ARID Family from Brachypodium

Brachypodium families updated 2023 based on Maize family rules

Required domains for ARID family:PF01388

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The founding members of this family, murine Bright and Drosophila dead ringer (Dri), were independently cloned from mice and frutifly respectively, on the basis of their ability to bind to AT-rich DNA sequences, although encoded a known DNA binding domain. Mapping of the DNA binding abilities revealed a novel DNA binding domain, the consensus sequence of which extends across approximately 100 amino acids (Wilsker et. al., 2002). This novel DNA binding domain was designated AT-rich interactive domain (ARID), based on the behavior of Bright and Dri but is also referred to as the BRIGHT domain and has the pfam designation PF01388. The consensus sequence occurs in proteins from all sequenced eukaryotic organisms. The solution structure of the DNA-binding domain from the DEAD RINGER protein has been determined (1C20). The basic structure of the domain appears to be a series of six helices separated by ß-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. In humans the 15 human ARID family proteins can be divided into seven subfamilies based on the degree of sequence identity between individual members.  In one study it was found that the majority of ARID subfamilies (i.e. five out of seven) bind DNA without obvious sequence preference (Patsialou et al., 2005).

In plants it was found that there exist proteins that contain both an ARID and an HMG-box domain and these appear specific to plants and the protein combines DNA-binding properties characteristic of ARID and HMG-box proteins (Hansen et al., 2008). The Arabidopsis ARID-HMG protein HMGB11 (At1g55650) can bind double-stranded DNA with a weaker affinity (Kd = 475 ± 17.9 nM) compared to Arabidopsis HMGB1 protein (Kd = 39.8 ± 2.68 nM). AtHMGB11 also prefers AT-rich DNA as a substrate and shows structural bias for supercoiled DNA.  Molecular docking of the DNA-AtHMGB11 complex indicated that the protein interacts with the DNA major groove, mainly through its ARID domain and the junction region connecting the ARID and the HMG-box domain. Also, predicted by the docking model, mutation of Lys(85) from the ARID domain and Arg(199) & Lys(202) from the junction region affects the DNA binding affinity of AtHMGB11. In addition, AtHMGB11 and its truncated form containing the HMG-box domain can not only promote DNA mini-circle formation but are also capable of inducing negative supercoils into relaxed plasmid DNA suggesting the involvement of this protein in several nuclear events. In Arabidopsis another ARID-HMG protein AtHMGB15 was found to be required required for pollen tube growth. There are at least 11 members of the ARID TF family in maize.

Last updated June 2023 by John Gray


Wilsker D, Patsialou A, Dallas PB, Moran E. ARID proteins: a diverse family of DNA binding proteins implicated in the control of cell growth, differentiation, and development. Cell Growth Differ. 2002 Mar;13(3):95-106. PMID: 11959810.

Hansen FT, Madsen CK, Nordland AM, Grasser M, Merkle T, Grasser KD. A novel family of plant DNA-binding proteins containing both HMG-box and AT-rich interaction domains. Biochemistry. 2008 Dec 16;47(50):13207-14. doi: 10.1021/bi801772k. PMID: 19053246.

Patsialou A, Wilsker D, Moran E. DNA-binding properties of ARID family proteins. Nucleic Acids Res. 2005 Jan 7;33(1):66-80. doi: 10.1093/nar/gki145. PMID: 15640446; PMCID: PMC546134.

Roy A, Dutta A, Roy D, Ganguly P, Ghosh R, Kar RK, Bhunia A, Mukhopadhyay J, Chaudhuri S. Deciphering the role of the AT-rich interaction domain and the HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana. Plant Mol Biol. 2016 Oct;92(3):371-88. doi: 10.1007/s11103-016-0519-y. Epub 2016 Aug 9. Erratum in: Plant Mol Biol. 2016 Oct;92(3):389-90. Mukhobadhyay, Jayanta [corrected to Mukhopadhyay, Jayanta]. PMID: 27503561.

Xia C, Wang YJ, Liang Y, Niu QK, Tan XY, Chu LC, Chen LQ, Zhang XQ, Ye D. The ARID-HMG DNA-binding protein AtHMGB15 is required for pollen tube growth in Arabidopsis thaliana. Plant J. 2014 Sep;79(5):741-56. doi: 10.1111/tpj.12582. Epub 2014 Jul 23. PMID: 24923357.




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