Genome Engineering Program

Publicaciones

#	Año	Ficha	Ligas
1	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
2	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
3	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
4	2012	Tejerizo, G.T., Lozano, L.F., 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
5	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
6	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
7	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
8	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
9	2011	Villaseñor-Toledo, T., Dávalos, A., Lozano, L.F., 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
10	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
11	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
12	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
13	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*.	PUBMED: #19555380
14	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
15	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
16	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
17	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
18	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
19	2008	García-de los Santos, A., López, E., Cubillas, C.A., 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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	2007	Top, E. and Romero, D. (2007). "Evolution and Ecology - Summary". Plasmid. 57(2):223-225
29	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
30	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
31	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
32	2005	Santoyo, G. and Romero, D. (2005). "Gene Conversion and Concerted Evolution in Bacterial Genomes". FEMS Microbiol Rev. 29(2):169-183	PUBMED: #15808740
33	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
34	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
35	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
36	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
37	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
38	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
39	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
40	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
41	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
42	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
43	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
44	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
45	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
46	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
47	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
48	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
49	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
50	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
51	2000	Valencia-Morales, E. and Romero, D. (2000). *"Recombination Enhancement By Replication (RER) in Rhizobium etli". Genetics. 154*(3):971-983	PUBMED: #10757747
52	1999	Brom, S. and Romero, D. (1999). "Plasmid Biology 98: International Symposium on Plasmid Biology". Plasmid. 41(2):141-177	PUBMED: #10087219
53	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
54	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
55	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
56	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
57	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
58	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
59	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
60	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
61	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
62	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
63	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
64	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
65	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
66	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
67	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
68	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
69	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
70	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
71	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
72	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
73	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
74	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
75	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
76	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
77	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
78	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
79	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
80	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
81	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.

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Role of the extracitoplasmic (ECF) sigma factors in Rhizobium etli

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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.**

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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.

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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.

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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