Polar auxin transport and PLETHORA gene action regulate Arabidopsis development and architecture

The mature Arabidopsis embryo contains two stem cell niches that upon germination bring forth and maintain the root meristem (RM) and shoot apical meristem (SAM). During seedling growth, the RM enables indeterminate elongation of the primary root, while the SAM produces true leaves. The resulting seedling further increases in complexity by continuous de novo organ formation, which involves positioning, formation and patterning of organ primordia. These primordia can produce leaves, flowers or the new growth axes of lateral roots or inflorescence stems. Cells within meristems are required to divide, elongate and differentiate without consuming the meristem to facilitate organ growth. Plant growth is plastic, but displays profound regularities that are thought to result from the interplay between endogenously determined developmental cues and environmental factors. In this thesis we have attempted to understand better the endogenous factors and mechanisms that control Arabidopsis development and architecture. We show that embryonic root formation requires the redundant activity of four PLETHORA (PLT) genes (PLT1-4), which function in a gene-dosage-dependent manner. These PLT proteins accumulate in gradients throughout the RM, with the highest levels required for stem cell niche maintenance, intermediate levels promoting mitotic cell division and low levels required for cell elongation. Lateral root initiation involves the formation of local auxin activity maxima. We have combined experiments and computational modelling to study the mechanism that establish these maxima and thus determine root system architecture. We found that root bending induces lateral root initiation on the outside of the bend. We performed computational modelling and found that cell size changes due to bending perturb auxin transport in such a manner that it positions higher auxin levels at the positions where lateral roots normally form. We show that such differences can be amplified by auxin influx carriers, which allows the precise definition of a new lateral root initiation site. Lateral organ formation in roots and shoots appears to be very different, but auxin has been shown to regulate both. The pattern of root and shoot branching thus might relate to similar mechanisms that position and restrict auxin activity maxima. So far, no transcription factors have been found to regulate branching of both roots and shoots, which would indicate that these branching systems evolved separately. However, we demonstrate that both branching mechanisms depend on the activity of three PLT genes, PLT3, 5 and 7. These genes are expressed through auxin accumulation at the sites of lateral root formation and their absence results in the clustering of root initiation sites. In the shoot, they regulate accumulation patterns of the PIN1 auxin transport protein to position primordia. Strikingly, plants that fail to express these PLT genes switch their pattern of leaf initiation from spiral to other regular patterns that are often observed within other plant species.