An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy

Single cell sequencing has recently allowed the generation of exhaustive root cell atlases. However, some cell types are elusive and remain underrepresented. Here, we use a second- generation single cell approach, where we zoom in on the root transcriptome sorting with specific markers to profile the phloem poles at an unprecedented resolution. Our data highlight the similarities among the developmental trajectories and gene regulatory networks communal to protophloem sieve element (PSE) adjacent lineages in relation to PSE enucleation, a key event in phloem biology.As a signature for early PSE-adjacent lineages, we have identified a set of DNA-binding with one finger (DOF) transcription factors, the PINEAPPLEs (PAPL), that act downstream of PHLOEM EARLY DOF (PEAR) genes, and are important to guarantee a proper root nutrition in the transition to autotrophy.Our data provide a holistic view of the phloem poles that act as a functional unit in root development.

A giant cell enhancer achieves cell-type specificity through activation via TCP and repression by Dof transcription factors

Proper pattern formation relies on the tight coordination of cell fate specification and cell cycle regulation in growing tissues. How this can be organized at enhancers that activate gene expression necessary for differentiation is not well understood. One such example is the patterning of the Arabidopsis thaliana sepal epidermis where giant cell fate specification is associated with the endoreduplication cell cycle. Previously, we identified an enhancer region capable of driving giant cell-specific expression. In this study, we use the giant cell enhancer as a model to understand the regulatory logic that promotes cell-type specific expression. Our dissection of the enhancer revealed that giant cell specificity is achieved primarily through the combination of two elements: an activator and a repressor. TCP transcription factors are involved in activation of non-specific expression throughout the epidermis with higher expression in endoreduplicated giant cells than small cells. Dof transcription factors act via the second element to repress activity of the enhancer and limit expression to giant cells. Thus, we find that cell-type specific expression emerges from the combined activities of two broadly acting enhancer elements.

The DOF Transcription Factors in Seed and Seedling Development

The DOF (DNA binding with one finger) family of plant-specific transcription factors (TF) was first identified in maize in 1995. Since then, DOF proteins have been shown to be present in the whole plant kingdom, including the unicellular alga Chlamydomonas reinhardtii. The DOF TF family is characterised by a highly conserved DNA binding domain (DOF domain), consisting of a CX2C-X21-CX2C motif, which is able to form a zinc finger structure. Early in the study of DOF proteins, their relevance for seed biology became clear. Indeed, the PROLAMIN BINDING FACTOR (PBF), one of the first DOF proteins characterised, controls the endosperm-specific expression of the zein genes in maize. Subsequently, several DOF proteins from both monocots and dicots have been shown to be primarily involved in seed development, dormancy and germination, as well as in seedling development and other light-mediated processes. In the last two decades, the molecular network underlying these processes have been outlined, and the main molecular players and their interactions have been identified. In this review, we will focus on the DOF TFs involved in these molecular networks, and on their interaction with other proteins.

The DOF Transcription Factors in Seed and Seedling Development

The DOF (DNA binding with one finger) family of plant-specific transcription factors (TF) was first identified in maize in 1995. Since then, DOF proteins have been shown to be present in the whole plant kingdom including the unicellular alga Chlamydomonas reinhardtii. The DOF TF family is characterised by a highly conserved DNA binding domain (DOF domain), consisting of a CX2C-X21-CX2C motif which is able to form a zinc finger structure. Early in the study of DOF proteins it became clear their relevance for seed biology. Indeed, the Prolamine Binding Factor (PBF), one of the first DOF proteins characterised, controls the endosperm-specific expression of the zein genes in maize. Subsequently, several DOF proteins from both monocots and dicots have been shown to be primarily involved in seed development, dormancy and germination, as well as in seedling development and other light-mediated processes. In the last two decades the molecular network underlying these processes have been outlined, and the main molecular players and their interactions have been identified. In this review, we will focus on the DOF TFs involved in these molecular networs, and on their interaction with other proteins.