E-GEOD-18183 - Specific growth rate dependent transcriptome profiling of Escherichia coli K12 MG1655 in accelerostat cultures

Status
Submitted on 20 September 2009, released on 22 May 2010, last updated on 1 May 2014
Organism
Escherichia coli
Samples (8)
Array (1)
Protocols (9)
Description
Specific growth rate dependent gene expression changes of Escherichia coli K12 MG1655 were determined by microarray and real time PCR analyses. The bacteria were cultivated on glucose limited minimal medium using the accelerostat method (A-stat), where starting from steady state conditions in a chemostat culture, dilution rate is constantly increased. At specific growth rate (μ) 0.47 h-1, E. coli had focused its metabolism to glucose utilization by down-regulation of alternative substrate transporters expression compared to μ = 0.3 h-1. It was found that acetic acid accumulation began at μ = 0.34 ± 0.01 h-1 and two acetate synthesis pathways (phosphotransacetylase-acetate kinase (pta-ackA) and pyruvate oxidase (poxB)) contributed to the synthesis at the beginning of overflow metabolism, i.e. onset of acetate excretion. On the other hand, poxB, pta and ackA expression patterns suggest that pyruvate oxidase may be the only enzyme synthesizing acetate at μ = 0.47 h-1. Down-regulation of acs-yjcH-actP operon, the resulting loss of glucose and acetate co-utilization between specific growth rates 0.3 h-1 – 0.42 h-1 and acetic acid accumulation from μ = 0.34 ± 0.01 h-1 allows one to surmise that the acetate utilization operon expression might play an important role in overflow metabolism. DNA microarray analysis was performed from three A-stat cultivations, for which one has a technical replicate.
Experiment type
transcription profiling by array 
Contacts
Ranno Nahku <ranno@tftak.org>, Kaarel Adamberg, Kaspar Valgepea, Kristo Abner, Petri-Jaan Lahtvee, Raivo Vilu, Sten Erm
Citation
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-18183.idf.txt
Sample and data relationshipE-GEOD-18183.sdrf.txt
Raw data (1)E-GEOD-18183.raw.1.zip
Processed data (1)E-GEOD-18183.processed.1.zip
Array designA-GEOD-8067.adf.txt
R ExpressionSetE-GEOD-18183.eSet.r
Links