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A High-Throughput Mass Spectrometric Enzyme Activity Assay Enabling the Discovery of Cytochrome P450 Biocatalysts.

de Rond T, Gao J, Zargar A, de Raad M, Cunha J, Northen TR, Keasling JD.

Angew Chem Int Ed Engl. 2019 May 29. doi: 10.1002/anie.201901782. [Epub ahead of print]


Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases.

Barajas JF, McAndrew RP, Thompson MG, Backman TWH, Pang B, de Rond T, Pereira JH, Benites VT, Martín HG, Baidoo EEK, Hillson NJ, Adams PD, Keasling JD.

J Ind Microbiol Biotechnol. 2019 May 21. doi: 10.1007/s10295-019-02189-z. [Epub ahead of print]


Building a global alliance of biofoundries.

Hillson N, Caddick M, Cai Y, Carrasco JA, Chang MW, Curach NC, Bell DJ, Le Feuvre R, Friedman DC, Fu X, Gold ND, Herrgård MJ, Holowko MB, Johnson JR, Johnson RA, Keasling JD, Kitney RI, Kondo A, Liu C, Martin VJJ, Menolascina F, Ogino C, Patron NJ, Pavan M, Poh CL, Pretorius IS, Rosser SJ, Scrutton NS, Storch M, Tekotte H, Travnik E, Vickers CE, Yew WS, Yuan Y, Zhao H, Freemont PS.

Nat Commun. 2019 May 9;10(1):2040. doi: 10.1038/s41467-019-10079-2. No abstract available.


Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism.

Thompson MG, Blake-Hedges JM, Cruz-Morales P, Barajas JF, Curran SC, Eiben CB, Harris NC, Benites VT, Gin JW, Sharpless WA, Twigg FF, Skyrud W, Krishna RN, Pereira JH, Baidoo EEK, Petzold CJ, Adams PD, Arkin AP, Deutschbauer AM, Keasling JD.

MBio. 2019 May 7;10(3). pii: e02577-18. doi: 10.1128/mBio.02577-18.


Engineered Reversal of Function in Glycolytic Yeast Promoters.

Rajkumar AS, Özdemir E, Lis AV, Schneider K, Qin J, Jensen MK, Keasling JD.

ACS Synth Biol. 2019 May 15. doi: 10.1021/acssynbio.9b00027. [Epub ahead of print]


The Transcriptome and Flux Profiling of Crabtree-Negative Hydroxy Acid-Producing Strains of Saccharomyces cerevisiae Reveals Changes in the Central Carbon Metabolism.

Jessop-Fabre MM, Dahlin J, Biron MB, Stovicek V, Ebert BE, Blank LM, Budin I, Keasling JD, Borodina I.

Biotechnol J. 2019 Apr 10:e1900013. doi: 10.1002/biot.201900013. [Epub ahead of print]


Exploring small-scale chemostats to scale up microbial processes: 3-hydroxypropionic acid production in S. cerevisiae.

Lis AV, Schneider K, Weber J, Keasling JD, Jensen MK, Klein T.

Microb Cell Fact. 2019 Mar 11;18(1):50. doi: 10.1186/s12934-019-1101-5.


Coupling S-adenosylmethionine-dependent methylation to growth: Design and uses.

Luo H, Hansen ASL, Yang L, Schneider K, Kristensen M, Christensen U, Christensen HB, Du B, Özdemir E, Feist AM, Keasling JD, Jensen MK, Herrgård MJ, Palsson BO.

PLoS Biol. 2019 Mar 11;17(3):e2007050. doi: 10.1371/journal.pbio.2007050. eCollection 2019 Mar.


Complete biosynthesis of cannabinoids and their unnatural analogues in yeast.

Luo X, Reiter MA, d'Espaux L, Wong J, Denby CM, Lechner A, Zhang Y, Grzybowski AT, Harth S, Lin W, Lee H, Yu C, Shin J, Deng K, Benites VT, Wang G, Baidoo EEK, Chen Y, Dev I, Petzold CJ, Keasling JD.

Nature. 2019 Mar;567(7746):123-126. doi: 10.1038/s41586-019-0978-9. Epub 2019 Feb 27.


A rapid methods development workflow for high-throughput quantitative proteomic applications.

Chen Y, Vu J, Thompson MG, Sharpless WA, Chan LJG, Gin JW, Keasling JD, Adams PD, Petzold CJ.

PLoS One. 2019 Feb 14;14(2):e0211582. doi: 10.1371/journal.pone.0211582. eCollection 2019.


Production efficiency of the bacterial non-ribosomal peptide indigoidine relies on the respiratory metabolic state in S. cerevisiae.

Wehrs M, Prahl JP, Moon J, Li Y, Tanjore D, Keasling JD, Pray T, Mukhopadhyay A.

Microb Cell Fact. 2018 Dec 13;17(1):193. doi: 10.1186/s12934-018-1045-1.


Liquid Chromatography and Mass Spectrometry Analysis of Isoprenoid Intermediates in Escherichia coli.

Baidoo EEK, Wang G, Joshua CJ, Benites VT, Keasling JD.

Methods Mol Biol. 2019;1859:209-224. doi: 10.1007/978-1-4939-8757-3_11.


Short-chain ketone production by engineered polyketide synthases in Streptomyces albus.

Yuzawa S, Mirsiaghi M, Jocic R, Fujii T, Masson F, Benites VT, Baidoo EEK, Sundstrom E, Tanjore D, Pray TR, George A, Davis RW, Gladden JM, Simmons BA, Katz L, Keasling JD.

Nat Commun. 2018 Nov 1;9(1):4569. doi: 10.1038/s41467-018-07040-0.


Renewable production of high density jet fuel precursor sesquiterpenes from Escherichia coli.

Liu CL, Tian T, Alonso-Gutierrez J, Garabedian B, Wang S, Baidoo EEK, Benites V, Chen Y, Petzold CJ, Adams PD, Keasling JD, Tan T, Lee TS.

Biotechnol Biofuels. 2018 Oct 20;11:285. doi: 10.1186/s13068-018-1272-z. eCollection 2018.


Viscous control of cellular respiration by membrane lipid composition.

Budin I, de Rond T, Chen Y, Chan LJG, Petzold CJ, Keasling JD.

Science. 2018 Dec 7;362(6419):1186-1189. doi: 10.1126/science.aat7925. Epub 2018 Oct 25.


Synthetic Biology for Fundamental Biochemical Discovery.

Budin I, Keasling JD.

Biochemistry. 2019 Mar 19;58(11):1464-1469. doi: 10.1021/acs.biochem.8b00915. Epub 2018 Oct 31.


Synthetic Enzymology and the Fountain of Youth: Repurposing Biology for Longevity.

Lim YP, Go MK, Raida M, Inoue T, Wenk MR, Keasling JD, Chang MW, Yew WS.

ACS Omega. 2018 Sep 30;3(9):11050-11061. doi: 10.1021/acsomega.8b01620. Epub 2018 Sep 12.


Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification.

Li G, Jones KC, Eudes A, Pidatala VR, Sun J, Xu F, Zhang C, Wei T, Jain R, Birdseye D, Canlas PE, Baidoo EEK, Duong PQ, Sharma MK, Singh S, Ruan D, Keasling JD, Mortimer JC, Loqué D, Bartley LE, Scheller HV, Ronald PC.

BMC Biotechnol. 2018 Sep 4;18(1):54. doi: 10.1186/s12896-018-0464-8.


Commodity Chemicals From Engineered Modular Type I Polyketide Synthases.

Yuzawa S, Zargar A, Pang B, Katz L, Keasling JD.

Methods Enzymol. 2018;608:393-415. doi: 10.1016/bs.mie.2018.04.027. Epub 2018 May 26.


Modular 5'-UTR hexamers for context-independent tuning of protein expression in eukaryotes.

Petersen SD, Zhang J, Lee JS, Jakociunas T, Grav LM, Kildegaard HF, Keasling JD, Jensen MK.

Nucleic Acids Res. 2018 Nov 30;46(21):e127. doi: 10.1093/nar/gky734.


CasPER, a method for directed evolution in genomic contexts using mutagenesis and CRISPR/Cas9.

Jakočiūnas T, Pedersen LE, Lis AV, Jensen MK, Keasling JD.

Metab Eng. 2018 Jul;48:288-296. doi: 10.1016/j.ymben.2018.07.001. Epub 2018 Jul 5.


Probing the Flexibility of an Iterative Modular Polyketide Synthase with Non-Native Substrates in Vitro.

Curran SC, Hagen A, Poust S, Chan LJG, Garabedian BM, de Rond T, Baluyot MJ, Vu JT, Lau AK, Yuzawa S, Petzold CJ, Katz L, Keasling JD.

ACS Chem Biol. 2018 Aug 17;13(8):2261-2268. doi: 10.1021/acschembio.8b00422. Epub 2018 Jun 26.


De novo DNA synthesis using polymerase-nucleotide conjugates.

Palluk S, Arlow DH, de Rond T, Barthel S, Kang JS, Bector R, Baghdassarian HM, Truong AN, Kim PW, Singh AK, Hillson NJ, Keasling JD.

Nat Biotechnol. 2018 Aug;36(7):645-650. doi: 10.1038/nbt.4173. Epub 2018 Jun 18.


Alleviation of reactive oxygen species enhances PUFA accumulation in Schizochytrium sp. through regulating genes involved in lipid metabolism.

Zhang S, He Y, Sen B, Chen X, Xie Y, Keasling JD, Wang G.

Metab Eng Commun. 2018 Mar 27;6:39-48. doi: 10.1016/j.meteno.2018.03.002. eCollection 2018 Jun.


Engineering β-oxidation in Yarrowia lipolytica for methyl ketone production.

Hanko EKR, Denby CM, Sànchez I Nogué V, Lin W, Ramirez KJ, Singer CA, Beckham GT, Keasling JD.

Metab Eng. 2018 Jul;48:52-62. doi: 10.1016/j.ymben.2018.05.018. Epub 2018 May 28.


An Orthogonal and pH-Tunable Sensor-Selector for Muconic Acid Biosynthesis in Yeast.

Snoek T, Romero-Suarez D, Zhang J, Ambri F, Skjoedt ML, Sudarsan S, Jensen MK, Keasling JD.

ACS Synth Biol. 2018 Apr 20;7(4):995-1003. doi: 10.1021/acssynbio.7b00439. Epub 2018 Apr 5.


Biochemical Characterization of β-Amino Acid Incorporation in Fluvirucin B2 Biosynthesis.

Barajas JF, Zargar A, Pang B, Benites VT, Gin J, Baidoo EEK, Petzold CJ, Hillson NJ, Keasling JD.

Chembiochem. 2018 Jul 4;19(13):1391-1395. doi: 10.1002/cbic.201800169. Epub 2018 May 14.


Industrial brewing yeast engineered for the production of primary flavor determinants in hopped beer.

Denby CM, Li RA, Vu VT, Costello Z, Lin W, Chan LJG, Williams J, Donaldson B, Bamforth CW, Petzold CJ, Scheller HV, Martin HG, Keasling JD.

Nat Commun. 2018 Mar 20;9(1):965. doi: 10.1038/s41467-018-03293-x.


Discovery of enzymes for toluene synthesis from anoxic microbial communities.

Beller HR, Rodrigues AV, Zargar K, Wu YW, Saini AK, Saville RM, Pereira JH, Adams PD, Tringe SG, Petzold CJ, Keasling JD.

Nat Chem Biol. 2018 May;14(5):451-457. doi: 10.1038/s41589-018-0017-4. Epub 2018 Mar 19.


Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli.

George KW, Thompson MG, Kim J, Baidoo EEK, Wang G, Benites VT, Petzold CJ, Chan LJG, Yilmaz S, Turhanen P, Adams PD, Keasling JD, Lee TS.

Metab Eng. 2018 May;47:60-72. doi: 10.1016/j.ymben.2018.03.004. Epub 2018 Mar 9.


Engineered Production of Short-Chain Acyl-Coenzyme A Esters in Saccharomyces cerevisiae.

Krink-Koutsoubelis N, Loechner AC, Lechner A, Link H, Denby CM, Vögeli B, Erb TJ, Yuzawa S, Jakociunas T, Katz L, Jensen MK, Sourjik V, Keasling JD.

ACS Synth Biol. 2018 Apr 20;7(4):1105-1115. doi: 10.1021/acssynbio.7b00466. Epub 2018 Mar 12.


Synthetic biology of polyketide synthases.

Yuzawa S, Backman TWH, Keasling JD, Katz L.

J Ind Microbiol Biotechnol. 2018 Jul;45(7):621-633. doi: 10.1007/s10295-018-2021-9. Epub 2018 Feb 9.


Improving methyl ketone production in Escherichia coli by heterologous expression of NADH-dependent FabG.

Goh EB, Chen Y, Petzold CJ, Keasling JD, Beller HR.

Biotechnol Bioeng. 2018 May;115(5):1161-1172. doi: 10.1002/bit.26558. Epub 2018 Mar 1.


Isolation and characterization of novel mutations in the pSC101 origin that increase copy number.

Thompson MG, Sedaghatian N, Barajas JF, Wehrs M, Bailey CB, Kaplan N, Hillson NJ, Mukhopadhyay A, Keasling JD.

Sci Rep. 2018 Jan 25;8(1):1590. doi: 10.1038/s41598-018-20016-w.


Engineered polyketides: Synergy between protein and host level engineering.

Barajas JF, Blake-Hedges JM, Bailey CB, Curran S, Keasling JD.

Synth Syst Biotechnol. 2017 Sep 7;2(3):147-166. doi: 10.1016/j.synbio.2017.08.005. eCollection 2017 Sep. Review.


Constraining Genome-Scale Models to Represent the Bow Tie Structure of Metabolism for 13C Metabolic Flux Analysis.

Backman TWH, Ando D, Singh J, Keasling JD, García Martín H.

Metabolites. 2018 Jan 4;8(1). pii: E3. doi: 10.3390/metabo8010003.


Toward industrial production of isoprenoids in Escherichia coli: Lessons learned from CRISPR-Cas9 based optimization of a chromosomally integrated mevalonate pathway.

Alonso-Gutierrez J, Koma D, Hu Q, Yang Y, Chan LJG, Petzold CJ, Adams PD, Vickers CE, Nielsen LK, Keasling JD, Lee TS.

Biotechnol Bioeng. 2018 Apr;115(4):1000-1013. doi: 10.1002/bit.26530. Epub 2018 Feb 7.


Design, Engineering, and Characterization of Prokaryotic Ligand-Binding Transcriptional Activators as Biosensors in Yeast.

Ambri F, Snoek T, Skjoedt ML, Jensen MK, Keasling JD.

Methods Mol Biol. 2018;1671:269-290. doi: 10.1007/978-1-4939-7295-1_17.


Assembly and Multiplex Genome Integration of Metabolic Pathways in Yeast Using CasEMBLR.

Jakočiūnas T, Jensen ED, Jensen MK, Keasling JD.

Methods Mol Biol. 2018;1671:185-201. doi: 10.1007/978-1-4939-7295-1_12.


Autonomous control of metabolic state by a quorum sensing (QS)-mediated regulator for bisabolene production in engineered E. coli.

Kim EM, Woo HM, Tian T, Yilmaz S, Javidpour P, Keasling JD, Lee TS.

Metab Eng. 2017 Nov;44:325-336. doi: 10.1016/j.ymben.2017.11.004. Epub 2017 Nov 10.


A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering.

Dossani ZY, Reider Apel A, Szmidt-Middleton H, Hillson NJ, Deutsch S, Keasling JD, Mukhopadhyay A.

Yeast. 2018 Mar;35(3):273-280. doi: 10.1002/yea.3292. Epub 2017 Dec 7.


Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts.

Yaegashi J, Kirby J, Ito M, Sun J, Dutta T, Mirsiaghi M, Sundstrom ER, Rodriguez A, Baidoo E, Tanjore D, Pray T, Sale K, Singh S, Keasling JD, Simmons BA, Singer SW, Magnuson JK, Arkin AP, Skerker JM, Gladden JM.

Biotechnol Biofuels. 2017 Oct 23;10:241. doi: 10.1186/s13068-017-0927-5. eCollection 2017.


ClusterCAD: a computational platform for type I modular polyketide synthase design.

Eng CH, Backman TWH, Bailey CB, Magnan C, García Martín H, Katz L, Baldi P, Keasling JD.

Nucleic Acids Res. 2018 Jan 4;46(D1):D509-D515. doi: 10.1093/nar/gkx893.


Heterologous Gene Expression of N-Terminally Truncated Variants of LipPks1 Suggests a Functionally Critical Structural Motif in the N-terminus of Modular Polyketide Synthase.

Yuzawa S, Bailey CB, Fujii T, Jocic R, Barajas JF, Benites VT, Baidoo EEK, Chen Y, Petzold CJ, Katz L, Keasling JD.

ACS Chem Biol. 2017 Nov 17;12(11):2725-2729. doi: 10.1021/acschembio.7b00714. Epub 2017 Oct 17.


Oxidative cyclization of prodigiosin by an alkylglycerol monooxygenase-like enzyme.

de Rond T, Stow P, Eigl I, Johnson RE, Chan LJG, Goyal G, Baidoo EEK, Hillson NJ, Petzold CJ, Sarpong R, Keasling JD.

Nat Chem Biol. 2017 Nov;13(11):1155-1157. doi: 10.1038/nchembio.2471. Epub 2017 Sep 11.


The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization.

Morrell WC, Birkel GW, Forrer M, Lopez T, Backman TWH, Dussault M, Petzold CJ, Baidoo EEK, Costello Z, Ando D, Alonso-Gutierrez J, George KW, Mukhopadhyay A, Vaino I, Keasling JD, Adams PD, Hillson NJ, Garcia Martin H.

ACS Synth Biol. 2017 Dec 15;6(12):2248-2259. doi: 10.1021/acssynbio.7b00204. Epub 2017 Sep 8.


Engineering glucose metabolism of Escherichia coli under nitrogen starvation.

Chubukov V, Desmarais JJ, Wang G, Chan LJG, Baidoo EE, Petzold CJ, Keasling JD, Mukhopadhyay A.

NPJ Syst Biol Appl. 2017 Jan 5;3:16035. doi: 10.1038/npjsba.2016.35. eCollection 2017.


Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks.

d'Espaux L, Ghosh A, Runguphan W, Wehrs M, Xu F, Konzock O, Dev I, Nhan M, Gin J, Reider Apel A, Petzold CJ, Singh S, Simmons BA, Mukhopadhyay A, García Martín H, Keasling JD.

Metab Eng. 2017 Jul;42:115-125. doi: 10.1016/j.ymben.2017.06.004. Epub 2017 Jun 10.


Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism.

Shymansky CM, Wang G, Baidoo EEK, Gin J, Apel AR, Mukhopadhyay A, García Martín H, Keasling JD.

Front Bioeng Biotechnol. 2017 May 24;5:31. doi: 10.3389/fbioe.2017.00031. eCollection 2017.


Intracellular cellobiose metabolism and its applications in lignocellulose-based biorefineries.

Parisutham V, Chandran SP, Mukhopadhyay A, Lee SK, Keasling JD.

Bioresour Technol. 2017 Sep;239:496-506. doi: 10.1016/j.biortech.2017.05.001. Epub 2017 May 4. Review.


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