Natural Genetic Competence in Bacillus subtilis Natto OK2

Sayaka Ashikaga; Hideaki Nanamiya; Yoshiaki Ohashi; Fujio Kawamura

doi:10.1128/jb.182.9.2411-2415.2000

. 2000 May;182(9):2411–2415. doi: 10.1128/jb.182.9.2411-2415.2000

Natural Genetic Competence in Bacillus subtilis Natto OK2

Sayaka Ashikaga ¹, Hideaki Nanamiya ¹, Yoshiaki Ohashi ^1,^†, Fujio Kawamura ^1,^*

PMCID: PMC111301 PMID: 10762239

Abstract

We isolated a Bacillus subtilis natto strain, designated OK2, from a lot of commercial fermented soybean natto and studied its ability to undergo natural competence development using a comG-lacZ fusion at the amyE locus. Although transcription of the late competence genes was not detected in the B. subtilis natto strain OK2 during competence development, these genes were constitutively transcribed in the OK2 strain carrying either the mecA or the clpC mutation derived from B. subtilis 168. In addition, both OK2 mutants exhibited high transformation frequencies, comparable with that observed for B. subtilis 168. Moreover, as expected from these results, overproduction of ComK derived from strain 168 in strain OK2 resulted in a high transformation frequency as well as in induction of the late competence genes. These results clearly indicated that ComK produced in both the mecA and clpC mutants of strain OK2 (ComK_OK2) could activate the transcription of the whole set of late competence genes and suggested that ComK_OK2 was not activated in strain OK2 during competence development. We therefore sequenced the comS gene of OK2 and compared it with that of 168. The comS_OK2 had a single-base change, resulting in the replacement of Ser (strain 168) by Cys (strain OK2) at position 11.

Some species of the genus Bacillus have been used not only for producing industrially useful exoenzymes, antibiotics, and insecticides, but also for making traditional foods such as natto, which is soybeans fermented by a Bacillus subtilis natto strain. Moreover, B. subtilis has been extensively studied because of its ability to sporulate as well as to be efficiently transformed. Based on its high natural transformability, B. subtilis has been utilized as a host bacterium for genetic engineering. The transformation system of B. subtilis is exquisitely regulated. During the development of natural genetic competence, the cells develop the ability to incorporate external DNA and to undergo homologous recombination between chromosomal and incoming single-stranded DNA (24). Among B. subtilis strains, the B. subtilis Marburg strain can be transformed at a high frequency, whereas other B. subtilis strains, including B. subtilis natto strains, give transformants at a frequency similar to that of spontaneous mutation.

The genome sequence of B. subtilis Marburg 168, which can develop competence, was completed in 1997 (15). Competence development in B. subtilis 168 is part of a complex signal transduction network influenced by the level of nutrients in the environment and by the cell density (3). The decisive step in the development of genetic competence is the synthesis of a transcriptional factor, ComK (3, 7, 9, 11, 28–30). The ComK protein in B. subtilis 168 can induce the transcription of recA as well as comK itself and all of the late competence operons (the comC gene and the comE, comF, and comG operons) that are essential for the uptake of exogenous DNA in macromolecular form (3, 7, 10). During the exponential-growth phase, ComK is inhibited by a direct protein-protein interaction with MecA and ClpC (14, 27). The bound ComK is also targeted for degradation by the ATP-dependent protease ClpCP (26). From the end of the exponential phase, ComS is synthesized as the end product of a quorum-sensing pathway. ComS causes the release of ComK from the ternary complex with ClpC and MecA, probably by altering the conformation of MecA and reducing its affinity for ComK (20). When ComS binds to MecA, the rate of ComK degradation by ClpCP decreases, because ComK is released (26). Thus, MecA, ClpC, and ComK, together with the signaling peptide ComS, form a regulatory mechanism controlling the activity of ComK.

Seki and Oshima examined DNA homology by DNA-DNA hybridization among Bacillus species and showed that the chromosomal DNA of B. subtilis natto strains is highly homologous to that of B. subtilis 168 (22). Moreover DNA extracted from natto strains can transform strain 168 as efficiently as DNA from strain 168. In fact, our preliminary transformation experiments showed that eight genetic markers at different positions on the chromosome of strain 168 could be efficiently transformed by DNA from the natto strain OK2, which was used in this study. Because of the industrial importance of the natto strain, we examined its ability to develop genetic competence and especially the expression of the late competence genes required for incorporation of exogenous DNA. In this paper, we present evidence that the natto strain has all the active late competence genes but that ComS in the natto strain is different from that in strain 168.

MATERIALS AND METHODS

Bacterial strains.

The bacterial strains used in this study are listed in Table 1. The B. subtilis natto strain OK2 was isolated from a commercial fermented soybean natto, “Okame natto,” produced by Takano Foods Co. in Ibaraki, Japan. This strain can ferment soybeans to make natto, carries two kinds of plasmids which have been recognized in many B. subtilis natto strains (25), and requires biotin for its growth. Spontaneous rifampin (rif21_OK2)- or streptomycin (strA22_OK2)-resistant mutants of strain OK2 were isolated by spreading on Luria-Bertani (LB) agar plates containing 2 μg of rifampin/ml or 500 μg of streptomycin/ml. Both mecA and clpC (mecB) mutants derived from strain 168 were kindly provided by D. Dubnau. The construction of the strain carrying a translational comG-lacZ fusion at the amyE locus has been described previously (14).

TABLE 1.

B. subtilis 168 and natto strains used in this study

Strain	Relevant genotype or description	Source or reference
Marburg strains
168	trpC2
BD2123	hisB2 leu-8 metB5 amyE::comG-lacZ mecA::spc	14
BD2243	hisB2 leu-8 metB5 amyE::comG-lacZ clpC::spc	14
RIK1001	trpC2 amyE::[comG-lacZ (Cm^r)]	17
RIK1027	trpC2 amyE::[comG-lacZ (Cm^r)] pULI7KS27	This work
RIK1023	trpC2 rif1728 strA7	12; this work
Natto strains
OK2	bio	This work
RIK7101	bio amyE::[comG-lacZ (Cm^r)]	This work
RIK7102	bio amyE::[comG-lacZ (Cm^r)] mecA::spc	This work
RIK7103	bio amyE::[comG-lacZ (Cm^r)] clpC::spc	This work
RIK7127	bio amyE::[comG-lacZ (Cm^r)] pULI7KS27	This work
RIK7121	bio rif21_OK2	This work
RIK7122	bio strA22_OK2	This work

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Media and antibiotics.

The media used were LB (21), LB agar, and 2× SG medium (16). Media for preparation of competent cells consisted of Spizizen's minimal glucose (0.5% [wt/vol]) medium (1) supplemented with 0.05% and 0.025% yeast extract (Difco) for CI and CII (see below), respectively. For the B. subtilis natto strain, biotin was added at a final concentration of 0.1 μg/ml. When present in selective media, antibiotics were used at the following concentrations: chloramphenicol, 5 μg/ml; kanamycin, 7.5 μg/ml; spectinomycin, 50 μg/ml; and rifampin, 2 μg/ml.

Preparation of DNA.

Chromosomal DNA from B. subtilis was prepared as follows. Cells precultured at 28°C overnight were inoculated into LB medium containing appropriate antibiotics and were grown at 37°C with shaking until early-stationary phase. A 1.5-ml portion of the culture was centrifuged, and the cell pellet was resuspended in 150 μl of SETL solution (20% sucrose, 20 mM EDTA, 20 mM Tris-HCl [pH 8.0], and 2 mg of lysozyme/ml) containing 5 μl of RNase A (10 mg/ml). After incubation at 37°C for 5 min, 600 μl of lysing buffer (20 mM Tris-HCl [pH 8.0], 1 mM EDTA, and 1% sodium dodecyl sulfate [SDS]) was added and gently mixed. Thirty-five microliters of 3 M sodium acetate (pH 5.2) was added and mixed well, and then phenol-chloroform treatment was carried out three times. DNA was precipitated with an equal volume of 2-propanol and washed twice with 1 ml of 70% ethanol. DNA was dissolved in 200 μl of TE (20 mM Tris-HCl [pH 8.0] and 1 mM EDTA) after drying in a vacuum desiccator.

Plasmid DNAs were prepared from cells grown until early-stationary phase in L broth at 37°C in the presence of appropriate antibiotics as described previously (2).

Preparation of competent cells and transformation.

Competent cells were prepared according to the two-step protocol as described previously (6). Cells were precultured on an LB plate at 28°C for about 16 h, inoculated into 5 ml of CI medium at an optical density at 660 nm (OD₆₆₀) of ca. 0.05, and grown at 37°C until early-stationary phase. A 0.5-ml portion of the culture was centrifuged, and the cell pellet was suspended in 1 ml of CII medium. An aliquot of 0.1 ml of the cell suspension was mixed with DNA and incubated at 37°C for 90 min with shaking. After the addition of 0.3 ml of LB medium to the culture, the culture was further incubated for 1 or 2 h, depending on the drug resistance markers used, and plated onto LB plates containing antibiotics suitable for selection.

Construction of plasmids.

The 1.7-kb EcoRI-BamHI fragment of pAG58 (13) containing the Pspac promoter and lacI gene was ligated with the 3.8-kb EcoRI-BamHI fragment of pUB110 and transformed into B. subtilis 168 competent cells to construct pULI7. To construct the inducible comK expression plasmid pULI7KS27, the 601-bp comK-containing PCR fragment from B. subtilis 168 DNA was cloned into the XbaI site of pULI7. The PCR primers 5′-CAT CTC TAG AGA TGG AGG CCA TAA TAT GAG TCAG-3′ and 5′-TTA GTC TAG ACT AAT ACC GTT CCC CGA GCT CACG-3′, which have XbaI recognition sequences (underlined), were used for cloning the comK gene of B. subtilis 168 into pULI7 to produce pULI7KS27, as shown in Fig. 1.

FIG. 1 — Construction of pULI7KS27 carrying the Pspac-controlled *comK* gene. The 601-bp fragment containing the Shine-Dalgarno (SD) and coding sequences of the *B. subtilis* 168 *comK* gene was amplified by PCR and was inserted at the *Xba*I site of pULI7 as described in Materials and Methods.

Assay of β-galactosidase activity.

The β-galactosidase specific activity was determined as described previously (17). Strains were grown in CI or LB medium with or without isopropyl-β-d-thiogalactopyranoside (IPTG; 0.1 to 1 mM), 200- to 500-μl samples were collected at the indicated times, and β-galactosidase activities were measured. One unit is equivalent to 1,000 × A₄₂₀/OD₆₆₀/ml/min, where A₄₂₀ is the absorbance at 420 nm.

Other reagents and instruments.

Restriction enzymes, the PCR amplification kit, the DNA ligation kit, and X-Gal (5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside) were purchased from Takara Shuzo Co. (Shiga, Japan). For PCR, we used a model PJ2000 apparatus (Perkin-Elmer).

RESULTS

Transformation ability of the B. subtilis natto strain OK2.

We isolated the B. subtilis natto strain, designated OK2, from a commercial fermented soybean natto lot as described in Materials and Methods. To examine whether strain OK2 has transformation ability, we carried out transformation experiments with the chromosomal DNA prepared from RIK7121, a rifampin-resistant (rif21_OK2) mutant of OK2. As shown in Table 2, strain OK2 gave only a few Rif^r colonies per 0.1 ml. To examine whether these Rif^r colonies were real transformants, strain OK2 was transformed with chromosomal DNA extracted from a rif1728 strA7 double mutant of strain 168, and the linkage between rif1728 and strA7 markers was determined. The cotransformation frequency of Rif^r with Str^r was found to be about 40%, indicating that these Rif^r and Str^r colonies were real transformants obtained via a homologous-recombination process (19). These results suggested that the homologous-recombination system in competent cells of strain OK2 functioned at a detectable level. Table 2 also shows that plasmid transformation with pUB110 DNA occurred at a frequency similar to that obtained with chromosomal DNA, indicating that strain OK2 cannot take up exogenous DNA. These results strongly suggested that a complete set of genes required for competence development does exist in strain OK2 but that they function inefficiently.

TABLE 2.

Transformation frequency in mecA and clpC mutants of the B. subtilis natto strain OK2

Recipient	Genotype	Donor DNA
Recipient	Genotype	Rif^r mutant DNA^a (no. of Rif^r transformants/ml)	pUB110^b (no. of Km^r transformants/ml)
B. subtilis 168	trpC2	1.3 × 10⁵	1.1 × 10⁴
B. subtilis OK2	bio	6.0 × 10	2.0 × 10
RIK7101	bio amyE::comG-lacZ	2.0 × 10	1.5 × 10
RIK7102	bio amyE::comG-lacZ mecA::spc	3.9 × 10⁴	1.5 × 10⁴
RIK7103	bio amyE::comG-lacZ clpC::spc	2.1 × 10⁴	1.1 × 10³

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DNA extracted from RIK7121 (bio rif21_OK2) was used for transformation experiments at a final concentration of 2 μg/ml. Cells were collected 4 h after inoculation. After the addition of LB medium, cells were incubated at 37°C for 2 h with shaking and plated onto LB plates containing 2 μg of rifampin/ml.

pUB110 DNA extracted from strain 168(pUB110) was used for transformation experiments at a final concentration of 5 μg/ml. Cells were collected 4 h after inoculation. After the addition of LB medium, the cell culture was incubated at 37°C for 1 h with shaking and plated onto LB plates containing 7.5 μg of kanamycin/ml.

Extensive studies on competence development in B. subtilis Marburg 168 derivative strains have shown that the ComK protein can induce the transcription of all the late competence genes that are responsible for the uptake of exogenous DNA in macromolecular form (4, 8, 28–30). To examine whether an active ComK protein was produced, we first tried to introduce a translational comG-lacZ fusion at the amyE locus (14) of the OK2 chromosome. Two Cm^r transformants of strain OK2 were obtained using the chromosomal DNA from strain 168 carrying a comG-lacZ fusion. To confirm whether these OK2 transformants contain the intact comG-lacZ fusion, strain 168 was transformed with their chromosomal DNAs and β-galactosidase activities in all Cm^r transformants of strain 168 tested were induced during the development of competence (data not shown). The results in Fig. 2 show that comG-lacZ is not expressed. A possible explanation, based on our knowledge of B. subtilis 168, is that the level of ComK is greatly reduced in OK2.

FIG. 2 — Expression of *comG-lacZ* in *B. subtilis* 168 and the *B. subtilis* natto strain OK2. Cells were grown in CI medium, and samples (200 to 500 μl) were collected at the indicated times. β-Galactosidase activities were determined as described in Materials and Methods. Time zero is defined as the end of exponential growth. Symbols: ○, RIK1001 (168 *amyE*::*comG-lacZ*); ●, RIK7101 (OK2 *amyE*::*comG-lacZ*).

Expression of comG-lacZ in a mecA or clpC mutant of OK2.

It has been shown that the late competence genes, including the comG operon, are constitutively expressed even in rich media such as LB in either mecA or clpC (mecB) mutants (5). It has also been shown recently that these gene products in combination with ClpP protein inhibit the expression of the late competence genes by degrading ComK protein (26, 27). We therefore introduced a deletion of mecA or clpC into an OK2-derived strain carrying a comG-lacZ fusion and examined the transformation abilities and ComK activities of the mecA and clpC mutants by measuring comG-lacZ expression during competence development in CI medium (Table 2; Fig. 3). It seems plausible that an active ComK protein exists in strain OK2 and also that ComK produced in both mecA and clpC mutants of strain OK2 can activate the transcription of the comG operon as well as of the other late competence genes, since the transformation ability of strain OK2 was greatly enhanced by the introduction of either the mecA or the clpC mutation (Table 2).

FIG. 3 — The effect of *mecA* or *clpC* mutation on *comG-lacZ* expression in the *B. subtilis* natto strain OK2. Growth conditions and measurement of β-galactosidase activities were as specified in the legend to Fig. 2. Time zero is defined as the end of exponential growth. Symbols: ○, RIK7101 (OK2 *amyE*::*comG-lacZ*); ●, RIK7102 (OK2 *amyE*::*comG-lacZ mecA*::*spc*); ▵, RIK7103 (OK2 *amyE*::*comG-lacZ clpC*::*spc*).

Overproduction of ComK₁₆₈ can develop genetic competence in strain OK2.

The results described above promptly led us to the idea that the transformation ability of OK2 would be enhanced by overproducing the ComK protein of strain 168 (ComK₁₆₈). We therefore constructed plasmid pULI7KS27 (see Materials and Methods) (Fig. 1), containing a Pspac-controlled comK gene derived from 168, and examined the effect of overproduction of ComK₁₆₈ on comG expression in strain 168 during the exponential-growth phase in LB medium. As shown in Fig. 4, the results indicate that plasmid pULI7KS27 produces sufficient ComK protein to induce the transcription of the late competence genes after the addition of 0.1 mM IPTG. During the construction of pULI7KS27, we found that 168 cells carrying this plasmid cannot form colonies on LB plates containing 1 mM IPTG, indicating that overproduction of ComK₁₆₈ protein is toxic for the growth of 168.

FIG. 4 — Effect of *comK* induction on *comG-lacZ* expression in *B. subtilis* 168 during exponential growth. RIK1027 cells carrying pULI7KS27 (Fig. 1) were grown in LB medium containing 7.5 μg of kanamycin/ml. When the cell density reached an OD₆₆₀ of 0.1, IPTG was added to the culture at various concentrations. Symbols: ○, 0 mM IPTG; ●, 0.1 mM IPTG; ▵, 1 mM IPTG.

We next introduced pULI7KS27 into OK2 carrying a translational comG-lacZ fusion to obtain RIK7127 and examined the effect of ComK₁₆₈ overproduction on the late competence genes in OK2. The expression of comG-lacZ in RIK7127 was significantly induced by the addition of 1 mM IPTG 3 h after the inoculation of RIK7127 cells into CI medium (Fig. 5). We also carried out the transformation experiment in which RIK7127 cells were collected 1 h after the addition of 1 mM IPTG, suspended in CII medium, and then mixed with RIK7121 (bio rif21_OK2) DNA at a final concentration of 2 μg/ml. We could obtain 2.4 × 10³ Rif^r transformants/ml. These results clearly showed that all of the late competence genes, as well as the homologous-recombination activity in OK2, could be induced by the overproduction of ComK₁₆₈ protein.

FIG. 5 — Effect of *comK* induction on *comG-lacZ* expression in OK2 during competence development. RIK7127 cells carrying plasmid pULI7KS27 were grown in CI medium containing 7.5 μg of kanamycin/ml and 0.1 μg of biotin/ml as described in Materials and Methods. At the point shown by the arrow (T₀, defined as the end of exponential growth), IPTG was added to the culture at the indicated concentrations, and β-galactosidase activities were measured as specified in the legend to Fig. 2. Symbols: ○, 0 mM IPTG; ●, 0.1 mM IPTG; ▵, 1 mM IPTG.

Difference in ComS between strains OK2 and 168.

The results described above, together with the information that ComS disrupts the ternary complex consisting of MecA, ClpC, and ComK (26, 27), clearly indicated that a complete set of late genes required for competence exists in OK2 and also suggested that ComS or ComK of strain OK2 may differ from that of 168. We first determined the nucleotide sequence of the comK gene of OK2 and could not find any difference in the predicted amino acid sequence of the ComK protein in spite of 11 differences in nucleotides between OK2 and 168. Furthermore, the AT-rich motif recognized by ComK (11) is conserved upstream of the comK promoter of OK2. We next determined the nucleotide sequences of the comS genes of OK2 and the other three natto strains, including strains Naruse, Takahashi, and Miyagino, which are widely used for natto fermentation in Japan, and found only a 1-base difference between the coding sequence of the comS gene of 168 and those of the natto strains. This single-base change resulted in the replacement of Ser (AGC) (strain 168) by Cys (TGC) (natto strains) at position 11 in the N terminus of ComS.

DISCUSSION

High transformation ability is observed in B. subtilis Marburg and its derivative strains but not in other B. subtilis strains. We isolated a B. subtilis natto strain, designated OK2, from a commercial natto preparation and examined whether it could develop genetic competence. We first carried out transformation experiments with OK2 using DNA extracted from a rif1728 strA7 (Rif^r Str^r) (12) double mutant of 168. Since the frequency of simultaneously spontaneous mutation in these two genes is expected to be about 10⁻⁸ × 10⁻⁸, or 10⁻¹⁶, it is difficult to obtain the spontaneous Str^r Rif^r double mutants. The frequency of cotransformation was 40%, and this value was in good agreement with those obtained in strain 168 (19, 23). We performed plasmid transformation experiments using pUB110, since plasmid transformation is known to be independent of RecA activity. The frequency of plasmid transformation was as low as that obtained with chromosomal marker transformation (Table 2). These results indicated that there was some defect in the function and/or expression of the late competence genes.

In B. subtilis 168, when ComK is activated, the transcription of all genes which are required for the uptake of external DNA is induced (8, 28–30). ComK activity can be easily monitored by measuring the expression of the comG operon using a translational comG-lacZ fusion (29). We therefore first introduced the translational comG-lacZ fusion (14) into OK2 and 168 and then measured β-galactosidase activity in CI medium. Although strong expression of comG was observed in strain 168 after the end of exponential growth, comG expression was not detected in OK2 throughout growth, suggesting that the absence of active ComK is the cause of the low transformation ability in OK2.

Based on these results, together with the fact that the late competence genes are constitutively expressed in 168 carrying a mecA or clpC mutation, we introduced a mecA or clpC mutation (14) into OK2 carrying the comG-lacZ translational fusion and examined the expression of the comG operon as well as transformability. We found that comG expression is strongly induced in both OK2 mutants during competence development (Fig. 3). Moreover, high transformation ability with Rif^r chromosomal and pUB110 plasmid DNA was observed in these mutants (Table 2). It is thus likely that the comK gene of OK2 produces a functional ComK protein (ComK_OK2) but that it is not fully activated during competence development in OK2 cells. To confirm this, we determined the nucleotide sequence of the comK gene in OK2 and examined the effect of ComK₁₆₈ overproduction in OK2 cells. There was no difference between the deduced amino acid sequences of the ComK proteins of 168 and OK2, in spite of several differences in the nucleotide sequence. Furthermore, strain OK2 bearing pULI7KS27 showed strong expression of comG and high transformation ability when ComK₁₆₈ was induced by the addition of IPTG (Fig. 5). These results again indicate that there is no difference in the ComK gene as well as the late competence genes between OK2 and 168.

Why cannot ComK_OK2 in OK2 be activated? We assumed that ComK_OK2 is not released from degradation by the MecA–ClpC–ClpP ternary complex in OK2. We therefore determined the nucleotide sequence of comS, whose product releases ComK from the ternary complex in 168 cells. We found only a 1-base change, resulting in a difference between the 11th amino acid of ComS_OK2 (Cys [TGC]) and that of ComS₁₆₈ (Ser [AGC]) (15). It has recently been shown that comG-lacZ expression was significantly reduced by the substitution of alanine for Ser11 of ComS₁₆₈ (18). It has also been shown that ComS activity was greatly reduced by alanine substitution in the region between the 11th and 15th residues. In particular, the altered ComS with an alanine substitution at Ser13 completely lost its ability to bind to MecA (18). Furthermore, it was suggested that this N-terminal region containing Ser11 in ComS has an important role in binding to MecA (18). It is thus most likely that the alteration of ComS of strain OK2 affects its efficient interaction with MecA and that ComK is thereby constitutively degraded, resulting in the failure of expression of the late competence genes. Although it remains to be clarified whether the quorum-sensing signal transduction pathway in OK2 functions or not, the transformable B. subtilis natto strains are now available, as described in this paper. These transformable natto strains will be useful not only for genetic analysis but also for engineering improvements in natto strains.

ACKNOWLEDGMENTS

We are grateful to D. Dubnau for bacterial strains and critical reading of the manuscript. We thank R. H. Doi, P. Zuber, and M. M. Nakano for helpful discussions and critical reading of the manuscript. We also thank Y. Chijiiwa for technical assistance.

This work was supported in part by a grant-in-aid for Scientific Research (C) from the Ministry of Education, Science, Sports, and Culture of Japan and by a grant, JSPS-RFTH96L00105, from the Japan Society for Promotion of Science.

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PERMALINK

Natural Genetic Competence in Bacillus subtilis Natto OK2

Sayaka Ashikaga

Hideaki Nanamiya

Yoshiaki Ohashi

Fujio Kawamura

Abstract