Gene coexpression clusters and putative regulatory elements underlying seed storage reserve accumulation in Arabidopsis

Fred Y Peng,Randall J Weselake

doi:10.1186/1471-2164-12-286

Abstract

BackgroundIn Arabidopsis, a large number of genes involved in the accumulation of seed storage reserves during seed development have been characterized, but the relationship of gene expression and regulation underlying this physiological process remains poorly understood. A more holistic view of this molecular interplay will help in the further study of the regulatory mechanisms controlling seed storage compound accumulation.ResultsWe identified gene coexpression networks in the transcriptome of developing Arabidopsis (Arabidopsis thaliana) seeds from the globular to mature embryo stages by analyzing publicly accessible microarray datasets. Genes encoding the known enzymes in the fatty acid biosynthesis pathway were found in one coexpression subnetwork (or cluster), while genes encoding oleosins and seed storage proteins were identified in another subnetwork with a distinct expression profile. In the triacylglycerol assembly pathway, only the genes encoding diacylglycerol acyltransferase 1 (DGAT1) and a putative cytosolic "type 3" DGAT exhibited a similar expression pattern with genes encoding oleosins. We also detected a large number of putative cis-acting regulatory elements in the promoter regions of these genes, and promoter motifs for LEC1 (LEAFY COTYLEDON 1), DOF (DNA-binding-with-One-Finger), GATA, and MYB transcription factors (TF), as well as SORLIP5 (Sequences Over-Represented in Light-Induced Promoters 5), are overrepresented in the promoter regions of fatty acid biosynthetic genes. The conserved CCAAT motifs for B3-domain TFs and binding sites for bZIP (basic-leucine zipper) TFs are enriched in the promoters of genes encoding oleosins and seed storage proteins.ConclusionsGenes involved in the accumulation of seed storage reserves are expressed in distinct patterns and regulated by different TFs. The gene coexpression clusters and putative regulatory elements presented here provide a useful resource for further experimental characterization of protein interactions and regulatory networks in this process.

Highlights

In Arabidopsis, a large number of genes involved in the accumulation of seed storage reserves during seed development have been characterized, but the relationship of gene expression and regulation underlying this physiological process remains poorly understood
To examine the overall transcriptome changes across the eight seed development stages, we performed a principal component analysis (PCA) in the ‘Sample’ space, and the results indicated that the global transcriptional program changes constantly during seed maturation (Figure 1)
This result suggests that staging of seed development based on the embryo’s morphological shape alone may not necessarily reflect the transcriptome state in the seed, which is attributable to the fact that molecular events, such as gene expression, occur prior to morphological changes

Summary

Introduction

In Arabidopsis, a large number of genes involved in the accumulation of seed storage reserves during seed development have been characterized, but the relationship of gene expression and regulation underlying this physiological process remains poorly understood. Additional TFs such as WRINKLED 1 (WRI1), a member of plant-specific APETALA 2 (AP2) - ethylene response element binding factor (EREB) family, is known to control transcription of many FA biosynthetic genes [26], and recent studies show it acts via binding to the AW-box motif present in the promoter region of 19 FA biosynthetic genes [27]. Distinct regulatory mechanisms are present in controlling the accumulation processes of oils and proteins, perhaps with cross-talk to coordinate the synthesis of seed storage compounds. This coordination could help to explain the well-documented negative correlation (correlation coefficient ranging from -0.60 to -0.90) between oil and protein content in seeds of many oleaginous species [[3] and references therein]. Several TFs, such as LEC1, ABI3 and FUS3, have been demonstrated to regulate many genes in the synthesis of both oils and storage proteins in developing seeds [30,31,32]

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