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Journal of Bacteriology, May 2005, p. 3133-3138, Vol. 187, No. 9
0021-9193/05/$08.00+0 doi:10.1128/JB.187.9.3133-3138.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Department of Biological Sciences, Purdue University, West Lafayette, Indiana
Received 15 July 2004/ Accepted 13 December 2004
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It has been speculated that the absence of a functional plcR gene in B. anthracis is the first step in the ultimate removal of the genes encoding the extracellular factors that are no longer needed for pathogenicity (19). One scenario is that B. anthracis was derived from a B. cereus isolate, a so-called transitional strain (22) containing a functional PlcR regulon, by acquiring the two plasmids, pXO1 and pXO2, necessary for pathogenicity. These plasmids encode critical pathogenicity factors and some key regulators (8, 12). One of these, AtxA, is involved in the regulation of both the capsule and the toxin genes, among others, and appears to be antagonistic to PlcR, at least for sporulation (19). This is one explanation for the nonfunctional plcR gene in B. anthracis although the genome sequence of an atypical B. cereus isolate that contains a pXO1 plasmid has both intact atxA and plcR genes (13).
While the synthesis of many of these pathogenic factors is substantially reduced in B. anthracis, there is an array of genes encoding extracellular proteases (NCBI protein database for B. anthracis Ames, accession no. AE017031.1). Some of these may have a function in pathogenesis, such as the InhA2 metalloprotease in B. thuringiensis (9, 11), while others could play a role by providing nutrients for postexponential survival and sporulation. If so, there are likely to be regulatory protein(s) other than PlcR.
In the course of examining the spore coat profile of B. anthracis, a novel protein of 43 kDa, designated Cot43, was found which is a Rap-like protein encoded on the pXO1 plasmid (21). Rap proteins are members of the tetratricopeptide repeat family (6) which, together with an interacting pentapeptide encoded within a small downstream open reading frame (ORF), serves to modulate the phosphorelay initiating sporulation in Bacillus subtilis (23). Surprisingly, the PlcR pleiotropic regulator is also a member of this tetratricopeptide family and is activated by a pentapeptide (27) that is processed from a secreted oligopeptide of 48 amino acids and then taken up by an oligopeptide permease (10). It was thus conceivable that Cot43, in addition to its presence in spore coats, served a similar regulatory function, especially given the absence of a functional PlcR in B. anthracis. This possibility has been explored by examining the pattern of extracellular enzymes secreted by strains lacking or containing the cot43 gene. The results are consistent with regulation by Cot43 of the pattern and amounts of several extracellular proteases.
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Cells were grown in 30 ml nutrient sporulation medium (NSM) (26), brain heart infusion broth (BHI), or the latter containing 0.5 M sorbitol. B. cereus and B. thuringiensis were also grown in a yeast extract-glucose medium (G-Tris) (4). Growth was in sidearm flasks and the density was monitored in a Klett colorimeter (660-nm filter [K600]). One-milliliter aliquots were removed and centrifuged in an Eppendorf microcentrifuge for 8 min, and the supernatants were passed through 0.2-µm-pore-size Nalgene syringe filters. In some cases the supernatants were dried in a lyophilizer and dissolved in water adjusting the volumes to equate K660 values. Alternatively, the sample volumes for protease assays or for sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) were adjusted to compensate for differences in the K660 values.
Cloning. The Cot43 protein was originally identified as a band in SDS-15% PAGE gels of spore coat extracts of the Sterne strain but not of B. cereus. The band was excised and partially sequenced (MIVSVKGNEQITKMLND?YI), and this sequence was aligned with the amino terminal end of Orf136 in the pXO1 plasmid (21). For expression, a primer for a region 246 bp upstream of the start of translation (5'-CTCCTTTCACGCAGACGTGACATAATCCG) and one for the terminus (5'-TTTTCTTCCTTTTAAAGCCTCCTTTTC) were used. In order to include the downstream ORF of 46 amino acids (an alternative reading frame), the second primer was replaced with 5'-GTTTATTTATGATCCGCCAGTATGGCC. The PCR products were cloned into pCRT7/CT-TOPO (Invitrogen), and the inserts were sequenced. Each was excised with XbaI and HincII and subcloned into the E. coli/Bacillus shuttle vector, pHT315 (3) digested with XbaI and SmaI (referred to as cot43 and cot43P, respectively).
For disruption of the cot43 gene, primers 500 bp up- and downstream of the coding region were used: 5'-CGTTATCCAATAGGTTAAGGTCTCCC and 5'-GCTTTCCATGACTGGAAACTAGCACTG. The PCR product was cloned as described above, and a neomycin resistance gene cassette excised with SmaI from plasmid pBEST501 (14) was inserted into the unique EcoRV site within the cot43 gene. The entire disrupted gene region was then excised with XbaI and HindIII and cloned into the shuttle vector, pUTE29 (17). Electroporation and screening for neomycin-resistant (Neor), tetracycline-sensitive (Tcs) colonies were done as described previously (15). Clones were checked by PCR for the Neor insert in cot43 and by immunoblotting of spores and extracts from postexponential cells for the absence of Cot43 antigen.
A lacZ fusion to 246 bp of the region upstream plus 50 bp into the coding region of the cot43 gene was constructed by PCR amplification with primer 5'-CTCCTTTCCTGCAGACGTGACATAATCCG containing a PstI site and primer 5'-GTCTGGCACGTATCTCTAGATACCAGTC containing an XbaI site. Following purification with a QIAGEN kit, the PCR product was digested with these enzymes and ligated into an identically digested vector, pHT304-18Z, containing a promoterless lacZ gene (1).
The upstream regions (130 to 140 bp) of genes encoding two extracellular proteases were cloned by PCR. For a serine protease (NP846139), primers 5'-GCTGATTACTATAATCTCTGCAGTAGAAAGG and 5'-CTCTAGACGCACACATTTTTTGAAAC were used. These primers contained a PstI or XbaI site, respectively, and the resulting oligonucleotide (144 bp) was cloned into PHT305-18Z as described above. The same strategy was used to clone the upstream region of an immune inhibitor protease (NP843199) by employing primers 5'-GCCTTTTTATATAGGGACTGCAGAAAG and 5'-GACGATAACACTTCTAGAGGCGC.
The three plasmids containing lacZ fusions were electroporated into the Sterne strain, and the two protease fusion plasmids were electroporated into the d2 strain as well. Transformants were grown in 30 ml of NSM plus 25 µg of erythromycin ml1 in sidearm flasks. One-milliliter duplicate samples were removed periodically and centrifuged for 6 min in an Eppendorf microcentrifuge. The pellets were frozen at 80°C and subsequently assayed for ß-galactosidase activity (7). The specific activities are the averages of duplicate samples, and plots show the ranges for one standard deviation.
Extracellular enzyme assays. The initial screening was done by spotting cells onto BHI agar containing 5% low-fat milk (Parmalat), 5% sheep red blood cells, or 5% egg yolk (Difco) and incubating at 37°C for 16 to 36 h (19). Total protease in cell supernatants was measured by using succinylated-casein (QuantiCleave protease assay kit; Pierce) under the conditions specified in the notes to Table 1. Reaction conditions were selected to ensure a linear increase of color with time (over 60 min) and proportional increases with quantities of supernatants (2.5 to 10 µl). Zymogen profiles were determined in SDS-8% PAGE containing Parmalat 2% milk at a 5% (vol/vol) final concentration. Gelatin (Difco) at 2% (w/vol) was also used, but there were fewer bands. Stock solutions (0.01 M) of the protease inhibitors O-phenanthroline and phenylmethylsulfonyl fluoride (PMSF) were dissolved in ethanol; EGTA (Sigma) and E-64 (Sigma), an inhibitor of cysteine proteases, were dissolved in deionized water. Inhibitors were added to the supernatants to a 2.5 mM final concentration, and the solutions were incubated at 27°C for 5 min before loading on gels. A control with an equal concentration of ethanol was also included. After electrophoresis, the gels were treated as described previously (16). A purified protease of 36 kDa from Bacillus polymyxa (Sigma) served as a molecular weight marker.
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TABLE 1. Protease activity in supernatants of Bacillus speciesa
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Zymogen profiles of the two B. anthracis strains were compared with sampling during growth and at various stages of sporulation (Fig. 1). Five protease activities were resolved (Fig. 1, bands A to E). For all of the relative sampling times, protease bands A to D in the plasmid-cured strain were more intense than the comparable bands in the Sterne strain. For the latter, bands A to D increased to late sporulation, whereas band E peaked in early sporulation. There was another protease activity of ca. 40 kDa found predominantly in exponentially growing cells (see Fig. 6 and the band just above band E). On the basis of the effects of protease inhibitors (Fig. 2), band A and perhaps bands C and D, which were less intense in the presence of PMSF (lane 3), are likely to be serine proteases. Bands B to D were not detected in the presence of EGTA (lane 2), and so are probably calcium-dependent proteases. Band E was less intense in the presence of the cysteine protease inhibitor, E64, when the bands in lanes 4 and 5 were compared, but its intensity varied with the time of sampling (Fig. 1), and so there is less certainty as to the type of protease.
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FIG. 1. Zymogen profiles of a gel containing low-fat milk. Lanes 1 to 5 are supernatants from the Sterne strain grown in NSM at 37°C with samples removed at 60-min intervals, commencing at the end of growth. Phase-white endospores were present in >80% of the cells by sample 4. Lanes 6 to 8 are for the plasmid-free strain, St-13, sampled at the same time as lanes 2, 4, and 5. Bands labeled A to E are discussed in the text (Fig. 2). In all cases, 5 µl of the supernatants was loaded from cultures grown to a Klett value of 230 or the equivalent (see Materials and Methods).
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FIG. 6. A clone of the cot43 gene regulates the intensity of the protease bands. Supernatants of strain St-13 (lanes 1, 4, and 7), strain St-13/cot43 (lanes 2, 5, and 8), and strain St-13/cot43P (lanes 3, 6, and 9) were used. Samples were removed during late exponential growth (lanes 1 to 3), at the end of growth (lanes 4 to 6), and 90 min later (lanes 7 to 9). Amounts were loaded as described in the legend to Fig. 1.
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FIG. 2. Effect of inhibitors on extracellular proteases. Lane 1, 5 µl of the supernatant from the Sterne strain grown in NSM at 37°C and harvested as described for lane 4, Fig. 1; lane 2, addition of EGTA to a concentration of 2.5 mM prior to loading; lane 3, 2.5 mM PMSF; lane 4, 2.5 mM O-phenanthroline; lane 5, 2.5 mM E64. A molecular weight marker was a metalloprotease of 36 kDa from B. polymyxa (Sigma P-6141) which migrated a little bit more slowly than band E (Fig. 5).
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FIG. 3. Zymogen profiles with variations in strains, media, and temperature of growth. Lane 1, B. cereus T grown in G-tris medium at 30°C; lane 2, B. cereus T grown in NSM at 30°C; lane 3, B. cereus T grown at 37°C in G-tris; lane 4, B. cereus T grown at 37°C in NSM; lane 5, Sterne strain grown at 30°C in NSM; lane 6, Sterne strain grown at 30°C in BHI plus 0.5 M sorbitol; lane 7, Sterne strain grown at 37°C in NSM; lane 8, Sterne strain grown at 37°C in BHI plus 0.5 M sorbitol; lanes 9 and 10, Sterne strain grown at 37°C in NSM and samples incubated at 27°C for 30 min prior to loading (lane 9 supernatant from cells sampled 90 min earlier than the samples in the other lanes). Supernatants in lanes 1 to 8 and 10 are from samples taken 3 h after the end of growth (20 to 30% phase-dull spores in each). See legend to Fig. 1 for the amounts loaded.
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FIG. 4. Time course of the increase in the specific activity of ß-galactosidase in the Sterne strain containing a lacZ fusion to the cot43 upstream region. Sampling and analysis were performed as described in Materials and Methods.
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FIG. 5. Enhanced protease in strains lacking Cot43. Lane 1, B. polymyxa metalloprotease (the lower band is 36 kDa); lane 2, Sterne strain with a disruption of the cot43 gene (strain d2); lane 3, strain UT44; lane 4, strain St-13; lane 5, Sterne strain; Lanes 6 to 9, the same strains used in lanes 2 to 5, respectively, but with cells harvested 90 min earlier. Strains were grown at 37°C in NSM until 90 min after the end of growth (lanes 6 to 9) or 180 min after the end of growth (lanes 2 to 5). Bands labeled A to E are as discussed in the legend to Fig. 2 and the text. Amounts loaded are as described in the legend to Fig. 1.
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FIG. 7. Differential effects of the presence of Cot43 on the zymogen profiles of a mutant with a disruption of the atxA gene. Lane 1, strain UM44; lane 2, strain UT53; lane 3, strain UT53/cot43P. All strains were grown at 37°C in NSM until 1 h after the end of exponential growth. Amounts were loaded as described in the legend of Fig 1.
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FIG. 8. Specific activities of ß-galactosidase of a fusion of the upstream region of the immune inhibitor protease to lacZ in the Sterne strain and in mutant d2. Time zero is the end of growth, with phase-dull endospores present in >70% of the cells by 4 h.
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An examination of the ORFs in the Ames genome (entrez protein search of the B. anthracis Ames genome, accession no. AE017031.1) indicates that there are ca. 10 proteases with potential signal sequences (5) ranging in size from about 40 to 100 kDa. Nothing is known about the expression or secretion patterns of these enzymes. Two appear to be similar to the InhA protease secreted by B. thuringiensis which may function to destroy host immune proteins and thus aid in establishing infection (9, 11). None of these protease genes contained the consensus palindrome recognized by the PlcR regulator (19), at least within 50 bp of the start codon. There was in the upstream regions, however, a consensus sequence present among six of these protease genes. Its role, if any, in regulation by Cot43 is being examined.
Among the six protease bands identified here, four were present primarily in postexponential cells and at least three were down-regulated in the Sterne strain relative to a derivative devoid of the pXO1 plasmid (Fig. 5). It was noted that a pXO1 gene designated cot43 encoded a tetratricopeptide repeat protein and that there was a potential downstream ORF of 46 amino acids. Cot43 is similar in sequence to the Rap proteins in B. subtilis, many of which also contain a small downstream ORF (23). In addition, the PlcR regulator from B. thuringiensis is a member of this family, and thus the possibility that Cot43 had a regulatory function was explored. While this protein was originally identified in spore coat extracts of the Sterne strain, disruption of the cot43 gene resulted in overexpression of the proteases in a pattern similar to that in the plasmid-free strain. Expression of Cot43 on a plasmid resulted in extensive inhibition of protease activity, especially if the clone contained a downstream orf encoding a 46-amino-acid peptide. Variations in the level of expression of the cot43 operon could thus modulate extracellular postexponential protease synthesis. It appears that Cot43 has a dual function: as part of the B. anthracis spore coat where it modulates germination (A. I. Aronson and H. Hu, unpublished data) and directly or indirectly as a transcriptional regulator of several extracellular proteases.
A small but significant enhanced expression was found for the cot43 mutant strain relative to the plasmid-free strain (Table 1 and Fig. 5), implying that another pXO1 gene was involved as an inducer. One candidate would be the AtxA regulator of pathogenic factors (8, 12), and a strain with a disruption of this gene produced somewhat less protease than the parental strain (Fig. 7). The two plasmid-encoded proteins, Cot43 and AtxA, may serve to modulate extracellular protease synthesis, at least for the six proteases resolved in this analysis.
It is intriguing that chromosomally encoded proteases are regulated by pXO1 factors. A similar regulatory pattern was found for the S-layer proteins that are encoded on the chromosome and regulated by AtxA (20). It is tempting to speculate that in both cases, there is some relation of this pattern of regulation to pathogenicity. This interplay implies that pathogenic B. anthracis strains have evolved beyond a B. cereus"transition strain" containing pXO1 and pXO2 as autonomously functioning plasmids.
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