Publications 2015 – 2020


Haslinger K., Prather K.L.J. Heterologous caffeic acid biosynthesis in Escherichia coli is affected by choice of tyrosine ammonia lyase and redox partners for bacterial Cytochrome P450. Microb Cell Fact. 19(1):26. (2020) DOI: 10.1186/s12934-020-01300-9.

Dinh C.V., Chen X., Prather K.L.J. Development of a Quorum-Sensing Based Circuit for Control of Coculture Population Composition in a Naringenin Production System. ACS Synth Biol. 9(3): 590-597 (2020) DOI: 10.1021/acssynbio.9b00451.

Prather, K.L.J. 2020 “Accelerating and expanding nature to address its greatest challenges.” Nat. Catal. 3:181–183. DOI: 10.1038/s41929-020-0422-4.

Dinh, C.V. and K. L.J. Prather. 2020. “Layered and multi-input autonomous dynamic control strategies for metabolic engineering.” Curr. Opin. Biotechnol. 65: 156-162.  DOI: 10.1016/j.copbio.2020.02.015.

Fox, K.J. and K.L.J. Prather. 2020. “Carbon catabolite repression relaxation in Escherichia coli: global and sugar-specific methods for glucose and secondary sugar co-utilization.”  Curr. Opin. Chem. Eng. 30:9-16.  DOI:  10.1016/j.coche.2020.05.005.

Marques, W.L., L.A. Anderson, L. Sandoval, M.A. Hicks, K.L.J. Prather. 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.  DOI:  10.1016/j.enzmictec.2020.109623

Fox, K.J. and K.L.J. Prather.  2020. “Production of D-glyceric acid from D-galacturonate in Escherichia coli.” J. Ind. Microbiol. Biotechnol. 47:1075–1081.  DOI: 10.1007/s10295-020-02323-2

Zu, Y., K.L.J. Prather, G. Stephanopoulos.  2020. “Metabolic engineering strategies to overcome precursor limitations in isoprenoid biosynthesis,” Curr. Opin. Biotechnol. 66:171-178.  DOI: 10.1016/j.copbio.2020.07.005


Dinh C.V., Prather K.L.J. Development of an autonomous and bifunctional quorum-sensing circuit for metabolic flux control in engineered Escherichia coli. Proc Natl Acad Sci U S A. :116(51):25562-25568. (2019) DOI: 10.1073/pnas.1911144116.

Kunjapur A.M., Prather K.L.J. “Development of a Vanillate Biosensor for the
Vanillin Biosynthesis Pathway in E. coli”. ACS Synth Biol 8(9):1958-1967. (2019) DOI: 10.1021/acssynbio.9b00071.

Amorim C., Silvério S.C., Prather K.L.J., Rodrigues L.R. “From lignocellulosic
residues to market: Production and commercial potential of xylooligosaccharides.”
Biotechnol Adv. pii: S0734-9750(19)30078-3 (2019) DOI: 10.1016/j.biotechadv.2019.05.003. 

Prather K.L.J. “Chemistry as biology by design.” Microb Biotechnol. 12(1):30-31 (2019). DOI: 10.1111/1751-7915.13345.

Amorim, C., S.C. Silvério, R.F S. Gonçalves, A.C. Pinheiro, S. Silva, E. Coelho, M.A. Coimbra, Prather K.L.J., L.R. Rodrigues, “Downscale fermentation for xylooligosaccharides production by recombinant Bacillus subtilis 3610.” Carbohydrate Polymers 205:176-183 (2019). DOI: 10.1016/j.carbpol.2018.09.088

Boock, J.T., A.J.E. Freedman, G.A. Tompsett, S.K. Muse, A.J. Allen, L.A. Jackson, B. Castro-Dominguez, M.T. Timko, Prather K.L.J. (co-corresponding author), J.R. Thompson, “Engineered microbial biofuel production and recovery under supercritical carbon dioxide.” Nat. Commun. 10:587 (2019). DOI: 10.1038/s41467-019-08486-6


Tompsett, G.A., J.T. Boock, C. DiSpirito, E. Stoltz, D.R. Knutson, A.G. Rivard, M.R. Overdevest, C. N. Conlon, K.L.J. Prather, J.R. Thompson, M.T. Timko, “Extraction rate and energy efficiency of supercritical carbon dioxide recovery of higher alcohols from dilute aqueous solution.” Energy Technology 6(4): 683-693 (2018). DOI: 10.1002/ente.201700626.

Amorim, C., S.C. Silvério, S.P. Silva, E. Coelho, M.A. Coimbra, K.L.J. Prather, L.R. Rodrigues, “Single-step production of arabino-xylooligosaccharides by recombinant Bacillus subtilis 3610 cultivated in brewers’ spent grain.” Carbohydrate Polymers 199:546–554 (2018). DOI: 10.1016/j.carbpol.2018.07.017.

Freedman, A.J., K.C. Peet, J.T. Boock, K. Penn, K.L.J. Prather, J.R. Thompson. 2018. “Isolation, development, and genomic analysis of Bacillus megaterium SR7 for growth and metabolite production under supercritical carbon dioxide.” Front. Microbiol. 9:2152DOI: 10.3389/fmicb.2018.02152.

Haris S., Fang C., Bastidas-Oyanedel J.R., Prather K.J., Schmidt J.E., Thomsen M.H., “Natural antibacterial agents from arid-region pretreated lignocellulosic biomasses and extracts for the control of lactic acid bacteria in yeast fermentation.“ AMB Express 8(127) (2018). DOI: 10.1186/s13568-018-0654-8.

Bonk B.M., Tarasova Y., Hicks M.A., Tidor B. and K.L.J. Prather, “Rational design of thiolase substrate specificity for metabolic engineering applications.“ Biotechnol. Bioeng. (2018). DOI: 10.1002/bit.26737

de Lorenzo V., Prather K.L., Chen G.Q., O’Day E., von Kameke C., Oyarzún D.A., Hosta-Rigau L., Alsafar H., Cao C., Ji W., Okano H., Roberts R.J., Ronaghi M., Yeung K., Zhang F., Lee S.Y., “The power of synthetic biology for bioproduction, remediation and pollution control: The UN’s Sustainable Development Goals will inevitably require the application of molecular biology and biotechnology on a global scale.” EMBO Rep. 19(4): e45658 (2018). DOI: 10.15252/embr.201745658

Doong S.J., Gupta A. and K.L.J. Prather, “Layered dynamic regulation for improving metabolic pathway productivity in Escherichia coli.” Proc. Natl. Acad. Sci. U S A 115(12):2964-2969 (2018). DOI: 10.1073/pnas.1716920115

Anderson L.A., Islam M.A. and K.L.J. Prather, “Synthetic biology strategies for improving microbial synthesis of “green” biopolymers.” J. Biol. Chem. 293(14):5053-5061 (2018). DOI: 10.1074/jbc.TM117.000368

Tan S.Z., Reisch C.R. and K.L.J. Prather, “A Robust CRISPR Interference Gene Repression System in Pseudomonas.” J. Bacteriol. 200:7: e00575-17 (2018). DOI: 10.1128/JB.00575-1710.1128/JB.00575-17


Haslinger, K. and K.L. J. Prather, “Pathway towards renewable chemicals.” Nat. Microbiol. 2(12):1580-1581 (2017). DOI:10.1038/s41564-017-0071-9.

Tan, S.Z. and K. L. J. Prather, “Dynamic pathway regulation: recent advances and methods of construction.” Curr. Opin. Chem. Biol. 41:28-35 (2017). DOI:10.1016/j.cbpa.2017.10.004

Reisch, C.R. and K.L. J. Prather, “Scarless Cas9 Assisted Recombineering (no-SCAR) in Escherichia coli, an easy to use system for genome editing.” Curr. Prot. Mol. Biol. 117:31.8.1-31.8.20 (2017). DOI:10.1002/cpmb.29

Khlystov, N.A., W.Y. Chan, A.M. Kunjapur, W. Shi, K.L. J. Prather and B.D. Olsen. “Material properties of the cyanobacterial reserve polymer multi-L-arginyl-poly-L-aspartate (cyanophycin).” Polymer. 109 pp: 238-245 (2017). DOI:10.1016/j.polymer.2016.11.058

Gupta, A., I.M. Brockman Reizman, C.R. Reisch and K.L. J. Prather. “Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit.” in press, Nat. Biotechnol. 35:273-279 (2017). DOI:10.1038/nbt.3796


Sheppard, M. J.*, Kunjapur, A. M.* and K. L. J. Prather. “Modular and selective biosynthesis of gasoline-range alkanes.” Metab. Eng. 33, 28–40 (2016). *equal contribution. DOI: 10.1016/j.ymben.2015.10.010

Kunjapur, A.M., B. Cervantes, K.L.J. Prather. “Coupling carboxylic acid reductase to inorganic pyrophosphatase enhances cell-free in vitro aldehyde biosynthesis.” Biochem. Eng. J. 109: 19–27 (2016). doi:  10.1016/j.bej.2015.12.018

Tan, S.T., S. Manchester, K.L J. Prather. “Controlling central carbon metabolism for improved pathway yields in Saccharomyces cerevisiae.” ACS Syn. Biol. 5(2) pp: 116-124 (2016).. DOI:10.1021/acssynbio.5b00164

Simcikova, M., D.M. Prazeres, K.L J. Prather, G.A. Monteiro. “Towards an effective non-viral gene delivery vector.” Biotechnol. Genet. Eng. Rev. 31(1-2) pp: 82-107 (2016). DOI:10.1080/02648725.2016.1178011

Kunjapur, A.M., J.C. Hyun, K.L J. Prather. “Deregulation of S-adenosylmethionine biosynthesis and regeneration improves methylation in the E. coli de novo vanillin biosynthesis pathway.” Microb. Cell Fact. 15:61 (2016). DOI:10.1186/s12934-016-0459-x

Simcikova, M., C.P.A. Alves, L. Brito, K.L J. Prather, D.M.F. Prazeres, G.A. Monteiro. “Improvement of DNA minicircle production by optimization of the secondary structure of the 5′-UTR of ParA resolvase.” Appl. Microbiol. Biotechnol. 100(15) pp: 6725-6737 (2016). DOI:10.1007/s00253-016-7565-x

Gupta, A.L., M.A. Hicks, S.P. Manchester, K.L J. Prather. “Porting the synthetic D-glucaric acid pathway from Escherichia coli to Saccharomyces cerevisiae.” Biotechnol. J. 11(9) pp: 1201-1208 (2016). DOI:10.1002/biot.201500563


Rodrigues, J.L., K.L J. Prather, L.D. Kluskens, L.R. Rodrigues. “Heterologous production of curcuminoids: a review.” Microbiol. Mol. Biol. Rev. 79 pp: 39-60 (2015). DOI:10.1128/MMBR.00031-14

Kunjapur, A. M., and K.L.J. Prather. “Microbial engineering for aldehyde synthesis.” Appl. Environ. Microbiol. 81 pp: 1892-1901. (2015). DOI:10.1128/AEM.03319-14

Brockman, I.M., and K.L.J. Prather. “Dynamic knockdown of E. coli central metabolism for redirecting fluxes of primary metabolites.” Metab. Eng. 28 pp: 104-113 (2015). DOI:10.1016/j.ymben.2014.12.005

Shiue, E., I.M. Brockman, K. L. J. Prather. “Improving product yields on D-glucose in Escherichia coli via alternative carbon sources.” Biotechnol. Bioeng.112(3) pp: 579-587 (2015).  DOI:10.1002/bit.25470

Lopes, M.B., G.A.L. Gonçalves, D. Felício-Silva, K. L. J. Prather. G.A. Monteiro, D.M.F. Prazeres, C.R.C. Calado. “In-situ NIR monitoring of plasmid bioproduction processes: effect of the cultivation medium composition, the cultivation strategy, and the Escherichia coli strain.” J. Chem. Technol. Biotechnol. 90(2) pp: 255-261 (2015). DOI:10.1002/jctb.4431

Pfleger, B. F., and K. L. J. Prather. “Biological synthesis unbounded?” Nat. Biotechnol. 33, 1148–9 (2015). DOI:10.1038/nbt.3399

Tan, S. Z., Manchester, S., and K. L. J. Prather. “Controlling central carbon metabolism for improved pathway yields in Saccharomyces cerevisiae.” ACS Synth. Biol. 5(2) pp: 116-124 (2015).  DOI:10.1021/acssynbio.5b00164

Boock, J. T., Gupta, A., and K. L. J. Prather. “Screening and modular design for metabolic pathway optimization.” Curr. Opin. Biotechnol. 36, 189–198 (2015).

Reizman, I. M. B., Stenger, A. R., Reisch, C. R., Gupta, A., Connors, N. C., and K. L. J. Prather. “Improvement of glucaric acid production in E. coli via dynamic control of metabolic fluxes.” Metab. Eng. Commun. 2, 109–116 (2015). DOI:10.1016/j.meteno.2015.09.002

Reisch, C. R., and K. L. J. Prather. “The no-SCAR (Scarless Cas9 Assisted Recombineering) system for genome editing in Escherichia coli.” Sci. Rep. 5, 15096 (2015). DOI:10.1038/srep15096

Brockman, I. M., and K. L. J. Prather. “Dynamic metabolic engineering: New strategies for developing responsive cell factories.” Biotechnol. J. 10, 1360–9 (2015). DOI:10.1002/biot.201400422

Rodrigues, J. L., Araújo, R. G., K. L. J. Prather, Kluskens, L. D. & Rodrigues, L. R. “Heterologous production of caffeic acid from tyrosine in Escherichia coli.” Enzyme Microb. Technol. 71, 36–44 (2015). DOI:10.1016/j.enzmictec.2015.01.001

Rodrigues, J.L., R. G. Araújo, K. L. J. Prather, Kluskens, L. D., Rodrigues, L. R. “Production of curcuminoids from tyrosine by a metabolically engineered Escherichia coli.” Biotechnol. J. 10(4) 599-609 (2015). DOI:10.1002/biot.201400637

Cheng, D., R. Wang, K. L. J. Prather, Chow, I.-M. Hsing. “Tackling codon usage bias for heterologous expression in Rhodobacter sphaeroides by supplementation of rare tRNAs.” Enzyme Microbiol. Technol. 72:25-34 (2015). DOI:10.1016/j.enzmictec.2015.02.003