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Emerging Systems and Synthetic Biology Approaches to Hydrocarbon Biotechnology

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Abstract:

Systems Biology is a conceptual frame for studying living systems that departs from the extreme reductionism of traditional Molecular Biology and pursues the quantitative understanding of complete biological entities rather than the mere comprehension of their parts. The development of the field stems from the popularization of high-throughput DNA sequencing technologies that have allowed the complete determination and archiving of the whole genetic complement of a number of individual species from microorganisms, and even complete ecosystems. This has then been followed by a plethora of omics disciplines (genomics, proteomics, metabolomics) that endow Biotechnologists upfront with wealth of information on any biological catalyst of interest. This article examines questions at stake in the application of Systems Biology to microbial biotransformations of petroleum components, in particular, the type of abstractions needed for modeling the scenarios where microorganisms meet organic molecules. Concepts such as epi-metabolome, pan-enzymes, and ectopic metabolism are paramount to comprehend microbial activities in sites where mixtures of chemical structures are exposed to multispecies metabolic networks. The ensuing process is constrained by the abiotic characteristics of the locations, as physico-chemical conditions determine the dynamic interplay between the contaminants and the biological catalysts. The availability of genes, genomes, and metagenomes of biodegradative microorganisms make it possible to model and predict the fate of chemicals through the global microbial metabolism. Moreover, the field is capitalizing quickly on the new field of Synthetic Biology (SB) in view of the possibilities of designing superior biocatalysts for biodegradation and biotransformations of desired chemicals.

Keywords:

  • Biodegradation
  • metabolic networks
  • biocatalysis
  • catabolic landscape
  • epi-metabolome
  • pan-enzymes
  • ectopic metabolism

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Notes

  1. 1.

    A is orthogonal to B, if A does not influence B. Orthogonality guarantees that changes made in a component of a system neither creates nor propagates side effects to other components of the system.

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Acknowledgments

The work made in Authors’ Laboratory was supported by research grants of the Spanish Ministry of Science and Innovation, by contracts of the Framework Programme of the EU and by Funds of the Autonomous Community of Madrid.

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de Lorenzo*, V., Fraile, S., Jiménez, J.I. (2010). Emerging Systems and Synthetic Biology Approaches to Hydrocarbon Biotechnology. In: Timmis, K.N. (eds) Handbook of Hydrocarbon and Lipid Microbiology. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-77587-4_97

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