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Conserved Regulatory Mechanism Controls the Development of Cells

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Conserved Regulatory Mechanism Controls the Development of Cells Conserved regulatory mechanism controls the PNAS PLUS development of cells with rooting functions in land plants Thomas Ho Yuen Tam, Bruno Catarino, and Liam Dolan1 Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom Edited by Philip N. Benfey, Duke University, Durham, NC, and approved June 11, 2015 (received for review August 22, 2014) Land plants develop filamentous cells—root hairs, rhizoids, and the moss Physcomitrella patens (8–12). To test whether the con- caulonemata—at the interface with the soil. Members of the servation of RSL function is unique or indicative of a more gen- group XI basic helix–loop–helix (bHLH) transcription factors en- eral, conserved regulatory mechanism, we determined whether coded by LOTUS JAPONICUS ROOTHAIRLESS1-LIKE (LRL) genes other components of the gene-regulatory network controlling an- positively regulate the development of root hairs in the angio- giosperm root-hair development are conserved among land plants. sperms Lotus japonicus, Arabidopsis thaliana, and rice (Oryza sat- Group XI bHLH transcription factors encoded by LOTUS iva). Here we show that auxin promotes rhizoid and caulonema JAPONICUS ROOTHAIRLESS1-LIKE (LRL) genes are also development by positively regulating the expression of PpLRL1 key regulators of root-hair development in angiosperms. LRL and PpLRL2, the two LRL genes in the Physcomitrella patens ge- genes encode several proteins that regulate root-hair devel- nome. Although the group VIII bHLH proteins, AtROOT HAIR opment in diverse angiosperms, including ROOTHAIRLESS1 DEFECTIVE6 and AtROOT HAIR DEFECTIVE SIX-LIKE1, promote root- (LjRHL1) in Lotus japonicus, AtLRL1, AtLRL2, AtLRL3 in hair development by positively regulating the expression of AtLRL3 A. thaliana (13, 14), and ROOTHAIRLESS1 (OsRHL1) in Oryza in A. thaliana, LRL genes promote rhizoid development indepen- sativa (15). Other LRL genes include OsPTF1, involved in dently of PpROOT HAIR DEFECTIVE SIX-LIKE1 and PpROOT HAIR phosphate starvation tolerance in rice (16), and AtUNE12, in- DEFECITVE SIX-LIKE2 (PpRSL1 and PpRSL2) gene function in volved in female gametophyte development in Arabidopsis PLANT BIOLOGY P. patens. Together, these data demonstrate that both LRL and (17). Here we define the function of LRL genes in the moss RSL genes are components of an ancient auxin-regulated gene P. patens and conclude that, together, LRL and RSL genes form network that controls the development of tip-growing cells with the core of an ancient network that operated in the common rooting functions among most extant land plants. Although this net- ancestor of the mosses and angiosperms that existed in the work has diverged in the moss and the angiosperm lineages, our data Silurian Period 415–435 million years ago. demonstrate that the core network acted in the last common ancestor of the mosses and angiosperms that existed sometime before 420 mil- Results lion years ago. Two LRL Genes Are Present in the Genome of the Moss P. patens. The LRL transcription factors belong to group XI of plant bHLH auxin | bHLH | evolution | rhizoids | root hairs transcription factors (18) and share a conserved LRL domain of 36 amino acids between the bHLH domain and the C terminus he evolution of rooting structures was a key morphological (Fig. 1A). To identify LRL homologs in P. patens, we performed Tinnovation that occurred when plants colonized the relatively BLAST searches in selected land plant genomes using the dry continental surfaces of the planet sometime before 470 million AtLRL3 (At5g58010) sequence as a query. Phylogenetic anal- year ago. The rooting structures of the earliest diverging groups of yses identified two LRL genes in P. patens,designatedPpLRL1 land plants comprised systems of rhizoids. Rhizoids are either unicellular filaments (in liverworts and hornworts) or multicel- Significance lular (in mosses) and elongate into the growth substrate or air surrounding the plant. Bryophyte (liverwort, moss, and hornwort) This work describes the discovery of an ancient genetic mech- rhizoids develop on gametophytes, the multicellular haploid stage anism that was used to build rooting systems when plants col- in the life cycle. The evolution of vascular plants was accompanied onized the relatively dry continental surfaces >470 million years by an increase in the morphological diversity of the sporophyte, ago. We demonstrate that a group of basic helix–loop–helix the diploid multicellular stage of the plant life cycle (1). Roots, transcription factors—the LOTUS JAPONICUS ROOTHAIRLESS1- multicellular axes derived from meristems with protective caps, LIKE proteins—is part of a conserved auxin-regulated gene were a key innovation that first appeared in the fossil record network that controls the development of tip-growing cells with ∼ — 380 million years ago and likely evolved at least twice at least rooting functions among extant land plants. This result suggests once among the Lycophytes and at least once in the Euphyllo- that this mechanism was active in the common ancestor of most phyte clade (2). Roots generally grow into the soil and expand land plants and facilitated the development of early land plant – the plant soil interface into different soil horizons. For example, filamentous rooting systems, crucial for the successful coloniza- some root systems extend deep into the soil (taproots), whereas tion of the land by plants. others proliferate in the nutrient-rich horizons near the soil sur- face. However, unicellular, filamentous protuberances called root Author contributions: T.H.Y.T. and L.D. designed research; T.H.Y.T. and B.C. performed hairs, which are morphologically similar to rhizoids, develop on research; T.H.Y.T., B.C., and L.D. analyzed data; and T.H.Y.T., B.C., and L.D. wrote all roots with few exceptions (2–5). Despite the different contexts the paper. in which they develop, root hairs and rhizoids carry out similar The authors declare no conflict of interest. rooting functions, including nutrient uptake and anchorage (6, 7). This article is a PNAS Direct Submission. Group VIII basic helix–loop–helix (bHLH) transcription fac- Freely available online through the PNAS open access option. tors encoded by ROOT HAIR DEFECTIVE SIX-LIKE (RSL) 1To whom correspondence should be addressed. Email: [email protected]. genes positively regulate root-hair development in the angio- This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. sperm Arabidopsis thaliana and both rhizoid and caulonema in 1073/pnas.1416324112/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1416324112 PNAS | Published online July 6, 2015 | E3959–E3968 Downloaded by guest on September 25, 2021 Fig. 1. (A) Schematic representation of gene structure and amino acid alignment of LRL transcription factors. Only the bHLH and LRL domains are shown. (B) Tree of LRL proteins and related groups of bHLH proteins based on ML statistics. This tree resolved PpLRL1, PpLRL2, OsRHL1, AtLRL1, AtLRL2, AtLRL3, AtLRL4, and AtUNE12 within a monophyletic group, which also contains four additional rice and four additional Selaginella moellendorffii genes (Fig. S1). aLRT values are indicated above the nodes. Two other groups of plant bHLHs involved in root-hair and rhizoid development, group VIIIc (1) encoded by the class I RSL genes, and group VIIIc (2) encoded by the class II RSL genes, are labeled in red and green, respectively. The full ML and Bayesian trees are shown in Fig. S1.(C) Unrooted tree showing the relationships of different LRL proteins in land plants using Bayesian statistics. The location of selected LRL proteins from the moss P. patens (Pp), the monocot O. sativa (Os), and the eudicot A. thaliana (At) are indicated in the diagram. The full ML and Bayesian trees are shown in Fig. S2. (Pp1s173_83V6.1) and PpLRL2 (Pp1s209_22V6.2), respectively of a uniseriate filamentous network (protonema) comprising (Fig. 1B). Maximum- likelihood (ML) analysis resolved PpLRL1, cells with large chloroplasts and transverse cell walls (chlor- PpLRL2, AtLRL1 (At2g24260), AtLRL2 (At4g30980), AtLRL3, onema cells). Subsequently, increasingly longer cells with oblique AtLRL4 (At1g03040), AtUNE12 (At4g02590), five rice proteins cell walls (caulonema cells) develop. Caulonema cells are mor- including OsRHL1 (Os06g08500), and four Selaginella moellen- phologically and genetically similar to rhizoids (19). Both dorffii proteins into a monophyletic group (Fig. 1B, Fig. S1, and PpLRL1 and PpLRL2 were expressed in the central region of the Dataset S1). The LRL domains of PpLRL1 and PpLRL2 are protonema, which is rich in chloronema and from which caulo- 97.2% identical to each other and are 77.8% and 80.6% identical nema develop (Fig. 2 A and B). No expression was detected in to the LRL domain of the AtLRL3 protein, respectively. The two the very edges of the 30-d-old protonema, where caulonema is PpLRL proteins have conserved bHLH domains that are 100% the dominant cell type. These observations suggest that PpLRL1 identical to each other (Fig. 1A). The bHLH domains of the and PpLRL2 are active in cells that develop caulonema. PpLRL proteins are 92.4% identical to the bHLH domain of PpLRL1 promoter was also active in the rhizoid-forming re- the AtLRL3 protein. To infer the phylogenetic relationship of the gion at the base of the gametophore in plants in which the different proteins containing the LRL domain, we constructed PpLRL1 CDS was replaced by the GUS-reporter gene (Fig. 2 C phylogenetic trees using Bayesian and ML methods (Fig. 1C and and D). However, no GUS expression was detected in rhizoids Fig. S2). These trees showed that LRL homologs are present in all themselves. This expression pattern is consistent with a role for 32 land plant species sampled (Fig. S3). The LRL proteins com- PpLRL1 in the regulation of the earliest stages of rhizoid de- prise three major groups, designated XIa, XIb, and XIc (Fig. 1C velopment. PpLRL1 promoter was also active in the gameto- and Fig. S2). Genes that control the development of root hairs are phore apex and leaves, suggesting that this gene likely controls present in group XIa (Fig.
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