Nucleotide sequences that signal the initiation of transcription and translation in Bacillus subtilis

In vivo transcription initiation and termination sites of an alpha-amylase gene from Bacillus amyloliquefaciens cloned in Bacillus subtilis

The alpha-amylase gene, originally isolated by molecular cloning from chromosomal DNA of Bacillus amyloliquefaciens, is efficiently expressed from its own promoter in a Bacillus subtilis host when present in the multicopy plasmid vector pUB110. The flanking regions of this gene were sequenced and the ends of the in vivo-generated messenger RNA were mapped by the S1 procedure. Outside the coding sequence, the mRNA for alpha-amylase contains about 30 nucleotides at the 5' end and 51 nucleotides at the 3' end. The promoter region has -10 sequence TAAAAT starting eleven nucleotides upstream from the transcription start point, pppU, and the -35 hexanucleotide TTGTTA is separated from it by 16 nucleotides. As indicated by its sequence, the terminator is bidirectional and of the rho-independent kind, and the mRNA can form a long hairpin structure at the very 3' end. The 3' terminus of the transcript does not seem to include a U stretch, although the DNA template codes for U3AU6 at the 3' end of the hairpin sequence. The bulk of the amylase mRNA does not contain any 3'-terminal poly(A).

Characterization of the Bacillus subtilis tryptophan promoter region

The nucleotide sequence of the control region of the trp operon of Bacillus subtilis has been determined. The region was shown to contain the trp promoter by deletion analysis and by determination of the transcription start site. The trp promoter shows similarity to the consensus sequence for Escherichia coli and B. subtilis promoters. The presence of the trp control region on a high-copy-number plasmid confers resistance to the tryptophan analogue 5-methyltryptophan. It appears that an approximately 120-base-pair region comprising not only the trp promoter but also adjacent direct repeat sequences is necessary to confer 5-methyltryptophan resistance. We postulate that this region is involved in tryptophan regulation and confers 5-methyltryptophan resistance by titration of a trp regulatory protein. Removal of either the trp promoter or the adjacent direct repeat sequences abolished the 5-methyltryptophan-resistance phenotype. Placement of unrelated promoters adjacent to the direct repeat sequences restored 5-methyltryptophan resistance. This suggests that promoter activity is necessary for the regulatory function.

Bacillus megaterium spore protein C-3: nucleotide sequence of its gene and the amino acid sequence at its spore protease cleavage site

The nucleotide sequence of the Bacillus megaterium gene coding for spore-specific protein C-3 has been determined. The gene codes for 65 amino acids and the coding sequence is preceded by an efficient ribosome-binding site. The predicted protein C-3 sequence agrees with both the amino acid composition and the amino terminal sequence of protein C-3, and shows homology (approx. 65% of all residues are identical) with the sequences of the analogous proteins A and C of B. megaterium. Protein C-3 is cleaved by the sequence-specific B. megaterium spore protease, and the amino acid sequence at the new amino-terminus generated is identical to that predicted from the gene sequence, and homologous to the spore protease cleavage sites in the A and C proteins. The protein C-3 gene also shares a number of features with the previously sequenced protein C gene in both upstream and downstream flanking sequence.

Enzymatic and nucleotide sequence studies of a kanamycin-inactivating enzyme encoded by a plasmid from thermophilic bacilli in comparison with that encoded by plasmid pUB110

The product of a kanamycin resistance gene encoded by plasmid pTB913 isolated from a thermophilic bacillus was identified as a kanamycin nucleotidyltransferase which is similar to that encoded by plasmid pUB110 from a mesophile, Staphylococcus aureus. The enzyme encoded by pTB913 was more thermostable than that encoded by pUB110. In view of a close resemblance of restriction endonuclease cleavage maps around the BglII site in the structural genes of both enzymes, ca. 1,200 base pairs were sequenced, followed by amino-terminal amino acid sequencing of the enzyme. The two nucleotide sequences were found to be identical to each other except for only one base in the midst of the structural gene. Each structural gene, initiating from a GUG codon as methionine, was composed of 759 base pairs and 253 amino acid residues (molecular weight, ca. 29,000). The sole difference was transversion from a cytosine (pUB110) to an adenine (pTB913) at a position + 389, counting the first base of the initiation codon as + 1. That is, a threonine at position 130 for the pUB110-coded kanamycin nucleotidyltransferase was replaced by a lysine for the pTB913-coded enzyme. The difference in thermostability between the two enzymes caused by a single amino acid replacement is discussed in light of electrostatic effects.

Cloning of the neutral protease gene of Bacillus subtilis and the use of the cloned gene to create an in vitro-derived deletion mutation

The neutral protease gene of Bacillus subtilis has been cloned, and its nucleotide sequence has been determined. The cloned gene was used to create an in vitro-derived deletion mutation, which was used to replace the wild-type copy of the gene. This deletion, in combination with a deletion of the alkaline protease gene, completely abolished protease production. The loss of the proteases had no detectable effect on growth, morphology, or sporulation.

Expression of human dihydrofolate reductase cDNA and its induction by chloramphenicol in Bacillus subtilis

A bifunctional plasmid (pMP358) able to replicate and to express cloned human dihydrofolate reductase cDNA (cDHFR) in both Escherichia coli and Bacillus subtilis was constructed. The expression of cDHFR in B. subtilis was the result of a deletion that placed the cDNA fragment under the control of the chloramphenicol acetyltransferase (CAT) gene promoter of Staphylococcus aureus plasmid pC194. By sequence analysis of plasmid pMP358, we observed a gene fusion occurring between the cDHFR and the 32nd codon of the CAT gene. We report that such a "hybrid" gene is able to direct the synthesis of a 25-kDal "hybrid" protein, which was found to be inducible by supplementing B. subtilis cells with sublethal doses of chloramphenicol.

Construction of a promoter-probe vector for a Bacillus subtilis host by using the trpD+ gene of Bacillus amyloliquefaciens

The trp gene cluster of Bacillus amyloliquefaciens was found to be structurally similar to that of the Enterobacteriaceae. The translation termination codon of the putative trpE gene and the initiation codon for the putative trpD gene overlap at the trpE-trpD junction, and a promoter for the putative trpC gene is suggested to exist. A promoter-probe vector of Bacillus subtilis, pFTB281, was constructed with a DNA fragment of B. amyloliquefaciens, complementing the trpC and trpD mutations of B. subtilis, a 42-base-pair DNA fragment of M13mp7, and the larger EcoRI-PvuII fragment of pUB110, which confers an autonomous replication function and the kanamycin-resistance phenotype to the chimeric plasmid. pFTB281 has BamHI, EcoRI, and SalI cloning sites in the 5'-upstream portion of the protein-coding region of the putative trpD gene, and the insertion of a certain DNA fragment at any of these sites allowed the plasmid to transform a trpD mutant of B. subtilis to the TrpD+ phenotype. DNA fragments showing the promoter function for the trpD gene were obtained from B. amyloliquefaciens and Saccharomyces cerevisiae chromosomes and rho 11 and lambda phage DNAs, but rarely from the DNAs of Escherichia coli and pBR322.

Genes for alkaline protease and neutral protease from Bacillus amyloliquefaciens contain a large open reading frame between the regions coding for signal sequence and mature protein

The genes for alkaline protease (apr[BamP]) and neutral protease (npr[BamP]) from Bacillus amyloliquefaciens have been isolated and expressed in Bacillus subtilis. The DNA sequences of apr[BamP] and npr[BamP] revealed, in each case, the presence of a large open reading frame. The inferred amino acid sequence of either gene contained a signal sequence and an additional polypeptide sequence ('pro' sequence) preceding the mature protein. Based on DNA sequence, the start point of translation has been identified as amino acid residue - 107 for apr[BamP] and -221 for npr[BamP]. To demonstrate that the start point of translation of apr[BamP] in vivo is probably at codon -107, codon -103 (AAA) was changed to an ochre (TAA) by site-directed mutagenesis. Alkaline protease was produced from this ochre mutant derivative of apr[BamP] only when the host strain was Su+. The presence of a pro sequence may be common to all of the secreted proteases from bacilli.

Functional expression of the genes of Escherichia coli in gram-positive Corynebacterium glutamicum

Hybrid plasmids were constructed by combining in vitro the Escherichia coli plasmid pGA22, which carries the genes determining resistance to kanamycin, tetracycline, chloramphenicol and ampicillin, with the cryptic plasmids, pCG1 and pCG2, of Corynebacterium glutamicum. The hybrid plasmids were introduced into C. glutamicum and E. coli and replicated in both hosts. They expressed all the E. coli resistance phenotypes except ampicillin resistance in C. glutamicum. The levels of antibiotic inactivating enzymes encoded on these plasmids were about four to ten times lower in C. glutamicum than in E. coli. Despite the lack of expression of ampicillin resistance, beta-lactamase activity was detected in C. glutamicum carrying hybrid plasmids.

The DNA sequence of the gene and genetic control sites for the excreted B. subtilis enzyme beta-glucanase

The sequence of a 1409 base pair restriction fragment containing the B. subtilis gene for (1-3), (1-4)-beta-D-glucan endoglucanase is reported. The gene is encoded in a 726 base pair segment. The deduced amino acid sequence of the protein has a hydrophobic signal peptide at the NH2-terminus similar to those found in five other secreted proteins from Bacillus. The gene is preceded by a sequence resembling promoters for the vegetative B. subtilis RNA polymerase. This is followed by a sequence resembling a B. subtilis ribosome binding site nine nucleotides before the first codon of the gene. Two sequences, one before and one after the gene, can be arranged in secondary structures similar to transcriptional terminators. There is also a short open reading frame coding for a hydrophobic protein on the minus strand just upstream from the beta-glucanase gene. A possible role for this gene in the control of expression of beta-glucanase is suggested.

A promoter whose utilization is temporally regulated during sporulation in Bacillus subtilis

The formation of endospores in the Gram-positive bacterium Bacillus subtilis proceeds according to a temporally ordered program of gene activation. To investigate timing mechanisms in sporulation gene expression, we have isolated and sequenced the promoter region for a B. subtilis gene known as 0.3 kb whose transcription is switched on at about stage III of development. The 5' terminus of the 0.3 kb mRNA was mapped by the S1 nuclease procedure to a position just upstream from its apparent ribosome binding site and initiation codon and just downstream from the transcription termination site for an adjacent gene. This information enabled us to construct a transcriptional fusion in which the 5' region of the 0.3 kb gene was joined to the lacZ gene of Escherichia coli. When introduced into cells of B. subtilis, the 0.3 kb-lacZ fusion caused the synthesis of a fusion-specified RNA that originated from within the 0.3 kb promoter region and extended into the adjacent E. coli DNA, and the induction of beta-galactosidase synthesis at the third to fourth hour of sporulation. Enzyme synthesis required the 0.3 kb promoter, since a deletion of the 5' region of the 0.3 kb gene in the transcription fusion eliminated the production of beta-galactosidase. Induction of the 0.3 kb-lacZ fusion was under developmental control, since the production of beta-galactosidase was blocked or substantially impaired by chromosomal mutations in the sporulation genes spoOB, spoIIA, spoIIE and spoIIIE, but not by a spoIIC mutation. We conclude that the 0.3 kb gene promoter is subject to a developmental clock, which delays its utilization until an intermediate stage of sporulation, and discuss models for how the timing of gene expression is regulated.

Functional substitution of the recE gene of Bacillus subtilis by the recA gene of Proteus mirabilis

Rec mutants of Bacillus subtilis have been tested for complementation by the recA gene of Proteus mirabilis (recApm) which was introduced into B. subtilis via the plasmid pHP334. In the recE4 mutant of B. subtilis the plasmid pHP334 restored significantly the defects in RecE functions tested: UV-sensitivity, homologous recombination (transduction and transformation) and prophage induction. Although serological methods to detect the presence of RecApm protein in B. subtilis have been unsuccessful, our results strongly indicate that the recE function of B. subtilis is analogous to the recA function of P. mirabilis.

Escherichia coli and Pseudomonas putida RNA polymerases display identical contacts with promoters

Methylation protection experiments with four promoters (P1 and P2 of the pBR322 plasmid, lacUV5 and lambda P0) have shown that the RNA polymerases from Escherichia coli and Pseudomonas putida, while differing in the primary structure of the subunits involved in DNA binding, display identical patterns of DNA contacts. Nor do these enzymes differ in covalent cross-linking patterns with a partially apurinized promoter. We conclude that the two RNA polymerases have very similar structures of DNA binding centers. The evolutionary conservation of this structure may account for the fact that diverse RNA polymerases often recognize and efficiently use promoters of distant bacterial species.

Restriction and modification in Bacillus subtilis: nucleotide sequence, functional organization and product of the DNA methyltransferase gene of bacteriophage SPR

Bacillus subtilis phage SPR codes for a DNA methyltransferase (Mtase) which methylates the 5' cytosine in the sequence GGCC and both cytosines in the sequence CCGG. A 2126-bp fragment of SPR DNA containing the Mtase gene has been sequenced. This fragment has only one significant open reading frame of 1347 bp, which corresponds to the Mtase gene. Within the sequence the Mtase promoter has been defined by S1 mapping. The size of the SPR Mtase predicted from the deduced amino acid composition is 49.9 kDal. This is in agreement with both the Mr of the purified enzyme and with that of the SPR Mtase gene product identified here by minicell technique. Base changes leading to mutants affected in Mtase activity were localized within the Mtase gene.

Regulatory regions that control expression of two chloramphenicol-inducible cat genes cloned in Bacillus subtilis

Plasmid pPL603 is a promoter cloning vector for Bacillus subtilis and consists of a 1.1-kilobase fragment of Bacillus pumilus DNA inserted between the EcoRI and BamHI sites of pUB110. The gene cat-86, specifying chloramphenicol-inducible chloramphenicol acetyltransferase, is located on the 1.1-kilobase cloned DNA. When pPL603 is present in B. subtilis, cat-86 is unexpressed during vegetative growth but expressed during sporulation. The regulation of cat-86 in pPL603 is due to sequences within two restriction fragments, designated P1 and R1, that precede the main coding portion of the gene. The P1 fragment promotes transcription of cat-86 only during sporulation, whereas the adjacent R1 fragment lacks promoter function but contains sequences essential to chloramphenicol inducibility. A second B. pumilus gene, cat-66, was cloned in B. subtilis and is expressed throughout the vegetative growth and sporulation cycle. The cat-66 coding region is preceded by two adjacent restriction fragments designated as P2 and R2. P1 and P2 are identical in size and share 95% conservation of base sequence. R1 and R2 are also identical in size and share 91% conservation of base sequence. Fragment substitution experiments demonstrate that R2 can functionally replace R1. The substitution of P2 for P1 promotes cat-86 expression throughout vegetative growth and sporulation. Analysis of a derivative of pPL603 in which P2 has replaced P1 demonstrates that P2 promotes transcription of cat-86 during vegetative growth and that P2 contains the start site for transcription of cat-86. Thus, P1 and P2 differ strikingly in vegetative promoter function, yet they differ by single-base substitutions at only 11 positions of 203.

Transfer and expression of recombinant plasmids carrying pneumococcal mal genes in Bacillus subtilis

The pneumococcal mal recombinant plasmid pLS70, which carries two strong promoters for transcription, could not be transferred and maintained intact in Bacillus subtilis. Although it could be established at low frequency, pLS70 was unstable and was rapidly replaced by deleted forms of the plasmid. A deleted derivative plasmid, pLS69, could be transferred at high frequency and maintained intact. In pLS69 the deletion reduces function of both the malM (amylomaltase) and malX (X-fragment) promoters. This mutant mal plasmid still codes for an intact amylomaltase, and the enzyme is produced in both S. pneumoniae and B. subtilis. The amylomaltase, which is inducible by maltose in S. pneumoniae, is synthesized constitutively in B. subtilis and is localized in the cytosol. Although pLS69 enables S. pneumoniae to grow with maltose, the plasmid did not enhance the ability of B. subtilis to use this sugar, presumably because the latter does not transport free maltose into the cell. Minicells of B. subtilis containing pLS69 synthesized the amylomaltase polypeptide but no X-fragment. In S. pneumoniae carrying pLS69, production of the X-fragment is also reduced more than the amylomaltase, when compared to cells carrying pLS70, which produce equal amounts of the two proteins. Inasmuch as the down promoter mutation leaves unchanged both structural genes, their ribosome-binding sites and -10 and -35 promoter sequences, the unequal effect is attributed to differential reduction in AT composition proximal to the promoters. Vector proteins were revealed in minicells as several bands, all located in the cytosol except for an Mr 35000 polypeptide located in the membrane.

Complete nucleotide sequence and start sites for transcription and translation of the Bacillus megaterium protein C gene

The nucleotide sequence of the Bacillus megaterium protein C gene, encompassing the coding region and 341 base pairs of flanking regions, has been determined. The gene codes for a 72-residue protein whose predicted amino acid sequence is identical to that previously determined for protein C with the exception of an amino-terminal methionine predicted from the gene sequence, but not found in the mature protein. The translational initiation codon is preceded by an 11-base pair sequence highly complementary to the 3' terminus of B. megaterium 16S rRNA. Protection against S1 nuclease digestion by hybridization of a protein C gene fragment to RNA containing high levels of protein C mRNA localized the transcription initiation site 108 base pairs upstream from the translation start site. Upstream from the transcription initiation site there are no obvious homologies with conserved regions of promoters for previously described B. subtilis vegetative or sporulation genes.

Expression of the Bacillus subtilis glutamine synthetase gene in Escherichia coli

The structural gene for glutamine synthetase (glnA) in Bacillus subtilis ( glnAB ) cloned in the lambda vector phage Charon 4A was used to transduce a lysogenic glutamine auxotrophic Escherichia coli strain to prototrophy. The defective E. coli gene ( glnAE ) was still present in the transductant since it could be transduced. In addition, curing of the prototroph resulted in the restoration of glutamine auxotrophy. Proteins in crude extracts of the transductant were examined by a "Western blotting" procedure for the presence of B. subtilis or E. coli glutamine synthetase antigen; only the former was detected. Growth of the strain in media without glutamine was not curtailed even when the bacteriophage lambda pL and pRM promoters were hyperrepressed . The specific activities and patterns of derepression of glutamine synthetase in the transductant were similar to those of B. subtilis, with no evidence for adenylylation. The information necessary for regulation of glnAB must be closely linked to the gene and appears to function in E. coli.

Promoter recognition by sigma-37 RNA polymerase from Bacillus subtilis

Bacillus subtilis possesses at least five different forms of RNA polymerase holoenzyme which are distinguished by their sigma subunit and their promoter recognition specificity. Sigma-37 RNA polymerase, a minor form of RNA polymerase, recognizes a class of promoters, which includes promoters for genes transcribed early during endospore formation. We have used site-directed bisulfite mutagenesis to construct a series of single and multiple base substitutions in a promoter recognized by sigma-37 RNA polymerase. In vitro transcription analysis of this series of mutant promoters demonstrated that single base substitutions at positions -36, -16, -15 and -14 most dramatically reduced the efficiency of promoter utilization by sigma-37 RNA polymerase. These results support a model in which sigma-37 RNA polymerase recognizes its cognate promoters by interacting with a sequence of nucleotides near the -10 region and the -35 region of the promoter--a sequence not recognized by B. subtilis sigma-55 RNA polymerase or Escherichia coli RNA polymerase.

DNA sequence and regulation of ermD, a macrolide-lincosamide-streptogramin B resistance element from Bacillus licheniformis

The DNA sequence of ermD , a macrolide-lincosamide-streptogramin B (MLS) resistance determinant cloned from the chromosome of Bacillus licheniformis, has been determined. ermD encodes an erythromycin inducible protein of molecular weight 32,796. S1 nuclease mapping of the ermD promoter has revealed the presence of an approximately 354 base leader sequence on the ermD transcript. This leader contains a short open reading frame sufficient to encode a 14 amino acid peptide, which is preceded by a potential ribosomal binding site. The leader sequence has the potential to fold into several base paired structures, in some of which the ribosomal binding site for the ermD product would be sequestered. Deletion analysis demonstrated that the leader contains regulatory sequences. Removal of the ermD promoter and fusion to an upstream promoter did not interfere with induction, strongly suggestion that ermD regulation is posttranscriptional. Based on these features it appears likely that ermD is regulated by a translational attenuation mechanism, analogous to that suggested for ermC , a resistance element from Staphylococcus aureus ( Gryczan et al. 1980; Horinouchi and Weisblum 1980). Comparison of the ermD sequence and that of its product to two other sequenced MLS determinants reveals substantial phylogenetic relatedness, although the three genes are not homologous by the criterion of Southern blot hybridization.

Expression of the mouse dihydrofolate reductase cDNA in B. subtilis: a system to select mutant cDNAs coding for methotrexate resistant enzymes

With the aim to obtain a cDNA coding for a mammalian methotrexate resistant dihydrofolate reductase (Dhfr) a plasmid ( pQS1 ) harboring the mouse wild type Dhfr cDNA was constructed and used to transform a methotrexate sensitive bacteria: B. subtilis. A plasmid, pQS4 , expressing large amount of Dhfr in both E. coli and B. subtilis was isolated through a two steps selection with two substrate analogues, trimethoprim followed by methotrexate. This new plasmid has a 54 bp duplication including the beta-lactamase promoter and a deletion of 564 bp removing the 5' end of the beta-lactamase coding region. These changes create a new -35 region TTGAAA and a potentially stronger binding site for both E. coli and B. subtilis 16S ribosomal RNA. pQS4 transformed B. subtilis were then grown in the presence of high level of methotrexate and resistant mutants isolated. One of them, pQS6 , which codes for an enzyme about 50 times more resistant to methotrexate than the wild type Dhfr was sequenced. It shows that a point mutation replaces the glutamine residue at position 35 by a proline.

Nucleotide sequence of the 5' region of the Bacillus licheniformis alpha-amylase gene: comparison with the B. amyloliquefaciens gene

The DNA sequence of the 5' region of the Bacillus licheniformis alpha-amylase gene is reported. Comparison of the inferred amino acid sequence of the B. licheniformis alpha-amylase gene with that of the Bacillus amyloliquefaciens gene shows that whereas the amino acid sequences of the mature proteins have considerable homology, the sequences for the signal peptides are distinct.

Streptomyces lividans RNA polymerase recognizes and uses Escherichia coli transcriptional signals

We report here the use of a novel genetic approach for the study of transcriptional control in Streptomyces lividans. Using up-promoter mutants of the ampC beta-lactamase gene of Escherichia coli, we have shown that mutations in each of the regions that define the major determinants of promoter strength in E. coli-i.e., the -35 region, the -10 region, and the intervening "spacer" region-lead to increased synthesis of ampC mRNA in S. lividans, just as they do in their host of origin. Results are also presented showing that the ampC transcriptional terminator is functional in S. lividans. Taken together, these findings indicate that Streptomyces have an RNA polymerase that recognizes and uses the various components of E. coli transcriptional signals, and imply that, notwithstanding the high GC content (i.e., 73%) of the Streptomyces genome, these organisms have indigenous promoters similar to those found in E. coli.

Characterization of the precursor form of the exocellular levansucrase from Bacillus subtilis

Expression of the cloned levansucrase gene (sacB) was demonstrated in E. coli minicells by assay of the enzyme in crude extracts, SDS-polyacrylamide gel electrophoresis and immunoblotting. The existence of a precursor form of the enzyme of MW 53000 was also demonstrated and confirmed by the DNA sequence corresponding to the NH2 terminal region of the protein.

Nucleotide sequence surrounding transcription initiation site of xylABC operon on TOL plasmid of Pseudomonas putida

The xylABC operon on the TOL plasmid directs the synthesis of enzymes for conversion of toluene to benzoate and is positively controlled by the regulatory gene xylR. In the study here the nucleotide sequence was determined for the regulatory region of this operon. The in vivo transcription initiation site of the operon was determined by S1 nuclease and reverse transcriptase mapping. RNA was prepared from m-methylbenzyl alcohol-induced cells of Pseudomonas putida and Escherichia coli carrying pTN2, a derivative of the TOL plasmid containing the structural and regulatory genes of the entire toluene-degrading pathway. The amount of E. coli mRNA was estimated to be only 10% of that of P. putida mRNA. Consensus sequences of the -10 region (Pribnow box) and the -35 region (RNA polymerase recognition site) in E. coli genes were not found in the region preceding the transcription initiation site, whereas a sequence complementary to the 3' end of the 16S rRNA of Pseudomonas aeruginosa and E. coli existed in front of the predicted start codon of the xylA gene. These results explain the inefficient expression of TOL genes in E. coli.

Use of chromosomal integration in the establishment and expression of blaZ, a Staphylococcus aureus beta-lactamase gene, in Bacillus subtilis

With several different vectors, attempts were made to establish blaZ, a Staphylococcus aureus beta-lactamase gene, in Bacillus subtilis. Stable establishment of blaZ in B. subtilis was achieved by use of a vector that allowed the integration of a single copy of the gene into the chromosome of that host. blaZ was expressed in the heterologous host since B. subtilis strains carrying integrated blaZ produced beta-lactamase and were more resistant to ampicillin than was wild-type B. subtilis. blaZ was stably inherited in such strains, as no loss of the ability to produce beta-lactamase was observed after growth in nonselective liquid medium or on solid medium. In contrast, a blaZ-containing restriction fragment could not be established in B. subtilis with either pUB110- or pC194-based vectors. Similarly, a pC194-based shuttle vector (pGX318) containing the 5' end of blaZ (including the promoter and the coding region for the signal sequence and the first few amino acids of the mature protein) was unable to transform B. subtilis. Two derivatives of pGX318 that could be stably established in B. subtilis were isolated. The structures of these derivatives suggested that inactivation of the blaZ promoter was associated with the acquisition of the ability to be established.

The complete DNA sequence and regulatory regions of the Bacillus licheniformis spoOH gene

We have determined the sequence of a 1228 base-pair cloned DNA fragment from Bacillus licheniformis capable of specifically complementing mutations in the spoOH gene, which is required for the early stage of sporulation in B. subtilis. The sequence has only one long open reading frame consisting of 168 codons. In vivo and in vitro transcription mapping studies indicate the size of complementary RNA to be around 1 kb with the 5' initiation site at base 79 and the 3' termination site in the area of base 1138. This indicates the presence of a 5' untranslated RNA and a fairly long 3' extension. The promoter sequence of this gene is 5'TATAAT3' at -10, and 5'TTGACG3' at -35, a typical E. coli-like promoter sequence, and is transcribed in vitro specifically only by RNA polymerase containing delta 55 and not delta 37-containing holoenzyme.

In vitro transcription of the Bacillus subtilis phage phi 29 DNA by Bacillus subtilis and Escherichia coli RNA polymerases

The Escherichia coli RNA polymerase bound to phage phi 29 DNA has been visualized by electron microscopy. Thirteen specific binding sites have been observed at 1.7,2.6,5.5,10.4,13.7,25.2,25.7,26.3,33.5,59.5,69.2,91.7 and 99.6 DNA length units and they have been named A1,A1I,A1II,A1III,A1IV,A2,A2I, A3, A4,B1,B1I,C1 and C2, respectively. The binding sites A1,A2,A3,B1,C1 and C2 coincide with those found with Bacillus subtilis RNA polymerase. The transcription of phage phi 29 DNA with B. subtilis or E. coli RNA polymerases has been studied. With the B. subtilis RNA polymerase eight transcripts were found, starting at positions corresponding to the binding sites A1, A1III, A2,A3,B1I,B2,C1 and C2, respectively. With the E. coli RNA polymerase the same transcripts were found and a new one starting at position corresponding to the A4 binding site. The RNAs starting at binding sites A1,A1III,A2,B1I, B2,C1 and C2 are transcribed from right to left, as expected for early RNA. The RNAs which initiate at positions A3 and A4 are transcribed from left to right and probably correspond to late RNAs.

Bacillus subtilis requires a "stringent" Shine-Dalgarno region for gene expression

A series of plasmids was constructed differing only in the sequence of the Shine-Dalgarno region preceding the leukocyte interferon-A gene. This series of plasmids was used to test the efficiency of interferon expression in both Bacillus subtilis and Escherichia coli. In B. subtilis, interferon expression was much more sensitive to changes in the sequence of the Shine-Dalgarno region than in E. coli and it appeared to require more homology to the 3' end of 16S ribosomal RNA.

Recognition of messenger RNA during translational initiation in Escherichia coli

The structural aspects of recognition by E. coli ribosomes of translational initiation regions on homologous messenger RNAs have been reviewed. Also discussed is the location of initiation region on mRNA, its confines, typical nucleotide sequences responsible for initiation signal, and the influence of RNA macrostructure on protein synthesis initiation. Most of the published DNA nucleotide sequences surrounding the start of various E. coli genes and those of its phages have been collected.

Overproduction of proteins in recombinant organisms

In a qualitative way, the materials and methods available to the recombinant DNA genetic engineer for overproducing proteins have been explained. The status of technology development for overproduction using E. coli, B. subtilis, and yeast as host microorganisms has been briefly assessed. Potential and actual genetic engineering solutions to the plasmid-shedding problem have been outlined. Since plasmid shedding presents a serious problem to the fermentation engineer responsible for scale-up to commercial production levels and since the ways around this problem appear mostly to have their solutions in the realm of genetic engineering coupled with appropriate fermentation protocol, the genetic engineer should work closely with the fermentation engineer to make scale-up realizable. Neither the genetic engineer nor the fermentation engineer can afford to be ignorant of the tools available to each profession if fermentation scale-up of genetically engineered microorganisms is to be accomplished economically.

Nucleotide sequence of the staphylokinase gene from Staphylococcus aureus

We have determined the entire nucleotide sequence of a 1,4-kilobase segment containing the staphylokinase gene, sak, molecularly cloned from the bacteriophage S phi-C genome of Staphylococcus aureus. The probable coding region is 489 base pairs long and these base pairs are translated into a polypeptide of 163 amino acid residues (Mr = 18,490) with a presumed signal sequence of 27 amino acid residues at the NH2-terminal end. In regions adjacent to the sak structural gene a possible promoter sequence and three possible terminator sequences for transcription were found about 100 base pairs upstream from the initiation codon and about 300, 400, and 500 base pairs downstream from the termination codon, respectively; they are active in an in vitro transcription system using Escherichia coli RNA polymerase. The immunoactive 18,500-dalton and 15,500-dalton proteins corresponding to a precursor form before secretion and a mature form after secretion of the sak gene products, respectively, were identified by the E. coli maxicell system.

Structure of the Bacillus sphaericus R modification methylase gene

A 2.5 X 10(3) base-pair segment of Bacillus sphaericus R DNA cloned in Escherichia coli has previously been shown to carry the functional BspRI modification methylase gene. The approximate location of the gene on this DNA segment and its direction of transcription were established by subcloning experiments. The nucleotide sequence of the relevant region was determined by the Maxam-Gilbert procedure. An open reading frame that can code for a 424 amino acid protein was found. The calculated molecular weight (48,264) of this protein is in fair agreement with previous estimates (50,000 to 52,000). The synthesis of this protein was demonstrated in E. coli minicells. The initiation point of transcription by E. coli RNA polymerase was localized by in vitro transcription experiments. The open reading frame starts 29 base-pairs downstream from the transcription initiation site and it is preceded by a sequence showing extensive Shine-Dalgarno complementarity. Subcloning experiments and translation in minicells suggest that after removal of this translational initiation site, a secondary start site 29 amino acids downstream can also start translation in E. coli, and this shorter protein retains the methylase activity. The overall base composition of the gene and the codon usage indicate a strong preference for A.T base-pairs.

Cloning and expression of the Escherichia coli recA gene in Bacillus subtilis

By means of homopolymer dG-dC tailing, using PstI linearized pBR327 as vector, we constructed small plasmids containing the entire Escherichia coli recA gene. The 1.8-kb inserts were recloned in the Bacillus subtilis expression vector pPL608 in a B. subtilis recE4 strain. Analysis of plasmid-coded proteins showed expression of the E. coli recA gene both in minicells and whole cells of B. subtilis. Expression was under control of the bacteriophage SP02 promoter, which is part of pPL608. A recA-expressing plasmid completely abolished the transformation deficiency of the recE4 mutant as well as its sensitivity to mitomycin C (MC). The expressed recA gene also restored recombination in other B. subtilis strains lacking the recE gene product. These results indicate a high similarity between the functions of the E. coli RecA and B. subtilis RecE proteins.

Developmental and genetic regulation of Bacillus subtilis genes transcribed by sigma 28-RNA polymerase

Sigma-28 RNA polymerase is a minor form of Bacillus subtilis RNA polymerase that is highly specific for transcription from a small number of promoter sites in the B. subtilis genome. We have followed transcription from two of these loci (P28-1 and P28-2) in vivo using a quantitative S1 nuclease mapping procedure. Both promoters are used at a modest rate in vegetatively growing cells (about 10 RNA copies per cell) and transcripts are initiated at the same start sites as found in vitro with the purified sigma 28-RNA polymerase. Transcription from the sigma 28 promoters varies somewhat with growth conditions and is shut off rapidly and almost completely after the first hour of sporulation. Neither sigma 28 transcripts is detected in vegetative cells of certain B. subtilis mutants (spoO classes A, B, E, and F) that are defective in sporulation. Transcription from these promoters is restored in second site revertants that are able to sporulate. Hence the action of sigma 28-RNA polymerase appears to be regulated by the spoO genes and the functions controlled by sigma 28-promoters may be closely tied to the system involved in the initiation of sporulation.

Ribosomal RNA precursors of Bacillus subtilis

The DNA sequence of the region corresponding to the 5'-end of a 16S rRNA gene of B. subtilis 168 was determined. Comparison of this sequence with the sequences flanking other 16S and 23S rRNA coding regions (1-4) indicated that large RNA stem structures, surrounding the mature 16S and 23S rRNAs, could form in a precursor rRNA. The 5'-ends of the precursors of 16S and 23S rRNAs (p16S and p23S) were mapped to the middles of these potential RNA stem structures. We propose that the initial cleavages of the primary rRNA transcript occur near the "opposed G's" which interrupt the basepairing of each of these stem structures. This model is supported by the finding that the 5'-end of the 5S rRNA precursor, p5A (5), maps to the region of the "opposed G's" in the 23S rRNA stem structure.

Alpha-amylase genes (amyR2 and amyE+) from an alpha-amylase-hyperproducing Bacillus subtilis strain: molecular cloning and nucleotide sequences

amyR2, amyE+, and aroI+ alleles from an alpha-amylase-hyperproducing strain, Bacillus subtilis NA64, were cloned in temperate B. subtilis phage p11, and the amyR2 and amyE+ genes were then recloned in plasmid pUB110, which was designated pTUB4. The order of the restriction sites, ClaI-EcoRI-PstI-SalI-SmaI, found in the DNA fragment carrying amyR2 and amyE+ from the phage genome was also found in the 2.3-kilobase insert of pTUB4. Approximately 2,600 base pairs of the DNA nucleotide sequence of the amyR2 and amyE+ gene region in pTUB4 were determined. Starting from an ATG initiator codon, an open reading frame was composed of a total 1,776 base pairs (592 amino acids). Among the 1,776 base pairs, 1,674 (558 amino acids) were found in the cloned DNA fragment, and 102 base pairs (34 amino acids) were in the vector pUB110 DNA. The COOH terminal region of the alpha-amylase of pTUB4 was encoded in pUB110. The electrophoretic mobility in a 7.5% polyacrylamide gel of the alpha-amylase was slightly faster than that of the parental alpha-amylases. The NH2 termination portion of the gene encoded a 41-amino acid-long signal sequence (Ohmura et al., Biochem. Biophys. Res. Commun. 112:687-683, 1983). The DNA sequence of the mature extracellular alpha-amylase, a potential RNA polymerase recognition site and Pribnow box (TTGATAGAGTGATTGTGATAATTTAAAAT), and an AT-rich inverted repeat structure which has free energy of -8.2 kcal/mol (-34.3 kJ/mol) were identified. The AT-rich inverted repeat structure seemed to correspond to the hyperproducing character. The nucleotide sequence around the region was quite different from the promoter region of the B. subtilis 168 alpha-amylase gene which was cloned in the Escherichia coli vector systems.

DNA sequence of the tandem ribosomal RNA promoter for B. subtilis operon rrnB

A new ribosomal RNA operon designated rrnB has been identified by screening a Charon 4a library of cloned B. subtilis sequences. Clones containing the promoter region of this operon are unstable in E. coli unless a special vector possessing a transcriptional terminator is used. DNA sequence data suggests that this operon contains two tandem putative promotor regions not unlike those found in E. coli. There are 92 base pairs separating the two "-10 regions" of the promotors. The second is 180 bp upstream from the start site for mature 16S RNA. A potential 29 base pair stem structure necessary for processing of the mature 16S RNA sequence can also be predicted from this analysis.

Structure and organization of rRNA operons in the region of the replication origin of the Bacillus subtilis chromosome

Structure and organization of two complete ribosomal RNA (rRNA) gene sets, rrnO and rrnA, were determined for the first time in Bacillus subtilis. They are located at the region of the replication origin of the chromosome. Each set constitutes a single operon of: two tandem promoters - leader sequence - 16S rRNA gene - Ile-tRNA gene - Ala-tRNA gene - 23S rRNA gene - 5S rRNA gene - termination signal. The first promoter (P1) of rrnO differs from that of rrnA in sequence and function. P1 of rrnO was used very little for transcription either in vivo or in vitro while P1 was predominantly used in rrnA. A putative transcript of the entire operon was determined and constructed into a secondary structure. Analysis of in vivo transcripts by S1 mapping revealed primary processing sites at the loop and stem structure of 16S rRNA in rrnO and rrnA. A unique sequence in the leader region of rrnO can be formed into a highly complexed secondary structure and affects processing of mature 16S rRNA. The sequences of the two spacer tRNA genes are highly conserved between B. subtilis and Escherichia coli.

Bacillus cereus 569/H beta-lactamase I: cloning in Escherichia coli and signal sequence determination

The gene, penPC, for beta-lactamase I of Bacillus cereus 569/H has been cloned and its expression studied in Escherichia coli. The protein product from the in vitro translation of penPC was shown by gel electrophoresis to have an Mr of 36 000 which is larger than the in vivo products found in B. cereus and E. coli. The DNA sequence of the signal region was determined. It revealed that the smallest known mature form present in B. cereus culture fluids is preceded by 45-48 amino acids in pre-beta-lactamase I, considering that there are 3 initiation codons in the same reading frame, one or more of which might be initiating translation. Unlike the Bacillus licheniformis 749/C beta-lactamase, which has a membrane-bound thioether lipoprotein form, the single Cys residue in the B. cereus beta-lactamase I signal sequence is unmodified and a single processed form of the enzyme is present in E. coli cells carrying penPC.

Nucleotide sequence of the Streptococcus faecalis plasmid gene encoding the 3'5"-aminoglycoside phosphotransferase type III

We have cloned in Escherichia coli and sequenced a 1489-bp DNA fragment conferring resistance to kanamycin and originating from the streptococcal plasmid pJH1. The resistance gene was located by analysis of the initiation and termination codons in an open reading frame (ORF) of 792 bp. The deduced gene product, a 3'5''-aminoglycoside phosphotransferase of type III, has an Mr of 29,200. Comparison of its amino acid sequence with those of type I (Oka et al., 1981) and type II (Beck et al., 1982) 3' phosphotransferase, from transposable elements Tn903 and Tn5, respectively, indicated a statistically significant structural relationship between these enzymes from phylogenetically remote bacterial genera. The degree of homology observed indicate that phosphotransferase type III and type I genes have diverged from a common ancestor and that the phosphotransferase type II gene has emerged more recently from the type I evolutionary pathway.

Deletion analysis of a complex promoter for a developmentally regulated gene from Bacillus subtilis

SpoVG is a developmentally regulated gene from the spore-forming bacterium Bacillus subtilis. The transcription initiation region for spoVG consists of two overlapping promoters whose startpoints of RNA synthesis are ten base pairs apart (Moran et al., 1981a). These startpoints are separately utilized by two forms of RNA polymerase holoenzyme containing different species of B. subtilis sigma factor. We have constructed a series of deletion mutations that extend into the spoVG promoter region from the downstream and from the upstream directions. Transcription studies with these mutated promoters showed that the functional boundaries of the spoVG promoters extended from the region of the transcription startpoints into an upstream A + T-rich box, which was located 76 to 51 base pairs preceding the downstream startsite. We have unexpectedly discovered that propagation of the spoVG promoter region on a high copy number plasmid in B. subtilis interferes with the process of sporulation by impairing development at an early stage. This was not a general effect of promoter amplification, since the propagation on plasmids of two other strong Bacillus promoters had little or no effect on spore formation. Deletion analysis established that the region of spoVG causing sporulation inhibition closely correlated with DNA sequences required for efficient promoter utilization in vitro. We propose that amplification of spoVG titrates a sporulation-specific regulatory protein that binds at or near the region of transcription initiation.

Molecular cloning and expression of a Bacillus subtilis beta-glucanase gene in Escherichia coli

A Bacillus subtilis gene coding for an endo-beta-1,3-1,4-glucanase has been transferred to Escherichia coli by molecular cloning using bacteriophage lambda and plasmid vectors. The gene is contained within a 1.6-kb EcoRI-PvuI DNA fragment and directs the synthesis in E. coli of a beta-glucanase which specifically degrades barley glucan and lichenan. A novel dye-staining method has been developed to detect beta-glucanase activity in colonies on agar plates.

In vitro transcription of the cloned chromosomal crystal gene from Bacillus thuringiensis

We have determined the conditions required for in vitro transcription of the cloned chromosomal crystal gene from Bacillus thuringiensis using either the homologous vegetative RNA polymerase or a sporulation specific form of this enzyme. The gene is actively transcribed by the latter enzyme (form II) but not by the vegetative one. Evidence for a specific recognition between the form II enzyme and the promotor site of the crystal gene was obtained by binding experiments. They showed that the binding is increased by the presence of some additional factors, which change the specificity of the vegetative core-enzyme. The sequence of the promoter has been determined and the start-point of the transcription deduced. Two hexanucleotide sequences, TACAAT and CCTACG, centered at - 10 and - 35 bp are present, but are somewhat different from the consensus sequences previously described in other bacilli.

Expression of antibiotic resistance genes from Escherichia coli in Bacillus subtilis

Bifunctional recombinant plasmids were constructed, comprised of the E. coli vectors pBR322, pBR325 and pACYC184 and different plasmids from Gram-positive bacteria, e.g. pBSU161-1 of B. subtilis and pUB110 and pC221 of S. aureus. The beta-lactamase (bla) gene and the chloramphenicol acetyltransferase (cat) gene from the E. coli plasmids were not transcribed and therefore not expressed in B. subtilis. However, tetracycline resistance from the E. coli plasmids was expressed in B. subtilis. Transcription of the tetracycline resistance gene(s) started in B. subtilis at or near the original E. coli promoter, the sequence of which is almost identical with the sequence recognized by sigma 55 of B. subtilis RNA polymerase.