Oxidative stress tolerance in plants: novel interplay between auxin and reactive oxygen species signaling

A single viral amino acid shapes the root system architecture of a plant host upon virus infection

BACKGROUND

Grapevine fanleaf virus (GFLV) is one of the most detrimental viral pathogens of grapevines worldwide but no information is available on its effect on the root system architecture (RSA) of plant hosts. We used two wildtype GFLV strains and their single amino acid mutants to assess RSA traits in infected Nicotiana benthamiana and evaluate transcriptomic changes in host root gene expression in replicated time course 3'RNA-Seq experiments. Mutations targeted the multi-functional GFLV-encoded protein 1EPol*/Sd, a putative RNA-dependent RNA polymerase and determinant of foliar symptoms in N. benthamiana plants.

RESULTS

Plant infection with wildtype GFLV strain GHu and mutant GFLV strain F13 1EPol G802K, both carrying a lysine in position 802 of protein 1EPol*/Sd, resulted in a significantly lower number of root tips (-30%), and a significantly increased average root diameter (+ 20%) at 17 days post inoculation (dpi) in comparison with roots of mock inoculated plants. In contrast, the RSA of plants infected with wildtype GFLV strain F13 and mutant GFLV strain GHu 1EPol K802G, both carrying a glycine in position 802 of protein 1EPol*/Sd, resembled that of mock inoculated plants. Modifications of RSA traits were not associated with GFLV titer. Root tissue transcriptome analysis at 17 dpi indicated dysregulation of pattern recognition receptors, plant hormones, RNA silencing, and genes related to the production of reactive oxygen species (ROS). For wildtype GFLV strain GHu, RSA modifications were correlated with an abundant accumulation of ROS in the pericycle of primary roots at 7 dpi and the duration of vein clearing symptom expression in apical leaves. Dysegulation of a hypersensitive response was an overarching gene ontology found through enrichment analyses of 3'RNA-Seq data.

CONCLUSIONS

Our findings revealed the causative role of lysine in position 802 of protein 1EPol*/Sd in a novel RSA phenotype during viral infection and documented GFLV-N. benthamiana interactions at the root level based on (i) antiviral response, (ii) receptor mediated production of ROS, and (iii) hormone regulation. A correlation between above and below ground symptoms was reported for the first time in plants infected with wildtype GFLV strain GHu. Further work is warranted to test whether the modified RSA of a plant host might impact GFLV acquisition and transmission by the ectoparasitic dagger nematode Xiphinema index.

Comparative transcriptomics analysis reveals defense mechanisms of Manihot esculenta Crantz against Sri Lanka Cassava MosaicVirus

BACKGROUND

Cassava mosaic disease (CMD), caused by Sri Lankan cassava mosaic virus (SLCMV) infection, has been identified as a major pernicious disease in Manihot esculenta Crantz (cassava) plantations. It is widespread in Southeast Asia, especially in Thailand, which is one of the main cassava supplier countries. With the aim of restricting the spread of SLCMV, we explored the gene expression of a tolerant cassava cultivar vs. a susceptible cassava cultivar from the perspective of transcriptional regulation and the mechanisms underlying plant immunity and adaptation.

RESULTS

Transcriptomic analysis of SLCMV-infected tolerant (Kasetsart 50 [KU 50]) and susceptible (Rayong 11 [R 11]) cultivars at three infection stages-that is, at 21 days post-inoculation (dpi) (early/asymptomatic), 32 dpi (middle/recovery), and 67 dpi (late infection/late recovery)-identified 55,699 expressed genes. Differentially expressed genes (DEGs) between SLCMV-infected KU 50 and R 11 cultivars at (i) 21 dpi to 32 dpi (the early to middle stage), and (ii) 32 dpi to 67 dpi (the middle stage to late stage) were then identified and validated by real-time quantitative PCR (RT-qPCR). DEGs among different infection stages represent genes that respond to and regulate the viral infection during specific stages. The transcriptomic comparison between the tolerant and susceptible cultivars highlighted the role of gene expression regulation in tolerant and susceptible phenotypes.

CONCLUSIONS

This study identified genes involved in epigenetic modification, transcription and transcription factor activities, plant defense and oxidative stress response, gene expression, hormone- and metabolite-related pathways, and translation and translational initiation activities, particularly in KU 50 which represented the tolerant cultivar in this study.

Exploration of key drug target proteins highlighting their related regulatory molecules, functional pathways and drug candidates associated with delirium: evidence from meta-data analyses

BACKGROUND

Delirium is a prevalent neuropsychiatric medical phenomenon that causes serious emergency outcomes, including mortality and morbidity. It also increases the suffering and the economic burden for families and carers. Unfortunately, the pathophysiology of delirium is still unknown, which is a major obstacle to therapeutic development. The modern network-based system biology and multi-omics analysis approach has been widely used to recover the key drug target biomolecules and signaling pathways associated with disease pathophysiology. This study aimed to identify the major drug target hub-proteins associated with delirium, their regulatory molecules with functional pathways, and repurposable drug candidates for delirium treatment.

METHODS

We used a comprehensive proteomic seed dataset derived from a systematic literature review and the Comparative Toxicogenomics Database (CTD). An integrated multi-omics network-based bioinformatics approach was utilized in this study. The STRING database was used to construct the protein-protein interaction (PPI) network. The gene set enrichment and signaling pathways analysis, the regulatory transcription factors and microRNAs were conducted using delirium-associated genes. Finally, hub-proteins associated repurposable drugs were retrieved from CMap database.

RESULTS

We have distinguished 11 drug targeted hub-proteins (MAPK1, MAPK3, TP53, JUN, STAT3, SRC, RELA, AKT1, MAPK14, HSP90AA1 and DLG4), 5 transcription factors (FOXC1, GATA2, YY1, TFAP2A and SREBF1) and 6 microRNA (miR-375, miR-17-5, miR-17-5p, miR-106a-5p, miR-125b-5p, and miR-125a-5p) associated with delirium. The functional enrichment and pathway analysis revealed the cytokines, inflammation, postoperative pain, oxidative stress-associated pathways, developmental biology, shigellosis and cellular senescence which are closely connected with delirium development and the hallmarks of aging. The hub-proteins associated computationally identified repurposable drugs were retrieved from database. The predicted drug molecules including aspirin, irbesartan, ephedrine-(racemic), nedocromil, and guanidine were characterized as anti-inflammatory, stimulating the central nervous system, neuroprotective medication based on the existing literatures. The drug molecules may play an important role for therapeutic development against delirium if they are investigated more extensively through clinical trials and various wet lab experiments.

CONCLUSION

This study could possibly help future research on investigating the delirium-associated therapeutic target biomarker hub-proteins and repurposed drug compounds. These results will also aid understanding of the molecular mechanisms that underlie the pathophysiology of delirium onset and molecular function.

Mitigation of arsenic toxicity in rice by the co-inoculation of arsenate reducer yeast with multifunctional arsenite oxidizing bacteria

The study aimed to explicate the role of microbial co-inoculants for the mitigation of arsenic (As) toxicity in rice. Arsenate (AsV) reducer yeast Debaryomyces hansenii NBRI-Sh2.11 (Sh2.11) with bacterial strains of different biotransformation potential was attempted to develop microbial co-inoculants. An experiment to test their efficacy (yeast and bacterial strains) on plant growth and As uptake was conducted under a stressed condition of 20 mg kg-1 of arsenite (AsIII). A combination of Sh2.11 with an As(III)-oxidizer, Citrobacter sp. NBRI-B5.12 (B5.12), resulted in ∼90% decrease in grain As content as compared to Sh2.11 alone (∼40%). Reduced As accumulation in rice roots under co-treated condition was validated with SEM-EDS analysis. Enhanced As expulsion in the selected combination under in vitro conditions was found to be correlated with higher As content in the soil during their interaction with plants. Selected co-inoculant mediated enhanced nutrient uptake in association with better production of indole acetic acid (IAA) and gibberellic acid (GA) in shoot, support microbial co-inoculant mediated better biomass under stressful condition. Boosted defense response in association with enhanced glutathione-S-transferase (GST) and glutathione reductase (GR), activities under in vitro and in vivo conditions were observed. These results indicated that the As(III) oxidizer-B5.12 accelerated the As detoxification property of the As(V) reducer-Sh2.11. Henceforth, the results confer that the coupled reduction-oxidation process of the co-inoculant reduces the accumulation of As in rice grain. These co-inoculants can be further developed for field trials to achieve higher biomass with alleviated As toxicity in rice.

Foliar-applied nanoscale zero-valent iron (nZVI) and iron oxide (Fe3O4) induce differential responses in growth, physiology, antioxidative defense and biochemical indices in Leonurus cardiaca L

The impacts of nZVI and iron oxides on growth, physiology and elicitation of bioactive antioxidant metabolites in medicinal aromatic plants must be critically assessed to ensure their safe utilization within the food chain and achieve nutritional gains. The present study investigated and compared the morpho-physiological and biochemical changes of Leonurus cardiaca L. plants as affected by various concentrations (0, 250, 500 and 1000 mg L^-1) of nZVI and Fe₃O₄. The foliar uptake of nZVI was verified through Scanning Electron Microscopy (SEM) images and Energy Dispersive X-ray (EDX) analytical spectra. Plants exposed to nZVI at low concentration showed comparatively monotonic deposition of NPs on the surface of leaves, however, the agglomerate size of nZVI was raised as their doses increased, leading to remarkable changes in anatomical and biochemical traits. 250 mg L^-1 nZVI and 500 mg L^-1 Fe₃O₄ significantly (P < 0.05) increased plant dry matter accumulation by 37.8 and 27% over the control, respectively. The treatments of nZVI and Fe₃O₄ at 250 mg L^-1 significantly (P < 0.01) improved chlorophyll a content by 22.4% and 15.3% as compared to the control, and then a rapid decrease (by 14.8% and 4.1%) followed at 1000 mg L^-1, respectively. Both nZVI and Fe₃O₄ at 250 mg L^-1 had no significant impact on malondialdehyde (MDA) formation, however, at an exposure of 500-1000 mg L^-1, the MDA levels and cellular electrolyte leakage were increased. Although nZVI particles could be utilized by plants and enhanced the synthesis of chlorophylls and secondary metabolites, they appeared to be more toxic than Fe₃O₄ at 1000 mg L^-1. Exposure to nZVI levels showed positive, negative and or neutral impacts on leaf water content compared to control, while no significant difference was observed with Fe₃O₄ treatments. Soluble sugar, total phenolics and hyperoside content were significantly increased upon optimum concentrations of employed treatments-with 250 mg L^-1 nZVI being most superior. Among the extracts, those obtained from plants treated with 250-500 mg L^-1 nZVI revealed the strong antioxidant activity in terms of scavenging free radical (DPPH) and chelating ferrous ions. These results suggest that nZVI (at lower concentration) has alternative and additional benefits both as nano-fertilizer and nano-elicitor for biosynthesis of antioxidant metabolites in plants, but at high concentrations is more toxic than Fe₃O₄.

IbTLD modulates reactive oxygen species scavenging and DNA protection to confer salinity stress tolerance in tobacco

Plants accumulate reactive oxygen species (ROS) that may damage the cells under prolonged stress conditions. Reduction of the excessive ROS production can alleviate oxidative damage and enhance the survival rates under stress. TLDc-containing protein (TLD) was reported to confer tolerance to oxidative stress, but the regulatory mechanism of TLD remains unclear. In this study, we ectopically overexpressed the Ipomoea batatas TLDc gene (IbTLD) in tobacco and characterized its functions. RNA-sequencing analysis and Gene Ontology term enrichment analysis revealed that IbTLD up-regulates auxin-responsive genes in response to oxidative stress. Under salinity stress, the IbTLD transgenic lines showed higher germination rates, chlorophyll contents, and root lengths than wild type (W38). In addition, the IbTLD transgenic lines showed higher expression of ROS scavenging genes, nudix hydrolases, ROS scavenging enzyme activity, and lesser DNA damage compared to W38 under salinity stress. Therefore, our results suggest that IbTLD activates the expression of ROS scavenging genes and confers tolerance to salinity stress in planta.

Single-base resolution methylomes of somatic embryogenesis in Theobroma cacao L. reveal epigenome modifications associated with somatic embryo abnormalities

Propagation by somatic embryogenesis in Theobroma cacao has some issues to be solved, as many morphologically abnormal somatic embryos that do not germinate into plants are frequently observed, thus hampering plant production on a commercial scale. For the first time the methylome landscape of T. cacao somatic embryogenesis was examined, using whole-genome bisulfite sequencing technique, with the aim to understand the epigenetic basis of somatic embryo abnormalities. We identified 873 differentially methylated genes (DMGs) in the CpG context between zygotic embryos, normal and abnormal somatic embryos, with important roles in development, programmed cell death, oxidative stress, and hypoxia induction, which can help to explain the morphological abnormalities of somatic embryos. We also identified the role of ethylene and its precursor 1-aminocyclopropane-1-carboxylate in several biological processes, such as hypoxia induction, cell differentiation and cell polarity, that could be associated to the development of abnormal somatic embryos. The biological processes and the hypothesis of ethylene and its precursor involvement in the somatic embryo abnormalities in cacao are discussed.

Cannabis Seedlings Inherit Seed-Borne Bioactive and Anti-Fungal Endophytic Bacilli

Throughout the hundreds of millions of years of co-evolution, plants and microorganisms have established intricate symbiotic and pathogenic relationships. Microbial communities associated with plants are in constant flux and can ultimately determine whether a plant will successfully reproduce or be destroyed by their environment. Inheritance of beneficial microorganisms is an adaptation plants can use to protect germinating seeds against biotic and abiotic stresses as seedlings develop. The interest in Cannabis as a modern crop requires research into effective biocontrol of common fungal pathogens, an area that has seen little research. This study examines the seed-borne endophytes present across 15 accessions of Cannabis grown to seed across Western Canada. Both hemp and marijuana seedlings inherited a closely related group of bioactive endophytic Bacilli. All Cannabis accessions possessed seed-inherited Paenibacillus mobilis with the capacity to solubilize mineral phosphate. Additionally, seeds were found to carry genera of fungal isolates known to be Cannabis pathogens and post-harvest molds: Alternaria, Penicillium, Cladosporium, Chaetomium, Aspergillus, Rhizopus, and Fusarium. Thirteen seed-borne endophytes showed antibiotic activity against Alternaria, Aspergillus, Penicillium, and Fusarium. This study suggests both fungal pathogens and bacterial endophytes that antagonize them are vectored across generations in Cannabis as they compete over this shared niche.

Changes in the Differentiation Program of Birch Cambial Derivatives following Trunk Girdling

The mechanisms regulating the tree trunk radial growth can be studied in original experiments. One technique for studying cambium activity (the meristem involved in radial growth) under conditions of an increased photoassimilate level is trunk girdling. We girdled the trunks of 17- to 22-year-old silver birch plants (Betula pendula Roth var. pendula) during the active growth period and collected xylem and phloem samples at two height levels (1 cm and 35 cm) above girdle, 10, 20, and 30 days after girdling. We investigated the changes that occurred at the anatomical level, as well as the activities of sucrose-metabolizing enzymes and antioxidant-system enzymes and the expression of genes that encode proteins involved in sucrose and auxin transport and metabolism. A moderate increase in photoassimilates (35 cm above the girdle) resulted in a change in the ratio of phloem to xylem increments and an increase in the proportion of parenchyma in the conducting tissues. The increase of photoassimilates above the level at which they can be used in the processes of normal tissue growth and development (1 cm above the girdle) led to xylogenesis suppression and the stimulation of phloem formation, a significant increase in the parenchyma proportion in the conducting tissues, and formation of large sclereid complexes. The differentiation of parenchyma and sclereid cells coincided with biochemical and molecular markers of abnormal conducting tissue formation in Karelian birch, which are also characterized by high proportions of parenchyma and sclereid near the cambium. The results obtained are important in understanding the cambium responses to the photoassimilate distribution changes and estimating tree productivity and survival under changing environmental conditions.

Overexpression of VvASMT1 from grapevine enhanced salt and osmotic stress tolerance in Nicotiana benthamiana

Salt and drought stresses are major environmental conditions that severely limit grape growth and productivity, while exogenous melatonin can alleviate the drought and salt damage to grapevines. N-acetylserotonin methyltransferase (ASMT) is the key enzyme in melatonin synthesis, which plays a critical role in regulating stress responses. However, the roles of ASMTs from grapevine under drought and salt stresses responses remain largely unclear. In this study, the VvASMT1 gene was isolated from grapevine, and its physiological functions in salt and mimic drought stress tolerance were investigated. Expression pattern analysis revealed that VvASMT1 was significantly induced by different salt and osmotic stresses. Ectopic expression of VvASMT1 in Nicotiana benthamiana significantly enhanced melatonin production in transgenic plants. Compared with wild-type plants, the transgenic lines exhibited a higher germination ratio, longer root length, lower degree of leaf wilting and relative water content (RWC) under salt and osmotic stresses. In addition, under salt and osmotic stresses, overexpression of VvASMT1 improved proline and malondialdehyde (MDA) contents, increased the activity of antioxidant enzymes and decreased the accumulation of reactive oxygen species (ROS). Taken together, our results demonstrate the explicit role of VvASMT1 in salt and osmotic stress responses, which provides a theoretical foundation for the genetic engineering of grapevine.

Advances in the Understanding of Reactive Oxygen Species-Dependent Regulation on Seed Dormancy, Germination, and Deterioration in Crops

Reactive oxygen species (ROS) play an essential role in the regulation of seed dormancy, germination, and deterioration in plants. The low level of ROS as signaling particles promotes dormancy release and triggers seed germination. Excessive ROS accumulation causes seed deterioration during seed storage. Maintaining ROS homeostasis plays a central role in the regulation of seed dormancy, germination, and deterioration in crops. This study highlights the current advances in the regulation of ROS homeostasis in dry and hydrated seeds of crops. The research progress in the crosstalk between ROS and hormones involved in the regulation of seed dormancy and germination in crops is mainly summarized. The current understandings of ROS-induced seed deterioration are reviewed. These understandings of ROS-dependent regulation on seed dormancy, germination, and deterioration contribute to the improvement of seed quality of crops in the future.

Detoxification of phenanthrene in Arabidopsis thaliana involves a Dioxygenase For Auxin Oxidation 1 (AtDAO1)

Polycyclic aromatic hydrocarbon (PAH) contamination has a negative impact on ecosystems. PAHs are a large group of toxins with two or more benzene rings that are persistent in the environment. Some PAHs can be cytotoxic, teratogenic, and/or carcinogenic. In the bacterium Pseudomonas, PAHs can be modified by dioxygenases, which increase the reactivity of PAHs. We hypothesize that some plant dioxygenases are capable of PAH biodegradation. Herein, we investigate the involvement of Arabidopsis thaliana At1g14130 in the degradation of phenanthrene, our model PAH. The At1g14130 gene encodes Dioxygenase For Auxin Oxidation 1 (AtDAO1), an enzyme involved in the oxidative inactivation of the hormone auxin. Expression analysis using a β-glucuronidase (GUS) reporter revealed that At1g14130 is prominently expressed in new leaves of plants exposed to media with phenanthrene. Analysis of the oxidative state of gain-of-function mutants showed elevated levels of H₂O₂ after phenanthrene treatments, probably due to an increase in the oxidation of phenanthrene by AtDAO1. Biochemical assays with purified AtDAO1 and phenanthrene suggest an enzymatic activity towards the PAH. Thus, data presented in this study support the hypothesis that an auxin dioxygenase, AtDAO1, from Arabidopsis thaliana contributes to the degradation of phenanthrene and that there is possible toxic metabolite accumulation after PAH exposure.

Changes in the fatty acid composition of pine needle lipids under the aluminum smelter emissions

Changes in the fatty acid (FA) composition of total lipids of Pinus sylvestris needles at different pollution levels caused by emissions from a large aluminum smelter (BrAS) have been studied. In the needles of trees from unpolluted (background) territories, the FA spectrum is represented by 24 acids with prevalence of unsaturated FAs (71.6%). The main unsaturated FA are represented by oleic (C18: 1ω9), linoleic (C18: 2ω6), and α-linolenic (C18: 3ω3) acids. Under the influence of BrAS emissions, the total amount of identified FAs in the needles and the proportion of unsaturated FAs decrease, while the fraction of saturated FAs, on the contrary, increases from 25.4% in unpolluted needles to 33.2% in polluted ones. The content of palmitic FA (C16:0) in the needles exceeds background values by 1.5 times, behenic acid (C22:0) - by 1.6-2.5 times, arachidic acid (C20:0) - by 1.5 times, palmitic margaric acid (C17:0) - by 1.5-2.3 times. These FAs play the important role in the protection of plant membranes from the effects of abiotic stress factors, making them less permeable. The sum of short-chain saturated FAs (C12:0, C14:0, C15:0) increase by 4.8 times in needles of trees that are highly polluted. Pentadecanoic (C15:0) acid is found in the needles only in the background areas and at the low pollution level. With a more severe pollution, C15:0 is not identified, but lauric acid with the cis-configuration of double bonds in the structure (izo-C12:0) appears. The presence of "relict" ∆5-polymethylene FAs in the composition of pine needle membrane lipids is determined. In the background areas, they account for 12.9% of the total FAs. With the industrial pollution intensification, their total content increases and reaches 14.1%. ∆5-polymethylene FAs are also able to protect membranes against negative influences. Thus, changes in the quantitative and qualitative FA composition of pine needle total lipids indicate the activation of the stabilization mechanisms of membrane lipids due to their tight packing in a bilayer. It is one of the adaptive reactions of Pinus sylvestris in response to the impact of the aluminum industry emissions.

Permissive action of H2O2 mediated ClUGT75 expression for auxin glycosylation and Al3+- tolerance in watermelon

Although Al³⁺-toxicity is one of the limiting factors for crop production in acidic soils, little is known about the Al³⁺-tolerance mechanism in watermelon, a fairly acid-tolerant crop. This work aimed to identify the interaction between the H₂O₂ scavenging pathway and auxin glycosylation relevant to watermelon Al³⁺-tolerance. By analyzing expressions of hormone-related ClUGTs and antioxidant enzyme genes in Al³⁺-tolerant (ZJ) and Al³⁺-sensitive (NBT) cultivars, we identified ClUGT75s (B1, B2, and D1) and ClSOD1-2-ClCAT as crucial components associated with Al³⁺-tolerance. Al³⁺-stress significantly increased H₂O₂ content by 92.7% in NBT and 42.3% in ZJ, accompanied by less Al³⁺-, auxin (IAA and IBA), and MDA contents in ZJ than NBT. These findings coincided with significant ClSOD1-2 expression and stable dismutation activity in NBT than ZJ. Hence, higher H₂O₂ content in the root apex of NBT than ZJ correlated with a significant increase in auxin content and ClSOD1-2 up-regulation. Moreover, Al³⁺-activated ClUGT75D1 and ClUGT75B2 in ZJ coincided with no considerable change in IBA content, suggesting that glycosylation-mediated changes in IBA content might be relevant to Al³⁺-tolerance in watermelon. Furthermore, exogenous H₂O₂ and IBA indicated ClUGT75D1 modulating IBA is likely dependent on H₂O₂ background. We hypothesize that a higher H₂O₂ level in NBT represses ClUGT75, resulting in increased auxin than those in ZJ roots. Thus, excess in both H₂O₂ and auxin aggravated the inhibition of root elongation under Al³⁺-stress. Our findings provide insights on the permissive action of H₂O₂ in the mediation of auxin glycosylation by ClUGT75 in root apex for Al³⁺-tolerance in watermelon.

Morphogenic responses and biochemical alterations induced by the cover crop Urochloa ruziziensis and its component protodioscin in weed species

Urochloa ruziziensis, a cover plant used in no-till systems, can suppress weeds in the field through their chemical compounds, but the mode of action of these compounds is still unknown. The present study aimed to investigate the effects of a saponin-rich butanolic extract from U. ruziziensis straw (BfUr) and one of its components, protodioscin on an eudicot Ipomoea grandifolia and a monocot Digitaria insularis weed. The anatomy and the morphology of the root systems and several parameters related to energy metabolism and antioxidant defense systems were examined. The IC₅₀ values for the root growth inhibition by BfUr were 108 μg mL^-1 in D. insularis and 230 μg mL^-1 in I. grandifolia. The corresponding values for protodioscin were 34 μg mL^-1 and 54 μg mL^-1. I. grandifolia exhibited higher ROS-induced peroxidative damage in its roots compared with D. insularis. In the roots of both weeds, the BfUr and protodioscin induced a reduction in the meristematic and elongation zones with a precocious appearance of lateral roots, particularly in I. grandifolia. The roots also exhibited features of advanced cell differentiation in the vascular cylinder. These alterations were similar to stress-induced morphogenic responses (SIMRs), which are plant adaptive strategies to survive in the presence of toxicants. At concentrations above their IC₅₀ values, the BfUr or protodioscin strongly inhibited the development of both weeds. Such findings demonstrated that U. ruziziensis mulches may contribute to the use of natural and renewable weed control tools.

Exogenous Nitric Oxide Reinforces Photosynthetic Efficiency, Osmolyte, Mineral Uptake, Antioxidant, Expression of Stress-Responsive Genes and Ameliorates the Effects of Salinity Stress in Wheat

Salinity stress is one of the major environmental constraints responsible for a reduction in agricultural productivity. This study investigated the effect of exogenously applied nitric oxide (NO) (50 μM and 100 μM) in protecting wheat plants from NaCl-induced oxidative damage by modulating protective mechanisms, including osmolyte accumulation and the antioxidant system. Exogenously sourced NO proved effective in ameliorating the deleterious effects of salinity on the growth parameters studied. NO was beneficial in improving the photosynthetic efficiency, stomatal conductance, and chlorophyll content in normal and NaCl-treated wheat plants. Moreover, NO-treated plants maintained a greater accumulation of proline and soluble sugars, leading to higher relative water content maintenance. Exogenous-sourced NO at both concentrations up-regulated the antioxidant system for averting the NaCl-mediated oxidative damage on membranes. The activity of antioxidant enzymes increased the protection of membrane structural and functional integrity and photosynthetic efficiency. NO application imparted a marked effect on uptake of key mineral elements such as nitrogen (N), potassium (K), and calcium (Ca) with a concomitant reduction in the deleterious ions such as Na⁺. Greater K and reduced Na uptake in NO-treated plants lead to a considerable decline in the Na/K ratio. Enhancing of salt tolerance by NO was concomitant with an obvious down-regulation in the relative expression of SOS1, NHX1, AQP, and OSM-34, while D2-protein was up-regulated.

Transcriptomic analyses of cacao flavonoids produced in photobioreactors

BACKGROUND

Theobroma cacao is a major source of flavonoids such as catechins and their monomers proanthocyanidins (PAs), widely studied for their potential benefits in cardiovascular diseases. Light has been shown to promote plant secondary metabolite production in vitro. In this study, cacao cells cultured in 7.5 L stirred tank photobioreactors (STPs) were exposed to a change of white to blue LED lights for 28 days (d).

RESULTS

Transcriptomic analyses were performed in three time points comparing changing expression patterns, after cell exposure to white light (d0-VS-d14), after a shift from white to blue light (d14-VS-d15), and after an extended period of blue light for the following 15 days (d15-VS-d28). Under white light, there was enrichment in metabolic pathways associated with cell growth (carbon, glycolysis, and amino acid biosynthesis) accompanied by a significant increase in the PAs content. In the shift to blue light, further increase in PAs content was observed concomitantly with the significant expression of TWO-COMPONENT RESPONSE REGULATOR genes involved in the early stress responses via circadian clock and hormone pathways. Under blue light exposure, we observed a depletion of PAs content associated with ROS-mediated stress pathways.

CONCLUSIONS

Light effects on large-scale cell cultures in photobioreactors are complex and pleiotropic; however, we have been able to identify key regulatory players upstream cacao flavonoid biosynthesis in STPs, including TWO-COMPONENT SYSTEM and ROS-signaling genes. The crosstalk between flavonoid biosynthesis and regulatory networks led to understand the dynamics of flavonoid production and degradation in response to light-driven ROS signals. This can be used to optimize the time, and the yield of in vitro targeted metabolites in large-scale culture systems.

Plant Responses to Abiotic Stresses and Rhizobacterial Biostimulants: Metabolomics and Epigenetics Perspectives

In response to abiotic stresses, plants mount comprehensive stress-specific responses which mediate signal transduction cascades, transcription of relevant responsive genes and the accumulation of numerous different stress-specific transcripts and metabolites, as well as coordinated stress-specific biochemical and physiological readjustments. These natural mechanisms employed by plants are however not always sufficient to ensure plant survival under abiotic stress conditions. Biostimulants such as plant growth-promoting rhizobacteria (PGPR) formulation are emerging as novel strategies for improving crop quality, yield and resilience against adverse environmental conditions. However, to successfully formulate these microbial-based biostimulants and design efficient application programs, the understanding of molecular and physiological mechanisms that govern biostimulant-plant interactions is imperatively required. Systems biology approaches, such as metabolomics, can unravel insights on the complex network of plant-PGPR interactions allowing for the identification of molecular targets responsible for improved growth and crop quality. Thus, this review highlights the current models on plant defence responses to abiotic stresses, from perception to the activation of cellular and molecular events. It further highlights the current knowledge on the application of microbial biostimulants and the use of epigenetics and metabolomics approaches to elucidate mechanisms of action of microbial biostimulants.

Diclofenac modified the root system architecture of Arabidopsis via interfering with the hormonal activities of auxin

Diclofenac, a pharmaceutical and personal care product, is accumulating in various environmental matrices worldwide. Increased irrigation has facilitated an influx of environmental diclofenac into agricultural products, which potentially threatens non-target living organisms. In this study, we demonstrated that diclofenac modified the growth and root developmental processes of plants by disturbing the activity of auxin, a group of major phytohormones. Exogenous diclofenac treatment retarded growth and induced oxidative stress in young seedlings of Arabidopsis thaliana. In the developmental perspective, diclofenac altered the root system architecture, which was also similarly observed under exogenous IAA (a natural form of phytoalexins) treatment. The effects of diclofenac on the root development of A. thaliana were mediated through canonical auxin signaling pathways. However, when diclofenac and IAA were treated in combination, diclofenac suppressed the activity of IAA in root system architecture. At the molecular level, diclofenac significantly inhibited the activity of IAA upregulating the expression of early auxin-responsive marker genes. In conclusion, diclofenac modified the root development of A. thaliana via interfering with the activities of natural auxin. These results indicate that diclofenac could potentially act as an environmental contaminant disturbing the natural developmental processes of plants.

Auxin treatment increases lifespan in Caenorhabditis elegans

The auxin-inducible degradation system (AID) has proven to be a highly versatile technology for rapid, robust and reversible depletion of proteins in multiple model systems. In recent years, AID has been adapted into the nematode Caenorhabditis elegans as a tool for conditional protein knockdown. Numerous transgenic strains have been created that, upon auxin exposure, undergo protein inactivation in the worm germline or somatic tissues, both during development and in young adults. Since longevity assays often involve long-term gene- and protein-manipulation, the facility for spatiotemporally precise and extended protein removal makes AID a potentially highly valuable tool for aging biology. However, whether auxins themselves impact worm longevity has not been directly addressed. Here, we show that prolonged exposure to indole 3-acetic acid (IAA), the auxin used in worm AID studies, extends lifespan. We also report that two transgenic strains expressing Arabidopsis proteins that are key components of the AID platform are longer lived than wild-type animals. Together, our results highlight the necessity for exercising caution while utilizing AID for longevity studies and in interpreting the resulting data.

This article has an associated First Person interview with the first author of the paper.

Summary: We report that auxin and auxin-inducible protein degradation tools alter lifespan in C. elegans.

Main nitric oxide (NO) hallmarks to relieve arsenic stress in higher plants

Arsenic (As) is a toxic metalloid that adversely affects plant growth, and poses severe risks to human health. It induces disturbance to many physiological and metabolic pathways such as nutrient, water and redox imbalance, abnormal photosynthesis and ATP synthesis and loss of membrane integrity. Nitric oxide (NO) is a free radical molecule endogenously generated in plant cells which has signalling properties. Under As-stress, the endogenous NO metabolism is significantly affected in a clear connection with the metabolism of reactive oxygen species (ROS) triggering nitro-oxidative stress. However, the exogenous NO application provides beneficial effects under As-stress conditions which can relieve oxidative damages by stimulating the antioxidant systems, regulation of the expression of the transporter and other defence-related genes, modification of root cell wall composition or the biosynthesis of enriched sulfur compounds such phytochelatins (PCs). This review aims to provide up-to-date information on the key NO hallmarks to relieve As-stress in higher plants. Furthermore, it will be analyzed the diverse genetic engineering techniques to increase the endogenous NO content which could open new biotechnological applications, especially in crops under arsenic stress.

tRNA ADENOSINE DEAMINASE 3 is required for telomere maintenance in Arabidopsis thaliana

KEY MESSAGE: tRNA Adenosine Deaminase 3 helps to sustain telomere tracts in a telomerase-independent fashion, likely through regulating cellular metabolism. Telomere length maintenance is influenced by a complex web of chromatin and metabolism-related factors. We previously reported that a lncRNA termed AtTER2 regulates telomerase activity in Arabidopsis thaliana in response to DNA damage. AtTER2 was initially shown to partially overlap with the 5' UTR of the tRNA ADENOSINE DEAMINASE 3 (TAD3) gene. However, updated genome annotation showed that AtTER2 was completely embedded in TAD3, raising the possibility that phenotypes ascribed to AtTER2 could be derived from TAD3. Here we show through strand-specific RNA-Seq, strand-specific qRT-PCR and bioinformatic analyses that AtTER2 does not encode a stable lncRNA. Further examination of the original tad3 (ter2-1/tad3-1) mutant revealed expression of an antisense transcript driven by a cryptic promoter in the T-DNA. Hence, a new hypomorphic allele of TAD3 (tad3-2) was examined. tad3-2 mutants showed hypersensitivity to DNA damage, but no deregulation of telomerase, suggesting that the telomerase phenotype of tad3-1 mutants reflects an off-target effect. Unexpectedly, however, tad3-2 plants displayed progressive loss of telomeric DNA over successive generations that was not accompanied by alteration of terminal architecture or end protection. The phenotype was exacerbated in plants lacking the telomerase processivity factor POT1a, indicating that TAD3 promotes telomere maintenance through a non-canonical, telomerase-independent pathway. The transcriptome of tad3-2 mutants revealed significant dysregulation of genes involved in auxin signaling and glucosinolate biosynthesis, pathways that intersect the stress response, cell cycle regulation and DNA metabolism. These findings indicate that the TAD3 locus indirectly contributes to telomere length homeostasis by altering the metabolic profile in Arabidopsis.

Overexpression of MzASMT 1, a Gene From Malus zumi Mats, Enhances Salt Tolerance in Transgenic Tobacco

Melatonin, widely found in various plants as a new antioxidant, could protect plants from various biotic and/or abiotic stresses, including salt stress. MzASMT 1 (KJ123721), a gene from Malus zumi Mats, is a key enzyme required for melatonin synthesis. However, whether the overexpression of MzASMT 1 could regulate the synthesis of melatonin and improve the salt tolerance in tobacco remains unknown. In this study, the overexpression of MzASMT 1 in tobacco increased the melatonin content, and the transgenic lines owned higher salt tolerance capacity. The transgenic lines overexpressing MzASMT 1 exhibited lower degree of leaf wilting; much more fresh weight; higher plant height; longer root; higher relative water content (RWC) of leaves, stem, and root; and higher chlorophyll content and Fv/Fm, which makes transgenic lines better adapt to salt stress. The transgenic lines also had higher accumulation of proline, lower accumulation of malondialdehyde (MDA), and improved antioxidant systems, which protected plants from cell damage and oxidative stress due to excess reactive oxygen species (ROS) accumulation under salt treatment. The transcription of salt response genes was much more highly activated in transgenic lines than in wild type under salt stress. The above results contributed to the understanding of functions for MzASMT 1 in tobacco under salt stress and provided a new choice for the application of MzASMT 1 in improving plant salt tolerance.

VdNPS, a Nonribosomal Peptide Synthetase, Is Involved in Regulating Virulence in Verticillium dahliae

Nonribosomal peptide synthetases (NPS) are known for the biosynthesis of antibiotics, toxins, and siderophore production. They are also a virulence determinant in different phytopathogens. However, until now, the functional characterization of NPS in Verticillium dahliae has not been reported. Deletion of the NPS gene in V. dahliae led to the decrease of conidia, microsclerotia, and pathogenicity. ΔVdNPS strains were tolerant to H₂O₂, and the genes involved in H₂O₂ detoxification, iron/copper transport, and cytoskeleton were differentially expressed in ΔVdNPS. Interestingly, ΔVdNPS strains exhibited hypersensitivity to salicylic acid (SA), and the genes involved in SA hydroxylation were up-regulated in ΔVdNPS compared with wild-type V. dahliae under SA stress. Additionally, during infection, ΔVdNPS induced more pathogenesis-related gene expression, higher reactive oxygen species production, and stronger SA-mediated signaling transduction in host to overcome pathogen. Uncovering the function of VdNPS in pathogenicity could provide a reliable theoretical basis for the development of cultivars with durable resistance against V. dahliae-associated diseases.

Molecular genetic analyses of abiotic stress responses during plant reproductive development

Plant responses to abiotic stresses during vegetative growth have been extensively studied for many years. Daily environmental fluctuations can have dramatic effects on plant vegetative growth at multiple levels, resulting in molecular, cellular, physiological, and morphological changes. Plants are even more sensitive to environmental changes during reproductive stages. However, much less is known about how plants respond to abiotic stresses during reproduction. Fortunately, recent advances in this field have begun to provide clues about these important processes, which promise further understanding and a potential contribution to maximize crop yield under adverse environments. Here we summarize information from several plants, focusing on the possible mechanisms that plants use to cope with different types of abiotic stresses during reproductive development, and present a tentative molecular portrait of plant acclimation during reproductive stages. Additionally, we discuss strategies that plants use to balance between survival and productivity, with some comparison among different plants that have adapted to distinct environments.

Over-expression of a γ-tocopherol methyltransferase gene in vitamin E pathway confers PEG-simulated drought tolerance in alfalfa

BACKGROUND

α-Tocopherol is one of the most important vitamin E components present in plant. α-Tocopherol is a potent antioxidant, which can deactivate photoproduced reactive oxygen species (ROS) and prevent lipids from oxidation when plants suffer drought stress. γ-Tocopherol methyltransferase (γ-TMT) catalyzes the formation of α-tocopherol in the tocopherol biosynthetic pathway. Our previous studies showed that over-expression of γ-TMT gene can increase the accumulation of α-tocopherol in alfalfa (Medicago sativa). However, whether these transgenic plants confer increased drought tolerance and the underlying mechanism are still unknown.

RESULTS

In the present study, we further evaluate transgenic alfalfa lines, and found that over-expression of MsTMT led to an increase in α-tocopherol and total tocopherol level in the transgenic lines compared with the control plant. It was revealed that drought tolerance of the transgenic alfalfa was remarkably increased, with alleviated oxidative damage and accumulation of more osmolytic substances. The stomatal development in transgenic plants was significantly inhibited on both sides of leaves, which may be resulted from the repression of MsSPCHLESS (MsSPCH) gene. The reduced stomatal density of transgenic plants contributes to a lower stomatal conductance and higher water use efficiency (WUE). Moreover, both RNA-seq and qRT-PCR analyses indicate that regulatory mechanism of MsTMT in drought involved in both ABA-dependent and ABA-independent pathways.

CONCLUSION

Our results suggest that MsTMT gene plays a positive role in regulating alfalfa response to PEG-simulated drought stress, which might involve complex mechanisms, including ROS scavenging system, stomatal development and multiple phytohormone signaling pathways. This study will broaden our view on the function of γ-TMT gene and provide new strategy for genetic engineering in alfalfa breeding.

Oxidative stress induced by cadmium in lettuce (Lactuca sativa Linn.): Oxidative stress indicators and prediction of their genes

Environmental contamination with heavy metals is of concern as plants have the ability to absorb chemical toxicants facilitating the entry of toxic metals into the food chain. Lettuce (Lactuca sativa Linn.) was cultured in four nutrient solutions containing different concentrations of cadmium (0, 3, 6, and 9 mmol). The impact of heavy metal on the morphological features, antioxidant properties and antioxidant enzymes activity were investigated with primary focus on superoxide dismutase, ascorbate peroxidase, peroxidase and catalase enzymes. In silico methods were utilized in the study of the genes of these enzymes. Significant changes were observed in the morphological features of the plant with plants appearing stunted, more spherical and yellow in colour. A decrease in the dry mass of the plant was also detected. The Translocation factor (TF) for cadmium was significantly high in lettuce. Enhanced antioxidant enzymatic activity suggests that these enzymes are integrally involved in the defense mechanism of the plant to heavy metal stress. Also observed was an increase in total soluble protein, and total phenolic content. Total flavonoid content was not significantly affected. Fourteen genes encoding for ascorbate peroxidase and nineteen genes for superoxide dismutase were identified in lettuce. These enzymes varied from each other with regards to the number of exons and amino acids present, as well as their location within the cell. Plants exhibit various response mechanisms to combat heavy metal contamination.

Oleuropein Transcriptionally Primes Lactobacillus plantarum to Interact With Plant Hosts

Oleuropein (OLE) is a secoiridoid unique to Oleaceae known to play a role in the plant–herbivore interaction. However, it is not clear how this molecule is induced to mediate plant responses to microbes and how microbes, in turn, withstand with OLE. To better understand how OLE affects the plant–microbe interaction, the contribution of differential gene expression in the adaptation to OLE was characterized by whole genome transcriptional profiling in Lactobacillus plantarum, a bacterium associated to the olive. OLE downregulated functions associated to rapid growth, remodeled membrane phospholipid biosynthesis pathways and markedly repressed the expression of several ABC transporters from L. plantarum. Genes encoding the plantaricin and lamABDCA quorum-sensing (QS) systems were down-regulated indicating the potential of OLE as a QS-antagonist. Notably, OLE diminished the expression of a set of genes encoding inmunomodulatory components and reoriented metabolic pathways to increase protein acetylation, probably to attenuate plant immunity. Responses were also triggered to repress the transport of acetoin and to buffer reactive oxygen species accumulation, two signals involved in plant development. The results suggest that OLE could act as a signaling molecule in the plant–microbe interaction and facilitate the accommodation of beneficial microbes such as L. plantarum by the plant host, via controlled expression of bacterial molecular players involved in this reciprocal interplay.

Regulation of physiological processes in winter wheat by growth regulators in conditions of powdery mildew infection

An important way of regulating the key units of metabolism in the plant organism under the action of stressors is the use of biologically active substances with regulating properties – plant growth regulators. They affect endogenous regulatory systems, altering key metabolic pathways and thus increasing the plant's sustainability and productive potential in adverse environmental conditions. The aim of the research was to establish the possibility of regulation of physiological processes in winter wheat varieties by exogenous treatment of plants with growth regulators of synthetic (salicylic acid) and natural (Emistim C and Biolan) origin to increase their resistance to the phytopathogen Erysiphe graminis DC f. sp. tritici Em. Marchal , the causative agent of powdery mildew. The intensity of the physiological processes in plants was evaluated by the dynamics of the activity of antioxidant enzymes – ascorbate peroxidase and catalase, the release of ethylene and the integrity of the cell membranes. The objects were selected varieties of soft winter wheat, which were grown in controlled growing conditions against the background of infection by powdery mildew. The treatment of plants was carried out using aqueous salicylic acid solutions in the concentration of 10–5 M (experimentally established by us), Emistim C and Biolan (manufacturer Agrobiotech) in the concentration specified by the manufacturer at the rate of 20 mL/ha, when the development of the disease reached 5% of the total natural background of the infection in the plants during the stages of heading-beginning of flowering. Infection of winter wheat with powdery mildew leads to disruption of cell membrane integrity, increased activity of catalase and ascorbate peroxidase in leaves of the susceptible winter wheat variety. The intensification of ethylene release by leaves of the resistant variety was observed, which was caused by the hypersensitive reaction of the hormone to the effect of stress. The use of plant treatment by growth regulators contributes to maintaining the integrity of membrane structures, adaptive changes in the activity of antioxidant enzymes and regulation of the synthesis of the stress hormone ethylene in both winter wheat varieties under stress. Such changes in the physiological processes induced by plant growth regulators are accompanied by the preservation of the grain productivity of winter wheat and the increase of their resistance to the development of the disease.

The Roles of Environmental Factors in Regulation of Oxidative Stress in Plant

Exposure to a variety of environmental factors such as salinity, drought, metal toxicity, extreme temperature, air pollutants, ultraviolet-B (UV-B) radiation, pesticides, and pathogen infection leads to subject oxidative stress in plants, which in turn affects multiple biological processes via reactive oxygen species (ROS) generation. ROS include hydroxyl radicals, singlet oxygen, and hydrogen peroxide in the plant cells and activates signaling pathways leading to some changes of physiological, biochemical, and molecular mechanisms in cellular metabolism. Excessive ROS, however, cause oxidative stress, a state of imbalance between the production of ROS and the neutralization of free radicals by antioxidants, resulting in damage of cellular components including lipids, nucleic acids, metabolites, and proteins, which finally leads to the death of cells in plants. Thus, maintaining a physiological level of ROS is crucial for aerobic organisms, which relies on the combined operation of enzymatic and nonenzymatic antioxidants. In order to improve plants' tolerance towards the harsh environment, it is vital to reinforce the comprehension of oxidative stress and antioxidant systems. In this review, recent findings on the metabolism of ROS as well as the antioxidative defense machinery are briefly updated. The latest findings on differential regulation of antioxidants at multiple levels under adverse environment are also discussed here.

The auxin influx carrier, OsAUX3, regulates rice root development and responses to aluminium stress

In rice, there are five members of the auxin carrier AUXIN1/LIKE AUX1 family; however, the biological functions of the other four members besides OsAUX1 remain unknown. Here, by using CRISPR/Cas9, we constructed two independent OsAUX3 knock-down lines, osaux3-1 and osaux3-2, in wild-type rice, Hwayoung (WT/HY) and Dongjin (WT/DJ). osaux3-1 and osaux3-2 have shorter primary roots (PRs), decreased lateral root (LR) density, and longer root hairs (RHs) compared with their WT. OsAUX3 expression in PRs, LRs, and RHs further supports that OsAUX3 plays a critical role in the regulation of root development. OsAUX3 locates at the plasma membrane and functions as an auxin influx carrier affecting acropetal auxin transport. OsAUX3 is up-regulated in the root apex under aluminium (Al) stress, and osaux3-2 is insensitive to Al treatments. Furthermore, 1-naphthylacetic acid accented the sensitivity of WT/DJ and osaux3-2 to respond to Al stress. Auxin concentrations, Al contents, and Al-induced reactive oxygen species-mediated damage in osaux3-2 under Al stress are lower than in WT, indicating that OsAUX3 is involved in Al-induced inhibition of root growth. This study uncovers a novel pathway alleviating Al-induced oxidative damage by inhibition of acropetal auxin transport and provides a new option for engineering Al-tolerant rice species.

Prioritization of Candidate Genes in QTL Regions for Physiological and Biochemical Traits Underlying Drought Response in Barley (Hordeum vulgare L.)

Drought is one of the most adverse abiotic factors limiting growth and productivity of crops. Among them is barley, ranked fourth cereal worldwide in terms of harvested acreage and production. Plants have evolved various mechanisms to cope with water deficit at different biological levels, but there is an enormous challenge to decipher genes responsible for particular complex phenotypic traits, in order to develop drought tolerant crops. This work presents a comprehensive approach for elucidation of molecular mechanisms of drought tolerance in barley at the seedling stage of development. The study includes mapping of QTLs for physiological and biochemical traits associated with drought tolerance on a high-density function map, projection of QTL confidence intervals on barley physical map, and the retrievement of positional candidate genes (CGs), followed by their prioritization based on Gene Ontology (GO) enrichment analysis. A total of 64 QTLs for 25 physiological and biochemical traits that describe plant water status, photosynthetic efficiency, osmoprotectant and hormone content, as well as antioxidant activity, were positioned on a consensus map, constructed using RIL populations developed from the crosses between European and Syrian genotypes. The map contained a total of 875 SNP, SSR and CGs, spanning 941.86 cM with resolution of 1.1 cM. For the first time, QTLs for ethylene, glucose, sucrose, maltose, raffinose, α-tocopherol, γ-tocotrienol content, and catalase activity, have been mapped in barley. Based on overlapping confidence intervals of QTLs, 11 hotspots were identified that enclosed more than 60% of mapped QTLs. Genetic and physical map integration allowed the identification of 1,101 positional CGs within the confidence intervals of drought response-specific QTLs. Prioritization resulted in the designation of 143 CGs, among them were genes encoding antioxidants, carboxylic acid biosynthesis enzymes, heat shock proteins, small auxin up-regulated RNAs, nitric oxide synthase, ATP sulfurylases, and proteins involved in regulation of flowering time. This global approach may be proposed for identification of new CGs that underlies QTLs responsible for complex traits.

Silicon Mechanisms to Ameliorate Heavy Metal Stress in Plants

The increased contaminants caused by anthropogenic activities in the environment and the importance of finding pathways to reduce pollution caused the silicon application to be considered an important detoxification agent. Silicon, as a beneficial element, plays an important role in amelioration of abiotic stress, such as an extreme dose of heavy metal in plants. There are several mechanisms involved in silicon mediation in plants, including the reduction of heavy metal uptake by plants, changing pH value, formation of Si heavy metals, and stimulation of enzyme activity, which can work by chemical and physical pathways. The aim of this paper is to investigate the major silicon-related mechanisms that reduce the toxicity of heavy metals in plants and then to assess the role of silicon in increasing the antioxidant enzyme and nonenzyme activities to protect the plant cell.

Levofloxacin is phytotoxic and modifies the protein profile of lupin seedlings

The toxicity of levofloxacin to yellow lupin plants was evaluated in this study. Recommended indexes of plant (roots and shoots) growth were determined and new indexes were proposed which better characterise the phytotoxicity of levofloxacin. These were, in particular, the activity of antioxidative enzymes, the content of free radicals, as well as the root protein content and the root protein profile. The results showed that levofloxacin considerably affected EC₅₀, measured as the activity of catalase in roots, and leaves (1.05 and 0.069 mM, respectively). The activity of peroxidase in the roots and the dry weight of seedlings were the least sensitive parameters (EC₅₀ was 1.8 and 1.76 mM, respectively). Units of toxicity clearly showed that the activity of catalase is a better measure of toxicity for low concentrations of the drug, and it is a better index of plant physiological state than the morphological parameters of seedlings. Moreover, levofloxacin changed the location of free radicals and the protein profile in plants. The changes in location of reactive oxygen species in roots were an important symptom of the drug toxicity to lupin seedlings. Our results have shown that the toxicity of levofloxacin was manifested mainly by changes in the protein profile. The content of the glyceraldehyde-3-phosphate dehydrogenase, 14-3-3-like protein A, expansin-B3-like precursor, fructose-bisphosphate aldolase, lipoxygenase, nucleotide-binding subunit of vacuolar ATPase and pyruvate dehydrogenase were found to decrease. On the other hand, plant exposure to levofloxacin resulted in an increase in the content of enolase, protein LlR18A, class III chitinase, ascorbate peroxidase, aspartate aminotransferase, alcohol dehydrogenase 1, leghemoglobin reductase-like 17 and heat shock cognate protein 80-like.

In-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa

Pathogenesis related (PR) proteins are low molecular weight family of proteins induced in plants under various biotic and abiotic stresses. They play an important role in plant-defense mechanism. PRs have wide range of functions, acting as hydrolases, peroxidases, chitinases, anti-fungal, protease inhibitors etc. In the present study, an attempt has been made to analyze promoter regions of PR1, PR2, PR5, PR9, PR10 and PR12 of Arabidopsis thaliana and Oryza sativa. Analysis of cis-element distribution revealed the functional multiplicity of PRs and provides insight into the gene regulation. CpG islands are observed only in rice PRs, which indicates that monocot genome contains more GC rich motifs than dicots. Tandem repeats were also observed in 5' UTR of PR genes. Thus, the present study provides an understanding of regulation of PR genes and their versatile roles in plants.

Seed-vectored endophytic bacteria modulate development of rice seedlings

AIM

The aim of the present study was to evaluate the effects of the removal of indigenous bacteria from rice seeds on seedling growth and development. Here we report the presence of three indigenous endophytic bacteria in rice seeds that play important roles in modulating seedling development (shoot and root lengths, and formation of root hairs and secondary roots) and defence against pathogens.

METHODS AND RESULTS

Seed-associated bacteria were removed using surface sterilization with NaOCl (bleach) followed by antibiotic treatment. When bacteria were absent, growth of seedlings in terms of root hair development and overall seedling size was less than that of seedlings that contained bacteria. Reactive oxygen staining of seedlings showed that endophytic bacteria became intracellular in root parenchyma cells and root hairs. Roots containing endophytic bacteria were seen to stain densely for reactive oxygen, while roots free of bacteria stained lightly for reactive oxygen. Bacteria were isolated and identified as Enterobacter asburiae (VWB1), Pantoea dispersa (VWB2) and Pseudomonas putida (VWB3) by 16S rDNA sequencing. Bacteria were found to produce indole acetic acid (auxins), inhibited the pathogen Fusarium oxysporum and solubilized phosphate. Reinoculation of bacteria onto seedlings derived from surface-disinfected rice and Bermuda grass seeds significantly restored seedling growth and development.

CONCLUSION

Rice seeds harbour indigenous bacterial endophytes that greatly influence seedling growth and development, including root and shoot lengths, root hair formation and disease susceptibility of rice seedlings.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study shows that seeds of rice naturally harbour bacterial endophytes that play key roles in modulation of seedling development.

Effect of proline on biochemical and molecular mechanisms in lettuce (Lactuca sativa L.) exposed to UV-B radiation

The purpose of the present study was to evaluate the role of proline (Pro) in relieving UV-B radiation-induced oxidative stress in lettuce. Lettuce seedlings were exposed to 3.3 W m-2 UV-B radiation for 12 h after pre-treatment sprayed with 20 mM Pro. The data for malondialdehyde (MDA), hydrogen peroxide (H2O2), endogenous Pro level, the activities of antioxidant enzymes [superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), and peroxidase (POD)], total phenolic concentration, antioxidant capacity, expression of phenylalanine ammonia lyase (PAL), γ-tocopherol methyltransferase (γ-TMT) and proline dehydrogenase (ProDH) genes, phytohormone levels such as abscisic acid (ABA), gibberellic acid (GA), indole acetic acid (IAA) and salicylic acid (SA), soluble sugars and organic acids were recorded. It was found that Pro alleviated the oxidative damage in the seedlings of lettuce as demonstrated by lower lipid peroxidation and H2O2 content, increasing the endogenous Pro level, the activity of antioxidant enzymes, total phenolic concentration and the antioxidant capacity. Additionally, it was revealed that exogenous application of Pro enhanced the levels of GA, IAA, the concentrations of soluble sugars and organic acids and expressions of PAL, γ-TMT and ProDH genes as compared to the control. The results obtained in this study suggest that pre-treatment with exogenous Pro provides important contributions to the increase in the UV-B tolerance of lettuce by regulating the biochemical mechanisms of UV-B response.

Deletion of a Stay-Green Gene Associates with Adaptive Selection in Brassica napus

Chlorophyll levels provide important information about plant growth and physiological plasticity in response to changing environments. The stay-green gene NON-YELLOWING 1 (NYE1) is believed to regulate chlorophyll degradation during senescence, concomitantly affecting the disassembly of the light-harvesting complex and hence indirectly influencing photosynthesis. We identified Brassica napus accessions carrying an NYE1 deletion associated with increased chlorophyll content, and with upregulated expression of light-harvesting complex and photosynthetic reaction center (PSI and PSII) genes. Comparative analysis of the seed oil content of accessions with related genetic backgrounds revealed that the B. napus NYE1 gene deletion (bnnye1) affected oil accumulation, and linkage disequilibrium signatures suggested that the locus has been subject to artificial selection by breeding in oilseed B. napus forms. Comparative analysis of haplotype diversity groups (haplogroups) between three different ecotypes of the allopolyploid B. napus and its A-subgenome diploid progenitor, Brassica rapa, indicated that introgression of the bnnye1 deletion from Asian B. rapa into winter-type B. napus may have simultaneously improved its adaptation to cooler environments experienced by autumn-sown rapeseed.

Indole-3-acetic acid-induced oxidative burst and an increase in cytosolic calcium ion concentration in rice suspension culture

Indole-3-acetic acid (IAA) is the major natural auxin involved in the regulation of a variety of growth and developmental processes such as division, elongation, and polarity determination in growing plant cells. It has been shown that dividing and/or elongating plant cells accompanies the generation of reactive oxygen species (ROS) and a number of reports have suggested that hormonal actions can be mediated by ROS through ROS-mediated opening of ion channels. Here, we surveyed the link between the action of IAA, oxidative burst, and calcium channel activation in a transgenic cells of rice expressing aequorin in the cytosol. Application of IAA to the cells induced a rapid and transient generation of superoxide which was followed by a transient increase in cytosolic Ca2+ concentration ([Ca2+]c). The IAA-induced [Ca2+]c elevation was inhibited by Ca2+ channel blockers and a Ca2+ chelator. Furthermore, ROS scavengers effectively blocked the action of IAA on [Ca2+]c elevation.

Integration of small RNAs, degradome and transcriptome sequencing in hyperaccumulator Sedum alfredii uncovers a complex regulatory network and provides insights into cadmium phytoremediation

The hyperaccumulating ecotype of Sedum alfredii Hance is a cadmium (Cd)/zinc/lead co-hyperaccumulating species of Crassulaceae. It is a promising phytoremediation candidate accumulating substantial heavy metal ions without obvious signs of poisoning. However, few studies have focused on the regulatory roles of miRNAs and their targets in the hyperaccumulating ecotype of S. alfredii. Here, we combined analyses of the transcriptomics, sRNAs and the degradome to generate a comprehensive resource focused on identifying key regulatory miRNA-target circuits under Cd stress. A total of 87 721 unigenes and 356 miRNAs were identified by deep sequencing, and 79 miRNAs were differentially expressed under Cd stress. Furthermore, 754 target genes of 194 miRNAs were validated by degradome sequencing. A gene ontology (GO) enrichment analysis of differential miRNA targets revealed that auxin, redox-related secondary metabolism and metal transport pathways responded to Cd stress. An integrated analysis uncovered 39 pairs of miRNA targets that displayed negatively correlated expression profiles. Ten miRNA-target pairs also exhibited negative correlations according to a real-time quantitative PCR analysis. Moreover, a coexpression regulatory network was constructed based on profiles of differentially expressed genes. Two hub genes, ARF4 (auxin response factor 4) and AAP3 (amino acid permease 3), which might play central roles in the regulation of Cd-responsive genes, were uncovered. These results suggest that comprehensive analyses of the transcriptomics, sRNAs and the degradome provided a useful platform for investigating Cd hyperaccumulation in S. alfredii, and may provide new insights into the genetic engineering of phytoremediation.

H2O2 and ABA signaling are responsible for the increased Na+ efflux and water uptake in Gossypium hirsutum L. roots in the non-saline side under non-uniform root zone salinity

Non-uniform root salinity increases the Na(+)efflux, water use, and growth of the root in non-saline side, which may be regulated by some form of signaling induced by the high-salinity side. However, the signaling and its specific function have remained unknown. Using a split-root system to simulate a non-uniform root zone salinity in Gossypium hirsutum L., we showed that the up-regulated expression of sodium efflux-related genes (SOS1, SOS2, PMA1, and PMA2) and water uptake-related genes (PIP1 and PIP2) was possibly involved in the elevated Na(+) efflux and water use in the the roots in the non-saline side. The increased level of indole acetic acid (IAA) in the non-saline side was the likely cause of the increased root growth. Also, the abscisic acid (ABA) and H2O2 contents in roots in the non-saline side increased, possibly due to the increased expression of their key biosynthesis genes, NCED and RBOHC, and the decreased expression of ABA catabolic CYP707A genes. Exogenous ABA added to the non-saline side induced H2O2 generation by up-regulating the RBOHC gene, but this was decreased by exogenous fluridone. Exogenous H2O2 added to the non-saline side reduced the ABA content by down-regulating NCED genes, which can be induced by diphenylene iodonium (DPI) treatment in the non-saline side, suggesting a feedback mechanism between ABA and H2O2.Both exogenous ABA and H2O2 enhanced the expression of SOS1, PIP1;7 ,PIP2;2, and PIP2;10 genes, but these were down-regulated by fluridone and DPI, suggesting that H2O2 and ABA are important signals for increasing root Na(+) efflux and water uptake in the roots in the non-saline side.

The Thioredoxin GbNRX1 Plays a Crucial Role in Homeostasis of Apoplastic Reactive Oxygen Species in Response to Verticillium dahliae Infection in Cotton

Examining the proteins that plants secrete into the apoplast in response to pathogen attack provides crucial information for understanding the molecular mechanisms underlying plant innate immunity. In this study, we analyzed the changes in the root apoplast secretome of the Verticillium wilt-resistant island cotton cv Hai 7124 (Gossypium barbadense) upon infection with Verticillium dahliae Two-dimensional differential gel electrophoresis and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry analysis identified 68 significantly altered spots, corresponding to 49 different proteins. Gene ontology annotation indicated that most of these proteins function in reactive oxygen species (ROS) metabolism and defense response. Of the ROS-related proteins identified, we further characterized a thioredoxin, GbNRX1, which increased in abundance in response to V. dahliae challenge, finding that GbNRX1 functions in apoplastic ROS scavenging after the ROS burst that occurs upon recognition of V. dahliae Silencing of GbNRX1 resulted in defective dissipation of apoplastic ROS, which led to higher ROS accumulation in protoplasts. As a result, the GbNRX1-silenced plants showed reduced wilt resistance, indicating that the initial defense response in the root apoplast requires the antioxidant activity of GbNRX1. Together, our results demonstrate that apoplastic ROS generation and scavenging occur in tandem in response to pathogen attack; also, the rapid balancing of redox to maintain homeostasis after the ROS burst, which involves GbNRX1, is critical for the apoplastic immune response.

The auxin conjugate indole-3-acetyl-aspartate affects responses to cadmium and salt stress in Pisum sativum L

The synthesis of IAA-amino acid conjugates is one of the crucial regulatory mechanisms for the control of auxin activity during physiological and pathophysiological responses. Indole-3-acetyl-aspartate (IAA-Asp) is a low molecular weight amide conjugate that predominates in pea (Pisum sativum L.) tissues. IAA-Asp acts as an intermediate during the auxin degradation pathway. However, some recent investigations suggest a direct signaling function of this conjugate in various processes. In this study, we examine the effect of 100 μM IAA-Asp alone and in combination with salt stress (160 mM NaCl) or heavy metal stress (250 μM CdCl2) on H2O2 concentration, protein carbonylation as well as catalase and ascorbate (APX) and guaiacol peroxidase (GPX) activities in 7-day-old pea seedlings. As revealed by spectrophotometric analyses, IAA-Asp increased the carbonylated protein level and reduced the H2O2 concentration. Moreover, IAA-aspartate potentiated the effect of both Cd(2+) ions and NaCl on the H2O2 level. The enzymatic activities (catalase and peroxidases) were examined using spectrophotometric and native-PAGE assays. IAA-Asp alone did not affect catalase activity, whereas the two peroxidases were regulated differently. IAA-Asp reduced the APX activity during 48h cultivation. APX activity was potentiated by IAA-Asp+NaCl after 48h. Guaiacol peroxidase activity was diminished by all tested compounds. Based on these results, we suggest that IAA-Asp can directly and specifically affect the pea responses to abiotic stress.

Transcriptomic Analysis of Grapevine (cv. Summer Black) Leaf, Using the Illumina Platform

Proceeding to illumina sequencing, determining RNA integrity numbers for poly RNA were separated from each of the four developmental stages of cv. Summer Black leaves by using Illumina HiSeq^™ 2000. The sums of 272,941,656 reads were generated from vitis vinifera leaf at four different developmental stages, with more than 27 billion nucleotides of the sequence data. At each growth stage, RNA samples were indexed through unique nucleic acid identifiers and sequenced. KEGG annotation results depicted that the highest number of transcripts in 2,963 (2Avs4A) followed by 1Avs4A (2,920), and 3Avs4A (2,294) out of 15,614 (71%) transcripts were recorded. In comparison, a total of 1,532 transcripts were annotated in GOs, including Cellular component, with the highest number in “Cell part” 251 out of 353 transcripts (71.1%), followed by intracellular organelle 163 out of 353 transcripts (46.2%), while in molecular function and metabolic process 375 out of 525 (71.4%) transcripts, multicellular organism process 40 out of 525 (7.6%) transcripts in biological process were most common in 1Avs2A. While in case of 1Avs3A, cell part 476 out of 662 transcripts (71.9%), and membrane-bounded organelle 263 out of 662 transcripts (39.7%) were recorded in Cellular component. In the grapevine transcriptome, during the initial stages of leaf development 1Avs2A showed single transcript was down-regulated and none of them were up-regulated. While in comparison of 1A to 3A showed one up-regulated (photosystem II reaction center protein C) and one down regulated (conserved gene of unknown function) transcripts, during the hormone regulating pathway namely SAUR-like auxin-responsive protein family having 2 up-regulated and 7 down-regulated transcripts, phytochrome-associated protein showed 1 up-regulated and 9 down-regulated transcripts, whereas genes associated with the Leucine-rich repeat protein kinase family protein showed 7 up-regulated and 1 down-regulated transcript, meanwhile Auxin Resistant 2 has single up-regulated transcript in second developmental stage, although 3 were down-regulated at lateral growth stages (3A and 4A). In the present study, 489 secondary metabolic pathways related genes were identified during leaf growth, which mainly includes alkaloid (40), anthocyanins (21), Diterpenoid (144), Monoterpenoid (90) and Flavonoids (93). Quantitative real-time PCR was applied to validate 10 differentially expressed transcripts patterns from flower, leaf and fruit metabolic pathways at different growth stages.

A Global View of Gene Expression of Aspergillus nidulans on Responding to the Deficiency in Soluble Potassium

Many researchers have suggested that microbes can accelerate the weathering of silicate minerals. However, many genes and metabolic pathways related to microorganisms obtaining potassium (K) from silicate remain undiscovered. It is feasible to detect the gene expression within the scope of the whole genome through high-throughput sequencing. Surprisingly, only a few reports have shown fungal weathering of silicate using this technology. This study explored differences in gene expression of Aspergillus nidulans, which was cultured with different K sources, KCl, and K-feldspar. A. nidulans RNA was extracted by the construction of a cDNA library. Identification of K-acquisition-related genes with GO and KEGG pathway analysis revealed that primarily differentially expressed genes were related to the biosynthesis of amino acids. When these genes were grouped in accordance with the physiological functions, the genes involved in the synthesis of protease, ribosome, and mitochondria, trans-membrane transport, and oxidative phosphorylation were significantly different. Moreover, 20 genes selected were further tested using RT-qPCR. One half (10 genes) exhibited differential expression, which was consistent with the results of RNA-seq. Combining the results of RNA-seq and RT-qPCR, we summarised a possible way to obtain mineral K in A. nidulans as well. The differentially expressed genes and their associated metabolic pathways revealed will improve the understanding of the molecular mechanisms of microbial weathering of silicate minerals.