Nucleoside Diphosphate Kinase Gene Research Articles

Identification of Salt Stress-Responsive Proteins in Maize (Zea may) Seedlings Using iTRAQ-Based Proteomic Technique.

Background: Soil salinity is a major abiotic stress that limits plant growth and yield worldwide. Objective: To better understand the mechanism of salt stress adaptation in maize (Zea may), proteomic analysis of maize responses to salt stress were analyzed in seedling.Materials and Methods: Taking maize seedlings untreated and treated with NaCl for 24 h as material, isobaric tags for relative and absolute quantitation (iTRAQ) were used to analyze the protein expression profile of maize seedlings after salt stress.Results: The result showed that 270 differentially expression proteins (DEPs) were identified in maize seedlings after salt stress. The majority proteins had functions related to translation, ribosomal structure and biogenesis (15%), posttranslational modification, protein turnover, chaperones (14%) and others metabolism. Quantitative real-time PCR analysis showed that the EF-Tu, peroxiredoxin, FoF1-type ATP synthase, glutamate dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, Acetyl-CoA acetyltransferase and nucleoside diphosphate kinase genes were up-regulated in the adaptation of maize to salt stress.Conclusions: The coped with salt stress of maize seedlings might be included nitrogen and glutamate (Glu) metabolism and energy homeostasis, nucleotide transport and metabolism, soluble sugar, fatty acid and nucleoside triphosphates synthesis. Moreover, the enhancement of plant to scavenge ROS, such as peroxiredoxin, might play significant roles in the adaptation of maize to salt stress.Taken together, these proteins might have important roles in defense mechanisms against salt stress in maize.We hope that this study provides valuable information for the further utilization and study on the molecular mechanisms of defense mechanisms in maize.

Cloning and bioinformatics analysis of nucleoside diphosphate kinase gene from Rehmannia glutinosa

Nucleoside diphosphate kinase(NDPK) is a highly conserved multifunctional protein,can catalyze substrate phosphorylation and participate in many metabolic processes,such as plant growth and development,abiotic stress,susceptible stress,photosynthesis and energy metabolism.In order to understand the structure,function and character of NDPK gene in Rehmannia glutinosa (RgNDPKⅠ),full length c DNA of RgNDPKⅠwas obtained by silico cloning from the transcriptome data of Rehmannia glutinosa.The length of RgNDPKⅠwas 765 bp.According to bioinformatics analysis,with an open reading frame of 447 bp,RgNDPKⅠencodes 148 amino acids,and has typical nucleoside diphosphate kinase domain and other phosphorylation active sites.The protein encoded by RgNDPKⅠwas located in the cytoplasm,and it was hydrophilic protein without transmembrane region.The protein was similar to nucleoside diphosphate kinase of Sesamum indicum and Handroanthus impetiginosus,97% and 96% respectively.NDPK gene has been cloned in many organisms,and there are many similar conservative domains in the amino acid sequences of different plants,so it is presumed that RgNDPKⅠis a member of the nucleoside diphosphate kinase superfamily.This study provides an important theoretical basis for further exploring the character,structure,function and expression mechanism of RgNDPKⅠ.

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.

Correction to: Isolation, Characterization, and Expression Profiling of Nucleoside Diphosphate Kinase Gene from Tall Fescue (Festuca arundinacea Schreb.) (FaNDPK) under Salt Stress

Fifty tall fescue (Festuca arundinacea Schreb.) half-sib families were screened under salinity stress during germination stage, and five tolerant and five sensitive half-sib families were selected. After studying morphological and biochemical characteristics of 10 selected families, the most salt-tolerant family was used for gene expression analysis. Real-time PCR analysis showed that the NDPK expression in plants treated by 200-mM sodium chloride has increased 36.782-fold greater than that in the control ones. The full length of encoding region of NDPK in tall fescue was obtained using the rapid amplification of cDNA ends technique. The homology comparison of DNA sequences, deduced amino acid sequences, and protein sequences were carried out using CLASTALW program in NCBI. The fragment composed of 822 nucleotides (gene’s ORF was 508 nucleotides), and corresponding protein consist 168 amino acids with a predicted molecular mass of 19.4 kD. Blast search for isolated fragment showed that our sequenced fragment is highly similar to UMP/CMP kinase of Oryza sativa japonica (95%). In Blastp, the amino acid sequence of isolated fragment was similar to UMP/CMP kinase of Sorghum bicolor (95%). The results of study confirm that the NDPK is related to UMP/CMP kinase.

Comparative transcriptome analysis revealed genes involved in the fruiting body development of Ophiocordyceps sinensis.

Ophiocordyceps sinensis is a highly valued fungus that has been used as traditional Asian medicine. This fungus is one of the most important sources of income for the nomadic populations of the Tibetan Plateau. With global warming and excessive collection, the wild O. sinensis resources declined dramatically. The cultivation of O. sinensis hasn’t been fully operational due to the unclear genetic basis of the fruiting body development. Here, our study conducted pairwise comparisons between transcriptomes acquired from different growth stages of O. sinensis including asexual mycelium (CM), developing fruiting body (DF) and mature fruiting body (FB). All RNA-Seq reads were aligned to the genome of O. sinensis CO18 prior to comparative analyses. Cluster analysis showed that the expression profiles of FB and DF were highly similar compared to CM. Alternative splicing analysis (AS) revealed that the stage-specific splicing genes may have important functions in the development of fruiting body. Functional enrichment analyses showed that differentially expressed genes (DEGs) were enriched in protein synthesis and baseline metabolism during fruiting body development, indicating that more protein and energy might be required for fruiting body development. In addition, some fruiting body development-associated genes impacted by ecological factors were up-regulated in FB samples, such as the nucleoside diphosphate kinase gene (ndk), β subunit of the fatty acid synthase gene (cel-2) and the superoxide dismutase gene (sod). Moreover, the expression levels of several cytoskeletons genes were significantly altered during all these growth stages, suggesting that these genes play crucial roles in both vegetative growth and the fruiting body development. Quantitative PCR (qPCR) was used to validate the gene expression profile and the results supported the accuracy of the RNA-Seq and DEGs analysis. Our study offers a novel perspective to understand the underlying growth stage-specific molecular differences and the biology of O. sinensis fruiting body development.

Isolation, Characterization, and Expression Profiling of Nucleoside Diphosphate Kinase Gene from Tall Fescue (Festuca arundinaceous Schreb.) (FaNDPK) under Salt Stress

Isolation, Characterization, and Expression Profiling of Nucleoside Diphosphate Kinase Gene from Tall Fescue (Festuca arundinaceous Schreb.) (FaNDPK) under Salt Stress

Delayed processing of bone marrow samples reveals a prognostic pattern of NME mRNA expression in cytogenetically normal acute myeloid leukemia

Improvements in the therapy of cytogenetically normal acute myeloid leukemia (CN-AML) will depend largely on the characterization of functional subtypes identified by prognostic markers. Exposing leukemic cells to stress ex vivo may reveal relevant phenotypic markers not apparent in freshly explanted cells. Here, we assess the prognostic relevance of expression of the nucleoside diphosphate kinase genes NME1 and NME2 in a cohort of 78 patients with CN-AML aged < 60 years using archived mononuclear cell samples originally prepared from bone marrow either directly (n = 25) or following 2–3 days of transport (n = 53). The stress conditions arising during transport resulted in the development of a prognostic pattern of NME mRNA with maintenance of high NME2 mRNA being a strong indicator of increased event-free survival independent of FLT3-internal tandem duplication. Prospective analysis of CN-AML bone marrow (n = 7) confirmed that NME1 mRNA is always decreased during storage, while NME2 mRNA is either decreased or maintained. We conclude that ex vivo stress can reveal novel prognostic markers.

The Nucleoside Diphosphate Kinase Gene Nme3 Acts as Quantitative Trait Locus Promoting Non-Mendelian Inheritance

The t-haplotype, a variant form of the t-complex region on mouse chromosome 17, acts as selfish genetic element and is transmitted at high frequencies (>95%) from heterozygous (t/+) males to their offspring. This phenotype is termed transmission ratio distortion (TRD) and is caused by the interaction of the t-complex responder (Tcr) with several quantitative trait loci (QTL), the t-complex distorters (Tcd1 to Tcd4), all located within the t-haplotype region. Current data suggest that the distorters collectively impair motility of all sperm derived from t/+ males; t-sperm is rescued by the responder, whereas +-sperm remains partially dysfunctional. Recently we have identified two distorters as regulators of RHO small G proteins. Here we show that the nucleoside diphosphate kinase gene Nme3 acts as a QTL on TRD. Reduction of the Nme3 dosage by gene targeting of the wild-type allele enhanced the transmission rate of the t-haplotype and phenocopied distorter function. Genetic and biochemical analysis showed that the t-allele of Nme3 harbors a mutation (P89S) that compromises enzymatic activity of the protein and genetically acts as a hypomorph. Transgenic overexpression of the Nme3 t-allele reduced t-haplotype transmission, proving it to be a distorter. We propose that the NME3 protein interacts with RHO signaling cascades to impair sperm motility through hyperactivation of SMOK, the wild-type form of the responder. This deleterious effect of the distorters is counter-balanced by the responder, SMOKTcr, a dominant-negative protein kinase exclusively expressed in t-sperm, thus permitting selfish behaviour and preferential transmission of the t-haplotype. In addition, the previously reported association of NME family members with RHO signaling in somatic cell motility and metastasis, in conjunction with our data involving RHO signaling in sperm motility, suggests a functional conservation between mechanisms for motility control in somatic cells and spermatozoa.

A novel connection between nucleotide and carbohydrate metabolism in mitochondria: sugar regulation of the Arabidopsis nucleoside diphosphate kinase 3a gene

Sugar metabolism is intricately connected with mitochondria through the conversion of sugars to ATP, and through the production of carbon skeletons that can be used in anabolic processes. Sugar molecules also take part in signalling cascades. In this study we investigated the impact of sucrose on the expression of the Arabidopsis thaliana Nucleoside Diphosphate Kinase gene family (NDPK, EC 2.7.4.6), focusing on NDPK3a, the product of which is located predominantly in mitochondria. Using quantitative PCR we show that the NDPK3a gene is subject to sucrose and glucose induction, while no other Arabidopsis NDPK gene are sucrose-inducible. The induction reaches a half-maximum after about 6 hours and is stable for at least 48 h. Sucrose and glucose inductions were found not to be affected by the presence of a hexokinase inhibitor, N-acetyl-glucosamine. Furthermore, turanose, a sucrose analogue that is not metabolised in plant cells, did not induce NDPK3a gene expression. An analysis of the NDPK3a gene revealed two WBOXHWISO1 boxes in the promoter region, elements that have previously been reported to be involved in sugar signalling in barley via the SUSIBA2 protein. SUSIBA2 belongs to the WRKY group of transcription factors. In this study we used two mutants containing T-DNA insertions in WRKY-genes, AtWrky4 and AtWrky34, to investigate the possible involvement of WRKY transcription factors in the sugar induction of NDPK3a.

Cloning, expression and characterization of a nucleoside diphosphate kinase (NDPK) gene from tobacco

Abstract Nucleoside diphosphate kinase (NDPK) is a housekeeping enzyme that maintains the intracellular levels of all (d)NTPs used in biosynthesis except ATP. Here we report that a full-length cDNA encoding nucleoside diphosphate kinase (NDPK) was cloned using yeast two-hybrid approach. A tobacco NDPK gene was obtained and designated as NtNDPK1. NtNDPK1 is 704 bp in length and encodes a putative 16.2 kD protein of 148 amino acids. Phylogenic analysis showed that NtNDPK1 is highly homologous to other plant NDPK genes and identified as type i (NDPK1). RNA-gel blot analysis showed that there was no significant difference of NtNDPK1 expression in roots, stems, leaves and buds. And expression of NtNSPK1 was induced by ABA and PEG and repressed by NaCl, but not significantly affected by Paraquat, wounding and low temperature (4°C) treatments, indication that NtNDPK1 may play a certain role in response to abiotic stress. In vitro phosphorylation assay demonstrated that NtNDPK1 had autophosphorylation activity. *...

Histidine Phosphorylation of the Potassium Channel KCa3.1 by Nucleoside Diphosphate Kinase B Is Required for Activation of KCa3.1 and CD4 T Cells

The Ca2+ -activated K+ channel KCa3.1 is required for Ca2+ influx and the subsequent activation of B and T cells. Inhibitors of KCa3.1 are in development to treat autoimmune diseases and transplant rejection, underscoring the importance in understanding how these channels are regulated. We show that nucleoside diphosphate kinase B (NDPK-B), a mammalian histidine kinase, functions downstream of PI(3)P to activate KCa3.1. NDPK-B directly binds and activates KCa3.1 by phosphorylating histidine 358 in the carboxyl terminus of KCa3.1. Endogenous NDPK-B is also critical for KCa3.1 channel activity and the subsequent activation of CD4 T cells. These findings provide one of the best examples whereby histidine phosphorylation regulates a biological process in mammals, and provide an example whereby a channel is regulated by histidine phosphorylation. The critical role for NDPK-B in the reactivation of CD4 T cells indicates that understanding NDPK-B regulation should uncover novel pathways required for T cell activation.

Crystal structure of nucleoside diphosphate kinase required for coleoptile elongation in rice ( Oryza sativa L.)

Nucleoside diphosphate kinase (NDK) is a ubiquitous enzyme found in all organisms and cell types, and catalyzes the transfer of the phosphoryl group from a nucleoside triphosphate to a nucleoside diphosphate. The enzyme is involved in and required for coleoptile elongation in rice as the level of the rice NDK (rNDK) changes during seed germination and the early stages of seedling growth. The expression of rice NDK gene is up-regulated in the growing coleoptiles when the anaerobic stress persists. The rNDK structure determined at 2.5 Å resolution consists of a four-stranded anti-parallel β-sheet, of which the surfaces are partially covered with six α-helices; its overall and active site structures are similar to those of homologous enzymes except the major conformation variations of residue 132–138 regions, involving significant structural contacts. The model contains 148 residues of 149 residues in total and averaged 19 water molecules per monomer for 12 molecules in an asymmetric unit. A mold of 12 superimposed molecules shows that the αA-α2 area has greater variations and higher temperature factors, indicating the flexibility for a substrate entrance. Hexameric molecular packing in both crystal and solution implies that rNDK functions as hexamers. This rNDK structure, which is the first NDK structure from a higher plant system, provides the structural information essential to understand the functional significance of this enzyme during growth and development in both rice and other plants.

Molecular evolution of nucleoside diphosphate kinase genes: conserved core structures and multiple-layered regulatory regions.

Genomic data regarding the nucleoside diphosphate (NDP) kinase genes have been accumulated from diverged phyla. Comparison of their regulatory sequences have shed light on the multiple facets of gene regulation systems. Phylogenetic studies, including CpG island and intron-mapping, and homologous sequence comparison, have suggested that the regions of the major mammalian genes, the ortholog (rat alpha or nm23-H2) and its paralog (rat beta or nm23-H1), have been constructed by a stepwise gain and loss of alien genes resulting in "multiple-layered" regulatory systems. They contain representative cis-elements for the constitutive, stage/lineage-specific, and early response expression. These elements' binding capacities to nuclear proteins were confirmed by electrophoretic mobility shift assay. Further, these regulatory systems generate heterogeneous mRNA at the 5' untranslated region, which influences their own translation efficiencies. In terms of this process, the transcription system would control another layer of gene expression: posttranscriptional (translational) regulation.

Suspected utility of enzymes with multiple activities in the small genome Mycoplasma species: the replacement of the missing "household" nucleoside diphosphate kinase gene and activity by glycolytic kinases.

The small genome Mollicutes whose DNAs are completely sequenced (Mycoplasma genitalium, Mycoplasma pneumoniae, Mycoplasma pulmonis, and Ureaplasma urealyticum [parvum]) lack a gene (ndk) for the presumably essential nucleoside diphosphate kinase (NDPK). We hypothesized that other activities might replace NDPK activity. We found in M. genitalium G37(T), Mycoplasma pneumoniae FH(T), Mycoplasma fermentans PG18(T), and Mycoplasma capricolum subsp. capricolum Kid(T) that their 6-phosphofructokinases (6-PFKs), phosphoglycerate kinases (PGKs), pyruvate kinases (PKs), and acetate kinases (AKs), besides reactant ADP/ATP, could use other ribo- and deoxyribo-purine and pyrimidine NDPs and NTPs. These activities could compensate for the absence of an orthologous ndk gene in the Mycoplasmataceae. They suggest a metabolically varied and consequential role for unrelated and perhaps unsuspected "replacement" or compensatory enzymes that may confound metabolic prediction. We partially purified and biochemically characterized the PKs, 6-PFKs, PGKs, and AKs from M. capricolum subsp. capricolum Kid(T) and M. fermentans PG18(T).

NME6: a new member of the nm23/nucleoside diphosphate kinase gene family located on human chromosome 3p21.3.

The NME (nm23/nucleoside diphosphate kinase) gene family in human is involved in the phosphorylation of nucleoside diphosphates and a variety of regulatory phenomena associated with development, oncogenic transformation, and metastasis. Here we report the cDNA sequence for a sixth member of this family, NME6. The cDNA sequence predicts a 186-residue protein that includes the characteristic active site motif of a nucleoside diphosphate (NDP) kinase, as well as the other residues previously identified as crucial for nucleotide binding and catalysis. The NME6 protein sequence is only 34-41% identical to the five previously reported human NME proteins, and is similarly related to prokaryotic and primitive eukaryotic NDP kinases. Compared to typical proteins of this family such as NME1 and NME2, NME6 has three additional residues located in the Kpn loop, and a 22-residue extension at the COOH-terminal. Using radiation hybrid mapping, the NME6 gene was localized to chromosome 3p21.3. The 1.3-kb transcript of NME6 is expressed at a moderately low level in many human tissues, and is most abundant in kidney, prostate, ovary, intestine, and spleen. Homologous cDNAs were also cloned and sequenced for rat and mouse. The sequence of the first 171 residues of the mouse homologue (Nm23-M6) is 94% identical to the deduced human NME6 protein.

Differential expression of nucleoside diphosphate kinases (NDPK/NM23) during Xenopus early development.

In Xenopus laevis, three nucleoside diphosphate kinase (NDPK) monomers have been described (NDPK X1, X2 and X3) (Ouatas et al., 1997). In eucaryotes, this kinase is known as a hetero- or homohexamer. Here, we examine the distribution of the enzyme and its different subunit mRNAs during oogenesis and early embryogenesis of Xenopus laevis, respectively by immunohistofluorescence and whole-mount in situ hybridization. These analyses show that NDPKs and their mRNAs are differentially distributed throughout the oocyte and early embryos with a high level of transcription in somites and brain. We emphasize two points. First, each mRNA displays a distinct subcellular localization in somites, suggesting a complex regulation of NDPK genes both at the transcriptional and translational level and a possible involvement of NDPK X2 homohexamers in the dorsal muscle differentiation. Second, in oocytes and early embryos, the proteins are mainly localized in the nucleus, suggesting a new mechanism for their nuclear import, since they do not possess any known nuclear import sequences.

Nm23 -H4, a new member of the family of human nm23 /nucleoside diphosphate kinase genes localised on chromosome 16p13

A novel human nm23/nucleoside diphosphate (NDP) kinase gene, called nm23-H4, was identified by screening a human stomach cDNA library with a probe generated by amplification by reverse transcription-polymerase chain reaction. The primers were designed from publicly available database cDNA sequences selected according to their homology to the human nn23-H1 putative metastasis suppressor gene. The full-length cDNA sequence predicts a 187 amino acid protein possessing the region homologous to NDP kinases with all residues crucial for nucleotide binding and catalysis, strongly suggesting that Nm23-H4 possesses NDP kinase activity. It shares 56, 55 and 60% identity with Nm23-H1, Nm23-H2 and DR-Nm23, respectively, the other human Nm23 proteins isolated so far. Compared with these proteins, Nm23-H4 contains an additional NH2-terminal region that is rich in positively charged residues and could indicate routing to mitochondria. The nm23-H4 gene has been localised to human chromosomal band 16p13.3. The corresponding 1.2 kb mRNA is widely distributed and expressed in a tissue-dependent manner, being found at very high levels in prostate, heart, liver, small intestine and skeletal muscle tissues and in low amounts in the brain and in blood leucocytes. Nm23-H4 naturally possesses the Pro-Ser substitution equivalent to the K-pn mutation (P97S) of Drosophila.

XI. Yeast sequencing reports. Sequence of a 20·7 kb region of yeast chromosome XI includes theNUP100 gene, an open reading frame (ORF) possibly representing a nucleoside diphosphate kinase gene, tRNAS for His, Val and Trp in addition to seven ORFs with weak or no significant similarity to known proteins

The complete DNA sequence of cosmid clone pEKG080 comprising 20,723 base pairs was determined from an ordered set of subclones. The sequence contains nine open reading frames (ORFs) longer than 100 amino acids. The deduced amino acid sequence of YKL067 exhibits significant similarity to nucleoside diphosphate kinases from a number of species and probably represents this gene in yeast. YKL068 is identical to the NUP100 gene recently cloned and sequenced. The gene codes for a nuclear pore complex protein. YKL073 is identical to Hsp70 proteins from yeast and Hydra at about 20% of the amino acids. The significance of this similarity is uncertain. The remaining six ORFs do not share homology with known proteins. Three tRNAs for histidine, valine and tryptophan respectively were identified, the latter interrupted by a 34 bp intron. Solo delta sequences were found at three locations.

Human c-myc transcription factor PuF identified as nm23-H2 nucleoside diphosphate kinase, a candidate suppressor of tumor metastasis.

A human gene encoding the c-myc purine-binding transcription factor PuF was identified by screening of a cervical carcinoma cell complementary DNA library with a DNA fragment containing PuF binding sites. The 17-kilodalton bacterially produced PuF was shown to have biological activity and properties similar to that of human PuF. DNA sequence analysis of recombinant PuF revealed perfect identity with the human nm23-H2 nucleoside diphosphate kinase gene, a potential negative regulator of cancer metastasis. These results provide a link between nm23 and the c-myc oncogene and suggest that the nm23 protein can function in vitro in the transcriptional regulation of c-myc expression.