scholarly journals Linking genomics and metabolomics to chart specialized metabolic diversity

2020 ◽  
Vol 49 (11) ◽  
pp. 3297-3314 ◽  
Author(s):  
Justin J. J. van der Hooft ◽  
Hosein Mohimani ◽  
Anelize Bauermeister ◽  
Pieter C. Dorrestein ◽  
Katherine R. Duncan ◽  
...  
Keyword(s):  
Chemical Diversity ◽  
Ecological Interactions ◽  
Metabolic Diversity ◽  
Metabolomics Data ◽  
Specialized Metabolites

Microbial and plant specialized metabolites play key roles in mediating ecological interactions between organisms. Analysis and integration of genomics and metabolomics data facilitates charting their immense chemical diversity.

scholarly journals Metabolome-Scale Genome-Wide Association Studies Reveal Chemical Diversity and Genetic Control of Maize Specialized Metabolites

2019 ◽  
Vol 31 (5) ◽  
pp. 937-955 ◽  
Author(s):  
Shaoqun Zhou ◽  
Karl A. Kremling ◽  
Nonoy Bandillo ◽  
Annett Richter ◽  
Ying K. Zhang ◽  
...  
Keyword(s):  
Genetic Control ◽  
Association Studies ◽  
Chemical Diversity ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Specialized Metabolites ◽  
Genome Wide

scholarly journals A Review of the Ephedra genus: Distribution, Ecology, Ethnobotany, Phytochemistry and Pharmacological Properties

Molecules ◽  
2020 ◽  
Vol 25 (14) ◽  
pp. 3283
Author(s):  
Daphne E. González-Juárez ◽  
Abraham Escobedo-Moratilla ◽  
Joel Flores ◽  
Sergio Hidalgo-Figueroa ◽  
Natalia Martínez-Tagüeña ◽  
...  
Keyword(s):  
Chemical Constituents ◽  
Nasal Congestion ◽  
Building Blocks ◽  
Relevant Information ◽  
Chemical Diversity ◽  
Future Research ◽  
Pharmacological Properties ◽  
Ecological Interactions ◽  
Phytochemical Study ◽  
Promising Area

Ephedra is one of the largest genera of the Ephedraceae family, which is distributed in arid and semiarid regions of the world. In the traditional medicine from several countries some species from the genus are commonly used to treat asthma, cold, flu, chills, fever, headache, nasal congestion, and cough. The chemical constituents of Ephedra species have been of research interest for decades due to their contents of ephedrine-type alkaloids and its pharmacological properties. Other chemical constituents such as phenolic and amino acid derivatives also have resulted attractive and have provided evidence-based supporting of the ethnomedical uses of the Ephedra species. In recent years, research has been expanded to explore the endophytic fungal diversity associated to Ephedra species, as well as, the chemical constituents derived from these fungi and their pharmacological bioprospecting. Two additional aspects that illustrate the chemical diversity of Ephedra genus are the chemotaxonomy approaches and the use of ephedrine-type alkaloids as building blocks in organic synthesis. American Ephedra species, especially those that exist in Mexico, are considered to lack ephedrine type alkaloids. In this sense, the phytochemical study of Mexican Ephedra species is a promising area of research to corroborate their ephedrine-type alkaloids content and, in turn, discover new chemical compounds with potential biological activity. Therefore, the present review represents a key compilation of all the relevant information for the Ephedra genus, in particular the American species, the species distribution, their ecological interactions, its ethnobotany, its phytochemistry and their pharmacological activities and toxicities, in order to promote clear directions for future research.

scholarly journals Complex evolutionary dynamics govern the diversity and distribution of biosynthetic gene clusters and their encoded specialized metabolites

2020 ◽  
Author(s):  
Alexander B. Chase ◽  
Douglas Sweeney ◽  
Mitchell N. Muskat ◽  
Dulce Guillén-Matus ◽  
Paul R. Jensen
Keyword(s):  
Evolutionary Dynamics ◽  
Gene Clusters ◽  
Ecological Interactions ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Evolutionary Processes ◽  
Specialized Metabolites ◽  
Marine Actinomycete ◽  
Species Specific ◽  
Gain Loss

ABSTRACTWhile specialized metabolites are thought to mediate ecological interactions, the evolutionary processes driving their distributions, particularly among closely related lineages, remain poorly understood. Here, we examine the evolutionary dynamics governing the diversity and distribution of biosynthetic gene clusters (BGCs) in 118 strains across nine described species within the marine actinomycete genus Salinispora. While previous evidence indicated that horizontal gene transfer largely contributed to BGC diversity, we find that a majority of BGCs in Salinispora genomes are maintained by processes of vertical descent. In particular, we identified species-specific signatures that were associated with both BGC distributions and the production of their encoded specialized metabolites. By analyzing nine experimentally characterized BGCs that range in conservation from species to genus specific, we find that the distribution of BGCs among Salinispora species is maintained by selection, while BGC diversification is constrained by recombination among closely related strains and strengthened by gain/loss events between species. Notably, the evolutionary processes driving BGC diversification had direct consequences for compound production, elucidating the mechanisms that lead to chemical diversification. These results support the concept that specialized metabolites, and their cognate BGCs, represent functional traits associated with ecological differentiation among Salinispora species.GRAPHICAL ABSTRACT

scholarly journals A global survey of specialized metabolic diversity encoded in bacterial genomes

2021 ◽  
Author(s):  
Athina Gavriilidou ◽  
Satria A Kautsar ◽  
Nestor Zaburannyi ◽  
Daniel Krug ◽  
Rolf Mueller ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Evolutionary History ◽  
Gene Clusters ◽  
Chemical Diversity ◽  
Metabolic Diversity ◽  
Bacterial Genomes ◽  
Biosynthetic Gene Clusters ◽  
Taxonomic Rank ◽  
New Antibiotics ◽  
Biosynthetic Machinery

Bacterial secondary metabolites have been studied for decades for their usefulness as drugs, such as antibiotics. However, the identification of new structures has been decelerating, in part due to rediscovery of known compounds. Meanwhile, multi-resistant pathogens continue to emerge, urging the need for new antibiotics. It is unclear how much chemical diversity exists in Nature and whether discovery efforts should be focused on established antibiotic producers or rather on understudied taxa. Here, we surveyed around 170,000 bacterial genomes as well as several thousands of Metagenome Assembled Genomes (MAGs) for their diversity in Biosynthetic Gene Clusters (BGCs) known to encode the biosynthetic machinery for producing secondary metabolites. We used two distinct algorithms to provide a global overview of the biosynthetic diversity present in the sequenced part of the bacterial kingdom. Our results indicate that only 3% of genomic potential for natural products has been experimentally discovered. We connect the emergence of most biosynthetic diversity in evolutionary history close to the taxonomic rank of genus. Despite enormous differences in potential among taxa, we identify Streptomyces as by far the most biosynthetically diverse based on currently available data. Simultaneously, our analysis highlights multiple promising high-producing taxas that have thus far escaped investigation.

scholarly journals Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity

Antibiotics ◽  
2018 ◽  
Vol 7 (4) ◽  
pp. 86 ◽  
Author(s):  
Cláudia Vicente ◽  
Annabelle Thibessard ◽  
Jean-Noël Lorenzi ◽  
Mabrouka Benhadj ◽  
Laurence Hôtel ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Sequence Data ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Core Gene ◽  
Chemical Diversity ◽  
Specific Gene ◽  
Biosynthetic Gene ◽  
Single Strain ◽  
Specialized Metabolites

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.

scholarly journals Metabotyping and its application in targeted nutrition: an overview

2017 ◽  
Vol 117 (12) ◽  
pp. 1631-1644 ◽  
Author(s):  
Anna Riedl ◽  
Christian Gieger ◽  
Hans Hauner ◽  
Hannelore Daniel ◽  
Jakob Linseisen
Keyword(s):  
Statistical Methods ◽  
Dietary Intervention ◽  
Metabolic Diseases ◽  
Population Based ◽  
Data Sets ◽  
Nutrient Requirements ◽  
Metabolic Diversity ◽  
Dietary Interventions ◽  
Metabolomics Data ◽  
Nutritional Interventions

AbstractMetabolic diversity leads to differences in nutrient requirements and responses to diet and medication between individuals. Using the concept of metabotyping – that is, grouping metabolically similar individuals – tailored and more efficient recommendations may be achieved. The aim of this study was to review the current literature on metabotyping and to explore its potential for better targeted dietary intervention in subjects with and without metabolic diseases. A comprehensive literature search was performed in PubMed, Google and Google Scholar to find relevant articles on metabotyping in humans including healthy individuals, population-based samples and patients with chronic metabolic diseases. A total of thirty-four research articles on human studies were identified, which established more homogeneous subgroups of individuals using statistical methods for analysing metabolic data. Differences between studies were found with respect to the samples/populations studied, the clustering variables used, the statistical methods applied and the metabotypes defined. According to the number and type of the selected clustering variables, the definitions of metabotypes differed substantially; they ranged between general fasting metabotypes, more specific fasting parameter subgroups like plasma lipoprotein or fatty acid clusters and response groups to defined meal challenges or dietary interventions. This demonstrates that the term ‘metabotype’ has a subjective usage, calling for a formalised definition. In conclusion, this literature review shows that metabotyping can help identify subgroups of individuals responding differently to defined nutritional interventions. Targeted recommendations may be given at such metabotype group levels. Future studies should develop and validate definitions of generally valid metabotypes by exploiting the increasingly available metabolomics data sets.

scholarly journals Evolution of metabolic novelty: A trichome-expressed invertase creates specialized metabolic diversity in wild tomato

2019 ◽  
Vol 5 (4) ◽  
pp. eaaw3754 ◽  
Author(s):  
Bryan J. Leong ◽  
Daniel B. Lybrand ◽  
Yann-Ru Lou ◽  
Pengxiang Fan ◽  
Anthony L. Schilmiller ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Gland Cell ◽  
Metabolic Enzyme ◽  
South American ◽  
Metabolic Diversity ◽  
Solanum Pennellii ◽  
Wild Tomato ◽  
Specialized Metabolites ◽  
New Class ◽  
In The Wild

Plants produce a myriad of taxonomically restricted specialized metabolites. This diversity—and our ability to correlate genotype with phenotype—makes the evolution of these ecologically and medicinally important compounds interesting and experimentally tractable. Trichomes of tomato and other nightshade family plants produce structurally diverse protective compounds termed acylsugars. While cultivated tomato (Solanum lycopersicum) strictly accumulates acylsucroses, the South American wild relative Solanum pennellii produces copious amounts of acylglucoses. Genetic, transgenic, and biochemical dissection of the S. pennellii acylglucose biosynthetic pathway identified a trichome gland cell–expressed invertase-like enzyme that hydrolyzes acylsucroses (Sopen03g040490). This enzyme acts on the pyranose ring–acylated acylsucroses found in the wild tomato but not on the furanose ring–decorated acylsucroses of cultivated tomato. These results show that modification of the core acylsucrose biosynthetic pathway leading to loss of furanose ring acylation set the stage for co-option of a general metabolic enzyme to produce a new class of protective compounds.

Molecular Networking Discloses the Chemical Diversity of Flavonoids and Selaginellins in Selaginella convoluta

Planta Medica ◽  
2020 ◽  
Author(s):  
Fernanda Priscila Santos Reginaldo ◽  
Paula Carolina Pires Bueno ◽  
Isabelly Cristina de Matos Costa ◽  
Alan de Araújo Roque ◽  
Arthur Germano Fett-Neto ◽  
...  
Keyword(s):  
Natural Habitat ◽  
Resistance Mechanism ◽  
Chemical Diversity ◽  
Semiarid Region ◽  
Structural Annotation ◽  
Molecular Networking ◽  
Specialized Metabolites ◽  
New Information ◽  
Brazilian Semiarid ◽  
Web Platform

Abstract Selaginella convoluta is a desiccation tolerant plant native to the Brazilian semiarid region (Caatinga), endowed with an effective drought resistance mechanism. As part of our research efforts to understand the chemical diversity of S. convoluta, dehydrated (harvested in their natural habitat in the dry season) and hydrated (plant acclimated in a laboratory after rehydration) specimens were analyzed by HR-LC-ESI-MS/MS followed by a structural annotation on the Global Natural Products Social Molecular Networking Web platform. The molecular networking approach allowed for putative annotation of 39 metabolites, mainly selaginellins and flavonoids. Based on MS/MS data, three unprecedented selaginellins were annotated: 29-hydroxy selaginellin O, 29-hydroxy selaginellin A, and 4-{[2-(4-hydrophenyl)-6-[2-(4-hydroxyphenyl)ethynyl]phenyl](4-oxocyclohexa-2,5-dien-1-ylidene)methyl}benzaldehyde. Th results pointed out that valuable scientific knowledge can be obtained from studies conducted with plants in their natural habitat by allowing a more realistic profile of chemical diversity. The present study adds new information on specialized metabolites of S. convoluta, mainly flavonoids and selaginellins, and highlights the species as an untapped source of chemobiodiversity from Caatinga.

scholarly journals Comparative Genomics and Metabolomics in the Genus Nocardia

mSystems ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Daniel Männle ◽  
Shaun M. K. McKinnie ◽  
Shrikant S. Mantri ◽  
Katharina Steinke ◽  
Zeyin Lu ◽  
...  
Keyword(s):  
Natural Product ◽  
Gene Cluster ◽  
Gene Clusters ◽  
Chemical Diversity ◽  
Biosynthetic Gene ◽  
Compound Identification ◽  
Biosynthetic Gene Clusters ◽  
Metabolomics Data ◽  
Similarity Networks ◽  
Gene Similarity

ABSTRACT Using automated genome analysis tools, it is often unclear to what degree genetic variability in homologous biosynthetic pathways relates to structural variation. This hampers strain prioritization and compound identification and can lead to overinterpretation of chemical diversity. Here, we assessed the metabolic potential of Nocardia, an underinvestigated actinobacterial genus that is known to comprise opportunistic human pathogens. Our analysis revealed a plethora of putative biosynthetic gene clusters of various classes, including polyketide, nonribosomal peptide, and terpenoid pathways. Furthermore, we used the highly conserved biosynthetic pathway for nocobactin-like siderophores to investigate how gene cluster differences correlate to structural differences in the produced compounds. Sequence similarity networks generated by BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) showed the presence of several distinct gene cluster families. Metabolic profiling of selected Nocardia strains using liquid chromatography-mass spectrometry (LC-MS) metabolomics data, nuclear magnetic resonance (NMR) spectroscopy, and GNPS (Global Natural Product Social molecular networking) revealed that nocobactin-like biosynthetic gene cluster (BGC) families above a BiG-SCAPE threshold of 70% can be assigned to distinct structural types of nocobactin-like siderophores. IMPORTANCE Our work emphasizes that Nocardia represent a prolific source for natural products rivaling better-characterized genera such as Streptomyces or Amycolatopsis. Furthermore, we showed that large-scale analysis of biosynthetic gene clusters using similarity networks with high stringency allows the distinction and prediction of natural product structural variations. This will facilitate future genomics-driven drug discovery campaigns.

scholarly journals Mass Spectrometry: A Rosetta Stone to Learn How Fungi Interact and Talk

Life ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 89
Author(s):  
Erika Calla-Quispe ◽  
Hammerly Lino Fuentes-Rivera ◽  
Pablo Ramírez ◽  
Carlos Martel ◽  
Alfredo J. Ibañez
Keyword(s):  
Mass Spectrometry ◽  
Dominant Role ◽  
Chemical Compounds ◽  
Rapid Identification ◽  
Ecological Interactions ◽  
Specialized Metabolites ◽  
Rosetta Stone ◽  
False Positive Identification ◽  
Analytical Strategies ◽  
Chemical Mediators

Fungi are a highly diverse group of heterotrophic organisms that play an important role in diverse ecological interactions, many of which are chemically mediated. Fungi have a very versatile metabolism, which allows them to synthesize a large number of still little-known chemical compounds, such as soluble compounds that are secreted into the medium and volatile compounds that are chemical mediators over short and long distances. Mass spectrometry (MS) is currently playing a dominant role in mycological studies, mainly due to its inherent sensitivity and rapid identification capabilities of different metabolites. Furthermore, MS has also been used as a reliable and accurate tool for fungi identification (i.e., biotyping). Here, we introduce the readers about fungal specialized metabolites, their role in ecological interactions and provide an overview on the MS-based techniques used in fungal studies. We particularly present the importance of sampling techniques, strategies to reduce false-positive identification and new MS-based analytical strategies that can be used in mycological studies, further expanding the use of MS in broader applications. Therefore, we foresee a bright future for mass spectrometry-based research in the field of mycology.

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