Processing of DNase domain during translocation of colicin E7 across the membrane of Escherichia coli.

Translocation of colicin across the membrane of sensitive cells has been studied extensively. However, processing of the toxicity domain of colicin during translocation has been the subject of much controversy. To investigate the final translocation product of colicin across the membrane of Escherichia coli, an endogenously expressed His-tagged Im7 protein was constructed to detect any translocation product containing the DNase domain traversed the inner membrane into cytoplasm of the E. coli cells. As a result, a final processed DNase domain of ColE7 was identified in the intracellular space of the cells treated with Col-Im complex. In the presence of periplasmic extracts, in vitro processing of DNase domain of ColE7 was also observed. These results suggest that the processing of ColE7 has occurred for translocation of the DNase-type colicin across the membrane and the process is probably taking place in the periplasmic space of the membrane.

Cloning of two new cry genes from Bacillus thuringiensis subsp. wuhanensis strain.

With PCR products as probes, we have cloned two new cry-type genes from Bacillus thuringiensis subsp. wuhanensis. The deduced amino acid sequence of the first clone is 77.3% identical to Cry1Ga1. The deduced protein sequence of the second clone is 69.8-78.7% identical to that of Cry1B group. The nomenclature assignment of these two clones is, therefore, named Cry1Gb1 and Cry1Bd1, respectively. The Cry1Bd1 is toxic to Plutella xylostella larvae, and the Cry1Gb1 is toxic to Pieris rapae larvae.

Hierarchical order of critical residues on the immunity-determining region of the Im7 protein which confer specific immunity to its cognate colicin.

The directed mutagenesis study of the Im7 protein of colicin E7 revealed that three residues, D31, D35, and E39, located in the loop 1 and helix 2 regions of the protein were critical for initiating the complex formation with its cognate colicin E7. Interestingly, the importance of these three critical residues in conferring specific immunity to its own colicin was exhibited in a hierarchical order, respectively. Moreover, we found that existence of the three critical residues was common among the DNase-type Im proteins. Most likely the three residues of the DNase-type immunity proteins are critical for initiating the unique protein-protein interactions with their cognate colicin. In addition, replacement of the helix 2 of Im7 by the corresponding region of Im8 produced a phenotype of the mutant protein very similar to that of Im8. This result suggests that the DNase-type Im proteins indeed share a "homologous-structural framework" and evolution of the Im proteins may be engendered by minor amino acid changes in this specific immunity-determining region without causing structural alteration of the proteins.

The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein.

BACKGROUND: Colicin E7 (ColE7) is one of the bacterial toxins classified as a DNase-type E-group colicin. The cytotoxic activity of a colicin in a colicin-producing cell can be counteracted by binding of the colicin to a highly specific immunity protein. This biological event is a good model system for the investigation of protein recognition. RESULTS: The crystal structure of a one-to-one complex between the DNase domain of colicin E7 and its cognate immunity protein Im7 has been determined at 2.3 A resolution. Im7 in the complex is a varied four-helix bundle that is identical to the structure previously determined for uncomplexed Im7. The structure of the DNase domain of ColE7 displays a novel alpha/beta fold and contains a Zn2+ ion bound to three histidine residues and one water molecule in a distorted tetrahedron geometry. Im7 has a V-shaped structure, extending two arms to clamp the DNase domain of ColE7. One arm (alpha1(*)-loop12-alpha2(*); where * represents helices in Im7) is located in the region that displays the greatest sequence variation among members of the immunity proteins in the same subfamily. This arm mainly uses acidic sidechains to interact with the basic sidechains in the DNase domain of ColE7. The other arm (loop 23-alpha3(*)-loop 34) is more conserved and it interacts not only with the sidechain but also with the mainchain atoms of the DNase domain of ColE7. CONCLUSIONS: The protein interfaces between the DNase domain of ColE7 and Im7 are charge-complementary and charge interactions contribute significantly to the tight and specific binding between the two proteins. The more variable arm in Im7 dominates the binding specificity of the immunity protein to its cognate colicin. Biological and structural data suggest that the DNase active site for ColE7 is probably near the metal-binding site.

Change of thermal stability of colicin E7 triggered by acidic pH suggests the existence of unfolded intermediate during the membrane-translocation phase.

Purified colicin E7 was analyzed by CD spectrum and gel filtration chromatography in a mimicking membrane-translocation phase. It was found that the CD spectra of colicin E7 at pH 7 and pH 2.5 were similar. Although the melting temperature of the protein shifted from 54.5 degrees C to 34 degrees C at low pH, the thermal denaturation curves of colicin E7 at different pH conditions still fit a two-state model. These experimental results imply that a minor structural change, triggered by acidic pH, for instance, may reduce the energy required for protein melting. In contrast to the minor change in secondary structure at different pH conditions, we observed that, in vitro, all monomeric colicin E7s converted into multimer-like conformations after recovering from the partial unfolding process. This multimeric form of colicin can only be dissociated by formamide and guanidine hydrochloride, indicating that this protein complex is indeed formed by aggregation of the monomeric colicins. Most interestingly, the aggregated colicins still perform in vivo bacteriocidal activity. We suggest that in a partial unfolding state the colicin is prepared for binding to the specific targets for translocation through the membrane. However, in the absence of specific targets in vitro these unfold intermediates may therefore aggregate into the multimeric form of colicins.

A novel role of ImmE7 in the autoregulatory expression of the ColE7 operon and identification of possible RNase active sites in the crystal structure of dimeric ImmE7.

Site-specific cleavage of mRNA has been identified in vivo for the polycistronic colicin E7 operon (ColE7), which occurs between G and A nucleotides located at the Asp52 codon (GAT) of the immunity gene (ceiE7). In vitro, this specific cleavage occurs only in the presence of the ceiE7 gene product (ImmE7). The crystal structure of dimeric ImmE7 has been determined at 1.8 A resolution by X-ray crystallographic analysis. We found that several residues located at the interface of dimeric ImmE7 bear surprising resemblance to the active sites of some RNases. These results suggest that dimeric ImmE7 may possess a novel RNase activity that cleaves its own mRNA at a specific site and thus autoregulates translational expression of the downstream celE7 gene as well as degradation of the upstream ceaE7 mRNA.

Two overlapping SOS-boxes in ColE operons are responsible for the viability of cells harboring the Col plasmid.

In this study, oligonucleotide-directed site-specific mutagenesis was used to change the consensus sequences of the LexA binding motifs in either one of the two SOS-boxes of the ColE7 operon. The results indicated that both mutants produced larger amounts of colicin than cells harboring the wild-type ColE7 plasmid. This finding would imply that two biologically functional SOS boxes exist in the ColE7 operon. In the non-induced state, no lysis of cells harboring wild-type plasmids occurred at 37 degrees C, whereas, cells harboring recombinant plasmids containing either one of the mutated SOS boxes underwent lysis within 100 min under the same conditions. This result indicated that adaptation of two SOS boxes of the ColE operon would obviously tightly control the expression of ColE operons. In such a way that it may prevent excessive expression of the lysis (cel) gene, thus safeguard the host cells from being lysed in ordinary living conditions.

The crystal structure of the immunity protein of colicin E7 suggests a possible colicin-interacting surface.

The immunity protein of colicin E7 (ImmE7) can bind specifically to the DNase-type colicin E7 and inhibit its bactericidal activity. Here we report the 1.8-angstrom crystal structure of the ImmE7 protein. This is the first x-ray structure determined in the superfamily of colicin immunity proteins. The ImmE7 protein consists of four antiparallel alpha-helices, folded in a topology similar to the architecture of a four-helix bundle structure. A region rich in acidic residues is identified. This negatively charged area has the greatest variability within the family of DNase-type immunity proteins; thus, it seems likely that this area is involved in specific binding to colicin. Based on structural, genetic, and kinetic data, we suggest that all the DNase-type immunity proteins, as well as colicins, share a "homologous-structural framework" and that specific interaction between a colicin and its cognate immunity protein relies upon how well these two proteins' charged residues match on the interaction surface, thus leading to specific immunity of the colicin.

Identification of novel cry-type genes from Bacillus thuringiensis strains on the basis of restriction fragment length polymorphism of the PCR-amplified DNA.

Two pairs of universal oligonucleotide primers were designed to probe the most conserved regions of all known cryI-type gene sequences so that the amplified PCR fragments of the DNA template from Bacillus thuringiensis strains may contain all possible cryI-type gene sequences. The restriction fragment length polymorphism (RFLP) patterns of the PCR-amplified fragments revealed that 14 distinct cry-type genes have been identified from 20 B. thuringiensis strains. Those cry-type genes included cryIA(a), cryIA(a), cryIA(b), cryIA(b), cryIA(c), cryIB, cryIC, cryIC, cryIC(b), cryID, cryIE, cryIF, cryIF, and cryIII (a dagger at the end of a gene designation indicates a novel cry-type gene determined by restriction mapping or DNA sequences). Among them, the sequences of cryIA(a), cryIA(b), cryIB, cryIC, cryIF, and cryIII were found to be different from the corresponding published cry gene sequences. Interestingly, five cry-type genes [cryIA(a)-, cryIB-, cryIC-, cryIC(b)-, and cryIF-type genes] and seven cry-type genes [cryIA(a)-, cryIA(b)-, cryIB-, cryIC-, cryIC(b)-, cryIF-, and cryIII-type genes] have been detected from B. thuringiensis subsp. morrisoni HD-12 and B. thuringiensis subsp. wuhanensis, respectively. Therefore, the PCR-RFLP typing system is a facile method to detect both known and novel cry genes existing in B. thuringiensis strains.

Crystallization and preliminary X-ray crystallographic analysis of ImmE7 protein of colicin E7.

The ImmE7 protein, which can bind specifically to the DNase colicin E7 and neutralize its bactericidal activity, has been purified and crystallized in two different crystal forms by vapor diffusion method. The orthorhombic crystals belong to space group I222 or I2(1)2(1)2(1) and have unit cell dimensions a = 75.1 A, b = 50.5 A, and c = 45.4 A. The second form is monoclinic space group P2(1) with cell dimensions a = 29.3 A, b = 102.7 A, c = 53.0 A, and beta = 91.5 degrees. The orthorhombic crystals diffract to 1.8 A resolution, and are suitable for high-resolution X-ray analysis.

Expression of the crystal protein gene under the control of the alpha-amylase promoter in Bacillus thuringiensis strains.

The expression of an insecticidal crystal protein gene of Bacillus thuringiensis under the control of the alpha-amylase gene promoter was investigated. The cryIC gene, which encodes a protein known to have a unique activity against Spodoptera (armyworm) species, was used in this investigation. The cryIC gene was placed, along with the alpha-amylase promoter from B. subtilis, in a B. thuringiensis-derived cloning vector, generating a pair of recombinant plasmids, pSB744 and pSB745. The cloning vector that contains the minimal replicon of B. thuringiensis subsp. kurstaki HD73 is stably maintained in a variety of B. thuringiensis strains, as previously reported by Gamel and Piot (Gene 120:17-26, 1992). The present study confirmed that the recombinant plasmids are also stably maintained in B. thuringiensis subsp. kurstaki Cry-B and HD73 growing in media without selection pressure for at least 48 h. The cryIC gene on the recombinant plasmids were notably expressed at high levels in both recombinant strains. Expression of the introduced cryIC gene on the recombinant plasmid in B. thuringiensis subsp. kurstaki HD73 did not impair expression of the resident cryIA(c) gene. The CryIA(c) protein is known to have a high level of activity against loopers such as Trichoplusia ni (the cabbage looper). As a result of coexpression of the introduced cryIC gene and the resident cryIA(c) gene, recombinant strain HD73 acquired an additional insecticidal activity against Spodoptera exigua (the beet armyworm) whereas the original activity level against T. ni was maintained.

Determination and Distribution of cry-Type Genes of Bacillus thuringiensis Isolates from Taiwan.

Using PCR with a set of specific oligonucleotide primers to detect cryI-type genes, we were able to screen the cry-type genes of 225 Bacillus thuringiensis soil isolates from Taiwan without much cost in time or labor. Some combinations of cry genes (the cry-type profile) in a single isolate were unique. We identified five distinct profiles of crystal genes from the B. thuringiensis soil isolates from Taiwan. The cry genes included cryIA(a), cryIA(b), cryIA(c), cryIC, cryID, and cryIV. Interestingly, 501 B. thuringiensis isolates (93.5% of the total number that we identified) were isolated from areas at high altitudes. The profiles of cry-type genes were distinct in all isolation areas. The distribution of cry-type genes of our isolates therefore depended on geography. Using PCR footprinting to detect cryIC-type genes, we identified two distinct cryIC footprints from some of our isolates, indicating that these isolates may contain novel cryIC-type genes. B. thuringiensis isolates containing cryIA(a)-, cryIA(b)-, and cryIA(c)-type genes exhibited much greater activity against Plutella xylostella than did other isolates, indicating that multiple cry-type genes may be used as markers for the prediction of insecticidal activities.

Mapping of transcriptional start sites of the cea and cei genes of the ColE7 operon.

Two transcriptional start sites were identified 77 and 78 nucleotides upstream of the translation initiation codon of the colicin E7 gene (ceaE7). The guanosine nucleotide located at the fifth position of the SOS box is probably a universal transcriptional start site of all E group colicins. Major and minor transcripts of the immunity gene (cei) are initiated at the 3' end of the cea gene. Relative to the -10 sequence, CAAAAT, of the major ceiE7 promoter, the corresponding region of the cei gene of other E group colicins has an increased content of guanosine nucleotides. However the -10 sequence of the minor ceiE7 promoter, TATGAT, was found to be conserved in other colicin promoters. The results indicate that the structure of the major promoter of the ceiE7 gene is unique among the E group colicins.

Expression of the ColE3 operon in maxicells.

The cea, cei, and cel genes of the ColE3 operon were localized and characterized by subcloning and by transposon mutagenesis. Plasmids containing different portions of the ColE3 operon were transformed into an E. coli maxicell strain CSR603. Proteins encoded by these plasmids were analyzed by SDS-PAGE after UV irradiation of the cells. The results showed that the molecular weights of Col, ImmE8, ImmE3 and Lys were 60 kDa, 15 kDa, 10 kDa, and 4-5 kDa, respectively. These results indicated that the maxicell system provides an easy and simple method for the identification of plasmid-encoded proteins.

Complete nucleotide sequence and identification of a putative promoter region for the expression in Escherichia coli of the cryIA(b) gene from Bacillus thuringiensis var. aizawai HD133.

The sequence of a cry gene from Bacillus thuringiensis var. aizawai HD133 was determined. This cry gene encodes a protein of 1155 amino acids, the molecular weight of which is 130622 Da. When the nucleotide sequence of this cry gene was compared with the nucleotide sequence from B.t. var. aizawai IPL7 and var. berliner 1715, only five nucleotide changes were found. Therefore, this cry gene should be grouped into the cryIA(b) gene type. A 72 nucleotide sequence upstream of the open reading frame of the cry gene was enough to conduct the transcription of the cry gene in E. coli. Using a promoter probe vector system, it was demonstrated that any DNA fragment containing this 72 nt sequence exhibited promoter activity in vivo. It is likely that a putative promoter sequence may be present within this 72 nucleotides region for the expression of this cry gene in E. coli.

Characterization of the cea gene of the ColE7 plasmid.

The complete nucleotide sequence (1731 nucleotides) of the gene encoding colicin E7 (cea) of plasmid ColE7-K317 was determined. This sequence encoded a deduced polypeptide of 576 amino acids of molecular weight 61349 Da. Comparison of the nucleotide and amino acid sequences of cea E7 with those of other E-group colicins revealed that colicin E7 was closely related to colicin E2, both in gene sequence and in predicted secondary structure of the deduced protein. Judging from the results of cross-immunity tests, we postulated that ColE7 is probably a proximate ancestor of ColE2 and ColE8. Based on results from colicin production tests on cells harboring a 5' end deleted form of the cea E7 gene, we propose that a previously unknown, non-inducible promoter may be involved in regulation of the constitutive expression of the cea E7 gene.

Cloning and characterization of the ColE7 plasmid.

The 6.2 kb ColE7-K317 plasmid was mapped and the DNA fragments of the colicin E7 operon subcloned into pUC18 and pUC19. The size of the functional colicin E7 operon deduced by subcloning was 2.3 kb. The colicin E7 gene product was purified by carboxymethylcellulose chromatography. Both colicin E7 and E9 were demonstrated to exhibit a non-specific DNAase-type activity by in vitro biological assay. The molecular mass of colicin E7 was 61 kDa, as determined by SDS-PAGE. From DNA sequence data, the estimated sizes of the E7 immunity protein and the E7 lysis protein were 9926 Da and 4847 Da, respectively. Comparison of restriction maps and DNA sequence data suggests that ColE7 and ColE2 are more closely related than other E colicin plasmids.

Characterization of the Bacillus thuringiensis strains isolated from Taiwan.

Over 100 Bacillus thuringiensis (Bt) isolates which produced phase bright inclusions have been isolated from soil samples from different areas in Taiwan. Three types of crystal proteins were visualized by phase contrast microscopy. Among these isolates, only 14 different types of plasmid profiles have been observed. They all possess a variety of plasmids ranging from a few kb to around 250 kb in size. With respect to the crystal protein profiles, the plasmid profiles, and the shapes of crystal proteins, we found that the majority of our isolates (87%) were different from most of the known Bt strains. Our other two types of isolates (10 and 3%) resembled Bt var. kurstaki HD1 and Bt var. israelensis, respectively. Most of our isolates were active against Bombyx mori (Lepidoptera) and Aedes aegypti (Diptera). Most interestingly, two of our isolates, Nos. 82 and 96, were found highly toxic to Heliothis virescens, even compared with the standard strain, Bt var. kurstaki HD1. Using insecticidal crystal protein (ICP) gene probe from Bt var. aizawai HD-133 to probe the total DNA of our isolates, we observed that at least one plasmid from each of the tested strains reacted with the probe. A 10 kb plasmid from some of our isolates hybridized with the probe. This probably is the first evidence demonstrating that the ICP gene sequence can be found in a low molecular weight plasmid.

Cloning and expression in Escherichia coli of an insecticidal crystal protein gene from Bacillus thuringiensis var. aizawai HD-133.

Using a gene probe derived from the cloned var. sotto insecticidal crystal protein (ICP) gene, we have cloned a Bacillus thuringiensis var. aizawai HD-133 ICP gene in Escherichia coli. The gene encodes a polypeptide that is toxic to Lepidoptera in vivo and in vitro. The protein is expressed at a level sufficient to produce phase-bright inclusions in recombinant E. coli strains, and these inclusions can be partially purified using discontinuous sucrose density gradients. Immunoblotting shows that the inclusions contain a 135 kDa polypeptide which reacts strongly with antiserum raised against the B. thuringiensis var. kurstaki HD-1 P1 polypeptide.

Isolation and characterization of a clone of the spoVE locus of Bacillus subtilis.

The Bacillus subtilis spoVE locus was isolated from a lambda clone bank and a 4.7 kbp EcoRV fragment subcloned into the shuttle vector pHV33. The resulting plasmid complemented chromosomal spoVE mutations. Its structure was stable in recE4 strains, but plasmid and chromosomal rearrangements occurred in rec+ strains. New spoVE mutations were obtained by mutagenesis of the plasmid; all the mutations tested mapped within three adjacent HindIII fragments of total length 1140 bp.