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The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production

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Synthetic and Systems Biotechnology 2016年第2期1卷 69-79页

作者： tilmann weber Hyun Uk Kim The Novo Nordisk Foundation Center for Biosustainability Technical University of DenmarkKogle Alle 62970 HosholmDenmark BioInformatics Research Center Korea Advanced Institute of Science and Technology(KAIST)Daejeon 34141Republic of Korea

Natural products are among the most important sources of lead molecules for drug *** the development of affordable whole-genome sequencing technologies and other‘omics tools,the field of natural products research is currently undergoing a shift in ***,for decades,mainly analytical and chemical methods gave access to this group of compounds,nowadays genomics-based methods offer complementary approaches to find,identify and characterize such *** paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily *** this context,this review gives a summary of tools and databases that currently are available to mine,identify and characterize natural product biosynthesis pathways and their producers based on‘omics data.A web portal called Secondary Metabolite Bioinformatics Portal(SMBP at http://***)is introduced to provide a one-stop catalog and links to these bioinformatics *** addition,an outlook is presented how the existing tools and those to be developed will influence synthetic biology approaches in the natural products field.

关键词： Antibiotics Biosynthesis Bioinformatics NRPS PKS Natural product

Designing sgRNAs for CRISPR-BEST base editing applications with CRISPyweb 2.0

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Synthetic and Systems Biotechnology 2020年第2期5卷 99-102页

作者： Kai Blin Simon Shaw Yaojun Tong tilmann weber The Novo Nordisk Foundation Center for Biosustainability Technical University of DenmarkKgs.LyngbyDenmark

CRISPR/Cas9 systems are an established tool in genome *** double strand breaks caused by the standard Cas9-based knock-out techniques can be problematic in some organisms,new systems were developed that can efficiently create knock-outs without causing double strand breaks to elegantly sidestep these *** recently published CRISPR-BEST base editor system for actinobacteria is built around a C to T or A to G base *** base editing systems however require additional constraints to be considered for designing the ***,we present an updated version of the interactive CRISPy-web single guide RNA design tool https://***/that was built to support“classical”CRISPR and now also CRISPRBEST workflows.

关键词： CRISPR Base editor sgRNA Webserver CRISPR-BEST Genome editing

Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets

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Synthetic and Systems Biotechnology 2022年第3期7卷 900-910页

作者： Omkar S.Mohite Colton J.Lloyd Jonathan M.Monk tilmann weber Bernhard O.Palsson The Novo Nordisk Foundation Center for Biosustainability Technical University of DenmarkKongens Lyngby2800Denmark Department of Bioengineering University of California San DiegoLa JollaCA92093USA

In silico genome mining provides easy access to secondary metabolite biosynthetic gene clusters(BGCs)encoding the biosynthesis of many bioactive compounds,which are the basis for many important drugs used in human ***,the association between BGCs and other functions encoded in the genomes of producers have remained ***,we present a systems biology workflow that integrates genome mining with a detailed pangenome analysis for detecting genes associated with a particular *** analyzed 3,889 enterobacterial genomes and found 13,266 BGCs,represented by 252 distinct BGC families and 347 additional singletons.A pangenome analysis revealed 88 genes putatively associated with a specific BGC coding for the colon cancer-related colibactin that code for diverse metabolic and regulatory *** presented workflow opens up the possibility to discover novel secondary metabolites,better understand their physiological roles,and provides a guide to identify and analyze BGC associated gene sets.

关键词： Pangenome analysis Workflow Secondary metabolites Colibactin Enterobacteria Secretion systems

Depiction of secondary metabolites and antifungal activity of Bacillus velezensis DTU001

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Synthetic and Systems Biotechnology 2019年第3期4卷 142-149页

作者： Sagarika Devi Heiko T.Kiesewalter Renato Kovacs Jens Christian Frisvad tilmann weber Thomas Ostenfeld Larsen Akos T.Kovacs Ling Ding Department of Biotechnology and Biomedicine Technical University of Denmark2800Kgs LyngbyDenmark Department of Medical Microbiology Faculty of MedicineUniversity of Debrecen4032DebrecenHungary Center for Biosustainability Technical University of Denmark2800Kgs LyngbyDenmark

For a safe and sustainable environment,effective microbes as biocontrol agents are in high *** have isolated a new Bacillus velezensis strain DTU001,investigated its antifungal spectrum,sequenced its genome,and uncovered the production of lipopeptides in HPLC-HRMS *** test the antifungal efficacy,extracts of *** DTU001 was tested against a range of twenty human or plant pathogenic *** demonstrate that inhibitory potential of *** DTU001 against selected fungi is superior in comparison to single lipopeptide,either iturin or *** isolate showed analogous biofilm formation to other closely related *** further support the biocontrol properties of the isolate,coculture with Candida albicans demonstrated that *** DTU001 exhibited excellent antiproliferation effect against *** summary,the described isolate is a potential antifungal agent with a broad antifungal spectrum that might assist our aims to avoid hazardous pathogenic fungi and provide alternative to toxicity caused by chemicals.

关键词： Bacillus velezensis Candida albicans Secondary metabolites Biocontrol Biofilm

Identification and heterologous expression of the globomycin biosynthetic gene cluster

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Synthetic and Systems Biotechnology 2023年第2期8卷 206-212页

作者： Daniel Oves-Costales Tetiana Gren Eva Baggesgaard Sterndorff Jesús Martín Francisco Javier Ortiz-Lopez Tue S.Jørgensen Xinglin Jiang Fernando Roman-Hurtado Fernando Reyes Olga Genilloud tilmann weber Fundacion MEDINA Centro de Excelencia en Investigaci´on de Medicamentos Innovadores en AndalucíaAvda del Conocimiento 3418016ArmillaGranadaSpain The Novo Nordisk Foundation Center for Biosustainability Technical University of DenmarkKemitorvetbuilding 2202800 Kgs.LyngbyDenmark

Globomycin is a cyclic lipodepsipeptide originally isolated from several Streptomyces species which displays strong and selective antibacterial activity against Gram-negative *** mode of action is based on the competitive inhibition of the lipoprotein signal peptidase II(LspA),which is absent in eukaryotes and considered an attractive target for the development of new *** its interesting biological properties,the gene cluster encoding its biosynthesis has not yet been *** this study we employed a genome-mining approach in the globomycin-producing Streptomyces ***-278952 to identify a candidate gene cluster responsible for its biosynthesis.A null mutant was constructed using CRISPR base editing where production was abolished,strongly suggesting its involvement in the *** putative gene cluster was then cloned and heterologously expressed in Streptomyces albus J1074 and Streptomyces coelicolor M1146,therefore unambigu-ously linking globomycin and its biosynthetic gene *** work paves the way for the biosynthesis of new globomycin derivatives with improved pharmacological properties.

关键词： Globomycin Signal peptidase II Cyclic lipodepsipeptide Genome mining CRISPR-cBEST Heterologous expression

Discovery of gargantulides B and C,new 52-membered macrolactones from Amycolatopsis *** absolute stereochemistry of the gargantulide family

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Organic Chemistry Frontiers 2022年第2期9卷 462-470页

作者： Daniel Carretero-Molina Francisco Javier Ortiz-López Tetiana Gren Daniel Oves-Costales Jesús Martín Fernando Román-Hurtado Tue Sparholt Jorgensen Mercedes de la Cruz Caridad Díaz Francisca Vicente Kai Blin Fernando Reyes tilmann weber Olga Genilloud Fundación MEDINA Centro de Excelencia en Investigación de Medicamentos Innovadores en AndalucíaAvda.del Conocimiento 3418016 ArmillaGranadaSpain The Novo Nordisk Foundation Center for Biosustainability Technical University of DenmarkKemitorvetbuilding 2202800 Kgs.LyngbyDenmark

Gargantulides B and C,two new and highly complex 52-membered glycosylated macrolactones,were isolated from Amycolatopsis *** CA-230715 during an antibacterial screening *** structures of these giant macrolides were elucidated by 2D NMR spectroscopy and shown to be related to gargantulide A,although containing additional β-glucopyranose and/orα-arabinofuranose monosaccharides separately attached to their *** sequencing allowed the identification of a strikingly large 216 kbp biosynthetic gene cluster,among the largest type Ⅰ PKS clusters described so far,and the proposal of a previously unreported biosynthetic pathway for gargantulides *** absolute configurations of gargantulides B and C were assigned based on a combination of NMR and bioinformatics analysis of ketoreductase and enoylreductase domains within the multimodular type Ⅰ *** addition,the absolute stereochemistry of gargantulide A has now been revised and *** B and C display potent antibacterial activity against a set of drug-resistant Gram-positive bacteria and moderate activity against the clinically relevant Gram-negative pathogen Acinetobacter baumannii.

关键词： absolute membered backbone

Strategies for the Airline Industry on the African Continent

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Journal of Transportation Technologies 2025年第1期15卷 17-49页

作者： tilmann Gabriel African Aviation & Aerospace University Abuja Nigeria

African Aviation continues to fall short of serving the demands of the fast-growing African population. For major air transport in and out of the African continent, African travellers rely mainly on non-African Airlines. There is, however, one successful airline on the continent at the writing of this paper: Ethiopian Airlines and the Ethiopian Aviation Group. Why are no further successful airlines possible on a continent of 1.4 billion people (25% of the world’s population) and only a 2%-share of global air transport? At the introduction of SAATM, which is anticipated as the start of the domestic African aviation boom, most African countries seem unprepared to build a success story like Ethiopia. Transportation infrastructure in sub-Saharan Africa does not start with roads and rail but with runways and airlines. This research investigates the basic requirements needed to equip Africa with a competitive aviation industry that would contribute some 5% to the continent’s GDP and create hundreds of thousands of workplaces. Interviews with African SAATM leaders signal a slowdown in the effort to succeed. The research is also concerned about the lack of inclusion in the implementation of a NetZero CO2 emission scheme in Africa.

关键词： African Aviation SAATM African Air Transport Industry African Airlines NetZero

Programmable polyketide biosynthesis platform for production of aromatic compounds in yeast

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Synthetic and Systems Biotechnology 2020年第1期5卷 11-18页

作者： Tadas Jakočiūnas Andreas K.Klitgaard Eftychia Eva Kontou Julie Bang Nielsen Emil Thomsen David Romero-Suarez Kai Blin Christopher J.Petzold Jennifer W.Gin Yaojun Tong Charlotte Held Gotfredsen Pep Charusanti Rasmus J.N.Frandsen tilmann weber Sang Yup Lee Michael K.Jensen Jay D.Keasling The Novo Nordisk Foundation Center for Biosustainability Technical University of DenmarkKgs.LyngbyDenmark Joint BioEnergy Institute EmeryvilleCAUSA Biological Systems&Engineering Division Lawrence Berkeley National LaboratoryBerkeleyCAUSA Department of Chemical and Biomolecular Engineering&Department of Bioengineering University of California BerkeleyCAUSA Center for Synthetic Biochemistry Institute for Synthetic BiologyShenzhen Institutes for Advanced TechnologiesShenzhenChina Department of Chemistry Technical University of DenmarkKgs.LyngbyDenmark Department of Biotechnology and Biomedicine Technical University of DenmarkKgs.LyngbyDenmark Department of Chemical and Biomolecular Engineering(BK21 Plus Program) Korea Advanced Institute of Science and Technology(KAIST)291 Daehak-roYuseong-guDaejeon34141Republic of Korea

To accelerate the shift to bio-based production and overcome complicated functional implementation of natural and artificial biosynthetic pathways to industry relevant organisms,development of new,versatile,bio-based production platforms is *** we present a novel yeast-based platform for biosynthesis of bacterial aromatic *** platform is based on a synthetic polyketide synthase system enabling a first demonstration of bacterial aromatic polyketide biosynthesis in a eukaryotic host.

关键词： Natural products Synthetic biology Aromatic polyketides CRISPR/Cas9 Polyketide Production platform in eukaryotes Metabolic engineering Biotechnology

Automated optimization and uncertainty quantification of convergence parameters in plane wave density functional theory calculations

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npj Computational Materials 2024年第1期10卷 428-438页

作者： Jan Janssen Edgar Makarov tilmann Hickel Alexander V.Shapeev Jörg Neugebauer Max Planck Institute for Sustainable Materials DüsseldorfGermany Skolkovo Institute of Science and Technology Skolkovo Innovation CenterMoscowRussia BAM Federal Institute for Materials Research and Testing BerlinGermany

First principles approaches have revolutionized our ability in using computers to predict,explore,and designmaterials.A major advantage commonly associated with these approaches is that they are fully ***,numerically solving the underlying equations requires to choose a set of convergence *** the advent of high-throughput calculations,it becomes exceedingly important to achieve a truly parameter-free *** uncertainty quantification(UQ)and linear decomposition we derive a numerically highly efficient representation of the statistical and systematic error in the multidimensional space of the convergence parameters for plane wave density functional theory(DFT)*** on this formalism we implement a fully automated approach that requires as input the target precision rather than convergence *** performance and robustness of the approach are shown by applying it to a large set of elements crystallizing in a cubic fcc lattice.

关键词： convergence plane wave