Arabidopsis CPL4 is an essential C-terminal domain phosphatase that suppresses xenobiotic stress responses

C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3 contributes to GA-mediated growth and flowering by interaction with DELLA proteins

Gibberellic acid (GA) plays a central role in many plant developmental processes and is crucial for crop improvement. DELLA proteins, the core suppressors in the GA signaling pathway, are degraded by GA via the 26S proteasomal pathway to release the GA response. However, little is known about the phosphorylation-mediated regulation of DELLA proteins. In this study, we combined GA response assays with protein-protein interaction analysis to infer the connection between Arabidopsis thaliana DELLAs and the C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3 (CPL3), a phosphatase involved in the dephosphorylation of RNA polymerase II. We show that CPL3 directly interacts with DELLA proteins and promotes DELLA protein stability by inhibiting its degradation by the 26S proteasome. Consequently, CPL3 negatively modulates multiple GA-mediated processes of plant development, including hypocotyl elongation, flowering time, and anthocyanin accumulation. Taken together, our findings demonstrate that CPL3 serves as a novel regulator that could improve DELLA stability and thereby participate in GA signaling transduction.

Deciphering Macromolecular Interactions Involved in Abiotic Stress Signaling: A Review of Bioinformatics Analysis

Plant functioning and responses to abiotic stresses largely involve regulations at the transcriptomic level via complex interactions of signal molecules, signaling cascades, and regulators. Nevertheless, all the signaling networks involved in responses to abiotic stresses have not yet been fully established. The in-depth analysis of transcriptomes in stressed plants has become a relevant state-of-the-art methodology to study these regulations and signaling pathways that allow plants to cope with or attempt to survive abiotic stresses. The plant science and molecular biology community has developed databases about genes, proteins, protein-protein interactions, protein-DNA interactions and ontologies, which are valuable sources of knowledge for deciphering such regulatory and signaling networks. The use of these data and the development of bioinformatics tools help to make sense of transcriptomic data in specific contexts, such as that of abiotic stress signaling, using functional biological approaches. The aim of this chapter is to present and assess some of the essential online tools and resources that will allow novices in bioinformatics to decipher transcriptomic data in order to characterize the cellular processes and functions involved in abiotic stress responses and signaling. The analysis of case studies further describes how these tools can be used to conceive signaling networks on the basis of transcriptomic data. In these case studies, particular attention was paid to the characterization of abiotic stress responses and signaling related to chemical and xenobiotic stressors.

CPL2 and CPL3 act redundantly in FLC activation and flowering time regulation in Arabidopsis

Reproductive success of plants greatly depends on the proper timing of the floral transition, which is precisely controlled by a complex genetic network. FLOWERING LOCUS C (FLC), a central floral repressor, is transcriptionally activated by the FRIGIDA (FRI) activator complex including FLC EXPRESSOR (FLX) and FLX-LIKE 4 (FLX4). C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3 (CPL3) forms a protein complex with FLX and FLX4 to mediate the dephosphorylation of FLX4, thereby promoting FLC expression to repress flowering in both winter and summer annuals. Here, we show that CPL2 acts redundantly with CPL3 to mediate FLC activation and flowering time. Similar to CPL3, CPL2 inhibits the floral transition, and is required for basal FLC expression in summer annuals and FLC activation in winter annuals. CPL2 directly interacts with FLX which further bridges the interaction between CPL2 and FLX4. Our results suggest that CPL2 and CPL3 function redundantly in regulating FLC expression to prevent precocious flowering.

Functional diversity of Medicago truncatula RNA polymerase II CTD phosphatase isoforms produced in the Arabidopsis thaliana superexpression platform

Medicago truncatula is a model system for legume plants, which has substantially expanded the genome relative to the prototypical model dicot plant, Arabidopsis thaliana. An essential transcriptional regulator, FCP1 (transcription factor IIF-interacting RNA polymerase II carboxyl-terminal phosphatase 1) ortholog, is encoded by a single essential gene CPL4 (CTD-phosphatase-like 4), whereas M. truncatula genome contains four genes homologous to FCP1/AtCPL4, and splicing variants of MtCPL4 are observed. Functional diversification of MtCPL4 family proteins was analyzed using recombinant proteins (MtCPL4a1, MtCPL4a2, and MtCPL4b) produced in Arabidopsis cell culture system developed for plant protein overexpression. In vitro CTD phosphatase assay using highly purified MtCPL4 preparations revealed a potent CTD phosphatase activity in MtCPL4b, but not two splicing variants of MtCPL4a. On the other hand, in planta binding assay to RNA polymerase II (pol II) revealed a greater pol II-binding activity of both MtCPL4a variants. Our results indicate functional diversification of MtCPL4 isoforms and suggest the presence of a large number of functionally specialized CTD-phosphatase-like proteins in plants.

Cyclin-Dependent Kinases and CTD Phosphatases in Cell Cycle Transcriptional Control: Conservation across Eukaryotic Kingdoms and Uniqueness to Plants

Cell cycle control is vital for cell proliferation in all eukaryotic organisms. The entire cell cycle can be conceptually separated into four distinct phases, Gap 1 (G1), DNA synthesis (S), G2, and mitosis (M), which progress sequentially. The precise control of transcription, in particular, at the G1 to S and G2 to M transitions, is crucial for the synthesis of many phase-specific proteins, to ensure orderly progression throughout the cell cycle. This mini-review highlights highly conserved transcriptional regulators that are shared in budding yeast (Saccharomyces cerevisiae), Arabidopsis thaliana model plant, and humans, which have been separated for more than a billion years of evolution. These include structurally and/or functionally conserved regulators cyclin-dependent kinases (CDKs), RNA polymerase II C-terminal domain (CTD) phosphatases, and the classical versus shortcut models of Pol II transcriptional control. A few of CDKs and CTD phosphatases counteract to control the Pol II CTD Ser phosphorylation codes and are considered critical regulators of Pol II transcriptional process from initiation to elongation and termination. The functions of plant-unique CDKs and CTD phosphatases in relation to cell division are also briefly summarized. Future studies towards testing a cooperative transcriptional mechanism, which is proposed here and involves sequence-specific transcription factors and the shortcut model of Pol II CTD code modulation, across the three eukaryotic kingdoms will reveal how individual organisms achieve the most productive, large-scale transcription of phase-specific genes required for orderly progression throughout the entire cell cycle.

Transcriptomics Reveals Fast Changes in Salicylate and Jasmonate Signaling Pathways in Shoots of Carbonate-Tolerant Arabidopsis thaliana under Bicarbonate Exposure

High bicarbonate concentrations of calcareous soils with high pH can affect crop performance due to different constraints. Among these, Fe deficiency has mostly been studied. The ability to mobilize sparingly soluble Fe is a key factor for tolerance. Here, a comparative transcriptomic analysis was performed with two naturally selected Arabidopsis thaliana demes, the carbonate-tolerant A1(c+) and the sensitive T6(c-). Analyses of plants exposed to either pH stress alone (pH 5.9 vs. pH 8.3) or to alkalinity caused by 10 mM NaHCO3 (pH 8.3) confirmed better growth and nutrient homeostasis of A1(c+) under alkaline conditions. RNA-sequencing (RNA-seq) revealed that bicarbonate quickly (3 h) induced Fe deficiency-related genes in T6(c-) leaves. Contrastingly, in A1(c+), initial changes concerned receptor-like proteins (RLP), jasmonate (JA) and salicylate (SA) pathways, methionine-derived glucosinolates (GS), sulfur starvation, starch degradation, and cell cycle. Our results suggest that leaves of carbonate-tolerant plants do not sense iron deficiency as fast as sensitive ones. This is in line with a more efficient Fe translocation to aerial parts. In A1(c+) leaves, the activation of other genes related to stress perception, signal transduction, GS, sulfur acquisition, and cell cycle precedes the induction of iron homeostasis mechanisms yielding an efficient response to bicarbonate stress.

The Arabidopsis RNA Polymerase II Carboxyl Terminal Domain (CTD) Phosphatase-Like1 (CPL1) is a biotic stress susceptibility gene

Crop breeding for improved disease resistance may be achieved through the manipulation of host susceptibility genes. Previously we identified multiple Arabidopsis mutants known as enhanced stress response1 (esr1) that have defects in a KH-domain RNA-binding protein and conferred increased resistance to the root fungal pathogen Fusarium oxysporum. Here, screening the same mutagenized population we discovered two further enhanced stress response mutants that also conferred enhanced resistance to F. oxysporum. These mutants also have enhanced resistance to a leaf fungal pathogen (Alternaria brassicicola) and an aphid pest (Myzus persicae), but not to the bacterial leaf pathogen Pseudomonas syringae. The causal alleles in these mutants were found to have defects in the ESR1 interacting protein partner RNA Polymerase II Carboxyl Terminal Domain (CTD) Phosphatase-Like1 (CPL1) and subsequently given the allele symbols cpl1-7 and cpl1-8. These results define a new role for CPL1 as a pathogen and pest susceptibility gene. Global transcriptome analysis and oxidative stress assays showed these cpl1 mutants have increased tolerance to oxidative stress. In particular, components of biotic stress responsive pathways were enriched in cpl1 over wild-type up-regulated gene expression datasets including genes related to defence, heat shock proteins and oxidative stress/redox state processes.

Cytokinin-overinduced transcription factors and thalianol cluster genes in CARBOXYL-TERMINAL DOMAIN PHOSPHATASE-LIKE 4-silenced Arabidopsis roots during de novo shoot organogenesis

Cytokinin (CK) is one of key phytohormones for de-differentiation and de novo organogenesis in plants. During the CK-mediated organogenesis not only genes in CK homeostasis, perception and signal transduction, but also factors regulating basic transcription, splicing and chromatin remodeling contribute to coordinate a sequence of events leading to formation of new organs. We have found that silencing of RNA polymerase II CTD-phosohatase-like 4 (CPL4_RNAi) in Arabidopsis induces CK-oversensitive de novo shoot organogenesis (DNSO) from roots, partly by early activation of transcription factors such as WUSCHEL and SHOOT MERISTEMLESS during pre-incubation on callus induction media. Here we show that a cluster of thalianol-biogenesis genes is highly expressed in the CPL4_RNAi during DNSO, implying involvement of CPL4 in transcriptional regulation of the thalianol pathway in DNSO.

Low doses of triazine xenobiotics mobilize ABA and cytokinin regulations in a stress- and low-energy-dependent manner

The extent of residual contaminations of pesticides through drift, run-off and leaching is a potential threat to non-target plant communities. Arabidopsis thaliana responds to low doses of the herbicide atrazine, and of its degradation products, desethylatrazine and hydroxyatrazine, not only in the long term, but also under conditions of short-term exposure. In order to investigate underlying molecular mechanisms of low-dose responses and to decipher commonalities and specificities between different chemical treatments, parallel transcriptomic studies of the early effects of the atrazine-desethylatrazine-hydroxyatrazine chemical series were undertaken using whole-genome microarrays. All of the triazines under study produced coordinated and specific changes in gene expression. Hydroxyatrazine-responsive genes were mainly linked to root development, whereas atrazine and desethylatrazine mostly affected molecular signaling networks implicated in stress and hormone responses. Analysis of signaling-related genes, promoter sites and shared-function interaction networks highlighted the involvement of energy-, stress-, abscisic acid- and cytokinin-regulated processes, and emphasized the importance of cold-, heat- and drought-related signaling in the perception of low doses of triazines. These links between low-dose xenobiotic impacts and stress-hormone crosstalk pathways give novel insights into plant-pesticide interactions and plant-pollution interactions that are essential for toxicity evaluation in the context of environmental risk assessment.

Cytokinin at the Crossroads of Abiotic Stress Signalling Pathways

Cytokinin is a multifaceted plant hormone that plays major roles not only in diverse plant growth and development processes, but also stress responses. We summarize knowledge of the roles of its metabolism, transport, and signalling in responses to changes in levels of both macronutrients (nitrogen, phosphorus, potassium, sulphur) and micronutrients (boron, iron, silicon, selenium). We comment on cytokinin's effects on plants' xenobiotic resistance, and its interactions with light, temperature, drought, and salinity signals. Further, we have compiled a list of abiotic stress-related genes and demonstrate that their expression patterns overlap with those of cytokinin metabolism and signalling genes.

Silencing Arabidopsis CARBOXYL-TERMINAL DOMAIN PHOSPHATASE-LIKE 4 induces cytokinin-oversensitive de novo shoot organogenesis

De novo shoot organogenesis (DNSO) is a post-embryonic development programme that has been widely exploited by plant biotechnology. DNSO is a hormonally regulated process in which auxin and cytokinin (CK) coordinate suites of genes encoding transcription factors, general transcription factors, and RNA metabolism machinery. Here we report that silencing Arabidopsis thaliana carboxyl-terminal domain (CTD) phosphatase-like 4 (CPL4_RNAi ) resulted in increased phosphorylation levels of RNA polymerase II (pol II) CTD and altered lateral root development and DNSO efficiency of the host plants. Under standard growth conditions, CPL4_RNAi lines produced no or few lateral roots. When induced by high concentrations of auxin, CPL4_RNAi lines failed to produce focused auxin maxima at the meristem of lateral root primordia, and produced fasciated lateral roots. In contrast, root explants of CPL4_RNAi lines were highly competent for DNSO. Efficient DNSO of CPL4_RNAi lines was observed even under 10 times less the CK required for the wild-type explants. Transcriptome analysis showed that CPL4_RNAi , but not wild-type explants, expressed high levels of shoot meristem-related genes even during priming on medium with a high auxin/CK ratio, and during subsequent shoot induction with a lower auxin/CK ratio. Conversely, CPL4_RNAi enhanced the inhibitory phenotype of the shoot redifferentiation defective2-1 mutation, which affected snRNA biogenesis and formation of the auxin gradient. These results indicated that CPL4 functions in multiple regulatory pathways that positively and negatively affect DNSO.

Purification and characterization of Arabidopsis thaliana oligosaccharyltransferase complexes from the native host: a protein super-expression system for structural studies

The oligosaccharyltransferase (OT) complex catalyzes N-glycosylation of nascent secretory polypeptides in the lumen of the endoplasmic reticulum. Despite their importance, little is known about the structure and function of plant OT complexes, mainly due to lack of efficient recombinant protein production systems suitable for studies on large plant protein complexes. Here, we purified Arabidopsis OT complexes using the tandem affinity-tagged OT subunit STAUROSPORINE AND TEMPERATURE SENSITIVE3a (STT3a) expressed by an Arabidopsis protein super-expression platform. Mass-spectrometry analysis of the purified complexes identified three essential OT subunits, OLIGOSACCHARYLTRANSFERASE1 (OST1), HAPLESS6 (HAP6), DEFECTIVE GLYCOSYLATION1 (DGL1), and a number of ribosomal subunits. Transmission-electron microscopy showed that STT3a becomes incorporated into OT-ribosome super-complexes formed in vivo, demonstrating that this expression/purification platform is suitable for analysis of large protein complexes. Pairwise in planta interaction analyses of individual OT subunits demonstrated that all subunits identified in animal OT complexes are conserved in Arabidopsis and physically interact with STT3a. Genetic analysis of newly established OT subunit mutants for OST1 and DEFENDER AGAINST APOTOTIC DEATH (DAD) family genes revealed that OST1 and DAD1/2 subunits are essential for the plant life cycle. However, mutations in these individual isoforms produced much milder growth/underglycosylation phenotypes than previously reported for mutations in DGL1, OST3/6 and STT3a.

Mechanical stress-induced subcellular re-localization of N-terminally truncated tobacco Nt-4/1 protein

The Nicotiana tabacum 4/1 protein (Nt-4/1) of unknown function expressed in plant vasculature has been shown to localize to cytoplasmic bodies associated with endoplasmic reticulum. Here, we analyzed molecular interactions of an Nt-4/1 mutant with a deletion of 90 N-terminal amino acid residues (Nt-4/1d90) having a diffuse GFP-like localization. Upon transient co-expression with VAP27, a membrane protein known to localize to the ER, ER-plasma membrane contact sites and plasmodesmata, Nt-4/1d90 was concentrated around the cortical ER tubules, forming a network matching the shape of the cortical ER. Additionally, in response to mechanical stress, Nt-4/1d90 was re-localized to small spherical bodies, whereas the subcellular localization of VAP27 remained essentially unaffected. The Nt-4/1d90-containing bodies associated with microtubules, which underwent noticeable bundling under the conditions of mechanical stress. The Nt-4/1d90 re-localization to spherical bodies could also be induced by incubation at an elevated temperature, although under heat shock conditions the re-localization was less efficient and incomplete. An Nt-4/1d90 mutant, which had phosphorylation-mimicking mutations in a predicted cluster of four potentially phosphorylated residues, was found to both inefficiently re-localize to spherical bodies and tend to revert back to the initial diffuse localization. The presented data show that Nt-4/1 has a potential for response to stresses that is manifested by its deletion mutant Nt-4/1d90, and this response can be mediated by protein dephosphorylation.

Improved recombinant protein production in Arabidopsis thaliana

Production and isolation of recombinant proteins are key steps in modern Molecular Biology. Expression vectors and platforms for various hosts, including both prokaryotic and eukaryotic systems, have been used. In basic plant research, Arabidopsis thaliana is the central model for which a wealth of genetic and genomic resources is available, and enormous knowledge has been accumulated over the past years - especially since elucidation of its genome in 2000. However, until recently an Arabidopsis platform had been lacking for preparative-scale production of homologous recombinant proteins. We recently established an Arabidopsis-based super-expression system, and used it for a structural pilot study of a multi-subunit integral membrane protein complex. This review summarizes the benefits and further potential of the model plant system for protein productions.

ABBREVIATIONS

Nb, Nicotiana benthamiana; OT, oligosaccharyltransferase.

Transcriptome Comparison Reveals the Adaptive Evolution of Two Contrasting Ecotypes of Zn/Cd Hyperaccumulator Sedum alfredii Hance

Hyperaccumulating ecotype (HE) and non-hyperaccumulating ecotype (NHE) of Sedum alfredii Hance belong to the same species but exhibit contrasting characteristics regarding hyperaccumulation and hypertolerance to cadmium and zinc. The Illumina Hiseq 2500 platform was employed to sequence HE and NHE to study the genetic evolution of this contrasting trait. Greater than 90 million clean reads were obtained and 118,479/228,051 unigenes of HE/NHE were annotated based on seven existing databases. We identified 149,668/319,830 single nucleotide polymorphisms (SNPs) and 12,691/14,428 simple sequence repeats (SSRs) of HE/NHE. We used a branch-site model to identify 18 divergent orthologous genes and 57 conserved orthologous genes of S. alfredii Hance. The divergent orthologous genes were mainly involved in the transcription and translation processes, protein metabolism process, calcium (Ca²⁺) pathway, stress response process and signal transduction process. To the best of our knowledge, this is the first study to use RNA-seq to compare the genetic evolution of hyperaccumulating and non-hyperaccumulating plants from the same species. In addition, this study made the sole concrete for further studies on molecular markers and divergent orthologous genes to depict the evolution process and formation of the hyperaccumulation and hypertolerance traits in S. alfredii Hance.

Herbicide-related signaling in plants reveals novel insights for herbicide use strategies, environmental risk assessment and global change assessment challenges

Herbicide impact is usually assessed as the result of a unilinear mode of action on a specific biochemical target with a typical dose-response dynamics. Recent developments in plant molecular signaling and crosstalk between nutritional, hormonal and environmental stress cues are however revealing a more complex picture of inclusive toxicity. Herbicides induce large-scale metabolic and gene-expression effects that go far beyond the expected consequences of unilinear herbicide-target-damage mechanisms. Moreover, groundbreaking studies have revealed that herbicide action and responses strongly interact with hormone signaling pathways, with numerous regulatory protein-kinases and -phosphatases, with metabolic and circadian clock regulators and with oxidative stress signaling pathways. These interactions are likely to result in mechanisms of adjustment that can determine the level of sensitivity or tolerance to a given herbicide or to a mixture of herbicides depending on the environmental and developmental status of the plant. Such regulations can be described as rheostatic and their importance is discussed in relation with herbicide use strategies, environmental risk assessment and global change assessment challenges.

Genome-Wide Transcriptional Profiling and Metabolic Analysis Uncover Multiple Molecular Responses of the Grass Species Lolium perenne Under Low-Intensity Xenobiotic Stress

Lolium perenne, which is a major component of pastures, lawns, and grass strips, can be exposed to xenobiotic stresses due to diffuse and residual contaminations of soil. L. perenne was recently shown to undergo metabolic adjustments in response to sub-toxic levels of xenobiotics. To gain insight in such chemical stress responses, a de novo transcriptome analysis was carried out on leaves from plants subjected at the root level to low levels of xenobiotics, glyphosate, tebuconazole, and a combination of the two, leading to no adverse physiological effect. Chemical treatments influenced significantly the relative proportions of functional categories and of transcripts related to carbohydrate processes, to signaling, to protein-kinase cascades, such as Serine/Threonine-protein kinases, to transcriptional regulations, to responses to abiotic or biotic stimuli and to responses to phytohormones. Transcriptomics-based expressions of genes encoding different types of SNF1 (sucrose non-fermenting 1)-related kinases involved in sugar and stress signaling or encoding key metabolic enzymes were in line with specific qRT-PCR analysis or with the important metabolic and regulatory changes revealed by metabolomic analysis. The effects of pesticide treatments on metabolites and gene expression strongly suggest that pesticides at low levels, as single molecule or as mixture, affect cell signaling and functioning even in the absence of major physiological impact. This global analysis of L. perenne therefore highlighted the interactions between molecular regulation of responses to xenobiotics, and also carbohydrate dynamics, energy dysfunction, phytohormones and calcium signaling.