Unlocking Nature’s Secrets: How Microbial Cell Factories Can Illuminate Hidden Plant Molecules

The new research, published in the Jan. 17 edition of Science, could aid in advancing sustainable agricultural practices by providing deeper insights into how plants synthesize and utilize their innate hormones to adapt and thrive.

Scientist across the globe have been intrigued by strigolactones due to their functions in governing plant growth, managing the plant’s symbiotic interaction with adjacent soil microorganisms, and instigating the germination of parasitic flora.

However, the advancement in grasping these strigolactones has somewhat stagnated, partly because these molecules appear in such minimal quantities within plants. Consequently, researchers have had to employ tedious methods, frequently using substantial amounts of plant material, merely to procure sufficient material for identification.

Currently, experts at the UC San Diego Jacobs School of Engineering, in partnership with UC Riverside and Utsunomiya University in Japan, have implemented a genomics-based strategy for their research, utilizing a microbial cell factory to address the abundance issue.

“We have this engineering strategy that simplifies everything and transforms previously impossible tasks into achievable ones,” said Yanran Li, a co-corresponding author of the study, and a professor in the Aiiso Yufeng Li Family Department of Chemical and Nano Engineering at the UC San Diego Jacobs School of Engineering, specializing in synthetic biology and metabolic engineering.

The team’s strategy harnessed the potential of E. coli and Baker’s yeast to fabricate strigolactones. By co-cultivating these two hosts, the researchers established a microbial cell factory yielding strigolactones over 125 times greater than earlier microbial consortiums. Traditional approaches for studying strigolactone, conversely, may necessitate extracting a minimum of 340 liters of xylem sap — equivalent to 7 or 8 poplar trees. In reality, that amount should be closer to 1000 liters, as Li explained, to compensate for losses incurred during the isolation and purification of the compound.

“By utilizing this microbial cell factory, you can circumvent extracting vast quantities of xylem sap, thereby preserving numerous trees in the quest to identify molecules vital for plant physiology,” noted Li.

Engineering Strategy

The initial discovery of strigolactone occurred in the 1960s, but it wasn’t until 2008 that the hormonal function of this class of compounds was acknowledged. As hormones, strigolactones direct plant growth and its responses to environmental stressors, such as reduced water or nutrient conditions. Following the 2008 revelation, plant biologists have been striving to unravel the chemistry and functions of strigolactones and their associated compounds. Thus far, findings have tended to be more speculative than definitive, partly due to the extremely low quantities of hormone compounds found in flora.

Approximately 30 strigolactones have been identified thus far, all descending from a common ancestor. The transformation of that precursor into many of these strigolactones is driven by a specific protein-coding gene (CPY722C) commonly found among flowering plants. Due to the widespread presence of related genes among seed plants, Li and her team proposed that these sister genes, designated as CYP722A and CYP722B, might also produce strigolactones with crucial biological functions.

To explore this, the researchers examined the behavior of the sister genes within a microbial cell factory, created by the co-cultivation of E. coli and Baker’s yeast, which they had developed earlier. Utilizing this platform, they expressed the CYP722A and CYP722B genes from 16 plant species, such as poplar, pepper, pea, and peach. Through further metabolic engineering, first author Anqi Zhou, a chemical engineering Ph.D. student in Li’s laboratory, discovered effective methods to optimize the output concentrations of strigolactones, exceeding 125 times the previous levels.

This enhanced concentration affords the researchers a sufficient quantity of material to ascertain the structure of any resultant compounds, which could potentially serve a significant role in plant physiology.

One such crucial molecule could be the novel compound generated by CYP722A or CYP722B: a strigolactone referred to as 16-hydroxy-carlactonic acid (16-OH-CLA).

Shoots over Roots

Although 16-OH-CLA has been noted previously, its precise structure and potential significance remained partially understood. The capacity to produce adequate amounts of 16-OH-CLA—thanks to the microbial cell factory—enabled the team to determine its precise structure for the first time.

Interestingly, when the researchers searched for 16-OH-CLA in plants, they only found it in the shoots rather than the roots, in contrast to all other recognized strigolactones. Furthermore, the compound is not consistently present. For annual plants such as pepper or common peas, it vanishes once the plant has matured. For trees like poplar, its presence is seasonal.

While the exact role of 16-OH-CLA is still unclear, its frequent occurrence among seed plants and in an atypical plant region indicates that it may have a vital, yet undervalued function, in plant signaling or adaptation to environmental pressures. Thanks to the novel engineering strategy, researchers will readily possess the quantities necessary to explore deeper—which is precisely the focus of Li and the team at present.

*These authors contributed equally to this work.

This research was backed by the National Science Foundation (CAREER Award CBET-2144626, IOS-1856741, and IOS-2329271, CAREER Award 2047396, Research Traineeship Program Grant DGE-1922642 “Plants3D”), USDA-NIFA (AFRI Predoctoral Fellowship 2023-67011-40396), Japan Science and Technology Agency (FOREST, JPMJFR220F), and JSPS (KAKENHI, 21H02125).