5. Conclusions
The metabolite profiles of the B. subtilis cells are similarly independent on the carbon sources regardless of whether they suppress others or are suppressed by others. All the similar profiles were measured at the maximum growth rate, suggesting that B. subtilis has a predetermined metabolite profile optimized for the maximum growth rate. Differences in carbon sources induced local perturbations in the predetermined profile. One of such perturbations was the accumulation of the starting metabolites in the suppressed carbon sources. Combined analysis of the metabolite profile and DNA microarrays revealed that the first reaction in the catabolism was rate-limiting when B. subtilis was grown on suppressed carbon sources, although the enzyme genes of the reactions were upregulated. The present analysis suggests that the decrease or increase in the gene expression of an enzyme does not always result in the accumulation or decrease in its substrates or products, because of the multiplicity of metabolic pathway networks. Metabolome and transcriptome data that supplement each other provide much informatiion to study the global regulation of metabolism.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Yoshida K, Kobayashi K, Miwa Y, Kang CM, Matsunaga M, Yamaguchi H, Tojo S, Yamamoto M, Nishi R, Ogasawara N, Nakayama, T, Fujita Y (2001) Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis. Nucleic Acids Res 29:683–692
Zheng D, Constantinidou C, Hobman JL, Minchin SD (2004) Identification of the CRP regulon using in vitro and in vivo transcriptional profiling. Nucleic Acids Res 32:5874–5893
Kolb A, Busby S, Buc H, Garges, S, Adhya S (1993) Transcriptional regulation by cAMP and its receptor protein. Annu Rev Biochem 62:749–795
Saier M, Ramseier, T, Reizer J (1996) Regulation of carbon utilization. In: Neidhardt F, Curtiss R, Ingraham J, et al (eds) Escherichia coli and Salmonella: cellular and molecular biology, vol. 1. ASM Press, Washington, DC, pp 1325–1343
Fujita Y, Miwa Y, Galinier, A, Deutscher J (1995) Specific recognition of the Bacillus subtilis gnt cis-acting catabolite-responsive element by a protein complex formed between CcpA and seryl-phosphorylated HPr. Mol Microbiol 17:953–960
Soga T, Ueno Y, Naraoka H, Matsuda K, Tomita, M, Nishioka T (2002) Pressure-assisted capillary electrophoresis electrospray ionization mass spectrometry for analysis of multivalent anions. Anal Chem 74:6224–6229
Soga T, Ueno Y, Naraoka H, Ohashi Y, Tomita, M, Nishioka T (2002b) Smultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry. Anal Chem 74:2233–2239.
Fujita, Y, Freese E (1979) Purification and properties of fructose-1,6-bisphosphatase of Bacillus subtilis. J Biol Chem 254:5340–5349
Arita M (2003) In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. Genome Res 13:2455–2466.
Arita M (2004) The metabolic world of Escherichia coli is not small. Proc Natl Acad Sci USA 101:1543–1547
Deutscher J, Galinier, A, Martin-Verstraete I (2002) Carbohydrate uptake and metabolism. In: Sonenshein A, Hoch J, Losick R (eds) Bacillus subtilis and its closest relatives from genes to cells. ASM Press, Washington DC, pp 129–162
Doan T, Servant P, Tojo S, Yamaguchi H, Lerondel G, Yoshida K-I, Fujita, Y, Aymerich S (2003) The Bacillus subtilis ywkA gene encodes a malic enzyme and its transcription is activated by the YufL/YufM two-component system in response to malate. Microbiology 149:2331–2343
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Tokyo
About this chapter
Cite this chapter
Nishioka, T., Matsuda, K., Fujita, Y. (2005). Combined Analysis of Metabolome and Transcriptome: Catabolism in Bacillus subtilis. In: Tomita, M., Nishioka, T. (eds) Metabolomics. Springer, Tokyo. https://doi.org/10.1007/4-431-28055-3_9
Download citation
DOI: https://doi.org/10.1007/4-431-28055-3_9
Publisher Name: Springer, Tokyo
Print ISBN: 978-4-431-25121-7
Online ISBN: 978-4-431-28055-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)