How do production systems in biological cells maintain their function in changing environments?
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ORIGINAL ARTICLE
How do production systems in biological cells maintain their function in changing environments? Moritz Emanuel Beber • Marc-Thorsten Hu¨tt
Received: 27 August 2012 / Accepted: 17 September 2012 / Published online: 29 September 2012 Ó Springer-Verlag Berlin Heidelberg 2012
Abstract Metabolism is a fascinating natural production and distribution process. Metabolic systems can be represented as a layered network, where the input layer consists of all the nutrients in the environment (raw materials entering the production process in the cell), subsequently to be processed by a complex network of biochemical reactions (middle layer) and leading to a well-defined output pattern, optimizing, for example, cell growth. Mathematical frameworks exploiting this layered-network representation of metabolism allow the prediction of metabolic fluxes (the cell’s ‘material flow’) under diverse conditions. In combination with suitable minimal models, it is possible to identify fundamental design principles and understand the efficiency and robustness of metabolic systems. Here, we summarize some design principles of metabolic systems from the perspective of production logistics and explore, how these principles can serve as templates for the design of robust manufacturing systems. Keywords Systems biology Metabolic networks Enzymes Design principles Simulated evolution
1 Introduction There is a deep intrinsic parallel between the metabolism of biological cells and industrial production. Cells function
M. E. Beber (&) M.-T. Hu¨tt School of Engineering and Science, Jacobs University, Campus Ring 1, 28759 Bremen, Germany e-mail: [email protected] M.-T. Hu¨tt e-mail: [email protected] URL: http://sysbio.jacobs-university.de/
efficiently under typical environmental conditions. At the same time, they are viable (thus maintaining a certain level of function) across a vast range of atypical environments. It is precisely this robustness with respect to large changes (and significant fluctuations) in the composition of the environment (the ‘input pattern’) that makes metabolic networks a potentially very interesting role model for technical production and distribution systems (see, e.g., [1]). The network of metabolic reactions in a cell is responsible for providing a wide range of substances at the right time in the right proportions for a specific purpose of consumption. At the same time, metabolic systems construct complicated chemical substances out of nutrients taken up from the environment. With several thousands of interacting machines (enzymes, catalyzing biochemical reactions), the underlying production network is about as complex as the most involved processes of industrial production. The key challenges are comparable: How do systems in both domains ensure robustness with respect to perturbations? How can these systems react rapidly to important changes in their environment by ensuring the achievement of the logistics targets? For metabolism, the young scientific discipline addres
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