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 S, Bekel T, Dondrup M, Hüser AT, Winnebald J, Schneider J, Kalinowski J, Goesmann A (2009)
BMC Systems Biology 3(1): 82.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
Background: The rapid progress of post-genomic analyses, such as transcriptomics, proteomics, and metabolomics has resulted in the generation of large amounts of quantitative data covering and connecting the complete cascade from genotype to phenotype for individual organisms. Various benefits can be achieved when these ''Omics'' data are integrated, such as the identification of unknown gene functions or the elucidation of regulatory networks of whole organisms. In order to be able to obtain deeper insights in the generated datasets, it is of utmost importance to present the data to the researcher in an intuitive, integrated, and knowledge-based environment. Therefore, various visualization paradigms have been established during the last years. The visualization of ''Omics'' data using metabolic pathway maps is intuitive and has been applied in various software tools. It has become obvious that the application of web-based and user driven software tools has great potential and benefits from the use of open and standardized formats for the description of pathways. Results: In order to combine datasets from heterogeneous ''Omics'' sources, we present the web-based ProMeTra system that visualizes and combines datasets from transcriptomics, proteomics, and metabolomics on user defined metabolic pathway maps. Therefore, structured exchange of data with our ''Omics'' applications Emma 2, Qupe and MeltDB is employed. Enriched SVG images or animations are generated and can be obtained via the user friendly web interface. To demonstrate the functionality of ProMeTra, we use quantitative data obtained during a fermentation experiment of the L-lysine producing strain Corynebacterium glutamicum DM1730. During fermentation, oxygen supply was switched off in order to perturb the system and observe its reaction. At six different time points, transcript abundances, intracellular metabolite pools, as well as extracellular glucose, lactate, and L-lysine levels were determined. Conclusion: The interpretation and visualization of the results of this complex experiment was facilitated by the ProMeTra software. Both transcriptome and metabolome data were visualized on a metabolic pathway map. Visual inspection of the combined data confirmed existing knowledge but also delivered novel correlations that are of potential biotechnological importance.
Erscheinungsjahr
2009
Zeitschriftentitel
BMC Systems Biology
Band
3
Ausgabe
1
Art.-Nr.
82
ISSN
1752-0509
Page URI
https://pub.uni-bielefeld.de/record/1783813

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Neuweger H, Persicke M, Albaum S, et al. Visualizing post genomics data-sets on customized pathway maps by ProMeTra – aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. BMC Systems Biology. 2009;3(1): 82.
Neuweger, H., Persicke, M., Albaum, S., Bekel, T., Dondrup, M., Hüser, A. T., Winnebald, J., et al. (2009). Visualizing post genomics data-sets on customized pathway maps by ProMeTra – aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. BMC Systems Biology, 3(1), 82. https://doi.org/10.1186/1752-0509-3-82
Neuweger, Heiko, Persicke, Marcus, Albaum, Stefan, Bekel, Thomas, Dondrup, Michael, Hüser, Andrea T., Winnebald, Jörn, Schneider, Jessica, Kalinowski, Jörn, and Goesmann, Alexander. 2009. “Visualizing post genomics data-sets on customized pathway maps by ProMeTra – aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example”. BMC Systems Biology 3 (1): 82.
Neuweger, H., Persicke, M., Albaum, S., Bekel, T., Dondrup, M., Hüser, A. T., Winnebald, J., Schneider, J., Kalinowski, J., and Goesmann, A. (2009). Visualizing post genomics data-sets on customized pathway maps by ProMeTra – aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. BMC Systems Biology 3:82.
Neuweger, H., et al., 2009. Visualizing post genomics data-sets on customized pathway maps by ProMeTra – aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. BMC Systems Biology, 3(1): 82.
H. Neuweger, et al., “Visualizing post genomics data-sets on customized pathway maps by ProMeTra – aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example”, BMC Systems Biology, vol. 3, 2009, : 82.
Neuweger, H., Persicke, M., Albaum, S., Bekel, T., Dondrup, M., Hüser, A.T., Winnebald, J., Schneider, J., Kalinowski, J., Goesmann, A.: Visualizing post genomics data-sets on customized pathway maps by ProMeTra – aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. BMC Systems Biology. 3, : 82 (2009).
Neuweger, Heiko, Persicke, Marcus, Albaum, Stefan, Bekel, Thomas, Dondrup, Michael, Hüser, Andrea T., Winnebald, Jörn, Schneider, Jessica, Kalinowski, Jörn, and Goesmann, Alexander. “Visualizing post genomics data-sets on customized pathway maps by ProMeTra – aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example”. BMC Systems Biology 3.1 (2009): 82.
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33 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community.
Pinu FR, Beale DJ, Paten AM, Kouremenos K, Swarup S, Schirra HJ, Wishart D., Metabolites 9(4), 2019
PMID: 31003499
From correlation to causation: analysis of metabolomics data using systems biology approaches.
Rosato A, Tenori L, Cascante M, De Atauri Carulla PR, Martins Dos Santos VAP, Saccenti E., Metabolomics 14(4), 2018
PMID: 29503602
When Transcriptomics and Metabolomics Work Hand in Hand: A Case Study Characterizing Plant CDF Transcription Factors.
Pérez-Alonso MM, Carrasco-Loba V, Medina J, Vicente-Carbajosa J, Pollmann S., High Throughput 7(1), 2018
PMID: 29495643
Analysis of metabolomic data: tools, current strategies and future challenges for omics data integration.
Cambiaghi A, Ferrario M, Masseroli M., Brief Bioinform 18(3), 2017
PMID: 27075479
Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris.
Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ., Microbiology 163(8), 2017
PMID: 28795660
Integration of omics: more than the sum of its parts.
Buescher JM, Driggers EM., Cancer Metab 4(), 2016
PMID: 26900468
MarVis-Pathway: integrative and exploratory pathway analysis of non-targeted metabolomics data.
Kaever A, Landesfeind M, Feussner K, Mosblech A, Heilmann I, Morgenstern B, Feussner I, Meinicke P., Metabolomics 11(3), 2015
PMID: 25972773
Bioinformatics: the next frontier of metabolomics.
Johnson CH, Ivanisevic J, Benton HP, Siuzdak G., Anal Chem 87(1), 2015
PMID: 25389922
PathVisio 3: an extendable pathway analysis toolbox.
Kutmon M, van Iersel MP, Bohler A, Kelder T, Nunes N, Pico AR, Evelo CT., PLoS Comput Biol 11(2), 2015
PMID: 25706687
Defining bacterial regulons using ChIP-seq.
Myers KS, Park DM, Beauchene NA, Kiley PJ., Methods 86(), 2015
PMID: 26032817
Protein S-mycothiolation functions as redox-switch and thiol protection mechanism in Corynebacterium glutamicum under hypochlorite stress.
Chi BK, Busche T, Van Laer K, Bäsell K, Becher D, Clermont L, Seibold GM, Persicke M, Kalinowski J, Messens J, Antelmann H., Antioxid Redox Signal 20(4), 2014
PMID: 23886307
Adaptation of Bacillus subtilis carbon core metabolism to simultaneous nutrient limitation and osmotic challenge: a multi-omics perspective.
Kohlstedt M, Sappa PK, Meyer H, Maaß S, Zaprasis A, Hoffmann T, Becker J, Steil L, Hecker M, van Dijl JM, Lalk M, Mäder U, Stülke J, Bremer E, Völker U, Wittmann C., Environ Microbiol 16(6), 2014
PMID: 24571712
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, Pühler A, Eisenreich W, Wittmann C, Niehaus K, Vorhölter FJ., Mol Biosyst 10(10), 2014
PMID: 25072918
Tools for the functional interpretation of metabolomic experiments.
Chagoyen M, Pazos F., Brief Bioinform 14(6), 2013
PMID: 23063930
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, Pühler A, Niehaus K, Vorhölter FJ., J Biotechnol 167(2), 2013
PMID: 23395674
Computational tools for the secondary analysis of metabolomics experiments.
Booth SC, Weljie AM, Turner RJ., Comput Struct Biotechnol J 4(), 2013
PMID: 24688685
Identification of a gene involved in plasmid structural instability in Corynebacterium glutamicum.
Kitade Y, Okino S, Gunji W, Hiraga K, Suda M, Suzuki N, Inui M, Yukawa H., Appl Microbiol Biotechnol 97(18), 2013
PMID: 23703324
Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding.
Myers KS, Yan H, Ong IM, Chung D, Liang K, Tran F, Keleş S, Landick R, Kiley PJ., PLoS Genet 9(6), 2013
PMID: 23818864
MeltDB 2.0-advances of the metabolomics software system.
Kessler N, Neuweger H, Bonte A, Langenkämper G, Niehaus K, Nattkemper TW, Goesmann A., Bioinformatics 29(19), 2013
PMID: 23918246
The bacterial response regulator ArcA uses a diverse binding site architecture to regulate carbon oxidation globally.
Park DM, Akhtar MS, Ansari AZ, Landick R, Kiley PJ., PLoS Genet 9(10), 2013
PMID: 24146625
EasyLCMS: an asynchronous web application for the automated quantification of LC-MS data.
Fructuoso S, Sevilla A, Bernal C, Lozano AB, Iborra JL, Cánovas M., BMC Res Notes 5(), 2012
PMID: 22884039
Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data.
García-Alcalde F, García-López F, Dopazo J, Conesa A., Bioinformatics 27(1), 2011
PMID: 21098431
Diversity of metabolic shift in response to oxygen deprivation in Corynebacterium glutamicum and its close relatives.
Yamamoto S, Sakai M, Inui M, Yukawa H., Appl Microbiol Biotechnol 90(3), 2011
PMID: 21327408
Pathogenomics of Xanthomonas: understanding bacterium-plant interactions.
Ryan RP, Vorhölter FJ, Potnis N, Jones JB, Van Sluys MA, Bogdanove AJ, Dow JM., Nat Rev Microbiol 9(5), 2011
PMID: 21478901
Visualization of omics data for systems biology.
Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin AC., Nat Methods 7(3 suppl), 2010
PMID: 20195258
Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments.
Albaum SP, Neuweger H, Fränzel B, Lange S, Mertens D, Trötschel C, Wolters D, Kalinowski J, Nattkemper TW, Goesmann A., Bioinformatics 25(23), 2009
PMID: 19808875

57 References

Daten bereitgestellt von Europe PubMed Central.

Metabolomics in systems biology.
Weckwerth W., Annu Rev Plant Biol 54(), 2003
PMID: 14503007
Metabolite profiling: from diagnostics to systems biology.
Fernie AR, Trethewey RN, Krotzky AJ, Willmitzer L., Nat. Rev. Mol. Cell Biol. 5(9), 2004
PMID: 15340383
Metabolomics and systems biology: making sense of the soup.
Kell DB., Curr. Opin. Microbiol. 7(3), 2004
PMID: 15196499
Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism.
Broeckling CD, Huhman DV, Farag MA, Smith JT, May GD, Mendes P, Dixon RA, Sumner LW., J. Exp. Bot. 56(410), 2004
PMID: 15596476
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
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, Walk TC, Zhang P, Karp PD., Nucleic Acids Res. 36(Database issue), 2007
PMID: 17965431
VANTED: a system for advanced data analysis and visualization in the context of biological networks.
Junker BH, Klukas C, Schreiber F., BMC Bioinformatics 7(), 2006
PMID: 16519817
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
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.
Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M., Plant J. 37(6), 2004
PMID: 14996223
KaPPA-view: a web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps.
Tokimatsu T, Sakurai N, Suzuki H, Ohta H, Nishitani K, Koyama T, Umezawa T, Misawa N, Saito K, Shibata D., Plant Physiol. 138(3), 2005
PMID: 16010003
PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways.
Mlecnik B, Scheideler M, Hackl H, Hartler J, Sanchez-Cabo F, Trajanoski Z., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980551
The MetaCyc Database.
Karp PD, Riley M, Paley SM, Pellegrini-Toole A., Nucleic Acids Res. 30(1), 2002
PMID: 11752254
AraCyc: a biochemical pathway database for Arabidopsis.
Mueller LA, Zhang P, Rhee SY., Plant Physiol. 132(2), 2003
PMID: 12805578
The Pathway Tools cellular overview diagram and Omics Viewer.
Paley SM, Karp PD., Nucleic Acids Res. 34(13), 2006
PMID: 16893960
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
CellDesigner: a process diagram editor for gene-regulatory and biochemical networks
Funahashi A, Morohashi M, Kitano H, Tanimura N., 2003
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
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.
Al-Shahrour F, Carbonell J, Minguez P, Goetz S, Conesa A, Tarraga J, Medina I, Alloza E, Montaner D, Dopazo J., Nucleic Acids Res. 36(Web Server issue), 2008
PMID: 18515841
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Huang da W, Sherman BT, Lempicki RA., Nat Protoc 4(1), 2009
PMID: 19131956
Industrial production of amino acids by coryneform bacteria.
Hermann T., J. Biotechnol. 104(1-3), 2003
PMID: 12948636
Biotechnological production of amino acids and derivatives: current status and prospects.
Leuchtenberger W, Huthmacher K, Drauz K., Appl. Microbiol. Biotechnol. 69(1), 2005
PMID: 16195792
Process for producing -lysine
Nakayama K, Araki K., 1973
Genetic and biochemical analysis of the aspartokinase from Corynebacterium glutamicum.
Kalinowski J, Cremer J, Bachmann B, Eggeling L, Sahm H, Puhler A., Mol. Microbiol. 5(5), 1991
PMID: 1956296
The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.
Kalinowski J, Bathe B, Bartels D, Bischoff N, Bott M, Burkovski A, Dusch N, Eggeling L, Eikmanns BJ, Gaigalat L, Goesmann A, Hartmann M, Huthmacher K, Kramer R, Linke B, McHardy AC, Meyer F, Mockel B, Pfefferle W, Puhler A, Rey DA, Ruckert C, Rupp O, Sahm H, Wendisch VF, Wiegrabe I, Tauch A., J. Biotechnol. 104(1-3), 2003
PMID: 12948626
A novel methodology employing Corynebacterium glutamicum genome information to generate a new L-lysine-producing mutant.
Ohnishi J, Mitsuhashi S, Hayashi M, Ando S, Yokoi H, Ochiai K, Ikeda M., Appl. Microbiol. Biotechnol. 58(2), 2002
PMID: 11876415
Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source.
Huser AT, Becker A, Brune I, Dondrup M, Kalinowski J, Plassmeier J, Puhler A, Wiegrabe I, Tauch A., J. Biotechnol. 106(2-3), 2003
PMID: 14651867
Emerging Corynebacterium glutamicum systems biology.
Wendisch VF, Bott M, Kalinowski J, Oldiges M, Wiechert W., J. Biotechnol. 124(1), 2006
PMID: 16406159
Proteomics of Corynebacterium glutamicum: essential industrial bacterium.
Burkovski A., Methods Biochem Anal 49(), 2006
PMID: 16929678
Utilization of soluble starch by a recombinant Corynebacterium glutamicum strain: growth and lysine production.
Seibold G, Auchter M, Berens S, Kalinowski J, Eikmanns BJ., J. Biotechnol. 124(2), 2006
PMID: 16488498

Gamma E, Helm R, Johnson R, Vlissides J., 1995
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
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
CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data.
Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Huser AT, Kalinowski J, Oehm S, Puhler A, Rahmann S, Weile J, Goesmann A., BMC Syst Biol 1(), 2007
PMID: 18034885
BRIGEP--the BRIDGE-based genome-transcriptome-proteome browser.
Goesmann A, Linke B, Bartels D, Dondrup M, Krause L, Neuweger H, Oehm S, Paczian T, Wilke A, Meyer F., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980569
GenBank.
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL., Nucleic Acids Res. 36(Database issue), 2007
PMID: 18073190
Metabolic analysis of Corynebacterium glutamicum during lactate and succinate productions under oxygen deprivation conditions.
Inui M, Murakami S, Okino S, Kawaguchi H, Vertes AA, Yukawa H., J. Mol. Microbiol. Biotechnol. 7(4), 2004
PMID: 15383716
Anaerobic growth and potential for amino acid production by nitrate respiration in Corynebacterium glutamicum.
Takeno S, Ohnishi J, Komatsu T, Masaki T, Sen K, Ikeda M., Appl. Microbiol. Biotechnol. 75(5), 2007
PMID: 17380327
The respiratory chain of Corynebacterium glutamicum.
Bott M, Niebisch A., J. Biotechnol. 104(1-3), 2003
PMID: 12948635
Anaerobic growth of Corynebacterium glutamicum using nitrate as a terminal electron acceptor.
Nishimura T, Vertes AA, Shinoda Y, Inui M, Yukawa H., Appl. Microbiol. Biotechnol. 75(4), 2007
PMID: 17347820
ArnR, a novel transcriptional regulator, represses expression of the narKGHJI operon in Corynebacterium glutamicum.
Nishimura T, Teramoto H, Vertes AA, Inui M, Yukawa H., J. Bacteriol. 190(9), 2008
PMID: 18296524
Transcriptional analysis of the F0F1 ATPase operon of Corynebacterium glutamicum ATCC 13032 reveals strong induction by alkaline pH.
Barriuso-Iglesias M, Barreiro C, Flechoso F, Martin JF., Microbiology (Reading, Engl.) 152(Pt 1), 2006
PMID: 16385111
Transcriptional profiling of Corynebacterium glutamicum metabolism during organic acid production under oxygen deprivation conditions.
Inui M, Suda M, Okino S, Nonaka H, Puskas LG, Vertes AA, Yukawa H., Microbiology (Reading, Engl.) 153(Pt 8), 2007
PMID: 17660414
Production of D-lactic acid by Corynebacterium glutamicum under oxygen deprivation.
Okino S, Suda M, Fujikura K, Inui M, Yukawa H., Appl. Microbiol. Biotechnol. 78(3), 2008
PMID: 18188553
Characterization of a Corynebacterium glutamicum lactate utilization operon induced during temperature-triggered glutamate production.
Stansen C, Uy D, Delaunay S, Eggeling L, Goergen JL, Wendisch VF., Appl. Environ. Microbiol. 71(10), 2005
PMID: 16204505
Expression control and specificity of the basic amino acid exporter LysE of Corynebacterium glutamicum.
Bellmann A, Vrljic M, Patek M, Sahm H, Kramer R, Eggeling L., Microbiology (Reading, Engl.) 147(Pt 7), 2001
PMID: 11429454
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