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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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Home › Our Science › Science Programs › DNA Synthesis Science Program › Synthetic Biology Publications

Synthetic Biology Publications

All JGI Publications

  • 2022
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2022

Baisya, Dipankar et al. (2022) Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica. Nature Communications 13(1), 922. 10.1038/s41467-022-28540-0
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Banerjee, Deepro et al. (2022) EnZymClass: Substrate specificity prediction tool of plant acyl-ACP thioesterases based on ensemble learning. Current Research in Biotechnology 4, 1-9. 10.1016/j.crbiot.2021.12.002
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D'Angelo, Francesca et al. (2022) Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host. eLife 11, e70936. 10.7554/elife.70936
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de Vries, Lisanne et al. (2022) pHBMT1, a BAHD-family monolignol acyltransferase, mediates lignin acylation in poplar. Plant Physiology 188(2), 1014-1027. 10.1093/plphys/kiab546
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Ke, Jing et al. (2022) Development of platforms for functional characterization and production of phenazines using a multi-chassis approach via CRAGE. Metabolic Engineering 69, 188-197. 10.1016/j.ymben.2021.11.012
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Lee, Jong-Won et al. (2022) Controlling selectivity of modular microbial biosynthesis of butyryl-CoA-derived designer esters. Metabolic Engineering 69, 262-274. 10.1016/j.ymben.2021.12.001
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Macdonald, Spencer S. et al. (2022) A Synthetic Gene Library Yields a Previously Unknown Glycoside Phosphorylase That Degrades and Assembles Poly-β-1,3-GlcNAc, Completing the Suite of β‑Linked GlcNAc Polysaccharides. ACS Central Science . 10.1021/acscentsci.1c01570
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Niu, Puhua et al. (2022) Protocol for condition-dependent metabolite yield prediction using the TRIMER pipeline. STAR Protocols 3(1), 101184. 10.1016/j.xpro.2022.101184
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Rybnicky, Grant A. et al. (2022) Development of a Freeze-Dried CRISPR-Cas12 Sensor for Detecting Wolbachia in the Secondary Science Classroom. ACS Synthetic Biology 11(2), 835-842. 10.1021/acssynbio.1c00503
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Rybnicky, Grant A. et al. (2022) Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences. Nucleic Acids Research 50(6), 3523-3534. 10.1093/nar/gkac142
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Sasaki, Yusuke et al. (2022) Metabolic engineering for valorization of macroalgae biomass. Metabolic Engineering 71, 42-61. 10.1016/j.ymben.2022.01.005
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Sharon, Itai et al. (2022) Structure and Function of the β‑Asp-Arg Polymerase Cyanophycin Synthetase 2. ACS Chemical Biology 17(3), 670-679. 10.1021/acschembio.1c01007
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Wimmer, Franziska et al. (2022) A TXTL-Based Assay to Rapidly Identify PAMs for CRISPR-Cas Systems with Multi-Protein Effector Complexes. , 391-411. 10.1007/978-1-0716-1998-8_24
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Wimmer, Franziska et al. (2022) Rapid cell-free characterization of multi-subunit CRISPR effectors and transposons. Molecular Cell 82(6), 1210-1224.e6. 10.1016/j.molcel.2022.01.026
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2021

Arellano-Saab, A. et al. (2021) Three mutations repurpose a plant karrikin receptor to a strigolactone receptor. Proceedings of the National Academy of Sciences of the United States of America 118(30). 10.1073/pnas.2103175118
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Bomble, Yannick J. et al. (2021) Editorial: Cell Free Biocatalysis for the Production of Bioproducts. Frontiers in Energy Research 9, 781552. 10.3389/fenrg.2021.781552
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Bowman, E. K. et al. (2021) Sorting for secreted molecule production using a biosensor-in-microdroplet approach. Proceedings of the National Academy of Sciences of the United States of America 118(36). 10.1073/pnas.2106818118
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Chou, Alexander et al. (2021) An orthogonal metabolic framework for one-carbon utilization. Nature Metabolism 3(10), 1385-1399. 10.1038/s42255-021-00453-0
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del Cerro, C. et al. (2021) Intracellular pathways for lignin catabolism in white-rot fungi. Proceedings of the National Academy of Sciences of the United States of America 118(9), 10. 10.1073/pnas.2017381118
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Destan, Ebru et al. (2021) Structural insights into bifunctional thaumarchaeal crotonyl-CoA hydratase and 3-hydroxypropionyl-CoA dehydratase from Nitrosopumilus maritimus. Scientific Reports 11(1), 22849. 10.1038/s41598-021-02180-8
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DiMario, R. J. et al. (2021) Kinetic variation in grass phosphoenolpyruvate carboxylases provides opportunity to enhance C-4 photosynthetic efficiency. Plant Journal 105(6), 1677-1688. 10.1111/tpj.15141
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Fackler, N. et al. (2021) Stepping on the Gas to a Circular Economy: Accelerating Development of Carbon-Negative Chemical Production from Gas Fermentation. Annual Review of Chemical and Biomolecular Engineering 12, 439-470. 10.1146/annurev-chembioeng-120120-021122
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Fackler, N. et al. (2021) Transcriptional control of Clostridium autoethanogenum using CRISPRi. Synthetic Biology 6(1). 10.1093/synbio/ysab008
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Iwata, M. et al. (2021) Omics analyses and biochemical study of Phlebiopsis gigantea elucidate its degradation strategy of wood extractives. Scientific Reports 11(1). 10.1038/s41598-021-91756-5
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Jabusch, L. K. et al. (2021) Microfabrication of a chamber for high-resolution, in situ imaging of the whole root for plant–microbe interactions. International Journal of Molecular Sciences 22(15). 10.3390/ijms22157880
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Ke, J. et al. (2021) Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture. Trends in Biotechnology 39(3), 244-261. 10.1016/j.tibtech.2020.07.008
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Ke, Jing et al. (2021) CRAGE-CRISPR facilitates rapid activation of secondary metabolite biosynthetic gene clusters in bacteria. Cell Chemical Biology 29. https://doi.org/10.1016/j.chembiol.2021.08.009
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Khlystov, N. A. et al. (2021) A plant host, Nicotiana benthamiana, enables the production and study of fungal lignin-degrading enzymes. Communications Biology 4(1). 10.1038/s42003-021-02464-9
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Lee, J. W. et al. (2021) Probing specificities of alcohol acyltransferases for designer ester biosynthesis with a high-throughput microbial screening platform. Biotechnology and Bioengineering . 10.1002/bit.27926
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Mondal, D. et al. (2021) Flavin-dependent halogenases catalyze enantioselective olefin halocyclization. Nature Communications 12(1). 10.1038/s41467-021-23503-3
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Niu, Puhua et al. (2021) TRIMER: Transcription Regulation Integrated with Metabolic Regulation. iScience 24(11), 103218. 10.1016/j.isci.2021.103218
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Rasor, B. J. et al. (2021) An integrated in vivo/in vitro framework to enhance cell-free biosynthesis with metabolically rewired yeast extracts. Nature Communications 12. 10.1038/s41467-021-25233-y
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Rasor, B. J. et al. (2021) Toward sustainable, cell-free biomanufacturing. Current Opinion in Biotechnology 69, 136-144. 10.1016/j.copbio.2020.12.012
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Scheffen, M. et al. (2021) A new-to-nature carboxylation module to improve natural and synthetic CO2 fixation. Nature Catalysis 4(2), 105-115. 10.1038/s41929-020-00557-y
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Schmid, S. et al. (2021) Dissolved inorganic carbon accumulating complexes from autotrophic bacteria from extreme environments. Journal of Bacteriology , JB.00377-21. doi:10.1128/JB.00377-21
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Seo, H. et al. (2021) Engineering promiscuity of chloramphenicol acetyltransferase for microbial designer ester biosynthesis. Metabolic Engineering 66, 179-190. 10.1016/j.ymben.2021.04.005
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Sharon, I. et al. (2021) Structures and function of the amino acid polymerase cyanophycin synthetase. Nature Chemical Biology 17(10), 1101-1110. 10.1038/s41589-021-00854-y
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Smith, M. D. et al. (2021) p-Nitrophenyl esters provide new insights and applications for the thiolase enzyme OleA. Computational and Structural Biotechnology Journal 19, 3087-3096. 10.1016/j.csbj.2021.05.031
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Svoboda, Jessee et al. (2021) Evaluation of inducible promoter–riboswitch constructs for heterologous protein expression in the cyanobacterial species Anabaena sp. PCC 7120. Synthetic Biology 6(1), ysab019. 10.1093/synbio/ysab019
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Takino, J. et al. (2021) Biochemistry-Guided Prediction of the Absolute Configuration of Fungal Reduced Polyketides. Angewandte Chemie - International Edition 60(43), 23403-23411. 10.1002/anie.202110658
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Wang, Jue et al. (2021) Enzyme engineering and in vivo testing of a formate reduction pathway. Synthetic Biology 6(1), ysab020. 10.1093/synbio/ysab020
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Wang, Q. et al. (2021) Aerobic bacterial methane synthesis. Proceedings of the National Academy of Sciences of the United States of America 118(27). 10.1073/pnas.2019229118
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Zhao, H. M. et al. (2021) Editorial overview: Energy biotechnology. Current Opinion in Biotechnology 67, III-V. 10.1016/j.copbio.2021.01.018
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2020

Banerjee, D. et al. (2020) Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale. Nature Communications 11(1). 10.1038/s41467-020-19171-4
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Bowman, E. K. et al. (2020) Bidirectional titration of yeast gene expression using a pooled CRISPR guide RNA approach. Proc Natl Acad Sci U S A 117(31), 18424-18430. 10.1073/pnas.2007413117
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Cao, M. et al. (2020) A genetic toolbox for metabolic engineering of Issatchenkia orientalis. Metab Eng 59, 87-97. 10.1016/j.ymben.2020.01.005
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Ding, Y. et al. (2020) Genetic elucidation of interconnected antibiotic pathways mediating maize innate immunity. Nat Plants 6(11), 1375-1388. 10.1038/s41477-020-00787-9
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Karim, A. S. et al. (2020) Modular cell-free expression plasmids to accelerate biological design in cells. Synth Biol (Oxf) 5(1), ysaa019. 10.1093/synbio/ysaa019
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Karunanithi, P. S. et al. (2020) The foxtail millet (Setaria italica) terpene synthase gene family. Plant J . 10.1111/tpj.14771
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Kruger, A. et al. (2020) Development of a clostridia-based cell-free system for prototyping genetic parts and metabolic pathways. Metab Eng 62, 95-105. 10.1016/j.ymben.2020.06.004
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Liu, H. et al. (2020) Bacterial genome editing by coupling Cre-lox and CRISPR-Cas9 systems. PLoS One 15(11), e0241867. 10.1371/journal.pone.0241867
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Marques, W. L. et al. (2020) Sequence-based bioprospecting of myo-inositol oxygenase (Miox) reveals new homologues that increase glucaric acid production in Saccharomyces cerevisiae. Enzyme Microb Technol 140, 109623. 10.1016/j.enzmictec.2020.109623
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Marques, Wesley Leoricy et al. (2020) Sequence-based bioprospecting of myo-inositol oxygenase (Miox) reveals new homologues that increase glucaric acid production in Saccharomyces cerevisiae. Enzyme and Microbial Technology 140, 109623. 10.1016/j.enzmictec.2020.109623
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Mazzoli, R. et al. (2020) Construction of lactic acid overproducing Clostridium thermocellum through enhancement of lactate dehydrogenase expression. Enzyme Microb Technol 141. 10.1016/j.enzmictec.2020.109645
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2019

Armstrong, Zachary et al. (2019) Systematic Screening of Synthetic Gene-Encoded Enzymes for Synthesis of Modified Glycosides. ACS Catalysis 9(4), 3219-3227. 10.1021/acscatal.8b05179
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Bernhardsgrutter, I. et al. (2019) Awakening the Sleeping Carboxylase Function of Enzymes: Engineering the Natural CO2-Binding Potential of Reductases. J Am Chem Soc 141(25), 9778-9782. 10.1021/jacs.9b03431
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Close, D. M. et al. (2019) Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis. Mol Microbiol 112(6), 1784-1797. 10.1111/mmi.14393
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Ding, Yezhang et al. (2019) Multiple genes recruited from hormone pathways partition maize diterpenoid defences. Nature Plants 5(10), 1043-1056. 10.1038/s41477-019-0509-6
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Doud, D. F. R. et al. (2019) Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere. ISME J . 10.1038/s41396-019-0557-y
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Dudley, Q. M. et al. (2019) Cell-free biosynthesis of limonene using enzyme-enriched Escherichia coli lysates. Synth Biol (Oxf) 4(1), ysz003. 10.1093/synbio/ysz003
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Felczak, M. M. et al. (2019) Expression of Phosphofructokinase Is Not Sufficient to Enable Embden-Meyerhof-Parnas Glycolysis in Zymomonas mobilis ZM4. Front Microbiol 10, 2270. 10.3389/fmicb.2019.02270
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Fisher, B. F. et al. (2019) Site-Selective C-H Halogenation Using Flavin-Dependent Halogenases Identified via Family-Wide Activity Profiling. ACS Cent Sci 5(11), 1844-1856. 10.1021/acscentsci.9b00835
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Fleming, S. R. et al. (2019) Flexizyme-Enabled Benchtop Biosynthesis of Thiopeptides. J Am Chem Soc 141(2), 758-762. 10.1021/jacs.8b11521
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Glasgow, E. M. et al. (2019) Extent and Origins of Functional Diversity in a Subfamily of Glycoside Hydrolases. J Mol Biol 431(6), 1217-1233. 10.1016/j.jmb.2019.01.024
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Huang, J. et al. (2019) Rare earth element alcohol dehydrogenases widely occur among globally distributed, numerically abundant and environmentally important microbes. ISME J . 10.1038/s41396-019-0414-z
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Hussey, S. G. et al. (2019) A Standardized Synthetic Eucalyptus Transcription Factor and Promoter Panel for Re-engineering Secondary Cell Wall Regulation in Biomass and Bioenergy Crops. ACS Synth Biol 8(2), 463-465. 10.1021/acssynbio.8b00440
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Karunanithi, P. S. et al. (2019) Terpene Synthases as Metabolic Gatekeepers in the Evolution of Plant Terpenoid Chemical Diversity. Front Plant Sci 10, 1166. 10.3389/fpls.2019.01166
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Ke, J. et al. (2019) Multi-chassis engineering for heterologous production of microbial natural products. Curr Opin Biotechnol 62, 88-97. 10.1016/j.copbio.2019.09.005
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Mouncey, N. J. et al. (2019) New voyages to explore the natural product galaxy. J Ind Microbiol Biotechnol 46(3-4), 273-279. 10.1007/s10295-018-02122-w
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Muchlinski, A. et al. (2019) Biosynthesis and Emission of Stress-Induced Volatile Terpenes in Roots and Leaves of Switchgrass (Panicum virgatum L.). Front Plant Sci 10, 1144. 10.3389/fpls.2019.01144
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Murphy, K. M. et al. (2019) A Customizable Approach for the Enzymatic Production and Purification of Diterpenoid Natural Products. J Vis Exp (152). 10.3791/59992
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Nguyen, N. D. et al. (2019) ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks. BMC Genomics 20(Suppl 12), 1003. 10.1186/s12864-019-6329-2
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Nora, L. C. et al. (2019) A toolset of constitutive promoters for metabolic engineering of Rhodosporidium toruloides. Microb Cell Fact 18(1), 117. 10.1186/s12934-019-1167-0
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Pelot, K. A. et al. (2019) Diterpene Synthase-Catalyzed Biosynthesis of Distinct Clerodane Stereoisomers. Chembiochem 20(1), 111-117. 10.1002/cbic.201800580
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Schwartz, C. et al. (2019) Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica. Metab Eng 55, 102-110. 10.1016/j.ymben.2019.06.007
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Shulse, C. N. et al. (2019) Engineered root bacteria release plant-available phosphate from phytate. Appl Environ Microbiol . 10.1128/AEM.01210-19
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Stoffel, G. M. M. et al. (2019) Four amino acids define the CO2 binding pocket of enoyl-CoA carboxylases/reductases. Proc Natl Acad Sci U S A . 10.1073/pnas.1901471116
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Venetz, J. E. et al. (2019) Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality. Proc Natl Acad Sci U S A 116(16), 8070-8079. 10.1073/pnas.1818259116
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Wang, X. et al. (2019) Rational Reprogramming of O-Methylation Regioselectivity for Combinatorial Biosynthetic Tailoring of Benzenediol Lactone Scaffolds. J Am Chem Soc 141(10), 4355-4364. 10.1021/jacs.8b12967
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2018

Bernhardsgrutter, I. et al. (2018) The multicatalytic compartment of propionyl-CoA synthase sequesters a toxic metabolite. Nat Chem Biol 14(12), 1127-1132. 10.1038/s41589-018-0153-x
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Coates, R. C. et al. (2018) An integrated workflow for phenazine-modifying enzyme characterization. J Ind Microbiol Biotechnol . 10.1007/s10295-018-2025-5
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Dippel, A. B. et al. (2018) Chemiluminescent Biosensors for Detection of Second Messenger Cyclic di-GMP. ACS Chem Biol . 10.1021/acschembio.7b01019
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Gao, J. et al. (2018) Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions. J Vis Exp (134). 10.3791/57170
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Higgins, D. A. et al. (2018) Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast. Genetics 210(1), 219-234. 10.1534/genetics.118.301161
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Kuang, M. C. et al. (2018) Repeated cis-regulatory tuning of a metabolic bottleneck gene during evolution. Mol Biol Evol . 10.1093/molbev/msy102
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Li, G. et al. (2018) Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification. BMC Biotechnol 18(1), 54. 10.1186/s12896-018-0464-8
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Mafu, S. et al. (2018) Discovery, Biosynthesis and Stress-Related Accumulation of Dolabradiene-Derived Defenses in Maize. Plant Physiol 176(4), 2677-2690. 10.1104/pp.17.01351
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Murphy, K. M. et al. (2018) Functional Characterization of Two Class II Diterpene Synthases Indicates Additional Specialized Diterpenoid Pathways in Maize (Zea mays). Front Plant Sci 9, 1542. 10.3389/fpls.2018.01542
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Pelot, K. A. et al. (2018) Functional Diversity of Diterpene Synthases in the Biofuel Crop Switchgrass. Plant Physiol 178(1), 54-71. 10.1104/pp.18.00590
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Vogeli, B. et al. (2018) Combining Promiscuous Acyl-CoA Oxidase and Enoyl-CoA Carboxylase/Reductases for Atypical Polyketide Extender Unit Biosynthesis. Cell Chem Biol 25(7), 833-839 e4. 10.1016/j.chembiol.2018.04.009
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Xie, L. et al. (2018) Methylglucosylation of aromatic amino and phenolic moieties of drug-like biosynthons by combinatorial biosynthesis. Proc Natl Acad Sci U S A 115(22), E4980-E4989. 10.1073/pnas.1716046115
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2017

Danby, Phillip M. et al. (2017) Glycosyl Cations versus Allylic Cations in Spontaneous and Enzymatic Hydrolysis. Journal of the American Chemical Society 139(31), 10629-10632. 10.1021/jacs.7b05628
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Ding, Y. et al. (2017) Selinene Volatiles Are Essential Precursors for Maize Defense Promoting Fungal Pathogen Resistance. Plant Physiol 175(3), 1455-1468. 10.1104/pp.17.00879
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Dossani, Z. Y. et al. (2017) A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering. Yeast . 10.1002/yea.3292
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Mukherjee, S. et al. (2017) 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nat Biotechnol . 10.1038/nbt.3886
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Oberortner, E. et al. (2017) Streamlining the Design-to-Build Transition with Build-Optimization Software Tools. ACS Synth Biol . 10.1021/acssynbio.6b00200
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2016

Frei, C. S. et al. (2016) Analysis of Amino Acid Substitutions in AraC Variants that Respond to Triacetic Acid Lactone. Protein Sci . 10.1002/pro.2873
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Gach, P. C. et al. (2016) A Droplet Microfluidic Platform for Automating Genetic Engineering. ACS Synth Biol . 10.1021/acssynbio.6b00011
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Hillson, N. J. et al. (2016) Improving Synthetic Biology Communication: Recommended Practices for Visual Depiction and Digital Submission of Genetic Designs. ACS Synth Biol 5(6), 449-51. 10.1021/acssynbio.6b00146
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Javidpour, P. et al. (2016) Investigation of Proposed Ladderane Biosynthetic Genes from Anammox Bacteria by Heterologous Expression in E. coli. PLoS One 11(3), e0151087. 10.1371/journal.pone.0151087
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Schwander, T. et al. (2016) A synthetic pathway for the fixation of carbon dioxide in vitro. Science 354(6314), 900-904. 10.1126/science.aah5237
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Tsementzi, D. et al. (2016) SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature 536(7615), 179-83. 10.1038/nature19068
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2015

Bianchetti, C. M. et al. (2015) Active site and laminarin binding in glycoside hydrolase family 55. J Biol Chem 290(19), 11819-32. 10.1074/jbc.M114.623579
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Christen, M. et al. (2015) Genome Calligrapher: A Web Tool for Refactoring Bacterial Genome Sequences for de Novo DNA Synthesis. ACS Synth Biol 4(8), 927-34. 10.1021/acssynbio.5b00087
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Deng, K. et al. (2015) Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS. Front Bioeng Biotechnol 3, 153. 10.3389/fbioe.2015.00153
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Mak, W. S. et al. (2015) Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. Nat Commun 6, 10005. 10.1038/ncomms10005
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Siegel, J. B. et al. (2015) Computational protein design enables a novel one-carbon assimilation pathway. Proc Natl Acad Sci U S A 112(12), 3704-9. 10.1073/pnas.1500545112
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2014

Heins, R. A. et al. (2014) Phylogenomically Guided Identification of Industrially Relevant GH1 beta-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry. Acs Chemical Biology 9(9), 2082-2091. 10.1021/Cb500244v
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Karannagoda, Nadeeshani et al. Eucalyptus grandis AUX/INDOLE-3-ACETIC ACID 13 (EgrIAA13) is a novel transcriptional regulator of xylogenesis. Plant Molecular Biology , 1-15. 10.1007/s11103-022-01255-y
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Liew, Fungmin Eric et al. Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale. Nature Biotechnology 40(3), 335-344. 10.1038/s41587-021-01195-w
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