Plant Gene Seeker -PGS
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Plant Gene Seeker -PGS
Absolutely Fascinated for plant & genomes
Curated by Andres Zurita
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Inflorescences: concepts, function, development and evolution

Inflorescences: concepts, function, development and evolution | Plant Gene Seeker -PGS | Scoop.it
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Background Inflorescences are complex structures with many functions. At anthesis they present the flowers in ways that allow for the transfer of pollen and optimization of the plant's reproductive success. During flower and fruit development they provide nutrients to the developing flowers and fruits. At fruit maturity they support the fruits prior to dispersal, and facilitate effective fruit and seed dispersal. From a structural point of view, inflorescences have played important roles in systematic and phylogenetic studies. As functional units they facilitate reproduction, and are largely shaped by natural selection.

Scope The papers in this Special Issue bridge the gap between structural and functional approaches to inflorescence evolution. They include a literature review of inflorescence function, an experimental study of inflorescences as essential contributors to the display of flowers, and two papers that present new methods and concepts for understanding inflorescence diversity and for dealing with terminological problems. The transient model of inflorescence development is evaluated in an ontogenetic study, and partially supported. Four papers present morphological and ontogenetic studies of inflorescence development in monophyletic groups, and two of these evaluate the usefulness of Hofmeister's Rule and inhibitory fields to predict inflorescence structure. In the final two papers, Bayesian and Monte-Carlo methods are used to elucidate inflorescence evolution in the Panicoid grasses, and a candidate gene approach is used in an attempt to understand the evolutionary genetics of inflorescence evolution in the genus Cornus (Cornaceae). Taken as a whole, the papers in this issue provide a glimpse of contemporary approaches to the study of the structure, development, and evolution of inflorescences, and suggest fruitful new directions for research.

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Maize ARGOS1 (ZAR1) transgenic alleles increase hybrid maize yield

Maize ARGOS1 (ZAR1) transgenic alleles increase hybrid maize yield | Plant Gene Seeker -PGS | Scoop.it
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Crop improvement for yield and drought tolerance is challenging due to the complex genetic nature of these traits and environmental dependencies. This study reports that transgenic over-expression of Zea mays AR GOS1 (ZAR1) enhanced maize organ growth, grain yield, and drought-stress tolerance. The ZAR1 transgene exhibited environmental interactions, with yield increase under Temperate Dry and yield reduction under Temperate Humid or High Latitude environments. Native ZAR1 allele variation associated with drought-stress tolerance. Two founder alleles identified in the mid-maturity germplasm of North America now predominate in Pioneer’s modern breeding programme, and have distinct proteins, promoters and expression patterns. These two major alleles show heterotic group partitioning, with one predominant in Pioneer’s female and the other in the male heterotic groups, respectively. These two alleles also associate with favourable crop performance when heterozygous. Allele-specific transgene testing showed that, of the two alleles discussed here, each allele differed in their impact on yield and environmental interactions. Moreover, when transgenically stacked together the allelic pair showed yield and environmental performance advantages over either single allele, resembling heterosis effects. This work demonstrates differences in transgenic efficacy of native alleles and the differences reflect their association with hybrid breeding performance.

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Plant biomechanics and mechanobiology are convergent paths to flourishing interdisciplinary research

Plant biomechanics and mechanobiology are convergent paths to flourishing interdisciplinary research | Plant Gene Seeker -PGS | Scoop.it
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‘One sole point of view is always false.’

Paul Valéry (1871–1945)

Over recent decades, there has been a real renaissance of interest in how inner and outer mechanical forces influence biological systems at all scales from macromolecules up to functional ecology. Many areas of animal and medical science are being reshaped by considering biomechanical and mechanobiological aspects, like stiffness-driven differentiation of stem cells, embryo development, tumour invasion, bone and cartilage adaptation, cardiac and arterial remodelling, brain neurobiology, touch and haptics, motion control, and proprioception (e.g. Discher et al., 2005;Stoltz et al., 2005, Boccafoschi et al., 2013; Bukoreshtliev et al., 2013). The same is true and no less impressive in plant sciences where researchers continue to be fascinated by the features that plants have evolved in order to grow and sense, withstand, acclimate, and adapt to the mechanical challenges they face. But what are the major frontiers in plant biomechanics and mechanobiology, the hotspots where physical and biological disciplines cross over? Is this really a new field or can we trace it back in time, and if so, how far? And what exactly do the seemingly mirror-image names biomechanics and mechanobiology mean?

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Environment: Waste production must peak this century

Environment: Waste production must peak this century | Plant Gene Seeker -PGS | Scoop.it
Without drastic action, population growth and urbanization will outpace waste reduction, warn Daniel Hoornweg, Perinaz Bhada-Tata and Chris Kennedy.
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Solid waste — the stuff we send down our chutes, discard at work and put on the curb every week — is a striking by-product of civilization. The average person in the United States throws away their body weight in rubbish every month. When waste management works well, we give it little thought: out of sight and, usually, quickly out of mind. Discarded materials are collected, some are recycled or composted, and most are landfilled or incinerated. But the global view is troubling.

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Liana Bianco-Caputo's curator insight, July 8, 2015 1:14 AM

This article has good links to reliable sources.

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Plant Callus: Mechanisms of Induction and Repression

Plant Callus: Mechanisms of Induction and Repression | Plant Gene Seeker -PGS | Scoop.it
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Plants develop unorganized cell masses like callus and tumors in response to various biotic and abiotic stimuli. Since the historical discovery that the combination of two growth-promoting hormones, auxin and cytokinin, induces callus from plant explants in vitro, this experimental system has been used extensively in both basic research and horticultural applications. The molecular basis of callus formation has long been obscure, but we are finally beginning to understand how unscheduled cell proliferation is suppressed during normal plant development and how genetic and environmental cues override these repressions to induce callus formation. In this review, we will first provide a brief overview of callus development in nature and in vitro and then describe our current knowledge of genetic and epigenetic mechanisms underlying callus formation.


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Draft genome of the kiwifruit Actinidia chinensis : Nature Communications : Nature Publishing Group

Draft genome of the kiwifruit Actinidia chinensis : Nature Communications : Nature Publishing Group | Plant Gene Seeker -PGS | Scoop.it
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The kiwifruit (Actinidia chinensis) is an economically and nutritionally important fruit crop with remarkably high vitamin C content. Here we report the draft genome sequence of a heterozygous kiwifruit, assembled from ~140-fold next-generation sequencing data. The assembled genome has a total length of 616.1 Mb and contains 39,040 genes. Comparative genomic analysis reveals that the kiwifruit has undergone an ancient hexaploidization event (γ) shared by core eudicots and two more recent whole-genome duplication events. Both recent duplication events occurred after the divergence of kiwifruit from tomato and potato and have contributed to the neofunctionalization of genes involved in regulating important kiwifruit characteristics, such as fruit vitamin C, flavonoid and carotenoid metabolism. As the first sequenced species in the Ericales, the kiwifruit genome sequence provides a valuable resource not only for biological discovery and crop improvement but also for evolutionary and comparative genomics analysis, particularly in the asterid lineage.

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Learning from halophytes: physiological basis and strategies to improve abiotic stress tolerance in crops

Learning from halophytes: physiological basis and strategies to improve abiotic stress tolerance in crops | Plant Gene Seeker -PGS | Scoop.it
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Background Global annual losses in agricultural production from salt-affected land are in excess of US$12 billion and rising. At the same time, a significant amount of arable land is becoming lost to urban sprawl, forcing agricultural production into marginal areas. Consequently, there is a need for a major breakthrough in crop breeding for salinity tolerance. Given the limited range of genetic diversity in this trait within traditional crops, stress tolerance genes and mechanisms must be identified in extremophiles and then introduced into traditional crops.

Scope and Conclusions This review argues that learning from halophytes may be a promising way of achieving this goal. The paper is focused around two central questions: what are the key physiological mechanisms conferring salinity tolerance in halophytes that can be introduced into non-halophyte crop species to improve their performance under saline conditions and what specific genes need to be targeted to achieve this goal? The specific traits that are discussed and advocated include: manipulation of trichome shape, size and density to enable their use for external Na+ sequestration; increasing the efficiency of internal Na+sequestration in vacuoles by the orchestrated regulation of tonoplast NHX exchangers and slow and fast vacuolar channels, combined with greater cytosolic K+ retention; controlling stomata aperture and optimizing water use efficiency by reducing stomatal density; and efficient control of xylem ion loading, enabling rapid shoot osmotic adjustment while preventing prolonged Na+ transport to the shoot.

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Hyperdominance in the Amazonian Tree Flora

Hyperdominance in the Amazonian Tree Flora | Plant Gene Seeker -PGS | Scoop.it
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The vast extent of the Amazon Basin has historically restricted the study of its tree communities to the local and regional scales. Here, we provide empirical data on the commonness, rarity, and richness of lowland tree species across the entire Amazon Basin and Guiana Shield (Amazonia), collected in 1170 tree plots in all major forest types. Extrapolations suggest that Amazonia harbors roughly 16,000 tree species, of which just 227 (1.4%) account for half of all trees. Most of these are habitat specialists and only dominant in one or two regions of the basin. We discuss some implications of the finding that a small group of species—less diverse than the North American tree flora—accounts for half of the world’s most diverse tree community.

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Trends in Plant Science - Ammonium stress in Arabidopsis: signaling, genetic loci, and physiological targets

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HighlightsWe review genetic loci, signaling pathways, and physiological targets of NH4+stress in the model system Arabidopsis thaliana.Differing NH4+ stress responses between belowground and aboveground sources are dissected.New experimental approaches to the study of NH4+ toxicity are outlined.An integrated view of behavior and signaling in response to NH4+ stress is proposed.Summary

Ammonium (NH4+) toxicity is a significant ecological and agricultural issue, and an important phenomenon in cell biology. As a result of increasing soil nitrogen input and atmospheric deposition, plants have to deal with unprecedented NH4+ stress from sources below and above ground. In this review, we describe recent advances in elucidating the signaling pathways and identifying the main physiological targets and genetic loci involved in the effects of NH4+ stress in the roots and shoots of Arabidopsis thaliana. We outline new experimental approaches that are being used to study NH4+ toxicity in Arabidopsis and propose an integrated view of behavior and signaling in response to NH4+ stress in the Arabidopsis system.

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Accumulation of anthocyanins in tomato skin extends shelf life - Bassolino - 2013 - New Phytologist - Wiley Online Library

Accumulation of anthocyanins in tomato skin extends shelf life - Bassolino - 2013 - New Phytologist - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it
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SummaryShelf life is one of the most important traits for the tomato (Solanum lycopersicum) industry. Two key factors, post-harvest over-ripening and susceptibility to post-harvest pathogen infection, determine tomato shelf life.Anthocyanins accumulate in the skin of Aft/Aft atv/atv tomatoes, the result of introgressing alleles affecting anthocyanin biosynthesis in fruit from two wild relatives of tomato, which results in extended fruit shelf life. Compared with ordinary, anthocyanin-less tomatoes, the fruits of Aft/Aft atv/atv keep longer during storage and are less susceptible to Botrytis cinerea, a major tomato pathogen, post-harvest.Using genetically modified tomatoes over-producing anthocyanins, we confirmed that skin-specific accumulation of anthocyanins in tomato is sufficient to reduce the susceptibility of fruit to Botrytis cinerea.Our data indicate that accumulation of anthocyanins in tomato fruit, achieved either by traditional breeding or genetic engineering can be an effective way to extend tomato shelf life.
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Violet/Blue Chrysanthemums—Metabolic Engineering of the Anthocyanin Biosynthetic Pathway Results in Novel Petal Colors

Violet/Blue Chrysanthemums—Metabolic Engineering of the Anthocyanin Biosynthetic Pathway Results in Novel Petal Colors | Plant Gene Seeker -PGS | Scoop.it
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Chrysanthemums (Chrysanthemum×morifolium Ramat.) are an important cut-flower and potted plant crop in the horticultural industry world wide. Chrysanthemums express the flavonoid 3′-hydroxylase (F3′H) gene and thus accumulate anthocyanins derived from cyanidin in their inflorescences which appear pink/red. Delphinidin-based anthocyanins are lacking due to the deficiency of a flavonoid 3′, 5′-hydroxylase (F3′5′H), and so violet/blue chrysanthemum flower colors are not found. In this study, together with optimization of transgene expression and selection of the host cultivars and gene source, F3′5′H genes have been successfully utilized to produce transgenic bluish chrysanthemums that accumulate delphinidin-based anthocyanins. HPLC analysis and feeding experiments with a delphinidin precursor identified 16 cultivars of chrysanthemums out of 75 that were predicted to turn bluish upon delphinidin accumulation. A selection of eight cultivars were successfully transformed with F3′5′H genes under the control of different promoters. A pansy F3′5′H gene under the control of a chalcone synthase promoter fragment from rose resulted in the effective diversion of the anthocyanin pathway to produce delphinidin in transgenic chrysanthemum flower petals. The resultant petal color was bluish, with 40% of total anthocyanidins attributed to delphinidin. Increased delphinidin levels (up to 80%) were further achieved by hairpin RNA interference-mediated silencing of the endogenous F3′H gene. The resulting petal colors were novel bluish hues, not possible by hybridization breeding. This is the first report of the production of anthocyanins derived from delphinidin in chrysanthemum petals leading to novel flower color.


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Three distinct mutational mechanisms acting on a single gene underpin the origin of yellow flesh in peach - Falchi - 2013 - The Plant Journal - Wiley Online Library

Three distinct mutational mechanisms acting on a single gene underpin the origin of yellow flesh in peach - Falchi - 2013 - The Plant Journal - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it
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Peach flesh color (white or yellow) is among the most popular commercial criteria for peach classification, and has implications for consumer acceptance and fruit nutritional quality. Despite the increasing interest in improving cultivars of both flesh types, little is known about the genetic basis for the carotenoid content diversity in peach. Here we describe the association between genotypes at a locus encoding the carotenoid cleavage dioxygenase 4 (PpCCD4), localized in pseudomolecule 1 of the Prunus persica reference genome sequence, and the flesh color for 37 peach varieties, including two somatic revertants, and three ancestral relatives of peach, providing definitive evidence that this locus is responsible for flesh color phenotype. We show that yellow peach alleles have arisen from various ancestral haplotypes by at least three independent mutational events involving nucleotide substitutions, small insertions and transposable element insertions, and that these mutations, despite being located within the transcribed portion of the gene, also result in marked differences in transcript levels, presumably as a consequence of differential transcript stability involving nonsense-mediated mRNA decay. The PpCCD4 gene provides a unique example of a gene for which humans, in their quest to diversify phenotypic appearance and qualitative characteristics of a fruit, have been able to select and exploit multiple mutations resulting from a variety of mechanisms.


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Plant Physiol. Focus Issue: Calcium signaling

Plant Physiol. Focus Issue: Calcium signaling | Plant Gene Seeker -PGS | Scoop.it

Want to talk about calcium signaling? Of course you do! It's important in the regulation of stomatal aperture, stress response, interactions with microbes etc.

Check out the focus issue of Plant Physiology on calcium signalling - lots of uptakes, reviews and new research, with an overview by Alex Webb here: www.plantphysiol.org/content/163/2/457.full.html


Via Mary Williams
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Great Issue with several interesting topics, and free acce$$

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Responses of foliar antioxidative and photoprotective defence systems of trees to drought: a meta-analysis

Responses of foliar antioxidative and photoprotective defence systems of trees to drought: a meta-analysis | Plant Gene Seeker -PGS | Scoop.it
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Current climate change predictions hint to more frequent extreme weather events, including extended droughts, making better understanding of the impacts of water stress on trees even more important. At the individual plant level, stomatal closure as a result of water deficit leads to reduced CO2 availability in the leaf, which can lead to photo-oxidative stress. Photorespiration and the Mehler reaction can maintain electron transport rates under low internal CO2, but result in production of reactive oxygen species (ROS). If electron consumption is decreased, upstream photochemical processes can be affected and light energy is absorbed in excess of photochemical requirements. Trees evolved to cope with excess energy and elevated concentration of ROS by activating photoprotective and antioxidative defence systems. The meta-analysis we present here assessed responses of these defence systems reported in 50 studies. We found responses to vary depending on stress intensity, foliage type and habitat, and on whether experiments were done in the field or in controlled environments. In general, drought increased concentrations of antioxidants and photoprotective pigments. However, severe stress caused degradation of antioxidant concentrations and oxidation of antioxidant pools. Evergreen trees seemed to preferentially reinforce membrane-bound protection systems zeaxanthin and tocopherol, whereas deciduous species showed greater responses in water-soluble antioxidants ascorbic acid and glutathione. Trees and shrubs from arid versus humid habitats vary in their antioxidative and photoprotective defence responses. In field experiments, drought had greater effects on some defence compounds than under controlled conditions.

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ATLs and BTLs, plant-specific and general eukaryotic structurally-related E3 ubiquitin ligases

ATLs and BTLs, plant-specific and general eukaryotic structurally-related E3 ubiquitin ligases | Plant Gene Seeker -PGS | Scoop.it
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Major components of the ubiquitin proteasome system are the enzymes that operate on the transfer of ubiquitin to selected target substrate, known as ubiquitin ligases. The RING finger is a domain that is present in key classes of ubiquitin ligases. This domain coordinates the interaction with a suitable E2 conjugase and the transfer of ubiquitin from the E2 to protein targets. Additional domains coupled to the same polypeptide are important for modulating the function of these ubiquitin ligases. Plants contain several types of E3 ubiquitin ligases that in many cases have expanded as multigene families. Some families are specific to the plant lineage, whereas others may have a common ancestor among plants and other eukaryotic lineages. Arabidopsis Tóxicos en Levadura (ATLs) and BCA2 zinc finger ATLs (BTLs) are two families of ubiquitin ligases that share some common structural features. These are intronless genes that encode a highly related RING finger domain, and yet during evolutionary history, their mode of gene expansion and function is rather different. In each of these two families, the co-occurrence of transmembrane helices or C2/C2 (BZF finger) domains with a selected variation on the RING finger has been subjected to strong selection pressure in order to preserve their unique domain architectures during evolution.

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Decoupling of soil nutrient cycles as a function of aridity in global drylands : Nature : Nature Publishing Group

Decoupling of soil nutrient cycles as a function of aridity in global drylands : Nature : Nature Publishing Group | Plant Gene Seeker -PGS | Scoop.it
The biogeochemical cycles of carbon (C), nitrogen (N) and phosphorus (P) are interlinked by primary production, respiration and decomposition in terrestrial ecosystems.
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The biogeochemical cycles of carbon (C), nitrogen (N) and phosphorus (P) are interlinked by primary production, respiration and decomposition in terrestrial ecosystems1. It has been suggested that the C, N and P cycles could become uncoupled under rapid climate change because of the different degrees of control exerted on the supply of these elements by biological and geochemical processes1, 2, 3, 4, 5. Climatic controls on biogeochemical cycles are particularly relevant in arid, semi-arid and dry sub-humid ecosystems (drylands) because their biological activity is mainly driven by water availability6, 7, 8. The increase in aridity predicted for the twenty-first century in many drylands worldwide9, 10, 11 may therefore threaten the balance between these cycles, differentially affecting the availability of essential nutrients12, 13, 14. Here we evaluate how aridity affects the balance between C, N and P in soils collected from 224 dryland sites from all continents except Antarctica. We find a negative effect of aridity on the concentration of soil organic C and total N, but a positive effect on the concentration of inorganic P. Aridity is negatively related to plant cover, which may favour the dominance of physical processes such as rock weathering, a major source of P to ecosystems, over biological processes that provide more C and N, such as litter decomposition12, 13, 14. Our findings suggest that any predicted increase in aridity with climate change will probably reduce the concentrations of N and C in global drylands, but increase that of P. These changes would uncouple the C, N and P cycles in drylands and could negatively affect the provision of key services provided by these ecosystems.

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The BRASSINOSTEROID INSENSITIVE1–LIKE3 Signalosome Complex Regulates Arabidopsis Root Development

The BRASSINOSTEROID INSENSITIVE1–LIKE3 Signalosome Complex Regulates Arabidopsis Root Development | Plant Gene Seeker -PGS | Scoop.it
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Brassinosteroid (BR) hormones are primarily perceived at the cell surface by the leucine-rich repeat receptor-like kinase BRASSINOSTEROID INSENSITIVE1 (BRI1). In Arabidopsis thaliana, BRI1 has two close homologs, BRI1-LIKE1 (BRL1) and BRL3, respectively, which are expressed in the vascular tissues and regulate shoot vascular development. Here, we identify novel components of the BRL3 receptor complex in planta by immunoprecipitation and mass spectrometry analysis. Whereas BRI1 ASSOCIATED KINASE1 (BAK1) and several other known BRI1 interactors coimmunoprecipitated with BRL3, no evidence was found of a direct interaction between BRI1 and BRL3. In addition, we confirmed that BAK1 interacts with the BRL1 receptor by coimmunoprecipitation and fluorescence microscopy analysis. Importantly, genetic analysis of brl1 brl3 bak1-3 triple mutants revealed that BAK1, BRL1, and BRL3 signaling modulate root growth and development by contributing to the cellular activities of provascular and quiescent center cells. This provides functional relevance to the observed protein–protein interactions of the BRL3 signalosome. Overall, our study demonstrates that cell-specific BRreceptor complexes can be assembled to perform different cellular activities during plant root growth, while highlighting that immunoprecipitation of leucine-rich repeat receptor kinases in plants is a powerful approach for unveiling signaling mechanisms with cellular resolution in plant development.


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Jasmonate signalling: a copycat of auxin signalling? - Plant, Cell & Environment

Jasmonate signalling: a copycat of auxin signalling? - Plant, Cell & Environment | Plant Gene Seeker -PGS | Scoop.it
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Plant hormones regulate almost all aspects of plant growth and development. The past decade has provided breakthrough discoveries in phytohormone sensing and signal transduction, and highlighted the striking mechanistic similarities between the auxin and jasmonate (JA) signalling pathways. Perception of auxin and JA involves the formation of co-receptor complexes in which hormone-specific E3-ubiquitin ligases of the SKP1-Cullin-F-box protein (SCF) type interact with specific repressor proteins. Across the plant kingdom, the Aux/IAA and the JASMONATE-ZIM DOMAIN (JAZ) proteins correspond to the auxin- and JA-specific repressors, respectively. In the absence of the hormones, these repressors form a complex with transcription factors (TFs) specific for both pathways. They also recruit several proteins, among which the general co-repressor TOPLESS, and thereby prevent the TFs from activating gene expression. The hormone-mediated interaction between the SCF and the repressors targets the latter for 26S proteasome-mediated degradation, which, in turn, releases the TFs to allow modulating hormone-dependent gene expression. In this review, we describe the similarities and differences in the auxin and JA signalling cascades with respect to the protein families and the protein domains involved in the formation of the pathway-specific complexes.

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Auxin and cytokinin control formation of the quiescent centre in the adventitious root apex of arabidopsis

Auxin and cytokinin control formation of the quiescent centre in the adventitious root apex of arabidopsis | Plant Gene Seeker -PGS | Scoop.it
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Background and Aims Adventitious roots (ARs) are part of the root system in numerous plants, and are required for successful micropropagation. In the Arabidopsis thaliana primary root (PR) and lateral roots (LRs), the quiescent centre (QC) in the stem cell niche of the meristem controls apical growth with the involvement of auxin and cytokinin. In arabidopsis, ARs emerge in planta from the hypocotyl pericycle, and from different tissues in in vitro cultured explants, e.g. from the stem endodermis in thin cell layer (TCL) explants. The aim of this study was to investigate the establishment and maintenance of the QC in arabidopsis ARs, in planta and in TCL explants, because information about this process is still lacking, and it has potential use for biotechnological applications.

Methods Expression of PR/LR QC markers and auxin influx (LAX3)/efflux (PIN1) genes was investigated in the presence/absence of exogenous auxin and cytokinin. Auxin was monitored by the DR5::GUS system and cytokinin by immunolocalization. The expression of the auxin-biosynthetic YUCCA6 gene was also investigated by in situ hybridization in planta and in AR-forming TCLs from the indole acetic acid (IAA)-overproducing superroot2-1 mutant and its wild type.

Key Results The accumulation of auxin and the expression of the QC marker WOX5 characterized the early derivatives of the AR founder cells,in planta and in in vitro cultured TCLs. By determination of PIN1 auxin efflux carrier and LAX3 auxin influx carrier activities, an auxin maximum was determined to occur at the AR tip, to which WOX5 expression was restricted, establishing the positioning of the QC. Cytokinin caused a restriction of LAX3 and PIN1 expression domains, and concomitantly the auxin biosynthesis YUCCA6 gene was expressed in the apex.

Conclusions In ARs formed in planta and TCLs, the QC is established in a similar way, and auxin transport and biosynthesis are involved through cytokinin tuning.

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Root Systems Biology: bridging regulatory networks to rhizosphere-scale processes

Root Systems Biology: bridging regulatory networks to rhizosphere-scale processes | Plant Gene Seeker -PGS | Scoop.it
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Our understanding of root biology has advanced over the last decade, in large part due to genetic and genomic approaches in model organisms. Recently, researchers have started to study the mechanisms controlling root growth and development using systems biology approaches. Modeling is set to become much more important as our knowledge of root regulatory pathways becomes increasingly complex and their outputs less intuitive. In order to relate root genotype to phenotype we must move beyond the network scales and employ multiscale modeling approaches to predict emergent properties at the tissue, organ, organism and rhizosphere levels. The interplay between scales is complex and an integrative approach is essential to understand the underlying biological mechanisms. We describe examples where such approaches have been successful and conclude by discussing the merits of developing digital plant models able to span the network to population scales and interact with their environment.

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Foraging strategies in trees of different root morphology: the role of root lifespan

Foraging strategies in trees of different root morphology: the role of root lifespan | Plant Gene Seeker -PGS | Scoop.it
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Resource exploitation of patches is influenced not simply by the rate of root production in the patches but also by the lifespan of the roots inhabiting the patches. We examined the effect of sustained localized nitrogen (N) fertilization on root lifespan in four tree species that varied widely in root morphology and presumed foraging strategy. The study was conducted in a 12-year-old common garden in central Pennsylvania using a combination of data from minirhizotron and root in-growth cores. The two fine-root tree species, Acer negundo L. and Populus tremuloidesMichx., exhibited significant increases in root lifespan with local N fertilization; no significant responses were observed in the two coarse-root tree species, Sassafras albidum Nutt. and Liriodendron tulipifera L. Across species, coarse-root tree species had longer median root lifespan than fine-root tree species. Localized N fertilization did not significantly increase the N concentration or the respiration of the roots growing in the N-rich patch. Our results suggest that some plant species appear to regulate the lifespan of different portions of their root system to improve resource acquisition while other species do not. Our results are discussed in the context of different strategies of foraging of nutrient patches in species of different root morphology.

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Cytokinin Induces Cell Division in the Quiescent Center of the Arabidopsis Root Apical Meristem

Cytokinin Induces Cell Division in the Quiescent Center of the Arabidopsis Root Apical Meristem | Plant Gene Seeker -PGS | Scoop.it

SummaryBackground

In the root apical meristem, which contains the stem cells that feed into root development, the phytohormones auxin and cytokinin play opposing roles, with auxin promoting cell division and cytokinin promoting cell differentiation. Cytokinin acts in the root tip in part by modulating auxin transport through regulation of the level of the PIN auxin efflux carriers. Auxin plays a key role in the specification of the quiescent center (QC), which is essential for maintaining the stem cell fate of the surrounding cells.

Results

We demonstrate that cytokinin promotes cell division in the QC, which is generally mitotically inactive. Cytokinin downregulates the expression of several key regulatory genes in the root tip, including SCARECROW, WOX5, and the auxin influx carriers AUX1 and LAX2. The decrease in LAX2 expression in response to cytokinin requires ARR1 and ARR12, two type B ARRs that mediate the primary transcriptional response to cytokinin. ARR1 was found to bind directly to the LAX2 gene in vivo, which indicates that type B ARRs directly regulate genes that are repressed by cytokinin. Disruption of the LAX2 gene results in a phenotype similar to that observed in response to cytokinin, including increased division of the cells in the QC and decreased expression of WOX5 and the auxin response reporter DR5.

Conclusions

Cytokinin acts to regulate auxin distribution in the root apical meristem by regulating both the PINs and LAX2. This redistribution of auxin, potentially coupled with other auxin-independent effects of cytokinin, regulates the mitotic activity in the QC.

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Current Biology - Halotropism Is a Response of Plant Roots to Avoid a Saline Environment

Current Biology - Halotropism Is a Response of Plant Roots to Avoid a Saline Environment | Plant Gene Seeker -PGS | Scoop.it

Via Mary Williams
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Scooped by Andres Zurita
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RAB5 Activation is Required for Multiple Steps in Arabidopsis thaliana Root Development

RAB5 Activation is Required for Multiple Steps in Arabidopsis thaliana Root Development | Plant Gene Seeker -PGS | Scoop.it
Plant and Cell Physiology
Andres Zurita's insight:

Rab GTPases regulate the tethering and fusion of transport vesicles to target membranes in membrane trafficking by acting as a molecular switch, cycling between GDP- and GTP-bound states. RAB5 is a member of the Rab GTPase family, the members of which have been shown to perform various functions in the endocytic pathway, including the regulation of endosomal fusion and motility in animal cells. RAB5-mediated endosomal trafficking has also been found to play important roles in various higher order plant functions, which include the regulation of the polar transport of auxin and responses to environmental conditions. The regulatory mechanisms and functions of plant RAB5 have also been investigated at the molecular and cellular levels. However, the significance of RAB5 activity at the tissue and organ levels has hardly been investigated thus far. In the present study, we examined the effect of a mutation inVPS9a, which encodes the sole guanine nucleotide exchange factor for all RAB5s in the vegetative stages of Arabidopsis thaliana. We found that multiple developmental processes were impaired in the mutant plants, including the growth and pattern formation of the roots and establishment of auxin maxima. Our results indicate that RAB5 plays distinctive pivotal roles in the development of plants.

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RHD3 Dynamin-Like GTPases Mediates Homotypic Endoplasmic Reticulum Fusion and Is Essential for Arabidopsis Development

RHD3 Dynamin-Like GTPases Mediates Homotypic Endoplasmic Reticulum Fusion and Is Essential for Arabidopsis Development | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

In all eukaryotic cells, the endoplasmic reticulum (ER) forms a tubular network whose generation requires the fusion of ER membranes. In Arabidopsis (Arabidopsis thaliana), the membrane-bound GTPase ROOT HAIR DEFECTIVE3 (RHD3) is a potential candidate to mediate ER fusion. In addition, Arabidopsis has two tissue-specific isoforms of RHD3, namely RHD3-like (RL) proteins, and their function is not clear. Here, we show that a null allele of RHD3, rhd3-8, causes growth defects and shortened root hairs. A point mutant, rhd3-1, exhibits a more severe growth phenotype than the null mutant, likely because it exerts a dominant-negative effect on the RL proteins. Genetic analysis reveals that the double deletion of RHD3 and RL1 is lethal and that the rhd3 rl2 plants produce no viable pollen, suggesting that the RL proteins are redundant to RHD3. RHD3 family proteins can replace Sey1p, the homolog of RHD3 in yeast (Saccharomyces cerevisiae), in the maintenance of ER morphology, and they are able to fuse membranes both in vivo and in vitro. Our results suggest that RHD3 proteins mediate ER fusion and are essential for plant development and that the formation of the tubular ER network is of general physiological significance.

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