Publications 2009 – 2014


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. DOI:10.1038/ncomms6031

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

Gonçalves, 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. DOI:10.1128/AEM.03303-13

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


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 K.L.J. Prather. 2012. “Controlled biosynthesis of odd-chain fuels and chemcials via engineered modular metabolic pathways.” PNAS109(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. Bioeng109(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


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. Biol21(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


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


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 putidaJ. Biotechnol. 139(1): 61-67 (2009) DOI:10.1016/j/jbiotec.2008.09.002

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