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1.
  • Amstutz, Cynthia L., et al. (author)
  • An atypical short-chain dehydrogenase–reductase functions in the relaxation of photoprotective qH in Arabidopsis
  • 2020
  • In: Nature Plants. - : Nature Publishing Group. - 2055-026X .- 2055-0278. ; 6, s. 154-166
  • Journal article (peer-reviewed)abstract
    • Photosynthetic organisms experience wide fluctuations in light intensity and regulate light harvesting accordingly to prevent damage from excess energy. The antenna quenching component qH is a sustained form of energy dissipation that protects the photosynthetic apparatus under stress conditions. This photoprotective mechanism requires the plastid lipocalin LCNP and is prevented by SUPPRESSOR OF QUENCHING1 (SOQ1) under non-stress conditions. However, the molecular mechanism of qH relaxation has yet to be resolved. Here, we isolated and characterized RELAXATION OF QH1 (ROQH1), an atypical short-chain dehydrogenase–reductase that functions as a qH-relaxation factor in Arabidopsis. The ROQH1 gene belongs to the GreenCut2 inventory specific to photosynthetic organisms, and the ROQH1 protein localizes to the chloroplast stroma lamellae membrane. After a cold and high-light treatment, qH does not relax in roqh1 mutants and qH does not occur in leaves overexpressing ROQH1. When the soq1 and roqh1 mutations are combined, qH can neither be prevented nor relaxed and soq1 roqh1 displays constitutive qH and light-limited growth. We propose that LCNP and ROQH1 perform dosage-dependent, antagonistic functions to protect the photosynthetic apparatus and maintain light-harvesting efficiency in plants.
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2.
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3.
  • Bhalerao, Rishikesh P. (author)
  • Root hydrotropism is controlled via a cortex-specific growth mechanism
  • 2017
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 3
  • Journal article (peer-reviewed)abstract
    • Plants can acclimate by using tropisms to link the direction of growth to environmental conditions. Hydrotropism allows roots to forage for water, a process known to depend on abscisic acid (ABA) but whose molecular and cellular basis remains unclear. Here we show that hydrotropism still occurs in roots after laser ablation removed the meristem and root cap. Additionally, targeted expression studies reveal that hydrotropism depends on the ABA signalling kinase SnRK2.2 and the hydrotropism-specific MIZ1, both acting specifically in elongation zone cortical cells. Conversely, hydrotropism, but not gravitropism, is inhibited by preventing differential cell-length increases in the cortex, but not in other cell types. We conclude that root tropic responses to gravity and water are driven by distinct tissue-based mechanisms. In addition, unlike its role in root gravitropism, the elongation zone performs a dual function during a hydrotropic response, both sensing a water potential gradient and subsequently undergoing differential growth.
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4.
  • Bourdon, Matthieu, et al. (author)
  • Ectopic callose deposition into woody biomass modulates the nano-architecture of macrofibrils
  • 2023
  • In: Nature Plants. - : Springer Nature. - 2055-0278 .- 2055-026X. ; 9:9, s. 1530-1546
  • Journal article (peer-reviewed)abstract
    • Plant biomass plays an increasingly important role in the circular bioeconomy, replacing non-renewable fossil resources. Genetic engineering of this lignocellulosic biomass could benefit biorefinery transformation chains by lowering economic and technological barriers to industrial processing. However, previous efforts have mostly targeted the major constituents of woody biomass: cellulose, hemicellulose and lignin. Here we report the engineering of wood structure through the introduction of callose, a polysaccharide novel to most secondary cell walls. Our multiscale analysis of genetically engineered poplar trees shows that callose deposition modulates cell wall porosity, water and lignin contents and increases the lignin–cellulose distance, ultimately resulting in substantially decreased biomass recalcitrance. We provide a model of the wood cell wall nano-architecture engineered to accommodate the hydrated callose inclusions. Ectopic polymer introduction into biomass manifests in new physico-chemical properties and offers new avenues when considering lignocellulose engineering.
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5.
  • Camara-Leret, R., et al. (author)
  • Fundamental species traits explain provisioning services of tropical American palms
  • 2017
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 3:2
  • Journal article (peer-reviewed)abstract
    • The well-being of the global human population rests on provisioning services delivered by 12% of the Earth's similar to 400,000 plant species(1). Plant utilization by humans is influenced by species traits(2-4), but it is not well understood which traits underpin different human needs(5). Here, we focus on palms (Arecaceae), one of the most economically important plant groups globally(6), and demonstrate that provisioning services related to basic needs, such as food and medicine, show a strong link to fundamental functional and geographic traits. We integrate data from 2,201 interviews on plant utilization from three biomes in South America-spanning 68 communities, 43 ethnic groups and 2,221 plant uses-with a dataset of 4 traits (leaf length, stem volume, fruit volume, geographic range size) and a species-level phylogeny(7). For all 208 palm species occurring in our study area, we test for relations between their traits and perceived value. We find that people preferentially use large, widespread species rather than small, narrow-ranged species, and that different traits are linked to different uses. Further, plant size and geographic range size are stronger predictors of ecosystem service realization for palm services related to basic human needs than less-basic needs (for example, ritual). These findings suggest that reliance on plant size and availability may have prevented our optimal realization of wild-plant services, since ecologically rare yet functionally important (for example, chemically) clades may have been overlooked. Beyond expanding our understanding of how local people use biodiversity in mega-diverse regions, our traitand phylogeny-based approach helps to understand the processes that underpin ecosystem service realization, a necessary step to meet societal needs in a changing world with a growing human population(5,8).
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6.
  • Capovilla, Giovanna, et al. (author)
  • PORCUPINE regulates development in response to temperature through alternative splicing
  • 2018
  • In: Nature plants. - : Nature Publishing Group. - 2055-026X .- 2055-0278. ; 4:8, s. 534-539
  • Journal article (peer-reviewed)abstract
    • Recent findings suggest that alternative splicing has a critical role in controlling the responses of plants to temperature variations. However, alternative splicing factors in plants are largely uncharacterized. Here we establish the putative splice regulator, PORCUPINE (PCP), as temperature-specific regulator of development in Arabidopsis thaliana. Our findings point to the misregulation of WUSCHEL and CLAVATA3 as the possible cause for the meristem defects affecting the pcp-1 loss-of-function mutants at low temperatures.
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7.
  • Chen, Ming, et al. (author)
  • Distinct structural modulation of photosystem I and lipid environment stabilizes its tetrameric assembly
  • 2020
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 6:3, s. 314-
  • Journal article (peer-reviewed)abstract
    • Photosystem I (PSI) is able to form different oligomeric states across various species. To reveal the structural basis for PSI dimerization and tetramerization, we structurally investigated PSI from the cyanobacterium Anabaena. This revealed a disrupted trimerization domain due to lack of the terminal residues of PsaL in the lumen, which resulted in PSI dimers with loose connections between monomers and weaker energy-coupled chlorophylls than in the trimer. At the dimer surface, specific phospholipids, cofactors and interactions in combination facilitated recruitment of another dimer to form a tetramer. Taken together, the relaxed luminal connections and lipid specificity at the dimer interface account for membrane curvature. PSI tetramer assembly appears to increase the surface area of the thylakoid membrane, which would contribute to PSI crowding. Photosystem I from the cyanobacterium Anabaena has a disrupted trimerization domain resulting in dimers with loose connections between monomers. Phospholipids and cofactors at the dimer surface facilitate further dimerization to form a tetramer.
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8.
  • Conn, Vanessa M., et al. (author)
  • A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation
  • 2017
  • In: Nature Plants. - : Nature Publishing Group. - 2055-026X .- 2055-0278. ; 3:5
  • Journal article (peer-reviewed)abstract
    • Circular RNAs (circRNAs) are a diverse and abundant class of hyper-stable, non-canonical RNAs that arise through a form of alternative splicing (AS) called back-splicing. These single-stranded, covalently-closed circRNA molecules have been identified in all eukaryotic kingdoms of life(1), yet their functions have remained elusive. Here, we report that circRNAs can be used as bona fide biomarkers of functional, exon-skipped AS variants in Arabidopsis, including in the homeotic MADS-box transcription factor family. Furthermore, we demonstrate that circRNAs derived from exon 6 of the SEPALLATA3 (SEP3) gene increase abundance of the cognate exon-skipped AS variant (SEP3.3 which lacks exon 6), in turn driving floral homeotic phenotypes. Toward demonstrating the underlying mechanism, we show that the SEP3 exon 6 circRNA can bind strongly to its cognate DNA locus, forming an RNA: DNA hybrid, or R-loop, whereas the linear RNA equivalent bound significantly more weakly to DNA. R-loop formation results in transcriptional pausing, which has been shown to coincide with splicing factor recruitment and AS(2-4). This report presents a novel mechanistic insight for how at least a subset of circRNAs probably contribute to increased splicing efficiency of their cognate exon-skipped messenger RNA and provides the first evidence of an organismal-level phenotype mediated by circRNA manipulation.
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9.
  • Derkacheva, Maria, et al. (author)
  • H2A deubiquitinases UBP12/13 are part of the Arabidopsis polycomb group protein system
  • 2016
  • In: Nature plants. - 2055-026X .- 2055-0278. ; 2:9
  • Journal article (peer-reviewed)abstract
    • Polycomb group (PcG) proteins form an epigenetic memory system in plants and animals, but interacting proteins are poorly known in plants. Here, we have identified Arabidopsis UBIQUITIN SPECIFIC PROTEASES (USP; UBP in plant and yeasts) 12 and 13 as partners of the plant-specific PcG protein LIKE HETEROCHROMATIN PROTEIN 1 (LHP1). UBP12 binds to chromatin of PcG target genes and is required for histone H3 lysine 27 trimethylation and repression of a subset of PcG target genes. Plants lacking UBP12 and UBP13 developed autonomous endosperm in the absence of fertilization. We have identified UBP12 and UBP13 as new proteins in the plant PcG regulatory network. UBP12 and UBP13 belong to an ancient gene family and represent plant homologues of metazoan USP7. We have found that Drosophila USP7 shares a function in heterochromatic gene repression with UBP12/13 and their homologue UBP26. In summary, we demonstrate that USP7-like proteins are essential for gene silencing in diverse genomic contexts.
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10.
  • Derkacheva, Maria, et al. (author)
  • H2A deubiquitinases UBP12/13 are part of the Arabidopsis polycomb group protein system
  • 2016
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 2
  • Journal article (peer-reviewed)abstract
    • Polycomb group (PcG) proteins form an epigenetic memory system in plants and animals, but interacting proteins are poorly known in plants. Here, we have identified Arabidopsis UBIQUITIN SPECIFIC PROTEASES (USP; UBP in plant and yeasts) 12 and 13 as partners of the plant-specific PcG protein LIKE HETEROCHROMATIN PROTEIN 1 (LHP1). UBP12 binds to chromatin of PcG target genes and is required for histone H3 lysine 27 trimethylation and repression of a subset of PcG target genes. Plants lacking UBP12 and UBP13 developed autonomous endosperm in the absence of fertilization. We have identified UBP12 and UBP13 as new proteins in the plant PcG regulatory network. UBP12 and UBP13 belong to an ancient gene family and represent plant homologues of metazoan USP7. We have found that Drosophila USP7 shares a function in heterochromatic gene repression with UBP12/13 and their homologue UBP26. In summary, we demonstrate that USP7-like proteins are essential for gene silencing in diverse genomic contexts.
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11.
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12.
  • Eriksson, Dennis (author)
  • Options for regulating new genomic techniques for plants in the European Union
  • 2023
  • In: Nature Plants. - 2055-026X .- 2055-0278. ; 9, s. 1958–1961-
  • Journal article (peer-reviewed)abstract
    • Which option for regulating plants derived from new genomic techniques in European Union law is feasible and justifiable scientifically? The European Commission has proposed a new regulation on plants obtained by specific new genomic techniques, which is now subject to discussion in the legislative process. From the perspective of the European Commission's envisaged legal reforms of European Union law towards the integration of greater sustainability, we conclude that the option focusing on plant traits delivering sustainability benefits should be chosen, which is most fitting to facilitate a contribution to climate action, the transition towards climate neutrality, and promptly integrate sustainability into all food-related policies. To assist the decision-making in the legislative process, we outline six regulatory options resulting from regulatory research involving interdisciplinary teams.This Perspective discusses six regulatory options following the proposition of the European Commission to amend European Union's legislation for plants obtained with new genomic techniques.
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13.
  • Feng, Ming, et al. (author)
  • A conserved graft formation process in Norway spruce and Arabidopsis identifies the PAT gene family as central regulators of wound healing
  • 2024
  • In: Nature Plants. - 2055-026X .- 2055-0278. ; 10, s. 53–65-
  • Journal article (peer-reviewed)abstract
    • The widespread use of plant grafting enables eudicots and gymnosperms to join with closely related species and grow as one. Gymnosperms have dominated forests for over 200 million years, and despite their economic and ecological relevance, we know little about how they graft. Here we developed a micrografting method in conifers using young tissues that allowed efficient grafting with closely related species and between distantly related genera. Conifer graft junctions rapidly connected vasculature and differentially expressed thousands of genes including auxin and cell-wall-related genes. By comparing these genes to those induced during Arabidopsis thaliana graft formation, we found a common activation of cambium, cell division, phloem and xylem-related genes. A gene regulatory network analysis in Norway spruce (Picea abies) predicted that PHYTOCHROME A SIGNAL TRANSDUCTION 1 (PAT1) acted as a core regulator of graft healing. This gene was strongly up-regulated during both spruce and Arabidopsis grafting, and Arabidopsis mutants lacking PAT genes failed to attach tissues or successfully graft. Complementing Arabidopsis PAT mutants with the spruce PAT1 homolog rescued tissue attachment and enhanced callus formation. Together, our data show an ability for young tissues to graft with distantly related species and identifies the PAT gene family as conserved regulators of graft healing and tissue regeneration.
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14.
  • Fernandez-Martinez, M., et al. (author)
  • Nutrient scarcity as a selective pressure for mast seeding
  • 2019
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 5:12
  • Journal article (peer-reviewed)abstract
    • Mast seeding is one of the most intriguing reproductive traits in nature. Despite its potential drawbacks in terms of fitness, the widespread existence of this phenomenon suggests that it should have evolutionary advantages under certain circumstances. Using a global dataset of seed production time series for 219 plant species from all of the continents, we tested whether masting behaviour appears predominantly in species with low foliar nitrogen and phosphorus concentrations when controlling for local climate and productivity. Here, we show that masting intensity is higher in species with low foliar N and P concentrations, and especially in those with imbalanced N/P ratios, and that the evolutionary history of masting behaviour has been linked to that of nutrient economy. Our results support the hypothesis that masting is stronger in species growing under limiting conditions and suggest that this reproductive behaviour might have evolved as an adaptation to nutrient limitations and imbalances.
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15.
  • Figueiredo, Duarte, et al. (author)
  • Auxin production couples endosperm development to fertilization
  • 2015
  • In: Nature Plants. - 2055-026X .- 2055-0278. ; 1
  • Journal article (peer-reviewed)abstract
    • In flowering plants, seed development is preceded by a double fertilization event, whereby two male sperm cells fuse with two female gametes: the egg and central cells. The fertilized egg cell will form the embryo, and the fertilized central cell will give rise to the triploid endosperm, whose function is to nourish and support the embryo. Even though the endosperm has an unparalleled role for human nutrition, the molecular bases for its development are yet to be understood. Our results reveal that increasing auxin levels after fertilization drive the replication of the central cell in Arabidopsis thaliana. Auxin is sufficient to trigger central cell division and is necessary for correct endosperm development, a process dependent on the MADS-box transcription factor AGL62 (AGAMOUS-LIKE 62). We propose that the epigenetic regulators of the Polycomb group (PcG) family block central cell division before fertilization by repressing the expression of auxin biosynthesis genes in the female gametophyte.
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16.
  • Franklin, Oskar, et al. (author)
  • Organizing principles for vegetation dynamics
  • 2020
  • In: Nature plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 6:5, s. 444-453
  • Journal article (peer-reviewed)abstract
    • Plants and vegetation play a critical-but largely unpredictable-role in global environmental changes due to the multitude of contributing processes at widely different spatial and temporal scales. In this Perspective, we explore approaches to master this complexity and improve our ability to predict vegetation dynamics by explicitly taking account of principles that constrain plant and ecosystem behaviour: natural selection, self-organization and entropy maximization. These ideas are increasingly being used in vegetation models, but we argue that their full potential has yet to be realized. We demonstrate the power of natural selection-based optimality principles to predict photosynthetic and carbon allocation responses to multiple environmental drivers, as well as how individual plasticity leads to the predictable self-organization of forest canopies. We show how models of natural selection acting on a few key traits can generate realistic plant communities and how entropy maximization can identify the most probable outcomes of community dynamics in space- and time-varying environments. Finally, we present a roadmap indicating how these principles could be combined in a new generation of models with stronger theoretical foundations and an improved capacity to predict complex vegetation responses to environmental change. Integrating natural selection and other organizing principles into next-generation vegetation models could render them more theoretically sound and useful for earth system applications and modelling climate impacts.
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17.
  • Fridman, Jonas, et al. (author)
  • The global biogeography of tree leaf form and habit
  • 2023
  • In: Nature Plants. - 2055-026X .- 2055-0278. ; 9, s. 1795-1809
  • Journal article (peer-reviewed)abstract
    • Understanding what controls global leaf type variation in trees is crucial for comprehending their role in terrestrial ecosystems, including carbon, water and nutrient dynamics. Yet our understanding of the factors influencing forest leaf types remains incomplete, leaving us uncertain about the global proportions of needle-leaved, broadleaved, evergreen and deciduous trees. To address these gaps, we conducted a global, ground-sourced assessment of forest leaf-type variation by integrating forest inventory data with comprehensive leaf form (broadleaf vs needle-leaf) and habit (evergreen vs deciduous) records. We found that global variation in leaf habit is primarily driven by isothermality and soil characteristics, while leaf form is predominantly driven by temperature. Given these relationships, we estimate that 38% of global tree individuals are needle-leaved evergreen, 29% are broadleaved evergreen, 27% are broadleaved deciduous and 5% are needle-leaved deciduous. The aboveground biomass distribution among these tree types is approximately 21% (126.4Gt), 54% (335.7Gt), 22% (136.2Gt) and 3% (18.7Gt), respectively. We further project that, depending on future emissions pathways, 17-34% of forested areas will experience climate conditions by the end of the century that currently support a different forest type, highlighting the intensification of climatic stress on existing forests. By quantifying the distribution of tree leaf types and their corresponding biomass, and identifying regions where climate change will exert greatest pressure on current leaf types, our results can help improve predictions of future terrestrial ecosystem functioning and carbon cycling. Integrating inventory data with machine learning models reveals the global composition of tree types-needle-leaved evergreen individuals dominate, followed by broadleaved evergreen and deciduous trees-and climate change risks.
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18.
  • Giacomello, Stefania, et al. (author)
  • Spatially resolved transcriptome profiling in model plant species
  • 2017
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 3:6
  • Journal article (peer-reviewed)abstract
    • Understanding complex biological systems requires functional characterization of specialized tissue domains. However, existing strategies for generating and analysing high-throughput spatial expression profiles were developed for a limited range of organisms, primarily mammals. Here we present the first available approach to generate and study highresolution, spatially resolved functional profiles in a broad range of model plant systems. Our process includes highthroughput spatial transcriptome profiling followed by spatial gene and pathway analyses. We first demonstrate the feasibility of the technique by generating spatial transcriptome profiles from model angiosperms and gymnosperms microsections. In Arabidopsis thaliana we use the spatial data to identify differences in expression levels of 141 genes and 189 pathways in eight inflorescence tissue domains. Our combined approach of spatial transcriptomics and functional profiling offers a powerful new strategy that can be applied to a broad range of plant species, and is an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology.
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19.
  • Gutierrez, Emilio, et al. (author)
  • Phenolic acid-induced phase separation and translation inhibition mediate plant interspecific competition
  • 2023
  • In: Nature Plants. - 2055-026X .- 2055-0278. ; 9, s. 1481–1499-
  • Journal article (peer-reviewed)abstract
    • Phenolic acids (PAs) secreted by donor plants suppress the growth of their susceptible plant neighbours. However, how structurally diverse ensembles of PAs are perceived by plants to mediate interspecific competition remains a mystery. Here we show that a plant stress granule (SG) marker, RNA-BINDING PROTEIN 47B (RBP47B), is a sensor of PAs in Arabidopsis. PAs, including salicylic acid, 4-hydroxybenzoic acid, protocatechuic acid and so on, directly bind RBP47B, promote its phase separation and trigger SG formation accompanied by global translation inhibition. Salicylic acid-induced global translation inhibition depends on RBP47 family members. RBP47s regulate the proteome rather than the absolute quantity of SG. The rbp47 quadruple mutant shows a reduced sensitivity to the inhibitory effect of the PA mixture as well as to that of PA-rich rice when tested in a co-culturing ecosystem. In this Article, we identified the long sought-after PA sensor as RBP47B and illustrated that PA-induced SG-mediated translational inhibition was one of the PA perception mechanisms.Allelopathy-the chemical competition between neighbouring plants-has been observed for centuries. This study identifies a sensor of phenolic allelochemicals and reveals translational control as a key mechanism.
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20.
  • Jonsson, Micael, et al. (author)
  • Levels of forest ecosystem services depend on specific mixtures of commercial tree species.
  • 2019
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-0278 .- 2055-026X. ; 5, s. 141-147
  • Journal article (peer-reviewed)abstract
    • Global and local ecosystem change resulting in diversity loss has motivated efforts to understand relationships between species diversity and ecosystem services. However, it is unclear how such a general understanding can inform policies for the management of ecosystem services in production systems, because these systems are primarily used for food or fibre, and are rarely managed for the conservation of species diversity. Here, using data from a nationwide forest inventory covering an area of 230,000km2, we show that relative abundances of commercial tree species in mixed stands strongly influence the potential to provide ecosystem services. The mixes provided higher levels of ecosystem services compared to respective plant monocultures (overyielding or transgressive overyielding) in 35% of the investigated cases, and lower (underyielding) in 9% of the cases. We further show that relative abundances, not just species richness per se, of specific tree-species mixtures affect the potential of forests to provide multiple ecosystem services, which is crucial information for policy and sustainable forest management.
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21.
  • Karady, Michal, et al. (author)
  • PIN-driven auxin transport emerged early in streptophyte evolution
  • 2019
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 5, s. 1114-1119
  • Journal article (peer-reviewed)abstract
    • PIN-FORMED (PIN) transporters mediate directional, intercellular movement of the phytohormone auxin in land plants. To elucidate the evolutionary origins of this developmentally crucial mechanism, we analysed the single PIN homologue of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized auxin exporter in land plants and heterologous models. While its role in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within streptophytes.
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22.
  • Lafon-Placette, Clément, et al. (author)
  • Paternally expressed imprinted genes associate with hybridization barriers in Capsella
  • 2018
  • In: Nature plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 4:6, s. 352-357
  • Journal article (peer-reviewed)abstract
    • Hybrid seed lethality is a widespread type of reproductive barrier among angiosperm taxa(1,2) that contributes to species divergence by preventing gene flow between natural populations(3,4). Besides its ecological importance, it is an important obstacle to plant breeding strategies(5). Hybrid seed lethality is mostly due to a failure of the nourishing endosperm tissue, resulting in embryo arrest(3,6,7). The cause of this failure is a parental dosage imbalance in the endosperm that can be a consequence of either differences in parental ploidy levels or differences in the 'effective ploidy', also known as the endosperm balance number (EBN)(8,9). Hybrid seed defects exhibit a parent-of-origin pattern(3,6,7), suggesting that differences in number or expression strength of parent-of-origin-specific imprinted genes underpin, as the primary or the secondary cause, the molecular basis of the EBN7,10. Here, we have tested this concept in the genus Capsella and show that the effective ploidy of three Capsella species correlates with the number and expression level of paternally expressed genes (PEGs). Importantly, the number of PEGs and the effective ploidy decrease with the selfing history of a species: the obligate outbreeder Capsella grandiflora had the highest effective ploidy, followed by the recent selfer Capsella rubella and the ancient selfer Capsella orientalis. PEGs were associated with the presence of transposable elements and their silencing mark, DNA methylation in CHH context (where H denotes any base except C). This suggests that transposable elements have driven the imprintome divergence between Capsella species. Together, we propose that variation in transposable element insertions, the resulting differences in PEG number and divergence in their expression level form one component of the effective ploidy variation between species of different breeding system histories, and, as a consequence, allow the establishment of endosperm-based hybridization barriers.
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23.
  • Ma, Yuan, et al. (author)
  • Multiple mechanisms behind plant bending
  • 2023
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 9, s. 13-21
  • Journal article (peer-reviewed)abstract
    • To survive, plants constantly adapt their body shape to their environment. This often involves remarkably rapid bending of their organs such as stems, leaves and roots. Since plant cells are enclosed by stiff cell walls, they use various strategies for bending their organs, which differ from bending mechanisms of soft animal tissues and involve larger physical forces. Here we attempt to summarize and link different viewpoints on bending mechanisms: genes and signalling, mathematical modelling and biomechanics. We argue that quantifying cell growth and physical forces could open a new level in our understanding of bending and resolve some of its paradoxes.
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24.
  • Mao, Hailiang, et al. (author)
  • Arabidopsis BTB/POZ protein-dependent PENETRATION3 trafficking and disease susceptibility
  • 2017
  • In: Nature Plants. - : NATURE PUBLISHING GROUP. - 2055-026X .- 2055-0278. ; 3:11, s. 854-858
  • Journal article (peer-reviewed)abstract
    • The outermost cell layer of plant roots (epidermis) constantly encounters environmental challenges. The epidermal outer plasma membrane domain harbours the PENETRATION3 (PEN3)/ABCG36/PDR8 ATP-binding cassette transporter that confers non-host resistance to several pathogens. Here, we show that the Arabidopsis ENDOPLASMIC RETICULUM-ARRESTED PEN3 (EAP3) BTB/POZ-domain protein specifically mediates PEN3 exit from the endoplasmic reticulum and confers resistance to a root-penetrating fungus, providing prime evidence for BTB/POZ-domain protein-dependent membrane trafficking underlying disease resistance.
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25.
  • Martinez-Arias, Germán, et al. (author)
  • Silencing in sperm cells is directed by RNA movement from the surrounding nurse cell
  • 2016
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 2
  • Journal article (peer-reviewed)abstract
    • Plant small interfering RNAs (siRNAs) communicate from cell to cell and travel long distances through the vasculature. However, siRNA movement into germ cells has remained controversial, and has gained interest because the terminally differentiated pollen vegetative nurse cell surrounding the sperm cells undergoes a programmed heterochromatin decondensation and transcriptional reactivation of transposable elements (TEs). Transcription of TEs leads to their post-transcriptional degradation into siRNAs, and it has been proposed that the purpose of this TE reactivation is to generate and load TE siRNAs into the sperm cells. Here, we identify the molecular pathway of TE siRNA production in the pollen grain and demonstrate that siRNAs produced from pollen vegetative cell transcripts can silence TE reporters in the sperm cells. Our data demonstrates that TE siRNAs act non-cell-autonomously, inhibiting TE activity in the germ cells and potentially the next generation.
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26.
  • Mortier, Thomas, et al. (author)
  • A framework for tracing timber following the Ukraine invasion
  • 2024
  • In: NATURE PLANTS. - 2055-026X .- 2055-0278. ; 10, s. 390-401
  • Journal article (peer-reviewed)abstract
    • Scientific testing including stable isotope ratio analysis (SIRA) and trace element analysis (TEA) is critical for establishing plant origin, tackling deforestation and enforcing economic sanctions. Yet methods combining SIRA and TEA into robust models for origin verification and determination are lacking. Here we report a (1) large Eastern European timber reference database (Betula, Fagus, Pinus, Quercus) tailored to sanctioned products following the Ukraine invasion; (2) statistical test to verify samples against a claimed origin; (3) probabilistic model of SIRA, TEA and genus distribution data, using Gaussian processes, to determine timber harvest location. Our verification method rejects 40–60% of simulated false claims, depending on the spatial scale of the claim, and maintains a low probability of rejecting correct origin claims. Our determination method predicts harvest location within 180 to 230km of true location. Our results showcase the power of combining data types with probabilistic modelling to identify and scrutinize timber harvest location claims.
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27.
  • Mozgova, Iva, et al. (author)
  • Chromatin assembly factor CAF-1 represses priming of plant defence response genes
  • 2015
  • In: Nature Plants. - 2055-026X .- 2055-0278. ; 1
  • Journal article (peer-reviewed)abstract
    • Plants have evolved efficient defence systems against pathogens that often rely on specific transcriptional responses. Priming is part of the defence syndrome, by establishing a hypersensitive state of defence genes such as after a first encounter with a pathogen. Because activation of defence responses has a fitness cost, priming must be tightly controlled to prevent spurious activation of defence. However, mechanisms that repress defence gene priming are poorly understood. Here, we show that the histone chaperone CAF-1 is required to establish a repressed chromatin state at defence genes. Absence of CAF-1 results in spurious activation of a salicylic acid-dependent pathogen defence response in plants grown under non-sterile conditions. Chromatin at defence response genes in CAF-1 mutants under non-inductive (sterile) conditions is marked by low nucleosome occupancy and high H3K4me3 at transcription start sites, resembling chromatin in primed wild-type plants. We conclude that CAF-1-mediated chromatin assembly prevents the establishment of a primed state that may under standard non-sterile growth conditions result in spurious activation of SA-dependent defence responses and consequential reduction of plant vigour.
  •  
28.
  • Müller, Niels A., et al. (author)
  • A single gene underlies the dynamic evolution of poplar sex determination.
  • 2020
  • In: Nature Plants. - : Springer Nature. - 2055-0278 .- 2055-026X. ; 6:6, s. 630-637
  • Journal article (peer-reviewed)abstract
    • Although hundreds of plant lineages have independently evolved dioecy (that is, separation of the sexes), the underlying genetic basis remains largely elusive. Here we show that diverse poplar species carry partial duplicates of the ARABIDOPSIS RESPONSE REGULATOR 17 (ARR17) orthologue in the male-specific region of the Y chromosome. These duplicates give rise to small RNAs apparently causing male-specific DNA methylation and silencing of the ARR17 gene. CRISPR–Cas9-induced mutations demonstrate that ARR17 functions as a sex switch, triggering female development when on and male development when off. Despite repeated turnover events, including a transition from the XY system to a ZW system, the sex-specific regulation of ARR17 is conserved across the poplar genus and probably beyond. Our data reveal how a single-gene-based mechanism of dioecy can enable highly dynamic sex-linked regions and contribute to maintaining recombination and integrity of sex chromosomes.
  •  
29.
  • Niittylä, Totte (author)
  • Sucrose synthases are not involved in starch synthesis in Arabidopsis leaves
  • 2022
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278.
  • Journal article (peer-reviewed)abstract
    • Many plants accumulate transitory starch reserves in their leaves during the day to buffer their carbohydrate supply against fluctuating light conditions, and to provide carbon and energy for survival at night. It is universally accepted that transitory starch is synthesized from ADP-glucose (ADPG) in the chloroplasts. However, the consensus that ADPG is made in the chloroplasts by ADPG pyrophosphorylase has been challenged by a controversial proposal that ADPG is made primarily in the cytosol, probably by sucrose synthase (SUS), and then imported into the chloroplasts. To resolve this long-standing controversy, we critically re-examined the experimental evidence that appears to conflict with the consensus pathway. We show that when precautions are taken to avoid artefactual changes during leaf sampling, Arabidopsis thaliana mutants that lack SUS activity in mesophyll cells (quadruple sus1234) or have no SUS activity (sextuple sus123456) have wild-type levels of ADPG and starch, while ADPG is 20 times lower in the pgm and adg1 mutants that are blocked in the consensus chloroplastic pathway of starch synthesis. We conclude that the ADPG needed for starch synthesis in leaves is synthesized primarily by ADPG pyrophosphorylase in the chloroplasts.Mutant analysis shows that sucrose synthase makes no substantial contribution to transitory starch synthesis in Arabidopsis leaves, resolving a 20-year-old controversy about one of the most important pathways of photosynthetic metabolism.
  •  
30.
  • Novak, Ondrej, et al. (author)
  • Local auxin metabolism regulates environment-induced hypocotyl elongation
  • 2016
  • In: Nature Plants. - 2055-026X .- 2055-0278. ; 2
  • Journal article (peer-reviewed)abstract
    • A hallmark of plants is their adaptability of size and form in response to widely fluctuating environments. The metabolism and redistribution of the phytohormone auxin play pivotal roles in establishing active auxin gradients and resulting cellular differentiation. In Arabidopsis thaliana, cotyledons and leaves synthesize indole-3-acetic acid (IAA) from tryptophan through indole-3-pyruvic acid (3-IPA) in response to vegetational shade. This newly synthesized auxin moves to the hypocotyl where it induces elongation of hypocotyl cells. Here we show that loss of function of VAS2 (IAA-amido synthetase Gretchen Hagen 3 (GH3). 17) leads to increases in free IAA at the expense of IAA-Glu (IAA-glutamate) in the hypocotyl epidermis. This active IAA elicits shade- and high temperature-induced hypocotyl elongation largely independently of 3-IPA-mediated IAA biosynthesis in cotyledons. Our results reveal an unexpected capacity of local auxin metabolism to modulate the homeostasis and spatial distribution of free auxin in specialized organs such as hypocotyls in response to shade and high temperature.
  •  
31.
  • Perez-Boerema, Annemarie, et al. (author)
  • Structure of a minimal photosystem I from the green alga Dunaliella salina
  • 2020
  • In: Nature plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 6:3, s. 321-327
  • Journal article (peer-reviewed)abstract
    • Solar energy harnessed by oxygenic photosynthesis supports most of the life forms on Earth. In eukaryotes, photosynthesis occurs in chloroplasts and is achieved by membrane-embedded macromolecular complexes that contain core and peripheral antennae with multiple pigments. The structure of photosystem I (PSI) comprises the core and light-harvesting (LHCI) complexes, which together form PSI-LHCI. Here we determined the structure of PSI-LHCI from the salt-tolerant green alga Dunaliella salina using X-ray crystallography and electron cryo-microscopy. Our results reveal a previously undescribed configuration of the PSI core. It is composed of only 7 subunits, compared with 14-16 subunits in plants and the alga Chlamydomonas reinhardtii, and forms the smallest known PSI. The LHCI is poorly conserved at the sequence level and binds to pigments that form new energy pathways, and the interactions between the individual Lhca1-4 proteins are weakened. Overall, the data indicate the PSI of D. salina represents a different type of the molecular organization that provides important information for reconstructing the plasticity and evolution of PSI. The photosystem I light-harvesting complex from the salt-tolerant green alga Dunaliella salina has a core configuration composed of only seven subunits. This unusual molecular organization could inform the reconstruction of photosystem evolution.
  •  
32.
  • Perez Boerema, Annemarie, et al. (author)
  • Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor
  • 2018
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 4, s. 212-217
  • Journal article (peer-reviewed)abstract
    • Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions underpinning this process in plants take place in the chloroplast. Chloroplasts evolved ~1.2 billion years ago from an engulfed primordial diazotrophic cyanobacterium, and chlororibosomes are responsible for synthesis of the core proteins driving photochemical reactions. Chlororibosomal activity is spatiotemporally coupled to the synthesis and incorporation of functionally essential co-factors, implying the presence of chloroplast-specific regulatory mechanisms and structural adaptation of the chlororibosome1,2. Despite recent structural information3,4,5,6, some of these aspects remained elusive. To provide new insights into the structural specialities and evolution, we report a comprehensive analysis of the 2.9–3.1 Å resolution electron cryo-microscopy structure of the spinach chlororibosome in complex with its recycling factor and hibernation-promoting factor. The model reveals a prominent channel extending from the exit tunnel to the chlororibosome exterior, structural re-arrangements that lead to increased surface area for translocon binding, and experimental evidence for parallel and convergent evolution of chloro- and mitoribosomes.
  •  
33.
  • Plomion, Christophe, et al. (author)
  • Oak genome reveals facets of long lifespan
  • 2018
  • In: NATURE PLANTS. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 4:7, s. 440-452
  • Journal article (peer-reviewed)abstract
    • Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes' but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times(2). With 450 species spread throughout Asia, Europe and America(3), oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical(4) and modelling(5) approaches have shown that intra-organismal genetic heterogeneity can be selected for(6) and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes(7). However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.
  •  
34.
  • Radhakrishnan, Guru V., et al. (author)
  • An ancestral signalling pathway is conserved in intracellular symbioses-forming plant lineages
  • 2020
  • In: NATURE PLANTS. - : NATURE PUBLISHING GROUP. - 2055-026X .- 2055-0278. ; 6:3, s. 280-289
  • Journal article (peer-reviewed)abstract
    • Plants are the foundation of terrestrial ecosystems, and their colonization of land was probably facilitated by mutualistic associations with arbuscular mycorrhizal fungi. Following this founding event, plant diversification has led to the emergence of a tremendous diversity of mutualistic symbioses with microorganisms, ranging from extracellular associations to the most intimate intracellular associations, where fungal or bacterial symbionts are hosted inside plant cells. Here, through analysis of 271 transcriptomes and 116 plant genomes spanning the entire land-plant diversity, we demonstrate that a common symbiosis signalling pathway co-evolved with intracellular endosymbioses, from the ancestral arbuscular mycorrhiza to the more recent ericoid and orchid mycorrhizae in angiosperms and ericoid-like associations of bryophytes. By contrast, species forming exclusively extracellular symbioses, such as ectomycorrhizae, and those forming associations with cyanobacteria, have lost this signalling pathway. This work unifies intracellular symbioses, revealing conservation in their evolution across 450 million yr of plant diversification. An extensive phylogenomics study based on hundreds of genomes and transcriptomes provides a new interpretation of the evolution of different types of symbiotic associations in land plants, and reveals a conserved ancestral symbiosis pathway.
  •  
35.
  • Simura, Jan, et al. (author)
  • Auxin export from proximal fruits drives arrest in temporally competent inflorescences
  • 2020
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 6, s. 699-707
  • Journal article (peer-reviewed)abstract
    • The authors investigate the mechanisms behind floral arrest in Arabidopsis. Despite what was previously believed, they show that it is not a global process but a locally regulated mechanism, driven by the export of auxin from fertile fruits.A well-defined set of regulatory pathways control entry into the reproductive phase in flowering plants, but little is known about the mechanistic control of the end-of-flowering despite this being a critical process for optimization of fruit and seed production. Complete fruit removal, or lack of fertile fruit-set, prevents timely inflorescence arrest in Arabidopsis, leading to a previous proposal that a cumulative fruit/seed-derived signal causes simultaneous 'global proliferative arrest'. Recent studies have suggested that inflorescence arrest involves gene expression changes in the inflorescence meristem that are, at least in part, controlled by the FRUITFULL-APETALA2 pathway; however, there is limited understanding of how this process is coordinated at the whole-plant level. Here, we provide a framework for the communication previously inferred in the global proliferative arrest model. We show that the end-of-flowering in Arabidopsis is not 'global' and does not occur synchronously between branches, but rather that the arrest of each inflorescence is a local process, driven by auxin export from fruit proximal to the inflorescence apex. Furthermore, we show that inflorescences are competent for arrest only once they reach a certain developmental age. Understanding the regulation of inflorescence arrest will be of major importance to extending and maximizing crop yields.
  •  
36.
  • Soh, W. K., et al. (author)
  • Palaeo leaf economics reveal a shift in ecosystem function associated with the end-Triassic mass extinction event
  • 2017
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 3:8
  • Journal article (peer-reviewed)abstract
    • Climate change is likely to have altered the ecological functioning of past ecosystems, and is likely to alter functioning in the future; however, the magnitude and direction of such changes are difficult to predict. Here we use a deep-time case study to evaluate the impact of a well-constrained CO 2 -induced global warming event on the ecological functioning of dominant plant communities. We use leaf mass per area (LMA), a widely used trait in modern plant ecology, to infer the palaeoecological strategy of fossil plant taxa. We show that palaeo-LMA can be inferred from fossil leaf cuticles based on a tight relationship between LMA and cuticle thickness observed among extant gymnosperms. Application of this new palaeo-LMA proxy to fossil gymnosperms from East Greenland reveals significant shifts in the dominant ecological strategies of vegetation found across the Triassic-Jurassic transition. Late Triassic forests, dominated by low-LMA taxa with inferred high transpiration rates and short leaf lifespans, were replaced in the Early Jurassic by forests dominated by high-LMA taxa that were likely to have slower metabolic rates. We suggest that extreme CO2-induced global warming selected for taxa with high LMA associated with a stress-tolerant strategy and that adaptive plasticity in leaf functional traits such as LMA contributed to post-warming ecological success.
  •  
37.
  • Stymne, Sten (author)
  • Tweaking enzymes for exotic plant oils
  • 2018
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 4, s. 633-634
  • Other publication (peer-reviewed)abstract
    • Plants are amazing chemical factories. Within the plant kingdom, more than 450 distinct fatty acid structures have been described. Two new C-24 dihydroxy fatty acids have now been discovered that are synthesized by an unprecedented biosynthetic route termed 'discontinuous elongation'.
  •  
38.
  • Yu, Lei, et al. (author)
  • Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina)
  • 2023
  • In: Nature Plants. - 2055-026X .- 2055-0278. ; 9:8, s. 1207-1220
  • Journal article (peer-reviewed)abstract
    • Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Two west-to-east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival of Z. marina in the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present there for ~243ky (thousand years). Mediterranean populations were founded ~44kya, while extant distributions along western and eastern Atlantic shores were founded at the end of the Last Glacial Maximum (~19kya), with at least one major refuge being the North Carolina region. The recent colonization and five- to sevenfold lower genomic diversity of the Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.
  •  
39.
  • Amunts, Alexey (author)
  • The revolution evolution
  • 2022
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-0278. ; 8:1, s. 14-17
  • Journal article (other academic/artistic)
  •  
40.
  • Benson, Samuel L, et al. (author)
  • An intact light harvesting complex I antenna system is required for complete state transitions in Arabidopsis
  • 2015
  • In: Nature plants. - : Nature Publishing Group. - 2055-026X. ; 1:12
  • Journal article (peer-reviewed)abstract
    • Efficient photosynthesis depends on maintaining balance between the rate of light-driven electron transport occurring in photosystem I (PSI) and photosystem II (PSII), located in the chloroplast thylakoid membranes. Balance is achieved through a process of 'state transitions' that increases energy transfer towards PSI when PSII is overexcited (state II), and towards PSII when PSI is overexcited (state I). This is achieved through redox control of the phosphorylation state of light-harvesting antenna complex II (LHCII). PSI is served by both LHCII and four light-harvesting antenna complex I (LHCI) subunits, Lhca1, 2, 3 and 4. Here we demonstrate that despite unchanged levels of LHCII phosphorylation, absence of specific Lhca subunits reduces state transitions in Arabidopsis. The severest phenotype-observed in a mutant lacking Lhca4 (Delta Lhca4)-displayed a 69% reduction compared with the wild type. Yet, surprisingly, the amounts of the PSI-LHCI-LHCII supercomplex isolated by blue native polyacrylamide gel electrophoresis (BN-PAGE) from digitonin-solubilized thylakoids were similar in the wild type and Delta Lhca mutants. Fluorescence excitation spectroscopy revealed that in the wild type this PSI-LHCI-LHCII supercomplex is supplemented by energy transfer from additional LHCII trimers in state II, whose binding is sensitive to digitonin, and which are absent in Delta Lhca4. The grana margins of the thylakoid membrane were found to be the primary site of interaction between this 'extra' LHCII and the PSI-LHCI-LHCII supercomplex in state II. The results suggest that the LHCI complexes mediate energetic interactions between LHCII and PSI in the intact membrane.
  •  
41.
  • da Fonseca, Rute R., et al. (author)
  • The origin and evolution of maize in the Southwestern United States
  • 2015
  • In: Nature Plants. - 2055-026X. ; 1:1
  • Journal article (peer-reviewed)abstract
    • The origin of maize (Zea mays mays) in the US Southwest remains contentious, with conflicting archaeological data supporting either coastal(1-4) or highland(5,6) routes of diffusion of maize into the United States. Furthermore, the genetics of adaptation to the new environmental and cultural context of the Southwest is largely uncharacterized(7). To address these issues, we compared nuclear DNA from 32 archaeological maize samples spanning 6,000 years of evolution to modern landraces. We found that the initial diffusion of maize into the Southwest about 4,000 years ago is likely to have occurred along a highland route, followed by gene flow from a lowland coastal maize beginning at least 2,000 years ago. Our population genetic analysis also enabled us to differentiate selection during domestication for adaptation to the climatic and cultural environment of the Southwest, identifying adaptation loci relevant to drought tolerance and sugar content.
  •  
42.
  • Dall'Osto, Luca, et al. (author)
  • Two mechanisms for dissipation of excess light in monomeric and trimeric light-harvesting complexes
  • 2017
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-0278. ; 3
  • Journal article (peer-reviewed)abstract
    • Oxygenic photoautotrophs require mechanisms for rapidly matching the level of chlorophyll excited states from light harvesting with the rate of electron transport from water to carbon dioxide. These photoprotective reactions prevent formation of reactive excited states and photoinhibition. The fastest response to excess illumination is the so-called non-photochemical quenching which, in higher plants, requires the luminal pH sensor PsbS and other yet unidentified components of the photosystem II antenna. Both trimeric light-harvesting complex II (LHCII) and monomeric LHC proteins have been indicated as site(s) of the heat-dissipative reactions. Different mechanisms have been proposed: Energy transfer to a lutein quencher in trimers, formation of a zeaxanthin radical cation in monomers. Here, we report on the construction of a mutant lacking all monomeric LHC proteins but retaining LHCII trimers. Its non-photochemical quenching induction rate was substantially slower with respect to the wild type. A carotenoid radical cation signal was detected in the wild type, although it was lost in the mutant. We conclude that non-photochemical quenching is catalysed by two independent mechanisms, with the fastest activated response catalysed within monomeric LHC proteins depending on both zeaxanthin and lutein and on the formation of a radical cation. Trimeric LHCII was responsible for the slowly activated quenching component whereas inclusion in supercomplexes was not required. This latter activity does not depend on lutein nor on charge transfer events, whereas zeaxanthin was essential.
  •  
43.
  • Fan, Lei, et al. (author)
  • Satellite-observed pantropical carbon dynamics
  • 2019
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-0278. ; 5:9, s. 944-951
  • Journal article (peer-reviewed)abstract
    • Changes in terrestrial tropical carbon stocks have an important role in the global carbon budget. However, current observational tools do not allow accurate and large-scale monitoring of the spatial distribution and dynamics of carbon stocks1. Here, we used low-frequency L-band passive microwave observations to compute a direct and spatially explicit quantification of annual aboveground carbon (AGC) fluxes and show that the tropical net AGC budget was approximately in balance during 2010 to 2017, the net budget being composed of gross losses of −2.86 PgC yr−1 offset by gross gains of −2.97 PgC yr−1 between continents. Large interannual and spatial fluctuations of tropical AGC were quantified during the wet 2011 La Niña year and throughout the extreme dry and warm 2015–2016 El Niño episode. These interannual fluctuations, controlled predominantly by semiarid biomes, were shown to be closely related to independent global atmospheric CO2 growth-rate anomalies (Pearson’s r = 0.86), highlighting the pivotal role of tropical AGC in the global carbon budget.
  •  
44.
  • Feeley, Kenneth J., et al. (author)
  • Changing forests under climate change
  • 2022
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-0278.
  • Journal article (other academic/artistic)
  •  
45.
  • Giaume, Francesca, et al. (author)
  • Two florigens and a florigen-like protein form a triple regulatory module at the shoot apical meristem to promote reproductive transitions in rice
  • 2023
  • In: Nature Plants. - : Springer Nature. - 2055-0278. ; 9:4, s. 525-534
  • Journal article (peer-reviewed)abstract
    • Many plant species monitor and respond to changes in day length (photoperiod) for aligning reproduction with a favourable season. Day length is measured in leaves and, when appropriate, leads to the production of floral stimuli called florigens that are transmitted to the shoot apical meristem to initiate inflorescence development. Rice possesses two florigens encoded by HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1). Here we show that the arrival of Hd3a and RFT1 at the shoot apical meristem activates FLOWERING LOCUS T-LIKE 1 (FT-L1), encoding a florigen-like protein that shows features partially differentiating it from typical florigens. FT-L1 potentiates the effects of Hd3a and RFT1 during the conversion of the vegetative meristem into an inflorescence meristem and organizes panicle branching by imposing increasing determinacy to distal meristems. A module comprising Hd3a, RFT1 and FT-L1 thus enables the initiation and balanced progression of panicle development towards determinacy.
  •  
46.
  • Herendeen, Patrick, et al. (author)
  • Palaeobotanical redux: revisiting the age of the angiosperms
  • 2017
  • In: Nature Plants. - London : Springer Science and Business Media LLC. - 2055-0278. ; 3, s. 1-8
  • Journal article (peer-reviewed)abstract
    • Angiosperms (flowering plants) are the most diverse of all major lineages of land plants and the dominant autotrophs in most terrestrial ecosystems. Their evolutionary and ecological appearance is therefore of considerable interest and has significant implications for understanding patterns of diversification in other lineages, including insects and other animals. More than half a century ago, influential reviews showed that while angiosperms are richly represented in sediments of Late Cretaceous and younger ages, there are no reliable records of angiosperms from pre-Cretaceous rocks. The extensive new macrofossil, mesofossil, and microfossil data that have accumulated since have confirmed and reinforced this pattern. Recently, however, molecular dating methods have raised the possibility that angiosperms may have existed much earlier, and there have been scattered reports of putative angiosperms from Triassic and Jurassic rocks. Critical assessment of these reports shows that, so far, none provide unequivocal evidence of pre-Cretaceous angiosperms. Angiosperms may ultimately be recognized from Jurassic or earlier rocks, but credible palaeobotanical evidence will require unambiguous documentation of the diagnostic structural features that separate angiosperms from other groups of extant and extinct seed plants.
  •  
47.
  • Hovenden, Mark J., et al. (author)
  • Globally consistent influences of seasonal precipitation limit grassland biomass response to elevated CO2
  • 2019
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-0278. ; 5, s. 167-173
  • Journal article (peer-reviewed)abstract
    • © 2019, The Author(s), under exclusive licence to Springer Nature Limited. Rising atmospheric carbon dioxide concentration should stimulate biomass production directly via biochemical stimulation of carbon assimilation, and indirectly via water savings caused by increased plant water-use efficiency. Because of these water savings, the CO 2 fertilization effect (CFE) should be stronger at drier sites, yet large differences among experiments in grassland biomass response to elevated CO 2 appear to be unrelated to annual precipitation, preventing useful generalizations. Here, we show that, as predicted, the impact of elevated CO 2 on biomass production in 19 globally distributed temperate grassland experiments reduces as mean precipitation in seasons other than spring increases, but that it rises unexpectedly as mean spring precipitation increases. Moreover, because sites with high spring precipitation also tend to have high precipitation at other times, these effects of spring and non-spring precipitation on the CO 2 response offset each other, constraining the response of ecosystem productivity to rising CO 2 . This explains why previous analyses were unable to discern a reliable trend between site dryness and the CFE. Thus, the CFE in temperate grasslands worldwide will be constrained by their natural rainfall seasonality such that the stimulation of biomass by rising CO 2 could be substantially less than anticipated.
  •  
48.
  • Li, Tao, et al. (author)
  • Amplification of plant volatile defence against insect herbivory in a warming Arctic tundra
  • 2019
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-0278. ; 5, s. 568-574
  • Journal article (peer-reviewed)abstract
    • Plant-emitted volatile organic compounds (VOCs) play fundamental roles in atmospheric chemistry and ecological processes by contributing to aerosol formation1 and mediating species interactions2. Rising temperatures and the associated shifts in vegetation composition have been shown to be the primary drivers of plant VOC emissions in Arctic ecosystems3. Although herbivorous insects also strongly alter plant VOC emissions2, no studies have addressed the impact of herbivory on plant VOC emissions in the Arctic. Here we show that warming dramatically increases the amount, and alters the blend, of VOCs released in response to herbivory. We observed that a tundra ecosystem subjected to warming, by open-top chambers, for 8 or 18 years showed a fourfold increase in leaf area eaten by insect herbivores. Herbivory by autumnal moth (Epirrita autumnata) larvae, and herbivory-mimicking methyl jasmonate application, on the widespread circumpolar dwarf birch (Betula nana) both substantially increased emissions of terpenoids. The long-term warming treatments and mimicked herbivory caused, on average, a two- and fourfold increase in monoterpene emissions, respectively. When combined, emissions increased 11-fold, revealing a strong synergy between warming and herbivory. The synergistic effect was even more pronounced for homoterpene emissions. These findings suggest that, in the rapidly warming Arctic, insect herbivory may be a primary determinant of VOC emissions during periods of active herbivore feeding.
  •  
49.
  • Naschberger, Andreas, et al. (author)
  • Algal photosystem I dimer and high-resolution model of PSI-plastocyanin complex
  • 2022
  • In: Nature Plants. - : Springer Science and Business Media LLC. - 2055-0278. ; 8:10, s. 1191-1201
  • Journal article (peer-reviewed)abstract
    • Photosystem I (PSI) enables photo-electron transfer and regulates photosynthesis in the bioenergetic membranes of cyanobacteria and chloroplasts. Being a multi-subunit complex, its macromolecular organization affects the dynamics of photosynthetic membranes. Here we reveal a chloroplast PSI from the green alga Chlamydomonas reinhardtii that is organized as a homodimer, comprising 40 protein subunits with 118 transmembrane helices that provide scaffold for 568 pigments. Cryogenic electron microscopy identified that the absence of PsaH and Lhca2 gives rise to a head-to-head relative orientation of the PSI–light-harvesting complex I monomers in a way that is essentially different from the oligomer formation in cyanobacteria. The light-harvesting protein Lhca9 is the key element for mediating this dimerization. The interface between the monomers is lacking PsaH and thus partially overlaps with the surface area that would bind one of the light-harvesting complex II complexes in state transitions. We also define the most accurate available PSI–light-harvesting complex I model at 2.3 Å resolution, including a flexibly bound electron donor plastocyanin, and assign correct identities and orientations to all the pigments, as well as 621 water molecules that affect energy transfer pathways.
  •  
50.
  • Naschberger, Andreas, et al. (author)
  • Structure of plant photosystem I in a native assembly state defines PsaF as a regulatory checkpoint
  • 2024
  • In: Nature plants. - 2055-026X.
  • Journal article (peer-reviewed)abstract
    • Plant photosystem I (PSI) consists of at least 13 nuclear-encoded and 4 chloroplast-encoded subunits that together act as a sunlight-driven oxidoreductase. Here we report the structure of a PSI assembly intermediate that we isolated from greening oat seedlings. The assembly intermediate shows an absence of at least eight subunits, including PsaF and LHCI, and lacks photoreduction activity. The data show that PsaF is a regulatory checkpoint that promotes the assembly of LHCI, effectively coupling biogenesis to function. This study reports the structure of a photosystem I assembly intermediate isolated from greening oat seedlings. It defines PsaF as a regulatory checkpoint promoting the association of LHCI that couples biogenesis to function.
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