Topic 199

engineering enzyme metabolic production biosynthetic products acid enzymes chemicals fatty reactions metabolism bacteria streptomyces synthetic precursor amino produced polyketide engineered carbon modifications reaction chemical active alanine coa heterologous biochemistry product mg biosynthesis intermediates work catabolic apertor lygos napigen amyris demetrix synthase commodity kingdom chassis coelicolor gram acids catalyzed catalytic catabolism beneficial tryptophan maple exchanges catabolized dehydro dikarya pathway switch genus bio industry gladioli nrps phenylethanol hydrolysis synthases strains encoded engineer supply bacterium lipomycin lippks2 lippks1 strain demonstrates genomes ascomycota bimodular efforts microbiology basidiomycota coli widely loop discovery establishing clusters terpene titer siderophore albus crispri residue stripe essential bgcs ferric specialty

34 items. Top items listed below.

Functional analysis of the fatty acid and alcohol metabolism of Pseudomonas putida using RB-TnSeq 199 67 12

Discovery and biosynthesis of gladiochelins: unusual lipodepsipeptide siderophores from Burkholderia gladioli 199 79 12

Enzyme-constrained models and omics analysis of Streptomyces coelicolor reveal metabolic changes that enhance heterologous production 199 67 12

Rational engineering of Kluyveromyces marxianus to create a chassis for the production of aromatic products 199 67 12

A bimodular PKS platform that expands the biological design space 199 129 67

Engineering of critical enzymes and pathways for improved triterpenoid biosynthesis in yeast 199 67 12

Chemoinformatic-guided engineering of polyketide synthases 199 129 67 63 8

Deglutarylation of GCDH by SIRT5 controls lysine metabolism in mice 199 67 63 3

Modulation of plant Acetyl CoA Synthetase activity by acetylation 199 129 63 16 8 3

Engineering Yarrowia lipolytica as a chassis for de novo synthesis of five aromatic-derived natural products and chemicals 199 67 12

Branch point control at malonyl-CoA node: A computational framework to uncover the design principles of an ideal genetic-metabolic switch 199 38 8

High titer methyl ketone production with tailored Pseudomonas taiwanensis VLB120 199 67

Trophic cooperation promotes bacterial survival of Staphylococcus aureus and Pseudomonas aeruginosa 199 79 12 10

A multi-sensor system provides spatiotemporal oxygen regulation of gene expression in a Rhizobium-legume symbiosis 199 16 12 3

A novel and conserved cell wall enzyme that can substitute for the Lipid II synthase MurG 199 79 12 3

Desulfovibrio diazotrophica sp. nov., a sulphate reducing bacterium from the human gut capable of nitrogen fixation 199 12 5

Two-stage Dynamic Deregulation of Metabolism Improves Process Robustness & Scalability in Engineered E. coli. 199 67 33 18

Algal Neurotoxin Biosynthesis Repurposes the Terpene Cyclase Structural Fold Into an N-prenyltransferase 199 129 63 8

An Interpreted Atlas of Biosynthetic Gene Clusters from 1000 Fungal Genomes 199 121 40 12 5 4

Novel two-stage processes for optimal chemical production in microbes 7

Phylogenomic analyses of non-Dikarya fungi supports horizontal gene transfer driving diversification of secondary metabolism in the amphibian gastrointestinal symbiont, Basidiobolus 199 121 40 12 5

Rapid mechanoenzymatic saccharification of lignocellulosic biomass without bulk water or chemical pre-treatment 199 115 67 12

A secreted NlpC/P60 endopeptidase from Photobacterium damselae subsp. piscicida cleaves the peptidoglycan of potentially competing bacteria 199 79 12 8

Multistable and dynamic CRISPRi-based synthetic circuits 199 33 18

Soybean Yellow Stripe-like7 is a symbiosome membrane peptide transporter essential for nitrogen fixation 199 16 3

Recombinant production of active microbial transglutaminase in E. coli using self-cleavable zymogen with mutated propeptide 199 129 63 8

Analysis of Metabolic Network Disruption in Engineered Microbial Hosts due to Enzyme Promiscuity 67 38 33 12

Ferric Heme as a CO/NO Sensor in the Nuclear Receptor Reverbβ by Coupling Gas binding to Electron Transfer 199 8 3

Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia 129 63 8

Engineering DNA templated nonribosomal peptide synthesis 199 129 8

Food-Poisoning Bacteria Employ a Citrate Synthase and a Type II NRPS to Synthesize Bolaamphiphilic Lipopeptide Antibiotics 199 12

A Lysate Proteome Engineering Strategy for Enhancing Cell-Free Metabolite Production 67 18

Cell-free styrene biosynthesis at high titers 67 18 12

Genetically encoded biosensors for branched-chain amino acid metabolism to monitor mitochondrial and cytosolic production of isobutanol and isopentanol in yeast 67 12

ArlCDE form the archaeal switch complex 199 8

iPSC-derived hepatocytes from patients with nonalcoholic fatty liver disease display a disease-specific gene expression profile 199

A High-efficacy CRISPRi System for Gene Function Discovery in Zymomonas mobilis 33 12

Formaldehyde-responsive proteins, TtmR and EfgA, reveal a tradeoff between formaldehyde resistance and efficient transition to methylotrophy in Methylorubrum extorquens 67 12 3

Computational genomic discovery of diverse gene clusters harboring Fe-S flavoenzymes in anaerobic gut microbiota 143 29 12 5

Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites 33 12

Machine Learning and Optimal Control of Enzyme Activities to Preserve Solvent Capacity in the Cell 67 38 26 4

Phylogenetic analysis of the salinipostin γ-butyrolactone gene cluster uncovers new potential for bacterial signaling-molecule diversity 121 79 12 5

Vibrio campbellii chitoporin: thermostability study and implications for the development of therapeutic agents against Vibrio infections 199 129 8

Exposure to Mites Sensitizes Intestinal Stem Cell Maintenance, Splenic Marginal Zone B Cell Homeostasis, And Heart Development to Notch Dosage and Cooperativity. 199 3

Comparative genome and transcriptome analyses revealing interspecies variations in the expression of fungal biosynthetic gene clusters 121 9 5

Developing an endogenous quorum-sensing based CRISPRi circuit for autonomous and tunable dynamic regulation of multiple targets in industrial Streptomyces 67 33 18

Secondary metabolism in the gill microbiota of shipworms (Teredinidae) as revealed by comparison of metagenomes and nearly complete symbiont genomes 143 121 29 12 5

Refactoring the formicamycin biosynthetic gene cluster to make high-level producing strains and new molecules 52 12

Elucidating the diversity and potential function of nonribosomal peptide and polyketide biosynthetic gene clusters in the root microbiome 29 12 5

Modeling a co-culture of Clostridium autoethanogenum and Clostridium kluyveri to increase syngas conversion to medium-chain fatty-acids 7

Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments 158 112 4

Directed evolution of Anabaena variabilis phenylalanine ammonia-lyase (PAL) identifies mutants with enhanced activities 129 63 33

Metabolite sequestration enables rapid recovery from fatty acid depletion in Escherichia coli 158 67 38 12

Cellular and structural basis of synthesis of the unique intermediate dehydro-F420-0 in mycobacteria 63 8

Structural and Dynamic Basis of Molecular Recognition between Acyltransferase and Carrier Protein in E. coli Fatty Acid Synthesis 63 8 3

Activity Mapping the Acyl Carrier Protein - Elongating Ketosynthase Interaction in Fatty Acid Biosynthesis 63 8

Development of a genome-scale metabolic model of Clostridium thermocellum and its applications for integration of multi-omics datasets and strain design 67 33 4

Production of diverse beauveriolide analogs in closely related fungi: a rare case of fungal chemodiversity 67 12 5

Computational study on ratio-sensing in yeast galactose utilization pathway 158 38

Post-translational control of PlsB is sufficient to coordinate membrane synthesis with growth in Escherichia coli 67 8 3

Genomic and chemical diversity of Bacillus subtilis secondary metabolites against plant pathogenic fungi 121 12 5

The NarX-NarL two-component system is a global regulator of biofilm formation, natural product biosynthesis, and host-associated survival in Burkholderia pseudomallei 79 12 3

Genome-scale metabolic rewiring to achieve predictable titers rates and yield of a non-native product at scale 67 12

Single amino acid-promoted reactions link a non-enzymatic chemical network to the early evolution of enzymatic pentose phosphate pathway 129 67 63 8

Regulation of antimycin biosynthesis is controlled by the ClpXP protease 79 3

Breaking a Strong Amide Bond: Structure and Properties of Dimethylformamidase. 63 8

Diagnosing and predicting mixed culture fermentations with unicellular and guild-based metabolic models 158 29 12

The Ketosynthase Domain Constrains the Design of Polyketide Synthases 129 63 8

Bacterial-like nonribosomal peptide synthetases produce cyclopeptides in the zygomycetous fungus Mortierella alpina 129 67 12

PQS-Induced Outer Membrane Vesicles Enhance Biofilm Dispersion in Pseudomonas aeruginosa 52 12 10 3

The defining genomic and predicted metabolic features of the Acetobacterium genus 121 67 12 5

Further biochemical profiling of Hypholoma fasciculare metabolome reveals its chemo-genetic diversity 12

Mechanism-based enzyme activating compounds 63 8

Engineering of Phytosterol-Producing Yeast Platforms for Functional Reconstitution of Downstream Biosynthetic Pathways 7

Ceragenins and antimicrobial peptides kill bacteria through distinct mechanisms 52 12

Harnessing the central dogma for stringent multi-level control of gene expression 38 33 18

A multiplexed, automated evolution pipeline enablesscalable discovery and characterization of biosensors 18 4

A Single Chromosome Strain of S. cerevisiae Exhibits Diminished Ethanol Metabolism and Tolerance. 67 16 3

Resistance to serine in Bacillus subtilis: Identification of the serine transporter YbeC and of a metabolic network that links serine and threonine metabolism 79 67 12 3

Benchmarking kinetic models of Escherichia coli metabolism 38 4

Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins 63 8


Pathway-based and phylogenetically adjusted quantification of metabolic interaction between microbial species 143 29 4

From iron to antibiotics: Identification of conserved bacterial-fungal interactions across diverse partners 143 29 12 5

A real-time, transient kinetic study of Drosophila melanogaster Dicer-2 elucidates mechanism of termini-dependent cleavage of dsRNA. 199 8

Optimizing mevalonate pathway for squalene production in Yarrowia lipolytica 67 12

Single cell characterization of a synthetic bacterial clock with a hybrid feedback loop containing dCas9-sgRNA 33 18

Modular cell-free expression plasmids to accelerate biological design in cells 33 18 4

Resource reallocation in engineered Escherichia coli strains with reduced genomes 67 12

Reconstruction of Fur pan-regulon uncovers the complexity and diversity of transcriptional regulation in E. coli 79 12 9 3

The Macerprep: a minimalist kit- and enzyme-free high-yield miniprep utilising alkaline lysis and alkaline hydrolysis principles 199 115

Uptake of exogenous serine is important to maintain sphingolipid homeostasis in Saccharomyces cerevisiae 69 34 3

Metabolism of long-chain fatty acids affects disulfide bond formation in Escherichia coli and activates envelope stress response pathways as a combat strategy 67 12 3

Repurposing the yeast peroxisome to compartmentalize a toxic enzyme enables improved (S)-reticuline production 67 33 3

Phenotypic changes of bacteria through opportunity and global methylation leads to antibiotic resistance 158 79 52 12

Integrated metabolic modeling, culturing and transcriptomics explains enhanced virulence of V. cholerae during co-infection with ETEC 114 12

Cheminformatics Analysis of Natural Product Scaffolds: Comparison of Scaffolds Produced by Animals, Plants, Fungi and Bacteria 129 4

Evolution-based design of chorismate mutase enzymes 129 63 8

Cell-free synthesis of natural compounds from genomic DNA of biosynthetic gene clusters 196 129 67 18 8

A Penicillium rubens platform strain for secondary metabolite production 67 12