Useful Products Engineered into E. coli “Poop” (Thank Goodness)

I can’t sit back and let the internet become saturated with misleading phrasing regarding by-products genetically engineered into E. coli metabolism. The latest sensation stems from the commercial production of the artificial sweetener aspartame. It was reported this week, well…read it for yourself (notice the language used):

This scientific jargon obfuscates (perhaps deliberately) a truly disturbing process:
1.) ‘Cloned microorganisms’ (which the patent later reveals to be genetically modified E. coli) are cultivated in tanks whose environments are tailored to help them thrive.
2.) The well-fed E. coli cultures defecate the proteins that contain the aspartic acid-phenylalanine amino acid segment needed to make aspartame.
3.) The proteins containing the Asp-Phe segments are ‘harvested’ (i.e. lab assistants collect the bacteria’s feces).
4.) The feces are then treated. This includes a process of methylation (adding an excess of the toxic alcohol, methanol, to the protected dipeptide).

While common sense dictates that this abomination doesn’t belong anywhere near our bodies, the patent’s authors made no secret about their belief that aspartame constitutes a safe and nutritious sweetener:


It was picked up on the UPI under “Science News” with a headline reading:

The use of the words ‘poop’, ‘feces’, ‘defecate’, and ‘excrement’ is truly unfortunate and used to sensationalize the process. Natural News has an agenda, or several agendas. First they are against genetic modifications to living organisms even though almost all discoveries and breakthroughs in modern medicine can be contributed to some form of genetic modification. Second, they are publicly against the use of aspartame in commercial products.

The truth about E. coli ‘poop’

First, E. coli do not ‘poop’ in the sense a human can relate. These are single-celled organisms and are rather leaky to certain molecules naturally. E. coli produce by-products, not poop. Metabolic end products are considered waste to the E. coli cell, but these natural end products include carbon dioxide, hydrogen gas, acetate (vinegar), and water. Their poop doesn’t sound so bad now does it?

The evolution of E. coli ‘poop’

E. coli has been the organism of choice for decades in myriad research areas. Simple genetic modifications like gene deletion and gene insertion are the norm and can easily be performed in a lab. Scientists and doctors have used this technique to engineer novel strains of E. coli that tweaks their metabolism to produce useful products for the general public. One great example occurred in 1978 by Herbert Boyer who inserted the gene for human insulin into E. coli. Recombinant insulin was approved by the FDA in 1982 and is now the source of 70% of the insulin sold today.

Human growth factor is another by-product engineered into E. coli to treat different forms of dwarfism. For hemophiliacs, E. coli are utilized to produce missing clotting factors like tissue plasminogen activator and factor VIII. It should be noted that before producing these therapeutics in E. coli, they were harvested from cadavers. Patients with immunodeficiency can receive recombinant interferon, used to treat viral infections, produced in bacteria.

E. coli and other bacteria are used in other industries as well. They have been modified to produce large amounts of succinate, a precursor for the solvent 1,4-butanediol. It can then be used to make some plastics and even Spandex. E. coli are also used in the production of polyhydroxybutyrate, or PHB, for the production of plastics. E. coli is also used for production of polyamines for synthesis of polyamide plastics.

Over the past decade, a lot of research has taken place in the field of renewable energy. One approach to lessen our dependence on foreign oil is the microbial conversion of cellulosic (non-food) plant material into viable fuels like ethanol and butanol. This task has given E. coli and other microbes ‘poop potential’. Through genetic engineering and synthetic biology techniques, E. coli can produce large amounts of free fatty acids which are one catalytic step away from the same diesel fuel derived from petroleum. E. coli is also engineered to produce precursors for jet fuel.

In this post, I have focused on only one microbe, E. coli, since this was the bacterium sensationalized this week in the press.

Moving towards the renewables: biotech and more

Moving towards the renewables: biotech and more.

Illustration: Synthetic Biology; Turning bacteria poop into a hot commodity

bacteria art, E. coli art, bioenergy, biomass, biodiesel
Illustration showing the concept of E. coli engineered to digest plant cell wall material (green) and produce fatty acids (white) that can be used as diesel as a waste product. The fatty acids shown are actual 3D structures of linoleic acid.

Mother Nature’s Lego Collection: Unfinished illustration of cellulose degrading polycellulosomes

biofuel, bioenergy, bacteria, microbiology, clostridium, bacteria art
Illustration of Clostridium thermocellum with two polycellulosomes (green) degrading cellulose fibers (brown). Size 2400 x 1920 px

It is amazing, to me anyways, how much we borrow from Mother Nature. Legos are no different. These small pieces of plastic that can be connected with infinite possibilities have stirred the imagination of children and adults alike.

There is a perfect example of Nature’s Lego set within the genomes of microorganisms that degrade plant matter using large protein complexes called cellulosomes (see this post). Clostridium thermocellum is a model organism for this.

Micrograph image of C. thermocellum showing cellulosomes attached to its cell surface. Image source here.

Thanks to its ability to interchange components, both the enzymes to degrade cellulose and the protein scaffold to attach these enzymes, C. thermocellum can optimize degradation any different sources of plant material. Shown in the my illustration above is only one assembly. The cellulosomes illustrated are of the actual protein structures (or models if no structure known) of the components. Essentially, there is one scaffold protein, OlpB, which can have up to 7 other scaffold proteins attached. In the case above, I have attached 7 CipA scaffoldins each with 9 cellulose degrading enzymes. So in total, each cellulosome shown has 63 enzymes to beakdown the cellulose polymers shown in brown. Those are actual cellulose polymers based upon the reported structure of cellulose in a crystal lattice.

I haven’t shown yet, however, larger cellulosomes or the other approach microorganisms use to break down plant material. Others can use excreted cellulases that release the sugar molecules for the microbe to transport into the cell. This has been demonstrated now in the bacterial “lab rat” organism E. coli. The goal is to find the right strategy to make this process cost effective and scalable for mass production of biofuels. The ultimate coal is consolidated bioprocessing in which a single organism or culture can both degrade the biomass and convert it into a particular biofuel like ethanol or diesel products. I hope to have an animation of this, but that is a more long term goal. Hope you are able to better understand strategies bacteria (and scientists and engineers) use to break down plant cell wall material.

Illustration of a bacterium that poops electricity and can save the world: Geobacter Hi-Res

Geobacter, nanowire, bacteria, bacteria art, science art