CYTOKININ-RESPONSIVE GROWTH REGULATOR regulates cell expansion and cytokinin-mediated cell cycle progression.

The cytokinin (CK) phytohormones have long been known to activate cell proliferation in plants. However, how CKs regulate cell division and cell expansion remains unclear. Here, we reveal that a basic helix-loop-helix transcription factor, CYTOKININ-RESPONSIVE GROWTH REGULATOR (CKG), mediates CK-dependent regulation of cell expansion and cell cycle progression in Arabidopsis thaliana. The overexpression of CKG increased cell size in a ploidy-independent manner and promoted entry into the S phase of the cell cycle, especially at the seedling stage. Furthermore, CKG enhanced organ growth in a pleiotropic fashion, from embryogenesis to reproductive stages, particularly of cotyledons. In contrast, ckg loss-of-function mutants exhibited smaller cotyledons. CKG mainly regulates the expression of genes involved in the regulation of the cell cycle including WEE1. We propose that CKG provides a regulatory module that connects cell cycle progression and organ growth to CK responses.

Cytokinin-Mediated Regulation of Reactive Oxygen Species Homeostasis Modulates Stomatal Immunity in Arabidopsis.

Stomata play an important role in preinvasive defense responses by limiting pathogen entry into leaves. Although the stress hormones salicylic acid (SA) and abscisic acid (ABA) are known to regulate stomatal immunity, the role of growth promoting hormones is far from understood. Here, we show that in Arabidopsis thaliana, cytokinins (CKs) function in stomatal defense responses. The cytokinin receptor HISTIDINE KINASE3 (AHK3) and RESPONSE REGULATOR2 (ARR2) promote stomatal closure triggered by pathogen-associated molecular pattern (PAMP) and resistance to Pseudomonas syringae pv tomato bacteria. Importantly, the cytokinin trans-zeatin induces stomatal closure and accumulation of reactive oxygen species (ROS) in guard cells through AHK3 and ARR2 in an SA-dependent and ABA-independent manner. Using pharmacological and reverse genetics approaches, we found that CK-mediated stomatal responses involve the apoplastic peroxidases PRX4, PRX33, PRX34, and PRX71, but not the NADPH oxidases RBOHD and RBOHF. Moreover, ARR2 directly activates the expression of PRX33 and PRX34, which are required for SA- and PAMP-triggered ROS production. Thus, the CK signaling pathway regulates ROS homeostasis in guard cells, which leads to enhanced stomatal immunity and plant resistance to bacteria.

Overexpression of INCREASED CAMBIAL ACTIVITY, a putative methyltransferase, increases cambial activity and plant growth.

Cambial activity is a prerequisite for secondary growth in plants; however, regulatory factors controlling the activity of the secondary meristem in radial growth remain elusive. Here, we identified INCREASED CAMBIAL ACTIVITY (ICA), a gene encoding a putative pectin methyltransferase, which could function as a modulator for the meristematic activity of fascicular and interfascicular cambium in Arabidopsis. An overexpressing transgenic line, 35S::ICA, showed accelerated stem elongation and radial thickening, resulting in increased accumulation of biomass, and increased levels of cytokinins (CKs) and gibberellins (GAs). Expression of genes encoding pectin methylesterases involved in pectin modification together with pectin methyltransferases was highly induced in 35S::ICA, which might contribute to an increase of methanol emission as a byproduct in 35S::ICA. Methanol treatment induced the expression of GA- or CK-responsive genes and stimulated plant growth. Overall, we propose that ectopic expression of ICA increases cambial activity by regulating CK and GA homeostasis, and methanol emission, eventually leading to stem elongation and radial growth in the inflorescence stem.

DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis.

BACKGROUND: Plants memorize previous pathogen attacks and are "primed" to produce a faster and stronger defense response, which is critical for defense against pathogens. In plants, cytosines in transposons and gene bodies are reported to be frequently methylated. Demethylation of transposons can affect disease resistance by regulating the transcription of nearby genes during defense response, but the role of gene body methylation (GBM) in defense responses remains unclear. RESULTS: Here, we find that loss of the chromatin remodeler decrease in DNA methylation 1 (ddm1) synergistically enhances resistance to a biotrophic pathogen under mild chemical priming. DDM1 mediates gene body methylation at a subset of stress-responsive genes with distinct chromatin properties from conventional gene body methylated genes. Decreased gene body methylation in loss of ddm1 mutant is associated with hyperactivation of these gene body methylated genes. Knockout of glyoxysomal protein kinase 1 (gpk1), a hypomethylated gene in ddm1 loss-of-function mutant, impairs priming of defense response to pathogen infection in Arabidopsis. We also find that DDM1-mediated gene body methylation is prone to epigenetic variation among natural Arabidopsis populations, and GPK1 expression is hyperactivated in natural variants with demethylated GPK1. CONCLUSIONS: Based on our collective results, we propose that DDM1-mediated GBM provides a possible regulatory axis for plants to modulate the inducibility of the immune response.

A systems approach for identifying resistance factors to Rice stripe virus.

Rice stripe virus (RSV) causes disease that can severely affect the productivity of rice (Oryza sativa). Several RSV-resistant cultivars have been developed. However, host factors conferring RSV resistance in these cultivars are still elusive. Here, we present a systems approach for identifying potential rice resistance factors. We developed two near-isogenic lines (NIL), RSV-resistant NIL22 and RSV-susceptible NIL37, and performed gene expression profiling of the two lines in RSV-infected and RSV-uninfected conditions. We identified 237 differentially expressed genes (DEG) between NIL22 and NIL37. By integrating with known quantitative trait loci (QTL), we selected 11 DEG located within the RSV resistance QTL as RSV resistance factor candidates. Furthermore, we identified 417 DEG between RSV-infected and RSV-uninfected conditions. Using an interaction network-based method, we selected 20 DEG highly interacting with the two sets of DEG as RSV resistance factor candidates. Among the 31 candidates, we selected the final set of 21 potential RSV resistance factors whose differential expression was confirmed in the independent samples using real-time reverse-transcription polymerase chain reaction. Finally, we reconstructed a network model delineating potential association of the 21 selected factors with resistance-related processes. In summary, our approach, based on gene expression profiling, revealed potential host resistance factors and a network model describing their relationships with resistance-related processes, which can be further validated in detailed experiments.

PDA Biosimilars Workshop Report (September 27-28, 2018)-Getting It Right the First Time for Biosimilar Marketing Applications.

This workshop report summarizes the presentations, the breakout session outcomes, and the speaker panel discussions from the PDA Biosimilars Workshop held September 27-28, 2018, in Washington, DC. This format was deliberately selected for the workshop with the expectation of delivering a post-workshop paper on current best practices and existing challenges for sponsors. The event, co-chaired by Dr. Stephan Krause (AstraZeneca Biologics) and Dr. Emanuela Lacana (CDER/FDA), was attended by 140 agency and industry representatives. The workshop was separated into three major sessions P1: Regulatory Perspective, P2: Challenges in Biosimilar Development, and P3: Demonstrating Analytical Similarity. Each of the three sessions started with agency and industry presentations. Participants then split into two concurrent roundtable discussion groups to hear the answers to questions that had been provided to all participants one week prior to the event. The sessions were recorded. This paper provides consolidated answers to specific case studies for current challenges to sponsors and agencies. In addition, the panel discussion notes following each breakout roundtable session, as well as brief talk summaries of all speakers, are provided. The first session explored the challenges encountered with submission of biosimilar marketing applications from the perspectives of regulatory agencies. Expectations for a successful submission of the chemistry, manufacturing, and controls (CMC) information were described. The second session addressed high-level technical challenges and how to avoid pitfalls frequently encountered during biosimilar candidate development, including data quality expectations, creation of the final control strategy, and strategic choices necessary for candidate selection and development. Both regulatory perspectives and industry experience were shared. The last session explored the use of statistical tools to provide meaningful contributions to the demonstration of analytical similarity. The presentations highlighted common issues and practical challenges that arise during the application of statistical tools.LAY ABSTRACT: Significant challenges are still-remaining for sponsors and agencies to successfully develop and license Biosimilars. A Biosimilars Workshop was therefore held on 27-28 September 2018 in Washington, DC, to find practical solutions to the remaining challenges. The workshop planning committee with members from industry and agencies prepared specific case studies focused on some of most difficult situations. The workshop was separated into three major sessions (P1 - Regulatory Perspective; P2 - Challenges in Biosimilar Development; P3 - Demonstrating Analytical Similarity) and each session attempted to provide practical solutions to the relevant case studies. This first session explored the challenges encountered with submission of biosimilar marketing applications from the regulatory agencies' perspectives. Expectations for a successful submission of the CMC information were described. The second session addressed high-level technical challenges frequently encountered during biosimilar candidate development, including data quality expectations, the creation of the final control strategy, and strategic choices necessary for candidate selection and development. The last session explored the use of statistical tools to provide meaningful contributions to the demonstration of analytical similarity and practical challenges that arise during the application of statistical tools.

iNID: an analytical framework for identifying network models for interplays among developmental signaling in Arabidopsis.

Integration of internal and external cues into developmental programs is indispensable for growth and development of plants, which involve complex interplays among signaling pathways activated by the internal and external factors (IEFs). However, decoding these complex interplays is still challenging. Here, we present a web-based platform that identifies key regulators and Network models delineating Interplays among Developmental signaling (iNID) in Arabidopsis. iNID provides a comprehensive resource of (1) transcriptomes previously collected under the conditions treated with a broad spectrum of IEFs and (2) protein and genetic interactome data in Arabidopsis. In addition, iNID provides an array of tools for identifying key regulators and network models related to interplays among IEFs using transcriptome and interactome data. To demonstrate the utility of iNID, we investigated the interplays of (1) phytohormones and light and (2) phytohormones and biotic stresses. The results revealed 34 potential regulators of the interplays, some of which have not been reported in association with the interplays, and also network models that delineate the involvement of the 34 regulators in the interplays, providing novel insights into the interplays collectively defined by phytohormones, light, and biotic stresses. We then experimentally verified that BME3 and TEM1, among the selected regulators, are involved in the auxin-brassinosteroid (BR)-blue light interplay. Therefore, iNID serves as a useful tool to provide a basis for understanding interplays among IEFs.

Plant hormonal regulation of nitrogen-fixing nodule organogenesis.

Legumes have evolved symbiotic interactions with rhizobial bacteria to efficiently utilize nitrogen. Recent progress in symbiosis has revealed several key components of host plants required for nitrogen-fixing nodule organogenesis, in which complicated metabolic and signaling pathways in the host plant are reprogrammed to generate nodules in the cortex upon perception of the rhizobial Nod factor. Following the recognition of Nod factors, plant hormones are likely to be essential throughout nodule organogenesis for integration of developmental and environmental signaling cues into nodule development. Here, we review the molecular events involved in plant hormonal regulation and signaling cross-talk for nitrogen-fixing nodule development, and discuss how these signaling networks are integrated into Nod factor-mediated signaling during plant-microbe interactions.

The Rice Oligonucleotide Array Database: an atlas of rice gene expression.

BACKGROUND: Microarray technologies facilitate high-throughput gene expression analysis. However, the diversity of platforms for rice gene expression analysis hinders efficient analysis. Tools to broadly integrate microarray data from different platforms are needed. RESULTS: In this study, we developed the Rice Oligonucleotide Array Database (ROAD, http://www.ricearray.org) to explore gene expression across 1,867 publicly available rice microarray hybridizations. The ROAD's user-friendly web interface and variety of visualization tools facilitate the extraction of gene expression profiles using gene and microarray element identifications. The ROAD supports meta-analysis of genes expressed in different tissues and at developmental stages. Co-expression analysis tool provides information on co-regulation between genes under general, abiotic and biotic stress conditions. Additionally, functional analysis tools, such as Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology, are embedded in the ROAD. These tools facilitate the identification of meaningful biological patterns in a list of query genes. CONCLUSIONS: The Rice Oligonucleotide Array Database provides comprehensive gene expression profiles for all rice genes, and will be a useful resource for researchers of rice and other grass species.

Cytokinins and plant immunity: old foes or new friends?

Cytokinins are plant growth promoting hormones involved in the specification of embryonic cells, maintenance of meristematic cells, shoot formation and development of vasculature. Cytokinins have also emerged as a major factor in plant-microbe interactions during nodule organogenesis and pathogenesis. Microbe-originated cytokinins confer abnormal hypersensitivity of cytokinins to plants, augmenting the sink activity of infected regions. However, recent findings have shed light on a distinct role of cytokinins in plant immune responses. Plant-borne cytokinins systemically induce resistance against pathogen infection. This resistance is orchestrated by endogenous cytokinin and salicylic acid signaling. Here, we discuss how plant- and pathogen-derived cytokinins inversely affect the plant defense response. In addition, we consider the molecular mechanisms underlying plant-derived cytokinin action in plant immunity.