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Publications from the Prather Group:

2008 | 2009 | 2010 | 2011 | 2012 | 2013 | 2014| 2015| 2016| 2017

Publications by Kristala Jones Prather:

Prather, K. L. J., Edmonds, M. C., and Herod, J. W. Identification and characterization of IS1 transposition in plasmid amplification mutants of E. coli clones producing DNA vaccines. Appl. Micrbiol. Biotechnol. 73:815-826 (2006).

Montgomery, D. L., and Prather, K. J. "Design of plasmid DNA constructs for vaccines." in DNA Vaccines: Methods and Protocols (eds. Saltzman, W.M., Shen, H. & Brandsma, J.L.), 2nd Ed., Humana Press, Totowa, NJ, 2006.

Prather, K. J., Sagar, S., Murphy, J., and Chartrain, M. Industrial scale production of plasmid DNA for vaccine and gene therapy: plasmid design, production, and purification. Enz. Microbiol. Technol. 33: 865-883 (2003).

1998-2002 | 2003-2006

Reisch, C.R. and K.L J. Prather, L.D. Kluskens, L.R. Rodrigues. "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).

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).

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. (2017).

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).

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).

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).

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).

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).

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).

Kunjapur, A. M., and K.L.J. Prather. "Microbial engineering for aldehyde synthesis." Appl. Environ. Microbiol. 81 pp: 1892-1901. (2015).

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).

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).

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).

Pfleger, B. F. and K. L. J. Prather. "Biological synthesis unbounded?" Nat. Biotechnol. 33, 1148–9 (2015).

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).

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).

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).

Brockman, I. M. and K. L. J. Prather. "Dynamic metabolic engineering: New strategies for developing responsive cell factories." Biotechnol. J. 10, 1360–9 (2015).

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).

Rodrigues, J.L., R. G. Ara˙jo, 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).

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).

Sheppard, M.J., A.M. Kunjapur, S.J. Wenck, and K.L.J. Prather. 2014. "Retro-biosynthetic screening of a modular pathway design achieves selective route for microbial synthesis of 4-methyl-pentanol." Nat. Commun. 5 5031.

Kunjapur, A.M., Y. Tarasova, and K.L.J. Prather. 2014. "Synthesis and accumulation of aromatic aldehydes in an engineered strain of Escherichia coli." J. Am. Chem. Soc. 136(33): 11644-11654.
doi: 10.1021/ja506664a

Gonçalves, G.A.L., K.L.J. Prather, G.A. Monteiro, D.M.F. Prazeres. 2014. “Engineering of Escherichia coli strains for plasmid biopharmaceutical production: scale-up challenges.”  Vaccine 32(24): 2847-2850.
doi: 10.1016/j.vaccine.2014.02.023

Simcikova, M., K.L.J. Prather, D.M.F. Prazeres and G.A. Monteiro. 2014. “On the dual effect of glucose during production of pBAD/AraC-based minicircles.”  Vaccine 32(24): 2843-2846.
doi: 10.1016/j.vaccine.2014.02.035

Hicks, M.A. and K.L.J. Prather.  2014.  “Bioprospecting in the Genomic Age.” In Sima Sariaslani, Geoffrey Gadd, editors: Advances in Applied Microbiology, Vol 87, AAM, UK: Academic Press, pp. 111-146.
doi: 10.1016/B978-0-12-800261-2.00003-7

Gonšalves, G.A.L., K.L.J. Prather, G.A. Monteiro, A.E. Carnes, D.M.F. Prazeres.  2014. “Plasmid DNA production with Escherichia coli GALG20, a pgi-gene knockout strain: fermentation strategies and impact on downstream processing.”  J. Biotechnol. 186: 119-127.
doi: 10.1016/j.jbiotec.2014.06.008

Shiue, E. and K.L.J. Prather. 2014.  “Improving D-glucaric acid production from myo-inositol in E. coli by increasing MIOX stability and myo-inositol transport.”  Metab. Eng. 22:22-31.
doi: 10.1016/j.ymben.2013.12.002

McMahon, M.D. and K. L. J. Prather. 2014. “Functional screening and in vitro analysis reveals thioesterases with enhanced substrate specificity profiles that improve medium-chain fatty acid production titers in Escherichia coli.” Appl. Environ. Microbiol. 80(3):1042-1050.

Abin-Fuentes, A., J. C. Leung, M. E. Mohamed, D.I.C. Wang and K.L.J. Prather. 2014. “Rate-limiting step analysis of the microbial desulfurization of dibenzothiophene in a model oil system.”  Biotechnol. Bioeng.111(5):876-884.
doi: 10.1002/bit.25148

Dhamankar, H., Y. Tarasova, C.H. Martin, and K.L.J. Prather. 2014. “Engineering E. coli for the biosynthesis of 3-hydroxy-γ-butyrolactone (3HBL) as a value added chemical from glucose as a sole carbon source.”  Metab. Eng. 25:72-81.
doi: 10.1016/j.ymben.2014.06.004

Rodrigues, J.L., M. Sousa, K.L.J. Prather, L.D. Kluskens, L.R. Rodrigues. 2014. “Selection of Escherichia coli heat shock promoters towards their application as stress probes.”  J. Biotechnol.188:61-71.
doi: 10.1016/j.jbiotec.2014.08.005

Pirie, C., M. De Mey, K.L.J. Prather and P.K. Ajikumar. 2013. “Integrating the protein and metabolic engineering toolkits for next-generation chemical biosynthesis.” ACS Chem. Biol.8:662-672. doi: 10.1021/cb300634b

Abin-Fuentes, A., M.E-S. Mohamed, D.I.C. Wang, and K.L.J. Prather. 2013. "Exploring the mechanism of biocatalyst inhibition in microbial desulfurization." Appl. Environ. Microbiol. 79:24 7546.
doi: 10.1128/AEM.03415-13

Martin, C. H.*, H. Dhamankar*, H.C. Tseng, M.J. Sheppard, C.R. Reisch, K.L.J. Prather. 2013. "A platform pathway for production of 3-hydroxyacids provides a biosynthetic route to 3-hydroxy-γ-butyrolactone." Nat. Commun. 4:1414. *Authors contributed equally to this work.
doi: 10.1038/ncomms2418

Solomon, K.V., T.S. Moon, B. Ma, T.M. Sanders, and K.L.J. Prather. 2013.  “Tuning primary metabolism for heterologous productivity.” ACS Synth. Biol. 2(3): 126-135. doi: 10.1021/sb300055e

Gonçalves, G.A.L., D.M.F. Prazeres, G.A. Monteiro, K.L.J. Prather. 2013. “De novo creation of MG1655-derived E. coli strains specifically designed for plasmid DNA production.”  Appl. Microbiol. Biotechnol. 97(2): 611-620. doi: 10.1007/s00253-012-4308-5


Dueber, J.E., Wu, G.C., Malmirchegini, G.R., Moon, T.S., Petzold, C.J., Ullal, A.V., Prather, K.J., Keasling, J.D. "Synthetic protein scaffolds provide modular control over metabolic flux." Nature Biotechnol. 27(8): 753-759 (2009). doi:10.1038/nbt.1557

Oliveira, P.H., Prather, K.J., Prazeres, D.M., and Monteiro, G. in press. "Structural instabilities of plasmid biopharmaceuticals: challenges and implications."Trends Biotechnol. 27(9):503-511 (2009). doi:10.1016/j.tibtech.2009.06.004

Moon, T.S., Yoon, S.-H., Tsang Mui Ching, M.-J., Lanza, A.M., and Prather, K.L.J. "Enzymatic assay of D-glucoronate using uronate dehydrogenase." Analytical Biochemistry. 392: 183-185 (2009). doi:10.1016/j.ab.2009.05.032

Nielsen, D.R., Leonard, E., Yoon, S.-H., Tseng, H.-C., Yuan, C. and Prather, K.J. "Engineering alternative butanol production platforms in heterologous bacteria." Metab. Eng.11: 262-273 (2009). doi:10.1016/j.ymben.2009.05.003

Tseng, H-C, Martin, C, Nielsen, D.R., and Prather, K.L.J. 2009. “Metabolic engineering of Escherichia coli for the enhanced production of (R)- and (S)-3-hydroxybutyrate.”  Appl. Environ. Microbiol. 75(10):3137-3145. doi:10.1128/AEM.02667-08

Leonard, E., Runguphan, W., O’Connor, S., and Prather, K.J. “Opportunities in metabolic engineering to facilitate scalable alkaloid production.”  Nature Chem. Biol 5(5): 292-300 (2009).doi:10.1038/nchembio.160

Martin, C.H., Nielsen, D.R., Solomon, K.V., and Prather, K.L.J. Synthetic metabolism: Engineering biology at the protein and pathway scales. Chem. Biol.16(3): 277-286 (2009). doi:10.1016/j.chembiol.2009.01.010

Bower, D.M., and Prather, K.L.J. Engineering of bacterial strains and vectors for the production of plasmid DNA. Appl. Microbiol. Biotechnol. 82(5): 805-813 (2009) doi:10.1007/s00253-009-1889-8

Yoon, S.-H., Moon, T.S., Iranpour, P., Lanza, A.M., and Prather, K.J. Cloning and characterization of uronate dehydrogenases from two Pseudomonads and Agrobacterium tumefaciens str. C58 J. Bacteriol. 191(5): 1565-1573 (2009) doi:10.1128/JB.00586-08

Moon, T.S., Yoon, S.-H., Lanza, A.M., Roy-Mayhew, J.D. and Prather, K.L.J. Production of glucaric acid from a synthetic pathway in recombinant Escherichia coli. Appl. Environ. Microbiol. 75: 589-595 (2009) doi:10.1128/AEM.00973-08

Martin, C.H. and Prather, K.L.J. High-titer production of monomeric hydroxyvalerates from levulinic acid in Pseudomonas putida. J. Biotechnol. 139(1): 61-67 (2009) doi:10.1016/j/jbiotec.2008.09.002

Nielsen, D.R. and Prather, K.L.J. In situ product recovery of n-butanol using polymeric resins. Biotechnol. Bioeng. 102: 811-821 (2009) doi:10.1002/bit.2210

Leonard, E., Nielsen, D., Solomon, K., and Prather, K.J. Engineering microbes with synthetic biology frameworks. Trends Biotechnol. 26(12): 674-681 (2008) doi:10.1016/j.tibtech.2008.08.003

Rodrigo, G., Carrera, J., Prather, K.L.J., and Jaramillo, A. DESHARKY: Automated design of metabolic pathways for optimal cell growth. Bioinformatics. 24(21): 2554-2556 (2008). doi:10.1093/bioinformatics/btn471

Prather, K.L.J. and Martin, C.H. De novo biosynthetic pathways: rational design of microbial chemical factories. Curr. Opin. Biotechnol. 19(5): 468-474 (2008). doi:10.1016/j.copbio.2008.07.009

Lippow, S.M., Moon, T.S., Basu, S., Yoon, S.-H., Li, X., Chapman, B.A., Robison, K., Lipovsek, D. and Prather, K.L.J. “Engineering Enzyme Specificity Using Computational Design of a Defined-Sequence Library.”  Chem. Biol. 17: 1306-1315 (2010) . doi: 10.1016/j.chembiol.2010.10.012

Tseng, H-C, Harwell, C.L., Martin, C.H., and Prather, K.L.J. “Biosynthesis of chiral 3-hydroxyvalerate from single propionate-unrelated carbon sources in metabolically engineered E. coli.”  Microb. Cell Fact. 9(96) (2010). doi: 10.1186/1475-2859-9-96

Leonard, E., Ajikumar, P.K., Thayer, K., Xiao, W.-H., Mo, J.D., Tidor, B., Stephanopoulos, and Prather, K.J. “Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control.”  PNAS 107(31): 13654-13659 (2010).doi:10.1073/pnas.1006138107

Fischer, C.R., Tseng, H-C, Tai, M., Prather, K.L.J., and Stepanopoulos, G. “Assessment of heterologous butyrate and butanol pathway activity by measurement of intracellular pathway intermediates in recombinant Escherichia coli.”  Appl. Microbiol. Biotechnol. 88(1):265-275 (2010) . doi: 10.1007/s00253-010-2749-2

Moon, T.S., Dueber, J.E., and Prather, K.L.J. "Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli." Metabolic Engineering . 12: 298-305 (2010) . doi:10.1016/j.ymben.2010.01.003.

Nielsen, D.R., Yoon, S.-H., Yuan, C.J., Prather, K.J. "Engineering acetoin and meso-2,3 butanediol biosynthesis in E. coli." Biotechnology Journal. 5: 274-284 (2010). doi:10.1002/biot200900279.

Nielsen, D.R., Amarasiriwardena, G.S., Prather, K.J. "Predicting the adsorption of second generation biofuels by polymeric resins with applications for in situ product recovery (ISPR) ." Bioresource Technology. 101: 2762-2769 (2010). doi:10.1016/j.biortech.2009.12.003

Martin, C.H., Wu, D., Prather, K.J. "Integrated Bioprocessing for the pH-Dependent Production of 4-Valerolactone from Levulinate in Pseudomonas putida KT2440." App. Environ. Microbiol. 76: 417-424 (2010) .doi:10.1128/AEM.01769-09

Dhamankar, H and K. L. J. Prather. 2011. “Microbial chemical factories: recent advances in pathway engineering for synthesis of value added chemicals.” Curr. Opin. Struct. Biol. 21(4):488-494. doi: 10.1016/

Oliveira, P.H., K. L. J. Prather, D. M. F. Prazeres and G. A. Monteiro .  2011. “Mutation detection in plasmid biopharmaceuticals.”  Biotechnol. J. 6(4):378-391. doi: 10.1002/biot.201000372

Aldor, I.S., Kim, S.-W., Prather, K.L.J., and Keasling, J.D. Metabolic engineering of a novel propionate-independent pathway for the production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) in recombinant Salmonella enterica serovar Typhimurium. Appl. Envir. Microbiol. 68: 3848-3854 (2002).

Jones, K.L., Kim, S.-W., and Keasling, J.D. Low-copy plasmids can perform as well as or better than high-copy plasmids for metabolic engineering of bacteria. Metabolic Engineering. 2: 328-338 (2000).

Carrier, T.A., Jones, K.L., and Keasling, J.D. mRNA stability and plasmid copy number effects on gene expression from an inducible promoter system. Biotechnol. Bioeng. 59: 666-672 (1998).

Jones, K.L. and Keasling, J.D. Construction and characterization of F plasmid-based expression vectors. Biotechnol. Bioeng. 59: 659-665 (1998).
Solomon, K.V., T.M. Sanders, and K.L.J. Prather.  2012.  “A dynamic metabolite valve for the control of central carbon metabolism.”  Metab. Eng.  14:661-671. doi: 10.1016/j.ymben.2012.08.006

Bower, D.M. and K.L.J. Prather. 2012.  “Development of new plasmid DNA vaccine vectors with R1-based replicons.”  Microb. Cell Fact. 11:107. doi:  10.1186/1475-2859-11-107

Tseng, H.-C., and KLJ Prather. 2012. "Controlled biosynthesis of odd-chain fuels and chemcials via engineered modular metabolic pathways." PNAS. 109(44): 17925-17930. doi: 10.1073/pnas.1209002109

Fernandes, F.,  J. Vidigal, M. Dias, K.L.J. Prather, M.J.T. Carrondo, A.S. Coroadinha, A.P. Teixeira, P.M. Alves. 2012. “Flipase-mediated cassette exchange in Sf9 insect cells for stable gene expression.”  Biotechnol. Bioeng. 109(11): 2836-2844.  doi: 10.1002/bit.24542

Shiue, E. and K.L.J. Prather.  2012. “Synthetic biology devices as tools for metabolic engineering.”  Biochem. Eng. J. 65:82-89.
doi: 10.1016/j.bej.2012.04.006

Bower, D.M., K.S. Lee, R.J. Ram, and K.L.J. Prather.  2012.  “Fed-batch microbioreactor platform for scale down and analysis of a plasmid DNA production process.” Biotechnol. Bioeng. 109(8):1976-1986.
doi: 10.1002/bit.24498

Moon, T.S., D.R. Nielsen, K.L.J. Prather. 2012.  “Sensitivity analysis of a proposed model mechanism for newly created glucose-6-oxidases.” AIChE J. 58(8): 2303-2308. doi: 10.1002/aic.12762

Gonçalves, G.L.,  D.M. Bower, D.M. F. Prazeres, G.A. Monteiro, K.L.J. Prather. 2012. “Rational engineering of E. coli strains for plasmid :biopharmaceutical manufacturing.” Biotechnol. J. 7: 251-261.
doi: 10.1002/biot.201100062

Solomon, K.V. and K. L. J. Prather. 2012. “The zero-sum game of pathway optimization: emerging paradigms for tuning gene expression.”  Biotechnol. J. 6(9): 1064-1070. doi: 10.1002/biot.201100086