To see the other types of publications on this topic, follow the link: Specialized metabolome.
Journal articles on the topic 'Specialized metabolome'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 journal articles for your research on the topic 'Specialized metabolome.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.
1
Solanki, Hiren, Manon Pierdet, Olivier P. Thomas, and Mayalen Zubia. "Insights into the Metabolome of the Cyanobacterium Leibleinia gracilis from the Lagoon of Tahiti and First Inspection of Its Variability." Metabolites 10, no. 5 (May 24, 2020): 215. http://dx.doi.org/10.3390/metabo10050215.
Full textAbstract:
Cyanobacteria are known to produce a large diversity of specialized metabolites that can cause severe (eco)toxicological effects. In the lagoon of Tahiti, the benthic cyanobacterium Leibleinia gracilis is commonly found overgrowing the proliferative macroalga Turbinaria ornata or dead branching corals. The specialized metabolome of the cyanobacterium L. gracilis was therefore investigated together with its variability on both substrates and changes in environmental parameters. For the study of the metabolome variability, replicates of L. gracilis were collected in the same location of the lagoon of Tahiti before and after a raining event, both on dead corals and on T. ornata. The variability in the metabolome was inferred from a comparative non-targeted metabolomic using high resolution mass spectrometry (MS) data and a molecular network analysis built through MS/MS analyses. Oxidized fatty acid derivatives including the unusual 11-oxopalmitelaidic acid were found as major constituents of the specialized metabolome of this species. Significant variations in the metabolome of the cyanobacteria were observed, being more important with a change in environmental factors. Erucamide was found to be the main chemical marker highly present when the cyanobacterium grows on the macroalga. This study highlights the importance of combined approaches in metabolomics and molecular networks to inspect the variability in the metabolome of cyanobacteria with applications for ecological questions.
2
Schweiger, Rabea, Eva Castells, Luca Da Sois, Jordi Martínez-Vilalta, and Caroline Müller. "Highly Species-Specific Foliar Metabolomes of Diverse Woody Species and Relationships with the Leaf Economics Spectrum." Cells 10, no. 3 (March 13, 2021): 644. http://dx.doi.org/10.3390/cells10030644.
Full textAbstract:
Plants show an extraordinary diversity in chemical composition and are characterized by different functional traits. However, relationships between the foliar primary and specialized metabolism in terms of metabolite numbers and composition as well as links with the leaf economics spectrum have rarely been explored. We investigated these relationships in leaves of 20 woody species from the Mediterranean region grown as saplings in a common garden, using a comparative ecometabolomics approach that included (semi-)polar primary and specialized metabolites. Our analyses revealed significant positive correlations between both the numbers and relative composition of primary and specialized metabolites. The leaf metabolomes were highly species-specific but in addition showed some phylogenetic imprints. Moreover, metabolomes of deciduous species were distinct from those of evergreens. Significant relationships were found between the primary metabolome and nitrogen content and carbon/nitrogen ratio, important traits of the leaf economics spectrum, ranging from acquisitive (mostly deciduous) to conservative (evergreen) leaves. A comprehensive understanding of various leaf traits and their coordination in different plant species may facilitate our understanding of plant functioning in ecosystems. Chemodiversity is thereby an important component of biodiversity.
3
Rai, Megha, Amit Rai, Tetsuya Mori, Ryo Nakabayashi, Manami Yamamoto, Michimi Nakamura, Hideyuki Suzuki, Kazuki Saito, and Mami Yamazaki. "Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus." International Journal of Molecular Sciences 22, no. 16 (August 17, 2021): 8835. http://dx.doi.org/10.3390/ijms22168835.
Full textAbstract:
Mallotus japonicus is a valuable traditional medicinal plant in East Asia for applications as a gastrointestinal drug. However, the molecular components involved in the biosynthesis of bioactive metabolites have not yet been explored, primarily due to a lack of omics resources. In this study, we established metabolome and transcriptome resources for M. japonicus to capture the diverse metabolite constituents and active transcripts involved in its biosynthesis and regulation. A combination of untargeted metabolite profiling with data-dependent metabolite fragmentation and metabolite annotation through manual curation and feature-based molecular networking established an overall metabospace of M. japonicus represented by 2129 metabolite features. M. japonicus de novo transcriptome assembly showed 96.9% transcriptome completeness, representing 226,250 active transcripts across seven tissues. We identified specialized metabolites biosynthesis in a tissue-specific manner, with a strong correlation between transcripts expression and metabolite accumulations in M. japonicus. The correlation- and network-based integration of metabolome and transcriptome datasets identified candidate genes involved in the biosynthesis of key specialized metabolites of M. japonicus. We further used phylogenetic analysis to identify 13 C-glycosyltransferases and 11 methyltransferases coding candidate genes involved in the biosynthesis of medicinally important bergenin. This study provides comprehensive, high-quality multi-omics resources to further investigate biological properties of specialized metabolites biosynthesis in M. japonicus.
4
Li, Dapeng, Rayko Halitschke, Ian T. Baldwin, and Emmanuel Gaquerel. "Information theory tests critical predictions of plant defense theory for specialized metabolism." Science Advances 6, no. 24 (June 2020): eaaz0381. http://dx.doi.org/10.1126/sciadv.aaz0381.
Full textAbstract:
Different plant defense theories have provided important theoretical guidance in explaining patterns in plant specialized metabolism, but their critical predictions remain to be tested. Here, we systematically explored the metabolomes of Nicotiana attenuata, from single plants to populations, as well as of closely related species, using unbiased tandem mass spectrometry (MS/MS) analyses and processed the abundances of compound spectrum–based MS features within an information theory framework to test critical predictions of optimal defense (OD) and moving target (MT) theories. Information components of plant metabolomes were consistent with the OD theory but contradicted the main prediction of the MT theory for herbivory-induced dynamics of metabolome compositions. From micro- to macroevolutionary scales, jasmonate signaling was confirmed as the master determinant of OD, while ethylene signaling provided fine-tuning for herbivore-specific responses annotated via MS/MS molecular networks.
5
Darghouth, Dhouha, Bérengère Koehl, Geoffrey Madalinski, Jean-François Heilier, Petra Bovee, Ying Xu, Marie-Françoise Olivier, et al. "Pathophysiology of sickle cell disease is mirrored by the red blood cell metabolome." Blood 117, no. 6 (February 10, 2011): e57-e66. http://dx.doi.org/10.1182/blood-2010-07-299636.
Full textAbstract:
Abstract Emerging metabolomic tools can now be used to establish metabolic signatures of specialized circulating hematopoietic cells in physiologic or pathologic conditions and in human hematologic diseases. To determine metabolomes of normal and sickle cell erythrocytes, we used an extraction method of erythrocytes metabolites coupled with a liquid chromatography-mass spectrometry–based metabolite profiling method. Comparison of these 2 metabolomes identified major changes in metabolites produced by (1) endogenous glycolysis characterized by accumulation of many glycolytic intermediates; (2) endogenous glutathione and ascorbate metabolisms characterized by accumulation of ascorbate metabolism intermediates, such as diketogulonic acid and decreased levels of both glutathione and glutathione disulfide; (3) membrane turnover, such as carnitine, or membrane transport characteristics, such as amino acids; and (4) exogenous arginine and NO metabolisms, such as spermine, spermidine, or citrulline. Finally, metabolomic analysis of young and old normal red blood cells indicates metabolites whose levels are directly related to sickle cell disease. These results show the relevance of metabolic profiling for the follow-up of sickle cell patients or other red blood cell diseases and pinpoint the importance of metabolomics to further depict the pathophysiology of human hematologic diseases.
6
Desmet, Sandrien, Yvan Saeys, Kevin Verstaen, Rebecca Dauwe, Hoon Kim, Claudiu Niculaes, Atsushi Fukushima, et al. "Maize specialized metabolome networks reveal organ-preferential mixed glycosides." Computational and Structural Biotechnology Journal 19 (2021): 1127–44. http://dx.doi.org/10.1016/j.csbj.2021.01.004.
Full text
7
Ostash, I., M. Deneka, M. Lopatniuk, T. Busche, J. Kalinowski, A. Luzhetskyy, V. Fedorenko, and B. Ostash. "Mining the cryptic specialized metabolome of Streptomyces cyanogenus S136." Visnyk of Lviv University. Biological series, no. 91 (June 7, 2024): 14–21. http://dx.doi.org/10.30970/vlubs.2024.91.02.
Full textAbstract:
Streptomyces cyanogenus S136 is known to produce landomycin family antibiotics, particularly its largest congener, landomycin A. Except for landomycins and polyene lucensomycin, no other specialized metabolites were sourced from S136. Nevertheless, S136 genome sequencing revealed over 40 biosynthetic gene clusters (BGCs), implying underappreciated potential of this strain for the production of novel bioactive natural compounds. We set out to gain deeper insight into the specialized metabolome of this strain. First, transcriptomic analysis of S136 grown under landomycin production conditions has been carried out, revealing that most of them are expressed at a basal level. This, likely, leads to a phenotypic silence of most of the BGCs. Nevertheless, several notable exceptions have been spotted. First of all, landomycin BGC is expressed at high level (at least 100 Transcripts Per Million mapped reads (TPM); and around 1000 TPM for minimal polyketide synthase genes lanFABC). Similarly, high levels of expression showed BGCs # 2, 4, 7 and 33, of which #2, encoding unknown saccharide, is the most dissimilar to the described precedents. RNAseq data also allowed us to delineate better the borders of several presumed BGCs. In the next phase of the work we singled out a few BGCs within S136 that appeared to be promising. First, these BGCs exhibited low similarity to the other gene clusters directing the production of known natural products. Second, the BGCs harbored cluster-situated regulatory genes that can be employed in the attempts to activate the expression of cryptic pathways. For one such BGC we constructed two plasmids for expression of several such regulatory genes and introduced them into S136 and its derivative deficient in production of landomycin A. Bioassays showed no differences in bioactivity of the recombinant strains as compared to the initial strains. Liquid chromatography coupled to mass spectrometry (LC-MS) analysis of several S. cyanogenus samples revealed the effects of genotype, growth conditions and extraction on specialized metabolome of this species, setting reference point for further studies.
8
Dubery, Ian A., Lerato P. Nephali, Fidele Tugizimana, and Paul A. Steenkamp. "Data-Driven Characterization of Metabolome Reprogramming during Early Development of Sorghum Seedlings." Metabolites 14, no. 2 (February 7, 2024): 112. http://dx.doi.org/10.3390/metabo14020112.
Full textAbstract:
Specialized metabolites are produced via discrete metabolic pathways. These small molecules play significant roles in plant growth and development, as well as defense against environmental stresses. These include damping off or seedling blight at a post-emergence stage. Targeted metabolomics was followed to gain insights into metabolome changes characteristic of different developmental stages of sorghum seedlings. Metabolites were extracted from leaves at seven time points post-germination and analyzed using ultra-high performance liquid chromatography coupled to mass spectrometry. Multivariate statistical analysis combined with chemometric tools, such as principal component analysis, hierarchical clustering analysis, and orthogonal partial least squares–discriminant analysis, were applied for data exploration and to reduce data dimensionality as well as for the selection of potential discriminant biomarkers. Changes in metabolome patterns of the seedlings were analyzed in the early, middle, and late stages of growth (7, 14, and 29 days post-germination). The metabolite classes were amino acids, organic acids, lipids, cyanogenic glycosides, hormones, hydroxycinnamic acid derivatives, and flavonoids, with the latter representing the largest class of metabolites. In general, the metabolite content showed an increase with the progression of the plant growth stages. Most of the differential metabolites were derived from tryptophan and phenylalanine, which contribute to innate immune defenses as well as growth. Quantitative analysis identified a correlation of apigenin flavone derivatives with growth stage. Data-driven investigations of these metabolomes provided new insights into the developmental dynamics that occur in seedlings to limit post-germination mortality.
9
Hao, Da-Cheng, Pei Li, Pei-Gen Xiao, and Chun-Nian He. "Dissection of full-length transcriptome and metabolome of Dichocarpum (Ranunculaceae): implications in evolution of specialized metabolism of Ranunculales medicinal plants." PeerJ 9 (November 5, 2021): e12428. http://dx.doi.org/10.7717/peerj.12428.
Full textAbstract:
Several main families of Ranunculales are rich in alkaloids and other medicinal compounds; many species of these families are used in traditional and folk medicine. Dichocarpum is a representative medicinal genus of Ranunculaceae, but the genetic basis of its metabolic phenotype has not been investigated, which hinders its sustainable conservation and utilization. We use the third-generation high-throughput sequencing and metabolomic techniques to decipher the full-length transcriptomes and metabolomes of five Dichocarpum species endemic in China, and 71,598 non-redundant full-length transcripts were obtained, many of which are involved in defense, stress response and immunity, especially those participating in the biosynthesis of specialized metabolites such as benzylisoquinoline alkaloids (BIAs). Twenty-seven orthologs extracted from trancriptome datasets were concatenated to reconstruct the phylogenetic tree, which was verified by the clustering analysis based on the metabolomic profile and agreed with the Pearson correlation between gene expression patterns of Dichocarpum species. The phylogenomic analysis of phytometabolite biosynthesis genes, e.g., (S)-norcoclaurine synthase, methyltransferases, cytochrome p450 monooxygenases, berberine bridge enzyme and (S)-tetrahydroprotoberberine oxidase, revealed the evolutionary trajectories leading to the chemodiversity, especially that of protoberberine type, aporphine type and bis-BIA abundant in Dichocarpum and related genera. The biosynthesis pathways of these BIAs are proposed based on full-length transcriptomes and metabolomes of Dichocarpum. Within Ranunculales, the gene duplications are common, and a unique whole genome duplication is possible in Dichocarpum. The extensive correlations between metabolite content and gene expression support the co-evolution of various genes essential for the production of different specialized metabolites. Our study provides insights into the transcriptomic and metabolomic landscapes of Dichocarpum, which will assist further studies on genomics and application of Ranunculales plants.
10
Piasecka, Anna, Aneta Sawikowska, Nicolas Jedrzejczak-Rey, Mariola Piślewska-Bednarek, and Paweł Bednarek. "Targeted and Untargeted Metabolomic Analyses Reveal Organ Specificity of Specialized Metabolites in the Model Grass Brachypodium distachyon." Molecules 27, no. 18 (September 13, 2022): 5956. http://dx.doi.org/10.3390/molecules27185956.
Full textAbstract:
Brachypodium distachyon, because of its fully sequenced genome, is frequently used as a model grass species. However, its metabolome, which constitutes an indispensable element of complex biological systems, remains poorly characterized. In this study, we conducted comprehensive, liquid chromatography-mass spectrometry (LC-MS)-based metabolomic examination of roots, leaves and spikes of Brachypodium Bd21 and Bd3-1 lines. Our pathway enrichment analysis emphasised the accumulation of specialized metabolites representing the flavonoid biosynthetic pathway in parallel with processes related to nucleotide, sugar and amino acid metabolism. Similarities in metabolite profiles between both lines were relatively high in roots and leaves while spikes showed higher metabolic variance within both accessions. In roots, differences between Bd21 and Bd3-1 lines were manifested primarily in diterpenoid metabolism, while differences within spikes and leaves concerned nucleotide metabolism and nitrogen management. Additionally, sulphate-containing metabolites differentiated Bd21 and Bd3-1 lines in spikes. Structural analysis based on MS fragmentation spectra enabled identification of 93 specialized metabolites. Among them phenylpropanoids and flavonoids derivatives were mainly determined. As compared with closely related barley and wheat species, metabolic profile of Brachypodium is characterized with presence of threonate derivatives of hydroxycinnamic acids.
11
Desmet, Sandrien, Kris Morreel, and Rebecca Dauwe. "Origin and Function of Structural Diversity in the Plant Specialized Metabolome." Plants 10, no. 11 (November 6, 2021): 2393. http://dx.doi.org/10.3390/plants10112393.
Full textAbstract:
The plant specialized metabolome consists of a multitude of structurally and functionally diverse metabolites, variable from species to species. The specialized metabolites play roles in the response to environmental changes and abiotic or biotic stresses, as well as in plant growth and development. At its basis, the specialized metabolism is built of four major pathways, each starting from a few distinct primary metabolism precursors, and leading to distinct basic carbon skeleton core structures: polyketides and fatty acid derivatives, terpenoids, alkaloids, and phenolics. Structural diversity in specialized metabolism, however, expands exponentially with each subsequent modification. We review here the major sources of structural variety and question if a specific role can be attributed to each distinct structure. We focus on the influences that various core structures and modifications have on flavonoid antioxidant activity and on the diversity generated by oxidative coupling reactions. We suggest that many oxidative coupling products, triggered by initial radical scavenging, may not have a function in se, but could potentially be enzymatically recycled to effective antioxidants. We further discuss the wide structural variety created by multiple decorations (glycosylations, acylations, prenylations), the formation of high-molecular weight conjugates and polyesters, and the plasticity of the specialized metabolism. We draw attention to the need for untargeted methods to identify the complex, multiply decorated and conjugated compounds, in order to study the functioning of the plant specialized metabolome.
12
Zhang, Ran, Junjie Zhou, Xiaoxuan Zhang, Huanteng Hou, Xianqing Liu, Chenkun Yang, Shuangqian Shen, and Jie Luo. "Insights into Tissue-Specific Specialized Metabolism in Wampee (Clausena lansium (Lour.) Skeels) Varieties." Foods 13, no. 19 (September 27, 2024): 3092. http://dx.doi.org/10.3390/foods13193092.
Full textAbstract:
Wampee (Clausena lansium (Lour.) Skeels) has natural bioactive components with diverse health benefits, but its detailed metabolism and tissue distribution are not fully understood. Here, widely targeted metabolomics analysis methods were employed to analyze the wampee fruit (peel, pulp, and seed) of 17 different varieties. A total of 1286 metabolites were annotated, including lipids, flavonoids, polyphenols, carbazole alkaloids, coumarins, and organic acids, among others. The quantitative analysis and matrix-assisted laser desorption/ionization–mass spectrometry imaging (MALDI-MSI) analysis indicated remarkable variations in metabolite categories and content in the peel, pulp, and seed of wampee fruit. Additionally, the difference analysis found that the metabolic components of peel contributed dominantly to the differences among varieties, and 7 potential biomarkers were identified. In this study, a comprehensive metabolome landscape of wampee fruit was established, which provided important information for the isolation and identification of functional components, food industry application, and nutritional improvement breeding.
13
Nicault, Matthieu, Abdoul-Razak Tidjani, Anthony Gauthier, Stéphane Dumarcay, Eric Gelhaye, Cyril Bontemps, and Pierre Leblond. "Mining the Biosynthetic Potential for Specialized Metabolism of a Streptomyces Soil Community." Antibiotics 9, no. 5 (May 23, 2020): 271. http://dx.doi.org/10.3390/antibiotics9050271.
Full textAbstract:
The diversity and distribution of specialized metabolite gene clusters within a community of bacteria living in the same soil habitat are poorly documented. Here we analyzed the genomes of 8 Streptomyces isolated at micro-scale from a forest soil that belong to the same species or to different species. The results reveal high levels of diversity, with a total of 261 biosynthesis gene clusters (BGCs) encoding metabolites such as terpenes, polyketides (PKs), non-ribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs) with potential bioactivities. A significant part of these BGCs (n = 53) were unique to only one strain when only 5 were common to all strains. The metabolites belong to very diverse chemical families and revealed that a large diversity of metabolites can potentially be produced in the community. Although that analysis of the global metabolome using GC-MS revealed that most of the metabolites were shared between the strains, they exhibited a specific metabolic pattern. We also observed that the presence of these accessory pathways might result from frequent loss and gain of genes (horizontal transfer), showing that the potential of metabolite production is a dynamic phenomenon in the community. Sampling Streptomyces at the community level constitutes a good frame to discover new biosynthetic pathways and it appears as a promising reservoir for the discovery of new bioactive compounds.
14
Melnyk, S., P. Hrab, and B. Ostash. "Genomic potential of Streptomyces roseochromogenes NRRL 3504 for the production of specialized metabolites: analysis in silico." Visnyk of Lviv University. Biological series, no. 87 (November 11, 2022): 45–53. http://dx.doi.org/10.30970/vlubs.2022.87.04.
Full textAbstract:
Streptomyces roseochromogenes NRRL 3504 is the only known producer of aminocoumarin antibiotic clorobiocin – an inhibitor of bacterial DNA-gyrase and topoisomerase IV. Sequencing of NRRL 3504 genome revealed a plethora of specialized metabolite biosynthetic gene clusters (BGCs) within the latter, attesting to the significant potential of this species for the production of various as-yet-unknown bioactive compounds. Here we report bioinformatic analysis of NRRL 3504 genome aimed to better understand what kind of small molecules this strain could produce and genetic mechanisms that may limit their production. In addition to the most commonly applied bioinformatic service for BGCs detection antiSMASH, we turned to alternative tools for secondary metabolome in silico analysis such as PRISM, DeepBGC, ARTS, SEMPI and GECCO. While different genome mining applications pointed to a common core set of BGCs within the NRRL 3504, each tool having its own algorithm of BGCs detection also discovered certain number of non-overlapping clusters. This was especially true for machine learning tool DeepBGC that unearthed the biggest number of BGCs. To summarize the obtained results we used BGCViz tool, which visualizes and integrates BGC annotations from various sources by using genomic coordinates. We discuss the genetic and structural diversity of the BGCs and outline the most interesting, in opinion, targets for further investigations. Most of the described BGCs are most likely silent due to very low or zero transcription. Therefore, it might be needed to find the ways to activate the transcription of the BGCs of interest. To this end, we mined NRRL 3504 genome for the orthologs of global regulatory genes known to be involved in regulation of specialized metabolism of S. coelicolor A3(2). We were able to identify almost all plausible global regulators of interest in NRRL 3504, implying that overall scheme of regulation of specialized metabolism in A3(2) and NRRL 3504 might be similar. Results of our work set the stage for a more detailed experimental scrutiny of silent specialized metabolome of NRRL 3504.
15
Fuchs, Amanda L., Stephanann M. Costello, Sage M. Schiller, Brian P. Tripet, and Valérie Copié. "Primary Human M2 Macrophage Subtypes Are Distinguishable by Aqueous Metabolite Profiles." International Journal of Molecular Sciences 25, no. 4 (February 18, 2024): 2407. http://dx.doi.org/10.3390/ijms25042407.
Full textAbstract:
The complexity of macrophage (MΦ) plasticity and polarization states, which include classically activated pro-inflammatory (M1) and alternatively activated anti-inflammatory (M2) MΦ phenotypes, is becoming increasingly appreciated. Within the M2 MΦ polarization state, M2a, M2b, M2c, and M2d MΦ subcategories have been defined based on their expression of specific cell surface receptors, secreted cytokines, and specialized immune effector functions. The importance of immunometabolic networks in mediating the function and regulation of MΦ immune responses is also being increasingly recognized, although the exact mechanisms and extent of metabolic modulation of MΦ subtype phenotypes and functions remain incompletely understood. In this study, proton (1H) nuclear magnetic resonance (NMR) metabolomics was employed to determine the polar metabolomes of M2 MΦ subtypes and to investigate the relationship between aqueous metabolite profiles and M2 MΦ functional phenotypes. Results from this study demonstrate that M2a MΦs are most distinct from M2b, M2c, and M2d MΦ subtypes, and that M2b MΦs display several metabolic traits associated with an M1-like MΦ phenotype. The significance of metabolome differences for metabolites implicated in glycolysis, the tricarboxylic acid (TCA) cycle, phospholipid metabolism, and creatine–phosphocreatine cycling is discussed. Altogether, this study provides biochemical insights into the role of metabolism in mediating the specialized effector functions of distinct M2 MΦ subtypes and supports the concept of a continuum of macrophage activation states rather than two well-separated and functionally distinct M1/M2 MΦ classes, as originally proposed within a classical M1/M2 MΦ framework.
16
Mishra, Ajay Kumar, Naganeeswaran Sudalaimuthuasari, Khaled M. Hazzouri, Esam Eldin Saeed, Iltaf Shah, and Khaled M. A. Amiri. "Tapping into Plant–Microbiome Interactions through the Lens of Multi-Omics Techniques." Cells 11, no. 20 (October 17, 2022): 3254. http://dx.doi.org/10.3390/cells11203254.
Full textAbstract:
This review highlights the pivotal role of root exudates in the rhizosphere, especially the interactions between plants and microbes and between plants and plants. Root exudates determine soil nutrient mobilization, plant nutritional status, and the communication of plant roots with microbes. Root exudates contain diverse specialized signaling metabolites (primary and secondary). The spatial behavior of these metabolites around the root zone strongly influences rhizosphere microorganisms through an intimate compatible interaction, thereby regulating complex biological and ecological mechanisms. In this context, we reviewed the current understanding of the biological phenomenon of allelopathy, which is mediated by phytotoxic compounds (called allelochemicals) released by plants into the soil that affect the growth, survival, development, ecological infestation, and intensification of other plant species and microbes in natural communities or agricultural systems. Advances in next-generation sequencing (NGS), such as metagenomics and metatranscriptomics, have opened the possibility of better understanding the effects of secreted metabolites on the composition and activity of root-associated microbial communities. Nevertheless, understanding the role of secretory metabolites in microbiome manipulation can assist in designing next-generation microbial inoculants for targeted disease mitigation and improved plant growth using the synthetic microbial communities (SynComs) tool. Besides a discussion on different approaches, we highlighted the advantages of conjugation of metabolomic approaches with genetic design (metabolite-based genome-wide association studies) in dissecting metabolome diversity and understanding the genetic components of metabolite accumulation. Recent advances in the field of metabolomics have expedited comprehensive and rapid profiling and discovery of novel bioactive compounds in root exudates. In this context, we discussed the expanding array of metabolomics platforms for metabolome profiling and their integration with multivariate data analysis, which is crucial to explore the biosynthesis pathway, as well as the regulation of associated pathways at the gene, transcript, and protein levels, and finally their role in determining and shaping the rhizomicrobiome.
17
Vicente, Cláudia, Annabelle Thibessard, Jean-Noël Lorenzi, Mabrouka Benhadj, Laurence Hôtel, Djamila Gacemi-Kirane, Olivier Lespinet, Pierre Leblond, and Bertrand Aigle. "Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity." Antibiotics 7, no. 4 (October 2, 2018): 86. http://dx.doi.org/10.3390/antibiotics7040086.
Full textAbstract:
Specialized metabolites are of great interest due to their possible industrial and clinical applications. The increasing number of antimicrobial resistant infectious agents is a major health threat and therefore, the discovery of chemical diversity and new antimicrobials is crucial. Extensive genomic data from Streptomyces spp. confirm their production potential and great importance. Genome sequencing of the same species strains indicates that specialized metabolite biosynthetic gene cluster (SMBGC) diversity is not exhausted, and instead, a pool of novel specialized metabolites still exists. Here, we analyze the genome sequence data from six phylogenetically close Streptomyces strains. The results reveal that the closer strains are phylogenetically, the number of shared gene clusters is higher. Eight specialized metabolites comprise the core metabolome, although some strains have only six core gene clusters. The number of conserved gene clusters common between the isolated strains and their closest phylogenetic counterparts varies from nine to 23 SMBGCs. However, the analysis of these phylogenetic relationships is not affected by the acquisition of gene clusters, probably by horizontal gene transfer events, as each strain also harbors strain-specific SMBGCs. Between one and 15 strain-specific gene clusters were identified, of which up to six gene clusters in a single strain are unknown and have no identifiable orthologs in other species, attesting to the existing SMBGC novelty at the strain level.
18
Lazcano-Ramírez, Hugo Gerardo, Roberto Gamboa-Becerra, Irving J. García-López, Ricardo A. Chávez Montes, David Díaz-Ramírez, Octavio Martínez de la Vega, José Juan Ordaz-Ortíz, et al. "Effects of the Developmental Regulator BOLITA on the Plant Metabolome." Genes 12, no. 7 (June 29, 2021): 995. http://dx.doi.org/10.3390/genes12070995.
Full textAbstract:
Transcription factors are important regulators of gene expression. They can orchestrate the activation or repression of hundreds or thousands of genes and control diverse processes in a coordinated way. This work explores the effect of a master regulator of plant development, BOLITA (BOL), in plant metabolism, with a special focus on specialized metabolism. For this, we used an Arabidopsis thaliana line in which the transcription factor activity can be induced. Fingerprinting metabolomic analyses of whole plantlets were performed at different times after induction. After 96 h, all induced replicas clustered as a single group, in contrast with all controls which did not cluster. Metabolomic analyses of shoot and root tissues enabled the putative identification of differentially accumulated metabolites in each tissue. Finally, the analysis of global gene expression in induced vs. non-induced root samples, together with enrichment analyses, allowed the identification of enriched metabolic pathways among the differentially expressed genes and accumulated metabolites after the induction. We concluded that the induction of BOL activity can modify the Arabidopsis metabolome. Future work should investigate whether its action is direct or indirect, and the implications of the metabolic changes for development regulation and bioprospection.
19
Silva, Sónia, Maria Celeste Dias, Diana C. G. A. Pinto, and Artur M. S. Silva. "Metabolomics as a Tool to Understand Nano-Plant Interactions: The Case Study of Metal-Based Nanoparticles." Plants 12, no. 3 (January 21, 2023): 491. http://dx.doi.org/10.3390/plants12030491.
Full textAbstract:
Metabolomics is a powerful tool in diverse research areas, enabling an understanding of the response of organisms, such as plants, to external factors, their resistance and tolerance mechanisms against stressors, the biochemical changes and signals during plant development, and the role of specialized metabolites. Despite its advantages, metabolomics is still underused in areas such as nano-plant interactions. Nanoparticles (NPs) are all around us and have a great potential to improve and revolutionize the agri-food sector and modernize agriculture. They can drive precision and sustainability in agriculture as they can act as fertilizers, improve plant performance, protect or defend, mitigate environmental stresses, and/or remediate soil contaminants. Given their high applicability, an in-depth understanding of NPs’ impact on plants and their mechanistic action is crucial. Being aware that, in nano-plant interaction work, metabolomics is much less addressed than physiology, and that it is lacking a comprehensive review focusing on metabolomics, this review gathers the information available concerning the metabolomic tools used in studies focused on NP-plant interactions, highlighting the impact of metal-based NPs on plant metabolome, metabolite reconfiguration, and the reprogramming of metabolic pathways.
20
Perez de Souza, Leonardo, Federico Scossa, Sebastian Proost, Elena Bitocchi, Roberto Papa, Takayuki Tohge, and Alisdair R. Fernie. "Multi‐tissue integration of transcriptomic and specialized metabolite profiling provides tools for assessing the common bean (Phaseolus vulgaris) metabolome." Plant Journal 97, no. 6 (January 15, 2019): 1132–53. http://dx.doi.org/10.1111/tpj.14178.
Full text
21
Kim, Uijin, Dong-Hyuk Kim, Deok-Kun Oh, Ha Youn Shin, and Choong Hwan Lee. "Gene Expression and Metabolome Analysis Reveals Anti-Inflammatory Impacts of 11,17diHDoPE on PM10-Induced Mouse Lung Inflammation." International Journal of Molecular Sciences 25, no. 10 (May 14, 2024): 5360. http://dx.doi.org/10.3390/ijms25105360.
Full textAbstract:
Oxylipins, the metabolites of polyunsaturated fatty acids, are vital in regulating cell proliferation and inflammation. Among these oxylipins, specialized pro-resolving mediators notably contribute to inflammation resolution. Previously, we showed that the specialized pro-resolving mediators isomer 11,17dihydroxy docosapentaenoic acid (11,17diHDoPE) can be synthesized in bacterial cells and exhibits anti-inflammatory effects in mammalian cells. This study investigates the in vivo impact of 11,17diHDoPE in mice exposed to particulate matter 10 (PM10). Our results indicate that 11,17diHDoPE significantly mitigates PM10-induced lung inflammation in mice, as evidenced by reduced pro-inflammatory cytokines and pulmonary inflammation-related gene expression. Metabolomic analysis reveals that 11,17diHDoPE modulates inflammation-related metabolites such as threonine, 2-keto gluconic acid, butanoic acid, and methyl oleate in lung tissues. In addition, 11,17diHDoPE upregulates the LA-derived oxylipin pathway and downregulates arachidonic acid- and docosahexaenoic acid-derived oxylipin pathways in serum. Correlation analyses between gene expression and metabolite changes suggest that 11,17diHDoPE alleviates inflammation by interfering with macrophage differentiation. These findings underscore the in vivo role of 11,17diHDoPE in reducing pulmonary inflammation, highlighting its potential as a therapeutic agent for respiratory diseases.
22
Padilla-González, Guillermo F., Evelyn Amrehn, Maximilian Frey, Javier Gómez-Zeledón, Alevtina Kaa, Fernando B. Da Da Costa, and Otmar Spring. "Metabolomic and Gene Expression Studies Reveal the Diversity, Distribution and Spatial Regulation of the Specialized Metabolism of Yacón (Smallanthus sonchifolius, Asteraceae)." International Journal of Molecular Sciences 21, no. 12 (June 26, 2020): 4555. http://dx.doi.org/10.3390/ijms21124555.
Full textAbstract:
Smallanthus sonchifolius, also known as yacón, is an Andean crop species commercialized for its nutraceutical and medicinal properties. The tuberous roots of yacón accumulate a diverse array of probiotic and bioactive metabolites including fructooligosaccharides and caffeic acid esters. However, the metabolic diversity of yacón remains unexplored, including the site of biosynthesis and accumulation of key metabolite classes. We report herein a multidisciplinary approach involving metabolomics, gene expression and scanning electron microscopy, to provide a comprehensive analysis of the diversity, distribution and spatial regulation of the specialized metabolism in yacón. Our results demonstrate that different metabolic fingerprints and gene expression patterns characterize specific tissues, organs and cultivars of yacón. Manual inspection of mass spectrometry data and molecular networking allowed the tentative identification of 71 metabolites, including undescribed structural analogues of known bioactive compounds. Imaging by scanning electron microscopy revealed the presence of a new type of glandular trichome in yacón bracts, with a distinctive metabolite profile. Furthermore, the high concentration of sesquiterpene lactones in capitate glandular trichomes and the restricted presence of certain flavonoids and caffeic acid esters in underground organs and internal tissues suggests that these metabolites could be involved in protective and ecological functions. This study demonstrates that individual organs and tissues make specific contributions to the highly diverse and specialized metabolome of yacón, which is proving to be a reservoir of previously undescribed molecules of potential significance in human health.
23
Boutet, Stéphanie, Léa Barreda, François Perreau, Jean‐Chrisologue Totozafy, Caroline Mauve, Bertrand Gakière, Etienne Delannoy, et al. "Untargeted metabolomic analyses reveal the diversity and plasticity of the specialized metabolome in seeds of different Camelina sativa genotypes." Plant Journal 110, no. 1 (February 6, 2022): 147–65. http://dx.doi.org/10.1111/tpj.15662.
Full text
24
Devi, Amna, Mamta Masand, Balraj Sharma, Aasim Majeed, and Ram Kumar Sharma. "Integrated transcriptome and metabolome analysis decrypting molecular insights of specialized metabolism in Valeriana jatamansi Jones." Industrial Crops and Products 214 (August 2024): 118504. http://dx.doi.org/10.1016/j.indcrop.2024.118504.
Full text
25
Li, Dapeng, and Emmanuel Gaquerel. "Next-Generation Mass Spectrometry Metabolomics Revives the Functional Analysis of Plant Metabolic Diversity." Annual Review of Plant Biology 72, no. 1 (June 17, 2021): 867–91. http://dx.doi.org/10.1146/annurev-arplant-071720-114836.
Full textAbstract:
The remarkable diversity of specialized metabolites produced by plants has inspired several decades of research and nucleated a long list of theories to guide empirical ecological studies. However, analytical constraints and the lack of untargeted processing workflows have long precluded comprehensive metabolite profiling and, consequently, the collection of the critical currencies to test theory predictions for the ecological functions of plant metabolic diversity. Developments in mass spectrometry (MS) metabolomics have revolutionized the large-scale inventory and annotation of chemicals from biospecimens. Hence, the next generation of MS metabolomics propelled by new bioinformatics developments provides a long-awaited framework to revisit metabolism-centered ecological questions, much like the advances in next-generation sequencing of the last two decades impacted all research horizons in genomics. Here, we review advances in plant (computational) metabolomics to foster hypothesis formulation from complex metabolome data. Additionally, we reflect on how next-generation metabolomics could reinvigorate the testing of long-standing theories on plant metabolic diversity.
26
Hu, Huaran, Lei Du, Ruihao Zhang, Qiuyue Zhong, Fawan Liu, Weifen Li, and Min Gui. "Dissection of Metabolome and Transcriptome—Insights into Capsaicin and Flavonoid Accumulation in Two Typical Yunnan Xiaomila Fruits." International Journal of Molecular Sciences 25, no. 14 (July 16, 2024): 7761. http://dx.doi.org/10.3390/ijms25147761.
Full textAbstract:
Pepper is an economically important vegetable worldwide, containing various specialized metabolites crucial for its development and flavor. Capsaicinoids, especially, are genus-specialized metabolites that confer a spicy flavor to Capsicum fruits. In this work, two pepper cultivars, YB (Capsicum frutescens L.) and JC (Capsicum baccatum L.) pepper, showed distinct differences in the accumulation of capsaicin and flavonoid. However, the molecular mechanism underlying them was still unclear. Metabolome analysis showed that the JC pepper induced a more abundant accumulation of metabolites associated with alkaloids, flavonoids, and capsaicinoids in the red ripening stages, leading to a spicier flavor in the JC pepper. Transcriptome analysis confirmed that the increased expression of transcripts associated with phenylpropanoid and flavonoid metabolic pathways occurred in the JC pepper. Integrative analysis of metabolome and transcriptome suggested that four structural genes, 4CL7, 4CL6, CHS, and COMT, were responsible for the higher accumulation of metabolites relevant to capsaicin and flavonoids. Through weighted gene co-expression network analyses, modules related to flavonoid biosynthesis and potential regulators for candidate genes were identified. The promoter analysis of four candidate genes showed they contained several cis-elements that were bonded to MYB, bZIP, and WRKY transcription factors. Further RT-qPCR examination verified three transcription factors, MYB, bZIP53, and WRKY25, that exhibited increased expression in the red ripening stage of the JC pepper compared to YB, which potentially regulated their expression. Altogether, our findings provide comprehensive understanding and valuable information for pepper breeding programs in the future.
27
Zhou, Shaoqun, Karl A. Kremling, Nonoy Bandillo, Annett Richter, Ying K. Zhang, Kevin R. Ahern, Alexander B. Artyukhin, et al. "Metabolome-Scale Genome-Wide Association Studies Reveal Chemical Diversity and Genetic Control of Maize Specialized Metabolites." Plant Cell 31, no. 5 (March 28, 2019): 937–55. http://dx.doi.org/10.1105/tpc.18.00772.
Full text
28
Blatt-Janmaat, Kaitlyn L., Steffen Neumann, Jörg Ziegler, and Kristian Peters. "Host Tree and Geography Induce Metabolic Shifts in the Epiphytic Liverwort Radula complanata." Plants 12, no. 3 (January 27, 2023): 571. http://dx.doi.org/10.3390/plants12030571.
Full textAbstract:
Bryophytes are prolific producers of unique, specialized metabolites that are not found in other plants. As many of these unique natural products are potentially interesting, for example, pharmacological use, variations in the production regarding ecological or environmental conditions have not often been investigated. Here, we investigate metabolic shifts in the epiphytic Radula complanata L. (Dumort) with regard to different environmental conditions and the type of phorophyte (host tree). Plant material was harvested from three different locations in Sweden, Germany, and Canada and subjected to untargeted liquid chromatography high-resolution mass-spectrometry (UPLC/ESI-QTOF-MS) and data-dependent acquisition (DDA-MS). Using multivariate statistics, variable selection methods, in silico compound identification, and compound classification, a large amount of variation (39%) in the metabolite profiles was attributed to the type of host tree and 25% to differences in environmental conditions. We identified 55 compounds to vary significantly depending on the host tree (36 on the family level) and 23 compounds to characterize R. complanata in different environments. Taken together, we found metabolic shifts mainly in primary metabolites that were associated with the drought response to different humidity levels. The metabolic shifts were highly specific to the host tree, including mostly specialized metabolites suggesting high levels of ecological interaction. As R. complanata is a widely distributed generalist species, we found it to flexibly adapt its metabolome according to different conditions. We found metabolic composition to also mirror the constitution of the habitat, which makes it interesting for conservation measures.
29
Weed, Rebecca A., Kyryll G. Savchenko, Leandro M. Lessin, Lori M. Carris, and David R. Gang. "Untargeted Metabolomic Investigation of Wheat Infected with Stinking Smut Tilletia caries." Phytopathology® 111, no. 12 (December 2021): 2343–54. http://dx.doi.org/10.1094/phyto-09-20-0383-r.
Full textAbstract:
Tilletia caries infection of wheat (Triticum aestivum) has become an increasing problem in organic wheat agriculture throughout the world. Little is known about how this pathogen alters host metabolism to ensure a successful infection. We investigated how T. caries allocates resources from wheat for its growth over the life cycle of the pathogen. An untargeted metabolomics approach that combined gas chromatography time-of-flight mass spectrometry and ultraperformance liquid chromatography tandem mass spectrometry platforms was used to determine which primary or specialized metabolite pathways are targeted and altered during T. caries infection. We found that T. caries does not dramatically alter the global metabolome of wheat but instead alters key metabolites for its own nutrient uptake and to antagonize host defenses by reducing wheat’s sweet immunity response and other related pathways. Our results highlight metabolic characteristics needed for selecting wheat varieties that are resistant to T. caries infection for organic agriculture. In addition, several wheat metabolites were identified that could be used in developing a diagnostic tool for early detection of T. caries infection.
30
Li, Dapeng, Sven Heiling, Ian T. Baldwin, and Emmanuel Gaquerel. "Illuminating a plant’s tissue-specific metabolic diversity using computational metabolomics and information theory." Proceedings of the National Academy of Sciences 113, no. 47 (November 7, 2016): E7610—E7618. http://dx.doi.org/10.1073/pnas.1610218113.
Full textAbstract:
Secondary metabolite diversity is considered an important fitness determinant for plants’ biotic and abiotic interactions in nature. This diversity can be examined in two dimensions. The first one considers metabolite diversity across plant species. A second way of looking at this diversity is by considering the tissue-specific localization of pathways underlying secondary metabolism within a plant. Although these cross-tissue metabolite variations are increasingly regarded as important readouts of tissue-level gene function and regulatory processes, they have rarely been comprehensively explored by nontargeted metabolomics. As such, important questions have remained superficially addressed. For instance, which tissues exhibit prevalent signatures of metabolic specialization? Reciprocally, which metabolites contribute most to this tissue specialization in contrast to those metabolites exhibiting housekeeping characteristics? Here, we explore tissue-level metabolic specialization in Nicotiana attenuata, an ecological model with rich secondary metabolism, by combining tissue-wide nontargeted mass spectral data acquisition, information theory analysis, and tandem MS (MS/MS) molecular networks. This analysis was conducted for two different methanolic extracts of 14 tissues and deconvoluted 895 nonredundant MS/MS spectra. Using information theory analysis, anthers were found to harbor the most specialized metabolome, and most unique metabolites of anthers and other tissues were annotated through MS/MS molecular networks. Tissue–metabolite association maps were used to predict tissue-specific gene functions. Predictions for the function of two UDP-glycosyltransferases in flavonoid metabolism were confirmed by virus-induced gene silencing. The present workflow allows biologists to amortize the vast amount of data produced by modern MS instrumentation in their quest to understand gene function.
31
Quer, Elodie, Susana Pereira, Thomas Michel, Mathieu Santonja, Thierry Gauquelin, Guillaume Simioni, Jean-Marc Ourcival, et al. "Amplified Drought Alters Leaf Litter Metabolome, Slows Down Litter Decomposition, and Modifies Home Field (Dis)Advantage in Three Mediterranean Forests." Plants 11, no. 19 (September 30, 2022): 2582. http://dx.doi.org/10.3390/plants11192582.
Full textAbstract:
In Mediterranean ecosystems, the projected rainfall reduction of up to 30% may alter plant–soil interactions, particularly litter decomposition and Home Field Advantage (HFA). We set up a litter transplant experiment in the three main forests encountered in the northern part of the Medi-terranean Basin (dominated by either Quercus ilex, Quercus pubescens, or Pinus halepensis) equipped with a rain exclusion device, allowing an increase in drought either throughout the year or concentrated in spring and summer. Senescent leaves and needles were collected under two precipitation treatments (natural and amplified drought plots) at their “home” forest and were left to decompose in the forest of origin and in other forests under both drought conditions. MS-based metabolomic analysis of litter extracts combined with multivariate data analysis enabled us to detect modifications in the composition of litter specialized metabolites, following amplified drought treatment. Amplified drought altered litter quality and metabolomes, directly slowed down litter decomposition, and induced a loss of home field (dis)advantage. No indirect effect mediated by a change in litter quality on decomposition was observed. These results may suggest major alterations of plant–soil interactions in Mediterranean forests under amplified drought conditions.
32
Pang, Zhiqiang, Charles Viau, Julius N. Fobil, Niladri Basu, and Jianguo Xia. "Comprehensive Blood Metabolome and Exposome Analysis, Annotation, and Interpretation in E-Waste Workers." Metabolites 14, no. 12 (December 2, 2024): 671. https://doi.org/10.3390/metabo14120671.
Full textAbstract:
Background: Electronic and electrical waste (e-waste) production has emerged to be of global environmental public health concern. E-waste workers, who are frequently exposed to hazardous chemicals through occupational activities, face considerable health risks. Methods: To investigate the metabolic and exposomic changes in these workers, we analyzed whole blood samples from 100 male e-waste workers and 49 controls from the GEOHealth II project (2017–2018 in Accra, Ghana) using LC-MS/MS. A specialized computational workflow was established for exposomics data analysis, incorporating two curated reference libraries for metabolome and exposome profiling. Two feature detection algorithms, asari and centWave, were applied. Results: In comparison to centWave, asari showed better sensitivity in detecting MS features, particularly at trace levels. Principal component analysis demonstrated distinct metabolic profiles between e-waste workers and controls, revealing significant disruptions in key metabolic pathways, including steroid hormone biosynthesis, drug metabolism, bile acid biosynthesis, vitamin metabolism, and prostaglandin biosynthesis. Correlation analyses linked metal exposures to alterations in hundreds to thousands of metabolic features. Functional enrichment analysis highlighted significant perturbations in pathways related to liver function, vitamin metabolism, linoleate metabolism, and dynorphin signaling, with the latter being observed for the first time in e-waste workers. Conclusions: This study provides new insights into the biological impact of prolonged metal exposure in e-waste workers.
33
Lin, Shuang, Shaohua Zeng, Biao A, Xiaoman Yang, Tianshun Yang, Guoqi Zheng, Guilian Mao, and Ying Wang. "Integrative Analysis of Transcriptome and Metabolome Reveals Salt Stress Orchestrating the Accumulation of Specialized Metabolites in Lycium barbarum L. Fruit." International Journal of Molecular Sciences 22, no. 9 (April 23, 2021): 4414. http://dx.doi.org/10.3390/ijms22094414.
Full textAbstract:
Salt stress seriously affects yield and quality of crops. The fruit of Lycium barbarum (LBF) is extensively used as functional food due to its rich nutrient components. It remains unclear how salt stress influences the quality of LBF. In this study, we identified 71 differentially accumulated metabolites (DAMs) and 1396 differentially expressed genes (DEGs) among ripe LBF with and without 300 mM of NaCl treatment. Pearson correlation analysis indicated that the metabolomic changes caused by salt stress were strongly related to oxidoreductases; hydrolases; and modifying enzymes, in particular, acyltransferases, methyltransferases and glycosyltransferases. Further analysis revealed that salt stress facilitated flavonoid glycosylation and carotenoid esterification by boosting the expression of structural genes in the biosynthetic pathways. These results suggested that salt stress prompts the modification of flavonoids and carotenoids to alleviate ROS damage, which in turn improves the quality of LBF. Our results lay a solid foundation for uncovering the underlying molecular mechanism of salt stress orchestrating LBF quality, and the candidate genes identified will be a valuable gene resource for genetic improvement of L. barbarum.
34
Mirza, Bilal, Wei Wang, Jie Wang, Howard Choi, Neo Christopher Chung, and Peipei Ping. "Machine Learning and Integrative Analysis of Biomedical Big Data." Genes 10, no. 2 (January 28, 2019): 87. http://dx.doi.org/10.3390/genes10020087.
Full textAbstract:
Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues.
35
Sabharwal, Usha, Piyush Kant Rai, Kamlesh Choure, R. B. Subramanian, Jeong Chan Joo, and Ashutosh Pandey. "Investigating the Effect of Pipecolic Acid on Specialized Metabolites Involved in Tomato Plant Defense Mechanisms Against Ralstonia solanacearum Wilt Pathogens." Analytica 6, no. 1 (January 9, 2025): 2. https://doi.org/10.3390/analytica6010002.
Full textAbstract:
The role of pipecolic acid (Pip) in plant immune responses, particularly against bacterial wilt pathogens, is significant. This research aimed to understand the interaction between plant defense-responsive enzymes and Pip by analyzing methanolic extracts from different treatments of tolerant (GAT5) and susceptible (GT2) tomato cultivars. LC-MS analysis demonstrated that the foliar application of Pip significantly influenced tomato metabolites, especially in bacterial wilt-infected plants, with a more pronounced effect in tolerant varieties. Principal component analysis (PCA) revealed that Pip-treated plants of tolerant varieties exhibited better coordinated metabolome profiles than those of susceptible varieties. Notable variations were observed in the levels of specialized metabolites, such as salicylic acid (SA), N-hydroxy pipecolic acid (NHP), and Pip, which are essential for producing defense compounds. Molecular docking studies further explored Pip’s interactions with key plant enzymes involved in defense mechanisms and showed that Pip acts as an effective organic inducer of systemic acquired resistance (SAR). These findings highlight Pip’s potential as a natural agent for enhancing plant tolerance to pathogens, offering promising implications for agricultural practices and improving crop resilience against diseases. This study enhances our understanding of Pip’s role in plant defense and provides a foundation for developing Pip-based strategies for sustainable agriculture.
36
Rai, Amit, Taiki Nakaya, Yohei Shimizu, Megha Rai, Michimi Nakamura, Hideyuki Suzuki, Kazuki Saito, and Mami Yamazaki. "De Novo Transcriptome Assembly and Characterization of Lithospermum officinale to Discover Putative Genes Involved in Specialized Metabolites Biosynthesis." Planta Medica 84, no. 12/13 (May 29, 2018): 920–34. http://dx.doi.org/10.1055/a-0630-5925.
Full textAbstract:
Abstract Lithospermum officinale is a valuable source of bioactive metabolites with medicinal and industrial values. However, little is known about genes involved in the biosynthesis of these metabolites, primarily due to the lack of genome or transcriptome resources. This study presents the first effort to establish and characterize de novo transcriptome assembly resource for L. officinale and expression analysis for three of its tissues, namely leaf, stem, and root. Using over 4Gbps of RNA-sequencing datasets, we obtained de novo transcriptome assembly of L. officinale, consisting of 77,047 unigenes with assembly N50 value as 1524 bps. Based on transcriptome annotation and functional classification, 52,766 unigenes were assigned with putative genes functions, gene ontology terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. KEGG pathway and gene ontology enrichment analysis using highly expressed unigenes across three tissues and targeted metabolome analysis showed active secondary metabolic processes enriched specifically in the root of L. officinale. Using co-expression analysis, we also identified 20 and 48 unigenes representing different enzymes of lithospermic/chlorogenic acid and shikonin biosynthesis pathways, respectively. We further identified 15 candidate unigenes annotated as cytochrome P450 with the highest expression in the root of L. officinale as novel genes with a role in key biochemical reactions toward shikonin biosynthesis. Thus, through this study, we not only generated a high-quality genomic resource for L. officinale but also propose candidate genes to be involved in shikonin biosynthesis pathways for further functional characterization.
37
Ramabulana, Anza-Tshilidzi, Paul A. Steenkamp, Ntakadzeni E. Madala, and Ian A. Dubery. "Application of Plant Growth Regulators Modulates the Profile of Chlorogenic Acids in Cultured Bidens pilosa Cells." Plants 10, no. 3 (February 25, 2021): 437. http://dx.doi.org/10.3390/plants10030437.
Full textAbstract:
Plant cell culture offers an alternative to whole plants for the production of biologically important specialised metabolites. In cultured plant cells, manipulation by auxin and cytokinin plant growth regulators (PGRs) may lead to in vitro organogenesis and metabolome changes. In this study, six different combination ratios of 2,4-dichlorophenoxyacetic acid (2,4-D) and benzylaminopurine (BAP) were investigated with the aim to induce indirect organogenesis from Bidens pilosa callus and to investigate the associated induced changes in the metabolomes of these calli. Phenotypic appearance of the calli and total phenolic contents of hydromethanolic extracts indicated underlying biochemical differences that were investigated using untargeted metabolomics, based on ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC–qTOF–MS), combined with multivariate data analysis. The concentration and combination ratios of PGRs were shown to induce differential metabolic responses and, thus, distinct metabolomic profiles, dominated by chlorogenic acids consisting of caffeoyl- and feruloyl-derivatives of quinic acid. Although organogenesis was not achieved, the results demonstrate that exogenous application PGRs can be used to manipulate the metabolome of B. pilosa for in vitro production of specialised metabolites with purported pharmacological properties.
38
Padilla-González, Guillermo F., Mauricio Diazgranados, and Fernando B. Da Costa. "Effect of the Andean Geography and Climate on the Specialized Metabolism of Its Vegetation: The Subtribe Espeletiinae (Asteraceae) as a Case Example." Metabolites 11, no. 4 (April 4, 2021): 220. http://dx.doi.org/10.3390/metabo11040220.
Full textAbstract:
The Andean mountains are ‘center stage’ to some of the most spectacular examples of plant diversifications, where geographic isolation and past climatic fluctuations have played a major role. However, the influence of Andean geography and climate as drivers of metabolic variation in Andean plants is poorly elucidated. Here, we studied the influence of those factors on the metabolome of the subtribe Espeletiinae (Asteraceae) using liquid chromatography coupled to high-resolution mass spectrometry data of over two hundred samples from multiple locations. Our results demonstrate that metabolic profiles can discriminate Espeletiinae taxa at different geographic scales, revealing inter- and intraspecific metabolic variations: at the country level, segregation between Colombian and Venezuelan taxa was observed; regionally, between páramo massifs; and locally, between páramo complexes. Metabolic differences in Espeletiinae were mainly explained by geographic isolation, although differences in taxonomic genera, temperature, and elevation, were also important. Furthermore, we found that different species inhabiting the same páramo complex showed stronger chemical similarities than the same species at different locations, corroborating that geographic isolation represents the main driver of metabolic change in Espeletiinae. The current study serves as a starting point to fill in the gaps in how Andean geography and climate have shaped the metabolism of its vegetation and reveal the potential of untargeted metabolomics to study the environmental physiology of plants.
39
Benninghaus, Vincent Alexander, Nicole van Deenen, Boje Müller, Kai-Uwe Roelfs, Ines Lassowskat, Iris Finkemeier, Dirk Prüfer, and Christian Schulze Gronover. "Comparative proteome and metabolome analyses of latex-exuding and non-exuding Taraxacum koksaghyz roots provide insights into laticifer biology." Journal of Experimental Botany 71, no. 4 (November 19, 2019): 1278–93. http://dx.doi.org/10.1093/jxb/erz512.
Full textAbstract:
Abstract Taraxacum koksaghyz has been identified as one of the most promising alternative rubber crops. Its high-quality rubber is produced in the latex of laticifers, a specialized cell type that is organized in a network of elongated tubules throughout the entire plant body. In order to gain insights into the physiological role(s) of latex and hence laticifer biology, we examine the effects of barnase-induced latex RNA degradation on the metabolite and protein compositions in the roots. We established high-quality datasets that enabled precise discrimination between cellular and physiological processes in laticifers and non-laticifer cell types of roots at different vegetative stages. We identified numerous latex-specific proteins, including a perilipin-like protein that has not been studied in plants yet. The barnase-expressing plants revealed a phenotype that did not exude latex, which may provide a valuable genetic basis for future studies of plant–environment interactions concerning latex and also help to clarify the evolution and arbitrary distribution of latex throughout the plant kingdom. The overview of temporal changes in composition and protein abundance provided by our data opens the way for a deeper understanding of the molecular interactions, reactions, and network relationships that underlie the different metabolic pathways in the roots of this potential rubber crop.
40
Hosmer, Jennifer, Marufa Nasreen, Rabeb Dhouib, Ama-Tawiah Essilfie, Horst Joachim Schirra, Anna Henningham, Emmanuelle Fantino, Peter Sly, Alastair G. McEwan, and Ulrike Kappler. "Access to highly specialized growth substrates and production of epithelial immunomodulatory metabolites determine survival of Haemophilus influenzae in human airway epithelial cells." PLOS Pathogens 18, no. 1 (January 27, 2022): e1010209. http://dx.doi.org/10.1371/journal.ppat.1010209.
Full textAbstract:
Haemophilus influenzae (Hi) infections are associated with recurring acute exacerbations of chronic respiratory diseases in children and adults including otitis media, pneumonia, chronic obstructive pulmonary disease and asthma. Here, we show that persistence and recurrence of Hi infections are closely linked to Hi metabolic properties, where preferred growth substrates are aligned to the metabolome of human airway epithelial surfaces and include lactate, pentoses, and nucleosides, but not glucose that is typically used for studies of Hi growth in vitro. Enzymatic and physiological investigations revealed that utilization of lactate, the preferred Hi carbon source, required the LldD L-lactate dehydrogenase (conservation: 98.8% of strains), but not the two redox-balancing D-lactate dehydrogenases Dld and LdhA. Utilization of preferred substrates was directly linked to Hi infection and persistence. When unable to utilize L-lactate or forced to rely on salvaged guanine, Hi showed reduced extra- and intra-cellular persistence in a murine model of lung infection and in primary normal human nasal epithelia, with up to 3000-fold attenuation observed in competitive infections. In contrast, D-lactate dehydrogenase mutants only showed a very slight reduction compared to the wild-type strain. Interestingly, acetate, the major Hi metabolic end-product, had anti-inflammatory effects on cultured human tissue cells in the presence of live but not heat-killed Hi, suggesting that metabolic endproducts also influence HI-host interactions. Our work provides significant new insights into the critical role of metabolism for Hi persistence in contact with host cells and reveals for the first time the immunomodulatory potential of Hi metabolites.
41
Dhaou, Dounia, Virginie Baldy, Dao Van Tan, Jean-Rémi Malachin, Nicolas Pouchard, Anaïs Roux, Sylvie Dupouyet, et al. "Allelopathic Potential of Mangroves from the Red River Estuary against the Rice Weed Echinochloa crus-galli and Variation in Their Leaf Metabolome." Plants 11, no. 19 (September 21, 2022): 2464. http://dx.doi.org/10.3390/plants11192464.
Full textAbstract:
Mangroves are the only forests located at the sea–land interface in tropical and subtropical regions. They are key elements of tropical coastal ecosystems, providing numerous ecosystem services. Among them is the production of specialized metabolites by mangroves and their potential use in agriculture to limit weed growth in cultures. We explored the in vitro allelopathic potential of eight mangrove species’ aqueous leaf extracts (Avicennia marina, Kandelia obovata, Bruguiera gymnorhiza, Sonneratia apetala, Sonneratia caseolaris, Aegiceras corniculatum, Lumnitzera racemosa and Rhizophora stylosa) on the germination and growth of Echinochloa crus-galli, a weed species associated with rice, Oryza sativa. Leaf methanolic extracts of mangrove species were also studied via UHPLC-ESI/qToF to compare their metabolite fingerprints. Our results highlight that A. corniculatum and S. apetala negatively affected E. crus-galli development with a stimulating effect or no effect on O. sativa. Phytochemical investigations of A. corniculatum allowed us to putatively annotate three flavonoids and two saponins. For S. apetala, three flavonoids, a tannin and two unusual sulfated ellagic acid derivatives were found. Some of these compounds are described for the first time in these species. Overall, A. corniculatum and S. apetala leaves are proposed as promising natural alternatives against E. crus-galli and should be further assessed under field conditions.
42
Symonsy, Stephan, Christian Zipplies, Florian Battke, and Kay Nieselt. "Integrative Systems Biology Visualization with MAYDAY." Journal of Integrative Bioinformatics 7, no. 3 (December 1, 2010): 1–14. http://dx.doi.org/10.1515/jib-2010-115.
Full textAbstract:
SummaryVisualization is pivotal for gaining insight in systems biology data. As the size and complexity of datasets and supplemental information increases, an efficient, integrated framework for general and specialized views is necessary. MAYDAY is an application for analysis and visualization of general ‘omics’ data. It follows a trifold approach for data visualization, consisting of flexible data preprocessing, highly customizable data perspective plots for general purpose visualization and systems based plots. Here, we introduce two new systems biology visualization tools for MAYDAY. Efficiently implemented genomic viewers allow the display of variables associated with genomic locations. Multiple variables can be viewed using our new track-based ChromeTracks tool. A functional perspective is provided by visualizing metabolic pathways either in KEGG or BioPax format. Multiple options of displaying pathway components are available, including Systems Biology Graphical Notation (SBGN) glyphs. Furthermore, pathways can be viewed together with gene expression data either as heatmaps or profiles.We apply our tools to two ‘omics’ datasets of Pseudomonas aeruginosa. The general analysis and visualization tools of MAYDAY as well as our ChromeTracks viewer are applied to a transcriptome dataset. We furthermore integrate this dataset with a metabolome dataset and compare the activity of amino acid degradation pathways between these two datasets, by visually enhancing the pathway diagrams produced by MAYDAY.
43
Stilo, Federico, Giulia Tredici, Carlo Bicchi, Albert Robbat, Joshua Morimoto, and Chiara Cordero. "Climate and Processing Effects on Tea (Camellia sinensis L. Kuntze) Metabolome: Accurate Profiling and Fingerprinting by Comprehensive Two-Dimensional Gas Chromatography/Time-of-Flight Mass Spectrometry." Molecules 25, no. 10 (May 24, 2020): 2447. http://dx.doi.org/10.3390/molecules25102447.
Full textAbstract:
This study applied an untargeted–targeted (UT) fingerprinting approach, based on comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-TOF MS), to assess the effects of rainfall and temperature (both seasonal and elevational) on the tea metabolome. By this strategy, the same compound found in multiple samples need only to be identified once, since chromatograms and mass spectral features are aligned in the data analysis process. Primary and specialized metabolites of leaves from two Chinese provinces, Yunnan (pu′erh) and Fujian (oolong), and a farm in South Carolina (USA, black tea) were studied. UT fingerprinting provided insight into plant metabolism activation/inhibition, taste and trigeminal sensations, and antioxidant properties, not easily attained by other analytical approaches. For example, pu′erh and oolong contained higher relative amounts of amino acids, organic acids, and sugars. Conversely, black tea contained less of all targeted compounds except fructose and glucose, which were more similar to oolong tea. Findings revealed compounds statistically different between spring (pre-monsoon) and summer (monsoon) in pu′erh and oolong teas as well as compounds that exhibited the greatest variability due to seasonal and elevational differences. The UT fingerprinting approach offered unique insights into how differences in growing conditions and commercial processing affect the nutritional benefits and sensory characteristics of tea beverages.
44
Zhao, Ruoxi, Shou Yan, Yadong Hu, Dan Rao, Hongjie Li, Ze Chun, and Shigang Zheng. "Metabolic and Transcriptomic Profile Revealing the Differential Accumulating Mechanism in Different Parts of Dendrobium nobile." International Journal of Molecular Sciences 25, no. 10 (May 14, 2024): 5356. http://dx.doi.org/10.3390/ijms25105356.
Full textAbstract:
Dendrobium nobile is an important orchid plant that has been used as a traditional herb for many years. For the further pharmaceutical development of this resource, a combined transcriptome and metabolome analysis was performed in different parts of D. nobile. First, saccharides, organic acids, amino acids and their derivatives, and alkaloids were the main substances identified in D. nobile. Amino acids and their derivatives and flavonoids accumulated strongly in flowers; saccharides and phenols accumulated strongly in flowers and fruits; alkaloids accumulated strongly in leaves and flowers; and a nucleotide and its derivatives and organic acids accumulated strongly in leaves, flowers, and fruits. Simultaneously, genes for lipid metabolism, terpenoid biosynthesis, and alkaloid biosynthesis were highly expressed in the flowers; genes for phenylpropanoids biosynthesis and flavonoid biosynthesis were highly expressed in the roots; and genes for other metabolisms were highly expressed in the leaves. Furthermore, different members of metabolic enzyme families like cytochrome P450 and 4-coumarate-coA ligase showed differential effects on tissue-specific metabolic accumulation. Members of transcription factor families like AP2-EREBP, bHLH, NAC, MADS, and MYB participated widely in differential accumulation. ATP-binding cassette transporters and some other transporters also showed positive effects on tissue-specific metabolic accumulation. These results systematically elucidated the molecular mechanism of differential accumulation in different parts of D. nobile and enriched the library of specialized metabolic products and promising candidate genes.
45
Mohanty, Bijayalaxmi, Seyed Mohammad Majedi, Shruti Pavagadhi, Shu Harn Te, Chek Yin Boo, Karina Yew-Hoong Gin, and Sanjay Swarup. "Effects of Light and Temperature on the Metabolic Profiling of Two Habitat-Dependent Bloom-Forming Cyanobacteria." Metabolites 12, no. 5 (April 29, 2022): 406. http://dx.doi.org/10.3390/metabo12050406.
Full textAbstract:
Rapid proliferation of cyanobacteria in both benthic and suspended (planktonic) habitats is a major threat to environmental safety, as they produce nuisance compounds such as cytotoxins and off-flavors, which degrade the safety and quality of water supplies. Temperature and light irradiance are two of the key factors in regulating the occurrence of algal blooms and production of major off-flavors. However, the role of these factors in regulating the growth and metabolism is poorly explored for both benthic and planktonic cyanobacteria. To fill this gap, we studied the effects of light and temperature on the growth and metabolic profiling of both benthic (Hapalosiphon sp. MRB220) and planktonic (Planktothricoides sp. SR001) environmental species collected from a freshwater reservoir in Singapore. Moreover, this study is the first report on the metabolic profiling of cyanobacteria belonging to two different habitats in response to altered environmental conditions. The highest growth rate of both species was observed at the highest light intensity (100 μmol photons/m²/s) and at a temperature of 33 °C. Systematic metabolite profiling analysis suggested that temperature had a more profound effect on metabolome of the Hapalosiphon, whereas light had a greater effect in the case of Planktothricoides. Interestingly, Planktothricoides sp. SR001 showed a specialized adaptation mechanism via biosynthesis of arginine, and metabolism of cysteine and methionine to survive and withstand higher temperatures of 38 °C and higher. Hence, the mode of strategies for coping with different light and temperature conditions was correlated with the growth and alteration in metabolic activities for physiological and ecological adaptations in both species. In addition, we putatively identified a number of unique metabolites with a broad range of antimicrobial activities in both species in response to both light and temperature. These metabolites could play a role in the dominant behavior of these species in suppressing competition during bloom formation. Overall, this study elucidated novel insights into the effects of environmental factors on the growth, metabolism, and adaptation strategies of cyanobacteria from two different habitats, and could be useful in controlling their harmful effects on human health and environmental concerns.
46
Raghuvanshi, Ruma, Allyssa G. Grayson, Isabella Schena, Onyebuchi Amanze, Kezia Suwintono, and Robert A. Quinn. "Microbial Transformations of Organically Fermented Foods." Metabolites 9, no. 8 (August 10, 2019): 165. http://dx.doi.org/10.3390/metabo9080165.
Full textAbstract:
Fermenting food is an ancient form of preservation ingrained many in human societies around the world. Westernized diets have moved away from such practices, but even in these cultures, fermented foods are seeing a resurgent interested due to their believed health benefits. Here, we analyze the microbiome and metabolome of organically fermented vegetables, using a salt brine, which is a common ‘at-home’ method of food fermentation. We found that the natural microbial fermentation had a strong effect on the food metabolites, where all four foods (beet, carrot, peppers and radishes) changed through time, with a peak in molecular diversity after 2–3 days and a decrease in diversity during the final stages of the 4-day process. The microbiome of all foods showed a stark transition from one that resembled a soil community to one dominated by Enterobacteriaceae, such as Erwinia spp., within a single day of fermentation and increasing amounts of Lactobacillales through the fermentation process. With particular attention to plant natural products, we observed significant transformations of polyphenols, triterpenoids and anthocyanins, but the degree of this metabolism depended on the food type. Beets, radishes and peppers saw an increase in the abundance of these compounds as the fermentation proceeded, but carrots saw a decrease through time. This study showed that organically fermenting vegetables markedly changed their chemistry and microbiology but resulted in high abundance of Enterobacteriaceae which are not normally considered as probiotics. The release of beneficial plant specialized metabolites was observed, but this depended on the fermented vegetable.
47
Genesiska, Joana Falcao Salles, and Kira Juliane Tiedge. "Untangling the rhizosphere specialized metabolome." Phytochemistry Reviews, November 20, 2024. http://dx.doi.org/10.1007/s11101-024-10036-y.
Full text
48
Pellissier, Leonie, Arnaud Gaudry, Salomé Vilette, Nicole Lecoultre, Adriano Rutz, Pierre-Marie Allard, Laurence Marcourt, et al. "Comparative metabolomic study of fungal foliar endophytes and their long-lived host Astrocaryum sciophilum: a model for exploring the chemodiversity of host-microbe interactions." Frontiers in Plant Science 14 (December 19, 2023). http://dx.doi.org/10.3389/fpls.2023.1278745.
Full textAbstract:
IntroductionIn contrast to the dynamics observed in plant/pathogen interactions, endophytic fungi have the capacity to establish enduring associations within their hosts, leading to the development of a mutually beneficial relationship that relies on specialized chemical interactions. Research indicates that the presence of endophytic fungi has the ability to significantly modify the chemical makeup of the host organism. Our hypothesis proposes the existence of a reciprocal exchange of chemical signals between plants and fungi, facilitated by specialized chemical processes that could potentially manifest within the tissues of the host. This research aimed to precisely quantify the portion of the cumulative fungal endophytic community's metabolome detectable within host leaves, and tentatively evaluate its relevance to the host-endophyte interplay. The understory palm Astrocaryum sciophilum (Miq.) Pulle was used as a interesting host plant because of its notable resilience and prolonged life cycle, in a tropical ecosystem.MethodUsing advanced metabolome characterization, including UHPLC-HRMS/MS and molecular networking, the study explored enriched metabolomes of both host leaves and 15 endophytic fungi. The intention was to capture a metabolomic "snapshot" of both host and endophytic community, to achieve a thorough and detailed analysis.Results and discussionThis approach yielded an extended MS-based molecular network, integrating diverse metadata for identifying host- and endophyte-derived metabolites. The exploration of such data (>24000 features in positive ionization mode) enabled effective metabolome comparison, yielding insights into cultivable endophyte chemodiversity and occurrence of common metabolites between the holobiont and its fungal communities. Surprisingly, a minor subset of features overlapped between host leaf and fungal samples despite significant plant metabolome enrichment. This indicated that fungal metabolic signatures produced in vitro remain sparingly detectable in the leaf. Several classes of primary metabolites were possibly shared. Specific fungal metabolites and/or compounds of their chemical classes were only occasionally discernible in the leaf, highlighting endophytes partial contribution to the overall holobiont metabolome. To our knowledge, the metabolomic study of a plant host and its microbiome has rarely been performed in such a comprehensive manner. The general analytical strategy proposed in this paper seems well-adapted for any study in the field of microbial- or microbiome-related MS and can be applied to most host-microbe interactions.
49
Singh, Nikhil Kumar, Sabina Moser Tralamazza, Leen Nanchira Abraham, Gaétan Glauser, and Daniel Croll. "Genome-wide association mapping reveals genes underlying population-level metabolome diversity in a fungal crop pathogen." BMC Biology 20, no. 1 (October 8, 2022). http://dx.doi.org/10.1186/s12915-022-01422-z.
Full textAbstract:
Abstract Background Fungi produce a wide range of specialized metabolites (SMs) involved in biotic interactions. Pathways for the production of SMs are often encoded in clusters of tightly arranged genes identified as biosynthetic gene clusters. Such gene clusters can undergo horizontal gene transfers between species and rapid evolutionary change within species. The acquisition, rearrangement, and deletion of gene clusters can generate significant metabolome diversity. However, the genetic basis underlying variation in SM production remains poorly understood. Results Here, we analyzed the metabolite production of a large population of the fungal pathogen of wheat, Zymoseptoria tritici. The pathogen causes major yield losses and shows variation in gene clusters. We performed untargeted ultra-high performance liquid chromatography-high resolution mass spectrometry to profile the metabolite diversity among 102 isolates of the same species. We found substantial variation in the abundance of the detected metabolites among isolates. Integrating whole-genome sequencing data, we performed metabolite genome-wide association mapping to identify loci underlying variation in metabolite production (i.e., metabolite-GWAS). We found that significantly associated SNPs reside mostly in coding and gene regulatory regions. Associated genes encode mainly transport and catalytic activities. The metabolite-GWAS identified also a polymorphism in the 3′UTR region of a virulence gene related to metabolite production and showing expression variation. Conclusions Taken together, our study provides a significant resource to unravel polymorphism underlying metabolome diversity within a species. Integrating metabolome screens should be feasible for a range of different plant pathogens and help prioritize molecular studies.
50
Dadras, Armin, Tim P. Rieseberg, Jaccoline M. S. Zegers, Janine M. R. Fürst-Jansen, Iker Irisarri, Jan de Vries, and Sophie de Vries. "Accessible versatility underpins the deep evolution of plant specialized metabolism." Phytochemistry Reviews, March 30, 2023. http://dx.doi.org/10.1007/s11101-023-09863-2.
Full textAbstract:
AbstractThe evolution of several hallmark traits of land plants is underpinned by phytochemical innovations. The specialized metabolism of plants can appear like a teeming chaos that has yielded an ungraspable array of chemodiversity. Yet, this diversity is the result of evolutionary processes including neutral evolution, drift, and selection that have shaped the metabolomic networks. Deciphering the evolutionary history of the specialized metabolome in the context of plant terrestrialization has only just begun. Studies on phytochemistry of model organisms and crop plants enabled the sketch of a blueprint for the biochemical landscape of land plants and a good idea on the diversity that can be explored. Evolutionary metabolomics has in the past been successfully used to identify traits that were critical for domestication of angiosperms or to unravel key innovations in land plants. Owing to recent advances in the study of non-model land plants and their close streptophyte algal relatives we can now begin to appreciate the variation of metabolic networks across the green lineage—and understand convergent solutions to similar environmental challenges and effects that plant terrestrialization had on these networks. Here, we highlight the significant progress made with regard to identifying metabolomic diversity by adding non-model organisms to the equation. We discuss the role of neutral evolution in the context of metabolomic diversity and the effects that environmental challenges had on the lineage-specific specialized metabolism from an evolutionary point of view.