Genomics-assisted breeding for ear rot resistances and reduced mycotoxin contamination in maize: methods, advances and prospects.
Genomics-assisted breeding for ear rot resistances and reduced mycotoxin contamination in maize: methods, advances and prospects.
Theor Appl Genet. 2019 Aug 22;:
Authors: Gaikpa DS, Miedaner T
KEY MESSAGE: Genetic mapping, genomic profiling and bioinformatic approaches were used to identify putative resistance genes for ear rots and low mycotoxin contamination in maize. Genomic selection seems to have good perspectives. Maize is globally an indispensable crop for humans and livestock. About 30% of yield is lost by fungal diseases with Gibberella, Fusarium and Aspergillus ear rots (ERs) having a high economic impact in most maize-growing regions of the world. They reduce not only yield, but also contaminate grains with mycotoxins like deoxynivalenol, zearalenone, fumonisins and aflatoxins, respectively. These mycotoxins pose serious health problems to humans and animals. A number of studies have been conducted to dissect the genetic architecture of resistance to these three major ear rots over the past decade. The review concentrates on studies carried out to locate quantitative trait loci (QTL) and candidate genes (CG) on the maize genome as well as the application of genomic selection in maize for resistance against Fusarium graminearum, Fusarium verticillioides and Aspergillus flavus. QTL studies by linkage or genome-wide association mapping, omic technologies (genomics, proteomics, transcriptomics and metabolomics) and bioinformatics are the methods used in the current studies to propose resistance genes against ear rot pathogens. Though a number of QTL and CG are reported, only a few specific genes were found to directly confer ER resistance in maize. A combination of two or more gene identification methods would provide a more powerful and reliable tool. Genomic selection seems to be promising for ER resistance breeding, but there are only a limited number of studies in this area. A strategy that can accurately validate and predict genotypes with major effect QTL and CG for selection will be worthwhile for practical breeding against ERs and mycotoxin contamination in maize.
PMID: 31440772 [PubMed - as supplied by publisher]
The Origin and Evolution of Plant Flavonoid Metabolism.
Front Plant Sci. 2019;10:943
Authors: Yonekura-Sakakibara K, Higashi Y, Nakabayashi R
During their evolution, plants have acquired the ability to produce a huge variety of compounds. Unlike the specialized metabolites that accumulate in limited numbers of species, flavonoids are widely distributed in the plant kingdom. Therefore, a detailed analysis of flavonoid metabolism in genomics and metabolomics is an ideal way to investigate how plants have developed their unique metabolic pathways during the process of evolution. More comprehensive and precise metabolite profiling integrated with genomic information are helpful to emerge unexpected gene functions and/or pathways. The distribution of flavonoids and their biosynthetic genes in the plant kingdom suggests that flavonoid biosynthetic pathways evolved through a series of steps. The enzymes that form the flavonoid scaffold structures probably first appeared by recruitment of enzymes from primary metabolic pathways, and later, enzymes that belong to superfamilies such as 2-oxoglutarate-dependent dioxygenase, cytochrome P450, and short-chain dehydrogenase/reductase modified and varied the structures. It is widely accepted that the first two enzymes in flavonoid biosynthesis, chalcone synthase, and chalcone isomerase, were derived from common ancestors with enzymes in lipid metabolism. Later enzymes acquired their function by gene duplication and the subsequent acquisition of new functions. In this review, we describe the recent progress in metabolomics technologies for flavonoids and the evolution of flavonoid skeleton biosynthetic enzymes to understand the complicate evolutionary traits of flavonoid metabolism in plant kingdom.
PMID: 31428108 [PubMed]
Ginger and its Active Compounds in Cancer Therapy: From Folk uses to Nano-therapeutic Applications.
Semin Cancer Biol. 2019 Aug 11;:
Authors: Mahomoodally MF, Aumeeruddy MZ, Rengasamy KRR, Roshan S, Hammad S, Pandohee J, Hu X, Zengin G
Ginger is a spice that is renowned for its characteristic aromatic fragrance and pungent taste, with documented healing properties. Field studies conducted in several Asian and African countries revealed that ginger is used traditionally in the management of cancer. The scientific community has probed into the biological validation of its extracts and isolated compounds including the gingerols, shogaols, zingiberene, and zingerone, through in-vitro and in-vivo studies. Nonetheless, an updated compilation of these data together with a deep mechanistic approach is yet to be provided. Accordingly, this review highlights the mechanisms and therapeutics of ginger and its bioactive compounds focused on a cancer context and these evidence are based on the (i) cytotoxic effect against cancer cell lines, (ii) enzyme inhibitory action, (iii) combination therapy with chemotherapeutic and phenolic compounds, (iv) possible links to the microbiome and (v) the use of nano-formulations of ginger bioactive compounds as a more effective drug delivery strategy in cancer therapy.
PMID: 31412298 [PubMed - as supplied by publisher]
Bacillus velezensis: phylogeny, useful applications, and avenues for exploitation.
Appl Microbiol Biotechnol. 2019 May;103(9):3669-3682
Authors: Adeniji AA, Loots DT, Babalola OO
Some members of the Bacillus velezensis (Bv) group (e.g., Bv FZB42T and AS3.43) were previously assigned grouping with B. subtilis and B. amyloliquefaciens, based on the fact that they shared a 99% DNA-DNA percentage phylogenetic similarity. However, hinging on current assessments of the pan-genomic reassignments, the differing phylogenomic characteristics of Bv from B. subtilis and B. amyloliquefaciens are now better understood. Within this re-grouping/reassignment, the various strains within the Bv share a close phylogenomic resemblance, and a number of these strains have received a lot of attention in recent years, due to their genomic robustness, and the growing evidence for their possible utilization in the agricultural industry for managing plant diseases. Only a few applications for their use medicinally/pharmaceutically, environmentally, and in the food industry have been reported, and this may be due to the fact that the majority of those strains investigated are those typically occurring in soil. Although the intracellular unique biomolecules of Bv strains have been revealed via in silico genome modeling and investigated using transcriptomics and proteomics, a further inquisition into the Bv metabolome using newer technologies such as metabolomics could elucidate additional applications of this economically relevant Bacillus species, beyond that of primarily the agricultural sector.
PMID: 30911788 [PubMed - indexed for MEDLINE]
Development of Robust Yeast Strains for Lignocellulosic Biorefineries Based on Genome-Wide Studies.
Prog Mol Subcell Biol. 2019;58:61-83
Authors: Zhang MM, Chen HQ, Ye PL, Wattanachaisaereekul S, Bai FW, Zhao XQ
Lignocellulosic biomass has been widely studied as the renewable feedstock for the production of biofuels and biochemicals. Budding yeast Saccharomyces cerevisiae is commonly used as a cell factory for bioconversion of lignocellulosic biomass. However, economic bioproduction using fermentable sugars released from lignocellulosic feedstocks is still challenging. Due to impaired cell viability and fermentation performance by various inhibitors that are present in the cellulosic hydrolysates, robust yeast strains resistant to various stress environments are highly desired. Here, we summarize recent progress on yeast strain development for the production of biofuels and biochemical using lignocellulosic biomass. Genome-wide studies which have contributed to the elucidation of mechanisms of yeast stress tolerance are reviewed. Key gene targets recently identified based on multiomics analysis such as transcriptomic, proteomic, and metabolomics studies are summarized. Physiological genomic studies based on zinc sulfate supplementation are highlighted, and novel zinc-responsive genes involved in yeast stress tolerance are focused. The dependence of host genetic background of yeast stress tolerance and roles of histones and their modifications are emphasized. The development of robust yeast strains based on multiomics analysis benefits economic bioconversion of lignocellulosic biomass.
PMID: 30911889 [PubMed - indexed for MEDLINE]
Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test.
Metabolomics. 2018 03 02;14(4):43
Authors: Pinu FR, Granucci N, Daniell J, Han TL, Carneiro S, Rocha I, Nielsen J, Villas-Boas SG
INTRODUCTION: Microbial cells secrete many metabolites during growth, including important intermediates of the central carbon metabolism. This has not been taken into account by researchers when modeling microbial metabolism for metabolic engineering and systems biology studies.
MATERIALS AND METHODS: The uptake of metabolites by microorganisms is well studied, but our knowledge of how and why they secrete different intracellular compounds is poor. The secretion of metabolites by microbial cells has traditionally been regarded as a consequence of intracellular metabolic overflow.
CONCLUSIONS: Here, we provide evidence based on time-series metabolomics data that microbial cells eliminate some metabolites in response to environmental cues, independent of metabolic overflow. Moreover, we review the different mechanisms of metabolite secretion and explore how this knowledge can benefit metabolic modeling and engineering.
PMID: 30830324 [PubMed - indexed for MEDLINE]
Sample Preparation Focusing on Plant Omics.
Adv Exp Med Biol. 2019;1073:161-185
Authors: Galazzi RM, de Jesus JR, Arruda MAZ
Because of strong impact of omics in many fields, and the complexity of the samples when focusing on areas such as genomics, (metallo)proteomics, metabolomics, among others, it is easy to rationalize the great importance that sample preparation has for achieving reliable results, mainly considering plant science. Then, this chapter points out applications of the sample preparation focusing on such areas, and a diversity of strategies, techniques, and procedures is highlighted and commented.
PMID: 31236843 [PubMed - indexed for MEDLINE]
Advances in understanding salt tolerance in rice.
Theor Appl Genet. 2019 Apr;132(4):851-870
Authors: Ganie SA, Molla KA, Henry RJ, Bhat KV, Mondal TK
KEY MESSAGE: This review presents a comprehensive overview of the recent research on rice salt tolerance in the areas of genomics, proteomics, metabolomics and chemical genomics. Salinity is one of the major constraints in rice cultivation globally. Traditionally, rice is a glycophyte except for a few genotypes that have been widely used in salinity tolerance breeding of rice. Both seedling and reproductive stages of rice are considered to be the salt-susceptible stages; however, research efforts have been biased towards improving the understanding of seedling-stage salt tolerance. An extensive literature survey indicated that there have been very few attempts to develop reproductive stage-specific salt tolerance in rice probably due to the lack of salt-tolerant phenotypes at the reproductive stage. Recently, the role of DNA methylation, genome duplication and codon usage bias in salinity tolerance of rice have been studied. Furthermore, the study of exogenous salt stress alleviants in rice has opened up another potential avenue for understanding and improving its salt tolerance. There is a need to not only generate additional genomic resources in the form of salt-responsive QTLs and molecular markers and to characterize the genes and their upstream regulatory regions, but also to use them to gain deep insights into the mechanisms useful for developing tolerant varieties. We analysed the genomic locations of diverse salt-responsive genomic resources and found that rice chromosomes 1-6 possess the majority of these salinity-responsive genomic resources. The review presents a comprehensive overview of the recent research on rice salt tolerance in the areas of genomics, proteomics, metabolomics and chemical genomics, which should help in understanding the molecular basis of salinity tolerance and its more effective improvement in rice.
PMID: 30759266 [PubMed - indexed for MEDLINE]
Advances in metabolic flux analysis toward genome-scale profiling of higher organisms.
Biosci Rep. 2018 12 21;38(6):
Authors: Basler G, Fernie AR, Nikoloski Z
Methodological and technological advances have recently paved the way for metabolic flux profiling in higher organisms, like plants. However, in comparison with omics technologies, flux profiling has yet to provide comprehensive differential flux maps at a genome-scale and in different cell types, tissues, and organs. Here we highlight the recent advances in technologies to gather metabolic labeling patterns and flux profiling approaches. We provide an opinion of how recent local flux profiling approaches can be used in conjunction with the constraint-based modeling framework to arrive at genome-scale flux maps. In addition, we point at approaches which use metabolomics data without introduction of label to predict either non-steady state fluxes in a time-series experiment or flux changes in different experimental scenarios. The combination of these developments allows an experimentally feasible approach for flux-based large-scale systems biology studies.
PMID: 30341247 [PubMed - indexed for MEDLINE]
Seed quality and carbon primary metabolism.
Plant Cell Environ. 2019 Jul 19;:
Authors: Domergue JB, Abadie C, Limami A, Way D, Tcherkez G
Improving seed quality is amongst the most important challenges of contemporary agriculture. In fact, using plant varieties with better germination rates that are more tolerant to stress during seedling establishment may improve crop yield considerably. Therefore, intense efforts are currently being devoted to improve seed quality in many species, mostly using genomics tools. However, despite its considerable importance during seed imbibition and germination processes, primary carbon metabolism in seeds is less studied. Our knowledge of the physiology of seed respiration and energy generation and the impact of these processes on seed performance has made limited progress over the past three decades. In particular, (isotope-assisted) metabolomics of seeds has only been assessed occasionally, and there is limited information on possible quantitative relationships between metabolic fluxes and seed quality. Here, we review the recent literature and provide an overview of potential links between metabolic efficiency, metabolic biomarkers and seed quality, and discuss implications for future research, including a climate change context.
PMID: 31323691 [PubMed - as supplied by publisher]
Systems Genetics for Evolutionary Studies.
Methods Mol Biol. 2019;1910:635-652
Authors: Prins P, Smant G, Arends D, Mulligan MK, Williams RW, Jansen RC
Systems genetics combines high-throughput genomic data with genetic analysis. In this chapter, we review and discuss application of systems genetics in the context of evolutionary studies, in which high-throughput molecular technologies are being combined with quantitative trait locus (QTL) analysis in segregating populations.The recent explosion of high-throughput data-measuring thousands of RNAs, proteins, and metabolites, using deep sequencing, mass spectrometry, chromatin, methyl-DNA immunoprecipitation, etc.-allows the dissection of causes of genetic variation underlying quantitative phenotypes of all types. To deal with the sheer amount of data, powerful statistical tools are needed to analyze multidimensional relationships and to extract valuable information and new modes and mechanisms of changes both within and between species. In the context of evolutionary computational biology, a well-designed experiment and the right population can help dissect complex traits likely to be under selection using proven statistical methods for associating phenotypic variation with chromosomal locations.Recent evolutionary expression QTL (eQTL) studies focus on gene expression adaptations, mapping the gene expression landscape, and, tentatively, define networks of transcripts and proteins that are jointly modulated sets of eQTL networks. Here, we discuss the possibility of introducing an evolutionary "prior" in the form of gene families displaying evidence of positive selection, and using that prior in the context of an eQTL experiment for elucidating host-pathogen protein-protein interactions.Here we review one exemplar evolutionairy eQTL experiment and discuss experimental design, choice of platforms, analysis methods, scope, and interpretation of results. In brief we highlight how eQTL are defined; how they are used to assemble interacting and causally connected networks of RNAs, proteins, and metabolites; and how some QTLs can be efficiently converted to reasonably well-defined sequence variants.
PMID: 31278680 [PubMed - in process]
[Characteristics and pro-health benefits of herbhoneys].
Pol Merkur Lekarski. 2019 Jun 28;46(276):263-267
Authors: Janda K, Kałduńska J, Jamniuk A, Jakubczyk K
Herbhoneys are bee origin products. However, they differ from traditional honeys in the production method. The process of making herbhoneys is based on feeding bees with nourishments, which are a combination of sugar syrup and plant extracts. For the preparation of the nourishment, plants that do not produce nectar or honeydew are often used. Thanks to this treatment, ready-made herbhoney, apart from a rich composition of mineral compounds, may also contain active substances. Herbhoneys have a characteristic color, which is associated with its plant origin and chemical composition. They are used in the therapy and prevention of many diseases, and their healthpromoting effect is associated with the plant material used to prepare the nutrient solution. Research shows positive influence of pine herbhoney in the treatment of upper respiratory tract infections, or the use of nettle herbhoney in gastrointestinal disorders. There are diverse data on the elemental composition of herbhoneys compared to natural honey. However, the essential factor conditioning the mineral content is the origin of honey and herbahoneys used for analysis. Herbhoneys, like traditional honey, have antimicrobial activity. They have been shown to be bactericidal against gram-positive and gram-negative pathogenic bacteria. The content of bioactive substances in herbhoneys determines their high antioxidant potential. Studies also indicate the presence of polyphenols, which occurrence is not observed in natural honeys. Herbhoneys, despite numerous health-promoting properties, are not a popular products on the Polish market.
PMID: 31260436 [PubMed - in process]
Expanding phytoremediation to the realms of known and unknown organic chemicals of concern.
Int J Phytoremediation. 2019 Jul 01;:1-12
Authors: Hedgespeth ML, Nichols EG
Recent advancements in analytical chemistry and data analyses via high-resolution mass spectrometry (HRMS) are evolving scientific understanding of the potential totality of organic chemical exposure and pollutant risk. This review addresses the importance of HRMS approaches, namely suspect screening and nontarget chemical analyses, to the realm of phytoremediation. These analytical approaches are not without caveats and constraints, but they provide an opportunity to understand in greater totality how plant-based technologies contribute, mitigate, and reduce organic chemical exposure across scales of experimental and system-level studies. These analytical tools can enlighten the complexity and efficacy of plant-contaminant system design and expand our understanding of biogenic and anthropogenic chemicals at work in phytoremediation systems. Advances in data analytics from biological sciences, such as metabolomics, are crucial to HRMS analysis. This review provides an overview of targeted, suspect screening, and nontarget HRMS approaches, summarizes the expanding knowledge of regulated and unregulated organic chemicals in the environment, addresses requisite HRMS instrumentation, analysis cost, uncertainty, and data processing techniques, and offers potential bridges of HRMS analyses to phytoremediation research and application.
PMID: 31257906 [PubMed - as supplied by publisher]
Bioinoculant capability enhancement through metabolomics and systems biology approaches.
Brief Funct Genomics. 2019 Jun 24;:
Authors: Chaudhary T, Shukla P
Bioinoculants are eco-friendly microorganisms, and their products are utilized for improving the potential of soil and fulfill the nutrients requirement for the host plant. The agricultural yield has increased due to the use of bioinoculants over chemical-based fertilizers, and thus it generates interest in understanding the innovation process by various methods. By gene-editing tool, the desired gene product can be changed for engineered microbial inoculants. We have also described various modern biotechnological tools like constraint-based modeling, OptKnock, flux balance analysis and modeling of the biological network for enhancing the bioinoculant capability. These fluxes give the fascinating perception of the metabolic network in the absence of comprehensive kinetic information. These tools also help in the stimulation of the metabolic networks by incorporation of enzyme-encoding genes. The present review explains the use of systems biology and gene-editing tools for improving the capability of bioinoculants. Moreover, this review also emphasizes on the challenges and future perspective of systems biology and its multidisciplinary facets.
PMID: 31232454 [PubMed - as supplied by publisher]
Using metabolome data for mathematical modeling of plant metabolic systems.
Curr Opin Biotechnol. 2018 12;54:138-144
Authors: Hirai MY, Shiraishi F
Plant metabolism is characterized by a wide diversity of metabolites, with systems far more complicated than those of microorganisms. Mathematical modeling is useful for understanding dynamic behaviors of plant metabolic systems for metabolic engineering. Time-series metabolome data has great potential for estimating kinetic model parameters to construct a genome-wide metabolic network model. However, data obtained by current metabolomics techniques does not meet the requirement for constructing accurate models. In this article, we highlight novel strategies and algorithms to handle the underlying difficulties and construct dynamic in vivo models for large-scale plant metabolic systems. The coarse but efficient modeling enables the prediction of unknown mechanisms regulating plant metabolism.
PMID: 30195121 [PubMed - indexed for MEDLINE]
A review on remediation of cyanide containing industrial wastes using biological systems with special reference to enzymatic degradation.
A review on remediation of cyanide containing industrial wastes using biological systems with special reference to enzymatic degradation.
World J Microbiol Biotechnol. 2019 Apr 22;35(5):70
Authors: Sharma M, Akhter Y, Chatterjee S
Cyanide is a nitrile which is used extensively in many industries like jewelry, mining, electroplating, plastics, dyes, paints, pharmaceuticals, food processing, and coal coking. Cyanides pose a serious health hazard due to their high affinity towards metals and cause malfunction of cellular respiration by inhibition of cytochrome c oxidase. This inhibition ultimately leads to histotoxic hypoxia, increased acidosis, reduced the functioning of the central nervous system and myocardial activity. Different physicochemical processes including oxidation by hydrogen peroxide, alkaline chlorination, and ozonization have been used to reduce cyanide waste from the environment. Microbial cyanide degradation which is considered as one the most successful techniques is used to take place through different biochemical/metabolic pathways involving reductive, oxidative, hydrolytic or substitution/transfer reactions. Groups of enzymes involved in microbial degradation are cyanidase, cyanide hydratase, formamidase, nitrilase, nitrile hydratase, cyanide dioxygenase, cyanide monooxygenase, cyanase and nitrogenase. In the future, more advancement of omics technologies and protein engineering will help us to recoup the environment from cyanide effluent. In this review, we have discussed the origin and environmental distribution of cyanide waste along with different bioremediation pathways and enzymes involved therein.
PMID: 31011828 [PubMed - indexed for MEDLINE]
Anticancer Drug Targets of Salvia Phytometabolites: Chemistry, Biology and Omics.
Curr Drug Targets. 2018;19(1):1-20
Authors: Hao DC, Ge GB, Xiao PG
BACKGROUND: Salvia displays diverse anticancer properties, which are attributable to their diterpene and phenolic contents. There is no comprehensive review on the anticancer diversity and molecular targets of Salvia components.
OBJECTIVE: We investigate the diversity and molecular targets of Salvia phytometabolites responsible for the prevention and treatment of cancer and sarcoma.
RESULTS AND CONCLUSION: Traditional therapeutic knowledge suggests that Salvia species can be used to develop anticancer drugs. Lots of concerns have been raised for tanshinone (Tan) IIA and cryptotanshinone. Some Salvia compounds disturb cell cycle and induce apoptosis of tumor cells or enhance immune activities, while others inhibit the proliferation, invasion, angiogenesis, and metastasis, or reverse the multi-drug resistance of cancer cells. Salvia phytometabolites regulate most cancer hallmarks defined by Hanahan and Weinberg. The same class of phytometabolite could exert the anticancer activity via multiple pathways. ADME/T properties and pharmacokinetic bebaviors of some phytometabolites have been revealed. Fluorescent probes are powerful tools for screening substrates, inhibitors or inducers of drug metabolizing enzymes/transporters from Salvia phytometabolites. Omics platform will greatly help mining more potentially useful phytometabolites from Salvia plants. More Salvia plants have application potential in pharmaceutical industry and clinical cancer therapy.
PMID: 27924725 [PubMed - indexed for MEDLINE]
Metabolomics 20 years on: what have we learned and what hurdles remain?
Plant J. 2018 06;94(6):933-942
Authors: Alseekh S, Fernie AR
The term metabolome was coined in 1998, by analogy to genome, transcriptome and proteome. The first research papers using the terms metabolomics, metabonomics, metabolic profiling or metabolite profiling were published shortly thereafter. In this short review we reflect on the major achievements brought about by the use of these approaches, and document the knowledge and technology gaps that are currently constraining its further development. Finally, we detail why we think that the time is ripe to refocus our efforts on the understanding of metabolic function.
PMID: 29734513 [PubMed - indexed for MEDLINE]
Metabolomics for a millenniums-old crop - tea plant (Camellia sinensis).
J Agric Food Chem. 2019 May 22;:
Authors: Jiang C, Ma JQ, Apostolides Z, Chen L
Tea cultivation and utilization dates back to antiquity. Today it is the most widely consumed beverage on earth due to its pleasant taste, and several beneficial health properties attributing to specific metabolites. Metabolomics has a tremendous potential to correlate tea metabolites with taste and health properties in humans. Our review on the current application of metabolomics in the tea science suggests that metabolomics is a promising frontier in the evaluation of tea quality, identification of functional genes responsible for key metabolites, investigation of their metabolic regulation and pathway analysis in the tea plant. Furthermore, the challenges, possible solutions and the prospects of metabolomics in the tea science are reviewed.
PMID: 31117495 [PubMed - as supplied by publisher]
[Comparation and utilization of crop-omics databases].
Yi Chuan. 2018 Jul 20;40(7):534-545
Authors: Song J, Wu YB, Zhou YH, Liu BJ, Wang N, Hao ZF, Wu YQ
Omics plays an important role in life sciences, which studies all the components and their interrelations as a whole. The omics databases collected and sorted out the relevant information to support omics research. The crop-omics database, based on the major food crop information, especially on the sequencing information and data mining, is set up to improve the basic research level of crop sciences and production, which potentially benefit our grain stock. Here, we summarize crop genomics, transcriptomics, proteomics, metabolomics and phenomics, explore the development and utilization status of crop-omics, and reveal that the comprehensive utilization of multiple omics databases has become an important research method for crop sciences in the era of high throughput information.
PMID: 30021717 [PubMed - indexed for MEDLINE]