CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice

Gonin Mathieu, Jeong Kwanho, Coudert Yoan, Lavarenne Jeremy, Hoang Giang Thi, Bes Martine, To Huong Thi Mai, Thiaw Marie-Rose Ndella, Do Toan Van, Moukouanga Daniel, Guyomarc'h Soazig, Bellande Kevin, Brossier Jean-Rémy, Parizot Boris, Nguyen Hieu Trang, Beeckman Tom, Bergougnoux Véronique, Rouster Jacques, Sallaud Christophe, Laplaze Laurent, Champion Anthony, Gantet Pascal. 2022. CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice. Plant Journal, 111 (2) : 546-566.

https://doi.org/10.1111/tpj.15838

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Résumé : In cereals, the root system is mainly composed of post-embryonic shoot-borne roots, named crown roots. The CROWN ROOTLESS1 (CRL1) transcription factor, belonging to the ASYMMETRIC LEAVES2-LIKE/LATERAL ORGAN BOUNDARIES DOMAIN (ASL/LBD) family, is a key regulator of crown root initiation in rice (Oryza sativa). Here, we show that CRL1 can bind, both in vitro and in vivo, not only the LBD-box, a DNA sequence recognized by several ASL/LBD transcription factors, but also another not previously identified DNA motif that was named CRL1-box. Using rice protoplast transient transactivation assays and a set of previously identified CRL1-regulated genes, we confirm that CRL1 transactivates these genes if they possess at least a CRL1-box or an LBD-box in their promoters. In planta, ChIP-qPCR experiments targeting two of these genes that include both a CRL1- and an LBD-box in their promoter show that CRL1 binds preferentially to the LBD-box in these promoter contexts. CRISPR/Cas9-targeted mutation of these two CRL1-regulated genes, which encode a plant Rho GTPase (OsROP) and a basic helix–loop–helix transcription factor (OsbHLH044), show that both promote crown root development. Finally, we show that OsbHLH044 represses a regulatory module, uncovering how CRL1 regulates specific processes during crown root formation.

Mots-clés Agrovoc : Oryza sativa, système racinaire, Transcription génique, transcription d'ADN, adn, racine, expression des gènes, facteur de transcription, séquence nucléotidique, Houppier

Mots-clés libres : ASL/LBD transcription factor, CRL1, DNA binding domain, Crown root, Development, Rice, Gene regulatory network, Oryza sativa

Agences de financement hors UE : Ministry of Science and Technology of Vietnam, Ambassade de France au Vietnam, Agence Nationale de la Recherche

Projets sur financement : (VNM) Application of functional genomics and association genetics to characterize genes involved in abiotic stresses tolerance in rice, (FRA) Détermination de gènes régulateurs maîtres du développement des racines coronaires pour l'ingénierie de la tolérance au déficit hydrique des céréales., (FRA) Agricultural Sciences for sustainable Development

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