Functional Genomics of Prokaryotes Program

Publicaciones

#	Año	Ficha	Ligas
1	2013	Aparicio-Fabre, R., Guillén, G., Loredo, M., Arellano, J., Valdés-López, O., Ramirez, M., Iñiguez-Rabago, L.P., Panzeri, D., Castiglioni, B., Cremonesi, P., Strozzi, F., Stella, A., Girard, L., Sparvoli, F. and Hernández, G. (2013). *"Common Bean (Phaseolus vulgaris* L.) PvTIFY Orchestrates Global Changes In Transcript Profile Response To Jasmonate and Phosphorus Deficiency"*. Bmc Plant Biology*. 13:26	PUBMED: #23402340
2	2013	Ramirez, M., Guillén, G., Fuentes, S.I., Iñiguez-Rabago, L.P., Aparicio-Fabre, R., Zamorano-Sánchez, D., Encarnación, S., Panzeri, D., Castiglioni, B., Cremonesi, P., Sparvoli, F. and Hernández, G. (2013). "Transcript Profiling of Common Bean Nodules Subjected to Oxidative Stress". Physiol Plant.	PUBMED: #23432573
3	2013	Ramirez, M., Flores-Pacheco, G., Reyes, J.L., Álvarez, A.L., Drevon, J.J., Girard, L. and Hernández, G. (2013). "Two Common Bean Genotypes With Contrasting Response To Phosphorus Deficiency Show Variations In the microRNA 399-mediated PvPHO2 Regulation within the PvPHR1 Signaling Pathway". International Journal of Molecular Sciences. 14:1-x
4	2012	Ávila-Calderón, E.D., López-Merino, A.E., Jain, N., Peralta, H., López-Villegas, E.O., Sriranganathan, N., Boyle, S.M., Witonsky, S. and Contreras-RodrÍguez, A. (2012). *"Characterization Of Outermembrane Vesicles from Brucella Melitensis* and Protection Induced in Mice"*. Clin Dev Immunol*.	PUBMED: #22242036
5	2012	Ávila-Calderón, E.D., López-Merino, A., Jain, N., Peralta, H., López-Villegas, E.O., Sriranganathan, N., Boyle, S.M., Witonsky, S. and Contreras-Rodríguez, A. (2012). *"Characterization Of Outer Membrane Vesicles from Brucella Melitensis* and Protection Induced in Mice"*. Clin Dev Immunol. 2012*
6	2012	Cancino-Rodezno, A., Lozano, L.F., Oppert, C., Castro, J.I., Lanz-Mendoza, H., Encarnación, S., Evans, A.E., Gill, S.S., Soberon, M., Jurat-Fuentes, J.L. and Bravo, A. (2012). *"Comparative Proteomic Analysis Of Aedes Aegypti* Larval Midgut after Intoxication With Cry11Aa Toxin From Bacillus thuringiensis"*. Plos One*. 7(5):e37034	PUBMED: #22615881
7	2012	Chino-Flores, C., Dantan-González, E., Vázquez-Ramos, A., Tinoco-Valencia, R., Díaz-Mendez, R., Sánchez-Salinas, E., Castrejón-Godinez, M.L., Ramos-Quintana, F. and Ortíz-Hernandez, M.L. (2012). *"Isolation of the opdE* Gene that Encodes for a New Hydrolase of Enterobacter sp Capable of Degrading Organophosphorus Pesticides"*. Biodegradation*. 23(3):387-397	PUBMED: #22065283
8	2012	García-García, J.D., Olin-Sandoval, V., Saavedra, E., Girard, L., Hernández, G. and Moreno-Sánchez, R. (2012). *"Sulfate Uptake In Photosynthetic Euglena Gracilis. Mechanisms of Regulation and Contribution to Cysteine Homeostasis". Bba-gen Subjects. 1820*(10):1567-1575	PUBMED: #22609877
9	2012	Gutiérrez-Roman, M.I., Holguin-Melendez, F., Bello-Mendoza, R., Guillén-Navarro, K., Dunn, M.F. and Huerta-Palacios, G. (2012). *"Production Of Prodigiosin and Chitinases by Tropical Serratia marcescens* Strains with Potential to Control Plant Pathogens"*. World J Microbiol Biotechnol*. 28(1):145-153	PUBMED: #22806790
10	2012	Juárez-Verdayes, M.A., González-Uribe, P.M., Peralta, H., Rodríguez-Martínez, S., Jan-Roblero, J., Escamilla-Hernández, R., Cancino-Díaz, M.E. and Cancino-Díaz, J.C. (2012). *"Detection Of hssS, hssR, hrtA* and hrtB Genes and their Expression by Hemin in Staphylococcus Epidermidis"*. Can J Microbiol*. 58(9):1063-1072	PUBMED: #22906238
11	2012	Martínez-Gómez, K., Flores, N., Castañeda, H.M., Martínez-Batallar, Á.G., Hernández-Chávez, G., Ramírez, O.T., Gosset, G., Encarnación, S. and Bolivar, F. (2012). *"New Insights Into Escherichia coli* Metabolism: Carbon Scavenging, Acetate Metabolism And Carbon Recycling Responses during Growth on Glycerol"*. Microb Cell Fact*. 11:46	PUBMED: #22513097
12	2012	Resendis-Antonio, O., Hernández, M., Mora, Y. and Encarnación, S. (2012). "Functional Modules, Structural Topology, and Optimal Activity in Metabolic Networks". Plos Comput Biol. 8(10):e1002720	PUBMED: #23071431
13	2012	Sánchez, D.G., Otero, L.H., Hernández, M., Serra, A.L., Encarnación, S., Domenech, C.E. and Lisa, A.T. (2012). *"A Pseudomonas Aeruginosa* Pa01 Acetylcholinesterase is Encoded by the PA4921 Gene and Belongs to the SGNH Hydrolase Family"*. Microbiological Research. 167*(6):317-325	PUBMED: #22192836
14	2012	Talbi, C., Sánchez, C., Hidalgo-García, A., González, E.M., Arrese-Igor, C., Girard, L., Bedmar, E.J. and Delgado, M.J. (2012). *"Enhanced Expression of Rhizobium etli* cbb3 Oxidase Improves Drought Tolerance of Common Bean Symbiotic Nitrogen Fixation"*. J Exp Bot*. 63(14):5053-5043	PUBMED: #22511804
15	2012	Zamorano-Sánchez, D., Reyes-González, A., Gómez-Hernández, N., Rivera, P., Georgellis, D. and Girard, L. (2012). *"FxkR Provides the Missing Link in the fixL-fixK* Signal Transduction Cascade in Rhizobium etli CFN42"*. Mol Plant Microbe Interactions*. 25(11):1506-1517	PUBMED: #22809273
16	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
17	2011	Díaz-Mendez, R., Vargas, M.C., Villalobos-López, M.A., Peralta, H., Mora, Y., Encarnación, S., Girard, L. and Mora, J. (2011). *"Argc Orthologs From Rhizobiales* Show Diverse Profiles of Transcriptional Efficiency and Functionality in Sinorhizobium meliloti"*. J Bacteriol. 193*(2):460-472	PUBMED: #21075924
18	2011	Dunn, M.F. (2011). *"Anaplerotic Function Of Phosphoenolpyruvate Carboxylase In Bradyrhizobium* japonicum USDA110"*. Curr Microbiol*. 62(5):1782-1788	PUBMED: #21479798
19	2011	Gómez-Hernández, N., Reyes-González, A., Sanchez, C., Mora, Y., Delgado, M.J. and Girard, L. (2011). *"Regulation and Symbiotic Role of nirK* and norC Expression in Rhizobium etli"*. Mol Plant Microbe Interactions*. 24(2):233-245	PUBMED: #21043576
20	2011	Higareda-Almaraz, J.C., Enríquez, M.R., Hernández, M., Resendis-Antonio, O. and Encarnación, S. (2011). "Proteomic Patterns of Cervical Cancer Cell Lines, a Network Perspective". Bmc Syst Biol. 5	PUBMED: #21696634
21	2011	Peralta, H., Guerrero, G., Aguilar, A. and Mora, J. (2011). *"Sequence Variability of Rhizobiales* Orthologs and Relationship with Physico-chemical Characteristics of Proteins"*. Biol Direct*. 6	PUBMED: #21970442
22	2011	Resendis-Antonio, O., Hernández, M., Salazar, E., Contreras-Martínez, S., Martínez-Batallar, Á.G., Mora, Y. and Encarnación, S. (2011). "Systems Biology of Bacterial Nitrogen Fixation: High-throughput Technology and Its Integrative Description with Constraint-based Modeling". Bmc Syst Biol. 5	PUBMED: #21801415
23	2010	Dávila-Martínez, Y., Ramos-Vega, A.L., Contreras-Martínez, S., Encarnación, S., Geiger, O. and López-Lara, I.M. (2010). *"Smc01553 Is The Sixth Acyl Carrier Protein in Sinorhizobium meliloti* 1021"*. Microbiology-sgm. 156*:230-239	PUBMED: #19797355
24	2010	González, V., Acosta, J.L., Santamaria, R.I., Bustos, P., Fernández, J.L., Hernández-González, I., Díaz-Mendez, R., Flores, M., Palacios, R., Mora, J. and Dávila, G. (2010). *"Conserved Symbiotic Plasmid Dna Sequences in the Multireplicon Pangenomic Structure of Rhizobium etli". Appl Environ Microbiol*. 76(5):1604-1614	PUBMED: #20048063
25	2010	Meneses, N., Mendonza-Hernández, G. and Encarnación, S. (2010). *"The Extracellular Proteome of Rhizobium etli* CE3 in Exponential and Stationary Growth Phase"*. Proteome Sci*. 8:51	PUBMED: #20942974
26	2010	Resendis-Antonio, O., Checa, A. and Encarnación, S. (2010). "Modeling Core Metabolism in Cancer Cells: Surveying the Topology Underlying the Warburg Effect". Plos One. 5(8)	PUBMED: #20811631
27	2010	Salazar, E., Díaz-Mejía, J.J., Moreno-Hagelsieb, G., Martínez-Batallar, Á.G., Mora, Y., Mora, J. and Encarnación, S. (2010). *"Characterization Of The NifA-RpoN Regulon in Rhizobium etli* in Free Life and in Symbiosis with Phaseolus vulgaris"*. Appl Environ Microbiol*. 76(13):4510-4520	PUBMED: #20453139
28	2010	Sánchez, C., Gates, A.J., Meakin, G.E., Uchiumi, T., Girard, L., Richardson, D.J., Bedmar, E.J. and Delgado, M.J. (2010). "Production of Nitric Oxide and Nitrosylleghemoglobin Complexes in Soybean Nodules in Response to Flooding". Mol Plant Microbe Interactions. 23(5):702-711	PUBMED: #20367476
29	2010	Talbi, C., Delgado, M.J., Girard, L., Ramírez-Trujillo, J.A., Caballero-Mellado, J. and Bedmar, E.J. (2010). *"Burkholderia* Phymatum Strains Capable Of Nodulating Phaseolus vulgaris Are Present In Moroccan Soils"*. Appl Environ Microbiol*. 76(13):4587-4591	PUBMED: #20472732
30	2009	Balleza, E., López-Bojorquez, L., Martínez-Antonio, A., Resendis-Antonio, O., Lozada-Chávez, I., Balderas-Martinez, Y.I., Encarnación, S. and Collado-Vides, J. (2009). "Regulation By Transcription Factors in Bacteria: beyond Description". FEMS Microbiol Rev. 33(1):133-151	PUBMED: #19076632
31	2009	Dunn, M.F., Ramírez-Trujillo, J.A. and Hernández-Lucas, I. (2009). "Major Roles of Isocitrate Lyase and Malate Synthase in Bacterial and Fungal Pathogenesis". Microbiology. 155(Pt 10):3166-3175	PUBMED: #19684068
32	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
33	2009	Onofre-Lemus, J., Hernández-Lucas, I., Girard, L. and Caballero-Mellado, J. (2009). *"Acc (1-aminocyclopropane-1-carboxylate) Deaminase Activity, a Widespread Trait in Burkholderia* Species, and Its Growth-promoting Effect on Tomato Plants"*. Appl Environ Microbiol*.	PUBMED: #19700546
34	2009	Ramos-Vega, A.L., Dávila-Martínez, Y., Sohlenkamp, C., Contreras-Martínez, S., Encarnación, S., Geiger, O. and López-Lara, I.M. (2009). *"SMb20651 Is Another Acyl Carrier Protein from Sinorhizobium meliloti". Microbiology. 155*:257-267	PUBMED: #19118366
35	2009	Resendis-Antonio, O. (2009). "Filling Kinetic Gaps: Dynamic Modeling of Metabolism where Detailed Kinetic Information is Lacking". Plos One. 4(3):e4967	PUBMED: #19305506
36	2009	Rodríguez-Alvarez, M., Mendoza-Hernández, G., Encarnación, S., Calva, J.J. and López-Vidal, Y. (2009). "Phenotypic Differences between Bcg Vaccines at the Proteome Level". Tuberculosis. 89(2):126-135	PUBMED: #19231290
37	2008	Contreras-Rodriguez, A, Quiroz-Limon, J, Martins, AM, Peralta, H., Avila-Calderon, E, Sriranganathan, N, Boyle, SM and Lopez-Merino, A (2008). *"Enzymatic, Immunological And Phylogenetic Characterization of Brucella suis* Urease"*. BMC Microbiol*. 8:121	PUBMED: #18638408
38	2008	Hernández-Lucas, I., Gallego-Hernandez, A.L., Encarnación, S., Fernandez-Mora, M., Martínez-Batallar, Á.G., Salgado, H., Oropeza, R. and Calva, E. (2008). *"The LysR-type Transcriptional Regulator Leuo Controls Expression of Several Genes in Salmonella enterica* Serovar Typhi"*. J Bacteriol. 190*(5):1658-1670	PUBMED: #18156266
39	2008	Martínez-Aguilar, L., Díaz-Mendez, R., Pena-Cabriales, J.J., Estrada-de los Santos, P., Dunn, M.F. and Caballero-Mellado, J. (2008). *"Multichromosomal Genome Structure And Confirmation of Diazotrophy in Novel Plant-associated Burkholderia* Species"*. Appl Environ Microbiol*. 74(14):4574-4579	PUBMED: #18502926
40	2008	Rodriguez-Perez, MA, Medina-Aunon, A, Encarnación, S., Bernal-Silvia, S, Barrera-Saldana, H and Albar-Ramirez, JP (2008). "In Silico Analysis of Protein Neoplastic Biomarkers for Cervix and Uterine Cancer". Clin Transl Oncol. 10(10):604-617	PUBMED: #18940741
41	2008	Taboada, H., Encarnación, S., Vargas, M.C., Mora, Y., Miranda-Ríos, J., Soberón, M. and Mora, J. (2008). *"Thiamine Limitation Determines The Transition from Aerobic to Fermentative-like Metabolism in Rhizobium etli* CE3"*. FEMS Microbiol Lett. 279*(1):48-55	PUBMED: #18177306
42	2008	Valdés-López, O., Arenas-Huertero, C., Ramirez, M., Girard, L., Sánchez, F., Vance, C.P., Reyes, J.L. and Hernández, G. (2008). "Essential Role Of Myb Transcription Factor: PvPHR1 And microRNA: PvmiR399 in Phosphorus-deficiency Signalling in Common Bean Roots". Plant Cell Environ. 31(12):1834-1843	PUBMED: #18771575
43	2007	Flores, M., Morales, L., Gonzaga-Jáuregui, C., Domínguez-Vidaña, R., Zepeda-Mendoza, C.J., Yáñez, O., Gutierrez-Arcelus, M., Lemus, T., Valle-García, D., Ávila, M.C., Blanco, D., Medina-Ruiz, S., Meza-Sosa, K.F., Ayala, E., García-Alonso, D., Bustos, P., González, V., Girard, L., Tusie-Luna, T., Dávila, G. and Palacios, R. (2007). "Recurrent DNA Inversion Rearrangements in the Human Genome". P Nat Acad Sci USA. 104(15):6099-6106	PUBMED: #17389356
44	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
45	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
46	2007	Resendis-Antonio, O., Reed, J.L., Encarnación, S., Collado-Vides, J. and Palsson, B.O. (2007). *"Metabolic Reconstruction And Modeling of Nitrogen Fixation in Rhizobium etli". Plos Comput Biol*. 3(10):1887-1895	PUBMED: #17922569
47	2007	Velázquez-Arellano, A. and Encarnación, S. (2007). "Role of Proteomics in the Study of Nutrition". Journal of Nutrigenetics and Nutrigenomics. 1:55-58
48	2006	Batista, C.V.F., DSuze, G., Gómez-Lagunas, F., Zamudio, F.Z., Encarnación, S., Sevcik, C. and Possani, L.D. (2006). *"Proteomic Analysis of Tityus discrepans* Scorpion Venom and Amino Acid Sequence of Novel Toxins"*. Proteomics*. 6(12):3718-3727	PUBMED: #16705749
49	2006	Encarnación, S. (2006). "GenÓmica y GenÓmica Funcional en MicrobiologÍa". Revista Latinoamericana de Microbiología. 48(2):131-132
50	2006	Encarnación, S., Salazar, E., Martínez-Batallar, Á.G., Hernández, M., Reyes-Pérez, A., Contreras-Martínez, S., Vargas, M.C., Domínguez-Vidaña, R., Gonzaga-Jáuregui, C., Mora, Y., Rivero Zaragoza, R. and Mora, J. (2006). "GenÓmica Funcional en Rizobiaceas". Revista Latinoamericana de Microbiología. 48(2):135-141
51	2005	Bueno, E., Gómez-Hernández, N., Girard, L., Bedmar, E.J. and Delgado, M.J. (2005). *"Function Of the Rhizobium etli* CFN42 nirK Gene in Nitrite Metabolism"*. Biochem Soc Trans*. 33:162-163	PUBMED: #15667294
52	2005	Encarnación, S., Hernández, M., Martínez-Batallar, Á.G., Contreras-Martínez, S., Vargas, M.C. and Mora, J. (2005). "Comparative Proteomics Using 2-D Gel Electrophoresis and Mass Spectrometry as Tools to Dissect Stimulons and Regulons in Bacteria with Sequenced or Partially Sequenced Genomes". Biol Proced Online. 117-135	PUBMED: #16145578
53	2005	Flores, M., Morales, L., Ávila, A., González, V., Bustos, P., García-Alonso, D., Mora, Y., Guo, X.W., Collado-Vides, J., Pinero, D., Dávila, G., Mora, J. and Palacios, R. (2005). *"Diversification of DNA Sequences in the Symbiotic Genome of Rhizobium etli". J Bacteriol. 187*(21):7185-7192	PUBMED: #16237002
54	2005	Guerrero, G., Peralta, H., Aguilar, A., Díaz-Mendez, R., Villalobos-López, M.A., Medrano-Soto, A. and Mora, J. (2005). *"Evolutionary, Structural And Functional Relationships Revealed by Comparative Analysis of Syntenic Genes in Rhizobiales". BMC Evol Biol*. 5:55	PUBMED: #16229745
55	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
56	2005	Guillén-Navarro, K., Encarnación, S. and Dunn, M.F. (2005). *"Biotin Biosynthesis, Transport And Utilization in Rhizobia". FEMS Microbiol Lett. 246*(2):159-165	PUBMED: #15899401
57	2004	Batista, C.V.F., Del Pozo, L., Zamudio, F.Z., Contreras-Martínez, S., Becerril, B., Wanke, E. and Possani, L.D. (2004). *"Proteomics of the Venom from the Amazonian Scorpion Tityus Cambridgei* and the Role of Prolines on Mass Spectrometry Analysis of Toxins"*. J Chromatogr B. 803*(1):55-66	PUBMED: #15025998
58	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
59	2004	Dunn, M.F., Araíza, G. and Mora, J. (2004). *"Biochemical Characterization Of a Rhizobium etli* Monovalent Cation-stimulated Acyl-coenzyme a Carboxylase with a High Substrate Specificity Constant for Propionyl-coenzyme a"*. Microbiology-sgm. 150*:399-406	PUBMED: #14766918
60	2004	Peralta, H., Mora, Y., Salazar, E., Encarnación, S., Palacios, R. and Mora, J. (2004). *"Engineering The Nifh Promoter Region and Abolishing Poly-beta-hydroxybutyrate Accumulation in Rhizobium etli* Enhance Nitrogen Fixation in Symbiosis with Phaseolus vulgaris"*. Appl Environ Microbiol*. 70(6):3272-3281	PUBMED: #15184121
61	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
62	2003	Encarnación, S., Guzmán, Y., Dunn, M.F., Hernández, M., Vargas, M.C. and Mora, J. (2003). *"Proteome Analysis Of Aerobic and Fermentative Metabolism in Rhizobium etli* CE3"*. Proteomics*. 3(6):1077-1085	PUBMED: #12833533
63	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
64	2003	Medina, G., Juarez, K., Díaz-Mendez, R. and Soberón-Chávez, G. (2003). *"Transcriptional Regulation Of Pseudomonas Aeruginosa rhlR, Encoding a Quorum-sensing Regulatory Protein". Microbiology-sgm. 149*:3073-3081	PUBMED: #14600219
65	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
66	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
67	2002	Dunn, M.F., Araíza, G., Encarnación, S., Vargas, M.C. and Mora, J. (2002). *"Effect Of aniA* (carbon Flux Regulator) and phaC (poly-beta-hydroxybutyrate Synthase) Mutations on Pyruvate Metabolism in Rhizobium etli"*. J Bacteriol. 184*(8):2296-2299	PUBMED: #11914362
68	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
69	2001	Dunn, M.F., Araíza, G. and Finan, T.M. (2001). *"Cloning And Characterization of the Pyruvate Carboxylase from Sinorhizobium meliloti* Rm1021"*. Arch Microbiol. 176*(5):355-363	PUBMED: #11702077
70	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
71	2000	Castillo, A., Taboada, H., Mendoza, A., Valderrama, B., Encarnación, S. and Mora, J. (2000). *"Role Of GOGAT in Carbon and Nitrogen Partitioning in Rhizobium etli". Microbiology-uk. 146*:1627-1637	PUBMED: #10878127
72	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
73	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
74	1999	Mandon, K., Michel-Reydellet, N., Encarnación, S., Kaminski, P.A., Leija, A., Cevallos, M.A., Elmerich, C. and Mora, J. (1999). *"Poly-beta-hydroxybutyrate Turnover In Azorhizobium caulinodans* is Required for Growth and Affects nifA Expression"*. J Bacteriol. 180*(19):5070-5076	PUBMED: #9748438
75	1999	Ramirez, M., Valderrama, B., Arredondo-Peter, R., Soberón, M., Mora, J. and Hernández, G. (1999). *"Rhizobium etli* Genetically Engineered For The Heterologous Expression of Vitreoscilla sp. Hemoglobin: Effects on Free-living and Symbiosis"*. Mol Plant Microbe Interactions*. 12(11):1008-1015
76	1999	Soberón, M., López, O., Morera, C., Girard, L., Tabche, M.L. and Miranda, J. (1999). *"Enhanced Nitrogen Fixation In A Rhizobium etli* Ntrc Mutant that Overproduces the Bradyrhizobium japonicum Symbiotic Terminal Oxidase Cbb(3)"*. Appl Environ Microbiol*. 65(5):2015-2019	PUBMED: #10223993
77	1998	Dunn, M.F. (1998). *"Tricarboxylic Acid Cycle And Anaplerotic Enzymes in Rhizobia". FEMS Microbiol Rev*. 22(2):105-123	PUBMED: #9729766
78	1998	Encarnación, S., Calderón, J., Gelbard, A.S., Cooper, A.J.L. and Mora, J. (1998). *"Glutamine Biosynthesis and The Utilization of Succinate and Glutamine by Rhizobium etli* and Sinorhizobium meliloti"*. Microbiology-uk. 144*:2629-2638	PUBMED: #9782512
79	1998	Flores, M., Mavingui, P., Girard, L., Perret, X., Broughton, W.J., Martínez-Romero, E., Dávila, G. and Palacios, R. (1998). *"Three Replicons Of Rhizobium* Sp. Strain NGR234 Harbor Symbiotic Gene Sequences"*. J Bacteriol. 180*(22):6052-6053	PUBMED: #9811668
80	1998	Mendoza, A., Valderrama, B., Leija, A. and Mora, J. (1998). *"Nifa-dependent Expression Of Glutamate Dehydrogenase in Rhizobium etli* Modifies Nitrogen Partitioning during Symbiosis"*. Mol Plant Microbe Interactions*. 11(2):83-90	PUBMED: #9450332
81	1997	Dunn, M.F., Araíza, G., Cevallos, M.A. and Mora, J. (1997). *"Regulation Of Pyruvate Carboxylase in Rhizobium etli". FEMS Microbiol Lett. 157*(2):301-306	PUBMED: #9435112
82	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
83	1997	Ramírez-Romero, M.Á., Bustos, P., Girard, L., Rodríguez, O., Cevallos, M.A. and Dávila, G. (1997). *"Sequence, Localization And Characteristics of the Replicator Region of the Symbiotic Plasmid of Rhizobium etli". Microbiology-uk. 143*:2825-2831	PUBMED: #9274036
84	1996	Cevallos, M.A., Encarnación, S., Leija, A., Mora, Y. and Mora, J. (1996). *"Genetic And Physiological Characterization of a Rhizobium etli* Mutant Strain Unable to Synthesize Poly-beta-hydroxybutyrate"*. J Bacteriol. 178*(6):1646-1654	PUBMED: #8626293
85	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
86	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
87	1996	Taboada, H., Encarnación, S., Vargas, M.C., Mora, Y., Martínez-Romero, E. and Mora, J. (1996). *"Glutamine Synthetase Ii Constitutes A Novel Taxonomic Marker in Rhizobium* etli and other Rhizobium Species"*. Int J Syst Bact*. 46(2):485-491
88	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
89	1995	Encarnación, S., Dunn, M.F., Willms, K. and Mora, J. (1995). *"Fermentative And Aerobic Metabolism in Rhizobium etli". J Bacteriol. 177*(11):3058-3066	PUBMED: #7768801
90	1995	Mendoza, A., Leija, A., Martínez-Romero, E., Hernández, G. and Mora, J. (1995). *"The Enhancement of Ammonium Assimilation in Rhizobium etli* Prevents Nodulation of Phaseolus vulgaris"*. Mol Plant Microbe Interactions*. 8(4):584-592	PUBMED: #8589413
91	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
92	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
93	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
94	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
95	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
96	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
97	1990	Calderón, J., Martínez, L.M. and Mora, J. (1990). *"Isolation And Characterization of a Neurospora crassa* Mutant Altered in the Alpha-polypeptide of Glutamine Synthetase"*. J Bacteriol. 172*(9):4996-5000	PUBMED: #1975579
98	1990	Mora, J. (1990). *"Glutamine Metabolism And Cycling in Neurospora crassa". Microbiol Rev*. 54(3):293-304	PUBMED: #2145504
99	1989	Calderón, J. and Mora, J. (1989). *"Glutamine Assimilation Pathways In Neurospora crassa* Growing on Glutamine as Sole Nitrogen and Carbon Source"*. J. Gen. Microbiol.. 135*:2699-2707	PUBMED: #2576659
100	1989	Calderón, J., Cooper, A.J.L., Gelbard, A.S. and Mora, J. (1989). *"N-13 Isotope Studies of Glutamine Assimilation Pathways in Neurospora crassa". J Bacteriol. 171*(3):1772-1774	PUBMED: #2522094
101	1988	Bravo, A. and Mora, J. (1988). *"Ammonium Assimilation In Rhizobium* phaseoli By the Glutamine Synthetase-glutamate Synthase Pathway"*. J Bacteriol. 170*(2):980-984	PUBMED: #2892829
102	1988	Bravo, A., Becerril, B. and Mora, J. (1988). *"Introduction Of The Escherichia coli* Gdha Gene into Rhizobium phaseoli: Effect on Nitrogen Fixation"*. J Bacteriol. 170*(2):985-988	PUBMED: #2892830
103	1987	Lomnitz, A., Calderón, J., Hernández, G. and Mora, J. (1987). "Functional-analysis of Ammonium Assimilation Enzymes in Neurospora-crassa". J. Gen. Microbiol.. 133:2333-2340
104	1987	Mora, Y., Hernández, G. and Mora, J. (1987). *"Regulation Of Carbon and Nitrogen Flow by Glutamate Synthase in Neurospora crassa". J. Gen. Microbiol.. 133*(7):1667-1674	PUBMED: #2959749
105	1986	Hernández, G. and Mora, J. (1986). *"Glutamine Synthesis Regulates Sucrose Catabolism In Neurospora crassa". J. Gen. Microbiol.. 132*:3315-3323
106	1986	Hernández, G., Mora, Y. and Mora, J. (1986). *"Regulation Of Glutamine Synthesis by Glycine and Serine in Neurospora crassa". J Bacteriol. 165*(1):133-138	PUBMED: #2867084
107	1986	Leija, A., Ruíz-Herrera, J. and Mora, J. (1986). *"Effect Of L-amino Acids on Mucor rouxii* Dimorphism"*. J Bacteriol. 168*(2):843-850	PUBMED: #3096961
108	1985	Calderón, J. and Mora, J. (1985). *"Glutamine Cycling In Neurospora crassa". J. Gen. Microbiol.. 131*(12):3237-3242
109	1985	Calderón, J., Morett, E. and Mora, J. (1985). *"Omega-amidase Pathway in the Degradation of Glutamine in Neurospora crassa". J Bacteriol. 161*(2):807-809	PUBMED: #2857167
110	1985	Quinto, C., de la Vega, H., Flores, M., Leemans, J., Cevallos, M.A., Pardo, M.A., Azpiroz, R., Girard, L., Calva, E. and Palacios, R. (1985). *"Nitrogenase Reductase: A Functional Multigene Family In Rhizobium* phaseoli"*. P Nat Acad Sci USA*. 82(4):1170-1174	PUBMED: #16593543
111	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
112	1983	González, A., Tenorio, M., Vaca, G. and Mora, J. (1983). *"Neurospora crassa* Mutant Impaired In Glutamine Regulation"*. J Bacteriol. 155*(1):1-7	PUBMED: #6134713
113	1983	Hernández, G., Sánchez-Pescador, R., Palacios, R. and Mora, J. (1983). *"Nitrogen Source Regulates Glutamate Dehydrogenase Nadp Synthesis in Neurospora crassa". J Bacteriol. 154*(1):524-528	PUBMED: #6300039
114	1982	Lara-Flores, M., Blanco, L., Campomanes, M., Calva, E., Palacios, R. and Mora, J. (1982). *"Physiology Of Ammonium Assimilation in Neurospora crassa". J Bacteriol. 150*(1):105-112	PUBMED: #6120927
115	1980	Hummelt, G. and Mora, J. (1980). *"Regulation And Function of Glutamate Synthase in Neurospora crassa". Biochem Biophys Res Commun*. 96(4):1688-1694	PUBMED: #6449930

Programa de Genómica Funcional de Procariotes

Responsable del Programa: Jaime Mora-Celis, M. D. Ph. D.

Con genómica comparativa encontramos que en R.etli, S.meliloti, M.loti, A.tumefaciens y B.melitensis una alta proporción de sus genes cromosomales son sinténicos (conservan el orden) y en comparación con los no sinténicos muestran mayor organización en operones, restricción al cambio, esencialidad e interacción funcional. Los sinténicos muestran una proporción de residuos comunes y otra de propios (la firma de la especie). ¿Hay mayor interrelación evolutiva en los sinténicos?, ¿Cuál es el significado funcional de la firma de la especie? Para ello seguimos 2 líneas:

1) Analizamos los genes sinténicos y no sinténicos comunes en esos Rhizobiales por identidad, similitud y filogenia.
2) Mutagenizamos argC (sinténico esencial de la síntesis de arginina) en S.meliloti y lo sustituimos con el gene de los otros Rhizobiales para evaluar la influencia de las firmas en el ajuste enzimático, la restitución de la prototrofía y la formación de metabolones.

Además, en el Laboratorio de Proteómica se analizan el proteoma, fosfoproteoma y transcriptoma de R.etli y S.meliloti para determinar la expresión global del genoma en el metabolismo fermentativo y aeróbico, simbiosis, en condiciones de estrés y en desarrollo de biofilms, de una sola especie y en comunidad con eucariotes como S.cerevisiae. De igual forma, hemos iniciado proyectos de proteómica buscando factores específicos en cáncer cervicouterino, como biomarcadores en plasma de pacientes con esta patología, y cambios en el fosofoproteoma en líneas celulares de cáncer.

REPOSITORIO DE ARTÍCULOS SELECCIONADOS POR EL DR. JAIME MORA.

Los artículos que aparecen en esta sección, son una selección del Dr. Mora hecha a través de varios años y de diversas revistas. Cada artículo cuenta con el resumen (abstract) del mismo, así como una liga para obtener el documento en formato PDF.

En próximas fechas estará disponible una red interactiva de las palabras clave de cada uno de los artículos contenidos en el Repositorio. Se les mantendrá informados cuando esta herramienta se active.

El Repositorio se encuentra ubicado en la siguiente dirección:

Rhizogenómica/lib

Rhizogenómica. Portal del Programa de Genómica Funcional de Procariotes, que dirige el Dr. Jaime Mora. Además de presentar información sobre los proyectos de investigación, en especial está dedicado a herramientas computacionales para el análisis genómico. Contiene los programas perl utilizados para la genómica comparativa de Rhizobiales, artículos publicados recientemente y otras ligas de interés.

Genomic analysis of orthologs in Rhizobiales

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Improvement of nitrogen fixation capacity of Rhizobium

The biofertilizers have a great perspective of application in the agricultural fields in Mexico because they are environmentally friendly, have a low cost and they are easily transported and applied. On the other hand, the nitrogen chemical fertilization represents high economic costs for the farmers, but the most serious effects of the massive fertilization in the world are environmental: industrial production contaminates the air, soils are deteriorated by the salinity, as well as the water-bearing mantles. Studying the

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Proteomic and transcriptomic analysis of Rhizobium

When we began the proteomic project with R. etli the genomic sequence was not available. Now, with the finished sequence, we also extended the analysis to the Sinorhizobium meliloti genome. To date, applying the 2D polyacrilamide gel electrophoresis technique (2D-PAGE) we have analyzed several physiological conditions of these

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Carbon and nitrogen metabolism in Rhizobium

We began our studies in the determination of the cycle of the glutamine synthetase in the fungus Neurospora crassa and the enzymes that participate in the glutamate-glutamine interconversion in N. crassa and in the new model organism Rhizobium etli .