Reference Work Entry

Handbook of Hydrocarbon and Lipid Microbiology

pp 1411-1435

Emerging Systems and Synthetic Biology Approaches to Hydrocarbon Biotechnology

  • V. de Lorenzo*Affiliated withSystems Biology Program, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco Email author 
  • , S. FraileAffiliated withSystems Biology Program, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco
  • , J. I. JiménezAffiliated withSystems Biology Program, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco


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.


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