20.109(F10):Metabolic Engineering Research

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Initial Research Ideas

  • Enhance the hydrocarbon metabolic pathway in microorganisms.
  • Certain bacteria can metabolize hydrocarbons (for example, oil). We want to enhance these metabolic pathways so that these bacteria can be used for metabolizing hydrocarbons for industrial purposes (for example: to clean up oil spills and/ or other wastes and pollutants). We will research available methods of enhancing metabolic systems, and suggest further research in the application of those methods that seem particularly promising in their application to these bacterial systems.
  • We also imagine an engineered system in which the bacteria use these hydrocarbon wastes as a fuel source to produce a useful product. This product can either be useful for industrial purposes (ie: to produce therapeutics or chemicals), or it can be useful for recycling purposes or "green" purposes. For example: we can engineer these bacteria to live symbiotically with certain plants, so that the bacteria metabolize wastes into materials useful for plant growth and development (these bacteria and plants can be useful in land fills, for example).


Headl I.M., Jonesl M.D., Roling W.F.M., Marine microorganisms make a meal of oil." Nature Reviews Microbiology. 2004 Mar 4: 173-82.

  • These bacteria use hydrocarbons almost exclusively as a carbon source: Alcanivorax spp., Cycloclasticus spp., Oleiphilus spp., Oleispira spp., Thalassolituus spp. and some members of the genus Planomicrobium (previously known as Planococcus).
  • In oil-spill bioremediation experiments carried out in laboratory microcosms and in the field, 16S ribosomal RNA (rRNA)-gene sequences from Alcanivorax spp. were undetectable in control experiments in which samples were not treated with oil, but within 2 weeks of oil treatment, they constituted more than 30% of the sequences in libraries of 16S-rRNA-gene clones constructed from oil-treated sediments and > 70% of the sequences recovered from sediment treated with oil and inorganic nutrients.
  • Results mirrored by detection of alkB genes, which encode the catalytic component of alkane hydroxylase, only in samples where Alcanivorax spp. 16S-rRNA genes were abundant.
  • It is thought that these organisms are normally present in very small numbers, and by providing conditions that allow them to take advantage of the hydrocarbons as a carbon and energy source, they grow and multiply rapidly.
  • In the field, rate and extent of oil degradation have been found to be lower, probably as a result of the lower mean temperature, which ranged from > 20°C to < 5°C.
  • In laboratory microcosms, phenanthrene and dibenzothiophenes were degraded, but such degradation was not observed in the above field experiment.

Steen E.J., Kang Y., Bokinsky G., Hu Z., Schirmer A., McClure A., Del Cardayre S.B., Keasling JD. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature. 2010 Jan 28:463(7280):559-62.

  • Researchers engineered E. coli to produce structurally tailored fatty esters (biodiesel), fatty alcohols and waxes directly from simple sugars by overexpressing thioesterases and acyl-CoA ligases to improve the E. coli fatty acid pathway.
  • Esters produced by expressing an acyltransferease in conjunction with an alcohol-forming pathway and biodiesel was produced by introduction of an ethanol pathway.
  • Expressing and secreting xylanases allowed for the utilization of hemicellulose, a moajor component of plant-derived biomass.
  • Process utilizes microbial catalysis the ability to compile several complex, biosynthetic pathways into a single cell, simplifying process and raw material requirements and decreasing costs.
  • The engineering strategy supports yields of these products within an order of magnitude that is required for commercial production as well as demonstrates possibility to realize a consolidated bioprocess.


  • Phosphorous requirement for hydrocarbon-metabolizing bacteria in the sea


  • Comprehensive overview of synthetic metabolism


  • Reverse of our idea: engineer bugs to eat waste and produce oil
  • No source cited for article? Maybe find primary source...


  • Article describing the history of research that has been done/is currently being done on oil-eating bacteria
  • Nice review, but we should find the primary sources that the article is talking about/describing


  • Talks about synthetic metabolism in plants for chemical synthesis