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1.
  • Abdelkader, Amal F., 1969, et al. (author)
  • High salt stress induces swollen prothylakoids in dark-grown wheat and alters both prolamellar body transformation and reformation after irradiation
  • 2007
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 58:10, s. 2553-2564
  • Journal article (peer-reviewed)abstract
    • High salinity causes ion imbalance and osmotic stress in plants. Leaf sections from 8-d-old dark-grown wheat (Triticum aestivum cv. Giza 168) were exposed to high salt stress (600 mM) and the native arrangements of plastid pigments together with the ultrastructure of the plastids were studied using low-temperature fluorescence spectroscopy and transmission electron microscopy. Although plastids from salt-treated leaves had highly swollen prothylakoids (PTs) the prolamellar bodies (PLBs) were regular. Accordingly, a slight intensity decrease of the short-wavelength protochlorophyllide (Pchlide) form was observed, but no change was found in the long-wavelength Pchlide form emitting at 656 nm. After irradiation, newly formed swollen thylakoids showed traversing stromal strands. The PLB dispersal was partly inhibited and remnants of the PLBs formed an electron-dense structure, which remained after prolonged (8 h) irradiation. The difference in fluorescence emission maximum of the main chlorophyll form in salt-stressed leaves (681 nm) and in control leaves (683 nm) indicated a restrained formation of the photosynthetic apparatus. Overall chlorophyll accumulation during prolonged irradiation was inhibited. Salt-stressed leaves returned to darkness after 3 h of irradiation had, compared with the control, a reduced amount of Pchlide and reduced reformation of regular net-like PLBs. Instead, the size of the electron-dense structures increased. This study reports, for the first time, the salt-induced swelling of PTs and reveals traversing stromal strands in newly formed thylakoids. Although the PLBs were intact and the Pchlide fluorescence emission spectra appeared normal after salt stress in darkness, plastid development to chloroplasts was highly restricted during irradiation.
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2.
  • Abraham, Edit, et al. (author)
  • Immunodetection of retinoblastoma-related protein and its phosphorylated form in interphase and mitotic alfalfa cells
  • 2011
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 62:6, s. 2155-2168
  • Journal article (peer-reviewed)abstract
    • 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.
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3.
  • Aguilera, Anabella, et al. (author)
  • Do photosynthetic cells communicate with each other during cell death? From cyanobacteria to vascular plants
  • 2022
  • In: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 73:22, s. 7219-7242
  • Research review (peer-reviewed)abstract
    • As in metazoans, life in oxygenic photosynthetic organisms relies on the accurate regulation of cell death. During development and in response to the environment, photosynthetic cells activate and execute cell death pathways that culminate in the death of a specific group of cells, a process known as regulated cell death (RCD). RCD control is instrumental, as its misregulation can lead to growth penalties and even the death of the entire organism. Intracellular molecules released during cell demise may act as ‘survival’ or ‘death’ signals and control the propagation of cell death to surrounding cells, even in unicellular organisms. This review explores different signals involved in cell-cell communication and systemic signalling in photosynthetic organisms, in particular Ca2+, reactive oxygen species, lipid derivates, nitric oxide, and eATP. We discuss their possible mode-of-action as either ‘survival’ or ‘death’ molecules and their potential role in determining cell fate in neighbouring cells. By comparing the knowledge available across the taxonomic spectrum of this coherent phylogenetic group, from cyanobacteria to vascular plants, we aim at contributing to the identification of conserved mechanisms that control cell death propagation in oxygenic photosynthetic organisms 
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4.
  • Andersson, Inger (author)
  • Catalysis and regulation in Rubisco.
  • 2008
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 59:7, s. 1555-1568
  • Journal article (peer-reviewed)abstract
    • 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.
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5.
  • Andersson, Mariette, et al. (author)
  • Inhibition of plastid PPase and NTT leads to major changes in starch and tuber formation in potato
  • 2018
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 69, s. 1913-1924
  • Journal article (peer-reviewed)abstract
    • The importance of a plastidial soluble inorganic pyrophosphatase (psPPase) and an ATP/ ADP translocator (NTT) for starch composition and tuber formation in potato (Solanum tuberosum) was evaluated by individual and simultaneous down-regulation of the corresponding endogenous genes. Starch and amylose content of the transgenic lines were considerably lower, and granule size substantially smaller, with down-regulation of StpsPPase generating the most pronounced effects. Single-gene down-regulation of either StpsPPase or StNTT resulted in increased tuber numbers per plant and higher fresh weight yield. In contrast, when both genes were inhibited simultaneously, some lines developed only a few, small and distorted tubers. Analysis of metabolites revealed altered amounts of sugar intermediates, and a substantial increase in ADP-glucose content of the StpsPPase lines. Increased amounts of intermediates of vitamin C biosynthesis were also observed. This study suggests that hydrolysis of pyrophosphate (PPi) by action of a psPPase is vital for functional starch accumulation in potato tubers and that no additional mechanism for consuming, hydrolysing, or exporting PPi exists in the studied tissue. Additionally, it demonstrates that functional PPi hydrolysis in combination with efficient ATP import is essential for tuber formation and development.
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6.
  • Baez, Luis Alonso, et al. (author)
  • Cell wall dynamics : novel tools and research questions
  • 2023
  • In: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 74:21, s. 6448-6467
  • Research review (peer-reviewed)abstract
    • Years ago, a classic textbook would define plant cell walls based on passive features. For instance, a sort of plant exoskeleton of invariable polysaccharide composition, and probably painted in green. However, currently, this view has been expanded to consider plant cell walls as active, heterogeneous, and dynamic structures with a high degree of complexity. However, what do we mean when we refer to a cell wall as a dynamic structure? How can we investigate the different implications of this dynamism? While the first question has been the subject of several recent publications, defining the ideal strategies and tools needed to address the second question has proven to be challenging due to the myriad of techniques available. In this review, we will describe the capacities of several methodologies to study cell wall composition, structure, and other aspects developed or optimized in recent years. Keeping in mind cell wall dynamism and plasticity, the advantages of performing long-term non-invasive live-imaging methods will be emphasized. We specifically focus on techniques developed for Arabidopsis thaliana primary cell walls, but the techniques could be applied to both secondary cell walls and other plant species. We believe this toolset will help researchers in expanding knowledge of these dynamic/evolving structures.
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7.
  • Bai, Bing, et al. (author)
  • SeedTransNet : a directional translational network revealing regulatory patterns during seed maturation and germination
  • 2023
  • In: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 74:7, s. 2416-2432
  • Journal article (peer-reviewed)abstract
    • Seed maturation is the developmental process that prepares the embryo for the desiccated waiting period before germination. It is associated with a series of physiological changes leading to the establishment of seed dormancy, seed longevity, and desiccation tolerance. We studied translational changes during seed maturation and observed a gradual reduction in global translation during seed maturation. Transcriptome and translatome profiling revealed specific reduction in the translation of thousands of genes. By including previously published data on germination and seedling establishment, a regulatory network based on polysome occupancy data was constructed: SeedTransNet. Network analysis predicted translational regulatory pathways involving hundreds of genes with distinct functions. The network identified specific transcript sequence features suggesting separate translational regulatory circuits. The network revealed several seed maturation-associated genes as central nodes, and this was confirmed by specific seed phenotypes of the respective mutants. One of the regulators identified, an AWPM19 family protein, PM19-Like1 (PM19L1), was shown to regulate seed dormancy and longevity. This putative RNA-binding protein also affects the translational regulation of its target mRNA, as identified by SeedTransNet. Our data show the usefulness of SeedTransNet in identifying regulatory pathways during seed phase transitions.
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8.
  • Bejai, Sarosh, et al. (author)
  • ML3: a novel regulator of herbivory-induced responses in Arabidopsis thaliana
  • 2013
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 64, s. 935-948
  • Journal article (peer-reviewed)abstract
    • ML (MD2-related lipid recognition) proteins are known to enhance innate immune responses in mammals. This study reports the analysis of the putative ML gene family in Arabidopsis thaliana and suggests a role for the ML3 gene in herbivory-associated responses in plants. Feeding by larvae of the Lepidopteran generalist herbivore Spodoptera littoralis and larvae of the specialist herbivore Plutella xylostella activated ML3 transcription in leaf tissues. ML3 loss-of-function Arabidopsis plants were compromised in the upregulation of herbivory-induced genes and displayed a semi-dwarf phenotype. Herbivory bioassays showed that larvae of S. littoralis fed on ml3 mutant plants gained more weight compared to larvae fed on wild-type plants while larvae of P. xylostella did not show any significant difference. Virus-induced gene silencing of ML3 expression in plants compromised in jasmonic acid (JA) and salicylic acid (SA) signalling revealed a complex role of ML3 in JA/defence signalling affecting both JA- and SA-dependent responses. The data suggest that ML3 is involved in herbivory-mediated responses in Arabidopsis and that it has a potential role in herbivory-associated molecular pattern recognition.
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9.
  • Berghuijs, Herman (author)
  • In silico study of the role of cell growth factors in photosynthesis using a virtual leaf tissue generator coupled to a microscale photosynthesis gas exchange model
  • 2020
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 71, s. 997-1009
  • Journal article (peer-reviewed)abstract
    • Computational tools that allow in silico analysis of the role of cell growth and division on photosynthesis are scarce. We present a freely available tool that combines a virtual leaf tissue generator and a two-dimensional microscale model of gas transport during C-3 photosynthesis. A total of 270 mesophyll geometries were generated with varying degrees of growth anisotropy, growth extent, and extent of schizogenous airspace formation in the palisade mesophyll. The anatomical properties of the virtual leaf tissue and microscopic cross-sections of actual leaf tissue of tomato (Solanum lycopersicum L.) were statistically compared. Model equations for transport of CO2 in the liquid phase of the leaf tissue were discretized over the geometries. The virtual leaf tissue generator produced a leaf anatomy of tomato that was statistically similar to real tomato leaf tissue. The response of photosynthesis to intercellular CO2 predicted by a model that used the virtual leaf tissue geometry compared well with measured values. The results indicate that the light-saturated rate of photosynthesis was influenced by interactive effects of extent and directionality of cell growth and degree of airspace formation through the exposed surface of mesophyll per leaf area. The tool could be used further in investigations of improving photosynthesis and gas exchange in relation to cell growth and leaf anatomy.
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10.
  • Betti, Marco, et al. (author)
  • Manipulating photorespiration to increase plant productivity : recent advances and perspectives for crop improvement
  • 2016
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 67:10, s. 2977-2988
  • Research review (peer-reviewed)abstract
    • 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.
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11.
  • Bhalerao, Rishikesh P., et al. (author)
  • Environmental and hormonal control of cambial stem cell dynamics
  • 2017
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 68, s. 79-87
  • Research review (peer-reviewed)abstract
    • Perennial trees have the amazing ability to adjust their growth rate to both adverse and favorable seasonally reoccurring environmental conditions over hundreds of years. In trunks and stems, the basis for the tuning of seasonal growth rate is the regulation of cambial stem cell activity. Cambial stem cell quiescence and dormancy protect the tree from potential physiological and genomic damage caused by adverse growing conditions and may permit a long lifespan. Cambial dormancy and longevity are both aspects of a tree's life for which the study of cambial stem cell behavior in the annual model plant Arabidopsis is inadequate. Recent functional analyses of hormone perception and catabolism mutants in Populus indicate that shoot-derived long-range signals, as well as local cues, steer cambial activity. Auxin is central to the regulation of cambial activity and probably also maintenance. Emerging genome editing and phenotyping technologies will enable the identification of down-stream targets of hormonal action and facilitate the genetic dissection of complex traits of cambial biology.
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12.
  • Blanco, Nicolas E., et al. (author)
  • Dual and dynamic intracellular localization of Arabidopsis thaliana SnRK1.1
  • 2019
  • In: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 70:8, s. 2325-2338
  • Journal article (peer-reviewed)abstract
    • 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.
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13.
  • Bollhoner, Benjamin, et al. (author)
  • Xylem cell death : emerging understanding of regulation and function
  • 2012
  • In: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 63:3, s. 1081-1094
  • Research review (peer-reviewed)abstract
    • 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.
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14.
  • Boussardon, Clément, et al. (author)
  • Comparison of plastid proteomes points towards a higher plastidial redox turnover in vascular tissues than in mesophyll cells
  • 2023
  • In: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 74:14, s. 4110-4124
  • Journal article (peer-reviewed)abstract
    • Plastids are complex organelles that vary in size and function depending on the cell type. Accordingly, they can be referred to as amyloplasts, chloroplasts, chromoplasts, etioplasts, or proplasts, to only cite a few. Over the past decades, methods based on density gradients and differential centrifugation have been extensively used for the purification of plastids. However, these methods need large amounts of starting material, and hardly provide a tissue-specific resolution. Here, we applied our IPTACT (Isolation of Plastids TAgged in specific Cell Types) method, which involves the biotinylation of plastids in vivo using one-shot transgenic lines expressing the Translocon of the Outer Membrane 64 (TOC64) gene coupled with a biotin ligase receptor particle and the BirA biotin ligase, to isolate plastids from mesophyll and companion cells of Arabidopsis using tissue specific pCAB3 and pSUC2 promoters, respectively. Subsequently, a proteome profiling was performed, which allowed the identification of 1672 proteins, among which 1342 were predicted to be plastidial, and 705 were fully confirmed according to the SUBA5 database. Interestingly, although 92% of plastidial proteins were equally distributed between the two tissues, we observed an accumulation of proteins associated with jasmonic acid biosynthesis, plastoglobuli (e.g. NAD(P)H dehydrogenase C1, vitamin E deficient 1, plastoglobulin of 34 kDa, ABC1-like kinase 1) and cyclic electron flow in plastids originating from vascular tissue. Besides demonstrating the technical feasibility of isolating plastids in a tissue-specific manner, our work provides strong evidence that plastids from vascular tissue have a higher redox turnover to ensure optimal functioning, notably under high solute strength as encountered in vascular cells.
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15.
  • Bozhkov, Peter, et al. (author)
  • Autophagy-related approaches for improving nutrient use efficiency and crop yield protection
  • 2018
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 69, s. 1335-1353
  • Research review (peer-reviewed)abstract
    • Autophagy is a eukaryotic catabolic pathway essential for growth and development. In plants, it is activated in response to environmental cues or developmental stimuli. However, in contrast to other eukaryotic systems, we know relatively little regarding the molecular players involved in autophagy and the regulation of this complex pathway. In the framework of the COST (European Cooperation in Science and Technology) action TRANSAUTOPHAGY (2016-2020), we decided to review our current knowledge of autophagy responses in higher plants, with emphasis on knowledge gaps. We also assess here the potential of translating the acquired knowledge to improve crop plant growth and development in a context of growing social and environmental challenges for agriculture in the near future.
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16.
  • Bozhkov, Peter, et al. (author)
  • Concentrating and sequestering biomolecules in condensates: impact on plant biology
  • 2023
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 74, s. 1303-1308
  • Journal article (peer-reviewed)abstract
    • Biomolecules can exist in a variety of forms, ranging from single entities to mesoscale assemblies akin to small organelles, also known as ‘biomolecular condensates’. The formation of biomolecular condensates is expedited by phase separation, in which molecules de-mix to form dilute and condensed phases. Phase separation results in concentrating or sequestering certain molecules, thus altering their abundance or other features in the phases and in this way inhibiting or promoting biochemical reactions. Here, we discuss recent research implicating biomolecular condensates in the regulation of biochemical reactions in plants.
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17.
  • Bozhkov, Peter (author)
  • Plant autophagy: mechanisms and functions
  • 2018
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 69, s. 1281-1285
  • Other publication (peer-reviewed)abstract
    • Autophagy (from Greek: 'self-eating') is a major catabolic process in eukaryotic cells in which cytoplasmic components are collected and delivered to the lysosomes or vacuoles for recycling. It plays a paramount role in plant fitness and immunity. At present, the frontiers of our understanding of the process are extending exponentially, with new, plant-specific mechanisms and functions being uncovered. In this special issue, original research articles and reviews enlighten this knowledge from lipid metabolism and dynamics, membrane trafficking and proteolysis to pathogen-mediated modulation of the process and the emerging role of autophagy-related approaches in crop improvement.
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18.
  • Bozhkov, Peter (author)
  • Somatic embryogenesis: life and death processes during apical - basal patterning
  • 2014
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 65, s. 1343-1360
  • Research review (peer-reviewed)abstract
    • Early embryos consist of the apical domain which gives rise to the mature embryo and the basal domain which is gradually eliminated by PCD. Molecular pathways regulating development of each domain are reviewed.Somatic embryogenesis (SE) is a process of differentiation of cells into a plant bypassing the fusion of gametes. As such, it represents a very powerful tool in biotechnology for propagation of species with a long reproductive cycle or low seed set and production of genetically modified plants with improved traits. SE is also a versatile model to study cellular and molecular mechanisms of plant embryo patterning. The morphology and molecular regulation of SE resemble those of zygotic embryogenesis and begin with establishment of apicalbasal asymmetry. The apical domain, the embryo proper, proliferates and eventually gives rise to the plantlet, while the basal part, the embryo suspensor, is terminally differentiated and gradually removed via vacuolar programmed cell death (PCD). This PCD is essential for normal development of the apical domain. Emerging evidence demonstrates that signalling events in the apical and basal domains share homologous components. Here we provide an overview of the main pathways controlling the life and death events during SE.
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19.
  • Brouwer, Bastiaan, et al. (author)
  • In response to partial plant shading, the lack of phytochrome A does not directly induce leaf senescence but alters the fine-tuning of chlorophyll biosynthesis
  • 2014
  • In: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 65:14, s. 4037-4049
  • Journal article (peer-reviewed)abstract
    • 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.
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20.
  • Bygdell, Joakim, et al. (author)
  • Protein expression in tension wood formation monitored at high tissue resolution in Populus
  • 2017
  • In: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 68:13, s. 3405-3417
  • Journal article (peer-reviewed)abstract
    • Tension wood (TW) is a specialized tissue with contractile properties that is formed by the vascular cambium in response to gravitational stimuli. We quantitatively analysed the proteomes of Populus tremula cambium and its xylem cell derivatives in stems forming normal wood (NW) and TW to reveal the mechanisms underlying TW formation. Phloem-, cambium-, and wood-forming tissues were sampled by tangential cryosectioning and pooled into nine independent samples. The proteomes of TW and NW samples were similar in the phloem and cambium samples, but diverged early during xylogenesis, demonstrating that reprogramming is an integral part of TW formation. For example, 14-3-3, reactive oxygen species, ribosomal and ATPase complex proteins were found to be up-regulated at early stages of xylem differentiation during TW formation. At later stages of xylem differentiation, proteins involved in the biosynthesis of cellulose and enzymes involved in the biosynthesis of rhamnogalacturonan-I, rhamnogalacturonan-II, arabinogalactan-II and fasciclin-like arabinogalactan proteins were up-regulated in TW. Surprisingly, two isoforms of exostosin family proteins with putative xylan xylosyl transferase function and several lignin biosynthesis proteins were also up-regulated, even though xylan and lignin are known to be less abundant in TW than in NW. These data provided new insight into the processes behind TW formation.
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21.
  • Capovilla, Giovanna, et al. (author)
  • Contribution of major FLM isoforms to temperature-dependent flowering in Arabidopsis thaliana
  • 2017
  • In: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 68:18, s. 5117-5127
  • Journal article (peer-reviewed)abstract
    • 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.
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22.
  • Capovilla, Giovanna, et al. (author)
  • Control of flowering by ambient temperature
  • 2015
  • In: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 66:1, s. 59-69
  • Journal article (peer-reviewed)abstract
    • 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.
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23.
  • Carlsbecker, Annelie, 1972-, et al. (author)
  • Xylem versus phloem in secondary growth : a balancing act mediated by gibberellins
  • 2021
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 72:10, s. 3489-3492
  • Journal article (other academic/artistic)abstract
    • Secondary growth generates wood, which constitutes most of the plant biomass. Despite considerable efforts over the last decade to uncover the genetic and molecular regulation of the vascular cambium, there is still much to learn about how it produces wood (xylem) inward and bast (phloem) outward. Ben-Targem et al. (2021) now provide novel insight into how the hormones auxin and gibberellic acid (GA) govern the activity of the cambium, promoting a transition from formation of equal amounts of xylem and phloem to a stage where xylem formation dominates phloem in Arabidopsis hypocotyls, resembling wood formation in trees.
  •  
24.
  • Carlsson, Gunilla H., et al. (author)
  • The elusive ligand complexes of the DWARF14 strigolactone receptor
  • 2018
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 69:9, s. 2345-2354
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
25.
  • Chawade, Aakash, et al. (author)
  • Functional phenomics for improved climate resilience in Nordic agriculture
  • 2022
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431.
  • Research review (peer-reviewed)abstract
    • The five Nordic countries span the most northern region for field cultivation in the world. This presents challenges per se, with short growing seasons, long days, and a need for frost tolerance. Climate change has additionally increased risks for micro-droughts and water logging, as well as pathogens and pests expanding northwards. Thus, Nordic agriculture demands crops that are adapted to the specific Nordic growth conditions and future climate scenarios. A focus on crop varieties and traits important to Nordic agriculture, including the unique resource of nutritious wild crops, can meet these needs. In fact, with a future longer growing season due to climate change, the region could contribute proportionally more to global agricultural production. This also applies to other northern regions, including the Arctic. To address current growth conditions, mitigate impacts of climate change, and meet market demands, the adaptive capacity of crops that both perform well in northern latitudes and are more climate resilient has to be increased, and better crop management systems need to be built. This requires functional phenomics approaches that integrate versatile high-throughput phenotyping, physiology, and bioinformatics. This review stresses key target traits, the opportunities of latitudinal studies, and infrastructure needs for phenotyping to support Nordic agriculture.
  •  
26.
  • Cheregi, Otilia, et al. (author)
  • Presence of state transitions in the cryptophyte alga Guillardia theta
  • 2015
  • In: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 66:20, s. 6461-6470
  • Journal article (peer-reviewed)abstract
    • Plants and algae have developed various regulatory mechanisms for optimal delivery of excitation energy to the photosystems even during fluctuating light conditions; these include state transitions as well as non-photochemical quenching. The former process maintains the balance by redistributing antennae excitation between the photosys-tems, meanwhile the latter by dissipating excessive excitation inside the antennae. In the present study, these mecha-nisms have been analysed in the cryptophyte alga Guillardia theta. Photoprotective non-photochemical quenching was observed in cultures only after they had entered the stationary growth phase. These cells displayed a diminished overall photosynthetic efficiency, measured as CO2 assimilation rate and electron transport rate. However, in the logarithmic growth phase G. theta cells redistributed excitation energy via a mechanism similar to state transitions. These state transitions were triggered by blue light absorbed by the membrane integrated chlorophyll a/c antennae, and green light absorbed by the lumenal biliproteins was ineffective. It is proposed that state transitions in G. thetaare induced by small re-arrangements of the intrinsic antennae proteins, resulting in their coupling/uncoupling to the photosystems in state 1 or state 2, respectively. G. theta therefore represents a chromalveolate algae able to perform state transitions.
  •  
27.
  • Crawford, Tim, et al. (author)
  • The role of retrograde signals during plant stress responses
  • 2018
  • In: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 69:11, s. 2783-2795
  • Research review (peer-reviewed)abstract
    • 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.
  •  
28.
  • Dauphinee, Adrian (author)
  • Hsp70 plays a role in programmed cell death during the remodelling of leaves of the lace plant (Aponogeton madagascariensis)
  • 2020
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 71, s. 907-918
  • Journal article (peer-reviewed)abstract
    • Lace plant leaves utilize programmed cell death (PCD) to form perforations during development. The role of heat shock proteins (Hsps) in PCD during lace plant leaf development is currently unknown. Hsp70 amounts were measured throughout lace plant leaf development, and the results indicate that it is highest before and during PCD. Increased Hsp70 amounts correlate with raised anthocyanin content and caspase-like protease (CLP) activity. To investigate the effects of Hsp70 on leaf development, whole plants were treated with either of the known regulators of PCD [reactive oxygen species (ROS) or antioxidants] or an Hsp70 inhibitor, chlorophenylethynylsulfonamide (PES-Cl). ROS treatment significantly increased Hsp70 2-fold and CLP activity in early developing leaves, but no change in anthocyanin and the number of perforations formed was observed. Antioxidant treatment significantly decreased Hsp70, anthocyanin, and CLP activity in early leaves, resulting in the fewest perforations. PES-Cl (25 mu M) treatment significantly increased Hsp70 4-fold in early leaves, while anthocyanin, superoxide, and CLP activity significantly declined, leading to fewer perforations. Results show that significantly increased (4-fold) or decreased Hsp70 amounts lead to lower anthocyanin and CLP activity, inhibiting PCD induction. Our data support the hypothesis that Hsp70 plays a role in regulating PCD at a threshold in lace plant leaf development.
  •  
29.
  • de Jonge, Jennifer, et al. (author)
  • Salicylic acid interferes with GFP fluorescence in vivo
  • 2017
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 68, s. 1689-1696
  • Journal article (peer-reviewed)abstract
    • Fluorescent proteins have become essential tools for cell biologists. They are routinely used by plant biologists for protein and promoter fusions to infer protein localization, tissue-specific expression and protein abundance. When studying the effects of biotic stress on chromatin, we unexpectedly observed a decrease in GFP signal intensity upon salicylic acid (SA) treatment in Arabidopsis lines expressing histone H1-GFP fusions. This GFP signal decrease was dependent on SA concentration. The effect was not specific to the linker histone H1-GFP fusion but was also observed for the nucleosomal histone H2A-GFP fusion. This result prompted us to investigate a collection of fusion proteins, which included different promoters, subcellular localizations and fluorophores. In all cases, fluorescence signals declined strongly or disappeared after SA application. No changes were detected in GFP-fusion protein abundance when fluorescence signals were lost indicating that SA does not interfere with protein stability but GFP fluorescence. In vitro experiments showed that SA caused GFP fluorescence reduction only in vivo but not in vitro, suggesting that SA requires cellular components to cause fluorescence reduction. Together, we conclude that SA can interfere with the fluorescence of various GFP-derived reporter constructs in vivo. Assays that measure relocation or turnover of GFP-tagged proteins upon SA treatment should therefore be evaluated with caution.
  •  
30.
  • DELUCIA, EH, et al. (author)
  • THE POTENTIAL FOR PHOTOINHIBITION OF PINUS-SYLVESTRIS L SEEDLINGS EXPOSED TO HIGH LIGHT AND LOW SOIL-TEMPERATURE
  • 1991
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 42:238, s. 611-617
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
31.
  • Derkacheva, Maria, et al. (author)
  • Variations on a theme: Polycomb group proteins in plants
  • 2014
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 65, s. 2769-2784
  • Research review (peer-reviewed)abstract
    • Polycomb group (PcG) proteins evolved early in evolution, probably in the common ancestor of animals and plants. In some unicellular organisms, such as Chlamydomonas and Tetrahymena, PcG proteins silence genes in heterochromatin, suggesting an ancestral function in genome defence. In angiosperms, the PcG system controls many developmental transitions. A PcG function in the vernalization response evolved especially in Brassicaceaea. Thus, the role of PcG proteins has changed during evolution to match novel needs. Recent studies identified many proteins associated with plant PcG protein complexes. Possible functions of these interactions are discussed here. We highlight recent findings about recruitment of PcG proteins in plants in comparison with animal system. Through the new data, a picture emerges in which PcG protein complexes do not function in sequential linear pathways but as dynamically interacting networks allowing stabilizing feedback loops. We discuss how the interplay between different PcG protein complexes can enable establishment, maintenance, and epigenetic inheritance of H3K27me3.
  •  
32.
  • Dikaya, Varvara, et al. (author)
  • Insights into the role of alternative splicing in plant temperature response
  • 2021
  • In: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 72:21, s. 7384-7403
  • Research review (peer-reviewed)abstract
    • Alternative splicing occurs in all eukaryotic organisms. Since the first description of multiexon genes and the splicing machinery, the field has expanded rapidly, especially in animals and yeast. However, our knowledge about splicing in plants is still quite fragmented. Though eukaryotes show some similarity in the composition and dynamics of their splicing machinery, observations of unique plant traits are only starting to emerge. For instance, plant alternative splicing is closely linked to their ability to perceive various environmental stimuli. Due to their sessile lifestyle, temperature is a central source of information, allowing plants to adjust their development to match current growth conditions. Hence, seasonal temperature fluctuations and day-night cycles can strongly influence plant morphology across developmental stages. Here we discuss available data on temperature-dependent alternative splicing in plants. Given its fragmented state, it is not always possible to fit specific observations into a coherent picture, yet it is sufficient to estimate the complexity of this field and the need for further research. Better understanding of alternative splicing as a part of plant temperature response and adaptation may also prove to be a powerful tool for both fundamental and applied sciences.
  •  
33.
  • Dinant, S., et al. (author)
  • Synchrotron FTIR and Raman spectroscopy provide unique spectral fingerprints for Arabidopsis floral stem vascular tissues
  • 2019
  • In: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 70:3, s. 871-883
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
34.
  • Dob, Asma, et al. (author)
  • Jasmonate inhibits adventitious root initiation through repression of CKX1 and activation of RAP2.6L transcription factor in Arabidopsis
  • 2021
  • In: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 72:20, s. 7107-7118
  • Journal article (peer-reviewed)abstract
    • Adventitious rooting is a de novo organogenesis process that enables plants to propagate clonally and cope with environmental stresses. Adventitious root initiation (ARI) is controlled by interconnected transcriptional and hormonal networks, but there is little knowledge of the genetic and molecular programs orchestrating these networks. Thus, we have applied genome-wide transcriptome profiling to elucidate the transcriptional reprogramming events preceding ARI. These reprogramming events are associated with the down-regulation of cytokinin (CK) signaling and response genes, which could be triggers for ARI. Interestingly, we found that CK free base (iP, tZ, cZ, and DHZ) content declined during ARI, due to down-regulation of de novo CK biosynthesis and up-regulation of CK inactivation pathways. We also found that MYC2-dependent jasmonate (JA) signaling inhibits ARI by down-regulating the expression of the CYTOKININ OXIDASE/DEHYDROGENASE1 (CKX1) gene. We also demonstrated that JA and CK synergistically activate expression of the transcription factor RELATED to APETALA2.6 LIKE (RAP2.6L), and constitutive expression of this transcription factor strongly inhibits ARI. Collectively, our findings reveal that previously unknown genetic interactions between JA and CK play key roles in ARI.
  •  
35.
  • Dockter, Christoph, et al. (author)
  • Improving barley culm robustness for secured crop yield in a changing climate.
  • 2015
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 66:12, s. 3499-3509
  • Research review (peer-reviewed)abstract
    • The Green Revolution combined advancements in breeding and agricultural practice, and provided food security to millions of people. Daily food supply is still a major issue in many parts of the world and is further challenged by future climate change. Fortunately, life science research is currently making huge progress, and the development of future crop plants will be explored. Today, plant breeding typically follows one gene per trait. However, new scientific achievements have revealed that many of these traits depend on different genes and complex interactions of proteins reacting to various external stimuli. These findings open up new possibilities for breeding where variations in several genes can be combined to enhance productivity and quality. In this review we present an overview of genes determining plant architecture in barley, with a special focus on culm length. Many genes are currently known only through their mutant phenotypes, but emerging genomic sequence information will accelerate their identification. More than 1000 different short-culm barley mutants have been isolated and classified in different phenotypic groups according to culm length and additional pleiotropic characters. Some mutants have been connected to deficiencies in biosynthesis and reception of brassinosteroids and gibberellic acids. Still other mutants are unlikely to be connected to these hormones. The genes and corresponding mutations are of potential interest for development of stiff-straw crop plants tolerant to lodging, which occurs in extreme weather conditions with strong winds and heavy precipitation.
  •  
36.
  • Doyle, Siamsa, et al. (author)
  • Small molecules unravel complex interplay between auxin biology and endomembrane trafficking
  • 2015
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 66, s. 4971-4982
  • Research review (peer-reviewed)abstract
    • The establishment and maintenance of controlled auxin gradients within plant tissues are essential for a multitude of developmental processes. Auxin gradient formation is co-ordinated via local biosynthesis and transport. Cell to cell auxin transport is facilitated and precisely regulated by complex endomembrane trafficking mechanisms that target auxin carrier proteins to their final destinations. In turn, auxin and cross-talk with other phytohormones regulate the endomembrane trafficking of auxin carriers. Dissecting such rapid and complicated processes is challenging for classical genetic experiments due to trafficking pathway diversity, gene functional redundancy, and lethality in lossof-function mutants. Many of these difficulties can be bypassed via the use of small molecules to modify or disrupt the function or localization of proteins. Here, we will review examples of the knowledge acquired by the use of such chemical tools in this field, outlining the advantages afforded by chemical biology approaches.
  •  
37.
  • Eklund, D. Magnus, et al. (author)
  • Physcomitrella patens : a model to investigate the role of RAC/ROP GTPase signalling in tip growth
  • 2010
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 61:7, s. 1917-1937
  • Research review (peer-reviewed)abstract
    • 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.
  •  
38.
  • Ekman, Asa, et al. (author)
  • Carbon partitioning between oil and carbohydrates in developing oat (Avena sativa L.) seeds
  • 2008
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 59:15, s. 4247-4257
  • Journal article (peer-reviewed)abstract
    • Cereals accumulate starch in the endosperm as their major energy reserve in the grain. In most cereals the embryo, scutellum, and aleurone layer are high in oil, but these tissues constitute a very small part of the total seed weight. However, in oat (Avena sativa L.) most of the oil in kernels is deposited in the same endosperm cells that accumulate starch. Thus oat endosperm is a desirable model system to study the metabolic switches responsible for carbon partitioning between oil and starch synthesis. A prerequisite for such investigations is the development of an experimental system for oat that allows for metabolic flux analysis using stable and radioactive isotope labelling. An in vitro liquid culture system, developed for detached oat panicles and optimized to mimic kernel composition during different developmental stages in planta, is presented here. This system was subsequently used in analyses of carbon partitioning between lipids and carbohydrates by the administration of C-14-labelled sucrose to two cultivars having different amounts of kernel oil. The data presented in this study clearly show that a higher amount of oil in the high-oil cultivar compared with the medium-oil cultivar was due to a higher proportion of carbon partitioning into oil during seed filling, predominantly at the earlier stages of kernel development.
  •  
39.
  •  
40.
  • Elander, Pernilla, et al. (author)
  • Autophagy in turnover of lipid stores: trans-kingdom comparison
  • 2018
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 69, s. 1301-1311
  • Research review (peer-reviewed)abstract
    • Lipids and their cellular utilization are essential for life. Not only are lipids energy storage molecules, but their diverse structural and physical properties underlie various aspects of eukaryotic biology, such as membrane structure, signalling, and trafficking. In the ever-changing environment of cells, lipids, like other cellular components, are regularly recycled to uphold the housekeeping processes required for cell survival and organism longevity. The ways in which lipids are recycled, however, vary between different phyla. For example, animals and plants have evolved distinct lipid degradation pathways. The major cell recycling system, autophagy, has been shown to be instrumental for both differentiation of specialized fat storing-cells, adipocytes, and fat degradation in animals. Does plant autophagy play a similar role in storage and degradation of lipids? In this review, we discuss and compare implications of bulk autophagy and its selective route, lipophagy, in the turnover of lipid stores in animals, fungi, and plants.
  •  
41.
  • Escamez, Sacha, 1987-, et al. (author)
  • Extracellular peptide Kratos restricts cell death during vascular development and stress in Arabidopsis
  • 2019
  • In: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 70:7, s. 2199-2210
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
42.
  • Escamez, Sacha, et al. (author)
  • Programmes of cell death and autolysis in tracheary elements : when a suicidal cell arranges its own corpse removal
  • 2014
  • In: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 65:5, s. 1313-1321
  • Research review (peer-reviewed)abstract
    • 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.
  •  
43.
  • Fan, Kaijian, et al. (author)
  • The pentatricopeptide repeat protein EMP603 is required for the splicing of mitochondrial Nad1 intron 2 and seed development in maize
  • 2021
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 72:20, s. 6933-6948
  • Journal article (peer-reviewed)abstract
    • Intron splicing is an essential event in post-transcriptional RNA processing in plant mitochondria, which requires the participation of diverse nuclear-encoded splicing factors. However, it is presently unclear how these proteins cooperatively take part in the splicing of specific introns. In this study, we characterized a nuclear-encoded mitochondrial P-type pentatricopeptide repeat (PPR) protein named EMP603. This protein is essential for splicing of intron 2 in the Nad1 gene and interacts with the mitochondria-localized DEAD-box RNA helicase PMH2-5140, the RAD52-like proteins ODB1-0814 and ODB1-5061, and the CRM domain-containing protein Zm-mCSF1. Further study revealed that the N-terminal region of EMP603 interacts with the DEAD-box of PMH2-5140, the CRM domain of Zm-mCSF1, and OBD1-5061, but not with OBD1-0814, whereas the PPR domain of EMP603 can interact with ODB1-0814, ODB1-5061, and PMH2-5140, but not with Zm-mCSF1. Defects in EMP603 severely disrupt the assembly and activity of mitochondrial complex I, leading to impaired mitochondrial function, and delayed seed development. The interactions revealed between EMP603 and PMH2-5140, ODB1-0814, ODB1-5061, and Zm-mCSF1 indicate a possible involvement of a dynamic 'spliceosome-like' complex in intron splicing, and may accelerate the elucidation of the intron splicing mechanism in plant mitochondria.
  •  
44.
  • Forsberg, Simon K. G., et al. (author)
  • On the relationship between epistasis and genetic variance heterogeneity.
  • 2017
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 68:20, s. 5431-5438
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
45.
  • Fricke, W, et al. (author)
  • The short-term growth response to salt of the developing barley leaf
  • 2006
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 57:5, s. 1079-1095
  • Journal article (peer-reviewed)abstract
    • Recent results concerning the short-term growth response to salinity of the developing barley leaf are reviewed. Plants were grown hydroponically and the growth response of leaf 3 was studied between 10 min and 5 d following addition of 100 mM NaCl to the root medium. The aim of the experiments was to relate changes in variables that are likely to affect cell elongation to changes in leaf growth. Changes in hormone content (ABA, cytokinins), water and solute relationships (osmolality, turgor, water potential, solute concentrations), gene expression (water channel), cuticle deposition, membrane potential, and transpiration were followed, while leaf elongation velocity was monitored. Leaf elongation decreased close to zero within seconds following addition of NaCl. Between 20 and 30 min after exposure to salt, elongation velocity recovered rather abruptly, to about 46% of the pre-stress level, and remained at the reduced rate for the following 5 d, when it reached about 70% of the level in non-stressed plants. Biophysical and physiological analyses led to three major conclusions. (i) The immediate reduction and sudden recovery in elongation velocity is due to changes in the water potential gradient between leaf xylem and peripheral elongating cells. Changes in transpiration, ABA and cytokinin content, water channel expression, and plasma membrane potential are involved in this response. (ii) Significant solute accumulation, which aids growth recovery, is detectable from 1 h onwards; growing and non-growing leaf regions and mesophyll and epidermis differ in their solute response. (iii) Cuticular wax density is not affected by short-term exposure to salt; transpirational changes are due to stomatal control.
  •  
46.
  • Fristedt, R., et al. (author)
  • PSB33 sustains photosystem II D1 protein under fluctuating light conditions
  • 2017
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 68:15, s. 4281-4293
  • Journal article (peer-reviewed)abstract
    • On Earth, solar irradiance varies as the sun rises and sets over the horizon, and sunlight is thus in constant fluctuation, following a slow dark-low-high-low-dark curve. Optimal plant growth and development are dependent on the capacity of plants to acclimate and regulate photosynthesis in response to these changes of light. Little is known of regulative processes for photosynthesis during nocturnal events. The nucleus-encoded plant lineage-specific protein PSB33 has been described as stabilizing the photosystem II complex, especially under light stress conditions, and plants lacking PSB33 have a dysfunctional state transition. To clarify the localization and function of this protein, we used phenomic, biochemical and proteomics approaches in the model plant Arabidopsis. We report that PSB33 is predominantly located in non-appressed thylakoid regions and dynamically associates with a thylakoid protein complex in a light-dependent manner. Moreover, plants lacking PSB33 show an accelerated D1 protein degradation in nocturnal periods, and show severely stunted growth when challenged with fluctuating light. We further show that the function of PSB33 precedes the STN7 kinase to regulate or balance the excitation energy of photosystems I and II in fluctuating light conditions.
  •  
47.
  • Fritioff, Åsa, et al. (author)
  • Fate of Cadmium in Elodea canadensis
  • 2007
  • In: Journal of Experimental Botany. - : Elsevier BV. - 0022-0957 .- 1460-2431. ; 67:2, s. 365-375
  • Journal article (peer-reviewed)abstract
    • 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 .
  •  
48.
  • Gaston, Amelia, et al. (author)
  • PFRU, a single dominant locus regulates the balance between sexual and asexual plant reproduction in cultivated strawberry
  • 2013
  • In: Journal of Experimental Botany. - : OXFORD UNIV PRESS. - 0022-0957 .- 1460-2431. ; 64:7, s. 1837-1848
  • Journal article (peer-reviewed)abstract
    • Strawberry (Fragaria sp.) stands as an interesting model for studying flowering behaviour and its relationship with asexual plant reproduction in polycarpic perennial plants. Strawberry produces both inflorescences and stolons (also called runners), which are lateral stems growing at the soil surface and producing new clone plants. In this study, the flowering and runnering behaviour of two cultivated octoploid strawberry (Fragariaananassa Duch., 2n856) genotypes, a seasonal flowering genotype CF1116 and a perpetual flowering genotype Capitola, were studied along the growing season. The genetic bases of the perpetual flowering and runnering traits were investigated further using a pseudo full-sibling F1 population issued from a cross between these two genotypes. The results showed that a single major quantitative trait locus (QTL) named FaPFRU controlled both traits in the cultivated octoploid strawberry. This locus was not orthologous to the loci affecting perpetual flowering (SFL) and runnering (R) in Fragaria vesca, therefore suggesting different genetic control of perpetual flowering and runnering in the diploid and octoploid Fragaria spp. Furthermore, the FaPFRU QTL displayed opposite effects on flowering (positive effect) and on runnering (negative effect), indicating that both traits share common physiological control. These results suggest that this locus plays a major role in strawberry plant fitness by controlling the balance between sexual and asexual plant reproduction.
  •  
49.
  • Gentili, Francesco, et al. (author)
  • Physiological and molecular diversity of feather moss associative N2-fixing cyanobacteria.
  • 2005
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 56:422, s. 3121-7
  • Journal article (peer-reviewed)abstract
    • Cyanobacteria colonizing the feather moss Pleurozium schreberi were isolated from moss samples collected in northern Sweden and subjected to physiological and molecular characterization. Morphological studies of isolated and moss-associated cyanobacteria were carried out by light microscopy. Molecular tools were used for cyanobacteria identification, and a reconstitution experiment of the association between non-associative mosses and cyanobacteria was conducted. The influence of temperature on N2 fixation in the different cyanobacterial isolates and the influence of light and temperature on N2-fixation rates in the moss were studied using the acetylene reduction assay. Two different cyanobacteria were effectively isolated from P. schreberi: Nostoc sp. and Calothrix sp. A third genus, Stigonema sp. was identified by microscopy, but could not be isolated. The Nostoc sp. was found to fix N2 at lower temperatures than Calothrix sp. Nostoc sp. and Stigonema sp. were the predominant cyanobacteria colonizing the moss. The attempt to reconstitute the association between the moss and cyanobacteria was successful. The two isolated genera of cyanobacteria in feather moss samples collected in northern Sweden differ in their temperature optima, which may have important ecological implications.
  •  
50.
  • Ghifari, Abi S., et al. (author)
  • The dual-targeted prolyl aminopeptidase PAP1 is involved in proline accumulation in response to stress and during pollen development
  • 2022
  • In: Journal of Experimental Botany. - : Oxford University Press (OUP). - 0022-0957 .- 1460-2431. ; 73:1, s. 78-93
  • Journal article (peer-reviewed)abstract
    • Plant endosymbiotic organelles such as mitochondria and chloroplasts harbour a wide array of biochemical reactions. As a part of protein homeostasis to maintain organellar activity and stability, unwanted proteins and peptides need to be completely degraded in a stepwise mechanism termed the processing pathway, where at the last stage single amino acids are released by aminopeptidases. Here, we determined the molecular and physiological functions of a prolyl aminopeptidase homologue PAP1 (At2g14260) that is able to release N-terminal proline. Transcript analyses demonstrate that an alternative transcription start site gives rise to two alternative transcripts, generating two in-frame proteins PAP1.1 and PAP1.2. Subcellular localization studies revealed that the longer isoform PAP1.1, which contains a 51 residue N-terminal extension, is exclusively targeted to chloroplasts, while the truncated isoform PAP1.2 is located in the cytosol. Distinct expression patterns in different tissues and developmental stages were observed. Investigations into the physiological role of PAP1 using loss-of-function mutants revealed that PAP1 activity may be involved in proline homeostasis and accumulation, required for pollen development and tolerance to osmotic stress. Enzymatic activity, subcellular location, and expression patterns of PAP1 suggest a role in the chloroplastic peptide processing pathway and proline homeostasis.
  •  
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