Decoding stem cell dynamics in plant growth and evolution

Advancing our understanding of plant epigenetics, a new study led by Ruben Gutzat from the “plant stem cell team” in Ortrun Mittelsten Scheid's laboratory at the Gregor Mendel Institute, unveils a genomic battle between plant stem cells and transposons. In the few stem cells in the shoot tip that give rise to future generations, plants’ genomic defense fights an onslaught of transposon activity. The findings are published on January 30 in the journal The Plant Cell.

Plants exhibit a development strikingly different from that of animals and can adjust their growth and organ formation in response to environmental conditions. This developmental plasticity, for instance, allows for the creation of Bonsai from trees, a process that is, of course, impossible with animals.

Stem cells, located at the tip of the plants and embedded in structures known as shoot apical meristems, orchestrate this development. Complete plant structures, including flowers, develop from these stem cells. Despite their crucial role in plant development, our knowledge about them remains limited, partly because isolating stem cells from plant tissue presents significant challenges.

In the new study, the “stem cell team” in Ortrun Mittelsten Scheid`s laboratory, spearheaded by Ruben Gutzat along with two PhD students, first authors Vu Nguyen and Gabriele Bradamante, has characterized shoot stem cells with a very high resolution. Doing so, the group pursued their long-standing interest in epigenetics. “Epigenetics encompasses everything inherited in addition to the genetic code. Epigenetic inheritance allows environmental influences to be passed from parent to offspring, potentially accelerating evolution”, explains postdoctoral fellow Gutzat and corresponding author of the study. Being the cells from which the future plant generation derives, stem cells are the theatre in which epigenetics plays out – a reason for the team to characterize them further.

The role of Argonautes in stem cell defense

Within the stem cells of the shoot apical meristem, the team has identified specific genes that are active in a special layer of cells in the subepidermis, which serve as progenitors for reproductive cells. In particular, two Argonaute (AGO) genes – AGO5 and AGO9 – are expressed at high levels in these cells. AGO proteins bind to small RNAs and use them as guides to silence transposable elements. “Transposons are egoistic genomic elements that can excise themselves, proliferate, and insert into a different location in the host genome,” explains Gutzat. “By jumping around the genome, transposons could significantly disrupt genome integrity – hence why defense mechanisms like AGO proteins arose to protect the genome.” Like antibodies in human immunity, the system of AGO proteins and small RNAs is adaptable to respond to different pathogens, including transposons as genomic pathogens.

Identifying that AGO5 and AGO9 are expressed in different combination in stem cells allowed the researchers to further characterize this cell population: the researchers labelled the cells with fluorescent reporters for both AGOs and then selected only the cells expressing both AGO5 and AGO9 for single-cell sequencing. This showed that transposons are highly active in these stem cells. Also, these transposons are processed into small RNAs by the cellular immune system and loaded onto AGO5 and AGO9.

The battle within: transposons vs. genome

“Usually, cells silence transposons. In the cells giving rise to the future generations, we now see a battle waged between transposons and the host genome”, Gutzat says. “From transposons’ point of view, this makes sense: If transposons want to replicate, they must be active in cells that are passed on to the next generation. And stem cells in turn must defend themselves against the transposons’ attack. An interplay between transposon activity and epigenetic control plays out, that we were previously not aware of.”

This discovery sheds new light on a long-standing debate in plant developmental and evolutionary biology regarding the extent to which plants possess quiescent cells that serve as direct precursors to reproductive cells, namely sperm and egg cells. For instance, it raises the question: Can a century-old tree yield seeds bursting with the same youthful vigor as those spawned by a tree in the prime of its life?

Previously, there was only indirect evidence to suggest that plants contain such quiescent cells, similar to animal germline cells, which play a critical role in preserving genomic integrity across generations. This study, however, offers pioneering evidence that subepidermal stem cells in plants might indeed host a plant 'germline' starting from early developmental stages.

Furthermore, this research also gives a glimpse into the early dynamics of stem cells in plant meristems. “As we lacked markers to focus on selective plant stem cells, we knew surprisingly little about this group of cells”, adds Mittelsten Scheid. “Now we know that plant stem cells differ in their behavior and activity even fairly early on, depending on their location within the meristem. The insights into the variability of stem cells paves the way for further research on transposon behavior, in particular how transposons are controlled through generations.”