SWI/SNF-SWI3 Family from Maize

Required domains for SWI/SNF-SWI3 family:PF04433

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SWI/SNF-SWI3 gene family members possess a conserved SWIRM domain (PF04433, IPR007526). The SWIRM domain is a small α-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain mediates protein-protein interactions in the assembly of chromatin-protein complexes (Aravind et al., 2002). The yeast SWI3 SWIRM structure revealed that it forms a four-helix globular domain containing a helix-turn-helix motif (Da et al., 2006).

Plant SWIRM domain proteins can be divided into three distinct types: Swi-type, LSD1-type, and Ada2-type. Generally, the SWIRM domain forms a helix-turn-helix motif commonly found in DNA-binding proteins. Based on the domain architectures and the amino acid sequence homology, the SWIRM domains can be classified into three main types: Swi3/MYSM1 (human MYb-like, Swirm, and Mpn domain-containing protein-1), LSD1 (Lysine-specific demethylase 1), and Ada2 (Adenosine deaminase isoenzymes 2) types (Yoneyama et al., 2007). Swi3p-type SWIRM domain-containing proteins are homologous to the ATP-dependent chromatin remodeling complexes SWI/SNF. LSD1-type SWIRM domain-containing proteins belong to Lysine-specific demethylase. LSD1 is the first histone demethylase discovered, and it belongs to the superfamily of the flavin adenine dinucleotide (FAD)-dependent amine oxidases (Tochio et al., 2006). Ada2-types SWIRM domain-containing proteins are homologs of transcriptional adaptor ADA2a, which promotes histone lysine acetylation and transcriptional activation and acts as a molecular scaffold within the SAGA remodeling complex (Sterner et al., 2002).

The genes encoding SWIRM domain proteins in Oryza sativa are widely expressed, especially in pistils. In addition, OsCHB701 and OsHDMA701 were downregulated by cold stress, whereas OsHDMA701 and OsHDMA702 were significantly induced by heat stress. These observations indicate that SWIRM domain proteins may play an essential role in plant development and plant responses to environmental stress (Gao et al., 2012).  There are at least 5 SWI3 members in maize. SWI3B is an Arabidopsis thaliana homologue of yeast SWI3, a subunit of the SWI/SNF complex. It has been shown to interact with HAB1(hypersensitive to ABA 1), a protein that plays a key role as a negative regulator of ABA signaling. HAB1 modulates ABA response through its interaction with SWI3B and thus, the regulation of the SWI/SNF complex (Saez et al., 2008, Kumari et al., 2022).

Last updated June 2023 by John Gray


Aravind L, Iyer LM. The SWIRM domain: a conserved module found in chromosomal proteins points to novel chromatin-modifying activities. Genome Biol. 2002 Jul 24;3(8):RESEARCH0039. doi: 10.1186/gb-2002-3-8-research0039. Epub 2002 Jul 24. PMID: 12186646; PMCID: PMC126233.

Da G, Lenkart J, Zhao K, Shiekhattar R, Cairns BR, Marmorstein R. Structure and function of the SWIRM domain, a conserved protein module found in chromatin regulatory complexes. Proc Natl Acad Sci U S A. 2006 Feb 14;103(7):2057-62. doi: 10.1073/pnas.0510949103. Epub 2006 Feb 3. PMID: 16461455; PMCID: PMC1413740.

Gao Y, Yang S, Yuan L, Cui Y, Wu K. Comparative Analysis of SWIRM Domain-Containing Proteins in Plants. Comp Funct Genomics. 2012;2012:310402. doi: 10.1155/2012/310402. Epub 2012 Jul 17. PMID: 22924025; PMCID: PMC3424641.

Yoneyama M, Tochio N, Umehara T, Koshiba S, Inoue M, Yabuki T, Aoki M, Seki E, Matsuda T, Watanabe S, Tomo Y, Nishimura Y, Harada T, Terada T, Shirouzu M, Hayashizaki Y, Ohara O, Tanaka A, Kigawa T, Yokoyama S. Structural and functional differences of SWIRM domain subtypes. J Mol Biol. 2007 May 25;369(1):222-38. doi: 10.1016/j.jmb.2007.03.027. Epub 2007 Mar 19. PMID: 17428495.

Tochio N, Umehara T, Koshiba S, Inoue M, Yabuki T, Aoki M, Seki E, Watanabe S, Tomo Y, Hanada M, Ikari M, Sato M, Terada T, Nagase T, Ohara O, Shirouzu M, Tanaka A, Kigawa T, Yokoyama S. Solution structure of the SWIRM domain of human histone demethylase LSD1. Structure. 2006 Mar;14(3):457-68. doi: 10.1016/j.str.2005.12.004. PMID: 16531230.

Sterner DE, Wang X, Bloom MH, Simon GM, Berger SL. The SANT domain of Ada2 is required for normal acetylation of histones by the yeast SAGA complex. J Biol Chem. 2002 Mar 8;277(10):8178-86. doi: 10.1074/jbc.M108601200. Epub 2002 Jan 2. PMID: 11777910.

Saez A, Rodrigues A, Santiago J, Rubio S, Rodriguez PL. HAB1-SWI3B interaction reveals a link between abscisic acid signaling and putative SWI/SNF chromatin-remodeling complexes in Arabidopsis. Plant Cell. 2008 Nov;20(11):2972-88. doi: 10.1105/tpc.107.056705. Epub 2008 Nov 25. PMID: 19033529; PMCID: PMC2613670.

Kumari P, Khan S, Wani IA, Gupta R, Verma S, Alam P, Alaklabi A. Unravelling the Role of Epigenetic Modifications in Development and Reproduction of Angiosperms: A Critical Appraisal. Front Genet. 2022 May 18;13:819941. doi: 10.3389/fgene.2022.819941. PMID: 35664328; PMCID: PMC9157814.





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