Seed dormancy is one of the most crucial process transitions in a plant's life cycle. Its timing is tightly controlled by the expression level of the Delay of Germination 1 gene (DOG1). DOG1 is the major quantitative trait locus for seed dormancy in Arabidopsis and has been shown to control dormancy in many other plant species. This is reflected by the evolutionary conservation of the functional short alternatively polyadenylated form of the DOG1 mRNA. Notably, the 3′ region of DOG1, including the last exon that is not included in this transcript isoform, shows a high level of conservation at the DNA level, but the encoded polypeptide is poorly conserved. Here, we demonstrate that this region of DOG1 contains a promoter for the transcription of a noncoding antisense RNA, asDOG1, that is 5′ capped, polyadenylated, and relatively stable. This promoter is autonomous and asDOG1 has an expression profile that is different from known DOG1 transcripts. Using several approaches we show that asDOG1 strongly suppresses DOG1 expression during seed maturation in cis, but is unable to do so in trans. Therefore, the negative regulation of seed dormancy by asDOG1 in cis results in allele-specific suppression of DOG1 expression and promotes germination. Given the evolutionary conservation of the asDOG1 promoter, we propose that this cis-constrained noncoding RNA-mediated mechanism limiting the duration of seed dormancy functions across the Brassicaceae.seed dormancy | DOG1 gene | cis-acting ncRNA | antisense transcript P lants have evolved elaborate adaptation mechanisms to cope with unexpected and rapid changes in their natural environment (1). The division of the plant life cycle into consecutive developmental phases can be viewed as one such mechanism. This compartmentalization allows plants to focus their resources on particular tasks. The most pronounced developmental phases in plant development are seed dormancy, the juvenile phase, vegetative growth, flowering, and senescence (2). The transition between each successive phase has to be tightly controlled and aligned with the plant's internal metabolic state and external conditions.Seeds are characterized by their remarkable ability to withstand harsh environmental conditions (3). This is in part because of a seed dormancy mechanism that imposes a block on the ability of seeds to sense permissive conditions and initiate germination (4, 5). This mechanism allows seeds to temporarily bypass favorable conditions to germinate in an environment that will support the entire plant life cycle. Seed dormancy is under strong evolutionary selection because the improper timing of germination often results in immediate death (6). In addition, from an agronomical point of view, seed dormancy has been a subject of intensive selection, because on the one hand strong dormancy leads to uneven germination, but on the other hand weak dormancy may result in preharvest sprouting because of germination on the mother plant (7).An analysis of seed dormancy variability among Arabidopsis thaliana ac...

ORCID IDs: 0000-0001-7449-8081 (M.C.); 0000-0001-8764-6370 (F.L.).DOG1 (Delay of Germination 1) is a key regulator of seed dormancy in Arabidopsis (Arabidopsis thaliana) and other plants. Interestingly, the C terminus of DOG1 is either absent or not conserved in many plant species. Here, we show that in Arabidopsis, DOG1 transcript is subject to alternative polyadenylation. In line with this, mutants in RNA 39 processing complex display weakened seed dormancy in parallel with defects in DOG1 proximal polyadenylation site selection, suggesting that the short DOG1 transcript is functional. This is corroborated by the finding that the proximally polyadenylated short DOG1 mRNA is translated in vivo and complements the dog1 mutant. In summary, our findings indicate that the short DOG1 protein isoform produced from the proximally polyadenylated DOG1 mRNA is a key player in the establishment of seed dormancy in Arabidopsis and characterizes a set of mutants in RNA 39 processing complex required for production of proximally polyadenylated functional DOG1 transcript.

Plants have developed multiple strategies to sense the external environment and to adapt growth accordingly. () is a major quantitative trait locus (QTL) for seed dormancy strength in that is reported to be expressed exclusively in seeds. is extensively regulated, with an antisense transcript () suppressing its expression in seeds. Here, we show that shows high levels in mature plants where it suppresses expression under standard growth conditions. Suppression is released by shutting down antisense transcription, which is induced by the plant hormone abscisic acid (ABA) and drought. Loss of results in constitutive high-level expression, conferring increased drought tolerance, while inactivation of causes enhanced drought sensitivity. The unexpected role of in environmental adaptation of mature plants is separate from its function in seed dormancy regulation. The requirement of to respond to ABA and drought demonstrates that antisense transcription is important for sensing and responding to environmental changes in plants.

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The phytoalexin deficient 4 (PAD4) gene in Arabidopsis thaliana (AtPAD4) is involved in the regulation of plant--pathogen interactions. The role of PAD4 in woody plants is not known; therefore, we characterized its function in hybrid aspen and its role in reactive oxygen species (ROS)-dependent signalling and wood development. Three independent transgenic lines with different suppression levels of poplar PAD expression were generated. All these lines displayed deregulated ROS metabolism, which was manifested by an increased H2O2 level in the leaves and shoots, and higher activities of manganese superoxide dismutase (MnSOD) and catalase (CAT) in the leaves in comparison to the wild-type plants. However, no changes in non-photochemical quenching (NPQ) between the transgenic lines and wild type were observed in the leaves. Moreover, changes in the ROS metabolism in the pad4 transgenic lines positively correlated with wood formation. A higher rate of cell division, decreased tracheid average size and numbers, and increased cell wall thickness were observed. The results presented here suggest that the Populus tremula × tremuloides PAD gene might be involved in the regulation of cellular ROS homeostasis and in the cell division--cell death balance that is associated with wood development.

SNF1-related protein kinases 2 (SnRK2s) are key signaling elements that regulate abscisic acid (ABA)-dependent plant development and responses to environmental stresses. Our previous data showed that the SnRK2-interacting Calcium Sensor (SCS) is an inhibitor of SnRK2 activity. In Arabidopsis thaliana, the use of alternative transcription start sites located within AtSCS gene results in two in-frame transcripts and subsequently two proteins, which differ only by the sequence position of the N-terminus. We described the longer AtSCS-A earlier, and now we describe the shorter AtSCS-B and compare both isoforms. The two forms differ significantly in their expression profiles in plant organs and in response to environmental stresses, in calcium binding properties, and conformational dynamics in the presence and absence of Ca2+. The results show that only AtSCS-A has the features of a calcium sensor. Both forms inhibit SnRK2 activity, but differ with respect to calcium dependence, as AtSCS-A requires calcium for inhibition, while AtSCS-B does not. Analysis of Arabidopsis plants stably expressing 35S::AtSCS-A-c-myc or 35S::AtSCS-B-c-myc in the scs-1 knockout mutant revealed that in planta both forms are negative regulators of the SnRK2 activity induced in response to ABA and regulate plant defense against water deficit. Moreover, the data present biochemical, biophysical, and functional properties of EF-hand-like motifs in plant proteins.One sentence SummaryTwo isoforms of SnRK2-interacting calcium sensor are expressed in Arabidopsis; they differ in calcium binding properties, but both of them inhibit SnRK2s and subsequently fine tune ABA signaling.