Negative regulation of conserved RSL class I bHLH transcription factors evolved independently among land plants

Abstract

Basic helix-loop-helix transcription factors encoded by RSL class I genes control a gene regulatory network that positively regulates the development of filamentous rooting cells – root hairs and rhizoids – in land plants. The GLABRA2 transcription factor negatively regulates these genes in the angiosperm Arabidopsis thaliana. To find negative regulators of RSL class I genes in early diverging land plants we conducted a mutant screen in the liverwort Marchantia polymorpha. This identified FEW RHIZOIDS1 (MpFRH1) microRNA (miRNA) that negatively regulates the RSL class I gene MpRSL1. The miRNA and its mRNA target constitute a feedback mechanism that controls epidermal cell differentiation. MpFRH1 miRNA target sites are conserved among liverwort RSL class I mRNAs but are not present in RSL class I mRNAs of other land plants. These findings indicate that while RSL class I genes are ancient and conserved, independent negative regulatory mechanisms evolved in different lineages during land plant evolution.

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

“…Relatives of M. polymorpha have been extensively used to study fundamental questions of evolutionary ecology and population biology (Stark et al, 2005;Groen et al, 2010;Stieha et al, 2014;Brzyski et al, 2018). More recently, the phylogenetic position of M. polymorpha has made this species critical for understanding the evolution of gene regulatory networks across land plants (Breuninger et al, 2016;Bowman et al, 2017;Honkanen et al, 2018). Phylogenomic data now indicate that liverworts and mosses are monophyletic, and that the tracheophytes (vascular plants) are sister to the clade of bryophytes including mosses, liverworts, and hornworts (Wickett et al, 2014;Cox, 2018;Puttick et al, 2018).…”

Genome-wide Survey of bHLH Super Gene Family in Brassica napus and Their Roles in Roots

“…Accordingly, to date, many members in nine subfamilies of this gene family (S5, S7, S15, S23-S28) have been identified to regulate many root processes (Table 1). For example, AtbHLH156/LHW from subfamily S23 plays an essential role in establishing vascular cells and the size of the vascular initial population in the root meristem [38], and AtbHLH024/SPT in S24 regulates root growth by controlling the size of root meristem [42]; homologs of AtbHLH002/GL3 (S5), AtLRLs (S26) and AtRSLs (S28) are involved in root hair development [35,[43][44][45][46][47][48][49][50][51][52]; AtbHLH92 in S7 and AtbHLH129 in S27 regulate root elongation [53,54]; AtbHLH74 of S25 regulates seedling root growth [55]. Accordingly, BnbHLH orthologs of those functionally-characterized bHLHs also showed high expression levels in roots ( Fig.…”

Independent evolution of lateral inhibition mechanisms in different lineages of land plants: MpFEW RHIZOIDS1 miRNA-mediated lateral inhibition controls rhizoid cell patterning in Marchantia polymorpha

“…MpRSL1 promotes the expression of MpFRH1 which encodes a 21-nucleotide microRNA 64 (Honkanen et al, 2018). Evidence that MpFRH1 represses rhizoid cell development by 65 negatively regulating MpRSL1 activity include (i) FRH1 miRNA directly targets RSL1 mRNA for 66 DICERLIKE1-mediated cleavage and (ii) the rhizoidless phenotype of MpFRH1 overexpression 67 is suppressed by co-expressing an MpFRH1 miRNA-resistant version of MpRSL1 (Honkanen 68 et al, 2018).…”

“…The MpRSL1-MpFRH1 mechanism of lateral inhibition that controls the patterning of 358 rhizoid cells is liverwort-specific. MpFRH1 is a liverwort-specific miRNA and the miRNA 359 target sequence has been identified in the RSL genes of many liverwort taxa but has not 360 been found in RSL genes from any other lineage of land plants (Honkanen et al, 2018). This 361 indicates that the mechanism of lateral inhibition in the liverwort lineage is entirely 362 different from the two mechanisms that has been described among the angiosperms (Myb 363 repressor and EPF2).…”

“…Since MpRSL1 mRNA is the only confirmed target of MpFRH1, the production of this 330 hypothetical signal would likely also be MpRSL1-dependent (Honkanen et al, 2018). Third, 331 the repressive signal could be transmitted by cell contact through an unknown mechanism.…”