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Rescooped by Shaikhul Islam from Plant-Microbe Symbiosis
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Evolution of species interactions determines microbial community productivity in new environments

Evolution of species interactions determines microbial community productivity in new environments | Molecular Biology and Life Science | Scoop.it
Diversity generally increases ecosystem productivity over short timescales. Over longer timescales, both ecological and evolutionary responses to new environments could alter productivity and diversity–productivity relationships. In turn, diversity might affect how component species adapt to new conditions. We tested these ideas by culturing artificial microbial communities containing between 1 and 12 species in three different environments for ~60 generations. The relationship between community yields and diversity became steeper over time in one environment. This occurred despite a general tendency for the separate yields of isolates of constituent species to be lower at the end if they had evolved in a more diverse community. Statistical comparisons of community and species yields showed that species interactions had evolved to be less negative over time, especially in more diverse communities. Diversity and evolution therefore interacted to enhance community productivity in a new environment.

Via Jean-Michel Ané
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Rescooped by Shaikhul Islam from Publications from The Sainsbury Laboratory
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Plant Journal: Probing formation of cargo/importin-α transport complexes in plant cells using a pathogen effector (2014)

Plant Journal: Probing formation of cargo/importin-α transport complexes in plant cells using a pathogen effector (2014) | Molecular Biology and Life Science | Scoop.it

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The Sainsbury Lab's curator insight, October 7, 2014 4:34 AM

Importin-αs are essential adapter proteins that recruit cytoplasmic proteins destined for active nuclear import to the nuclear transport machinery. Cargo proteins interact with the importin-α armadillo repeat domain via nuclear localization sequences (NLSs), short amino acids motifs enriched in Lys and Arg residues. Plant genomes typically encode several importin-α paralogs that can have both specific and partially redundant functions. Although some cargos are preferentially imported by a distinct importin-α, it remains unknown how this specificity is generated and to what extent cargos compete for binding to nuclear transport receptors. Here we report that the effector protein HaRxL106 from the oomycete pathogen Hyaloperonospora arabidopsidis co-opts the host cell's nuclear import machinery. We use HaRxL106 as a probe to determine redundant and specific functions of importin-α paralogs from Arabidopsis thaliana. A crystal structure of the importin-α3/MOS6 armadillo repeat domain suggests that five of the six Arabidopsis importin-αs expressed in rosette leaves have an almost identical NLS binding site. Comparison of the importin-α binding affinities of HaRxL106 and other cargos in vitro and in plant cells suggests that relatively small affinity differences in vitro affect the rate of transport complex formation in vivo. Our results suggest that cargo affinity for importin-α, sequence variation at the importin-α NLS binding sites and tissue-specific expression levels of importin-αs determine formation of cargo/importin-α transport complexes in plant cells.

Rescooped by Shaikhul Islam from Plant roots and rhizosphere
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Variation in Virus Symptom Development and Root Architecture Attributes at the Onset of Storage Root Initiation in ‘Beauregard’ Sweetpotato Plants Grown with or without Nitrogen

Variation in Virus Symptom Development and Root Architecture Attributes at the Onset of Storage Root Initiation in ‘Beauregard’ Sweetpotato Plants Grown with or without Nitrogen | Molecular Biology and Life Science | Scoop.it

It has been shown that virus infections, often symptomless, significantly limit sweetpotato productivity, especially in regions characterized by low input agricultural systems. In sweetpotatoes, the successful emergence and development of lateral roots (LRs), the main determinant of root architecture, determines the competency of adventitious roots to undergo storage root initiation. This study aimed to investigate the effect of some plant viruses on root architecture attributes during the onset of storage root initiation in ‘Beauregard’ sweetpotatoes that were grown with or without the presence of nitrogen. In two replicate experiments, virus-tested plants consistently failed to show visible symptoms at 20 days regardless of nitrogen treatment. In both experiments, the severity of symptom development among infected plants ranged from 25 to 118% when compared to the controls (virus tested plants grown in the presence of nitrogen). The presence of a complex of viruses (Sweet potato feathery mottle virus, Sweet potato virus G, Sweet potato virus C, and Sweet potato virus 2) was associated with 51% reduction in adventitious root number among plants grown without nitrogen. The effect of virus treatments on first order LR development depended on the presence or absence of nitrogen. In the presence of nitrogen, only plants infected with Sweet potato chlorotic stunt virus showed reductions in first order LR length, number, and density, which were decreased by 33%, 12%, and 11%, respectively, when compared to the controls. In the absence of nitrogen, virus tested and infected plants manifested significant reductions for all first order LR attributes. These results provide evidence that virus infection directly influences sweetpotato yield potential by reducing both the number of adventitious roots and LR development. These findings provide a framework for understanding how virus infection reduces sweetpotato yield and could lead to the development of novel strategies to mitigate virus effects on sweetpotato productivity.


Via Christophe Jacquet
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Rescooped by Shaikhul Islam from Plant roots and rhizosphere
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The ABC Transporter ABCG1 Is Required for Suberin Formation in Potato Tuber Periderm

The ABC Transporter ABCG1 Is Required for Suberin Formation in Potato Tuber Periderm | Molecular Biology and Life Science | Scoop.it

The lipid biopolymer suberin plays a major role as a barrier both at plant-environment interfaces and in internal tissues, restricting water and nutrient transport. In potato (Solanum tuberosum), tuber integrity is dependent on suberized periderm. Using microarray analyses, we identified ABCG1, encoding an ABC transporter, as a gene responsive to the pathogen-associated molecular pattern Pep-13. Further analyses revealed that ABCG1 is expressed in roots and tuber periderm, as well as in wounded leaves. Transgenic ABCG1-RNAi potato plants with downregulated expression of ABCG1 display major alterations in both root and tuber morphology, whereas the aerial part of the ABCG1-RNAi plants appear normal. The tuber periderm and root exodermis show reduced suberin staining and disorganized cell layers. Metabolite analyses revealed reduction of esterified suberin components and hyperaccumulation of putative suberin precursors in the tuber periderm of RNA interference plants, suggesting that ABCG1 is required for the export of suberin components.


Via Christophe Jacquet
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Rescooped by Shaikhul Islam from Plant roots and rhizosphere
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Evidence supporting distinct functions of three cytosolic glutamine synthetases and two NADH-glutamate synthases in rice

Evidence supporting distinct functions of three cytosolic glutamine synthetases and two NADH-glutamate synthases in rice | Molecular Biology and Life Science | Scoop.it

The functions of the three isoenzymes of cytosolic glutamine synthetase (GS1;1, GS1;2, and GS1;3) and two NADH-glutamate synthases (NADH-GOGAT1 and NADH-GOGAT2) in rice (Oryza sativa L.) were characterized using a reverse genetics approach and spatial expression of the corresponding genes. OsGS1;2 and OsNADH-GOGAT1 were mainly expressed in surface cells of rice roots in an NH4 +-dependent manner. Disruption of either gene by the insertion of endogenous retrotransposon Tos17 caused reduction in active tiller number and hence panicle number at harvest. Re-introduction of OsGS1;2 cDNA under the control of its own promoter into the knockout mutants successfully restored panicle number to wild-type levels. These results indicate that GS1;2 and NADH-GOGAT1 are important in the primary assimilation of NH4 + taken up by rice roots. OsGS1;1 and OsNADH-GOGAT2 were mainly expressed in vascular tissues of mature leaf blades. OsGS1;1 mutants showed severe reduction in growth rate and grain filling, whereas OsNADH-GOGAT2 mutants had marked reduction in spikelet number per panicle. Complementation of phenotypes seen in the OsGS1;1 mutant was successfully observed when OsGS1;1 was re-introduced. Thus, these two enzymes could be important in remobilization of nitrogen during natural senescence. Metabolite profiling data showed a crucial role of GS1;1 in coordinating metabolic balance in rice. Expression of OsGS1:3 was spikelet-specific, indicating that it is probably important in grain ripening and/or germination. Thus, these isoenzymes seem to possess distinct and non-overlapping functions and none was able to compensate for the individual function of another.


Via Christophe Jacquet
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Rescooped by Shaikhul Islam from Plant roots and rhizosphere
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Signal interactions in the regulation of root nitrate uptake

Signal interactions in the regulation of root nitrate uptake | Molecular Biology and Life Science | Scoop.it

In most aerobic soils, nitrate (NO3 –) is the main nitrogen source for plants and is often limiting for plant growth and development. To adapt to a changing environment, plants have developed complex regulatory mechanisms that involve short and long-range signalling pathways in response to both NO3 – availability in the soil and other physiological processes like growth or nitrogen (N) and carbon (C) metabolisms. Over the past decade, transcriptomic approaches largely contributed to the identification of molecular elements involved in these regulatory mechanisms, especially at the level of root NO3 – uptake. Most strikingly, the data obtained revealed the high level of interaction between N and both hormone and C signalling pathways, suggesting a strong dependence on growth, development, and C metabolism to adapt root NO3 – uptake to both external NO3 – availability and the N status of the plant. However, the signalling mechanisms involved in the cross-talk between N, C, and hormones for the regulation of root NO3 – uptake remain largely obscure. The aim of this review is to discuss the recent advances concerning the regulatory pathways controlling NO3 – uptake in response to N signalling, hormones, and C in the model plant Arabidopsis thaliana. Then, to further characterize the level of interaction between these signalling pathways we built on publicly available transcriptome data to determine how hormones and C treatments modify the gene network connecting root NO3 – transporters and their regulators.


Via Christophe Jacquet
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Rescooped by Shaikhul Islam from Plant-Microbe Symbiosis
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MinION USB stick gene sequencer finally comes to market

MinION USB stick gene sequencer finally comes to market | Molecular Biology and Life Science | Scoop.it
Oxford Nanopore Technologies has finally delivered on its promise to bring personalized genome sequencing to the desktop. It is now time to see what their MinIon USB device can do.

Via Jean-Michel Ané
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Jean-Michel Ané's curator insight, September 26, 2014 1:03 AM

Watch the video... Now you know what I want for Christmas!

Rescooped by Shaikhul Islam from The Plant Microbiome
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Nature Communications: Shoot-derived cytokinins systemically regulate root nodulation

Nature Communications: Shoot-derived cytokinins systemically regulate root nodulation | Molecular Biology and Life Science | Scoop.it
Legumes establish symbiotic associations with nitrogen-fixing bacteria (rhizobia) in root nodules to obtain nitrogen. Legumes control nodule number through long-distance communication between roots and shoots, maintaining the proper symbiotic balance. Rhizobial infection triggers the production of mobile CLE-RS1/2 peptides in Lotus japonicus roots; the perception of the signal by receptor kinase HAR1 in shoots presumably induces the production of an unidentified shoot-derived inhibitor (SDI) that translocates to roots and blocks further nodule development. Here we show that, CLE-RS1/2-HAR1 signalling activates the production of shoot-derived cytokinins, which have an SDI-like capacity to systemically suppress nodulation. In addition, we show that LjIPT3 is involved in nodulation-related cytokinin production in shoots. The expression of LjIPT3 is activated in an HAR1-dependent manner. We further demonstrate shoot-to-root long-distance transport of cytokinin in L. japonicus seedlings. These findings add essential components to our understanding of how legumes control nodulation to balance nutritional requirements and energy status.

Via Ryohei Thomas Nakano, Stéphane Hacquard
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Rescooped by Shaikhul Islam from TAL effector science
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TAL effectors – pathogen strategies and plant resistance engineering - New Phytol.

TAL effectors – pathogen strategies and plant resistance engineering - New Phytol. | Molecular Biology and Life Science | Scoop.it

(via T. Schreiber, thx)

Boch et al, 2014

Transcription activator-like effectors (TALEs) from plant pathogenic Xanthomonas spp. and the related RipTALs from Ralstonia solanacearum are DNA-binding proteins with a modular DNA-binding domain. This domain is both predictable and programmable, which simplifies elucidation of TALE function in planta and facilitates generation of DNA-binding modules with desired specificity for biotechnological approaches. Recently identified TALE host target genes that either promote or stop bacterial disease provide new insights into how expression of TALE genes affects the plant–pathogen interaction. Since its elucidation the TALE code has been continuously refined and now provides a mature tool that, in combination with transcriptome profiling, allows rapid isolation of novel TALE target genes. The TALE code is also the basis for synthetic promoter-traps that mediate recognition of TALE or RipTAL proteins in engineered plants. In this review, we will summarize recent findings in plant-focused TALE research. In addition, we will provide an outline of the newly established gene isolation approach for TALE or RipTAL host target genes with an emphasis on potential pitfalls.


Via dromius
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Rescooped by Shaikhul Islam from Plant microbiome studies
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Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics

Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics | Molecular Biology and Life Science | Scoop.it
Symbioses represent a frequent and successful lifestyle on earth and lichens are one of their classic examples. Recently, bacterial communities were identified as stable, specific and structurally integrated partners of the lichen symbiosis, but their role has remained largely elusive in comparison to the well-known functions of the fungal and algal partners. We have explored the metabolic potentials of the microbiome using the lung lichen Lobaria pulmonaria as the model. Metagenomic and proteomic data were comparatively assessed and visualized by Voronoi treemaps. The study was complemented with molecular, microscopic and physiological assays. We have found that more than 800 bacterial species have the ability to contribute multiple aspects to the symbiotic system, including essential functions such as (i) nutrient supply, especially nitrogen, phosphorous and sulfur, (ii) resistance against biotic stress factors (that is, pathogen defense), (iii) resistance against abiotic factors, (iv) support of photosynthesis by provision of vitamin B12, (v) fungal and algal growth support by provision of hormones, (vi) detoxification of metabolites, and (vii) degradation of older parts of the lichen thallus. Our findings showed the potential of lichen-associated bacteria to interact with the fungal as well as algal partner to support health, growth and fitness of their hosts. We developed a model of the symbiosis depicting the functional multi-player network of the participants, and argue that the strategy of functional diversification in lichens supports the longevity and persistence of lichens under extreme and changing ecological conditions.

Via Jean-Michel Ané, Francis Martin, Stéphane Hacquard, Nina Dombrowski
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Rescooped by Shaikhul Islam from Plant-Microbe Symbiosis
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Expression of novel cytosolic malate dehydrogenases (cMDH) in Lupinus angustifolius nodules during phosphorus starvation

During P deficiency, the increased activity of malate dehydrogenase (MDH, EC 1.1.1.37) can lead to malate accumulation. Cytosolic- and nodule-enhanced MDH (cMDH and neMDH, respectively) are known isoforms, which contribute to MDH activity in root nodules. The aim of this study was to investigate the role of the cMDH isoforms in nodule malate supply under P deficiency. Nodulated lupins (Lupinus angustifolius var. Tanjil) were hydroponically grown at adequate P (+P) or low P (–P). Total P concentration in nodules decreased under P deficiency, which coincided with an increase in total MDH activity. A consequence of higher MDH activity was the enhanced accumulation of malate derived from dark CO2 fixation via PEPC and not from pyruvate. Although no measurable neMDH presence could be detected via PCR, gene-specific primers detected two 1 kb amplicons of cMDH, designated LangMDH1 (corresponding to +P, HQ690186) andLangMDH2 (corresponding to–P, HQ690187), respectively. Sequencing analyses of these cMDH amplicons showed them to be 96% identical on an amino acid level. There was a high degree of diversification between proteins detected in this study and other known MDH proteins, particularly those from other leguminous plants. Enhanced malate synthesis in P-deficient nodules was achieved via increased anaplerotic CO2fixation and subsequent higher MDH activities. Novel isoforms of cytosolic MDH may be involved, as shown by gene expression of specific genes under P deficiency.


Via Jean-Michel Ané
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Rescooped by Shaikhul Islam from Plants and Microbes
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Frontiers: Effector proteins of rust fungi (2014)

Frontiers: Effector proteins of rust fungi (2014) | Molecular Biology and Life Science | Scoop.it

Rust fungi include many species that are devastating crop pathogens. To develop resistant plants, a better understanding of rust virulence factors, or effector proteins, is needed. Thus far, only six rust effector proteins have been described: AvrP123, AvrP4, AvrL567, AvrM, RTP1 and PGTAUSPE-10-1. Although some are well established model proteins used to investigate mechanisms of immune receptor activation (avirulence activities) or entry into plant cells, how they work inside host tissues to promote fungal growth remains unknown. The genome sequences of four rust fungi (two Melampsoraceae and two Pucciniaceae) have been analyzed so far. Genome-wide analyses of these species, as well as transcriptomics performed on a broader range of rust fungi, revealed hundreds of small secreted proteins considered as rust candidate secreted effector proteins (CSEPs). The rust community now needs high-throughput approaches (effectoromics) to accelerate effector discovery/characterization and to better understand how they function in planta. However, this task is challenging due to the non-amenability of rust pathosystems (obligate biotrophs infecting crop plants) to traditional molecular genetic approaches mainly due to difficulties in culturing these species in vitro. The use of heterologous approaches should be promoted in the future.


Via Kamoun Lab @ TSL
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Rescooped by Shaikhul Islam from Plant roots and rhizosphere
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Frontiers | The role of mycorrhizal associations in plant potassium nutrition | Plant Traffic and Transport

Frontiers | The role of mycorrhizal associations in plant potassium nutrition | Plant Traffic and Transport | Molecular Biology and Life Science | Scoop.it
Potassium (K+) is one of the most abundant elements of soil composition but its 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.

Via Christophe Jacquet
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Rescooped by Shaikhul Islam from Plants and Microbes
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Nature Communications: Long-distance endosome trafficking drives fungal effector production during plant infection (2014)

Nature Communications: Long-distance endosome trafficking drives fungal effector production during plant infection (2014) | Molecular Biology and Life Science | Scoop.it

To cause plant disease, pathogenic fungi can secrete effector proteins into plant cells to suppress plant immunity and facilitate fungal infection. Most fungal pathogens infect plants using very long strand-like cells, called hyphae, that secrete effectors from their tips into host tissue. How fungi undergo long-distance cell signalling to regulate effector production during infection is not known. Here we show that long-distance retrograde motility of early endosomes (EEs) is necessary to trigger transcription of effector-encoding genes during plant infection by the pathogenic fungus Ustilago maydis. We demonstrate that motor-dependent retrograde EE motility is necessary for regulation of effector production and secretion during host cell invasion. We further show that retrograde signalling involves the mitogen-activated kinase Crk1 that travels on EEs and participates in control of effector production. Fungal pathogens therefore undergo long-range signalling to orchestrate host invasion.


Via Kamoun Lab @ TSL
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Rescooped by Shaikhul Islam from Plant-Microbe Symbiosis
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Orchids and fungi: An unexpected case of symbiosis

Orchids and fungi: An unexpected case of symbiosis | Molecular Biology and Life Science | Scoop.it
The majority of orchids are found in habitats where light may be a limiting factor. However, orchids are found in a wide range of habitats and range in their photosynthetic capabilities. For those orchids that are fully photosynthetic, and presumably capable of acquiring their own organic carbon, are they less reliant on a specific suite of mycorrhizal fungi? A new study that examines fungal diversity in orchids in open sunny habitats, questions this assumption.

Via Jean-Michel Ané
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Rescooped by Shaikhul Islam from Plant roots and rhizosphere
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Growth rate distribution in the forming lateral root of arabidopsis

Growth rate distribution in the forming lateral root of arabidopsis | Molecular Biology and Life Science | Scoop.it

Background and Aims Microscopic observations of lateral roots (LRs) in Arabidopsis thaliana reveal that the cross-sectional shape of the organ changes from its basal to its apical region. The founder cells for LRs are elongated along the parent root axis, and thus from the site of initiation the base of LRs resemble an ellipse. The circumference of the apical part of LRs is usually a circle. The objective of this study was to analyse the characteristics of changes in the growth field of LRs possessing various shapes in their basal regions.

Methods The LRs of the wild type (Col-0) and two transgenic arabidopsis lines were analysed. On the basis of measurements of the long and short diameters (DL and DS, respectively) of the ellipse-like figure representing the bases of particular LRs, their asymmetry ratios (DL/DS) were determined. Possible differences between accessions were analysed by applying statistical methods.

Key Results No significant differences between accessions were detected. Comparisons were therefore made of the maximal, minimal and mean value of the ratio of all the LRs analysed. Taking into consideration the lack of circular symmetry of the basal part, rates of growth were determined at selected points on the surface of LRs by the application of the growth tensor method, a mathematical tool previously applied only to describe organs with rotational symmetry. Maps showing the distribution of growth rates were developed for surfaces of LRs of various asymmetry ratios.

Conclusions The maps of growth rates on the surfaces of LRs having various shapes of the basal part show differences in both the geometry and the manner of growth, thus indicating that the manner of growth of the LR primordium is correlated to its shape. This is the first report of a description of growth of an asymmetric plant organ using the growth tensor method. The mathematical modelling adopted in the study provides new insights into plant organ formation and shape.


Via Christophe Jacquet
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Rescooped by Shaikhul Islam from Plant roots and rhizosphere
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Natural products in Glycyrrhiza glabra (licorice) rhizome imaged at the cellular level by atmospheric pressure matrix-assisted laser desorption/ionization tandem mass spectrometry imaging

Natural products in Glycyrrhiza glabra (licorice) rhizome imaged at the cellular level by atmospheric pressure matrix-assisted laser desorption/ionization tandem mass spectrometry imaging | Molecular Biology and Life Science | Scoop.it
The rhizome of Glycyrrhiza glabra (licorice) was analyzed by high-resolution mass spectrometry imaging and tandem mass spectrometry imaging. An atmospheric pressure matrix-assisted laser desorption/ionization imaging ion source was combined with an orbital trapping mass spectrometer in order to obtain high-resolution imaging in mass and space. Sections of the rhizome were imaged with a spatial resolution of 10 μm in the positive ion mode, and a large number of secondary metabolites were localized and identified based on their accurate mass and MS/MS fragmentation patterns. Major tissue-specific metabolites, including free flavonoids, flavonoid glycosides and saponins, were successfully detected and visualized in images, showing their distributions at the cellular level. The analytical power of the technique was tested in the imaging of two isobaric licorice saponins with a mass difference of only 0.02 Da. With a mass resolving power of 140 000 and a bin width of 5 ppm in the image processing, the two compounds were well resolved in full-scan mode, and appeared with different distributions in the tissue sections. The identities of the compounds and their distributions were validated in a subsequent MS/MS imaging experiment, thereby confirming their identities and excluding possible analyte interference. The use of high spatial resolution, high mass resolution and tandem mass spectrometry in imaging experiments provides significant information about the biosynthetic pathway of flavonoids and saponins in legume species, combing the spatially resolved chemical information with morphological details at the microscopic level. Furthermore, the technique offers a scheme capable of high-throughput profiling of metabolites in plant tissues.

Via Christophe Jacquet
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Rescooped by Shaikhul Islam from Plant roots and rhizosphere
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Light modulated activity of root alkaline/neutral invertase involves the interaction with 14-3-3 proteins

Light modulated activity of root alkaline/neutral invertase involves the interaction with 14-3-3 proteins | Molecular Biology and Life Science | Scoop.it

Alkaline/neutral invertases (A/N-Invs) are now recognized as essential proteins in plant life. They catalyze the irreversible break-down of sucrose into glucose and fructose and thus supply the cells with energy as well as signaling molecules. In this study we report on a mechanism that affects the activity of the cytosolic invertase AtCINV1 (At-A/N-InvG or AT1G35580). We demonstrate that Ser547 at the extreme C-terminus of the AtCINV1 protein is a substrate of calcium-dependent kinases (CPK3 and 21) and that phosphorylation creates a high-affinity binding site for 14-3-3 proteins. The invertase as such has basal activity, but we provide evidence that interaction with 14-3-3 proteins enhances its activity. The analysis of three quadruple 14-3-3 mutants generated from six T-DNA insertion mutants of the non-epsilon family shows both specificity as well as redundancy for this function of 14-3-3 proteins. The strong reduction in hexose levels in the roots of one 14-3-3 quadruple mutant plant is in line with the activating function of 14-3-3 proteins. The physiological relevance of this mechanism that affects A/N invertase activity is underscored by the light induced activation and is another example of the central role of 14-3-3 proteins in mediating dark/light signaling. The nature of the light induced signal that travels from the shoot to root and the question whether this signal is transmitted via cytosolic Ca++ changes that activate calcium-dependent kinases, await further study.


Via Christophe Jacquet
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Rescooped by Shaikhul Islam from Plant-Microbe Symbiosis
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Nitrogen signalling in plant interactions with associative and endophytic diazotrophic bacteria

Nitrogen signalling in plant interactions with associative and endophytic diazotrophic bacteria | Molecular Biology and Life Science | Scoop.it

Some beneficial plant-interacting bacteria can biologically fix N2 to plant-available ammonium.


Via Jean-Michel Ané
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Rescooped by Shaikhul Islam from The Plant Microbiome
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PNAS: Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest

PNAS: Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest | Molecular Biology and Life Science | Scoop.it

Abstract The phyllosphere—the aerial surfaces of plants, including leaves—is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density–growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant–microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function.


Via Stéphane Hacquard
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Rescooped by Shaikhul Islam from The Plant Microbiome
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Nature communications: Niche and host-associated functional signatures of the root surface microbiome

Nature communications: Niche and host-associated functional signatures of the root surface microbiome | Molecular Biology and Life Science | Scoop.it

Plant microbiomes are critical to host adaptation and impact plant productivity and health. Root-associated microbiomes vary by soil and host genotype, but the contribution of these factors to community structure and metabolic potential has not been fully addressed. Here we characterize root microbial communities of two disparate agricultural crops grown in the same natural soil in a controlled and replicated experimental system. Metagenomic (genetic potential) analysis identifies a core set of functional genes associated with root colonization in both plant hosts, and metatranscriptomic (functional expression) analysis revealed that most genes enriched in the root zones are expressed. Root colonization requires multiple functional capabilities, and these capabilities are enriched at the community level. Differences between the root-associated microbial communities from different plants are observed at the genus or species level, and are related to root-zone environmental factors.


Via Stéphane Hacquard
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Rescooped by Shaikhul Islam from MycorWeb Plant-Microbe Interactions
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Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains | Molecular Biology and Life Science | Scoop.it

Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently~11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.


Via Francis Martin
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Diffuse symbioses: roles of plant–plant, plant–microbe and microbe–microbe interactions in structuring the soil microbiome - Bakker - 2013 - Molecular Ecology - Wiley Online Library

Diffuse symbioses: roles of plant–plant, plant–microbe and microbe–microbe interactions in structuring the soil microbiome - Bakker - 2013 - Molecular Ecology - Wiley Online Library | Molecular Biology and Life Science | Scoop.it

A conceptual model emphasizing direct host–microbe interactions has dominated work on host-associated microbiomes. To understand plant–microbiome associations, however, broader influences on microbiome composition and functioning must be incorporated, such as those arising from plant–plant and microbe–microbe interactions. We sampled soil microbiomes associated with target plant species (Andropogon gerardii, Schizachyrium scoparium, Lespedeza capitata, Lupinus perennis) grown in communities varying in plant richness (1-, 4-, 8- or 16-species). We assessed Streptomyces antagonistic activity and analysed bacterial and Streptomyces populations via 454 pyrosequencing. Host plant species and plant richness treatments altered networks of coassociation among bacterial taxa, suggesting the potential for host plant effects on the soil microbiome to include changes in microbial interaction dynamics and, consequently, co-evolution. Taxa that were coassociated in the rhizosphere of a given host plant species often showed consistent correlations between operational taxonomic unit (OTU) relative abundance and Streptomyces antagonistic activity, in the rhizosphere of that host. However, in the rhizosphere of a different host plant species, the same OTUs showed no consistency, or a different pattern of responsiveness to such biotic habitat characteristics. The diversity and richness of bacterial and Streptomyces communities exhibited distinct relationships with biotic and abiotic soil characteristics. The rhizosphere soil microbiome is influenced by a complex and nested array of factors at varying spatial scales, including plant community, plant host, soil edaphics and microbial taxon and community characteristics.


Via Nina Dombrowski
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Rescooped by Shaikhul Islam from Plant-Microbe Symbiosis
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RNA-seq transcriptome profiling reveals that Medicago truncatula nodules acclimate N2 fixation before emerging P deficiency reaches the nodules

Legume nodules are plant tissues with an exceptionally high concentration of phosphorus (P), which, when there is scarcity of P, is preferentially maintained there rather than being allocated to other plant organs. The hypothesis of this study was that nodules are affected before the P concentration in the organ declines during whole-plant P depletion. Nitrogen (N2) fixation and P concentration in various organs were monitored during a whole-plant P-depletion process in Medicago truncatula. Nodule gene expression was profiled through RNA-seq at day 5 of P depletion. Until that point in time P concentration in leaves reached a lower threshold but was maintained in nodules. N2-fixation activity per plant diverged from that of fully nourished plants beginning at day 5 of the P-depletion process, primarily because fewer nodules were being formed, while the activity of the existing nodules was maintained for as long as two weeks into P depletion. RNA-seq revealed nodule acclimation on a molecular level with a total of 1140 differentially expressed genes. Numerous genes for P remobilization from organic structures were increasingly expressed. Various genes involved in nodule malate formation were upregulated, while genes involved in fermentation were downregulated. The fact that nodule formation was strongly repressed with the onset of P deficiency is reflected in the differential expression of various genes involved in nodulation. It is concluded that plants follow a strategy to maintain N2 fixation and viable leaf tissue as long as possible during whole-plant P depletion to maintain their ability to react to emerging new P sources (e.g. through active P acquisition by roots).


Via Jean-Michel Ané
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Rescooped by Shaikhul Islam from Plants and Microbes
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New Phytologist: Hitchhiker's guide to multi-dimensional plant pathology (2014)

New Phytologist: Hitchhiker's guide to multi-dimensional plant pathology (2014) | Molecular Biology and Life Science | Scoop.it

Filamentous pathogens pose a substantial threat to global food security. One central question in plant pathology is how pathogens cause infection and manage to evade or suppress plant immunity to promote disease. With many technological advances over the past decade, including DNA sequencing technology, an array of new tools has become embedded within the toolbox of next-generation plant pathologists. By employing a multidisciplinary approach plant pathologists can fully leverage these technical advances to answer key questions in plant pathology, aimed at achieving global food security. This review discusses the impact of: cell biology and genetics on progressing our understanding of infection structure formation on the leaf surface; biochemical and molecular analysis to study how pathogens subdue plant immunity and manipulate plant processes through effectors; genomics and DNA sequencing technologies on all areas of plant pathology; and new forms of collaboration on accelerating exploitation of big data. As we embark on the next phase in plant pathology, the integration of systems biology promises to provide a holistic perspective of plant–pathogen interactions from big data and only once we fully appreciate these complexities can we design truly sustainable solutions to preserve our resources.


Via Kamoun Lab @ TSL
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Marie Zen Attitude's curator insight, July 26, 2014 8:21 AM

Un petit lien spécial pour Emeric ;)