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Plant-mPLoc: A Top-Down Strategy to Augment the Power for Predicting Plant Protein Subcellular Localization

Chou, Kuo-Chen; Shen, Hong-Bin
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 28/06/2010 Português
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One of the fundamental goals in proteomics and cell biology is to identify the functions of proteins in various cellular organelles and pathways. Information of subcellular locations of proteins can provide useful insights for revealing their functions and understanding how they interact with each other in cellular network systems. Most of the existing methods in predicting plant protein subcellular localization can only cover three or four location sites, and none of them can be used to deal with multiplex plant proteins that can simultaneously exist at two, or move between, two or more different location sites. Actually, such multiplex proteins might have special biological functions worthy of particular notice. The present study was devoted to improve the existing plant protein subcellular location predictors from the aforementioned two aspects. A new predictor called “Plant-mPLoc” is developed by integrating the gene ontology information, functional domain information, and sequential evolutionary information through three different modes of pseudo amino acid composition. It can be used to identify plant proteins among the following 12 location sites: (1) cell membrane...

New Technologies for 21st Century Plant Science

Ehrhardt, David W.; Frommer, Wolf B.
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Português
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Plants are one of the most fascinating and important groups of organisms living on Earth. They serve as the conduit of energy into the biosphere, provide food, and shape our environment. If we want to make headway in understanding how these essential organisms function and build the foundation for a more sustainable future, then we need to apply the most advanced technologies available to the study of plant life. In 2009, a committee of the National Academy highlighted the “understanding of plant growth” as one of the big challenges for society and part of a new era which they termed “new biology.” The aim of this article is to identify how new technologies can and will transform plant science to address the challenges of new biology. We assess where we stand today regarding current technologies, with an emphasis on molecular and imaging technologies, and we try to address questions about where we may go in the future and whether we can get an idea of what is at and beyond the horizon.

Vitamin Deficiencies in Humans: Can Plant Science Help?[W]

Fitzpatrick, Teresa B.; Basset, Gilles J.C.; Borel, Patrick; Carrari, Fernando; DellaPenna, Dean; Fraser, Paul D.; Hellmann, Hanjo; Osorio, Sonia; Rothan, Christophe; Valpuesta, Victoriano; Caris-Veyrat, Catherine; Fernie, Alisdair R.
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Português
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The term vitamin describes a small group of organic compounds that are absolutely required in the human diet. Although for the most part, dependency criteria are met in developed countries through balanced diets, this is not the case for the five billion people in developing countries who depend predominantly on a single staple crop for survival. Thus, providing a more balanced vitamin intake from high-quality food remains one of the grandest challenges for global human nutrition in the coming decade(s). Here, we describe the known importance of vitamins in human health and current knowledge on their metabolism in plants. Deficits in developing countries are a combined consequence of a paucity of specific vitamins in major food staple crops, losses during crop processing, and/or overreliance on a single species as a primary food source. We discuss the role that plant science can play in addressing this problem and review successful engineering of vitamin pathways. We conclude that while considerable advances have been made in understanding vitamin metabolic pathways in plants, more cross-disciplinary approaches must be adopted to provide adequate levels of all vitamins in the major staple crops to eradicate vitamin deficiencies from the global population.

The Gatsby Plant Science Summer School: Inspiring the Next Generation of Plant Science Researchers[OA]

Levesley, Aurora; Jopson, Juliet; Knight, Celia
Fonte: American Society of Plant Biologists Publicador: American Society of Plant Biologists
Tipo: Artigo de Revista Científica
Português
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We provide evidence from a 5-year study to show that a single concerted effort at the start of undergraduate study can have a clear and lasting effect on the attitudes of students toward plant science. Attendance at a week-long residential plant science summer school in the first year of an undergraduate degree resulted in many students changing courses to include more plant science and increased numbers of graduates selecting plant-based PhDs. The evidence shows that the Gatsby Plant Science Summer School has increased the pool of high-quality plant science related PhD applicants in the UK and has had a positive impact on students’ career aspirations. The results are discussed within the context of enhancing the pipeline of future plant scientists and reversing the decline of this vulnerable and strategically important subject relevant to addressing food security and other major global challenges. We have shown that a single well-designed and timely intervention can influence future student behavior and as such offers a framework of potential use to other vulnerable disciplines.

Signal Molecules Mediate the Impact of the Earthworm Aporrectodea caliginosa on Growth, Development and Defence of the Plant Arabidopsis thaliana

Puga-Freitas, Ruben; Barot, Sébastien; Taconnat, Ludivine; Renou, Jean-Pierre; Blouin, Manuel
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 03/12/2012 Português
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Earthworms have generally a positive impact on plant growth, which is often attributed to a trophic mechanism: namely, earthworms increase the release of mineral nutrients from soil litter and organic matter. An alternative hypothesis has been proposed since the discovery of a signal molecule (Indole Acetic Acid) in earthworm faeces. In this study, we used methodologies developed in plant science to gain information on ecological mechanisms involved in plant-earthworm interaction, by looking at plant response to earthworm presence at a molecular level. First, we looked at plant overall response to earthworm faeces in an in vitro device where only signal molecules could have an effect on plant growth; we observed that earthworms were inducing positive or negative effects on different plant species. Then, using an Arabidopsis thaliana mutant with an impaired auxin transport, we demonstrated the potential of earthworms to stimulate root growth and to revert the dwarf mutant phenotype. Finally, we performed a comparative transcriptomic analysis of Arabidopsis thaliana in the presence and absence of earthworms; we found that genes modulated in the presence of earthworms are known to respond to biotic and abiotic stresses, or to the application of exogenous hormones. A comparison of our results with other studies found in databases revealed strong analogies with systemic resistance...

Catalyzing plant science research with RNA-seq

Martin, Laetitia B. B.; Fei, Zhangjun; Giovannoni, James J.; Rose, Jocelyn K. C.
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
Publicado em 01/04/2013 Português
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Next generation DNA sequencing technologies are driving increasingly rapid, affordable and high resolution analyses of plant transcriptomes through sequencing of their associated cDNA (complementary DNA) populations; an analytical platform commonly referred to as RNA-sequencing (RNA-seq). Since entering the arena of whole genome profiling technologies only a few years ago, RNA-seq has proven itself to be a powerful tool with a remarkably diverse range of applications, from detailed studies of biological processes at the cell type-specific level, to providing insights into fundamental questions in plant biology on an evolutionary time scale. Applications include generating genomic data for heretofore unsequenced species, thus expanding the boundaries of what had been considered “model organisms,” elucidating structural and regulatory gene networks, revealing how plants respond to developmental cues and their environment, allowing a better understanding of the relationships between genes and their products, and uniting the “omics” fields of transcriptomics, proteomics, and metabolomics into a now common systems biology paradigm. We provide an overview of the breadth of such studies and summarize the range of RNA-seq protocols that have been developed to address questions spanning cell type-specific-based transcriptomics...

Perspectives on deciphering mechanisms underlying plant heat stress response and thermotolerance

Bokszczanin, Kamila L.; ; Fragkostefanakis, Sotirios
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
Publicado em 23/08/2013 Português
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Global warming is a major threat for agriculture and food safety and in many cases the negative effects are already apparent. The current challenge of basic and applied plant science is to decipher the molecular mechanisms of heat stress response (HSR) and thermotolerance in detail and use this information to identify genotypes that will withstand unfavorable environmental conditions. Nowadays X-omics approaches complement the findings of previous targeted studies and highlight the complexity of HSR mechanisms giving information for so far unrecognized genes, proteins and metabolites as potential key players of thermotolerance. Even more, roles of epigenetic mechanisms and the involvement of small RNAs in thermotolerance are currently emerging and thus open new directions of yet unexplored areas of plant HSR. In parallel it is emerging that although the whole plant is vulnerable to heat, specific organs are particularly sensitive to elevated temperatures. This has redirected research from the vegetative to generative tissues. The sexual reproduction phase is considered as the most sensitive to heat and specifically pollen exhibits the highest sensitivity and frequently an elevation of the temperature just a few degrees above the optimum during pollen development can have detrimental effects for crop production. Compared to our knowledge on HSR of vegetative tissues...

The use of nanoscale fluorescence microscopic to decipher cell wall modifications during fungal penetration

Ellinger, Dorothea; Voigt, Christian A.
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
Publicado em 18/06/2014 Português
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Plant diseases are one of the most studied subjects in the field of plant science due to their impact on crop yield and food security. Our increased understanding of plant–pathogen interactions was mainly driven by the development of new techniques that facilitated analyses on a subcellular and molecular level. The development of labeling technologies, which allowed the visualization and localization of cellular structures and proteins in live cell imaging, promoted the use of fluorescence and laser-scanning microscopy in the field of plant–pathogen interactions. Recent advances in new microscopic technologies opened their application in plant science and in the investigation of plant diseases. In this regard, in planta Förster/Fluorescence resonance energy transfer has demonstrated to facilitate the measurement of protein–protein interactions within the living tissue, supporting the analysis of regulatory pathways involved in plant immunity and putative host–pathogen interactions on a nanoscale level. Localization microscopy, an emerging, non-invasive microscopic technology, will allow investigations with a nanoscale resolution leading to new possibilities in the understanding of molecular processes.

Revealing changes in molecular composition of plant cell walls on the micron-level by Raman mapping and vertex component analysis (VCA)

Gierlinger, Notburga
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
Publicado em 30/06/2014 Português
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At the molecular level the plant cell walls consist of a few nanometer thick semi-crystalline cellulose fibrils embedded in amorphous matrix polymers such as pectins, hemicelluloses, and lignins. The arrangement of these molecules within the cell wall in different plant tissues, cells and cell wall layers is of crucial importance for a better understanding and thus optimized utilization of plant biomass. During the last years Confocal Raman microscopy evolved as a powerful method in plant science by revealing the different molecules in context with the microstructure. In this study two-dimensional spectral maps have been acquired of micro-cross-sections of spruce (softwood) and beech (hardwood). Raman images have been derived by using univariate (band integration, height ratios) and multivariate methods [vertex component analysis (VCA)]. While univariate analysis only visualizes changes in selected band heights or areas, VCA separates anatomical regions and cell wall layers with the most different molecular structures. Beside visualization of the distinguished regions and features the underlying molecular structure can be derived based on the endmember spectra. VCA revealed that the lumen sided S3 layer has a similar molecular composition as the pit membrane...

1064 nm FT-Raman spectroscopy for investigations of plant cell walls and other biomass materials

Agarwal, Umesh P.
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
Publicado em 23/09/2014 Português
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Raman spectroscopy with its various special techniques and methods has been applied to study plant biomass for about 30 years. Such investigations have been performed at both macro- and micro-levels. However, with the availability of the Near Infrared (NIR) (1064 nm) Fourier Transform (FT)-Raman instruments where, in most materials, successful fluorescence suppression can be achieved, the utility of the Raman investigations has increased significantly. Moreover, the development of several new capabilities such as estimation of cellulose-crystallinity, ability to analyze changes in cellulose conformation at the local and molecular level, and examination of water-cellulose interactions have made this technique essential for research in the field of plant science. The FT-Raman method has also been applied to research studies in the arenas of biofuels and nanocelluloses. Moreover, the ability to investigate plant lignins has been further refined with the availability of near-IR Raman. In this paper, we present 1064-nm FT-Raman spectroscopy methodology to investigate various compositional and structural properties of plant material. It is hoped that the described studies will motivate the research community in the plant biomass field to adapt this technique to investigate their specific research needs.

Mechanosensitive control of plant growth: bearing the load, sensing, transducing, and responding

Moulia, Bruno; Coutand, Catherine; Julien, Jean-Louis
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
Publicado em 23/02/2015 Português
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As land plants grow and develop, they encounter complex mechanical challenges, especially from winds and turgor pressure. Mechanosensitive control over growth and morphogenesis is an adaptive trait, reducing the risks of breakage or explosion. This control has been mostly studied through experiments with artificial mechanical loads, often focusing on cellular or molecular mechanotransduction pathway. However, some important aspects of mechanosensing are often neglected. (i) What are the mechanical characteristics of different loads and how are loads distributed within different organs? (ii) What is the relevant mechanical stimulus in the cell? Is it stress, strain, or energy? (iii) How do mechanosensing cells signal to meristematic cells? Without answers to these questions we cannot make progress analyzing the mechanobiological effects of plant size, plant shape, tissue distribution and stiffness, or the magnitude of stimuli. This situation is rapidly changing however, as systems mechanobiology is being developed, using specific biomechanical and/or mechanobiological models. These models are instrumental in comparing loads and responses between experiments and make it possible to quantitatively test biological hypotheses describing the mechanotransduction networks. This review is designed for a general plant science audience and aims to help biologists master the models they need for mechanobiological studies. Analysis and modeling is broken down into four steps looking at how the structure bears the load...

Beyond the Western front: targeted proteomics and organelle abundance profiling

Parsons, Harriet T.; Heazlewood, Joshua L.
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
Publicado em 05/05/2015 Português
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The application of westerns or immunoblotting techniques for assessing the composition, dynamics, and purity of protein extracts from plant material has become common practice. While the approach is reproducible, can be readily applied and is generally considered robust, the field of plant science suffers from a lack of antibody variety against plant proteins. The development of approaches that employ mass spectrometry to enable both relative and absolute quantification of many hundreds of proteins in a single sample from a single analysis provides a mechanism to overcome the expensive impediment in having to develop antibodies in plant science. We consider it an opportune moment to consider and better develop the adoption of multiple reaction monitoring (MRM)-based analyses in plant biochemistry.

Selection for High Oridonin Yield in the Chinese Medicinal Plant Isodon (Lamiaceae) Using a Combined Phylogenetics and Population Genetics Approach

Schoville, Sean D.; Dong, Chengming; Wang, Wenquan; Jian, Zaiyou; Zhao, Zhongzhen; Cao, Shugeng; Eisenberg, David Miles; Clardy, Jon C.; Harris, Eric S. J.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Português
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Oridonin is a diterpenoid with anti-cancer activity that occurs in the Chinese medicinal plant Isodon rubescens and some related species. While the bioactivity of oridonin has been well studied, the extent of natural variation in the production of this compound is poorly known. This study characterizes natural variation in oridonin production in order to guide selection of populations of Isodon with highest oridonin yield. Different populations of I. rubescens and related species were collected in China, and their offspring were grown in a greenhouse. Samples were examined for oridonin content, genotyped using 11 microsatellites, and representatives were sequenced for three phylogenetic markers (ITS, rps16, trnL-trnF). Oridonin production was mapped on a molecular phylogeny of the genus Isodon using samples from each population as well as previously published Genbank sequences. Oridonin has been reported in 12 out of 74 species of Isodon examined for diterpenoids, and the phylogeny indicates that oridonin production has arisen at least three times in the genus. Oridonin production was surprisingly consistent between wild-collected parents and greenhouse-grown offspring, despite evidence of gene flow between oridonin-producing and non-producing populations of Isodon. Additionally...

Relationship between Hexokinase and the Aquaporin PIP1 in the Regulation of Photosynthesis and Plant Growth

Kelly, Gilor; Sade, Nir; Attia, Ziv; Secchi, Francesca; Zwieniecki, Maciej; Holbrook, N. Michele; Levi, Asher; Alchanatis, Victor; Moshelion, Menachem; Granot, David
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Português
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Increased expression of the aquaporin NtAQP1, which is known to function as a plasmalemma channel for CO2 and water, increases the rate of both photosynthesis and transpiration. In contrast, increased expression of Arabidopsis hexokinase1 (AtHXK1), a dual-function enzyme that mediates sugar sensing, decreases the expression of photosynthetic genes and the rate of transpiration and inhibits growth. Here, we show that AtHXK1 also decreases root and stem hydraulic conductivity and leaf mesophyll CO2 conductance (gm). Due to their opposite effects on plant development and physiology, we examined the relationship between NtAQP1 and AtHXK1 at the whole-plant level using transgenic tomato plants expressing both genes simultaneously. NtAQP1 significantly improved growth and increased the transpiration rates of AtHXK1-expressing plants. Reciprocal grafting experiments indicated that this complementation occurs when both genes are expressed simultaneously in the shoot. Yet, NtAQP1 had only a marginal effect on the hydraulic conductivity of the double-transgenic plants, suggesting that the complementary effect of NtAQP1 is unrelated to shoot water transport. Rather, NtAQP1 significantly increased leaf mesophyll CO2 conductance and enhanced the rate of photosynthesis...

Genetics of boron tolerance in barley / by Mandy Jane Jenkin.

Jenkin, Mandy Jane
Fonte: Adelaide Thesis (Ph.D.) -- University of Adelaide, Department of Plant Science Publicador: Adelaide Thesis (Ph.D.) -- University of Adelaide, Department of Plant Science
Tipo: Tese de Doutorado Formato: 68101 bytes; application/pdf
Publicado em //1993 Português
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Thesis (Ph.D.)--University of Adelaide, Dept. of Plant Science, Waite Agricultural Research Institute, 1993; 1 v.; Title page, contents and abstract only. The complete thesis in print form is available from the University Library.

The organic chemistry of plant residues: comparison of NMR and pyrolysis data using multivariate statistical approaches

Plant, E.; Smernik, R.; Greenwood, P.; Macdonald, L.; van Leeuwen, J.
Fonte: Bentham Science Publ Ltd Publicador: Bentham Science Publ Ltd
Tipo: Artigo de Revista Científica
Publicado em //2013 Português
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To effectively characterise and distinguish between different organic matter samples, multiple chemical characterisation techniques are often employed. Due to the structural complexity of organic matter and the unique information provided by different characterisation techniques, it is often difficult to compare and combine data obtained from different analytical methods. In this study, we show how non-parametric multivariate statistical approaches can be used to compare the relative pattern of similarity/dissimilarity between organic samples characterised by two common solid-state analytical techniques: 13C nuclear magnetic resonance (NMR) spectroscopy and flash pyrolysis-gas chromatography mass spectrometry (py-GCMS). These analytical methods were used to characterise a suite of plant residues including the leaf, flower, bark and wood of several species. Using non-parametric multivariate statistical approaches we identified similarities between the plant residue data using ordination plots, which enabled us to identify where NMR and py-GCMS distinguished between residues differently. A mantel-type test called RELATE showed that there was significant (P<0.05) similarity between the NMR and py-GCMS data in terms of their ability to differentiate between plant residues of different type; 61% of the sample discrimination was common to both profiling techniques...

Plant Science research productivity in Chile during the past 20 years

Krauskopf, Erwin
Fonte: Sociedad de Biología de Chile Publicador: Sociedad de Biología de Chile
Tipo: Artigo de Revista Científica
Português
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http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602008000200002&lng=es&nrm=iso; The purpose of this study was to carry out a bibliometric analysis of the articles published in Chile during 1987-2006 that were categorized into the Plant Science discipline by ISI. The data was extracted from the Web of Science datábase, obtaining a total of 911 articles for analysis. Almost half of the articles were the outcome of an international collaboration, the United States being the country with more collaborative links with Chile within this discipline. A list was made with the 10 most-cited articles and 10 most frequently used journals. The analysis showed that almost 50% of the articles were concentrated in 10 different journals. The number of articles produced each year revealed a steady growth in scientific production since 1987. This is probably related to the progressive interaction between industry and public-research institutions.

Massive Mitochondrial Gene Transfer in a Parasitic Flowering Plant Clade

Xi, Zhenxiang; Wang, Yuguo; Bradley, Robert K.; Sugumaran, M.; Marx, Christopher J; Rest, Joshua S.; Davis, Charles Cavender
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Português
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Recent studies have suggested that plant genomes have undergone potentially rampant horizontal gene transfer (HGT), especially in the mitochondrial genome. Parasitic plants have provided the strongest evidence of HGT, which appears to be facilitated by the intimate physical association between the parasites and their hosts. A recent phylogenomic study demonstrated that in the holoparasite Rafflesia cantleyi (Rafflesiaceae), whose close relatives possess the world's largest flowers, about 2.1% of nuclear gene transcripts were likely acquired from its obligate host. Here, we used next-generation sequencing to obtain the 38 protein-coding and ribosomal RNA genes common to the mitochondrial genomes of angiosperms from R. cantleyi and five additional species, including two of its closest relatives and two host species. Strikingly, our phylogenetic analyses conservatively indicate that 24%–41% of these gene sequences show evidence of HGT in Rafflesiaceae, depending on the species. Most of these transgenic sequences possess intact reading frames and are actively transcribed, indicating that they are potentially functional. Additionally, some of these transgenes maintain synteny with their donor and recipient lineages, suggesting that native genes have likely been displaced via homologous recombination. Our study is the first to comprehensively assess the magnitude of HGT in plants involving a genome (i.e....

Effects of a Research-Infused Botanical Curriculum on Undergraduates’ Content Knowledge, STEM Competencies, and Attitudes toward Plant Sciences

Ward, Jennifer Rhode; Clarke, H. David; Horton, Jonathan L.
Fonte: American Society for Cell Biology Publicador: American Society for Cell Biology
Tipo: Artigo de Revista Científica
Publicado em //2014 Português
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This research-infused botanical curriculum increased students' knowledge and awareness of plant science topics, improved their scientific writing, and enhanced their statistical knowledge.

The role of mycorrhizal associations in plant potassium nutrition

Garcia, Kevin; Zimmermann, Sabine D.
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
Publicado em 17/07/2014 Português
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Potassium (K+) is one of the most abundant elements of soil composition but it's very low availability limits plant growth and productivity of ecosystems. Because this cation participates in many biological processes, its constitutive uptake from soil solution is crucial for the plant cell machinery. Thus, the understanding of strategies responsible of K+ nutrition is a major issue in plant science. Mycorrhizal associations occurring between roots and hyphae of underground fungi improve hydro-mineral nutrition of the majority of terrestrial plants. The contribution of this mutualistic symbiosis to the enhancement of plant K+ nutrition is not well understood and poorly studied so far. This mini-review examines the current knowledge about the impact of both arbuscular mycorrhizal and ectomycorrhizal symbioses on the transfer of K+ from the soil to the plants. A model summarizing plant and fungal transport systems identified and hypothetically involved in K+ transport is proposed. In addition, some data related to benefits for plants provided by the improvement of K+ nutrition thanks to mycorrhizal symbioses are presented.