Reference Work Entry

Handbook of Hydrocarbon and Lipid Microbiology

pp 1297-1325

A Genomic View of the Catabolism of Aromatic Compounds in Pseudomonas

  • J. I. JiménezAffiliated withDepartment of Microbial Biotechnology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas
  • , J. NogalesAffiliated withDepartment of Molecular Microbiology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas
  • , J. L. GarcíaAffiliated withDepartment of Molecular Microbiology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas
  • , E. DíazAffiliated withDepartment of Molecular Microbiology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas

Abstract:

The genetic, and the more recent genomic, proteomic, and metabolomic, approaches that have been undertaken to study the catabolism of aromatic compounds in different Pseudomonas strains have contributed significantly to the acceleration and completion of our understanding on different aspects of the physiology, ecology, biochemistry, and regulatory mechanisms underlying a secondary metabolism that allows the use of this highly abundant carbon source by some bacteria. Comparative genomics suggests that the overall organization of catabolic clusters is conserved across the Pseudomonas genus. However, species-specific and strain-specific variations account for differences in gene arrangements, substrate specificities, and regulatory elements. Moreover, genomic analyses point to the existence of parologous genes likely involved in the degradation of aromatic compounds, suggesting that our current knowledge about the degradative potential of Pseudomonas is still far from complete. On the other hand, many aromatic compounds, e.g., hydrocarbons and phenolic compounds, simultaneously serve as potential nutrients to be metabolized by bacteria but also as cellular stressors. The transcriptomic and proteomic approaches carried out with some Pseudomonas strains provide some light on the biodegradation versus stress dilemma. The increased use of the “omic” techniques, together with the genome-scale metabolic reconstructions developed for some Pseudomonas strains, will certainly contribute significantly to unravel the intricate regulatory and metabolic networks that govern the biodegradation of aromatic compounds, as well as their distribution and ecophysiological relevance. All the basic knowledge generated so far about the metabolism of aromatic compounds in Pseudomonas paves the way for a wealth of biotechnological applications, e.g., bioremediation, biotransformations, biosensors, etc., and it is of great potential in Synthetic Biology. Therefore, Pseudomonas becomes a paradigmatic bacterial genus both for increasing basic knowledge and for applied research within the field of aromatic compounds degradation.