Purification and characterization of extracellular soluble and membrane-bound insoluble alkaline phosphatases possessing phosphodiesterase activities in Bacillus subtilis

Iron limitation of microbial phosphorus acquisition in the tropical North Atlantic

In certain regions of the predominantly nitrogen limited ocean, microbes can become co-limited by phosphorus. Within such regions, a proportion of the dissolved organic phosphorus pool can be accessed by microbes employing a variety of alkaline phosphatase (APase) enzymes. In contrast to the PhoA family of APases that utilize zinc as a cofactor, the recent discovery of iron as a cofactor in the more widespread PhoX and PhoD implies the potential for a biochemically dependant interplay between oceanic zinc, iron and phosphorus cycles. Here we demonstrate enhanced natural community APase activity following iron amendment within the low zinc and moderately low iron Western North Atlantic. In contrast we find no evidence for trace metal limitation of APase activity beneath the Saharan dust plume in the Eastern Atlantic. Such intermittent iron limitation of microbial phosphorus acquisition provides an additional facet in the argument for iron controlling the coupling between oceanic nitrogen and phosphorus cycles.

Crystal structure of the Bacillus subtilis phosphodiesterase PhoD reveals an iron and calcium-containing active site

The PhoD family of extra-cytoplasmic phosphodiesterases are among the most commonly occurring bacterial phosphatases. The exemplars for this family are the PhoD protein of Bacillus subtilis and the phospholipase D of Streptomyces chromofuscus. We present the crystal structure of B. subtilis PhoD. PhoD is most closely related to purple acid phosphatases (PAPs) with both types of enzyme containing a tyrosinate-ligated Fe³⁺ ion. However, the PhoD active site diverges from that found in PAPs and uses two Ca²⁺ ions instead of the single extra Fe²⁺, Mn²⁺, or Zn²⁺ ion present in PAPs. The PhoD crystals contain a phosphate molecule that coordinates all three active site metal ions and that is proposed to represent a product complex. A C-terminal helix lies over the active site and controls access to the catalytic center. The structure of PhoD defines a new phosphatase active site architecture based on Fe³⁺ and Ca²⁺ ions.

Assembly-free metagenomic analysis reveals new metabolic capabilities in surface ocean bacterioplankton

Uncovering the metabolic capabilities of microbes is key to understanding global energy flux and nutrient transformations. Since the vast majority of environmental microorganisms are uncultured, metagenomics has become an important tool to genotype the microbial community. This study uses a recently developed computational method to confidently assign metagenomic reads to microbial clades without the requirement of metagenome assembly by comparing the evolutionary pattern of nucleotide sequences at non-synonymous sites between metagenomic and orthologous reference genes. We found evidence for new, ecologically relevant metabolic pathways in several lineages of surface ocean bacterioplankton using the Global Ocean Survey (GOS) metagenomic data, including assimilatory sulfate reduction and alkaline phosphatase capabilities in the alphaproteobacterial SAR11 clade, and proteorhodopsin-like genes in the cyanobacterial genus Prochlorococcus. These findings raise new hypotheses about microbial roles in energy flux and organic matter transformation in the ocean.

Role of the phosphatase PhoX in the phosphorus metabolism of the marine bacterium Ruegeria pomeroyi DSS-3

Marine microbes are adapted to surviving in a variable phosphorus (P) environment. This adaptation frequently involves the presence of periplasmic or cell membrane-associated enzymes that enable them access to alternative sources of P when phosphate is depleted. In a recent study we identified the phosphatase PhoX as an enzyme that may be essential in mediating organic P acquisition in the ocean. Here we have investigated the role of this enzyme in the utilization of different P sources, using as a model the marine bacterium Ruegeria pomeroyi DSS-3. Although our previous study had demonstrated that PhoX accounts for more than 90% of the alkaline phosphatase (APase) activity in R. pomeroyi, a PhoX mutant strain was able to grow on monophosphate esters at the same rate as the wild type. Nevertheless, further APase kinetic analyses with both strains demonstrated that the Km of the wild-type strain was an order of magnitude lower than the mutant strain, indicating that PhoX is crucial for the use of these substrates at low concentrations, typically found in seawater. We also showed that PhoX is required for efficient hydrolysation of nucleotides like ADP and ATP.

Prediction of functional class of novel bacterial proteins without the use of sequence similarity by a statistical learning method

A substantial percentage of the putative protein-encoding open reading frames (ORFs) in bacterial genomes have no homolog of known function, and their function cannot be confidently assigned on the basis of sequence similarity. Methods not based on sequence similarity are needed and being developed. One method, SVMProt (http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi), predicts protein functional family irrespective of sequence similarity (Nucleic Acids Res. 2003;31:3692-3697). While it has been tested on a large number of proteins, its capability for non-homologous proteins has so far been evaluated for a relatively small number of proteins, and additional tests are needed to more fully assess SVMProt. In this work, 90 novel bacterial proteins (non-homologous to known proteins) are used to evaluate the capability of SVMProt. These proteins are such that none of their homologs are in the Swiss-Prot database, their functions not clearly described in the literature, and they themselves and their homologs are not included in the training sets of SVMProt. They represent proteins whose function cannot be confidently predicted by sequence similarity methods at present. The predicted functional class of 76.7% of each of these proteins shows various levels of consistency with the literature-described function, compared to the overall accuracy of 87% for the SVMProt functional class assignment of 34,582 proteins that have at least one homolog of known function. Our study suggests that SVMProt is capable of assigning functional class for novel bacterial proteins at a level not too much lower than that of sequence alignment methods for homologous proteins.

Mutational analysis of the phoD promoter in Bacillus subtilis: implications for PhoP binding and promoter activation of Pho regulon promoters

The PhoP-PhoR two-component regulatory system controls the phosphate deficiency response in B. subtilis. A number of Pho regulon genes which require PhoP approximately P for activation or repression have been identified. The studies reported here were initiated to understand the PhoP-DNA interaction necessary for Pho promoter regulation. The regulatory region of phoD was characterized in detail using oligo-directed mutagenesis, DNase I footprinting, and in vivo transcription assays. These data reveal basic principles of PhoP binding relevant to PhoP's interaction with other Pho regulon promoters. Our results show that: (i) a dimer of PhoP approximately P is able to bind two consensus repeats in a stable fashion; (ii) PhoP binding is highly cooperative within the core promoter region, which is located from -66 to -17 on the coding strand and contains four TT(A/T/C)ACA-like repeats; (iii) specific bases comprising the TT(A/T/C)ACA consensus are essential for transcriptional activation, but the specific base pairs of the intervening sequences separating the consensus repeats are not important for either PhoP binding or promoter activation; (iv) the spacing between two consensus repeats within a putative dimer binding site in the core region is important for both PhoP binding and promoter activation; (v) the exact spacing between two dimer binding sites within the core region is important for promoter activation but less so for PhoP binding affinity, as long as the repeats are on the same face of the helix; and (vi) the 5' secondary binding region is important for coordinated PhoP binding to the core binding region, making it nearly essential for promoter activation.

Cloning and sequencing of a cyclodextrin glycosyltransferase gene from Brevibacillus brevis CD162 and its expression in Escherichia coli

A cyclodextrin glycosyltransferase (CGTase) gene of Brevibacillus brevis CD162 was cloned into Escherichia coli using pUC19 as a vector. Determination of the nucleotide sequence showed the presence of an open reading frame of 2079 bp encoding a polypeptide of 693 amino acid residues, composed of a 20-amino acid signal sequence and a 673-amino acid mature enzyme. Neither a TATA- nor a TTGA-like sequence was observed within the cloned DNA fragment. However, the fragment was expressed in Escherichia coli by the lac promoter of pUC19 and 74% of the total activity was secreted into the fermentation medium. The amino acid sequence of the mature CGTase showed the highest homology of 86% to that of Bacillus sp. KC201. The CGTase purified to homogeneity from the recombinant E. coli exhibited the same properties as those of native CGTase from Brevibacillus brevis CD162 in terms of molecular mass, reaction conditions, stability and the production of cyclodextrins.

Sites internal to the coding regions of phoA and pstS bind PhoP and are required for full promoter activity

Bacillus subtilis PhoP and PhoR, a pair of two-component regulatory proteins, regulate the phosphate starvation response. Here, we used two other pho regulon promoters, the phoA and pstS promoters, to examine the mechanism of PhoP-specific activation of its target promoters. Both gel shift and DNase I footprinting assays indicate that PhoP bound to the two promoters. Unphosphorylated PhoP bound only to the multiple TTAACA-like sequences upstream of these two promoters, while phosphorylated PhoP extended the binding region in both the 5' and the 3' direction and, additionally, protected sequences internal to the coding region of these two genes. The PhoP binding sites in the coding region were necessary for full induction from either promoter during phosphate starvation. Deletion of these sites eliminated approximately 75% and 45% of the induced promoter activity of the phoA and pstS promoters respectively. In vitro transcription assays using the phoA promoters with various 3' ends confirmed the requirement of the PhoP-P binding to the coding region for full promoter activity. The multiple TTAACA-like sequences in the phoA and pstS promoters were essential for promoter activity, and deletion of one or more of these sequences in either promoter eliminated the promoter activity. Two pairs of TTAACA-like sequences were required for efficient PhoP binding and were suggested to be one B. subtilis Pho box. Based on our data, we have proposed a model for activation of the phoA and the pstS promoter by PhoP.

Production of two extracellular alkaline phosphatases by a psychrophilic arthrobacter strain

We surveyed our collection of psychrophilic bacteria to determine the types of phosphatases they produce and whether any had heat-labile activities with potential applications. Assays at different temperatures showed that the activity from one isolate was optimal at 45(deg)C and decreased dramatically above 55(deg)C. This isolate, D10, had the rod-coccus morphological cycle and cell wall amino acids associated with members of the Arthrobacter genus. Interestingly, we found that this strain made two extracellular phosphatases that could be separated by ammonium sulfate fractionation and migration during polyacrylamide gel electrophoresis. One enzyme, designated D10A, hydrolyzed both X-phos (5-bromo-4-chloro-3-indolyl phosphate) and para-nitrophenyl phosphate as substrates and had activity over a broad pH range of 7 to 11. The second enzyme, D10B, lacked activity against X-phos and had a narrow pH range of about 8 to 9. In addition, the D10B enzyme required calcium for activity. The levels of activity of both enzymes decreased for cells grown in media containing more than 100 (mu)M P(infi). These results not only demonstrate the existence of different enzymes from one Arthrobacter strain but also suggest ways in which other studies may have missed phosphatases with unknown requirements.

Phosphodiesterase activity is a novel property of alkaline phosphatase from osseous plate

Phosphodiesterase activity is a novel property of the still-enigmatic alkaline phosphatase from osseous plate. Bis-(p-nitrophenyl) phosphate was hydrolysed at both pH 7.5 and 9.4 with an apparent dissociation constant (K0.5) of 1.9 mM and 3.9 mM respectively. The hydrolysis of p-nitrophenyl-5'-thymidine phosphate followed hyberbolic kinetics with a K0.5 of 500 microM. For p-nitrophenyl phenylphosphonate, site-site interactions [Hill coefficient (h) = 1.3] were observed in the range between 0.2 and 100 microM, and K0.5 was 32.8 mM. The hydrolysis of cyclic AMP by the enzyme followed more complex kinetics, showing site-site interactions (h = 1.7) and K0.5 = 300 microM for high-affinity sites. The low-affinity sites, representing 85% of total activity, also showed site-site interactions (h = 3.8) and a K0.5 of about 22 mM. ATP and cyclic AMP were competitive inhibitors of bis-(p-nitrophenyl) phosphatase activity of the enzyme and Ki values (25 mM and 0.6 mM for cyclic AMP and ATP respectively) very close to those of the K0.5 (22 mM and 0.7 mM for cyclic AMP and ATP respectively), determined by direct assay, indicated that a single catalytic site was responsible for the hydrolysis of both substrates. Non-denaturing PAGE of detergent-solubilized enzyme showed coincident bands on the gel for phosphomonohydrolase and phosphodiesterase activities. Additional evidence for a single catalytic site was the similar pKa values (8.5 and 9.7) found for the two ionizing groups participating in the hydrolysis of bis-(p-nitrophenyl) phosphate and p-nitrophenyl phosphate. The alkaline apparent pH optima, the requirement for bivalent metal ions and the inhibition by methylxanthines, amrinone and amiloride demonstrated that rat osseous-plate alkaline phosphatase was a type I phosphodiesterase. Considering that there is still confusion as to which is the physiological substrate for the enzyme, the present results describing a novel property for this enzyme could be of relevance in understanding the mineralization process.

Bacillus subtilis PrsA is required in vivo as an extracytoplasmic chaperone for secretion of active enzymes synthesized either with or without pro-sequences

In prsA (protein secretion) mutants of Bacillus subtilis, decreased levels of exoproteins, including alpha-amylase and subtilisins, are found extracellularly. The effect of prsA on subtilisin secretion is elaborated here. Extracytoplasmic folding and secretion of active subtilisin is assisted by the N-terminal pro-sequence of its precursor. In this paper we present evidence that the product of the prsA gene is additionally required for these processes in vivo. We examined inducible expression of different subtilisin-alkaline phosphatase fusion genes in the prsA3 mutant. We found massive degradation of the fusion proteins, and a lack of enzymatic activity in the protein secreted. We suggest that PrsA is a novel chaperone with a predicted extracytoplasmic location, and is important in vivo for the proper conformation of various exoproteins, including those with pro-sequence (like subtilisin) and those without (like alpha-amylase).

Purification and properties of two membrane alkaline phosphatases from Bacillus subtilis 168

Two alkaline phosphatases were extracted from the membranes of Bacillus subtilis 168 stationary-phase cells and purified as homogeneous proteins by hydroxyapatite column chromatography. Alkaline phosphatases I and II differed in several properties such as subunit molecular weight, substrate specificity, thermostability, Km, pH stability, and peptide maps.

Evidence for two structural genes for alkaline phosphatase in Bacillus subtilis

Two secreted alkaline phosphatase proteins were purified from cultures of Bacillus subtilis JH646MS. The two proteins showed slight differences in subunit molecular weight, substrate specificity, and charge characteristics. A total of 62% of the first 22 amino-terminal amino acids were identical. Both sequences showed conservation of structural features identified in Escherichia coli and human alkaline phosphatases. One alkaline phosphatase was a monomer and the other was a dimer. Southern analysis of genomic DNA with degenerative oligomers based on the amino acid sequences suggest that there are two structural genes for alkaline phosphatase in the genome of B. subtilis.

The utilization of inorganic and organic phosphorous compounds as nutrients by eukaryotic microalgae: a multidisciplinary perspective: part 1

This comprehensive literature review of the phosphorus nutrition and metabolism of eukaryotic microalgae deals sequentially with (1) extracellular P-compounds available for algal utilization and growth; (2) orthophosphate uptake mechanisms, kinetics, and influence from environmental variables; (3) phosphatase-mediated utilization of organic phosphates involving multiple enzymes, induction and cellular location of repressible and irrepressible phosphatases, and their role in growth physiological processes; (4) intracellular phosphate metabolism covering diversity of phosphometabolites. ATP-linked energy regulation, polyphosphate pools and storage roles, phospholipids and phospholipases; (5) steady-state and transient-state models relating phosphate utilization to growth; (6) ecological aspects covering manifestations of phosphorus limitation, interspecific competition for phosphonutrients among microorganisms, and current views on phosphorus cycling and turnover in aquatic ecosystems. Although concentrating on the microalgae, the review often points out sounder conclusions drawn from bacteria and fungi, and includes specific macroalgae in considering certain subtopics where such algae were better investigated and provided a good basis for comparison with the microalgae.

Extracellular and membrane-bound proteases from Bacillus subtilis

Bacillus subtilis YY88 synthesizes increased amounts of extracellular and membrane-bound proteases. More than 99% of the extracellular protease activity is accounted for by an alkaline serine protease and a neutral metalloprotease. An esterase having low protease activity accounts for less than 1% of the secreted protease. These enzymes were purified to homogeneity. Molecular weights of approximately 28,500 and 39,500 were determined for the alkaline and neutral proteases, respectively. The esterase had a molecular weight of approximately 35,000. Amino-terminal amino acid sequences were determined, and the actions of a number of inhibitors were examined. Membrane vesicles contained bound forms of alkaline and neutral proteases and a group of previously undetected proteases (M proteases). Membrane-bound proteases were extracted with Triton X-100. Membrane-bound alkaline and neutral proteases were indistinguishable from the extracellular enzymes by the criteria of molecular weight, immunoprecipitation, and sensitivity to inhibitors. The M protease fraction accounted for approximately 7% of the total activity in Triton X-100 extracts of membrane vesicles. The M protease fraction was partially fractionated into four species (M1 through M4) by ion-exchange chromatography. Immunoprecipitation and sensitivity to inhibitors distinguished membrane-bound alkaline and neutral proteases from M proteases. In contrast to alkaline and neutral proteases, proteases M2 and M3 exhibited exopeptidase activity.

Alkaline phosphatase possessing alkaline phosphodiesterase activity and other phosphodiesterases in Bacillus subtilis

In Bacillus subtilis Marburg strain, single-point mutations in the phoP locus brought about simultaneous losses of the major activities of alkaline phosphatase (APase) and alkaline phosphodiesterase (APDase). Revertants recovered the two activities. APases with APDase activity were purified from the membrane fraction of B. subtilis 6160-BC6 and from the culture fluid of an APase-secreting B. subtilis mutant strain, RAN 1. In addition to these major APases with APDase activity, at least two kinds of phosphodiesterase (PDase) without phosphatase activity were found in the cytoplasmic supernatants of RAN 1 and an APase-less B. subtilis mutant strain, SP25. Another minor APase with a molecular weight of about 80,000, which had almost no PDase activity, was isolated from the membrane fraction of strain 6160-BC6. Enzyme distribution in subcellular fractions from various strains cultured in high- and low-phosphate media was analyzed. The PDases did not cross-react with rabbit antiserum against the RAN 1 APase with APDase activity. The main component of the PDases had a molecular weight of about 80,000 and was most active at pH 8.0. These results suggest that APase with APDase activity is different from PDases detected in cytoplasmic supernatants and that phoP is the structural gene for the phosphate-repressible APase with APDase activity.