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A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes

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Abstract

The proteins harboring RING finger motif(s) have been shown to mediate protein–protein interactions that are relevant to a variety of cellular processes. In an effort to elucidate the evolutionary dynamics of the rice RING finger protein family, we have attempted to determine their genomic locations, expression diversity, and co-expressed genes via in silico analysis and semi-quantitative RT–PCR. A total of 425 retrieved genes appear to be distributed over all 12 of the chromosomes of rice with different distributions, and are reflective of the evolutionary dynamics of the rice genome. A genome-wide dataset harboring 155 gene expression omnibus sample plates evidenced some degree of differential evolutionary fates between members of RING-H2 and RING-HC types. Additionally, responses to abiotic stresses, such as salinity and drought, demonstrated that some degree of expression diversity existed between members of the RING finger protein genes. Interestingly, we determined that one RING-H2 finger protein gene (Os04g51400) manifested striking differences in expression patterns in response to abiotic stresses between leaf and culm-node tissues, further revealing responses highly similar to the majority of randomly selected co-expressed genes. The gene network of genes co-expressed with Os04g51400 may suggest some role in the salt response of the gene. These findings may shed further light on the evolutionary dynamics and molecular functional diversity of these proteins in complex cellular regulations.

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Acknowledgments

This work was supported by a grant from the BioGreen21 Program (no. 20080401034015), Rural Development Administration, Republic of Korea and a research program of Oriental Bio-herb Research Institute, Kangwon National University to CSJ and a research program of Dongguk University to BML.

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Authors and Affiliations

  1. Plant Genomics Lab, Department of Applied Plant Sciences Technology, Kangwon National University, Chuncheon, 200-713, Korea

    Sung Don Lim & Cheol Seong Jang

  2. Department of Plant Biotechnology, Dongguk University, Seoul, 100-715, Korea

    Sung Don Lim, Won Cheol Yim & Byung-Moo Lee

  3. Institute of Life Science and Natural Resources, Korea University, Seoul, 136-713, Korea

    Jun-Cheol Moon

  4. Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup, 580-185, Korea

    Dong Sub Kim

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  1. Sung Don Lim
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  2. Won Cheol Yim
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Correspondence to Byung-Moo Lee or Cheol Seong Jang.

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11103_2009_9576_MOESM4_ESM.png

Supplemental Fig. 1 Phylogenetic relationship among the 425 RING finger protein genes in rice. The phylogenetic tree was constructed via the neighbor-joining algorithm with 1,000 bootstrap replicates. (PNG 902 kb)

11103_2009_9576_MOESM5_ESM.pptx

Supplemental Fig. 2 Expression profiles of 369 RING finger protein genes in rice. Clustering analysis was conducted using the average linkage hierarchical clustering via uncentered Pearson’s correlation. The expression values of each RING finger protein genes were retrieved from 155 GSM samples of the Affymetrix GeneChip rice genome array. (PPTX 521 kb)

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Lim, S.D., Yim, W.C., Moon, JC. et al. A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes. Plant Mol Biol 72, 369–380 (2010). https://doi.org/10.1007/s11103-009-9576-9

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