Computational tools for the synthetic design of biochemical pathways

The rise of synthetic biology defines a new era in the metabolic engineering of microorganisms, an era characterized by the biosynthesis of biofuels and natural products through the de novo construction of biochemical pathways using parts from disparate origins. The development and effective implementation of computational tools is crucial to make such approaches possible.Several algorithms have been devised to find the metabolic pathways that are theoretically most suitable for thermodynamically efficient production of a certain compound. After detection of all possible pathways on the basis of enzyme classifications and/or possible chemical transformations, they can be ranked according to, for example, pathway length, thermodynamic efficiency and maximum predicted yields.Promising pathways can be integrated into genome-scale metabolic models of candidate host organisms to test how well the topology of their metabolic networks can accommodate the synthetic heterologous pathway. Such metabolic models can now be reconstructed rapidly because of the emergence of high-throughput model generation software, and pathway visualization tools facilitate quick and efficient analysis of modelling results.Various strategies are available for the computational identification of candidate parts, depending on the type and diversity of the parts that are searched for. For the identification of single enzyme-encoding genes, homology searches coupled to phylogenetic analysis can sometimes suffice. In more complex cases, automated in silico prediction of substrate specificities in enzyme families may allow more efficient prioritization of possible targets. Additionally, several algorithms have recently been developed for detecting multigene modules, such as biosynthetic operons or gene clusters.In order to effectively integrate foreign enzymatic parts into a given host organism, the codon usage of the genes encoding the enzymes can be matched to that of the host. Thus, the probability of obtaining efficient translation is increased. Using computer-aided design, the codon-optimized parts can then be integrated into transcriptional units with designed regulatory circuits that can be simulated in silico before commencing the DNA synthesis of the final constructs.There is still a wide range of opportunities for developing novel computational tools in this field. If these developments go hand-in-hand with developments in experimental approaches, the field of synthetic microbiology is likely to obtain a central position in the field of microbial biotechnology.