Time series omics experiments are critical for studying a range of biological processes, such as cell differentiation and developmental programs or responses to pathogens and environmental cues. While statistical tools for differential analysis across static conditions have matured, a comparable comprehensive methodology is lacking for time series data. Here, we introduce cpam, a novel method and user-friendly R package that performs temporal differential analysis of omics time series data, including pseudobulked single-cell sequence data. Powerful features include change-point detection and shape-constrained temporal trend estimation to allocate omics data into similar clusters. The software handles case-only and case-control designs, incorporates quantification uncertainty, and provides an interactive interface with customisable visualisations, offering graphical and statistical insight into molecular processes. Performance evaluation shows that cpam outperforms existing time series methods in terms of control of the false discovery rate versus power to detect temporal changes and accurate changepoint estimation. Application to published data illustrates RNA isoform-level modelling with high-resolution clustering during human embryogenesis and the identification of 910 novel genes that respond to excess-light in Arabidopsis.

Summary The phytohormone strigolactone (SL) inhibits shoot branching, whereas the signalling metabolite trehalose 6‐phosphate (Tre6P) promotes branching. How Tre6P and SL signalling may interact and which molecular mechanisms might be involved remains largely unknown. Transcript profiling of Arabidopsis SL mutants revealed a cluster of differentially expressed genes highly enriched in the Tre6P pathway compared with wild‐type (WT) plants or brc1 mutants. Tre6P‐related genes were also differentially expressed in axillary buds of garden pea (Pisum sativum) SL mutants. Tre6P levels were elevated in the SL signalling mutant more axillary (max) growth 2 compared with other SL mutants or WT plants indicating a role of MAX2‐dependent SL signalling in regulating Tre6P levels. A transgenic approach to increase Tre6P levels demonstrated that all SL mutant lines and brc1 flowered earlier, showing all of these mutants were responsive to Tre6P. Elevated Tre6P led to increased branching in WT plants but not in max2 and max4 mutants, indicating some dependency between the SL pathway and Tre6P regulation of shoot branching. By contrast, elevated Tre6P led to an enhanced branching phenotype in brc1 mutants indicating independence between BRC1 and Tre6P. A model is proposed whereby SL signalling represses branching via Tre6P and independently of the BRC1 pathway.

Video 3 from PLK1 Induces Chromosomal Instability and Overrides Cell-Cycle Checkpoints to Drive Tumorigenesis

Strigolactones (SLs) and karrikins (KARs) are butenolides that influence multiple aspects of plant growth and development. D14 and KAI2 are members of the α/β-fold hydrolase superfamily and act as receptors of SLs and KARs, as well as of unidentified endogenous KAI2-ligands (KLs). Phylogenetic analyses suggest that plant KAI2 was derived from bacterial RsbQ via horizontal gene transfer (HGT) before the emergence of streptophytes. The D14/KAI2 and RsbQ proteins share conserved tertiary structures and functional features. In this opinion article, we suggest that the acquisition of RsbQ by plant cells was fundamental to the formation of butenolide sensing systems. Recruitment of additional signal transduction components and gene duplication subsequently led to versatile butenolide signaling systems throughout land plants.

Boron (B) is an essential element for plant growth but its cellular functions are poorly defined. We conducted transcriptome analysis of shoot apices of pea (Pisum sativum L.) growing for up to 18 days in the presence or absence of borate. Shoots of B deficient plants exhibited impaired elongation of the apex but increased growth of lateral shoots. Transcriptome analysis at days 10, 14 and 18 revealed 42, 517 and 2684 differentially expressed genes (DEGs), respectively, relating to diverse aspects of cell growth, metabolism, membrane function and cell signaling. Genes involved in jasmonate signaling and cell wall metabolism were upregulated in the B deficient plants. Many DEGs encoded transcription factors (TFs) potentially involved in these responses including many MYB and ethylene-responsive transcription factor (ERF) proteins and two orthologs of MYC2 which has been implicated in jasmonate signaling. Treatment of detached apices with B or jasmonic acid (JA) led to rapid changes in the expression of several of these DEGs. These results are consistent with a major role for borate in cell wall structure, perturbation of which can activate jasmonate signaling and cell wall remodeling. Such changes can help to explain how B deficiency leads to changes in shoot growth and architecture.

Seeds of the root parasitic plant Striga hermonthica can sense very low concentrations of strigolactones (SLs) exuded from host roots. The S. hermonthica hyposensitive to light (ShHTL) proteins are putative SL receptors, among which ShHTL7 reportedly confers sensitivity to picomolar levels of SL when expressed in Arabidopsis thaliana. However, the molecular mechanism underlying ShHTL7 sensitivity is unknown. Here we determined the ShHTL7 crystal structure and quantified its interactions with various SLs and key interacting proteins. We established that ShHTL7 has an active-site pocket with broad-spectrum response to different SLs and moderate affinity. However, in contrast to other ShHTLs, we observed particularly high affinity of ShHTL7 for F-box protein AtMAX2. Furthermore, ShHTL7 interacted with AtMAX2 and with transcriptional regulator AtSMAX1 in response to nanomolar SL concentration. ShHTL7 mutagenesis analyses identified surface residues that contribute to its high-affinity binding to AtMAX2 and residues in the ligand binding pocket that confer broad-spectrum response to SLs with various structures. Crucially, yeast-three hybrid experiments showed that AtMAX2 confers responsiveness of the ShHTL7-AtSMAX1 interaction to picomolar levels of SL in line with the previously reported physiological sensitivity. These findings highlight the key role of SL-induced MAX2-ShHTL7-SMAX1 complex formation in determining the sensitivity to SL. Moreover, these data suggest a strategy to screen for compounds that could promote suicidal seed germination at physiologically relevant levels.

The levels of plant hormones are broadly determined by their relative rates of biosynthesis and degradation, but a degradation pathway for strigolactones has been missing. Now an enzyme has been discovered that can break down strigolactones and thereby influence plant development.

In photosynthetic cells, chloroplasts and mitochondria are the sites of the core redox reactions underpinning energy metabolism. Such reactions generate reactive oxygen species (ROS) when oxygen is partially reduced. ROS signaling leads to responses by cells which enable them to adjust to changes in redox status. Recent studies in Arabidopsis thaliana reveal that chloroplast NADH can be used to generate malate which is exported to the mitochondrion where its oxidation regenerates NADH. Oxidation of this NADH produces mitochondrial ROS (mROS) which can activate signaling systems to modulate energy metabolism, and in certain cases can lead to programmed cell death (PCD). We propose the term 'malate circulation' to describe such redistribution of reducing equivalents to mediate energy homeostasis in the cell.

Wildfires can encourage the establishment of invasive plants by releasing potent germination stimulants, such as karrikins. Seed germination of Brassica tournefortii , a noxious weed of Mediterranean climates, is strongly stimulated by KAR 1 , the archetypal karrikin produced from burning vegetation. In contrast, the closely-related yet non-fire-associated ephemeral Arabidopsis thaliana is unusual because it responds preferentially to KAR 2 . The α/β-hydrolase KARRIKIN INSENSITIVE 2 (KAI2) is the putative karrikin receptor identified in Arabidopsis . Here we show that B. tournefortii expresses three KAI2 homologues, and the most highly-expressed homologue is sufficient to confer enhanced responses to KAR 1 relative to KAR 2 when expressed in Arabidopsis . We identify two amino acid residues near the KAI2 active site that explain the ligand selectivity, and show that this combination has arisen independently multiple times within dicots. Our results suggest that duplication and diversification of KAI2 proteins could confer differential responses to chemical cues produced by environmental disturbance, including fire.

Rice tillering is an important agronomic trait affecting grain yield. Here, we identified a high-tillering mutant tillering20 (t20), which could be restored to the wild type by treatment with the strigolactone (SL) analog rac-GR24. T20 encodes a chloroplast ζ-carotene isomerase (Z-ISO), which is involved in the biosynthesis of carotenoids and their metabolites, SL and abscisic acid (ABA). The t20 mutant has reduced SL and ABA, raising the question of how SL and ABA biosynthesis is coordinated, and whether they have overlapping functions in tillering. We discovered that rac-GR24 stimulated T20 expression and enhanced all-trans-β-carotene biosynthesis. Importantly, rac-GR24 also stimulated expression of Oryza sativa 9-CIS-EPOXYCAROTENOID DIOXYGENASE 1 (OsNCED1) through induction of Oryza sativa HOMEOBOX12 (OsHOX12), promoting ABA biosynthesis in shoot base. On the other hand, ABA treatment significantly repressed SL biosynthesis and the ABA biosynthetic mutants displayed elevated SL biosynthesis. ABA treatment reduced the number of basal tillers in both t20 and wild-type plants. Furthermore, while ABA-deficient mutants aba1 and aba2 had the same number of basal tillers as wild type, they had more unproductive upper tillers at maturity. This work demonstrates complex interactions in the biosynthesis of carotenoid, SLs and ABA, and reveals a role for ABA in the regulation of rice tillering.

Strigolactone and karrikin signaling pathways trigger polyubiquitination and degradation of SMXL2 to regulate hypocotyl elongation and gene expression in Arabidopsis. Strigolactones (SLs) and karrikins (KARs) are related butenolide signaling molecules that control plant development. In Arabidopsis (Arabidopsis thaliana), they are recognized separately by two closely related receptors but use the same F-box protein MORE AXILLARY GROWTH2 (MAX2) for signal transduction, targeting different members of the SMAX1-LIKE (SMXL) family of transcriptional repressors for degradation. Both signals inhibit hypocotyl elongation in seedlings, raising the question of whether signaling is convergent or parallel. Here, we show that synthetic SL analog GR24(4DO) enhanced the interaction between the SL receptor DWARF14 (D14) and SMXL2, while the KAR surrogate GR24(ent-5DS) induced association of the KAR receptor KARRIKIN INSENSITIVE2 (KAI2) with SMAX1 and SMXL2. Both signals trigger polyubiquitination and degradation of SMXL2, with GR24(4DO) dependent on D14 and GR24(ent-5DS) dependent mainly on KAI2. SMXL2 is critical for hypocotyl responses to GR24(4DO) and functions redundantly with SMAX1 in hypocotyl response to GR24(ent-5DS). Furthermore, GR24(4DO) induced response of D14-LIKE2 and KAR-UP F-BOX1 through SMXL2, whereas GR24(ent-5DS) induced expression of these genes via both SMAX1 and SMXL2. These findings demonstrate that both SLs and KARs could trigger polyubiquitination and degradation of SMXL2, thus uncovering an unexpected but important convergent pathway in SL- and KAR-regulated gene expression and hypocotyl elongation.

Abstract Karrikins are simple organic chemicals produced by wildfires that stimulate germination of dormant seeds in the soil. They are present in the smoke and char produced by the fire and are washed into the soil by the following rains. Many plant species have evolved such that their seeds remain dormant in the soil until they encounter karrikins, whereupon they can germinate. This strategy has the advantage that emerging seedlings will have plenty of light and a supply of nutrients released by the fire. Such plants are termed ‘fire ephemerals’ because they appear after fires, then flower, produce seed and die. It is believed that karrikins mimic an unidentified endogenous germination hormone. Karrikins are also similar to endogenous hormones called strigolactones that control plant development. Karrikin perception by seeds apparently requires a protein closely related to the strigolactone receptor. Karrikins or smoke can be used to stimulate germination in horticulture and landscape revegetation. Key Concepts Wildfires stimulate seeds in the soil to germinate which contributes to rapid revegetation. Seeds from many plant species are adapted to respond to chemicals produced by fire. The most active germination stimulant produced by wildfires is a butenolide named ‘karrikin’. Karrikins can influence germination and also seedling development. The receptor protein and molecular components of the response pathway have been identified. Karrikins mimic an ancient endogenous plant hormone that has not yet been identified. Karrikins stimulate germination of agricultural weeds and so might be useful for their control. Karrikins provide tools and knowledge to help us manage our natural landscapes. Karrikins might be useful in seed conservation work and in seed banks. The karrikin signalling system might be applied in crop breeding for environmental resilience.

The breeding of cereals with altered gibberellin (GA) signaling propelled the 'Green Revolution' by generating semidwarf plants with increased tiller number. The mechanism by which GAs promote shoot height has been studied extensively, but it is not known what causes the inverse relationship between plant height and tiller number. Here we show that rice tiller number regulator MONOCULM 1 (MOC1) is protected from degradation by binding to the DELLA protein SLENDER RICE 1 (SLR1). GAs trigger the degradation of SLR1, leading to stem elongation and also to the degradation of MOC1, and hence a decrease in tiller number. This discovery provides a molecular explanation for the coordinated control of plant height and tiller number in rice by GAs, SLR1 and MOC1.

This article is a Commentary on Footitt et al. (2020), 225: 2035–2047.

Shoot architecture is determined by the organization and activities of apical, axillary, intercalary, secondary, and inflorescence meristems and by the subsequent development of stems, leaves, shoot branches, and inflorescences. In this review, we discuss the unifying principles of hormonal and genetic control of shoot architecture including advances in our understanding of lateral branch outgrowth; control of stem elongation, thickness, and angle; and regulation of inflorescence development. We focus on recent progress made mainly in Arabidopsis thaliana, rice, pea, maize, and tomato, including the identification of new genes and mechanisms controlling shoot architecture. Key advances include elucidation of mechanisms by which strigolactones, auxins, and genes such as IDEAL PLANT ARCHITECTURE1 and TEOSINTE BRANCHED1 control shoot architecture. Knowledge now available provides a foundation for rational approaches to crop breeding and the generation of ideotypes with defined architectural features to improve performance and productivity.

The control of seed germination in response to environmental conditions is important for plant success. We investigated the role of the karrikin receptor KARRIKIN INSENSITIVE2 (KAI2) in the response of Arabidopsis seeds to osmotic stress, salinity and high temperature. Germination of the kai2 mutant was examined in response to NaCl, mannitol and elevated temperature. The effect of karrikin on germination of wild-type seeds, hypocotyl elongation and the expression of karrikin-responsive genes was also examined in response to such stresses. The kai2 seeds germinated less readily than wild-type seeds and germination was more sensitive to inhibition by abiotic stress. Karrikin-induced KAI2 signalling stimulated germination of wild-type seeds under favourable conditions, but, surprisingly, inhibited germination in the presence of osmolytes or at elevated temperature. By contrast, GA stimulated germination of wild-type seeds and mutants under all conditions. Karrikin induced expression of DLK2 and KUF1 genes and inhibited hypocotyl elongation independently of osmotic stress. Under mild osmotic stress, karrikin enhanced expression of DREB2A, WRKY33 and ERF5 genes, but not ABA signalling genes. Thus, the karrikin-KAI2 signalling system can protect against abiotic stress, first by providing stress tolerance, and second by inhibiting germination under conditions unfavourable to seedling establishment.

Some proteins are put to work in more than one job, in a form of evolutionary improvisation. They are often described as “moonlighting” proteins, referring to the practice of people taking a second job, typically after dark, to help pay the bills. A classic example of a moonlighting protein is

Karrikins are butenolide compounds present in post-fire environments that can stimulate seed germination in many species, including Arabidopsis thaliana. Plants also produce endogenous butenolide compounds that serve as hormones, namely strigolactones (SLs). The receptor for karrikins (KARRIKIN INSENSITIVE 2; KAI2) and the receptor for SLs (DWARF14; D14) are homologous proteins that share many similarities. The mode of action of D14 as a dual enzyme receptor protein is well established, but the nature of KAI2-dependent signalling and its function as a receptor are not fully understood. To expand our knowledge of how KAI2 operates, we screened ethyl methanesulphonate (EMS)-mutagenized populations of A. thaliana for mutants with kai2-like phenotypes and isolated 13 new kai2 alleles. Among these alleles, kai2-10 encoded a D184N protein variant that was stable in planta. Differential scanning fluorimetry assays indicated that the KAI2 D184N protein could interact normally with bioactive ligands. We developed a KAI2-active version of the fluorescent strigolactone analogue Yoshimulactone Green to show that KAI2 D184N exhibits normal rates of ligand hydrolysis. KAI2 D184N degraded in response to treatment with exogenous ligands, suggesting that receptor degradation is a consequence of ligand binding and hydrolysis, but is insufficient for signalling activity. Remarkably, KAI2 D184N degradation was hypersensitive to karrikins, but showed a normal response to strigolactone analogues, implying that these butenolides may interact differently with KAI2. These results demonstrate that the enzymatic and signalling functions of KAI2 can be decoupled, and provide important insights into the mechanistic events that underpin butenolide signalling in plants.

Tiller angle in cereals is a key shoot architecture trait that strongly influences grain yield. Studies in rice (Oryza sativa) have implicated shoot gravitropism in the regulation of tiller angle. However, the functional link between shoot gravitropism and tiller angle is unknown. Here, we conducted a large-scale transcriptome analysis of rice shoots in response to gravistimulation and identified two new nodes of a shoot gravitropism regulatory gene network that also controls rice tiller angle. We demonstrate that HEAT STRESS TRANSCRIPTION FACTOR 2D (HSFA2D) is an upstream positive regulator of the LAZY1-mediated asymmetric auxin distribution pathway. We also show that two functionally redundant transcription factor genes, WUSCHEL RELATED HOMEOBOX6 (WOX6) and WOX11, are expressed asymmetrically in response to auxin to connect gravitropism responses with the control of rice tiller angle. These findings define upstream and downstream genetic components that link shoot gravitropism, asymmetric auxin distribution, and rice tiller angle. The results highlight the power of the high-temporal-resolution RNA-seq data set and its use to explore further genetic components controlling tiller angle. Collectively, these approaches will identify genes to improve grain yields by facilitating the optimization of plant architecture.

There are many endogenous signaling and regulatory molecules which can influence the growth, development and physiology of plants. Hormones are produced specifically for signaling. They are often transported from sites of synthesis to distant sites of action and they operate at very low concentrations. In contrast, some other chemicals may provide signals, but it may not be their main function or activity, such as primary metabolites, reactive oxygen species (ROS) and inorganic ions, and they often act locally within individual cells. The hormone family includes auxins, cytokinins (CK), gibberellins (GA), abscisic acid (ABA), ethylene (ETH), brassinosteroids (BR), strigolactones (SL), salicylic acid (SA), jasmonates (JA), and peptides. They are synthesized from common metabolic precursors, but use specialized pathways, and their production is very strictly controlled, both spatially and temporally. All hormones influence multiple aspects of plant function, and they influence the synthesis and actions of each other. The interactions between hormones, environmental signals, and developmental programs are so complex that the description and modeling of the whole system is very challenging. Some hormone receptors are membrane anchored (CK, ETH, BR, and peptides) while others are soluble (auxin, GA, ABA, SA, jasmonic acid (JA), and SL). Co-receptor complexes are formed during perception of hormones including auxin (with IAA/AUX transcriptional repressor proteins), JA (with JAZ transcriptional repressor proteins), and ABA (with phosphoprotein phosphatase PPC2). Hormone perception can lead to signal transduction through protein phosphorylation cascades (e.g., ABA, CK, BR, and peptides). Other hormone-receptor complexes trigger interaction with F-box proteins and ubiquitination enzymes that target proteins such as transcriptional repressors for degradation by the 26S proteasome (e.g., auxin, GA, SA, JA, and SL). Such signaling changes protein activities and gene transcription, with consequent changes to plant development and physiology. The effects of hormones are so profound that through breeding and agrochemical approaches in the 20th century, they gave us high-yielding, nutritious and resilient crops. In the 21st century we look to plant hormones to help meet the increasing demand for food production under ever-more challenging environmental conditions.