Diaz RJ, Rosenberg R: Spreading dead zones and consequences for marine ecosystems. Science. 2008, 321: 926-929. 10.1126/science.1156401
Article
CAS
PubMed
Google Scholar
Deakin WJ, Broughton WJ: Symbiotic use of pathogenic strategies: rhizobial protein secretion systems. Nat Rev Microbiol. 2009, 7: 312-320.
CAS
PubMed
Google Scholar
Lodwig E, Poole P: Metabolism of Rhizobium bacteroids. Critical Reviews in Plant Sciences. 2003, 22: 37-78. 10.1080/713610850.
Article
CAS
Google Scholar
Prell J, Poole P: Metabolic changes of rhizobia in legume nodules. Trends Microbiol. 2006, 14: 161-168. 10.1016/j.tim.2006.02.005
Article
CAS
PubMed
Google Scholar
Sarma AD, Emerich DW: Global protein expression pattern of Bradyrhizobium japonicum bacteroids: a prelude to functional proteomics. Proteomics. 2005, 5: 4170-4184. 10.1002/pmic.200401296
Article
CAS
PubMed
Google Scholar
Oehrle NW, Sarma AD, Waters JK, Emerich DW: Proteomic analysis of soybean nodule cytosol. Phytochemistry. 2008, 69: 2426-2438. 10.1016/j.phytochem.2008.07.004
Article
CAS
PubMed
Google Scholar
Feist AM, Palsson BO: The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol. 2008, 26: 659-667. 10.1038/nbt1401
Article
PubMed Central
CAS
PubMed
Google Scholar
Resendis-Antonio O, Reed JL, Encarnacion S, Collado-Vides J, Palsson BO: Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli. PLoS Comput Biol. 2007, 3: 1887-1895.
Article
CAS
PubMed
Google Scholar
Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, Godzik A: Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science. 2009, 325: 1544-1549. 10.1126/science.1174671
Article
PubMed Central
CAS
PubMed
Google Scholar
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO: Integrating high-throughput and computational data elucidates bacterial networks. Nature. 2004, 429: 92-96. 10.1038/nature02456
Article
CAS
PubMed
Google Scholar
Gonzalez V, Santamaria RI, Bustos P, Hernandez-Gonzalez I, Medrano-Soto A, Moreno-Hagelsieb G, Janga SC, Ramirez MA, Jimenez-Jacinto V, Collado-Vides J, Davila G: The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons. Proc Natl Acad Sci USA. 2006, 103: 3834-3839. 10.1073/pnas.0508502103
Article
PubMed Central
PubMed
Google Scholar
Dixon R, Kahn D: Genetic regulation of biological nitrogen fixation. Nat Rev Microbiol. 2004, 2: 621-631. 10.1038/nrmicro954
Article
CAS
PubMed
Google Scholar
Tatusov RL, Koonin EV, Lipman DJ: A genomic perspective on protein families. Science. 1997, 278: 631-637. 10.1126/science.278.5338.631
Article
CAS
PubMed
Google Scholar
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA: The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003, 4: 41- 10.1186/1471-2105-4-41
Article
PubMed Central
PubMed
Google Scholar
Barnett MJ, Toman CJ, Fisher RF, Long SR: A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote-host interaction. Proc Natl Acad Sci USA. 2004, 101: 16636-16641. 10.1073/pnas.0407269101
Article
PubMed Central
CAS
PubMed
Google Scholar
Becker A, Berges H, Krol E, Bruand C, Ruberg S, Capela D, Lauber E, Meilhoc E, Ampe F, de Bruijn FJ, Fourment J, Francez-Charlot A, Kahn D, Küster H, Liebe C, Pühler A, Weidner S, Batut J: Global changes in gene expression in Sinorhizobium meliloti 1021 under microoxic and symbiotic conditions. Mol Plant Microbe Interact. 2004, 17: 292-303. 10.1094/MPMI.2004.17.3.292
Article
CAS
PubMed
Google Scholar
Uchiumi T, Ohwada T, Itakura M, Mitsui H, Nukui N, Dawadi P, Kaneko T, Tabata S, Yokoyama T, Tejima K, Saeki K, Omori H, Hayashi M, Maekawa T, Sriprang R, Murooka Y, Tajima S, Simomura K, Nomura M, Suzuki A, Shimoda Y, Sioya K, Abe M, Minamisawa K: Expression islands clustered on the symbiosis island of the Mesorhizobium loti genome. J Bacteriol. 2004, 186: 2439-2448. 10.1128/JB.186.8.2439-2448.2004
Article
PubMed Central
CAS
PubMed
Google Scholar
Encarnacion S, Hernandez M, Martinez-Batallar G, Contreras S, Vargas Mdel C, Mora J: 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. 2005, 7: 117-135. 10.1251/bpo110
Article
PubMed Central
CAS
PubMed
Google Scholar
Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BO: Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol. 2009, 7: 129-143.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hyduke DR, Palsson BO: Towards genome-scale signalling-network reconstructions. Nat Rev Genet. 11: 297-307.
Google Scholar
Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28: 27-30. 10.1093/nar/28.1.27
Article
PubMed Central
CAS
PubMed
Google Scholar
Segre D, Vitkup D, Church GM: Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA. 2002, 99: 15112-15117. 10.1073/pnas.232349399
Article
PubMed Central
CAS
PubMed
Google Scholar
de las Nieves, Peltzer M, Roques N, Poinsot V, Aguilar OM, Batut J, Capela D: Auxotrophy accounts for nodulation defect of most Sinorhizobium meliloti mutants in the branched-chain amino acid biosynthesis pathway. Mol Plant Microbe Interact. 2008, 21: 1232-1241. 10.1094/MPMI-21-9-1232
Article
Google Scholar
Mahadevan R, Schilling CH: The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng. 2003, 5: 264-276. 10.1016/j.ymben.2003.09.002
Article
CAS
PubMed
Google Scholar
Becker SA, Feist AM, Mo ML, Hannum G, Palsson BO, Herrgard MJ: Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc. 2007, 2: 727-738. 10.1038/nprot.2007.99
Article
CAS
PubMed
Google Scholar
Dunn MF: Tricarboxylic acid cycle and anaplerotic enzymes in rhizobia. FEMS Microbiol Rev. 1998, 22: 105-123. 10.1111/j.1574-6976.1998.tb00363.x
Article
CAS
PubMed
Google Scholar
Thony-Meyer L, Kunzler P: The Bradyrhizobium japonicum aconitase gene (acnA) is important for free-living growth but not for an effective root nodule symbiosis. J Bacteriol. 1996, 178: 6166-6172.
PubMed Central
CAS
PubMed
Google Scholar
McDermott TR, Kahn ML: Cloning and mutagenesis of the Rhizobium meliloti isocitrate dehydrogenase gene. J Bacteriol. 1992, 174: 4790-4797.
PubMed Central
CAS
PubMed
Google Scholar
Soto MJ, Sanjuan J, Olivares J: The disruption of a gene encoding a putative arylesterase impairs pyruvate dehydrogenase complex activity and nitrogen fixation in Sinorhizobium meliloti. Mol Plant Microbe Interact. 2001, 14: 811-815. 10.1094/MPMI.2001.14.6.811
Article
CAS
PubMed
Google Scholar
Tate R, Ferraioli S, Filosa S, Cermola M, Riccio A, Iaccarino M, Patriarca EJ: Glutamine utilization by Rhizobium etli. Mol Plant Microbe Interact. 2004, 17: 720-728. 10.1094/MPMI.2004.17.7.720
Article
CAS
PubMed
Google Scholar
Romanov VI, Hernandez-Lucas I, Martinez-Romero E: Carbon Metabolism Enzymes of Rhizobium tropici Cultures and Bacteroids. Appl Environ Microbiol. 1994, 60: 2339-2342.
PubMed Central
CAS
PubMed
Google Scholar
Jiang G, Krishnan AH, Kim YW, Wacek TJ, Krishnan HB: A functional myo-inositol dehydrogenase gene is required for efficient nitrogen fixation and competitiveness of Sinorhizobium fredii USDA191 to nodulate soybean (Glycine max [L.] Merr.). J Bacteriol. 2001, 183: 2595-2604. 10.1128/JB.183.8.2595-2604.2001
Article
PubMed Central
CAS
PubMed
Google Scholar
Cevallos MA, Encarnacion S, Leija A, Mora Y, Mora J: Genetic and physiological characterization of a Rhizobium etli mutant strain unable to synthesize poly-beta-hydroxybutyrate. J Bacteriol. 1996, 178: 1646-1654.
PubMed Central
CAS
PubMed
Google Scholar
Encarnacion S, del Carmen Vargas M, Dunn MF, Davalos A, Mendoza G, Mora Y, Mora J: AniA regulates reserve polymer accumulation and global protein expression in Rhizobium etli. J Bacteriol. 2002, 184: 2287-2295. 10.1128/JB.184.8.2287-2295.2002
Article
PubMed Central
CAS
PubMed
Google Scholar
Dombrecht B, Tesfay MZ, Verreth C, Heusdens C, Napoles MC, Vanderleyden J, Michiels J: The Rhizobium etli gene iscN is highly expressed in bacteroids and required for nitrogen fixation. Mol Genet Genomics. 2002, 267: 820-828. 10.1007/s00438-002-0715-0
Article
CAS
PubMed
Google Scholar
Randhawa GS, Hassani R: Role of rhizobial biosynthetic pathways of amino acids, nucleotide bases and vitamins in symbiosis. Indian J Exp Biol. 2002, 40: 755-764.
CAS
PubMed
Google Scholar
Walshaw DL, Poole PS: The general L-amino acid permease of Rhizobium leguminosarum is an ABC uptake system that also influences efflux of solutes. Mol Microbiol. 1996, 21: 1239-1252. 10.1046/j.1365-2958.1996.00078.x
Article
CAS
PubMed
Google Scholar
Hosie AH, Allaway D, Galloway CS, Dunsby HA, Poole PS: Rhizobium leguminosarum has a second general amino acid permease with unusually broad substrate specificity and high similarity to branched-chain amino acid transporters (Bra/LIV) of the ABC family. J Bacteriol. 2002, 184: 4071-4080. 10.1128/JB.184.15.4071-4080.2002
Article
PubMed Central
CAS
PubMed
Google Scholar
Newman JD, Diebold RJ, Schultz BW, Noel KD: Infection of soybean and pea nodules by Rhizobium spp. purine auxotrophs in the presence of 5-aminoimidazole-4-carboxamide riboside. J Bacteriol. 1994, 176: 3286-3294.
PubMed Central
CAS
PubMed
Google Scholar
Okazaki S, Hattori Y, Saeki K: The Mesorhizobium loti purB gene is involved in infection thread formation and nodule development in Lotus japonicus. J Bacteriol. 2007, 189: 8347-8352. 10.1128/JB.00788-07
Article
PubMed Central
CAS
PubMed
Google Scholar
Buendia-Claveria AM, Moussaid A, Ollero FJ, Vinardell JM, Torres A, Moreno J, Gil-Serrano AM, Rodriguez-Carvajal MA, Tejero-Mateo P, Peart JL, Brewin NJ, Ruiz-Sainz JE: A purL mutant of Sinorhizobium fredii HH103 is symbiotically defective and altered in its lipopolysaccharide. Microbiology. 2003, 149: 1807-1818. 10.1099/mic.0.26099-0
Article
CAS
PubMed
Google Scholar
Vineetha KE, Vij N, Prasad CK, Hassani R, Randhawa GS: Ultrastructural studies on nodules induced by pyrimidine auxotrophs of Sinorhizobium meliloti. Indian J Exp Biol. 2001, 39: 371-377.
CAS
PubMed
Google Scholar
Sarma AD, Emerich DW: A comparative proteomic evaluation of culture grown vs nodule isolated Bradyrhizobium japonicum. Proteomics. 2006, 6: 3008-3028. 10.1002/pmic.200500783
Article
CAS
PubMed
Google Scholar
Salazar E, Diaz-Mejia JJ, Moreno-Hagelsieb G, Martinez-Batallar G, Mora Y, Mora J, Encarnacion S: Characterization of the NifA-RpoN regulon in Rhizobium etli in free life and in symbiosis with Phaseolus vulgaris. Appl Environ Microbiol. 2010, 76: 4510-4520. 10.1128/AEM.02007-09
Article
PubMed Central
CAS
PubMed
Google Scholar
Encarnacion S, Dunn M, Willms K, Mora J: Fermentative and aerobic metabolism in Rhizobium etli. J Bacteriol. 1995, 177: 3058-3066.
PubMed Central
CAS
PubMed
Google Scholar
Peralta H, Mora Y, Salazar E, Encarnacion S, Palacios R, Mora J: 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. 2004, 70: 3272-3281. 10.1128/AEM.70.6.3272-3281.2004
Article
PubMed Central
CAS
PubMed
Google Scholar
Vries S, Hoge H, Bisseling : Isolation of total and polysomal RNA from plant tissues. Plant Molecular Biology Manual. 1988, 6: 1-13.
Google Scholar
Hegde P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R, Hughes JE, Snesrud E, Lee N, Quackenbush J: A concise guide to cDNA microarray analysis. Biotechniques. 2000, 29: 548-550. 552-544, 556 passim,
CAS
PubMed
Google Scholar
Livak KJ, Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001, 25: 402-408. 10.1006/meth.2001.1262
Article
CAS
PubMed
Google Scholar