SNF2 Family from Maize
Required domains for SNF2 family:PF00176
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Sucrose nonfermenting 2 (Snf2) family of helicase related proteins are responsible for ATP dependent chromatin remodeling found in all eukaryotes, therefore playing role in wide range of nuclear processes like replication, transcription, DNA repair and homologous recombination. Members of this family are defined by helicase-like motifs containing highly conserved sequence blocks. The helicase-like region consists of SNF2_N and helicase_C conserved domains (Flaus et al., 2006). The Arabidopsis genome consists of 41 SNF2 proteins belonging to 19 subfamilies and the rice genome includes 40 SNF2 proteins divided into 18 subfamilies (Knizewski et al., 2008, Hu et al., 2013). From GEO database microarray and RT PCR based data for two week old rice seedlings treated with drought, cold and salt stress, some rice SNF2 members play divergent roles in response to these stress. Expression profiles for transcripts from different tissues at different developmental stages analysis indicated that some rice SNF2 members showed tissue specific expression (Hu et al., 2013).
Two redundant SNF2 family members, SNF2-RING-HELICASE-LIKE1 and 2 (FRG1 and 2) are associated with RNA dependent DNA methylation (RdDM) pathway, since methylation related defects were associated at RdDM targeted loci in FRG1 and 2 double mutants. From coimmunoprecipitation (Co-IP) assay, FGR1 physically interacts with a known RdDM component, a putative methyltransferase SUVR2 (Groth et al., 2014). From the tomato genome, 45 Snf2s were identified, distributed on 11 chromosomes and clustered in 6 groups. All identified Snf2s had variable amino acids in SNF2_N domain and about 80 amino acids in helicase_C domain. Tomato Snf2s show a wide range of distribution in different tissues during development and some Snf2s respond differently to various environmental stimuli such as salt, cold, salicyclic acid abscisic acid (Zhang et al., 2019). Rice snf2s shows tissue/organ specific expression during plant development. OsCHR722, OsCHR742, OsCHR735 and OsCHR746 are specifically expressed in SAM, OsCHR715 in Sti, OsCHR703 in S2 and OsCHR717 in S3 and also there are pistil development specific rice Snf2s, therefore aiding our understanding in rice Snf2s roles during vegetative and reproductive stage development. Rice Snf2s also play a role in biotic/abiotic stress response. In response to salt stress, seven of the rice snf2s (OsCHR705, OsCHR706, OsCHR710, OsCHR714, OsCHR721, OsCHR726, and OsCHR737) were upregulated and OsCHR712 gene was downregulated in response to drought stress. In response to Magnaporthe oryzaeinfection, most genes were induced immediately 12 h post infection (Guo et al., 2022). Rice endospermless1 (enl1) encoding snf2 family protein, produces seed without endosperm but functional embryo and contains ameboid nuclei caused due to mitotic chromosomal segregation malfunction during syncytial endosperm development. PIK1 Interacting Checkpoint Helicase (PICH) is human ortholog to ENL1 and plays a role in DNA catenation during anaphase. However, root meristem karyokinesis is affected due dysfunctional ENL1. Arabidopsis ortholog of ENL1, CHR24 loss of function results in normal plant development with less effect on endosperm nuclei. Thus, rice ENL1 is needed for syncytial endosperm development (Hara et al., 2014).Soybean genome consists of 66 snf2 family members distributed unevenly across 20 chromosomes. Based on real time PCR and expression analysis, most of the snf2s regulate soybean symbiotic nodulation since they are expressed in roots and nodule tissues and their expression is significantly downregulated in response to rhizobial infection (Wang et al., 2023). Among 32 snf2s genes present in barley, seven of them were highly expressed and showed diverse expression profiles during spike development, thus implying snf2s role in regulating spike development in barley (Chen et al., 2022). Rice endospermless 1 (enl1) encoding snf2 family protein, produces seed without endosperm but functional embryo and contains ameboid nuclei caused due to mitotic chromosomal segregation malfunction during syncytial endosperm development. PIK1 Interacting Checkpoint Helicase (PICH) is human ortholog to ENL1 and plays a role in DNA catenation during anaphase. However, root meristem karyokinesis is affected due dysfunctional ENL1. Arabidopsis ortholog of ENL1, CHR24 loss of function results in normal plant development with less effect on endosperm nuclei. Thus, rice ENL1 is needed for syncytial endosperm development (Hara et al., 2014).
Last updated June 2023 by Ankita Abnave
Flaus A, Martin DM, Barton GJ, Owen-Hughes T. Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucleic Acids Res. 2006 May 31;34(10):2887-905. doi: 10.1093/nar/gkl295. PMID: 16738128; PMCID: PMC1474054.
Hu Y, Zhu N, Wang X, Yi Q, Zhu D, Lai Y, Zhao Y. Analysis of rice Snf2 family proteins and their potential roles in epigenetic regulation. Plant Physiol Biochem. 2013 Sep;70:33-42. doi: 10.1016/j.plaphy.2013.05.001. Epub 2013 May 17. PMID: 23770592.
Knizewski L, Ginalski K, Jerzmanowski A. Snf2 proteins in plants: gene silencing and beyond. Trends Plant Sci. 2008 Oct;13(10):557-65. doi: 10.1016/j.tplants.2008.08.004. Epub 2008 Sep 9. PMID: 18786849.
Groth M, Stroud H, Feng S, Greenberg MV, Vashisht AA, Wohlschlegel JA, Jacobsen SE, Ausin I. SNF2 chromatin remodeler-family proteins FRG1 and -2 are required for RNA-directed DNA methylation. Proc Natl Acad Sci U S A. 2014 Dec 9;111(49):17666-71. doi: 10.1073/pnas.1420515111. Epub 2014 Nov 25. PMID: 25425661; PMCID: PMC4267348.
Zhang D, Gao S, Yang P, Yang J, Yang S, Wu K. Identification and Expression Analysis of Snf2 Family Proteins in Tomato (Solanum lycopersicum). Int J Genomics. 2019 Mar 28;2019:5080935. doi: 10.1155/2019/5080935. PMID: 31049349; PMCID: PMC6458923.
Guo M, Zhao H, He Z, Zhang W, She Z, Mohammadi MA, Shi C, Yan M, Tian D, Qin Y. Comparative Expression Profiling of Snf2 Family Genes During Reproductive Development and Stress Responses in Rice. Front Plant Sci. 2022 May 31;13:910663. doi: 10.3389/fpls.2022.910663. PMID: 35712583; PMCID: PMC9194907.
Wang J, Sun Z, Liu H, Yue L, Wang F, Liu S, Su B, Liu B, Kong F, Fang C. Genome-Wide Identification and Characterization of the Soybean Snf2 Gene Family and Expression Response to Rhizobia. Int J Mol Sci. 2023 Apr 14;24(8):7250. doi: 10.3390/ijms24087250. PMID: 37108411; PMCID: PMC10138738.
Chen G, Mishina K, Zhu H, Kikuchi S, Sassa H, Oono Y, Komatsuda T. Genome-Wide Analysis of Snf2 Gene Family Reveals Potential Role in Regulation of Spike Development in Barley. Int J Mol Sci. 2022 Dec 27;24(1):457. doi: 10.3390/ijms24010457. PMID: 36613901; PMCID: PMC9820626.
Hara T, Katoh H, Ogawa D, Kagaya Y, Sato Y, Kitano H, Nagato Y, Ishikawa R, Ono A, Kinoshita T, Takeda S, Hattori T. Rice SNF2 family helicase ENL1 is essential for syncytial endosperm development. Plant J. 2015 Jan;81(1):1-12. doi: 10.1111/tpj.12705. Epub 2014 Nov 11. PMID: 25327517.