Current Opinion in Plant Biology

The genetic control of flower-pollinator specificity.

Publication Date: 2013 Jun 10 PMID: 23763819
Authors: Yuan, Y. W. - Byers, K. J. - Bradshaw, H. Jr
Journal: Curr Opin Plant Biol

The ca. 275,000 species of flowering plants are the result of a recent adaptive radiation driven largely by the coevolution between plants and their animal pollinators. Identification of genes and mutations responsible for floral trait variation underlying pollinator specificity is crucial to understanding how pollinator shifts occur between closely related species. Petunia, Mimulus, and Antirrhinum have provided a high standard of experimental evidence to establish causal links from genes to floral traits to pollinator responses. In all three systems, MYB transcription factors seem to play a prominent role in the diversification of pollinator-associated floral traits.

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What's the 'buzz' about? The ecology and evolutionary significance of buzz-pollination.

Publication Date: 2013 Jun 7 PMID: 23751734
Authors: De Luca, P. A. - Vallejo-Marin, M.
Journal: Curr Opin Plant Biol

Many plant species have evolved floral characteristics that restrict pollen access. Some of these species are visited by insects, principally bees, which make use of vibrations to extract pollen from anthers. Buzz-pollination, as this phenomenon is generally known, is a widespread method of fertilization for thousands of species in both natural and agricultural systems. Despite its prevalence in pollination systems, the ecological and evolutionary conditions that favour the evolution of buzz-pollination are poorly known. We briefly summarize the biology of buzz-pollination and review recent studies on plant and pollinator characteristics that affect pollen removal. We suggest that buzz-pollination evolves as the result of an escalation in the competition between plants and pollen-consuming floral visitors (including pollen thieves and true pollinators) to control the rate of pollen removal from flowers.

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Genes, communities & invasive species: understanding the ecological and evolutionary dynamics of host-pathogen interactions.

Publication Date: 2013 Jun 6 PMID: 23746668
Authors: Burdon, J. - Thrall, P. - Ericson, L.
Journal: Curr Opin Plant Biol

Reciprocal interactions between hosts and pathogens drive ecological, epidemiological and co-evolutionary trajectories, resulting in complex patterns of diversity at population, species and community levels. Recent results confirm the importance of negative frequency-dependent rather than 'arms-race' processes in the evolution of individual host-pathogen associations. At the community level, complex relationships between species abundance and diversity dampen or alter pathogen impacts. Invasive pathogens challenge these controls reflecting the earliest stages of evolutionary associations (akin to arms-race) where disease effects may be so great that they overwhelm the host's and community's ability to respond. Viewing these different stabilization/destabilization phases as a continuum provides a valuable perspective to assessment of the role of genetics and ecology in the dynamics of both natural and invasive host-pathogen associations.

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Physiology and metabolism: water for thought.

Publication Date: 2013 Jun PMID: 23714378
Authors: Farmer, E. E. - Browse, J.
Journal: Curr Opin Plant Biol

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Genome studies and molecular genetics: understanding the functional genome based on the rice model.

Publication Date: 2013 May PMID: 23706861
Authors: Zhang, Q. - Wing, R.
Journal: Curr Opin Plant Biol

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Development of genomics-based genotyping platforms and their applications in rice breeding.

Publication Date: 2013 May PMID: 23706659
Authors: Chen, H. - He, H. - Zhou, F. - Yu, H. - Deng, X. W.
Journal: Curr Opin Plant Biol

Breeding by design has been an aspiration of researchers in the plant sciences for a decade. With the rapid development of genomics-based genotyping platforms and available of hundreds of functional genes/alleles in related to important traits, however, it may now be possible to turn this enduring ambition into a practical reality. Rice has a relatively simple genome comparing to other crops, and its genome composition and genetic behavior have been extensively investigated. Recently, rice has been taken as a model crop to perform breeding by design. The essential process of breeding by design is to integrate functional genes/alleles in an ideal genetic background, which requires high throughput genotyping platforms to screen for expected genotypes. With large amount of genome resequencing data and high-throughput genotyping technologies available, quite a number of genomics-based genotyping platforms have been developed. These platforms are widely used in genetic mapping, integration of target traits via marker-assisted backcrossing (MABC), pyramiding, recurrent selection (MARS) or genomic selection (GS). Here, we summarize and discuss recent exciting development of rice genomics-based genotyping platforms and their applications in molecular breeding.

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Systems-integration of plant metabolism: means, motive and opportunity.

Publication Date: 2013 Jun PMID: 23642787
Authors: Stitt, M.
Journal: Curr Opin Plant Biol

System integration of metabolism is considered in analogy to the investigation of corporate misdemeanour. Motive, or goal-oriented explanation, provides hypotheses that can guide the investigation of network structure. Opportunity can be established by correlative analysis using large-scale omics resources. However, correlative approaches on their own remain inconclusive and seldom identify all the links in a network. Establishment of means, or the ability to act on other network components and contribute to a phenotype, is therefore crucial. This requires functional information. Integration of quantitative data in the context of pathway models provides a powerful approach to establish 'means'. This is illustrated by discussing: first, how protein abundance is regulated by a network including transcript abundance, translation and protein degradation and second, how a combination of experimentation and modelling provides information about pathway flux, an emergent network property that integrates changes in proteins and metabolites and determines composition and biomass.

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Phytochemical genomics-a new trend.

Publication Date: 2013 Jun PMID: 23628002
Authors: Saito, K.
Journal: Curr Opin Plant Biol

Phytochemical genomics is a recently emerging field, which investigates the genomic basis of the synthesis and function of phytochemicals (plant metabolites), particularly based on advanced metabolomics. The chemical diversity of the model plant Arabidopsis thaliana is larger than previously expected, and the gene-to-metabolite correlations have been elucidated mostly by an integrated analysis of transcriptomes and metabolomes. For example, most genes involved in the biosynthesis of flavonoids in Arabidopsis have been characterized by this method. A similar approach has been applied to the functional genomics for production of phytochemicals in crops and medicinal plants. Great promise is seen in metabolic quantitative loci analysis in major crops such as rice and tomato, and identification of novel genes involved in the biosynthesis of bioactive specialized metabolites in medicinal plants.

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Root responses to flooding.

Publication Date: 2013 Jun PMID: 23608517
Authors: Sauter, M.
Journal: Curr Opin Plant Biol

Soil water-logging and submergence pose a severe threat to plants. Roots are most prone to flooding and the first to suffer from oxygen shortage. Roots are vital for plant function, however, and maintenance of a functional root system upon flooding is essential. Flooding-resistant plants possess a number of adaptations that help maintain oxygen supply to the root. Plants are also capable of initiating organogenesis to replace their original root system with adventitious roots if oxygen supply becomes impossible. This review summarizes current findings on root development and de novo root genesis in response to flooding.

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In vivo biochemistry: applications for small molecule biosensors in plant biology.

Publication Date: 2013 Jun PMID: 23587939
Authors: Jones, A. M. - Grossmann, G. - Danielson, J. A. - Sosso, D. - Chen, L. Q. - Ho, C. H. - Frommer, W. B.
Journal: Curr Opin Plant Biol

Revolutionary new technologies, namely in the areas of DNA sequencing and molecular imaging, continue to impact new discoveries in plant science and beyond. For decades we have been able to determine properties of enzymes, receptors and transporters in vitro or in heterologous systems, and more recently been able to analyze their regulation at the transcriptional level, to use GFP reporters for obtaining insights into cellular and subcellular localization, and tp measure ion and metabolite levels with unprecedented precision using mass spectrometry. However, we lack key information on the location and dynamics of the substrates of enzymes, receptors and transporters, and on the regulation of these proteins in their cellular environment. Such information can now be obtained by transitioning from in vitro to in vivo biochemistry using biosensors. Genetically encoded fluorescent protein-based sensors for ion and metabolite dynamics provide highly resolved spatial and temporal information, and are complemented by sensors for pH, redox, voltage, and tension. They serve as powerful tools for identifying missing processes (e.g., glucose transport across ER membranes), components (e.g., SWEET sugar transporters for cellular sugar efflux), and signaling networks (e.g., from systematic screening of mutants that affect sugar transport or cytosolic and vacuolar pH). Combined with the knowledge of properties of enzymes and transporters and their interactions with the regulatory machinery, biosensors promise to be key diagnostic tools for systems and synthetic biology.

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Rice breaks ground for cadmium-free cereals.

Publication Date: 2013 Jun PMID: 23587938
Authors: Uraguchi, S. - Fujiwara, T.
Journal: Curr Opin Plant Biol

It is important to reduce the risk of long-term cadmium (Cd) exposure through ingestion. Cd in plant-derived foods (especially rice grain in Japan) is a major source of human Cd intake. In rice, Cd uptake and xylem loading in roots, remobilization from leaf blades and intervascular transfer in nodes to redirect Cd transport are crucial for grain Cd accumulation. Different metal transporters mediate these processes with cell-type specific expressions. In this review, we summarize and discuss the recent rapid advance in molecular understanding of Cd transport in rice. The achievements and perspectives in developing 'low-Cd rice' by the use of various alleles of Cd transporter genes are also discussed.

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Evolution of flexible non-photochemical quenching mechanisms that regulate light harvesting in oxygenic photosynthesis.

Publication Date: 2013 Jun PMID: 23583332
Authors: Niyogi, K. K. - Truong, T. B.
Journal: Curr Opin Plant Biol

All photosynthetic organisms need to regulate light harvesting for photoprotection. Three types of flexible non-photochemical quenching (NPQ) mechanisms have been characterized in oxygenic photosynthetic cyanobacteria, algae, and plants: OCP-, LHCSR-, and PSBS-dependent NPQ. OCP-dependent NPQ likely evolved first, to quench excess excitation in the phycobilisome (PB) antenna of cyanobacteria. During evolution of eukaryotic algae, PBs were lost in the green and secondary red plastid lineages, while three-helix light-harvesting complex (LHC) antenna proteins diversified, including LHCSR proteins that function in dissipating excess energy rather than light harvesting. PSBS, an independently evolved member of the LHC protein superfamily, seems to have appeared exclusively in the green lineage, acquired a function as a pH sensor that turns on NPQ, and eventually replaced LHCSR in vascular plants.

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Hydraulic signals in long-distance signaling.

Publication Date: 2013 Jun PMID: 23545219
Authors: Christmann, A. - Grill, E. - Huang, J.
Journal: Curr Opin Plant Biol

Higher plants are sessile organisms that continuously adapt their metabolism and development in response to a changing environment. Control of water uptake and the maintenance of water status are key for the survival and optimal growth of plants. Environmental factors such as radiation, air temperature, rainfall, and humidity have a high impact on plant water relations. Hence, plants require a coordinated and timely response in above-ground and below-ground organs to cope with the changing need to take up and preserve water. In this review we will focus on changes in plant water availability and on how information on the water status is communicated to remote plant organs. We will summarize the current knowledge of long-distance signaling by hydraulic cues and of potential sensors required to convert a physical signal into a chemical messenger, namely the plant hormone abscisic acid (ABA).

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Biochemical pathways in seed oil synthesis.

Publication Date: 2013 Jun PMID: 23529069
Authors: Bates, P. D. - Stymne, S. - Ohlrogge, J.
Journal: Curr Opin Plant Biol

Oil produced in plant seeds is utilized as a major source of calories for human nutrition, as feedstocks for non-food uses such as soaps and polymers, and can serve as a high-energy biofuel. The biochemical pathways leading to oil (triacylglycerol) synthesis in seeds involve multiple subcellular organelles, requiring extensive lipid trafficking. Phosphatidylcholine plays a central role in these pathways as a substrate for acyl modifications and likely as a carrier for the trafficking of acyl groups between organelles and membrane subdomains. Although much has been clarified regarding the enzymes and pathways responsible for acyl-group flux, there are still major gaps in our understanding. These include the identity of several key enzymes, how flux between alternative pathways is controlled and the specialized cell biology leading to biogenesis of oil bodies that store up to 80% of carbon in seeds.

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C4 photosynthesis: from evolutionary analyses to strategies for synthetic reconstruction of the trait.

Publication Date: 2013 Jun PMID: 23510604
Authors: Denton, A. K. - Simon, R. - Weber, A. P.
Journal: Curr Opin Plant Biol

C4 photosynthesis represents the most productive modes of photosynthesis in land plants and some of the most productive crops on the planet, such as maize and sugarcane, and many ecologically important native plants use this type of photosynthesis. Despite its ecological and economic importance, the genetic basis of C4 photosynthesis remains largely unknown. Even many fundamental aspects of C4 biochemistry, such as the molecular identity of solute transporters, and many aspects of C4 plant leaf development, such as the Kranz anatomy, are currently not understood. Here, we review recent progress in gaining a mechanistic understanding of the complex C4 trait through comparative evolutionary analyses of C3 and C4 species.

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Plant sphingolipids: function follows form.

Publication Date: 2013 Jun PMID: 23499054
Authors: Markham, J. E. - Lynch, D. V. - Napier, J. A. - Dunn, T. M. - Cahoon, E. B.
Journal: Curr Opin Plant Biol

Plant sphingolipids are structurally diverse molecules that are important as membrane components and bioactive molecules. An appreciation of the relationship between structural diversity and functional significance of plant sphingolipids is emerging through characterization of Arabidopsis mutants coupled with advanced analytical methods. It is increasingly apparent that modifications such as hydroxylation and desaturation of the sphingolipid nonpolar long-chain bases and fatty acids influence their metabolic routing to particular complex sphingolipid classes and their functions in signaling pathways and other cellular processes, such as membrane protein targeting. Here, we review recent reports investigating some of the more prevalent sphingolipid structural modifications and their functional importance in plants.

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Confluence of structural and chemical biology: plant polyketide synthases as biocatalysts for a bio-based future.

Publication Date: 2013 Jun PMID: 23481348
Authors: Stewart, C. Jr - Vickery, C. R. - Burkart, M. D. - Noel, J. P.
Journal: Curr Opin Plant Biol

Type III plant polyketide synthases (PKSs) biosynthesize a dazzling array of polyphenolic products that serve important roles in both plant and human health. Recent advances in structural characterization of these enzymes and new tools from the field of chemical biology have facilitated exquisite probing of plant PKS iterative catalysis. These tools have also been used to exploit type III PKSs as biocatalysts to generate new chemicals. Going forward, chemical, structural and biochemical analyses will provide an atomic resolution understanding of plant PKSs and will serve as a springboard for bioengineering and scalable production of valuable molecules in vitro, by fermentation and in planta.

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Daylength mediated control of seasonal growth patterns in perennial trees.

Publication Date: 2013 Jun PMID: 23473967
Authors: Petterle, A. - Karlberg, A. - Bhalerao, R. P.
Journal: Curr Opin Plant Biol

Daylength is a key regulator of seasonal growth patterns in perennial trees in temperate regions. Cessation of growth is induced by short day signal in these trees before the advent of winter and constitutes a major adaptive developmental program. In this review, we report on the recent progress made in identifying the molecular mechanisms that underlie the daylength mediated control of seasonal growth in perennial trees. A major finding that has emerged from the analysis of this process is that the regulation of growth cessation in perennial trees and flowering time by daylength in annuals such as Arabidopsis thaliana involves identical signalling components.

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Regulation of the mitochondrial tricarboxylic acid cycle.

Publication Date: 2013 Jun PMID: 23462640
Authors: Nunes-Nesi, A. - Araujo, W. L. - Obata, T. - Fernie, A. R.
Journal: Curr Opin Plant Biol

Recent years have seen considerable advances in our understanding of the particular physiological roles of the constituent enzymes of the tricarboxylic acid (TCA) cycle. Despite acquiring a fairly comprehensive overview of the functional importance of these proteins relatively little is known concerning how this important pathway is regulated. In this review we concentrate on the mitochondrial reactions since this organelle is the only one in which a full cycle can, at least theoretically, operate. We summarize what is known about the regulation of the enzymes of the pathway both from historical kinetic studies as well as discussing more recent transcriptional and proteomic studies and our enhanced understanding of subcellular compartmentation within the context of metabolic regulation.

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Natural variation and genetic constraints on drought tolerance.

Publication Date: 2013 Jun PMID: 23462639
Authors: Juenger, T. E.
Journal: Curr Opin Plant Biol

Drought is a central abiotic stress for both natural plant populations and agricultural crops. Substantial natural genetic variation in drought resistance traits has been identified in plant populations, crop species, and laboratory model systems. In particular, studies in Arabidopsis thaliana have discovered variation in a number of key physiological traits involved in plant-water relations that may underlie evolved drought stress responses among accessions. Despite this abundant variation, we still know little about the complex genetic architecture of drought tolerance or its role in constraining evolution. Unfortunately, few natural allelic variants have been cloned for drought related traits-progress cloning QTL, the use of RNA-sequencing methods for evaluating gene expression responses to soil drying, and improved methodology for exploring complex multivariate data all hold promise for moving the field forward. In particular, a better understanding of the molecular nature of pleiotropic gene action and the genetics of phenotypic plasticity will give insight into local adaptation in plants and provide new avenues for improving crops.

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Succinate dehydrogenase: the complex roles of a simple enzyme.

Publication Date: 2013 Jun PMID: 23453781
Authors: Huang, S. - Millar, A. H.
Journal: Curr Opin Plant Biol

Succinate dehydrogenase (SDH) oxidises succinate to fumarate as a component of the tricarboxylic acid cycle and ubiquinone to ubiquinol in the mitochondrial electron transport chain. Studies of SDH mutants have revealed far-reaching effects of altering succinate oxidation in plant cells. The plant SDH complex composition, structure and assembly are all beginning to be understood but the implications of the divergence across eukaryotes is still unclear. We propose an integration of the reported physiological roles of SDH in plants which influence photosynthesis, the function of stomata, root elongation and fungal defence. Future SDH research needed in plants should involve tissue-specific studies of mutants, analysis of the pathways induced by succinate-dependent reactive oxygen species generation and assessment of the impact of succinate accumulation on metabolism.

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Embolism resistance as a key mechanism to understand adaptive plant strategies.

Publication Date: 2013 Jun PMID: 23453076
Authors: Lens, F. - Tixier, A. - Cochard, H. - Sperry, J. S. - Jansen, S. - Herbette, S.
Journal: Curr Opin Plant Biol

One adaptation of plants to cope with drought or frost stress is to develop wood that is able to withstand the formation and distribution of air bubbles (emboli) in its water conducting xylem cells under negative pressure. The ultrastructure of interconduit pits strongly affects drought-induced embolism resistance, but also mechanical properties of the xylem are involved. The first experimental evidence for a lower embolism resistance in stems of herbaceous plants compared to stems of their secondarily woody descendants further supports this mechanical-functional trade-off. An integrative approach combining (ultra)structural observations of the xylem, safety-efficiency aspects of the hydraulic pipeline, and xylem-phloem interactions will shed more light on the multiple adaptive strategies of embolism resistance in plants.

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Iron transport in plants: better be safe than sorry.

Publication Date: 2013 Jun PMID: 23415557
Authors: Thomine, S. - Vert, G.
Journal: Curr Opin Plant Biol

Iron is essential for plant cell function and more specifically for photosynthesis. Plants have evolved highly efficient systems to take up iron from the soil. However, activating iron uptake is a double jeopardy: not only iron itself is toxic but iron uptake systems are poorly selective and allow the entry of other potentially toxic metals. Plants therefore tightly control iron uptake at the transcriptional and post-translational level and have evolved mechanisms to cope with the concomitant entry of toxic metals. In plant cells, iron has to be distributed to chloroplasts and mitochondria or may be stored safely in vacuole. Distinct transcriptional networks regulating uptake and intracellular distribution are being uncovered, while iron sensing mechanisms remain elusive.

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