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Transcriptional dynamics during cell wall removal and regeneration reveals key genes involved in cell wall development in rice

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Abstract

Efficient and cost-effective conversion of plant biomass to usable forms of energy requires a thorough understanding of cell wall biosynthesis, modification and degradation. To elucidate these processes, we assessed the expression dynamics during enzymatic removal and regeneration of rice cell walls in suspension cells over time. In total, 928 genes exhibited significant up-regulation during cell wall removal, whereas, 79 genes were up-regulated during cell wall regeneration. Both gene sets are enriched for kinases, transcription factors and genes predicted to be involved in cell wall-related functions. Integration of the gene expression datasets with a catalog of known and/or predicted biochemical pathways from rice, revealed metabolic and hormonal pathways involved in cell wall degradation and regeneration. Rice lines carrying Tos17 mutations in genes up-regulated during cell wall removal exhibit dwarf phenotypes. Many of the genes up-regulated during cell wall development are also up-regulated in response to infection and environmental perturbations indicating a coordinated response to diverse types of stress.

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Abbreviations

MeV:

MultiExperiment Viewer

CAZy:

Carbohydrate-Active enZymes

GEO:

Gene expression omnibus

ERF:

Ethylene response factors

JA:

Jasmonic acid

GT:

Glycosyltransferase

GH:

Glycoside hydrolase

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Acknowledgments

This work was supported by a US Department of Energy (DEFG0207ER6445907110980) and USDA (2007355041824007110980) grant to PCR and ZP; an Office of Science, Office of Biological and Environmental Research of the US DOE contract no. DE-AC02-05CH11231 to the Joint BioEnergy Institute and a grant from the Next-Generation BioGreen 21 Program (No. SSAC2011), Rural Development Administration, Republic of Korea to KHJ. We thank Dr. Peijian Cao for helping with data normalization.

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Authors and Affiliations

  1. Department of Plant Pathology, University of California, Davis, CA, 95616, USA

    Rita Sharma, Ki-Hong Jung, Manoj K. Sharma & Pamela C. Ronald

  2. Joint Bioenergy Institute, Emeryville, CA, 94710, USA

    Rita Sharma, Manoj K. Sharma & Pamela C. Ronald

  3. Department of Biochemistry and Molecular Biology, Mississippi State University, Starkville, MS, 39762, USA

    Feng Tan & Zhaohua Peng

  4. Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446–701, Korea

    Ki-Hong Jung & Pamela C. Ronald

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  1. Rita Sharma
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Correspondence to Pamela C. Ronald.

Electronic supplementary material

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Online Resource 1. List of quantitative PCR primers used for validation of microarray data. (XLS 17 kb)

11103_2011_9819_MOESM2_ESM.xls

Online Resource 2a. List of genes up-regulated during cell wall removal. 2b. List of genes down-regulated during cell wall removal. (XLS 180 kb)

11103_2011_9819_MOESM3_ESM.xls

Online Resource 3a. List of genes up-regulated during cell wall regeneration. 3b. List of genes down-regulated during cell wall regeneration. (XLS 52 kb)

11103_2011_9819_MOESM4_ESM.eps

Online Resource 4. Hierarchical cluster display showing log2 fold changes exhibited by cell wall-related genes during cell wall removal and regeneration. Green represents down-regulation and red signifies up-regulation of genes with respect to suspension cells and protoplasts during cell wall removal and regeneration, respectively. The time points analyzed are shown at the top. S: suspension cell; D1: 2 h; D2: 6 h after enzymatic treatment; P: protoplasts at 0 h on regeneration medium; R1: 4 h; R2: 12 h and R3: 48 h after incubation in regeneration medium. The dendrogram at the left represents hierarchical clustering of genes. The LOCUS IDs of genes are on the right. (EPS 1869 kb)

Online Resource 5. List of genes up-regulated during cell wall removal and different stress treatments. (XLSX 115 kb)

11103_2011_9819_MOESM6_ESM.xlsx

Online Resource 6. List of genes up-regulated during cell wall regeneration and different stress treatments. (XLSX 60 kb)

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Sharma, R., Tan, F., Jung, KH. et al. Transcriptional dynamics during cell wall removal and regeneration reveals key genes involved in cell wall development in rice. Plant Mol Biol 77, 391 (2011). https://doi.org/10.1007/s11103-011-9819-4

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