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Publications from the Prather Group:

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

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

Kunjapur, A. M., and K.L.J. Prather. In press. "Microbial engineering for aldehyde synthesis." Appl. Environ. Microbiol.
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

Shiue, E., I.M. Brockman, K.L.J. Prather. In press. "Improving product yields on D-glucose in Escherichia coli via alternative carbon sources." Biotechnol. Bioeng.

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 press. "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.

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

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

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