Large-scale identification of gibberellin-related transcription factors defines group VII ETHYLENE RESPONSE FACTORS as functional DELLA partners

RAP2.3 negatively regulates nitric oxide biosynthesis and related responses through a rheostat-like mechanism in Arabidopsis

Nitric oxide (NO) is sensed through a mechanism involving the degradation of group-VII ERF transcription factors (ERFVIIs) that is mediated by the N-degron pathway. However, the mechanisms regulating NO homeostasis and downstream responses remain mostly unknown. To explore the role of ERFVIIs in regulating NO production and signaling, genome-wide transcriptome analyses were performed on single and multiple erfvii mutants of Arabidopsis following exposure to NO. Transgenic plants overexpressing degradable or non-degradable versions of RAP2.3, one of the five ERFVIIs, were also examined. Enhanced RAP2.3 expression attenuated the changes in the transcriptome upon exposure to NO, and thereby acted as a brake for NO-triggered responses that included the activation of jasmonate and ABA signaling. The expression of non-degradable RAP2.3 attenuated NO biosynthesis in shoots but not in roots, and released the NO-triggered inhibition of hypocotyl and root elongation. In the guard cells of stomata, the control of NO accumulation depended on PRT6-triggered degradation of RAP2.3 more than on RAP2.3 levels. RAP2.3 therefore seemed to work as a molecular rheostat controlling NO homeostasis and signaling. Its function as a brake for NO signaling was released upon NO-triggered PRT6-mediated degradation, thus allowing the inhibition of growth, and the potentiation of jasmonate- and ABA-related signaling.

Origin and evolution of gibberellin signaling and metabolism in plants

Gibberellins modulate multiple aspects of plant behavior. The molecular mechanism by which these hormones are perceived and how this information is translated into transcriptional changes has been elucidated in vascular plants: gibberellins are perceived by the nuclear receptor GID1, which then interacts with the DELLA nuclear proteins and promote their degradation, resulting in the modification of the activity of transcription factors with which DELLAs interact physically. However, several important questions are still pending: how does a single molecule perform such a vast array of functions along plant development? What property do gibberellins add to plant behavior? A closer look at gibberellin action from an evolutionary perspective can help answer these questions. DELLA proteins are conserved in all land plants, and predate the emergence of a full gibberellin metabolic pathway and the GID1 receptor in the ancestor of vascular plants. The origin of gibberellin signaling is linked to the exaptation by GID1 of the N-terminal domain in DELLA, which already acted as a transcriptional coactivator domain in the ancestral DELLA proteins. At least the ability to control plant growth seems to be encoded already in the ancestral DELLA protein too, suggesting that gibberellins' functional diversity is the direct consequence of DELLA protein activity. Finally, comparative network analysis suggests that gibberellin signaling increases the coordination of transcriptional responses, providing a theoretical framework for the role of gibberellins in plant adaptation at the evolutionary scale, which further needs experimental testing.

Evolution of Plant Hormone Response Pathways

This review focuses on the evolution of plant hormone signaling pathways. Like the chemical nature of the hormones themselves, the signaling pathways are diverse. Therefore, we focus on a group of hormones whose primary perception mechanism involves an Skp1/Cullin/F-box-type ubiquitin ligase: auxin, jasmonic acid, gibberellic acid, and strigolactone. We begin with a comparison of the core signaling pathways of these four hormones, which have been established through studies conducted in model organisms in the Angiosperms. With the advent of next-generation sequencing and advanced tools for genetic manipulation, the door to understanding the origins of hormone signaling mechanisms in plants beyond these few model systems has opened. For example, in-depth phylogenetic analyses of hormone signaling components are now being complemented by genetic studies in early diverging land plants. Here we discuss recent investigations of how basal land plants make and sense hormones. Finally, we propose connections between the emergence of hormone signaling complexity and major developmental transitions in plant evolution.

Allele mining of TaGRF-2D gene 5'-UTR in Triticum aestivum and Aegilops tauschii genotypes

The low diversity of the D-subgenome of bread wheat requires the involvement of new alleles for breeding. In grasses, the allelic state of Growth Regulating Factor (GRF) gene is correlated with nitrogen uptake. In this study, we characterized the sequence of TaGRF-2D and assessed its diversity in bread wheat and goatgrass Aegilops tauschii (genome DD). In silico analysis was performed for reference sequence searching, primer pairs design and sequence assembly. The gene sequence was obtained using Illumina and Sanger sequencing. The complete sequences of TaGRF-2D were obtained for 18 varieties of wheat. The polymorphism in the presence/absence of two GCAGCC repeats in 5' UTR was revealed and the GRF-2D-SSR marker was developed. Our results showed that the alleles 5' UTR-250 and 5' UTR-238 were present in wheat varieties, 5' UTR-250 was presented in the majority of wheat varieties. In Ae. tauschii ssp. strangulata (likely donor of the D-subgenome of polyploid wheat), most accessions carried the 5' UTR-250 allele, whilst most Ae. tauschii ssp. tauschii have 5' UTR-244. The developed GRF-2D-SSR marker can be used to study the genetic diversity of wheat and Ae. tauschii.

GROWTH-REGULATING FACTORS Interact with DELLAs and Regulate Growth in Cold Stress

DELLA proteins are repressors of the gibberellin (GA) hormone signaling pathway that act mainly by regulating transcription factor activities in plants. GAs induce DELLA repressor protein degradation and thereby control a number of critical developmental processes as well as responses to stresses such as cold. The strong effect of cold temperatures on many physiological processes has rendered it difficult to assess, based on phenotypic criteria, the role of GA and DELLAs in plant growth during cold stress. Here, we uncover substantial differences in the GA transcriptomes between plants grown at ambient temperature (21°C) and plants exposed to cold stress (4°C) in Arabidopsis (Arabidopsis thaliana). We further identify over 250, to the largest extent previously unknown, DELLA-transcription factor interactions using the yeast two-hybrid system. By integrating both data sets, we reveal that most members of the nine-member GRF (GROWTH REGULATORY FACTOR) transcription factor family are DELLA interactors and, at the same time, that several GRF genes are targets of DELLA-modulated transcription after exposure to cold stress. We find that plants with altered GRF dosage are differentially sensitive to the manipulation of GA and hence DELLA levels, also after cold stress, and identify a subset of cold stress-responsive genes that qualify as targets of this DELLA-GRF regulatory module.

The plant N-degron pathways of ubiquitin-mediated proteolysis

The amino-terminal residue of a protein (or amino-terminus of a peptide following protease cleavage) can be an important determinant of its stability, through the Ubiquitin Proteasome System associated N-degron pathways. Plants contain a unique combination of N-degron pathways (previously called the N-end rule pathways) E3 ligases, PROTEOLYSIS (PRT)6 and PRT1, recognizing non-overlapping sets of amino-terminal residues, and others remain to be identified. Although only very few substrates of PRT1 or PRT6 have been identified, substrates of the oxygen and nitric oxide sensing branch of the PRT6 N-degron pathway include key nuclear-located transcription factors (ETHYLENE RESPONSE FACTOR VIIs and LITTLE ZIPPER 2) and the histone-modifying Polycomb Repressive Complex 2 component VERNALIZATION 2. In response to reduced oxygen or nitric oxide levels (and other mechanisms that reduce pathway activity) these stabilized substrates regulate diverse aspects of growth and development, including response to flooding, salinity, vernalization (cold-induced flowering) and shoot apical meristem function. The N-degron pathways show great promise for use in the improvement of crop performance and for biotechnological applications. Upstream proteases, components of the different pathways and associated substrates still remain to be identified and characterized to fully appreciate how regulation of protein stability through the amino-terminal residue impacts plant biology.

ARGONAUTE1 and ARGONAUTE4 Regulate Gene Expression and Hypoxia Tolerance

In plants, hypoxia can be induced by submergence, and the lack of oxygen impairs mitochondrial respiration, thus affecting the plant's energy status. Hypoxia has major effects on gene expression; these changes induce key responses that help meet the needs of the stressed plant. However, little is known about the possible role of RNA signaling in the regulation of gene expression under limited oxygen availability. Here, we report the contribution of ARGONAUTE1 (AGO1) to hypoxia-induced gene regulation in Arabidopsis (Arabidopsis thaliana). Submergence induced changes in levels of the microRNAs miR2936 and miR398, but this had no obvious effects on their putative target mRNA levels. However, we found that ago1-27 plants are intolerant to submergence and transcriptome analysis identified genes whose regulation requires functional AGO1. Analysis of mutants affected in various branches of RNA signaling highlighted the convergence of AGO1 signaling with the AGO4-dependent RNA-directed DNA methylation (RdDM) pathway. AGO4-dependent RdDM represses the expression of HOMOLOG OF RPW8 4 (HR4) and alters its response to submergence. Remarkably, methylation of the second exon of HR4 is not only reduced in ago4-1 but also in plants overexpressing a constitutively stable version of the oxygen sensor RELATED TO APETALA2 12 (RAP2.12), indicating convergence of oxygen signaling with epigenetic regulation of gene expression. Therefore, our results identify a role for AGO1 and AGO4 RNA-silencing pathways in low-oxygen signaling in Arabidopsis.

Silencing of transcription factor encoding gene StTCP23 by small RNAs derived from the virulence modulating region of potato spindle tuber viroid is associated with symptom development in potato

Viroids are small, non-protein-coding RNAs which can induce disease symptoms in a variety of plant species. Potato (Solanum tuberosum L.) is the natural host of Potato spindle tuber viroid (PSTVd) where infection results in stunting, distortion of leaves and tubers and yield loss. Replication of PSTVd is accompanied by the accumulation of viroid-derived small RNAs (sRNAs) proposed to play a central role in disease symptom development. Here we report that PSTVd sRNAs direct RNA silencing in potato against StTCP23, a member of the TCP (teosinte branched1/Cycloidea/Proliferating cell factor) transcription factor family genes that play an important role in plant growth and development as well as hormonal regulation, especially in responses to gibberellic acid (GA). The StTCP23 transcript has 21-nucleotide sequence complementarity in its 3ʹ untranslated region with the virulence-modulating region (VMR) of PSTVd strain RG1, and was downregulated in PSTVd-infected potato plants. Analysis using 3ʹ RNA ligase-mediated rapid amplification of cDNA ends (3ʹ RLM RACE) confirmed cleavage of StTCP23 transcript at the expected sites within the complementarity with VMR-derived sRNAs. Expression of these VMR sRNA sequences as artificial miRNAs (amiRNAs) in transgenic potato plants resulted in phenotypes reminiscent of PSTVd-RG1-infected plants. Furthermore, the severity of the phenotypes displayed was correlated with the level of amiRNA accumulation and the degree of amiRNA-directed down-regulation of StTCP23. In addition, virus-induced gene silencing (VIGS) of StTCP23 in potato also resulted in PSTVd-like phenotypes. Consistent with the function of TCP family genes, amiRNA lines in which StTCP23 expression was silenced showed a decrease in GA levels as well as alterations to the expression of GA biosynthesis and signaling genes previously implicated in tuber development. Application of GA to the amiRNA plants minimized the PSTVd-like phenotypes. Taken together, our results indicate that sRNAs derived from the VMR of PSTVd-RG1 direct silencing of StTCP23 expression, thereby disrupting the signaling pathways regulating GA metabolism and leading to plant stunting and formation of small and spindle-shaped tubers.

Potato spindle tuber viroid (PSTVd) is a small RNA pathogen that causes severe pandemic diseases in potato. How this non-protein-coding RNA induces disease symptom development in potato is unknown, thereby hindering the development of effective control measures. Here we report the first evidence that PSTVd disease is caused by the silencing of StTCP23, a potato transcription factor encoding gene, by PSTVd-derived small-interfering RNA (siRNAs). Specifically, we demonstrate that 3ʹ untranslated region (UTR) region of StTCP23 mRNA contains a 21-nt sequence that is complementary to the virulence-modulating region (VMR) of PSTVd. Furthermore, we show that StTCP23 expression is repressed in PSTVd-infected potato, and this repression is accompanied by StTCP23 transcript cleavage within the identified region of complementary. In planta expression of VMR sequences as 21-nt artificial microRNAs (amiRNAs) or infection of potato plants with a virus-induced gene silencing vector containing a portion the StTCP23 coding sequence, results in reduced StTCP23 transcript abundance and the expression of PSTVd-like disease symptoms. Consistent with the predicted functional role of StTCP23 in regulating the gibberellic acid (GA) biosynthesis and signaling pathways, GA levels were reduced both in PSTVd-infected and amiRNA-expressing plants. Our results provide compelling evidence that StTCP23 positively regulates potato sprouting and tuber development via a GA-related mechanism, and that the disease symptoms that develop upon PSTVd infection result from silencing of StTCP23 by VMR-derived siRNAs.

Nitric oxide molecular targets: reprogramming plant development upon stress

Plants are sessile organisms that need to complete their life cycle by the integration of different abiotic and biotic environmental signals, tailoring developmental cues and defense concomitantly. Commonly, stress responses are detrimental to plant growth and, despite the fact that intensive efforts have been made to understand both plant development and defense separately, most of the molecular basis of this trade-off remains elusive. To cope with such a diverse range of processes, plants have developed several strategies including the precise balance of key plant growth and stress regulators [i.e. phytohormones, reactive nitrogen species (RNS), and reactive oxygen species (ROS)]. Among RNS, nitric oxide (NO) is a ubiquitous gasotransmitter involved in redox homeostasis that regulates specific checkpoints to control the switch between development and stress, mainly by post-translational protein modifications comprising S-nitrosation of cysteine residues and metals, and nitration of tyrosine residues. In this review, we have sought to compile those known NO molecular targets able to balance the crossroads between plant development and stress, with special emphasis on the metabolism, perception, and signaling of the phytohormones abscisic acid and salicylic acid during abiotic and biotic stress responses.

Origin of Gibberellin-Dependent Transcriptional Regulation by Molecular Exploitation of a Transactivation Domain in DELLA Proteins

DELLA proteins are plant-specific transcriptional regulators known to interact through their C-terminal GRAS domain with over 150 transcription factors in Arabidopsis thaliana. Besides, DELLAs from vascular plants can interact through the N-terminal domain with the gibberellin receptor encoded by GID1, through which gibberellins promote DELLA degradation. However, this regulation is absent in nonvascular land plants, which lack active gibberellins or a proper GID1 receptor. Current knowledge indicates that DELLAs are important pieces of the signaling machinery of vascular plants, especially angiosperms, but nothing is known about DELLA function during early land plant evolution or if they exist at all in charophytan algae. We have now elucidated the evolutionary origin of DELLA proteins, showing that algal GRAS proteins are monophyletic and evolved independently from those of land plants, which explains why there are no DELLAs outside land plants. DELLA genes have been maintained throughout land plant evolution with only two major duplication events kept among plants. Furthermore, we show that the features needed for DELLA interaction with the receptor were already present in the ancestor of all land plants and propose that these DELLA N-terminal motifs have been tightly conserved in nonvascular land plants for their function in transcriptional coactivation, which allowed subsequent exaptation for the interaction with the GID1 receptor when vascular plants developed gibberellin synthesis and the corresponding perception module.

Gibberellins Act Downstream of Arabis PERPETUAL FLOWERING1 to Accelerate Floral Induction during Vernalization

Regulation of flowering by endogenous and environmental signals ensures that reproduction occurs under optimal conditions to maximize reproductive success. Involvement of the growth regulator gibberellin (GA) in the control of flowering by environmental cues varies among species. Arabis alpina Pajares, a model perennial member of the Brassicaceae, only undergoes floral induction during vernalization, allowing definition of the role of GA specifically in this process. The transcription factor PERPETUAL FLOWERING1 (PEP1) represses flowering until its mRNA levels are reduced during vernalization. Genome-wide analyses of PEP1 targets identified genes involved in GA metabolism and signaling, and many of the binding sites in these genes were specific to the A. alpina lineage. Here, we show that the pep1 mutant exhibits an elongated-stem phenotype, similar to that caused by treatment with exogenous GA, consistent with PEP1 repressing GA responses. Moreover, in comparison with the wild type, the pep1 mutant contains higher GA4 levels and is more sensitive to GA prior to vernalization. Upon exposure to cold temperatures, GA levels fall to low levels in the pep1 mutant and in wild-type plants, but GA still promotes floral induction and the transcription of floral meristem identity genes during vernalization. Reducing GA levels strongly impairs flowering and inflorescence development in response to short vernalization treatments, but longer treatments overcome the requirement for GA. Thus, GA accelerates the floral transition during vernalization in A. alpina, the down-regulation of PEP1 likely increases GA sensitivity, and GA responses contribute to determining the length of vernalization required for flowering and reproduction.

The BAP Module: A Multisignal Integrator Orchestrating Growth

Coordination of cell proliferation, cell expansion, and differentiation underpins plant growth. To maximise reproductive success, growth needs to be fine-tuned in response to endogenous and environmental cues. This developmental plasticity relies on a cellular machinery that integrates diverse signals and coordinates the downstream responses. In arabidopsis, the BAP regulatory module, which includes the BRASSINAZOLE RESISTANT 1 (BZR1), AUXIN RESPONSE FACTOR 6 (ARF6), and PHYTOCHROME INTERACTING FACTOR 4 (PIF4) transcription factors (TFs), has been shown to coordinate growth in response to multiple growth-regulating signals. In this Opinion article, we provide an integrative view on the BAP module control of cell expansion and discuss whether its function is conserved or diversified, thus providing new insights into the molecular control of growth.

Constitutive expression of a stabilized transcription factor group VII ethylene response factor enhances waterlogging tolerance in wheat without penalizing grain yield

Waterlogging causes oxygen deprivation within plant roots and affects crop growth and yield. In crop wheat (Triticum aestivum), molecular responses to waterlogging are poorly understood. Here, we performed a genome-wide analysis of group VII ethylene response factor (ERFVII) genes in hexaploid wheat and identified 25 genes, which were induced by waterlogging with diverse manner. Among them, TaERFVII.1 exhibited differential expression patterns between waterlogging-tolerant wheat Nonglin46 and susceptible wheat Yangmai16 under waterlogging. Constitutive expression of TaERFVII.1 with an MYC-peptide tag at its N terminus in wheat enhanced tolerance to waterlogging as evidenced by increased grain weight per plant, survival rate, and chlorophyll content of leaves and by increased expression of waterlogging-responsive genes, while silencing of TaERFVII.1 compromised the expression of waterlogging-responsive genes. Notably, constitutive expression of the stabilized TaERFVII.1 did not negatively impact both plant development and grain yield under standard conditions. We further demonstrated that constitutive expression of stabilized TaERFVII.1 elevated the transcriptional level of TaSAB18.1, the ortholog of Arabidopsis HRA1 and rice SAB18, consequently reduced the expression of waterlogging-responsive genes under standard conditions. These results suggest that TaERFVII.1 plays an important role in wheat tolerance to waterlogging, and it could be a candidate for improving crop waterlogging tolerance.

Endogenous Hypoxia in Lateral Root Primordia Controls Root Architecture by Antagonizing Auxin Signaling in Arabidopsis

As non-photosynthesizing organs, roots are dependent on diffusion of oxygen from the external environment and, in some instances, from the shoot for their aerobic metabolism. Establishment of hypoxic niches in the developing tissues of plants has been postulated as a consequence of insufficient diffusion of oxygen to satisfy the demands throughout development. Here, we report that such niches are established at specific stages of lateral root primordia development in Arabidopsis thaliana grown under aerobic conditions. Using gain- and loss-of-function mutants, we show that ERF-VII transcription factors, which mediate hypoxic responses, control root architecture by acting in cells with a high level of auxin signaling. ERF-VIIs repress the expression of the auxin-induced genes LBD16, LBD18, and PUCHI, which are essential for lateral root development, by binding to their promoters. Our results support a model in which the establishment of hypoxic niches in the developing lateral root primordia contributes to the shutting down of key auxin-induced genes and regulates the production of lateral roots.

A Crucial Role of GA-Regulated Flavonol Biosynthesis in Root Growth of Arabidopsis

Flavonols have been demonstrated to play many important roles in plant growth, development, and communication with other organisms. Flavonol biosynthesis is spatiotemporally regulated by the subgroup 7 R2R3-MYB (SG7 MYB) transcription factors including MYB11/MYB12/MYB111. However, whether SG7-MYB activity is subject to post-translational regulation remains unclear. Here, we show that gibberellic acid (GA) inhibits flavonol biosynthesis via DELLA proteins in Arabidopsis. Protein-protein interaction analyses revealed that DELLAs (RGA and GAI) interacted with SG7 MYBs (MYB12 and MYB111) both in vitro and in vivo, leading to enhanced affinity of MYB binding to the promoter regions of key genes for flavonol biosynthesis and thus increasing their transcriptional levels. We observed that the level of auxin in the root tip was negatively correlated with root flavonol content. Furthermore, genetic assays showed that loss-of-function mutations in MYB12, which is predominantly expressed in roots, partially rescued the short-root phenotype of the GA-deficient mutant ga1-3 by increasing root meristem size and mature cell size. Consistent with these observations, exogenous application of the flavonol quercetin restored the root meristem size of myb12 ga1-3 to that of ga1-3. Taken together, our data elucidate a molecular mechanism by which GA promotes root growth by directly reducing flavonol biosynthesis.

Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects

Soil flooding creates composite and complex stress in plants known as either submergence or waterlogging stress depending on the depth of the water table. In nature, these stresses are important factors dictating the species composition of the ecosystem. On agricultural land, they cause economic damage associated with long-term social consequences. The understanding of the plant molecular responses to these two stresses has benefited from research studying individual components of the stress, in particular low-oxygen stress. To a lesser extent, other associated stresses and plant responses have been incorporated into the molecular framework, such as ion and ROS signaling, pathogen susceptibility, and organ-specific expression and development. In this review, we aim to highlight known or suspected components of submergence/waterlogging stress that have not yet been thoroughly studied at the molecular level in this context, such as miRNA and retrotransposon expression, the influence of light/dark cycles, protein isoforms, root architecture, sugar sensing and signaling, post-stress molecular events, heavy-metal and salinity stress, and mRNA dynamics (splicing, sequestering, and ribosome loading). Finally, we explore biotechnological strategies that have applied this molecular knowledge to develop cultivars resistant to flooding or to offer alternative uses of flooding-prone soils, like bioethanol and biomass production.

Somatic Embryogenesis in the Medicago truncatula Model: Cellular and Molecular Mechanisms

Medicago truncatula is now widely regarded as a legume model where there is an increasing range of genomic resources. Highly regenerable lines have been developed from the wild-type Jemalong cultivar, most likely due to epigenetic changes. These lines with high rates of somatic embryogenesis (SE) can be compared with wild-type where SE is rare. Much of the research has been with the high SE genotype Jemalong 2HA (2HA). SE can be induced from leaf tissue explants or isolated mesophyll protoplasts. In 2HA, the exogenous phytohormones 1-naphthaleneacetic acid (NAA) and 6-benzylaminopurine (BAP) are central to SE. However, there are interactions with ethylene, abscisic acid (ABA), and gibberellic acid (GA) which produce maximum SE. In the main, somatic embryos are derived from dedifferentiated cells, undergo organellar changes, and produce stem-like cells. There is evidence that the SE is induced as a result of a stress and hormone interaction and this is discussed. In M. truncatula, there are connections between stress and specific up-regulated genes and specific hormones and up-regulated genes during the SE induction phase. Some of the transcription factors have been knocked down using RNAi to show they are critical for SE induction (MtWUSCHEL, MtSERF1). SE research in M. truncatula has utilized high throughput transcriptomic and proteomic studies and the more detailed investigation of some individual genes. In this review, these studies are integrated to suggest a framework and timeline for some of the key events of SE induction in M. truncatula.

Screening Arrayed Libraries with DNA and Protein Baits to Identify Interacting Proteins

Molecular interactions are an integral part of the regulatory mechanisms controlling gene expression. The yeast one- and two-hybrid systems (Y1H/Y2H) have been widely used by many laboratories to detect DNA-protein (Y1H) and protein-protein interactions (Y2H). The development of efficient cloning systems have promoted the generation of large open reading frame (ORF) clone collections (libraries) for several organisms. Functional analyses of such large collections require the establishment of adequate protocols. Here, we describe a simple straightforward procedure for high-throughput screenings of arrayed libraries with DNA or protein baits that can be carried out by one person with minimal labor and not requiring robotics. The protocol can also be scaled up or down and is compatible with several library formats. Procedures to make yeast stocks for long-term storage (tube and microplate formats) are also provided.

Hypoxia and the group VII ethylene response transcription factor HRE2 promote adventitious root elongation in Arabidopsis

Soil water-logging and flooding are common environmental stress conditions that can impair plant fitness. Roots are the first organs to be confronted with reduced oxygen tension as a result of flooding. While anatomical and morphological adaptations of roots are extensively studied, the root system architecture is only now becoming a focus of flooding research. Adventitious root (AR) formation shifts the root system higher up the plant, thereby facilitating supply with oxygen, and thus improving root and plant survival. We used Arabidopsis knockout mutants and overexpressors of ERFVII transcription factors to study their role in AR formation under hypoxic conditions and in response to ethylene. Results show that ethylene inhibits AR formation. Hypoxia mainly promotes AR elongation rather than formation mediated by ERFVII transcription factors, as indicated by reduced AR elongation in erfVII seedlings. Overexpression of HRE2 induces AR elongation to the same degree as hypoxia, while ethylene overrides HRE2-induced AR elongation. The ERFVII transcription factors promote establishment of an AR system that is under negative control by ethylene. Inhibition of growth of the main root system and promotion of AR elongation under hypoxia strengthens the root system in upper soil layers where oxygen shortage may last for shorter time periods.

Multiple Links between HD-Zip Proteins and Hormone Networks

HD-Zip proteins are unique to plants, and contain a homeodomain closely linked to a leucine zipper motif, which are involved in dimerization and DNA binding. Based on homology in the HD-Zip domain, gene structure and the presence of additional motifs, HD-Zips are divided into four families, HD-Zip I–IV. Phylogenetic analysis of HD-Zip genes using transcriptomic and genomic datasets from a wide range of plant species indicate that the HD-Zip protein class was already present in green algae. Later, HD-Zips experienced multiple duplication events that promoted neo- and sub-functionalizations. HD-Zip proteins are known to control key developmental and environmental responses, and a growing body of evidence indicates a strict link between members of the HD-Zip II and III families and the auxin machineries. Interactions of HD-Zip proteins with other hormones such as brassinolide and cytokinin have also been described. More recent data indicate that members of different HD-Zip families are directly involved in the regulation of abscisic acid (ABA) homeostasis and signaling. Considering the fundamental role of specific HD-Zip proteins in the control of key developmental pathways and in the cross-talk between auxin and cytokinin, a relevant role of these factors in adjusting plant growth and development to changing environment is emerging.

Regulation of xylem fiber differentiation by gibberellins through DELLA-KNAT1 interaction

The thickening of plant organs is supported by secondary growth, a process by which new vascular tissues (xylem and phloem) are produced. Xylem is composed of several cell types, including xylary fibers, parenchyma and vessel elements. In Arabidopsis, it has been shown that fibers are promoted by the class-I KNOX gene KNAT1 and the plant hormones gibberellins, and are repressed by a small set of receptor-like kinases; however, we lack a mechanistic framework to integrate their relative contributions. Here, we show that DELLAs, negative elements of the gibberellin signaling pathway, physically interact with KNAT1 and impair its binding to KNAT1-binding sites. Our analysis also indicates that at least 37% of the transcriptome mobilized by KNAT1 is potentially dependent on this interaction, and includes genes involved in secondary cell wall modifications and phenylpropanoid biosynthesis. Moreover, the promotion by constitutive overexpression of KNAT1 of fiber formation and the expression of genes required for fiber differentiation were still reverted by DELLA accumulation, in agreement with post-translational regulation of KNAT1 by DELLA proteins. These results suggest that gibberellins enhance fiber development by promoting KNAT1 activity.

A Shoot Fe Signaling Pathway Requiring the OPT3 Transporter Controls GSNO Reductase and Ethylene in Arabidopsis thaliana Roots

Ethylene, nitric oxide (NO) and glutathione (GSH) increase in Fe-deficient roots of Strategy I species where they participate in the up-regulation of Fe acquisition genes. However, S-nitrosoglutathione (GSNO), derived from NO and GSH, decreases in Fe-deficient roots. GSNO content is regulated by the GSNO-degrading enzyme S-nitrosoglutathione reductase (GSNOR). On the other hand, there are several results showing that the regulation of Fe acquisition genes does not solely depend on hormones and signaling molecules (such as ethylene or NO), which would act as activators, but also on the internal Fe content of plants, which would act as a repressor. Moreover, different results suggest that total Fe in roots is not the repressor of Fe acquisition genes, but rather the repressor is a Fe signal that moves from shoots to roots through the phloem [hereafter named LOng Distance Iron Signal (LODIS)]. To look further in the possible interactions between LODIS, ethylene and GSNOR, we compared Arabidopsis WT Columbia and LODIS-deficient mutant opt3-2 plants subjected to different Fe treatments that alter LODIS content. The opt3-2 mutant is impaired in the loading of shoot Fe into the phloem and presents constitutive expression of Fe acquisition genes. In roots of both Columbia and opt3-2 plants we determined 1-aminocyclopropane-1-carboxylic acid (ACC, ethylene precursor), expression of ethylene synthesis and signaling genes, and GSNOR expression and activity. The results obtained showed that both 'ethylene' (ACC and the expression of ethylene synthesis and signaling genes) and 'GSNOR' (expression and activity) increased in Fe-deficient WT Columbia roots. Additionally, Fe-sufficient opt3-2 roots had higher 'ethylene' and 'GSNOR' than Fe-sufficient WT Columbia roots. The increase of both 'ethylene' and 'GSNOR' was not related to the total root Fe content but to the absence of a Fe shoot signal (LODIS), and was associated with the up-regulation of Fe acquisition genes. The possible relationship between GSNOR(GSNO) and ethylene is discussed.

ERF72 interacts with ARF6 and BZR1 to regulate hypocotyl elongation in Arabidopsis

The phytohormones brassinosteroid (BR), auxin, and gibberellin (GA) regulate photomorphogenesis-related hypocotyl elongation in Arabidopsis via the co-operative interaction of BZR-ARF-PIF/DELLA (BAP/D) transcription factors/regulators. In addition, ethylene activates the PIF3 or ERF1 pathway through EIN3/EIL1 to balance hypocotyl elongation in Arabidopsis seedlings. However, the mechanism by which ethylene is co-ordinated with other phytohormones to produce light-regulated hypocotyl growth remains elusive. In this study, we found that hypocotyl cell elongation is regulated by a network involving ethylene, auxin, and BR signalling, which is mediated by interactions among ERF72, ARF6, and BZR1. ERF72 interacted directly with ARF6 and BZR1 in vitro and in vivo, and it antagonised regulation by ARF6 and BZR1 of the transcription of BEE3 and XTH7. In addition, light modulated the subcellular localisation of ERF72 and transcription of ERF72 through the EIN2-EIN3/EIL1 pathway, facilitating the function of ERF72 in photomorphogenesis. The expression of BEE3 and XTH7 was also regulated by the EIN2-EIN3/EIL1 pathway. Our findings indicate that a revised BZR-ARF-PIF/DELLA-ERF (BAP/DE) module integrates light and hormone signals to regulate hypocotyl elongation in Arabidopsis.

Gibberellins negatively modulate ovule number in plants

Ovule formation is a complex developmental process in plants, with a strong impact on the production of seeds. Ovule primordia initiation is controlled by a gene network, including components of the signaling pathways of auxin, brassinosteroids and cytokinins. By contrast, gibberellins (GAs) and DELLA proteins, the negative regulators of GA signaling, have never been shown to be involved in ovule initiation. Here, we provide molecular and genetic evidence that points to DELLA proteins as novel players in the determination of ovule number in Arabidopsis and in species of agronomic interest, such as tomato and rapeseed, adding a new layer of complexity to this important developmental process. DELLA activity correlates positively with ovule number, acting as a positive factor for ovule initiation. In addition, ectopic expression of a dominant DELLA in the placenta is sufficient to increase ovule number. The role of DELLA proteins in ovule number does not appear to be related to auxin transport or signaling in the ovule primordia. Possible crosstalk between DELLA proteins and the molecular and hormonal network controlling ovule initiation is also discussed.

Transcriptome analysis unravels spatiotemporal modulation of phytohormone-pathway expression underlying gibberellin-induced parthenocarpic fruit set in San Pedro-type fig (Ficus carica L.)

BACKGROUND

Gibberellin (GA) treatments can induce parthenocarpy in the main crop of San Pedro-type figs, the native non-parthenocarpic fruit, however, the underlying mechanism is still largely unclear.

RESULTS

In our study, GA3 was applied to San Pedro-type fig main crop at anthesis. Sharply increased GA3 content was detected in both female flowers and receptacle, along with significantly decreased indole-3-acetic acid (IAA), zeatin and abscisic acid (ABA) levels in female flowers, and increased zeatin peak intensity and earlier ABA peak in receptacles. Transcriptome comparison between control and treatment groups identified more differentially expressed genes (DEGs) in receptacles than in female flowers 2 and 4 days after treatment (DAT); 10 DAT, the number of DEGs became similar in the two tissues. Synchronized changing trends of phytohormone-associated DEGs were observed in female flowers and receptacles with fruit development. Modulation of ethylene and GA signaling and auxin metabolism by exogenous GA3 occurred mainly 2 DAT, whereas changes in auxin, cytokinin and ABA signaling occurred mainly 10 DAT. Auxin-, ethylene- and ABA-metabolism and response pathways were largely regulated in the two tissues, mostly 2 and 10 DAT. The major components altering fig phytohormone metabolic and response patterns included downregulated GA2ox, BAS1, NCED and ACO, and upregulated ABA 8'-h and AUX/IAA.

CONCLUSIONS

Thus GA-induced parthenocarpy in fig is co-modulated by the female flowers and receptacle, and repression of ABA and ethylene biosynthesis and GA catabolism might be the main forces deflecting abscission and producing fig parthenocarpy.

Converging Light, Energy and Hormonal Signaling Control Meristem Activity, Leaf Initiation, and Growth

The development of leaf primordia is subject to light control of meristematic activity. Light regulates the expression of thousands of genes with roles in cell proliferation, organ development, and differentiation of photosynthetic cells. Previous work has highlighted roles for hormone homeostasis and the energy-dependent Target of Rapamycin (TOR) kinase in meristematic activity, yet a picture of how these two regulatory mechanisms depend on light perception and interact with each other has yet to emerge. Their relevance beyond leaf initiation also is unclear. Here, we report the discovery that the dark-arrested meristematic region of Arabidopsis (Arabidopsis thaliana) experiences a local energy deprivation state and confirm previous findings that the PIN1 auxin transporter is diffusely localized in the dark. Light triggers a rapid removal of the starvation state and the establishment of PIN1 polar membrane localization consistent with auxin export, both preceding the induction of cell cycle- and cytoplasmic growth-associated genes. We demonstrate that shoot meristematic activity can occur in the dark through the manipulation of auxin and cytokinin activity as well as through the activation of energy signaling, both targets of photomorphogenesis action, but the organ developmental outcomes differ: while TOR-dependent energy signals alone stimulate cell proliferation, the development of a normal leaf lamina requires photomorphogenesis-like hormonal responses. We further show that energy signaling adjusts the extent of cell cycle activity and growth of young leaves non-cellautonomously to available photosynthates and leads to organs constituted of a greater number of cells developing under higher irradiance. This makes energy signaling perhaps the most important biomass growth determinant under natural, unstressed conditions.

Group VII Ethylene Response Factors in Arabidopsis: Regulation and Physiological Roles

The role of ERF-VII TFs in higher plants is to coordinate their signature response to oxygen deficiency, but additional layers of modulation of ERF-VII activity enrich their regulatory range.

Gene Regulation and Survival under Hypoxia Requires Starch Availability and Metabolism

Plants respond to hypoxia, often caused by submergence, by expressing a specific set of genes that contribute to acclimation to this unfavorable environmental condition. Genes induced by low oxygen include those encoding enzymes for carbohydrate metabolism and fermentation, pathways that are required for survival. Sugar availability is therefore of crucial importance for energy production under hypoxia. Here, we show that Arabidopsis (Arabidopsis thaliana) plants require starch for surviving submergence as well as for ensuring the rapid induction of genes encoding enzymes required for anaerobic metabolism. The starchless pgm mutant is highly susceptible to submergence and also fails to induce anaerobic genes at the level of the wild type. Treating wild-type plants under conditions inducing sugar starvation results in a weak induction of alcohol dehydrogenase and other anaerobic genes. Induction of gene expression under hypoxia requires transcription factors belonging to group VII ethylene response factors (ERF-VII) that, together with plant Cys oxidases, act as an oxygen-sensing mechanism. We show that repression of this pathway by sugar starvation occurs downstream of the hypoxia-dependent stabilization of ERF-VII proteins and independently of the energy sensor protein kinases SnRK1.1 (SNF1-related kinase 1.1).

Emerging role of the plant ERF transcription factors in coordinating wound defense responses and repair

Plants react to wounding through the activation of both defense and repair pathways, but how these two responses are coordinated is unclear. Here, we put forward the hypothesis that diverse members of the subfamily X of the plant-specific ethylene response factor (ERF) transcription factors coordinate stress signaling with the activation of wound repair mechanisms. Moreover, we highlight the observation that tissue repair is strongly boosted through the formation of a heterodimeric protein complex that comprises ERF and transcription factors of the GRAS domain type. This interaction turns ERFs into highly potent and stress-responsive activators of cell proliferation. The potency to induce stem cell identity suggests that these heterodimeric transcription factor complexes could become valuable tools to increase crop regeneration and transformation efficiency.

AP2/ERF Family Transcription Factors ORA59 and RAP2.3 Interact in the Nucleus and Function Together in Ethylene Responses

The gaseous plant hormone ethylene is a key signaling molecule regulating plant growth, development, and defense against pathogens. Octadecanoid-responsive arabidopsis 59 (ORA59) is an ethylene response factor (ERF) transcription factor and has been suggested to integrate ethylene and jasmonic acid signaling and regulate resistance to necrotrophic pathogens. Here we screened for ORA59 interactors using the yeast two-hybrid system to elucidate the molecular function of ORA59. This led to the identification of RELATED TO AP2.3 (RAP2.3), another ERF transcription factor belonging to the group VII ERF family. In binding assays, ORA59 and RAP2.3 interacted in the nucleus and showed ethylene-dependent nuclear localization. ORA59 played a positive role in ethylene-regulated responses, including the triple response, featured by short, thick hypocotyl and root, and exaggerated apical hook in dark-grown seedlings, and resistance to the necrotrophic pathogen Pectobacterium carotovorum, as shown by the increased and decreased ethylene sensitivity and disease resistance in ORA59-overexpressing (ORA59OE) and null mutant (ora59) plants, respectively. In genetic crosses, ORA59OE rap2.3 crossed lines lost ORA59-mediated positive effects and behaved like rap2.3 mutant. These results suggest that ORA59 physically interacts with RAP2.3 and that this interaction is important for the regulatory roles of ORA59 in ethylene responses.

Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)

RNA-seq has been used to perform global expression analysis of the achene and the receptacle at four stages of fruit ripening, and of the roots and leaves of strawberry (Fragaria × ananassa). About 967 million reads and 191 Gb of sequence were produced, using Illumina sequencing. Mapping the reads in the related genome of the wild diploid Fragaria vesca revealed differences between the achene and receptacle development program, and reinforced the role played by ethylene in the ripening receptacle. For the strawberry transcriptome assembly, a de novo strategy was followed, generating separate assemblies for each of the ten tissues and stages sampled. The Trinity program was used for these assemblies, resulting in over 1.4 M isoforms. Filtering by a threshold of 0.3 FPKM, and doing Blastx (E-value < 1 e-30) against the UniProt database of plants reduced the number to 472,476 isoforms. Their assembly with the MIRA program (90% homology) resulted in 26,087 contigs. From these, 91.34 percent showed high homology to Fragaria vesca genes and 87.30 percent Fragaria iinumae (BlastN E-value < 1 e-100). Mapping back the reads on the MIRA contigs identified polymorphisms at nucleotide level, using FREEBAYES, as well as estimate their relative abundance in each sample.

The Cys-Arg/N-End Rule Pathway Is a General Sensor of Abiotic Stress in Flowering Plants

Abiotic stresses impact negatively on plant growth, profoundly affecting yield and quality of crops. Although much is known about plant responses, very little is understood at the molecular level about the initial sensing of environmental stress. In plants, hypoxia (low oxygen, which occurs during flooding) is directly sensed by the Cys-Arg/N-end rule pathway of ubiquitin-mediated proteolysis, through oxygen-dependent degradation of group VII Ethylene Response Factor transcription factors (ERFVIIs) via amino-terminal (Nt-) cysteine [1, 2]. Using Arabidopsis (Arabidopsis thaliana) and barley (Hordeum vulgare), we show that the pathway regulates plant responses to multiple abiotic stresses. In Arabidopsis, genetic analyses revealed that response to these stresses is controlled by N-end rule regulation of ERFVII function. Oxygen sensing via the Cys-Arg/N-end rule in higher eukaryotes is linked through a single mechanism to nitric oxide (NO) sensing [3, 4]. In plants, the major mechanism of NO synthesis is via NITRATE REDUCTASE (NR), an enzyme of nitrogen assimilation [5]. Here, we identify a negative relationship between NR activity and NO levels and stabilization of an artificial Nt-Cys substrate and ERFVII function in response to environmental changes. Furthermore, we show that ERFVIIs enhance abiotic stress responses via physical and genetic interactions with the chromatin-remodeling ATPase BRAHMA. We propose that plants sense multiple abiotic stresses through the Cys-Arg/N-end rule pathway either directly (via oxygen sensing) or indirectly (via NO sensing downstream of NR activity). This single mechanism can therefore integrate environment and response to enhance plant survival.

Exploiting DELLA Signaling in Cereals

The spectacular yield increases in rice and wheat during the green revolution were partly realized by reduced gibberellin (GA) synthesis or sensitivity, both causing the accumulation of DELLA proteins. Although insights into the regulation of plant growth and development by DELLA proteins advanced rapidly in arabidopsis (Arabidopsis thaliana), DELLA-mediated regulation of downstream responses in cereals has received little attention to date. Furthermore, translating this research from arabidopsis to cereals is challenging given their different growth patterns and our phylogenetic analysis which reveals that DELLA-related DGLLA proteins exist in cereals but not in arabidopsis. Therefore, understanding the molecular basis of DELLA function in cereals holds great potential to improve yield. In this review, we propose to extend the focus of DELLA functional research to cereals, and highlight the appropriate tools that are now available to achieve this.

Root Bending Is Antagonistically Affected by Hypoxia and ERF-Mediated Transcription via Auxin Signaling

When plants encounter soil water logging or flooding, roots are the first organs to be confronted with reduced gas diffusion resulting in limited oxygen supply. Since roots do not generate photosynthetic oxygen, they are rapidly faced with oxygen shortage rendering roots particularly prone to damage. While metabolic adaptations to low oxygen conditions, which ensure basic energy supply, have been well characterized, adaptation of root growth and development have received less attention. In this study, we show that hypoxic conditions cause the primary root to grow sidewise in a low oxygen environment, possibly to escape soil patches with reduced oxygen availability. This growth behavior is reversible in that gravitropic growth resumes when seedlings are returned to normoxic conditions. Hypoxic root bending is inhibited by the group VII ethylene response factor (ERFVII) RAP2.12, as rap2.12-1 seedlings show exaggerated primary root bending. Furthermore, overexpression of the ERFVII member HRE2 inhibits root bending, suggesting that primary root growth direction at hypoxic conditions is antagonistically regulated by hypoxia and hypoxia-activated ERFVIIs. Root bending is preceded by the establishment of an auxin gradient across the root tip as quantified with DII-VENUS and is synergistically enhanced by hypoxia and the auxin transport inhibitor naphthylphthalamic acid. The protein abundance of the auxin efflux carrier PIN2 is reduced at hypoxic conditions, a response that is suppressed by RAP2.12 overexpression, suggesting antagonistic control of auxin flux by hypoxia and ERFVII. Taken together, we show that hypoxia triggers an escape response of the primary root that is controlled by ERFVII activity and mediated by auxin signaling in the root tip.

Genome-wide identification and characterization of TCP transcription factor genes in upland cotton (Gossypium hirsutum)

TCP proteins are plant-specific transcription factors (TFs), and perform a variety of physiological functions in plant growth and development. In this study, 74 non-redundant TCP genes were identified in upland cotton (Gossypium hirsutum L.) genome. Cotton TCP family can be classified into two classes (class I and class II) that can be further divided into 11 types (groups) based on their motif composition. Quantitative RT-PCR analysis indicated that GhTCPs display different expression patterns in cotton tissues. The majority of these genes are preferentially or specifically expressed in cotton leaves, while some GhTCP genes are highly expressed in initiating fibers and/or elongating fibers of cotton. Yeast two-hybrid results indicated that GhTCPs can interact with each other to form homodimers or heterodimers. In addition, GhTCP14a and GhTCP22 can interact with some transcription factors which are involved in fiber development. These results lay solid foundation for further study on the functions of TCP genes during cotton fiber development.

A transcriptome analysis of two grapevine populations segregating for tendril phyllotaxy

The shoot structure of cultivated grapevine Vitis vinifera L. typically exhibits a three-node modular repetitive pattern, two sequential leaf-opposed tendrils followed by a tendril-free node. In this study, we investigated the molecular basis of this pattern by characterizing differentially expressed genes in 10 bulk samples of young tendril tissue from two grapevine populations showing segregation of mutant or wild-type shoot/tendril phyllotaxy. One population was the selfed progeny and the other one, an outcrossed progeny of a Vitis hybrid, 'Roger's Red'. We analyzed 13 375 expressed genes and carried out in-depth analyses of 324 of them, which were differentially expressed with a minimum of 1.5-fold changes between the mutant and wild-type bulk samples in both selfed and cross populations. A significant portion of these genes were direct cis-binding targets of 14 transcription factor families that were themselves differentially expressed. Network-based dependency analysis further revealed that most of the significantly rewired connections among the 10 most connected hub genes involved at least one transcription factor. TCP3 and MYB12, which were known important for plant-form development, were among these transcription factors. More importantly, TCP3 and MYB12 were found in this study to be involved in regulating the lignin gene PRX52, which is important to plant-form development. A further support evidence for the roles of TCP3-MYB12-PRX52 in contributing to tendril phyllotaxy was the findings of two other lignin-related genes uniquely expressed in the mutant phyllotaxy background.

Hormonal control of the floral transition: Can one catch them all?

The transition to flowering marks a key adaptive developmental switch in plants which impacts on their survival and fitness. Different signaling pathways control the floral transition, conveying both endogenous and environmental cues. These cues are often relayed and/or modulated by different hormones, which might confer additional developmental flexibility to the floral process in the face of varying conditions. Among the different hormonal pathways, the phytohormone gibberellic acid (GA) plays a dominant role. GA is connected with the other floral pathways through the GA-regulated DELLA proteins, acting as versatile interacting modules for different signaling proteins. In this review, I will highlight the role of DELLAs as spatial and temporal modulators of different consolidated floral pathways. Next, building on recent data, I will provide an update on some emerging themes connecting other hormone signaling cascades to flowering time control. I will finally provide examples for some established as well as potential cross-regulatory mechanisms between hormonal pathways mediated by the DELLA proteins.

Transcriptional analysis of defense mechanisms in upland tetraploid switchgrass to greenbugs

BACKGROUND

Aphid infestation of switchgrass (Panicum virgatum) has the potential to reduce yields and biomass quality. Although switchgrass-greenbug (Schizaphis graminum; GB) interactions have been studied at the whole plant level, little information is available on plant defense responses at the molecular level.

RESULTS

The global transcriptomic response of switchgrass cv Summer to GB was monitored by RNA-Seq in infested and control (uninfested) plants harvested at 5, 10, and 15 days after infestation (DAI). Differentially expressed genes (DEGs) in infested plants were analyzed relative to control uninfested plants at each time point. DEGs in GB-infested plants induced by 5-DAI included an upregulation of reactive burst oxidases and several cell wall receptors. Expression changes in genes linked to redox metabolism, cell wall structure, and hormone biosynthesis were also observed by 5-DAI. At 10-DAI, network analysis indicated a massive upregulation of defense-associated genes, including NAC, WRKY, and MYB classes of transcription factors and potential ancillary signaling molecules such as leucine aminopeptidases. Molecular evidence for loss of chloroplastic functions was also detected at this time point. Supporting these molecular changes, chlorophyll content was significantly decreased, and ROS levels were elevated in infested plants 10-DAI. Total peroxidase and laccase activities were elevated in infested plants at 10-DAI relative to control uninfested plants. The net result appeared to be a broad scale defensive response that led to an apparent reduction in C and N assimilation and a potential redirection of nutrients away from GB and towards the production of defensive compounds, such as pipecolic acid, chlorogenic acid, and trehalose by 10-DAI. By 15-DAI, evidence of recovery in primary metabolism was noted based on transcript abundances for genes associated with carbon, nitrogen, and nutrient assimilation.

CONCLUSIONS

Extensive remodeling of the plant transcriptome and the production of ROS and several defensive metabolites in an upland switchgrass cultivar were observed in response to GB feeding. The early loss and apparent recovery in primary metabolism by 15-DAI would suggest that these transcriptional changes in later stages of GB infestation could underlie the recovery response categorized for this switchgrass cultivar. These results can be exploited to develop switchgrass lines with more durable resistance to GB and potentially other aphids.

Transcriptomic Analysis Implies That GA Regulates Sex Expression via Ethylene-Dependent and Ethylene-Independent Pathways in Cucumber (Cucumis sativus L.)

Sex differentiation of flower buds is an important developmental process that directly affects fruit yield of cucumber (Cucumis sativus L.). Plant hormones, such as gibberellins (GAs) and ethylene can promote development of male and female flowers, respectively, however, the regulatory mechanisms of GA-induced male flower formation and potential involvement of ethylene in this process still remain unknown. In this study, to unravel the genes and gene networks involved in GA-regulated cucumber sexual development, we performed high throughout RNA-Seq analyses that compared the transcriptomes of shoot tips between GA₃ treated and untreated gynoecious cucumber plants. Results showed that GA₃ application markedly induced male flowers but decreased ethylene production in shoot tips. Furthermore, the transcript levels of M (CsACS2) gene, ethylene receptor CsETR1 and some ethylene-responsive transcription factors were dramatically changed after GA₃ treatment, suggesting a potential involvement of ethylene in GA-regulated sex expression of cucumber. Interestingly, GA₃ down-regulated transcript of a C-class floral homeotic gene, CAG2, indicating that GA may also influence cucumber sex determination through an ethylene-independent process. These results suggest a novel model for hormone-mediated sex differentiation and provide a theoretical basis for further dissection of the regulatory mechanism of male flower formation in cucumber. Statement: We reveal that GA can regulate sex expression of cucumber via an ethylene-dependent manner, and the M (CsACS2), CsETR1, and ERFs are probably involved in this process. Moreover, CAG2, a C-class floral homeotic gene, may also participate in GA-modulated cucumber sex determination, but this pathway is ethylene-independent.

Yeast One- and Two-Hybrid High-Throughput Screenings Using Arrayed Libraries

Since their original description more than 25 years ago, the yeast one- and two-hybrid systems (Y1H/Y2H) have been used by many laboratories to detect DNA-protein (Y1H) and protein-protein interactions (Y2H). These systems use yeast cells (Saccharomyces cerevisiae) as a eukaryotic "test tube" and are amenable for most labs in the world. The development of highly efficient cloning methods has fostered the generation of large collections of open reading frames (ORFs) for several organisms that have been used for yeast screenings. Here, we describe a simple mating based method for high-throughput screenings of arrayed ORF libraries with DNA (Y1H) or protein (Y2H) baits not requiring robotics. One person can easily carry out this protocol in approximately 10 h of labor spread over 5 days. It can also be scaled down to test one-to-one (few) interactions, scaled up (i.e., robotization) and is compatible with several library formats (i.e., 96, 384-well microtiter plates).

Evolutionary Analysis of DELLA-Associated Transcriptional Networks

DELLA proteins are transcriptional regulators present in all land plants which have been shown to modulate the activity of over 100 transcription factors in Arabidopsis, involved in multiple physiological and developmental processes. It has been proposed that DELLAs transduce environmental information to pre-wired transcriptional circuits because their stability is regulated by gibberellins (GAs), whose homeostasis largely depends on environmental signals. The ability of GAs to promote DELLA degradation coincides with the origin of vascular plants, but the presence of DELLAs in other land plants poses at least two questions: what regulatory properties have DELLAs provided to the behavior of transcriptional networks in land plants, and how has the recruitment of DELLAs by GA signaling affected this regulation. To address these issues, we have constructed gene co-expression networks of four different organisms within the green lineage with different properties regarding DELLAs: Arabidopsis thaliana and Solanum lycopersicum (both with GA-regulated DELLA proteins), Physcomitrella patens (with GA-independent DELLA proteins) and Chlamydomonas reinhardtii (a green alga without DELLA), and we have examined the relative evolution of the subnetworks containing the potential DELLA-dependent transcriptomes. Network analysis indicates a relative increase in parameters associated with the degree of interconnectivity in the DELLA-associated subnetworks of land plants, with a stronger effect in species with GA-regulated DELLA proteins. These results suggest that DELLAs may have played a role in the coordination of multiple transcriptional programs along evolution, and the function of DELLAs as regulatory 'hubs' became further consolidated after their recruitment by GA signaling in higher plants.

Gibberellins Regulate Ovule Integument Development by Interfering with the Transcription Factor ATS

Gibberellins (GAs) are plant hormones that regulate most plant life cycle aspects, including flowering and fruit development. Here, we demonstrate the implication of GAs in ovule development. DELLA proteins, negative GA response regulators, act as positive factors for ovule integument development in a mechanism that involves transcription factor ABERRANT TESTA SHAPE (ATS). The seeds of the della global mutant, a complete loss-of-function of DELLA, and the ats-1 mutant are remarkably similar, with a round shape, a disorganized testa, and viviparism. These defects are the result of an alteration in integuments that fail to fully develop and are shorter than in wild-type plants. ats-1 also shows some GA-related phenotypes, for example, higher germination rates and early flowering. In fact, ats-1 has elevated GA levels due to the activation of GA biosynthesis genes, which indicates that ATS inhibits GA biosynthesis. Moreover, DELLAs and ATS proteins interact, which suggests the formation of a transcriptional complex that regulates the expression of genes involved in integument growth. Therefore, the repression of GA biosynthesis by ATS would result in the stabilization of DELLAs to ensure correct ATS-DELLA complex formation. The requirement of both activities to coordinate proper ovule development strongly argues that the ATS-DELLA complex acts as a key molecular factor. This work provides the first evidence for a role of GAs in ovule and seed development.

A Transcriptional and Metabolic Framework for Secondary Wall Formation in Arabidopsis

Plant cell walls are essential for plant growth and development. The cell walls are traditionally divided into primary walls, which surround growing cells, and secondary walls, which provide structural support to certain cell types and promote their functions. While much information is available about the enzymes and components that contribute to the production of these two types of walls, much less is known about the transition from primary to secondary wall synthesis. To address this question, we made use of a transcription factor system in Arabidopsis (Arabidopsis thaliana) in which an overexpressed master secondary wall-inducing transcription factor, VASCULAR-RELATED NAC DOMAIN PROTEIN7, can be redirected into the nucleus by the addition of dexamethasone. We established the time frame during which primary wall synthesis changed into secondary wall production in dexamethasone-treated seedlings and measured transcript and metabolite abundance at eight time points after induction. Using cluster- and network-based analyses, we integrated the data sets to explore coordination between transcripts, metabolites, and the combination of the two across the time points. We provide the raw data as well as a range of network-based analyses. These data reveal links between hormone signaling and metabolic processes during the formation of secondary walls and provide a framework toward a deeper understanding of how primary walls transition into secondary walls.

From start to finish: amino-terminal protein modifications as degradation signals in plants

Contents 1188 I. 1188 II. 1189 III. 1190 IV. 1191 V. 1192 1192 References 1192 SUMMARY: The amino- (N-) terminus (Nt) of a protein can undergo a diverse array of co- and posttranslational modifications. Many of these create degradation signals (N-degrons) that mediate protein destruction via the N-end rule pathway of ubiquitin-mediated proteolysis. In plants, the N-end rule pathway has emerged as a major system for regulated control of protein stability. Nt-arginylation-dependent degradation regulates multiple growth, development and stress responses, and recently identified functions of Nt-acetylation can also be linked to effects on the in vivo half-lives of Nt-acetylated proteins. There is also increasing evidence that N-termini could act as important protein stability determinants in plastids. Here we review recent advances in our understanding of the relationship between the nature of protein N-termini, Nt-processing events and proteolysis in plants.

The ERF11 Transcription Factor Promotes Internode Elongation by Activating Gibberellin Biosynthesis and Signaling

The phytohormone gibberellin (GA) plays a key role in promoting stem elongation in plants. Previous studies show that GA activates its signaling pathway by inducing rapid degradation of DELLA proteins, GA signaling repressors. Using an activation-tagging screen in a reduced-GA mutant ga1-6 background, we identified AtERF11 to be a novel positive regulator of both GA biosynthesis and GA signaling for internode elongation. Overexpression of AtERF11 partially rescued the dwarf phenotype of ga1-6 AtERF11 is a member of the ERF (ETHYLENE RESPONSE FACTOR) subfamily VIII-B-1a of ERF/AP2 transcription factors in Arabidopsis (Arabidopsis thaliana). Overexpression of AtERF11 resulted in elevated bioactive GA levels by up-regulating expression of GA3ox1 and GA20ox genes. Hypocotyl elongation assays further showed that overexpression of AtERF11 conferred elevated GA response, whereas loss-of-function erf11 and erf11 erf4 mutants displayed reduced GA response. In addition, yeast two-hybrid, coimmunoprecipitation, and transient expression assays showed that AtERF11 enhances GA signaling by antagonizing the function of DELLA proteins via direct protein-protein interaction. Interestingly, AtERF11 overexpression also caused a reduction in the levels of another phytohormone ethylene in the growing stem, consistent with recent finding showing that AtERF11 represses transcription of ethylene biosynthesis ACS genes. The effect of AtERF11 on promoting GA biosynthesis gene expression is likely via its repressive function on ethylene biosynthesis. These results suggest that AtERF11 plays a dual role in promoting internode elongation by inhibiting ethylene biosynthesis and activating GA biosynthesis and signaling pathways.

The Role of SWI/SNF Chromatin Remodeling Complexes in Hormone Crosstalk

SWI/SNF-type ATP-dependent chromatin remodeling complexes (CRCs) are evolutionarily conserved multiprotein machineries controlling DNA accessibility by regulating chromatin structure. We summarize here recent advances highlighting the role of SWI/SNF in the regulation of hormone signaling pathways and their crosstalk in Arabidopsis thaliana. We discuss the functional interdependences of SWI/SNF complexes and key elements regulating developmental and hormone signaling pathways by indicating intriguing similarities and differences in plants and humans, and summarize proposed mechanisms of SWI/SNF action on target loci. We postulate that, given their viability, several plant SWI/SNF mutants may serve as an attractive model for searching for conserved functions of SWI/SNF CRCs in hormone signaling, cell cycle control, and other regulatory pathways.

GA signalling and cross-talk with other signalling pathways

Gibberellins (GAs) are phytohormones that regulate growth and development. DELLA proteins repress GA responses. GA binding to its receptor triggers a series of events that culminate in the destruction of DELLA proteins by the 26S proteasome, which removes the repression of GA signalling. DELLA proteins are transcription co-activators that induce the expression of genes which encode products that inhibit GA responses. In addition to repressing GA responses, DELLA proteins influence the activity of other signalling pathways and serve as a central hub from which other pathways influence GA signalling. In this role, DELLA proteins bind to and inhibit proteins, including transcription factors that act in the signalling pathways of other hormones and light. The binding of these proteins to DELLA proteins also inhibits DELLA activity. GA signalling is subject to homoeostatic regulation through GA-induced repression of GA biosynthesis gene expression, and increased production of the GA receptor and enzymes that catabolize bioactive GAs. This review also discusses the nature of mutant DELLA alleles that are used to produce high-yielding 'Green Revolution' cereal varieties, and highlights important gaps in our knowledge of GA signalling.

Bioinformatic landscapes for plant transcription factor system research

Diverse bioinformatic resources have been developed for plant transcription factor (TF) research. This review presents the bioinformatic resources and methodologies for the elucidation of plant TF-mediated biological events. Such information is helpful to dissect the transcriptional regulatory systems in the three reference plants Arabidopsis , rice, and maize and translation to other plants. Transcription factors (TFs) orchestrate diverse biological programs by the modulation of spatiotemporal patterns of gene expression via binding cis-regulatory elements. Advanced sequencing platforms accompanied by emerging bioinformatic tools revolutionize the scope and extent of TF research. The system-level integration of bioinformatic resources is beneficial to the decoding of TF-involved networks. Herein, we first briefly introduce general and specialized databases for TF research in three reference plants Arabidopsis, rice, and maize. Then, as proof of concept, we identified and characterized heat shock transcription factor (HSF) members through the TF databases. Finally, we present how the integration of bioinformatic resources at -omics layers can aid the dissection of TF-mediated pathways. We also suggest ways forward to improve the bioinformatic resources of plant TFs. Leveraging these bioinformatic resources and methodologies opens new avenues for the elucidation of transcriptional regulatory systems in the three model systems and translation to other plants.