C3H Family from Brachypodium

Brachypodium families updated 2023 based on Maize family rules

Required domains for C3H family:PF00642

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The CCCH (C3H) zinc finger motif (PF00642) is a nucleic acid binding motif that is described in proteins with diverse functions in many different pathways in plants. A typical CCCH protein usually contains 1-6 CCCH-type zinc finger motifs. Based on the different numbers of amino acid spacers between cysteines and histidines in the CCCH motif, a consensus sequence for these motifs was defined as C-X4-15-C-X46-C-X3-H (X represents any amino acid) based on the whole-genome analysis of rice and Arabidopsis CCCH proteins. The domain has been shown in proteins that bind to single stranded DNA and RNA.  In general, it has been reported that CCCH zinc-finger proteins function in plant development and tolerance to abiotic stresses such as salt, drought, flooding, cold temperatures and oxidative stress (Han et al., 2021).

In maize, a genome scan identified a total of 68 CCCH genes (ZmC3H1-68) in maize and these could be divided into seven groups by phylogenetic analysis. These 68 genes were found to be unevenly distributed on 10 chromosomes with 15 segmental duplication events, suggesting that segmental duplication played a major role in expansion of the maize CCCH family.  Twelve maize CCCH genes grouped with other known stress-responsive genes from Arabidopsis and were found to contain putative stress-responsive cis-elements in their promoter regions. Seven of these genes chosen for further quantitative real-time PCR analysis showed differential expression patterns among five representative maize tissues and over time in response to abscisic acid and drought treatments (Peng et al ., 2012).

In rice, the DCM1 protein contains five tandem CCCH motifs and interacts with nuclear poly (A) binding proteins (PABNs) in nuclear speckles. The expression profiles of genes related to callose synthesis and degradation are significantly modified in dcm1. It is proposed that DCM1 plays an essential role in male meiotic cytokinesis by preserving callose from premature dissolution in rice (Zhang et al., 2018).

Last updated June 2023 by John Gray


Peng X, Zhao Y, Cao J, Zhang W, Jiang H, Li X, Ma Q, Zhu S, Cheng B. CCCH-type zinc finger family in maize: genome-wide identification, classification and expression profiling under abscisic acid and drought treatments. PLoS One. 2012;7(7):e40120. doi: 10.1371/journal.pone.0040120. Epub 2012 Jul 6. PMID: 22792223; PMCID: PMC3391233.

Zhang C, Shen Y, Tang D, Shi W, Zhang D, Du G, Zhou Y, Liang G, Li Y, Cheng Z. The zinc finger protein DCM1 is required for male meiotic cytokinesis by preserving callose in rice. PLoS Genet. 2018 Nov 12;14(11):e1007769. doi: 10.1371/journal.pgen.1007769. PMID: 30419020; PMCID: PMC6258382.

Han G, Qiao Z, Li Y, Wang C, Wang B. The Roles of CCCH Zinc-Finger Proteins in Plant Abiotic Stress Tolerance. Int J Mol Sci. 2021 Aug 3;22(15):8327. doi: 10.3390/ijms22158327. PMID: 34361093; PMCID: PMC8347928.




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