Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

Schatschneider S, Schneider J, Blom J, Letisse F, Niehaus K, Goesmann A, Vorhölter F-J (2017)
MICROBIOLOGY-SGM 163(8): 1117-1144.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Abstract / Bemerkung
Bacteria of the genus Xanthomonas are a major group of plant pathogens. They are hazardous to important crops and closely related to human pathogens. Being collectively a major focus of molecular phytopathology, an increasing number of diverse and intricate mechanisms are emerging by which they communicate, interfere with host signalling and keep competition at bay. Interestingly, they are also biotechnologically relevant polysaccharide producers. Systems biotechnology techniques have revealed their central metabolism and a growing number of remarkable features. Traditional analyses of Xanthomonas metabolism missed the Embden-Meyerhof-Parnas pathway (glycolysis) as being a route by which energy and molecular building blocks are derived from glucose. As a consequence of the emerging full picture of their metabolism process, xanthomonads were discovered to have three alternative catabolic pathways and they use an unusual and reversible phosphofructokinase as a key enzyme. In this review, we summarize the synthetic and systems biology methods and the bioinformatics tools applied to reconstruct their metabolic network and reveal the dynamic fluxes within their complex carbohydrate metabolism. This is based on insights from omics disciplines; in particular, genomics, transcriptomics, proteomics and metabolomics. Analysis of high-throughput omics data facilitates the reconstruction of organism-specific large-and genome-scale metabolic networks. Reconstructed metabolic networks are fundamental to the formulation of metabolic models that facilitate the simulation of actual metabolic activities under specific environmental conditions.
plant pathogenesis; infection; bioinformatics tools; OMICS; metabolic; modelling; biotechnology
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Schatschneider S, Schneider J, Blom J, et al. Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. MICROBIOLOGY-SGM. 2017;163(8):1117-1144.
Schatschneider, S., Schneider, J., Blom, J., Letisse, F., Niehaus, K., Goesmann, A., & Vorhölter, F. - J. (2017). Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. MICROBIOLOGY-SGM, 163(8), 1117-1144. doi:10.1099/mic.0.000473
Schatschneider, Sarah, Schneider, Jessica, Blom, Jochen, Letisse, Fabien, Niehaus, Karsten, Goesmann, Alexander, and Vorhölter, Frank-Jörg. 2017. “Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris”. MICROBIOLOGY-SGM 163 (8): 1117-1144.
Schatschneider, S., Schneider, J., Blom, J., Letisse, F., Niehaus, K., Goesmann, A., and Vorhölter, F. - J. (2017). Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. MICROBIOLOGY-SGM 163, 1117-1144.
Schatschneider, S., et al., 2017. Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. MICROBIOLOGY-SGM, 163(8), p 1117-1144.
S. Schatschneider, et al., “Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris”, MICROBIOLOGY-SGM, vol. 163, 2017, pp. 1117-1144.
Schatschneider, S., Schneider, J., Blom, J., Letisse, F., Niehaus, K., Goesmann, A., Vorhölter, F.-J.: Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. MICROBIOLOGY-SGM. 163, 1117-1144 (2017).
Schatschneider, Sarah, Schneider, Jessica, Blom, Jochen, Letisse, Fabien, Niehaus, Karsten, Goesmann, Alexander, and Vorhölter, Frank-Jörg. “Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris”. MICROBIOLOGY-SGM 163.8 (2017): 1117-1144.

337 References

Daten bereitgestellt von Europe PubMed Central.

Realizing the potential of synthetic biology.
Church GM, Elowitz MB, Smolke CD, Voigt CA, Weiss R., Nat. Rev. Mol. Cell Biol. 15(4), 2014
PMID: 24622617
Computational systems biology.
Kitano H., Nature 420(6912), 2002
PMID: 12432404
Integrating 'omic' information: a bridge between genomics and systems biology.
Ge H, Walhout AJ, Vidal M., Trends Genet. 19(10), 2003
PMID: 14550629
In silico biology through "omics".
Palsson B., Nat. Biotechnol. 20(7), 2002
PMID: 12089538
Gross RW, Holcapek M., Anal. Chem. 86(17), 2014
PMID: 25103272
Lipidomics: coming to grips with lipid diversity.
Shevchenko A, Simons K., Nat. Rev. Mol. Cell Biol. 11(8), 2010
PMID: 20606693
Lipidomics: new tools and applications.
Wenk MR., Cell 143(6), 2010
PMID: 21145456
Glycomic analysis: an array of technologies.
Krishnamoorthy L, Mahal LK., ACS Chem. Biol. 4(9), 2009
PMID: 19728746
Quantitative glycomics strategies.
Mechref Y, Hu Y, Desantos-Garcia JL, Hussein A, Tang H., Mol. Cell Proteomics 12(4), 2013
PMID: 23325767
Glycomics: an integrated systems approach to structure-function relationships of glycans.
Raman R, Raguram S, Venkataraman G, Paulson JC, Sasisekharan R., Nat. Methods 2(11), 2005
PMID: 16278650
Recent advances in high-throughput 13C-fluxomics.
Heux S, Berges C, Millard P, Portais JC, Letisse F., Curr. Opin. Biotechnol. 43(), 2016
PMID: 27838571
How to measure metabolic fluxes: a taxonomic guide for (13)C fluxomics.
Niedenfuhr S, Wiechert W, Noh K., Curr. Opin. Biotechnol. 34(), 2014
PMID: 25531408
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.
Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L., Science 292(5518), 2001
PMID: 11340206
Multiple high-throughput analyses monitor the response of E. coli to perturbations.
Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, Ho PY, Kakazu Y, Sugawara K, Igarashi S, Harada S, Masuda T, Sugiyama N, Togashi T, Hasegawa M, Takai Y, Yugi K, Arakawa K, Iwata N, Toya Y, Nakayama Y, Nishioka T, Shimizu K, Mori H, Tomita M., Science 316(5824), 2007
PMID: 17379776
Integrating multiple 'omics' analysis for microbial biology: application and methodologies.
Zhang W, Li F, Nie L., Microbiology (Reading, Engl.) 156(Pt 2), 2009
PMID: 19910409
Systems biotechnology of animal cells: the road to prediction.
Carinhas N, Oliveira R, Alves PM, Carrondo MJ, Teixeira AP., Trends Biotechnol. 30(7), 2012
PMID: 22541337
Systems metabolic engineering in an industrial setting.
Sagt CM., Appl. Microbiol. Biotechnol. 97(6), 2013
PMID: 23397485
Industrial biotechnology: tools and applications.
Tang WL, Zhao H., Biotechnol J 4(12), 2009
PMID: 19844915
Metabolomics: an integral technique in systems biology.
Weckwerth W., Bioanalysis 2(4), 2010
PMID: 21083277
Mechanistic pathway modeling for industrial biotechnology: challenging but worthwhile.
Wiechert W, Noack S., Curr. Opin. Biotechnol. 22(5), 2011
PMID: 21353523
Industrial systems biology.
Otero JM, Nielsen J., Biotechnol. Bioeng. 105(3), 2010
PMID: 19891008
Systems metabolic engineering, industrial biotechnology and microbial cell factories.
Lee SY, Mattanovich D, Villaverde A., Microb. Cell Fact. 11(), 2012
PMID: 23232052
Engineering of microorganisms for the production of biofuels and perspectives based on systems metabolic engineering approaches.
Jang YS, Park JM, Choi S, Choi YJ, Seung do Y, Cho JH, Lee SY., Biotechnol. Adv. 30(5), 2011
PMID: 21889585
Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol.
Antoniewicz MR, Kraynie DF, Laffend LA, Gonzalez-Lergier J, Kelleher JK, Stephanopoulos G., Metab. Eng. 9(3), 2007
PMID: 17400499
Metabolic engineering for the microbial production of 1,3-propanediol.
Nakamura CE, Whited GM., Curr. Opin. Biotechnol. 14(5), 2003
PMID: 14580573
Genome-scale analysis of Mannheimia succiniciproducens metabolism.
Kim TY, Kim HU, Park JM, Song H, Kim JS, Lee SY., Biotechnol. Bioeng. 97(4), 2007
PMID: 17405177
Genome-based metabolic engineering of Mannheimia succiniciproducens for succinic acid production.
Lee SJ, Song H, Lee SY., Appl. Environ. Microbiol. 72(3), 2006
PMID: 16517641
Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory.
Otero JM, Cimini D, Patil KR, Poulsen SG, Olsson L, Nielsen J., PLoS ONE 8(1), 2013
PMID: 23349810

Werpy, 2004
A systems biology approach to infectious disease research: innovating the pathogen-host research paradigm.
Aderem A, Adkins JN, Ansong C, Galagan J, Kaiser S, Korth MJ, Law GL, McDermott JG, Proll SC, Rosenberger C, Schoolnik G, Katze MG., MBio 2(1), 2011
PMID: 21285433
Carbon metabolism of intracellular bacterial pathogens and possible links to virulence.
Eisenreich W, Dandekar T, Heesemann J, Goebel W., Nat. Rev. Microbiol. 8(6), 2010
PMID: 20453875
A review on computational systems biology of pathogen-host interactions.
Durmus S, Cakır T, Ozgur A, Guthke R., Front Microbiol 6(), 2015
PMID: 25914674

Salmonella: a model for bacterial pathogenesis.
Ohl ME, Miller SI., Annu. Rev. Med. 52(), 2001
PMID: 11160778
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.
Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen FC, Fleming RM, Hsiung CA, De Keersmaecker SC, Liao YC, Marchal K, Mo ML, Ozdemir E, Raghunathan A, Reed JL, Shin SI, Sigurbjornsdottir S, Steinmann J, Sudarsan S, Swainston N, Thijs IM, Zengler K, Palsson BO, Adkins JN, Bumann D., BMC Syst Biol 5(), 2011
PMID: 21244678
Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling.
Ansong C, Deatherage BL, Hyduke D, Schmidt B, McDermott JE, Jones MB, Chauhan S, Charusanti P, Kim YM, Nakayasu ES, Li J, Kidwai A, Niemann G, Brown RN, Metz TO, McAteer K, Heffron F, Peterson SN, Motin V, Palsson BO, Smith RD, Adkins JN., Curr. Top. Microbiol. Immunol. 363(), 2013
PMID: 22886542
SEEK: a systems biology data and model management platform.
Wolstencroft K, Owen S, Krebs O, Nguyen Q, Stanford NJ, Golebiewski M, Weidemann A, Bittkowski M, An L, Shockley D, Snoep JL, Mueller W, Goble C., BMC Syst Biol 9(), 2015
PMID: 26160520
Conservation of Salmonella infection mechanisms in plants and animals.
Schikora A, Virlogeux-Payant I, Bueso E, Garcia AV, Nilau T, Charrier A, Pelletier S, Menanteau P, Baccarini M, Velge P, Hirt H., PLoS ONE 6(9), 2011
PMID: 21915285
Establishment, in silico analysis, and experimental verification of a large-scale metabolic network of the xanthan producing Xanthomonas campestris pv. campestris strain B100.
Schatschneider S, Persicke M, Watt SA, Hublik G, Puhler A, Niehaus K, Vorholter FJ., J. Biotechnol. 167(2), 2013
PMID: 23395674
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
The Arabidopsis thaliana-pseudomonas syringae interaction.
Katagiri F, Thilmony R, He SY., Arabidopsis Book 1(), 2002
PMID: 22303207
The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants.
Crossman LC, Gould VC, Dow JM, Vernikos GS, Okazaki A, Sebaihia M, Saunders D, Arrowsmith C, Carver T, Peters N, Adlem E, Kerhornou A, Lord A, Murphy L, Seeger K, Squares R, Rutter S, Quail MA, Rajandream MA, Harris D, Churcher C, Bentley SD, Parkhill J, Thomson NR, Avison MB., Genome Biol. 9(4), 2008
PMID: 18419807
10.11 Xanthan
Hublik, 2012
Structure of extracellular polysaccharide from Xanthomonas campestris.
Jansson PE, Kenne L, Lindberg B., Carbohydr. Res. 45(), 1975
PMID: 1212669
Location of a second O-acetyl group in xanthan gum by the reductive-cleavage method.
Stankowski JD, Mueller BE, Zeller SG., Carbohydr. Res. 241(), 1993
PMID: 8472258
Xanthomonas campestris pv. campestris gum mutants: effects on xanthan biosynthesis and plant virulence.
Katzen F, Ferreiro DU, Oddo CG, Ielmini MV, Becker A, Puhler A, Ielpi L., J. Bacteriol. 180(7), 1998
PMID: 9537354
Biological role of xanthomonadin pigments in Xanthomonas campestris pv. campestris.
Poplawsky AR, Urban SC, Chun W., Appl. Environ. Microbiol. 66(12), 2000
PMID: 11097878

Xanthan Pyruvilation Is Essential for the Virulence of Xanthomonas campestris pv. campestris.
Bianco MI, Toum L, Yaryura PM, Mielnichuk N, Gudesblat GE, Roeschlin R, Marano MR, Ielpi L, Vojnov AA., Mol. Plant Microbe Interact. 29(9), 2016
PMID: 27464764
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
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
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
Born, 2005

CRISPR-mediated adaptive immune systems in bacteria and archaea.
Sorek R, Lawrence CM, Wiedenheft B., Annu. Rev. Biochem. 82(), 2013
PMID: 23495939
What makes Xanthomonas albilineans unique amongst xanthomonads?
Pieretti I, Pesic A, Petras D, Royer M, Sussmuth RD, Cociancich S., Front Plant Sci 6(), 2015
PMID: 25964795
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
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.
Salzberg SL, Sommer DD, Schatz MC, Phillippy AM, Rabinowicz PD, Tsuge S, Furutani A, Ochiai H, Delcher AL, Kelley D, Madupu R, Puiu D, Radune D, Shumway M, Trapnell C, Aparna G, Jha G, Pandey A, Patil PB, Ishihara H, Meyer DF, Szurek B, Verdier V, Koebnik R, Dow JM, Ryan RP, Hirata H, Tsuyumu S, Won Lee S, Seo YS, Sriariyanum M, Ronald PC, Sonti RV, Van Sluys MA, Leach JE, White FF, Bogdanove AJ., BMC Genomics 9(), 2008
PMID: 18452608
Analysis of CRISPR system function in plant pathogen Xanthomonas oryzae.
Semenova E, Nagornykh M, Pyatnitskiy M, Artamonova II, Severinov K., FEMS Microbiol. Lett. 296(1), 2009
PMID: 19459963
Xylella and Xanthomonas Mobil'omics.
Monteiro-Vitorello CB, de Oliveira MC, Zerillo MM, Varani AM, Civerolo E, Van Sluys MA., OMICS 9(2), 2005
PMID: 15969647
The role of prophage in plant-pathogenic bacteria.
Varani AM, Monteiro-Vitorello CB, Nakaya HI, Van Sluys MA., Annu Rev Phytopathol 51(), 2013
PMID: 23725471
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

Draft genome of the xanthan producer Xanthomonas campestris NRRL B-1459 (ATCC 13951).
Wibberg D, Alkhateeb RS, Winkler A, Albersmeier A, Schatschneider S, Albaum S, Niehaus K, Hublik G, Puhler A, Vorholter FJ., J. Biotechnol. 204(), 2015
PMID: 25865276
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
Comparison of two Xanthomonas campestris pathovar campestris genomes revealed differences in their gene composition.
Vorholter FJ, Thias T, Meyer F, Bekel T, Kaiser O, Puhler A, Niehaus K., J. Biotechnol. 106(2-3), 2003
PMID: 14651861
BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.
Bartels D, Kespohl S, Albaum S, Druke T, Goesmann A, Herold J, Kaiser O, Puhler A, Pfeiffer F, Raddatz G, Stoye J, Meyer F, Schuster SC., Bioinformatics 21(7), 2004
PMID: 15514001
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence.
Thieme F, Koebnik R, Bekel T, Berger C, Boch J, Buttner D, Caldana C, Gaigalat L, Goesmann A, Kay S, Kirchner O, Lanz C, Linke B, McHardy AC, Meyer F, Mittenhuber G, Nies DH, Niesbach-Klosgen U, Patschkowski T, Ruckert C, Rupp O, Schneiker S, Schuster SC, Vorholter FJ, Weber E, Puhler A, Bonas U, Bartels D, Kaiser O., J. Bacteriol. 187(21), 2005
PMID: 16237009
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

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
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

Identification, genetic and biochemical analysis of genes involved in synthesis of sugar nucleotide precursors of xanthan gum.
Harding NE, Raffo S, Raimondi A, Cleary JM, Ielpi L., J. Gen. Microbiol. 139(3), 1993
PMID: 20050414
Xanthan gum biosynthesis and application: a biochemical/genetic perspective.
Becker A, Katzen F, Puhler A, Ielpi L., Appl. Microbiol. Biotechnol. 50(2), 1998
PMID: 9763683
Xanthomonas campestris pv. campestris gum mutants: effects on xanthan biosynthesis and plant virulence.
Katzen F, Ferreiro DU, Oddo CG, Ielmini MV, Becker A, Puhler A, Ielpi L., J. Bacteriol. 180(7), 1998
PMID: 9537354
Expression of the gum operon directing xanthan biosynthesis in Xanthomonas campestris and its regulation in planta.
Vojnov AA, Slater H, Daniels MJ, Dow JM., Mol. Plant Microbe Interact. 14(6), 2001
PMID: 11386372
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
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
Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp.
Bogdanove AJ, Koebnik R, Lu H, Furutani A, Angiuoli SV, Patil PB, Van Sluys MA, Ryan RP, Meyer DF, Han SW, Aparna G, Rajaram M, Delcher AL, Phillippy AM, Puiu D, Schatz MC, Shumway M, Sommer DD, Trapnell C, Benahmed F, Dimitrov G, Madupu R, Radune D, Sullivan S, Jha G, Ishihara H, Lee SW, Pandey A, Sharma V, Sriariyanun M, Szurek B, Vera-Cruz CM, Dorman KS, Ronald PC, Verdier V, Dow JM, Sonti RV, Tsuge S, Brendel VP, Rabinowicz PD, Leach JE, White FF, Salzberg SL., J. Bacteriol. 193(19), 2011
PMID: 21784931
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
Genome Sequence of Xanthomonas campestris pv. campestris Strain Xca5.
Bolot S, Guy E, Carrere S, Barbe V, Arlat M, Noel LD., Genome Announc 1(1), 2013
PMID: 23405315
Genome Sequences of Three Atypical Xanthomonas campestris pv. campestris Strains, CN14, CN15, and CN16.
Bolot S, Roux B, Carrere S, Jiang BL, Tang JL, Arlat M, Noel LD., Genome Announc 1(4), 2013
PMID: 23846270
Draft Genome Sequence of the Xanthan Producer Xanthomonas campestris LMG 8031.
Schmid J, Huptas C, Wenning M., Genome Announc 4(5), 2016
PMID: 27789631
EDGAR: a software framework for the comparative analysis of prokaryotic genomes.
Blom J, Albaum SP, Doppmeier D, Puhler A, Vorholter FJ, Zakrzewski M, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19457249
EDGAR 2.0: an enhanced software platform for comparative gene content analyses.
Blom J, Kreis J, Spanig S, Juhre T, Bertelli C, Ernst C, Goesmann A., Nucleic Acids Res. 44(W1), 2016
PMID: 27098043
Natural genetic variation of Xanthomonas campestris pv. campestris pathogenicity on arabidopsis revealed by association and reverse genetics.
Guy E, Genissel A, Hajri A, Chabannes M, David P, Carrere S, Lautier M, Roux B, Boureau T, Arlat M, Poussier S, Noel LD., MBio 4(3), 2013
PMID: 23736288
Transcriptome analysis using next-generation sequencing.
Mutz KO, Heilkenbrinker A, Lonne M, Walter JG, Stahl F., Curr. Opin. Biotechnol. 24(1), 2012
PMID: 23020966
Identifying bacterial genes and endosymbiont DNA with Glimmer.
Delcher AL, Bratke KA, Powers EC, Salzberg SL., Bioinformatics 23(6), 2007
PMID: 17237039
Improved microbial gene identification with GLIMMER.
Delcher AL, Harmon D, Kasif S, White O, Salzberg SL., Nucleic Acids Res. 27(23), 1999
PMID: 10556321
CRITICA: coding region identification tool invoking comparative analysis.
Badger JH, Olsen GJ, Woese CR., Mol. Biol. Evol. 16(4), 1999
PMID: 10331277
REGANOR: a gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes.
Linke B, McHardy AC, Neuweger H, Krause L, Meyer F., Appl. Bioinformatics 5(3), 2006
PMID: 16922601
GISMO--gene identification using a support vector machine for ORF classification.
Krause L, McHardy AC, Nattkemper TW, Puhler A, Stoye J, Meyer F., Nucleic Acids Res. 35(2), 2006
PMID: 17175534
Prodigal: prokaryotic gene recognition and translation initiation site identification.
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ., BMC Bioinformatics 11(), 2010
PMID: 20211023
Small non-coding RNAs in plant-pathogenic Xanthomonas spp.
Abendroth U, Schmidtke C, Bonas U., RNA Biol 11(5), 2014
PMID: 24667380
Rfam 12.0: updates to the RNA families database.
Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD., Nucleic Acids Res. 43(Database issue), 2014
PMID: 25392425
Conveyor: a workflow engine for bioinformatic analyses.
Linke B, Giegerich R, Goesmann A., Bioinformatics 27(7), 2011
PMID: 21278189
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
The xylan utilization system of the plant pathogen Xanthomonas campestris pv campestris controls epiphytic life and reveals common features with oligotrophic bacteria and animal gut symbionts.
Dejean G, Blanvillain-Baufume S, Boulanger A, Darrasse A, Duge de Bernonville T, Girard AL, Carrere S, Jamet S, Zischek C, Lautier M, Sole M, Buttner D, Jacques MA, Lauber E, Arlat M., New Phytol. 198(3), 2013
PMID: 23442088
The N-Glycan cluster from Xanthomonas campestris pv. campestris: a toolbox for sequential plant N-glycan processing.
Dupoiron S, Zischek C, Ligat L, Carbonne J, Boulanger A, Duge de Bernonville T, Lautier M, Rival P, Arlat M, Jamet E, Lauber E, Albenne C., J. Biol. Chem. 290(10), 2015
PMID: 25586188
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
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
Phosphatidylcholine biosynthesis in Xanthomonas campestris via a yeast-like acylation pathway.
Moser R, Aktas M, Narberhaus F., Mol. Microbiol. 91(4), 2014
PMID: 24329598
A perspective on microarrays: current applications, pitfalls, and potential uses.
Jaluria P, Konstantopoulos K, Betenbaugh M, Shiloach J., Microb. Cell Fact. 6(), 2007
PMID: 17254338
Navigating gene expression using microarrays--a technology review.
Schulze A, Downward J., Nat. Cell Biol. 3(8), 2001
PMID: 11483980
EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data.
Dondrup M, Albaum SP, Griebel T, Henckel K, Junemann S, Kahlke T, Kleindt CK, Kuster H, Linke B, Mertens D, Mittard-Runte V, Neuweger H, Runte KJ, Tauch A, Tille F, Puhler A, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19200358
EMMA: a platform for consistent storage and efficient analysis of microarray data.
Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651856
Insights into the extracytoplasmic stress response of Xanthomonas campestris pv. campestris: role and regulation of {sigma}E-dependent activity.
Bordes P, Lavatine L, Phok K, Barriot R, Boulanger A, Castanie-Cornet MP, Dejean G, Lauber E, Becker A, Arlat M, Gutierrez C., J. Bacteriol. 193(1), 2010
PMID: 20971899
Transcriptional reprogramming and phenotypical changes associated with growth of Xanthomonas campestris pv. campestris in cabbage xylem sap.
Duge de Bernonville T, Noel LD, SanCristobal M, Danoun S, Becker A, Soreau P, Arlat M, Lauber E., FEMS Microbiol. Ecol. 89(3), 2014
PMID: 24784488
Insights into the genome of the xanthan-producing phytopathogen Xanthomonas arboricola pv. pruni 109 by comparative genomic hybridization.
Mayer L, Vendruscolo CT, Silva WP, Vorholter FJ, Becker A, Puhler A., J. Biotechnol. 155(1), 2011
PMID: 21539867
Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris.
Zhou L, Vorholter FJ, He YQ, Jiang BL, Tang JL, Xu Y, Puhler A, He YW., BMC Genomics 12(), 2011
PMID: 21745409
High-resolution transcriptional analysis of the regulatory influence of cell-to-cell signalling reveals novel genes that contribute to Xanthomonas phytopathogenesis.
An SQ, Febrer M, McCarthy Y, Tang DJ, Clissold L, Kaithakottil G, Swarbreck D, Tang JL, Rogers J, Dow JM, Ryan RP., Mol. Microbiol. 88(6), 2013
PMID: 23617851
ReadXplorer--visualization and analysis of mapped sequences.
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A., Bioinformatics 30(16), 2014
PMID: 24790157
From RNA-seq reads to differential expression results.
Oshlack A, Robinson MD, Young MD., Genome Biol. 11(12), 2010
PMID: 21176179
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data.
Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, Mason CE, Socci ND, Betel D., Genome Biol. 14(9), 2013
PMID: 24020486
Transcriptome profiling of Xanthomonas campestris pv. campestris grown in minimal medium MMX and rich medium NYG.
Liu W, Yu YH, Cao SY, Niu XN, Jiang W, Liu GF, Jiang BL, Tang DJ, Lu GT, He YQ, Tang JL., Res. Microbiol. 164(5), 2013
PMID: 23470514

Diffusible signals and interspecies communication in bacteria.
Ryan RP, Dow JM., Microbiology (Reading, Engl.) 154(Pt 7), 2008
PMID: 18599814
A bacterial cell-cell communication signal with cross-kingdom structural analogues.
Wang LH, He Y, Gao Y, Wu JE, Dong YH, He C, Wang SX, Weng LX, Xu JL, Tay L, Fang RX, Zhang LH., Mol. Microbiol. 51(3), 2004
PMID: 14731288
The cAMP receptor-like protein CLP is a novel c-di-GMP receptor linking cell-cell signaling to virulence gene expression in Xanthomonas campestris.
Chin KH, Lee YC, Tu ZL, Chen CH, Tseng YH, Yang JM, Ryan RP, McCarthy Y, Dow JM, Wang AH, Chou SH., J. Mol. Biol. 396(3), 2009
PMID: 20004667
The diffusible factor synthase XanB2 is a bifunctional chorismatase that links the shikimate pathway to ubiquinone and xanthomonadins biosynthetic pathways.
Zhou L, Wang JY, Wu J, Wang J, Poplawsky A, Lin S, Zhu B, Chang C, Zhou T, Zhang LH, He YW., Mol. Microbiol. 87(1), 2012
PMID: 23113660
Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions.
Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J, Stadler PF, Bonas U., Nucleic Acids Res. 40(5), 2011
PMID: 22080557
Identification of four novel small non-coding RNAs from Xanthomonas campestris pathovar campestris.
Jiang RP, Tang DJ, Chen XL, He YQ, Feng JX, Jiang BL, Lu GT, Lin M, Tang JL., BMC Genomics 11(), 2010
PMID: 20482898
ReadXplorer 2-detailed read mapping analysis and visualization from one single source.
Hilker R, Stadermann KB, Schwengers O, Anisiforov E, Jaenicke S, Weisshaar B, Zimmermann T, Goesmann A., Bioinformatics 32(24), 2016
PMID: 27540267
Rapid identification of proteins by peptide-mass fingerprinting.
Pappin DJ, Hojrup P, Bleasby AJ., Curr. Biol. 3(6), 1993
PMID: 15335725
Comprehensive analysis of the extracellular proteins from Xanthomonas campestris pv. campestris B100.
Watt SA, Wilke A, Patschkowski T, Niehaus K., Proteomics 5(1), 2005
PMID: 15619296
Qualitative and comparative proteomic analysis of Xanthomonas campestris pv. campestris 17.
Chung WJ, Shu HY, Lu CY, Wu CY, Tseng YH, Tsai SF, Lin CH., Proteomics 7(12), 2007
PMID: 17566974
Xylem sap proteomics.
de Bernonville TD, Albenne C, Arlat M, Hoffmann L, Lauber E, Jamet E., Methods Mol. Biol. 1072(), 2014
PMID: 24136537
Bioinformatics support for high-throughput proteomics.
Wilke A, Ruckert C, Bartels D, Dondrup M, Goesmann A, Huser AT, Kespohl S, Linke B, Mahne M, McHardy A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651857
Comparative proteomics reveal new HrpX-regulated proteins of Xanthomonas oryzae pv. oryzae.
Robin GP, Ortiz E, Szurek B, Brizard JP, Koebnik R., J Proteomics 97(), 2013
PMID: 23603630
Secretome analysis of the rice bacterium Xanthomonas oryzae (Xoo) using in vitro and in planta systems.
Wang Y, Kim SG, Wu J, Huh HH, Lee SJ, Rakwal R, Agrawal GK, Park ZY, Young Kang K, Kim ST., Proteomics 13(12-13), 2013
PMID: 23512849
Insights into xanthomonas axonopodis pv. citri biofilm through proteomics.
Zimaro T, Thomas L, Marondedze C, Garavaglia BS, Gehring C, Ottado J, Gottig N., BMC Microbiol. 13(), 2013
PMID: 23924281
Regulation and control of metabolic fluxes in microbes.
Gerosa L, Sauer U., Curr. Opin. Biotechnol. 22(4), 2011
PMID: 21600757
Dynamic protein phosphorylation during the growth of Xanthomonas campestris pv. campestris B100 revealed by a gel-based proteomics approach.
Musa YR, Basell K, Schatschneider S, Vorholter FJ, Becher D, Niehaus K., J. Biotechnol. 167(2), 2013
PMID: 23792782
Posttranslational regulation of microbial metabolism.
Kochanowski K, Sauer U, Noor E., Curr. Opin. Microbiol. 27(), 2015
PMID: 26048423
Current trends in quantitative proteomics.
Elliott MH, Smith DS, Parker CE, Borchers C., J Mass Spectrom 44(12), 2009
PMID: 19957301
Quantitative proteomics by metabolic labeling of model organisms.
Gouw JW, Krijgsveld J, Heck AJ., Mol. Cell Proteomics 9(1), 2009
PMID: 19955089
Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments.
Albaum SP, Neuweger H, Franzel B, Lange S, Mertens D, Trotschel C, Wolters D, Kalinowski J, Nattkemper TW, Goesmann A., Bioinformatics 25(23), 2009
PMID: 19808875
Mass spectrometry-based metabolomics.
Dettmer K, Aronov PA, Hammock BD., Mass Spectrom Rev 26(1), 2007
PMID: 16921475
Mass spectrometry in metabolome analysis.
Villas-Boas SG, Mas S, Akesson M, Smedsgaard J, Nielsen J., Mass Spectrom Rev 24(5), 2005
PMID: 15389842
Metabolomics for functional genomics, systems biology, and biotechnology.
Saito K, Matsuda F., Annu Rev Plant Biol 61(), 2010
PMID: 19152489
Novel biological insights through metabolomics and 13C-flux analysis.
Zamboni N, Sauer U., Curr. Opin. Microbiol. 12(5), 2009
PMID: 19744879

MeltDB 2.0-advances of the metabolomics software system.
Kessler N, Neuweger H, Bonte A, Langenkamper G, Niehaus K, Nattkemper TW, Goesmann A., Bioinformatics 29(19), 2013
PMID: 23918246
MeltDB: a software platform for the analysis and integration of metabolomics experiment data.
Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A., Bioinformatics 24(23), 2008
PMID: 18765459
Metabolic flux pattern of glucose utilization by Xanthomonas campestris pv. campestris: prevalent role of the Entner-Doudoroff pathway and minor fluxes through the pentose phosphate pathway and glycolysis.
Schatschneider S, Huber C, Neuweger H, Watt TF, Puhler A, Eisenreich W, Wittmann C, Niehaus K, Vorholter FJ., Mol Biosyst 10(10), 2014
PMID: 25072918
KEGG: Kyoto Encyclopedia of Genes and Genomes.
Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M., Nucleic Acids Res. 27(1), 1999
PMID: 9847135
Genome-scale models of bacterial metabolism: reconstruction and applications.
Durot M, Bourguignon PY, Schachter V., FEMS Microbiol. Rev. 33(1), 2008
PMID: 19067749
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 modeling in systems biology: algorithms and resources.
Najafi A, Bidkhori G, Bozorgmehr JH, Koch I, Masoudi-Nejad A., Curr. Genomics 15(2), 2014
PMID: 24822031
The nature of systems biology.
Bruggeman FJ, Westerhoff HV., Trends Microbiol. 15(1), 2006
PMID: 17113776
Software platforms to facilitate reconstructing genome-scale metabolic networks.
Hamilton JJ, Reed JL., Environ. Microbiol. 16(1), 2013
PMID: 24148076
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
Keseler IM, Mackie A, Santos-Zavaleta A, Billington R, Bonavides-Martinez C, Caspi R, Fulcher C, Gama-Castro S, Kothari A, Krummenacker M, Latendresse M, Muniz-Rascado L, Ong Q, Paley S, Peralta-Gil M, Subhraveti P, Velazquez-Ramirez DA, Weaver D, Collado-Vides J, Paulsen I, Karp PD., Nucleic Acids Res. 45(D1), 2016
PMID: 27899573
AraCyc: a biochemical pathway database for Arabidopsis.
Mueller LA, Zhang P, Rhee SY., Plant Physiol. 132(2), 2003
PMID: 12805578
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
The Pathway Tools software.
Karp PD, Paley S, Romero P., Bioinformatics 18 Suppl 1(), 2002
PMID: 12169551
The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks.
Swainston N, Smallbone K, Mendes P, Kell D, Paton N., J Integr Bioinform 8(2), 2011
PMID: 22095399
High-throughput generation, optimization and analysis of genome-scale metabolic models.
Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL., Nat. Biotechnol. 28(9), 2010
PMID: 20802497
The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum.
Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J., PLoS Comput. Biol. 9(3), 2013
PMID: 23555215
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
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
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T., Genome Res. 13(11), 2003
PMID: 14597658
BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.
Barthelmes J, Ebeling C, Chang A, Schomburg I, Schomburg D., Nucleic Acids Res. 35(Database issue), 2007
PMID: 17202167
Toward the automated generation of genome-scale metabolic networks in the SEED.
DeJongh M, Formsma K, Boillot P, Gould J, Rycenga M, Best A., BMC Bioinformatics 8(), 2007
PMID: 17462086
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24293654
Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A., Methods Mol. Biol. 406(), 2007
PMID: 18287689
Comparative glucose catabolism of Xanthomonas species.
Zagallo AC, Wang CH., J. Bacteriol. 93(3), 1967
PMID: 6025434
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
Classic and contemporary approaches to modeling biochemical reactions.
Chen WW, Niepel M, Sorger PK., Genes Dev. 24(17), 2010
PMID: 20810646
Kinetic modeling of biological systems.
Resat H, Petzold L, Pettigrew MF., Methods Mol. Biol. 541(), 2009
PMID: 19381542
Modeling a bacterium’s life: a petri-net library in modelica
Proß, 2009
Stoichiometric and constraint-based modelling
Klamt, 2006
Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol.
Yim H, Haselbeck R, Niu W, Pujol-Baxley C, Burgard A, Boldt J, Khandurina J, Trawick JD, Osterhout RE, Stephen R, Estadilla J, Teisan S, Schreyer HB, Andrae S, Yang TH, Lee SY, Burk MJ, Van Dien S., Nat. Chem. Biol. 7(7), 2011
PMID: 21602812
Identification of potential drug targets in Salmonella enterica sv. Typhimurium using metabolic modelling and experimental validation.
Hartman HB, Fell DA, Rossell S, Jensen PR, Woodward MJ, Thorndahl L, Jelsbak L, Olsen JE, Raghunathan A, Daefler S, Poolman MG., Microbiology (Reading, Engl.) 160(Pt 6), 2014
PMID: 24777662
Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery.
Kim HU, Kim SY, Jeong H, Kim TY, Kim JJ, Choy HE, Yi KY, Rhee JH, Lee SY., Mol. Syst. Biol. 7(), 2011
PMID: 21245845
Blueprint for antimicrobial hit discovery targeting metabolic networks.
Shen Y, Liu J, Estiu G, Isin B, Ahn YY, Lee DS, Barabasi AL, Kapatral V, Wiest O, Oltvai ZN., Proc. Natl. Acad. Sci. U.S.A. 107(3), 2010
PMID: 20080587
Polysaccharides, microbial
Morris, 2009
13C metabolic flux analysis.
Wiechert W., Metab. Eng. 3(3), 2001
PMID: 11461141
The benefits of being transient: isotope-based metabolic flux analysis at the short time scale.
Noh K, Wiechert W., Appl. Microbiol. Biotechnol. 91(5), 2011
PMID: 21732247
Metabolic networks in motion: 13C-based flux analysis.
Sauer U., Mol. Syst. Biol. 2(), 2006
PMID: 17102807
Advances in analysis of microbial metabolic fluxes via (13)C isotopic labeling.
Tang YJ, Martin HG, Myers S, Rodriguez S, Baidoo EE, Keasling JD., Mass Spectrom Rev 28(2), 2009
PMID: 19025966
Fluxome analysis using GC-MS.
Wittmann C., Microb. Cell Fact. 6(), 2007
PMID: 17286851
(13)C-based metabolic flux analysis.
Zamboni N, Fendt SM, Ruhl M, Sauer U., Nat Protoc 4(6), 2009
PMID: 19478804
OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis.
Quek LE, Wittmann C, Nielsen LK, Kromer JO., Microb. Cell Fact. 8(), 2009
PMID: 19409084
OpenMebius: an open source software for isotopically nonstationary 13C-based metabolic flux analysis.
Kajihata S, Furusawa C, Matsuda F, Shimizu H., Biomed Res Int 2014(), 2014
PMID: 25006579
13CFLUX2--high-performance software suite for (13)C-metabolic flux analysis.
Weitzel M, Noh K, Dalman T, Niedenfuhr S, Stute B, Wiechert W., Bioinformatics 29(1), 2012
PMID: 23110970
Characterization of the pyrophosphate-dependent 6-phosphofructokinase from Xanthomonas campestris pv. campestris.
Frese M, Schatschneider S, Voss J, Vorholter FJ, Niehaus K., Arch. Biochem. Biophys. 546(), 2014
PMID: 24508689
Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions.
Bordbar A, Lewis NE, Schellenberger J, Palsson BO, Jamshidi N., Mol. Syst. Biol. 6(), 2010
PMID: 20959820
13C-flux spectral analysis of host-pathogen metabolism reveals a mixed diet for intracellular Mycobacterium tuberculosis.
Beste DJ, Noh K, Niedenfuhr S, Mendum TA, Hawkins ND, Ward JL, Beale MH, Wiechert W, McFadden J., Chem. Biol. 20(8), 2013
PMID: 23911587
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.
Sigurdsson MI, Jamshidi N, Steingrimsson E, Thiele I, Palsson BO., BMC Syst Biol 4(), 2010
PMID: 20959003
Glycan foraging in vivo by an intestine-adapted bacterial symbiont.
Sonnenburg JL, Xu J, Leip DD, Chen CH, Westover BP, Weatherford J, Buhler JD, Gordon JI., Science 307(5717), 2005
PMID: 15790854
A community-driven global reconstruction of human metabolism.
Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bolling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novere N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BO., Nat. Biotechnol. 31(5), 2013
PMID: 23455439
Systems biology of host-microbe metabolomics.
Heinken A, Thiele I., Wiley Interdiscip Rev Syst Biol Med 7(4), 2015
PMID: 25929487
AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis.
de Oliveira Dal'Molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK., Plant Physiol. 152(2), 2009
PMID: 20044452
Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity.
Mintz-Oron S, Meir S, Malitsky S, Ruppin E, Aharoni A, Shlomi T., Proc. Natl. Acad. Sci. U.S.A. 109(1), 2011
PMID: 22184215
Recent advances in the reconstruction of metabolic models and integration of omics data.
Saha R, Chowdhury A, Maranas CD., Curr. Opin. Biotechnol. 29(), 2014
PMID: 24632194
Multiscale metabolic modeling: dynamic flux balance analysis on a whole-plant scale.
Grafahrend-Belau E, Junker A, Eschenroder A, Muller J, Schreiber F, Junker BH., Plant Physiol. 163(2), 2013
PMID: 23926077
Complete Genome Sequence of the Barley Pathogen Xanthomonas translucens pv. translucens DSM 18974T (ATCC 19319T).
Jaenicke S, Bunk B, Wibberg D, Sproer C, Hersemann L, Blom J, Winkler A, Schatschneider S, Albaum SP, Kolliker R, Goesmann A, Puhler A, Overmann J, Vorholter FJ., Genome Announc 4(6), 2016
PMID: 27908994
Genomic analysis of Xanthomonas translucens pathogenic on wheat and barley reveals cross-kingdom gene transfer events and diverse protein delivery systems.
Gardiner DM, Upadhyaya NM, Stiller J, Ellis JG, Dodds PN, Kazan K, Manners JM., PLoS ONE 9(1), 2014
PMID: 24416331
Construction of a genome-scale metabolic network of the plant pathogen Pectobacterium carotovorum provides new strategies for bactericide discovery.
Wang C, Deng ZL, Xie ZM, Chu XY, Chang JW, Kong DX, Li BJ, Zhang HY, Chen LL., FEBS Lett. 589(3), 2014
PMID: 25535697
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments.
Zhuang K, Izallalen M, Mouser P, Richter H, Risso C, Mahadevan R, Lovley DR., ISME J 5(2), 2010
PMID: 20668487
Xanthomonas campestris pv. vesicatoria Secretes Proteases and Xylanases via the Xps Type II Secretion System and Outer Membrane Vesicles.
Sole M, Scheibner F, Hoffmeister AK, Hartmann N, Hause G, Rother A, Jordan M, Lautier M, Arlat M, Buttner D., J. Bacteriol. 197(17), 2015
PMID: 26124239
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
Extracellular ATP acts as a damage-associated molecular pattern (DAMP) signal in plants.
Tanaka K, Choi J, Cao Y, Stacey G., Front Plant Sci 5(), 2014
PMID: 25232361

Regulation and secretion of Xanthomonas virulence factors.
Buttner D, Bonas U., FEMS Microbiol. Rev. 34(2), 2009
PMID: 19925633
News from the frontline: recent insights into PAMP-triggered immunity in plants.
Schwessinger B, Zipfel C., Curr. Opin. Plant Biol. 11(4), 2008
PMID: 18602859
TAL effectors--pathogen strategies and plant resistance engineering.
Boch J, Bonas U, Lahaye T., New Phytol. 204(4), 2014
PMID: 25539004
TAL Effectors Drive Transcription Bidirectionally in Plants.
Wang L, Rinaldi FC, Singh P, Doyle EL, Dubrow ZE, Tran TT, Perez-Quintero AL, Szurek B, Bogdanove AJ., Mol Plant 10(2), 2016
PMID: 27965000

Microbial life in the phyllosphere.
Vorholt JA., Nat. Rev. Microbiol. 10(12), 2012
PMID: 23154261
Characterization of bacteriophages Cp1 and Cp2, the strain-typing agents for Xanthomonas axonopodis pv. citri.
Ahmad AA, Ogawa M, Kawasaki T, Fujie M, Yamada T., Appl. Environ. Microbiol. 80(1), 2013
PMID: 24123743
CRISPR/Cas system and its role in phage-bacteria interactions.
Deveau H, Garneau JE, Moineau S., Annu. Rev. Microbiol. 64(), 2010
PMID: 20528693
Bacteria–phage interactions in natural environments
Díaz-Muñoz, 2014
Characterization of Xanthomonas phaseoli Bacteriophages.
Vidaver AK, Schuster ML., J. Virol. 4(3), 1969
PMID: 16789107
The DSF Family of Cell-Cell Signals: An Expanding Class of Bacterial Virulence Regulators.
Ryan RP, An SQ, Allan JH, McCarthy Y, Dow JM., PLoS Pathog. 11(7), 2015
PMID: 26181439
Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides.
Royer M, Koebnik R, Marguerettaz M, Barbe V, Robin GP, Brin C, Carrere S, Gomez C, Hugelland M, Voller GH, Noell J, Pieretti I, Rausch S, Verdier V, Poussier S, Rott P, Sussmuth RD, Cociancich S., BMC Genomics 14(), 2013
PMID: 24069909
Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology.
Goesmann A, Linke B, Rupp O, Krause L, Bartels D, Dondrup M, McHardy AC, Wilke A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651858
The Sequence Analysis and Management System -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies.
Bekel T, Henckel K, Kuster H, Meyer F, Mittard Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Puhler A, Stoye J, Goesmann A., J. Biotechnol. 140(1-2), 2009
PMID: 19297685
Structural and functional analysis of cellular networks with CellNetAnalyzer.
Klamt S, Saez-Rodriguez J, Gilles ED., BMC Syst Biol 1(), 2007
PMID: 17408509
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
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.
Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R., Brief. Bioinformatics 17(5), 2015
PMID: 26454094
Comparative RNA-seq analysis of early-infected peach leaves by the invasive phytopathogen Xanthomonas arboricola pv. pruni.
Socquet-Juglard D, Kamber T, Pothier JF, Christen D, Gessler C, Duffy B, Patocchi A., PLoS ONE 8(1), 2013
PMID: 23342103
Overlap between signaling pathways responsive to Xanthomonas oryzae pv. oryzae infection and drought stress in rice introgression line revealed by RNA-seq
Zhang, J Plant Growth Regul 14(), 2015
Xanthomonas axonopodis virulence is promoted by a transcription activator-like effector-mediated induction of a SWEET sugar transporter in cassava.
Cohn M, Bart RS, Shybut M, Dahlbeck D, Gomez M, Morbitzer R, Hou BH, Frommer WB, Lahaye T, Staskawicz BJ., Mol. Plant Microbe Interact. 27(11), 2014
PMID: 25083909
The PAS domain-containing histidine kinase RpfS is a second sensor for the diffusible signal factor of Xanthomonas campestris.
An SQ, Allan JH, McCarthy Y, Febrer M, Dow JM, Ryan RP., Mol. Microbiol. 92(3), 2014
PMID: 24617591
RNAseq analysis of cassava reveals similar plant responses upon infection with pathogenic and non-pathogenic strains of Xanthomonas axonopodis pv. manihotis.
Munoz-Bodnar A, Perez-Quintero AL, Gomez-Cano F, Gil J, Michelmore R, Bernal A, Szurek B, Lopez C., Plant Cell Rep. 33(11), 2014
PMID: 25120000
Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range.
Jalan N, Kumar D, Andrade MO, Yu F, Jones JB, Graham JH, White FF, Setubal JC, Wang N., BMC Genomics 14(), 2013
PMID: 23941402
A potential disease susceptibility gene CsLOB of citrus is targeted by a major virulence effector PthA of Xanthomonas citri subsp. citri.
Li Z, Zou L, Ye G, Xiong L, Ji Z, Zakria M, Hong N, Wang G, Chen G., Mol Plant 7(5), 2014
PMID: 24398629
RNA-seq pinpoints a Xanthomonas TAL-effector activated resistance gene in a large-crop genome.
Strauss T, van Poecke RM, Strauss A, Romer P, Minsavage GV, Singh S, Wolf C, Strauss A, Kim S, Lee HA, Yeom SI, Parniske M, Stall RE, Jones JB, Choi D, Prins M, Lahaye T., Proc. Natl. Acad. Sci. U.S.A. 109(47), 2012
PMID: 23132937
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
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
BRENDA, enzyme data and metabolic information.
Schomburg I, Chang A, Schomburg D., Nucleic Acids Res. 30(1), 2002
PMID: 11752250
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
TCDB: the Transporter Classification Database for membrane transport protein analyses and information.
Saier MH Jr, Tran CV, Barabote RD., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381841
Enzyme-specific profiles for genome annotation: PRIAM.
Claudel-Renard C, Chevalet C, Faraut T, Kahn D., Nucleic Acids Res. 31(22), 2003
PMID: 14602924
The ENZYME database in 2000.
Bairoch A., Nucleic Acids Res. 28(1), 2000
PMID: 10592255
EzCatDB: the Enzyme Catalytic-mechanism Database.
Nagano N., Nucleic Acids Res. 33(Database issue), 2005
PMID: 15608227
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics.
Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18838391
In vivo proteome analysis of Xanthomonas campestris pv. campestris in the interaction with the host plant Brassica oleracea.
Andrade AE, Silva LP, Pereira JL, Noronha EF, Reis FB Jr, Bloch C Jr, dos Santos MF, Domont GB, Franco OL, Mehta A., FEMS Microbiol. Lett. 281(2), 2008
PMID: 18318710
Proteome of the phytopathogen Xanthomonas citri subsp. citri: a global expression profile.
Soares MR, Facincani AP, Ferreira RM, Moreira LM, de Oliveira JC, Ferro JA, Ferro MI, Meneghini R, Gozzo FC., Proteome Sci 8(), 2010
PMID: 21062441
Comparative proteome analysis of Xanthomonas campestris pv. campestris in the interaction with the susceptible and the resistant cultivars of Brassica oleracea.
Villeth GR, Reis FB Jr, Tonietto A, Huergo L, de Souza EM, Pedrosa FO, Franco OL, Mehta A., FEMS Microbiol. Lett. 298(2), 2009
PMID: 19663914
A proteomic study of Xanthomonas oryzae pv. oryzae in rice xylem sap.
Gonzalez JF, Degrassi G, Devescovi G, De Vleesschauwer D, Hofte M, Myers MP, Venturi V., J Proteomics 75(18), 2012
PMID: 22835776
Data set from a comprehensive phosphoproteomic analysis of rice variety IRBB5 in response to bacterial blight.
Hou Y, Tong X, Wang Y, Qiu J, Li Z, Zhang W, Huang S, Zhang J., Data Brief 6(), 2015
PMID: 26862573
A comprehensive quantitative phosphoproteome analysis of rice in response to bacterial blight.
Hou Y, Qiu J, Tong X, Wei X, Nallamilli BR, Wu W, Huang S, Zhang J., BMC Plant Biol. 15(), 2015
PMID: 26112675
Identification of proteins in susceptible and resistant Brassica oleracea responsive to Xanthomonas campestris pv. campestris infection.
Villeth GRC, Carmo LST, Silva LP, Santos MF, de Oliveira Neto OB, Grossi-de-Sa MF, Ribeiro IS, Dessaune SN, Fragoso RR, Franco OL, Mehta A., J Proteomics 143(), 2016
PMID: 26825537
Phosphate regulated proteins of Xanthomonas citri subsp. citri: a proteomic approach.
Pegos VR, Nascimento JF, Sobreira TJ, Pauletti BA, Paes-Leme A, Balan A., J Proteomics 108(), 2014
PMID: 24846853
Comparative proteomic analysis reveals that T3SS, Tfp, and xanthan gum are key factors in initial stages of Citrus sinensis infection by Xanthomonas citri subsp. citri.
Facincani AP, Moreira LM, Soares MR, Ferreira CB, Ferreira RM, Ferro MI, Ferro JA, Gozzo FC, de Oliveira JC., Funct. Integr. Genomics 14(1), 2013
PMID: 24676796
The periplasmic PDZ domain-containing protein Prc modulates full virulence, envelops stress responses, and directly interacts with dipeptidyl peptidase of Xanthomonas oryzae pv. oryzae.
Deng CY, Deng AH, Sun ST, Wang L, Wu J, Wu Y, Chen XY, Fang RX, Wen TY, Qian W., Mol. Plant Microbe Interact. 27(2), 2014
PMID: 24200074
Proteomics analysis of the regulatory role of Rpf/DSF cell-to-cell signaling system in the virulence of Xanthomonas campestris.
O'Connell A, An SQ, McCarthy Y, Schulte F, Niehaus K, He YQ, Tang JL, Ryan RP, Dow JM., Mol. Plant Microbe Interact. 26(10), 2013
PMID: 23819805
Proteome analysis of the plant-pathogenic bacterium Xanthomonas oryzae pv. oryzae.
Xu S, Luo J, Pan X, Liang X, Wu J, Zheng W, Chen C, Hou Y, Ma H, Zhou M., Biochim. Biophys. Acta 1834(8), 2013
PMID: 23748134
Identification and functional characterization of small non-coding RNAs in Xanthomonas oryzae pathovar oryzae.
Liang H, Zhao YT, Zhang JQ, Wang XJ, Fang RX, Jia YT., BMC Genomics 12(), 2011
PMID: 21276262
Proteomic analysis of the regulatory function of DSF-dependent quorum sensing in Xanthomonas oryzae pv. oryzicola.
Zhao Y, Qian G, Yin F, Fan J, Zhai Z, Liu C, Hu B, Liu F., Microb. Pathog. 50(1), 2010
PMID: 20946946
A plant natriuretic peptide-like molecule of the pathogen Xanthomonas axonopodis pv. citri causes rapid changes in the proteome of its citrus host.
Garavaglia BS, Thomas L, Zimaro T, Gottig N, Daurelio LD, Ndimba B, Orellano EG, Ottado J, Gehring C., BMC Plant Biol. 10(), 2010
PMID: 20302677
Proteomic analysis of bacterial-blight defense-responsive proteins in rice leaf blades.
Mahmood T, Jan A, Kakishima M, Komatsu S., Proteomics 6(22), 2006
PMID: 17051650

High-throughput screening of structural proteomics targets using NMR.
Galvao-Botton LM, Katsuyama AM, Guzzo CR, Almeida FC, Farah CS, Valente AP., FEBS Lett. 552(2-3), 2003
PMID: 14527688
Unravelling potential virulence factor candidates in Xanthomonas citri. subsp. citri by secretome analysis.
Ferreira RM, Moreira LM, Ferro JA, Soares MRR, Laia ML, Varani AM, de Oliveira JCF, Ferro MIT., PeerJ 4(), 2016
PMID: 26925342
Differential proteome and secretome analysis during rice-pathogen interaction.
Wang Y, Kim SG, Wu J, Kim ST, Kang KY., Methods Mol. Biol. 1072(), 2014
PMID: 24136547
Metabolomic and transcriptomic analysis of the rice response to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae.
Sana TR, Fischer S, Wohlgemuth G, Katrekar A, Jung KH, Ronald PC, Fiehn O., Metabolomics 6(3), 2010
PMID: 20676379
Metabolomic profiling of bacterial leaf blight in rice
Fisher, Appl Note (), 2007

The Pathogen-Host Interactions database (PHI-base): additions and future developments.
Urban M, Pant R, Raghunath A, Irvine AG, Pedro H, Hammond-Kosack KE., Nucleic Acids Res. 43(Database issue), 2014
PMID: 25414340
PHISTO: pathogen-host interaction search tool.
Durmus Tekir S, Cakır T, Ardic E, Sayılırbas AS, Konuk G, Konuk M, Sarıyer H, Ugurlu A, Karadeniz I, Ozgur A, Sevilgen FE, Ulgen KO., Bioinformatics 29(10), 2013
PMID: 23515528
PHIDIAS: a pathogen-host interaction data integration and analysis system.
Xiang Z, Tian Y, He Y., Genome Biol. 8(7), 2007
PMID: 17663773
Integration and visualization of host-pathogen data related to infectious diseases.
Driscoll T, Gabbard JL, Mao C, Dalay O, Shukla M, Freifeld CC, Hoen AG, Brownstein JS, Sobral BW., Bioinformatics 27(16), 2011
PMID: 21712250
PATRIC, the bacterial bioinformatics database and analysis resource.
Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R, Machi D, Mao C, Nordberg EK, Olson R, Overbeek R, Pusch GD, Shukla M, Schulman J, Stevens RL, Sullivan DE, Vonstein V, Warren A, Will R, Wilson MJ, Yoo HS, Zhang C, Zhang Y, Sobral BW., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24225323
PhytoPath: an integrative resource for plant pathogen genomics.
Pedro H, Maheswari U, Urban M, Irvine AG, Cuzick A, McDowall MD, Staines DM, Kulesha E, Hammond-Kosack KE, Kersey PJ., Nucleic Acids Res. 44(D1), 2015
PMID: 26476449
HPIDB--a unified resource for host-pathogen interactions.
Kumar R, Nanduri B., BMC Bioinformatics 11 Suppl 6(), 2010
PMID: 20946599
Database of host-pathogen and related species interactions, and their global distribution.
Wardeh M, Risley C, McIntyre MK, Setzkorn C, Baylis M., Sci Data 2(), 2015
PMID: 26401317

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