Choose an application

• Reference Manager
• EndNote
• RefWorks (Direct export to RefWorks)

Understanding how microorganisms adapt their specialized metabolism in response to environmental signals is a major theme in modern microbiology. This knowledge is crucial to discover new molecules associated with the plethora of crypPc "Biosynthetic Gene Clusters" (BGCs), many of them being transcriptionally silent or low expressed under laboratory conditions. Our strategy to activate the expression of BGCs is "to learn from the biology of the producing microorganism itself ” by identifying the genetic information responsible for the expression of these BGCs and connecting it to environmental signals. For this purpose, our lab is developing the COMMBAT (COndiPons for Microbial Metabolite Biosynthesis Activated TranscripPon) bioinformatic tool which aims at predicting the environmental signals and their associated transcription factors (TF) that control BGC expression. For optimal utilization of this tool, we must in parallel fill the knowledge gap on the signal perceived and transported by specialized metabolite-producing bacteria. The first objective of my Master thesis was to use and test the COMMBAT tool to highlight novel signaling pathways from environmental elicitors to specialized metabolite production. Using the TF/elicitor couple DasR/N-acetylglucosamine (GlcNAc) as test example, we identified a series of BGCs that could possibly have their expression induced by the uptake of GlcNAc. We started to experimentally validate these predictions, by growing the selected strains on media under ON/OFF culture conditions (with and without the inducer: GlcNAc) and visualizing the repercussion on the production level of the metabolites by MALDI Imaging Mass Spectrometry (IMS). The GlcNAc-dependent production of cephamycin C by S. clavuligerus is the most significant new pathway discovered in this work. The second objective of my Master thesis was to contribute to the identification of the carbon source(s) transported by specialized metabolite-producing bacteria. The strategy to identify the carbon source associated with a predicted sugar transporter combined i) in silico analysis of genes of the transcription unit (TU) containing the genes for sugar transport, ii) finding the allosteric effector modulating the DNA-binding activity of the purified TF controlling the TU, and iii) a proteomic analysis of the expression of proteins of the TU in presence of the predicted carbon source. Our approach allowed to identify the genes/proteins required for ribose utilization in Streptomyces species while the identification of genes/proteins for rhamnose utilization still requires further investigation. Overall, the COMMBAT tool seems promising at unveiling novel pathways for the activation of specialized metabolites. The strategy for discovering the signal molecules transported by metabolite-producing bacteria as partially convincing, depending on the level of complexity of the TU investigated.

Biological Dark matter --- Cryptic biosynthetic gene clusters --- Novel bioactive compound discovery --- Sciences du vivant > Biochimie, biophysique & biologie moléculaire

Choose an application

• Reference Manager
• EndNote
• RefWorks (Direct export to RefWorks)

After the long history of screening, it is becoming difficult to find novel compounds from microorganisms and plants anywhere in the world. Until now, more than about 30,000 marine natural products have been reported. However, with the development of marine natural products research, the hit rate of new compounds is also decreasing. Scientists are now turning their attention to the deep sea, where a high hit rate of novel compounds is expected. Many small compounds and peptides from microorganisms and sponges are with therapeutic activity are shown in this book. This Special Issue Book, “Natural Products from the Deep Sea”, should be useful for the screening of novel and useful compounds from nature.

Medicine --- deep sea marine-derived fungus --- Myrothecium sp. --- myrothecol --- nitric oxide (NO) --- antioxidant activity --- macrolactam --- Deep-Sea-Derived Streptomyces --- abiotic formation --- natural product --- antifungal activity --- Thorectandra choanoides --- tryptophan alkaloid --- indoleamine 2,3-dioxygenase --- aplysinopsins --- GNPS molecular network --- cellular signal transduction --- bioactive metabolite --- deep-sea organisms --- anti-inflammatory agent --- anticancer agent --- Mariana Trench --- Micromonospora provocatoris MT25 --- desferrioxamine --- n-acetylglutaminyl glutamine amide --- 1H-15N 2D-NMR --- genomics --- biosynthetic gene clusters --- stress genes --- crustins --- antibacterial peptides --- hydrothermal vent --- anti-Gram-negative bacteria --- Al-crus 3 and Al-crus 7 --- Trichoderma --- harziane diterpenes --- NO inhibition --- thioester-containing benzoate --- deep-sea-derived fungus --- α-glucosidase inhibitory activity --- docking study

Choose an application

• Reference Manager
• EndNote
• RefWorks (Direct export to RefWorks)

Marine organisms are a treasure trove for the discovery of novel natural products, and, thus, marine natural products have been a focus of interest for researchers for decades. Some marine bacteria are prolific producers of natural products, occurring either free-living or, as recently shown, in symbiosis with marine animals. Recent advances in DNA sequencing have led to an enormous increase in published bacterial genomes and bioinformatics tools to analyze natural product biosynthetic potential by various “genome mining” approaches. Similarly, analytical NMR and MS methods for the characterization and comparison of metabolomes of natural product producers have advanced. Novel interdisciplinary approaches combine genomics and metabolomics data for accelerated and targeted natural product discovery. This Special Issue invites articles from both genomics- and metabolomics-driven studies on marine bacteria with a focus on natural product discovery and characterization. We particularly welcome articles that combine genomics and metabolomic approaches for the dereplication and characterization of marine bacterial natural products.

Moorena bouillonii --- marine natural products --- chemogeography --- metabolomics --- natural products --- dereplication --- antibiotics --- marine sponges --- plant pathogen --- cyclodepsipeptides --- marine Actinobacteria --- Streptomyces spp. --- antibiotic --- sea cucumber --- HCV --- Actinobacteria --- marine --- Polar --- genomics --- specialised metabolites --- chitin --- chitinase --- chitin degradation machinery --- Pseudoalteromonas --- secondary metabolites --- bacterial natural products --- mass spectrometry --- genome mining --- paired omics --- keratinases --- keratinolytic proteases --- marine-derived Streptomyces --- genomic comparison --- cyanobacteria --- symbionts --- comparative genomics --- biosynthetic gene clusters --- Indonesia --- biodiversity --- novel antibiotics --- drug screening --- bioactivity --- gene cluster networking --- GNPS --- enterococci --- genome-wide analysis --- bacteriocins --- probiotics --- wild marine species --- Neolyngbya --- anticancer --- drug discovery --- South China Sea --- wenchangamide --- Moorea producens --- CuSO4·5H2O assisted --- differential gDNA isolation --- filamentous bacteria --- micrococcin P1 and P2 --- stalked diatoms

Choose an application

• Reference Manager
• EndNote
• RefWorks (Direct export to RefWorks)

In the past few decades, awareness of the basic role that endophytic fungi play in shaping the fitness of both wild and crop plants has increased significantly. The number of papers on the subject is so large that it is becoming difficult to have a complete overview of the state-of-the-art with reference to specific crops. In the absence of readily available documents providing circumstantial information on the endophytic assemblage of plants, the isolation of a certain fungal species may appear to be occasional or trivial; hence, many important findings are at risk of going unnoticed. This Special Issue aims to present a collection of papers dealing with the occurrence and functions of endophytic fungi in crop species. It may represent a useful tool for stakeholders in this particular research field, with a view to stimulating a more thorough consideration of the opportunities deriving from their discoveries.

endophytic fungi --- Fusarium --- species complexes --- mycotoxins --- fusaric acid --- trichothecenes --- biosynthetic gene clusters --- Citrus spp. --- endophytes --- antagonism --- defensive mutualism --- plant growth promotion --- bioactive compounds --- entomopathogens --- crop protection --- integrated pest management --- Cordycipitaceae --- Alternaria --- Illumina MiSeq --- secondary raw materials --- compositae --- fungi --- herbs --- secondary metabolites --- symbiosis --- mutualism --- plant fitness --- latent pathogens --- Botryosphaeria rhodina --- Botryodiplodia theobromae --- onions --- amaryllis --- endosphere --- endobiome --- metabolome --- sage --- bioprospecting --- medicinal plants --- Lamiaceae --- biocontrol --- biostimulants --- induced systemic resistance --- ISR --- plant pathogens --- fungal entomopathogens --- Acacia --- Albizia --- Bauhinia --- Berberis --- Caesalpinia --- Cassia --- Cornus --- Hamamelis --- Jasminus --- Ligustrum --- Lonicera --- Nerium --- Robinia --- EFSA --- high-risk plants --- n/a

Choose an application

• Reference Manager
• EndNote
• RefWorks (Direct export to RefWorks)

In the past few decades, awareness of the basic role that endophytic fungi play in shaping the fitness of both wild and crop plants has increased significantly. The number of papers on the subject is so large that it is becoming difficult to have a complete overview of the state-of-the-art with reference to specific crops. In the absence of readily available documents providing circumstantial information on the endophytic assemblage of plants, the isolation of a certain fungal species may appear to be occasional or trivial; hence, many important findings are at risk of going unnoticed. This Special Issue aims to present a collection of papers dealing with the occurrence and functions of endophytic fungi in crop species. It may represent a useful tool for stakeholders in this particular research field, with a view to stimulating a more thorough consideration of the opportunities deriving from their discoveries.

Research & information: general --- endophytic fungi --- Fusarium --- species complexes --- mycotoxins --- fusaric acid --- trichothecenes --- biosynthetic gene clusters --- Citrus spp. --- endophytes --- antagonism --- defensive mutualism --- plant growth promotion --- bioactive compounds --- entomopathogens --- crop protection --- integrated pest management --- Cordycipitaceae --- Alternaria --- Illumina MiSeq --- secondary raw materials --- compositae --- fungi --- herbs --- secondary metabolites --- symbiosis --- mutualism --- plant fitness --- latent pathogens --- Botryosphaeria rhodina --- Botryodiplodia theobromae --- onions --- amaryllis --- endosphere --- endobiome --- metabolome --- sage --- bioprospecting --- medicinal plants --- Lamiaceae --- biocontrol --- biostimulants --- induced systemic resistance --- ISR --- plant pathogens --- fungal entomopathogens --- Acacia --- Albizia --- Bauhinia --- Berberis --- Caesalpinia --- Cassia --- Cornus --- Hamamelis --- Jasminus --- Ligustrum --- Lonicera --- Nerium --- Robinia --- EFSA --- high-risk plants --- endophytic fungi --- Fusarium --- species complexes --- mycotoxins --- fusaric acid --- trichothecenes --- biosynthetic gene clusters --- Citrus spp. --- endophytes --- antagonism --- defensive mutualism --- plant growth promotion --- bioactive compounds --- entomopathogens --- crop protection --- integrated pest management --- Cordycipitaceae --- Alternaria --- Illumina MiSeq --- secondary raw materials --- compositae --- fungi --- herbs --- secondary metabolites --- symbiosis --- mutualism --- plant fitness --- latent pathogens --- Botryosphaeria rhodina --- Botryodiplodia theobromae --- onions --- amaryllis --- endosphere --- endobiome --- metabolome --- sage --- bioprospecting --- medicinal plants --- Lamiaceae --- biocontrol --- biostimulants --- induced systemic resistance --- ISR --- plant pathogens --- fungal entomopathogens --- Acacia --- Albizia --- Bauhinia --- Berberis --- Caesalpinia --- Cassia --- Cornus --- Hamamelis --- Jasminus --- Ligustrum --- Lonicera --- Nerium --- Robinia --- EFSA --- high-risk plants