Growth asymmetry precedes differential auxin response during apical hook initiation in Arabidopsis.

The development of a hook-like structure at the apical part of the soil-emerging organs has fascinated botanists for centuries, but how it is initiated remains unclear. Here, we demonstrate with high-throughput infrared imaging and 2-D clinostat treatment that, when gravity-induced root bending is absent, apical hook formation still takes place. In such scenarios, hook formation begins with a de novo growth asymmetry at the apical part of a straightly elongating hypocotyl. Remarkably, such de novo asymmetric growth, but not the following hook enlargement, precedes the establishment of a detectable auxin response asymmetry, and is largely independent of auxin biosynthesis, transport and signaling. Moreover, we found that functional cortical microtubule array is essential for the following enlargement of hook curvature. When microtubule array was disrupted by oryzalin, the polar localization of PIN proteins and the formation of an auxin maximum became impaired at the to-be-hook region. Taken together, we propose a more comprehensive model for apical hook initiation, in which the microtubule-dependent polar localization of PINs may mediate the instruction of growth asymmetry that is either stochastically taking place, induced by gravitropic response, or both, to generate a significant auxin gradient that drives the full development of the apical hook.

Integrated Regulation of Apical Hook Development by Transcriptional Coupling of EIN3/EIL1 and PIFs in Arabidopsis.

The apical hook protects the meristems of dicot seedlings as they protrude through the soil; multiple factors, including phytohormones and light, mediate apical hook development. HOOKLESS1 (HLS1) plays an indispensable role, as HLS1 mutations cause a hookless phenotype. The ETHYLENE INSENSITIVE3 (EIN3) and EIN3-LIKE1 (EIL1) transcription factors integrate multiple signals (ethylene, gibberellins, and jasmonate) and activate HLS1 expression to enhance hook development. Here, we found that Arabidopsis thaliana PHYTOCHROME INTERACTING FACTOR (PIF) transcription factors act in parallel with EIN3/EIL1 and promote hook curvature by activating HLS1 transcription at a distinct binding motif. EIN3/EIL1 and PIFs can promote hook formation in the absence of the other. Jasmonate represses PIF function to inhibit hook development. Like EIN3 and EIL1, MYC2 interacts with PIF4 and hampers its activity. Acting together, EIN3/EIL1 and PIFs alleviate the negative effects of jasmonate/light and facilitate the positive effects of ethylene/gibberellins. Mutating EIN3/EIL1 and PIFs causes a complete hookless phenotype, marginal HLS1 expression, and insensitivity to upstream signals. Transcriptome profiling revealed that EIN3/EIL1 and PIFs additively and distinctly regulate a wide array of processes, including apical hook development. Together, our findings identify an integrated framework underlying the regulation of apical hook development and show that EIN3/EIL1 and PIFs fine-tune adaptive growth in response to hormone and light signals.

Ethylene-induced microtubule reorientation is essential for fast inhibition of root elongation in Arabidopsis.

Microtubule reorientation is a long-standing observation that has been implicated in regulating the inhibitory effect of ethylene on axial elongation of plant cells. However, the signaling mechanism underlying ethylene-induced microtubule reorientation has remained elusive. Here, we reveal, by live confocal imaging and kinetic root elongation assays, that the time courses of ethylene-induced microtubule reorientation and root elongation inhibition are highly correlated, and that microtubule reorientation is required for the full responsiveness of root elongation to ethylene treatment. Our genetic analysis demonstrated that the effect of ethylene on microtubule orientation and root elongation is mainly transduced through the canonical linear ethylene signaling pathway. By using pharmacological and genetic analyses, we demonstrate further that the TIR1/AFBs-Aux/IAAs-ARFs auxin signaling pathway, but not the ABP1-ROP6-RIC1 auxin signaling branch, is essential for ethylene-induced microtubule reorientation and root elongation inhibition. Together, these findings offer evidence for the functional significance and elucidate the signaling mechanism for ethylene-induced microtubule reorientation in fast root elongation inhibition in Arabidopsis.

A small-molecule screen identifies L-kynurenine as a competitive inhibitor of TAA1/TAR activity in ethylene-directed auxin biosynthesis and root growth in Arabidopsis.

The interactions between phytohormones are crucial for plants to adapt to complex environmental changes. One example is the ethylene-regulated local auxin biosynthesis in roots, which partly contributes to ethylene-directed root development and gravitropism. Using a chemical biology approach, we identified a small molecule, l-kynurenine (Kyn), which effectively inhibited ethylene responses in Arabidopsis thaliana root tissues. Kyn application repressed nuclear accumulation of the ETHYLENE INSENSITIVE3 (EIN3) transcription factor. Moreover, Kyn application decreased ethylene-induced auxin biosynthesis in roots, and TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1/TRYPTOPHAN AMINOTRANSFERASE RELATEDs (TAA1/TARs), the key enzymes in the indole-3-pyruvic acid pathway of auxin biosynthesis, were identified as the molecular targets of Kyn. Further biochemical and phenotypic analyses revealed that Kyn, being an alternate substrate, competitively inhibits TAA1/TAR activity, and Kyn treatment mimicked the loss of TAA1/TAR functions. Molecular modeling and sequence alignments suggested that Kyn effectively and selectively binds to the substrate pocket of TAA1/TAR proteins but not those of other families of aminotransferases. To elucidate the destabilizing effect of Kyn on EIN3, we further found that auxin enhanced EIN3 nuclear accumulation in an EIN3 BINDING F-BOX PROTEIN1 (EBF1)/EBF2-dependent manner, suggesting the existence of a positive feedback loop between auxin biosynthesis and ethylene signaling. Thus, our study not only reveals a new level of interactions between ethylene and auxin pathways but also offers an efficient method to explore and exploit TAA1/TAR-dependent auxin biosynthesis.

Ethylene-induced stabilization of ETHYLENE INSENSITIVE3 and EIN3-LIKE1 is mediated by proteasomal degradation of EIN3 binding F-box 1 and 2 that requires EIN2 in Arabidopsis.

Plant responses to ethylene are mediated by regulation of EBF1/2-dependent degradation of the ETHYLENE INSENSITIVE3 (EIN3) transcription factor. Here, we report that the level of EIL1 protein is upregulated by ethylene through an EBF1/2-dependent pathway. Genetic analysis revealed that EIL1 and EIN3 cooperatively but differentially regulate a wide array of ethylene responses, with EIL1 mainly inhibiting leaf expansion and stem elongation in adult plants and EIN3 largely regulating a multitude of ethylene responses in seedlings. When EBF1 and EBF2 are disrupted, EIL1 and EIN3 constitutively accumulate in the nucleus and remain unresponsive to exogenous ethylene application. Further study revealed that the levels of EBF1 and EBF2 proteins are downregulated by ethylene and upregulated by silver ion and MG132, suggesting that ethylene stabilizes EIN3/EIL1 by promoting EBF1 and EBF2 proteasomal degradation. Also, we found that EIN2 is indispensable for mediating ethylene-induced EIN3/EIL1 accumulation and EBF1/2 degradation, whereas MKK9 is not required for ethylene signal transduction, contrary to a previous report. Together, our studies demonstrate that ethylene similarly regulates EIN3 and EIL1, the two master transcription factors coordinating myriad ethylene responses, and clarify that EIN2 but not MKK9 is required for ethylene-induced EIN3/EIL1 stabilization. Our results also reveal that EBF1 and EBF2 act as essential ethylene signal transducers that by themselves are subject to proteasomal degradation.

AHD2.0: an update version of Arabidopsis Hormone Database for plant systematic studies.

Phytohormone studies enlightened our knowledge of plant responses to various changes. To provide a systematic and comprehensive view of genes participating in plant hormonal regulation, an online accessible database Arabidopsis Hormone Database (AHD) has been developed, which is a collection of hormone related genes of the model organism Arabidopsis thaliana (AHRGs). Recently we updated our database from AHD to a new version AHD2.0 by adding several pronounced features: (i) updating our collection of AHRGs based on most recent publications as well as constructing elaborate schematic diagrams of each hormone biosynthesis and signaling pathways; (ii) adding orthologs of sequenced plants listed in OrthoMCL-DB to each AHRG in the updated database; (iii) providing predicted miRNA splicing site(s) for each AHRG; (iv) integrating genes that genetically interact with each AHRG according to literatures mining; (v) providing links to a powerful online analysis platform WebLab for the convenience of in-time bioinformatics analysis and (vi) providing links to widely used protein databases and integrating more expression profiling information that would facilitate users for a more systematic and integrative analysis related to phytohormone research.

Model of Short- and Long-Term Outcomes of Emicizumab Prophylaxis Treatment for Persons with Hemophilia A.

BACKGROUND: Hemophilia A (HA) can result in bleeding events because of low or absent clotting factor VIII (FVIII). Prophylactic treatment for severe HA includes replacement FVIII infusions and emicizumab, a bispecific factor IXa- and factor X-directed antibody. OBJECTIVE: To develop an economic model to predict the short- and long-term clinical and economic outcomes of prophylaxis with emicizumab versus short-acting recombinant FVIII among persons with HA in the United States. METHODS: A Markov model was developed to compare clinical outcomes and costs of emicizumab versus FVIII prophylaxis among persons with severe HA from U.S. payer and societal perspectives. Patients started prophylaxis at age 1 year in the base case. Mutually exclusive health states considered were "no arthropathy," "arthropathy," "surgery," and "death." Serious adverse events, breakthrough bleeds, and inhibitor development were simulated throughout the modeled time horizon. In addition to the prophylaxis drug costs, patients could incur other direct costs related to breakthrough bleeds treatment, serious adverse events, development of inhibitors, arthropathy, and orthopedic surgery. Indirect costs associated with productivity loss (i.e., missed work or disabilities) were applied for adults. Model inputs were obtained from the HAVEN 3 trial, published literature, and expert opinion. The model used a lifetime horizon, and results for 1 year and 5 years were also reported. Deterministic sensitivity analyses and scenario analyses were conducted to assess robustness of the model. RESULTS: Over a lifetime horizon, the cumulative number of all treated bleeds and joint bleeds avoided on emicizumab versus FVIII prophylaxis were 278.2 and 151.7, respectively. Correspondingly, arthropathy (mean age at onset: 12.9 vs. 5.4 years) and FVIII inhibitor development (mean age at development: 13.9 vs. 1.1 years) were delayed. Total direct and indirect costs were lower for emicizumab versus FVIII prophylaxis for all modeled time horizons ($97,159 vs. $331,610 at 1 year; $603,146 vs. $1,459,496 at 5 years; and $15,238,072 vs. $22,820,281 over a lifetime horizon). The sensitivity analyses indicated that clinical outcomes were sensitive to efficacy inputs, while economic outcomes were driven by the discount rate, dosing schedules, and treatments after inhibitor development. Results for moderate to severe patients were consistent with findings in the severe HA population. CONCLUSIONS: The model suggests that emicizumab prophylaxis confers additional clinical benefits, resulting in a lower number of bleeding events and delayed onset of arthropathy and inhibitor development across all time assessment horizons. Compared with short-acting recombinant FVIII, emicizumab prophylaxis leads to superior patient outcomes and cost savings from U.S. payer and societal perspectives. DISCLOSURES: Funding for this study was provided by Genentech. Raimundo and Patel are employees of Genentech and own stock or stock options. Zhou, Han, Ji, Fang, Zhong, and Betts are employees of Analysis Group, which received consultancy fees from Genentech for conducting this study. Mahajerin received consultancy fees from Genentech for work on this study. Portions of this research were presented as a poster at the 2018 American Society of Hematology Conference; December 1-4, 2018; San Diego, CA.

Plant biology. Suppression of endogenous gene silencing by bidirectional cytoplasmic RNA decay in Arabidopsis.

Plant immunity against foreign gene invasion takes advantage of posttranscriptional gene silencing (PTGS). How plants elaborately avert inappropriate PTGS of endogenous coding genes remains unclear. We demonstrate in Arabidopsis that both 5'-3' and 3'-5' cytoplasmic RNA decay pathways act as repressors of transgene and endogenous PTGS. Disruption of bidirectional cytoplasmic RNA decay leads to pleiotropic developmental defects and drastic transcriptomic alterations, which are substantially rescued by PTGS mutants. Upon dysfunction of bidirectional RNA decay, a large number of 21- to 22-nucleotide endogenous small interfering RNAs are produced from coding transcripts, including multiple microRNA targets, which could interfere with their cognate gene expression and functions. This study highlights the risk of unwanted PTGS and identifies cytoplasmic RNA decay pathways as safeguards of plant transcriptome and development.

Coordinated regulation of apical hook development by gibberellins and ethylene in etiolated Arabidopsis seedlings.

Dark-grown Arabidopsis seedlings develop an apical hook when germinating in soil, which protects the cotyledons and apical meristematic tissues when protruding through the soil. Several hormones are reported to distinctly modulate this process. Previous studies have shown that ethylene and gibberellins (GAs) coordinately regulate the hook development, although the underlying molecular mechanism is largely unknown. Here we showed that GA(3) enhanced while paclobutrazol repressed ethylene- and EIN3-overexpression (EIN3ox)-induced hook curvature, and della mutant exhibited exaggerated hook curvature, which required an intact ethylene signaling pathway. Genetic study revealed that GA-enhanced hook development was dependent on HOOKLESS 1 (HLS1), a central regulator mediating the input of the multiple signaling pathways during apical hook development. We further found that GA(3) induced (and DELLA proteins repressed) HLS1 expression in an ETHYLENE INSENSITIVE 3/EIN3-LIKE 1 (EIN3/EIL1)-dependent manner, whereby EIN3/EIL1 activated HLS1 transcription by directly binding to its promoter. Additionally, DELLA proteins were found to interact with the DNA-binding domains of EIN3/EIL1 and repress EIN3/EIL1-regulated HLS1 expression. Treatment with naphthylphthalamic acid, a polar auxin transport inhibitor, repressed the constitutively exaggerated hook curvature of EIN3ox line and della mutant, supporting that auxin functions downstream of the ethylene and GA pathways in hook development. Taken together, our results identify EIN3/EIL1 as a new class of DELLA-associated transcription factors and demonstrate that GA promotes apical hook formation in cooperation with ethylene partly by inducing the expression of HLS1 via derepression of EIN3/EIL1 functions.