Class C ARFs evolved before the origin of land plants and antagonize differentiation and developmental transitions in Marchantia polymorpha

Abstract

A plethora of developmental and physiological processes in land plants is influenced by auxin, to a large extent via alterations in gene expression by AUXIN RESPONSE FACTORs (ARFs). The canonical auxin transcriptional response system is a land plant innovation, however, charophycean algae possess orthologues of at least some classes of ARF and AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) genes, suggesting that elements of the canonical land plant system existed in an ancestral alga. We reconstructed the phylogenetic relationships between streptophyte ARF and AUX/IAA genes and functionally characterized the solitary class C ARF, MpARF3, in Marchantia polymorpha. Phylogenetic analyses indicate that multiple ARF classes, including class C ARFs, existed in an ancestral alga. Loss- and gain-of-function MpARF3 alleles result in pleiotropic effects in the gametophyte, with MpARF3 inhibiting differentiation and developmental transitions in multiple stages of the life cycle. Although loss-of-function Mparf3 and Mpmir160 alleles respond to exogenous auxin treatments, strong miR-resistant MpARF3 alleles are auxin-insensitive, suggesting that class C ARFs act in a context-dependent fashion. We conclude that two modules independently evolved to regulate a pre-existing ARF transcriptional network. Whereas the auxin-TIR1-AUX/IAA pathway evolved to repress class A/B ARF activity, miR160 evolved to repress class C ARFs in a dynamic fashion.

Minimal auxin sensing levels in vegetative moss stem cells revealed by a ratiometric reporter

“…The PpR2D2 data indicate that low auxin sensing activity might have been a key trait of such an ancestral stem cell. In M. polymorpha, auxin-induced activation of the single type A activating ARF has been suggested to induce cell differentiation, while type C repressing ARFs promote pluripotency (Flores-Sandoval et al, 2018), lending further support to this hypothesis. Low auxin activity in ancestral land plant stem cells is congruent with the idea that TIR-mediated auxin regulation might have arisen to stimulate differentiation through regulation of pre-existing ARF precursors already acting to balance cell proliferation and differentiation (Flores-Sandoval et al, 2018).…”

“…In M. polymorpha, auxin-induced activation of the single type A activating ARF has been suggested to induce cell differentiation, while type C repressing ARFs promote pluripotency (Flores-Sandoval et al, 2018), lending further support to this hypothesis. Low auxin activity in ancestral land plant stem cells is congruent with the idea that TIR-mediated auxin regulation might have arisen to stimulate differentiation through regulation of pre-existing ARF precursors already acting to balance cell proliferation and differentiation (Flores-Sandoval et al, 2018). The fact that PIN-FORMED (PIN)-mediated auxin export has been implicated as important to maintain low auxin activity in most For each rhizoid, a differential interference contrast image from a selected Z-plane (left) and a maximum-intensity projection of a Zstack with channels detecting mDII-nVENUS (green) and DII-nTdTOMATO (magenta) merged (right) are shown.…”

“…The core mechanisms for auxin sensing are conserved in P. patens and M. polymorpha , indicating that they were already in place in the common ancestors of flowering plants and bryophytes (i.e. in the earliest land plants; Prigge et al ., ; Lavy et al ., , ; Eklund et al ., ; Flores‐Sandoval et al ., , ; Kato et al ., , ; Plavskin et al ., ; Mutte et al ., ; Tao & Estelle, ).…”

Design principles of a minimal auxin response system

“…MpARF1 is a major mediator of auxin-dependent transcription, as mutation causes strong developmental phenotypes, auxin-insensitivity and loss of auxin-dependent transcription 12 . An Mp arf3 mutant also shows developmental defects, but no evident changes in auxin response 4,13 . When expressed from the Mp ARF1 promoter, neither MpARF2 nor MpARF3 complemented developmental defects in the Mp arf1 mutant (Fig.…”

Corrigendum

“…Since its publication, the authors of Flores‐Sandoval et al . () have brought to our attention an error in their article. At the end of the first paragraph in the Results, subsection ‘Origin and evolution of land plant ARF genes’ (p. 1615) a reference to Nishiyama et al .…”