Download or read book Genome Mining and Marine Microbial Natural Products written by Kui Hong and published by MDPI. This book was released on 2020-01-07 with total page 202 pages. Available in PDF, EPUB and Kindle. Book excerpt: Two review papers, eight research articles, and one brief report were published in this Special Issue. They showed the rich resources that are present within the genomes of marine microorganisms and discussed the use of recently developed tools and technologies to exploit this genetic richness. Examples include the rational supply of precursors according to the relevant biosynthetic pathway and stress driven discovery together with the use of histone deacetylase inhibitors to facilitate the discovery of new bioactive molecules with potential biopharmaceutical applications. We believe that the content of this Special Issue reflects the current state-of-the-art research in this area and highlights the interesting strategies that are being employed to uncover increasing numbers of exciting novel compounds for drug discovery from marine genetic resources.
Download or read book Genome Mining and Marine Microbial Natural Products written by Alan Dobson and published by . This book was released on 2020 with total page 202 pages. Available in PDF, EPUB and Kindle. Book excerpt: Two review papers, eight research articles, and one brief report were published in this Special Issue. They showed the rich resources that are present within the genomes of marine microorganisms and discussed the use of recently developed tools and technologies to exploit this genetic richness. Examples include the rational supply of precursors according to the relevant biosynthetic pathway and stress driven discovery together with the use of histone deacetylase inhibitors to facilitate the discovery of new bioactive molecules with potential biopharmaceutical applications. We believe that the content of this Special Issue reflects the current state-of-the-art research in this area and highlights the interesting strategies that are being employed to uncover increasing numbers of exciting novel compounds for drug discovery from marine genetic resources.
Download or read book Genome Mining and Synthetic Biology in Marine Natural Products Discovery written by Maria Costantini and published by MDPI. This book was released on 2021-09-03 with total page 92 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, marine genomics has become a rapidly growing field, helped by the large amount of information that is becoming available to the international scientific community. Taking into account the current excitement in the field of marine biotechnology, this Special Issue entitled “Genome Mining and Synthetic Biology in Marine Natural Product Discovery” aims to to assess the impact of these molecular approaches on the discovery of bioactive compounds from marine organisms. The term “genome mining” is used to identify all bioinformatic investigations aimed at detecting the biosynthetic pathways of bioactive natural products and their possible functional and chemical interactions. Several studies are now reporting on marine organisms. Oceans cover nearly 70% of the Earth’s surface and host a huge ecological, chemical, and biological diversity. The natural conditions of the sea favor, in marine organisms, the production of a large variety of novel molecules with great pharmaceutical potential. Marine organisms are unique in their structural and functional features compared to terrestrial ones. Innovation in this field is very rapid, as revealed by the funding of several Seventh Framework Programme (FP7) and Horizon 2020 projects under the topic “Blue Growth”, with the urgent goal of discovering new drugs.
Download or read book Natural Product Genomics and Metabolomics of Marine Bacteria written by and published by . This book was released on 2022-02-24 with total page 244 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Genome Mining and Synthetic Biology in Marine Natural Products Discovery written by Maria Costantini and published by . This book was released on 2021 with total page 92 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, marine genomics has become a growning rapidly field, helped by the large amount of information that is becoming available to the international scientific community. Taking into account the current excitement in the field of marine biotechnology, this Special Issue entitled “Genome Mining and Synthetic Biology in Marine Natural Product Discovery” aims to to assess the impact of these molecular approaches on the discovery of bioactive compounds from marine organisms. The term “genome mining” is used to identify all bioinformatic investigations aimed at detecting the biosynthetic pathways of bioactive natural products and their possible functional and chemical interactions. Several studies are now reporting on marine organisms. Oceans cover nearly 70% of the Earth's surface and host a huge ecological, chemical, and biological diversity. The natural conditions of the sea favor, in marine organisms, the production of a large variety of novel molecules with great pharmaceutical potential. Marine organisms are unique in their structural and functional features compared to terrestrial ones. Innovation in this field is very rapid, as revealed by the funding of several Seventh Framework Programme (FP7) and Horizon 2020 projects under the topic “Blue Growth”, with the urgent goal of discovering new drugs.
Download or read book From Molecules to Genes and Back Again written by Michelle Antoinette Schorn and published by . This book was released on 2018 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nature has created elegant and efficient ways of assembling a wide variety of diverse chemical scaffolds. Microbes are prolific producers of these secondary metabolites, which can have profound bioactivities and be harnessed for use in medicine. Within their genomes, microbes possess the blueprints for making natural products, and recent advances in high-throughput DNA sequencing have revealed a much larger repertoire of specialized chemistry than what can be observed in the lab. This bacterial 'dark matter' has the potential to contain the instructions for making countless new chemical scaffolds and represents an untapped source for drug discovery. Connecting secondary metabolite compounds with their biosynthetic gene clusters can inform novel biosynthetic transformations, provide a renewable source of promising bioactive compounds, and inspire synthetic biology approaches to assembling new molecules. Chapter 2 of this dissertation connects two pharmaceutically relevant natural products with their corresponding biosynthetic gene clusters. The epoxyketone proteasome inhibitors epoxomicin and eponemycin are naturally produced by actinomycete bacteria, and whole genome sequencing revealed their genetic underpinnings and native resistance mechanism. This work represents the first elucidation of biosynthetic gene clusters for epoxyketone proteasome inhibitors. Chapter 3 takes a wider lens to examine an understudied group of bacteria: the rare marine actinomycetes. Whole genome sequencing of a group of rare marine actinomycetes revealed an incredible wealth of biosynthetic potential and diversity not yet represented in current sequencing databases. This study establishes rare marine actinomycetes as a group worthy of further exploration for genome mining and drug discovery. Chapter 4 investigates a more complex system with a focus on uncultivatable cyanobacterial sponge symbionts. Previous work showed that the genomes of these symbionts contained the genes necessary to produce environmentally relevant poly-brominated diphenyl ethers (PBDEs). In assembling high quality draft genomes of two symbionts of distinct sponges, their full secondary metabolite potential was revealed. Additionally, genome mining led to the identification of two novel dysinosin molecules, representing the first example of mining for gene clusters in a metagenome assembled genome leading to new chemistry.
Download or read book Marine Biotechnology in the Twenty First Century written by National Research Council and published by National Academies Press. This book was released on 2002-05-29 with total page 130 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dramatic developments in understanding the fundamental underpinnings of life have provided exciting opportunities to make marine bioproducts an important part of the U.S. economy. Several marine based pharmaceuticals are under active commercial development, ecosystem health is high on the public's list of concerns, and aquaculture is providing an ever greater proportion of the seafood on our tables. Nevertheless, marine biotechnology has not yet caught the public's, or investor's, attention. Two workshops, held in October 1999 and November 2001 at the National Academies, were successful in highlighting new developments and opportunities in environmental and biomedical applications of marine biotechnology, and also in identifying factors that are impeding commercial exploitation of these products. This report includes a synthesis of the 2001 sessions addressing drug discovery and development, applications of genomics and proteomics to marine biotechnology, biomaterials and bioengineering, and public policy and essays contributed by the workshop speakers.
Download or read book Mass Spectrometry guided Genome Mining of Peptidic and Glycosylated Microbial Natural Products written by Roland David Kersten and published by . This book was released on 2013 with total page 233 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientific progress in organic synthesis, biochemistry and biology and cures to many infectious diseases and cancer rely on discovery of microbial natural products and their biosynthetic pathways. `Omics' approaches such as genome mining have opened new opportunities for natural product discovery within the last decade as ~90% of pathways in microbial genomes are uncharacterized in their products. Genome mining for natural product discovery can be defined as the connection of a natural product (chemotype) with its biosynthetic genes (genotype) by applied biosynthetic knowledge. Traditional genome mining approaches are in silico-guided approaches in which the isolation of a new natural product is guided by bioinformatic predictions from a target cryptic gene cluster. The problem of in silico-guided genome mining in natural product discovery is its low-throughput rate as only one pathway is characterized per experiment. In this dissertation, mass spectrometry (MS)-guided genome mining approaches are introduced which rapidly connect a natural product with its biosynthetic genes by matching de novo tandem MS structures of biosynthetic building blocks such as amino acids and sugars to metabolite structures predicted from microbial genomes. As MS guided genome mining starts at the chemotype level by e.g. liquid chromatography-tandem mass spectrometry analysis of a microbial extract and subsequently connects putative natural products with their gene clusters, it has the potential for automation. In Chapter 2, peptidogenomics is introduced as a MS-guided genome mining approach for characterization of ribosomal and nonribosomal peptide chemotypes and their corresponding genotypes. Peptidogenomics characterized ten new peptide chemo- and genotypes from Streptomyces cultures including lanthipeptides, lassopeptides, linaridins and lipopeptides. In Chapter 3, a combination of imaging mass spectrometry, tandem MS and genome mining characterized the biosynthetic pathway of the didemnin anti-cancer agents in the marine alpha-proteobacterium Tistrella mobilis. In Chapter 4, glycogenomics is introduced as a MS-guided genome mining approach to connect chemo- and genotypes of glycosylated natural products. Glycogenomics enabled the discovery of putative arenimycin B, a glycosylated aromatic polyketide from the marine actinobacterium Salinispora arenicola and its biosynthetic pathway. In Chapter 5, bioactivity-guided genome mining combined with genetic knockouts and glycogenomics characterized the biosynthetic gene cluster of the lomaiviticins anti cancer agents in the marine actinobacterium Salinispora tropica.
Download or read book Natural Products from Marine Microorganisms written by Xian-Wen Yang and published by Frontiers Media SA. This book was released on 2020-01-22 with total page 142 pages. Available in PDF, EPUB and Kindle. Book excerpt: Natural products continue to serve as sources for the development of new medicines. There is currently a revival of interest in the discovery of bioactive compounds with new chemical structures from natural sources, largely due to the fact that synthetic libraries have not yielded the expected number of developmental candidates in the pharmaceutical industry during the last decade. In addition, the emergence of clinically relevant pathogens that are becoming increasingly resistant to currently used medicines strengthens the notion that natural product research is urgently required. Considering the fact that almost 10% of bioactive compounds are of microbial origin, and that marine microorganisms are relatively poorly studied compared to their terrestrial relatives, marine microorganisms are regarded as the most potential-laden resource for drug discovery.
Download or read book Drug Discovery from Natural Products written by Olga Genilloud and published by Royal Society of Chemistry. This book was released on 2012-08-21 with total page 435 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book offers an integrated review of the most recent trends in natural products drug discovery and key lead candidates that are outstanding for their chemistry and biology as a starting point in novel drug development. The authors focus on different trends that are and will continue to be impacting multiples stages of modern drug discovery from NPs that have not been included in other works. This is complemented with a series of case studies from leading experts from industry and academia on key molecules and derivatives that have been chosen for their novelty in chemistry, biology and clinical applications. The book intends to reflect the current confluence of different disciplines in chemical biology and synthetic chemistry supported by a more profound knowledge of systems biology that ensures the concurrency and synergisms of expertise from different research fields that impact in the discovery of novel molecules. In the first section the chapters reflect recent approaches to exploit the biosynthetic potential of microbial resources (including genome mining, metagenomic and epigenetic approaches), as well as biosynthetic chemistry tools to respond to product supply and novel screening alternatives that have lead to the discovery of novel chemistry. The second part reviews, in the form of case studies, some examples of bioactive molecules in the important therapeutic areas of antiinfectives, oncology and antiparasitics.
Download or read book Marine Microorganisms written by Leo M.L. Nollet and published by CRC Press. This book was released on 2016-09-19 with total page 130 pages. Available in PDF, EPUB and Kindle. Book excerpt: The marine environment covers 70% of the earth’s surface and accounts for 98% of the potentially habitable space. The bioactives from marine microorganisms include antibiotic compounds, polysaccharides, inhibitors, enzymes, peptides, and pigments. These are used in various fields of biology that range from nutraceuticals to cosmeceuticals. Recent scientific investigations have revealed that marine microbial compounds exhibit various beneficial biological effects, such as anti-inflammatory, anti-cancer, anti-HIV, anti-hypertensive, and anti-diabetic. Marine Microorganisms: Extraction and Analysis of Bioactive Compounds sheds light on the extraction, clean-up, and detection methods of major compounds from marine organisms. The book includes information on the different classes of marine microorganisms and the different bioactives that can be extracted from bacteria, fungi and microalgae. Divided into 7 chapters, the book covers bioactive marine natural products, such as marine microbes, seaweeds, and marine sponges as potential sources of drug discovery, and focuses on analysis methods of the biocomponents from marine microorganisms. A useful reference tool for researchers and students, this book provides current knowledge about isolation and analysis methods of the bioactives and provides insight into the various bioactives of marine microbes toward nutraceutical and pharmaceutical development.
Download or read book Genome Mining of Marine Bacteria for Bioactive Metabolites written by Jamshid Amiri Moghaddam and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Chemical Biology of Natural Products written by David J. Newman and published by CRC Press. This book was released on 2017-09-22 with total page 650 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical Biology of Natural Products This unique, long-awaited volume is designed to address contemporary aspects of natural product chemistry and its influence on biological systems, not solely on human interactions. The subjects covered include discovery, isolation and characterization, biosynthesis, biosynthetic engineering, pharmaceutical, and other applications of these compounds. Each chapter begins with a brief and simple introduction to the subject matter, and then proceeds to guide the reader towards the more contemporary, cutting-edge research in the field, with the contributing authors presenting current examples from their own work in order to exemplify key themes. Topics covered in the text include genome mining, heterologous expression, natural product synthesis, biosynthesis, glycosylation, chemical ecology, and therapeutic applications of natural products, both current and potential.
Download or read book Comparative Genomics and Genome Mining Insights Into Natural Product Rich Marine Cyanobacteria written by Tiago Ferreira Leao and published by . This book was released on 2019 with total page 114 pages. Available in PDF, EPUB and Kindle. Book excerpt: Numerous advantages of systematic genomics have been leveraged in other areas, such as transcriptomics, proteomics and human microbiome studies, but it has yet to be effective in stimulating the increased discovery of natural products (secondary metabolites). Since the discovery of the first microbial genome (2002), the surprisingly high percentage of cryptic biosynthetic pathways per genome (genes not connected to any known secondary metabolite, aka natural product) has continued as a consistent theme. Cyanobacteria from benthic environments are prolific producers of natural products but genomes from these organisms remain scarce in public repositories. Hence, this dissertation focused on sequencing and performing genomic analysis in prolific cyanobacteria collected from several tropical benthic ecosystems around the planet. First, we analyzed the relationship between a cyanobacterium host and its associated heterotrophic microbiome. By evaluation the non-axenic culture of Moorea producens JHB, we characterized a novel uncultured acidobacteria heterotroph living with the cyanobacterial host. This heterotroph was only 85% similar to the closest cultured representative, it presented a large number of genes encoding for transcriptional regulators and it was auxotrophic for several proteogenic amino acids. Next, we expanded our genome comparison by deeper analyzing 4 Moorea genomes. Our genome comparison revealed that Moorea, already a prolific producer of secondary metabolites, harbored an even richer metabolic potential, four times above the cyanobacterial average. We observed that Moorea conserved its primary metabolism while evolved an intricate secondary metabolism machinery, accounting for 20% of their genomic content. These findings were very promising for future genome mining efforts in those four strains. Thereby, we further expanded our sequencing efforts by sampling 165 metagenomes of filamentous marine cyanobacteria collected from around the globe. Our new metagenomic pipeline was able to generated 85 high-quality genomes, including 32 Moorea and 29 Okeania strains. Our genome comparison highlighted that these two genera are among the most diverse and prolific producers of natural products in our dataset (comparing pairwise 506 cyanobacterial genomes, 425 from the NCBI database). Gene networking revealed the abundance of unique (only encountered in a single strain) and "extended families" (found in several strains). Using genomes with paired mass spectrometry data, we correlated the distribution of gene families with the distribution of metabolic families and automatically annotated a new dehydromicrosclerodermin B homologue.
Download or read book Genome Mining and Metabolomics Approach Towards the Discovery of Marine Natural Products written by Kevin Jace Miranda and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Bioactive Compounds from Extremophiles written by Lesley-Ann Giddings and published by Springer. This book was released on 2015-01-07 with total page 63 pages. Available in PDF, EPUB and Kindle. Book excerpt: This SpringerBrief sheds new light on bioactive materials from extremophiles with the focus on the biosynthesis processes and related genomics. It deals with all aspects of the chemical compounds produced by organisms living under extreme conditions that may have potential as drugs or lead to novel drugs for human use.
Download or read book Natural Products from Actinomycetes written by Ravishankar V. Rai and published by Springer Nature. This book was released on 2022-04-15 with total page 512 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides in-depth information about the ecology, diversity and applications of Actinomycetes. The book is divided into two major parts. The first part discusses the diversity, chemical biology and ecology of Actinomycetes. It also covers the discovery of natural products from soil, endophytic and marine-derived Actinomycetes. It includes natural product discovery, chemical biology, new methods for discovering secondary metabolites, structure elucidation and biosynthetic research of natural products. The chapters in this part focus on the effects of biological and chemical elicitation at molecular level on secondary metabolism in Actinomycetes. The second part of the book discusses genomic and synthetic biology approaches in Actinomycetes drug discovery. This part includes chapters focused on the application of metabolic engineering to optimize natural product synthesis and the use of omics data in engineering of regulatory genes. It covers the advanced tools of synthetic biology and metabolic engineering including cluster assembly, CRISPR/Cas9 technologies, and chassis strain development for natural product overproduction in Actinomycetes. It describes the use of bioinformatics tools for reprogramming of biosynthetic pathways through polyketide synthase and non-ribosomal peptide synthetase engineering. These advanced genomic and molecular tools are expected to accelerate the discovery and development of new natural products from Actinomycetes with medicinal and other industrial applications. The book is useful to researchers and students in the field of microbiology, pharmaceutical sciences and drug discovery.
