In the old days of industrial fermentation, microbes produced lactic acid, beer, wine, cheese, and other desired products, yet no one knew exactly how the cells functioned.
Now the tools of systems biology are helping to understand, at all levels, what happens inside microbial cells.
“Today, one needs to have a thorough understanding of the cell as a whole. Systems biology provides a quantitative description of the cell and is an important source of new findings to optimize production systems,” according to Ralf Takors, Ph.D., director of the centre of bioprocess engineering at the University of Stuttgart, Germany.
Takors was one of several presenters at “BioSpain”, a conference organized by ASEBIO (Spanish Association of Biotechnology Companies) and held in Bilbao, Spain.
Dr. Takors uses Pseudomonas putida as a model system to illustrate possible applications of systems biology. P. putida has multiple properties that make it ideal for industrial applications. It degrades many types of substrates, its genome is sequenced, and the microbe has a high stress tolerance. These features make it a good model for systems biology studies that provide a holistic picture of metabolic and regulatory interactions.
“If we can understand the basic characteristics and properties of P. putida, we can transfer them to other microbes to improve industrial biotechnological processes,” said Dr. Takors.
In one set of experiments, Dr. Takors focused on butanol as the sole carbon source, which P. putida completely consumes. The energy charge generated was measured in relation to increasing butanol concentrations. Under steady-state conditions, the energy charge stayed at a constant level of 0.85. But when glucose was added, the energy charge fell to 0.4 and coincided with the highest fraction of butanol consumed.
A transcriptome analysis showed that as butanol concentration rose, 40 genes were overexpressed, including ones coding for ADH degradation, ABC efflux exporters, the AgmR cluster, and the tricarboxylic acid cycle (TCA). “These genes indicate a bacterial regulation scenario not expected so far,” said Dr. Takors.
Additionally, a metabolic flux analysis showed that in the presence of both glucose and butanol, their metabolism was decoupled. The TCA cycle totally consumed butanol, whereas glucose solely fueled glycolysis. “By understanding these events we can change systems to include only cells that are high producers of desired end products,” noted Dr. Takors.
Additionally, flow cytometry showed that over time the fraction of cells with single DNA content decreased as did the growth rate. At the same time, the fraction of cells with twice the DNA content and others with multiple copies of DNA increased and replicated. These different types of cell populations “lead to totally different scenarios of growth,” said Dr. Takors, and “likely affect the strain’s production.” He is working on a mechanistic model to explain these new events uncovered by systems biology.