Synthetic Biology

In our program we address diverse biological questions through the scales (molecules, cells, communities) using different disciplines such as systems biology, bioinformatics, functional genomics, biochemistry, ecology, molecular biology among others. We aim to study how biological systems evolve and how we can modify them to generate synthetic biology applications.

One of our current topics is to study bacterial populations’ ecological and evolutionary dynamics and their response to different environmental conditions. In particular, we are interested in studying the effect of antimicrobial substances on the complex dynamics of bacterial populations. We build synthetic communities and study their interactions using experimental evolution techniques and mathematical, computational models, and individual cell microfluidics.

Current research shows that proteins can start to fold and become functional while still being synthesized by the ribosome. In our lab we apply state of the art methods of homology detection, algorithms to detect rare codons and folding predictions to uncover the impact of the ribosome in the structure of the proteome. In our experimental strategies we use one of the most successful developments of synthetic biology: a cell free protein expression system. With this system we produce proteins in carefully determined environments without the restrictions that living cells impose; this allows us to precisely control the elements that influence protein folding during translation.

Another of our research topics include the use of functional genomics to understand and design microbial production strains. We are interested in the generation of genome scale computational tools to aid in the design of synthetic production phenotypes through the modification of the genotype-phenotype relationship ( i.e. through the regulatory network). We aim to engineer the transcriptional and translational machineries of model and non model bacteria, such as Escherichia coli and pseudomonas chlororaphis, to improve the allocation of cellular resources to synthetic functions.

We are a mix of young bioinformaticians and experimentalists, this setup provides the perfect blend for successful projects. In our lab we encourage creativity, innovation and critical thinking in a relaxed environment to promote the development of young bachelor, master, doctoral students and postdocs.

Group Staff

José Utrilla CarreriResearcherAssociate 3291686
Ayari Fuentes HernándezResearcherAssociate 3291686
José Arcadio Farías RicoResearcherAssistant 3291686
Omar Alejandro Aguilar VeraLaboratory TechnicianLaboratory 3139944
María Soledad Juárez RamírezSupport 3133881

Group Publications

2022León-González, J.A., Flatet, P., Juárez-Ramírez, M.S., Farías-Rico, J.A.. (2022). "Folding and Evolution of a Repeat Protein on the Ribosome.". Frontiers in molecular biosciences. 9():-. [doi:10.3389/fmolb.2022.851038]35707224
2022Reyes-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):212008-212008. [doi:10.1098/rsos.212008]35592760
2022Peralta, H., Aguilar, A., Cancino-Díaz, J.C., Cuevas-Rico, E.A., Carmona-González, A., Cruz-Maya, J.A., Jan-Roblero, J.. (2022). "Determination of the metabolic pathways for degradation of naphthalene and pyrene in Amycolatopsis sp. Poz14.". COMP BIOCHEM PHYS C. 254():-. [doi:10.1016/j.cbpc.2022.109268]35026398
2022Hidalgo, 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):-. [doi:10.1016/j.isci.2022.103879]35243241
2022Rodríguez-Santiago, J., Rodríguez-Medina, N., Tamayo-Legorreta, E.M., Silva-Sánchez, J., Téllez-Sosa, J., Duran-Bedolla, J., Aguilar-Vera, A., Lecona-Valera, A.N., Garza-Ramos, U., Alpuche-Aranda, C.. (2022). "Molecular and Genomic Insights of mcr-1 -Producing Escherichia coli Isolates from Piglets.". ANTIBIOTICS-BASEL. 11(2):-. [doi:10.3390/antibiotics11020157]35203760
2022Vargas-Lagunas, C., Mora, Y., Aguilar, A., Reyes-González, A.R., Arteaga-Ide, A., Dunn, M.F., Encarnación, S., Girard, L., Peralta, H., Mora, J.. (2022). "A Tar aspartate receptor and Rubisco-like protein substitute biotin in the growth of rhizobial strains.". MICROBIOLOGY-SGM. 168(1):-. [doi:10.1099/mic.0.001130]35077343
2022Romero-Leiton, J.P., Prieto, K., Reyes-Gonzalez, D., Fuentes-Hernandez, A.. (2022). "Optimal control and Bayes inference applied to complex microbial communities.". MATH BIOSCI ENG. 19(7):6860-6882. [doi:10.3934/mbe.2022323]35730286
2022Humberto, B.C., Jesús, S.S., Elena, C.A., Luis, L.A., Josefina, D.B., Alejandro, A.V., Elvira, G.G., Paola, B.I., Rayo, M.O., Rigoberto, H.C., Ulises, G.R.. (2022). "PCR system for the correct differentiation of the main bacterial species of the Klebsiella pneumoniae complex.". Archives Of Microbiology. 204(1):-. [doi:10.1007/s00203-021-02668-x]34951665
2021Hidalgo, D., Martínez-Ortiz, C.A., O. Palsson, B., Jiménez, J.I., Utrilla, J.. (2021). "Regulatory perturbations of ribosome allocation reshape the growth proteome with a trade-off in adaptation capacity". bioRxiv. ():-. [doi:]
2021Hernández-Beltrán, J.C.R., San Millán, A., Fuentes-Hernández, A., Peña-Miller, R.. (2021). "Mathematical Models of Plasmid Population Dynamics.". Frontiers in Microbiology. 12():-. [doi:10.3389/fmicb.2021.606396]34803935
2021Hernandez-Beltran, J.C.R., Rodríguez-Beltrán, J., Millán, A.S., Peña-Miller, R., Fuentes-Hernández, A.. (2021). "Quantifying plasmid dynamics using single-cell microfluidics and image bioinformatics.". Plasmid. 113():-. [doi:10.1016/j.plasmid.2020.102517]32535165
2020Rojas, E., Martinez-Pacheco, M., Rodriguez-Sastre, M.A., Ramos-Espinosa, P., Valverde, M.. (2020). "Post-transcriptional regulation of Rad51c by miR-222 contributes cellular transformation.". Plos One. 15(1):-. [doi:10.1371/journal.pone.0221681]31923208
2020Kim, 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. [doi:10.1016/j.copbio.2019.08.004]31580950
2020Ferruz N, Lobos F, Lemm D, Toledo-Patino S, Farías-Rico JA, Schmidt S, Höcker B. (2020). "Identification and Analysis of Natural Building Blocks for Evolution-Guided Fragment-Based Protein Design.". Journal Of Molecular Biology. 432(13):3898-3914. [doi:10.1016/j.jmb.2020.04.013]32330481
2020Cornejo-Páramo, P., Dissanayake, D.S.B., Lira-Noriega, A., Martínez-Pacheco, M.L., Acosta, A., Ramírez-Suástegui, C., Méndez-de-la-Cruz, F.R., Székely, T., Urrutia, A.O., Georges, A., Cortez, D.. (2020). "Viviparous Reptile Regarded to Have Temperature-Dependent Sex Determination Has Old XY Chromosomes.". Genome Biology And Evolution. 12(6):924-930. [doi:10.1093/gbe/evaa104]32433751
2020Lastiri-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. 16(9):1026-1033. [doi:10.1038/s41589-020-0593-y]32661378
2020de la Cruz, M., Ramírez, E.A., Sigala, J.C., Utrilla, J., Lara, A.R.. (2020). "Plasmid DNA Production in Proteome-Reduced Escherichia coli .". Microorganisms. 8(9):1-8. [doi:10.3390/microorganisms8091444]32967123
2020Moreno-Avitia, Fabian, Utrilla, Jose, Bolivar, Francisco, Nogales, Juan, Escalante, Adelfo. (2020). "Metabolic reconstruction ofPseudomonas chlororaphisATCC 9446 to understand its metabolic potential as a phenazine-1-carboxamide-producing strain". Applied Microbiology And Biotechnology. 104(23):10119-10132. [doi:10.1007/s00253-020-10913-4]32984920
2020Martínez-Pacheco, M., Tenorio, M., Almonte, L., Fajardo, V., Godínez, A., Fernández, D., Cornejo-Páramo, P., Díaz-Barba, K., Halbert, J., Liechti, A., Székely, T., Urrutia, A.O., Cortez, D.. (2020). "Expression Evolution of Ancestral XY Gametologs across All Major Groups of Placental Mammals.". Genome Biology And Evolution. 12(11):2015-2028. [doi:10.1093/gbe/evaa173]32790864
2020Rodriguez, Susana, Correa-Galeote, David, Sanchez-Perez, Mishael, Ramirez, Mario, Isidra-Arellano, Mariel C., Reyero-Saavedra, Maria del Rocio, Zamorano-Sanchez, David, Hernandez, Georgina, Valdes-Lopez, Oswaldo, Girard, Lourdes. (2020). "A Novel OmpR-Type Response Regulator Controls Multiple Stages of the Rhizobium etliPhaseolus vulgaris N2-Fixing Symbiosis". Frontiers in Microbiology. 11():-. [doi:10.3389/fmicb.2020.615775]33384681
2019Acosta, A., Martínez-Pacheco, M.L., Díaz-Barba, K., Porras, N., Gutiérrez-Mariscal, M., Cortez, D.. (2019). "Deciphering Ancestral Sex Chromosome Turnovers Based on Analysis of Male Mutation Bias.". Genome Biology And Evolution. 11(11):3054-3067. [doi:10.1093/gbe/evz221]31605487
2019Santos-Zavaleta, A., Pérez-Rueda, E., Sánchez-Pérez, M., Velázquez-Ramírez, D.A., Collado-Vides, J.. (2019). "Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes.". Bmc Genomics. 20(1):-. [doi:10.1186/s12864-019-5619-z]30991941
2019Astudillo-Melgar, Fernando, Ochoa-Leyva, Adrian, Utrilla, Jose, Huerta-Beristain, Gerardo. (2019). "Bacterial Diversity and Population Dynamics During the Fermentation of Palm Wine From Guerrero Mexico.". Frontiers in Microbiology. 10():-. [doi:10.3389/fmicb.2019.00531]30967846
2019Santos-Zavaleta, A., Salgado, H., Gama-Castro, S., Sánchez-Pérez, M., Gómez-Romero, L., Ledezma-Tejeida, D., García-Sotelo, J.S., Alquicira-Hernández, K., Muñiz-Rascado, L.J., Peña-Loredo, P., Ishida-Gutiérrez, C., Velázquez-Ramírez, D.A., Del Moral-Chávez, V., Bonavides-Martínez, C., Méndez-Cruz, C.F., Galagan, J., Collado-Vides, J.. (2019). "RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12". Nucleic Acids Research. 47(D1):212-220. [doi:10.1093/nar/gky1077]30395280
2018Latif, H., Federowicz, S., Ebrahim, A., Tarasova, J., Szubin, R., Utrilla, J., Zengler, K., Palsson, B.O.. (2018). "ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions". Plos One. 13(5):-. [doi:10.1371/journal.pone.0197272]29771928
2018Rodriguez-Beltran, J., Hernandez-Beltran, J.C.R., Delafuente, J., Escudero, J.A., Fuentes-Hernandez, A., MacLean, R.C., Peña-Miller, R., San Millan, A.. (2018). "Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation". Nature Ecology & Evolution. 2(5):873-881. [doi:10.1038/s41559-018-0529-z]29632354
2017Steffani-Vallejo, J.L., Zuñiga, C., Cruz-Morales, P., Lozano, L., Morales, M., Licona-Cassani, C., Revah, S., Utrilla, J.. (2017). "Draft genome sequence of Sphingobacterium sp. CZ-UAM, isolated from a methanotrophic consortium". Microbiology Resource Announcements. 5(33):-. [doi:10.1128/genomeA.00792-17]28818899
2017Moreno-Avitia, F., Lozano, L., Utrilla, J., Bolívar, F., Escalante, A.. (2017). "Draft genome sequence of pseudomonas chlororaphis ATCC 9446, a nonpathogenic bacterium with bioremediation and industrial potential". Microbiology Resource Announcements. 5(23):-. [doi:10.1128/genomeA.00474-17]28596401
2017Utrilla, Jose. (2017). "Evolutionary Engineering of Microorganisms to Overcome Toxicity During Lignocellulose Hydrolysates Utilization". Engineering of Microorganisms for the Production of Chemicals and Biofuels from Renewable Resources. ():181-200. [doi:]
2016Utrilla, Jose, Vargas-Tah, Alejandra, Trujillo-Martinez, Berenice, Gosset, Guillermo, Martinez, Alfredo. (2016). "Production of D-lactate from sugarcane bagasse and corn stover hydrolysates using metabolic engineered Escherichia coli strains". BIORESOURCE TECHNOLOGY. 220():208-214. [doi:10.1016/j.biortech.2016.08.067]27573474
2016Utrilla, 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 systems. 2(4):260-271. [doi:10.1016/j.cels.2016.04.003]27135538