Single-cell data reveal heterogeneity of investment in ribosomes across a bacterial population.

Ribosomes are responsible for the synthesis of proteins, the major component of cellular biomass. Classical experiments have established a linear relationship between the fraction of resources invested in ribosomal proteins and the rate of balanced growth of a microbial population. Very little is known, however, about how the investment in ribosomes varies over individual cells in a population.

Improving the genetic stability of bacterial growth control for long-term bioproduction.

Using microorganisms for bioproduction requires the reorientation of metabolic fluxes from biomass synthesis to the production of compounds of interest. We previously engineered a synthetic growth switch in Escherichia coli based on inducible expression of the β- and β'-subunits of RNA polymerase. Depending on the level of induction, the cells stop growing or grow at a rate close to that of the wild-type strain.

Green autofluorescence, a double edged monitoring tool for bacterial growth and activity in micro-plates.

The intrinsic green autofluorescence of an Escherichia coli culture has long been overlooked and empirically corrected in green fluorescent protein (GFP) reporter experiments. We show here, by using complementary methods of fluorescence analysis and HPLC, that this autofluorescence, principally arise from the secreted flavins in the external media. The cells secrete roughly 10 times more than what they keep inside.

Inference of quantitative models of bacterial promoters from time-series reporter gene data.

The inference of regulatory interactions and quantitative models of gene regulation from time-series transcriptomics data has been extensively studied and applied to a range of problems in drug discovery, cancer research, and biotechnology. The application of existing methods is commonly based on implicit assumptions on the biological processes under study. First, the measurements of mRNA abundance obtained in transcriptomics experiments are taken to be representative of protein concentrations.

A genome-wide screen for identifying all regulators of a target gene.

We have developed a new screening methodology for identifying all genes that control the expression of a target gene through genetic or metabolic interactions. The screen combines mutant libraries with luciferase reporter constructs, whose expression can be monitored in vivo and over time in different environmental conditions. We apply the method to identify the genes that control the expression of the gene acs, encoding the acetyl coenzyme A synthetase, in Escherichia coli.

Shared control of gene expression in bacteria by transcription factors and global physiology of the cell.

Gene expression is controlled by the joint effect of (i) the global physiological state of the cell, in particular the activity of the gene expression machinery, and (ii) DNA-binding transcription factors and other specific regulators. We present a model-based approach to distinguish between these two effects using time-resolved measurements of promoter activities. We demonstrate the strength of the approach by analyzing a circuit involved in the regulation of carbon metabolism in E.

Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria.

Background: Fluorescent and luminescent reporter genes have become popular tools for the real-time monitoring of gene expression in living cells. However, mathematical models are necessary for extracting biologically meaningful quantities from the primary data.

Results: We present a rigorous method for deriving relative protein synthesis rates (mRNA concentrations) and protein concentrations by means of kinetic models of gene expression.

WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data.

Motivation: Fluorescent and luminescent reporter gene systems in combination with automated microplate readers allow real-time monitoring of gene expression on the population level at high precision and sampling density. This generates large amounts of data for the analysis of which computer tools are missing to date.

Results: We have developed WellReader, a MATLAB program for the analysis of fluorescent and luminescent reporter gene data.