The role of auxin in cell specification during arabidopsis embryogenesis

Auxin is a structurally simple molecule, yet it elicits many different responses in plants. In Chapter 1 we have reviewed how specificity in the output of auxin signaling could be generated by distinct regulation and the unique properties of the members of the Aux/IAA and ARF transcription factor families. In Chapter 2 we further investigated the generation of specificity in auxin responses by generating a set of sensitive transcriptional reporter lines for all Arabidopsis ARFs. This facilitated a comprehensive identification of the ARF complement within a cell/tissue of interest. Our analysis of ARF expression in the root meristem revealed both ubiquitous and specific ARF expression patterns and ARF subsets that distinguished the actively dividing cells from those undergoing elongation. Moreover, a striking correlation between cell type and ARF expression patterns was revealed in the early Arabidopsis embryo, where each cell type expressed a unique ARF complement. In Chapter 3 we characterized a novel cell-autonomous auxin response is required for hypophysis specification and root meristem initiation, and identify Aux/IAA and ARF transcription factors that mediate this response. We show that auxin response components in the proembryo and the suspensor are intrinsically different, and their regulated, lineage-specific expression creates a prepattern enabling different developmental auxin responses. Surprisingly, we find that, in addition to mediating hypophysis specification, auxin response also acts to maintain suspensor cell identity. We show that auxin controlled maintenance of suspensor cell identity includes repression of the embryonic program. This finding gave us an experimental system in which to investigate suspensor cell identity and embryonic transformation. In Chapter 4 the targeted and specific inhibition of auxin response in the suspensor was coupled to new embryo dissection techniques and a microarray based approach was used to generate a unique dataset which was subsequently mined for cell identity regulators. Unexpectedly, inhibition of auxin response induced the misregulation of thousands of genes, prior to gross morphological changes, revealing a high degree of transcriptional plasticity in these cells. This complicated the identification of regulators. Moreover, the dataset also included secondary/indirect changes in embryo expressed genes, which were inevitable given the connectivity and developmental connectedness between the embryo and suspensor. One of the most striking findings from analysis of the dataset generated in Chapter 4 was the convergent regulation of members of many gene families involved in all facets of auxin homeostasis, as investigated in Chapter 5. It appears that transient auxin response inhibition is sensed as an auxin minimum and in general auxin homeostasis genes were activated or repressed in such a way that would increase cellular auxin levels (and response). Finally, many bHLH superfamily members were misregulated upon the inhibition of suspensor auxin response and subsequently found to have specific expression patterns in the embryo, the focus of in Chapter 6. Several bHLHs were shown to lose their lineage specific expression patterns upon inhibition of auxin response in the suspensor, validating further research to place these factors into the auxin response pathways controlling cell identity in the embryo.