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Yongjun Wei, Lei Zhang, Zhihua Zhou, Xing Yan
Polyketides (PKs) and nonribosomal peptides (NRPs) are widely applied as drugs in use today, and one potential source for novel PKs and NRPs is the marine sediment microbes. However, the diversities of microbes and their PKs and NRPs biosynthetic genes in the marine sediment are rarely reported. In this study, 16S rRNA gene fragments of the Yellow Sea sediment were analyzed, demonstrating that Proteobacteria and Bacteroidetes accounted for 62% of all the bacterial species and Actinobacteria bacteria which were seen as the typical PKs and NRPs producers only accounted for 0...
2018: Frontiers in Microbiology
Drew A Vander Wood, Adrian T Keatinge-Clay
Here, the term "module" is redefined for trans-acyltransferase (trans-AT) assembly lines to agree with how its domains cooperate and evolutionarily co-migrate. The key domain in both the polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) modules of assembly lines is the acyl carrier protein (ACP). ACPs not only relay growing acyl chains through the assembly line but also collaborate with enzymes in modules, both in cis and in trans, to add a specific chemical moiety. A ketosynthase (KS) downstream of ACP often plays the role of gatekeeper, ensuring that only a single intermediate generated by the enzymes of a module is passed downstream...
March 10, 2018: Proteins
Alexander S Moffett, Diwakar Shukla
Eukaryotic protein kinases (PKs) are a large family of proteins critical for cellular response to external signals, acting as molecular switches. PKs propagate biochemical signals by catalyzing phosphorylation of other proteins, including other PKs, which can undergo conformational changes upon phosphorylation and catalyze further phosphorylations. Although PKs have been studied thoroughly across the domains of life, the structures of these proteins are sparsely understood in numerous groups of organisms, including plants...
March 9, 2018: Biochemical Journal
Franziska Hemmerling, Karen Lebe, Johannes Wunderlich, Frank Hahn
The divinylcyclopropane (DVC) fragment of the ambruticins is proposed to be formed via a unique polyene cyclization mechanism in which the unusual didomain AmbG plays a key role. It is proposed to activate the branched thioester carboxylic acid resulting from the polyene cyclisation and to transfer it to its associated ACP. After oxidative decarboxylation, the intermediate is channeled back into polyketide synthase (PKS) processing. AmbG was previously annotated as an adenylation-thiolation didomain with a very unusual substrate selectivity code, but has not yet been biochemically studied...
March 8, 2018: Chembiochem: a European Journal of Chemical Biology
Rafael R C Cuadrat, Danny Ionescu, Alberto M R Dávila, Hans-Peter Grossart
Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations...
2018: Frontiers in Microbiology
Douglas R Cohen, Craig A Townsend
Despite the identification of a β-hydroxyhexaene produced by the enediyne polyketide synthases (PKSs), the post-PKS biosynthetic steps to the individual members of this antitumor antibiotic family remain largely unknown. The massive biosynthetic gene clusters (BGCs) that direct the formation of each product caution that many steps could be required. It was recently demonstrated that the enediyne PKS in the dynemicin A BGC from Micromonospora chersina gives rise to both the anthraquinone and enediyne "halves" of the molecule...
March 7, 2018: Angewandte Chemie
Jose Manuel Leão, Antonio Lozano-Leon, Jorge Giráldez, Óscar Vilariño, Ana Gago-Martínez
Tetrodotoxins (TTX) are a potent group of natural neurotoxins putatively produced by symbiotic microorganisms and affecting the aquatic environment. These neurotoxins have been recently found in some species of bivalves and gastropods along the European Coasts (Greece, UK, and The Netherlands) linked to the presence of high concentrations of Vibrio , in particular Vibrio parahaemolyticus . This study is focused on the evaluation of the presence of Vibrio species and TTX in bivalves (mussels, oysters, cockles, clams, scallops, and razor clams) from Galician Rias (northwest of Spain)...
March 6, 2018: Marine Drugs
Yusuke Sone, Shuto Nakamura, Makoto Sasaki, Fumihito Hasebe, Seung-Young Kim, Nobutaka Funa
1,8-Dihydroxynaphthalene (1,8-DHN) is a key intermediate in the biosynthesis of DHN melanin, which is specific to fungi. In this study, we characterized the enzymatic properties of the gene products of an operon consisting of soceCHS1 , bdsA , and bdsB from the gram-negative bacterium, Sorangium cellulosum Heterologous expression of soceCHS1 , bdsA , and bdsB in Streptomyces coelicolor caused secretion of a dark-brown pigment into the broth. High-performance liquid chromatography analysis of the broth revealed that the recombinant strain produced 1,8-DHN, indicating that the operon encoded a novel enzymatic system for the synthesis of 1,8-DHN...
March 2, 2018: Applied and Environmental Microbiology
Robert L Bertrand, Mona Abdel-Hameed, John L Sorensen
Lichens are symbionts of fungi and algae that produce diverse secondary metabolites with useful properties. Little is known of lichen natural product biosynthesis because of the challenges of working with lichenizing fungi. We describe the first attempt to comprehensively profile the genetic secondary metabolome of a lichenizing fungus. An Illumina platform combined with the Antibiotics and Secondary Metabolites Analysis Shell (FungiSMASH, version 4.0) was used to sequence and annotate assembled contigs of the fungal partner of Cladonia uncialis...
February 27, 2018: Journal of Natural Products
Muralikrishna Narra, Srinivas Kota, Yashodhara Velivela, Raghu Ellendula, V Rao Allini, Sadanandam Abbagani
Chloroplast transformation vectors require an expression cassette flanked by homologous plastid sequences to drive plastome recombination. The rrn 16- rrn 23 plastome region was selected and using this region, a new species-specific plastid transformation vector CuIA was developed with pKS+ II as a backbone by inserting the rrn 16- trnI and trnA - rrn 23 sequences from Cucumis sativus L. An independent expression cassette with aadA gene encoding aminoglycoside 3'-adenylyltransferase with psbA controlling elements is added into the trnI - trnA intergenic region that confers resistance to spectinomycin...
March 2018: 3 Biotech
Bee Gek Ng, Jae Woo Han, Dong Wan Lee, Gyung Ja Choi, Beom Seok Kim
Hahella chejuensis MB-1084 is a Gram-negative marine bacterial strain that produces unusual 17-membered carbocyclic tetraenes, chejuenolide A and B. Two fosmid clones responsible for chejuenolide production were identified from the genomic DNA library of the MB-1084 strain. Systematic inactivation of the open reading frames (ORFs) in the sequenced region defines the boundaries of the chejuenolide (che) biosynthetic gene cluster (24.9 kbp) that encodes one non-ribosomal peptide synthase (NRPS)-polyketide synthase (PKS) hybrid protein, three modular PKSs, two PKS domains, and an amine oxidase homolog...
February 26, 2018: Journal of Antibiotics
Fan Huang, Jianli Tang, Lian He, Xuezhi Ding, Shaoya Huang, Youming Zhang, Yunjun Sun, Liqiu Xia
BACKGROUND: Syringolin, synthesized by a mixed non-ribosomal peptide synthetase/polyketide synthetase in Pseudomonas syringae pv. syringae (Pss) B728a, is a novel eukaryotic proteasome inhibitor. Meanwhile, directly modifying large fragments in the PKS/NRPS gene cluster through traditional DNA engineering techniques is very difficult. In this study, we directly cloned the syl gene cluster from Pss B301D-R via Red/ET recombineering to effectively express syringolin in heterologous hosts...
February 26, 2018: Microbial Cell Factories
Nissim Kanekar, Tapasi Ghosh, Jayaram N Chengalur
We have used the Arecibo Telescope to carry out one of the deepest-ever integrations in radio astronomy, targeting the redshifted conjugate satellite OH 18 cm lines at z≈0.247 towards PKS 1413+135. The satellite OH 1720 and 1612 MHz lines are, respectively, in emission and absorption, with exactly the same line shapes due to population inversion in the OH ground state levels. Since the 1720 and 1612 MHz line rest frequencies have different dependences on the fine structure constant α and the proton-electron mass ratio μ, a comparison between their measured redshifts allows one to probe changes in α and μ with cosmological time...
February 9, 2018: Physical Review Letters
Jonathan Schnabel, Peter Hombach, Thomas Waksman, Giovanni Giuriani, Jan Petersen, John M Christie
Protein kinases (PKs) control many aspects of plant physiology by regulating signaling networks through protein phosphorylation. Phototropins (phots) are plasma membrane-associated serine/threonine PKs that control a range of physiological processes that serve collectively serve to optimize photosynthetic efficiency in plants. These include phototropism, leaf positioning and flattening, chloroplast movement and stomatal opening. Despite their identification over two decades ago, only a handful of substrates have been identified for these PKs...
February 23, 2018: Journal of Biological Chemistry
Ronaldo A Pereira-Junior, Carla Huarte-Bonnet, Flávia R S Paixão, Donald W Roberts, Christian Luz, Nicolás Pedrini, Éverton K K Fernandes
AIMS: The effect of nutritional supplementation of two Metarhizium species with riboflavin (Rb) during production of conidia was (a) evaluated on conidial tolerance (based on germination) to UV-B radiation and (b) on conidial expression following UV-B irradiation, of enzymes known to be active in photoreactivation, viz., photolyase (Phr), laccase (Lcc) and polyketide synthase (Pks). METHODS AND RESULTS: Metarhizium acridum (ARSEF 324) and Metarhizium robertsii (ARSEF 2575) were grown either on (a) potato dextrose agar medium (PDA), (b) PDA supplemented with 1% yeast extract (PDAY), (c) PDA supplemented with Rb (PDA+Rb), or (d) PDAY supplemented with Rb (PDAY+Rb)...
February 23, 2018: Journal of Applied Microbiology
Mehtap Danismazoglu, Remziye Nalcacioglu, Hacer Muratoglu, Zihni Demirbag
Entomopoxviruses are an important group of viruses infecting only insects. They belong to Poxviridae which infect both invertebrates and vertebrates, including humans. Protein kinases are known to have roles at virus morphogenesis, host selectivity, the regulation of cell division and apoptosis in some vertebrate poxviruses. In this study, 2 protein kinases (PKs) (AMV153 and AMV197) of Amsacta moorei entomopoxvirus (AMEV) were investigated for the interactions among 230 viral proteins using yeast two-hybrid system (Y2H)...
February 19, 2018: Virus Research
Stephen A Jackson, Lisa Crossman, Eduardo L Almeida, Lekha Menon Margassery, Jonathan Kennedy, Alan D W Dobson
The genus Streptomyces produces secondary metabolic compounds that are rich in biological activity. Many of these compounds are genetically encoded by large secondary metabolism biosynthetic gene clusters (smBGCs) such as polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS) which are modular and can be highly repetitive. Due to the repeats, these gene clusters can be difficult to resolve using short read next generation datasets and are often quite poorly predicted using standard approaches...
February 20, 2018: Marine Drugs
Helene L Robertsen, Ewa M Musiol-Kroll, Ling Ding, Kristina J Laiple, Torben Hofeditz, Wolfgang Wohlleben, Sang Yup Lee, Stephanie Grond, Tilmann Weber
Kirromycin is the main product of the soil-dwelling Streptomyces collinus Tü 365. The elucidation of the biosynthetic pathway revealed that the antibiotic is synthesised via a unique combination of trans-/cis-AT type I polyketide synthases and non-ribosomal peptide synthetases (PKS I/NRPS). This was the first example of an assembly line integrating the three biosynthetic principles in one pathway. However, information about other enzymes involved in kirromycin biosynthesis remained scarce. In this study, genes encoding tailoring enzymes KirM, KirHVI, KirOI, and KirOII, and the putative crotonyl-CoA reductase/carboxylase KirN were deleted, complemented, and the emerged products analysed by HPLC-HRMS and MS/MS...
February 19, 2018: Scientific Reports
Christopher R Vickery, Javier Cardenas, Marianne Bowman, Michael D Burkart, Nancy A Da Silva, Joseph P Noel
Polyketides are attractive compounds for uses ranging from biorenewable chemical precursors to high-value therapeutics. In many cases, synthesis in a heterologous host is required to produce these compounds in industrially relevant quantities. The type III polyketide synthase 2-pyrone synthase (2-PS) from Gerbera hybrida was used for the production of triacetic acid lactone (TAL) in Saccharomyces cerevisiae. Initial in vitro characterization of 2-PS led to the identification of active site variants with improved kinetic properties relative to wildtype...
February 19, 2018: Biotechnology and Bioengineering
Catarina Loureiro, Marnix H Medema, John van der Oost, Detmer Sipkema
Microorganisms are Nature's little engineers of a remarkable array of bioactive small molecules that represent most of our new drugs. The wealth of genomic and metagenomic sequence data generated in the last decade has shown that the majority of novel biosynthetic gene clusters (BGCs) is identified from cultivation-independent studies, which has led to a strong expansion of the number of microbial taxa known to harbour BGCs. The large size and repeat sequences of BGCs remain a bioinformatic challenge, but newly developed software tools have been created to overcome these issues and are paramount to identify and select the most promising BGCs for further research and exploitation...
February 14, 2018: Current Opinion in Biotechnology
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