Molecular and catalytic properties of Arabidopsis thaliana adenylyl sulfate (APS)-kinase.

A cDNA clone (Atakn1) from Arabidopsis thaliana encoding APS-kinase (EC 2.7.1.25) was investigated for structural and catalytic properties of the gene product. Recombinant his10-AtAkn1 formed PAPS at a Vmax of 7.35 U x mg(-1). The Km for APS was 0.14 microM and for ATP 147 microM. APS caused a severe substrate inhibition (K(i) 4.5 microM). The type of inhibition is uncompetitive with respect to MgATP. High ionic strength and reducing thiols stabilized the enzyme activity. Plant APS-kinase is regulated in vitro by the redox charge with thioredoxin as essential activator. Mutagenesis of a serine in S182C and S182F presumed to be involved in the transfer of the phosphoryl group had no effect upon catalytic activity. Using a yeast two-hybrid system with AtAkn1 as bait, an interacting clone was detected from a cDNA library of A. thaliana cv. Columbia that codes for an APS-kinase iso-form (Atakn2). Complementation of APS-kinase-deficient Saccharomyces cerevisiae met14 showed that AtAkn2 is functionally active as APS-kinase. It was immunologically related to AtAkn1 and presumably represents a plastidal iso-form of the plant APS-kinase gene family.

New thioredoxins and glutaredoxins as electron donors of 3'-phosphoadenylylsulfate reductase.

Reduction of inorganic sulfate to sulfite in prototrophic bacteria occurs with 3'-phosphoadenylylsulfate (PAPS) as substrate for PAPS reductase and is the first step leading to reduced sulfur for cellular biosynthetic reactions. The relative efficiency as reductants of homogeneous highly active PAPS reductase of the newly identified second thioredoxin (Trx2) and glutaredoxins (Grx1, Grx2, Grx3, and a mutant Grx1C14S) was compared with the well known thioredoxin (Trx1) from Escherichia coli. Trx1, Trx2, and Grx1 supported virtually identical rates of sulfite formation with a Vmax ranging from 6.6 units mg-1 (Trx1) to 5.1 units mg-1 (Grx1), whereas Grx1C14S was only marginally active, and Grx2 and Grx3 had no activity. The structural difference between active reductants had no effect upon Km PAPS (22.5 microM). Grx1 effectively replaced Trx1 with essentially identical Km-values: Km trx1 (13.7 microM), Km grx1 (14.9 microM), whereas the Km trx2 was considerably higher (34.2 microM). The results agree with previous in vivo data suggesting that Trx1 or Grx1 is essential for sulfate reduction but not for ribonucleotide reduction in E. coli.

Structural and kinetic properties of adenylyl sulfate reductase from Catharanthus roseus cell cultures.

A cDNA encoding a plant-type APS reductase was isolated from an axenic cell suspension culture of Catharanthus roseus (Genbank/EMBL-databank accession number U63784). The open reading frame of 1392 bp (termed par) encoded for a protein (Mr=51394) consisting of a N-terminal transit peptide, a PAPS reductase-like core and a C-terminal extension with homology to the thioredoxin-like domain of protein disulfide isomerase. The APS reductase precursor was imported into pea chloroplasts in vitro and processed to give a mature protein of approximately 45 kDa. The homologous protein from pea chloroplast stroma was detected using anti:par polyclonal antibodies. To investigate the catalytical function of the different domains deleted par proteins were purified. ParDelta1 lacking the transit sequence liberated sulfite from APS (Km 2.5+/-0.23 microM) in vitro with glutathione (Km 3+/-0.64 mM) as reductant (Vmax 2.6+/-0.14 U mg-1, molecular activity 126 min-1). ParDelta2 lacking the transit sequence and C-terminal domain had to be reconstituted with exogenous thioredoxin as reductant (Km 15. 3+/-1.27 microM, Vmax 0.6+/-0.014 U mg-1). Glutaredoxin, GSH or DTT were ineffective substitutes. ParDelta1 (35.4%) and parDelta2 (21. 8%) both exhibited insulin reductase activity comparable to thioredoxin (100%). Protein disulfide isomerase activity was observed for parDelta1.

Crystallization and preliminary X-ray diffraction studies of phospho-adenylylsulfate (PAPS) reductase from E. coli.

PAPS reductase from E. coli is involved in sulfur metabolism and catalyses the reduction of phospho-adenylyl-sulfate (PAPS) to sulfite. The protein has been cloned, overexpressed and purified from E. coli. Crystallization experiments resulted in crystals suitable for X-ray diffraction. The crystals belong to the orthorhombic space group C2221 with cell dimensions a = 81.9, b = 97.4, c = 109.5 A, and contain one molecule per asymmetric unit. At cryogenic (100 K) temperatures the crystals diffract to a resolution limit of 2.7 A using a rotating anode and to 2.0 A at a synchrotron source.

Isolation and characterization of a gene for assimilatory sulfite reductase from Arabidopsis thaliana.

Sulfite reductase (SIR) represents a key enzyme in sulfate assimilation in higher plants. The genomic DNA sequence of the sir gene from Arabidopsis thaliana including regulatory and structural regions was isolated and characterized. The sequence of a 6 kb fragment encoding SIR revealed a coding region of 2891 basepairs (bp) that consists of eight exons separated by seven introns between 83 and 139 bp in length. The transcription start point was determined 272 bp upstream of the translation start site. Southern analysis indicates a single locus for the sir gene that gives rise to a 2.4 (kb) mRNA in leaves and in roots. The promoter region was verified by functional expression of the gusA reporter gene in transgenic A. thaliana plants and was shown to provide correct expression in root and leaf.

Crystal structure of phosphoadenylyl sulphate (PAPS) reductase: a new family of adenine nucleotide alpha hydrolases.

BACKGROUND: Assimilatory sulphate reduction supplies prototrophic organisms with reduced sulphur for the biosynthesis of all sulphur-containing metabolites. This process is driven by a sequence of enzymatic steps involving phosphoadenylyl sulphate (PAPS) reductase. Thioredoxin is used as the electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP) and sulphite. Unlike most electron-transfer reactions, there are no cofactors or prosthetic groups involved in this reduction and PAPS reductase is one of the rare examples of an enzyme that is able to store two electrons. Determination of the structure of PAPS reductase is the first step towards elucidating the biochemical details of the reduction of PAPS to sulphite. RESULTS: We have determined the crystal structure of PAPS reductase at 2.0 A resolution in the open, reduced form, in which a flexible loop covers the active site. The protein is active as a dimer, each monomer consisting of a central six-stranded beta sheet with alpha helices packing against each side. A highly modified version of the P loop, the fingerprint peptide of mononucleotide-binding proteins, is present in the active site of the protein, which appears to be a positively charged cleft containing a number of conserved arginine and lysine residues. Although PAPS reductase has no ATPase activity, it shows a striking similarity to the structure of the ATP pyrophosphatase (ATP PPase) domain of GMP synthetase, indicating that both enzyme families have evolved from a common ancestral nucleotide-binding fold. CONCLUSIONS: The sequence conservation between ATP sulphurylases, a subfamily of ATP PPases, and PAPS reductase and the similarities in both their mechanisms and folds, suggest an evolutionary link between the ATP PPases and PAPS reductases. Together with the N type ATP PPases, PAPS reductases and ATP sulphurylases are proposed to form a new family of homologous enzymes with adenine nucleotide alpha-hydrolase activity. The open, reduced form of PAPS reductase is able to bind PAPS, whereas the closed oxidized form cannot. A movement between the two monomers of the dimer may allow this switch in conformation to occur.

A cDNA clone from Arabidopsis thaliana encoding plastidic ferredoxin:sulfite reductase.

A cDNA with an open reading frame of 1929 bp (termed sir) was isolated from a lambda ZapII library of Arabidopsis thaliana leaf tissue. The polypeptide sequence deduced from the cDNA is homologous to the ferredoxin-dependent sulfite reductase (EC 1.8.7.1) from Synechococcus PCC7942 and distantly related to the hemoprotein subunit of Escherichia coli NADPH-dependent sulfite reductase (EC 1.8.1.2). A molecular mass of 71.98 kDa can be predicted for a ferredoxin sulfite reductase from A. thaliana. The polypeptide consists of 642 amino acids including a transit peptide of 66 residues (6.72 kDa) that is assumed to direct the protein into the plastid. For expression and enzymatic characterization of a putative A. thaliana ferredoxin sulfite reductase, the DNA of the transit peptide was deleted by a PCR method. The truncated cDNA clone was expressed as his-tag fusion protein. The modified gene product was enzymatically inactive but specific cross-reaction with polyclonal antibodies against ferredoxin sulfite reductase from Synechococcus is seen as confirmation of its identity as higher plant ferredoxin sulfite reductase.

Reaction mechanism of thioredoxin: 3'-phospho-adenylylsulfate reductase investigated by site-directed mutagenesis.

Properties of purified recombinant adenosine 3'-phosphate 5'-phosphosulfate (PAdoPS) reductase from Escherichia coli were investigated. The Michaelis constants for reduced thioredoxin and PAdoPS are 23 microM and 10 microM, respectively; the enzyme has a Vmax of 94-99 mumol min-1 mg-1 and a molecular activity/catalytically active dimer of 95 s-1. Adenosine 3',5'-bisphosphate (PAdoP) inhibits competitively (Ki 4 microM) with respect to PAdoPS; adenosine 2',5'-bisphosphate and sulfite are not inhibitory. Alkylation by SH-group inhibitors irreversibly inactivates the enzyme. The structural gene (cysH) encodes for a small polypeptide with a single Cys residue located in a conserved cluster (KXECGI/LH) of amino acids. Involvement of the only Cys and of Tyr209 in the reduction of PAdoPS to sulfite was investigated by site-specific mutagenesis: cysH was mutated by single-strand-overlay extension PCR; the mutated genes were cloned in pBTac1 and expressed in E. coli RL 22 (delta cysHIJ). Homogenous Cys239Ser and Tyr209Phe mutant PAdoPS reductases were investigated for altered catalytic properties. Mutation of the single Cys reduced Vmax by a factor of 4.5 x 10(3) (Vmax = 0.02-0.013 mumol min-1 mg-1) with marginal effects on Km for PAdoPS (19 microM) and reduced thioredoxin (14 microM). Mutation of Tyr209 drastically affected saturation with thioredoxin (Km 1.5 microM) and decreased Vmax (0.22-0.25 mumol min-1 mg-1) in addition to a small increase in Km for PAdoPS (31 microM). Chromophores as prosthetic groups were absent from recombinant PAdoPS reductase. Difference absorption spectra between reduced and oxidized forms of wild-type and mutated proteins indicated that, in addition to Cys239 and Tyr209, an unidentified Trp (delta lambda max 292 nm) appears to be involved in the reduction. The data suggest a special ping-pong mechanism with PAdoPS reacting with the reduced enzyme isomer in a Theorell-Chance type mechanism.

APS-sulfotransferase activity is identical to higher plant APS-kinase (EC 2.7.1.25).

A cDNA from Arabidopsis thaliana L. Heynh encoding the APS-kinase (EC 2.7.1.25) was modified by deletion of a plastidic transit peptide to enable its expression in Escherichia coli. The resultant protein (MW 25,761) is enzymatically active as APS-kinase and restores prototrophic growth in an APS-kinase mutant. All transformants harbouring the modified plant DNA also acquired APS-sulfotransferase activity. In the absence of ATP but provided with DTT, a tetrameric form of recombinant APS-kinase exhibits APS-sulfotransferase activity. Monospecific polyclonal antibodies raised against the APS-kinase as immunogen also reacted against APS-sulfotransferase. We propose that APS-sulfotransferase activity is a nonphysiological side reaction of APS-kinase.

A cDNA for adenylyl sulphate (APS)-kinase from Arabidopsis thaliana.

A cDNA clone with an open reading frame of 831 nucleotides was isolated from a lambda ZapII-library of Arabidopsis thaliana. The nucleotide sequence of the cDNA is homologous to the APS-kinase genes from enterobacteria, diazotrophic bacteria, and yeast: Escherichia coli (cys C: 53.2%), Rhizobium meliloti (nod Q: 52.6%), and Saccharomyces cerevisiae (met 14:57.1%). The polypeptide deduced from the plant APS-kinase cDNA is comprised of 276 amino acid residues with a molecular weight of 29,790. It contains an N-terminal extension of 77 amino acids. This extension includes a putative transit peptide of 37 residues separated from the core protein by a VRACV processing site for stromal peptidase; a molecular weight of 26,050 is predicted for the processed protein. The relatedness between bacterial, fungal and plant APS-kinase polypeptides ranges from 47.5% (E. coli), 55.4% (S. cerevisiae), 52.6% (R. meliloti), and 50.3% (Azospirillum brasilense). The plant polypeptide contains eight cysteine residues; two cysteines flank a conserved purine nucleotide binding domain: GxxxxGK. Also conserved are a serine-182 as a possible phosphate transferring group and a K/LARAGxxxxFTG motif described for PAPS dependent enzymes. The identity of the gene was confirmed by analyzing the function of the gene product. The putative transit peptide was deleted by PCR and the truncated gene was expressed in a pTac1 vector system. A polypeptide of MW 25761 could be induced by IPTG. The gene product was enzymatically active as APS-kinase. It produced PAPS from APS and ATP--the absence of ATP but supplemented with thiols, the APS-kinase reacted as APS-sulphotransferase. APS-sulphotransferase is not a separate enzyme but identical with APS-kinase.

The ferredoxin:sulphite reductase gene from Synechococcus PCC7942.

The structural gene of the ferredoxin:sulphite reductase (EC 1.8.7.1) from the cyanobacterium Synechococcus PCC7942 (formerly 'Anacystis nidulans') was cloned and sequenced. The gene termed 'sir' was detected by heterologous Southern hybridisation with the structural gene cysI from Escherichia coli encoding the iron-sulphur haemoprotein of the NADPH:sulphite reductase. The open reading frame is comprised of 1875 bp encoding for a polypeptide of M(r) 70.028. The deduced amino acid sequence is 35.6% identical with the enterobacterial iron-sulphur haemoprotein. This putative fd-dependent sulphite reductase is only distantly related to the fd-dependent nitrite reductase (binary matching coefficient SAB: 0.23) or with the NADPH-sulphite reductase (SAB: 0.32). Highly conserved residues are found within the two Cys clusters forming the reactive Fe4S4-sirohaem centre of the enzyme. Expression of the sir gene using a fusion vector gave a single gene product which is immunologically related with the fd-sulphite reductase from the wild-type bacterium.

Primary structure of the Synechococcus PCC 7942 PAPS reductase gene.

The structural gene encoding a thioredoxin-dependent 5'-phosphoadenylyl sulphate (PAPS) reductase (EC 1.8.4.-) from cyanobacterium Synechococcus PCC 7942 ('Anacystis nidulans') was detected by heterologous hybridization with the cysH gene from Escherichia coli K12. The cyanobacterial gene (further called par gene) comprised 696 nt which are 57.8% homologous to the enterobacterial gene. The putative open reading frame encoded a polypeptide consisting of 232 amino acid residues (deduced molecular weight 26,635) which showed significant homologies to the polypeptide from E. coli (50.8%) and to the polypeptide from Saccharomyces cerevisiae (30.3%). A single cysteine located at the C-terminus of the polypeptide of E. coli (Cys239) was conserved in Synechococcus. Conservation of this cysteinyl residue seems indispensable for catalysis. Complementation of a cysH-deficient mutant of E. coli by the cyanobacterial gene indicated that the cloned DNA is the structural gene of the PAPS reductase.

Characterisation of the gene cysH and of its product phospho-adenylylsulphate reductase from Escherichia coli.

The nucleotide sequence of the gene cysH from Escherichia coli K12 was determined. The open reading frame was 735 nucleotides in length; it was flanked by a repetitive palindromic sequence centred 36 nucleotides upstream of cysH and a terminator-like structure located 20 nucleotides downstream. CysH encoded a polypeptide of Mr 27927 consisting of 244 amino acids. The gene product was isolated as a homodimer exhibiting phospho-adenylylsulphate reductase (PAPS reductase) activity. The active enzyme was devoid of electron transferring cofactors and contained only one cysteine per subunit. Reduction of the enzyme by dithiols resulted in a shift of the apparent molecular weight from 44,000 to 62,000 without formation of an enzyme-thioredoxin complex.

PAPS-reductase of Escherichia coli. Correlating the N-terminal amino acid sequence with the DNA of gene cys H.

The DNA of the gene complementing a PAPS-reductase-deficient strain of Escherichia coli was sequenced. The N-terminal amino acid sequence of the purified PAPS-reductase confirmed that cys H is the structural gene for this enzyme. The open reading frame extends 732 bases and encodes for a peptide of Mr = 27927. The gene product is functionally active when supplemented with thioredoxin and immunologically related with the wild type enzyme.

Yeast PAPS reductase: properties and requirements of the purified enzyme.

The enzymatic mechanism of sulphite formation in Saccharomyces cerevisiae was investigated using a purified 3'-phosphoadenylsulphate (PAPS) reductase and thioredoxin. The functionally active protein (MR 80-85 k) is represented by a dimer which reduces 3'-phosphoadenylyl sulphate to adenosine-3',5'-bisphosphate and free sulphite at a stoichiometry of 1:1. Reduced thioredoxin is required as cosubstrate. Examination of the reaction products showed that free anionic sulphite is formed with no evidence for "bound-sulphite(s)" as intermediate. Vmax of the enriched enzyme was 4-7 nmol sulphite.min-1.mg-1 using the homologous thioredoxin from yeast. The velocity of reaction decreased to 0.4 nmol sulphite.min-1.mg-1 when heterologous thioredoxin (from Escherichia coli) was used instead. The Km of homologous thioredoxin was 0.6.10(-6) M, for the heterologous cosubstrate it increased to 1.4.10(-6) M. The affinity for PAPS remained practically unaffected (Km PAPS: 19.10(-6) M in the homologous, and 21.10(-6) M in the heterologous system). From the kinetic data it is concluded that the enzyme followed an ordered mechanism with thioredoxin as first substrate followed by PAPS as the second. Parallel lines in the reciprocal and a common intersect in the Hanes-plots for thioredoxin were seen as indication of a ping-pong (with respect to thioredoxin) uni-bi (with respect to PAPS) mechanism.

PAPS-reductase from Escherichia coli: characterization of the enzyme as probe for thioredoxins.

PAPS-reductase from Escherichia coli was employed to detect thioredoxins from pro- and eukaryotic organisms. A simple method for the isolation of this enzyme and properties of the enzymatic assay were described. A comparison between thioredoxins detected by the PAPS-reductase and the Fructose-bisphosphatase or NADP malate dehydrogenase was used to assess the validity of the test. The high cross-reactivity of the bacterial enzyme was useful in the purification of heterologous thioredoxins from spinach, Synechococcus, and Saccharomyces cerevisiae.

Properties of the purified APS-kinase from Escherichia coli and Saccharomyces cerevisiae.

Adenylylsulphate kinase (EC 2.7.1.25, ATP:adenylylsulphate 3'-phosphotransferase) has been isolated from Escherichia coli and from Saccharomyces cerevisiae. As major steps of purification, affinity chromatography on Sepharose CL 6B ("blue" or "red") and chromatofocusing on polybuffer PBE 94tm were employed. The proteins were obtained in nearly homogeneous state after five chromatographic steps. The isolated enzymes from both sources appeared predominantly to exist as dimers. Upon reduction of the protein with dithiothreitol, it disintegrated into assumingly identical smaller subunits (E. coli rom Mr 90-85,000 to 45-40,000 and S. cerevisiae from 52-49,500 to 28-29,500). Both forms, dimer and monomer were found catalytically active. Preincubation of the isolated enzyme from either source in the presence of thioredoxin plus DTT, reduced glutathione or DTT increased the activity significantly. Treatment of the enzyme with SH-blocking reagents inactivated the enzyme irreversibly as compared to the inactivation caused by oxidants (2,6-dichlorophenol-indophenol, ferricyanide or oxydized glutathione). This oxidant induced inactivation was less pronounced for the fungal enzyme than for the bacterial protein. The enzyme from E. coli required thioredoxin in order to alleviate the GSSG-induced inactivation.

Expression of the plant sulphite reductase in cell suspension cultures from Catharanthus roseus L.

Sulphur-heterotrophic growth exhibited a dual response to the expression of sulphate-assimilating enzymes. The level of ATP-sulphurylase (EC 2.7.7.4) appeared "repressed" while sulphite reductase (EC 1.8.7.1) and O-acetyl-L-serine sulphhydrylase (EC 4.2.99.8) were "derepressed" and coordinated in their occurrence. The capability of the cells to reduce adenylylphosphosulphate or 3'-phospho adenylylphosphosulphate to cysteine coincided with the activity of sulphite reductase. The expression of these reducing steps lacked correlation with the regulation of ATP-sulphurylase.

Dissimilation of methionine in cell suspension cultures from Catharanthus roseus L.

Plant cell suspension cultures from Catharanthus roseus were investigated for their capability to dissimilate methionine or its analogs in order to reutilize the sulphane group for cysteine biosynthesis. Three steps have been described as prerequisites of this process: (a) oxidative degradation by the amino-acid oxidase of methionine giving rise to methanethiol production; (b) demethylation by methyltransferases leading to homocysteine and S-methylmethionine (c) replacement of the homocysteine sulphane sulphur by alkylthiol yielding methionine and free hydrogen sulphide. A reversal of the cystathionine pathway as a source of cysteine was ruled out because the cells lack cystathionine γ-lyase. The absence of this enzyme is compensated by the S-alkyl exchange of homocysteine with methylmercaptan. Hydrogen sulphide thus liberated is used for de novo synthesis of cysteine. The complete pathway can be catalyzed by the constitutive set of enzymes present in the higher plant.

On the role of S: Sulfotransferases in assimilatory sulfate reduction by plant cell suspension cultures.

Cell suspension cultures of Catharanthus roseus (L.) G. Don were grown under S-auxotrophic (1.8 mM sulfate) and under S-heterotrophic (0.5 and 1.0 mM cysteine or methionine) conditions. The development of activity of the thiol sulfotransferases was followed during the complete growth period. Under auxotrophic growth, an NADPH-dependent S: sulfotransferase and a GSH-dependent S: sulfotransferase developed identically, whereas under heterotrophic growth, differences in the amount of enzymes and in the time course of their development occurred. The NADPH-dependent sulfotransferase appeared "repressed" by the S-amino acids but the GSH-dependent enzyme was "derepressed." In that phenomenon, the development of the GSH sulfotransferase paralleled the development of the ATP-sulfurylase (EC 2774) activity of the cells.