Strategies to Engineer Microorganisms for Biofuel Production

Much of today’s commercial activity using advanced biotechnology for biofuel production focuses on the creation, selection or improvement of strains of desired microorganisms having enhanced properties for functions important for biofuel production. Longstanding methods for producing ethanol or other fuels, generally rely on the use of one or more selected microbial strains to drive the fermentation process. Traditionally, these methods have made use of naturally-occurring or classically selected microorganisms, but in recent years the power of the new biotechnologies to develop enhanced strains is being investigated or used by numerous companies. The following is a brief overview of some of the strategies that are being pursued. This is not meant to be a comprehensive summary of such strategies, and it is well beyond the scope of this blog to try to provide a thorough review of the multitude of published scientific papers describing genetic engineering approaches to improving biofuels organisms. For those seeking more scientific detail, there have been numerous review articles published in recent years, including Dien et al. 2003; Jarboe et al. 2007; Stephanopoulos 2007; Atsumi and Liao 2008; Fortman et al. 2008; Lee et al. 2008; Rude and Schirmer 2009 and Connor and Liao 2009

 Typical strategies include: 

  • Overexpress desired enzymes within host fermentation organisms (e.g. to improve ability to process or degrade cellulosic feedstocks).
    • Alter the timing or amount of expression of native enzymes
    • Express heterologous enzymes from other species
    • Express synthetic or engineered enzymes
  • Engineer microorganisms to manufacture novel or improved industrial enzymes for stand-alone use in biofuel production.
  • Create novel or synthetic microorganisms to enable production of renewable fuels.

Perhaps the most common strategy employed to date has been the use of recombinant DNA techniques to engineer microorganisms to overexpress desired enzymes, including heterologous enzymes derived from other species which are not naturally found in the host species. This is the strategy most often used by companies developing new microbial strains for cellulosic ethanol production: it would be advantageous from a process perspective to have a single microbial strain that can express the cellulases needed to break down the complex components of cellulosic feedstocks while also possessing the pathways to ferment the resulting sugars into ethanol, but there are few, if any, naturally occurring microorganisms that combine these features.  One approach is therefore to introduce into host organisms that are already optimized for ethanol fermentation genes from other species encoding the desired cellulytic enzymatic activities. As another example, genetic engineering could be used to give ethanol fermenting microbes the metabolic pathways needed to utilize sugar sources such as the 5-carbon xyloses and other pentoses that are released from hydrolysis of woody biomass. The alternative approach would be to splice genes encoding the enzymes making up the ethanol fermentation pathway into an organism lacking that trait but having the ability to digest the complex cellulosic components. Strategies like these are being pursued by companies like Mascoma Corporation, Verenium Corporation and others. It is also possible to use genetic engineering simply to enhance the efficiency of naturally-occurring ethanol-producing strains that in some cases already have sufficient activity to be used commercially: an example of a company pursuing this strategy is Qteros, which is moving towards commercial use of a natural microbial isolate while beginning in-house research to improve its activity using biotechnology.   

A variation of this strategy is to create and use engineered microbes to manufacture novel or improved industrial enzymes, which can then be used as a catalyst in fuel fermentations to enhance or accelerate biofuel production processes. Enzymes like cellulases, amylases, and other degradative enzymes can be used to pretreat cellulosic feedstocks, or can be added to an ethanol production process at any other suitable time. Companies pursuing this strategy are generally companies already manufacturing and selling other industrial enzymes, including several companies having decades of experience in this sector of the industry, such as Novozymes, the Genencor division of Danisco, and others. The field has also attracted some newer players, such as Iogen Corporation and Dyadic International, some of which are devoting a significant portion of their effort to the manufacture and sale of biofuel enzymes.  

Finally, a more ambitious strategy is to use synthetic biology, metabolic engineering, or other advanced techniques to create novel or synthetic microorganisms possessing enzymatic capabilities not found in the original host organism. This strategy might involve designing an “optimal” organism using combinations of enzymes from other sources, or even completely new enzymes designed and created using protein engineering to have maximal catalytic activity. Strategies like these are most often being pursued to create microorganisms or algae optimized to produce “designer” mixtures of hydrocarbons mimicking the composition of diesel, jet fuels or other petroleum fuels, including efforts by companies like LS9, Amyris Biotechnologies, Joule Biotechnologies, and (in algae) by Synthetic Genomics.  However, this approach is also being used to enable more efficient production of other fuels: for example, Joule Biotechnologies is using synthetic biology to create novel organisms that use photosynthesis to produce ethanol and other transportation fuels from sunlight and carbon dioxide without the need for a biomass feedstock. 

I’ll have more to say about these and other companies in later installments of this blog, when I focus on specific sectors of the industry and the technology strategies being pursued in each. 

D. Glass Associates, Inc. is a consulting company specializing in several fields of biotechnology. David Glass, Ph.D. is a veteran of nearly thirty years in the biotech industry, with expertise in patents, technology licensing, industrial biotechnology regulatory affairs, and market and technology assessments. This blog provides back-up and expanded content to complement a presentation Dr. Glass made at the EUEC 2010 conference on February 2, 2010 entitled “Prospects for the Use of Genetic Engineering in Biofuel Production.” The slides from that presentation are available at


2 thoughts on “Strategies to Engineer Microorganisms for Biofuel Production

  1. I am a scientist seeking to enter the algae renewable biofuels area. This report is very useful in bootstrapping my understanding the scientific basis and the nature of some of the business ventures of this emerging alternative energy industry. Thank you for providing this clear and comprehensive summary.

  2. Metabolic Engineering of Algae - Oilgae Blog

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