Basic helix-loop-helix (bHLH) proteins are a class of transcription factors found throughout eukaryotic organisms. Classification of the complete sets of bHLH proteins in the sequenced genomes of Arabidopsis thaliana and Oryza sativa (rice) has defined the diversity of these proteins among flowering plants. However, the evolutionary relationships of different plant bHLH groups and the diversity of bHLH proteins in more ancestral groups of plants are currently unknown. In this study, we use whole-genome sequences from nine species of land plants and algae to define the relationships between these proteins in plants. We show that few (less than 5) bHLH proteins are encoded in the genomes of chlorophytes and red algae. In contrast, many bHLH proteins (100-170) are encoded in the genomes of land plants (embryophytes). Phylogenetic analyses suggest that plant bHLH proteins are monophyletic and constitute 26 subfamilies. Twenty of these subfamilies existed in the common ancestors of extant mosses and vascular plants, whereas six further subfamilies evolved among the vascular plants. In addition to the conserved bHLH domains, most subfamilies are characterized by the presence of highly conserved short amino acid motifs. We conclude that much of the diversity of plant bHLH proteins was established in early land plants, over 440 million years ago.

Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants

Epidermis differentiation and maintenance are essential for plant survival. Constant cross-talk between epidermal cells and their immediate environment is at the heart of epidermal cell fate, and regulates epidermis-specific transcription factors. These factors in turn direct epidermal differentiation involving a whole array of epidermis-specific pathways including specialized lipid metabolism necessary to build the protective cuticle layer. An intact epidermis is crucial for certain key processes in plant development, shoot growth and plant defence. Here, we discuss the control of epidermal cell fate and the function of the epidermal cell layer in the light of recent advances in the field.

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/j.1469-8137.2010.03514.x

Epidermis: the formation and functions of a fundamental plant tissue

Seed dormancy controls the start of a plant’s life cycle by preventing germination of a viable seed in an unfavorable season. Freshly harvested seeds usually show a high level of dormancy, which is gradually released during dry storage (afterripening). Abscisic acid (ABA) has been identified as an essential factor for the induction of dormancy, whereas gibberellins (GAs) are required for germination. The molecular mechanisms controlling seed dormancy are not well understood. DELAY OF GERMINATION1 (DOG1) was recently identified as a major regulator of dormancy in Arabidopsis thaliana. Here, we show that the DOG1 protein accumulates during seed maturation and remains stable throughout seed storage and imbibition. The levels of DOG1 protein in freshly harvested seeds highly correlate with dormancy. The DOG1 protein becomes modified during after-ripening, and its levels in stored seeds do not correlate with germination potential. Although ABA levels in dog1 mutants are reduced and GA levels enhanced, we show that DOG1 does not regulate dormancy primarily via changes in hormone levels. We propose that DOG1 protein abundance in freshly harvested seeds acts as a timer for seed dormancy release, which functions largely independent from ABA.

/pdf/the-time-required-for-dormancy-release-in-arabidopsis-is-44xod5gfq4.pdf

The Time Required for Dormancy Release in Arabidopsis Is Determined by DELAY OF GERMINATION1 Protein Levels in Freshly Harvested Seeds

Differential expression of maternally and paternally inherited alleles of a gene is referred to as gene imprinting, a form of epigenetic gene regulation common to flowering plants and mammals. In plants, imprinting primarily occurs in the endosperm, a seed tissue that supports the embryo during its growth and development. Previously, we demonstrated that widespread DNA demethylation at remnants of transposable elements accompanies endosperm development and that a subset of these methylation changes are associated with gene imprinting. Here we assay imprinted gene expression genome-wide by performing high-throughput sequencing of RNA derived from seeds of reciprocal intraspecific crosses. We identify more than 200 loci that exhibit parent-of-origin effects on gene expression in the endosperm, including a large number of transcription factors, hormone biosynthesis and response genes, and genes that encode regulators of epigenetic information, such as methylcytosine binding proteins, histone methyltransferases, and chromatin remodelers. The majority of these genes are partially, rather than completely, imprinted, suggesting that gene dosage regulation is an important aspect of imprinted gene expression.

/pdf/genomic-analysis-of-parent-of-origin-allelic-expression-in-33d8798hax.pdf

Genomic Analysis of Parent-of-Origin Allelic Expression in Arabidopsis thaliana Seeds

https://www.cell.com/trends/plant-science/pdf/S1360-1385(14)00251-9.pdf

Only in dying, life: programmed cell death during plant development.

During Arabidopsis seed development, the growing embryo invades and consumes the surrounding endosperm tissue. The signalling pathways that coordinate the separation of the embryo from the endosperm and the concomitant breakdown of the endosperm are poorly understood. We have identified a novel bHLH transcription factor, ZHOUPI (ZOU), which mediates these processes. ZOU is expressed exclusively in the endosperm of developing seeds. It is activated in the central cell immediately after fertilization and is initially expressed uniformly in endosperm, subsequently resolving to the embryo surrounding region (ESR). However, zou mutant embryos have defects in cuticle formation and in epidermal cell adhesion, suggesting that ZOU functions non-autonomously to regulate embryonic development. In addition, the endosperm of zou mutant seeds fails to separate from the embryo, restricting embryo expansion and resulting in the production of shrivelled collapsed seeds. zou seeds retain more endosperm than do wild-type seeds at maturity, suggesting that ZOU also controls endosperm breakdown. We identify several target genes whose expression in the ESR is regulated by ZOU. These include ABNORMAL LEAF SHAPE1, which encodes a subtilisin-like protease previously shown to have a similar role to ZOU in regulating endosperm adhesion and embryonic epidermal development. However, expression of several other ESR-specific genes is independent of ZOU. Therefore, ZOU is not a general regulator of endosperm patterning, but rather controls specific signalling pathways that coordinate embryo invasion and breakdown of surrounding endosperm tissues.

Niamh Johnston

Papers

The endosperm-specific ZHOUPI gene of Arabidopsis thaliana regulates endosperm breakdown and embryonic epidermal development.