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polyketide synthase

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https://www.readbyqxmd.com/read/29040649/clustercad-a-computational-platform-for-type-i-modular-polyketide-synthase-design
#1
Clara H Eng, Tyler W H Backman, Constance B Bailey, Christophe Magnan, Héctor García Martín, Leonard Katz, Pierre Baldi, Jay D Keasling
ClusterCAD is a web-based toolkit designed to leverage the collinear structure and deterministic logic of type I modular polyketide synthases (PKSs) for synthetic biology applications. The unique organization of these megasynthases, combined with the diversity of their catalytic domain building blocks, has fueled an interest in harnessing the biosynthetic potential of PKSs for the microbial production of both novel natural product analogs and industrially relevant small molecules. However, a limited theoretical understanding of the determinants of PKS fold and function poses a substantial barrier to the design of active variants, and identifying strategies to reliably construct functional PKS chimeras remains an active area of research...
October 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29028314/heterologous-gene-expression-of-n-terminally-truncated-variants-of-lippks1-suggests-a-functionally-critical-structural-motif-in-the-n-terminus-of-modular-polyketide-synthase
#2
Satoshi Yuzawa, Constance B Bailey, Tatsuya Fujii, Renee Jocic, Jesus F Barajas, Veronica T Benites, Edward E K Baidoo, Yan Chen, Christopher J Petzold, Leonard Katz, Jay D Keasling
Streptomyces genomes have a high G + C content and typically use an ATG or GTG codon to initiate protein synthesis. Although gene-finding tools perform well in low GC genomes, it is known that the accuracy in predicting a translational start site (TSS) is much less for high GC genomes. LipPks1 is a Streptomyces-derived, well-characterized modular polyketide synthase (PKS). Using this enzyme as a model, we experimentally investigated the effects of alternative TSSs using a heterologous host, Streptomyces venezuelae...
October 17, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28993611/natural-product-diversity-associated-with-the-nematode-symbionts-photorhabdus-and-xenorhabdus
#3
Nicholas J Tobias, Hendrik Wolff, Bardya Djahanschiri, Florian Grundmann, Max Kronenwerth, Yi-Ming Shi, Svenja Simonyi, Peter Grün, David Shapiro-Ilan, Sacha J Pidot, Timothy P Stinear, Ingo Ebersberger, Helge B Bode
Xenorhabdus and Photorhabdus species dedicate a large amount of resources to the production of specialized metabolites derived from non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS). Both bacteria undergo symbiosis with nematodes, which is followed by an insect pathogenic phase. So far, the molecular basis of this tripartite relationship and the exact roles that individual metabolites and metabolic pathways play have not been well understood. To close this gap, we have significantly expanded the database for comparative genomics studies in these bacteria...
October 9, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28989652/elucidation-of-the-relative-and-absolute-stereochemistry-of-the-kalimantacin-batumin-antibiotics
#4
Iain R G Thistlethwaite, Freya M Bull, Chengsen Cui, Paul D Walker, Shu-Shan Gao, Luoyi Wang, Zhongshu Song, Joleen Masschelein, Rob Lavigne, Matthew P Crump, Paul R Race, Thomas J Simpson, Christine L Willis
Kalimantacin A and batumin exhibit potent and selective antibiotic activity against Staphylococcus species including MRSA. Both compounds are formed via a hybrid polyketide synthase/non-ribosomal peptide synthetase (PKS-NRPS) biosynthetic pathway and from comparison of the gene clusters it is apparent that batumin from Pseudomonas batumici and kalimantacin from P. fluorescens are the same compound. The linear structure of this unsaturated acid was assigned by spectroscopic methods, but the relative and absolute stereochemistry of the five stereocentres remained unknown...
September 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28985565/genetic-mapping-and-biochemical-basis-of-yellow-feather-pigmentation-in-budgerigars
#5
Thomas F Cooke, Curt R Fischer, Ping Wu, Ting-Xin Jiang, Kathleen T Xie, James Kuo, Elizabeth Doctorov, Ashley Zehnder, Chaitan Khosla, Cheng-Ming Chuong, Carlos D Bustamante
Parrot feathers contain red, orange, and yellow polyene pigments called psittacofulvins. Budgerigars are parrots that have been extensively bred for plumage traits during the last century, but the underlying genes are unknown. Here we use genome-wide association mapping and gene-expression analysis to map the Mendelian blue locus, which abolishes yellow pigmentation in the budgerigar. We find that the blue trait maps to a single amino acid substitution (R644W) in an uncharacterized polyketide synthase (MuPKS)...
October 5, 2017: Cell
https://www.readbyqxmd.com/read/28980673/dissecting-how-modular-polyketide-synthase-ketoreductases-interact-with-acyl-carrier-protein-attached-substrates
#6
Luisa Moretto, Steven Vance, Brennan Heames, R William Broadhurst
Interaction studies using fragments excised from the modular mycolactone polyketide synthase show that ketoreductase domains possess a generic binding site for acyl carrier protein domains and provide evidence that the pendant 5'-phosphopantetheine prosthetic group plays a key role in delivering acyl substrates to the active site in the correct orientation.
October 5, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28975513/genome-wide-analysis-of-microsatellites-in-alternaria-arborescens-and-elucidation-of-the-function-of-polyketide-synthase-pksj
#7
Prassan Choudhary, Prem Lal Kashyap, Sanjay Kumar Goswami, Hillol Chakdar, Alok Kumar Srivastava, Anil Kumar Saxena
Microsatellites or simple sequence repeats (SSRs) have been the most widely applied class of molecular markers used in genetic studies, having applications in genetic conservation, population studies, as well as diagnostics of fungi. Mining and analysis of SSRs of the whole genome sequence have been carried out in this study for the fungus Alternaria arborescens causing early blight of tomato and well known for producing mycotoxins like alternariol (AOH), alternariol monomethyl ether (AME), etc. A total of 4097 microsatellites were identified in A...
October 3, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28963198/first-draft-genome-sequence-of-a-clinical-strain-of-nocardia-cerradoensis
#8
Gema Carrasco, Sara Monzón, Pilar Jiménez, Isabel Cuesta, Joaquín Bartolomé-Alvarez, Sylvia Valdezate
This paper reports the first draft genome sequence for a strain of Nocardia cerradoensis obtained from an immunocompetent patient with a knee infection. The 8.2-Mb genome has 8,329 coding sequences, including intrinsic resistance genes, biosynthetic gene clusters for polyketide synthase and nonribosomal peptide synthase, virulence genes, and prophages.
September 28, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28950701/development-of-transcription-factor-based-designer-macrolide-biosensors-for-metabolic-engineering-and-synthetic-biology
#9
Christian Kasey, Mounir Zerrad, Yiwei Li, Thomas Ashton Cropp, Gavin J Williams
Macrolides are a large group of natural products that display broad and potent biological activities and are biosynthesized by type I polyketide synthases (PKSs) and associated enzymatic machinery. There is an urgent need to access macrolides and unnatural macrolide derivatives for drug discovery, drug manufacture, and probe development. Typically, efforts to engineer the biosynthesis of macrolides and macrolide analogues in various microbial hosts are hampered by the complexity of macrolide biosynthetic pathways and our limited ability to rationally reprogram type I PKSs and post-PKS machinery...
September 26, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28949419/both-modular-and-single-domain-type-i-polyketide-synthases-are-expressed-in-the-brevetoxin-producing-dinoflagellate-karenia-brevis-dinophyceae
#10
Frances M Van Dolah, Gurjeet S Kohli, Jeanine S Morey, Shauna A Murray
Dinoflagellates are prolific producers of polyketide compounds, many of which are potent toxins with adverse impacts on human and marine animal health. To identify polyketide synthase (PKS) genes in the brevetoxin-producing dinoflagellate, Karenia brevis, we assembled a transcriptome from 595 million Illumina reads, sampled under different growth conditions. The assembly included 125,687 transcripts greater than 300 nt in length, with over half having >100x coverage. We found 121 transcripts encoding Type I ketosynthase (KS) domains, of which 99 encoded single KS domains, while 22 contained multiple KS domains arranged in 1-3 protein modules...
September 26, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28946011/engineering-modular-polyketide-synthases-for-production-of-biofuels-and-industrial-chemicals
#11
REVIEW
Wenlong Cai, Wenjun Zhang
Polyketide synthases (PKSs) are one of the most profound biosynthetic factories for producing polyketides with diverse structures and biological activities. These enzymes have been historically studied and engineered to make un-natural polyketides for drug discovery, and have also recently been explored for synthesizing biofuels and industrial chemicals due to their versatility and customizability. Here, we review recent advances in the mechanistic understanding and engineering of modular PKSs for producing polyketide-derived chemicals, and provide perspectives on this relatively new application of PKSs...
September 22, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28933436/stereodivergent-synthesis-with-a-programmable-molecular-machine
#12
Salma Kassem, Alan T L Lee, David A Leigh, Vanesa Marcos, Leoni I Palmer, Simone Pisano
It has been convincingly argued that molecular machines that manipulate individual atoms, or highly reactive clusters of atoms, with Ångström precision are unlikely to be realized. However, biological molecular machines routinely position rather less reactive substrates in order to direct chemical reaction sequences, from sequence-specific synthesis by the ribosome to polyketide synthases, where tethered molecules are passed from active site to active site in multi-enzyme complexes. Artificial molecular machines have been developed for tasks that include sequence-specific oligomer synthesis and the switching of product chirality, a photo-responsive host molecule has been described that is able to mechanically twist a bound molecular guest, and molecular fragments have been selectively transported in either direction between sites on a molecular platform through a ratchet mechanism...
September 20, 2017: Nature
https://www.readbyqxmd.com/read/28932984/rnai-mediated-down-regulation-of-a-melanin-polyketide-synthase-pks1-gene-in-the-fungus-slafractonia-leguminicola
#13
Mohammad S Alhawatema, Sayed Gebril, Daniel Cook, Rebecca Creamer
The fungus Slafractonia leguminicola, the causal agent of blackpatch disease of legumes produces two mycotoxins slaframine and swainsonine, causing slobbers' symptoms and locoism of grazing animals, respectively. The genetics of this important fungus is poorly understood. This work aimed to develop a genetic transformation system and evaluate the efficacy of RNA interference (RNAi) in S. leguminicola. In this study, S. leguminicola was transformed using a PEG-mediated method with a fungal construct that carries a hygromycin resistance cassette...
September 20, 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28928723/analysis-of-the-sequences-structures-and-functions-of-product-releasing-enzyme-domains-in-fungal-polyketide-synthases
#14
Lu Liu, Zheng Zhang, Chang-Lun Shao, Chang-Yun Wang
Product-releasing enzyme (PRE) domains in fungal non-reducing polyketide synthases (NR-PKSs) play a crucial role in catalysis and editing during polyketide biosynthesis, especially accelerating final biosynthetic reactions accompanied with product offloading. However, up to date, the systematic knowledge about PRE domains is deficient. In the present study, the relationships between sequences, structures, and functions of PRE domains were analyzed with 574 NR-PKSs of eight groups (I-VIII). It was found that the PRE domains in NR-PKSs could be mainly classified into three types, thioesterase (TE), reductase (R), and metallo-β-lactamase-type TE (MβL-TE)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28924162/insights-into-the-functionality-of-endophytic-actinobacteria-with-a-focus-on-their-biosynthetic-potential-and-secondary-metabolites-production
#15
Ajit Kumar Passari, Vineet Kumar Mishra, Garima Singh, Pratibha Singh, Brijesh Kumar, Vijai Kumar Gupta, Rupak Kumar Sharma, Ratul Saikia, Anthonia O' Donovan, Bhim Pratap Singh
Endophytic actinobacteria play an important role in growth promotion and development of host plant by producing enormous quantities of novel bioactive natural products. In the present investigation, 169 endophytic actinobacteria were isolated from endospheric tissues of Rhynchotoechum ellipticum. Based on their antimicrobial potential, 81 strains were identified by 16rRNA gene analysis, which were taxonomically grouped into 15 genera. All identified strains were screened for their plant growth promoting attributes and, for the presence of modular polyketide synthases (PKSI, PKSII and nonribosomal peptide synthetase (NRPS) gene clusters to correlate the biosynthetic genes with their functional properties...
September 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28921941/the-lactococcus-lactis-kf147-nonribosomal-peptide-synthetase-polyketide-synthase-system-confers-resistance-to-oxidative-stress-during-growth-on-plant-leaf-tissue-lysate
#16
Benjamin L Golomb, Annabelle O Yu, Laurynne C Coates, Maria L Marco
Strains of Lactococcus lactis isolated from plant tissues possess adaptations that support their survival and growth in plant-associated microbial habitats. We previously demonstrated that genes coding for a hybrid nonribosomal peptide synthetase/polyketide synthase (NRPS/PKS) system involved in production of an uncharacterized secondary metabolite are specifically induced in L. lactis KF147 during growth on plant tissues. Notably, this NRPS/PKS has only been identified in plant-isolated strains of L. lactis...
September 18, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28918535/bioprospecting-of-novel-and-bioactive-compounds-from-marine-actinomycetes-isolated-from-south-china-sea-sediments
#17
Na Yang, Fuhang Song
Marine actinomycetes are less investigated compared to terrestrial strains as potential sources of natural products. To date, few investigations have been performed on culturable actinomycetes associated with South China Sea sediments. In the present study, twenty-eight actinomycetes were recovered from South China Sea sediments after dereplication by traditional culture-dependent method. The 16S rRNA gene sequences analyses revealed that these strains related to five families and seven genera. Twelve representative strains possessed at least one of the biosynthetic genes coding for polyketide synthase I, II, and nonribosomal peptide synthetase...
September 16, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28916825/de-novo-transcriptome-of-the-cosmopolitan-dinoflagellate-amphidinium-carterae-to-identify-enzymes-with-biotechnological-potential
#18
Chiara Lauritano, Daniele De Luca, Alberto Ferrarini, Carla Avanzato, Andrea Minio, Francesco Esposito, Adrianna Ianora
Dinoflagellates are phytoplanktonic organisms found in both freshwater and marine habitats. They are often studied because related to harmful algal blooms but they are also known to produce bioactive compounds for the treatment of human pathologies. The aim of this study was to sequence the full transcriptome of the dinoflagellate Amphidinium carterae in both nitrogen-starved and -replete culturing conditions (1) to evaluate the response to nitrogen starvation at the transcriptional level, (2) to look for possible polyketide synthases (PKSs) in the studied clone (genes that may be involved in the synthesis of bioactive compounds), (3) if present, to evaluate if nutrient starvation can influence PKS expression, (4) to look for other possible enzymes of biotechnological interest and (5) to test strain cytotoxicity on human cell lines...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28902510/stereospecific-formation-of-e-and-z-disubstituted-double-bonds-by-dehydratase-domains-from-modules-1-and-2-of-the-fostriecin-polyketide-synthase
#19
Dhara D Shah, Young-Ok You, David E Cane
The dehydratase domain FosDH1 from module 1 of the fostriecin polyketide synthase (PKS) catalyzed the stereospecific interconversion of (3R)-3-hydroxybutyryl-FosACP1 (5) and (E)-2-butenoyl-FosACP1 (11), as established by a combination of direct LC-MS/MS and chiral GC-MS. FosDH1 did not act on either (3S)-3-hydroxybutyryl-FosACP1 (6) or (Z)-2-butenoyl-FosACP1 (12). FosKR2, the ketoreductase from module 2 of the fostriecin PKS that normally provides the natural substrate for FosDH2, was shown to catalyze the NADPH-dependent stereospecific reduction of 3-ketobutyryl-FosACP2 (23) to (3S)-3-hydroxybutyryl-FosACP2 (8)...
October 11, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28884166/crystal-structure-of-thioesterase-sgce10-supporting-common-polyene-intermediates-in-9-and-10-membered-enediyne-core-biosynthesis
#20
Thibault Annaval, Jeffrey D Rudolf, Chin-Yuan Chang, Jeremy R Lohman, Youngchang Kim, Lance Bigelow, Robert Jedrzejczak, Gyorgy Babnigg, Andrzej Joachimiak, George N Phillips, Ben Shen
Enediynes are potent natural product anticancer antibiotics, and are classified as 9- or 10-membered according to the size of their enediyne core carbon skeleton. Both 9- and 10-membered enediyne cores are biosynthesized by the enediyne polyketide synthase (PKSE), thioesterase (TE), and PKSE-associated enzymes. Although the divergence between 9- and 10-membered enediyne core biosynthesis remains unclear, it has been observed that nascent polyketide intermediates, tethered to the acyl carrier protein (ACP) domain of PKSE, could be released by TE in the absence of the PKSE-associated enzymes...
August 31, 2017: ACS Omega
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