Gibberellic acid and cGMP-dependent transcriptional regulation in Arabidopsis thaliana

Identification and molecular evolution of the GLX genes in 21 plant species: a focus on the Gossypium hirsutum

BACKGROUND

The glyoxalase system includes glyoxalase I (GLXI), glyoxalase II (GLXII) and glyoxalase III (GLXIII), which are responsible for methylglyoxal (MG) detoxification and involved in abiotic stress responses such as drought, salinity and heavy metal.

RESULTS

In this study, a total of 620 GLX family genes were identified from 21 different plant species. The results of evolutionary analysis showed that GLX genes exist in all species from lower plants to higher plants, inferring that GLX genes might be important for plants, and GLXI and GLXII account for the majority. In addition, motif showed an expanding trend in the process of evolution. The analysis of cis-acting elements in 21 different plant species showed that the promoter region of the GLX genes were rich in phytohormones and biotic and abiotic stress-related elements, indicating that GLX genes can participate in a variety of life processes. In cotton, GLXs could be divided into two groups and most GLXIs distributed in group I, GLXIIs and GLXIIIs mainly belonged to group II, indicating that there are more similarities between GLXII and GLXIII in cotton evolution. The transcriptome data analysis and quantitative real-time PCR analysis (qRT-PCR) show that some members of GLX family would respond to high temperature treatment in G.hirsutum. The protein interaction network of GLXs in G.hirsutum implied that most members can participate in various life processes through protein interactions.

CONCLUSIONS

The results elucidated the evolutionary history of GLX family genes in plants and lay the foundation for their functions analysis in cotton.

Genome-Wide Identification of Apple Atypical bHLH Subfamily PRE Members and Functional Characterization of MdPRE4.3 in Response to Abiotic Stress

Paclobutrazol Resistance (PRE) genes encode atypical basic helix–loop–helix (bHLH) transcription factor family. Typical bHLH proteins contain a bifunctional structure with a basic region involved in DNA binding and an adjacent helix–loop–helix domain involved in protein–protein interaction. PRE members lack the basic region but retain the HLH domain, which interacts with other typical bHLH proteins to suppress or enhance their DNA-binding activity. PRE proteins are involved in phytohormone responses, light signal transduction, and fruit pigment accumulation. However, apple (Malus domestica) PRE protein functions have not been studied. In this study, nine MdPRE genes were identified from the apple GDDH13 v1.1 reference genome and were mapped to seven chromosomes. The cis-acting element analysis revealed that MdPRE promoters possessed various elements related to hormones, light, and stress responses. Expression pattern analysis showed that MdPRE genes have different tissue expression profiles. Hormonal and abiotic stress treatments can induce the expression of several MdPRE genes. Moreover, we provide molecular and genetic evidence showing that MdPRE4.3 increases the apple’s sensitivity to NaCl, abscisic acid (ABA), and indoleacetic acid (IAA) and improves tolerance to brassinosteroids (BR); however, it does not affect the apple’s response to gibberellin (GA). Finally, the protein interaction network among the MdPRES proteins was predicted, which could help us elucidate the molecular and biological functions of atypical bHLH transcription factors in the apple.

Genome-Wide Identification, Transcript Profiling and Bioinformatic Analyses of GRAS Transcription Factor Genes in Rice

Our group has previously identified the activation of a GRAS transcription factor (TF) gene in the gain-of-function mutant population developed through activation tagging in rice (in an indica rice variety, BPT 5204) that was screened for water use efficiency. This family of GRAS transcription factors has been well known for their diverse roles in gibberellin signaling, light responses, root development, gametogenesis etc. Recent studies indicated their role in biotic and abiotic responses as well. Although this family of TFs received significant attention, not many genes were identified specifically for their roles in mediating stress tolerance in rice. Only OsGRAS23 (here named as OsGRAS22) was reported to code for a TF that induced drought tolerance in rice. In the present study, we have analyzed the expression patterns of rice GRAS TF genes under abiotic (NaCl and ABA treatments) and biotic (leaf samples infected with pathogens, Xanthomonas oryzae pv. oryzae that causes bacterial leaf blight and Rhizoctonia solani that causes sheath blight) stress conditions. In addition, their expression patterns were also analyzed in 13 different developmental stages. We studied their spatio-temporal regulation and correlated them with the in-silico studies. Fully annotated genomic sequences available in rice database have enabled us to study the protein properties, ligand interactions, domain analysis and presence of cis-regulatory elements through the bioinformatic approach. Most of the genes were induced immediately after the onset of stress particularly in the roots of ABA treated plants. OsGRAS39 was found to be a highly expressive gene under sheath blight infection and both abiotic stress treatments while OsGRAS8, OsSHR1 and OsSLR1 were also responsive. Our earlier activation tagging based functional characterization followed by the genome-wide characterization of the GRAS gene family members in the present study clearly show that they are highly appropriate candidate genes for manipulating stress tolerance in rice and other crop plants.

Identification and functional analysis of the MdLTPG gene family in apple

Cuticular wax is synthesized from intracellular lipids that are exported by epidermal cells, and plant lipid transfer proteins (LTPs) play an important role in this process. The glycosylphosphatidylinositol (GPI)-anchored LTPs (LTPGs) are a large subgroup within the LTP family and function in lipid transport and wax formation. Although LTPG family members have been identified in several plant species, the LTPG gene family of apple (Malus domestica) remains uncharacterized. In this paper, we identified 26 potential LTPG genes by searching apple whole-genome annotation files using "GPI-anchored" and "lipid transferase" as keywords. Twenty of the 26 putative LTPG genes were confirmed as MdLTPG family members based on their subcellular localization predictions. The MdLTPGs were divided into four classes based on phylogenetic analysis and functional domain prediction. One member of each class was analyzed for subcellular localization, and all identified members were located on the plasma membrane. Most MdLTPG genes were induced by abiotic stress treatments such as low temperature, NaCl, and ABA. Finally, the MdLTPG17 protein was shown to interact with the lysine-rich arabinogalactan protein MdAGP18 to perform its function in wax transport during plant growth and development.

LsHSP70 is induced by high temperature to interact with calmodulin, leading to higher bolting resistance in lettuce

High temperatures have significant impacts on heat-tolerant bolting in lettuce. In this study, it was found that high temperatures could facilitate the accumulation of GA in lettuce to induce bolting, with higher expression levels of two heat shock protein genes LsHsp70-3701 and LsHsp70-2711. By applying VIGS technology, these two Hsp70 genes were incompletely silenced and plant morphological changes under heat treatment of silenced plants were observed. The results showed that lower expression levels of these two genes could enhance bolting stem length of lettuce under high temperatures, which means these two proteins may play a significant role in heat-induced bolting tolerance. By using the yeast two-hybrid technique, it was found that a calmodulin protein could interact with LsHsp70 proteins in a high-temperature stress cDNA library, which was constructed for lettuce. Also, the Hsp70-calmodulin combination can be obtained at high temperatures. According to these results, it can be speculated that the interaction between Hsp70 and calmodulin could be induced under high temperatures and higher GA contents can be obtained at the same time. This study analyses the regulation of heat tolerance in lettuce and lays a foundation for additional studies of heat resistance in lettuce.

Genome wide analysis and functional identification of MdKCS genes in apple

Apple fruit is covered by cuticle wax, which plays important roles protecting fruits from adverse environmental conditions. β-Ketoacyl-CoA synthase (KCS) is the key rate-limiting enzyme in plant wax synthesis. In this study, we identified 28 KCS gene family members from apple (Malus × domestica Borkh.) by homology analysis. Multi-sequence alignment and phylogenetic analyses revealed that the 28 MdKCS genes were divided into four subgroups, including KCS1-like, FAE1-like, FDH-like, and CER6. A chromosomal localization analysis revealed that 27 apple KCS genes were located on 11 chromosomes, while MdKCS28 was localized to the unassembled genomic scaffold. Most of the MdKCS proteins were hydrophilic proteins and they had similar secondary and tertiary structures. The prediction of cis-acting elements of the MdKCS gene promoters suggested that the MdKCS genes may be widely involved in hormone signaling and the stress response. Furthermore, the quantitative real-time polymerase chain reaction results showed that eight MdKCS genes were highly expressed in the apple pericarp, and were significantly induced by drought, abscisic acid (ABA), and NaCl treatments. We transformed the MdKCS21 gene into apple calli, and found the MdKCS21 overexpressing transgenic apple calli exhibited higher tolerance to ABA treatment. Finally, the MdKCS proteins were localized to the endoplasmic reticulum and vacuolar membrane by confocal laser microscopy. This study established a foundation to further analyze the function of KCS genes and provided candidate genes for molecular improvement of wax content in apple.

CO2 enrichment enhanced drought resistance by regulating growth, hydraulic conductivity and phytohormone contents in the root of cucumber seedlings

The coordinated effects of CO2 enrichment and drought stress on cucumber leaves have attracted increasing research attention, but few studies have investigated the effects of CO2 enrichment on the root system under drought stress. So we analyzed the morphological parameters, hydraulic conductivity, aquaporin-related gene expression, and endogenous phytohormone contents in roots of cucumber seedlings cultured under different CO2 concentrations (approximately 400 and 800 ± 40 μmol mol-1) and drought stresses simulated by polyethylene glycol 6000 (0%, 5%, and 10%). The results showed that under drought stress, regardless of the CO2 concentration, the root biomass and hydraulic conductivity decreased, the contents of auxin (IAA), zeatin nucleoside (ZR), and gibberellin (GA) decreased, the abscisic acid (ABA) content and the transcript levels of the aquaporin-related genes CsPIP2-4 increased, and the transcript levels of the aquaporin-related genes CsPIP2-5 and CsPIP2-7 decreased compared with no drought stress. Under moderate drought stress, CO2 enrichment decreased ABA content and the transcript level of CsPIP2-4, increased root biomass and GA content and the transcript level of CsPIP2-7, improved contribution rate of cell-to-cell water transport (mediated by aquaporins) and roots hydraulic conductivity. In summary, drought stress changed the water transport capacity of the roots and inhibited the growth of cucumber seedlings. CO2 enrichment regulated phytohormone contents and aquaporin-related gene expression, maintained the normal contribution rate of cell-to-cell water transport, and improved the root biomass and hydraulic conductivity, thereby alleviated the negative effects of drought stress on cucumber seedlings.

Deciphering aquaporin regulation and roles in seed biology

Seeds are the typical dispersal and propagation units of angiosperms and gymnosperms. Water movement into and out of seeds plays a crucial role from the point of fertilization through to imbibition and seed germination. A class of membrane intrinsic proteins called aquaporins (AQPs) assist with the movement of water and other solutes within seeds. These highly diverse and abundant proteins are associated with different processes in the development, longevity, imbibition, and germination of seed. However, there are many AQPs encoded in a plant's genome and it is not yet clear how, when, or which AQPs are involved in critical stages of seed biology. Here we review the literature to examine the evidence for AQP involvement in seeds and analyse Arabidopsis seed-related transcriptomic data to assess which AQPs are likely to be important in seed water relations and explore additional roles for AQPs in seed biology.

Dual Activities of Plant cGMP-Dependent Protein Kinase and Its Roles in Gibberellin Signaling and Salt Stress

Cyclic GMP (cGMP) is an important regulator in eukaryotes, and cGMP-dependent protein kinase (PKG) plays a key role in perceiving cellular cGMP in diverse physiological processes in animals. However, the molecular identity, property, and function of PKG in plants remain elusive. In this study, we have identified PKG from plants and characterized its role in mediating the gibberellin (GA) response in rice (Oryza sativa). PKGs from plants are structurally unique with an additional type 2C protein phosphatase domain. Rice PKG possesses both protein kinase and phosphatase activities, and cGMP stimulates its kinase activity but inhibits its phosphatase activity. One of PKG's targets is GAMYB, a transcription factor in GA signaling, and the dual activities of PKG catalyze the reversible phosphorylation of GAMYB at Ser6 and modulate the nucleocytoplasmic distribution of GAMYB in response to GA. Loss of PKG impeded the nuclear localization of GAMYB and abolished GAMYB function in the GA response, leading to defects in GA-induced seed germination, internode elongation, and pollen viability. In addition to GAMYB, PKG has multiple potential targets and thus has broad effects, particularly in the salt stress response.

Spatio-temporal expression of phytoglobin: a determining factor in the NO specification of cell fate

Plant growth and development rely on the orchestration of cell proliferation, differentiation, and ultimately death. After varying rounds of divisions, cells respond to positional cues by acquiring a specific fate and embarking upon distinct developmental pathways which might differ significantly from those of adjacent cells exposed to diverse cues. Differential cell behavior is most apparent in response to stress, when some cells might be more vulnerable than others to the same stress condition. This appears to be the case for stem cells which show abnormal features of differentiation and ultimately signs of deterioration at the onset of specific types of stress such as hypoxia and water deficit. A determining factor influencing cell behavior during growth and development, and cell response during conditions of stress is nitric oxide (NO), the level of which can be regulated by phytoglobins (Pgbs), known scavengers of NO. The modulation of NO by Pgbs can be cell, tissue, and/or organ specific, as revealed by the expression patterns of Pgbs dictated by the presence of distinct cis-regulatory elements in their promoters. This review discusses how the temporal and spatial Pgb expression pattern influences NO-mediated responses and ultimately cell fate acquisition in plant developmental processes.

Identification of cis-regulatory regions responsible for developmental and hormonal regulation of HbHMGS1 in transgenic Arabidopsis thaliana

OBJECTIVES

3-Hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase (HMGS) is an important enzyme in mevalonate (MVA) pathway of isoprenoid biosynthesis, which regulates the rubber biosynthetic pathway in rubber tree (Hevea brasiliensis) in coordination with HMG-CoA reductase (HMGR). However, little information is available about the regulation of HMGS gene expression. To understand the mechanism controlling the HbHMGS1 gene expression, we characterized the HbHMGS1 promoter sequence in transgenic plants with the β-glucuronidase (GUS) reporter gene.

RESULTS

GUS activity analysis of the transgenic plants showed that the HbHMGS1 promoter is active in all organs of the transgenic Arabidopsis plants during various developmental stages (from 6 to 45-day-old). Deletion of different portions of the upstream HbHMGS1 promoter identified sequences responsible for either positive or negative regulation of the GUS expression. Particularly, the - 454 bp HbHMGS1 promoter resulted in a 2.19-fold increase in promoter activity compared with the CaMV 35S promoter, suggesting that the - 454 bp HbHMGS1 promoter is a super-strong near-constitutive promoter. In addition, a number of promoter regions important for the responsiveness to ethylene, methyl jasmonate (MeJA) and gibberellic acid (GA) were identified.

CONCLUSION

The - 454 bp HbHMGS1 promoter has great application potential in plant transformation studies as an alternative to the CaMV 35S promoter. The HbHMGS1 promoter may play important roles in regulating ethylene-, MeJA- and GA-mediated gene expression. The functional complexity of cis-elements revealed by this study remains to be elucidated.

Downstream Targets of Cyclic Nucleotides in Plants

Efficient integration of various external and internal signals is required to maintain adaptive cellular function. Numerous distinct signal transduction systems have evolved to allow cells to receive these inputs, to translate their codes and, subsequently, to expand and integrate their meanings. Two of these, cyclic AMP and cyclic GMP, together referred to as the cyclic nucleotide signaling system, are between them. The cyclic nucleotides regulate a vast number of processes in almost all living organisms. Once synthesized by adenylyl or guanylyl cyclases, cyclic nucleotides transduce signals by acting through a number of cellular effectors. Because the activities of several of these effectors are altered simultaneously in response to temporal changes in cyclic nucleotide levels, agents that increase cAMP/cGMP levels can trigger multiple signaling events that markedly affect numerous cellular functions. In this mini review, we summarize recent evidence supporting the existence of cNMP effectors in plant cells. Specifically, we highlight cAMP-dependent protein kinase A (PKA), cGMP-dependent kinase G (PKG), and cyclic nucleotide phosphodiesterases (PDEs). Essentially this manuscript documents the progress that has been achieved in recent decades in improving our understanding of the regulation and function of cNMPs in plants and emphasizes the current gaps and unanswered questions in this field of plant signaling research.

Cyclic Nucleotide Monophosphates in Plants and Plant Signaling

Cyclic nucleotide monophosphates (cNMPs) and the enzymes that can generate them are of increasing interest in the plant sciences. Arguably, the major recent advance came with the release of the complete Arabidopsis thaliana genome that has enabled the systematic search for adenylate (ACs) or guanylate cyclases (GCs) and did eventually lead to the discovery of a number of GCs in higher plants. Many of these proteins have complex domain architectures with AC or GC centers moonlighting within cytosolic kinase domains. Recent reports indicated the presence of not just the canonical cNMPs (i.e., cAMP and cGMP), but also the noncanonical cCMP, cUMP, cIMP, and cdTMP in plant tissues, and this raises several questions. Firstly, what are the functions of these cNMPs, and, secondly, which enzymes can convert the substrate triphosphates into the respective noncanonical cNMPs? The first question is addressed here by comparing the reactive oxygen species (ROS) response of cAMP and cGMP to that elicited by the noncanonical cCMP or cIMP. The results show that particularly cIMP can induce significant ROS production. To answer, at least in part, the second question, we have evaluated homology models of experimentally confirmed plant GCs probing the substrate specificity by molecular docking simulations to determine if they can conceivably catalytically convert substrates other than ATP or GTP. In summary, molecular modeling and substrate docking simulations can contribute to the evaluation of cyclases for noncanonical cyclic mononucleotides and thereby further our understanding of the molecular mechanism that underlie cNMP-dependent signaling in planta.

Genome-Wide Identification and Comprehensive Expression Profiling of Ribosomal Protein Small Subunit (RPS) Genes and their Comparative Analysis with the Large Subunit (RPL) Genes in Rice

Ribosomal proteins (RPs) are indispensable in ribosome biogenesis and protein synthesis, and play a crucial role in diverse developmental processes. Our previous studies on Ribosomal Protein Large subunit (RPL) genes provided insights into their stress responsive roles in rice. In the present study, we have explored the developmental and stress regulated expression patterns of Ribosomal Protein Small (RPS) subunit genes for their differential expression in a spatiotemporal and stress dependent manner. We have also performed an in silico analysis of gene structure, cis-elements in upstream regulatory regions, protein properties and phylogeny. Expression studies of the 34 RPS genes in 13 different tissues of rice covering major growth and developmental stages revealed that their expression was substantially elevated, mostly in shoots and leaves indicating their possible involvement in the development of vegetative organs. The majority of the RPS genes have manifested significant expression under all abiotic stress treatments with ABA, PEG, NaCl, and H2O2. Infection with important rice pathogens, Xanthomonas oryzae pv. oryzae (Xoo) and Rhizoctonia solani also induced the up-regulation of several of the RPS genes. RPS4, 13a, 18a, and 4a have shown higher transcript levels under all the abiotic stresses, whereas, RPS4 is up-regulated in both the biotic stress treatments. The information obtained from the present investigation would be useful in appreciating the possible stress-regulatory attributes of the genes coding for rice ribosomal small subunit proteins apart from their functions as house-keeping proteins. A detailed functional analysis of independent genes is required to study their roles in stress tolerance and generating stress- tolerant crops.

The Hippeastrum hybridum PepR1 gene (HpPepR1) encodes a functional guanylyl cyclase and is involved in early response to fungal infection

It is generally known that cyclic GMP widespread in prokaryotic and eukaryotic cells, is involved in essential cellular processes and stress signal transduction. However, in contrast to animals the knowledge about plant guanylyl cyclases (GCs) which catalyze the formation of cGMP from GTP is still quite obscure. Recent studies of plant GCs are focused on identification and functional analysis of a new family of membrane proteins called "moonlighting kinases with GC activity" with guanylyl cyclase catalytic center encapsulated within intracellular kinase domain. Here we report identification and characterization of plasma membrane receptor of peptide signaling molecules - HpPepR1 in Hippeastrum hybridum. Both bioinformatic analysis of amimo acid sequence and in vitro studies revealed that the protein can act as guanylyl cyclase. The predicted amino acid sequence contains highly conserved 14 aa-long search motif in the catalytic center of GCs from lower and higher eukaryotes. Here, we provide experimental evidence to show that the intracellular domain of HpPepR1 can generate cGMP in vitro. Moreover, it was shown that the accumulation of HpPepR1 transcript was sharply increased after Peyronellaea curtisii (=Phoma narcissi) fungal infection, whereas mechanical wounding has no influence on expression profile of studied gene. These results may indicate the participation of cGMP-dependent pathway in rapid, alarm plant reactions induced by pathogen infection.

The arabidopsis cyclic nucleotide interactome

BACKGROUND

Cyclic nucleotides have been shown to play important signaling roles in many physiological processes in plants including photosynthesis and defence. Despite this, little is known about cyclic nucleotide-dependent signaling mechanisms in plants since the downstream target proteins remain unknown. This is largely due to the fact that bioinformatics searches fail to identify plant homologs of protein kinases and phosphodiesterases that are the main targets of cyclic nucleotides in animals.

METHODS

An affinity purification technique was used to identify cyclic nucleotide binding proteins in Arabidopsis thaliana. The identified proteins were subjected to a computational analysis that included a sequence, transcriptional co-expression and functional annotation analysis in order to assess their potential role in plant cyclic nucleotide signaling.

RESULTS

A total of twelve cyclic nucleotide binding proteins were identified experimentally including key enzymes in the Calvin cycle and photorespiration pathway. Importantly, eight of the twelve proteins were shown to contain putative cyclic nucleotide binding domains. Moreover, the identified proteins are post-translationally modified by nitric oxide, transcriptionally co-expressed and annotated to function in hydrogen peroxide signaling and the defence response. The activity of one of these proteins, GLYGOLATE OXIDASE 1, a photorespiratory enzyme that produces hydrogen peroxide in response to Pseudomonas, was shown to be repressed by a combination of cGMP and nitric oxide treatment.

CONCLUSIONS

We propose that the identified proteins function together as points of cross-talk between cyclic nucleotide, nitric oxide and reactive oxygen species signaling during the defence response.

Cyclic GMP balance is critical for malaria parasite transmission from the mosquito to the mammalian host

Transmission of malaria occurs during Anopheles mosquito vector blood meals, when Plasmodium sporozoites that have invaded the mosquito salivary glands are delivered to the mammalian host. Sporozoites display a unique form of motility that is essential for their movement across cellular host barriers and invasion of hepatocytes. While the molecular machinery powering motility and invasion is increasingly well defined, the signaling events that control these essential parasite activities have not been clearly delineated. Here, we identify a phosphodiesterase (PDEγ) in Plasmodium, a regulator of signaling through cyclic nucleotide second messengers. Reverse transcriptase PCR (RT-PCR) analysis and epitope tagging of endogenous PDEγ detected its expression in blood stages and sporozoites of Plasmodium yoelii. Deletion of PDEγ (pdeγ⁻) rendered sporozoites nonmotile, and they failed to invade the mosquito salivary glands. Consequently, PDEγ deletion completely blocked parasite transmission by mosquito bite. Strikingly, pdeγ⁻ sporozoites showed dramatically elevated levels of cyclic GMP (cGMP), indicating that a perturbation in cyclic nucleotide balance is involved in the observed phenotypic defects. Transcriptome sequencing (RNA-Seq) analysis of pdeγ⁻ sporozoites revealed reduced transcript abundance of genes that encode key components of the motility and invasion apparatus. Our data reveal a crucial role for PDEγ in maintaining the cyclic nucleotide balance in the malaria parasite sporozoite stage, which in turn is essential for parasite transmission from mosquito to mammal.

Malaria is a formidable threat to human health worldwide, and there is an urgent need to identify novel drug targets for this parasitic disease. The parasite is transmitted by mosquito bite, inoculating the host with infectious sporozoite stages. We show that cellular signaling by cyclic nucleotides is critical for transmission of the parasite from the mosquito vector to the mammalian host. Parasite phosphodiesterase γ is essential for maintaining cyclic nucleotide balance, and its deletion blocks transmission of sporozoites. A deeper understanding of the signaling mechanisms involved in transmission might inform the discovery of novel drugs that interrupt this essential step in the parasite life cycle.

BIIDXI, the At4g32460 DUF642 gene, is involved in pectin methyl esterase regulation during Arabidopsis thaliana seed germination and plant development

BACKGROUND

DUF642 proteins constitute a highly conserved family of proteins that are associated with the cell wall and are specific to spermatophytes. Transcriptome studies have suggested that members of this family are involved in seed development and germination processes. Previous in vitro studies have revealed that At4g32460- and At5g11420-encoded proteins interact with the catalytic domain of pectin methyl esterase 3 (AtPME3, which is encoded by At3g14310). PMEs play an important role in plant development, including seed germination. The aim of this study was to evaluate the function of the DUF642 gene At4g32460 during seed germination and plant development and to determine its relation to PME activity regulation.

RESULTS

Our results indicated that the DUF642 proteins encoded by At4g32460 and At5g11420 could be positive regulators of PME activity during several developmental processes. Transgenic lines overexpressing these proteins showed increased PME activity during seed germination, and improved seed germination performance. In plants expressing At4g32460 antisense RNA, PME activity was decreased in the leaves, and the siliques were very short and contained no seeds. This phenotype was also present in the SALK_142260 and SALK_054867 lines for At4g32460.

CONCLUSIONS

Our results suggested that the DUF642 family contributes to the complexity of the methylesterification process by participating in the fine regulation of pectin status during plant development.

Nuclear factor Y-mediated H3K27me3 demethylation of the SOC1 locus orchestrates flowering responses of Arabidopsis

Nuclear factor Y (NF-Y) is a conserved heterotrimeric transcription factor complex that binds to the CCAAT motifs within the promoter region of many genes. In plants, a large number of genes code for variants of each NF-YA, B or C subunit that can assemble in a combinatorial fashion. Here, we report the discovery of an Arabidopsis NF-Y complex that exerts epigenetic control over flowering time by integrating environmental and developmental signals. We show that NF-Y interacts with CONSTANS in the photoperiod pathway and DELLAs in the gibberellin pathway, to directly regulate the transcription of SOC1, a major floral pathway integrator. This NF-Y complex binds to a unique cis-element within the SOC1 promoter to modulate trimethylated H3K27 levels, partly through a H3K27 demethylase REF6. Our findings establish NF-Y complexes as critical mediators of epigenetic marks that regulate the response to environmental or intrinsic signals in plants.

Pathogen and circadian controlled 1 (PCC1) protein is anchored to the plasma membrane and interacts with subunit 5 of COP9 signalosome in Arabidopsis

The Pathogen and Circadian Controlled 1 (PCC1) gene, previously identified and further characterized as involved in defense to pathogens and stress-induced flowering, codes for an 81-amino acid protein with a cysteine-rich C-terminal domain. This domain is essential for homodimerization and anchoring to the plasma membrane. Transgenic plants with the ß-glucuronidase (GUS) reporter gene under the control of 1.1 kb promoter sequence of PCC1 gene display a dual pattern of expression. At early post-germination, PCC1 is expressed only in the root vasculature and in the stomata guard cells of cotyledons. During the transition from vegetative to reproductive development, PCC1 is strongly expressed in the vascular tissue of petioles and basal part of the leaf, and it further spreads to the whole limb in fully expanded leaves. This developmental pattern of expression together with the late flowering phenotype of long-day grown RNA interference (iPCC1) plants with reduced PCC1 expression pointed to a regulatory role of PCC1 in the photoperiod-dependent flowering pathway. iPCC1 plants are defective in light perception and signaling but are not impaired in the function of the core CO-FT module of the photoperiod-dependent pathway. The regulatory effect exerted by PCC1 on the transition to flowering as well as on other reported phenotypes might be explained by a mechanism involving the interaction with the subunit 5 of the COP9 signalosome (CSN).

A cis-element responsible for cGMP in the promoter of the soybean chalcone synthase gene

The cyclic nucleotides cGMP and cAMP have been reported to play key roles in the regulation of plant processes and responses. We have previously reported that several genes encoding flavonoid biosynthetic enzymes, including chalcone synthase (CHS) in soybean (Glycine max L.), were induced by cGMP but not cAMP. The soybean genome contains nine CHS gene copies (GmCHS1-9). We investigated the responsiveness of several GmCHS genes to cGMP, cAMP, NO, and white light. Quantitative RT-PCR analysis showed that the transcript levels of GmCHS7 and GmCHS8 were increased by 3.6- and 3.8-fold, respectively, with cGMP whereas the transcript levels of GmCHS2 remained constant. Although cAMP had no effect on the transcript levels of the three genes, NO had an activation effect on all three. White light activated the three genes in a transient manner, with GmCHS2, GmCHS7, and GmCHS8 transcript levels increasing 3-fold after 3 h and decreasing to basal levels after 9 h. The GmCHS8 promoter contains several important cis-elements, including the G-box and H-box forming the Unit-I-like sequence and the MYB binding sequence, a target of the GmMYB176 transcription factor regulating the expression of GmCHS8. A transient gene expression assay revealed the activation of the Unit-I-like sequence, but not of the MYB binding sequence, by cGMP. The combination of G-box and H-box was necessary for cGMP responsiveness. Taken together, these results suggest that the Unit-I-like sequence in the promoters of GmCHS7 and GmCHS8 is a cGMP responsive cis-element in these genes and that NO exerts its effect via cis-elements other than the Unit-I-like sequence.

Molecular basis and evolutionary pattern of GA-GID1-DELLA regulatory module

The tetracyclic diterpenoid carboxylic acids, gibberellins (GAs), orchestrate a broad spectrum of biological programs. In nature, GAs or GA-like substance is produced in bacteria, fungi, and plants. The function of GAs in microorganisms remains largely unknown. Phytohormones GAs mediate diverse growth and developmental processes through the life cycle of plants. The GA biosynthetic and metabolic pathways in bacteria, fungi, and plants are remarkably divergent. In vascular plants, phytohormone GA, receptor GID1, and repressor DELLA shape the GA-GID1-DELLA module in GA signaling cascade. Sequence reshuffling, functional divergence, and adaptive selection are main driving forces during the evolution of GA pathway components. The GA-GID1-DELLA complex interacts with second messengers and other plant hormones to integrate environmental and endogenous cues, which is beneficial to phytohormones homeostasis and other biological events. In this review, we first briefly describe GA metabolism pathway, signaling perception, and its second messengers. Then, we examine the evolution of GA pathway genes. Finally, we focus on reviewing the crosstalk between GA-GID1-DELLA module and phytohormones. Deciphering mechanisms underlying plant hormonal interactions are not only beneficial to addressing basic biological questions, but also have practical implications for developing crops with ideotypes to meet the future demand.

A cyclic nucleotide sensitive promoter reporter system suitable for bacteria and plant cells

BACKGROUND

Cyclic AMP (cAMP) and cyclic GMP (cGMP) have roles in relaying external signals and modifying gene expression within cells in all phyla. Currently there are no reporter systems suitable for bacteria and plant cells that measure alterations in downstream gene expression following changes in intracellular levels of cyclic nucleotides. As the plant protein OLIGOPEPTIDE TRANSPORTER X (OPTX) is upregulated by cGMP, we fused the OPTX promoter to a luciferase reporter gene (OPTX:LUC) to develop a plant cell reporter of cGMP-induced gene expression. We prepared a second construct augmented with three mammalian cGMP response elements (OPTXcGMPRE:LUC) and a third construct containing five gibberellic acid response elements (OPTXGARE:LUC). All three constructs were tested in bacteria and isolated plant protoplasts.

RESULTS

Membrane permeable cGMP enhanced luciferase activity of OPTX:LUC and OPTXGARE:LUC in protoplasts. Treatment with the plant hormone gibberellic acid which acts via cGMP also generated downstream luciferase activity. However, membrane permeable cAMP induced similar responses to cGMP in protoplasts. Significantly increased luciferase activity occurred in bacteria transformed with either OPTXcGMPRE:LUC or OPTXGARE:LUC in response to membrane permeable cAMP and cGMP. Bacteria co-transformed with OPTXcGMPRE:LUC or OPTXGARE:LUC and the soluble cytoplasmic domain of phytosulfokine receptor1 (PSKR1; a novel guanylate cyclase) had enhanced luciferase activity following induction of PSKR1 expression.

CONCLUSIONS

We have developed promoter reporter systems based on the plant OPTX promoter that can be employed in bacteria and isolated plant cells. We have shown that it can be used in bacteria to screen recombinant proteins for guanylate cyclase activity as increases in intracellular cGMP levels result in altered gene transcription and luciferase activity.

Both cyclic-AMP and cyclic-GMP can act as regulators of the phenylpropanoid pathway in Arabidopsis thaliana seedlings

Cyclic nucleotides (cAMP and cGMP) are important signaling molecules that control a range of cellular functions and modulate different reactions. It is known that under abiotic or biotic stress plant cells synthesize these nucleotides and that they also enhance the activity of the phenylpropanoid pathway. Wondering what is the relation between these two facts, we investigated how the exogenously applied membrane-permeable derivatives, 8-Br-cAMP or 8-Br-cGMP, which are believed to act as the original cyclic nucleotides, affect the expression of the genes for and the specific activity of three enzymes of the phenylpropanoid pathway in Arabidopsis thaliana seedlings. We found that the expression of the genes of phenylalanine ammonia-lyase (PAL2), 4-coumarate:coenzyme A ligase (4CL1) and chalcone synthase (CHS), and the specific activities of PAL (EC 4.3.1.5), 4CL (EC 6.2.1.12) and CHS (EC 2.3.1.74) were induced in the same way by either of these cyclic nucleotides used at 5 μM concentration. None of the possible cAMP and cGMP degradation products (AMP, GMP, adenosine or guanosine) evoked such effects. Expression of PAL1, 4CL2 and 4CL3 were practically not affected. Although the investigated nucleotides induced rapid expression of the aforementioned enzymes, they did not affect the level of anthocyanins within the same period. We discuss the effects exerted by the exogenously administered cyclic nucleotides, their relation with stress and the role which the phenylpropanoid pathways the cyclic nucleotides may play in plants.

Proteomic signatures implicate cAMP in light and temperature responses in Arabidopsis thaliana

The second messenger 3'-5'-cyclic adenosine monophosphate (cAMP) and adenylyl cyclases (ACs), enzymes that catalyse the formation of cAMP from ATP, are increasingly recognized as important signaling molecules in a number of physiological responses in higher plants. Here we used proteomics to identify cAMP-dependent protein signatures in Arabidopsis thaliana and identify a number of differentially expressed proteins with a role in light- and temperature-dependent responses, notably photosystem II subunit P-1, plasma membrane associated cation-binding protein and chaperonin 60 β. Based on these proteomics results we conclude that, much like in cyanobacteria, algae and fungi, cAMP may have a role in light signaling and the regulation of photosynthesis as well as responses to temperature and we speculate that ACs could act as light and/or temperature sensors in higher plants.

BIOLOGICAL SIGNIFICANCE

This current study is significant since it presents the first proteomic response to cAMP, a novel and key second messenger in plants. It will be relevant to researchers in plant physiology and in particular those with an interest in second messengers and their role in biotic and abiotic stress responses.

The cyclic nucleotide cGMP is involved in plant hormone signalling and alters phosphorylation of Arabidopsis thaliana root proteins

The cyclic nucleotide cGMP has been shown to play important roles in plant development and responses to abiotic and biotic stress. Yet much controversy remains regarding the exact role of this second messenger. Progress in unravelling cGMP function in plants was hampered by laborious and time-consuming methodology to measure changes in cellular [cGMP] but the development of fluorescence-based reporters has removed this disadvantage. This study used the FlincG cGMP reporter to investigate potential interactions between phytohormone and cGMP signalling and found a rapid and significant effect of the hormones abscisic acid (ABA), auxin (IAA), and jasmonic acid (JA) on cytoplasmic cGMP levels. In contrast, brassinosteroids and cytokinin did not evoke a cGMP signal. The effects of ABA, IAA, and JA were apparent at external concentrations in the nanomolar range with EC50 values of around 1000, 300, and 0.03 nmoles for ABA, IAA, and JA respectively. To examine potential mechanisms for how hormone-induced cGMP signals are propagated, the role of protein phosphorylation was tested. A phosphoproteomics analysis on Arabidopsis thaliana root microsomal proteins in the absence and presence of membrane-permeable cGMP showed 15 proteins that rapidly (within minutes) changed in phosphorylation status. Out of these, nine were previously shown to also alter phosphorylation status in response to plant hormones, pointing to protein phosphorylation as a target for hormone-induced cGMP signalling.

Identification of a novel Arabidopsis thaliana nitric oxide-binding molecule with guanylate cyclase activity in vitro

While there is evidence of nitric oxide (NO)-dependent signalling via the second messenger cyclic guanosine 3',5'-monophosphate (cGMP) in plants, guanylate cyclases (GCs), enzymes that catalyse the formation of cGMP from guanosine 5'-triphosphate (GTP) have until recently remained elusive and none of the candidates identified to-date are NO-dependent. Using both a GC and heme-binding domain specific (H-NOX) search motif, we have identified an Arabidopsis flavin monooxygenase (At1g62580) and shown electrochemically that it binds NO, has a higher affinity for NO than for O(2) and that this molecule can generate cGMP from GTP in vitro in an NO-dependent manner.

Endogenous NO levels regulate nodule functioning: potential role of cGMP in nodule functioning?

Nitric oxide is a small gaseous signaling molecule which functions in the regulation of plant development and responses to biotic and abiotic stresses. Recently, we have shown that nitric oxide is required for development of functional nodules. Here, we show that inhibition of nitric oxide synthase enzymatic activity (using N(ω)-nitro-L-arginine) reduces nitric oxide content in soybean root nodules and this is coupled by reduction of endogenous cyclic guanosine monophosphate content in the nodules. We postulate that the regulation of soybean nodule development by nitric oxide is transduced via cyclic guanosine monophosphate through activation of nitric oxide-responsive soluble guanylate cyclase. Furthermore, we hypothesize that this signaling cascade is mediated via modulation of the activities of antioxidant metabolic pathways.