Studies on the ADP-ribose pyrophosphatase subfamily of the nudix hydrolases and tentative identification of trgB, a gene associated with tellurite resistance.

Four Nudix hydrolase genes, ysa1 from Saccharomyces cerevisiae, orf209 from Escherichia coli, yqkg from Bacillus subtilis, and hi0398 from Hemophilus influenzae were amplified, cloned into an expression vector, and transformed into E. coli. The expressed proteins were purified and shown to belong to a subfamily of Nudix hydrolases active on ADP-ribose. Comparison with other members of the subfamily revealed a conserved proline 16 amino acid residues downstream of the Nudix box, common to all of the ADP-ribose pyrophosphatase subfamily. In this same region, a conserved tyrosine designates another subfamily, the diadenosine polyphosphate pyrophosphatases, while an array of eight conserved amino acids is indicative of the NADH pyrophosphatases. On the basis of these classifications, the trgB gene, a tellurite resistance factor from Rhodobacter sphaeroides, was predicted to designate an ADP-ribose pyrophosphatase. In support of this hypothesis, a highly specific ADP-ribose pyrophosphatase gene from the archaebacterium, Methanococcus jannaschii, introduced into E. coli, increased the transformant's tolerance to potassium tellurite.     

Characterization of the arabidopsis formin-like protein AFH1 and its interacting protein

A partial cDNA encoding an Arabidopsis thaliana FH (Formin Homology) protein (AFH1) was used as a probe to clone a full length AFH1 cDNA. The deduced protein encoded by the cDNA contains a FH1 domain rich in proline residues and a C-terminal FH2 domain which is highly conserved amongst FH proteins. In contrast to FH proteins of other organisms, the predicted AFH1 protein also contains a putative signal peptide and a transmembrane domain suggesting its association with membrane. Cell fractionation by differential centrifugation demonstrated the presence of AFH1 in the Triton X-100 insoluble microsomal fraction. An Arabidopsis cDNA library was screened to identify proteins that interact with the C-terminal region of AFH1 using yeast two-hybrid assays, and one of the isolated cDNAs encoded a novel protein, FIP2. Experiments using recombinant proteins expressed in E. coli demonstrated that FIP2 interacted directly with AFH1. The amino acid sequence of FIP2 has partial homology to bacterial putative membrane proteins and animal A-type K+ ATPases. AFH1 may form a membrane anchored complex with FIP2, which might be involved in the organization of the actin cytoskeleton.     

Characterization of plant beta-ureidopropionase and functional overexpression in Escherichia coli

Pyrimidine bases are rapidly catabolized in growing plant tissues. The final enzyme of the catabolic pathway, beta-ureidopropionase (beta-UP; EC 3.5.1.6), was partially purified from the shoots of etiolated maize (Zea mays) seedlings. The enzyme had a K(m) for beta-ureidopropionate (the substrate derived from uracil) of 11 microM. Only one enantiomer of racemic beta-ureidoisobutyrate (derived from thymine) was processed with a K(m) of 6 microM. The enzyme was inactivated by dialysis against 1,10-phenanthroline and activity could be partially restored by addition of Zn(2+). Maize beta-UP was very sensitive to inactivation by iodoacetamide. This could be prevented by addition of substrate, indicating the presence of an active site Cys. The enzyme was strongly inhibited by short chain aliphatic acids and aryl propionates, the most potent inhibitor of which was 2-(2, 6-dinitrophenoxy)-propionate (I(50) = 0.5 microM). A gene for Arabidopsis beta-UP encodes a polypeptide of 405 amino acids and has about 55% homology with the enzymes from other eukaryotic organisms. Several highly conserved residues link the plant beta-UP with a larger class of prokaryotic and eukaryotic amidohydrolases. An Arabidopsis cDNA truncated at the N terminus by 14 residues was cloned and overexpressed in Escherichia coli. The recombinant enzyme (43.7 kD) was soluble, functional, and purified to homogeneity with yields of 15 to 20 mg per 30 g fresh weight of E. coli cells. The recombinant enzyme from Arabidopsis and the native enzyme from maize had molecular masses of approximately 440 kD, indicating the enzyme is a decamer at pH 7.     

Cloning, expression and characterization of a Nudix hydrolase that catalyzes the hydrolytic breakdown of ADP-glucose linked to starch biosynthesis in Arabidopsis thaliana

'Nudix' hydrolases are widely distributed nucleotide pyrophosphatases that possess a conserved GX5EX7REUXEEXGU motif where U is usually isoleucine, leucine or valine. Among them, Escherichia coli ADP-sugar pyrophosphatase (ASPP) has been shown to catalyze the hydrolytic breakdown of ADP-glucose linked to bacterial glycogen biosynthesis. Comparisons of the 31 different Nudix-encoding sequences of the Arabidopsis genome with those coding for known bacterial and mammalian ASPPs identified one sequence possessing important divergences in the Nudix motif that, once expressed in E. coli, produced a protein with ASPP activity. This protein, designated as AtASPP, shares strong homology with hypothetical rice and potato proteins, indicating that ASPPs are widely distributed in both mono- and dicotyledonous plants. As a first step to test the possible involvement of plant ASPPs in regulating the intracellular levels of ADP-glucose linked to starch biosynthesis, we produced and characterized AtASPP-overexpressing Arabidopsis plants. Source leaves from these plants exhibited a large reduction in the levels of both ADP-glucose and starch, indicating that plant ASPPs catalyze the hydrolytic breakdown of a sizable pool of ADP-glucose linked to starch biosynthesis. No pleiotropic changes in maximum catalytic activities of enzymes closely linked to starch metabolism could be detected in AtASPP-overexpressing leaves. The overall information provides the first evidence for the existence of plant Nudix hydrolases that have access to an intracellular pool of ADP-glucose linked to starch biosynthesis.     

Molecular characterization of an Arabidopsis thaliana cDNA encoding a small GTP-binding protein, Rha1.

We have isolated a cDNA encoding a small GTP-binding protein from an Arabidopsis thaliana cDNA library using an oligonucleotide probe derived from the most conserved domain of the ras superfamily. The cDNA encodes a 21.8 kDa protein, designated Rha1, which shows high homology to members of the ras superfamily in the regions involved in GTP binding, GTPase activity, and membrane attachment. The amino acid sequence is 60% identical to the sequence of the mammalian Rab5 protein, a small GTP-binding protein which is believed to be involved in endocytosis. Several regions, including the putative effector domain are completely conserved. This high percentage of amino acid identity suggests that the Rha1 protein is the functional plant counterpart of the Rab5 protein. When expressed in E. coli, the Rha1 protein was shown to bind GTP. The rha1 gene is most highly expressed in root and callus tissue, weakly expressed in stems and inflorescences and virtually not expressed in leaves and seed pods. Genomic Southern analysis revealed that rha 1 is part of a small multigene family.     

Identification of cytosolic Mg2+-dependent soluble inorganic pyrophosphatases in potato and phylogenetic analysis

Using polyclonal antibodies raised against a previously cloned potato Mg2+-dependent soluble inorganic pyrophosphatase (ppa1 gene) [8], a second gene, called ppa2, could be isolated. A single locus homologous to ppa2 was mapped on potato chromosomes, unlinked to the two loci identified for ppa1. From a phylogenetic and structural point of view, the PPA1 and PPA2 polypeptides are more closely related to prokaryotic than to eukaryotic Mg2+-dependent soluble inorganic pyrophosphatases (soluble PPases). Subcellular localization by immunogold electron microscopy, using sections from leaf parenchyma cells, showed that PPA1 and PPA2 are localized to the cytosol. Based on these observations, the likely phylogenetic origin and the physiological significance of the cytosolic soluble pyrophosphatases are discussed.     

High-level expression in Escherichia coli of the catalytically active flavin domain of corn leaf NADH:nitrate reductase and its comparison to human NADH:cytochrome B5 reductase

Higher plant nitrate reductase can be divided into three functional domains representing its prosthetic groups: 1) flavin; 2) cytochrome b; and 3) Mo-pterin. The flavin domain has been synthesized by heterologous expression in Escherichia coli using a fragment of a corn leaf NADH:nitrate reductase cDNA clone, Zmnr1, which we had previously isolated and sequenced. A Xho2-BamH1 fragment was cut from Zmnr1, containing the sequence for the flavin domain, and ligated in the BamH1 site of expression vector pET3c. When this construct was expressed in E. coli, a 30 kD polypeptide was found to be newly synthesized. The flavin domain was purified to homogeneity using blue Sepharose and shown to have a molecular weight of 30 kD. The recombinant flavin domain has a ferricyanide reductase specific activity of 1000 mumols NADH oxidized/min/mg protein and a visible spectrum virtually identical to that of human NADH:cytochrome b5 reductase.     

日本血吸虫新基因Sj-MA的克隆、表达及保护性免疫

为发现新基因 ,寻找日本血吸虫病新疫苗候选分子 ,采用Sj雄虫免疫血清筛选Sj成虫cDNA文库。经测序发现新基因Sj MA含有一个完整的阅读框 ,推测其由 2 4 9个氨基酸组成 ,编码分子量为 2 8.8kD的可溶性蛋白质 ,并带有多个能被磷酸化激活的位点 ,提示其可能为一重要的信息传递分子。将Sj MA的cDNA亚克隆至原核表达载体pGEX 5X ,获得Sj MA原核表达的重组体rSj MA/GST ,并在E .coli中高效表达为谷胱甘肽S 转移酶 (GST)融合蛋白 ,分子量为 5 4 .8kD ,Western印迹显示融合蛋白质能被抗雄虫和抗GST血清识别。融合蛋白质免疫小鼠可诱导 34.2 9%的减虫率 ,与对照组有显著性差异 (P <0 .0 0 1 )。表明新基因Sj MA表达的蛋白质能诱导小鼠的抗日本血吸虫的保护性免疫 ,提示其作为日本血吸虫疫苗候选分子的潜在价值     

Evolutionary aspects of inorganic pyrophosphatase.

Based on the primary structure, soluble inorganic pyrophosphatases can be divided into two families which exhibit no sequence similarity to each other. Family I, comprising most of the known pyrophosphatase sequences, can be further divided into prokaryotic, plant and animal/fungal pyrophosphatases. Interestingly, plant pyrophosphatases bear a closer similarity to prokaryotic than to animal/fungal pyrophosphatases. Only 17 residues are conserved in all 37 pyrophosphatases of family I and remarkably, 15 of these residues are located at the active site. Subunit interface residues are conserved in animal/fungal but not in prokaryotic pyrophosphatases.     

The Construction of γ-TIP Prokaryotic Expression Vector and Preparation of the γ- TIP Antibody

A prokaryotic expression vector, pGEX-TIP, was constructed from Arabidopsis thaliana (L.) Heynh. Employing PCR, 205 bp fragment near 3' end of γ-TIP cDNA, which has specific aquaporin activity, was amplified and cloned into pGEX-KG. Restriction endonuclease analysis and sequencing confirmed the correct construction, and 0.4 mmoL/L IPTC can induce high expression of GST-TIP fused protein which was about 50% in total of E. coli proteins. The IPTG induced E. coli was collected and ]ysed by supersonic treatment. The fusion protein was mainly recovered as an inclusion body. The expressed GST-TIP was purified by SDS-PAGE according to their molecular weight, which was about 32 kD. The purified protein was used to immune rabbits directly or was electrophoretically eluted before it was used for immunization. The highly qualified antibody for GST-TIP was obtained, which provides a very useful protein probe for the research on localization and function of aquaporins.     

Identification of an Arabidopsis inorganic pyrophosphatase capable of being imported into chloroplasts

An Arabidopsis cDNA coding for a previously uncharacterized isoform of inorganic pyrophosphatase was isolated. It was used to complement an E. coli mutant, demonstrating that it coded for an active enzyme. MgCl(2) was necessary for the protein's activity, whilst NaF inhibited it. The K(m) for pyrophosphate and the pH optimum of the protein was determined. The gene coding for this protein was expressed in all tissues, and its expression in rosette leaves was induced by incubation on metabolizable sugars. In vitro import experiments demonstrated that the protein could be imported into chloroplasts and localized to the stromal compartment.     

一种新的乙型肝炎病毒表面抗原结合蛋白的筛选、表达及其生物学活性的初步研究

为了研究乙肝病毒侵染肝细胞过程中的功能蛋白 ,通过印迹免疫分析技术从人肝cDNA噬菌体表达库中筛选出一株编码乙肝表面抗原结合蛋白 (hepatitisBsurfaceantigenbindingprotein ,HBsAg BP)的cDNA克隆 .基因测序结果表明 ,该cDNA具有独立的开放阅读框架 ,编码 1个由 344个氨基酸残基构成的可溶性蛋白分子 ,属于免疫球蛋白超家族成员 .将该基因克隆到原核表达载体pTriplEx后 ,在E .coliXL1 Blue菌株中获得 4 4kD的重组蛋白 .重组蛋白经Western印迹和ELISA实验证明具有与乙肝表面抗原特异性结合的能力 .进一步经流式细胞仪实验显示 ,在纯化的重组蛋白存在的情况下 ,天然的HBsAg与肝细胞株HepG2的亲和力显著增高 .结果显示 ,该乙肝表面抗原结合蛋白可能是介导乙肝病毒对肝细胞亲和侵染的可溶性辅助受体 .     

Cloning and characterization of the NADH pyrophosphatases from Caenorhabditis elegans and Saccharomyces cerevisiae, members of a Nudix hydrolase subfamily

Two genes from Caenorhabditis elegans and Saccharomyces cerevisiae, coding for enzymes homologous to the Nudix hydrolase family of nucleotide pyrophosphatases, have been cloned and expressed in Escherichia coli. The purified enzymes are homodimers of 39.1 and 43. 5 kDa, respectively, are activated by Mg(2+) and Mn(2+), and are 30 to 50 times more active on NADH than on NAD(+). They both have a conserved array of amino acids downstream of the Nudix box first seen in the orthologous enzyme from E. coli which designates them as members of an NADH pyrophosphatase subfamily of the Nudix hydrolases.     

Functional analysis of the Arabidopsis thaliana GCPE protein involved in plastid isoprenoid biosynthesis

Plastid isoprenoids are synthesized via the 2-C-methyl-D-erythritol 4-phosphate pathway. A few years after its discovery, most of the Escherichia coli genes involved in the pathway have been identified, including gcpE. In this work, we have identified an Arabidopsis thaliana protein with homology to the product of this gene. The plant polypeptide, GCPE, contains two structural domains that are absent in the E. coli protein: an N-terminal extension and a central domain of 30 kDa. We demonstrate that the N-terminal region targets the Arabidopsis protein to chloroplasts in vivo, consistent with its role in plastid isoprenoid biosynthesis. Although the presence of the internal extra domain may have an effect on activity, the Arabidopsis mature GCPE was able to complement a gcpE-defective E. coli strain, indicating the plant protein is a true functional homologue of the bacterial gcpE gene product.     

The TMK1 gene from Arabidopsis codes for a protein with structural and biochemical characteristics of a receptor protein kinase.

Genomic and cDNA clones that code for a protein with structural and biochemical properties similar to the receptor protein kinases from animals were obtained from Arabidopsis. Structural features of the predicted polypeptide include an amino-terminal membrane targeting signal sequence, a region containing blocks of leucine-rich repeat elements, a single putative membrane spanning domain, and a characteristic serine/threonine-specific protein kinase domain. The gene coding for this receptor-like transmembrane kinase was designated TMK1. Portions of the TMK1 gene were expressed in Escherichia coli, and antibodies were raised against the recombinant polypeptides. These antibodies immunodecorated a 120-kD polypeptide present in crude extracts and membrane preparations. The immunodetectable band was present in extracts from leaf, stem, root, and floral tissues. The kinase domain of TMK1 was expressed as a fusion protein in E. coli, and the purified fusion protein was found capable of autophosphorylation on serine and threonine residues. The possible role of the TMK1 gene product in transmembrane signaling is discussed.     

棉花生长素应答因子克隆和序列分析

通过电子克隆和RACE相结合的方法,从陆地棉中克隆到一个新ARF基因。序列分析表明,该基因序列全长为2393其中包括87bp的5′非编码区(5′UTR),1941bp的蛋白质编码区,终止密码子TAA和362bp的3′非编码区。该基因可编码647个氨基酸的蛋白质,分子量为71.9kD,等电点(PI)为8.2。该基因含有一个与拟南芥中ARF基因相似的B3结构域和一个Auxin_resp结合位点,表明该基因与拟南芥ARF基因有很高的同源性,推测具有相似或相同的功能。     

A potato gene encoding a WRKY-like transcription factor is induced in interactions with Erwinia carotovora subsp. atroseptica and Phytophthora infestans and is coregulated with class I endochitinase expression

A potato gene encoding a putative WRKY protein was isolated from a cDNA library enriched by suppression subtractive hybridization for sequences upregulated 1 h postinoculation with Erwinia carotovora subsp. atroseptica. The cDNA encodes a putative polypeptide of 172 amino acids, containing a single WRKY domain with a zinc finger motif and preceded by a potential nuclear localization site. St-WRKY1 was strongly upregulated in compatible, but only weakly in incompatible, interactions with Phytophthora infestans where, in all cases, it was coregulated with class I endochitinase, associating its expression with a known defense response. Whereas St-WRKY1 was strongly induced by E. carotovora culture filtrate (CF), confirming it to be an elicitor-induced gene, no such induction was detected after treatment with salicylic acid, methyl jasmonate, ethylene, or wounding. St-WRKY1 was upregulated by treatment of potato leaves with CFs from recombinant Escherichia coli containing plasmids expressing E. carotovora pectate lyase genes pelB and pelD, suggesting that either proteins encoded by these genes, or oligogalacturonides generated by their activity, elicit a potato defense pathway associated with St-WRKY1.     

Pro domain peptide of HGCP-Iv cysteine proteinase inhibits nematode cysteine proteinases

Cysteine proteinases (CPs) are synthesized as zymogens and converted to mature proteinase forms by proteolytic cleavage and release of their pro domain peptides. A cDNA encoding a papain-like CP, called hgcp-Iv, was isolated from a Heterodera glycines J2 cDNA library, expressed and utilized to assess the ability of its propeptide to inhibit proteinase in its active form. The hgcp-Iv cDNA sequence encodes a polypeptide of 374 amino acids with the same domain organization as other cathepsin L-like CPs, including a hydrophobic signal sequence and a pro domain region. HGCP-Iv, produced in Escherichia coli as a fusion protein with thioredoxin, degrades the synthetic peptide benzyloxycarbonyl-Phe-Arg-7-amido-4-methylcoumarin and is inhibited by E-64, a substrate and inhibitor commonly used for functional characterization of CPs. Recombinant propeptides of HGCP-Iv, expressed in E. coli, presented high inhibitory activity in vitro towards its cognate enzyme and proteinase activity of Meloidogyne incognita females, suggesting its usefulness in inhibiting nematode CPs in biological systems. Cysteine proteinases from other species produced no noticeable activity.     

Systematic characterization of the ADP-ribose pyrophosphatase family in the Cyanobacterium Synechocystis sp. strain PCC 6803

We have characterized four putative ADP-ribose pyrophosphatases Sll1054, Slr0920, Slr1134, and Slr1690 in the cyanobacterium Synechocystis sp. strain PCC 6803. Each of the recombinant proteins was overexpressed in Escherichia coli and purified. Sll1054 and Slr0920 hydrolyzed ADP-ribose specifically, while Slr1134 hydrolyzed not only ADP-ribose but also NADH and flavin adenine dinucleotide. By contrast, Slr1690 showed very low activity for ADP-ribose and had four substitutions of amino acids in the Nudix motif, indicating that Slr1690 is not an active ADP-ribose pyrophosphatase. However, the quadruple mutation of Slr1690, T73G/I88E/K92E/A94G, which replaced the mutated amino acids with those conserved in the Nudix motif, resulted in a significant (6.1 x 10(2)-fold) increase in the k(cat) value. These results suggest that Slr1690 might have evolved from an active ADP-ribose pyrophosphatase. Functional and clustering analyses suggested that Sll1054 is a bacterial type, while the other three and Slr0787, which was characterized previously (Raffaelli et al., FEBS Lett. 444:222-226, 1999), are phylogenetically diverse types that originated from an archaeal Nudix protein via molecular evolutionary mechanisms, such as domain fusion and amino acid substitution.