Overcoming metabolic stochasticity and population dynamics in microbial cell factories

acronym: CONTIbugs

RESULTS of CONTIbugs: Presentation can be found here.

Project coordinator
- Dr. Katja Bühler and Prof. Dr. Andreas Schmid - Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University - Germany
Project leaders
- Prof. Victor de Lorenzo - Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid - Spain
- Prof. Dr. Søren Molin - Infection Microbiology Group; Center for Systems Microbiology; Department of
Systems biology; Technical University of Denmark (DTU), Lyngby - Denmark
- Prof. Dr. Eytan Ruppin - School of Medicine & School of Computer Science; Tel-Aviv University (TAU) - Israel

The efficiency of industrial whole-cell production processes is most often afflicted by the formation of
subpopulations in a microbial culture during biotransformations and fermentations. A bioreactor
running in batch, fed-batch or continuous mode can be regarded as an artificial environment that is
permanently changing [CurrOpMicrobiol 2000, 3:248] and thus creating a diversity of functional
microhabitats which ultimately lead to the emergence of various pheno- and genotypes
[BiotechBioeng 2010, 105:705]. Phenotypic heterogeneity and variability represents a key -and
unwanted feature in the bacterial population that constitutes the biological catalyst. This project will
investigate the phenomena of metabolic stochasticity and population dynamics in microbial cell
factories using Pseudomonas sp. growing in suspended culture, as well as attached to surfaces as
catalytic biofilms. Biofilms are resilient to a wide variety of environmental stresses. This inherited
robustness make biofilms desirable as potent biocatalysts, especially regarding reactions involving
biological difficult substrates and/or products [TrendsBiotechnol 2009, 27:636].
This project addresses the phenomenon of catalytic heterogeneity of genetically identical bacterial
cells using a controllable system composed of non-pathogenic Pseudomonas strains as host of
reference. The biosynthesis of the short chain alcohol isobutanol will be employed as a model
reaction system. On the technical side, cultivation systems and molecular tools will be developed for
analyzing catalytic heterogeneity in bacterial cultures under process conditions (i). Following
identification of process relevant subpopulations (ii), the responsible signals and molecular
mechanisms controlling the formation of the respective mutations will be identified (iii) and strategies
to guide phenotypic and genotypic heterogeneity throughout an entire population will be developed
(iv). The main outcome of this project is a collection of Pseudomonas strains (CONTIbugs) optimized
as cell factories for hosting and stably expressing heterologous genes and maintaining productive
catalytic activities in controlled populations for industrial biotechnology.