Julie M. Pelletier, Raymond W. Kwong, Soomin Park, Brandon H. Le, Russell Baden, Alexandro Cagliari, Meryl Hashimoto, Matthew D. Munoz, Robert L. Fischer, Robert B. Goldberg, and John J. Harada

PNAS August 8 2017; Vol. 114; no.32: E6710–E6719, doi: 10.1073/pnas.1707957114

Significance

Seed development is biphasic, consisting of the morphogenesis phase when the basic plant body plan is established and the maturation phase when the embryo accumulates storage reserves and becomes desiccation tolerant. Despite the importance of seeds as human food and animal feed, little is known about the gene-regulatory networks that operate during these phases. We identified genes that are regulated genetically and transcriptionally by a master regulator of seed development, LEAFY COTYLEDON1 (LEC1). We show that LEC1 transcriptionally regulates genes involved in photosynthesis and other developmental processes in early and maturation genes in late seed development. Our results suggest that LEC1 partners with different transcription factors to regulate distinct gene sets and that LEC1 function is conserved in Arabidopsis and soybean seed development.

Abstract

LEAFY COTYLEDON1 (LEC1), an atypical subunit of the nuclear transcription factor Y (NF-Y) CCAAT-binding transcription factor, is a central regulator that controls many aspects of seed development including the maturation phase during which seeds accumulate storage macromolecules and embryos acquire the ability to withstand desiccation. To define the gene networks and developmental processes controlled by LEC1, genes regulated directly by and downstream of LEC1 were identified. We compared the mRNA profiles of wild-type and lec1-null mutant seeds at several stages of development to define genes that are down-regulated or up-regulated by the lec1 mutation. We used ChIP and differential gene-expression analyses in Arabidopsis seedlings overexpressing LEC1 and in developing Arabidopsis and soybean seeds to identify globally the target genes that are transcriptionally regulated by LEC1 in planta. Collectively, our results show that LEC1 controls distinct gene sets at different developmental stages, including those that mediate the temporal transition between photosynthesis and chloroplast biogenesis early in seed development and seed maturation late in development. Analyses of enriched DNA sequence motifs that may act as cis-regulatory elements in the promoters of LEC1 target genes suggest that LEC1 may interact with other transcription factors to regulate distinct gene sets at different stages of seed development. Moreover, our results demonstrate strong conservation in the developmental processes and gene networks regulated by LEC1 in two dicotyledonous plants that diverged ∼92 Mya.

See http://www.pnas.org/content/114/32/E6710.abstract.html?etoc

Figure 1: mRNA profiling of lec1 mutant seeds throughout development. (A) The number of diverse mRNAs detected in lec1-1–mutant seeds compared with wild-type seeds (17) at the indicated seed-development stages as determined in ATH1 GeneChip hybridization studies. Representative seeds and MG and PMG embryos as viewed by bright-field (24H), differential interference contrast (GLOB and LCOT), and dark-field whole-mount (MG and PMG) microscopy (Insets, MG and PMG seeds). (B) Numbers of mRNAs differentially expressed between lec1-1 and wild-type seeds at the indicated stages define lec1⁻–down-regulated (Left) and lec1⁻–up-regulated (Right) mRNAs. The green shading and percentages denote lec1⁻–up-regulated mRNAs that also are detected at significantly higher levels in seedlings than in seeds (seedling-enriched). Lists of the mRNAs and their levels that are present in lec1-1 mutants, that are lec1⁻ regulated, and that are seedling specific are given in Dataset S1. (C) Hierarchical clustering of lec1⁻–down-regulated mRNAs. The heatmap shows relative mRNA levels in each subregion at the preglobular, GLOB, heart, LCOT, BCOT, and MG stages (left to right, as indicated by the arrow). SUS mRNAs are shown at the GLOB stage.