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Qualitative changes in proteins contained in outer membrane vesicles produced by Rhizobium etli grown in the presence of the nod gene inducer naringenin.

Taboada H, Dunn MF, Meneses N, Vargas-Lagunas C, Buchs N, Andrade-Domínguez A, Encarnación S.

Arch Microbiol. 2019 Nov;201(9):1173-1194. doi: 10.1007/s00203-019-01682-4. Epub 2019 Jun 6.


Transcriptional analysis reveals the metabolic state of Burkholderia zhejiangensis CEIB S4-3 during methyl parathion degradation.

Castrejón-Godínez ML, Ortiz-Hernández ML, Salazar E, Encarnación S, Mussali-Galante P, Tovar-Sánchez E, Sánchez-Salinas E, Rodríguez A.

PeerJ. 2019 Apr 24;7:e6822. doi: 10.7717/peerj.6822. eCollection 2019.


Proteins in the periplasmic space and outer membrane vesicles of Rhizobium etli CE3 grown in minimal medium are largely distinct and change with growth phase.

Taboada H, Meneses N, Dunn MF, Vargas-Lagunas C, Buchs N, Castro-Mondragón JA, Heller M, Encarnación S.

Microbiology. 2019 Jun;165(6):638-650. doi: 10.1099/mic.0.000720. Epub 2018 Oct 25.


Analysis of differentially upregulated proteins in ptsHIcrr- and rppH- mutants in Escherichia coli during an adaptive laboratory evolution experiment.

Aguilar C, Martínez-Batallar G, Flores N, Moreno-Avitia F, Encarnación S, Escalante A, Bolívar F.

Appl Microbiol Biotechnol. 2018 Dec;102(23):10193-10208. doi: 10.1007/s00253-018-9397-3. Epub 2018 Oct 3.


Overproduction of Sinorhizobium meliloti ArgC (N-acetyl-gamma-glutamyl phosphate reductase) promotes growth delay and inefficient nodules.

Vargas-Lagunas C, Mora Y, Díaz R, Martínez-Batallar G, Girard L, Encarnación S, Peralta H, Mora J.

FEMS Microbiol Lett. 2017 Dec 15;364(23). doi: 10.1093/femsle/fnx233.


The naringenin-induced exoproteome of Rhizobium etli CE3.

Meneses N, Taboada H, Dunn MF, Vargas MDC, Buchs N, Heller M, Encarnación S.

Arch Microbiol. 2017 Jul;199(5):737-755. doi: 10.1007/s00203-017-1351-8. Epub 2017 Mar 2.


Infection with Plasmodium berghei ookinetes alters protein expression in the brain of Anopheles albimanus mosquitoes.

Alvarado-Delgado A, Perales Ortiz G, Tello-López ÁT, Encarnación S, Conde R, Martínez-Batallar ÁG, Moran-Francia K, Lanz-Mendoza H.

Parasit Vectors. 2016 Oct 11;9(1):542.


Genomic studies of nitrogen-fixing rhizobial strains from Phaseolus vulgaris seeds and nodules.

Peralta H, Aguilar A, Díaz R, Mora Y, Martínez-Batallar G, Salazar E, Vargas-Lagunas C, Martínez E, Encarnación S, Girard L, Mora J.

BMC Genomics. 2016 Sep 6;17:711. doi: 10.1186/s12864-016-3053-z.


Region 4 of Rhizobium etli Primary Sigma Factor (SigA) Confers Transcriptional Laxity in Escherichia coli.

Santillán O, Ramírez-Romero MA, Lozano L, Checa A, Encarnación SM, Dávila G.

Front Microbiol. 2016 Jul 13;7:1078. doi: 10.3389/fmicb.2016.01078. eCollection 2016.


The space of enzyme regulation in HeLa cells can be inferred from its intracellular metabolome.

Diener C, Muñoz-Gonzalez F, Encarnación S, Resendis-Antonio O.

Sci Rep. 2016 Jun 23;6:28415. doi: 10.1038/srep28415.


Transcriptomic analysis of the process of biofilm formation in Rhizobium etli CFN42.

Reyes-Pérez A, Vargas Mdel C, Hernández M, Aguirre-von-Wobeser E, Pérez-Rueda E, Encarnacion S.

Arch Microbiol. 2016 Nov;198(9):847-60. doi: 10.1007/s00203-016-1241-5. Epub 2016 May 25.


Proteomic and morphometric study of the in vitro interaction between Oncidium sphacelatum Lindl. (Orchidaceae) and Thanatephorus sp. RG26 (Ceratobasidiaceae).

López-Chávez MY, Guillén-Navarro K, Bertolini V, Encarnación S, Hernández-Ortiz M, Sánchez-Moreno I, Damon A.

Mycorrhiza. 2016 Jul;26(5):353-65. doi: 10.1007/s00572-015-0676-x. Epub 2016 Jan 6.


Nitrogen-fixing rhizobial strains isolated from common bean seeds: phylogeny, physiology, and genome analysis.

Mora Y, Díaz R, Vargas-Lagunas C, Peralta H, Guerrero G, Aguilar A, Encarnación S, Girard L, Mora J.

Appl Environ Microbiol. 2014 Sep;80(18):5644-54. doi: 10.1128/AEM.01491-14. Epub 2014 Jul 7.


Interspecies competition triggers virulence and mutability in Candida albicans-Pseudomonas aeruginosa mixed biofilms.

Trejo-Hernández A, Andrade-Domínguez A, Hernández M, Encarnación S.

ISME J. 2014 Oct;8(10):1974-88. doi: 10.1038/ismej.2014.53. Epub 2014 Apr 17.


The Salmonella enterica serovar Typhi ltrR-ompR-ompC-ompF genes are involved in resistance to the bile salt sodium deoxycholate and in bacterial transformation.

Villarreal JM, Becerra-Lobato N, Rebollar-Flores JE, Medina-Aparicio L, Carbajal-Gómez E, Zavala-García ML, Vázquez A, Gutiérrez-Ríos RM, Olvera L, Encarnación S, Martínez-Batallar AG, Calva E, Hernández-Lucas I.

Mol Microbiol. 2014 Jun;92(5):1005-24. doi: 10.1111/mmi.12610. Epub 2014 Apr 24.


A small heat-shock protein (Hsp20) regulated by RpoS is essential for cyst desiccation resistance in Azotobacter vinelandii.

Cocotl-Yañez M, Moreno S, Encarnación S, López-Pliego L, Castañeda M, Espín G.

Microbiology. 2014 Mar;160(Pt 3):479-487. doi: 10.1099/mic.0.073353-0. Epub 2014 Jan 2.


Eco-evolutionary feedbacks drive species interactions.

Andrade-Domínguez A, Salazar E, Vargas-Lagunas Mdel C, Kolter R, Encarnación S.

ISME J. 2014 May;8(5):1041-54. doi: 10.1038/ismej.2013.208. Epub 2013 Dec 5.


Analysis and prediction of pathways in HeLa cells by integrating biological levels of organization with systems-biology approaches.

Higareda-Almaraz JC, Valtierra-Gutiérrez IA, Hernandez-Ortiz M, Contreras S, Hernandez E, Encarnación-Guevara S.

PLoS One. 2013 Jun 10;8(6):e65433. doi: 10.1371/journal.pone.0065433. Print 2013. Erratum in: PLoS One. 2013;8(7). doi:10.1371/annotation/b212d5e5-7c4b-48c1-80ff-ba0d4ce87cfc. Encarnacion, Sergio [corrected to Encarnación-Guevara, Sergio].


Functional modules, structural topology, and optimal activity in metabolic networks.

Resendis-Antonio O, Hernández M, Mora Y, Encarnación S.

PLoS Comput Biol. 2012;8(10):e1002720. doi: 10.1371/journal.pcbi.1002720. Epub 2012 Oct 11.


Comparative proteomic analysis of Aedes aegypti larval midgut after intoxication with Cry11Aa toxin from Bacillus thuringiensis.

Cancino-Rodezno A, Lozano L, Oppert C, Castro JI, Lanz-Mendoza H, Encarnación S, Evans AE, Gill SS, Soberón M, Jurat-Fuentes JL, Bravo A.

PLoS One. 2012;7(5):e37034. doi: 10.1371/journal.pone.0037034. Epub 2012 May 16.


New insights into Escherichia coli metabolism: carbon scavenging, acetate metabolism and carbon recycling responses during growth on glycerol.

Martínez-Gómez K, Flores N, Castañeda HM, Martínez-Batallar G, Hernández-Chávez G, Ramírez OT, Gosset G, Encarnación S, Bolivar F.

Microb Cell Fact. 2012 Jul 4;11:46. doi: 10.1186/1475-2859-11-46.


A Pseudomonas aeruginosa PAO1 acetylcholinesterase is encoded by the PA4921 gene and belongs to the SGNH hydrolase family.

Sánchez DG, Otero LH, Hernández CM, Serra AL, Encarnación S, Domenech CE, Lisa AT.

Microbiol Res. 2012 Jun 20;167(6):317-25. doi: 10.1016/j.micres.2011.11.005. Epub 2011 Dec 20.


Systems biology of bacterial nitrogen fixation: high-throughput technology and its integrative description with constraint-based modeling.

Resendis-Antonio O, Hernández M, Salazar E, Contreras S, Batallar GM, Mora Y, Encarnación S.

BMC Syst Biol. 2011 Jul 29;5:120. doi: 10.1186/1752-0509-5-120.


argC Orthologs from Rhizobiales show diverse profiles of transcriptional efficiency and functionality in Sinorhizobium meliloti.

Díaz R, Vargas-Lagunas C, Villalobos MA, Peralta H, Mora Y, Encarnación S, Girard L, Mora J.

J Bacteriol. 2011 Jan;193(2):460-72. doi: 10.1128/JB.01010-10. Epub 2010 Nov 12.


The extracellular proteome of Rhizobium etli CE3 in exponential and stationary growth phase.

Meneses N, Mendoza-Hernández G, Encarnación S.

Proteome Sci. 2010 Oct 14;8:51. doi: 10.1186/1477-5956-8-51.


Modeling core metabolism in cancer cells: surveying the topology underlying the Warburg effect.

Resendis-Antonio O, Checa A, Encarnación S.

PLoS One. 2010 Aug 25;5(8):e12383. doi: 10.1371/journal.pone.0012383.


Characterization of the NifA-RpoN regulon in Rhizobium etli in free life and in symbiosis with Phaseolus vulgaris.

Salazar E, Díaz-Mejía JJ, Moreno-Hagelsieb G, Martínez-Batallar G, Mora Y, Mora J, Encarnación S.

Appl Environ Microbiol. 2010 Jul;76(13):4510-20. doi: 10.1128/AEM.02007-09. Epub 2010 May 7.


SMc01553 is the sixth acyl carrier protein in Sinorhizobium meliloti 1021.

Dávila-Martínez Y, Ramos-Vega AL, Contreras-Martínez S, Encarnación S, Geiger O, López-Lara IM.

Microbiology. 2010 Jan;156(Pt 1):230-9. doi: 10.1099/mic.0.033480-0. Epub 2009 Oct 1.


Role of the extracytoplasmic function sigma factor RpoE4 in oxidative and osmotic stress responses in Rhizobium etli.

Martínez-Salazar JM, Salazar E, Encarnación S, Ramírez-Romero MA, Rivera J.

J Bacteriol. 2009 Jul;191(13):4122-32. doi: 10.1128/JB.01626-08. Epub 2009 Apr 17.


Phenotypic differences between BCG vaccines at the proteome level.

Rodríguez-Alvarez M, Mendoza-Hernández G, Encarnación S, Calva JJ, López-Vidal Y.

Tuberculosis (Edinb). 2009 Mar;89(2):126-35. doi: 10.1016/ Epub 2009 Feb 20.


SMb20651 is another acyl carrier protein from Sinorhizobium meliloti.

Ramos-Vega AL, Dávila-Martínez Y, Sohlenkamp C, Contreras-Martínez S, Encarnación S, Geiger O, López-Lara IM.

Microbiology. 2009 Jan;155(Pt 1):257-67. doi: 10.1099/mic.0.022079-0.


Regulation by transcription factors in bacteria: beyond description.

Balleza E, López-Bojorquez LN, Martínez-Antonio A, Resendis-Antonio O, Lozada-Chávez I, Balderas-Martínez YI, Encarnación S, Collado-Vides J.

FEMS Microbiol Rev. 2009 Jan;33(1):133-51. doi: 10.1111/j.1574-6976.2008.00145.x. Review.


Thiamine limitation determines the transition from aerobic to fermentative-like metabolism in Rhizobium etli CE3.

Taboada H, Encarnación S, Vargas Mdel C, Mora Y, Miranda-Ríos J, Soberón M, Mora J.

FEMS Microbiol Lett. 2008 Feb;279(1):48-55. doi: 10.1111/j.1574-6968.2007.01006.x.


Role of proteomics in the study of nutrition.

Velázquez-Arellano A, Encarnación S.

J Nutrigenet Nutrigenomics. 2008;1(1-2):55-8. doi: 10.1159/000109875. Epub 2007 Oct 16. Review.


The LysR-type transcriptional regulator LeuO controls expression of several genes in Salmonella enterica serovar Typhi.

Hernández-Lucas I, Gallego-Hernández AL, Encarnación S, Fernández-Mora M, Martínez-Batallar AG, Salgado H, Oropeza R, Calva E.

J Bacteriol. 2008 Mar;190(5):1658-70. Epub 2007 Dec 21.


Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli.

Resendis-Antonio O, Reed JL, Encarnación S, Collado-Vides J, Palsson BØ.

PLoS Comput Biol. 2007 Oct;3(10):1887-95. Epub 2007 Aug 17.


Functional characterization of the Sinorhizobium meliloti acetate metabolism genes aceA, SMc00767, and glcB.

Ramírez-Trujillo JA, Encarnación S, Salazar E, de los Santos AG, Dunn MF, Emerich DW, Calva E, Hernández-Lucas I.

J Bacteriol. 2007 Aug;189(16):5875-84. Epub 2007 May 25.


Proteomic analysis of Tityus discrepans scorpion venom and amino acid sequence of novel toxins.

Batista CV, D'Suze G, Gómez-Lagunas F, Zamudio FZ, Encarnación S, Sevcik C, Possani LD.

Proteomics. 2006 Jun;6(12):3718-27.


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.

Encarnación S, Hernández M, Martínez-Batallar G, Contreras S, Vargas Mdel C, Mora J.

Biol Proced Online. 2005;7:117-35. Epub 2005 Aug 11.


Biotin biosynthesis, transport and utilization in rhizobia.

Guillén-Navarro K, Encarnación S, Dunn MF.

FEMS Microbiol Lett. 2005 May 15;246(2):159-65. Review.


Proteome analysis of aerobic and fermentative metabolism in Rhizobium etli CE3.

Encarnación S, Guzmán Y, Dunn MF, Hernández M, del Carmen Vargas M, Mora J.

Proteomics. 2003 Jun;3(6):1077-85.


Only one catalase, katG, is detectable in Rhizobium etli, and is encoded along with the regulator OxyR on a plasmid replicon.

Vargas Mdel C, Encarnación S, Dávalos A, Reyes-Pérez A, Mora Y, García-de los Santos A, Brom S, Mora J.

Microbiology. 2003 May;149(Pt 5):1165-76.


Effect of aniA (carbon flux regulator) and PhaC (poly-beta-hydroxybutyrate synthase) mutations on pyruvate metabolism in Rhizobium etli.

Dunn MF, Araíza G, Encarnación S, del Carmen Vargas M, Mora J.

J Bacteriol. 2002 Apr;184(8):2296-9.


AniA regulates reserve polymer accumulation and global protein expression in Rhizobium etli.

Encarnación S, del Carmen Vargas M, Dunn MF, Dávalos A, Mendoza G, Mora Y, Mora J.

J Bacteriol. 2002 Apr;184(8):2287-95.


Role of GOGAT in carbon and nitrogen partitioning in Rhizobium etli.

Castillo A, Taboada H, Mendoza A, Valderrama B, Encarnación S, Mora J.

Microbiology. 2000 Jul;146 ( Pt 7):1627-1637. doi: 10.1099/00221287-146-7-1627.


Glutamine biosynthesis and the utilization of succinate and glutamine by Rhizobium etli and Sinorhizobium meliloti.

Encarnación S, Calderón J, Gelbard AS, Cooper AJ, Mora J.

Microbiology. 1998 Sep;144 ( Pt 9):2629-38.


Poly-beta-hydroxybutyrate turnover in Azorhizobium caulinodans is required for growth and affects nifA expression.

Mandon K, Michel-Reydellet N, Encarnación S, Kaminski PA, Leija A, Cevallos MA, Elmerich C, Mora J.

J Bacteriol. 1998 Oct;180(19):5070-6.


Expression of thiamin biosynthetic genes (thiCOGE) and production of symbiotic terminal oxidase cbb3 in Rhizobium etli.

Miranda-Ríos J, Morera C, Taboada H, Dávalos A, Encarnación S, Mora J, Soberón M.

J Bacteriol. 1997 Nov;179(22):6887-93.


Pyruvate carboxylase from Rhizobium etli: mutant characterization, nucleotide sequence, and physiological role.

Dunn MF, Encarnación S, Araíza G, Vargas MC, Dávalos A, Peralta H, Mora Y, Mora J.

J Bacteriol. 1996 Oct;178(20):5960-70.

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