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Engineering of red cells of Arabidopsis thaliana and comparative genome-wide gene expression analysis of red cells versus wild-type cells

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Abstract

We report metabolic engineering of Arabidopsis red cells and genome-wide gene expression analysis associated with anthocyanin biosynthesis and other metabolic pathways between red cells and wild-type (WT) cells. Red cells of A. thaliana were engineered for the first time from the leaves of production of anthocyanin pigment 1-Dominant (pap1-D). These red cells produced seven anthocyanin molecules including a new one that was characterized by LC–MS analysis. Wild-type cells established as a control did not produce anthocyanins. A genome-wide microarray analysis revealed that nearly 66 and 65% of genes in the genome were expressed in the red cells and wild-type cells, respectively. In comparison with the WT cells, 3.2% of expressed genes in the red cells were differentially expressed. The expression levels of 14 genes involved in the biosynthetic pathway of anthocyanin were significantly higher in the red cells than in the WT cells. Microarray and RT-PCR analyses demonstrated that the TTG1–GL3/TT8–PAP1 complex regulated the biosynthesis of anthocyanins. Furthermore, most of the genes with significant differential expression levels in the red cells versus the WT cells were characterized with diverse biochemical functions, many of which were mapped to different metabolic pathways (e.g., ribosomal protein biosynthesis, photosynthesis, glycolysis, glyoxylate metabolism, and plant secondary metabolisms) or organelles (e.g., chloroplast). We suggest that the difference in gene expression profiles between the two cell lines likely results from cell types, the overexpression of PAP1, and the high metabolic flux toward anthocyanins.

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Abbreviations

PAP1:

Production of anthocyanin pigmentation 1

pap1-D :

Production of anthocyanin pigmentation 1-Dominant

HPLC–ESI–MS:

High-performance liquid chromatography–electrospray ionization–mass spectrometry

HPLC–TOF–MS:

High-performance liquid chromatography–time of flight–mass spectrometry

RT-PCR:

Reverse transcription-polymerase chain reaction

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Acknowledgments

We are very grateful to Dr. Heike Sederoff from the Department of Plant Biology at North Carolina State University for her suggestions in microarray data analysis. We thank Dr. Li–Li Zhou from our laboratory for her discussion about plant tissue culture and anthocyanin analysis. This work was financially supported by a USDA–NRI grant (USDA 2006-35318-17431) and North Carolina State University.

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  1. Department of Plant Biology, North Carolina State University, Raleigh, NC, 27695, USA

    Ming-Zhu Shi & De-Yu Xie

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  1. Ming-Zhu Shi
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Correspondence to De-Yu Xie.

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425_2010_1335_MOESM7_ESM.jpg

Fig. S1 A diagram of the chloroplast thylakoid membrane depicting the locations of 25 photosynthetic components encoded by nuclear genes that are expressed at least two-fold lower in red cells than in wild-type cells. “(16)” and “(19)” are used twice because of the overlaid locations of two proteins. Abbreviation: PC, plastocyanin; PQ: plastoquinone; Fdx: Ferredoxin; FNR: Ferredoxin-NADP reductase. (JPEG 786 kb)

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Shi, MZ., Xie, DY. Engineering of red cells of Arabidopsis thaliana and comparative genome-wide gene expression analysis of red cells versus wild-type cells. Planta 233, 787–805 (2011). https://doi.org/10.1007/s00425-010-1335-2

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