• Streptomyces bacteria produce numerous specialized metabolites with industrial and medicinal applications, and they contain many associated biosynthetic gene clusters (BGCs). (mdpi.com)
  • We identified several SM-encoding biosynthetic gene clusters (BGCs) from the metagenomic data of lean and obese individuals and found significant association between some BGCs, including those that produce hitherto unknown SM, and obesity. (hindawi.com)
  • The biosynthesis of SMs is controlled by enzymes encoded by biosynthetic gene clusters (BGCs). (hindawi.com)
  • Most microbial BGCs that have been identified so far contain genes encoding core biosynthetic enzymes such as polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS). (hindawi.com)
  • CLiPs are nonribosomally synthesized by modular mega-enzymes so-called NonRibosomal Peptide Synthetases (NRPSs) that are encoded by large biosynthetic gene clusters (BGCs) spanning over dozens of kb in the genomes. (fems-microbiology.org)
  • Subsequent trait-based analyses revealed numerous biosynthetic gene clusters (BGCs) overrepresented in the endophytic bacterial families of plants under pathogen attack, including BGCs involved in signal transduction, extracellular enzyme and secondary metabolite production. (apsnet.org)
  • BGCs are well known in the bacterial world but their role in plants is not fully understood. (sciencedaily.com)
  • Using genome mining, we have discovered a pair of lasso peptide biosynthetic gene clusters (BGCs) that include cytochrome P450 genes. (rsc.org)
  • In addition, the involved biosynthetic gene clusters (BGCs) will be recombined to produce novel natural products. (mpg.de)
  • A new study researchers at the Swiss Federal Institute of Technology Zurich (ETH Zurich) in collaboration with experts from the Institut de Ciències del Mar (ICM-CSIC), published in the prestigious journal Nature has revealed the existence of a new family of marine bacteria whose genetic capacity, through the immense number of biosynthetic gene clusters in their genomes (BGCs), could lead to numerous biotechnological applications. (cbinsights.com)
  • A primary purpose of the UCSF study was to identify the biosynthetic gene clusters (BGCs) that contain the genetic blueprints for creating such molecules. (drugdiscoverynews.com)
  • When they used this algorithm to systematically analyze genes in the human microbiome, they identified 3,000 BGCs at different body sites. (drugdiscoverynews.com)
  • The advent of next generation DNA-sequencing has revealed a vastly rich pool of NP biosynthetic gene clusters (BGCs) among bacterial genomes, most of which with no corresponding NP. (up.pt)
  • Mining this resource revealed ∼40,000 putative biosynthetic gene clusters (BGCs), many from unknown phylogenetic groups. (uibk.ac.at)
  • In silico analysis of NL19 genome sequence revealed the presence of 17 biosynthetic gene clusters (BGCs) for different classes of BNPs, including nonribosomal peptide (NRPs), polyketides (PKs), ribosomally synthesized and posttranslationally modified peptides (RiPPs), siderophores, terpenes and several hybrid NRPs-PKs. (ua.pt)
  • describes BGDM Docker - a tool specifically designed to evaluate bacterial pan-genomes. (peerj.com)
  • Binning of the metagenomic sequences allowed de novo assembly of mulitple high quality genomes of different endophytic bacterial genera. (apsnet.org)
  • But once whole bacterial genomes were sequenced, we realized that we have only discovered a small fraction of the natural products coded in the genome. (genengnews.com)
  • This knowledge meant the scientists could focus on searching for certain types of gene clusters in samples rather than having to sequence and analyse the whole genomes of bacteria. (eurekalert.org)
  • A prerequisite for this work are high-quality genomes of the bacterial producers: Only they allow manipulations to the required extent. (mpg.de)
  • The work of the team in LOEWE-TBG includes the identification and structural characterization of the natural products, the manipulation of the bacterial genomes using synthetic biology methods, mass spectrometry, biochemistry, and molecular microbiology. (mpg.de)
  • Omnitrophota genomes in 6 classes are reduced, but maintain major biosynthetic and energy conservation pathways, including acetogenesis (with or without the Wood-Ljungdahl pathway) and diverse respirations. (bigelow.org)
  • At least 64% of Omnitrophota genomes encode gene clusters typical of bacterial symbionts, suggesting host-associated lifestyles. (bigelow.org)
  • In the microbial genomes we reconstructed from DNA extracted from ancient tooth tartar, we found a gene cluster that was shared by a high proportion of Neanderthals and anatomically modern humans living during the Middle and Upper Paleolithic that lasted from 300,000 to 12,000 years ago. (nflbulletin.com)
  • Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. (uibk.ac.at)
  • These can include the secondary biosynthetic pathways that have been identified from any genome sequence. (wikipedia.org)
  • Takano is developing robotic systems to explore the potential biosynthetic pathways, testing thousands of new compounds every year. (wikipedia.org)
  • Koreenceine-type pathways are widely distributed among Pseudomonas species, and koreenceine C was detected in another Pseudomonas species from a distantly related cluster. (nih.gov)
  • A BGC is a group of genes located close together in the genome that are involved in the same metabolic pathways. (sciencedaily.com)
  • The BGC cluster of the beautyberry plant contains genes that encode two distinct terpenoid pathways. (sciencedaily.com)
  • This study shows the natural occurrence of serratiochelins, photobactin, enterobactin, and aerobactin in a single bacterial species and illuminates the interplay between siderophore biosynthetic pathways and polyamine production, indicating routes of molecular diversification. (biomedcentral.com)
  • This work develops a general synthetic biology pipeline to systematically "animate" orphan biosynthetic pathways across kingdoms. (yale.edu)
  • BGDM Docker integrates a software for genome annotation (Prokka), a software for pan-genome analysis and classification (PanX) and a software dedicated to identify clusters of biosynthetic genes, along with the metabolites that can be produced from such clusters (anti-SMASH). (peerj.com)
  • Metabolites were isolated based on biological activity and were characterized using tandem mass spectrometry, multidimensional nuclear magnetic resonance, and Mosher ester analysis, leading to the discovery of a new family of bacterial tetrahydropyridine alkaloids, koreenceine A to D (metabolites 1 to 4). (nih.gov)
  • Of late there is a strong trend in the opposite direction ("from gene to secondary metabolites"), especially strengthened by the recent technological breakthroughs in genome sequencing and bioinformatics. (drexel.edu)
  • Gas chromatography MS is ideal for screening engineered bacterial strains for small metabolites like terpenes, fatty acids or small polyketides. (drexel.edu)
  • The clb gene cluster encodes the biosynthesis of metabolites known as precolibactins and colibactins. (omicsdi.org)
  • This cleavage pathway forms other known clb metabolites or biosynthetic intermediates and explains the difficulties in isolating fully mature biosynthetic products. (omicsdi.org)
  • At least five genes were shown to be essential for the synthesis of AHBA, five genes were determined to encode the modular type I PKS that uses AHBA as the starter unit, and 20 or more genes appear to govern modification of the polyketide-derived framework, and rifamycin resistance and export. (nih.gov)
  • Disruption of the PKS genes at the end of rifA abolished rifamycin B production and resulted in the formation of P8/1-OG, a known shunt product of rifamycin biosynthesis, whereas disruption of the orf6 and orf9 genes, which may encode deoxysugar biosynthesis enzymes, had no apparent effect. (nih.gov)
  • Here we combine sequence-based metagenomic mining with a motif search of bioinformatically predicted natural product structures to identify six biosynthetic gene clusters that we predicted encode MK-binding antibiotics (MBAs). (nature.com)
  • In this condition genes that encode putative efflux pumps as well as ferrous iron capture system, were significantly upregulated, which suggests redirection of cellular metabolism. (ua.pt)
  • Putative regulatory genes were also identified. (nih.gov)
  • Among several EPS-defective mutants, we identified a mutant, SL341P4, with a Tn5-insertion in a gene encoding a putative NDP-sugar epimerase, a putative membrane protein with sugar-modifying moiety, in a reverse orientation to EPS biosynthesis gene cluster. (ppjonline.org)
  • These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. (uibk.ac.at)
  • To mine for undiscovered genomic treasure, the researchers first used computational tools to identify silent biosynthetic gene clusters-small groups of genes involved in making chemical products. (genengnews.com)
  • By sequencing and studying genomic variation across the tree of life, researchers hope to better understand the origin and functional adaptations of diversity from genes to ecosystems (comparative genomics). (mpg.de)
  • Their excision and integration at tRNA genes appear to drive the remodeling of genomic islands\textemdashkey reservoirs for flexible genes in bacteria. (bigelow.org)
  • We have tremendous experience with plant, animal, yeast and bacterial genomic BAC libraries. (biost.com)
  • There is great need for therapeutics against multi-drug resistant, Gram-negative bacterial pathogens. (sdsc.edu)
  • The UCSF study, which was published in Cell in September, found that lactocillan serves to kill common vaginal bacterial pathogens while sparing other bacteria known to dwell harmlessly in the vagina. (drugdiscoverynews.com)
  • The bacterial pathogens within the RSSC produce exopolysaccharide (EPS), a highly complicated nitrogen-containing heteropolymeric polysaccharide, as a major virulence factor. (ppjonline.org)
  • The colibactin peptidase ClbP deacylates synthetic precolibactin 886 to form a non-genotoxic pyridone, which suggests precolibactin 886 lies off the path of the major biosynthetic route. (omicsdi.org)
  • To reach this goal, a heterologous production strategy will be used to generate few generic chassis bacterial strains belonging to key genera, allowing the production of a broad range of structurally diverse CLiPs. (fems-microbiology.org)
  • Specifically, Dr. Zhao and colleagues, including colleagues from Singapore's Agency for Science, Technology, and Research, have been using a CRISPR/Cas9 knock-in strategy to activate silent biosynthetic gene clusters (BCGs) in bacteria. (genengnews.com)
  • Essentially, the scientists turned on unexpressed, or "silent," gene clusters in a common class of bacteria that naturally produce many compounds already used as antibiotics, anticancer agents, and other drugs. (genengnews.com)
  • In addition to being part of a very diverse bacterial group from a biosynthetic point of view, these bacteria are ubiquitously and abundantly distributed throughout the ocean water column," explains Shinichi Sunagawa, professor at ETH Zürich and head of the team that led the study. (cbinsights.com)
  • Here we report the 2.1 Å X-ray structure and molecular function of ClbS, a gene product that confers resistance to colibactin toxicity in host bacteria and which has been shown to be important for bacterial viability. (omicsdi.org)
  • This cluster bore the molecular hallmarks of very ancient DNA and belonged to the bacterial genus Chlorobium , a group of green sulfur bacteria capable of photosynthesis. (nflbulletin.com)
  • To identify genes in EPS production beyond the EPS biosynthetic gene operon, we selected the EPS-defective mutants of R. pseudosolanacearum strain SL341 from Tn5-inserted mutant pool. (ppjonline.org)
  • Details of this work appeared April 10 in the journal Nature Chemical Biology, in an article entitled, "CRISPR-Cas9 Strategy for Activation of Silent Streptomyces Biosynthetic Gene Clusters. (genengnews.com)
  • In the past, it was very difficult to turn on or off a specific gene in Streptomyces species. (genengnews.com)
  • As a demonstration, the researchers isolated and determined the structure of one of the novel compounds produced from a silent biosynthetic gene cluster and found that it has a fundamentally different structure from other Streptomyces -derived drugs-a potential diamond in the rough. (genengnews.com)
  • The aborycin biosynthetic gene cluster gul from marine sponge-associated Streptomyces sp. (bvsalud.org)
  • The biosynthetic gene cluster (BGC) for oviedomycin is primarily found in Streptomyces antibioticus. (bvsalud.org)
  • Several recent studies point to an even broader range of activity for MAIT cells including: the control of bacterial, fungal and viral infections, a role in autoimmune disease and possible involvement in the immune processes involved in attacking the proliferation of tumor cells. (joessciencescorner.net)
  • However, for every cultured bacterial species, there are 100 uncultivated species in the environment. (eurekalert.org)
  • Ralstonia solanacearum species complex (RSSC) is a soil borne plant pathogen causing bacterial wilt on various important crops, including Solanaceae plants. (ppjonline.org)
  • The phylogenetic analysis of the 16S rRNA, gyrB and Internal Transcribed Spacer (ITS) gene sequences identified this strain as belonging to the genus Pedobacter, and having P. himalayensis, P. cryoconitis, P. westerhofensis and P. hartonius as closely related species. (ua.pt)
  • Further polyphasic analysis showed that the strain is a new bacterial species, and which was named Pedobacter lusitanus NL19. (ua.pt)
  • Comparative analysis of the koreenceine cluster with the γ-coniceine pathway revealed distinct polyketide synthase routes to the defining tetrahydropyridine scaffold, suggesting convergent evolution. (nih.gov)
  • However, the biosynthetic pathway of the EPS in the RSSC has not been fully characterized. (ppjonline.org)
  • In E . coli , the biosynthetic pathway for the production of glycine betaine from choline has been well characterized at the genetic level ( Landfald and Strom, 1986 ). (scialert.net)
  • Most of the structural and functional diversity relies on CLiPs produced by 3 main bacterial genera Bacillus, Pseudomonas and Burkholderia. (fems-microbiology.org)
  • Astonishingly, homologues of the membrane-bound and D-asparagine-specific peptidase (XcnG) and the encoding NRPS for the starting module (XcnA) for the acylated D-asparagine residue were identified in many different bacterial genera. (uni-frankfurt.de)
  • Horizontal gene transfer accelerates microbial evolution. (bigelow.org)
  • Only in recent years, thanks to several ocean circumnavigation campaigns and the use of new molecular methods, we have begun to know what organisms, what genes, and what biotechnological potential is hidden under the skin of the ocean", exposes the ICM-CSIC researcher Josep M Gasol, who has participated in the study. (cbinsights.com)
  • SAN FRANCISCO-One of the most common bacterial organisms found in the vagina has helped scientists at the University of California, San Francisco (USCF) reveal the extent to which the human microbe could serve as a rich source for antibiotic compounds. (drugdiscoverynews.com)
  • Yet capturing this diversity, assigning functions to host organisms and exploring the biosynthetic potential in natural environments remains challenging. (uibk.ac.at)
  • Covering: up to 2017This review covers the biosynthetic and evolutionary aspects of lincosamide antibiotics, antitumour pyrrolobenzodiazepines (PBDs) and the quorum-sensing molecule hormaomycin. (shengsci.com)
  • Because of the diverse functions bacterial natural products have, many have been used as medical treatments such as antibiotics and anti-cancer drugs. (nflbulletin.com)
  • The inappropriate use of these antibiotics has led to an increase in bacterial resistance, which is a problem of worldwide concern, warning for the urgent need for new effective alternatives. (ua.pt)
  • Although its basic precursors (3-amino-5-hydroxy benzoic acid AHBA, and acetic and propionic acids) had been established, and several biosynthetic intermediates had been identified, very little was known about the origin of AHBA nor had the PKS and the various genes and enzymes that modify the initial intermediate been characterized. (nih.gov)
  • This process allowed us to identify not only what genes were present, but also their order in the genome and the ways they differ from bacterial genes known today - key information to uncovering their evolutionary history and function. (nflbulletin.com)
  • Originally discovered from members of the nematode symbiotic genus Photorhabdus, the biosynthetic gene cluster (BGC) encoding for the synthesis of darobactin A can also be found in other γ-proteobacterial families. (sdsc.edu)
  • Here, we report a novel family of DNA transposons\textemdash"tycheposons"\textemdashsome of which are viral satellites while others carry cargo, such as nutrient-acquisition genes, which shape the genetic variability in this globally abundant genus. (bigelow.org)
  • We report that Serratia plymuthica V4 produces a variety of siderophores, which we term the siderome , and which are assembled by the concerted action of enzymes encoded in two independent gene clusters. (biomedcentral.com)
  • The enzymes encoded by one of the gene clusters can independently assemble enterobactin. (biomedcentral.com)
  • We demonstrate that not only the presence of pathogen inherent molecular patterns induces immune responses, but that bacterial motility is linked to a host-cell-induced expression of additional immune modulators. (elifesciences.org)
  • The opportunistic pathogen may infect virtually any tissue and has evolved as a model to study bacterial adaptation to the conditions within the human host. (elifesciences.org)
  • The bacterial foodborne pathogen Listeria monocytogenes clonal 41 complex 1 (Lm-CC1) is the most prevalent clonal group associated with listeriosis, and is 42 strongly associated with cattle and dairy products. (cdc.gov)
  • Scientists have made significant progress toward mapping the bacterial ecosystems found in the gut, skin, nasal passages, mouth, vagina and other parts of the human body through research funded by the NIH's Human Microbiome Project . (drugdiscoverynews.com)
  • Candidate bacterial phylum Omnitrophota has not been isolated and is poorly understood. (bigelow.org)
  • Among these groups, we identified a lineage rich in biosynthetic gene clusters ('Candidatus Eudoremicrobiaceae') that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. (uibk.ac.at)
  • We confirmed host phylogeny using the sequencing method and analyzed the influence of host phylogeny and bioclimatic zone parameters on the rodent gut microbiome using high-throughput amplicon sequencing of 16S rRNA gene fragments. (microbial-ecology.net)
  • A genetic screen in P. koreensis identified a previously uncharacterized biosynthetic gene cluster responsible for the inhibitory activity. (nih.gov)
  • Joshua Herbeck: Are HIV genetic clusters enriched with transmitters? (birs.ca)
  • Such genes are difficult to detect and reconstruct from ancient DNA because very old genetic material breaks down over time, fragmenting into thousands or even millions of pieces. (nflbulletin.com)
  • Rifamycin production in A. mediterranei is governed by a single gene cluster consisting of structural, resistance and export, and regulatory genes. (nih.gov)
  • They have devised complex regulatory mechanisms responding to Fe 2+ unavailability that induce the expression of a series of genes to produce small iron chelators, termed siderophores [ 5 , 6 , 7 ], secrete them, and take up their iron-bound forms. (biomedcentral.com)
  • The paper 'Global Biogeography of Bacterial Secondary Metabolism' can be freely accessed online at http://dx.doi.org/10.7554/eLife.05048 . (eurekalert.org)
  • Traditionally, natural products, a key resource from secondary metabolism, have been studied at a chemical level before the gene clusters or enzymes responsible for their biosynthesis were known. (drexel.edu)
  • BAC libraries are essential elements in doing large-scale genome research such as screening for genes of target, biosynthetic gene cluster cloning, transgene identification, gene/gene cluster functional analyses, physical mapping and genome sequencing. (biost.com)
  • Researchers created a machine-learning algorithm that enabled a computer to identify known genes that produce small molecules with potential as drugs. (drugdiscoverynews.com)
  • Bacterial siderophores are small molecules with unmatched capacity to scavenge iron from proteins and the extracellular milieu, where it mostly occurs as insoluble Fe 3+ . (biomedcentral.com)
  • During this work, xenocoumacin 1 (XCN 1) and 2 (XCN 2), the major antimicrobial compounds produced by Xenorhabdus nematophila and their corresponding biosynthetic gene cluster were identified and studied in detail. (uni-frankfurt.de)
  • Certain commensal Escherichia coli contain the clb biosynthetic gene cluster that codes for small molecule prodrugs known as precolibactins. (omicsdi.org)
  • In this study, choline dehydrogenase ( betA ) gene encoding for glycine betaine biosynthesis in Escherichia coli isolated from salted shark ( Scoliodon sp. (scialert.net)
  • Scientists have previously identified clusters of bacterial genes that are particularly good at producing therapeutics. (eurekalert.org)
  • Based on the historical success of natural products as therapeutics, biosynthetic dark matter is likely to hold enormous potential for biomedicine," says Dr Brady. (eurekalert.org)
  • It spans the period from the first applications and subsequent development of modern stable-isotope labelling methods, the isolation, sequencing and expression of PKS genes, biochemical and structural charac. (shengsci.com)
  • We repurposed quantitative stable-isotope probing data from soils dominated by andesite, basalt or granite weathering and identified 3 families with high isotope uptake consistent with obligate bacterial predators. (bigelow.org)
  • NP structures inspire chemists to develop new syntheses, and NP biosynthetic enzymes add to the metabolic engineer's toolbox. (up.pt)
  • The scientists were also able to identify hotspots for 'biosynthetic dark matter' - gene clusters new to science. (eurekalert.org)
  • Also, NL19´ RNA-seq transcriptome data in high and low PC concentrations, allowed us to identify 261 differentially expressed genes (DEGs). (ua.pt)
  • Five different prexenocoumacins are formed by the xenocoumacin biosynthetic machinery as inactive prodrugs inside the cytoplasm. (uni-frankfurt.de)
  • 5) Characterize the structure of bacterial diversity through metataxonomic analysis (metabarcoding). (fapesp.br)
  • Furthermore, XCN 1 is secreted by an ABC transporter TolC-like protein complex and is thought to be involved in killing microbes living inside the insect gut or other bacterial food competitors during the infection cycle and the nematode development. (uni-frankfurt.de)
  • These findings suggest that mutant M22-2C43 can produce NA4/NA6 as a degradation product due to functional inactivation of the dagB gene through a point mutation (G474A), ultimately preventing further degradation of NA4/NA6 to NA2. (bvsalud.org)
  • Directly targeting menaquinone (MK), which plays an important role in bacterial electron transport, is an appealing, yet underexplored, mode of action due to a dearth of MK-binding molecules. (nature.com)
  • Our data indicate that normal and inflamed skin harbor distinct phageomes and suggest a causative relationship between changing viral and bacterial communities as a driver of skin pathology. (microbial-ecology.net)
  • But Dr. Zhao's team reports that they have now uncovered even more potential treasure formerly hidden in silent genes. (genengnews.com)
  • The study of the "biosynthetic" content of these soils shows their potential for drug discovery. (eurekalert.org)
  • The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. (uibk.ac.at)
  • For example, in a hot spring sample from New Mexico, they found clusters similar to those that produce epoxamicin. (eurekalert.org)
  • In samples from Brazil, they found genes that may be able to make new versions of bleomycin, an anticancer agent listed on the World Health Organisation's list of essential medicines. (eurekalert.org)
  • clb+ E. coli induce megalocytosis and DNA double-strand breaks in eukaryotic cells, but paradoxically, this gene cluster is found in the probiotic Nissle 1917. (omicsdi.org)
  • In general, at high concentrations of PC, in addition to the genes involved in pedopeptins biosynthesis, genes involved in the de novo biosynthesis of biotin were also found to be significantly downregulated. (ua.pt)
  • Then they used CRISPR technology to insert a strong promoter sequence before each gene that they wanted to activate, prompting the cell to make the natural products that the genes clusters coded for. (genengnews.com)
  • Numerous pharmaceutical drugs are derivatives of bacterial natural products. (mpg.de)
  • Precolibactins and colibactins represent a family of natural products that are encoded by the clb gene cluster and are produced by certain commensal, extraintestinal, and probiotic E. coli. (omicsdi.org)
  • The cellular machinery producing bacterial natural products is encoded in genes that are typically in close proximity to one another, forming what are called biosynthetic gene clusters . (nflbulletin.com)
  • Additionally, the SL341P4 mutant exhibited reduced disease severity and incidence of bacterial wilt in tomato plants compared to the wild-type SL341 without alteration of bacterial multiplication. (ppjonline.org)
  • We inserted a synthetic version of this gene cluster into a "modern" bacterium called Pseudomona protegens so it could produce the chemical compounds encoded in the ancient genes. (nflbulletin.com)
  • The reactive organosulfur compounds form disulfide bonds with free sulfhydryl groups of enzymes and compromise the integrity of the bacterial membrane. (frontiersin.org)