Genome Engineering Program


# Año Ficha Ligas
1 2017 Bañuelos-Vazquez, L.A., Tejerizo, G.T. and Brom, S. (2017). "Regulation of Conjugative Transfer of Plasmids and Integrative Conjugative Elements". Plasmid. 91:82-89   PUBMED: #28438469
2 2017 Bustos, P., Santamaria, R.I., Pérez-Carrascal, O.M., Acosta, J.L., Lozano, L., Juárez, S., Martínez-Flores, I., Martínez-Romero, E., Romero, D., Dávila, G., Vinuesa, P., Miranda-Sánchez, F., Ormeño-Orrillo, E. and González, V. (2017). "Complete Genome Sequences Of Three Rhizobium gallicum Symbionts Associated With Common Bean (Phaseolus vulgaris)". Genome Announc. 5(11)   PUBMED: #28302777
3 2017 Contreras-Moreira, B., Cantalapiedra, C.P., García-Pereira, M.J., Gordon, S.P., Vogel, J.P., Igartua, E., Casas, A.M. and Vinuesa, P. (2017). "Analysis of Plant Pan-genomes and Transcriptomes with GET_HOMOLOGUES-est, a Clustering Solution for Sequences of the Same Species". Front Plant Sci. 8:184   PUBMED: #28261241
4 2017 Cubillas, C., Miranda-Sánchez, F., González-Sánchez, A., Elizalde, J.P., Vinuesa, P., Brom, S. and (2017). "A Comprehensive Phylogenetic Analysis of Copper Transporting P-1b ATPases from Bacteria of the Rhizobiales Order Uncovers Multiplicity, Diversity and Novel Taxonomic Subtypes". Microbiologyopen. 6(4):-e452   PUBMED: #28217917
5 2017 González-Sánchez, A., Cubillas, C., Miranda, F., Dávalos, A. and García-de los Santos, A. (2017). "The ropAe Gene Encode a Porin-like Protein Involved in Copper Transit in Rhizobium etli CFN42". Microbiologyopen.   PUBMED: #29280343
6 2017 Martinez-Flores, W.A., Palma-Garcia, J.M., Caballero-Ortega, H., Del Viento-Camacho, A., López-Escamilla, E., Martínez-Hernández, F., Vinuesa, P., Correa, D. and Maravilla, P. (2017). "Genotyping Toxoplasma Gondii with the B1 Gene in Naturally Infected Sheep from an Endemic Region in the Pacific Coast of Mexico". Vector-borne and Zoonotic Diseases. 17(7):495-502   PUBMED: #28530509
7 2017 Ochoa-Sanchez, L.E. and Vinuesa, P. (2017). "Evolutionary Genetic Analysis Uncovers Multiple Species With Distinct Habitat Preferences and Antibiotic Resistance Phenotypes in the Stenotrophomonas maltophilia Complex". Frontiers in Microbiology. 8:-1548   PUBMED: #28861062
8 2017 Santamaria, R.I., Bustos, P., Pérez-Carrascal O.M, Miranda-Sánchez, F., Vinuesa, P., Martínez-Flores, I., Juárez, S., Lozano, L., Martínez-Romero, E., Cevallos, M.A., Ormeño-Orrillo, E. and González, V. (2017). "Complete Genome Sequences Of Eight Rhizobium Symbionts Associated With Common Bean (Phaseolus vulgaris)". Genome Announc. 5(30)   PUBMED: #28751391
9 2017 Silva, C., Betancor, L., García, C., Astocondor, L., Hinostroza, N., Bisio, J., Rivera, J., Perezgasga, L., Escanda, V.P., Yim, L., Jacobs, J., García-del Portillo, F., Chabalgoity, J.A. and Puente, J.L. (2017). "Characterization Of Salmonella enterica Isolates Causing Bacteremia in Lima, Peru, Using Multiple Typing Methods". Plos One. 12(12):-e0189946   PUBMED: #29267322
10 2016 Carrascal, O.M.P., Juárez, S., Polz, M.F., Vinuesa, P. and González, V. (2016). "Population Genomics of The Symbiotic Plasmids of Sympatric Nitrogen-fixing Rhizobium Species Associated with Phaseolus vulgaris". Environ Microbiol. 18(8):2660-2676   PUBMED: #27312778
11 2016 Centeno-Leija, S., Vinuesa, P., Rodríguez-Peña, K., Trenado-Uribe, M., Cárdenas-Conejo, Y., Serrano-Posada, H., Rodríguez-Sanoja, R. and Sánchez, S. (2016). "Draft Genome Sequence Of an Endophytic Actinoplanes Species, Encoding Uncommon trans-Acyltransferase Polyketide Synthases". Genome Announc. 4(2):e00164-16   PUBMED: #27013046
12 2016 Hernández-Tamayo, R., Torres-Tejerizo, G., Brom, S. and Romero, D. (2016). "Site-Specific Bacterial Chromosome Engineering Mediated By Inta Integrase from Rhizobium etli". BMC Microbiol. 16   PUBMED: #27357704
13 2016 Miranda-Sánchez, F., Rivera, J. and Vinuesa, P. (2016). "Diversity Patterns of Rhizobiaceae Communities Inhabiting Soils, Root Surfaces and Nodules Reveal a Strong Selection of Rhizobial Partners by Legumes". Environ Microbiol. 18(8):2375-2391   PUBMED: #26395550
14 2016 Sandner-Miranda L., Vinuesa, P., Soberón-Chávez G. and Morales-Espinosa R. (2016). "Complete Genome Sequence Of Serratia marcescens SmUNAM836, a Nonpigmented Multidrug-resistant Strain Isolated from a Mexican Patient with Obstructive Pulmonary Disease". Genome Announc. 4(1):e01417-15   PUBMED: #26798087
15 2016 Silva C., Calva E., Puente J.L., Zaidi M.B. and Vinuesa, P. (2016). "Complete Genome Sequence Of Salmonella enterica Serovar Typhimurium Strain SO2 (sequence Type 302) Isolated from an Asymptomatic Child in Mexico". Genome Announc. 4(2):e00253-16   PUBMED: #27081133
16 2016 Silva C., Calva E., Puente J.L., Zaidi M.B. and Vinuesa, P. (2016). "Complete Genome Sequence Of Salmonella enterica Serovar Typhimurium Strain Yu15 (sequence Type 19) Harboring the Salmonella Genomic Island 1 and Virulence Plasmid pSTV". Genome Announc. 4(2):e00252-16   PUBMED: #27081132
17 2016 Vinuesa, P., Puente J.L., Calva E., Zaidi M.B. and Silva C. (2016). "Complete Genome Sequence Of Salmonella enterica Serovar Typhimurium Strain SO3 (sequence Type 302) Isolated from a Baby with Meningitis in Mexico". Genome Announc. 4(2):e00285-16   PUBMED: #27103717
18 2016 Yáñez, F., Castellanos, M. and Romero, D. (2016). "Biased Gene Conversion In Rhizobium etli is Caused by Preferential Double-strand Breaks on One of the Recombining Homologs". J Bacteriol. 198(3):591-599   PUBMED: #26598365
19 2015 Lopez-Fuentes, E., Torres-Tejeerizo, G., Cervantes, L. and Brom, S. (2015). "Genes Encoding Conserved Hypothetical Proteins Localized in The Conjugative Transfer Region of Plasmid pRet42a from Rhizobium etli CFN42 Participate in Modulating Transfer and Affect Conjugation from Different Donors". Frontiers in Microbiology. 5:-793   PUBMED: #25642223
20 2015 Riquelme, C., Camara, S., Dapkevicius, M.D.N.E., Vinuesa, P., da Silva, C.C.G., Malcata, F.X. and Rego, O.A. (2015). "Characterization of the Bacterial Biodiversity in Pico Cheese (an Artisanal Azorean Food)". International Journal of Food Microbiology. 192:86-94   PUBMED: #25440551
21 2015 Sachman-Ruíz, B., Narvaez-Padilla, V. and Reynaud, E. (2015). "Commercial Bombus Impatiens as Reservoirs of Emerging Infectious Diseases in Central Mexico". Biological Invasions. 17(7):2043-2053    
22 2015 Tejerizo, G.T., Banuelos, L.A., Cervantes, L., Gaytan, P., Pistorio, M., Romero, D. and Brom, S. (2015). "Development Of Molecular Tools to Monitor Conjugative Transfer in Rhizobia". Journal of Microbiological Methods. 117:155-163   PUBMED: #26272377
23 2015 Vinuesa, P. and Contreras-Moreira, B. (2015). "Robust Identification of Orthologues and Paralogues for Microbial Pan-genomics Using GET_HOMOLOGUES: a Case Study of pIncA/c Plasmids". Bacterial Pangenomics: Methods and Protocols. 1231:203-232   PUBMED: #25343868
24 2014 Chang, F.M.J., Coyne, H.J., Cubillas, C., Vinuesa, P., Fang, X.Y., Ma, Z., Ma, D.J., Helmann, J.D., García-de los Santos, A., Wang, Y.X., Dann, C.E. and Giedroc, D.P. (2014). "Cu(I)-mediated Allosteric Switching in a Copper-sensing Operon Repressor (CsoR)". J Biol Chem. 289(27):19204-19217   PUBMED: #24831014
25 2014 Cubillas, C., Vinuesa, P., Tabche, M.L., Vázquez, A., Hernández-Lucas, I., Romero, D. and García-de los Santos, A. (2014). "The Cation Diffusion Facilitator Protein EmfA of Rhizobium etli Belongs to a Novel Subfamily of Mn2+/fe2+ Transporters Conserved in Alpha-proteobacteria". Metallomics. 6(10):1808-1815   PUBMED: #25054342
26 2014 Rogel, M.A., Santamaria, R.I., González, V., Romero, D., Cevallos, M.A., Lozano, L., Castro-Mondragón, J., Martínez, J., Ormeño-Orrillo, E. and Martínez-Romero, E. (2014). "Genomic Basis Of Symbiovar Mimosae in Rhizobium etli". BMC Genomics. 15   PUBMED: #25005495
27 2014 Santamaria, R.I., Bustos, P., Lozano, L., Rodríguez, C., Fernández, J.L., Juárez, S., Kameyama, L., Guarneros, G., Dávila, G. and González, V. (2014). "Narrow-host-range Bacteriophages That Infect Rhizobium etli Associate with Distinct Genomic Types". Appl Environ Microbiol. 80(2):446-454   PUBMED: #24185856
28 2014 Tejerizo, G.T., Pistorio, M., Althabegoiti, M.J., Cervantes, L., Wibberg, D., Schluter, A., Puhler, A., Lagares, A., Romero, D. and Brom, S. (2014). "Rhizobial Plasmid pLPU83a Is Able To Switch between Different Transfer Machineries Depending on Its Genomic Background". FEMS Microbiol Ecol. 88(3):565-578   PUBMED: #24646299
29 2013 Contreras-Moreira, B. and Vinuesa, P. (2013). "GET_HOMOLOGUES, A Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis". Appl Environ Microbiol. 79(24):7696-7701   PUBMED: #24096415
30 2013 Cubillas, C., Vinuesa, P., Tabche, M.L. and García-de los Santos, A. (2013). "Phylogenomic Analysis of Cation Diffusion Facilitator Proteins Uncovers Ni2+/co2+ Transporters". Metallomics. 5(12):1634-1643   PUBMED: #24077251
31 2013 Estrada-de los Santos, P., Vinuesa, P., Martínez-Aguilar, L., Hirsch, A.M. and Caballero-Mellado, J. (2013). "Phylogenetic Analysis Of Burkholderia Species By multilocus Sequence Analysis". Curr Microbiol. 67(1):51-60   PUBMED: #23404651
32 2013 Hernández-Tamayo, R., Sohlenkamp, C., Puente, J.L., Brom, S. and Romero, D. (2013). "Characterization of Inta, a Bidirectional Site-Specific Recombinase Required for Conjugative Transfer of the Symbiotic Plasmid of Rhizobium etli CFN42". J Bacteriol. 195(20):4668-4677   PUBMED: #23935046
33 2012 Bonilla-Rosso, G., Eguiarte, L.E., Romero, D., Travisano, M. and Souza, V. (2012). "Understanding Microbial Community Diversity Metrics Derived from Metagenomes: Performance Evaluation Using Simulated Data Sets". FEMS Microbiol Ecol. 82(1):37-49   PUBMED: #22554028
34 2012 Castillo-Rodal, A.I., Mazari-Hiriart, M., Lloret-Sánchez, L.T., Sachman-Ruíz, B., Vinuesa, P. and López-Vidal, Y (2012). "Potentially Pathogenic Nontuberculous Mycobacteria Found in Aquatic Systems. Analysis from a Reclaimed Water and Water Distribution System in Mexico City". European Journal of Clinical Microbiology and Infectious Diseases. 31(5):683-694   PUBMED: #21805195
35 2012 Escalera-Zamudio, M., Cobian-Guemes, G., Soto-del Río, M.D., Isa, P., Sánchez-Betancourt, I., Parissi-Crivelli, A., Martinez-Cazares, M.T., Romero, P., Velázquez-Salinas, L., Huerta-Lozano, B., Nelson, M., Montero, H., Vinuesa, P., López, S. and Arias, C.F. (2012). "Characterization Of an Influenza a Virus in Mexican Swine that is Related to the a-H1N1-2009 Pandemic Clade". Virology. 433(1):176-182   PUBMED: #22921315
36 2012 Tejerizo, G.T., Lozano, L., González, V., Bustos, P., Romero, D. and Brom, S. (2012). "Draft Genome Sequence Of the Bean-nodulating Sinorhizobium fredii Strain GR64". J Bacteriol. 194(24):6978-6978   PUBMED: #23209231
37 2011 Acosta, J.L., Eguiarte, L.E., Santamaria, R.I., Bustos, P., Vinuesa, P., Martínez-Romero, E., Dávila, G. and González, V. (2011). "Genomic Lineages of Rhizobium etli Revealed by the Extent of Nucleotide Polymorphisms and Low Recombination". BMC Evol Biol. 11   PUBMED: #22004448
38 2011 Cervantes, L., Bustos, P., Girard, L., Santamaria, R.I., Dávila, G., Vinuesa, P., Romero, D. and Brom, S. (2011). "The Conjugative Plasmid of a Bean-nodulating Sinorhizobium fredii Strain is Assembled from Sequences of Two Rhizobium Plasmids and the Chromosome of a Sinorhizobium Strain". BMC Microbiol. 11(1):149   PUBMED: #21702991
39 2011 Landeta, C., Dávalos, A., Cevallos, M.A., Geiger, O., Brom, S. and Romero, D. (2011). "Plasmids With a Chromosome-like Role in Rhizobia". J Bacteriol. 193(6):1317-1326   PUBMED: #21217003
40 2011 Silva-Sanchez, J., Garza-Ramos, J.U., Reyna-Flores, F., Sánchez-Pérez, A, Rojas-Moreno, T., Andrade-Almaraz, V., Pastrana, J., Castro-Romero, J.I., Vinuesa, P., Barrios, H. and Cervantesde, C (2011). "Extended-spectrum Beta-lactamase-producing Enterobacteriaceae Causing Nosocomial Infections In Mexico. a Retrospective and Multicenter Study". Arch Med Res. 42(2):156-162   PUBMED: #21565630
41 2011 Villaseñor-Toledo, T., Dávalos, A., Lozano, L., Romero, D. and García-de los Santos, A. (2011). "Housekeeping Genes Essential For Pantothenate Biosynthesis Are Plasmid-encoded In Rhizobium etli and Rhizobium leguminosarum". BMC Microbiol. 11   PUBMED: #21463532
42 2010 Miranda-Miranda, E., Cossio-Bayugar, R., Quezada-Delgado, M.D.R., Sachman-Ruíz, B. and Reynaud, E. (2010). "Staphylococcus saprophyticus Is A Pathogen Of The Cattle Tick Rhipicephalus (Boophilus) microplus". Biocontrol Sci. Technol.. 20:1055-1067    
43 2009 Castellanos, M. and Romero, D. (2009). "The Extent of Migration of the Holliday Junction is a Crucial Factor for Gene Conversion in Rhizobium etli". J Bacteriol. 191(15):4987-4995   PUBMED: #19502410
44 2009 Contreras-Moreira, B., Sachman-Ruíz, B., Figueroa-Palacios, I. and Vinuesa, P. (2009). "Primers4clades: A Web Server that Uses Phylogenetic Trees to Design Lineage-Specific PCR Primers for Metagenomic and Diversity Studies". Nucl Acid Res. 37:W95-W100   PUBMED: #19465390
45 2009 Cummings, S.P., Gyaneshwar, P., Vinuesa, P., Farruggia, F.T., Andrews, M., Humphry, D., Elliot, G.N., Nelson, A., Orr, C., Pettitt, D., Shah, G.R., Santos, S.R., Krishnan, H.B., Odee, D., Moreira, F.M., Sprent, J.I., Young, J.P. and James, E.K. (2009). "Nodulation Of Sesbania Species By Rhizobium (Agrobacterium) Strain IRBG74 And Other Rhizobia". Environ Microbiol. 11(10):2510-2525   PUBMED: #19555380
46 2009 Martínez-Salazar, J.M., Salazar, E., Encarnación, S., Ramírez-Romero, M.Á. and Rivera, J. (2009). "Role Of the Extracytoplasmic Function Sigma Factor RpoE4 in Oxidative and Osmotic Stress Responses in Rhizobium etli". J Bacteriol. 191(13):4122-4132   PUBMED: #19376852
47 2009 Martínez-Salazar, J.M., Zuñiga-Castillo, J. and Romero, D. (2009). "Differential Roles of Proteins Involved in Migration of Holliday Junctions on Recombination and Tolerance to DNA Damaging Agents in Rhizobium etli". Gene. 432(1-2):26-32   PUBMED: #19071199
48 2009 Martínez-Salazar, J.M., Sandoval-Calderón, M., Guo, X.W., Castillo-Ramírez, S., Reyes-González, A., Loza-Correa, M., Rivera, J., Alvarado-Affantranger, X., Sánchez, F, González, V., Dávila, G. and Ramírez-Romero, M.Á. (2009). "The Rhizobium etli RpoH1 and RpoH2 Sigma Factors are Involved in Different Stress Responses". Microbiology-sgm. 155:386-397   PUBMED: #19202087
49 2008 Cerritos, R., Vinuesa, P., Eguiarte, L.E., Herrera-Estrella, L., Alcaraz-Peraza, L.D., Arvizu-Gomez, J.L., Olmedo, G., Ramirez, E., Siefert, J.L. and Souza, V. (2008). "Bacillus coahuilensis sp nov., a Moderately Halophilic Species from a Desiccation Lagoon in the Cuatro Cienegas Valley in Coahuila, Mexico". Int J Syst Evol Microbiol. 58:919-923   PUBMED: #18398195
50 2008 Crossman, LC., Castillo-Ramírez, S., McAnnula, C., Lozano, L., Vernikos, GS., Acosta, JL., Ghazoui, ZF., Hernández-González, I., Meakin, G., Walker, AW., Hynes, MF., Young, JP., Downie, JA., Romero, D., Johnston, AW., Dávila, G., Parkhill, J. and González, V. (2008). "A Common Genomic Framework for a Diverse Assembly of Plasmids in the Symbiotic Nitrogen Fixing Bacteria". Plos One. 3(7):e2567   PUBMED: #18596979
51 2008 García-de los Santos, A., López, E., Cubillas, C., Noel, K.D., Brom, S. and Romero, D. (2008). "Requirement of a Plasmid-encoded Catalase for Survival of Rhizobium etli CFN42 in a Polyphenol-rich Environment". Appl Environ Microbiol. 74(8):2398-2403   PUBMED: #18310436
52 2008 Renteria, M.E., Gandhi, N.S., Vinuesa, P., Helmerhorst, E. and Mancera, R.L. (2008). "A Comparative Structural Bioinformatics Analysis of the Insulin Receptor Family Ectodomain Based on Phylogenetic Information". Plos One. 3(11):-e3667   PUBMED: #18989367
53 2008 Sepúlveda, E., Perez-Mendoza, D., Ramírez-Romero, M.Á., Soto, M.J., López-Lara, I.M., Geiger, O., Sanjuan, J., Brom, S. and Romero, D. (2008). "Transcriptional Interference And Repression Modulate the Conjugative Ability of the Symbiotic Plasmid of Rhizobium etli". J Bacteriol. 190(12):4189-4197   PUBMED: #18424522
54 2008 Vinuesa, P., Rojas-Jimenez, K., Contreras-Moreira, B., Mahna, S.K., Prasad, B.N., Moe, H., Selvaraju, S.B., Thierfelder, H. and Werner, D. (2008). "Multilocus Sequence Analysis For Assessment of the Biogeography and Evolutionary Genetics of Four Bradyrhizobium Species that Nodulate Soybeans on the Asiatic Continent". Appl Environ Microbiol. 74(22):6987-6996   PUBMED: #18791003
55 2007 Granados-Baeza, M.J., Gómez-Hernández, N., Mora, Y., Delgado, M.J., Romero, D. and Girard, L. (2007). "Novel Reiterated Fnr-type Proteins Control the Production of the Symbiotic Terminal Oxidase Cbb(3) in Rhizobium etli CFN42". Mol Plant Microbe Interactions. 20(10):1241-1249   PUBMED: #17918626
56 2007 Pinero, S., Rivera, J., Romero, D., Cevallos, M.A., Martínez, A., Bolivar, F. and Gosset, G. (2007). "Tyrosinase From Rhizobium etli is Involved in Nodulation Efficiency and Symbiosis-associated Stress Resistance". J Mol Microbiol Biotechnol. 13(1-3):35-44   PUBMED: #17693711
57 2007 Poggio, S., Abreu-Goodger, C., Fabela, S., Osorio, A., Dreyfus, G., Vinuesa, P. and Camarena, L. (2007). "A Complete Set of Flagellar Genes Acquired by Horizontal Transfer Coexists with the Endogenous Flagellar System in Rhodobacter sphaeroides". J Bacteriol. 189(8):3208-3216   PUBMED: #17293429
58 2007 Ramírez-Trujillo, J.A., Encarnación, S., Salazar, E., García-de los Santos, A., Dunn, M.F., Emerich, D.W., Calva, E. and Hernández-Lucas, I. (2007). "Functional Characterization Of The Sinorhizobium meliloti Acetate Metabolism Genes aceA, SMc00767, and glcB". J Bacteriol. 189(16):5875-5884   PUBMED: #17526694
59 2007 Sohlenkamp, C., Galindo-Lagunas, K.A., Guan, Z.Q., Vinuesa, P., Robinson, S., Thomas-Oates, J., Raetz, C.R.H. and Geiger, O. (2007). "The Lipid Lysyl-phosphatidylglycerol Is Present In Membranes of Rhizobium tropici CIAT899 and Confers Increased Resistance to Polymyxin B under Acidic Growth Conditions". Mol Plant Microbe Interactions. 20(11):1421-1430   PUBMED: #17977153
60 2007 Top, E. and Romero, D. (2007). "Evolution and Ecology - Summary". Plasmid. 57(2):223-225    
61 2005 Guillén-Navarro, K., Araíza, G., García-de los Santos, A., Mora, Y. and Dunn, M.F. (2005). "The Rhizobium etli bioMNY Operon Is Involved in Biotin Transport". FEMS Microbiol Lett. 250(2):209-219   PUBMED: #16099603
62 2005 Pérez-Mendoza, D., Sepúlveda, E., Pando, V., Muñoz, S., Nogales, J., Olivares, J., Soto, M.J., Herrera-Cervera, J.A., Romero, D., Brom, S. and Sanjuan, J. (2005). "Identification of the rctA Gene, Which is Required for Repression of Conjugative Transfer of Rhizobial Symbiotic Megaplasmids". J Bacteriol. 187(21):7341-7350   PUBMED: #16237017
63 2005 Santoyo, G., Martínez-Salazar, J.M., Rodríguez, C. and Romero, D. (2005). "Gene Conversion Tracts Associated With Crossovers in Rhizobium etli". J Bacteriol. 187(12):4116-4126   PUBMED: #15937174
64 2005 Santoyo, G. and Romero, D. (2005). "Gene Conversion and Concerted Evolution in Bacterial Genomes". FEMS Microbiol Rev. 29(2):169-183   PUBMED: #15808740
65 2004 Brom, S., Girard, L., Tun-Garrido, C., García-de los Santos, A., Bustos, P., González, V. and Romero, D. (2004). "Transfer of The Symbiotic Plasmid of Rhizobium etli CFN42 Requires Cointegration with p42a, Which may be Mediated by Site-Specific Recombination". J Bacteriol. 186(22):7538-7548   PUBMED: #15516565
66 2004 Perez-Mendoza, D., Dominguez-Ferreras, A., Munoz, S., Soto, M.J., Olivares, J., Brom, S., Girard, L., Herrera-Cervera, J.A. and Sanjuan, J. (2004). "Identification of Functional Mob Regions in Rhizobium etli: Evidence for Self-transmissibility of the Symbiotic Plasmid pRetCFN42d". J Bacteriol. 186(17):5753-5761   PUBMED: #15317780
67 2004 Zuñiga-Castillo, J., Romero, D. and Martínez-Salazar, J.M. (2004). "The Recombination Genes addAB are not Restricted to Gram-positive Bacteria: Genetic Analysis of the Recombination Initiation Enzymes recF and addAB in Rhizobium etli". J Bacteriol. 186(23):7905-7913   PUBMED: #15547262
68 2003 González, V., Bustos, P., Ramírez-Romero, M.Á., Medrano-Soto, A., Salgado, H., Hernández-González, I., Hernandez-Celis, J.C., Quintero, V., Moreno-Hagelsieb, G., Girard, L., Rodríguez, O., Flores, M., Cevallos, M.A., Collado-Vides, J., Romero, D. and Dávila, G. (2003). "The Mosaic Structure of the Symbiotic Plasmid of Rhizobium etli CFN42 and Its Relation to other Symbiotic Genome Compartments". Genome Biol. 4(6)   PUBMED: #12801410
69 2003 Jahn, O.J., Dávila, G., Romero, D. and Noel, K.D. (2003). "Bacs: an Abundant Bacteroid Protein in Rhizobium etli Whose Expression Ex Planta Requires nifA". Mol Plant Microbe Interactions. 16(1):65-73   PUBMED: #12580283
70 2003 Tun-Garrido, C., Bustos, P., González, V. and Brom, S. (2003). "Conjugative Transfer of p42a from Rhizobium etli CFN42, Which is Required for Mobilization of the Symbiotic Plasmid, is Regulated by Quorum Sensing". J Bacteriol. 185(5):1681-1692   PUBMED: #12591886
71 2003 Vargas, M.C., Encarnación, S., Dávalos, A., Reyes-Pérez, A., Mora, Y., García-de los Santos, A., Brom, S. and Mora, J. (2003). "Only One Catalase, katG, is Detectable in Rhizobium etli, and is Encoded along with the Regulator OxyR on a Plasmid Replicon". Microbiology-sgm. 149:1165-1176   PUBMED: #12724378
72 2002 Brom, S., Girard, L., García-de los Santos, A., Sanjuan-Pinilla, J.M., Olivares, J. and Sanjuan, J. (2002). "Conservation Of Plasmid-encoded Traits Among Bean-nodulating Rhizobium Species". Appl Environ Microbiol. 68(5):2555-2561   PUBMED: #11976134
73 2002 Cevallos, M.A., Porta, H., Izquierdo, J., Tun-Garrido, C., García-de los Santos, A., Dávila, G. and Brom, S. (2002). "Rhizobium etli Cfn42 Contains At Least Three Plasmids of the repABC Family: a Structural and Evolutionary Analysis". Plasmid. 48(2):104-116   PUBMED: #12383728
74 2002 Encarnación, S., Vargas, M.C., Dunn, M.F., Dávalos, A., Mendoza, G., Mora, Y. and Mora, J. (2002). "Ania Regulates Reserve Polymer Accumulation and Global Protein Expression in Rhizobium etli". J Bacteriol. 184(8):2287-2295   PUBMED: #11914361
75 2002 Falcon, L.I., Escobar-Briones, E. and Romero, D. (2002). "Nitrogen Fixation Patterns Displayed by Cyanobacterial Consortia in Alchichica Crater-lake, Mexico". Hydrobiologia. 467(1-3):71-78    
76 2002 García-de los Santos, A., Morales, A., Baldoma, L., Clark, S.R.D., Brom, S., Yost, C.K., Hernández-Lucas, I., Aguilar, J. and Hynes, M.F. (2002). "The Glcb Locus of Rhizobium leguminosarum VF39 Encodes an Arabinose-inducible Malate Synthase". Can J Microbiol. 48(10):922-932   PUBMED: #12489782
77 2001 López, O., Morera, C., Miranda-Ríos, J., Girard, L., Romero, D. and Soberón, M. (2001). "Regulation of Gene Expression in Response to Oxygen in Rhizobium etli: Role of FnrN in fixNOQP Expression and in Symbiotic Nitrogen Fixation". J Bacteriol. 183(24):6999-7006   PUBMED: #11717256
78 2000 Brom, S., García-de los Santos, A., Cervantes, L., Palacios, R. and Romero, D. (2000). "In Rhizobium etli Symbiotic Plasmid Transfer, Nodulation Competitivity and Cellular Growth Require Interaction Among Different Replicons". Plasmid. 44(1):34-43   PUBMED: #10873525
79 2000 Flores, M., Mavingui, P., Perret, X., Broughton, W.J., Romero, D., Hernández, G., Dávila, G. and Palacios, R. (2000). "Prediction, Identification, And Artificial Selection Of DNA Rearrangements in Rhizobium: toward a Natural Genomic Design". P Nat Acad Sci USA. 97(16):9138-9143   PUBMED: #10922070
80 2000 Girard, L., Brom, S., Dávalos, A., López, O., Soberón, M. and Romero, D. (2000). "Differential Regulation Of fixN-reiterated Genes in Rhizobium etli by a Novel fixL-fixK-cascade". Mol Plant Microbe Interactions. 13(12):1283-1292   PUBMED: #11106020
81 2000 Martínez-Salazar, J.M. and Romero, D. (2000). "Role Of the ruvB Gene in Homologous and Homeologous Recombination in Rhizobium etli". Gene. 243(1-2):125-131   PUBMED: #10675620
82 2000 Reyes, J.D., Tabche, M.L., Morera, C., Girard, L., Romero, D., Krol, E., Miranda, J. and Soberón, M. (2000). "Expression Pattern Of Rhizobium etli ccmIEFH Genes Involved In c-type Cytochrome Maturation". Gene. 250(1-2):149-157   PUBMED: #10854788
83 2000 Valencia-Morales, E. and Romero, D. (2000). "Recombination Enhancement By Replication (RER) in Rhizobium etli". Genetics. 154(3):971-983   PUBMED: #10757747
84 1999 Brom, S. and Romero, D. (1999). "Plasmid Biology 98: International Symposium on Plasmid Biology". Plasmid. 41(2):141-177   PUBMED: #10087219
85 1999 Corvera, A., Prome, D., Prome, J.C., Martínez-Romero, E. and Romero, D. (1999). "The nolL Gene from Rhizobium etli Determines Nodulation Efficiency by Mediating the Acetylation of the Fucosyl Residue in the Nodulation Factor". Mol Plant Microbe Interactions. 12(3):236-246   PUBMED: #10065560
86 1999 Romero, D., Martínez-Salazar, J.M., Ortíz, E., Rodríguez, C. and Valencia-Morales, E. (1999). "Repeated Sequences in Bacterial Chromosomes and Plasmids: a Glimpse from Sequenced Genomes". Res Microbiol. 150(9-10):735-743   PUBMED: #10673011
87 1999 Wang, E.T., Rogel, M.A., García-de los Santos, A., Martínez, J., Cevallos, M.A. and Martínez-Romero, E. (1999). "Rhizobium etli Bv. Mimosae, A Novel Biovar Isolated from Mimosa affinis". Int J Syst Bact. 49:1479-1491   PUBMED: #10555329
88 1998 Mavingui, P., Laeremans, T., Flores, M., Romero, D., Martínez-Romero, E. and Palacios, R. (1998). "Genes Essential For Nod Factor Production And Nodulation Are Located on a Symbiotic Amplicon (AMPRtrCFN299pc60) in Rhizobium tropici". J Bacteriol. 180(11):2866-2874   PUBMED: #9603874
89 1998 Rodríguez, C. and Romero, D. (1998). "Multiple Recombination Events Maintain Sequence Identity Among Members Of the Nitrogenase Multigene Family in Rhizobium etli". Genetics. 149(2):785-794   PUBMED: #9611191
90 1997 García-de los Santos, A. and Brom, S. (1997). "Characterization of Two Plasmid-borne lps Beta loci of Rhizobium etli Required for Lipopolysaccharide Synthesis and for Optimal Interaction with Plants". Mol Plant Microbe Interactions. 10(7):891-902   PUBMED: #9304861
91 1997 Mavingui, P., Flores, M., Romero, D., Martínez-Romero, E. and Palacios, R. (1997). "Generation Of Rhizobium Strains with Improved Symbiotic Properties by Random DNA Amplification (RDA)". Nat Biotechnol. 15(6):564-569   PUBMED: #9181580
92 1997 Miranda-Ríos, J., Morera, C., Taboada, H., Dávalos, A., Encarnación, S., Mora, J. and Soberón, M. (1997). "Expression of Thiamin Biosynthetic Genes (thiCOGE) And Production of Symbiotic Terminal Oxidase Cbb(3), in Rhizobium etli". J Bacteriol. 179(22):6887-6893   PUBMED: #9371431
93 1997 Romero, D. and Palacios, R. (1997). "Gene Amplification and Genomic Plasticity in Prokaryotes". Annu Rev Genet. 31:91-111   PUBMED: #9442891
94 1996 Dunn, M.F., Encarnación, S., Araíza, G., Vargas, M.C., Dávalos, A., Peralta, H., Mora, Y. and Mora, J. (1996). "Pyruvate Carboxylase From Rhizobium etli: Mutant Characterization, Nucleotide Sequence, and Physiological Role". J Bacteriol. 178(20):5960-5970   PUBMED: #8830693
95 1996 García-de los Santos, A., Brom, S. and Romero, D. (1996). "Rhizobium Plasmids In Bacteria Legume Interactions". World J Microbiol Biotechnol. 12(2):119-125   PUBMED: #24415159
96 1996 Girard, L., Valderrama, B., Palacios, R., Romero, D. and Dávila, G. (1996). "Transcriptional Activity of the Symbiotic Plasmid of Rhizobium etli is Affected by Different Environmental Conditions". Microbiology-uk. 142:2847-2856    
97 1996 Valderrama, B., Dávalos, A., Girard, L., Morett, E. and Mora, J. (1996). "Regulatory Proteins And CIS-acting Elements Involved in the Transcriptional Control of Rhizobium etli Reiterated nifH Genes". J Bacteriol. 178(11):3119-3126   PUBMED: #8655489
98 1995 Caballero-Mellado, J., Fuentes-Ramírez, L.E., Reis, V.M. and Martínez-Romero, E. (1995). "Genetic Structure of Acetobacter diazotrophicus Populations And Identification of a New Genetically Distant Group". Appl Environ Microbiol. 61(8):3008-3013   PUBMED: #16535102
99 1995 Romero, D., Martínez-Salazar, J.M., Girard, L., Brom, S., Dávila, G., Palacios, R., Flores, M. and Rodríguez, C. (1995). "Discrete Amplifiable Regions (Amplicons) In The Symbiotic Plasmid of Rhizobium etli CFN42". J Bacteriol. 177(4):973-980   PUBMED: #7860608
100 1993 Flores, M., Brom, S., Stepkowsky, T., Girard, L., Dávila, G., Romero, D. and Palacios, R. (1993). "Gene Amplification In Rhizobium Identification And in vivo Cloning Of Discrete Amplifiable Dna Regions (Amplicons) From Rhizobium leguminosarum Biovar phaseoli". P Nat Acad Sci USA. 90(11):4932-4936   PUBMED: #8506337
101 1993 Morett, E. and Segovia, L. (1993). "The Sigma(54) Bacterial Enhancer-binding Protein Family - Mechanism of Action and Phylogenetic Relationship of their Functional Domains". J Bacteriol. 175(19):6067-6074   PUBMED: #8407777
102 1992 Brom, S., García-de los Santos, A., Stepkowsky, T., Flores, M., Dávila, G., Romero, D. and Palacios, R. (1992). "Different Plasmids Of Rhizobium leguminosarum Bv phaseoli Are Required for Optimal Symbiotic Performance". J Bacteriol. 174(16):5183-5189   PUBMED: #1644746
103 1991 Brom, S., García-de los Santos, A., Girard, L., Dávila, G., Palacios, R. and Romero, D. (1991). "High-frequency Rearrangements In Rhizobium leguminosarum Bv. phaseoli Plasmids". J Bacteriol. 173(3):1344-1346   PUBMED: #1991727
104 1991 Girard, L., Flores, M., Brom, S., Romero, D., Palacios, R. and Dávila, G. (1991). "Structural Complexity Of The Symbiotic Plasmid Of Rhizobium leguminosarum bv phaseoli". J Bacteriol. 173(8):2411-2419   PUBMED: #2013564
105 1991 Martínez-Romero, E., Segovia, L., Martins Mercante, F., Franco, A.A., Graham, P. and Pardo, M.A. (1991). "Rhizobium tropici, A Novel Species Nodulating Phaseolus vulgaris L. Beans And Leucaena Sp. Trees". International Journal of Systematic Bacteriol. 41(3):417-426   PUBMED: #1715738
106 1991 Martínez-Salazar, J.M., Romero, D., Girard, L. and Dávila, G. (1991). "Molecular Cloning and Characterization of the recA Gene of Rhizobium phaseoli and Construction of recA Mutants". J Bacteriol. 173(10):3035-3040   PUBMED: #2022610
107 1991 Romero, D., Brom, S., Martínez-Salazar, J.M., Girard, L., Palacios, R. and Dávila, G. (1991). "Amplification And Deletion of A nod-nif Region in the Symbiotic Plasmid of Rhizobium phaseoli". J Bacteriol. 173(8):2435-2441   PUBMED: #2013567
108 1991 Segovia, L., Piñero, D., Palacios, R. and Martínez-Romero, E. (1991). "Genetic-structure of A Soil Population of Nonsymbiotic Rhizobium leguminosarum". Appl Environ Microbiol. 57(2):426-433   PUBMED: #1707606
109 1991 Vázquez, M., Dávalos, A., De las Peñas, A., Sánchez, F. and Quinto, C. (1991). "Novel Organization Of The Common Nodulation Genes In Rhizobium leguminosarum bv. phaseoli Strains". J Bacteriol. 173(3):1250-1258   PUBMED: #1991718
110 1990 Martínez-Romero, E., Romero, D. and Palacios, R. (1990). "The Rhizobium Genome". Crit Rev Plant Sci. 9(1):59-93    
111 1989 Cevallos, M.A., Vázquez, M., Dávalos, A., Espín Ocampo, E.G., Sepúlveda, J. and Quinto, C. (1989). "Characterization Of Rhizobium phaseoli Sym Plasmid Regions Involved In Nodule Morphogenesis and Host-range Specificity". Mol Microbiol. 3(7):879-889   PUBMED: #2552255
112 1988 Brom, S., Martínez-Romero, E., Dávila, G. and Palacios, R. (1988). "Narrow-and Broad-host-range Symbiotic Plasmids Of Rhizobium spp. Strains that Nodulate Phaseolus vulgaris". Appl Environ Microbiol. 54(5):1280-1283   PUBMED: #16347637
113 1988 Martínez-Romero, E., Flores, M., Brom, S., Romero, D., Dávila, G. and Palacios, R. (1988). "Rhizobium phaseoli: A Molecular Genetics View". Plant Soil. 108(1):179-184    
114 1987 Flores, M., González, V., Brom, S., Martínez-Romero, E., Piñero, D., Romero, D., Dávila, G. and Palacios, R. (1987). "Reiterated Dna Sequences In Rhizobium and Agrobacterium spp.". J Bacteriol. 169(12):5782-5788   PUBMED: #3450286
115 1987 Garcíarrubio, A. and Covarrubias, A. (1987). "Promoter Selection By a Bacterial Enhancer-like Activator Element (BELE) in Escherichia coli". Gene. 54(2-3):275-280   PUBMED: #3308639
116 1985 León, P., Romero, D., Garcíarrubio, A., Bastarrachea, F. and Covarrubias, A. (1985). "Glutamine Synthetase-constitutive Mutation Affecting The glnALG Upstream Promoter Of Escherichia coli". J Bacteriol. 164(3):1032-1038   PUBMED: #2866175
117 1983 Dávila, G., Brom, S., Mora, Y., Palacios, R. and Mora, J. (1983). "Genetic and Biochemical Characterization of Glutamine Synthetase from Neurospora crassa Glutamine Auxotrophs and their Revertants". J Bacteriol. 156(3):993-1000   PUBMED: #6139363

Programa de Ingeniería Genómica

Program Responsible: Dr. David Romero.

Este programa está dedicado a la comprensión de las fuerzas y mecanismos que han forjado la arquitectura genómica de proteobacterias asociadas a plantas (específicamente Rhizobium sp.), tanto en el corto plazo como con una perspectiva evolutiva.

El objetivo a largo plazo es utilizar este conocimiento para desarrollar nuevas estrategias en ingeniería genómica. Para ese fin, nuestras líneas de investigación inciden en los mecanismos y consecuencias evolutivas de la recombinación homóloga, recombinación sitio-específica durante la conjugación de plásmidos, regulación de la transferencia conjugativa, genómica funcional de plásmidos (incluyendo el análisis de funciones codificadas en plásmidos y el papel de factores sigma extracitoplásmicos en respuestas a estrés), así como sistemática molecular, microevolución y filogeografía. Parte de este conocimiento se está integrando en la generación de nuevos enfoques para la generación de deleciones programadas y mutagénesis global del genoma.

Nuestro trabajo combina el análisis bioinformático con enfoques genéticos y de biología molecular así como de análisis de genética de poblaciones.

Identification of plasmid-encoded genes involved...

Identification of plasmid-encoded genes involved in the adaptation of Rhizobium etli to the rhizosphere of Phaseolus vulgaris using genetic and genomic approaches.


Search for the presence of site-specific recombination systems...

Search for the presence of site-specific recombination systems, similar to the one we found on R. etli CFN42 plasmids, on other Rhizobiacea.

Our previous work has shown the participation of a site-specific recombination in the formation or resolution of cointegrates between the symbiotic plasmid and a smaller, self-transmissible plasmid. These cointegrates are important to achieve conjugative transfer of the pSym. Our work will continue with the search of similar elements on other Rhizobiaceae.

Regulation of conjugative transfer of the symbiotic plasmid of Rhizobium etli

In this line, we are studying the mechanisms involved in repression of a conjugative system present on the pSym of R. etli. This system, which employs one repressor gene rctA) also has interactions with another gene product (RctB) whose overproduction apparently overrides the repression imposed by RctA. Characterization of the regions relevant for transcriptional repression as well as purification and analysis of RctA and RctB are the
objectives of this line.

Systematic analysis of Rhizobium plasmids by programmed deletions

Continuing with our interest in functions encoded in Rhizobium plasmids, we are generating a collection of programmed deletions in each of the six large plasmids of Rhizobium etli. Strains resulting from this work will be used in experiments of functional genomics.

Participants: Araceli Dávalos, Alejandro García, Susana Brom, David Romero

Generation of tools for genome engineering in Rhizobium

Genome Engineering is defined as the in vivo modification of the genome, using homologous or site-specific recombination. In this area, we are taking advantage of our previous experience in selection of genome rearrangements. Moreover, we are implementing several tools for


Program Responsible: Dr. David Romero.