Plant Metabolomics Reviews

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Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding.

June 20, 2017 - 10:41am
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Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding.

Front Plant Sci. 2017;8:757

Authors: Ghatak A, Chaturvedi P, Weckwerth W

Abstract
Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation. Therefore, it is essential to measure protein levels and post-translational protein modifications to reveal information about stress inducible signal perception and transduction, translational activity and induced protein levels. This information cannot be revealed by genomic or transcriptomic analysis. Eventually, these processes will provide more direct insight into stress perception then genetic markers and might build a complementary basis for future marker-assisted selection of drought resistance. In this review, we survey the role of proteomic studies to illustrate their applications in crop stress adaptation analysis with respect to productivity. Cereal crops such as wheat, rice, maize, barley, sorghum and pearl millet are discussed in detail. We provide a comprehensive and comparative overview of all detected protein changes involved in drought stress in these crops and have summarized existing knowledge into a proposed scheme of drought response. Based on a recent proteome study of pearl millet under drought stress we compare our findings with wheat proteomes and another recent study which defined genetic marker in pearl millet.

PMID: 28626463 [PubMed - in process]

Frontiers of high-throughput metabolomics.

June 20, 2017 - 10:41am
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Frontiers of high-throughput metabolomics.

Curr Opin Chem Biol. 2017 Feb;36:15-23

Authors: Zampieri M, Sekar K, Zamboni N, Sauer U

Abstract
Large scale metabolomics studies are increasingly used to investigate genetically different individuals and time-dependent responses to environmental stimuli. New mass spectrometric approaches with at least an order of magnitude more rapid analysis of small molecules within the cell's metabolome are now paving the way towards true high-throughput metabolomics, opening new opportunities in systems biology, functional genomics, drug discovery, and personalized medicine. Here we discuss the impact and advantages of the progress made in profiling large cohorts and dynamic systems with high temporal resolution and automated sampling. In both areas, high-throughput metabolomics is gaining traction because it can generate hypotheses on molecular mechanisms and metabolic regulation. We conclude with the current status of the less mature single cell analyses where high-throughput analytics will be indispensable to resolve metabolic heterogeneity in populations and compartmentalization of metabolites.

PMID: 28064089 [PubMed - indexed for MEDLINE]

The application of metabolomics for herbal medicine pharmacovigilance: a case study on ginseng.

June 20, 2017 - 10:41am
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The application of metabolomics for herbal medicine pharmacovigilance: a case study on ginseng.

Essays Biochem. 2016 Dec 15;60(5):429-435

Authors: Crighton E, Mullaney I, Trengove R, Bunce M, Maker G

Abstract
Herbal medicines are growing in popularity, use and commercial value; however, there remain problems with the quality and consequently safety of these products. Adulterated, contaminated and fraudulent products are often found on the market, a risk compounded by the fact that these products are available to consumers with little or no medical advice. Current regulations and quality control methods are lacking in their ability to combat these serious problems. Metabolomics is a biochemical profiling tool that may help address these issues if applied to quality control of both raw ingredients and final products. Using the example of the popular herbal medicine, ginseng, this essay offers an overview of the potential use of metabolomics for quality control in herbal medicines and also highlights where more research is needed.

PMID: 27980093 [PubMed - indexed for MEDLINE]

Livestock metabolomics and the livestock metabolome: A systematic review.

May 23, 2017 - 10:19am
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Livestock metabolomics and the livestock metabolome: A systematic review.

PLoS One. 2017;12(5):e0177675

Authors: Goldansaz SA, Guo AC, Sajed T, Steele MA, Plastow GS, Wishart DS

Abstract
Metabolomics uses advanced analytical chemistry techniques to comprehensively measure large numbers of small molecule metabolites in cells, tissues and biofluids. The ability to rapidly detect and quantify hundreds or even thousands of metabolites within a single sample is helping scientists paint a far more complete picture of system-wide metabolism and biology. Metabolomics is also allowing researchers to focus on measuring the end-products of complex, hard-to-decipher genetic, epigenetic and environmental interactions. As a result, metabolomics has become an increasingly popular "omics" approach to assist with the robust phenotypic characterization of humans, crop plants and model organisms. Indeed, metabolomics is now routinely used in biomedical, nutritional and crop research. It is also being increasingly used in livestock research and livestock monitoring. The purpose of this systematic review is to quantitatively and objectively summarize the current status of livestock metabolomics and to identify emerging trends, preferred technologies and important gaps in the field. In conducting this review we also critically assessed the applications of livestock metabolomics in key areas such as animal health assessment, disease diagnosis, bioproduct characterization and biomarker discovery for highly desirable economic traits (i.e., feed efficiency, growth potential and milk production). A secondary goal of this critical review was to compile data on the known composition of the livestock metabolome (for 5 of the most common livestock species namely cattle, sheep, goats, horses and pigs). These data have been made available through an open access, comprehensive livestock metabolome database (LMDB, available at http://www.lmdb.ca). The LMDB should enable livestock researchers and producers to conduct more targeted metabolomic studies and to identify where further metabolome coverage is needed.

PMID: 28531195 [PubMed - in process]

Proteomics survey of Solanaceae family: Current status and challenges ahead.

May 23, 2017 - 10:19am
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Proteomics survey of Solanaceae family: Current status and challenges ahead.

J Proteomics. 2017 May 18;:

Authors: Ghatak A, Chaturvedi P, Paul P, Agrawal GK, Rakwal R, Kim ST, Weckwerth W, Gupta R

Abstract
Solanaceae is one of the major economically important families of higher plants and has played a central role in human nutrition since the dawn of human civilization. Therefore, researchers have always been interested in understanding the complex behavior of Solanaceae members to identify key transcripts, proteins or metabolites, which are potentially associated with major traits. Proteomics studies have contributed significantly to understanding the physiology of Solanaceae members. A compilation of all the published reports showed that both gel-based (75%) and gel-free (25%) proteomic technologies have been utilized to establish the proteomes of different tissues, organs, and organelles under normal and adverse environmental conditions. Among the Solanaceae members, most of the research has been focused on tomato (42%) followed by potato (28%) and tobacco (20%), owing to their economic importance. This review comprehensively covers the progress made so far in the field of Solanaceae proteomics including novel methods developed to isolate the proteins from different tissues. Moreover, key proteins presented in this review can serve as a resource to select potential targets for crop improvement. We envisage that information presented in this review would enable us to design the stress tolerant plants with enhanced yields.
BIOLOGICAL SIGNIFICANCE: Solanaceae is one of the major economically important families of higher plants and has played a central role in human nutrition since the dawn of human civilization. Therefore, researchers have always been interested in understanding the complex behavior of Solanaceae members to identify key players associated with major traits. Proteomics studies have contributed significantly to understanding the physiology of Solanaceae members. This review comprehensively covers the progress made so far in the field of Solanaceae proteomics including novel methods developed to isolate the proteins from different tissues. Moreover, key proteins presented in this review can serve as a resource to select potential targets for crop improvement. We envisage that information presented in this review would enable us to design the stress tolerant plants with enhanced yields.

PMID: 28528990 [PubMed - as supplied by publisher]

Genomics of the Asian rice gall midge and its interactions with rice.

May 20, 2017 - 7:25am
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Genomics of the Asian rice gall midge and its interactions with rice.

Curr Opin Insect Sci. 2017 Feb;19:76-81

Authors: Sinha DK, Atray I, Agarrwal R, Bentur JS, Nair S

Abstract
Understanding virulence and manipulative strategies of gall formers will reveal new facets of plant defense and insect counter defense. Among the gall midges, the Asian rice gall midge (AGM) has emerged as a model for studies on plant-insect interactions. Data from several genomics, transcriptomics and metabolomics studies have revealed diverse strategies adopted by AGM to successfully invade the host while overcoming its defense. Adaptive skills of AGM transcend from its genomic and transcriptomic make-up. Information arising from studies on genetics, mitochondrial genome and miRNAs, amongst other parameters, highlights AGM's capacity to maneuver the host defense, reorient host metabolome and redirect its morphogenesis.

PMID: 28521946 [PubMed - in process]

More effort - more results: recent advances in integrative 'omics' data analysis.

May 20, 2017 - 7:25am
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More effort - more results: recent advances in integrative 'omics' data analysis.

Curr Opin Plant Biol. 2016 Apr;30:57-61

Authors: Rajasundaram D, Selbig J

Abstract
The development of 'omics' technologies has progressed to address complex biological questions that underlie various plant functions thereby producing copious amounts of data. The need to assimilate large amounts of data into biologically meaningful interpretations has necessitated the development of statistical methods to integrate multidimensional information. Throughout this review, we provide examples of recent outcomes of 'omics' data integration together with an overview of available statistical methods and tools.

PMID: 26890084 [PubMed - indexed for MEDLINE]

From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web-resources for mass spectral plant metabolomics.

May 19, 2017 - 7:30am
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From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web-resources for mass spectral plant metabolomics.

Gigascience. 2017 May 17;:

Authors: de Souza LP, Naake T, Tohge T, Fernie AR

Abstract
The grand challenge currently facing metabolomics is the expansion of the coverage of the metabolome from a minor percentage of the metabolic complement of the cell towards the level of coverage afforded by other post-genomic technologies such as transcriptomics and proteomics. In plants this problem is exacerbated by the sheer diversity of chemicals that constitute the metabolome with the number of metabolites in the plant kingdom generally being considered to be in excess of 200 000. In this review we focus on web-resources that can be exploited in order to improve analyte and ultimately metabolite identification and quantification. There is a wide range of available software that not only aids in this but also in the related area of peak alignment, however, for the uninitiated choosing which program to use is a daunting task. For this reason we provide an overview of the pros and cons of the software as well as comments regarding the level of programing skills required to effectively exploit their basic functions. In addition the torrent of available genome and transcriptome sequences that followed the advent of next-generation sequencing has opened up further valuable resources for metabolite identification. All things considered, we posit that only via a continued communal sharing of information such as that deposited in the databases described within the article are we likely to be able to make significant headway towards improving our coverage of the plant metabolome.

PMID: 28520864 [PubMed - as supplied by publisher]

Anticancer Chemodiversity of Ranunculaceae Medicinal Plants: Molecular Mechanisms and Functions.

May 16, 2017 - 10:18am
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Anticancer Chemodiversity of Ranunculaceae Medicinal Plants: Molecular Mechanisms and Functions.

Curr Genomics. 2017 Feb;18(1):39-59

Authors: Hao DC, He CN, Shen J, Xiao PG

Abstract
The buttercup family, Ranunculaceae, comprising more than 2,200 species in at least 62 genera, mostly herbs, has long been used in folk medicine and worldwide ethnomedicine since the beginning of human civilization. Various medicinal phytometabolites have been found in Ranunculaceae plants, many of which, such as alkaloids, terpenoids, saponins, and polysaccharides, have shown anti-cancer activities in vitro and in vivo. Most concerns have been raised for two epiphany molecules, the monoterpene thymoquinone and the isoquinoline alkaloid berberine. At least 17 genera have been enriched with anti-cancer phytometabolites. Some Ranunculaceae phytometabolites induce the cell cycle arrest and apoptosis of cancer cells or enhance immune activities, while others inhibit the proliferation, invasion, angiogenesis, and metastasis, or reverse the multi-drug resistance of cancer cells thereby regulating all known hallmarks of cancer. These phytometabolites could exert their anti-cancer activities via multiple signaling pathways. In addition, absorption, distribution, metabolism, and excretion/toxicity properties and structure/activity relationships of some phytometabolites have been revealed assisting in the early drug discovery and development pipelines. However, a comprehensive review of the molecular mechanisms and functions of Ranunculaceae anti-cancer phytometabolites is lacking. Here, we summarize the recent progress of the anti-cancer chemo- and pharmacological diversity of Ranunculaceae medicinal plants, focusing on the emerging molecular machineries and functions of anti-cancer phytometabolites. Gene expression profiling and relevant omics platforms (e.g. genomics, transcriptomics, proteomics, and metabolomics) could reveal differential effects of phytometabolites on the phenotypically heterogeneous cancer cells.

PMID: 28503089 [PubMed - in process]

Finger Millet: A "Certain" Crop for an "Uncertain" Future and a Solution to Food Insecurity and Hidden Hunger under Stressful Environments.

May 11, 2017 - 1:17pm
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Finger Millet: A "Certain" Crop for an "Uncertain" Future and a Solution to Food Insecurity and Hidden Hunger under Stressful Environments.

Front Plant Sci. 2017;8:643

Authors: Gupta SM, Arora S, Mirza N, Pande A, Lata C, Puranik S, Kumar J, Kumar A

Abstract
Crop growth and productivity has largely been vulnerable to various abiotic and biotic stresses that are only set to be compounded due to global climate change. Therefore developing improved varieties and designing newer approaches for crop improvement against stress tolerance have become a priority now-a-days. However, most of the crop improvement strategies are directed toward staple cereals such as rice, wheat, maize etc., whereas attention on minor cereals such as finger millet [Eleusine coracana (L.) Gaertn.] lags far behind. It is an important staple in several semi-arid and tropical regions of the world with excellent nutraceutical properties as well as ensuring food security in these areas even during harsh environment. This review highlights the importance of finger millet as a model nutraceutical crop. Progress and prospects in genetic manipulation for the development of abiotic and biotic stress tolerant varieties is also discussed. Although limited studies have been conducted for genetic improvement of finger millets, its nutritional significance in providing minerals, calories and protein makes it an ideal model for nutrition-agriculture research. Therefore, improved genetic manipulation of finger millets for resistance to both abiotic and biotic stresses, as well as for enhancing nutrient content will be very effective in millet improvement. Key message: Apart from the excellent nutraceutical value of finger millet, its ability to tolerate various abiotic stresses and resist pathogens make it an excellent model for exploring vast genetic and genomic potential of this crop, which provide us a wide choice for developing strategies for making climate resilient staple crops.

PMID: 28487720 [PubMed - in process]

Integrating cell biology and proteomic approaches in plants.

April 26, 2017 - 10:22am
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Integrating cell biology and proteomic approaches in plants.

J Proteomics. 2017 Apr 21;:

Authors: Takáč T, Šamajová O, Šamaj J

Abstract
Significant improvements of protein extraction, separation, mass spectrometry and bioinformatics nurtured advancements of proteomics during the past years. The usefulness of proteomics in the investigation of biological problems can be enhanced by integration with other experimental methods from cell biology, genetics, biochemistry, pharmacology, molecular biology and other omics approaches including transcriptomics and metabolomics. This review aims to summarize current trends integrating cell biology and proteomics in plant science. Cell biology approaches are most frequently used in proteomic studies investigating subcellular and developmental proteomes, however, they were also employed in proteomic studies exploring abiotic and biotic stress responses, vesicular transport, cytoskeleton and protein posttranslational modifications. They are used either for detailed cellular or ultrastructural characterization of the object subjected to proteomic study, for validation of proteomic results, or they might be used to expand proteomic data. In this respect, a broad spectrum of methods is employed to support proteomic studies including ultrastructural electron microscopy studies, histochemical staining, immunochemical localization, in vivo imaging of fluorescently tagged proteins and visualization of protein-protein interactions. Thus, cell biological observations on fixed or living cell compartments, cells, tissues and organs are feasible, and in some cases fundamental for the validation and complementation of proteomic data.
SIGNIFICANCE: Validation of proteomic data by independent experimental methods requires development of new complementary approaches. Benefits of cell biology methods and techniques are not sufficiently highlighted in current proteomic studies. This encouraged us to review most popular cell biology methods used in proteomic studies and to evaluate their relevance and potential for proteomic data validation and enrichment of purely proteomic analyses. We also provide examples of representative studies combining proteomic and cell biology methods for various purposes. Integrating cell biology approaches with proteomic ones allow validation and better interpretation of proteomic data. Moreover, cell biology methods remarkably extend the knowledge provided by proteomic studies and might be fundamental for the functional complementation of proteomic data. This review article summarizes current literature linking proteomics with cell biology.

PMID: 28438675 [PubMed - as supplied by publisher]

Justicidin B: A Promising Bioactive Lignan.

April 19, 2017 - 10:19am
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Justicidin B: A Promising Bioactive Lignan.

Molecules. 2016 Jun 23;21(7):

Authors: Hemmati S, Seradj H

Abstract
Adverse effects and drug resistance to the current onchopharmacologicals have increased the demand for alternative novel therapeutics. We herein introduce justicidin B, an arylnaphthalen lignan isolated from different plant origins, especially Justicia, Phyllanthus, Haplophyllum and Linum species. This cyclolignan exhibits a wide array of biological properties ranges from piscicidal to antifungal, antiviral and antibacterial activities. Activity against Trypanosoma brucei makes justicidin B a potential antiprotozoal agent for the treatment of neglected tropical diseases. Pharmacological properties like antiplatelet, anti-inflammatory and bone resorption inhibition have been also attributed to justicidin B. This compound is a potent cytotoxic substance on several cell lines, especially chronic myeloid and chronic lymphoid leukemia. Pharmacological values, natural variation, as well as biotechnological production of justicidin B by plant cell, tissue and organ culture are also described in this review. Chemical characteristics and chromatographic methods to identify justicidin B and its biosynthetic pathway have been discussed. Different approaches to the total synthesis of justicidin B are compared. This review would shed light on the role of justicidin B as an intriguing natural compound and provides a chance to optimize conditions for industrial applications.

PMID: 27347906 [PubMed - indexed for MEDLINE]

The Hedyotis diffusa Willd. (Rubiaceae): A Review on Phytochemistry, Pharmacology, Quality Control and Pharmacokinetics.

April 19, 2017 - 10:19am
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The Hedyotis diffusa Willd. (Rubiaceae): A Review on Phytochemistry, Pharmacology, Quality Control and Pharmacokinetics.

Molecules. 2016 May 30;21(6):

Authors: Chen R, He J, Tong X, Tang L, Liu M

Abstract
Hedyotis diffusa Willd (H. diffusa) is a well-known Chinese medicine with a variety of activities, especially its anti-cancer effect in the clinic. Up to now, 171 compounds have been reported from H. diffusa, including 32 iridoids, 26 flavonoids, 24 anthraquinones, 26 phenolics and their derivatives, 50 volatile oils and 13 miscellaneous compounds. In vitro and in vivo studies show these phytochemicals and plant extracts to exhibit a range of pharmacological activities of anti-cancer, antioxidant, anti-inflammatory, anti-fibroblast, immunomodulatory and neuroprotective effects. Although a series of methods have been established for the quality control of H. diffusa, a feasible and reliable approach is still needed in consideration of its botanical origin, collecting time and bioactive effects. Meanwhile, more pharmacokinetics researches are needed to illustrate the characteristics of H. diffusa in vivo. The present review aims to provide up-to-date and comprehensive information on the phytochemistry, pharmacology, quality control and pharmacokinetic characteristics of H. diffusa for its clinical use and further development.

PMID: 27248992 [PubMed - indexed for MEDLINE]

Insect Gallers and Their Plant Hosts: From Omics Data to Systems Biology.

April 11, 2017 - 10:20am
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Insect Gallers and Their Plant Hosts: From Omics Data to Systems Biology.

Int J Mol Sci. 2016 Nov 18;17(11):

Authors: Oates CN, Denby KJ, Myburg AA, Slippers B, Naidoo S

Abstract
Gall-inducing insects are capable of exerting a high level of control over their hosts' cellular machinery to the extent that the plant's development, metabolism, chemistry, and physiology are all altered in favour of the insect. Many gallers are devastating pests in global agriculture and the limited understanding of their relationship with their hosts prevents the development of robust management strategies. Omics technologies are proving to be important tools in elucidating the mechanisms involved in the interaction as they facilitate analysis of plant hosts and insect effectors for which little or no prior knowledge exists. In this review, we examine the mechanisms behind insect gall development using evidence from omics-level approaches. The secretion of effector proteins and induced phytohormonal imbalances are highlighted as likely mechanisms involved in gall development. However, understanding how these components function within the system is far from complete and a number of questions need to be answered before this information can be used in the development of strategies to engineer or breed plants with enhanced resistance.

PMID: 27869732 [PubMed - indexed for MEDLINE]

Microbial interactions with chromium: basic biological processes and applications in environmental biotechnology.

March 31, 2017 - 10:21am
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Microbial interactions with chromium: basic biological processes and applications in environmental biotechnology.

World J Microbiol Biotechnol. 2016 Dec;32(12):191

Authors: Gutiérrez-Corona JF, Romo-Rodríguez P, Santos-Escobar F, Espino-Saldaña AE, Hernández-Escoto H

Abstract
Chromium (Cr) is a highly toxic metal for microorganisms as well as plants and animal cells. Due to its widespread industrial use, Cr has become a serious pollutant in diverse environmental settings. The hexavalent form of the metal, Cr(VI), is considered a more toxic species than the relatively innocuous and less mobile Cr(III) form. The study of the interactions between microorganisms and Cr has been helpful to unravel the mechanisms allowing organisms to survive in the presence of high concentrations of Cr(VI) and to detoxify and remove the oxyanion. Various mechanisms of interactions with Cr have been identified in diverse species of bacteria and fungi, including biosorption, bioaccumulation, reduction of Cr(VI) to Cr(III), and chromate efflux. Some of these systems have been proposed as potential biotechnological tools for the bioremediation of Cr pollution using bioreactors or by in situ treatments. In this review, the interactions of microorganisms with Cr are summarised, emphasising the importance of new research avenues using advanced methodologies, including proteomic, transcriptomic, and metabolomic analyses, as well as the use of techniques based on X-ray absorption spectroscopy and electron paramagnetic resonance spectroscopy.

PMID: 27718146 [PubMed - indexed for MEDLINE]

Molecular Approaches to Genetically Improve the Accumulation of Health-Promoting Secondary Metabolites in Staple Crops-A Case Study: The Lipoxygenase-B1 Genes and Regulation of the Carotenoid Content in Pasta Products.

March 31, 2017 - 10:21am
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Molecular Approaches to Genetically Improve the Accumulation of Health-Promoting Secondary Metabolites in Staple Crops-A Case Study: The Lipoxygenase-B1 Genes and Regulation of the Carotenoid Content in Pasta Products.

Int J Mol Sci. 2016 Jul 21;17(7):

Authors: Borrelli GM, Trono D

Abstract
Secondary metabolites, also known as phytochemicals, represent a large subset of plant molecules that include compounds with health-promoting effects. Indeed, a number of epidemiological studies have shown that, when taken regularly and in adequate amounts, these molecules can have long-term beneficial effects on human health, through reduction of the incidence of degenerative diseases, such as cardiovascular diseases, obesity, diabetes, and cancer. As the dietary intake of these phytochemicals is often inadequate, various strategies are in use to improve their content in staple crops, and the end-products thereof. One of the most effective strategies is crop improvement through genetic approaches, as this is the only way to generate new cultivars in which the high accumulation of a given phytochemical is stably fixed. Efforts to genetically improve quality traits are rapidly evolving, from classical breeding to molecular-assisted approaches; these require sound understanding of the molecular bases underlying the traits, to identify the genes/alleles that control them. This can be achieved through global analysis of the metabolic pathway responsible for phytochemical accumulation, to identify the link between phytochemical content and the activities of key enzymes that regulate the metabolic pathway, and between the key enzymes and their encoding genes/alleles. Once these have been identified, they can be used as markers for selection of new improved genotypes through biotechnological approaches. This review provides an overview of the major health-promoting properties shown to be associated with the dietary intake of phytochemicals, and describes how molecular approaches provide means for improving the health quality of edible crops. Finally, a case study is illustrated, of the identification in durum wheat of the Lipoxygenase-B1 genes that control the final carotenoid content in semolina-based foods, such as pasta products.

PMID: 27455242 [PubMed - indexed for MEDLINE]

Bioinformatics resources for pollen.

March 31, 2017 - 10:21am
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Bioinformatics resources for pollen.

Plant Reprod. 2016 06;29(1-2):133-47

Authors: Ambrosino L, Bostan H, Ruggieri V, Chiusano ML

Abstract
KEY MESSAGE: Bioinformatics for Pollen. Pollen plays a key role in crop production, and its development is the most delicate phase in reproduction. Different metabolic pathways are involved in pollen development, and changes in the level of some metabolites, as well as responses to stress, are correlated with the reduction in pollen viability, leading consequently to a decrease in the fruit production. However, studies on pollen may be hard because gamete development and fertilization are complex processes that occur during a short window of time. The rise of the so-called -omics sciences provided key strategies to promote molecular research in pollen tissues, starting from model organisms and moving to increasing number of species. An integrated multi-level approach based on investigations from genomics, transcriptomics, proteomics and metabolomics appears now feasible to clarify key molecular processes in pollen development and viability. To this aim, bioinformatics has a fundamental role for data production and analysis, contributing varied and ad hoc methodologies, endowed with different sensitivity and specificity, necessary for extracting added-value information from the large amount of molecular data achievable. Bioinformatics is also essential for data management, organization, distribution and integration in suitable resources. This is necessary to catch the biological features of the pollen tissues and to design effective approaches to identifying structural or functional properties, enabling the modeling of the major involved processes in normal or in stress conditions. In this review, we provide an overview of the available bioinformatics resources for pollen, ranging from raw data collections to complete databases or platforms, when available, which include data and/or results from -omics efforts on the male gametophyte. Perspectives in the fields will also be described.

PMID: 27271281 [PubMed - indexed for MEDLINE]

Plant Metabolomics: An Indispensable System Biology Tool for Plant Science.

March 24, 2017 - 7:25am
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Plant Metabolomics: An Indispensable System Biology Tool for Plant Science.

Int J Mol Sci. 2016 Jun 01;17(6):

Authors: Hong J, Yang L, Zhang D, Shi J

Abstract
As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plant behavior under both normal and stressed conditions. Hereby, we summarize the current knowledge on the genetic and biochemical mechanisms underlying plant growth, development, and stress responses, focusing further on the contributions of metabolomics to practical applications in crop quality improvement and food safety assessment, as well as plant metabolic engineering. We also highlight the current challenges and future perspectives in this inspiring area, with the aim to stimulate further studies leading to better crop improvement of yield and quality.

PMID: 27258266 [PubMed - indexed for MEDLINE]

Metabolic engineering for the production of plant isoquinoline alkaloids.

March 24, 2017 - 7:25am
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Metabolic engineering for the production of plant isoquinoline alkaloids.

Plant Biotechnol J. 2016 06;14(6):1319-28

Authors: Diamond A, Desgagné-Penix I

Abstract
Several plant isoquinoline alkaloids (PIAs) possess powerful pharmaceutical and biotechnological properties. Thus, PIA metabolism and its fascinating molecules, including morphine, colchicine and galanthamine, have attracted the attention of both the industry and researchers involved in plant science, biochemistry, chemical bioengineering and medicine. Currently, access and availability of high-value PIAs [commercialized (e.g. galanthamine) or not (e.g. narciclasine)] is limited by low concentration in nature, lack of cultivation or geographic access, seasonal production and risk of overharvesting wild plant species. Nevertheless, most commercial PIAs are still extracted from plant sources. Efforts to improve the production of PIA have largely been impaired by the lack of knowledge on PIA metabolism. With the development and integration of next-generation sequencing technologies, high-throughput proteomics and metabolomics analyses and bioinformatics, systems biology was used to unravel metabolic pathways allowing the use of metabolic engineering and synthetic biology approaches to increase production of valuable PIAs. Metabolic engineering provides opportunity to overcome issues related to restricted availability, diversification and productivity of plant alkaloids. Engineered plant, plant cells and microbial cell cultures can act as biofactories by offering their metabolic machinery for the purpose of optimizing the conditions and increasing the productivity of a specific alkaloid. In this article, is presented an update on the production of PIA in engineered plant, plant cell cultures and heterologous micro-organisms.

PMID: 26503307 [PubMed - indexed for MEDLINE]

Potential role of CYP1B1 in the development and treatment of metabolic diseases.

March 23, 2017 - 10:20am
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Potential role of CYP1B1 in the development and treatment of metabolic diseases.

Pharmacol Ther. 2017 Mar 16;:

Authors: Li F, Zhu W, Gonzalez FJ

Abstract
Cytochrome P450 1B1 (CYP1B1), a member of CYP450s, is expressed in liver and extrahepatic tissues carries out the metabolism of numerous xenobiotics, including the metabolic activation of polycyclic aromatic hydrocarbons. Surprisingly, CYP1B1 was also shown to be important in regulating endogenous metabolic pathways, including the metabolism of steroid hormones, fatty acids, melatonin, and vitamins. CYP1B1 and nuclear receptors including peroxisome proliferator-activated receptors (PPARs), estrogen receptor (ER), and retinoic acid receptors (RAR) contribute to the maintenance of the homeostasis of these endogenous compounds. Many natural flavonoids and synthetic stilbenes show the inhibitory activity toward CYP1B1 expression and function, notably isorhamnetin and 2,4,3',5'-tetramethoxystilbene. Accumulating data indicate that modulation of CYP1B1 can decrease adipogenesis and tumorigenesis, and prevent obesity, hypertension, atherosclerosis, and cancer. Therefore, it may be feasible to consider CYP1B1 as a therapeutic target for the treatment of metabolic diseases.

PMID: 28322972 [PubMed - as supplied by publisher]

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