In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome

Kromer, Jens Olaf, Sorgenfrei, Oliver, Klopprogge, Kai, Heinzle, Elmar and Wittman, Christoph (2004) In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome. Journal of Bacteriology, 186 6: 1769-1784. doi:10.1128/JB.186.6.1769-1784.2004

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Author Kromer, Jens Olaf
Sorgenfrei, Oliver
Klopprogge, Kai
Heinzle, Elmar
Wittman, Christoph
Title In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome
Formatted title
In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome
Journal name Journal of Bacteriology   Check publisher's open access policy
ISSN 0021-9193
1067-8832
1098-5530
Publication date 2004-03
Sub-type Article (original research)
DOI 10.1128/JB.186.6.1769-1784.2004
Open Access Status File (Publisher version)
Volume 186
Issue 6
Start page 1769
End page 1784
Total pages 16
Place of publication Washington, DC, United States
Publisher American Society for Microbiology
Language eng
Abstract An in-depth analysis of the intracellular metabolite concentrations, metabolic fluxes, and gene expression (metabolome, fluxome, and transcriptome, respectively) of lysine-producing Corynebacterium glutamicum ATCC 13287 was performed at different stages of batch culture and revealed distinct phases of growth and lysine production. For this purpose, 13C flux analysis with gas chromatography-mass spectrometry-labeling measurement of free intracellular amino acids, metabolite balancing, and isotopomer modeling were combined with expression profiling via DNA microarrays and with intracellular metabolite quantification. The phase shift from growth to lysine production was accompanied by a decrease in glucose uptake flux, the redirection of flux from the tricarboxylic acid (TCA) cycle towards anaplerotic carboxylation and lysine biosynthesis, transient dynamics of intracellular metabolite pools, such as an increase of lysine up to 40 mM prior to its excretion, and complex changes in the expression of genes for central metabolism. The integrated approach was valuable for the identification of correlations between gene expression and in vivo activity for numerous enzymes. The glucose uptake flux closely corresponded to the expression of glucose phosphotransferase genes. A correlation between flux and expression was also observed for glucose-6-phosphate dehydrogenase, transaldolase, and transketolase and for most TCA cycle genes. In contrast, cytoplasmic malate dehydrogenase expression increased despite a reduction of the TCA cycle flux, probably related to its contribution to NADH regeneration under conditions of reduced growth. Most genes for lysine biosynthesis showed a constant expression level, despite a marked change of the metabolic flux, indicating that they are strongly regulated at the metabolic level. Glyoxylate cycle genes were continuously expressed, but the pathway exhibited in vivo activity only in the later stage. The most pronounced changes in gene expression during cultivation were found for enzymes at entry points into glycolysis, the pentose phosphate pathway, the TCA cycle, and lysine biosynthesis, indicating that these might be of special importance for transcriptional control in C. glutamicum.
Keyword Amino acid
Glucokinase
Glucose 6 phosphate dehydrogenase
Glutamic acid
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
Australian Institute for Bioengineering and Nanotechnology Publications
 
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Created: Thu, 12 Feb 2009, 16:05:51 EST by Paul Rollo on behalf of Aust Institute for Bioengineering & Nanotechnology