Microbial cell factories may help get to the root of understudied plant molecules

Sometimes just using a different tool makes the job a whole lot easier. A team of researchers co-led by the University of California San Diego has developed a method to produce a special class of plant hormones, known as strigolactones, at unprecedented levels using microbial cell factories.

By amplifying production of strigolactones, the researchers now have the ability to study these scarce and mysterious plant molecules in much greater depth than before.

The new study, published in the Jan. 17 issue of Science, could help improve sustainable agricultural practices by offering deeper insights into how plants make and use their natural hormones to adapt and survive.

Symbiosis and parasitism

Scientists worldwide have been interested in strigolactones due to their roles in controlling plant development, regulating the plant’s symbiotic relationship with nearby soil microbes, and triggering the germination of parasitic plants.

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But progress in understanding these strigolactones has grown a bit stagnant, partly because these molecules occur in such low amounts in plants. As a result, scientists have had to use laborious methods, often using large quantities of plant material, just to obtain enough material to identify them.

Now, researchers at the UC San Diego Jacobs School of Engineering, in collaboration with UC Riverside and Utsunomiya University in Japan, have introduced a genomics-driven tactic to the investigation, using a microbial cell factory, to overcome the abundancy challenge.

Microbial cell factory

“We have this engineering approach that makes everything much easier and previously impossible things now possible,” said study co-corresponding author Yanran Li, a professor in the Aiiso Yufeng Li Family Department of Chemical and Nano Engineering at the UC San Diego Jacobs School of Engineering who specializes in synthetic biology and metabolic engineering.

The team’s approach leveraged the capabilities of E. coli and baker’s yeast to produce strigolactones. By co-culturing these two hosts, researchers created a microbial cell factory that produces yields of strigolactones over 125 times higher than previous microbial consortiums. Traditional methods to study strigolactone, in contrast, can require extracting at least 340 liters of xylem sap — the equivalent of 7 or 8 poplar trees. Realistically, that amount needs to be closer to 1,000 liters, explained Li, to account for losses from isolating and purifying the compound.

“By using this microbial cell factory, you can bypass extracting tons of xylem sap and thus destroying dozens of trees to discover the molecules important for the physiology of plants,” said Li.

Engineering approach

The first strigolactone was discovered in the 1960s, but it wasn’t until 2008 when the hormonal role of this compound class was recognized. As hormones, strigolactones control the development of the plant and its responses to stress, like low water or low nutrient situations. Since the 2008 realization, plant biologists have been pushing to figure out the chemistry and purposes of strigolactones and their related compounds. Findings have so far been more speculative than conclusive, in part due to the very low amount of hormone compounds in plants.  

About 30 strigolactones have been discovered so far, and they all have a common ancestor. What drives the conversion of that precursor to many of those strigolactones is a specific protein coding gene (CPY722C) in most flowering plants. Because sisters to that gene are widely found among seed plants, Li and her team hypothesized that these sister genes, labeled as CYP722A and CYP722B, might also make strigolactones of essential biological roles.

Sister genes

To investigate, the researchers tested what happens with the sister genes in a microbial cell factory, made by co-culturing E. coli and baker’s yeast, that they previously developed. With this platform, they expressed the CYP722A and CYP722B genes from 16 different plant species, including poplar, pepper, pea and peach. Through further metabolic engineering, first author Anqi Zhou, a chemical engineering Ph.D. student in Li’s lab, found efficient ways to optimize the output concentrations of strigolactones, more than 125-fold than before. 

That enhanced concentration gives the researchers enough material to figure out the structure of any resulting compounds, which could potentially play an important role in plant physiology. 

And one such important molecule could be the novel compound produced by CYP722A or CYP722B: a strigolactone called 16-hydroxy-carlactonic acid (16-OH-CLA).

Shoots not roots

While 16-OH-CLA has been reported previously, its exact structure and why it might be important were not fully known. The ability to produce sufficient quantities of 16-OH-CLA — thanks to the microbial cell factory — allowed the team to uncover its precise structure for the first time. 

Interestingly, when the researchers looked for 16-OH-CLA in plants, they only detected it in the shoots and not the roots, unlike all the other known strigolactones. What’s more, the compound isn’t present at all times. For annual plants like pepper or the common pea, the compound disappears once the plant is mature and developed. For trees like poplar, it’s seasonal.

Although the specific function of 16-OH-CLA remains elusive, its common presence within seed plants and in an unusual plant region suggests that it may play a critical, yet underappreciated role, in plant signaling or adaptation to environmental challenges. Thanks to the new engineering approach, researchers will easily have the quantities they need to dig deeper — which is exactly what Li and the team are working on now.

Paper: “Evolution of inter-organismal strigolactone biosynthesis in seed plants.” Co-authors include Anqi Zhou, Kaibiao Wang, and Yanran Li, UC San Diego; Annalise Kane, Michell Santiago, and David C. Nelson, UC Riverside; Sheng Wu, Shanghai University of Traditional Chinese Medicine; Yui Ishiguro and Xiaonan Xie, Utsunomiya University; Kaori Yonegama, Saitama University; and Malathy Palagam, UC Davis.