Alfin-like Family from Maize

Required domains for Alfin-like family:PF12165

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The Alfin1-like (AL)  family was first described by its founding member, Alfin1. The cDNA of Alfin1 was obtained by differential screening of a poly(A)+ library from salt-tolerant alfalfa cells, which encodes a protein with a Cys4 and His/Cys3 putative zinc-binding domain. The putative consensus binding site for Alfin1 is shown to contain two to five G-rich triplets with the conserved core of GNGGTG or GTGGNG  (Bastola et al., 1998).  The AL proteins have been proposed to bind H3K4me3 through their PHD domain and to recruit PRC1 (Molitor et al., 2014; Peng et al., 2018). Since most AL proteins can bind to the conserved cis-element GNGGTG/GTGGNG (ALFIN1 elements) (Bastola et al., 1998; Wei et al., 2015), this raises the possibility that PRC1 could be tethered to specific sites by the AL proteins independently of VAL1/2. In support of this possibility, the promoters of genes upregulated in the bmi1abc mutant are enriched in ALFIN1 elements (Merini et al., 2017). Alfin1-binding sites occur in promoters of genes expressed in roots of a wide variety of plant species. Overexpression of Alfin1 in transgenic alfalfa plants driven by the CaMV 35S promoter confers a many-fold increase in root growth under normal and saline conditions and does not adversely affect shoot growth  (Winicov et al.,2000).  An RNA-seq meta analysis also links ALs to drought response (Benny et al., 2019).

Alfin1-like proteins in Arabidopsis thaliana have been shown to localize to the nucleus and binds to trimethylated lysine 4 on histone 3 (H3K4me3/2) via plant homeodomain (PHD) fingers Lee et al 2009. Later it was shown that Arabidopsis PHD-domain H3K4me3-binding ALFIN1-like proteins (ALs) functions as novel interactors of the Polycomb Repressive Complex 1 (PRC1) core components AtBMI1b and AtRING1a (Molitor et al., 2014).  This study proposed that AL PHD-PRC1 complexes, built around H3K4me3, lead to a switch from the H3K4me3-associated active to the H3K27me3-associated repressive transcription state of seed developmental genes during seed germination.  The PHD domain of AL proteins was reported to bind H3K4me3 (Zhao et al., 2018), and the PAL domain has been involved in the interaction with RING1 and BMI1 (Peng et al., 2018).

Last updated June 2023 by John Gray


Bastola D.R., Pethe V.V., Winicov I. Alfin1, a novel zinc-finger protein in alfalfa roots that binds to promoter elements in the salt-inducible MsPRP2 gene. Plant Mol. Biol. 1998;38:1123–1135 (PMID:9869418).

Winicov I. Alfin1 transcription factor overexpression enhances plant root growth under normal and saline conditions and improves salt tolerance in alfalfa. Planta. 2000 Feb;210(3):416-22. doi: 10.1007/PL00008150. PMID: 10750899.

Lee WY, Lee D, Chung WI, Kwon CS. Arabidopsis ING and Alfin1-like protein families localize to the nucleus and bind to H3K4me3/2 via plant homeodomain fingers. Plant J. 2009 May;58(3):511-24. doi: 10.1111/j.1365-313X.2009.03795.x. Epub 2009 Jan 18. PMID: 19154204.

Wei W., Zhang Y.-Q., Tao J.-J., Chen H.-W., Li Q.-T., Zhang W.-K., Ma B., Lin Q., Zhang J.-S., Chen S.-Y. The Alfin-like homeodomain finger protein AL5 suppresses multiple negative factors to confer abiotic stress tolerance in Arabidopsis. Plant J. 2015;81:871–883.

Merini W., Romero-Campero F.J., Gomez-Zambrano A., Zhou Y., Turck F., Calonje M. The Arabidopsis polycomb repressive complex 1 (PRC1) components AtBMI1A, B, and C impact gene networks throughout all stages of plant development. Plant Physiol. 2017;173:627–641.

Molitor AM, Bu Z, Yu Y, Shen WH. Arabidopsis AL PHD-PRC1 complexes promote seed germination through H3K4me3-to-H3K27me3 chromatin state switch in repression of seed developmental genes. PLoS Genet. 2014 Jan;10(1):e1004091. doi: 10.1371/journal.pgen.1004091. Epub 2014 Jan 23. PMID: 24465219; PMCID: PMC3900384.

Peng L, Wang L, Zhang Y, Dong A, Shen WH, Huang Y. Structural Analysis of the Arabidopsis AL2-PAL and PRC1 Complex Provides Mechanistic Insight into Active-to-Repressive Chromatin State Switch. J Mol Biol. 2018 Oct 19;430(21):4245-4259. doi: 10.1016/j.jmb.2018.08.021. Epub 2018 Aug 31. PMID: 30176245.

Zhao S, Zhang B, Yang M, Zhu J, Li H. Systematic Profiling of Histone Readers in Arabidopsis thaliana. Cell Rep. 2018 Jan 23;22(4):1090-1102. doi: 10.1016/j.celrep.2017.12.099. Epub 2018 Jan 28. PMID: 29386129.

Benny J, Pisciotta A, Caruso T, Martinelli F. Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data. BMC Plant Biol. 2019 May 10;19(1):194. doi: 10.1186/s12870-019-1794-y. PMID: 31077147; PMCID: PMC6511156.



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