Recruitment and remodeling of an ancient gene regulatory network during land plant evolution

Abstract

The evolution of multicellular organisms was made possible by the evolution of underlying gene regulatory networks. In animals, the core of gene regulatory networks consists of kernels, stable subnetworks of transcription factors that are highly conserved in distantly related species. However, in plants it is not clear when and how kernels evolved. We show here that RSL (ROOT HAIR DEFECTIVE SIX-LIKE) transcription factors form an ancient land plant kernel controlling caulonema differentiation in the moss Physcomitrella patens and root hair development in the flowering plant Arabidopsis thaliana. Phylogenetic analyses suggest that RSL proteins evolved in aquatic charophyte algae or in early land plants, and have been conserved throughout land plant radiation. Genetic and transcriptional analyses in loss of function A. thaliana and P. patens mutants suggest that the transcriptional interactions in the RSL kernel were remodeled and became more hierarchical during the evolution of vascular plants. We predict that other gene regulatory networks that control development in derived groups of plants may have originated in the earliest land plants or in their ancestors, the Charophycean algae.T he development of multicellular organisms is controlled by gene regulatory networks (GRNs) and the reorganization of GRN architecture is thought to be a major factor underlying morphological evolution (1-5). GRNs are hierarchic and modular structures where four major component classes can be identified (3): at the periphery of GRNs are differentiation gene batteries encoding proteins that execute cell type-specific functions (such as building a pigmented cell); upstream of these batteries are switches that allow or prevent subcircuits to function in specific developmental contexts, and "plug-ins," small subcircuits that are flexibly and repeatedly used during development (such as signal transduction pathways); at the core of GRNs are kernels, small conserved subcircuits that execute specific developmental functions (such as defining spatial patterns in an embryo). Kernels are comprised of transcription factors that are highly conserved in distantly related species and are unusually stable components of GRNs.Ancient kernels that regulate body plan and organ development are highly conserved among diverse groups of metazoans (animals) (6-10). In contrast, the core components of plant GRNs are difficult to identify because of the dynamic nature of plant genome evolution and the plastic character of plant development. Floral homeotic genes form a relatively recent kernel controlling flower development (11). Homologs of KNOX and LEAFY transcription factors control shoot development in vascular plants and sporophyte development in mosses (12-15). KNOX/BEL genes also control the development of the diploid phase in unicellular chlorophytes (16) and the haploid-to-diploid transition in mosses (15), suggesting that KNOX and LEAFY genes may be core members of ancient GRNs that control diploid development in plants. Auxin signaling (17,18), et...

Conserved regulatory mechanism controls the development of cells with rooting functions in land plants

“…The mechanism of auxin-regulated caulonema and rhizoid development in P. patens involves key components of the auxinsignaling pathway that is conserved among land plants (8,9,11,(20)(21)(22)(23)31). We showed here that auxin positively regulates the expression of PpLRL1 and PpLRL2 and that the PpLRL genes are necessary for auxin-induced caulonema and rhizoid development.…”

“…Group VIII basic helix-loop-helix (bHLH) transcription factors encoded by ROOT HAIR DEFECTIVE SIX-LIKE (RSL) genes positively regulate root-hair development in the angiosperm Arabidopsis thaliana and both rhizoid and caulonema in the moss Physcomitrella patens (8)(9)(10)(11)(12). To test whether the conservation of RSL function is unique or indicative of a more general, conserved regulatory mechanism, we determined whether other components of the gene-regulatory network controlling angiosperm root-hair development are conserved among land plants.…”

Tracheophytes Contain Conserved Orthologs of a Basic Helix-Loop-Helix Transcription Factor That Modulate ROOT HAIR SPECIFIC Genes

“…RSL transcription factors are divided into two classes, class I RSLs (RHD6 and RSL1) and class II RSLs (RSL2-5), where class I RSLs regulate class II RSLs (Pires et al, 2013). RSL4 is the direct target of RHD6 (Yi et al, 2010).…”

“…Interestingly, the RSL4-orthologous genes from these bryophytes include multiple RHE-like motifs in their promoter regions as do the tracheophyte orthologs (Supplemental Figure 5), suggesting that the RSL4-RHE regulatory module may be found in bryophytes as well. The hierarchical relationship between class I and class II RSLs, where class I RSLs modulate class II RSLs, is conserved in both moss and Arabidopsis (Pires et al, 2013), and class I RSLs play a role in rhizoid development in liverwort and moss (Menand et al, 2007;Proust et al, 2016). Considering the morphological and functional similarity between root hairs and rhizoids, it is conceivable that the RSL4-RHE module might have emerged during early land plant evolution.…”

ROS Regulation of Polar Growth in Plant Cells

“…Furthermore, the overexpression of RSL proteins in Brachypodium spp., rice (Oryza sativa), and wheat (Triticum aestivum) promotes root hair growth, and MpRSL1 in the liverwort Marchantia polymorpha (Proust et al, 2016) and PpRSL1 and PpRSL2 in the moss Physcomitrella patens (Jang and Dolan, 2011) are regulated by auxin and trigger cell expansion. Consequently, the auxin-RSL module is thought to have been conserved during plant evolution as a master regulator of polar growth and may have been derived from the first land plants that lived almost 500 million years ago (Pires et al, 2013;Proust et al, 2016). It is unclear if the auxin-RSL module controlled polar cell expansion by triggering ROS production in the early plant lineages.…”