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Journal of Bacteriology, October 2005, p. 7150-7154, Vol. 187, No. 20
0021-9193/05/$08.00+0     doi:10.1128/JB.187.20.7150-7154.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Biosynthesis of Active Bacillus subtilis Urease in the Absence of Known Urease Accessory Proteins

Jong Kyong Kim,1 Scott B. Mulrooney,2 and Robert P. Hausinger1,2,3*

Cell and Molecular Biology Program,1 Department of Microbiology and Molecular Genetics,2 Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-43203

Received 1 June 2005/ Accepted 27 July 2005


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ABSTRACT
 
Bacillus subtilis contains urease structural genes but lacks the accessory genes typically required for GTP-dependent incorporation of nickel. Nevertheless, B. subtilis was shown to possess a functional urease, and the recombinant enzyme conferred low levels of nickel-dependent activity to Escherichia coli. Additional investigations of the system lead to the suggestion that B. subtilis may use unidentified accessory proteins for in vivo urease activation.


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TEXT
 
Urease is a Ni-containing enzyme found in plants, fungi, and bacteria (15). This protein participates in the recycling of environmental nitrogen and serves as a virulence factor in pathogenic microorganisms associated with gastric ulceration and urinary stone formation (22). Most bacterial ureases possess three structural subunits (encoded by ureABC) associated into a trimer of trimers [({alpha}ß{gamma})3], with each UreC subunit containing a dinuclear Ni active site bridged by a carbamylated lysine (4, 16, 28). Helicobacter species have only two subunits (UreA, a fusion of the small subunits [ß and {gamma}] in other bacteria, and the large subunit, designated UreB) in a ({alpha}3ß3)4 macromolecular structure (14). Fungi and plants contain a homohexamer ({alpha}6) of a fusion of the three bacterial sequences (30). Synthesis of active urease requires the action of several accessory proteins (23), with the best-studied system found in Klebsiella aerogenes, in which the structural genes are found in a gene cluster containing four accessory genes (ureDABCEFG). By use of this system, UreD-UreF-UreG was identified as a GTP-dependent molecular chaperone that binds urease apoprotein (8, 32), while UreE was shown to function as a metallochaperone that delivers Ni2+ (11, 25, 31).

Genome sequence analysis has revealed that, in contrast to other ureolytic microorganisms, Bacillus subtilis contains only urease structural genes (ureABC) and lacks homologues to any accessory genes (18). Despite this dearth of urease genes, the organism exhibits urease activity and grows with urea as the sole nitrogen source unless ureC is inactivated (12).

Urease activity in B. subtilis. B. subtilis SF10 cells (wild type, SMY derivative; from Susan Fisher) (3) were cultured at 37°C in S7 minimal medium (37) plus 0.2% glutamate. A low but detectable level of urease activity (0.113 ± 0.006 U/mg protein, where one unit is the amount of enzyme required to hydrolyze 1 µmol of urea per min at 37°C in 50 mM HEPES buffer, pH 7.8, containing 50 mM urea) (38) was observed in cell extracts obtained by sonication followed by centrifugation (10,000 x g, 20 min, 4°C). This level of activity is comparable to the level of 0.103 ± 0.012 U/mg (after correction to the same units) described previously for extracts of these cells (3) and compares to ~2 U/mg for cell extracts of K. aerogenes (36) or 2,500 U/mg for the purified K. aerogenes urease (35). The addition of 100 µM NiCl2 to the culture had no effect on the urease activity (0.107 ± 0.016 U/mg), which suggests that the trace levels of Ni2+ in the minimal medium were sufficient for synthesis of active urease or that Ni2+ was not required.

Overexpression of B. subtilis ureABC in B. subtilis and Escherichia coli. To test whether Ni2+-dependent activity is observed in B. subtilis that overproduces the urease, pDR-BsABC was constructed by amplifying the B. subtilis ureABC genes from pURE91 (a pET23-derived plasmid provided by Susan Fisher), digesting with SalI and NheI, and cloning into pDR111 (7). B. subtilis RB247 (trpC2 pheA1) (from Rob Britton) containing pDR-BsABC was grown in LB medium supplemented with 100 µg/ml ampicillin, 0.5 mM NiCl2, and in some cases, IPTG (isopropyl-ß-D-thiogalactopyranoside). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis was used to analyze the proteins (19) with 15% polyacrylamide running gels and 4.5% stacking gels and Coomassie brilliant blue (Sigma) staining. As shown in Fig. 1A, urease expression was greatly enhanced in the recombinant cells, while SF10 cell extracts exhibited no visible urease proteins. Despite the larger amount of urease protein in cell extracts of the B. subtilis transformant, the activity level was lower (0.081 ± 0.026 U/mg) than in the nonrecombinant strain. Growth with 0.5 mM Ni2+ resulted in ~3.5-fold-higher level of activity (0.281 ± 0.105 U/mg) than that of nonrecombinant B. subtilis SF10. We conclude that urease apoprotein is activated with low efficiency in B. subtilis.



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  		FIG. 1. Expression of recombinant B. subtilis ureABC in B. subtilis and E. coli. (A) Cultures of B. subtilis RB247 cells transformed with pDR-BsABC were induced with 0.5 mM IPTG, and the cell extracts were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Lanes: M, molecular mass markers (for phosphorylase b, the Mr was 97,400; for bovine serum albumin, the Mr was 66,200; for ovalbumin, the Mr was 45,000; for carbonic anhydrase, the Mr was 31,000; for soybean trypsin inhibitor, the Mr was 21,000; and for lysozyme, the Mr was 14,400); STD, enriched B. subtilis urease standard; SF, cell extracts of SF10 cells grown in S7 minimal medium with glutamate as the nitrogen source; pDR-BsABC – and + (IPTG), cell extracts of the B. subtilis transformant. (B) Effects of various IPTG concentrations on expression of recombinant B. subtilis urease genes in E. coli C41(pURE91) cell extracts. Lanes: M, molecular mass markers; STD, 6 µg of purified K. aerogenes urease; –, uninduced control; 0.1 and 0.5 (mM IPTG), extracts of the cells induced with 0.1 mM and 0.5 mM IPTG, respectively.

Recombinant B. subtilis urease was produced in E. coli C41(DE3) cells (20) containing pURE91. Cultures were grown in Terrific Broth (TB) (Fisher Biotech) with ampicillin at 37°C to an optical density at 600 nm of ~0.4, induced with 0.5 mM IPTG, and harvested after 14 to 16 h. Urease was highly expressed (Fig. 1B); however, the level of activity measured in cell extracts was very low (0.14 ± 0.02 U/mg). Growth of the E. coli transformant in TB medium containing various Ni2+ concentrations revealed that urease activity was Ni2+ dependent, with maximal activity of 6.4 ± 0.9 U/mg observed when the medium was supplemented with 5 to 7 mM NiCl2 (higher [Ni2+] led to cell toxicity).

Activation of B. subtilis urease. We examined whether B. subtilis urease in cell extracts could be activated by incubation at 37°C for 90 min in 100 mM HEPES (pH 8.3), 150 mM NaCl, 100 mM NaHCO3, and 300 µM NiCl2. Although these conditions are known to activate ~15% of the K. aerogenes urease apoprotein (16, 26, 27), urease activity in nonrecombinant B. subtilis extracts decreased 50% and levels of activity in extracts of the B. subtilis transformant were unchanged. For extracts from E. coli C41(DE2)[pURE91] cells grown with 7 mM NiCl2, activation led to modest increases in activity (<10%). In contrast, for cells grown without supplemental Ni2+, the activity increased from 0.056 to 2.9 U/mg. Mn2+ also activated the enzyme (0.42 U/mg), while other metal ions had negligible effects. Notably, Mn2+ activates K. aerogenes urease apoprotein, yielding ~2% of the activity generated by Ni2+ activation (26, 39). The growth studies with various Ni2+ concentrations and in vitro activation results both suggest that the B. subtilis urease is a Ni-containing enzyme, like all other ureases that have been characterized (15).

Characterization of recombinant B. subtilis urease. In order to understand the low level of urease activity in E. coli C41(DE3) cells containing pURE91, even when grown with high Ni2+ and despite the high-level production of urease subunits, we characterized the properties of the enriched enzyme. Efforts to purify recombinant urease by using ion exchange and hydrophobic interaction chromatography resins, even with potential stabilizing agents, resulted in losses of activity. Although the basis of B. subtilis urease inactivation is incompletely defined, high salt concentrations (0.5 to 1.5 M KCl) caused UreA dissociation from the heterotrimeric enzyme, with UreBC precipitating out of the solution. Urease in cell extracts was highly enriched (~85% homogeneous according to the integrated band intensities [Kodak 1D Scientific Imaging Systems]) by Sephacryl S-300 chromatography with 20 mM Tris-Cl, 150 mM NaCl, and 1 mM EDTA buffer, pH 7.4. By inductively coupled plasma emission analysis (Chemical Analysis Laboratory, University of Georgia), two independent preparations of B. subtilis urease contained 0.13 to 0.29 mol of Ni and 0.063 to 0.070 mol of Zn per mole of {alpha}ß{gamma}, with no significant levels of other metals. The Ni2+ content roughly correlates with the observed activity level, i.e., ~0.2 Ni/{alpha}ß{gamma} correlates to ~1% dinuclear center.

Direct comparison of recombinant expression of B. subtilis ureABC and K. aerogenes ureABC. The urease activity in E. coli cells expressing B. subtilis ureABC prompted us to reevaluate recombinant cells containing only K. aerogenes ureABC. Prior studies suggested that the K. aerogenes structural genes were ineffective in producing functional enzyme (24), but a very low level of activity would have been undetected. To directly compare the two systems, pURE93 and pKAU602 were constructed by using PCR and site-directed mutagenesis to contain ureABC of B. subtilis and K. aerogenes with the same pET42b expression vector and cloning strategy. The plasmids were transformed into E. coli C41(DE3) and the cells grown identically. B. subtilis ureABC was expressed at higher levels than K. aerogenes ureABC (Fig. 2), and in both cases, the UreA subunit was overproduced compared to the other subunits. Excess UreA synthesis may be due to the efficient ribosome binding site provided by the expression vector, whereas this was not observed with pURE91 or pKK17 (29), for which ureA expression uses the endogenous ribosome binding sites.



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  		FIG. 2. Direct comparison of the levels of expression of K. aerogenes ureABC and B. subtilis ureABC from pET-42b derived vectors. Cultures of E. coli C41(DE3) cells carrying pKAU602 or pURE93 were induced with 0.5 mM IPTG, and the cell extracts were analyzed by denaturing polyacrylamide gel. Lanes: M, molecular weight markers; STD, K. aerogenes urease standard; pKAU602 – and + (IPTG), cell extracts containing K. aerogenes UreABC; pURE93 – and + (IPTG), cell extracts containing B. subtilis UreABC.

Urease activities were measured in extracts of the two E. coli transformants cultured with 7 mM NiCl2 with or without IPTG (isopropyl-ß-D-thiogalactopyranoside). Induced cell extracts containing B. subtilis and K. aerogenes UreABC exhibited ~9 U/mg and ~0.4 U/mg (Table 1), in approximate correspondence to the amount of UreC observed (Fig. 2). Although the level of activity found in cells harboring pKAU602 was low compared to that for cells containing pURE93, this result overturns prior dogma about ureDEFG-encoded accessory proteins being required for urease activation.


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  		TABLE 1. Urease activity in recombinant E. coli C41(DE3) cell extracts containing the indicated plasmids grown with 7 mM Ni2+ or grown without supplemental Ni2+ and subjected to activation conditions

To investigate the in vitro activation properties of K. aerogenes and B. subtilis UreABC, activation was performed with cell extracts from transformants cultured without supplemental Ni2+ (Table 1). For pKAU602, no activity was detected prior to activation, consistent with the ability of TB medium to sequester trace levels of the required metal ion, while in vitro activation yielded ~0.8 U/mg. For pURE93, the level of trace activity increased to 1.3 U/mg after activation.

Coexpression studies with urease accessory genes. We tested whether coexpression of B. subtilis ureABC with ureEFGD from K. aerogenes or Bacillus pasteurii would affect activity. Plasmid pACT-ABCdel was constructed by deleting ureABC from the K. aerogenes urease operon in pACT-KKWT (25) by using the QuickChange mutagenesis kit (Stratagene). pACT-BpEFGD (carrying B. pasteurii ureEFGD) was generated by PCR-based cloning by using pBU11 (17) as a template and pACT3 (13) as a vector. pACT, pACT-ABCdel, and pACT-BpEFGD were cotransformed with pURE93 into the E. coli host, and pACT and pACT-ABCdel were cotransformed with pKAU602. Gene expression from each of the vectors was visible (data not shown). While the compatible vectors containing the cognate K. aerogenes genes yielded high levels of urease activity, coexpression of pURE93 and pACT-ABCdel did not enhance the activity over that for pURE93 alone (Table 2). Rather, the observed level of activity decreased in the cotransformant compared to pURE93 alone, perhaps due to reduced expression efficiency for two plasmids versus one plasmid in the same host. This decrease in urease activity also occurred in the pACT3 control. Similarly, the B. pasteurii accessory proteins failed to enhance activity from the B. subtilis structural genes (Table 2). We conclude that the B. subtilis urease subunits do not interact with heterologous urease accessory proteins from K. aerogenes or B. pasteurii. It remains possible that endogenous E. coli components facilitate synthesis of active urease expressed from B. subtilis or K. aerogenes ureABC. One possibility for a facilitator protein is SlyD, known to assist in activation of Ni-containing hydrogenase (40). Countering the participation of SlyD in these constructs are studies showing no effect when the intact K. aerogenes urease gene cluster or that from which ureE was deleted was transformed into slyD versus wild-type E. coli cells (6). To summarize, trace levels of recombinant B. subtilis urease are activated in E. coli without the participation of known urease accessory genes.


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  		TABLE 2. Urease activity from E. coli cotransformants grown in medium containing 5 mM NiCl2

Evidence for novel accessory proteins in B. subtilis. Although B. subtilis lacks homologues to the established urease accessory genes, two lines of evidence support the existence of nonhomologous accessory gene(s) located at a locus (loci) separated from the subunit genes. First, the activity in B. subtilis is comparable to that in the recombinant E. coli cells, despite the vast overproduction of urease protein in the latter cultures. This result suggests an increased efficiency of activation in B. subtilis that could arise from increased intracellular Ni2+ or bicarbonate concentrations, folding issues in the heterologous host, or a novel accessory gene(s). Second, B. subtilis cells overexpressing recombinant B. subtilis ureABC lack enhanced urease activity. These cells are expected to contain Ni2+ and bicarbonate concentrations equivalent to those of the wild-type B. subtilis cells, and the folding machinery acts on homologous proteins, yet a much lower proportion of urease is activated. An unidentified accessory protein acting stoichiometrically could account for these results. Further studies are required to examine whether B. subtilis possesses one or more unidentified accessory genes.

Other urealytic systems lacking accessory proteins. Over 200 microbial genomes have been sequenced, and approximately 20% contain homologues to ureC. Additional targeted sequence information is available for urease gene clusters of numerous microorganisms. For most bacteria, the structural genes cluster with the accessory genes (with ureD sometimes referred to as ureH) in various arrangements (21, 22). Urease genes of selected microorganisms are interrupted by intervening sequences, such as the six open reading frames within ureABCDEFG of Agrobacterium tumefaciens. Similarly, ureDABC and ureEFG of Pseudomonas aeruginosa PAO1 and Pseudomonas syringae pv. tomato strains are separated by more than 15,000 bp (with additional open reading frames between ureA and ureB). Synechocystis sp. strain PCC 6803 and Thermosynechococcus elongatus BP-1 have urease genes dispersed throughout their genomes. Of greater relevance to the B. subtilis system are cases in which one or more urease accessory genes are missing. The urease gene cluster of the Mycobacterium tuberculosis Erdman strain contains only ureABCFG, yet it synthesizes active urease (10); however, the missing genes may be elsewhere on the chromosome. In contrast, the genomes of M. tuberculosis CDC1551, M. tuberculosis H37Rv, and Mycobacterium bovis AF2122/97, "Candidatus Blochmannia floridanus," Streptomyces avermitilis MA-4680, Streptomyces coelicolor A3 (2), Bradyrhizobium japonicum, Rhodopseudomonas palustris CGA009, and Nocardia farcinica lack homologues of ureE. Still, B. subtilis is the only urealytic organism that lacks all known accessory genes.

Activation of nonurease dinuclear hydrolases. Phosphotriesterase (5), dihydro-orotase (34), isoaspartyl dipeptidase (33), and three different hydantoinases (1, 2, 9) all contain active sites closely resembling that of urease (with a carbamylated lysine bridging two metal ions, typically zinc), yet no genetic or biochemical evidence implicates accessory proteins for their biosynthesis. We suggest that B. subtilis urease provides a link between activation of these enzymes and that of the typical urease systems. Urease can be activated without accessory proteins, but the efficiency is very low; accessory proteins greatly enhance the efficiency by a still poorly understood process coupled with GTP hydrolysis. Of related interest, the activation of Ni-containing hydrogenases, carbon monoxide dehydrogenase, and acetyl-coenzyme A decarbonylase-synthase also requires accessory genes for efficient metallocenter assembly (23).


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ACKNOWLEDGMENTS
 
We thank Susan Fisher for providing pURE91 and B. subtilis SF10 and Rob Britton for pDR111 and B. subtilis RB247, along with helpful discussions.

This work was supported by National Institutes of Health grant DK45686.


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FOOTNOTES
 
* Corresponding author. Mailing address: Microbiology and Molecular Genetics, 6193 Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320. Phone: (517) 355-6463, ext. 1610. Fax: (517) 353-8957. E-mail: hausinge{at}msu.edu. Back


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Journal of Bacteriology, October 2005, p. 7150-7154, Vol. 187, No. 20
0021-9193/05/$08.00+0     doi:10.1128/JB.187.20.7150-7154.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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