Publicaciones

27. Bedoya-Pérez, L.P., Aguilar-Vera, A., Sánchez-Pérez, M., Utrilla, J*. and Sohlenkamp, C.*, 2024. Enhancing Escherichia coli abiotic stress resistance through ornithine lipid formation. Applied Microbiology and Biotechnology, 108(1), p.288.

26. Castillo-Alfonso, F., Valadez-Cano, C., Cejas-Añón, G., Utrilla, J., Alanis, J.C.S., Le Borgne, S., Sales-Cruz, A.M., Vigueras-Ramírez, G. and Olivares-Hernández, R., 2024. Sequencing, assembly, and genomic annotation of Leucoagaricus gongylophorus LEU18496, a dikarya mutualistic species. Molecular Omics. 

25. Bello-González MA, Bedoya-Perez LP, Pantoja-Zepeda MA, Utrilla J*. Development of SynBio Tools for Pseudomonas chlororaphis: A Versatile Non-Pathogenic Bacterium Host. SynBio. 2024; 2(2):112-124. https://doi.org/10.3390/synbio2020007 

24. Lara, A.R., Utrilla, J., Martínez, L.M., Krausch, N., Kaspersetz, L., Hidalgo, D., Cruz-Bournazou, N., Neubauer, P., Sigala, J.C., Gosset, G. and Büchs, J., 2024. Recombinant protein expression in proteome-reduced cells under aerobic and oxygen-limited regimes. Biotechnology and Bioengineering. 

23 .Amaro-Reyes, A., Marcial-Ramírez, D., Vázquez-Landaverde, P.A., Utrilla, J., Escamilla-García, M., Regalado, C., Macias-Bobadilla, G., Campos-Guillén, J., Ramos-López, M.A. and Favela-Camacho, S.E., 2024. Electrostatic Fermentation: Molecular Response Insights for Tailored Beer Production. Foods, 13(4), p.600. 

22. Marquez‐Zavala, Elisa, and Jose Utrilla*. "Engineering resource allocation in artificially minimized cells: Is genome reduction the best strategy?." Microbial Biotechnology 16.5 (2023): 990-999. 

21. Reyes-González, D., De Luna-Valenciano, H., Utrilla, J., Sieber, M., Peña-Miller, R., & Fuentes-Hernández, A. (2022). Dynamic proteome allocation regulates the profile of interaction of auxotrophic bacterial consortia. Royal Society Open Science, 9(5). https://doi.org/10.1098/RSOS.212008

20. Hidalgo, D., Martínez-Ortiz, C. A., Palsson, B. O., Jiménez, J. I., & Utrilla, J. (2022). Regulatory perturbations of ribosome allocation in bacteria reshape the growth proteome with a trade-off in adaptation capacity. IScience, 25(3), 103879. https://doi.org/10.1016/j.isci.2022.103879

19.   Moreno-Avitia, F., Utrilla, J., Bolívar, F., Nogales, J. and Escalante, A., 2020. Metabolic reconstruction of Pseudomonas chlororaphis ATCC 9446 to understand its metabolic potential as a phenazine-1-carboxamide-producing strain. Applied Microbiology and Biotechnology, 104(23), pp.10119-10132. 

18.   de la Cruz, M., Ramírez, E.A., Sigala, J.C., Utrilla, J. and Lara, A.R., 2020. Plasmid DNA Production in Proteome-Reduced Escherichia coli. Microorganisms, 8(9), p.1444. 

17.   Lastiri-Pancardo, G., Mercado-Hernández, J. S., Kim, J., Jiménez, J. I., & Utrilla, J.* (2020). A quantitative method for proteome reallocation using minimal regulatory interventions. Nature Chemical Biology, 1–8. https://doi.org/10.1038/s41589-020-0593-y 

16.   Kim, J., Darlington, A., Salvador, M., Utrilla, J., & Jiménez, J. I. (2020). Trade-offs between gene expression, growth and phenotypic diversity in microbial populations. Current Opinion in Biotechnology, 62, 29–37. https://doi.org/10.1016/j.copbio.2019.08.004 (F.I. 2019: 8.23)

15.   Cheng, Chuankai, Edward J. O’Brien, Douglas McCloskey, Jose Utrilla, Connor Olson, Ryan A. LaCroix, Troy E. Sandberg, Adam M. Feist, Bernhard O. Palsson, and Zachary A. King. 2019. “Laboratory Evolution Reveals a Two-Dimensional Rate-Yield Tradeoff in Microbial Metabolism.”  PLOS Computational Biology 15 (6): e1007066 (F.I. 2019: 4.43)

14.   Astudillo-Melgar, Fernando, Adrián Ochoa-Leyva, José Utrilla*, and Gerardo Huerta-Beristain*. 2019. “Bacterial Diversity and Population Dynamics During the Fermentation of Palm Wine From Guerrero Mexico.” Frontiers in Microbiology 10: 531. doi:10.3389/fmicb.2019.00531. (Co-autor de correspondencia) 

13.   Latif, H., Federowicz, S., Ebrahim, A., Tarasova, J., Szubin, R., Utrilla, J., Zengler, K. and Palsson, B.O., 2018. ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions. PloS one, 13(5), p.e0197272. 

12.   Utrilla, J., Vargas-Tah, A., Trujillo-Martínez, B., Gosset, G., Martinez, A., 2016. Production of d-lactate from sugarcane bagasse and corn stover hydrolysates using metabolic engineered Escherichia coli strains. Bioresour. Technol. 220, 208–214  

11.   O’Brien, E.J., Utrilla, J., Palsson, B.O., 2016. Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments. PLOS Comput. Biol. 12, e1004998. doi:10.1371/journal.pcbi.1004998  

10.   Utrilla, J., O’Brien, E.J., Chen, K., McCloskey, D., Cheung, J., Wang, H., Armenta-Medina, D., Feist, A.M., Palsson, B.O., 2016. Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution. Cell Syst. 2, 260–271. doi:10.1016/j.cels.2016.04.003 

9.  LaCroix, R. a, Sandberg, T. E., O’Brien, E. J., Utrilla, J., Ebrahim, A., Guzman, G. I., … Feist, A. M. (2014). Discovery of key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal media using adaptive laboratory evolution. Applied and Environmental Microbiology, 81(1), 17–30. doi:10.1128/AEM.02246-14 

8.      Guzmán, G. I., Utrilla, J., Nurk, S., Brunk, E., Monk, J. M., Ebrahim, A.,  Feist, A. M. (2015). Model-driven discovery of underground metabolic functions in Escherichia coli. Proceedings of the National Academy of Sciences. doi:10.1073/pnas.1414218112 

7.  McCloskey,D., Utrilla, J., Naviaux, R. K., Palsson, B. O., & Feist, A. M. (2014). Fast Swinnex filtration (FSF): a fast and robust sampling and extraction method suitable for metabolomics analysis of cultures grown in complex media. Metabolomics. doi:10.1007/s11306-014-0686-2 

6.      Centeno-Leija, S., Utrilla, J., Flores, N., Rodriguez, A., Gosset, G., & Martinez, A. (2013). Metabolic and transcriptional response of Escherichia coli with a NADP+-dependent glyceraldehyde 3-phosphate dehydrogenase from Streptococcus mutans. Antonie van Leeuwenhoek. doi:10.1007/s10482-013-0010-6

5.      Utrilla, J., Licona-Cassani, C., Marcellin, E., Gosset, G., Nielsen, L.K., Martinez, A., 2012. Engineering and adaptive evolution of Escherichia coli for D-lactate fermentation reveals GatC as a xylose transporter. Metabolic engineering 14, 469–76. 

4.      Orencio-Trejo M, Utrilla J., Fernández-Sandoval M.T., Huerta-Beristain G., Gosset G., Martinez A. 2010. Engineering the Escherichia coli fermentative metabolism. Adv. Biochem. Eng.  121: 71–107

3.      Utrilla J, Gosset G, Martinez A. ATP limitation in a pyruvate formate lyase mutant of Escherichia coli MG1655 increases glycolytic flux to D- Lactate. (2009) Journal of Industrial Microbiology & Biotechnology Aug;36(8):1057-62. 

2.      Gerardo Huerta-Beristain, José Utrilla, Georgina Hernández-Chávez, Francisco Bolívar, Guillermo Gosset, Alfredo Martínez. Specific ethanol production rate in ethanologenic Escherichia coli KO11 strain is positively controlled by pyruvate decarboxylase from Zymomonas mobilis.(2008) Journal of Molecular Microbiology and Biotechnology. 15(1):55-64 

1.  Huerta-Beristain G.,Utrilla-Carreri J., Hernández-Chávez G., Bolivar F., Gosset G., Martinez A. (2005) Ingeniería Metabólica para incrementar el Flux y rendimiento de etanol en Escherichia coli Etanologénica. 4, 1:25-36 Revista Mexicana de Ingeniería Química. AMDIQ.