in the transgenic plants consistent with an increase of total cytokinin levels. This was confirmed by cytokinin quantification by LC-MS/MS. Our results indicate that PtSHR2B appears to function in the phellogen and therefore in the regulation of phellem and periderm formation, possibly acting through modulation of cytokinin homeostasis. Furthermore, this work points to a functional diversification of SHR after the divergence of the Populus and Arabidopsis lineages. This finding may contribute to selection and breeding strategies of cork oak in which, unlike Populus, the phellogen is active throughout the entire tree lifespan, being at the basis of a highly profitable cork industry.

  • 40.
    Mishra, Laxmi S.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mielke, Kati
    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.
    Reduced expression of the proteolytically inactive FtsH members has impacts on the Darwinian fitness of Arabidopsis thaliana2019In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 70, no 7, p. 2173-2184Article in journal (Refereed)
    Abstract [en]

    FtsH (filamentation-temperature-sensitive protein H) proteases are a family of membrane-bound enzymes present in eubacteria, animals, and plants. Besides the 12 genes encoding proteolytically active members of the FtsH family in the genome of Arabidopsis, there are five genes coding for members that are assumed to be proteolytically inactive due to mutations in the protease domain; these are termed FtsHi (i for inactive). Despite their lack of proteolytic activity, these FtsHi members seem to be important for chloroplast and plant development as four out of five homozygous knockout-mutants of FtsHis are embryo-lethal. Here, we analysed the Darwinian fitness of weak homozygous (ftshi1,3,4) and heterozygous (ftshi/FTSHi2,4,5) mutants. We compared the growth and development of these mutants to their respective wild-type Arabidopsis plants under controlled laboratory conditions and in the field, and we also evaluated the photosynthetic efficiency by pulse-amplitude modulation fluorescence. Homologous genotypes were subjected to various stress conditions in a greenhouse and gene co-expression as well as phylogenetic analyses were performed. Analysis of the gene-expression network of the five FTSHi genes indicated common clusters with genes encoding FtsH12, OTP51, and methylase. Phylogenetic analyses pointed to a common evolution (and common disappearance in grasses and gymnosperms) of FtsH12 and multiple presumably proteolytically inactive FtsHi enzymes. Our data show that the FtsHi enzymes are highly important during the seedling stage and for Darwinian fitness analyses in semi-natural conditions.

  • 41. Mounet, Fabien
    et al.
    Moing, Annick
    Kowalczyk, Mariusz
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Rohrmann, Johannes
    Petit, Johann
    Garcia, Virginie
    Maucourt, Mickael
    Yano, Kentaro
    Deborde, Catherine
    Aoki, Koh
    Berges, Helene
    Granell, Antonio
    Fernie, Alisdair R.
    Bellini, Catherine
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Rothan, Christophe
    Lemaire-Chamley, Martine
    Down-regulation of a single auxin efflux transport protein in tomato induces precocious fruit development2012In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 63, no 13, p. 4901-4917Article in journal (Refereed)
    Abstract [en]

    The PIN-FORMED (PIN) auxin efflux transport protein family has been well characterized in the model plant Arabidopsis thaliana, where these proteins are crucial for auxin regulation of various aspects of plant development. Recent evidence indicates that PIN proteins may play a role in fruit set and early fruit development in tomato (Solanum lycopersicum), but functional analyses of PIN-silenced plants failed to corroborate this hypothesis. Here it is demonstrated that silencing specifically the tomato SlPIN4 gene, which is predominantly expressed in tomato flower bud and young developing fruit, leads to parthenocarpic fruits due to precocious fruit development before fertilization. This phenotype was associated with only slight modifications of auxin homeostasis at early stages of flower bud development and with minor alterations of ARF and Aux/IAA gene expression. However, microarray transcriptome analysis and large-scale quantitative RT-PCR profiling of transcription factors in developing flower bud and fruit highlighted differentially expressed regulatory genes, which are potential targets for auxin control of fruit set and development in tomato. In conclusion, this work provides clear evidence that the tomato PIN protein SlPIN4 plays a major role in auxin regulation of tomato fruit set, possibly by preventing precocious fruit development in the absence of pollination, and further gives new insights into the target genes involved in fruit set.

  • 42. Murcha, Monika W.
    et al.
    Kmiec, Beata
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Kubiszewski-Jakubiak, Szymon
    Teixeira, Pedro F.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Glaser, Elzbieta
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Whelan, James
    Protein import into plant mitochondria: signals, machinery, processing, and regulation2014In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 65, no 22, p. 6301-6335Article, review/survey (Refereed)
    Abstract [en]

    The majority of more than 1000 proteins present in mitochondria are imported from nuclear-encoded, cytosolically synthesized precursor proteins. This impressive feat of transport and sorting is achieved by the combined action of targeting signals on mitochondrial proteins and the mitochondrial protein import apparatus. The mitochondrial protein import apparatus is composed of a number of multi-subunit protein complexes that recognize, translocate, and assemble mitochondrial proteins into functional complexes. While the core subunits involved in mitochondrial protein import are well conserved across wide phylogenetic gaps, the accessory subunits of these complexes differ in identity and/or function when plants are compared with Saccharomyces cerevisiae (yeast), the model system for mitochondrial protein import. These differences include distinct protein import receptors in plants, different mechanistic operation of the intermembrane protein import system, the location and activity of peptidases, the function of inner-membrane translocases in linking the outer and inner membrane, and the association/regulation of mitochondrial protein import complexes with components of the respiratory chain. Additionally, plant mitochondria share proteins with plastids, i.e. dual-targeted proteins. Also, the developmental and cell-specific nature of mitochondrial biogenesis is an aspect not observed in single-celled systems that is readily apparent in studies in plants. This means that plants provide a valuable model system to study the various regulatory processes associated with protein import and mitochondrial biogenesis.

  • 43.
    Pacurar, Daniel Ioan
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj Napoca, Romania.
    Pacurar, Monica Lacramioara
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj Napoca, Romania & Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden.
    Bussell, John Desmond
    Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden & Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley WA 6009, Australia.
    Schwambach, Joseli
    Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden & V.
    Pop, Tiberia Ioana
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj Napoca, Romania.
    Kowalczyk, Mariusz
    Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden.
    Gutierrez, Laurent
    Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden & Université de Picardie Jules Verne, CRRBM & BIOPI EA3900, 80039 Amiens, France.
    Cavel, Emilie
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Chaabouni, Salma
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Ljung, Karin
    Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden.
    Fett-Neto, Arthur Germano
    Centro de Biotecnologia, Laboratório de Fisiologia Vegetal, Universidade Federal do Rio Grande do Sul, 9500, CP15005, CEP 91501–970, Porto Alegre, RS, Brazil.
    Pamfil, Doru
    University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj Napoca, Romania.
    Bellini, Catherine
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech 78026 Versailles Cedex, France.
    Identification of new adventitious rooting mutants amongst suppressors of the Arabidopsis thaliana superroot2 mutation2014In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 65, no 6, p. 1605-1618Article in journal (Refereed)
    Abstract [en]

    The plant hormone auxin plays a central role in adventitious rooting and is routinely used with many economically important, vegetatively propagated plant species to promote adventitious root initiation and development on cuttings. Nevertheless the molecular mechanisms through which it acts are only starting to emerge. The Arabidopsis superroot2-1 (sur2-1) mutant overproduces auxin and, as a consequence, develops excessive adventitious roots in the hypocotyl. In order to increase the knowledge of adventitious rooting and of auxin signalling pathways and crosstalk, this study performed a screen for suppressors of superroot2-1 phenotype. These suppressors provide a new resource for discovery of genetic players involved in auxin signalling pathways or at the crosstalk of auxin and other hormones or environmental signals. This study reports the identification and characterization of 26 sur2-1 suppressor mutants, several of which were identified as mutations in candidate genes involved in either auxin biosynthesis or signalling. In addition to confirming the role of auxin as a central regulator of adventitious rooting, superroot2 suppressors indicated possible crosstalk with ethylene signalling in this process.

  • 44.
    Pacurar, Daniel Ioan
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Pacurar, Monica Lacramioara
    Street, Nathaniel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Bussell, John Desmond
    Pop, Tiberia Ioana
    Gutierrez, Laurent
    Bellini, Catherine
    A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions2012In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 63, no 7, p. 2491-2501Article in journal (Refereed)
    Abstract [en]

    The availability of a comprehensive set of resources including an entire annotated reference genome, sequenced alternative accessions, and a multitude of marker systems makes Arabidopsis thaliana an ideal platform for genetic mapping. PCR markers based on INsertions/DELetions (INDELs) are currently the most frequently used polymorphisms. For the most commonly used mapping combination, ColumbiaxLandsberg erecta (Col-0xLer-0), the Cereon polymorphism database is a valuable resource for the generation of polymorphic markers. However, because the number of markers available in public databases for accessions other than Col-0 and Ler-0 is extremely low, mapping using other accessions is far from straightforward. This issue arose while cloning mutations in the Wassilewskija (Ws-4) background. In this work, approaches are described for marker generation in Ws-4 x Col-0. Complementary strategies were employed to generate 229 INDEL markers. Firstly, existing Col-0/Ler-0 Cereon predicted polymorphisms were mined for transferability to Ws-4. Secondly, Ws-0 ecotype Illumina sequence data were analyzed to identify INDELs that could be used for the development of PCR-based markers for Col-0 and Ws-4. Finally, shotgun sequencing allowed the identification of INDELs directly between Col-0 and Ws-4. The polymorphism of the 229 markers was assessed in seven widely used Arabidopsis accessions, and PCR markers that allow a clear distinction between the diverged Ws-0 and Ws-4 accessions are detailed. The utility of the markers was demonstrated by mapping more than 35 mutations in a Col-0xWs-4 combination, an example of which is presented here. The potential contribution of next generation sequencing technologies to more traditional map-based cloning is discussed.

  • 45. Pencik, Ales
    et al.
    Casanova-Sáez, Ruben
    Pilarova, Veronika
    Zukauskaite, Asta
    Pinto, Rui
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Luis Micol, José
    Ljung, Karin
    Novák, Ondrej
    Ultra-rapid auxin metabolite profiling for high-throughput mutant screening in Arabidopsis2018In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 69, no 10, p. 2569-2579Article in journal (Refereed)
    Abstract [en]

    Auxin (indole-3-acetic acid, IAA) plays fundamental roles as a signalling molecule during numerous plant growth and development processes. The formation of local auxin gradients and auxin maxima/minima, which is very important for these processes, is regulated by auxin metabolism (biosynthesis, degradation, and conjugation) as well as transport. When studying auxin metabolism pathways it is crucial to combine data obtained from genetic investigations with the identification and quantification of individual metabolites. Thus, to facilitate efforts to elucidate auxin metabolism and its roles in plants, we have developed a high-throughput method for simultaneously quantifying IAA and its key metabolites in minute samples (<10 mg FW) of Arabidopsis thaliana tissues by in-tip micro solid-phase extraction and fast LC-tandem MS. As a proof of concept, we applied the method to a collection of Arabidopsis mutant lines and identified lines with altered IAA metabolite profiles using multivariate data analysis. Finally, we explored the correlation between IAA metabolite profiles and IAA-related phenotypes. The developed rapid analysis of large numbers of samples (>100 samples d(-1)) is a valuable tool to screen for novel regulators of auxin metabolism and homeostasis among large collections of genotypes.

  • 46.
    Persson, Jörgen
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Gardeström, Per
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Näsholm, Torgny
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Uptake, metabolism and distribution of organic and inorganic nitrogen sources by Pinus sylvestris2006In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 57, no 11, p. 2651-2659Article in journal (Refereed)
    Abstract [en]

    Although an increasing number of studies show that many plant species have the capacity to take up amino acids from exogenous sources, the importance of such uptake for plant nitrogen nutrition is largely unknown. Moreover, little is known regarding metabolism and distribution of amino acid-N following uptake or of the regulation of these processes in response to plant nitrogen status. Here results are presented from a study following uptake, metabolism, and distribution of nitrogen from Formula Formula Glu, or Ala in Scots pine (Pinus sylvestris L). In a parallel experiment, Ala uptake, processing, and shoot allocation were also monitored following a range of pretreatments intended to alter plant C- and N-status. Uptake data, metabolite profiles, N fluxes through metabolite pools and tissues, as well as alanine aminotransferase activity are presented. The results show that uptake of the organic N sources was equal to or larger than Formula uptake, while Formula uptake was comparatively low. Down-regulation of Ala uptake in response to pretreatments with NH4NO3 or methionine sulphoximine (MSX) indicates similarities between amino acid and inorganic N uptake regulation. N derived from amino acid uptake exhibited a rapid flux through the amino acid pool following uptake. Relative shoot allocation of amino acid-N was equal to that of Formula but smaller than for Formula Increased N status as well as MSX treatment significantly increased relative shoot allocation of Ala-N suggesting that Formula may have a role in the regulation of shoot allocation of amino acid-N.

  • 47. Petersen, Jan
    et al.
    Eriksson, Sylvia K.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Harryson, Pia
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Pierog, Steffen
    Colby, Thomas
    Bartels, Dorothea
    Roehrig, Horst
    The lysine-rich motif of intrinsically disordered stress protein CDeT11-24 from Craterostigma plantagineum is responsible for phosphatidic acid binding and protection of enzymes from damaging effects caused by desiccation2012In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 63, no 13, p. 4919-4929Article in journal (Refereed)
    Abstract [en]

    The late embryogenesis abundant (LEA)-like protein CDeT11-24 is one of the major desiccation-related phosphoproteins of the resurrection plant Craterostigma plantagineum. In this study, it was shown that CDeT11-24 is mostly intrinsically disordered and protects two different enzymes, citrate synthase and lactate dehydrogenase, against damaging effects caused by desiccation. Lipid-binding assays revealed that CDeT11-24 is able to interact with phosphatidic acid, although electrostatic repulsion was expected due to the overall negative net charge of the protein under the tested physiological conditions. CDeT11-24 carries an N-terminal lysine-rich sequence, which is predicted to form an amphipathic alpha-helix. Analysis of the truncated CDeT11-24 protein identified this region to be responsible for both activities: enzyme protection and phosphatidic acid interaction. Possible functions of the CDeT11-24 protein are discussed in the context of desiccation tolerance.

  • 48.
    Pocock, Tessa
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences, Engineering and Mathematics.
    Vetterli, Adrien
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences, Engineering and Mathematics.
    Falk, Stefan
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences, Engineering and Mathematics.
    Evidence for phenotypic plasticity in the Antarctic extremophile Chlamydomonas raudensis Ettl. UWO 2412011In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 62, no 3, p. 1169-1177Article in journal (Refereed)
    Abstract [en]

    Life in extreme environments poses unique challenges to photosynthetic organisms. The ability for an extremophilic green alga and its genetic and mesophilic equivalent to acclimate to changes in their environment was examined to determine the extent of their phenotypic plasticities. The Antarctic extremophile Chlamydomonas raudensis Ettl. UWO 241 (UWO) was isolated from an ice-covered lake in Antarctica, whereas its mesophilic counterpart C. raudensis Ettl. SAG 49.72 (SAG) was isolated from a meadow pool in the Czech Republic. The effects of changes in temperature and salinity on growth, morphology, and photochemistry were examined in the two strains. Differential acclimative responses were observed in UWO which include a wider salinity range for growth, and broader temperature- and salt-induced fluctuations in Fv/Fm, relative to SAG. Furthermore, the redox state of the photosynthetic electron transport chain, measured as 1–qP, was modulated in the extremophile whereas this was not observed in the mesophile. Interestingly, it is shown for the first time that SAG is similar to UWO in that it is unable to undergo state transitions. The different natural histories of these two strains exert different evolutionary pressures and, consequently, different abilities for acclimation, an important component of phenotypic plasticity. In contrast to SAG, UWO relied on a redox sensing and signalling system under the growth conditions used in this study. It is proposed that growth and adaptation of UWO under a stressful and extreme environment poises this extremophile for better success under changing environmental conditions.

  • 49.
    Rai, Neha
    et al.
    Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland.
    Neugart, Susanne
    Research Area of Plant Quality and Food Security, Leibniz Institute of Vegetable and Ornamental Crops e. V., Grossbeeren, Germany.
    Yan, Yan
    Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland.
    Wang, Fang
    Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland.
    Siipola, Sari M.
    Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland.
    Lindfors, Anders V.
    Finnish Meteorological Institute, Helsinki, Finland.
    Winkler, Jana Barbro
    Research Unit Environmental Simulation, Helmholtz Zentrum München, Neuherberg, Germany.
    Albert, Andreas
    Research Unit Environmental Simulation, Helmholtz Zentrum München, Neuherberg, Germany.
    Brosché, Mikael
    Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland.
    Lehto, Tarja
    School of Forest Sciences, University of Eastern Finland, Joensuu, Finland.
    Morales, Luis Orlando
    Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland.
    Aphalo, Pedro J.
    Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, Finland.
    How do cryptochromes and UVR8 interact in natural and simulated sunlight?2019In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431Article in journal (Refereed)
    Abstract [en]

    Cryptochromes (CRYs) and UV RESISTANCE LOCUS 8 (UVR8) photoreceptors perceive UV-A/blue (315–500 nm) and UV-B (280–315 nm) radiation in plants, respectively. While the roles of CRYs and UVR8 have been studied in separate controlled environment experiments, little is known about the interaction between these photoreceptors. Here, Arabidopsis thaliana wild-type Ler, CRYs and UVR8 photoreceptor mutants (uvr82, cry1cry2 and cry1cry2uvr82), and a flavonoid biosynthesis defective mutant (tt4) were grown in a sun simulator. Plants were exposed to filtered radiation for 17 d or for 6 h, to study the effects of blue, UV-A and UV-B radiation. Both CRYs and UVR8 independently enabled growth and survival of plants under solar levels of UV, while their joint absence was lethal under UV-B. CRYs mediated gene expression under blue light. UVR8 mediated gene expression under UV-B radiation, and in the absence of CRYs, also under UV-A. This negative regulation of UVR8-mediated gene expression by CRYs was also observed for UV-B. The accumulation of flavonoids was also consistent with this interaction between CRYs and UVR8. In conclusion, we provide evidence for an antagonistic interaction between CRYs and UVR8 and a role of UVR8 in UV-A perception.

  • 50.
    Ramachandran, Prashanth
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Physiological Botany.
    Carlsbecker, Annelie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Physiological Botany.
    Etchells, J. Peter
    Univ Durham, Dept Biosci, South Rd, Durham DH1 3LE, England..
    Class III HD- ZIPs govern vascular cell fate: an HD view on patterning and differentiation2017In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, no 1, p. 55-69Article, review/survey (Refereed)
    Abstract [en]

    Plant vasculature is required for the transport of water and solutes throughout the plant body. It is constituted of xylem, specialized for transport of water, and phloem, that transports photosynthates. These two differentiated tissues are specified early in development and arise from divisions in the procambium, which is the vascular meristem during primary growth. During secondary growth, the xylem and phloem are further expanded via differentiation of cells derived from divisions in the cambium. Almost all of the developmental fate decisions in this process, including vascular specification, patterning, and differentiation, are regulated by transcription factors belonging to the class III homeodomain-leucine zipper (HD-ZIP III) family. This review draws together the literature describing the roles that these genes play in vascular development, looking at how HD-ZIP IIIs are regulated, and how they in turn influence other regulators of vascular development. Themes covered vary, from interactions between HD-ZIP IIIs and auxin, cytokinin, and brassinosteroids, to the requirement for exquisite spatial and temporal regulation of HD-ZIP III expression through miRNA-mediated post-transcriptional regulation, and interactions with other transcription factors. The literature described places the HD-ZIP III family at the centre of a complex network required for initiating and maintaining plant vascular tissues.

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