PUB - Publikationen an der Universität Bielefeld

Pseudomonas cepacia mutants blocked in the Entner-Doudoroff pathway.
Allenza P, Lessie TG., J. Bacteriol. 150(3), 1982
PMID: 7076620

InterPro--an integrated documentation resource for protein families, domains and functional sites.
Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM; InterPro Consortium., Bioinformatics 16(12), 2000
PMID: 11159333

Bacterial polysaccharides suppress induced innate immunity by calcium chelation.
Aslam SN, Newman MA, Erbs G, Morrissey KL, Chinchilla D, Boller T, Jensen TT, De Castro C, Ierano T, Molinaro A, Jackson RW, Knight MR, Cooper RM., Curr. Biol. 18(14), 2008
PMID: 18639458

The ENZYME database in 2000.
Bairoch A., Nucleic Acids Res. 28(1), 2000
PMID: 10592255

The Universal Protein Resource (UniProt)
Bairoch, Nucleic Acids Research 33(), 2004

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.
Becker SA, Feist AM, Mo ML, Hannum G, Palsson BO, Herrgard MJ., Nat Protoc 2(3), 2007
PMID: 17406635

R factor transfer in Rhizobium leguminosarum.
Beringer JE., J. Gen. Microbiol. 84(1), 1974
PMID: 4612098

Metabolic flux distributions: genetic information, computational predictions, and experimental validation.
Blank LM, Kuepfer L., Appl. Microbiol. Biotechnol. 86(5), 2010
PMID: 20232063

Plant carbohydrate scavenging through tonB-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria.
Blanvillain S, Meyer D, Boulanger A, Lautier M, Guynet C, Denance N, Vasse J, Lauber E, Arlat M., PLoS ONE 2(2), 2007
PMID: 17311090

Integration of expression data in genome-scale metabolic network reconstructions.
Blazier AS, Papin JA., Front Physiol 3(), 2012
PMID: 22934050

Investigation of the central carbon metabolism of Sorangium cellulosum: metabolic network reconstruction and quantification of pathway fluxes.
Bolten CJ, Heinzle E, Muller R, Wittmann C., J. Microbiol. Biotechnol. 19(1), 2009
PMID: 19190405

Xanthan
Born, 2005

Identification and regulation of the N-acetylglucosamine utilization pathway of the plant pathogenic bacterium Xanthomonas campestris pv. campestris.
Boulanger A, Dejean G, Lautier M, Glories M, Zischek C, Arlat M, Lauber E., J. Bacteriol. 192(6), 2010
PMID: 20081036

UniProtKB/Swiss-Prot.
Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A., Methods Mol. Biol. 406(), 2007
PMID: 18287689

Regulation and secretion of Xanthomonas virulence factors.
Buttner D, Bonas U., FEMS Microbiol. Rev. 34(2), 2009
PMID: 19925633

Exocellular polysaccharides produced by lactic acid bacteria.
Cerning J., FEMS Microbiol. Rev. 7(1-2), 1990
PMID: 1702979

Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli.
Chen X, Alonso AP, Allen DK, Reed JL, Shachar-Hill Y., Metab. Eng. 13(1), 2010
PMID: 21129495

Enzyme-specific profiles for genome annotation: PRIAM.
Claudel-Renard C, Chevalet C, Faraut T, Kahn D., Nucleic Acids Res. 31(22), 2003
PMID: 14602924

Comparison of the genomes of two Xanthomonas pathogens with differing host specificities.
da Silva AC, Ferro JA, Reinach FC, Farah CS, Furlan LR, Quaggio RB, Monteiro-Vitorello CB, Van Sluys MA, Almeida NF, Alves LM, do Amaral AM, Bertolini MC, Camargo LE, Camarotte G, Cannavan F, Cardozo J, Chambergo F, Ciapina LP, Cicarelli RM, Coutinho LL, Cursino-Santos JR, El-Dorry H, Faria JB, Ferreira AJ, Ferreira RC, Ferro MI, Formighieri EF, Franco MC, Greggio CC, Gruber A, Katsuyama AM, Kishi LT, Leite RP, Lemos EG, Lemos MV, Locali EC, Machado MA, Madeira AM, Martinez-Rossi NM, Martins EC, Meidanis J, Menck CF, Miyaki CY, Moon DH, Moreira LM, Novo MT, Okura VK, Oliveira MC, Oliveira VR, Pereira HA, Rossi A, Sena JA, Silva C, de Souza RF, Spinola LA, Takita MA, Tamura RE, Teixeira EC, Tezza RI, Trindade dos Santos M, Truffi D, Tsai SM, White FF, Setubal JC, Kitajima JP., Nature 417(6887), 2002
PMID: 12024217

Fructose catabolism in Xanthomonas campestris pv. campestris. Sequence of the PTS operon, characterization of the fructose-specific enzymes.
de Crecy-Lagard V, Bouvet OM, Lejeune P, Danchin A., J. Biol. Chem. 266(27), 1991
PMID: 1655739

Fructose phosphotransferase system of Xanthomonas campestris pv. campestris: characterization of the fruB gene.
de Crecy-Lagard V, Binet M, Danchin A., Microbiology (Reading, Engl.) 141 ( Pt 9)(), 1995
PMID: 7496537

A gene cluster in Xanthomonas campestris pv. campestris required for pathogenicity controls the excretion of polygalacturonate lyase and other enzymes
Dow, Physiological and Molecular Plant Pathology 31(), 1987

Xanthan is not essential for pathogenicity in citrus canker but contributes to Xanthomonas epiphytic survival.
Dunger G, Relling VM, Tondo ML, Barreras M, Ielpi L, Orellano EG, Ottado J., Arch. Microbiol. 188(2), 2007
PMID: 17356870

Genome-scale models of bacterial metabolism: reconstruction and applications.
Durot M, Bourguignon PY, Schachter V., FEMS Microbiol. Rev. 33(1), 2008
PMID: 19067749

Response of Pseudomonas putida KT2440 to increased NADH and ATP demand.
Ebert BE, Kurth F, Grund M, Blank LM, Schmid A., Appl. Environ. Microbiol. 77(18), 2011
PMID: 21803911

In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data.
Edwards JS, Ibarra RU, Palsson BO., Nat. Biotechnol. 19(2), 2001
PMID: 11175725

Reconstruction of biochemical networks in microorganisms.
Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BO., Nat. Rev. Microbiol. 7(2), 2008
PMID: 19116616

Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.
Forster J, Famili I, Fu P, Palsson BO, Nielsen J., Genome Res. 13(2), 2003
PMID: 12566402

Xanthan gum: production, recovery, and properties.
Garcia-Ochoa F, Santos VE, Casas JA, Gomez E., Biotechnol. Adv. 18(7), 2000
PMID: 14538095

Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse.
Guo F, Gopaul DN, van Duyne GD., Nature 389(6646), 1997
PMID: 9288963

Correlation between TCA cycle flux and glucose uptake rate during respiro-fermentative growth of Saccharomyces cerevisiae.
Heyland J, Fu J, Blank LM., Microbiology (Reading, Engl.) 155(Pt 12), 2009
PMID: 19684065

Morphological heterogeneity among Salmonella lipopolysaccharide chemotypes in silver-stained polyacrylamide gels.
Hitchcock PJ, Brown TM., J. Bacteriol. 154(1), 1983
PMID: 6187729

Hopwood, 1985

Cloning and analysis of a 35.3-kilobase DNA region involved in exopolysaccharide production by Xanthomonas campestris pv. campestris.
Hotte B, Rath-Arnold I, Puhler A, Simon R., J. Bacteriol. 172(5), 1990
PMID: 2332409

10.11 – Xanthan
Hublik, 2012

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J; SBML Forum., Bioinformatics 19(4), 2003
PMID: 12611808

Chemical synthesis of the bacterial cell: polymerization, biosynthesis, fueling reactions, and transport
Ingraham, 1983

Energy requirements for microbial exopolysaccharide synthesis
Jarman, Archives of Microbiology 137(), 1984

The KEGG databases at GenomeNet.
Kanehisa M, Goto S, Kawashima S, Nakaya A., Nucleic Acids Res. 30(1), 2002
PMID: 11752249

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology.
Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R., Brief. Bioinformatics 11(1), 2009
PMID: 19955237

Metabolic flux analysis of Escherichia coli in glucose-limited continuous culture. I. Growth-rate-dependent metabolic efficiency at steady state.
Kayser A, Weber J, Hecht V, Rinas U., Microbiology (Reading, Engl.) 151(Pt 3), 2005
PMID: 15758216

Relationship between glucose catabolism and xanthan production in Xanthomonas oryzae pv. oryzae
Kim SY, Lee BM, Cho JY., Biotechnol. Lett. 32(4), 2010
PMID: IND44339310

Using process diagrams for the graphical representation of biological networks.
Kitano H, Funahashi A, Matsuoka Y, Oda K., Nat. Biotechnol. 23(8), 2005
PMID: 16082367

Structural and functional analysis of cellular networks with CellNetAnalyzer.
Klamt S, Saez-Rodriguez J, Gilles ED., BMC Syst Biol 1(), 2007
PMID: 17408509

Genetics of xanthan production in Xanthomonas campestris: the xanA and xanB genes are involved in UDP-glucose and GDP-mannose biosynthesis.
Koplin R, Arnold W, Hotte B, Simon R, Wang G, Puhler A., J. Bacteriol. 174(1), 1992
PMID: 1370280

Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes.
Kovach ME, Elzer PH, Hill DS, Robertson GT, Farris MA, Roop RM 2nd, Peterson KM., Gene 166(1), 1995
PMID: 8529885

The influence of metabolic network structures and energy requirements on xanthan gum yields.
Letisse F, Chevallereau P, Simon JL, Lindley N., J. Biotechnol. 99(3), 2002
PMID: 12385717

Kinetic analysis of growth and xanthan gum production with Xanthomonas campestris on sucrose, using sequentially consumed nitrogen sources.
Letisse F, Chevallereau P, Simon JL, Lindley ND., Appl. Microbiol. Biotechnol. 55(4), 2001
PMID: 11398920

Development of a phenomenological modeling approach for prediction of growth and xanthan gum production using Xanthomonas campestris.
Letisse F, Lindley ND, Roux G., Biotechnol. Prog. 19(3), 2003
PMID: 12790645

Evaluation of extraction methods for recovery of fatty acids from lipid-producing microheterotrophs.
Lewis T, Nichols PD, McMeekin TA., J. Microbiol. Methods 43(2), 2000
PMID: 11121609

The univector plasmid-fusion system, a method for rapid construction of recombinant DNA without restriction enzymes
Liu, Current Biology 8(), 1998

Mutations of Bacteria from Virus Sensitivity to Virus Resistance.
Luria SE, Delbruck M., Genetics 28(6), 1943
PMID: 17247100

Top 10 plant pathogenic bacteria in molecular plant pathology.
Mansfield J, Genin S, Magori S, Citovsky V, Sriariyanum M, Ronald P, Dow M, Verdier V, Beer SV, Machado MA, Toth I, Salmond G, Foster GD., Mol. Plant Pathol. 13(6), 2012
PMID: 22672649

Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology.
Milne CB, Kim PJ, Eddy JA, Price ND., Biotechnol J 4(12), 2009
PMID: 19946878

Acetylornithine transcarbamylase: a novel enzyme in arginine biosynthesis.
Morizono H, Cabrera-Luque J, Shi D, Gallegos R, Yamaguchi S, Yu X, Allewell NM, Malamy MH, Tuchman M., J. Bacteriol. 188(8), 2006
PMID: 16585758

Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example.
Neuweger H, Persicke M, Albaum SP, Bekel T, Dondrup M, Huser AT, Winnebald J, Schneider J, Kalinowski J, Goesmann A., BMC Syst Biol 3(), 2009
PMID: 19698148

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.
Nogales J, Palsson BO, Thiele I., BMC Syst Biol 2(), 2008
PMID: 18793442

Applications of genome-scale metabolic reconstructions.
Oberhardt MA, Palsson BO, Papin JA., Mol. Syst. Biol. 5(), 2009
PMID: 19888215

What is flux balance analysis?
Orth JD, Thiele I, Palsson BO., Nat. Biotechnol. 28(3), 2010
PMID: 20212490

Glucose metabolism in Xanthomonas campestris and influence of methionine on the carbon flow.
Pielken P, Schimz KL, Eggeling L, Sahm H., Can. J. Microbiol. 34(12), 1988
PMID: 3148363

Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology.
Puchalka J, Oberhardt MA, Godinho M, Bielecka A, Regenhardt D, Timmis KN, Papin JA, Martins dos Santos VA., PLoS Comput. Biol. 4(10), 2008
PMID: 18974823

Comparative and functional genomic analyses of the pathogenicity of phytopathogen Xanthomonas campestris pv. campestris.
Qian W, Jia Y, Ren SX, He YQ, Feng JX, Lu LF, Sun Q, Ying G, Tang DJ, Tang H, Wu W, Hao P, Wang L, Jiang BL, Zeng S, Gu WY, Lu G, Rong L, Tian Y, Yao Z, Fu G, Chen B, Fang R, Qiang B, Chen Z, Zhao GP, Tang JL, He C., Genome Res. 15(6), 2005
PMID: 15899963

Thirteen years of building constraint-based in silico models of Escherichia coli.
Reed JL, Palsson BO., J. Bacteriol. 185(9), 2003
PMID: 12700248

Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli
Resendis-Antonio, PLoS Computational Biology 3(), 2007

Review of xanthan gum production from unmodified starches by Xanthomonas comprestris sp.
Rosalam, Enzyme and Microbial Technology 39(), 2006

Kinetic and metabolic effects of nitrogen, magnesium and sulphur restriction in Xanthomonas campestris batch cultures
Roseiro, Journal of Applied Microbiology 75(), 1993

Pathogenomics of Xanthomonas: understanding bacterium-plant interactions.
Ryan RP, Vorholter FJ, Potnis N, Jones JB, Van Sluys MA, Bogdanove AJ, Dow JM., Nat. Rev. Microbiol. 9(5), 2011
PMID: 21478901

Growth efficiency of Xanthomonas campestris in continuous culture
Rye, Journal of General Microbiology 134(), 1988

Sambrook, 2001

Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism.
Sauer U, Lasko DR, Fiaux J, Hochuli M, Glaser R, Szyperski T, Wuthrich K, Bailey JE., J. Bacteriol. 181(21), 1999
PMID: 10542169

Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum.
Schafer A, Tauch A, Jager W, Kalinowski J, Thierbach G, Puhler A., Gene 145(1), 1994
PMID: 8045426

Genome-enabled determination of amino acid biosynthesis in Xanthomonas campestris pv. campestris and identification of biosynthetic pathways for alanine, glycine, and isoleucine by 13C-isotopologue profiling.
Schatschneider S, Vorholter FJ, Ruckert C, Becker A, Eisenreich W, Puhler A, Niehaus K., Mol. Genet. Genomics 286(3-4), 2011
PMID: 21853248

BRENDA, the enzyme information system in 2011.
Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Sohngen C, Stelzer M, Thiele J, Schomburg D., Nucleic Acids Res. 39(Database issue), 2010
PMID: 21062828

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.
Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BO., Nat Protoc 6(9), 2011
PMID: 21886097

Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis.
Schilling CH, Palsson BO., J. Theor. Biol. 203(3), 2000
PMID: 10716908

CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks.
Schneider J, Vorholter FJ, Trost E, Blom J, Musa YR, Neuweger H, Niehaus K, Schatschneider S, Tauch A, Goesmann A., Genet. Mol. Res. 9(3), 2010
PMID: 20799163

Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli.
Schuetz R, Kuepfer L, Sauer U., Mol. Syst. Biol. 3(), 2007
PMID: 17625511

Analysis of optimality in natural and perturbed metabolic networks.
Segre D, Vitkup D, Church GM., Proc. Natl. Acad. Sci. U.S.A. 99(23), 2002
PMID: 12415116

Identification of Xanthomonas campestris pv. campestris galactose utilization genes from transcriptome data.
Serrania J, Vorholter FJ, Niehaus K, Puhler A, Becker A., J. Biotechnol. 135(3), 2008
PMID: 18538881

The influence of acetyl and pyruvate substituents on the helix-coil transition behaviour of xanthan
Shatwell, Carbohydrate Research 206(), 1990

Towards a genome-scale kinetic model of cellular metabolism.
Smallbone K, Simeonidis E, Swainston N, Mendes P., BMC Syst Biol 4(), 2010
PMID: 20109182

In silico genome-scale metabolic analysis of Pseudomonas putida KT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival.
Sohn SB, Kim TY, Park JM, Lee SY., Biotechnol J 5(7), 2010
PMID: 20540110

Functional characterization of the Xcs and Xps type II secretion systems from the plant pathogenic bacterium Xanthomonas campestris pv vesicatoria.
Szczesny R, Jordan M, Schramm C, Schulz S, Cogez V, Bonas U, Buttner D., New Phytol. 187(4), 2010
PMID: 20524995

Xanthomonas campestris pv. campestris possesses a single gluconeogenic pathway that is required for virulence.
Tang DJ, He YQ, Feng JX, He BR, Jiang BL, Lu GT, Chen B, Tang JL., J. Bacteriol. 187(17), 2005
PMID: 16109965

Genome sequence of Xanthomonas campestris JX, an industrially productive strain for Xanthan gum.
Tao F, Wang X, Ma C, Yang C, Tang H, Gai Z, Xu P., J. Bacteriol. 194(17), 2012
PMID: 22887662

Predictions for oxygen supply control to enhance population stability of engineered production strains.
Varma A, Palsson BO., Biotechnol. Bioeng. 43(4), 1994
PMID: 18615690

Xanthomonas campestris pv. campestris (cause of black rot of crucifers) in the genomic era is still a worldwide threat to Brassica crops
Vicente, Molecular Plant Pathology 14(), 2012

Lipopolysaccharide biosynthesis in Xanthomonas campestris pv. campestris: a cluster of 15 genes is involved in the biosynthesis of the LPS O-antigen and the LPS core.
Vorholter FJ, Niehaus K, Puhler A., Mol. Genet. Genomics 266(1), 2001
PMID: 11589581

The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis.
Vorholter FJ, Schneiker S, Goesmann A, Krause L, Bekel T, Kaiser O, Linke B, Patschkowski T, Ruckert C, Schmid J, Sidhu VK, Sieber V, Tauch A, Watt SA, Weisshaar B, Becker A, Niehaus K, Puhler A., J. Biotechnol. 134(1-2), 2008
PMID: 18304669

Involvement of bacterial TonB-dependent signaling in the generation of an oligogalacturonide damage-associated molecular pattern from plant cell walls exposed to Xanthomonas campestris pv. campestris pectate lyases.
Vorholter FJ, Wiggerich HG, Scheidle H, Sidhu VK, Mrozek K, Kuster H, Puhler A, Niehaus K., BMC Microbiol. 12(), 2012
PMID: 23082751

Low molecular weight plant extract induces metabolic changes and the secretion of extracellular enzymes, but has a negative effect on the expression of the type-III secretion system in Xanthomonas campestris pv. campestris.
Watt TF, Vucur M, Baumgarth B, Watt SA, Niehaus K., J. Biotechnol. 140(1-2), 2008
PMID: 19114064

Glucose metabolism in Xanthomonas campestris
Whitfield, Journal of General Microbiology 128(), 1982

Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum.
Wiback SJ, Mahadevan R, Palsson BO., Biotechnol. Bioeng. 86(3), 2004
PMID: 15083512

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model.
Yizhak K, Benyamini T, Liebermeister W, Ruppin E, Shlomi T., Bioinformatics 26(12), 2010
PMID: 20529914

Xanthan induces plant susceptibility by suppressing callose deposition.
Yun MH, Torres PS, El Oirdi M, Rigano LA, Gonzalez-Lamothe R, Marano MR, Castagnaro AP, Dankert MA, Bouarab K, Vojnov AA., Plant Physiol. 141(1), 2006
PMID: 16531487

Comparative glucose catabolism of Xanthomonas species.
Zagallo AC, Wang CH., J. Bacteriol. 93(3), 1967
PMID: 6025434

An Escherichia coli K-12 tktA tktB mutant deficient in transketolase activity requires pyridoxine (vitamin B6) as well as the aromatic amino acids and vitamins for growth.
Zhao G, Winkler ME., J. Bacteriol. 176(19), 1994
PMID: 7928977