Genome‐wide analyses of epigenomic and transcriptomic profiles provide extensive resources for discovering epigenetic regulatory mechanisms. However, the construction of functionally relevant ...hypotheses from correlative patterns and the rigorous testing of these hypotheses may be challenging. We combined bioinformatics‐driven hypothesis building with mutant analyses to identify potential epigenetic mechanisms using the model plant Arabidopsis thaliana. Genome‐wide maps of nine histone modifications produced by ChIP‐seq were used together with a strand‐specific RNA‐seq dataset to profile the epigenome and transcriptome of Arabidopsis. Combinatorial chromatin patterns were described by 42 major chromatin states with selected states validated using the re‐ChIP assay. The functional relevance of chromatin modifications was analyzed using the ANchored CORrelative Pattern (ANCORP) method and a newly developed state‐specific effects analysis (SSEA) method, which interrogates individual chromatin marks in the context of combinatorial chromatin states. Based on results from these approaches, we propose the hypothesis that cytosine methylation (5mC) and histone methylation H3K36me may synergistically repress production of natural antisense transcripts (NATs) in the context of actively expressed genes. Mutant analyses supported this proposed model at a significant proportion of the tested loci. We further identified polymerase‐associated factor as a potential repressor for NAT abundance. Although the majority of tested NATs were found to localize to the nucleus, we also found evidence for cytoplasmically partitioned NATs. The significance of the subcellular localization of NATs and their biological functions remain to be defined.
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Arsenic (As) contamination in paddy soil can cause phytotoxicity and elevated As accumulation in rice grain. Rice varieties vary in As uptake and tolerance, but the underlying mechanisms remain ...unclear. In this study, the aus variety Kasalath was found to be more tolerant to arsenate As(V) than the japonica variety Nipponbare, but the two varieties showed similar arsenite As(III) tolerance. Nipponbare took up more phosphate (Pi) and As(V) than Kasalath. The expression of genes for Pi transporters or Pi homeostasis regulation was quantified. Nipponbare showed 2- to 3-fold higher expression of the Pi transporter genes OsPT2 and OsPT8 than Kasalath. Two ospt8 mutants were isolated from the Kasalath background and compared with an ospt8 mutant in the Nipponbare background. Mutation in OsPT8 in both backgrounds decreased As(V) uptake by 33–57%, increased As(V) tolerance assayed by root elongation by >100-fold, and abolished the varietal differences in As(V) uptake and tolerance. The results show that OsPT8 plays a key role in As(V) uptake and that As(V) uptake mediated by OsPT8 exerts a profound toxic effect on root elongation. The results also suggest that differential OsPT8 expression explains the varietal differences in As(V) uptake and tolerance between Kasalath and Nipponbare.
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Flavodiiron proteins (FLVs) catalyze the reduction of oxygen to water by using electrons from Photosystem I (PSI). In several photosynthetic organisms such as cyanobacteria, green algae, mosses and ...gymnosperms, FLV-dependent electron flow protects PSI from over-reduction and consequent damage especially under fluctuating light conditions. In this work we investigated biochemical and structural properties of FLVA and FLVB from the model moss Physcomitrium patens. The two proteins, expressed and purified from Escherichia coli, bind both iron and flavin cofactors and show NAD(P)H oxidase activity as well as oxygen reductase capacities. Moreover, the co-expression of both FLVA and FLVB, coupled to a tandem affinity purification procedure with two different affinity tags, enabled the isolation of the stable and catalytically active FLVA/B hetero tetrameric protein complex with cooperative nature. The multimeric organization was shown to be stabilized by inter-subunit disulfide bonds. This investigation provides valuable new information on the biochemical properties of FLVs, with new insights into their in vivo activity.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The contribution of SOS1 (for Salt Overly Sensitive 1), encoding a sodium/proton antiporter, to plant salinity tolerance was analyzed in wild-type and RNA interference (RNAi) lines of the halophytic ...Arabidopsis (Arabidopsis thaliana)-relative Thellungiella salsuginea. Under all conditions, SOS1 mRNA abundance was higher in Thellungiella than in Arabidopsis. Ectopic expression of the Thellungiella homolog ThSOS1 suppressed the salt-sensitive phenotype of a Saccharomyces cerevisiae strain lacking sodium ion (Na⁺) efflux transporters and increased salt tolerance of wild-type Arabidopsis. thsos1-RNAi lines of Thellungiella were highly salt sensitive. A representative line, thsos1-4, showed faster Na⁺ accumulation, more severe water loss in shoots under salt stress, and slower removal of Na⁺ from the root after removal of stress compared with the wild type. thsos1-4 showed drastically higher sodium-specific fluorescence visualized by CoroNa-Green, a sodium-specific fluorophore, than the wild type, inhibition of endocytosis in root tip cells, and cell death in the adjacent elongation zone. After prolonged stress, Na⁺ accumulated inside the pericycle in thsos1-4, while sodium was confined in vacuoles of epidermis and cortex cells in the wild type. RNAi-based interference of SOS1 caused cell death in the root elongation zone, accompanied by fragmentation of vacuoles, inhibition of endocytosis, and apoplastic sodium influx into the stele and hence the shoot. Reduction in SOS1 expression changed Thellungiella that normally can grow in seawater-strength sodium chloride solutions into a plant as sensitive to Na⁺ as Arabidopsis.
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An investigation was initiated to examine the effects of nanoscale zinc oxide particles on plant growth and development. In view of the widespread cultivation of peanut in India and in other parts of ...the globe and in view of the potential influence of zinc on its growth, this plant was chosen as the model system. Peanut seeds were separately treated with different concentrations of nanoscale zinc oxide (ZnO) and chelated bulk zinc sulfate (ZnSO
4
) suspensions (a common zinc supplement), respectively and the effect this treatment had on seed germination, seedling vigor, plant growth, flowering, chlorophyll content, pod yield and root growth were studied. Treatment of nanoscale ZnO (25 nm mean particle size) at 1000 ppm concentration promoted both seed germination and seedling vigor and in turn showed early establishment in soil manifested by early flowering and higher leaf chlorophyll content. These particles proved effective in increasing stem and root growth. Pod yield per plant was 34% higher compared to chelated bulk ZnSO
4
. Consequently, a field experiment was conducted during Rabi seasons of 2008-2009 and 2009-2010 with the foliar application of nanoscale ZnO particles at 15 times lower dose compared to the chelated ZnSO
4
recommended and we recorded 29.5% and 26.3% higher pod yield, respectively, compared to chelated ZnSO
4
. The inhibitory effect with higher nanoparticle concentration (2000 ppm) reveals the need for judicious usage of these particles in such applications. This is the first report on the effect of nanoscale particles on peanut growth and yield.
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Root nodules formed by plants of the nitrogen-fixing clade (NFC) are symbiotic organs that function in the maintenance and metabolic integration of large populations of nitrogen-fixing bacteria. ...These organs feature unique characteristics and processes, including their tissue organization, the presence of specific infection structures called infection threads, endocytotic uptake of bacteria, symbiotic cells carrying thousands of intracellular bacteria without signs of immune responses, and the integration of symbiont and host metabolism. The early stages of nodulation are governed by a few well-defined functions, which together constitute the common symbiosis-signaling pathway (CSSP). The CSSP activates a set of transcription factors (TFs) that orchestrate nodule organogenesis and infection. The later stages of nodule development require the activation of hundreds to thousands of genes, mostly expressed in symbiotic cells. Many of these genes are only active in symbiotic cells, reflecting the unique nature of nodules as plant structures. Although how the nodule-specific transcriptome is activated and connected to early CSSP-signaling is poorly understood, candidate TFs have been identified using transcriptomic approaches, and the importance of epigenetic and chromatin-based regulation has been demonstrated. We discuss how gene regulation analyses have advanced our understanding of nodule organogenesis, the functioning of symbiotic cells, and the evolution of symbiosis in the NFC.
Nitric oxide (NO) is a signaling and defense molecule of major importance in living organisms. In the model legume Medicago truncatula, NO production has been detected in the nitrogen fixation zone ...of the nodule, but the systems responsible for its synthesis are yet unknown and its role in symbiosis is far from being elucidated. In this work, using pharmacological and genetic approaches, we explored the enzymatic source of NO production in M. truncatula-Sinorhizobium meliloti nodules under normoxic and hypoxic conditions. When transferred from normoxia to hypoxia, nodule NO production was rapidly increased, indicating that NO production capacity is present in functioning nodules and may be promptly up-regulated in response to decreased oxygen availability. Contrary to roots and leaves, nodule NO production was stimulated by nitrate and nitrite and inhibited by tungstate, a nitrate reductase inhibitor. Nodules obtained with either plant nitrate reductase RNA interference double knockdown (MtNR1/2) or bacterial nitrate reductase-deficient (napA) and nitrite reductase-deficient (nirK) mutants, or both, exhibited reduced nitrate or nitrite reductase activities and NO production levels. Moreover, NO production in nodules was found to be inhibited by electron transfer chain inhibitors, and nodule energy state (ATP-ADP ratio) was significantly reduced when nodules were incubated in the presence of tungstate. Our data indicate that both plant and bacterial nitrate reductase and electron transfer chains are involved in NO synthesis. We propose the existence of a nitrate-NO respiration process in nodules that could play a role in the maintenance of the energy status required for nitrogen fixation under oxygen-limiting conditions.
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Summary
Microorganisms, or ‘microbes’, have formed intimate associations with plants throughout the length of their evolutionary history. In extant plant systems microbes still remain an integral ...part of the ecological landscape, impacting plant health, productivity and long‐term fitness. Therefore, to properly understand the genetic wiring of plants, we must first determine what perception systems plants have evolved to parse beneficial from commensal from pathogenic microbes. In this review, we consider some of the most recent advances in how plants respond at the molecular level to different microbial lifestyles. Further, we cover some of the means by which microbes are able to manipulate plant signaling pathways through altered destructiveness and nutrient sinks, as well as the use of effector proteins and micro‐RNAs (miRNAs). We conclude by highlighting some of the major questions still to be answered in the field of plant‐microbe research, and suggest some of the key areas that are in greatest need of further research investment. The results of these proposed studies will have impacts in a wide range of plant research disciplines and will, ultimately, translate into stronger agronomic crops and forestry stock, with immune perception and response systems bred to foster beneficial microbial symbioses while repudiating pathogenic symbioses.
Significance Statement
Ecological research is increasingly demonstrating that the microbes associated with plant tissues have as much, if not more, impact on plant physiology and fitness than the plant genome itself. Therefore, when studying plant systems, we must take into account the role of plant‐microbe symbioses. We review, here, recent advances in our understanding of how plants interact with their microbial community and highlight areas of pressing need for further research investment.
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