Data files

Experimental data set for the kinetic characterisation of G3PDH

Experimental data set for the kinetic characterisation of ALD

Experimental data set for the kinetic characterisation of ENO

Experimental data set for the kinetic characterisation of GAPDH

Experimental data set for the kinetic characterisation of LDH

Experimental data set for the kinetic characterisation of PGI

Experimental data set for the kinetic characterisation of HK

Experimental data set for the kinetic characterisation of PFK

Experimental data set for the kinetic characterisation of PGK

Experimental data set for the kinetic characterisation of TPI

Experimental data set for the kinetic characterisation of the glucose transport reaction

Experimental data set for the kinetic characterisation of PK

Experimental data for the phosphoglycerate mutase (EC 5.4.2.12) activity.

Timecourses of GLC (starting at 5 mM) and LAC, PYR, GLY in the closed system.

This files contains the parameter values, life-times, half-lives and errors associated with modeling the decay of the transcriptome, based on 3 models described in Deneke et al. "Complex degradation processes lead to non-exponential decay patters and age-dependent decay rates of messenger RNA". PLoS One. 2013;8(2):e55442

The file contains the normalized relative read counts (RPM) of 2 mRNA decay experiments. Columns in blue correspond to experiment 1, columns in violet correspond to experiment 2. The time points are in column headers. The last 3 columns contain parameters and half lives calculated from an exponantial fit of all data points. Normalization was done in 2 steps :first by calculating RPM i.e. reads per million of aligned reads to unique ORFs, second by normalizing this to the total amount of mRNA ...

WT 110901_SN865_B_L006_R1_GQC-28- ATCACG.fastq.gz 100 19.624.852 1,29

llumina fastq format 4 lines for each sequence: 1- Unique identifier, with the following format: @::::#/ 2- Sequence (A, T, C ,G or N (undetermined) only) 3- Orientation (always forward without mapping) 4- Quality value for each base, corresponding to a Phred-like score encoded in ASCII format, with an offset of of 33 (e.g. “J” gives a value of 41) and is in accordance with sanger FASTQ format. The sequence file is compressed ...

See wild type sample.

TbTryS activity was measured at 37°C in the in vivo-like buffer. All substrate stock solutions were prepared in the in vivo-like buffer and the pH was adjusted to 7.0. The assays were performed in a final volume of 2 ml and contained 0.2 mM NADH, 1 mM phosphoenolpyruvate, 4 units pyruvate kinase, 4 units L-lactate dehydrogenase, 0.17 µM TbTryS, 2.1 mM ATP and varying amounts of GSH, and Spd.

This data file shows results from the different chemostat experiments.Gene expression rates are presented.

Mutants with defects in glucose transport systems were analyzed in a bioreactor and the transcription of certain uptake systems analyzed. Transcription profiles between batch and chemostat conditions were compared

by-product formation rates and glucose uptake rates of mutants with linear electron transport chain at different aerobiosis levels

The ArcA phosphorylation state was determined for mutants with linear respiratory chain at defined aerobiosis levels.

Gene expression levels in mutants with linear ETC were determined by RealTime RT-PCR

RNA processing and degradation is initiated by endonucleolytic cleavage of the target RNAs. In many bacteria, this activity is performed by RNase E which is not present in Bacillus subtilis and other Gram-positive bacteria. Recently, the essential endoribonuclease RNase Y has been discovered in B. subtilis. This RNase is involved in the degradation of bulk mRNA suggesting a major role in mRNA metabolism. However, only a few targets of RNase Y have been identified so far. In order to assess the ...