Clades 4 and 5 contain sequences from protists that are both photosynthetic (algae) and non-photosynthetic. Like clade 3, clade 4 contains iterative type I PKSs with cis-AT domains. It is interesting to note that iterative PKSs from chlorophytes in clade 4 are distant from noniterative PKSs from the same algal phylum (clade 9). Similarly, photosynthetic heterokonts contribute to separate clades: While clade 4 includes iterative PKSs from Nannochloropsis oceanica, clade 8 contains sequences from A. anophagefferens that phylogenetically resemble noniterative PKSs from the haptophyte E. huxleyi, including Aan-sKS5 that is encoded on scaffold 46 (annotated as free-standing KS). This finding further supports the idea that A. anophagefferens contains several type I PKSs. Similar to the clear separation of iterative and noniterative PKSs from algae observed here, iterative and noniterative PKSs from bacteria and fungi also form separate clades [31].. PKSs from the dinoflagellate S. minutum are found in ...

18635006] Characterization of the azinomycin B biosynthetic gene cluster revealing a different iterative type I polyketide synthase for naphthoate biosynthesis. (Chem Biol. , 2008 ...

15797213] The neocarzinostatin biosynthetic gene cluster from Streptomyces carzinostaticus ATCC 15944 involving two iterative type I polyketide synthases. (Chem Biol. , 2005 ...

4JAR: Crystal structure of mycobacterium tuberculosis pks11 in complex with polyketide intermediates and evidence that it synthesize ALKYLPYRONES

Polyketides are a class of natural products that exhibit remarkable structural and functionally diversity and are highly sought after due to their medicinally important activities. For many decades now, polyketide synthases (PKSs), the mega-enzymes responsible for biosynthesis of polyketides have been the focus of extensive investigation to make new polyketides by polyketide engineering strategies. While there are many established methods to investigate polyketide enzymes and biosynthesis mechanisms, they have substantial shortcomings that have limited the extent of success with polyketide engineering efforts. This thesis focuses on developing simple, flexible yet powerful tools for examining polyketide biosynthesis by overcoming some deficiencies in currently used techniques. Reactive heterocylces have been designed for direct labeling of key polyketide synthase enzymes to provide a direct insight into its functions and mechanisms. First β-lactones and then β-lactams have been used as small molecule

Modular polyketide synthases (PKSs) are giant bacterial enzymes that synthesize many polyketides of therapeutic value. In contrast to PKSs that provide acyltransferase (AT) activities in cis, trans-AT PKSs lack integrated AT domains and exhibit unusual enzymatic features with poorly understood functions in polyketide assembly. This has retarded insight into the assembly of products such as mupirocin, leinamycin and bryostatin 1. We show that trans-AT PKSs evolved in a fundamentally different fashion from cis-AT systems, through horizontal recruitment and assembly of substrate-specific ketosynthase (KS) domains. The insights obtained from analysis of these KS mosaics will facilitate both the discovery of novel polyketides by genome mining, as we demonstrate for the thailandamides of Burkholderia thailandensis, and the extraction of chemical information from short trans-AT PCR products, as we show using metagenomic DNA of marine sponges. Our data also suggest new strategies for dissecting ...

A cis-acting enoyl reductase (ER) catalytic domain was isolated from a fungal highly reducing iterative polyketide synthase (HR-iPKS) for the first time and studied in vitro. The ER from the squalestatin tetraketide synthase forms a discrete dimeric protein in solution. The ER shows broad substrate selectivi

Combinatorial biosynthesis aspires to exploit the incorporation of different microbial anabolic pathways to engineer the synthesis of new chemical entities. The modular enzymes composed by functionally independent domains, e.g., polyketide synthases (PKS), are suitable test case for the modularization of secondary metabolic pathways into build-couple-pair synthetic schemes. Fungal benzenediol lactones (BDLs) polyketides provide an opportunity for combinatorial biosynthesis. Fungal BDLs are important pharmacophores with wide-ranging bioactivities, and their biosynthesis involves a pair of collaborating iterative polyketide synthases (iPKSs): A highly reducing iPKS (hrPKS) with product that is further elaborated by a non-reducing iPKS (nrPKS) to yield a 1,3-benzenediol moiety bridged by a macrolactone. Co-expressing random heterocombinations of hrPKSs and nrPKSs from different BDL biosynthetic pathways in Saccharomyces cerevisiae lead to the one-pot, one-step combinatorial biosynthesis of ...

Fungal highly reducing polyketide synthases (HRPKSs) are an enigmatic group of multidomain enzymes that catalyze the biosynthesis of structurally diverse compounds. This variety stems from their intrinsic programming rules, which permutate the use of tailoring domains and determine the overall number of iterative cycles. From genome sequencing and mining of the producing strain Eupenicillium brefeldianum ATCC 58665, we identified an HRPKS involved in the biosynthesis of an important protein transport-inhibitor Brefeldin A (BFA), followed by reconstitution of its activity in Saccharomyces cerevisiae and in vitro. Bref-PKS demonstrated an NADPH-dependent reductive tailoring specificity that led to the synthesis of four different octaketide products with varying degrees of reduction. Furthermore, contrary to what is expected from the structure of BFA, Bref-PKS is found to be a nonaketide synthase in the absence of an associated thiohydrolase Bref-TH. Such chain-length control by the partner ...

The minimal domains of a pks module are an acyltransferase at, ketosynthase ks and acyl carrier protein acp domain, where the at domain loads a coenzyme a-activated dicarboxylic acid extender unit onto the acp domain and the ks domain of the preceding domain catalyzes condensation of the nascent polyketide with the extender unit. So, according to this dictionary, the core difference in the two terms is that adamant applies centrally to resistance to being moved physically or figuratively, while tenacious applies centrally to resistance to being separated from something physically or figuratively. The unions are pressing for a three-year guarantee of job security and an eight percent across-the-board wage hike. The following assertions prove that the mock has come into effect. But 60s and older seniors online dating website truly free just before, rohit murdered and hid vikram and gul hassans daughter. No baggy clothes are permitted in ballet, in cold weather a light blue crossover can be bloch- ...

Polyketide natural products from filamentous fungi are highly diverse in both chemical structures and bioactivities, and they include the current top-selling dr...

The diversity of actinomycetes associated with marine sponges collected off Fsar Reef (Saudi Arabia) was investigated in the present study. Forty-seven actinomycetes were cultivated and phylogenetically identified based on 16S rRNA gene sequencing and were assigned to 10 different actinomycete genera. Eight putatively novel species belonging to genera Kocuria, Mycobacterium, Nocardia, and Rhodococcus were identified based on sequence similarity values below 98.2% to other 16S rRNA gene sequences available in the NCBI database. PCR-based screening for biosynthetic genes including type I and type II polyketide synthases (PKS-I, PKS-II) as well as nonribosomal peptide synthetases (NRPS) showed that 20 actinomycete isolates encoded each at least one type of biosynthetic gene. The organic extracts of nine isolates displayed bioactivity against at least one of the test pathogens, which were Gram-positive and Gram-negative bacteria, fungi, human parasites, as well as in a West Nile Virus protease enzymatic

Shop Probable polyketide biosynthesis zinc-dependent hydrolase ELISA Kit, Recombinant Protein and Probable polyketide biosynthesis zinc-dependent hydrolase Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.

A vast array of plant secondary metabolites are synthesized through the acetate-malonate pathway, where acetate units provided by malonyl-CoA are concatenated into a polyketide intermediate which may fold in a number of ways to produce, e.g., new aromatic ring systems. The best known example of these reactions is the formation of chalcone, the first precursor of the flavonoid branch of phenylpropanoids. Chalcone synthase together with other plant polyketide synthases form a super family with a common origin in evolution but wide variation in starter substrate selection, number of iteration steps and final folding of the product. In analogy to fatty acid biosynthesis, but in a highly selective manner, the growing polyketide chain may also be reduced during its synthesis, leading to further increased chemical variation. The associated PKR is known only for chalcone synthase, but reductive steps are needed for biosynthesis of, e.g., the raspberry ketone (raspberry), the glucosidic lactones gerberin ...

1MNQ: Insights into channel architecture and substrate specificity from crystal structures of two macrocycle-forming thioesterases of modular polyketide synthases

The present invention provides for a non-naturally occurring polyketide synthase (PKS) capable of synthesizing a carboxylic acid or a lactone, and a composition such that a carboxylic acid or lactone is included. The carboxylic acid or lactone, or derivative thereof, is useful as a biofuel. The present invention also provides for a recombinant nucleic acid or vector that encodes such a PKS, and host cells which also have such a recombinant nucleic acid or vector. The present invention also provides for a method of producing such carboxylic acids or lactones using such a PKS.

Polyketide Biosynthesis, Fungi - CHEMICAL BIOLOGY - reflects the multidimensional character of chemical biology, focusing in particular on the fundamental science of biological structures and systems, the use of chemical and biological techniques to elucidate

Author: Piel, J. et al.; Genre: Journal Article; Published in Print: 2004; Keywords: Biosynthesis|br/|Natural products|br/|Polyketicles|br/|Symbiosis|br/|Synthases|br/|Uncultivated bacteria.|br/|Biosynthetic gene-cluster|br/|Combinatorial biosynthesis|br/|Peptide synthetase|br/|Myxococcus-xanthus|br/|Escherichia-coli|br/|Antibiotic ta|br/|Superfamily|br/|Metabolism|br/|Sequence|br/|Acid.|br/|Chemistry & Analysis in Current Contents(R)/Life Sciences.; Title: Unprecedented diversity of catalytic domains in the first four modules of the putative pederin polyketide synthase

In this system, the expression of the hybrid DEBS1-TE is under the control of the actI promoter and the specific activator protein ActII-ORF4 (21). When S. coelicolor CH999/pIG1 was grown for 5 days in liquid medium and the fermentation broth was extracted with ethyl acetate, several polyketides not produced by a control fermentation of S. coelicolor CH999 were identified and were subsequently purified from the extract. The products included the triketide lactones3 and 4 arising from the use of the isobutyrate and 2-methylbutyrate starter units, respectively. The loading module swap does indeed generate a functional hybrid PKS and one that accepts starter units characteristic of the transplanted broad-specificityavr PKS loading module. The triketide lactones 1through 4 (Fig. 1A) were obtained in the approximate ratio of 2:8:2:5 (total yield 10 mg/liter). The fermentation conditions were not optimized, and yields might also have been improved by addition of suitable carboxylic acids to the ...

For the past two decades, we have studied and engineered enzymatic assembly lines called polyketide synthases that catalyze the biosynthesis of structurally complex and medicinally fascinating antibiotics in bacteria. An example of such an assembly line is found in the erythromycin biosynthetic pathway. Our current focus is on understanding the structure and mechanism of this polyketide synthase. At the same time, we are developing methods to decode the vast and growing number of orphan polyketide assembly lines in the sequence databases ...

Biosynthesis of the allylmalonyl-CoA extender unit for the FK506 polyketide synthase proceeds through a dedicated polyketide synthase and facilitates the mutasynthesis of analogues / S Mo; D H Kim; J H Lee; J W Park; D B Basnet; Y H Ban; Y J Yoo; S Chen; S R Park; E A Choi; E Kim; Y Y Jin; S K Lee; J Y Park; Y Liu; M O Lee; K S Lee; S J Kim; Doo Il Kim; Byoung Chul Park; S G Lee; H J Kwon; J W Suh; B S Moore; S K Lim; Y J Yoon , 2011 ...

Title: Polyketide bio-derivatization using thepromiscuous acyltransferase KirCIIAuthor: Musiol-Kroll, E.M., Zubeil, F., Schafhauser, T.,Hartner, T., Kulik, A., McArthur, J., Koryakina, I., Wohlleben, W., Grond, S.,Williams, G.J., Lee, S.Y., and Weber,

Title: Polyketide bio-derivatization using thepromiscuous acyltransferase KirCIIAuthor: Musiol-Kroll, E.M., Zubeil, F., Schafhauser, T.,Hartner, T., Kulik, A., McArthur, J., Koryakina, I., Wohlleben, W., Grond, S.,Williams, G.J., Lee, S.Y., and Weber,

immune Uncategorized buy 73573-88-3, Rabbit Polyclonal to CATZ (Cleaved-Leu62) Accurate and large-scale prediction of proteinCprotein connections directly from amino-acid sequences is among the great issues in computational biology. that in addition, it predicts interaction companions in a recently available dataset of polyketide synthases accurately. Analysis from the forecasted genome-wide two-component signaling systems implies that cognates (interacting kinase/regulator pairs, which rest adjacent over the genome) and orphans (which rest isolated) type two relatively unbiased the different parts of the signaling network in each genome. Furthermore, some buy 73573-88-3 genes are forecasted to have just a small amount of connections partners, we discover that 10% of orphans type a separate course of hub nodes that distribute and integrate indicators to and from up to tens of different connections partners. scoring system is used to recognize pairs of positions that present significant ...

NRPS/PKS substrate predictor uses a HMM-based approach to predict specificities of NRPS A-domains and PKS AT domains.. Reference:. ...

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Plasmid pKS104 from Dr. Jay Keaslings lab contains the insert fadD (M3351), atfA and is published in Nature. 2010 Jan 28;463(7280):559-62. This plasmid is available through Addgene.

Plasmid pKS100 from Dr. Jay Keaslings lab contains the insert fadD and is published in Nature. 2010 Jan 28;463(7280):559-62. This plasmid is available through Addgene.

Polyketide synthase (PKSs) and nonribosomal peptide synthetase (NRPSs) are large multimodular enzymes involved in biosynthesis of polyketide and peptide toxins produced by fungi. Furthermore, hybrid enzymes, in which a reducing PKS region is fused to a single NRPS module, are also responsible of the synthesis of peptide-polyketide metabolites in fungi. The genes encoding for PKSs and NRPSs have been exposed to complex evolutionary mechanisms, which have determined the great number and diversity of metabolites. In this study, we considered the most important polyketide and peptide mycotoxins and, for the first time, a phylogenetic analysis of both PKSs and NRPSs involved in their biosynthesis was assessed using two domains for each enzyme: β-ketosynthase (KS) and acyl-transferase (AT) for PKSs; adenylation (A) and condensation (C) for NRPSs. The analysis of both KS and AT domains confirmed the differentiation of the three classes of highly, partially and non-reducing PKSs. Hybrid PKS-NRPSs involved in

Background Polyketides are natural products with a wide range of biological functions and pharmaceutical applications. Discovery and utilization of polyketides can be facilitated by understanding the evolutionary processes that gave rise to the biosynthetic machinery and the natural product potential of extant organisms. Gene duplication and subfunctionalization, as well as horizontal gene transfer are proposed mechanisms in the evolution of biosynthetic gene clusters. To explain the amount of homology in some polyketide synthases in unrelated organisms such as bacteria and fungi, interkingdom horizontal gene transfer has been evoked as the most likely evolutionary scenario. However, the origin of the genes and the direction of the transfer remained elusive. Methodology/Principal Findings We used comparative phylogenetics to infer the ancestor of a group of polyketide synthase genes involved in antibiotic and mycotoxin production. We aligned keto synthase domain sequences of all available fungal 6

Several alternative sigma factors of M. tuberculosis regulate gene expression in response to stress, including SigH and SigE, which have been shown (SigH) or are hypothesized (SigE) to be regulated by ZASs. Though sigL is also linked to a likely ZAS gene (rslA), we did not identify oxidative or nitrosative stress conditions that either induced expression of this sigma factor or resulted in decreased survival of a sigL mutant relative to wild-type survival. These results suggest that SigL is not a stress response regulator and that other conditions encountered by the bacillus during infection in vivo may activate sigL expression.. By performing microarray analysis followed by primer extension and in vitro transcription experiments, we identified a limited set of genes that are directly regulated by SigL. Despite the small number of regulated promoters, we identified clear −35 and −10 element consensus sequences (TGAACC-N16-CGT) in the promoters recognized by SigL. Though this is similar to ...

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Many metabolic engineering applications require a combination of natural enzymes and ones engineered to catalyze a particular reaction or when the native enzyme is somehow insufficient. The Keasling Lab has engineered isoprenoid cyclases to have new or more focused activities, complexes of scaffolded enzymes to increase flux through metabolic pathways, and polyketide synthases to produce unnatural chemicals. The enzymes attached to the protein scaffold is an example where we learned how nature scaffolds enzymes and constructed a scaffolding system for application to metabolic pathways. The polyketide synthases are natures best examples of scaffolded enzymes. Example publications include:. ...

Author: Gajewski, J. et al.; Genre: Journal Article; Published in Print: 2017-04; Open Access; Title: Engineering fatty acid synthases for directed polyketide production.

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Abstract: Bacillus subtilis has long been a model bacterium for understanding biological mechanisms, such as fatty acid catabolism and polyketide biosynthesis. Our interest in the latter was centered on the polyketide synthase (PKS) mechanism responsible for ß-branching polyketides. The unique structural moiety is attributed to a HMG-CoA synthase homolog, such as the pksG gene in B. subtilis. The first goal was a metagenomic survey of local soils, using the conserved pksG homolog sequence as a genetic marker. After optimizing techniques for the extraction and purification of environmental DNA, the ß-branching polyketide population was not detected in any local soil samples. While working with a pksG homolog, an apparent sequence anomaly prompted us to verify the taxonomic classification of B. subtilis research strains ATCC 39374 and 39320. Comparison of DNA sequences (pksG homologs, hypervariable regions of 16S rRNA and rDNA) and species-specific genes showed the two ATCC strains are more ...

Description. UCI Chem 128 Introduction to Chemical Biology (Winter 2013) Lec 16. Introduction to Chemical Biology -- Glycobiology & Polyketides -- Part 2 View the complete course: http://ocw.uci.edu/courses/chem_128_introduction_to_chemical_biology.html Instructor: Gregory Weiss, Ph.D. License: Creative Commons BY-NC-SA Terms of Use: http://ocw.uci.edu/info. More courses at http://ocw.uci.edu Description: Introduction to the basic principles of chemical biology: structures and reactivity; chemical mechanisms of enzyme catalysis; chemistry of signaling, biosynthesis, and metabolic pathways. Introduction to Chemical Biology (Chem 128) is part of OpenChem: http://ocw.uci.edu/collections/open_chemistry.html This video is part of a 18-lecture undergraduate-level course titled Introduction to Chemical Biology taught at UC Irvine by Professor Gregory Weiss. Recorded March 5, 2013. Index of Topics: 0:00:33 Polysaccharides 0:08:45 Fatty Acid Synthase: Paradigm for a Polyketide Synthesis Machine 0:10:58 ...

Polyketides, a large family of complicated and structurally diverse natural products (> 10000 compounds identified), are an extremely rich source of bioactive molecules. The annual sales of polyketide-related drugs are more than $17 billions, illustrating the high impact of polyketides on pharmaceutical industry. Polyketides have been intensely pursued as total synthesis targets. In Nature, polyeketides are made by polyketide synthase (PKSs), a multi-domain enzyme cluster that catalyzes repeated chain elongations and chain modifications. By combining different PKS domains, Nature generates a large variation of polyketide natural products via a controlled variation in chain length, choice of chain-building units and optional chain modification. In light of natures strategy, we can perform total synthesis in a different approach. De novo polyketides can be synthesized by genetic engineering of PKS domains via domain rearrangement, as well as by in vivo feeding of synthetic precursors. In addition ...

After winning the most hateful student award, given by its department heads, Cale pulls the plug at the end his college days on July 6. He performs La Monte Youngs X for Henry Flynt by kneeling at the piano and smashing the keys with his elbows.. At the same show Robin Page came screaming down from the balcony, performing Cales Plant Piece. A potted plant was set on stage and the idea was to scream at it until it died. The plant survived, the audience was not that pleased. Piano Piece (unsequel music 212b) was the third Cale composition.. Goldsmiths College would bestow Cale with an Honorary Fellowship in 1997.. ...

Current search: plant type: perennial[x], height: ,1[x], habit: bushy[x], interests: fruit[x], interests: buds[x], interests: stems[x], uses: wildflower meadow[x], maintenance: slight[x]. ...

We address a mixed-model assembly-line sequencing problem with work overload minimization criteria.We consider time windows in work stations of the assembly line (closed stations) and different versions of a product to be assembled in the line, which require different processing time according to the work required in each work station. In a paced assembly line, products are feeded in the line at a predetermined constant rate (cycle time). Then, if many products with processing time greater than cycle time are feeded consecutively, work overload can be produced when the worker has insufficient time to finish his/her job. We propose a scatter search based hyper-heuristic for this NP-hard problem. In the low-level, the procedure makes use of priority rules through a constructive procedure. Computational experiments over a wide range of instances from the literature show the effectiveness of the proposed hyper-heuristics when compared to existing heuristics. The relevance of the priority rules was ...

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Consensus tree of alignment of acyltransferase core domains of cis‐ and trans‐AT‐type polyketide synthases. Outgroup is FabD from E. coli.

Natural organic compounds that contain fluorine are rare because living organisms -- with a few exceptions -- do not produce them. Scientists have now genetically engineered a microbial host for organofluorine metabolism, allowing it to produce a fluoridated intermediate known as a diketide. As reported, the diketide could then be used as a monomer for the in vivo production of fluorinated bioplastics ...

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Polyketides, natural products from microorganisms, have been a main source of antibiotics. Understanding the programming of the enzymes that produce these complex molecules has opened a new field of drug discovery.

Gavalda S., Bardou F., Laval F., Bon C., Malaga W., Chalut C., Guilhot C., Mourey L., Daffé M., Quémard A (2014) The polyketide synthase Pks13 catalyzes a novel mechanism of lipid transfer in mycobacteria. Chem. Biol., 21:1660-9. doi: 10.1016/j.chembiol.2014.10.011. Epub 2014 Nov 26.. Kaufmann S, Alves P, Fae K, Houthuys E, Dorhoi A, Kreuchwig A, Furkert J, Barison N, Diehl A, Munder A, Constant P, Skrahina T, Guhlich-Bornhof U, Klemm M, Koehler A-B, Bandermann S, Goosmann C, Mollenkopf H-J, Hurwitz R, Brinkmann V, Fillatreau S, Daffe M, Tummler B, Kolbe M, Oschkinat H, and Krause G. (2014) AhR sensing of bacterial pigments orchestrates antibacterial defense. Nature, 512:387-92.. Gonzalo-Asensio, J., Malaga, W, Pawlik, A., Astarie-Dequeker, C., Passemar, C., Moreau, F., Laval, F., Daffé, M., Martin, C., Brosch, R. and Guilhot, C. (2014) Evolutionary history of tuberculosis shaped by conserved mutations in the PhoPR virulence regulator. PNAS, 111:11491-6.. Daffé M.* and Zuber, B. (2014) The ...

Judith says that, historically, because of the finely honed skills required for each approach, there has been a tendency for the natural building industry to divide off into those that build with straw, and those that build with hempcrete. There are of course many other plant types that can be used, depending on the design criteria. She explains that we shouldnt assume that we could build the whole project out of plants either, and nor should we assume that only one plant type will be suitable for each of the different building elements. Judith uses walls as an example, where because they provide the dual functions of structure and insulation, it might make sense to separate those elements out and use different materials. She says that otherwise, wherever youre trying to get a particular product to perform multiple functions, you may well end up with significant compromises. ...

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Wyche TP, Piotrowski JS, Hou YP, Braun D, Deshpande R, McIlwain S, Ong IM, Myers CL, Guzei IA, Westler WM, et al. Forazoline A: Marine-Derived Polyketide with Antifungal In Vivo Efficacy. Angewandte Chemie-International Edition. 2014 ;53:11583-11586. ...

Angela Belcher found a way to turn natures zombies into a tiny assembly line. But creating a new power cell might be just the beginning.

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