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

Abstract

ATP-dependent SWI/SNF chromatin remodelling complexes are conserved multi-subunit assemblies that control genome activity. Functions of SWI/SNF complexes in plant development and growth have been well established, but the architecture of particular assemblies is unclear. In this study, we elucidate the organization of Arabidopsis SWI/SNF complexes formed around a BRM catalytic subunit, and define the requirement of bromodomain-containing proteins BRD1/2/13 for the formation and stability of the entire complex. Using affinity purification followed by mass spectrometry, we identify a set of BRM-associated subunits and demonstrate that the BRM complexes strongly resemble mammalian non-canonical BAF complexes. Furthermore, we identify BDH1 and 2 proteins as components of the BRM complex and, using mutant analyses, show that BDH1/2 are important for vegetative and generative development, as well as hormonal responses. We further show that BRD1/2/13 represent unique subunits of the BRM complexes, and their depletion severely affects the integrity of the complex, resulting in the formation of residual assemblies. Finally, analyses of BRM complexes after proteasome inhibition revealed the existence of a module consisting of the ATPase, ARP, and BDH proteins, assembled with other subunits in a BRD-dependent manner. Together, our results suggest modular organization of plant SWI/SNF complexes and provide a biochemical explanation for mutant phenotypes.

Spotlight on Plant Bromodomain Proteins

“…Specifically, BRD1 (At1g20670), BRD2 (At1g76380) and BRD13 (At5g55040) were co-purified with subunits of Arabidopsis SWI/SNF complexes [ 57 ]. Subsequent studies have demonstrated that BRD1, BRD2 and BRD13 are unique components of Arabidopsis SWI/SNF complexes, thereby introducing the presence of non-ATPase BRD-containing subunits in these complexes [ 58 , 59 , 60 ]; however, note that they do not contribute equally to their formation of BRM-containing SWI/SNF complexes [ 60 ]. Comparative analysis indicated that BRD1, BRD2 and BRD13 are highly similar and clustered into a single phylogenetic cluster.…”

“…brd1, brd2 and brd13 mutants display early flowering compared to wt plants, indicating that BRD1, BRD2 and BRD13 act as repressors of flowering. Since double mutants presented pronounced phenotypes, a functional redundancy of these BRD-proteins is thought to occur, even though the levels of redundancy differ between them [ 58 , 59 , 60 ]. In comparison to single and double mutants, brdx3 triple mutants exhibited a general reduction in size, along with the production of smaller, curled leaves, shorter roots, early flowering and reduced fertility [ 58 , 59 ], a phenotype similar to brm mutants [ 58 , 59 ].…”

Characterization of the SWI/SNF complex and nucleosome organization in sorghum

“…Most of the SWI/SNF complex subunits have been revealed to play important roles in multiple processes of plant development, such as leaf, root, floral organ and seed development, flowering time control, shoot apical meristem maintenance, chlorophyll biosynthesis, and response to phytohormone ( Shang and He, 2022 ). The multi-copies of some subunits exhibit redundant functions like MINU1/2, BRD1/2/13, BRIP1/2, BDH1/2, and TPF1/2 ( Sang et al., 2012 ; Yu et al., 2020 ; Jaronczyk et al., 2021 ; Diego-Martin et al., 2022 ; Stachula et al., 2023 ). On the contrary, SWI3 proteins act non-redundantly to control different aspects of development ( Sarnowski et al., 2005 ).…”