LFR Physically and Genetically Interacts With SWI/SNF Component SWI3B to Regulate Leaf Blade Development in Arabidopsis

Abstract

Leaves start to develop at the peripheral zone of the shoot apical meristem. Thereafter, symmetric and flattened leaf laminae are formed. These events are simultaneously regulated by auxin, transcription factors, and epigenetic regulatory factors. However, the relationships among these factors are not well known. In this study, we conducted protein-protein interaction assays to show that our previously reported Leaf and Flower Related (LFR) physically interacted with SWI3B, a component of the ATP-dependent chromatin remodeling SWI/SNF complex in Arabidopsis. The results of truncated analysis and transgenic complementation showed that the N-terminal domain (25–60 amino acids) of LFR was necessary for its interaction with SWI3B and was crucial for LFR functions in Arabidopsis leaf development. Genetic results showed that the artificial microRNA knockdown lines of SWI3B (SWI3B-amic) had a similar upward-curling leaf phenotype with that of LFR loss-of-function mutants. ChIP-qPCR assay was conducted to show that LFR and SWI3B co-targeted the promoters of YABBY1/FILAMENTOUS FLOWER (YAB1/FIL) and IAA carboxyl methyltransferase 1 (IAMT1), which were misexpressed in lfr and SWI3B-amic mutants. In addition, the association between LFR and the FIL and IAMT1 loci was partly hampered by the knockdown of SWI3B. These data suggest that LFR interacts with the chromatin-remodeling complex component, SWI3B, and influences the transcriptional expression of the important transcription factor, FIL, and the auxin metabolism enzyme, IAMT1, in flattened leaf lamina development.

BRM Complex in Arabidopsis Adopts ncBAF-like Composition and Requires BRD Subunits for Assembly and Stability

“…We noticed that a number of known SWI/SNF members, including SWI3A/B/D [ 7 ], BSH (an SNF5 homolog) [ 24 ], and LFR (a homolog of ARID1/2 subunits) [ 20 , 25 ], were not detected in the IP/MS experiments using BRM-GFP ( Figure 3 a, Table S2 ). We reasoned that the subunits frequently identified in BRM-GFP IPs represent the most abundant BRM complex, while the absent subunits are part of separate SWI/SNF complexes containing SYD, CHR12, or CHR23, but not BRM ATPase.…”

Chromatin‐remodeling complexes: Conserved and plant‐specific subunits in Arabidopsis

“…In the future, additional molecular mechanisms should be explored to reveal how these chromatin regulators coordinately function in transcriptional regulation. Four SWI/SNF‐type ATPases, including BRM, SYD, MINU1, and MINU2, and many conserved accessory subunits of SWI/SNF complexes have been identified in Arabidopsis (Brzeski et al, 1999; Sarnowski et al, 2002; Wagner and Meyerowitz, 2002; Farrona et al, 2004; Crane and Gelvin, 2007; Wang et al, 2009; Vercruyssen et al, 2014; Yu et al, 2020; Jarończyk et al, 2021; Lin et al, 2021). How many subtypes of SWI/SNF complexes are formed by these ATPases and the components for each subtype remain to be determined.…”

“…However, some of the interactions detected by Y2H assay require confirmation by in vivo assays. Immunoprecipitation combined with mass spectrometry (IP‐MS) has been used to identify the following Arabidopsis SWI/SNF components: LFR, which is an ARM (Armadillo)‐repeat protein and is homologous to the ARID2 (AT‐rich interaction domain 2) protein belonging to the human pBAF complex (Wang et al, 2009; Lin et al, 2021); three bromodomain‐containing proteins, that is, BRD1 (bromodomain‐containing protein 1), BRD2, and BRD13 (BRD1/2/13) (Vercruyssen et al, 2014; Jarończyk et al, 2021); and AN3 (ANGUSTIFOLIA3) (Vercruyssen et al, 2014). Two homologous GLTSCR domain‐containing proteins, BRIP1 (BRAHMA‐interacting protein 1) and BRIP2, were identified as components of BRM‐containing SWI/SNF complexes by IP‐MS (Yu et al, 2020) (Figure 1B).…”

“…A number of protein–protein interactions have been detected among different components of SWI/SNF complexes, advancing our understanding of how the SWI/SNF complexes are assembled in Arabidopsis . As determined by yeast two‐hybrid (Y2H) assays, SWI3A, SWI3B, and SWI3C interact with each other, while SWI3D interacts only with SWI3B (Sarnowski et al, 2002; Sarnowski et al, 2005); BSH and LFR (LEAF AND FLOWER RELATED) interact with SWI3A and SWI3B (Sarnowski et al, 2005; Lin et al, 2021); SWP73A interacts with SWI3C, whereas SWP73B interacts with both SWI3C and SWI3D (Sacharowski et al, 2015); BRM strongly interacts with SWI3C and weakly interacts with SWI3B (Farrona et al, 2004; Hurtado et al, 2006). However, some of the interactions detected by Y2H assay require confirmation by in vivo assays.…”

The roles of epigenetic modifications in the regulation of auxin biosynthesis

“…As a homologous protein of ARP6, ARP4 represses the transcription of YUC9 through exchanging H2A with the histone variant H2A.Z (Lee and Seo, 2017 ), but it remains unknown if the release of YUC9 transcriptional inhibition is related to HDA-PWR complex-mediated histone deacetylation. Moreover, in Arabidopsis leaf development, the expression of the auxin metabolism gene IAMT1 (encoding an enzyme that converts IAA into its methyl ester) and biosynthetic gene YUC6 were regulated by the subunit SWI3B of the chromatin remodeling complex SWI/SNF (Han et al, 2018 ; Lin et al, 2021 ).…”