574 research outputs found

    Genome-Wide Identification and Analysis of Grape Aldehyde Dehydrogenase (ALDH) Gene Superfamily

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    The completion of the grape genome sequencing project has paved the way for novel gene discovery and functional analysis. Aldehyde dehydrogenases (ALDHs) comprise a gene superfamily encoding NAD(P)(+)-dependent enzymes that catalyze the irreversible oxidation of a wide range of endogenous and exogenous aromatic and aliphatic aldehydes. Although ALDHs have been systematically investigated in several plant species including Arabidopsis and rice, our knowledge concerning the ALDH genes, their evolutionary relationship and expression patterns in grape has been limited.A total of 23 ALDH genes were identified in the grape genome and grouped into ten families according to the unified nomenclature system developed by the ALDH Gene Nomenclature Committee (AGNC). Members within the same grape ALDH families possess nearly identical exon-intron structures. Evolutionary analysis indicates that both segmental and tandem duplication events have contributed significantly to the expansion of grape ALDH genes. Phylogenetic analysis of ALDH protein sequences from seven plant species indicates that grape ALDHs are more closely related to those of Arabidopsis. In addition, synteny analysis between grape and Arabidopsis shows that homologs of a number of grape ALDHs are found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the speciation of the grape and Arabidopsis. Microarray gene expression analysis revealed large number of grape ALDH genes responsive to drought or salt stress. Furthermore, we found a number of ALDH genes showed significantly changed expressions in responses to infection with different pathogens and during grape berry development, suggesting novel roles of ALDH genes in plant-pathogen interactions and berry development.The genome-wide identification, evolutionary and expression analysis of grape ALDH genes should facilitate research in this gene family and provide new insights regarding their evolution history and functional roles in plant stress tolerance

    The bracteatus pineapple genome and domestication of clonally propagated crops

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    Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars 'Smooth Cayenne' and 'Queen' exhibited ancient and recent admixture, while 'Singapore Spanish' supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops

    Omeprazole, a proton-pump inhibitor on humans, acts as a growth enhancer and stress protectant in plants

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    L’omeprazolo (OP) è un derivato benzimidazolico utilizzato in campo umano per la terapia di patologie gastriche legate essenzialmente all’eccessiva produzione di acido cloridrico all’interno dello stomaco, essendo capace di inibire una pompa protonica necessaria alla sua produzione. Prima di questo studio, non era mai stato testato l’effetto di OP sulle piante. Ciò che è stato riscontrato nei vari esperimenti è che OP è bioattivo a concentrazioni micromolari. Il primo esperimento è stato condotto su piante di pomodoro coltivate in idroponica. Le piante trattate con OP hanno presentato un aumento della produzione di biomassa aerea e radicale, oltre che una maggiore protezione dell’apparato fotosintetico in condizioni di stress salino. In un successivo esperimento su pomodoro (in vaso), pur non riscontrando un effetto sulla crescita in condizioni ottimali, è risultato chiaro l’effetto che OP ha esercitato sulla tolleranza allo stress salino. Inoltre, OP ha portato ad un aumento di produzione, un parametro che non era stato possibile valutare nel primo esperimento data la breve durata dello stesso. In seguito abbiamo scelto di testare OP su due diverse varietà di basilico, Genovese e Napoletano, che presentano rispettivamente una costitutiva maggiore e minore tolleranza allo stress salino. Il risultato più interessante dell’esperimento è stato che, pur riscontrando una risposta simile delle due varietà in condizioni ottimali, in condizioni di stress salino la varietà meno tollerante ha beneficiato del trattamento con OP, a differenza della varietà più tollerante in cui non è stata riscontrata alcuna variazione nell’accumulo di biomassa. Per valutare in maggior dettaglio il meccanismo di azione dell’OP abbiamo valutato anche i suoi effetti su un sistema modello. Esperimenti su Arabidopsis thaliana condotti in piastre Petri hanno dimostrato che OP induce una maggiore produzione di radici laterali, e di conseguenza porta ad un’alterazione dell’architettura dell’apparato radicale, che può avere importanti implicazioni per quanto riguarda la capacità di una pianta di accedere ad acqua e nutrienti

    Genetic and Biochemical Dissection of Differential Functions of Cryptochrome 1 and 2 in the Mammalian Circadian Clock

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    Circadian clocks in mammals are based on a negative feedback loop in which transcriptional repression by the Cryptochromes, CRY1 and CRY2, lies at the heart of the mechanism. Despite similarities in their sequence, domain structure and biochemical activity, they play distinct roles in the mammalian clock function. However, detailed biochemical studies have not been straightforward and function of Cryptochrome (Cry) has not been examined in real clock cells using kinetic measurements. In this study, we demonstrate, through cell-based genetic complementation and real-time molecular recording, that Cry1 alone is able to maintain cell-autonomous circadian rhythms, while Cry2 cannot. Using this novel functional assay, we identify a Cryptochrome differentiating α-helical domain within the photolyase homology region (PHR) of CRY1 protein, designated as CRY1-PHR(313-426), that is required for clock function and distinguishes CRY1 from CRY2. Further, in contrast to speculation, we demonstrate that the divergent carboxyl-terminal tail domain (CTD) is dispensable for circadian clock function, but it serves to modulate rhythm amplitude and period length. Finally, we identify the biochemical basis of their distinct function; CRY1 is a much more potent repressor of BMAL1/CLOCK transcriptional activity than CRY2, and the strength of repression by various forms of CRY proteins significantly correlates with rhythm amplitude. Taken together, our results demonstrate that the CRY1-PHR(313-426), not the divergent CTD, is critical for clock function. These findings provide novel insights into the evolution of the diverse functions of the photolyase/cryptochrome family of flavoproteins and offer new opportunities for mechanistic studies of CRY function

    INVESTIGATION ON THE GENETIC BASIS OF ENVIRONMENTAL STRESS IN FRUIT TREE CROPS

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    Plant stress can be divided into two major categories: abiotic stress and biotic stress. Abiotic stress happens when plants are exposed to the environment either physically or chemically. There is an emergency in developing crop varieties that are tolerant to abiotic stresses to ensure food security and safety in the coming years. Multiple abiotic stress like drought, heat, frost at flowering and nutrient deficiency can cause an erratic fruiting behavior or following extreme events, the death of the plants. Plants require an optimal level of nutrients and essential minerals for their growth and development that are mainly acquired from soil by their roots. Nutrient deficiency is an environmental stress that can seriously affect fruit production and quality. In the past decades, agriculturalists relied only on the traditional methods to identify the stresses. In this postgenomic era, called the “omic” era, transcriptional and translational research on model plants has provided many valuable information on many horticultural species. In the present dissertation, the objective of the first study was to identify, and map key genes involved in drought response on leaves across different crops. The study is the first to provide RNA-Seq data analysis related to transcriptomic responses towards drought across different fruit tree crops. The second study was conducted to identify essential genes involved in general plant abiotic stress conditions and those involved in specific and unique in different abiotic stresses. A pipeline composed of pathway and gene set enrichment analysis, protein-protein interaction networks, and gene visualization tools were employed. The next study aims to identify genes that serve as potential targets to develop cultivars with enhanced drought and salinity resistance and/or tolerance across different fruit tree crops in a biotechnological sustainable way. An “omic” experimental plan was developed to investigate and understand a physiological stress presumably due to nutritional deficiencies causing premature flower bud abscission in pistachio that leads to alternate bearing behavior. The aim of this analysis was to provide insights into the transcript changes between inflorescence buds and fruits in bearing and non-bearing shoots to identify the molecular mechanism causing premature inflorescence bud abscission, which is linked to alternate bearing in the Italian pistachio cultivar Bianca. Key molecular physiological conclusions were generated based on the identification of conserved gene sets, pathways, and gene networks involved in abiotic stress resistance/tolerance. The experiment provides a valid approach to ask additional questions with respect to how plants respond to stress. Identifying key information in transcriptomic data is very important, especially when the “omic” study deals with plant responses to stresses in field conditions where a high number of variables and disturbing factors may affect the analysis. The proper understanding of plant stress response mechanisms under specific stresses can draw a better view for improving worldwide food production

    High-throughput profiling and analysis of plant responses over time to abiotic stress

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    Sorghum (Sorghum bicolor (L.) Moench) is a rapidly growing, high-biomass crop prized for abiotic stress tolerance. However, measuring genotype-by-environment (G x E) interactions remains a progress bottleneck. We subjected a panel of 30 genetically diverse sorghum genotypes to a spectrum of nitrogen deprivation and measured responses using high-throughput phenotyping technology followed by ionomic profiling. Responses were quantified using shape (16 measurable outputs), color (hue and intensity), and ionome (18 elements). We measured the speed at which specific genotypes respond to environmental conditions, in terms of both biomass and color changes, and identified individual genotypes that perform most favorably. With this analysis, we present a novel approach to quantifying colorbased stress indicators over time. Additionally, ionomic profiling was conducted as an independent, low-cost, and high-throughput option for characterizing G x E, identifying the elements most affected by either genotype or treatment and suggesting signaling that occurs in response to the environment. This entire dataset and associated scripts are made available through an open-access, user-friendly, web-based interface. In summary, this work provides analysis tools for visualizing and quantifying plant abiotic stress responses over time. These methods can be deployed as a time-efficient method of dissecting the genetic mechanisms used by sorghum to respond to the environment to accelerate crop improvement

    TRANSCRIPTIONAL REGULATION OF SPECIALIZED METABOLITES IN \u3cem\u3eARABIDOPSIS THALIANA\u3c/em\u3e AND \u3cem\u3eCATHARANTHUS ROSEUS\u3c/em\u3e

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    For millennia humans have utilized plant specialized metabolites for health benefits, fragrances, poisons, spices, and medicine. Valued metabolites are often produced in small quantities and may command high prices. Understanding when and how the plant synthesizes these compounds is important for improving their production. Phytohormone signaling cascades, such as jasmonate (JA) activate or repress transcription factors (TF) controlling expression of metabolite biosynthetic genes. TFs regulating specialized metabolite biosynthetic genes can be manipulated to engineer plants with increased metabolite production. WRKY transcription factor are known components of both JA signaling cascades and regulation of specialized metabolism. The presence of WRKY binding sites in promoters of several terpene indole alkaloids suggested their involvement in regulating biosynthesis of these compounds. A phylogenetic analysis was used to compare Arabidopsis and Catharanthus WRKY TFs families. Gene expression analysis identified WRKY TFs induced by JA in both Arabidopsis and Catharanthus, providing candidates for future characterization. WRKY TFs suggest a possible conserved regulatory network of TFs downstream of JA signaling cascades. The origin and conservation of JA signaling in plants remain ambiguous. Identification of the first algal TIFY factor helped determine when JA signaling appeared. The charophyte, Klebsormidium flaccidum does not possess genes encoding key green-plant JA signaling components, including CORONATINE INSENSTIVE1, JASMONATE-ZIM DOMAIN, NOVEL INTERACTOR OF JAZ, and the JAZ-interacting bHLH factors, yet their orthologs are present in the moss. A molecular clock analysis dated the evolution of JA signaling evolution to during the early Ediacaran to late Cambrian periods 628 to 491 million years ago – a time corresponding to rapid diversification of animal predators. The plant Mediator complex is a core component of gene expression. Conservation of the MED25 subunit in plants, and its known involvement in JA signaling implicates this factor in regulation of specialized metabolism. MED25 is involved in anthocyanin accumulation, but how it functions remains unknown. Characterization of MED25 in Arabidopsis revealed it interacts with the transcription factor GL3 as well as the JAZ1 repressor. Importantly, the interaction of JAZ1 with MED25 reveals a new mechanism by which JAZ proteins regulate gene expression, improving our understanding of JA signaling

    Towards a Better Understanding of the Molecular Mechanisms Underlying Plant Development and Stress Response

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    The spectacular array of diverse plant forms as well as the predominantly sessile life style of plants raises two questions that have been fascinating to scientists in the field of plant biology for many years: 1) how do plants develop to a specific size and shape? 2) how do plants respond to environmental stresses given its immobility? Plant organ development to a specific size and shape is controlled by cell proliferation and cell expansion. While the cell proliferation process is extensively studied, the cell expansion process remains largely unknown, and can be affected by several factors, such as cell wall remodeling and the incorporation of new wall materials. To better understand the genetic basis of plant development, we identified an Arabidopsis T-DNA insertion mutant named development related Myb-like 1 (drmy1), which showed altered size and shape in both vegetative and reproductive organs due to defective cell expansion. We further demonstrated that the defective cell expansion in the drmy1 mutant is linked to the change in cell wall composition. Complementation testing by introduction of DRMY1 into the mutant background rescued the phenotype, indicating that DRMY1 is a functional regulator of plant organ development. The DRMY1 protein contains a single Myb-like DNA binding domain and is localized in the nucleus, and may cooperate with other transcription factors to regulate downstream gene expression as DRMY1 itself does not possess transactivation ability. DRMY1 expression analysis revealed that its expression is reduced by the plant hormone ethylene (a negative regulator of cell expansion) while induced by ABA (a positive regulator of cell expansion). Furthermore, whole transcriptome profiling suggested that DRMY1 might control cell expansion directly by regulating genes related to cell wall biosynthesis/remodeling and ribosome biogenesis or indirectly through regulating genes involved in ethylene and ABA signaling pathways. Plants cannot “escape” from salinity stress but have evolved different mechanisms for salt tolerance over the time of adaptation to salinity. About 1% of plant species named halophytes can survive and thrive in environments containing high salt concentrations, which makes it important to understand their salt tolerance mechanisms and the responsible genes. Here, we investigated salt tolerance mechanisms in Supreme, the most salt-tolerant cultivar of a halophytic warm-seasoned perennial grass, Seashore paspalum (Paspalum vaginatum) at the physiological and transcriptomic levels by comparative study with another cultivar Parish, which possesses moderate salinity tolerance. Our results suggest that Na+ accumulation under normal conditions and further increased accumulation under high salinity conditions (400 mM NaCl), possibly by vacuolar sequestration is a crucial mechanism for salinity tolerance in Supreme. Our data suggests that Na+ accumulation in Supreme under normal conditions might trigger the secondary messenger Ca2+ for signal transduction and the resulting upregulation of salt stress related transcription factors in addition to serving as cheap osmolytes to facilitate water uptake. Moreover, the retention of K+ under salt treatment, which can counteract the toxicity of Na+, is a protective mechanism for both cultivars. A strong oxidation-reduction process and nucleic acid binding activity under high salinity conditions are two other contributors to the salinity tolerance in both cultivars. We also identified ion transporters including NHXs and H+-PPases for Na+ sequestration and K+ uptake transporters, which can be used as candidate genes for functional studies and potential targets to engineer plants for enhanced salinity tolerance, opening new avenues for future research

    Epigenetic and targeted metabolic changes in microbial biostimulant-treated maize plants under drought stress conditions

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    Abstract: Drought stress is one of the major limiting factors in agriculture globally, hampering crop yields in approximately 70% of arable farmlands. In this regard, microbial-biostimulants, such as plant growth-promoting bacteria (PGPR)-based formulations, have been proven to provide sustainable and economically favorable solutions that could introduce novel approaches to improve agricultural practices and crop productivity under adverse environmental conditions. However, to devise these novel biostimulants-based agricultural strategies, there is a necessity to firstly understand the physiology and biochemistry governing the interactions between biostimulants and plants. Herein, targeted metabolomics, epigenetics and gene expression analyses were employed to elucidate molecular mechanisms governing plant growth-promotion, stress priming and enhanced drought stress responses induced by a microbial-based biostimulant formulation (a consortium of five Bacillus sp. strains) in maize (Zea mays) plants...M.Sc. (Biochemistry
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