Each multicellular organism, much like the communities they belong to, is not a discrete biological unit, but an union of elements that require constant communication in order to sustain growth. In both animals and plants, small peptide hormones serve as one such means of intercellular correspondence, typically secreted into the apoplastic space to be perceived by receptors in neighbouring cells. These molecular messengers form intricate feedback pathways that allow connective tissue layers to coordinate their diverse roles and functions.

A large family of signaling molecules called CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) is conserved throughout the evolution of the land plant lineage. Its members encode prepropeptides that are processed into small 12-13 amino acid ligands, whose functions are implicated in diverse developmental processes, including cell fate acquisition, cell proliferation, and cell division plane orientation. The founding member of the CLE family is CLAVATA3 (CLV3), which is expressed at the shoot apex of the mustard plant Arabidopsis thaliana, to mediate activity of the stem cell niche there, also called the shoot apical meristem (SAM). The CLV3 signal is perceived by multiple receptor complexes in the underlying tissue layers, triggering a pathway that targets the homeodomain transcription factor WUSCHEL (WUS). WUS is a mobile protein that promotes stem cell identity within its area of effect, while also directly activating CLV3 expression. In turn, CLV3 signaling represses WUS expression and confines its domain to a few cells at the center of the SAM. The ensuing feedback loop between CLV3 and WUS thus maintains a small but stable stem cell population at the shoot tip, which proliferates to supply building materials for various growth processes aboveground, including vertical extension and generation of organs such as leaves, flowers, and axillary branches.

In this study, I characterized the biological functions of three genes related to CLV3, CLE16, CLE17, and CLE27, all of which are also expressed at the shoot apex of Arabidopsis. By themselves, CLE16, CLE17, and CLE27 appear to have no significant impact on stem cell activity at the SAM and overall plant architecture. However, via analyzing higher order mutants, I demonstrated that in the loss of endogenous CLV3 activity, the CLE16 and CLE17 peptides can independently act in its place to restrict stem cell accumulation, starting at the embryonic stage and throughout the entirety of the life cycle, ending at flower production. In contrast, CLE27 does not compensate for the loss of CLV3 signaling at least in the final stage of floral development. The ability of CLE16 and CLE17 to partially, but not fully, replace CLV3 function may stem from their binding affinity to a subset of CLV3’s cognate receptors. In addition, while the CLE16 and CLE17 signaling pathways appear to target WUS in a similar manner to CLV3, I provided evidence that both may have WUS-independent functions that are specific to the development of axillary branches. Together, these observations describe a complex interrelation that both expand upon the known CLV-WUS module, and reveal novel aspects in the regulation of shoot stem cell activity by CLE peptides.

Finally, I characterized functions of two other CLE genes in Arabidopsis leaves, CLE5 and CLE6. Both genes are expressed at the base of developing leaves, and appear to have a minor impact on overall leaf shape. Their expression levels are responsive to various transcription factors involved in leaf patterning, as well as the phytohormones auxin. This study provides the first instance of CLE peptides regulating leaf morphology, and thus opens up a new avenue for investigating the genetic regulation of leaf development in land plants.