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:

Source

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.

Bacteria; They’re not only for biofuel anymore. Unsung heroes for bioplastics

illustrated bacteria, microbiology, bioplastic, bioenergy, environment
Illustration of PHB within bacterial cells

I spend a lot of time on this blog illustrating and promoting the benefits of the things we can’t see, however, we can’t live without and finding new ways they can help us out. To focus on bacteria along for now, they are beneficial overwhelmingly more than they are hazardous. Lots of research is going into utilizing them in new arenas from ethanol to diesel and jet fuels.

Helping solve the forthcoming energy/climate crisis is not the only area these guys can help. Lots of bacteria, under certain environmental conditions, can and will produce huge internal polymers as carbon stores, especially when nitrogen supplies are limited. Think of this polymer like starch in plants and glycogen in mammals. Research is still ongoing into the mechanisms that regulate polymer synthesis and degradation.

The bacterial polymer is special, unlike the molecular make-up of starch or glycogen, this polymer is a class of polyhydroxyalkanoate (PHA).

Structure of poly-(R)-3-hydroxybutyrate (P3HB)
Structure of poly-(R)-3-hydroxybutyrate (P3HB) (Photo credit: Wikipedia)

One of the most prevalent forms of PHA is polyhydroxybutyrate, or PHB. Speaking from experience, PHB is an interesting macromolecule to study and observe under the microscope with cells treated with a fluorescent dye that stains PHB. PHB can account for up to 75%  of the total cell weight. PHB, and PHAs in general, can be used to make plastic thus replacing the need for petroleum based plastics.

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.

Living at the Boiling Point: What we can learn from extreme heat-loving microbes

Thanks to the decreasing costs of sequencing genomic DNA, finding novel microorganisms that add to our understanding of metabolism in myriad environments is becoming common place. Not only are we learning about the diversity of life in extreme environments, like heat, cold, pressure, and altitude, but we are also learning what life on other planets may be like. With each additional genome added into ‘the cloud’, our synthetic biology toolbox gets a little bit bigger and our ability to manipulate tiny organisms to produce novel compounds is possible. Enter the “rushing fireball”.

Pyrococcus furiosus is an archeal species that thrives near deep-sea thermal vents where temperatures are between 90 and 100 degrees Celsius (or 194 to 212 degrees F). P. furiosus can grow at temperatures as low as 70 degrees C (158 deg F). To live in such conditions, this organism’s proteins must be tolerant to what we would consider harsh conditions. This organism’s ambient conditions makes wild-type proteins well-suited for industrial processes where temperatures are near boiling.

So far, P. furiosus has been utilized to produce 3-hydroxypropionic acid, a common industrial chemical used to make various products including acrylics. The kicker is that these cells were wired to make this chemical from atmospheric carbon dioxide. It is not crazy to think of what other useful products can be produced by P. furiosus with small modifications within the genome; products like ethanol or butanol as biofuels.

Pyrococcus furiosus, bacteria, archea, illustration, microbiology
My illustration of Pyrococcus furiosus

Reference

Keller, M., Schut, G. J., Lipscomb, G. L., Menon, A., Iwuchukwu, I., Leuko, T., Thorgersen, M. P., Nixon, W. J., Hawkins, A., Kelly, R. M. and Adams, M. W. W. (2013) “Exploiting microbial hyperthermophilicity to produce an industrial chemical using hydrogen and carbon dioxide”Proc. Natl. Acad. Sci. U.S.A. (in press).

Illustration of the world of synthetic biology: a new phase in science

animated bacteria, bioenergy, synthetic biology graphic
With novel technologies, it is becoming commonplace to manipulate microbes to acquire desired effects. Shown is a bacterium with foreign gene pathways (glowing) that enable this cell to efficiently produce a desired product.

First, there was biology which began in earnest in the 19th century. Then came molecular biology in the 1920s and the foundation of mutagenesis set forth by Herman Muller in 1927. Then, genetic engineering was first applied in 1972 the lab of Paul Berg. Finally, humans had the ability to manipulate living organisms in a specific, directed way. Fast forward 38 years to the announcement by J. Craig Venter that the first synthetic organism was created with a completely synthetic genome. However, Mother Nature is very particular about what exactly humans can do with respect to organismal manipulation. The naive thought that simple addition of genes from one organism into a more suitable organism would lead to theoretical, effective production of desired chemicals was soon the way of the albatros.

This is when scientists had to take a step back and rethink their strategy. They had to consider gene regulation (positive and negative feedback), build-up of secondary metabolites, toxicity of produced end products, etc. It wasn’t enough to add genes coding for enzymes necessary for desired chemical production. Through the advancements of bioinformatics, computation biology, and a nascent field called systems biology, scientists are just now starting to see the fruits of their labor.

Humor me; type in “engineering bacteria” into Google News. Take a look at the headlines that pop up in your browser. Look at the amazing advancements that are happening currently and imagine what is to come…

Combing the Earth One Genome at a Time: In Pursuit of “The Next Big Thing” in Sustainability

animated bacteria, cellulose, bioenergy
Illustration of Clostridium thermocellum cells (orange) on the surface of a cellulose fibril (multicolor)

There is one thing that can be said about scientists: they’re never satisfied…thankfully. Observation and curiosity leave them on a never-ending quest to understand Mother Nature and improve humanity. One great example of this is the field of alternative energy science. Through the efforts of the Bioenergy Research Centers (BRCs) and Joint Genome Institute within the U.S. Department of Energy‘s Office of Science, there is a perpetual search for Nature’s best metabolic machinery. This search requires thinking outside the box and sometimes outside your comfort zone. For example, last year researchers from the Joint BioEnergy Institute published findings that originated in the El Yunque National Forest in Puerto Rico, a rain forest and home to Enterobacter lignolyticus, a bacterium that is tolerant to ionic liquids (liquids with salts that are not crystaline, but are liquid). This discovery began with the observation that soil microbes at El Yunque have a high rate of organic decomposition and tolerance to osmotic pressure.

Another example are bacteria from the genus Caldicellulosiruptor that are able to degrade biomass, however, they live in extremely thermophilic environments like hot springs from New Zealand to Russia to Yellowstone. Researchers at the BioEnergy Science Center were able to isolate these microbes and start characterizing the enzymes responsible for degrading woody biomass into simple sugars.

Or what about  researchers at the Great Lakes Bioenergy Research Center essentially dissecting a leaf-cutter ant colony in Panama to examine its ecology; from the fungus the ants use as food, to the bacteria that help degrade the leaves. Or what about isolating microbes from termite guts or wasp guts?

Then there is the champion for raising scientific curiosities, Clostridium thermocellum which holsters woody biomass degradation factories attached to the outside of its cell membrane. These factories are known as cellulosomes.