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Motif analysis unveils the possible co-regulation of chloroplast genes and nuclear genes encoding chloroplast proteins

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Abstract

Chloroplasts play critical roles in land plant cells. Despite their importance and the availability of at least 200 sequenced chloroplast genomes, the number of known DNA regulatory sequences in chloroplast genomes are limited. In this paper, we designed computational methods to systematically study putative DNA regulatory sequences in intergenic regions near chloroplast genes in seven plant species and in promoter sequences of nuclear genes in Arabidopsis and rice. We found that −35/−10 elements alone cannot explain the transcriptional regulation of chloroplast genes. We also concluded that there are unlikely motifs shared by intergenic sequences of most of chloroplast genes, indicating that these genes are regulated differently. Finally and surprisingly, we found five conserved motifs, each of which occurs in no more than six chloroplast intergenic sequences, are significantly shared by promoters of nuclear-genes encoding chloroplast proteins. By integrating information from gene function annotation, protein subcellular localization analyses, protein–protein interaction data, and gene expression data, we further showed support of the functionality of these conserved motifs. Our study implies the existence of unknown nuclear-encoded transcription factors that regulate both chloroplast genes and nuclear genes encoding chloroplast protein, which sheds light on the understanding of the transcriptional regulation of chloroplast genes.

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Acknowledgments

This project is supported by two National Science Foundation grants 1125676 and 1149955 (to HH). We sincerely appreciate the helpful comments by the two reviewers.

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Authors and Affiliations

  1. Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL, 32816, USA

    Ying Wang, Jun Ding & Haiyan Hu

  2. Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL, 32816, USA

    Henry Daniell & Xiaoman Li

  3. Harris Corporation and Engineering Center 346, University of Central Florida, Orlando, FL, 32816, USA

    Xiaoman Li

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  1. Ying Wang
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  2. Jun Ding
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  3. Henry Daniell
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  4. Haiyan Hu
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  5. Xiaoman Li
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Correspondence to Haiyan Hu or Xiaoman Li.

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Ying Wang and Jun Ding are co-first authors.

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Wang, Y., Ding, J., Daniell, H. et al. Motif analysis unveils the possible co-regulation of chloroplast genes and nuclear genes encoding chloroplast proteins. Plant Mol Biol 80, 177–187 (2012). https://doi.org/10.1007/s11103-012-9938-6

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