Discovery of Marine Natural Products
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Rescooped by Yue Yang from Natural Products Chemistry Breaking News
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Opportunistic Sampling of Roadkill as an Entry Point to Accessing Natural Products Assembled by Bacteria Associated with Non-anthropoidal Mammalian Microbiomes 

Opportunistic Sampling of Roadkill as an Entry Point to Accessing Natural Products Assembled by Bacteria Associated with Non-anthropoidal Mammalian Microbiomes  | Discovery of Marine Natural Products | Scoop.it

Click hFew secondary metabolites have been reported from mammalian microbiome bacteria despite the large numbers of diverse taxa that inhabit warm-blooded higher vertebrates. As a means to investigate natural products from these microorganisms, an opportunistic sampling protocol was developed, which focused on exploring bacteria isolated from roadkill mammals. This initiative was made possible through the establishment of a newly created discovery pipeline, which couples laser ablation electrospray ionization mass spectrometry (LAESIMS) with bioassay testing, to target biologically active metabolites from microbiome-associated bacteria. To illustrate this process, this report focuses on samples obtained from the ear of a roadkill opossum (Dideiphis virginiana) as the source of two bacterial isolates (Pseudomonas sp. and Serratia sp.) that produced several new and known cyclic lipodepsipeptides (viscosin and serrawettins, respectively). These natural products inhibited biofilm formation by the human pathogenic yeast Candida albicans at concentrations well below those required to inhibit yeast viability. Phylogenetic analysis of 16S rRNA gene sequence libraries revealed the presence of diverse microbial communities associated with different sites throughout the opossum carcass. A putative biosynthetic pathway responsible for the production of the new serrawettin analogues was identified by sequencing the genome of the Serratia sp. isolate. This study provides a functional roadmap to carrying out the systematic investigation of the genomic, microbiological, and chemical parameters related to the production of natural products made by bacteria associated with non-anthropoidal mammalian microbiomes. Discoveries emerging from these studies are anticipated to provide a working framework for efforts aimed at augmenting microbiomes to deliver beneficial natural products to a host.ere to edit the content


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NatProdChem's curator insight, November 27, 10:15 AM

Weirdest sampling pipeline !

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Annual Review of Ecology, Evolution, and Systematics: Adaptation in Natural Microbial Populations

Annual Review of Ecology, Evolution, and Systematics: Adaptation in Natural Microbial Populations | Discovery of Marine Natural Products | Scoop.it

Although their diversity greatly exceeds that of plants and animals, microbial organisms have historically received less attention in ecology and evolutionary biology research. This knowledge gap is rapidly closing, owing to recent technological advances and an increasing appreciation for the role microbes play in shaping ecosystems and human health. In this review, we examine when and how the process and patterns of bacterial adaptation might fundamentally differ from those of macrobes, highlight methods used to measure adaptation in natural microbial populations, and discuss the importance of examining bacterial adaptation across multiple scales. We emphasize the need to consider the scales of adaptation as continua, in which the genetic makeup of bacteria blur boundaries between populations, species, and communities and with them concepts of ecological and evolutionary time. Finally, we examine current directions of the field as we move beyond the stamp-collecting phase and toward a better understanding of microbial adaptation in nature.

 

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Plant Mol Biol: Fungal endophytes: modifiers of plant disease

Plant Mol Biol: Fungal endophytes: modifiers of plant disease | Discovery of Marine Natural Products | Scoop.it

Many recent studies have demonstrated that non-pathogenic fungi within plant microbiomes, i.e., endophytes (“endo” = within, “phyte” = plant), can significantly modify the expression of host plant disease. The rapid pace of advancement in endophyte ecology warrants a pause to synthesize our understanding of endophyte disease modification and to discuss future research directions. We reviewed recent literature on fungal endophyte disease modification, and here report on several emergent themes: (1) Fungal endophyte effects on plant disease span the full spectrum from pathogen antagonism to pathogen facilitation, with pathogen antagonism most commonly reported. (2) Agricultural plant pathosystems are the focus of research on endophyte disease modification. (3) A taxonomically diverse group of fungal endophytes can influence plant disease severity. And (4) Fungal endophyte effects on plant disease severity are context-dependent. Our review highlights the importance of fungal endophytes for plant disease across a broad range of plant pathosystems, yet simultaneously reveals that complexity within plant microbiomes presents a significant challenge to disentangling the biotic environmental factors affecting plant disease severity. Manipulative studies integrating eco-evolutionary approaches with emerging molecular tools will be poised to elucidate the functional importance of endophytes in natural plant pathosystems that are fundamental to biodiversity and conservation.


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Algae–bacteria interactions: Evolution, ecology and emerging applications

Algae–bacteria interactions: Evolution, ecology and emerging applications | Discovery of Marine Natural Products | Scoop.it
Algae and bacteria have coexisted ever since the early stages of evolution. This coevolution has revolutionized life on earth in many aspects. Algae and bacteria together influence ecosystems as varied as deep seas to lichens and represent all conceivable modes of interactions — from mutualism to parasitism. Several studies have shown that algae and bacteria synergistically affect each other's physiology and metabolism, a classic case being algae–roseobacter interaction. These interactions are ubiquitous and define the primary productivity in most ecosystems. In recent years, algae have received much attention for industrial exploitation but their interaction with bacteria is often considered a contamination during commercialization. A few recent studies have shown that bacteria not only enhance algal growth but also help in flocculation, both essential processes in algal biotechnology. Hence, there is a need to understand these interactions from an evolutionary and ecological standpoint, and integrate this understanding for industrial use. Here we reflect on the diversity of such relationships and their associated mechanisms, as well as the habitats that they mutually influence. This review also outlines the role of these interactions in key evolutionary events such as endosymbiosis, besides their ecological role in biogeochemical cycles. Finally, we focus on extending such studies on algal–bacterial interactions to various environmental and bio-technological applications.

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Jean-Michel Ané's curator insight, December 10, 2015 10:55 AM

Guess which ones we are interested in...

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Bacteria from the sea join the fight against cancer and infections

Bacteria from the sea join the fight against cancer and infections | Discovery of Marine Natural Products | Scoop.it

For decades, bacteria have served society by producing antibiotics – the chemical compounds that can cure infectious diseases. However, it is possible that many natural microorganisms carry the recipes for the medicines of the future hidden in their genetic material, without this part of their genetic code being activated or “switched on”.


But now, biotechnologists from SINTEF and NTNU are developing technology that will make it easier to find – and exploit – these hidden and unutilized medicine factories in bacteria that exist in the natural environment. The hunt will concentrate on marine bacteria, and is one of the projects run by the new Norwegian Centre for Digital Life.


“Our aim is to identify novel compounds that are capable, for example, of killing cancer cells or antibiotic-resistant bacteria. The technology that we are developing will reduce the time taken to search for these and to make the production process more efficient,” says Alexander Wentzel, a senior scientist at SINTEF.


As a strategy, scientists will clip out genetic material from a large number of microorganisms before they transfer their DNA to cultivable bacteria; organisms whose characteristics have already been studied and will be optimized by the researchers in the INBioPharm project. The alterations will enable these organisms to switch on production of new substances that cannot be produced in the microorganism from which the DNA has been extracted.


With the aid of systems biology and synthetic biology (see fact-box), the project will develop the microorganisms in a way which, when they are cultivated, will produce small test quantities of all the possible products, and later, enable mass-production of the most promising substances.


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Prospecting for new bacterial metabolites: a glossary of approaches for inducing, activating and upregulating the biosynthesis of bacterial cryptic or silent natural products

Prospecting for new bacterial metabolites: a glossary of approaches for inducing, activating and upregulating the biosynthesis of bacterial cryptic or silent natural products | Discovery of Marine Natural Products | Scoop.it

Over the centuries, microbial secondary metabolites have played a central role in the treatment of human diseases and have revolutionised the pharmaceutical industry. With the increasing number of sequenced microbial genomes revealing a plethora of novel biosynthetic genes, natural product drug discovery is entering an exciting second golden age. Here, we provide a concise overview as an introductory guide to the main methods employed to unlock or up-regulate these so called ‘cryptic’, ‘silent’ and ‘orphan’ gene clusters, and increase the production of the encoded natural product. With a predominant focus on bacterial natural products we will discuss the importance of the bioinformatics approach for genome mining, the use of first different and simple culturing techniques and then the application of genetic engineering to unlock the microbial treasure trove.

 

Joseph Scott Zarins-Tutt,a   Tania Triscari Barberi,a   Hong Gao,a   Andrew Mearns-Spragg,b   Lixin Zhang,c   David J. Newmand and   Rebecca Jane Miriam Goss*a  
 
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Nat. Prod. Rep., 2016, Advance Article


DOI: 10.1039/C5NP00111K

 

 


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Optimizing Crops for Biocontrol of Pests and Disease

Optimizing Crops for Biocontrol of Pests and Disease | Discovery of Marine Natural Products | Scoop.it

Research in Focus: Optimizing Crops for Biocontrol of Pests and Disease. This week we summarize an Opinion article from Trends in Plant Science on the potential applications of Volatile Organic Compounds and tritropic interactions for pest control. http://blog.aspb.org/…/optimizing-crops-for-biocontrol-of-…/ The article of the same name is published Open Access at Trends in Plant Science - check it out http://www.cell.com/…/pl…/abstract/S1360-1385%2815%2900208-3


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Eric Vincill's curator insight, October 18, 2015 4:39 PM

I see this as a paradigm shift in how we think about trait enhancement and crop breeding to protecting our food crops.

 

Instead of focusing on finding 'beneficial' bacteria and fungi that confer disease and herbivory resistance to the current cultivars of agronomically important plant species, why not focus on the plant and find 'beneficial' plant traits that will attract or increase the spectrum of compatibility with beneficial bacteria and fungi to confer disease or herbivory resistance. 

 

 

 

 

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Interaction of Piriformospora indica with Azotobacter chroococcum

Interaction of Piriformospora indica with Azotobacter chroococcum | Discovery of Marine Natural Products | Scoop.it
Microbial communities in rhizosphere interact with each other and form a basis of a cumulative impact on plant growth. Rhizospheric microorganisms like Piriformospora indica and Azotobacter chroococcum are well known for their beneficial interaction with plants. These features make P. indica /A. chroococcum co-inoculation of crops most promising with respect to sustainable agriculture and to understanding the transitions in the evolution of rhizospheric microbiome. Here, we investigated interactions of P. indica with A. chroococcum in culture. Out of five Azotobacter strains tested, WR5 exhibited growth-promoting while strain M4 exerted growth-inhibitory effect on the fungus in axenic culture. Electron microscopy of co-culture indicated an intimate association of the bacterium with the fungus. 2-D gel electrophoresis followed by mass spectrometry of P. indica cellular proteins grown with or without WR5 and M4 showed differential expression of many metabolic proteins like enolase-I, ureaseD, the GTP binding protein YPT1 and the transmembrane protein RTM1. Fungal growth as influenced by bacterial crude metabolites was also monitored. Taken together, the results conform to a model where WR5 and M4 influence the overall growth and physiology of P. indica which may have a bearing on its symbiotic relationship with plants.

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Exploiting the Complementarity between Dereplication and Computer-Assisted Structure Elucidation for the Chemical Profiling of Natural Cosmetic Ingredients: Tephrosia purpurea as a Case Study

Exploiting the Complementarity between Dereplication and Computer-Assisted Structure Elucidation for the Chemical Profiling of Natural Cosmetic Ingredients: Tephrosia purpurea as a Case Study | Discovery of Marine Natural Products | Scoop.it

The aqueous-ethanolic extract of Tephrosia purpurea seeds is currently exploited in the cosmetic industry as a natural ingredient of skin lotions. The aim of this study was to chemically characterize this ingredient by combining centrifugal partition extraction (CPE) as a fractionation tool with two complementary identification approaches involving dereplication and computer-assisted structure elucidation. Following two rapid fractionations of the crude extract (2 g), seven major compounds namely, caffeic acid, quercetin-3-O-rutinoside, ethyl galactoside, ciceritol, stachyose, saccharose, and citric acid, were unambiguously identified within the CPE-generated simplified mixtures by a recently developed 13C NMR-based dereplication method. The structures of four additional compounds, patuletin-3-O-rutinoside, kaempferol-3-O-rutinoside, guaiacylglycerol 8-vanillic acid ether, and 2-methyl-2-glucopyranosyloxypropanoic acid, were automatically elucidated by using the Logic for Structure Determination program based on the interpretation of 2D NMR (HSQC, HMBC, and COSY) connectivity data. As more than 80% of the crude extract mass was characterized without need for tedious and labor-intensive multistep purification procedures, the identification tools involved in this work constitute a promising strategy for an efficient and time-saving chemical profiling of natural extracts.

 

Jane Hubert*†, Sébastien Chollet†, Sylvain Purson†‡, Romain Reynaud‡, Dominique Harakat†, Agathe Martinez†, Jean-Marc Nuzillard†, and Jean-Hugues Renault
J. Nat. Prod., Article ASAPDOI: 10.1021/acs.jnatprod.5b00174

 

 


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What is Complexity Theory?

What is Complexity Theory? | Discovery of Marine Natural Products | Scoop.it

Chaos & Complexity are related; both are forms of “Coarse Damping”. While chaos is a form of coarse damping in “Time”, complexity on the other hand is a form of coarse damping in “Structure”!


Complexity arises from the ubiquitous “Collaborative Interplay of Entropy and Symmetry-Breaking” in all naturally damped-driven systems  –  Complexity is a form of coarse damping to uniformity!  A form of coarse symmetry! “Complexity is Coarse Entropy!”


Progressive Complexity arises from the ubiquitous “Competitive Interplay of Entropy and Coarse Entropy” in all naturally damped-driven systems  –  Evolution is a form of coarse damping to complexity! “Evolution is the Progressive Upheaval and Rejuvenation of Coarse Entropy!”


There are two fundamental forces at work in nature and all evolutionary systems; one is the entropic force of spontaneous decay and disorder (otherwise known as “The Second Law of Thermodynamics”); the other is a universal, and somewhat mysterious, capacity for self-organization and spontaneous emergence!


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Philippe Vallat's curator insight, May 12, 2015 11:31 AM

Excellent and clear article, describing many of the concepts of complexity theory. Must read!

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Secondary metabolites in plant innate immunity

Secondary metabolites in plant innate immunity | Discovery of Marine Natural Products | Scoop.it
Plant secondary metabolites carry out numerous functions in interactions between plants and a broad range of other organisms. Experimental evidence strongly supports the indispensable contribution of many constitutive and pathogen-inducible phytochemicals to plant innate immunity. Extensive studies on model plant species, particularly Arabidopsis thaliana, have brought significant advances in our understanding of the molecular mechanisms underpinning pathogen-triggered biosynthesis and activation of defensive secondary metabolites. However, despite the proven significance of secondary metabolites in plant response to pathogenic microorganisms, little is known about the precise mechanisms underlying their contribution to plant immunity. This insufficiency concerns information on the dynamics of cellular and subcellular localization of defensive phytochemicals during the encounters with microbial pathogens and precise knowledge on their mode of action. As many secondary metabolites are characterized by their in vitro antimicrobial activity, these compounds were commonly considered to function in plant defense as in planta antibiotics. Strikingly, recent experimental evidence suggests that at least some of these compounds alternatively may be involved in controlling several immune responses that are evolutionarily conserved in the plant kingdom, including callose deposition and programmed cell death.

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Molecular cartography of the human skin surface in 3D

Molecular cartography of the human skin surface in 3D | Discovery of Marine Natural Products | Scoop.it

The human skin is an organ with a surface area of 1.5–2 m2 that provides our interface with the environment. The molecular composition of this organ is derived from host cells, microbiota, and external molecules. The chemical makeup of the skin surface is largely undefined. Here we advance the technologies needed to explore the topographical distribution of skin molecules, using 3D mapping of mass spectrometry data and microbial 16S rRNA amplicon sequences. Our 3D maps reveal that the molecular composition of skin has diverse distributions and that the composition is defined not only by skin cells and microbes but also by our daily routines, including the application of hygiene products. The technological development of these maps lays a foundation for studying the spatial relationships of human skin with hygiene, the microbiota, and environment, with potential for developing predictive models of skin phenotypes tailored to individual health.


Amina Bouslimani, Carla Porto, Christopher M. Rath, Mingxun Wang, Yurong Guo, Antonio Gonzalez, Donna Berg-Lyon, Gail Ackermann, Gitte Julie Moeller Christensen, Teruaki Nakatsuji, Lingjuan Zhang, Andrew W. Borkowski, Michael J. Meehan, Kathleen Dorrestein, Richard L. Galla, Nuno Bandeira, Rob Knight, Theodore Alexandrova,j,k,l,2, and Pieter C. Dorrestein

PNAS

doi: 10.1073/pnas.1424409112


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Biogenetically-Inspired Total Synthesis of Epidithiodiketopiperazines and Related Alkaloids

Biogenetically-Inspired Total Synthesis of Epidithiodiketopiperazines and Related Alkaloids | Discovery of Marine Natural Products | Scoop.it

Natural products chemistry has historically been the prime arena for the discovery of new chemical transformations and the fountain of insights into key biological processes. It remains a fervent incubator of progress in the fields of chemistry and biology and an exchange mediating the flow of ideas between these allied fields of science. It is with this ethos that our group has taken an interest in and pursued the synthesis of a complex family of natural products termed the dimeric epipolythiodiketopiperazine (ETP) alkaloids. We present here an Account of the highly complex target molecules to which we pegged our ambitions, our systematic and relentless efforts toward those goals, the chemistry we developed in their pursuit, and the insight we have gained for their translational potential as potent anticancer molecules.


Justin Kim † and Mohammad Movassaghi Acc. Chem. Res., Article ASAPDOI: 10.1021/ar500454vPublication Date (Web): April 6, 2015



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Isolation and characterization of antagonistic endophytes from Dendrobium candidum Wall ex Lindl., and the biofertilizing potential of a novel Pseudomonas saponiphila strain

Isolation and characterization of antagonistic endophytes from Dendrobium candidum Wall ex Lindl., and the biofertilizing potential of a novel Pseudomonas saponiphila strain | Discovery of Marine Natural Products | Scoop.it
Many endophytic bacterial strains are now successfully used for plant-growth promotion (PGP) and as biocontrol agents (BCA) against plant diseases. This is a promising strategy for the improvement of crop productivity, thereby reducing the use of chemical pesticides and fertilizers. The objectives of this study were to isolate endophytic bacteria from the medicinal plant Dendrobium candidum Wall ex Lindl in China, and evaluate the biological control and PGP characteristics of these bacteria. Antagonistic tests were performed against fungal pathogens. Twenty-two of the 83 bacterial isolates showed antagonistic activities. These antagonistic isolates were screened in vitro for PGP traits, such as the production of indoleacetic acid (IAA), siderophores, proteases, and phosphate solubilization. Based on the tested PGP traits, strain YW was selected for further study. Strain YW was identified as Pseudomonas saponiphila based on its 16S rRNA and gyrB gene sequences. We detected the antifungal metabolite-encoding genes phlD, and hcnBC genes encoding 2,4-diacetylphloroglucinol (2,4-DAPG) and hydrogen cyanide (HCN) from strain YW. We measured the effect of strain YW on the growth of pepper seedlings under greenhouse conditions. Our results showed that its antifungal potential may be attributed to 2,4-DAPG and HCN antibiotics, as well as protease and siderophore production, and growth promotion may be related to the ability of isolate YW to synthesize IAA and solubilize phosphate. The PGP and antifungal activities of strain YW suggest that it may be exploited as a potential bioinoculant agent. This is the first report of a P. saponiphila strain with PGP attributes.

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The Biological Diversity and Production of Volatile Organic Compounds by Stem-Inhabiting Endophytic Fungi of Ecuador

The Biological Diversity and Production of Volatile Organic Compounds by Stem-Inhabiting Endophytic Fungi of Ecuador | Discovery of Marine Natural Products | Scoop.it
Fungal endophytes colonize every major lineage of land plants without causing apparent harm to their hosts. Despite their production of interesting and potentially novel compounds, endophytes—particularly those inhabiting stem tissues—are still a vastly underexplored component of microbial diversity. In this study, we explored the diversity of over 1500 fungal endophyte isolates collected from three Ecuadorian ecosystems: lowland tropical forest, cloud forest, and coastal dry forest. We sought to determine whether Ecuador’s fungal endophytes are hyperdiverse, and whether that biological diversity is reflected in the endophytes’ chemical diversity. To assess this chemical diversity, we analyzed a subset of isolates for their production of volatile organic compounds (VOCs), a representative class of natural products. This study yielded a total of 1526 fungal ITS sequences comprising some 315 operational taxonomic units (OTUs), resulting in a non-asymptotic OTU accumulation curve and characterized by a Fisher’s α of 120 and a Shannon Diversity score of 7.56. These figures suggest that the Ecuadorian endophytes are hyperdiverse. Furthermore, the 113 isolates screened for VOCs produced more than 140 unique compounds. These results present a mere snapshot of the remarkable biological and chemical diversity of stem-inhabiting endophytic fungi from a single neotropical country.

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Friends or foes? Emerging insights from fungal interactions with plants

Friends or foes? Emerging insights from fungal interactions with plants | Discovery of Marine Natural Products | Scoop.it

Fungi interact with plants in various ways, with each interaction giving rise to different alterations in both partners. While fungal pathogens have detrimental effects on plant physiology, mutualistic fungi augment host defence responses to pathogens and/or improve plant nutrient uptake. Tropic growth towards plant roots or stomata, mediated by chemical and topographical signals, has been described for several fungi, with evidence of species-specific signals and sensing mechanisms. Fungal partners secrete bioactive molecules such as small peptide effectors, enzymes and secondary metabolites which facilitate colonization and contribute to both symbiotic and pathogenic relationships. There has been tremendous advancement in fungal molecular biology, omics sciences and microscopy in recent years, opening up new possibilities for the identification of key molecular mechanisms in plant–fungal interactions, the power of which is often borne out in their combination. Our fragmentary knowledge on the interactions between plants and fungi must be made whole to understand the potential of fungi in preventing plant diseases, improving plant productivity and understanding ecosystem stability. Here, we review innovative methods and the associated new insights into plant–fungal interactions.


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Epigenetic stimulation of polyketide production in Chaetomium cancroideum by an NAD+-dependent HDAC inhibitor

Epigenetic stimulation of polyketide production in Chaetomium cancroideum by an NAD+-dependent HDAC inhibitor | Discovery of Marine Natural Products | Scoop.it
Exposure of the fungus Chaetomium cancroideum to an NAD+-dependent HDAC inhibitor, nicotinamide, enhanced the production of aromatic and branched aliphatic polyketides, which allowed us to isolate new secondary metabolites, chaetophenol G and cancrolides A and B. Their structures were determined using spectroscopic

 

Teigo Asai,*a   Shuntaro Morita,a   Tohru Taniguchi,b   Kenji Mondeb and   Yoshiteru Oshima*a  
 
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Org. Biomol. Chem., 2016, Advance Article


DOI: 10.1039/C5OB01595B


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Dimeric Octaketide Spiroketals from the Jellyfish-Derived Fungus Paecilomyces variotii J08NF-1

Dimeric Octaketide Spiroketals from the Jellyfish-Derived Fungus Paecilomyces variotii J08NF-1 | Discovery of Marine Natural Products | Scoop.it

Paeciloketals (1–3), new benzannulated spiroketal derivatives, were isolated from the marine fungus Paecilomyces variotii derived from the giant jellyfish Nemopilema nomurai. Compound 1 was present as a racemate and was resolved into enantiopure 1a and 1b by chiral-phase separation on a cellulose column. Compounds 2 and 3, possessing a novel benzannulated spiroketal skeleton, were rapidly interconvertible and yielded an equilibrium mixture on standing at room temperature. The relative and absolute configurations of compounds 2 and 3 were determined by NOESY analysis and ECD calculations. Compound 1 showed modest antibacterial activity against the marine pathogen Vibrio ichthyoenteri.

 

 

Haibo Wang†, Jongki Hong‡, Jun Yin§, Hyung Ryong Moon†, Yonghong Liu⊥, Xiaoyi Wei∥, Dong-Chan Oh∇, and Jee H. Jung
J. Nat. Prod., Article ASAP
DOI: 10.1021/acs.jnatprod.5b00594
Publication Date (Web): November 12, 2015

 


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Recognition of the role of Natural Products as drugs to treat neglected tropical diseases by the 2015 Nobel prize in physiology or medicine

Recognition of the role of Natural Products as drugs to treat neglected tropical diseases by the 2015 Nobel prize in physiology or medicine | Discovery of Marine Natural Products | Scoop.it
The 2015 Nobel Prize in Physiology or Medicine recognised the advances made in treating neglected tropical diseases, using drugs whose origins lie in natural products.

 

James H. McKerrowa  
 
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Nat. Prod. Rep., 2015, Advance Article


DOI: 10.1039/C5NP90043C


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NatProdChem's curator insight, November 4, 2015 9:03 AM

Also worth reading http://swarajyamag.com/culture/nobel-for-traditional-medicine-of-china-meanwhile-in-india/


were it is told about the story of Artemisinin and opinions regarding ayurgenomics in India ...

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Diversity and functions of volatile organic compounds produced by Streptomyces from a disease-suppressive soil

Diversity and functions of volatile organic compounds produced by Streptomyces from a disease-suppressive soil | Discovery of Marine Natural Products | Scoop.it
In disease-suppressive soils, plants are protected from infections by specific root pathogens due to the antagonistic activities of soil and rhizosphere microorganisms. For most disease-suppressive soils, however, the microorganisms and mechanisms involved in pathogen control are largely unknown. Our recent studies identified Actinobacteria as the most dynamic phylum in a soil suppressive to the fungal root pathogen Rhizoctonia solani. Here we isolated and characterized 300 isolates of rhizospheric Actinobacteria from the Rhizoctonia-suppressive soil. Streptomyces species were the most abundant, representing approximately 70% of the isolates. Streptomyces are renowned for the production of an exceptionally large number of secondary metabolites, including volatile organic compounds (VOCs). VOC profiling of 12 representative Streptomyces isolates by SPME-GC-MS allowed a more refined phylogenetic delineation of the Streptomyces isolates than the sequencing of 16S rRNA and the house-keeping genes atpD and recA only. VOCs of several Streptomyces isolates inhibited hyphal growth of R. solani and significantly enhanced plant shoot and root biomass. Coupling of Streptomyces VOC profiles with their effects on fungal growth, pointed to VOCs potentially involved in antifungal activity. Subsequent assays with five synthetic analogs of the identified VOCs showed that methyl 2-methylpentanoate, 1,3,5-trichloro-2-methoxy benzene and the VOCs mixture have antifungal activity. In conclusion, our results point to a potential role of VOC-producing Streptomyces in disease suppressive soils and show that VOC profiling of rhizospheric Streptomyces can be used as a complementary identification tool to construct strain-specific metabolic signatures.

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Direct Protocol for Ambient Mass Spectrometry Imaging on Agar Culture

Direct Protocol for Ambient Mass Spectrometry Imaging on Agar Culture | Discovery of Marine Natural Products | Scoop.it

Herein we describe a new protocol that allows direct mass spectrometry imaging (IMS) of agar cultures. A simple sample dehydration leads to a thin solid agar, which enables the direct use of spray-based ambient mass spectrometry techniques. To demonstrate its applicability, metal scavengers siderophores were imaged directly from agar culture of S. wadayamensis, and well resolved and intense images were obtained using both desorption electrospray ionization (DESI) and easy ambient sonic-spray ionization (EASI) with well-defined selective spatial distributions for the free and the metal-bound molecules, providing clues for their roles in cellular metabolism.


Célio Fernando F. Angolini †, Pedro Henrique Vendramini †, Francisca D. S. Araújo †, Welington L. Araújo ‡, Rodinei Augusti §, Marcos N. Eberlin †, and Luciana Gonzaga de OliveiraAnal. Chem., Article ASAPDOI: 10.1021/acs.analchem.5b01538  



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Lasso Peptides: An Intriguing Class of Bacterial Natural Products - Accounts of Chemical Research (ACS Publications)

Lasso Peptides: An Intriguing Class of Bacterial Natural Products - Accounts of Chemical Research (ACS Publications) | Discovery of Marine Natural Products | Scoop.it

«

Conspectus

Natural products of peptidic origin often represent a rich source of medically relevant compounds. The synthesis of such polypeptides in nature is either initiated by deciphering the genetic code on the ribosome during the translation process or driven by ribosome-independent processes. In the latter case, highly modified bioactive peptides are assembled by multimodular enzymes designated as nonribosomal peptide synthetases (NRPS) that act as a protein-template to generate chemically diverse peptides. On the other hand, the ribosome-dependent strategy, although relying strictly on the 20–22 proteinogenic amino acids, generates structural diversity by extensive post-translational-modification. This strategy seems to be highly distributed in all kingdoms of life. One example for this is the lasso peptides, which are an emerging class of ribosomally assembled and post-translationally modified peptides (RiPPs) from bacteria that were first described in 1991.

A wide range of interesting biological activities are known for these compounds, including antimicrobial, enzyme inhibitory, and receptor antagonistic activities. Since 2008, genome mining approaches allowed the targeted isolation and characterization of such molecules and helped to better understand this compound class and their biosynthesis. Their defining structural feature is a macrolactam ring that is threaded by the C-terminal tail and held in position by sterically demanding residues above and below the ring, resulting in a unique topology that is reminiscent of a lariat knot. The ring closure is achieved by an isopeptide bond formed between the N-terminal α-amino group of a glycine, alanine, serine, or cysteine and the carboxylic acid side chain of an aspartate or glutamate, which can be located at positions 7, 8, or 9 of the amino acid sequence.

In this Account, we discuss the newest findings about these compounds, their biosynthesis, and their physicochemical properties. This includes the suggested mechanism through which the precursor peptide is enzymatically processed into a mature lasso peptide and crucial residues for enzymatic recognition. Furthermore, we highlight new insights considering the protease and thermal stability of lasso peptides and discuss why seven amino acid residue rings are likely to be the lower limit feasible for this compound class. To elucidate their fascinating three-dimensional structures, NMR spectroscopy is commonly employed. Therefore, the general methodology to elucidate these structures by NMR will be discussed and pitfalls for these approaches are highlighted. In addition, new tools provided by recent investigations to assess and prove the lasso topology without a complete structure elucidation will be summarized. These include techniques like ion mobility–mass spectrometry and a combined approach of thermal and carboxypeptidase treatment with subsequent LC-MS analysis. Nevertheless, even though much was learned about these compounds in recent years, their true native function and the exact enzymatic mechanism of their maturation remain elusive. »


Julian D. Hegemann , Marcel Zimmermann , Xiulan Xie , and Mohamed A. Marahiel * Department of Chemistry, Biochemistry and LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein-Strasse 4, D-35032, Marburg, GermanyAcc. Chem. Res., Article ASAPDOI: 10.1021/acs.accounts.5b00156Publication Date (Web): June 16, 2015Copyright © 2015 American Chemical Society
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Rescooped by Yue Yang from Plant Biology Teaching Resources (Higher Education)
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Medicines from plants top trump game

Medicines from plants top trump game | Discovery of Marine Natural Products | Scoop.it

I love the "top trumps" format for teaching. Here's a set of trumps cards designed by Dr Sarah McLusky about medicine from plants, which you can find on the SAPS site. http://www.saps.org.uk/…/871-medicines-and-drugs-from-plant…. Generic instructions for Top Trumps are here http://www.toptrumps.com/how-to-play-top-trumps/
You can also have students design their own top trumps card games - the topic can be plant species, proteins, amino acids, pigments, pathogens, nutrients, etc.


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Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species

Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species | Discovery of Marine Natural Products | Scoop.it

Katherine R. Duncan1, 4, Max Crüsemann1, 4, Anna Lechner1, 4, Anindita Sarkar1, Jie Li1, Nadine Ziemert1, Mingxun Wang2, Nuno Bandeira2, Bradley S. Moore1, 3, , , Pieter C. Dorrestein3, , ,Paul R. Jensen

Genome sequencing has revealed that bacteria contain many more biosynthetic gene clusters than predicted based on the number of secondary metabolites discovered to date. While this biosynthetic reservoir has fostered interest in new tools for natural product discovery, there remains a gap between gene cluster detection and compound discovery. Here we apply molecular networking and the new concept of pattern-based genome mining to 35 Salinispora strains, including 30 for which draft genome sequences were either available or obtained for this study. The results provide a method to simultaneously compare large numbers of complex microbial extracts, which facilitated the identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. These efforts revealed considerable metabolite diversity and led to several molecular family-gene cluster pairings, of which the quinomycin-type depsipeptide retimycin A was characterized and linked to gene cluster NRPS40 using pattern-based bioinformatic approaches

doi:10.1016/j.chembiol.2015.03.010

 



 


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NatProdChem's curator insight, April 12, 2015 5:32 AM

Amazing job 

MB

Ally Evans's curator insight, March 30, 5:45 AM

Amazing job 

MB

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Large-Scale Metabolomics Reveals a Complex Response of Aspergillus nidulans to Epigenetic Perturbation

Large-Scale Metabolomics Reveals a Complex Response of Aspergillus nidulans to Epigenetic Perturbation | Discovery of Marine Natural Products | Scoop.it

The microbial world offers a rich source of bioactive compounds for those able to sift through it. Technologies capable of quantitatively detecting natural products while simultaneously identifying known compounds would expedite the search for new pharmaceutical leads. Prior efforts have targeted histone deacetylases in fungi to globally activate the production of new secondary metabolites, yet no study has directly assessed its effects with minimal bias at the metabolomic level. Using untargeted metabolomics, we monitored changes in >1000 small molecules secreted from the model fungus, Aspergillus nidulans, following genetic or chemical reductions in histone deacetylase activity (HDACi). Through quantitative, differential analyses, we found that nearly equal numbers of compounds were up- and down-regulated by >100 fold. We detected products from both known and unknown biosynthetic pathways and discovered that A. nidulans is capable of producing fellutamides, proteasome inhibitors whose expression was induced by ∼100 fold or greater upon HDACi. This work adds momentum to an “omics”-driven resurgence in natural products research, where direct detection replaces bioactivity as the primary screen for new pharmacophores.


Jessica C. Albright †, Matthew T. Henke ‡, Alexandra A. Soukup ∥, Ryan A. McClure †, Regan J. Thomson †, Nancy P. Keller ⊥#, and Neil L. Kelleher *†‡§†Department of Chemistry, ‡Department of Molecular Biosciences, §Feinberg School of Medicine,Northwestern University, Evanston, Illinois 60208, United States∥Department of Genetics, ⊥Department of Bacteriology, #Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United StatesACS Chem. Biol., Article ASAPDOI: 10.1021/acschembio.5b00025Publication Date (Web): March 27, 2015



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