• 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)
  • In this study, we elucidated the biosynthetic pathway encoded by , a hybrid polyketide synthase and nonribosomal peptide synthetase (PKS/NRPS) biosynthetic gene cluster (BGC), present in a number of globally distributed strains. (jcvi.org)
  • It was shown that strains in which either PKS or NRPS genes were identified produced a significantly higher number of metabolites and exhibited a larger number of unidentified, possibly new metabolites than other strains. (hs-flensburg.de)
  • Therefore, the presence of PKS and NRPS genes is a good indicator for the selection of strains to isolate new natural products. (hs-flensburg.de)
  • Several classes of structurally diverse secondary metabolites with a broad spectrum of bioactivities (e.g. antibacterial, insecticidal, antifungal) are known from different Xenorhabdus and Photorhabdus strains and are produced by nonribosomal peptide synthetases (NRPS) and the fatty acid synthase (FAS)-related polyketide synthases (PKS) or even hybrids thereof. (uni-frankfurt.de)
  • 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)
  • Cpr37, which belongs to the adenylation domain protein in the nonribosomal peptide synthase (NRPS), subsequently activates PABA and loads it to holo-Cpr36 Two proteins Cpr34 and Cpr35 work in concert to catalyze decarboxylative condensation between a thioester linked PABA and malonyl- S -acyl carrier protein (ACP) during aromatic polyketide biosynthesis catalyzed by type II polyketide synthases. (uky.edu)
  • Fabclavines are hybrid SMs derived from nonribosomal peptide synthetases (NRPS), polyunsaturated fatty acid (PUFA), and polyketide synthases (PKS). (beilstein-journals.org)
  • Enzymes of various catalytic functions in Streptomyces are useful as members of an artificial gene cluster constructed in Escherichia coli for fermentative production of plant-specific flavonoids, including isoflavones and unnatural compounds. (go.jp)
  • 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)
  • 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)
  • The clb gene cluster encodes the biosynthesis of metabolites known as precolibactins and colibactins. (omicsdi.org)
  • Certain commensal Escherichia coli contain the clb biosynthetic gene cluster that codes for small molecule prodrugs known as precolibactins. (omicsdi.org)
  • A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles. (mpg.de)
  • Cloning, sequencing and analysis of the enterocin biosynthesis gene cluster from the marine isolate 'Streptomyces maritimus': evidence for the derailment of an aromatic polyketide synthase. (mpg.de)
  • Natural metabolic diversity encoded by the enterocin biosynthesis gene cluster. (mpg.de)
  • 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)
  • The biosynthetic gene cluster of A-102395 was previously identified and includes 35 putative open reading frames responsible for biosynthesis and resistance. (uky.edu)
  • Cpr12, encoded by a gene that was originally proposed to be outside the gene cluster and sharing similarity to proteins annotated as ADC lyase, was revealed to catalyze the elimination of pyruvate to form PABA. (uky.edu)
  • Selected Xenorhabdus and Photorhabdus mutant strains were generated applying a chemically inducible promoter in front of the suggested fabclavine ( fcl ) biosynthesis gene cluster (BGC), followed by the analysis of the occurring fabclavines. (beilstein-journals.org)
  • There are several ways in which doxorubicin is believed to cause cardiomyopathy, including oxidative stress, downregulation of genes for contractile proteins, and p53-mediated apoptosis. (wikipedia.org)
  • The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. (nih.gov)
  • Genes that encode a variety of novel proteins were also identified. (nih.gov)
  • For this, it identifies and clusters co-localized genes encoding proteins of secretion systems using sequence similarity search with Hidden Markov Model (HMM) protein profiles. (bvsalud.org)
  • The 37-Mb genome was predicted to contain a total of 12,074 genes encoding proteins with a length greater than 100 amino acid residues (see Methods). (nature.com)
  • Downstream genes involved in type VII secretion systems, cell wall synthesis (polyketide biosynthesis proteins), and iron uptake were changed in response to the intracellular environment of macrophages. (biomedcentral.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)
  • Analysis of the genome revealed the presence of high numbers of secondary metabolic biosynthetic gene clusters. (scienceopen.com)
  • In recent years, genome mining methodologies have been widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. (scienceopen.com)
  • Furthermore, genome analysis of this strain suggested the presence of gene clusters involved in iron acquisition ( fhuABD , afuABC , fbpABC , and fepCDG ) and phosphate solubilization ( pstABCHS , phoABHLU , and phnCDEP ) and other phytohormone biosynthesis genes, including indole-3-acetic acid ( trpABCDEFG ), in the genome. (springeropen.com)
  • The biosynthesis gene clusters for grixazone and hexahydroxyperylenequinone are examples. (go.jp)
  • eSNaPD (environmental Surveyor of Natural Product Diversity) is a web-based bioinformatics and data aggregation platform that aids in the discovery of gene clusters encoding both novel natural products and new congeners of medicinally relevant natural products using (meta)genomic sequence data. (ecolowood.com)
  • 1990 Furthermore improvements in sequencing technologies and a corresponding increase in the number of newly sequenced genomes have shown that even extensively studied cultured bacteria contain an abundance of previously undetected cryptic biosynthetic gene clusters (Bentley et al. (ecolowood.com)
  • 2011 While much of the focus has been placed on accessing molecules from newly recognized biosynthetic gene clusters found in bacteria housed in culture selections culture-independent or metagenomic methods provide an alternate approach that can MK-3102 unlock access to a vast pool of biologically active small molecules encoded by environmental bacteria by bypassing the initial culturing step (Banik and Brady 2010 Brady 2007 Kampa et al. (ecolowood.com)
  • Small molecule discovery efforts from metagenomes however face a key challenge in the identification of biosynthetic gene clusters of interest from among a much larger pool of undesired DNA sequence. (ecolowood.com)
  • Repetitive use of highly conserved biosynthetic domains and the fact that a common ground metagenome may contain 104-105 unique bacterial species make it impractical to assemble large MK-3102 numbers of total biosynthetic gene clusters from metagenomic sequence data (Pop 2009 Rappé and Giovannoni 2003 MK-3102 Torsvik et al. (ecolowood.com)
  • 1990 Fortunately while the high degree of conservation seen in natural product biosynthetic genes makes the accurate assembly MK-3102 of metagenomic EDM1 gene clusters hard it also allows for a substantial amount of information pertaining to the biosynthetic pathways present in a metagenome to be gleaned through the use of a PCR-based sequence tag approach that targets these conserved genes (Udwary et al. (ecolowood.com)
  • 2010 We have exploited this correlation to develop a general method for functional classification of novel secondary metabolite biosynthetic gene clusters based solely around the minimal amount of sequence contained within a PCR amplicon (Owen et al. (ecolowood.com)
  • 2012 In this approach conserved biosynthetic domains are PCR amplified from (meta)genomic DNA and the individual next-generation sequencing reads derived from these amplicons termed natural product sequence tags or simply sequence tags are used to establish the relationship between gene clusters present within a pool of metagenomic DNA and a reference set of functionally characterized gene clusters (Figures 1 and ?and55). (ecolowood.com)
  • We were curious if detecting putative HGT events within fungi that are known to produce neuroactive metabolites would point us to novel biosynthetic gene clusters. (arcadiascience.com)
  • 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)
  • In addition, the presence of biosynthesis genes encoding polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) in 30 strains was established. (hs-flensburg.de)
  • As famílias de genes que codificam as enzimas PKSs (polyketides synthases) e halogenases flanqueadoras são consideradas de interesse biotecnológico pois são produzidas no metabolismo secundário de diversos organismos e são fundamentais para a síntese de compostos antimicrobianos e antitumor. (fiocruz.br)
  • The families of genes that encode enzymes PKSs (polyketides synthases) and flanking halogenases are considered of biotechnological interest because they are producedin the secondary metabolism of different organisms and are essential for the synthesis of antimicrobial compounds and antitumor. (fiocruz.br)
  • We have cloned and sequenced polyketide synthase (PKS) genes from the aclacinomycin producer Streptomyces galilaeus ATCC 31,615. (nih.gov)
  • Unprecedented diversity of catalytic domains in the first four modules of the putative pederin polyketide synthase. (mpg.de)
  • Nystatin biosynthesis and transport: nysH and nysG genes encoding a putative ABC transporter system in Streptomyces noursei ATCC 11455 are required for efficient conversion of 10-deoxynystatin to nystatin. (biosergen.net)
  • To overcome the host plant defense response, M. phaseolina encodes a significant number of P450s, MFS type membrane transporters, glycosidases, transposases, and secondary metabolites in comparison to all sequenced ascomycete species. (biomedcentral.com)
  • For the first time, a comprehensive investigation was performed with regard to phylogenetic strain identification, secondary metabolite profiling, bioactivity determination, and genetic exploration of biosynthetic genes, especially concerning the relationships of the abundance of biosynthesis gene fragments to the number and diversity of produced secondary metabolites. (hs-flensburg.de)
  • We set out to identify novel fungal genes involved in production of neuroactive metabolites that influence other organisms. (arcadiascience.com)
  • The blocks of A. oryzae -specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. (nature.com)
  • Our comprehensive analysis of the whole genome of F. equiseti provides basic data for studies of gene expression, regulatory and functional mechanisms, evolutionary processes, as well as disease prevention and control. (researchsquare.com)
  • The genome consisted of 3,007,472 bp with a GC content of 46.7% that was predicted to contain 2,818 genes, including 2,670 protein-coding genes. (kjom.org)
  • Here we show that the 37-megabase (Mb) genome of A. oryzae contains 12,074 genes and is expanded by 7-9 Mb in comparison with the genomes of Aspergillus nidulans 5 and Aspergillus fumigatus 6 . (nature.com)
  • Viral genome-encoded enzymes that facilitate the replication of RNA VIRUSES. (bvsalud.org)
  • The enzyme is capable of transferring the 4'-phosphopantetheine moiety of coenzyme A to a conserved serine residue in both the acyl carrier protein domain of the human cytosolic multifunctional fatty acid synthase and the acyl carrier protein associated independently with human mitochondria. (rhea-db.org)
  • In this scenario, hydride is predicted to be added to the re face to generate the S configuration resulting in the same stereochemical outcome as other 3-oxoacyl-ACP reductase (FabG) from bacterial type II fatty acid synthases.These findings are critical advancement for interrogating the biosynthesis of the unusual chemical components of the family of antibiotics of capuramycin. (uky.edu)
  • strain B2 with a G+C content of 70.1 % and 4,663 candidate protein-encoding genes. (scienceopen.com)
  • Acyltransferase Domain Exchange between Two Independent Type I Polyketide Synthases in the Same Producer Strain of Macrolide Antibiotics. (go.jp)
  • All strains were phylogenetically identified by 16S rRNA gene sequence analyses and were found to belong to the genera Actinoalloteichus, Micrococcus, Micromonospora, Nocardiopsis, and Streptomyces. (hs-flensburg.de)
  • molecular characterization of the niad and pyrg genes from penicillium camemberti, and their use as transformation markers. (liverpool.ac.uk)
  • The identification and functional characterization of 24 genes that are involved in iron homeostasis in A. fumigatus and/or Aspergillus nidulans , respectively, revealed significant insights into iron metabolism and its regulation (Table 1 ). (frontiersin.org)
  • Functional characterization of Cpr38, which has sequence similarity to the gene products encoded by pabA and pabB from E. coli , revealed that it functions as a 4-amino-4-deoxychorismate (ADC) synthase catalyzing a two-step reaction involving amidohydrolysis of L-Gln with ammonia channeled and incorporated into chorismic acid to generate ADC. (uky.edu)
  • Our research program targets the development of the next-generation natural compound production technology which leads the production of novel compounds by heterologous expression system applying on cryptic biosynthetic genes. (go.jp)
  • Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. (nih.gov)
  • 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)
  • Exploring the chemistry of uncultivated bacterial symbionts: Antitumor polyketides of the pederin family. (mpg.de)
  • Targeting modular polyketide synthases with iteratively acting acyltransferases from metagenomes of uncultured bacterial consortia. (mpg.de)
  • Antitumor polyketide biosynthesis by an uncultivated bacterial symbiont of the marine sponge Theonella swinhoei. (mpg.de)
  • As discovery of natural neuroactive molecules often relies on exploring specific systems that include both the source of the neuroactive molecules and the organism that experiences a behavior change (e.g. plants used to influence human behavior in traditional ceremonies), we aimed to identify a greater diversity of neuromodulators in a way that was not initially dependent on starting from known molecules or biosynthetic genes. (arcadiascience.com)
  • The invention furthermore relates to novel nucleic acid sequences which code for the Δ6-desaturases used in the method, gene constructs comprising these nucleic acid sequences, a vector and transgenic plants comprising at least one nucleic acid sequence or a gene construct. (rothamsted.ac.uk)
  • construction of a shuttle vector for heterologous expression of a novel fungal α-amylase gene in aspergillus oryzae. (liverpool.ac.uk)
  • We used a horizontal gene transfer detection pipeline to screen for novel fungal genes tied to neuroactivity. (arcadiascience.com)
  • The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. (nih.gov)
  • The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. (nih.gov)
  • In our previous sutdy, RNA-seq data has showed that the transcriptional level of many SM backbone genes could be upregulated by overexpressing LaeA. (elsevierpure.com)
  • The key steps in the A-factor regulatory cascade, including afsA , encoding the key enzyme for A-factor biosynthesis, arpA , encoding the A-factor receptor, and adpA , encoding a transcriptional activator, are elucidated. (go.jp)
  • The Mediator subunit OsMed15a is a transcriptional co-regulator of seed size/weight-modulating genes in rice. (nipgr.ac.in)
  • The target genes of the regulatory cascade include genes of various functions required for morphological development and secondary metabolite formation. (go.jp)
  • The assembly was characterized, including analyses of the genomic structure, with the aim of providing data to support the discovery of beneficial or harmful genes and to improve our understanding of the molecular pathogenesis. (researchsquare.com)
  • in this study, the nitrate reductase (niad) and orotidine-5'-monophosphate decarboxylase (pyrg) genes from penicillium camemberti were characterized, and their suitability as metabolic molecular markers for transformation was evaluated. (liverpool.ac.uk)
  • A detailed understanding of the molecular and cellular mechanisms underlying pigment cell specification in sea urchin embryos will first require isolation of the genes responsible for this developmental process. (silverchair.com)
  • Taken together, these results will aid in identifying the key genes associated with pollen fertility, which offered insights into the molecular mechanism underlying pollen development in tetraploid rice. (biomedcentral.com)
  • However, the molecular mechanism of these genes underlying pollen fertility process remained largely unknown in tetraploid rice. (biomedcentral.com)
  • In total, 13,134 functional genes were annotated, accounting for 94.97% of the total gene number. (researchsquare.com)
  • However, there are few in-depth studies on the functional genes. (researchsquare.com)
  • of which 101 genes were attributed to multiple functional descriptions. (kjom.org)
  • In addition to the minimal PKS, the cloned region included the PKS genes for polyketide ketoreductase (aknA), aromatase (aknE1) and oxygenase (aknX), as well as genes putatively encoding an aklanonic acid methyl transferase (aknG) and an aklanonic acid methyl ester cyclase (aknH) for post-polyketide steps were found. (nih.gov)
  • Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation. (nature.com)
  • The gedCΔ mutant was created by inserting the antibiotic marker hygromycin B (hyg) within the gedC gene that encodes emodin anthrone polyketide synthase (PKS), a primary gene responsible for initiating (+)-geodin biosynthesis. (upm.edu.my)
  • Oxidative conditions induced by H 2 O 2 increased water-soluble yellow pigment accumulation via up-regulation of the expression levels of relative genes and by increasing the precursors of pigment biosynthesis through redirection of metabolic flux. (biomedcentral.com)
  • A comparative genomic analysis supported the high quality of the F. equiseti assembly, exhibiting good collinearity with the reference strains, 3,483 species-specific genes, and 1,805 core genes. (researchsquare.com)
  • 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)
  • A gene family analysis revealed more than 2,500 single-copy orthologs. (researchsquare.com)
  • Gene expression analysis was carried out on a subset of 66 clones with real time quantitative PCR and 40 clones were positive. (silverchair.com)
  • RNA-seq analysis displayed a total of 5606 differentially expressed genes (DEGs) in ny1 compared to wild type (H1) during meiosis, of which 2977 were up-regulated and 2629 were down-regulated. (biomedcentral.com)
  • Transcriptome analysis can provide valuable insights into rice pollen development by detecting gene regulation. (biomedcentral.com)
  • Here the biofilm formation is not influenced by the competence system, despite gene expression analysis of the competence genes appears to be approximately the same in all models. (dub-signal.com)
  • MAP upregulates stress-responsive global gene regulators, such as two-component systems and sigma factors, in response to oxidative and cell wall stress. (biomedcentral.com)
  • Their organization as well as their protein sequences showed high similarity to those of other type II PKS genes. (nih.gov)
  • The former contains the enzymes for novel benzene ring formation and phenoxazinone formation, and the latter contains enzymes belonging to a type III polyketide synthase and a cytochrome P-450. (go.jp)
  • Engineering biodiversity with type II polyketide synthase genes. (mpg.de)
  • Inactivation of 10 of the 19 A. fumigatus genes caused defects in virulence. (frontiersin.org)
  • All of the virulence-associated genes are transcriptionally upregulated during iron starvation and encode functions that are important for survival during iron starvation, which emphasizes the crucial role of adaptation to iron starvation in virulence. (frontiersin.org)
  • Distribution and expression of the genes on chromosome 1. (nature.com)
  • When differentiated human THP-1 cells were infected with MAP, the expression of various genes associated with stress responses and metabolism was altered in both host and MAP at 3 h post-infection. (biomedcentral.com)
  • Notably, alterations in gene sets involved in arginine metabolism were observed in both the host and MAP, along with significant downregulation of NOS2 expression. (biomedcentral.com)
  • Evolution of genetic architecture and gene regulation in biphenyl/PCB-degrading bacteria. (go.jp)
  • The characteristics of genetic regulation in pollen development have been analyzed using reliable pollen development networks and novel pollen development-related genes. (biomedcentral.com)
  • The genetic study showed promising results in "silencing" the genes that translate into tau protein, the primary component behind dementia. (medicaldaily.com)
  • Dynamic cellular events beyond genetic encodings, such as epigenetics, and intermolecular protein interaction, play critical roles in dictating cellular functions. (go.jp)
  • New secondary mesenchyme specific genes, expressed exclusively in pigment cells, were isolated from sea urchin embryos using a differential screening of a macroarray cDNA library. (silverchair.com)
  • Using whole mount in situ hybridization, it was shown that these genes are specifically expressed in pigment cells. (silverchair.com)
  • The results suggest that S. purpuratus pks, fmo and sult could belong to a differentiation gene battery of pigment cells. (silverchair.com)
  • Our findings illustrate the widespread distribution of SM-encoding BGCs in the human microbiome and provide new insights into the causes of obesity. (hindawi.com)
  • The effects of emodin anthrone PKS gene disruption on (+)-geodin and lovastatin biosynthesis and the production of the precursors acetyl-CoA and malonyl-CoA were investigated with cultures based on glycerol alone and in combination with lactose. (upm.edu.my)
  • As a broad host range pathogen, M. phaseolina possesses a large number of pathogen-host interaction genes including those for adhesion, signal transduction, cell wall breakdown, purine biosynthesis, and potent mycotoxin patulin. (biomedcentral.com)