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Applied and Environmental Microbiology, January 2006, p. 245-251, Vol. 72, No. 1
0099-2240/06/$08.00+0 doi:10.1128/AEM.72.1.245-251.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Jie Zou,1,
Qiyu Bao,2
Wen-Li Chen,1
Li Wang,1
Huanming Yang,3 and
Cheng-Cai Zhang1,4*
National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China,1 Institute of Biomedical Informatics, Wenzhou Medical College, Wenzhou 325000, People's Republic of China,2 Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, People's Republic of China,3 Laboratoire de Chimie Bactérienne, IBSM, CNRS-UPR9043, 31 Chemin Joseph Aiguie, 13402 Marseille Cedex 20, France4
Received 13 September 2005/ Accepted 29 October 2005
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The family of PAPases belongs to a superfamily of metal-dependent phosphatases with various substrates. These enzymes contain a fructose-1,6-biphosphate 1-phosphatase (FBPase)/inositol monophosphatase (IMPase)/GlpX-like domain and are sensitive to lithium but dependent on magnesium. Two families have been defined for the FBPase/IMPase/GlpX-like domain-containing protein superfamily, the FBPase family, and the IMPase family. FBPases hydrolyze fructose-1,6-biphosphate and are involved in gluconeogenesis (4, 14, 28). The IMPase family includes PAPases, inositol polyphosphate 1-phosphatases (IPPases), IMPases, and PAP/inositol-1,4-bisphosphate phosphatases (PIPases). These enzymes share a common structural core within the active sites and critical residues required for metal binding. Among the well-characterized enzymes of this superfamily, Hal2p from Saccharomyces cerevisiae and AtAHL (Hal2p-like protein) from Arabidopsis thaliana are PAPases (9, 16, 17) and Tol1 from Schizosaccharomyces pombe and Sal1 from Arabidopsis thaliana are PIPases (15, 21).
Sulfate assimilation pathways are well conserved in plants, yeasts, and bacteria (23). PAPS reductase encoded by cysH is also found in a variety of bacterial genomes sequenced so far. However, to our knowledge, the enzymes involved in PAP hydrolysis are poorly defined for bacteria. The most likely candidate of PAPase is the gene product of cysQ from Escherichia coli, since this gene was shown to be required for sulfate assimilation, and its mutation could be complemented by a HAL2-like gene from rice (18, 20). However, the deduced amino acid sequence from cysQ is only distantly related to PAPases from plants and yeasts, and its enzyme activity has never been determined. We have initiated a study on the properties of a putative Hal2p homolog, called HalA, from the cyanobacterium Arthrospira (Spirulina) platensis. Although Arthrospira platensis is found in freshwater environments, this strain is highly resistant to salt and can even be grown in marine water (13, 26). The mechanism of salt resistance of this cyanobacterium is not known. Studies on PAPases from bacteria may help us to understand the structure-function relationship of salt sensitivity of these enzymes and provide information for the engineering of salt-resistant crops.
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Cloning and overexpression of halA in E. coli.
The coding region of the putative open reading frame of halA was amplified by PCR, with one primer containing an NdeI site at the 5' end and the other primer containing an EcoRI site right after the stop codon. The sequences of the two primers were as follows: 5'-CAAGGATCCCATATGCCCTACGATCGCGAAA-3' and 5'-CTTGAATTCGGCGGGTTGATGATTCTT-3'. The PCR product was cloned into the expression vector pET28a(+) after digestion with NdeI and EcoRI, and the resulting clone was named pET28a-ArHAL. In this construct, the open reading frame of halA was translationally fused to a sequence encoding a His tag which facilitates the purification of the recombinant protein. The accuracy of the cloned DNA fragment was confirmed by DNA sequencing. The construct was then transformed into E. coli strain BL21(DE3).
Protein purification and enzyme assays.
After the addition of 0.3 mM isopropyl-ß-D-thiogalactopyranoside (IPTG), cells were cultured for 4 h and then collected by centrifugation and resuspended in lysis buffer (30% sucrose, 0.25 M Tris [pH 8.0], 0.5 M KCl, 25 mM EDTA, 5 mM dithiothreitol, 0.2 mM phenylmethylsulfonyl fluoride). After sonication and treatment with DNase I, the supernatant was separated from cell debris by centrifugation. The expression of the recombinant protein was monitored by sodium dodecyl sulfate (SDS)-12% polyacrylamide gel electrophoresis.
The recombinant fusion protein His tag-HalA was purified by nickel affinity chromatography using a HisTrap kit (Amersham Inc.) under nondenaturing conditions following the manufacturer's instructions. The optimal concentrations of imidazole were 100 mM in the binding buffer and 200 mM in the elution buffer.
Phosphatase assays were performed as described previously with minor modifications (16). Briefly, a standard assay was conducted in a 100-µl reaction mixture containing 50 mM Tris (pH 8.0), 2 mM MgCl2, and the indicated amounts of purified protein and substrate. After 40 min of incubation at 30°C, the inorganic phosphate released during the reaction was quantified using the malachite green method as described by Baykov et al. (5). Under these conditions, the enzyme activity was linear with protein quantity (up to 300 ng) and reaction time (up to 1 h). The Km for PAP was determined by measuring reaction rates at substrate concentrations of 0.1, 0.2, 0.4, 0.7, and 1 mM. The Km for inositol-1,4-bisphosphate was determined by measuring reaction rates at substrate concentrations of 0.1, 0.2, 0.3, 0.4, and 0.5 mM. The Km for PAPS was determined by measuring reaction rates at substrate concentrations of 0.2, 0.4, 0.6, 0.8, and 1 mM. Specific activity was estimated by normalizing to the protein concentration determined by the Bradford method (Bio-Rad), which was consistent with the relative band intensity on the SDS-polyacrylamide gel, using bovine serum albumin as the standard.
Phylogenic analysis and structural modeling.
Phylogenetic construction and illustration were performed using MEGA3.1 and the neighbor-joining method (11). Bootstrap analysis was performed with 3,000 resampling replicates.
The alignment between HalA and Hal2p was produced with ClustalX1.8 (27) and manually optimized based on their secondary structures. This alignment was submitted as the input to the SWISS-MODEL server (http://swissmodel.expasy.org/SWISS-MODEL.html), with the high-resolution X-ray structure of Hal2p (PDB identification, 1ka1A) as a template to build the three-dimensional model of HalA. Swiss Pdb-Viewer was used to view the structure and the Ramachandran plot as well as to produce the stereo figures. The Ramachandran plot of the HalA model showed that 283 residues (88.7%) had their dihedral angles clustered in the most favored regions, 23 residues (7.2%; proline and glycine residues were not counted) in the additional allowed regions, and 9 residues (2.8%; proline and glycine residues were not counted) in the disallowed regions. All the residues having disallowed dihedral angles were located at the coil regions (on the surface of the structure) and far from the active center.
Nucleotide sequence accession number.
The sequence of halA has been deposited into the National Center for Biotechnology Information databank, and the accession number is DQ185137.
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FIG. 1. Phylogenic analysis of various IMPases. For each protein, the corresponding organisms and the accession number from the databanks are shown. The full names of the species under study, except those already mentioned in the text or the figure, were Agrobacterium tumefaciens C58, Aquifex aeolicus VF5, Brucella melitensis 16M, Caenorhabditis elegans, Cytophaga hutchinsonii, Desulfitobacterium hafniense, Gloeobacter violaceus PCC7421, Magnetospirillum magnetotacticum, Mesembryanthemum crystallinum, Mesorhizobium loti MAFF303099, Methylobacillus flagellatus KT, Mycobacterium tuberculosis, Neurospora crassa, Prochlorococcus marinus MIT9313, Prochlorococcus marinus CCMP1375, Prochlorococcus marinus CCMP1986, Pseudomonas syringae DC3000, Rhodobacter sphaeroides, Rhodospirillum rubrum, Streptomyces coelicolor A3(2), Synechococcus elongatus PCC6301, Thermosynechococcus elongatus BP-1, Xanthomonas axonopodis 306, and Xenopus laevis. Based on this analysis, five different clusters can be clearly defined (clades I through V). Proteins from cyanobacteria are marked with a triangle. Proteins of particular relevance to this work are shown in boldface. Bootstrap values are labeled on the major branches.
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HalA is a magnesium-dependent PAPase.
The coding region of halA was cloned in an expression vector, and its corresponding protein was produced in E. coli as a fusion product with the His tag. After induction with IPTG and protein separation on an SDS-12% polyacrylamide gel, a polypeptide with an apparent molecular mass of 41.8 kDa could be identified (Fig. 2). The size of this polypeptide was slightly higher than the theoretical molecular mass of the recombinant protein (36.4 kDa) predicted from the corresponding DNA sequence of halA together with the His tag sequence. As expected, the BL21(DE3) strain transformed with the vector pET28a(+) without insert did not give rise to the corresponding polypeptide (Fig. 2). Purification using a nickel affinity chromatography column (see Materials and Methods) yielded the recombinant protein with good homogeneity (Fig. 2).
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FIG. 2. Analysis of the purified HalA on an SDS-12% polyacrylamide electrophoresis gel stained with Coomassie brilliant blue. Lane 1, protein extract from E. coli transformed with plasmid pET28a(+) (control); lane 2, protein extract from E. coli transformed with plasmid pET28a-ArHAL (containing the coding region of the halA gene); lane 3, HalA after purification in a HisTrap affinity column; lane 4, molecular mass standards in kilodaltons.
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TABLE 1. Substrate specificity of the phosphatase activity of HalA
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FIG. 3. Effects of Mg2+ (A) and pH (B) on the activity of HalA. Error bars indicate standard deviations.
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Li+ inhibition.
Most PAPases from yeasts and plants are strongly inhibited by Li+ ions and to a lesser extent by Na+ ions (4, 8, 22). The effects of several ions on the activity of HalA were thus tested. When the concentration of Li+ was 2 mM or less, little inhibitory effect on the PAPase activity of HalA was observed. However, once the concentration of Li+ was increased to more than 2 mM, a drastic inhibitory effect on the enzyme activity was obtained. IC50, an index measuring the concentration of an inhibitor to reduce the enzyme activity by 50%, was estimated to be 3.6 mM (Fig. 4). To determine if the effect of Li+ on the activity of HalA was specific, LiCl was replaced with NaCl or KCl. The results showed that K+ at a concentration as high as 600 mM had no inhibitory effect on the activity of HalA. When the concentration of K+ was at 50 mM, a stimulatory effect was observed (Fig. 4). Low concentrations of Na+ stimulated the activity of HalA as K+, and as its concentrations increased, a weak inhibitory effect was found (IC50 = 600 mM).
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FIG. 4. Effects of various ions on the enzyme activity of HalA with 0.5 mM PAP as substrate. The activity was measured in a buffer containing 50 mM Tris, pH 8.0, and 2 mM MgCl2 at 30°C for 40 min. The activity obtained at optimal conditions was considered 100%, and that obtained in the presence of ions was normalized to the optimal activity. Error bars indicate standard deviations.
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FIG. 5. Effects of the expression of halA in E. coli on the tolerance toward LiCl. E. coli strain BL21 (DE3) was transformed with either pET28a-ArHAL (A and C) or pET28a(+) (B and D). The two transformed strains were grown in M9 medium supplemented with MgSO4 as the sulfur source and 0.04 mM IPTG as the inducer. For A and B, no LiCl was added; for C and D, 0.4 M LiCl was added. The growth rate was followed by measuring the optical density (OD) by spectroscopy at 600 nm. Error bars show the results of three independent experiments.
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Protein sequence alignment suggested that HalA could have a PAPase activity. This was confirmed by biochemical analysis indicating that HalA could use PAP as the best substrate tested. These data were comparable to those obtained with Hal2p-like protein (AtAHL) from Arabidopsis thaliana (9). The activity of AtAHL by using PAPS as the substrate was 52% of that obtained using PAP. By comparison with other PAPases from yeasts and plants, HalA had a high Km value and reaction velocity (Table 2). Structural modeling using the structure of Hal2p from yeast as a template suggested that a very similar substrate-binding pocket was present in HalA (Fig. 6). However, the putative substrate-binding motif of HalA has a proline residue (P254) which might lower its affinity with PAP.
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TABLE 2. Comparison of different parameters of various enzymes
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FIG. 6. Modeling of the substrate-binding site of HalA. The model was based on the high-resolution X-ray structure of Hal2p from yeast (2, 19). A major difference between Hal2p and HalA was found at the substrate-binding pocket with the presence of the ring structure of Pro254 in HalA.
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It has been shown that the expression of Sal1 of Arabidopsis thaliana enhances salt tolerance in yeast (21). Similarly, the expression of halA in E. coli enhances its resistance to lithium, suggesting that lithium tolerance mediated by HalA-like proteins could also take place in bacteria. This phenotype was observed only when sulfate was used as the sole sulfur source for the growth of E. coli (Fig. 5). In the rich LB medium, where amino acids were readily available, no difference in growth rate was observed between the strain expressing halA and the control strain. Similarly, when sulfite replaced sulfate, both strains grew better and no growth difference was observed with or without LiCl. These results correlate well with the inhibition of sulfur metabolism by lithium in bacteria and the fact that PAP is produced during the reduction of sulfate to sulfite (2, 17). The properties of HalA could be helpful for studying the structure-function relationship of PAPases and understanding their molecular basis of salt resistance. Furthermore, the relatively higher resistance of HalA to salt makes it a good candidate for expression in plants in order to improve the salt resistance of crops.
Sulfur metabolism is poorly understood in cyanobacteria. Several genes involved in sulfate transport have been characterized in Synechococcus elongatus strain PCC7942 (10, 12). Sulfur deprivation has a profound impact on the physiology and relocation of cell resources (7). But, in general, how sulfur metabolism is regulated in response to environmental changes remains largely unknown. Mutants of a cyanobacterial strain resistant to LiCl have been isolated, but the targets of these mutations have never been clearly identified (6). Characterization of enzymes involved in sulfur metabolism could be helpful for the understanding of the regulation of sulfur metabolism in cyanobacteria.
J.-Y.Z. and J.Z. contributed equally to this work. ![]()
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