A Possible Role for NDPK2 in the Regulation of Auxin-mediated Responses for Plant Growth and Development

Single-cell RNA sequencing reveals dynamics of gene expression for 2D elongation and 3D growth in Physcomitrium patens

The transition from two-dimensional (2D) to 3D growth likely facilitated plants to colonize land, but its heterogeneity is not well understood. In this study, we utilized single-cell RNA sequencing to analyze the moss Physcomitrium patens, whose morphogenesis involves a transition from 2D to 3D growth. We profiled over 17,000 single cells covering all major vegetative tissues, including 2D filaments (chloronema and caulonema) and 3D structures (bud and gametophore). Pseudotime analyses revealed larger numbers of candidate genes that determine cell fates for 2D tip elongation or 3D bud differentiation. Using weighted gene co-expression network analysis, we identified a module that connects β-type carbonic anhydrases (βCAs) with auxin. We further validated the cellular expression patterns of βCAs and demonstrated their roles in 3D gametophore development. Overall, our study provides insights into cellular heterogeneity in a moss and identifies molecular signatures that underpin the 2D-to-3D growth transition at single-cell resolution.

Genome-Wide Identification of NDPK Family Genes and Expression Analysis under Abiotic Stress in Brassica napus

The NDPK gene family is an important group of genes in plants, playing a crucial role in regulating energy metabolism, growth, and differentiation, cell signal transduction, and response to abiotic stress. However, our understanding of the NDPK gene family in Brassica napus L. remains limited. This paper systematically analyzes the NDPK gene family in B. napus, particularly focusing on the evolutionary differences within the species. In this study, sixteen, nine, and eight NDPK genes were identified in B. napus and its diploid ancestors, respectively. These genes are not only homologous but also highly similar in their chromosomal locations. Phylogenetic analysis showed that the identified NDPK proteins were divided into four clades, each containing unique motif sequences, with most NDPKs experiencing a loss of introns/exons during evolution. Collinearity analysis revealed that the NDPK genes underwent whole-genome duplication (WGD) events, resulting in duplicate copies, and most of these duplicate genes were subjected to purifying selection. Cis-acting element analysis identified in the promoters of most NDPK genes elements related to a light response, methyl jasmonate response, and abscisic acid response, especially with an increased number of abscisic acid response elements in B. napus. RNA-Seq results indicated that NDPK genes in B. napus exhibited different expression patterns across various tissues. Further analysis through qRT-PCR revealed that BnNDPK genes responded significantly to stress conditions such as salt, drought, and methyl jasmonate. This study enhances our understanding of the NDPK gene family in B. napus, providing a preliminary theoretical basis for the functional study of NDPK genes and offering some references for further revealing the phenomenon of polyploidization in plants.

Mitochondria-Associated Protein FgNdk1 Regulates the Development, Pathogenicity, and SDHI Fungicide Sensitivity of Fusarium graminearum by Interacting with Succinate Dehydrogenase

Nucleoside diphosphate kinase (NDK) plays an important role in many cellular processes in all organisms. In this study, we functionally characterized a nucleoside diphosphate kinase (FgNdk1) in Fusarium graminearum, a causal agent of Fusarium head blight (FHB). FgNdk1 was involved in the generation of energy in the electron-transfer chain by interacting with succinate dehydrogenase (FgSdhA, FgSdhC1, and FgSdhC2). Deletion of FgNdk1 not only resulted in abnormal mitochondrial morphology, decreased ATP content, defective fungal development, and impairment in the formation of the toxisome but also led to the suppressed expression level of DON biosynthesis enzymes, decreased DON biosynthesis, and declined pathogenicity as well. Furthermore, deletion of FgNdk1 caused increasing transcriptional levels of FgSdhC1 and FgdhC2, in the presence of pydiflumetofen, related to the decreased sensitivity to SDHI fungicides. Overall, this study identified a new regulatory mechanism of FgNdk1 in the pathogenicity and SDHI fungicide sensitivity of Fusarium graminearum.

Molecular prospective on the wheat grain development

Wheat grain development is an important biological process to determine grain yield and quality, which is controlled by the interplay of genetic, epigenetic, and environmental factors. Wheat grain development has been extensively characterized at the phenotypic and genetic levels. The advent of innovative molecular technologies allows us to characterize genes, proteins, and regulatory factors involved in wheat grain development, which have enhanced our understanding of the wheat seed development process. However, wheat is an allohexaploid with a large genome size, the molecular mechanisms underlying the wheat grain development have not been well understood as those in diploids. Understanding grain development, and how it is regulated, is of fundamental importance for improving grain yield and quality through conventional breeding or genetic engineering. Herein, we review the current discoveries on the molecular mechanisms underlying wheat grain development. Notably, only a handful of genes that control wheat grain development have, thus far, been well characterized, their interplay underlying the grain development remains elusive. The synergistic network-integrated genomics and epigenetics underlying wheat grain development and how the subgenome divergence dynamically and precisely regulates wheat grain development are unknown.

Genetic Dissection of Root Angle of Brassica napus in Response to Low Phosphorus

Plant root angle determines the vertical and horizontal distribution of roots in the soil layer, which further influences the acquisition of phosphorus (P) in topsoil. Large genetic variability for the lateral root angle (root angle) was observed in a linkage mapping population (BnaTNDH population) and an association panel of Brassica napus whether at a low P (LP) or at an optimal P (OP). At LP, the average root angle of both populations became smaller. Nine quantitative trait loci (QTLs) at LP and three QTLs at OP for the root angle and five QTLs for the relative root angle (RRA) were identified by the linkage mapping analysis in the BnaTNDH population. Genome-wide association studies (GWASs) revealed 11 single-nucleotide polymorphisms (SNPs) significantly associated with the root angle at LP (LPRA). The interval of a QTL for LPRA on A06 (qLPRA-A06c) overlapped with the confidence region of the leading SNP (Bn-A06-p14439400) significantly associated with LPRA. In addition, a QTL cluster on chromosome C01 associated with the root angle and the primary root length (PRL) in the "pouch and wick" high-throughput phenotyping (HTP) system, the root P concentration in the agar system, and the seed yield in the field was identified in the BnaTNDH population at LP. A total of 87 genes on A06 and 192 genes on C01 were identified within the confidence interval, and 14 genes related to auxin asymmetric redistribution and root developmental process were predicted to be candidate genes. The identification and functional analyses of these genes affecting LPRA are of benefit to the cultivar selection with optimal root system architecture (RSA) under P deficiency in Brassica napus.

A nucleoside diphosphate kinase gene OsNDPK4 is involved in root development and defense responses in rice (Oryza sativa L.)

Dysfunctional mutation of OsNDPK4 resulted in severe defects in root development of rice. However, the resistance of Osndpk4 against bacterial blight was significantly enhanced. Nucleoside diphosphate kinases (NDPKs) are an evolutionarily conserved family of important enzymes balancing the energy currency nucleoside triphosphates by catalyzing the transfer of their phosphate groups. The aim of this study was to elucidate the function of OsNDPK4 in rice. A dysfunctional rice mutant was employed to characterize the function of OsNDPK4. Its expression and subcellular localization were examined. The transcriptomic change in roots of Osndpk4 was analyzed by RNA-seq. The rice mutant Osndpk4 showed severe defects in root development from the early seedling stage. Further analysis revealed that meristematic activity and cell elongation were significantly inhibited in primary roots of Osndpk4, together with reduced accumulation of reactive oxygen species (ROS). Map-based cloning identified that the mutation occurred in the OsNDPK4 gene. OsNDPK4 was found to be expressed in a variety of tissues throughout the plant and OsNDPK4 was located in the cytosol. Osndpk4 showed enhanced resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo) and up-regulation of pathogenesis-related marker genes. In addition, transcriptomic analysis showed that OsNDPK4 was significantly associated with a number of biological processes, including translation, protein modification, metabolism, biotic stress response, etc. Detailed analysis revealed that the dysfunction of OsNDPK4 might reorchestrate energy homeostasis and hormone metabolism and signalling, resulting in repression of translation, DNA replication and cell cycle progression, and priming of biotic stress defense. Our results demonstrate that OsNDPK4 plays important roles in energy homeostasis, development process, and defense responses in rice.

Biological impacts of phosphomimic AtMYB75

The phosphorylation status of MYB75 at T-131 affects protein stability, flavonoid profiles, and patterns of gene expression. The Arabidopsis transcription factor Myeloblastosis protein 75 (MYB75, AT1G56650) is known to act as a positive transcriptional regulator of genes required for flavonoid and anthocyanin biosynthesis. MYB75 was also shown to negatively regulate lignin and other secondary cell wall biosynthetic genes (Bhargava et al. in Plant Physiol 154(3):1428-1438, 2010). While transcriptional regulation of MYB75 has been described in numerous publications, little is known about post-translational control of MYB75 protein function. In a recent publication, light-induced activation of a MAP kinase (MPK4, AT4G01370) in Arabidopsis was reported to lead to MYB75 phosphorylation at two canonical MPK target sites, threonines, T-126 and T-131. This double phosphorylation event positively influenced MYB75 protein stability (Li et al. in Plant Cell 28(11):2866-2883, 2016). We have examined this phenomenon through use of phosphomutant forms of MYB75 and found that MYB75 is phosphorylated primarily at T-131, and that the phosphorylation of MYB75 recombinant protein in vitro can be catalyzed by multiple MAP kinases, including MPK3 (AT3G45640), MPK6 (AT2G43790), MPK4 and MPK11 (AT1G01560). We also demonstrate that MYB75 can bind to a large number of Arabidopsis MPK's in vitro, suggesting it could be a target of multiple signalling pathways. The impact of MYB75 phosphorylation at T-131 on the function of this transcription factor, in terms of localization, stability, and protein-protein interactions with known binding partners was examined in transgenic lines expressing phosphomimic and phosphonull versions of MYB75, to capture the behaviour of permanently phosphorylated and unphosphorylated MYB75 protein, respectively. In addition, we describe how ectopic over-expression of different phosphovariant forms of MYB75 (MYB75^WT, MYB75^T131A, and MYB75^T131E) affects flavonoid biochemical profiles and global changes of gene expression in the corresponding transgenic Arabidopsis plants.

Comparative proteomic analysis provides new insights into the specialization of shoots and stolons in bermudagrass (Cynodon dactylon L.)

Background

Bermudagrass (Cynodon dactylon L.) is an important turfgrass species with two types of stems, shoots and stolons. Despite their importance in determining the morphological variance and plasticity of bermudagrass, the intrinsic differences between stolons and shoots are poorly understood.

Results

In this study, we compared the proteomes of internode sections of shoots and stolons in the bermudagrass cultivar Yangjiang. The results indicated that 376 protein species were differentially accumulated in the two types of stems. Pathway enrichment analysis revealed that five and nine biochemical pathways were significantly enriched in stolons and shoots, respectively. Specifically, enzymes participating in starch synthesis all preferentially accumulated in stolons, whereas proteins involved in glycolysis and diverse transport processes showed relatively higher abundance in shoots. ADP-glucose pyrophosphorylase (AGPase) and pyruvate kinase (PK), which catalyze rate-limiting steps of starch synthesis and glycolysis, showed high expression levels and enzyme activity in stolons and shoots, respectively, in accordance with the different starch and soluble sugar contents of the two types of stems.

Conclusions

Our study revealed the differences between the shoots and stolons of bermudagrass at the proteome level. The results not only expand our understanding of the specialization of stolons and shoots but also provide clues for the breeding of bermudagrass and other turfgrasses with different plant architectures.

Supplementary material

Supplementary information accompanies this paper at 10.1186/s12864-019-6077-3.

Functional analyses of NDPK2 in Populus trichocarpa and overexpression of PtNDPK2 enhances growth and tolerance to abiotic stresses in transgenic poplar

Nucleoside diphosphate kinases (NDPKs) are multifunctional proteins that regulate a variety of eukaryotic cellular activities, including cell proliferation, development, and differentiation. NDPK2 regulates the expression of antioxidant genes in plants. In a previous study, the Arabidopsis thaliana NDPK2 gene (AtNDPK2) was found to be associated with H₂O₂-mediated mitogen-activated protein kinase signaling in Arabidopsis thaliana. Proteins from transgenic plants overexpressing AtNDPK2 showed higher levels of autophosphorylation and NDPK activity and lower levels of reactive oxygen species (ROS) than those of wild-type (WT) plants. Therefore, constitutive overexpression of AtNDPK2 in Arabidopsis plants conferred enhanced tolerance to multiple environmental stresses that elicit ROS accumulation in situ. In this study, we cloned the Populus trichocarpa NDPK2 gene and analyzed its molecular structure and function. We generated and evaluated transgenic poplar plants expressing the PtNDPK2 gene under the control of the 35S promoter to achieve enhanced tolerance to various abiotic stresses. Transgenic poplar plants showed enhanced tolerance to salt and drought stress at the whole-plant level. The transgenic poplar plants showed significantly greater tolerance to 200 mM NaCl and drought stresses than WT poplar plants. In addition, the transgenic plants exhibited better growth due to increased expression of auxin-related indole acetic acid genes under normal growth conditions compared with WT plants. Our results suggest that induction of PtNDPK2 overexpression in poplars will be useful for increasing biomass production in the presence of various abiotic stresses.

Proteomics analysis of maize (Zea mays L.) grain based on iTRAQ reveals molecular mechanisms of poor grain filling in inferior grains

In maize, inferior grains (IG) located on the upper part of the ear have poor grain filling process compared to superior grains (SG) located on the middle and lower parts of the ear. This difference limits satisfactory yield and quality; however, the underlying molecular mechanisms remain unknown. Here, using the isobaric tag for relative and absolute quantification (iTRAQ) technology, the proteomes of IG and SG during early and middle grain filling stages were investigated. In total, 4720 proteins were identified in maize grain and 305 differentially accumulated proteins (DiAPs) were detected between IG and SG. These DiAPs were involved in diverse cellular and metabolic processes with preferred distribution in protein synthesis/destination and metabolism. Compared to SG, DiAPs related to cell growth/division and starch synthesis were lag-accumulated and down-regulated in IG, respectively, resulting in smaller sink sizes and lower sink activities in IG. Meanwhile, impediment of the glycolysis pathway in IG may lead to reduce energy supply and building materials for substance synthesis. Additionally, reactive oxygen species (ROS) homeostasis and the defense system were disturbed in IG, which might lead to reduce protection against various environmental stresses. The present study provides new information on the proteomic differences between IG and SG, and explains possible molecular mechanisms for poor grain filling in IG.

Protein Transphosphorylation During the Mutual Interaction between Phytochrome A and a Nuclear Isoform of Nucleoside Diphosphate Kinase Is Regulated by Red Light

The nuclear isoform of nucleoside diphosphate kinase isoenzyme NDPK-I_n undergoes strong catalytic activation upon its interaction with the active form of phytochrome A (Pfr) in red light. The autophosphorylation or intermolecular transphosphorylation of NDPK-I_n leads to the formation of phosphoester bonds stable in acidic solution. The phosphate residue of the phosphamide bond in the active center of NDPK-I_n can also be transferred to serine and threonine residues localized in other proteins, including phytochrome A. Phytochrome A, similarly to NDPK-I_n, undergoes autophosphorylation on serine and threonine residues and can phosphorylate some potential substrate proteins. The physical interaction between phytochrome A in the Pfr form and NDPK-I_n results in a significant increase in the kinase activity of NDPK-I_n. The results presented in this work indicate that NDPK-I_n may function as a protein kinase regulated by light.

White stripe leaf 12 (WSL12), encoding a nucleoside diphosphate kinase 2 (OsNDPK2), regulates chloroplast development and abiotic stress response in rice (Oryza sativa L.)

Chloroplast is a crucial organelle for plant photosynthesis and maintaining normal life activities in higher plants. Although some genes related to chloroplast development and pigment synthesis have been identified or cloned in rice, little is known about the relationship between these genes and abiotic stress response. In this study, we identified a novel mutant white stripe leaf 12 (wsl12) affecting pigment synthesis, chloroplast development and abiotic stress response in rice. The mutant phenotype was obvious at seeding and tillering stages and in response to the temperature change. Genetic analysis of reciprocal crosses between wsl12 and wild-type plants showed that wsl12 was a recessive mutant in a single nuclear locus. Map-based cloning revealed that the WSL12 locus encoded OsNDPK2, one of the three nucleoside diphosphate kinases (OsNDPKs). WSL12 expressed in all tested tissues, while it highly expressed in leaves and young tissues. The WSL12 protein localized to the chloroplast. The wsl12 mutant showed higher superoxide anion level and enhanced sensitivity to abscisic acid (ABA) and salinity. The transcription pattern of many genes involved in chlorophyll biosynthesis, ABA synthesis, light signaling pathway, reactive oxygen species-scavenging pathway and the other two OsNDPKs was altered in the wsl12 mutant. These results indicate that the OsNDPK2 encoded by WSL12 plays an important role in chloroplast development and chlorophyll biosynthesis by regulating the expression levels of related genes. In addition, WSL12 also affects the response to abiotic stress, such as ABA and salinity in rice, and is beneficial to molecular breeding of stress tolerance.

Transgenic alfalfa plants expressing AtNDPK2 exhibit increased growth and tolerance to abiotic stresses

In this study, we generated and evaluated transgenic alfalfa plants (Medicago sativa L. cv. Xinjiang Daye) expressing the Arabidopsis nucleoside diphosphate kinase 2 (AtNDPK2) gene under the control of the oxidative stress-inducible SWPA2 promoter (referred to as SN plants) to develop plants with enhanced tolerance to various abiotic stresses. We selected two SN plants (SN4 and SN7) according to the expression levels of AtNDPK2 and the enzyme activity of NDPK in response to methyl viologen (MV)-mediated oxidative stress treatment using leaf discs for further characterization. SN plants showed enhanced tolerance to high temperature, NaCl, and drought stress on the whole-plant level. When the plants were subjected to high temperature treatment (42 °C for 24 h), the non-transgenic (NT) plants were severely wilted, whereas the SN plants were not affected because they maintained high relative water and chlorophyll contents. The SN plants also showed significantly higher tolerance to 250 mM NaCl and water stress treatment than the NT plants. In addition, the SN plants exhibited better plant growth through increased expression of auxin-related indole acetic acid (IAA) genes (MsIAA3, MsIAA5, MsIAA6, MsIAA7, and MsIAA16) under normal growth conditions compared to NT plants. The results suggest that induced overexpression of AtNDPK2 in alfalfa will be useful for increasing biomass production under various abiotic stress conditions.

Clues to the functions of plant NDPK isoforms

This review describes the five nucleoside diphosphate kinase (NDPK) genes found in both model plants Arabidopsis thaliana (thale cress) and Oryza sativa L. (rice). Phylogenetic and sequence analyses of these genes allow the definition of four types of NDPK isoforms with different predicted subcellular localization. These predictions are supported by experimental evidence for most NDPK types. Data mining also provides evidence for the existence of a novel NDPK type putatively localized in the endoplasmic reticulum. Phylogenic analyses indicate that plant types I, II, and III belong to the previously identified Nme group I whereas type IV belongs to Nme group II. Additional analysis of the literature offers clues supporting the idea that the various plant NDPK types have different functions. Hence, cytosolic type I NDPKs are involved in metabolism, growth, and stress responses. Type II NDPKs are localized in the chloroplast and mainly involved in photosynthetic development and oxidative stress management. Type III NDPKs have dual targeting to the mitochondria and the chloroplast and are principally involved in energy metabolism. The subcellular localization and precise function of the novel type IV NDPKs, however, will require further investigations.

A functional TOC complex contributes to gravity signal transduction in Arabidopsis

Although plastid sedimentation has long been recognized as important for a plant's perception of gravity, it was recently shown that plastids play an additional function in gravitropism. The Translocon at the Outer envelope membrane of Chloroplasts (TOC) complex transports nuclear-encoded proteins into plastids, and a receptor of this complex, Toc132, was previously hypothesized to contribute to gravitropism either by directly functioning as a gravity signal transducer or by indirectly mediating the plastid localization of a gravity signal transducer. Here we show that mutations in multiple genes encoding TOC complex components affect gravitropism in a genetically sensitized background and that the cytoplasmic acidic domain of Toc132 is not required for its involvement in this process. Furthermore, mutations in TOC132 enhance the gravitropic defect of a mutant whose amyloplasts lack starch. Finally, we show that the levels of several nuclear-encoded root proteins are altered in toc132 mutants. These data suggest that the TOC complex indirectly mediates gravity signal transduction in Arabidopsis and support the idea that plastids are involved in gravitropism not only through their ability to sediment but also as part of the signal transduction mechanism.

Temporal analysis of poplar woody root response to bending stress

Temperate perennial woody plants use different environmental signals to coordinate their growth and development in relation to seasonal changes. Preliminary evidences suggest that, even during dormancy, plants maintain effective metabolic activities and molecular mechanisms ensuring them an eventual recording of mechanical loads during winter times. Despite their great importance for productivity and survival, plant biology investigations have poorly characterized the root growth cycle and its response to environmental stresses. In this study, we describe the proteomic changes occurring over the time in poplar root either in the absence or in response to a bending stress; corresponding expression of cell cycle regulator and auxin transporter genes was also evaluated by reverse transcription polymerase chain reaction analysis. Our results confirm previous evidences on the effect of the bending stress on the anticipation of root growth resumption, providing additional insights on a temporal modulation of various plant metabolic processes involved in dormancy break, growth resumption and stress response in the bent root; these events seem related to the differential compression and tension force distribution occurring over the plant taproot.

Initial characterization of shade avoidance response suggests functional diversity between Populus phytochrome B genes

Shade avoidance signaling involves perception of incident red/far-red (R/FR) light by phytochromes (PHYs) and modulation of downstream transcriptional networks. Although these responses are well studied in Arabidopsis, little is known about the role of PHYs and the transcriptional responses to shade in the woody perennial Populus. Tissue expression and subcellular localization of Populus PHYs was studied by quantitative real-time PCR (qRT-PCR) and protoplast transient assay. Transgenic lines with altered PHYB1 and/or PHYB2 expression were used in phenotypic assays and transcript profiling with qRT-PCR. RNA-Seq was used to identify transcriptional responses to enriched FR light. All three PHYs were differentially expressed among tissue types and PHYBs were targeted to the nucleus under white light. Populus PHYB1 rescued Arabidopsis phyB mutant phenotypes. Phenotypes of Populus transgenic lines and the expression of candidate shade response genes suggested that PHYB1 and PHYB2 have distinct yet overlapping functions. RNA-Seq analysis indicated that genes associated with cell wall modification and brassinosteroid signaling were induced under enriched FR light in Populus. This study is an initial attempt at deciphering the role of Populus PHYs by evaluating transcriptional reprogramming to enriched FR and demonstrates functional diversity and overlap of the Populus PHYB1 and PHYB2 in regulating shade responses.

Proteome characterization of developing grains in bread wheat cultivars (Triticum aestivum L.)

BACKGROUND

The analyses of protein synthesis, accumulation and regulation during grain development in wheat are more complex because of its larger genome size compared to model plants such as Arabidopsis and rice. In this study, grains from two wheat cultivars Jimai 20 and Zhoumai 16 with different gluten quality properties were harvested at five development stages, and were used to displayed variable expression patterns of grain proteins.

RESULTS

Proteome characterization during grain development in Chinese bread wheat cultivars Jimai 20 and Zhoumai 16 with different quality properties was investigated by 2-DE and tandem MALDI-TOF/TOF-MS. Identification of 117 differentially accumulated protein spots representing 82 unique proteins and five main expression patterns enabled a chronological description of wheat grain formation. Significant proteome expression differences between the two cultivars were found; these included 14 protein spots that accumulated in both cultivars but with different patterns and 27 cultivar-different spots. Among the cultivar-different protein spots, 14 accumulated in higher abundance in Jimai 20 than in Zhoumai 16, and included NAD-dependent isocitrate dehydrogenase, triticin precursor, LMW-s glutenin subunit and replication factor C-like protein. These proteins are likely to be associated with superior gluten quality. In addition, some proteins such as class II chitinase and peroxidase 1 with isoforms in developing grains were shown to be phosphorylated by Pro-Q Diamond staining and phosphorprotein site prediction. Phosphorylation could have important roles in wheat grain development. qRT-PCR analysis demonstrated that transcriptional and translational expression patterns of many genes were significantly different.

CONCLUSIONS

Wheat grain proteins displayed variable expression patterns at different developmental stages and a considerable number of protein spots showed differential accumulation between two cultivars. Differences in seed storage proteins were considered to be related to different quality performance of the flour from these wheat cultivars. Some proteins with isoforms were phosphorylated, and this may reflect their importance in grain development. Our results provide new insights into proteome characterization during grain development in different wheat genotypes.

Proteome characterization of developing grains in bread wheat cultivars (Triticum aestivum L.)

BACKGROUND

The analyses of protein synthesis, accumulation and regulation during grain development in wheat are more complex because of its larger genome size compared to model plants such as Arabidopsis and rice. In this study, grains from two wheat cultivars Jimai 20 and Zhoumai 16 with different gluten quality properties were harvested at five development stages, and were used to displayed variable expression patterns of grain proteins.

RESULTS

Proteome characterization during grain development in Chinese bread wheat cultivars Jimai 20 and Zhoumai 16 with different quality properties was investigated by 2-DE and tandem MALDI-TOF/TOF-MS. Identification of 117 differentially accumulated protein spots representing 82 unique proteins and five main expression patterns enabled a chronological description of wheat grain formation. Significant proteome expression differences between the two cultivars were found; these included 14 protein spots that accumulated in both cultivars but with different patterns and 27 cultivar-different spots. Among the cultivar-different protein spots, 14 accumulated in higher abundance in Jimai 20 than in Zhoumai 16, and included NAD-dependent isocitrate dehydrogenase, triticin precursor, LMW-s glutenin subunit and replication factor C-like protein. These proteins are likely to be associated with superior gluten quality. In addition, some proteins such as class II chitinase and peroxidase 1 with isoforms in developing grains were shown to be phosphorylated by Pro-Q Diamond staining and phosphorprotein site prediction. Phosphorylation could have important roles in wheat grain development. qRT-PCR analysis demonstrated that transcriptional and translational expression patterns of many genes were significantly different.

CONCLUSIONS

Wheat grain proteins displayed variable expression patterns at different developmental stages and a considerable number of protein spots showed differential accumulation between two cultivars. Differences in seed storage proteins were considered to be related to different quality performance of the flour from these wheat cultivars. Some proteins with isoforms were phosphorylated, and this may reflect their importance in grain development. Our results provide new insights into proteome characterization during grain development in different wheat genotypes.

Transgenic poplar expressing Arabidopsis NDPK2 enhances growth as well as oxidative stress tolerance

Nucleoside diphosphate kinase 2 (NDPK2) is known to regulate the expression of antioxidant genes in plants. Previously, we reported that overexpression of Arabidopsis NDPK2 (AtNDPK2) under the control of an oxidative stress-inducible SWPA2 promoter in transgenic potato and sweetpotato plants enhanced tolerance to various abiotic stresses. In this study, transgenic poplar (Populus alba × Poplus glandulosa) expressing the AtNDPK2 gene under the control of a SWPA2 promoter (referred to as SN) was generated to develop plants with enhanced tolerance to oxidative stress. The level of AtNDPK2 expression and NDPK activity in SN plants following methyl viologen (MV) treatment was positively correlated with the plant's tolerance to MV-mediated oxidative stress. We also observed that antioxidant enzyme activities such as ascorbate peroxidase, catalase and peroxidase were increased in MV-treated leaf discs of SN plants. The growth of SN plants was substantially increased under field conditions including increased branch number and stem diameter. SN plants exhibited higher transcript levels of the auxin-response genes IAA2 and IAA5. These results suggest that enhanced AtNDPK2 expression affects oxidative stress tolerance leading to improved plant growth in transgenic poplar.

Heat shock modulates phosphorylation status and activity of nucleoside diphosphate kinase in cultured sugarcane cells

Nucleoside diphosphate kinase (NDPK) is involved in the regeneration of nucleoside triphosphates (NTPs) through its phosphotransferase activity via an autophosphorylating histidine residue. Additionally, autophosphorylation of serine and/or threonine residues is documented for NDPKs from various organisms. However, the metabolic significance of serine/threonine phosphorylation has not been well characterized. In this study we report the cloning and characterization of NDPKI from cultured sugarcane (Saccharum officinarum L. line H50-7209) cells, and modulation of serine autophosphorylation of NDPK1 in response to heat-shock (HS). Heat-shock treatment at 40°C for 2 h resulted in a 40% reduction in labeled phosphoserine in NDPK1. This dephosphorylation was accompanied by an increase in NDPK enzyme activity. In contrast, NDPK1 in cultured tobacco (cv. W-38) cells did not show changes in autophosphorylation or increased enzyme activity in response to HS. The mRNA or protein level of NDPK1 did not increase in response to HS. Sugarcane cells sustain the constitutive protein synthesis in addition to heat-shock protein synthesis during HS, while constitutive protein synthesis is significantly reduced in tobacco cells during HS. Thus, HS modulation of NDPK1 activity and serine dephosphorylation in sugarcane cells may represent an important physiological role in maintaining cellular metabolic functions during heat stress.

ROS resistance in Pisum sativum cv. Alaska: the involvement of nucleoside diphosphate kinase in oxidative stress responses via the regulation of antioxidants

This study investigated the reactive oxygen species (ROS) tolerance mechanism of a paraquat-resistant Pisum sativum line (R3-1) compared with the wild type (WT). Physiological and biochemical analyses showed significant differences in the phenotypes, such as delayed leaf and floral development, superior branching, and greater biomass and yields in the R3-1 line, as well as an increased level of antioxidant pigments and a lower rate of cellular lipid peroxidation in the resistant R3-1. Additionally, the phosphorylation of crude proteins showed distinguishable differences in band mobility and intensity between the R3-1 and WT plants. cDNA cloning and sequence analysis of NDPKs, which were candidate phosphorylated proteins, revealed that two of the deduced amino acids in NDPK2 (IL12L and Glu205Lys) and one in NDPK3 (P45S) were mutated in R3-1. Using glutathione S-transferase-NDPK fusion constructs, we found that the precursor recombinant R3-1 NDPK2 showed an increased level of activity and autophosphorylation in R3-1 plants compared to WT plants. Native PAGE analysis of the crude proteins revealed that NDPK and catalase (CAT) activity co-existed in the same area of the gel. In a yeast two-hybrid assay, the N-terminal region of NDPK2 showed an interaction with the full-length CAT1 protein. Furthermore, we found that WT showed a decreased level of CAT activity compared with R3-1 under illumination and/or on media containing ROS-releasing reagents. Taken together, these results suggest that there is a strong interaction between NDPK2 and CAT1 in R3-1 plants, which possibly plays a vital role in the antioxidant defense against ROS.

Arabidopsis nucleoside diphosphate kinase-2 as a plant GTPase activating protein

Nucleoside diphosphate kinase (NDPK) is involved in multiple signaling pathways in mammalian systems, including G-protein signaling. Arabidopsis NDPK2, like its mammalian counterparts, is multifunctional despite its initial discovery phytochrome-interacting protein. This similarity raises the possibility that NDPK2 may play a role in G-protein signaling in plants. In the present study, we explore the potential relationship between NDPK2 and the small G proteins, Pra2 and Pra3, as well as the heterotrimeric G protein, GPA1. We report a physical interaction between NDPK2 and these small G proteins, and demonstrate that NDPK2 can stimulate their GTPase activities. Our results suggest that NDPK2 acts as a GTPase-activating protein for small G proteins in plants. We propose that NDPK2 might be a missing link between the phytochromemediated light signaling and G protein-mediated signaling.

The expression of tomato prosystemin gene in tobacco plants highly affects host proteomic repertoire

Systemin, an octadecapeptide isolated from tomato, is a primary signal molecule involved in the local and systemic responses to pest attack, elicited by activation of a set of defence genes. It derives from processing of prosystemin, a prohormone of almost 200 amino acids. Prosystemin orthologues have been found in other Solanaceae species but not in tobacco, where are present hydroxyproline-rich peptides functionally but not structurally related to tomato systemin. Molecular events leading to the release of signalling peptides from protein precursors are unknown in plants; the occurrence of a family of signal molecules suggests that initiation of wound response may involve different processing mechanisms. It has been previously shown that the protein product from an engineered tomato prosystemin gene is processed in tobacco, thus suggesting that the components responsible for its post-translational modifications are present in this species. By analyzing analysing the proteome repertoire of transformed tobacco plant leaves with 2-DE, here we demonstrate that the constitutive expression of the tomato prosystemin gene highly affected host protein synthesis. In particular, engineered plants showed a number of differentially synthesized proteins that were identified by PMF MALDI-TOF and microLC-ESI-IT-MS/MS experiments as polypeptide species involved in protection from pathogens and oxidative stress, or in carbon/energy metabolism. Significant differences in over-produced proteins were observed with respect to previous data reported on systemin-engineered tomato plants. Our results strongly support the need of using proteomic approaches during systematic analysis of plant tissues to investigate the principle of substantial equivalence in transgenic plants expressing a transgene coding for a signalling molecule.

Interaction of SOS2 with nucleoside diphosphate kinase 2 and catalases reveals a point of connection between salt stress and H2O2 signaling in Arabidopsis thaliana

SOS2, a class 3 sucrose-nonfermenting 1-related kinase, has emerged as an important mediator of salt stress response and stress signaling through its interactions with proteins involved in membrane transport and in regulation of stress responses. We have identified additional SOS2-interacting proteins that suggest a connection between SOS2 and reactive oxygen signaling. SOS2 was found to interact with the H2O2 signaling protein nucleoside diphosphate kinase 2 (NDPK2) and to inhibit its autophosphorylation activity. A sos2-2 ndpk2 double mutant was more salt sensitive than a sos2-2 single mutant, suggesting that NDPK2 and H2O2 are involved in salt resistance. However, the double mutant did not hyperaccumulate H2O2 in response to salt stress, suggesting that it is altered signaling rather than H2O2 toxicity alone that is responsible for the increased salt sensitivity of the sos2-2 ndpk2 double mutant. SOS2 was also found to interact with catalase 2 (CAT2) and CAT3, further connecting SOS2 to H2O2 metabolism and signaling. The interaction of SOS2 with both NDPK2 and CATs reveals a point of cross talk between salt stress response and other signaling factors including H2O2.

Localisation of Arabidopsis NDPK2--revisited

Phytochromes are light responsive photoreceptors in plants that influence development and differentiation during the entire plant life cycle. Plant nucleoside diphosphate kinase 2 (NDPK2) has been reported to be a component of the light-mediated signalling cascade and to interact physically with phytochrome A in the cytosol. By using diverse methods as in vitro imports, in vivo localisation of GFP-fusion proteins and immuno blotting of plant cell fractions we clearly localise NDPK2 only to chloroplasts but not to the cytosol, demonstrating that although high affinity protein-protein interactions can occur in vitro, their physiological relevance can be artificial if the proteins are localised to different cell compartments in vivo.

Arabidopsis MEKK1 can take a short cut: it can directly interact with senescence-related WRKY53 transcription factor on the protein level and can bind to its promoter

Despite the importance of the senescence processes in plants, our knowledge on regulatory mechanisms of senescence is still poor. WRKY transcription factors have been shown to be involved in the regulation of leaf senescence. However, almost nothing is known about the upstream regulation of the senescence specific expression of WRKY factors. Therefore, we characterized proteins that bind and activate the promoter of WRKY53, which participates in leaf senescence in Arabidopsis thaliana. Surprisingly, a mitogen activated protein kinase kinase kinase (MEKK1) was identified as a DNA-binding protein. The binding motif for MEKK1 in the WRKY53 promoter could be characterized and promoter:GUS analyses revealed that this region is important for the switch of WRKY53 expression from a leaf age dependent to a systemic plant age dependent expression during bolting time. In addition to its promotor-binding activity, MEKK1 was also able to interact with the WRKY53 protein. Using bimolecular fluorescence complementation assays the complex formation of MEKK1 and WRKY53 could be localized predominately in the nucleus of Arabidopsis cells. MEKK1 could also phosphorylate WRKY53 in vitro and phosphorylation could increase DNA-binding activity of WRKY53 in vitro and transcription of a WRKY53 promoter driven reporter gene in vivo. These results suggest that MEKK1 is a bifunctional protein: it binds to the promoter of the WRKY53 gene regulating the switch from a leaf age dependent to a plant age dependent expression and it can phosopharylate WRKY53 in vitro increasing its DNA binding activity. Thus, MEKK1 might be able to take a very direct short cut in mitogen-activated protein kinase (MAPK) signalling by directly phosphorylating a transcription factor.

Glutathione S-transferase interacting with far-red insensitive 219 is involved in phytochrome A-mediated signaling in Arabidopsis

Far-red (FR) insensitive 219 (FIN219) was previously shown to be involved in phytochrome A-mediated FR light signaling. To further understand its function and regulatory relation with other light-signaling components, a yeast two-hybrid approach was used to isolate FIN219-interacting partners. Here, we demonstrate that FIN219-interacting protein 1 (FIP1) interacts with FIN219 in vitro and in vivo and is composed of 217 amino acids that belong to the tau class of the large glutathione S-transferase gene family. FIP1 was further shown to have glutathione S-transferase activity. The gain of function and partial loss of function of FIP1 resulted in a hyposensitive hypocotyl phenotype under continuous FR (cFR) light and a delayed flowering phenotype under long-day conditions, which suggests that FIP1 may exist in a complex to function in the regulation of Arabidopsis (Arabidopsis thaliana) development. In addition, FIP1 mRNA was down-regulated in the suppressor of phytochrome A-105 1 mutant and differentially expressed in constitutive photomorphogenic 1-4 (cop1-4) and cop1-5 mutants under cFR. Intriguingly, FIP1 expression was up-regulated in the fin219 mutant under all light conditions, except cFR. Furthermore, promoter activity assays revealed that FIP1 expression was light dependent, mainly associated with vascular tissues, and developmentally regulated. Subcellular localization studies revealed that the beta-glucuronidase-FIP1 fusion protein was localized in the nucleus and cytoplasm. Taken together, these data indicate that FIP1 may interact with FIN219 to regulate cell elongation and flowering in response to light.

The GRAS protein SCL13 is a positive regulator of phytochrome-dependent red light signaling, but can also modulate phytochrome A responses

Phytochrome photoreceptors enable plants to perceive divergent light signals leading to adaptive changes in response to differing environmental conditions. However, the mechanism of light signal transduction is not fully understood. Here we report the identification of a new signaling intermediate from Arabidopsis thaliana, Scarecrow-like (SCL)13, which serves as a positive regulator of continuous red light signals downstream of phytochrome B (phyB). SCL13 antisense lines exhibit reduced sensitivity towards red light, but only a distinct subset of phyB-mediated responses is affected, indicating that SCL13 executes its major role in hypocotyl elongation during de-etiolation. Genetic evidence suggests that SCL13 is also needed to modulate phytochrome A (phyA) signal transduction in a phyB-independent way. The SCL13 protein is localized in the cytoplasm, but can also be detected in the nucleus. Overexpression of both a nuclear and cytoplasmic localized SCL13 protein leads to a hypersensitive phenotype under red light indicating that SCL13 is biologically active in both compartments. SCL13 is a member of the plant-specific GRAS protein family, which is involved in various different developmental and signaling pathways. A previously identified phytochrome A signaling intermediate, PAT1, belongs to the same subbranch of GRAS proteins as SCL13. Although both proteins are involved in phytochrome signaling, each is specific for a different light condition and regulates a different subset of responses.