Synthetic Biology Pubs

All JGI Publications

2024

• Alsup, Tyler A. et al. (2024) Characterization of UbiA terpene synthases with a precursor overproduction system in Escherichia coli. . 10.1016/bs.mie.2024.02.001
• Champagne, Sarah E. et al. (2024) Biocatalytic Stereoselective Oxidation of 2‑Arylindoles. Journal of the American Chemical Society 146(4), 2728-2735. 10.1021/jacs.3c12393
• Chiarelli, Daniela Prates et al. (2024) Expression and characterization of monofunctional alcohol dehydrogenase enzymes in Clostridium thermocellum. Metabolic Engineering Communications 19, e00243. 10.1016/j.mec.2024.e00243
• Chiarelli, Daniela Prates et al. (2024) Expression and characterization of monofunctional alcohol dehydrogenase enzymes in Clostridium thermocellum. Metabolic Engineering Communications 19, e00243. 10.1016/j.mec.2024.e00243
• Conway, Jonathan M. et al. (2024) Arabidopsis Root Microbiome Microfluidic (ARMM) Device for Imaging Bacterial Colonization and Morphogenesis of Arabidopsis Roots. Methods in Molecular Biology 2805, 213-228. 10.1007/978-1-0716-3854-5_15
• Conway, Jonathan M. et al. (2024) Arabidopsis Root Microbiome Microfluidic (ARMM) Device for Imaging Bacterial Colonization and Morphogenesis of Arabidopsis Roots. Methods in Molecular Biology 2805, 213-228. 10.1007/978-1-0716-3854-5_15
• Covington, Jonathan K. et al. (2024) Biochemical characterization of Fsa16295Glu from “Fervidibacter sacchari,” the first hyperthermophilic GH50 with β-1,3-endoglucanase activity and founding member of the subfamily GH50_3. Frontiers in Microbiology 15, 1355444. 10.3389/fmicb.2024.1355444
• Covington, Jonathan K. et al. (2024) Biochemical characterization of Fsa16295Glu from “Fervidibacter sacchari,” the first hyperthermophilic GH50 with β-1,3-endoglucanase activity and founding member of the subfamily GH50_3. Frontiers in Microbiology 15, 1355444. 10.3389/fmicb.2024.1355444
• DeChellis, Antonio et al. (2024) Supercharging Carbohydrate Binding Module Alone Enhances Endocellulase Thermostability, Binding, and Activity on Cellulosic Biomass. ACS Sustainable Chemistry & Engineering 12(9), 3500-3516. 10.1021/acssuschemeng.3c06266
• Grosjean, Nicolas et al. (2024) A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria. Nature Communications 15(1), 3167. 10.1038/s41467-024-47486-z
• Grosjean, Nicolas et al. (2024) A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria. Nature Communications 15(1), 3167. 10.1038/s41467-024-47486-z
• Haddad Momeni, Majid et al. (2024) Insights into the action of phylogenetically diverse microbial expansins on the structure of cellulose microfibrils. Biotechnology for Biofuels and Bioproducts 17(1), 56. 10.1186/s13068-024-02500-w
• Haddad Momeni, Majid et al. (2024) Insights into the action of phylogenetically diverse microbial expansins on the structure of cellulose microfibrils. Biotechnology for Biofuels and Bioproducts 17(1), 56. 10.1186/s13068-024-02500-w
• Hu, Zhijuan et al. (2024) Engineered Biosynthesis and Anticancer Studies of Ring-Expanded Antimycin-Type Depsipeptides. ACS Synthetic Biology 13(5), 1562-1571. 10.1021/acssynbio.4c00193
• Hu, Zhijuan et al. (2024) Engineered Biosynthesis and Anticancer Studies of Ring-Expanded Antimycin-Type Depsipeptides. ACS Synthetic Biology 13(5), 1562-1571. 10.1021/acssynbio.4c00193
• Kim, Youngchang et al. (2024) Revealing reaction intermediates in one-carbon elongation by thiamine diphosphate/CoA-dependent enzyme family. Communications Chemistry 7(1), 160. 10.1038/s42004-024-01242-y
• Kim, Youngchang et al. (2024) Revealing reaction intermediates in one-carbon elongation by thiamine diphosphate/CoA-dependent enzyme family. Communications Chemistry 7(1), 160. 10.1038/s42004-024-01242-y
• Koper, Kaan et al. (2024) Multisubstrate specificity shaped the complex evolution of the aminotransferase family across the tree of life. Proceedings of the National Academy of Sciences of the United States of America 121(26), e2405524121. 10.1073/pnas.2405524121
• Koper, Kaan et al. (2024) Multisubstrate specificity shaped the complex evolution of the aminotransferase family across the tree of life. Proceedings of the National Academy of Sciences of the United States of America 121(26), e2405524121. 10.1073/pnas.2405524121
• Lee, Ye-Gi et al. (2024) Self-Buffering system for Cost-Effective production of lactic acid from glucose and xylose using Acid-Tolerant Issatchenkia orientalis. Bioresource Technology 399, 130641. 10.1016/j.biortech.2024.130641
• Li, Li et al. (2024) Biosynthesis of Cytosporones in Leotiomycetous Filamentous Fungi. Journal of the American Chemical Society 146(9), 6189-6198. 10.1021/jacs.3c14066
• Panich, Justin et al. (2024) Functional plasticity of HCO3 – uptake and CO2 fixation in Cupriavidus necator H16. Bioresource Technology 410, 131214. 10.1016/j.biortech.2024.131214
• Panich, Justin et al. (2024) Functional plasticity of HCO3 – uptake and CO2 fixation in Cupriavidus necator H16. Bioresource Technology 410, 131214. 10.1016/j.biortech.2024.131214
• Roze, Ludmila V. et al. (2024) High Throughput Phosphoglycolate Phosphatase Activity Assay Using Crude Leaf Extract and Recombinant Enzyme to Determine Kinetic Parameters Km and Vmax Using a Microplate Reader. Methods in Molecular Biology 2792, 3-17. 10.1007/978-1-0716-3802-6_1
• Roze, Ludmila V. et al. (2024) High Throughput Phosphoglycolate Phosphatase Activity Assay Using Crude Leaf Extract and Recombinant Enzyme to Determine Kinetic Parameters Km and Vmax Using a Microplate Reader. Methods in Molecular Biology 2792, 3-17. 10.1007/978-1-0716-3802-6_1
• Sanford, Patrick A. et al. (2024) An efficient cre‐based workflow for genomic integration and expression of large biosynthetic pathways in Eubacterium limosum. Biotechnology and Bioengineering 121(10), 3360-3366. 10.1002/bit.28796
• Sanford, Patrick A. et al. (2024) Development of a Recombineering System for the Acetogen Eubacterium limosum with Cas9 Counterselection for Markerless Genome Engineering. ACS Synthetic Biology 13(8), 2505-2514. 10.1021/acssynbio.4c00253
• Sanford, Patrick A. et al. (2024) An efficient cre‐based workflow for genomic integration and expression of large biosynthetic pathways in Eubacterium limosum. Biotechnology and Bioengineering 121(10), 3360-3366. 10.1002/bit.28796
• Sanford, Patrick A. et al. (2024) Development of a Recombineering System for the Acetogen Eubacterium limosum with Cas9 Counterselection for Markerless Genome Engineering. ACS Synthetic Biology 13(8), 2505-2514. 10.1021/acssynbio.4c00253
• Shen, Yihui et al. (2024) Mitochondrial ATP generation is more proteome efficient than glycolysis. Nature Chemical Biology , 1-10. 10.1038/s41589-024-01571-y
• Stroud, Marissa N. Roghair et al. (2024) Optimized CRISPR Interference System for Investigating Pseudomonas alloputida Genes Involved in Rhizosphere Microbiome Assembly. ACS Synthetic Biology 13(9), 2912-2925. 10.1021/acssynbio.4c00312
• Stroud, Marissa N. Roghair et al. (2024) Optimized CRISPR Interference System for Investigating Pseudomonas alloputida Genes Involved in Rhizosphere Microbiome Assembly. ACS Synthetic Biology 13(9), 2912-2925. 10.1021/acssynbio.4c00312
• Tafrishi, Aida et al. (2024) Functional genomic screening in Komagataella phaffii enabled by high-activity CRISPR-Cas9 library. Metabolic Engineering 85, 73-83. 10.1016/j.ymben.2024.07.006
• Tafrishi, Aida et al. (2024) Functional genomic screening in Komagataella phaffii enabled by high-activity CRISPR-Cas9 library. Metabolic Engineering 85, 73-83. 10.1016/j.ymben.2024.07.006
• Wyatt, G. et al. (2024) Characterization of switchgrass (Panicum virgatum L.) PvKSL1 as a levopimaradiene/abietadiene‐type diterpene synthase. Plant Biology . 10.1111/plb.13708
• Wyatt, G. et al. (2024) Characterization of switchgrass (Panicum virgatum L.) PvKSL1 as a levopimaradiene/abietadiene‐type diterpene synthase. Plant Biology . 10.1111/plb.13708
• Yu, Yaochun et al. (2024) Substrate promiscuity of xenobiotic-transforming hydrolases from stream biofilms impacted by treated wastewater. Water Research 256, 121593. 10.1016/j.watres.2024.121593
• Yu, Yaochun et al. (2024) Substrate promiscuity of xenobiotic-transforming hydrolases from stream biofilms impacted by treated wastewater. Water Research 256, 121593. 10.1016/j.watres.2024.121593

2023

• Babaei, Mahsa et al. (2023) Coupling High-Throughput and Targeted Screening for Identification of Nonobvious Metabolic Engineering Targets. ACS Synthetic Biology 13(1), 168-182. 10.1021/acssynbio.3c00396
• Back, Daniel et al. (2023) Identification, Heterologous Expression, and Characterization of the Tolypodiol Biosynthetic Gene Cluster through an Integrated Approach. ACS Chemical Biology 18(8), 1797-1807. 10.1021/acschembio.3c00225
• Brown, Malory O. et al. (2023) Sterol methyltransferases in uncultured bacteria complicate eukaryotic biomarker interpretations. Nature Communications 14(1), 1859. 10.1038/s41467-023-37552-3
• Chiang, Chang-Hwa et al. (2023) Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction. Proceedings of the National Academy of Sciences of the United States of America 120(15), e2218248120. 10.1073/pnas.2218248120
• Dubinkina, Veronika et al. (2023) A transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strains. Microbiology Spectrum 12(1), e02536-23. 10.1128/spectrum.02536-23
• Dubinkina, Veronika et al. (2023) A transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strains. Microbiology Spectrum 12(1), e02536-23. 10.1128/spectrum.02536-23
• Dubinkina, Veronika et al. (2023) A transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strains. Microbiology Spectrum 12(1), e02536-23. 10.1128/spectrum.02536-23
• Gauttam, Rahul et al. (2023) Development of genetic tools for heterologous protein expression in a pentose‐utilizing environmental isolate of Pseudomonas putida. Microbial Biotechnology 16(3), 645-661. 10.1111/1751-7915.14205
• Gopal, Madan R. et al. (2023) Reductive Enzyme Cascades for Valorization of Polyethylene Terephthalate Deconstruction Products. ACS Catalysis 13(7), 4778-4789. 10.1021/acscatal.2c06219
• Kuch, Nathaniel J. et al. (2023) Contribution of calcium ligands in substrate binding and product release in the Acetovibrio thermocellus glycoside hydrolase family 9 cellulase CelR. Journal of Biological Chemistry 299(5), 104655. 10.1016/j.jbc.2023.104655
• Lee, Seung Hwan et al. (2023) Identification of 2‑Hydroxyacyl-CoA Synthases with High Acyloin Condensation Activity for Orthogonal One-Carbon Bioconversion. ACS Catalysis 13(18), 12007-12020. 10.1021/acscatal.3c02373
• Lillington, Stephen P et al. (2023) Expression and characterization of spore coat CotH kinases from the cellulosomes of anaerobic fungi (Neocallimastigomycetes). Protein Expression and Purification 210, 106323. 10.1016/j.pep.2023.106323
• Lin, Alex Y W et al. (2023) Statistical 3D morphology characterization of vaterite microspheres produced by engineered Escherichia coli. Biomaterials Advances 156, 213711. 10.1016/j.bioadv.2023.213711
• Lin, Alex Y W et al. (2023) Statistical 3D morphology characterization of vaterite microspheres produced by engineered Escherichia coli. Biomaterials Advances 156, 213711. 10.1016/j.bioadv.2023.213711
• Lin, Alex Y W et al. (2023) Statistical 3D morphology characterization of vaterite microspheres produced by engineered Escherichia coli. Biomaterials Advances 156, 213711. 10.1016/j.bioadv.2023.213711
• Nain, Priyanka et al. (2023) Reductive amination cascades in cell‐free and resting whole cell formats for valorization of lignin deconstruction products. Biotechnology and Bioengineering 121(2), 593-604. 10.1002/bit.28604
• Nain, Priyanka et al. (2023) Reductive amination cascades in cell‐free and resting whole cell formats for valorization of lignin deconstruction products. Biotechnology and Bioengineering 121(2), 593-604. 10.1002/bit.28604
• Nain, Priyanka et al. (2023) Reductive amination cascades in cell‐free and resting whole cell formats for valorization of lignin deconstruction products. Biotechnology and Bioengineering 121(2), 593-604. 10.1002/bit.28604
• Nattermann, Maren et al. (2023) Engineering a new-to-nature cascade for phosphate-dependent formate to formaldehyde conversion in vitro and in vivo. Nature Communications 14(1), 2682. 10.1038/s41467-023-38072-w
• Ramesh, Adithya et al. (2023) acCRISPR: an activity-correction method for improving the accuracy of CRISPR screens. Communications Biology 6(1), 617. 10.1038/s42003-023-04996-8
• Rasor, Blake J. et al. (2023) Cell Extracts from Bacteria and Yeast Retain Metabolic Activity after Extended Storage and Repeated Thawing. ACS Synthetic Biology 12(3), 904-908. 10.1021/acssynbio.2c00685
• Seo, Hyeongmin et al. (2023) Rewiring metabolism of Clostridium thermocellum for consolidated bioprocessing of lignocellulosic biomass poplar to produce short-chain esters. Bioresource Technology 384, 129263. 10.1016/j.biortech.2023.129263
• Seo, Hyeongmin et al. (2023) Engineering a Synthetic Escherichia coli Coculture for Compartmentalized de novo Biosynthesis of Isobutyl Butyrate from Mixed Sugars. ACS Synthetic Biology 13(1), 259-268. 10.1021/acssynbio.3c00493
• Takawira, Lazarus T. et al. (2023) Functional investigation of five R2R3-MYB transcription factors associated with wood development in Eucalyptus using DAP-seq-ML. Plant Molecular Biology , 1-25. 10.1007/s11103-023-01376-y
• Tian, Jiayi et al. (2023) Custom tuning of Rieske oxygenase reactivity. Nature Communications 14(1), 5858. 10.1038/s41467-023-41428-x
• Tian, Jiayi et al. (2023) Leveraging a Structural Blueprint to Rationally Engineer the Rieske Oxygenase TsaM. Biochemistry 62(11), 1807-1822. 10.1021/acs.biochem.3c00150
• Wu, Zong-Yen et al. (2023) Metabolic engineering of low-pH-tolerant non-model yeast, Issatchenkia orientalis, for production of citramalate. Metabolic Engineering Communications 16, e00220. 10.1016/j.mec.2023.e00220
• Yi, Xiunan et al. (2023) Establishing a versatile toolkit of flux enhanced strains and cell extracts for pathway prototyping. Metabolic Engineering 80, 241-253. 10.1016/j.ymben.2023.10.008
• Yi, Xiunan et al. (2023) Establishing a versatile toolkit of flux enhanced strains and cell extracts for pathway prototyping. Metabolic Engineering 80, 241-253. 10.1016/j.ymben.2023.10.008
• Yi, Xiunan et al. (2023) Establishing a versatile toolkit of flux enhanced strains and cell extracts for pathway prototyping. Metabolic Engineering 80, 241-253. 10.1016/j.ymben.2023.10.008
• Zhang, Weimin et al. (2023) Manipulating the 3D organization of the largest synthetic yeast chromosome. Molecular Cell 83(23), 4424-4437.e5. 10.1016/j.molcel.2023.10.015
• Zhang, Weimin et al. (2023) Manipulating the 3D organization of the largest synthetic yeast chromosome. Molecular Cell 83(23), 4424-4437.e5. 10.1016/j.molcel.2023.10.015
• Zhang, Weimin et al. (2023) Manipulating the 3D organization of the largest synthetic yeast chromosome. Molecular Cell 83(23), 4424-4437.e5. 10.1016/j.molcel.2023.10.015

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
• 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
• Cheng, Ming-Hsun et al. (2022) Cas9-Based Metabolic Engineering of Issatchenkia orientalis for Enhanced Utilization of Cellulosic Hydrolysates. Journal of Agricultural and Food Chemistry 70(38), 12085-12094. 10.1021/acs.jafc.2c04251
• 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
• DeMirci, Hasan et al. (2022) Intersubunit Coupling Enables Fast CO2‑Fixation by Reductive Carboxylases. ACS Central Science 8(8), 1091-1101. 10.1021/acscentsci.2c00057
• Gambacorta, Francesca V. et al. (2022) Combinatorial library design for improving isobutanol production in Saccharomyces cerevisiae. Frontiers in Bioengineering and Biotechnology 10, 1080024. 10.3389/fbioe.2022.1080024
• Han, Sang-Woo et al. (2022) Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes. Current Opinion in Microbiology 68, 102172. 10.1016/j.mib.2022.102172
• Karannagoda, Nadeeshani et al. (2022) Eucalyptus grandis AUX/INDOLE-3-ACETIC ACID 13 (EgrIAA13) is a novel transcriptional regulator of xylogenesis. Plant Molecular Biology 109(1-2), 51-65. 10.1007/s11103-022-01255-y
• Keown, Rachel A. et al. (2022) Novel Viral DNA Polymerases From Metagenomes Suggest Genomic Sources of Strand-Displacing Biochemical Phenotypes. Frontiers in Microbiology 13, 858366. 10.3389/fmicb.2022.858366
• Koper, Kaan et al. (2022) Evolutionary origin and functional diversification of aminotransferases. Journal of Biological Chemistry 298(8), 102122. 10.1016/j.jbc.2022.102122
• Koper, Kaan et al. (2022) Biochemical characterization of plant aromatic aminotransferases. 680, 35-83. 10.1016/bs.mie.2022.07.034
• Lee, Ye-Gi et al. (2022) Cas9-Based Metabolic Engineering of Issatchenkia orientalis for Enhanced Utilization of Cellulosic Hydrolysates. Journal of Agricultural and Food Chemistry 70(38), 12085-12094. 10.1021/acs.jafc.2c04251
• Liew, Fungmin Eric et al. (2022) 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
• Lupish, Brian et al. (2022) Genome‐wide CRISPR‐Cas9 screen reveals a persistent null‐hyphal phenotype that maintains high carotenoid production in Yarrowia lipolytica. Biotechnology and Bioengineering 119(12), 3623-3631. 10.1002/bit.28219
• 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 8(4), 430-440. 10.1021/acscentsci.1c01570
• 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
• Pasquini, Miriam et al. (2022) Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase. Cell Reports 39(7), 110834. 10.1016/j.celrep.2022.110834
• 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
• 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
• Sarkar, Snigdha et al. (2022) Applying Promiscuous RiPP Enzymes to Peptide Backbone N‑Methylation Chemistry. ACS Chemical Biology 17(8), 2165-2178. 10.1021/acschembio.2c00293
• Sasaki, Yusuke et al. (2022) Metabolic engineering for valorization of macroalgae biomass. Metabolic Engineering 71, 42-61. 10.1016/j.ymben.2022.01.005
• Seo, Hyeongmin et al. (2022) Proteome reallocation enables the selective de novo biosynthesis of non-linear, branched-chain acetate esters. Metabolic Engineering 73, 38-49. 10.1016/j.ymben.2022.05.003
• Seshadri, Rekha et al. (2022) Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes. Cell Genomics 2(12), 100213. 10.1016/j.xgen.2022.100213
• 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
• Sharon, Itai et al. (2022) A cryptic third active site in cyanophycin synthetase creates primers for polymerization. Nature Communications 13(1), 3923. 10.1038/s41467-022-31542-7
• Snodgrass, Harrison M. et al. (2022) Directed Evolution of Flavin-Dependent Halogenases for Site- and Atroposelective Halogenation of 3‑Aryl-4(3H)‑Quinazolinones via Kinetic or Dynamic Kinetic Resolution. Journal of the American Chemical Society 144(36), 16676-16682. 10.1021/jacs.2c07422
• Tiedge, Kira et al. (2022) Comparative transcriptomics and metabolomics reveal specialized metabolite drought stress responses in switchgrass (Panicum virgatum). New Phytologist 236(4), 1393-1408. 10.1111/nph.18443
• Vögeli, Bastian et al. (2022) Cell-free prototyping enables implementation of optimized reverse β-oxidation pathways in heterotrophic and autotrophic bacteria. Nature Communications 13(1), 3058. 10.1038/s41467-022-30571-6
• Wimmer, Franziska et al. (2022) A TXTL-Based Assay to Rapidly Identify PAMs for CRISPR-Cas Systems with Multi-Protein Effector Complexes. 2433, 391-411. 10.1007/978-1-0716-1998-8_24
• 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
• Wu, Ruonan et al. (2022) Structural characterization of a soil viral auxiliary metabolic gene product – a functional chitosanase. Nature Communications 13(1), 5485. 10.1038/s41467-022-32993-8
• Yi, Xiunan et al. (2022) Considering Strain Variation and Non-Type Strains for Yeast Metabolic Engineering Applications. Life 12(4), 510. 10.3390/life12040510
• Zhao, Zhiying et al. (2022) Discovering untapped biochemistry in microorganisms from hidden corners. Nature Reviews Microbiology 20(11), 639-639. 10.1038/s41579-022-00795-w
• Zhao, Zhiying et al. (2022) Chromosomal integration of complex DNA constructs using CRAGE and CRAGE-Duet systems. STAR Protocols 3(3), 101546. 10.1016/j.xpro.2022.101546
• 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
• 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
• 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
• 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
• de Vries, Lisanne et al. (2021) pHBMT1, a BAHD-family monolignol acyltransferase, mediates lignin acylation in poplar. Plant Physiology 188(2), 1014-1027. 10.1093/plphys/kiab546
• 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
• 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
• 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
• Fackler, N. et al. (2021) Transcriptional control of Clostridium autoethanogenum using CRISPRi. Synthetic Biology 6(1). 10.1093/synbio/ysab008
• 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
• 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
• 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
• 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
• 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
• Ke, Jing et al. (2021) 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
• 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
• 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
• Lee, Jong-Won et al. (2021) Controlling selectivity of modular microbial biosynthesis of butyryl-CoA-derived designer esters. Metabolic Engineering 69, 262-274. 10.1016/j.ymben.2021.12.001
• Mondal, D. et al. (2021) Flavin-dependent halogenases catalyze enantioselective olefin halocyclization. Nature Communications 12(1). 10.1038/s41467-021-23503-3
• Niu, Puhua et al. (2021) TRIMER: Transcription Regulation Integrated with Metabolic Regulation. iScience 24(11), 103218. 10.1016/j.isci.2021.103218
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• Zhao, H. M. et al. (2021) Editorial overview: Energy biotechnology. Current Opinion in Biotechnology 67, III-V. 10.1016/j.copbio.2021.01.018

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
• 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
• 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
• 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
• 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
• Karunanithi, P. S. et al. (2020) The foxtail millet (Setaria italica) terpene synthase gene family. Plant J . 10.1111/tpj.14771
• 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
• 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
• 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
• 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
• 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

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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• Fleming, S. R. et al. (2019) Flexizyme-Enabled Benchtop Biosynthesis of Thiopeptides. J Am Chem Soc 141(2), 758-762. 10.1021/jacs.8b11521
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• Pelot, K. A. et al. (2019) Diterpene Synthase-Catalyzed Biosynthesis of Distinct Clerodane Stereoisomers. Chembiochem 20(1), 111-117. 10.1002/cbic.201800580
• 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
• Shulse, C. N. et al. (2019) Engineered root bacteria release plant-available phosphate from phytate. Appl Environ Microbiol . 10.1128/AEM.01210-19
• 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
• 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
• 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

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
• Coates, R. C. et al. (2018) An integrated workflow for phenazine-modifying enzyme characterization. J Ind Microbiol Biotechnol . 10.1007/s10295-018-2025-5
• Dippel, A. B. et al. (2018) Chemiluminescent Biosensors for Detection of Second Messenger Cyclic di-GMP. ACS Chem Biol . 10.1021/acschembio.7b01019
• 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
• 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
• Kuang, M. C. et al. (2018) Repeated cis-regulatory tuning of a metabolic bottleneck gene during evolution. Mol Biol Evol . 10.1093/molbev/msy102
• 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
• 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
• 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
• 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
• 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
• 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

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
• 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
• Dossani, Z. Y. et al. (2017) A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering. Yeast . 10.1002/yea.3292
• 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
• Oberortner, E. et al. (2017) Streamlining the Design-to-Build Transition with Build-Optimization Software Tools. ACS Synth Biol . 10.1021/acssynbio.6b00200

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
• Gach, P. C. et al. (2016) A Droplet Microfluidic Platform for Automating Genetic Engineering. ACS Synth Biol . 10.1021/acssynbio.6b00011
• 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
• 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
• 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
• Tsementzi, D. et al. (2016) SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature 536(7615), 179-83. 10.1038/nature19068

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
• 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
• 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
• 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
• 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

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