The lipid‐binding START domain regulates the dimerization of ATML1 via modulating the ZIP motif activity in Arabidopsis thaliana

Abstract

In Arabidopsis thaliana, the epidermis is the outermost cell layer composed of many specialized types of epidermal cells, such as pavement cells, trichomes, and guard cells. The homeodomain-leucine zipper (HD-ZIP) class Ⅳ transcription factors (TFs), which are unique to the plant kingdom, have been recognized as key regulators of epidermis development. Unlike animal HD proteins, which can bind to DNA as monomers, plant HD-ZIP class Ⅳ TFs bind to DNA as dimers, although little is known about the regulation of their dimerization process. Here, we show that the homodimerization of ARABIDOPSIS THALIANA MERISTEM LAYER 1 (ATML1) -HD-ZIP class Ⅳ TF that is required for protoderm development -is regulated by the lipid-binding steroidogenic acute regulatory protein-related lipid transfer (START) domain. We found that ATML1 forms homodimer through interaction via its ZIP motif in yeast and plant cells, although the interaction is abolished by generating a mutation into the lipid-binding START domain to disrupt the lipid-binding ability. These results suggest that lipidic ligands function as key regulators of protoderm development via modulating the dimerization of ATML1.

A conserved mechanism determines the activity of two pivotal transcription factors that control epidermal cell differentiation in Arabidopsis thaliana

“…The yeast two-hybrid analysis was performed as previously described (Nagata and Abe 2021 ). Briefly, the appropriate plasmids were transformed into the yeast strain Y2HGold (Takara) using the lithium acetate method.…”

“…PDF2 and ATML1 are expressed predominantly in the outermost cell layer of aerial organs (Abe et al 2003 ; Lu et al 1996 ; Nagata et al 2021 ; Sessions et al 1999 ) and immature roots before root cap sloughing (Nagata et al 2021 ). These TFs orchestrate the expression of epidermal cell-specific genes, some of which are involved in cuticle formation (e.g., FIDDLEHEAD , 3-KETOACYL-COA SYNTHASE 20, PASTICCINO 2 ) (Nagata and Abe 2021 ; Nagata et al 2021 ; Rombolá-Caldentey et al 2014 ), as well as maintaining SAM structure and function (e.g., microRNA171 family genes) (Han et al 2020 ). Consistently, hypomorphic pdf2-1; atml1-1 double mutants lack an epidermal cell layer in the aerial tissue (Abe et al 2003 ) and show a severe developmental delay of lateral root primordia formation (Nagata et al 2021 ).…”

“…The HDs of PDF2 and ATML1 act as DNA-binding domains and specifically bind to the L1 box, a well-conserved cis -regulatory element within the promoter regions of epidermal cell-specific genes (Abe et al 2001 , 2003 ; Han et al 2020 ; Nakamura et al 2006 ). The ZIP motifs of PDF2 and ATML1, which are located immediately downstream of their HDs, act as dimerization motifs and mediate the homodimerization of PDF2 and ATML1, and heterodimerization between PDF2 and ATML1 (Nagata and Abe 2021 ; Rombolá-Caldentey et al 2014 ; San-Bento et al 2014 ). Additionally, the START domains of PDF2 and ATML1 are also lipid-binding and interact with specific lipid ligands (Nagata et al 2021 ; Wojciechowska et al 2021 ), therefore demonstrating the similarities that each PDF2 and ATML1 domain share in terms of their biochemical properties.…”

“…First, the START domains of PDF2, ATML1, and GLABRA2 (GL2) bind to lipid ligands to stimulate TF activity in yeast cells (Schrick et al 2014 ). Second, the START domains of ATML1 and GL2 bind to their lipid ligands to protect them from turnover and affect the level of dimeric proteins in plant cells (Mukherjee et al 2022 ; Nagata and Abe 2021 ; Nagata et al 2021 ). In particular, very-long-chain fatty acid-containing ceramides (VLCFA-Cers), which are lipid ligands in the START domain of PDF2 and ATML1, are thought to be generated predominantly in the outermost cells (Nagata et al 2021 ).…”

The dynamics of HD-ZIP III - ZPR protein interactions play essential roles in embryogenesis, meristem function and organ development

“…The Arabidopsis genome contains five HD-ZIP III genes [REVOLUTA/IFL1 (REV), PHABULOSA/ATHB14 (PHB), PHAVOLUTA/ATHB9 (PHV), CORONA/ATHB15 (CNA) and ATHB8]. Members of this group share five predicted structural domains: A Homeodomain -a DNA binding domain, a leucine zipper domaina protein dimerization domain, a START domain -a motif with putative lipid binding capability (Nagata & Abe, 2021), a SAD domain -a putative transcriptional activation domain (De Caestecker et al, 2000), and a MEKHLA domaina protein-protein interaction domain, present exclusively in the class III members, possibly involved in oxygen redox and light signaling (Chandler et al, 2007;Duclercq et al, 2011;Magnani & Barton, 2011;Mukherjee & Bürglin, 2006). HD-ZIP IIIs play essential roles in Arabidopsis shoot development.…”