Industrial bioengineering is now using genetically modified microbes to produce a wide array of products at industrial scale, including everything from biofuels to nutraceuticals such as resveratrol. But despite the diversity of output, the primary organisms producing them are modified E. coli bacteria and Saccharomyces cerevisiae, or baker’s yeast.
Despite the irony—or poetry—of using the same yeast used to brew Ancient Egyptian beer to brew nutraceuticals, some researchers are turning to other microorganisms, hoping to find new phenotypes that could offer new capabilities that both broaden and deepen the biotechnology toolbox and accelerate progress in genetic engineering.
“There is this sort of movement in the field where we are trying to develop genetic tools for other organisms,” says Eric Young, PhD, a professor of chemical engineering at Worcester Polytechnic Institute (WPI). Every organism has its own specializations, its own skill set, he adds, and there is a big diversification as “a lot of labs have their own organisms they are interested in developing genetic tools for.”
Young’s lab has recently received a half-million-dollar National Science Foundation grant to study Xanthophyllomyces dendrorhous, or red yeast.
“Our interest in red yeast is because it’s red,” he says. “It’s red for the same reason that a tomato is red, and we can actually make it orange in the same way a carrot is orange.”
Red yeast produce terpenoids, the large class of chemicals that includes the lycopene and carotene that give those produce items their hue, Young notes. “If we can put into the genome of red yeast a variety of terpene synthases, we think we can make a variety of different molecules.”
Terpenoids represent a wide range of natural products, from fragrance and flavor molecules such as limonene, a major component in oil citrus fruit peels, to vitamin A to the antimalarial compound artemisinin, found in the herb sweet wormwood.
The full variety of terpenoids are built up linearly by adding isoprene units, so that a monoterpene such as limonene has two isoprene units and a sesquiterpenoid like artemisinin has three such units and carotenoids, containing six isoprene units, are tetraterpenoids.
Proof of Concept
Young’s lab aims to make one of each type of terpenoid as a proof of concept, beginning with limonene. Ultimately, he aims to test whether red yeast may be fundamentally different from baker’s yeast when it comes to making certain compounds. A basidiomycetes yeast has more in common with mushroom producing fungus than baker’s yeast, he says, and “it might be easier to make plant chemicals like artemisinin in something like red yeast because the biology is different.”
This is a departure from recent practice, Young notes, where researchers find interesting genetics and chemistries in other organisms and then find a way to engineer those traits in S. cerevisiae or E. coli. “Now we’re saying, why don’t we leave all that interesting genetics in place where they naturally are and they work really well and just tweak it a little bit?”
There are some cases where the prolific workhorses of current biotechnology are at a definite disadvantage, according to Ian Wheeldon, PhD, an associate professor of chemical and environmental engineering at the University of California (UC), Riverside.
“Industrially we make a lot of protein using E. coli. The limitation becomes, how do you glycosylate? You couldn’t make an antibody against [SARS-CoV-2],” if it needs to be glycosylated, he says. The current solution is to use mammalian cells to make antibodies, but “it would be really nice to have a eukaryote, like a yeast, like the red yeast or K. marxianus, or Yarrowia lipolytica, that can produce those proteins with glycosylation and have it amenable to larger scale bioprocesses, like fermentation.”
Wheeldon’s lab is researching Y. lipolytica, a yeast that accumulates and metabolizes lipids.
“We developed genetic engineering tools to manipulate pathways inside that yeast that can amplify that trait,” he says. “Let’s say you want to make bio diesel or omega 3 fatty acids or something like that. You could use the power that yeast naturally has to produce long chain lipids and then give it a couple of new enzymes.”
So while Young may be engineering red yeast to produce fragrances today, he and Wheeldon both see such explorations of the tree of life yielding eventual products that sound almost like science fiction. Young is already in discussions with another WPI researcher to see if there could be biomedical applications for yeast that can produce cellulose, rather than sourcing it from trees.
Wheeldon is interested in bacteria that can produce conductive filaments, and other magnetic nanoparticles. “There is a process there that we can’t do very well or don’t do to the same extent with synthetic chemistry,” Wheeldon says. “Here is an example of a phenotype you could identify in nature, a microorganism that makes nanoparticles that are magnetic, and then it controls crystal facets. Great! So how do we hijack that?”
There are costs to this approach however, and even Young admits that exploring new organisms requires developing new genetic engineering tools specific to those organisms. His lab expects a long boot up time to get rolling with red yeast in a fashion comparable to S. cerevisiae.
“There will be applications for these organisms as well, but it takes time to bring them into industry at scale. The bacteria or the S. cerevisiae are well developed in the fermentation process side,” says Ajikumar Parayil, PhD, CEO of Manus Bio. The company is working to commercialize the microbial production of the kinds of materials Young and Wheeldon are imagining, from artemisinin to Reb M, a sweetener derived from the Stevia plant. Their tool of choice, however, is primarily what Parayil calls the “plain chassis,” the reliable E. coli bacterium.
“The proof of concept is very easy in higher organisms like yeast, but when you really want to make it as a workhouse for the industry, bacteria are sometimes superior,” he says.
But even as he puts E. coli to work, Parayil is nothing but supportive of the explorations of researchers like Young.
“He should look into the new organisms, new genetics, and how to develop tools for engineering these microorganisms, I am absolutely thrilled to hear that,” Parayil says. “I want people like Eric to be very dreamy and do this kind of work so everything runs faster.”