Current Opinion in Plant Biology

Mechanisms underlying CO(2) diffusion in leaves.

Publication Date: 2012 Jan 31 PMID: 22300606
Authors: Kaldenhoff, R.
Journal: Curr Opin Plant Biol

Plants provide an excellent system to study CO(2) diffusion because, under light saturated conditions, photosynthesis is limited by CO(2) availability. Recent findings indicate that CO(2) diffusion in leaves can be variable in a short time range. Mesophyll CO(2) conductance could change independently from stomata movement or CO(2) fixing reactions and it was suggested that, beside others, the membranes are mesophyll CO(2) conductance limiting components. Specific aquaporins as membrane intrinsic pore proteins are considered to have a function in the modification of membrane CO(2) conductivity. Because of conflicting data, the mechanism of membrane CO(2) diffusion in plants and animals is a matter of a controversy vivid debate in the scientific community. On one hand, data from biophysics are in favor of CO(2) diffusion limiting mechanisms completely independent from membrane structure and membrane components. On the other, there is increasing evidence from physiology that a change in membrane composition has an effect on CO(2) diffusion.

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A multi-biome gap in understanding of crop and ecosystem responses to elevated CO(2).

Publication Date: 2012 Jan 25 PMID: 22284851
Authors: Leakey, A. D. - Bishop, K. A. - Ainsworth, E. A.
Journal: Curr Opin Plant Biol

A key finding from elevated [CO(2)] field experiments is that the impact of elevated [CO(2)] on plant and ecosystem function is highly dependent upon other environmental conditions, namely temperature and the availability of nutrients and soil moisture. In addition, there is significant variation in the response to elevated [CO(2)] among plant functional types, species and crop varieties. However, experimental data on plant and ecosystem responses to elevated [CO(2)] are strongly biased to economically and ecologically important systems in the temperate zone. There is a multi-biome gap in experimental data that is most severe in the tropics and subtropics, but also includes high latitudes. Physiological understanding of the environmental conditions and species found at high and low latitudes suggest they may respond differently to elevated [CO(2)] than well-studied temperate systems. Addressing this knowledge gap should be a high priority as it is vital to understanding 21st century food supply and ecosystem feedbacks on climate change.

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Photorespiration has a dual origin and manifold links to central metabolism.

Publication Date: 2012 Jan 25 PMID: 22284850
Authors: Bauwe, H. - Hagemann, M. - Kern, R. - Timm, S.
Journal: Curr Opin Plant Biol

Photorespiration is a Janus-headed metabolic process: it makes oxygenic photosynthesis possible by scavenging its major toxic by-product, 2-phosphoglycolate, but also leads to high losses of freshly assimilated CO(2) from most land plants. Photorespiration has been often classified as a wasteful process but is now increasingly appreciated as a key ancillary component of photosynthesis and therefore the global carbon cycle. As such, the photorespiratory cycle is one of the major highways for the flow of carbon in the terrestrial biosphere. Recent research revealed that this important pathway originated as a partner of oxygenic photosynthesis billions of years ago and is multiply linked to other pathways of central metabolism of contemporary land plants.

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Towards understanding how molecular networks evolve in plants.

Publication Date: 2012 Jan 24 PMID: 22280840
Authors: Chae, L. - Lee, I. - Shin, J. - Rhee, S. Y.
Journal: Curr Opin Plant Biol

Residing beneath the phenotypic landscape of a plant are intricate and dynamic networks of genes and proteins. As evolution operates on phenotypes, we expect its forces to shape somehow these underlying molecular networks. In this review, we discuss progress being made to elucidate the nature of these forces and their impact on the composition and structure of molecular networks. We also outline current limitations and open questions facing the broader field of plant network analysis.

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In silico archeogenomics unveils modern plant genome organisation, regulation and evolution.

Publication Date: 2012 Jan 24 PMID: 22280839
Authors: Salse, J.
Journal: Curr Opin Plant Biol

Increasing access to plant genome sequences as well as high resolution gene-based genetic maps have recently offered the opportunity to compare modern genomes and model their evolutionary history from their reconstructed founder ancestors on an unprecedented scale. In silico paleogenomic data have revealed the evolutionary forces that have shaped present-day genomes and allowed us to gain insight into how they are organised and regulated today.

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Integrative systems biology: an attempt to describe a simple weed.

Publication Date: 2012 Jan 23 PMID: 22277598
Authors: Liberman, L. M. - Sozzani, R. - Benfey, P. N.
Journal: Curr Opin Plant Biol

Genome-scale studies hold great promise for revealing novel plant biology. Because of the complexity of these techniques, numerous considerations need to be made before embarking on a study. Here we focus on the Arabidopsis model system because of the wealth of available genome-scale data. Many approaches are available that provide genome-scale information regarding the state of a given organism (e.g. genomics, epigenomics, transcriptomics, proteomics, metabolomics interactomics, ionomics, phenomics, etc.). Integration of all of these types of data will be necessary for a comprehensive description of Arabidopsis. In this review we propose that 'triangulation' among transcriptomics, proteomics and metabolomics is a meaningful approach for beginning this integrative analysis and uncovering a systems level perspective of Arabidopsis biology.

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Lessons from eQTL mapping studies: non-coding regions and their role behind natural phenotypic variation in plants.

Publication Date: 2012 Jan 19 PMID: 22265229
Authors: Cubillos, F. A. - Coustham, V. - Loudet, O.
Journal: Curr Opin Plant Biol

Even if considerable progress has been achieved towards the understanding of natural variation in plant systems, the contribution of transcript abundance variation to phenotypic diversity remains unappreciated. Over the last decade, efforts to characterise the genome-wide expression variation in natural accessions, structured populations and hybrids have improved our knowledge of the contribution of non-coding polymorphisms to gene expression regulation. Moreover, new studies are helping to unravel the role of expression polymorphisms and their orchestrated performance. Recent advances involving classical linkage analysis, GWAS and improved eQTL mapping strategies will provide a greater resolution to determine the genetic variants shaping the broad diversity in plant systems.

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Signals of speciation within Arabidopsis thaliana in comparison with its relatives.

Publication Date: 2012 Jan 19 PMID: 22265228
Authors: Alcazar, R. - Pecinka, A. - Aarts, M. G. - Fransz, P. F. - Koornneef, M.
Journal: Curr Opin Plant Biol

The species within the now well-defined Arabidopsis genus provide biological materials suitable to investigate speciation and the development of reproductive isolation barriers between related species. Even within the model species A. thaliana, genetic differentiation between populations due to environmental adaptation or demographic history can lead to cases where hybrids between accessions are non-viable. Experimental evidence supports the importance of genome duplications and genetic epistatic interactions in the occurrence of reproductive isolation. Other examples of adaptation to specific environments can be found in Arabidopsis relatives where hybridization and chromosome doubling lead to new amphidiploid species. Molecular signals of speciation found in the Arabidopsis genus should provide a better understanding of speciation processes in plants from a genetic, molecular and evolutionary perspective.

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Taming the hydra of specialized metabolism: how systems biology and comparative approaches are revolutionizing plant biochemistry.

Publication Date: 2012 Jan 12 PMID: 22244679
Authors: Schilmiller, A. L. - Pichersky, E. - Last, R. L.
Journal: Curr Opin Plant Biol

Specialized (traditionally called 'secondary') metabolism can be thought of as a hydra with hundreds of thousands of compounds produced by thousands of enzymes across the entire plant kingdom. Until recently, plants that produce the most interesting and valuable metabolites were recalcitrant to modern molecular biology approaches for gene and pathway discovery. Recent advances in technologies for genomic, transcriptomic, proteomic, and metabolomic methods now allow for deployment of 'systems biology' approaches to help elucidate unknown steps in specialized metabolite pathways, for example through co-expression analyses. Inexpensive transcriptome and whole genome sequencing (WGS) promises to provide direct access to metabolic pathways in plants not currently used as reference organisms. For example, WGS has uncovered cases of physical proximity of genes of specialized metabolism. Further integration of multiple 'omics' datasets through advances in bioinformatics tools will increase our knowledge of pathway architecture and regulation at an ever-increasing rate. As such the era of systems biology is rapidly providing a broader and deeper understanding of plant specialized metabolism.

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Hormone signaling in plant development.

Publication Date: 2012 Feb PMID: 22244082
Authors: Durbak, A. - Yao, H. - McSteen, P.
Journal: Curr Opin Plant Biol

Hormone signaling plays diverse and critical roles during plant development. In particular, hormone interactions regulate meristem function and therefore control formation of all organs in the plant. Recent advances have dissected commonalities and differences in the interaction of auxin and cytokinin in the regulation of shoot and root apical meristem function. In addition, brassinosteroid hormones have recently been discovered to regulate root apical meristem size. Further insights have also been made into our understanding of the mechanism of crosstalk among auxin, cytokinin, and strigolactone in axillary meristems.

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Respiratory carbon fluxes in leaves.

Publication Date: 2012 Jan 11 PMID: 22244081
Authors: Tcherkez, G. - Boex-Fontvieille, E. - Mahe, A. - Hodges, M.
Journal: Curr Opin Plant Biol

Leaf respiration is a major metabolic process that drives energy production and growth. Earlier works in this field were focused on the measurement of respiration rates in relation to carbohydrate content, photosynthesis, enzymatic activities or nitrogen content. Recently, several studies have shed light on the mechanisms describing the regulation of respiration in the light and in the dark and on associated metabolic flux patterns. This review will highlight advances made into characterizing respiratory fluxes and provide a discussion of metabolic respiration dynamics in relation to important biological functions.

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Plant development-a snapshot in 2012.

Publication Date: 2012 Feb PMID: 22217656
Authors: Chen, X. - Laux, T.
Journal: Curr Opin Plant Biol

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Double fertilization on the move.

Publication Date: 2012 Feb PMID: 22153653
Authors: Hamamura, Y. - Nagahara, S. - Higashiyama, T.
Journal: Curr Opin Plant Biol

Double fertilization is a flowering plant mechanism whereby two immotile sperm cells fertilize two different female gametes. One of the two sperm cells fertilizes the egg cell to produce the embryo and the other fertilizes the central cell to produce the endosperm. Despite the biological and agricultural significance of double fertilization, the mechanism remains largely unknown owing to difficulties associated with the embedded structure of female gametes in the maternal tissue. However, molecular genetic approaches combined with novel live-cell imaging techniques have begun to clarify the actual behavior of the sperm cells, which is different from that described by previous hypotheses. In this review article, we discuss the mechanism of double fertilization based on the dynamics of the two sperm cells in Arabidopsis.

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Stem cell maintenance in shoot apical meristems.

Publication Date: 2012 Feb PMID: 22079787
Authors: Perales, M. - Reddy, G. V.
Journal: Curr Opin Plant Biol

Stem cell homeostasis in shoot apical meristems of higher plants is regulated through a dynamic balance between spatial regulation of gene expression, cell growth patterns and patterns of differentiation. Cell-cell communication mediated by both the local factors and long-range signals have been implicated in stem cell homeostasis. Here we have reviewed recent developments on spatio-temporal regulation of cell-cell communication processes with an emphasis on how ubiquitously utilized signals such as plant hormones function with local factors in mediating stem cell homeostasis. We also provide a brief overview of how the activity of ubiquitously utilized epigenetic regulators are modulated locally to orchestrate gene expression.

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The patterning of epidermal hairs in Arabidopsis-updated.

Publication Date: 2012 Feb PMID: 22079786
Authors: Grebe, M.
Journal: Curr Opin Plant Biol

Epidermal hairs of Arabidopsis thaliana emerge in regular spacing patterns providing excellent model systems for studies of biological pattern formation. A number of root-hair and leaf-trichome patterning mutants and tools for cell-specific and tissue-specific manipulation of patterning protein activities have been combined in cycles of experimentation and mathematical modelling. These approaches have provided insight into molecular mechanisms of epidermal patterning. During the last two years, endoreplication has, unexpectedly, been found to control cell-fate maintenance during trichome patterning. New genetic interactions between a downstream, positive transcriptional regulator and lateral inhibitors of trichome or non-root-hair fate specification have been uncovered. A lateral inhibitor and a new positive regulator have been identified as major loci affecting trichome patterning in natural Arabidopsis populations. Finally, factors that modify root-hair patterning from the underlying cell layer have been discovered.

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Axis formation in Arabidopsis - transcription factors tell their side of the story.

Publication Date: 2012 Feb PMID: 22079785
Authors: Jeong, S. - Volny, M. - Lukowitz, W.
Journal: Curr Opin Plant Biol

Apical-to-basal auxin flux is a defining feature of land plants and determines their main body axis. How is the axis first set up in the embryo? Recent studies reveal that the establishment of embryonic polarity with the asymmetric first division as well as the separation of shoot and root fates within the proembryo depend on transcriptional regulation in the zygote and early embryo. Although the functional connections need to be better defined, this transcriptional network likely provides the positional information required for initiating the machinery capable of processing the systemic signal auxin in a context-dependent manner.

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Making leaves.

Publication Date: 2012 Feb PMID: 22079784
Authors: Byrne, M. E.
Journal: Curr Opin Plant Biol

Leaves are determinate organs that develop from the flanks of the shoot apical meristem through founder cell recruitment, establishment of proximodistal, dorsoventral and mediolateral axes, and subsequent growth, expansion and differentiation along these axes. Maintenance of the shoot apical meristem and production of leaves requires balanced partitioning of cells between pluripotent and differentiation fates. Hormones have a significant role in this balance but it is becoming apparent that additional intrinsic and extrinsic inputs influence hormone signalling to control meristem function and leaf initiation. As leaves develop, temporal and spatial regulation of growth and maturation determines leaf shape and complexity. Remarkably genes involved in leaf development in the context of the shoot apical meristem are also involved in elaboration of the leaf shape to generate subtle marginal serrations, more prominent lobes or a dissected compound leaf. Potentially these common regulatory modules represent a fundamental means of setting up boundaries separating discrete zones of growth. Defining gene networks involved in leaf shape variation and exploring interspecies differences between such networks is enabling exciting insight into changes that contribute to natural variation of leaf form.

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Growth and development of the root apical meristem.

Publication Date: 2012 Feb PMID: 22079783
Authors: Perilli, S. - Di Mambro, R. - Sabatini, S.
Journal: Curr Opin Plant Biol

A key question in plant developmental biology is how cell division and cell differentiation are balanced to modulate organ growth and shape organ size. In recent years, several advances have been made in understanding how this balance is achieved during root development. In the Arabidopsis root meristem, stem cells in the apical region of the meristem self-renew and produce daughter cells that differentiate in the distal meristem transition zone. Several factors have been implicated in controlling the different functional zones of the root meristem to modulate root growth; among these, plant hormones have been shown to play a main role. In this review, we summarize recent findings regarding the role of hormone signaling and transcriptional networks in regulating root development.

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Secondary cell wall patterning during xylem differentiation.

Publication Date: 2012 Feb PMID: 22078063
Authors: Oda, Y. - Fukuda, H.
Journal: Curr Opin Plant Biol

Xylem cell differentiation involves temporal and spatial regulation of secondary cell wall deposition. The cortical microtubules are known to regulate the spatial pattern of the secondary cell wall by orientating cellulose deposition. However, it is largely unknown how the microtubule arrangement is regulated during secondary wall formation. Recent findings of novel plant microtubule-associated proteins in developing xylem vessels shed new light on the regulation mechanism of the microtubule arrangement leading to secondary wall patterning. In addition, in vitro culture systems allow the dynamics of microtubules and microtubule-associated proteins during secondary cell wall formation to be followed. Therefore, this review focuses on novel aspects of microtubule dynamics leading to secondary cell wall patterning with a focus on microtubule-associated proteins.

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Environmentally coordinated epigenetic silencing of FLC by protein and long noncoding RNA components.

Publication Date: 2012 Feb PMID: 22078062
Authors: Kim, D. H. - Sung, S.
Journal: Curr Opin Plant Biol

In Arabidopsis, the role of the vernalization pathway is to repress expression of a potent floral repressor, FLOWERING LOCUS C (FLC), after a sufficient period of winter cold has been perceived. Following winter, the lack of FLC expression allows unimpeded operation of the photoperiod pathway and hence rapid flowering of vernalized plants in spring via the activation of floral integrator genes. Molecular studies revealed that regulation of the key floral repressor, FLC, is under the control of the interplay between Trithorax group (TrxG)-mediated activation and Polycomb group (PcG)-mediated repression. On-off switch of genes by TrxG and PcG is an evolutionarily conserved mechanism to coordinate cellular identity in eukaryotes. Regulation of FLC by external cues provides an excellent model system to study mechanisms in which cell identity is influenced by environment. In this review, we discuss coordinated contributions by protein and long noncoding RNA components to this environmentally induced epigenetic switch of a developmental program in plants.

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Subterranean space exploration: the development of root system architecture.

Publication Date: 2012 Feb PMID: 22037466
Authors: Jones, B. - Ljung, K.
Journal: Curr Opin Plant Biol

The colonisation of terrestrial environments offered plants a host of advantages. It also presented them with major challenges. The foremost amongst these, the dichotomous nature of terrestrial environments, was clearly successfully met by the development of an integrated but divergent root-shoot structure. Whereas they share many similarities, roots and shoots evolved specialist functions in line with their principle roles and their growth environment. In this review, we discuss a number of areas where recent discoveries, principally in Arabidopsis, are shedding light on the mechanisms that enable the successful colonisation of the soil environment.

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Epigenetic regulation of reproductive development and the emergence of apomixis in angiosperms.

Publication Date: 2012 Feb PMID: 22037465
Authors: Grimanelli, D.
Journal: Curr Opin Plant Biol

Apomictic plants reproduce asexually through seeds by avoiding both meiosis and fertilization. While apomixis is genetically controlled, individual loci contributing to its expression have yet to be identified. Here, we review recent results indicating that RNA-dependent DNA methylation pathways acting during female reproduction are essential for proper reproductive development in plants, and may represent key regulators of the differentiation between apomictic and sexual reproduction.

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Epigenetic reprogramming during plant reproduction and seed development.

Publication Date: 2012 Feb PMID: 22035873
Authors: Wollmann, H. - Berger, F.
Journal: Curr Opin Plant Biol

Epigenetic processes such as DNA methylation are crucial for the development of flowering plants, and for protection of genome integrity via silencing of transposable elements (TEs). Recent advances in genome-wide profiling suggest that during reproduction DNA methylation patterns are at least partially transmitted or even enhanced in the next generation to ensure stable silencing of TEs. At the same time, parent-of-origin specific removal of DNA methylation in the accompanying tissue allows imprinted expression of genes. Here we summarize the dynamics of DNA methylation as a major epigenetic regulatory pathway during reproduction and seed development.

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Comparison of phytohormone signaling mechanisms.

Publication Date: 2012 Feb PMID: 22001935
Authors: Shan, X. - Yan, J. - Xie, D.
Journal: Curr Opin Plant Biol

Plant hormones are crucial signaling molecules that coordinate all aspects of plant growth, development and defense. A great deal of attention has been attracted from biologists to study the molecular mechanisms for perception and signal transduction of plant hormones during the last two decades. Tremendous progress has been made in identifying receptors and key signaling components of plant hormones. The holistic picture of hormone signaling pathways is extremely complicated, this review will give a general overview of perception and signal transduction mechanisms of auxin, gibberellin, cytokinin, abscisic acid, ethylene, brassinosteroid, and jasmonate.

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On evaluating models in Computational Morphodynamics.

Publication Date: 2012 Feb PMID: 22000039
Authors: Jonsson, H. - Gruel, J. - Krupinski, P. - Troein, C.
Journal: Curr Opin Plant Biol

Recent advances in experimental plant biology have led to an increased potential to investigate plant development at a systems level. The emerging research field of Computational Morphodynamics has the aim to lead this development by combining dynamic spatial experimental data with computational models of molecular networks, growth, and mechanics in a multicellular context. The increased number of published models may lead to a diversification of our understanding of the systems, and methods for evaluating, comparing, and sharing models are main challenges for the future. We will discuss this problem using ideas originating from physics and use recent computational models of plant development as examples.

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The end of innocence: flowering networks explode in complexity.

Publication Date: 2012 Feb PMID: 21974961
Authors: Pose, D. - Yant, L. - Schmid, M.
Journal: Curr Opin Plant Biol

Substantial recent advances in genome-scale transcription factor target mapping have provided a fresh view of the gene networks governing developmental transitions. In particular, our understanding of the fine-scale spatial and temporal dynamics underlying the floral transition at the shoot apex has seen great advances in the past two years. Single transcription factors are regularly observed to act in complex manners, directly promoting the expression of particular targets while directly repressing the expression of others, based at least partly on defined heterodimerization patterns. For single regulators this behavior reaches into distinct physiological processes, providing compelling evidence that particular transcription factors act to directly integrate diverse processes to orchestrate complex developmental transitions.

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Self/non-self discrimination in angiosperm self-incompatibility.

Publication Date: 2012 Feb PMID: 21968124
Authors: Iwano, M. - Takayama, S.
Journal: Curr Opin Plant Biol

Self-incompatibility (SI) in angiosperms prevents inbreeding and promotes outcrossing to generate genetic diversity. In many angiosperms, self/non-self recognition in SI is accomplished by male-specificity and female-specificity determinants (S-determinants), encoded at the S-locus. Recent studies using genetic, molecular biological and biochemical approaches have revealed that angiosperms utilize diverse self/non-self discrimination systems, which can be classified into two fundamentally different systems, self-recognition and non-self recognition systems. The self-recognition system, adopted by Brassicaceae and Papaveraceae, depends on a specific interaction between male and female S-determinants derived from the same S-haplotype. The non-self recognition system, found in Solanaceae, depends on non-self (different S-haplotype)-specific interaction between male and female S-determinants, and the male S-determinant genes are duplicated to recognize diverse non-self female S-determinants.

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