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Metabolic Engineering and Synthetic & Systems Biology Laboratory

Alfredo Martinez

Yandi Dharmadi


B.S., Biochemical Engineering. Universidad Autónoma Metropolitana. Mexico City, 1985.
M.Sc., Biotechnology. Universidad Nacional Autonoma de Mexico . Cuernavaca, Morelos, Mexico.1990.
PhD., Biotechnology. Universidad Nacional Autonoma de Mexico. Cuernavaca, Morelos, Mexico, 1997. México




Metabolic engineering and bioprocess development with Escherichia coli for biofuels (fuel ethanol) and lactate (biopolymer precursor) production. Physiological studies for biomass production with oleaginous microalgae for biofuel applications.



Present Position: (Aug 2012 – Jul 2013): Visiting Scholar, Chemical and Biomolecular Engineering, Rice University.                          

Current Position:    Professor, Department of Cellular Engineering and Biocatalyst. IBt-UNAM.
Biotechnology Institute (Instituto de Biotecnologia:IBt)
National Autonomous University of Mexico (Universidad Nacional Autónoma de México: UNAM)
For an up-to-date CV, click here. To visit the website of my group at the IBt-UNAM, click here.


REFEREED PUBLICATIONS   (click here to see publication details)

Utrilla José, Cuauhtemoc  Licona-Cassani, Esteban Marcellin, Guillermo Gosset, Lars K. Nielsen, A. Martinez. Engineering and adaptive evolution of Escherichia coli for D-lactate fermentation reveals GatC as a xylose transporter. In Press Metabolic Engineering.  2012.

Cabrera-Valladares Natividad, Luz M. Martínez, Noemi Flores, Georgina Hernández-Chávez, A. Martínez, Francisco Bolivar, Guillermo Gosset. Physiologic consequences of glucose transport and phosphoenolpyruvate node modifications in Bacillus subtilis 168. Journal of Molecular Microbiology and Biotechnology. 22:177-197. 2012.

Fernández-Sandoval MT., G. Huerta-Beristain, B. Trujillo-Martinez, P. Bustos, V. González, F. Bolivar, G. Gosset, A. Martinez. Laboratory metabolic evolution improves acetate tolerance and growth on acetate of ethanologenic Escherichia coli under non aerated conditions in glucose-mineral medium. In Press Applied Microbiology and Biotechnology. 2012.

Sabido, Andrea, Luz María Martínez, Ramón de Anda, A. Martinez, Francisco Bolívar, Guillermo Gosset. A novel plasmid vector designed for chromosomal gene integration and expression: Use for developing a genetically stable Escherichia coli melanin production strain. In Press Plasmid. 2012.

Chávez-Béjar M.I., J.L. Baez-Viveros, A. Martinez, F. Bolivar, G. Gosset. Biotechnological production of L-tyrosine and derived compounds. Process Biochemistry. 47:1017-1026. 2012

Muñoz-Gutiérrez Iván, Ricardo Oropeza, Guillermo Gosset, A. Martinez. Journal of Industrial Microbiology and Biotechnology. 39:1141-1152. 2012.

Muñoz A.J., G. Hernández-Chávez, R. de Anda, A. Martinez, F. Bolívar, G. Gosset. Metabolic engineering of Escherichia coli for improving L-3,4-dihydroxyphenylalanine (L-DOPA) synthesis from glucose. Journal of Industrial Microbiology and Biotechnology. 38:1845-1852. 2011.

Rojas-Rejón O.A., H.M. Poggi-Varaldo, A.C. Ramos-Valdivia, A. Martinez, E. Cristiani-Urbina, M. de la Torre Martínez, T. Ponce-Noyola. Production of cellulases and xylanases under catabolic repression conditions from mutant PR-22 of Cellulomonas flavigena. Journal of Industrial Microbiology and Biotechnology. 38:257-264. 2011.

Balderas-Hernández V.E., V. Hernández-Montalvo, F. Bolívar, G. Gosset, A. Martinez. Adaptive evolution of Escherichia coli inactivated in the phosphotransferase system operon improves co-utilization of xylose and glucose under anaerobic conditions. Applied Biochemistry and Biotechnology. 163 (4):485-496. 2011.

Orencio-Trejo M., J. Utrilla, M.T. Fernández-Sandoval, G. Huerta-Beristain, G. Gosset, A. Martinez. Engineering the Escherichia coli fermentative metabolism. Advances in Biochemical Engineering and Biotechnology. 121:71-107. 2010.

Quiroz-Castañeda R.E., E. Balcázar-López, E. Dantán-González, A. Martinez, J. Folch-Mallol, C. Martínez Anaya. Characterization of cellulolytic activities of Bjerkandera adusta and Pycnoporus sanguineus on solid wheat straw medium. Electronic Journal of Biotechnology.

Utrilla J., G. Gosset, A. Martinez. ATP limitation in a pyruvate formate lyase mutant of Escherichia coli MG1655 increases glycolytic flux to D-lactate. Journal of Industrial Microbiology and Biotechnology. 36:1057-1062. 2009.

Romero S., C. Hernández, E. Merino, G. Gosset, A. Martinez. Homolactic fermentation from glucose and cellobiose using Bacillus subtilis. Microbial Cell Factories. 8, 23:1- 8. 2009.

Balderas-Hernández V.E., A. Sabido-Ramos, P. Silva, N. Cabrera-Valladares, G. Hernandez-Chavez, J.L. Baez-Viveros, A. Martinez, F. Bolivar, G. Gosset. Metabolic engineering for improving anthranilate synthesis from glucose in Escherichia coli. Microbial Cell Factories. 8, 19:1-12. 2009.

Orencio-Trejo M., N. Flores, A. Escalante, G. Hernández-Chávez, F. Bolívar, G. Gosset, A. Martinez. Metabolic regulation analysis of an ethanologenic Escherichia coli strain based on RT-PCR and enzymatic activities. Biotechnology for Biofuels, 1, 8:1-13.

Chávez-Béjar M.I., A.R. Lara, H. López, G. Hernández-Chávez, A. Martinez, O.T. Ramírez, F. Bolívar, G. Gosset. Metabolic engineering of Escherichia coli for L-tyrosine production by the expression of the genes coding for the chorismate mutase domain from native P-protein and a cyclohexadienyl dehydrogenase from Zymomonas mobilis. Applied and Environmental Microbiology. 74:3284-3290. 2008.

Huerta-Beristain G., J. Utrilla, G. Hernández-Chávez, F. Bolívar, G. Gosset, A. Martinez. Specific ethanol production rate in ethanologenic Escherichia coli strainKO11 is limited by pyruvate decarboxylase. Journal of Molecular Microbiology and Biotechnology . 15:55-64. 2008.

Vázquez-Limón C., J. Vega-Badillo, A. Martinez, G. Espinosa-Molina, G. Gosset, X. Soberón, A. López-Munguía, J. Osuna. Growth rate of a non-fermentative Escherichia coli strain is influenced by NAD+ regeneration. Biotechnology Letters. 29:1857-1863. 2007.

Romero S., E. Merino, F. Bolívar, G. Gosset, A. Martinez. Metabolic engineering of Bacillus subtilis for ethanol production: Lactate dehydrogenase plays a key role in the fermentative metabolism. Applied and Environmental Microbiology. 73:5190-5198. 2007.

Martinez A., T.B. Grabar, K.T. Shanmugam, L.P. Yomano, S.W. York, L.O. Ingram. Low salt medium for lactate and ethanol production by recombinant Escherichia coli B. Biotechnology Letters. 29:397-404. 2007.

Flores N., L. Leal, J.C. Sigala, R. de Anda, A. Escalante, A. Martinez, O.T. Ramírez, G. Gosset, F. Bolivar. Growth recovery on glucose under aerobic conditions of an Escherichia coli strain carrying a phosphoenolpyruvate:carbohydrate phosphotransferase system deletion by inactivating arcA and overexpressing the genes coding for glucokinase and galactose permease. Journal of Molecular Microbiology and Biotechnology. 13: 105-116. 2007.

Treviño-Quintanilla L.G., A. Escalante, A.D. Caro, A. Martinez, R. González, J.L. Puente, F. Bolívar, G. Gosset. The Phosphotransferase system-dependent sucrose utilization regulon in enteropathogenic Escherichia coli strains is located in a variable chromosomal region containing iap sequences. Journal of Molecular Microbiology and Biotechnology. 13:117-125. 2007.

Piñero S., J. Rivera, D. Romero, M.A. Cevallos, A. Martinez, F. Bolívar, G. Gosset. Tyrosinase from Rhizobium etli is involved in nodulation efficiency and symbiosis-associated stress resistance. Journal of Molecular Microbiology and Biotechnology. 13:35-44. 2007.

Lagunas-Muños V.H., N. Cabrera-Valladares, F. Bolívar, G. Gosset, A. Martinez. Optimum melanin production using recombinant Escherichia coli. Journal of Applied Microbiology. 101:1002-1008. 2006.

Cabrera N, A. Martínez, S. Piñero, V.H. Lagunas-Muñoz, R. Tinoco, R. de Anda, R. Vázquez-Duhalt, F. Bolívar, G. Gosset. Expression of the melA gene from Rhizobium etli CFN42 in Escherichia coli and characterization of the encoded tyrosinase. Enzyme and Microbial Technology. 38:772-779. 2006.

Flores N., R. de Anda, S. Flores, A. Escalante, G. Hernández, A. Martinez, O.T. Ramírez, G. Gosset, F. Bolívar. The role of pyruvate oxidase in Escherichia coli strains lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system. Journal of Molecular Microbiology and Biotechnology. 8:209-221. 2004.

Escalante A., M.E. Rodríguez, A. Martinez, A. López-Munguía, F. Bolívar, G. Gosset. Characterization of bacterial diversity in Pulque, a traditional Mexican alcoholic fermented beverage, as determined by 16S rDNA analysis. FEMS Microbiology Letters. 235:273-279. 2004.

Garay-Arroyo A., A.A. Covarrubias, I. Clark, I. Niño, G. Gosset, A. Martinez. Response to different environmental stress conditions of industrial and laboratory Saccharomyces cerevisiae strains. Applied Microbiology and Biotechnology. 63:734-741. 2004.

Hernández-Montalvo V., A. Martinez, G. Hernández-Chávez, F. Bolívar, F. Valle, G. Gosset. Expression of galP and glk in a Escherichia coli PTS mutant restores glucose transport and increases glycolytic flux to fermentation products. Biotechnology and Bioengineering. 83:687–694. 2003.

Espinosa-de-los-Monteros, J., A. Martinez, F. Valle. Metabolic profiles and aprE expression in anaerobic cultures of Bacillus subtilis using nitrate as terminal electron acceptor. Applied Microbiology and Biotechnology. 57:379-384. 2001.

Tao, H., R. González, A. Martínez, M.E. Rodríguez, L.O. Ingram, J.F. Preston, K.T. Shanmugam. Engineering a homo-ethanol pathway in Escherichia coli: Increased glycolytic flux and levels of expression of glycolytic genes during xylose fermentation. Journal of Bacteriology. 183 (10):2979-2988. 2001.

Martinez, A., M.E. Rodríguez, M.L. Wells, S.W. York, J.F. Preston, L.O. Ingram. Detoxification of dilute acid hydrolysates of lignocellulose with lime. Biotechnology Progress. 17:287-293. 2001.

Martinez, A., M.E. Rodríguez, S.W. York, J.F. Preston, L.O. Ingram. Use of UV absorbance to monitor furans in dilute acid hydrolysates of biomass. Biotechnology Progress. 16:637-641. 2000.

Martinez, A., M.E. Rodríguez, S.W. York, J.F. Preston, L.O. Ingram. Effects of Ca(OH)2 treatments (“Overliming”) on the composition and toxicity of bagasse hemicellulose hydrolysate. Biotechnology and Bioengineering. 69:526-536. 2000.

Zaldivar, J., A. Martinez, L.O. Ingram. Effect of alcohols found in hemicellulose hydrolysate on the growth and fermentation of ethanologenic Escherichia coli. Biotechnology and Bioengineering. 68:524-530. 2000.

Martínez-Morales, F., A.C. Borges, A. Martinez, K.T. Shanmugam, L.O. Ingram. Chromosomal integration of heterologous DNA in Escherichia coli with precise removal of markers and replicons used during construction. Journal of Bacteriology.  181 (22):7143-7148. 1999.

Ingram, L.O., H.C. Aldrich, A.C.C. Borges, T.B. Causey, A. Martinez, F. Morales, A. Saleh, S.A. Underwood, L.P. Yomano, S.W. York, J. Zaldivar, S. Zhou. Enteric bacterial catalyst for fuel ethanol production. Biotechnology Progress. 15:855-866. 1999.

Martinez, A., S.W. York, L.P. Yomano, V.L. Pineda, F.C. Davis, J.C. Shelton, L.O. Ingram. Biosynthetic burden and plasmid burden limit expression of chromosomally integrated heterologous genes (pdc, adhB) in Escherichia coli. Biotechnology Progress. 15:891-897. 1999.

Sigüenza, R., N. Flores, G. Hernández, A. Martinez, F. Bolívar, F. Valle. Kinetic characterization in batch and continuous culture of Escherichia coli mutants affected in phosphoenolpyruvate metabolism: differences in acetic acid production. World Journal of Microbiology Biotechnology. 15:587-592. 1999.

Zaldivar, J., A. Martinez, L.O. Ingram. Effect of selected aldehydes on the growth and fermentation of ethanologenic Escherichia coli B. Biotechnology and Bioengineering. 65:24-33. 1999.

Martinez, A., O.T. Ramirez, F. Valle. Effect of growth rate on the production of ß-galactosidase from Escherichia coli in Bacillus subtilis using glucose-limited exponentially fed-batch cultures. Enzyme and Microbial Technology. 22:520-526. 1998.

Ponce, E., A. Martinez, F. Bolívar, F. Valle. Stimulation of glucose catabolism through the pentose pathway by the absence of the two pyruvate kinase isoenzyme from Escherichia coli. Biotechnology and Bioengineering. 58:292-295. 1998.

Martinez, A., O.T. Ramirez, F. Valle. Improvement of culture conditions to overproduce ß-galactosidase from Escherichia coli in Bacillus subtilis. Applied Microbiology and Biotechnology. 47:40-45. 1997.

Galindo, E., M.A. Argüello, D. Velasco, V. Albiter, A. Martinez. A comparison of cavern development in mixing a yield stress fluid by Rushton and InterMig impellers. Chemical Engineering Technology. 19:315-323. 1996.

Ponce, E., N. Flores, A. Martinez, F. Valle, F. Bolívar. Cloning of the pyruvate kinase isoenzyme structural genes from Escherichia coli: the relative roles of these enzymes in pyruvate biosynthesis. Journal of Bacteriology. 177 (9):5719-5722. 1995.

Gosset, G., R. de Anda, N. Cruz, A. Martinez, R. Quintero, F. Bolívar. Recombinant protein production in cultures of an Escherichia coli trp- strain. Applied Microbiology and Biotechnology. 39:541-546. 1993.

Bravo, A., R. Quintero, C. Díaz, A. Martinez, M. Soberón. Efficiency of insecticidal crystal protein production in a Bacillus thuringiensis mutant with derepressed expression of the terminal oxidase aa3 during sporulation. Applied Microbiology and Biotechnology. 39:558-562. 1993.

Sánchez, A., A. Martinez, L. Torres, E. Galindo. Power consumption of three impeller combinations in mixing xanthan fermentation broths. Process Biochemistry. 27:351-365. 1992.

Reséndiz, R., A. Martinez, G. Ascanio, E. Galindo. A new pneumatic bearing dynamometer for power input measurement in stirred tanks. Chemical Engineering Technology. 14:105-108. 1991.

Martinez, A., E. Galindo, M. Salvador. Sparger position effect over kLa in bench and pilot stirred-tank fermentors. Journal of Fermentation and Bioengineering. 68 (1):71-73. 1989.



A. Escalante, A. Martínez, M. Rivera, G. Gosset. Solute transport processes in the cell. The Metabolic Pathway Engineering Handbook. Ed. C.D. Smolke. CRC Press. Boca Raton, FL, EUA. 2009.

Chávez, M.I., A. Martínez, G. Gosset. Metabolic pathway engineering for microbial production of aromatic amino acids. Res. Adv. In Food Science. V5, pp. 11-20, 2005. New Delhi, India.

D. Velasco, A. Martínez, L.G. Torres, E. Galindo. Rheology and dual impeller mixing of an industrial fermentation broth containing Micromonospora purpurea. Proceedings of the 3rd International Conference on Bioreactors & Bioprocess Fluid Dynamics. BHR Group Limited, Cambridge, U.K. pp. 101-119, 1993.

D. Velasco, A. Martínez,E. Galindo. Hydrodynamics of industrial fermentations: rheology and power draw in rifamycin production. Industrial Mixing Technology: Chemical and Biological Applications. G.B. Tatterson, R.V. Calabrese and W.R. Penney (Eds.). AIChE Symp. Ser. 299, Vol. 90, pp. 157-165, 1994.



Member, Mexican National Research System (SNI), since July 1990

CONACyT (Mexican Council of Science and Technology) postdoctoral fellowship at the University of Florida, July 1988 – January 2000

Treasurer, Morelos Branch of the Mexican Society for Biotechnology and Bioengineering, July 2001 – June 2003

Member, Morelos Branch of the National Academy of Sciences, Since November 2007

Vice-President, Mexican Society for Biotechnology and Bioengineering, July 2008 – June 2010

Chairman, VII International Symposium for the Production of Alcohols and Yeasts, 2009

Chairman, XIII National (Mexican) Meeting of Biotechnology and Bioengineering, 2009

President, XIV National (Mexican) Meeting of Biotechnology and Bioengineering, 2011

President, Mexican Society for Biotechnology and Bioengineering, July 2010 – June 2012



    Mexican Society for Biotechnology and Bioengineering, since 1986

    American Society of Microbiology (USA), since April 1998

    Society of Industrial Microbiology (USA), since January 1999

    Mexican Network for Bioenergy, since February 2007

    Latin-American Society for Environmental and Algal Biotechnology, since 2009

    Mexican Network for Alternative Energies, since 2009

    Contact Information

    Department of Chemical and Biomolecular Engineering (CHBE)
    Abercrombie Lab, B235
    Rice University
    6100 Main St. MS-362
    Houston, TX. 77005
    Office: 713-348 5906
    Fax (713) 348-5478