Nucleotide sequences of transcription and translation initiation regions in Bacillus phage phi 29 early genes

Modulation of in vivo and in vitro transcription of bacteriophage phi 29 early genes

The majority of early transcripts of the phi 29 bacteriophage are produced throughout the lytic cycle but the levels of a class of transcripts from the right end of the phi 29 genome are significantly reduced late in the infection. We have isolated a phage early protein which selectively interferes with the initiation in vitro of transcription from promoters at the right end of the phi 29 genome. The amino acid sequence of the purified inhibitory protein correlates to the sequence predicted from the phi 29 gene 6 reading frame. In addition the inhibitory protein was not detectable in cells infected with phage mutated in gene 6 and the decrease in transcription did not occur in vivo when nonpermissive cells were infected with phi 29(sus6). The results indicate that the gene 6 protein modulates transcription from the right side of the phi 29 genome.

In vivo transcription of bacteriophage phi 29 DNA: transcription initiation sites

The initiation sites of the RNA transcripts synthesized in vivo in Bacillus subtilis infected with bacteriophage phi 29 have been mapped by S1 protection experiments. Nine transcription initiation sites were localized along the entire phi 29 genome, close to previously reported B. subtilis and Escherichia coli RNA polymerase-binding sites. Eight of these sites corresponded to early transcription and only one corresponded to late transcription. By using 5'-end-labeled RNA, four of the early sites and the late one were shown to be the main sites where initiation of transcription occurs in vivo in the phi 29 genome.

Separation and analysis of the RNA polymerase binding sites of a complex Bacillus subtilis promoter

The Bacillus subtilis veg promotor site was shown to be composed of two neighboring RNA polymerase binding sites, only one of which ("Site I") produces a transcript. The relationship between these sites has been investigated following insertion of ten base pairs of DNA between the sites and subsequent cloning of each site independent of the other, and deletion of DNA sequences upstream from the productive site. The effect of DNA insertion was to permit transcription initiation from the previously nonproductive Site II, in either the presence or absence of Site I. This could be attributed to insertion of a purine residue seven base pairs downstream from the Pribnow box of Site II. Transcription from Site I was slightly increased in the presence of Site II in cis, but was still efficient in the absence of Site II, indicating that there is no absolute dependence on Site II for in vitro transcription from Site I.

Nucleotide sequence analysis of the gene specifying the bifunctional 6'-aminoglycoside acetyltransferase 2"-aminoglycoside phosphotransferase enzyme in Streptococcus faecalis and identification and cloning of gene regions specifying the two activities

The gene specifying the bifunctional 6'-aminoglycoside acetyltransferase [AAC(6')] 2"-aminoglycoside phosphotransferase [APH(2")] enzyme from the Streptococcus faecalis plasmid pIP800 was cloned in Escherichia coli. A single protein with an apparent molecular weight of 56,000 was specified by this cloned determinant as detected in minicell experiments. Nucleotide sequence analysis revealed the presence of an open reading frame capable of specifying a protein of 479 amino acids and with a molecular weight of 56,850. The deduced amino acid sequence of the bifunctional AAC(6')-APH(2") gene product possessed two regions of homology with other sequenced resistance proteins. The N-terminal region contained a sequence that was homologous to the chloramphenicol acetyltransferase of Bacillus pumilus, and the C-terminal region contained a sequence homologous to the aminoglycoside phosphotransferase of Streptomyces fradiae. Subcloning experiments were performed with the AAC(6')-APH(2") resistance determinant, and it was possible to obtain gene segments independently specifying the acetyltransferase and phosphotransferase activities. These data suggest that the gene specifying the AAC(6')-APH(2") resistance enzyme arose as a result of a gene fusion.

Structure of a beta-galactosidase gene of Bacillus stearothermophilus

The nucleotide sequence of the bgaB gene, which encodes the thermostable beta-galactosidase I of Bacillus stearothermophilus, and its flanking region was determined. A 2,016-base-pair open reading frame observed was concluded to be for beta-galactosidase I (Mr 78,051) from observations that the amino acid composition of the enzyme and the sequence of 14 amino acids from the amino-terminus of the enzyme coincided with those deduced from this open frame. A 107-base-pair HaeIII-AluI fragment just upstream of the estimated Shine-Dalgarno sequence of the bgaB gene had promoter activity toward cat-86 (chloramphenicol acetyltransferase gene) and produced the enzyme at a level equivalent to 7% of the total cellular protein of B. subtilis. From the base sequence of this DNA region and the transcriptional start site determined by S1 nuclease mapping, the -35 and -10 sequences are estimated to be TTGACA and TAATTT, respectively, which are similar to the consensus sequence of B. subtilis sigma 43 RNA polymerase.

Characterization of signals promoting gene expression on the Staphylococcus aureus plasmid pUB110 and development of a gram-positive expression vector system

The transcriptional and translational initiation signals of a portion of the Staphylococcus aureus plasmid pUB110 were analyzed. An Mbo I-Pvu II fragment was sequenced and the site of transcriptional initiation was determined by in vitro mapping. To convert the plasmid into a cloning vector, a multilinker was introduced in different positions relative to a detected reading frame. The Gram-negative beta-galactosidase gene and the Gram-positive chloramphenicol acetyltransferase (cat) gene were fused and the level of expression was determined in Bacillus subtilis. Hybrid proteins consisting of corresponding CAT polypeptides were produced in each translational reading frame. Therefore this vector system can be used to express cloned DNA in the Gram-positive host Bacillus subtilis. Furthermore a derived lacZ fusion plasmid may be used for rapid screening of inserts.

Nucleotide sequence of the type A streptococcal exotoxin (erythrogenic toxin) gene from Streptococcus pyogenes bacteriophage T12

The gene specifying type A streptococcal exotoxin (speA), also known as erythrogenic toxin, was cloned from the Streptococcus pyogenes bacteriophage T12 genome and analyzed by nucleotide sequencing. The speA gene consists of 753 base pairs and codes for a 29,244-molecular-weight protein. The speA gene product contains a putative 30-amino acid signal peptide, resulting in a molecular weight of 25,787 for the secreted protein. A possible promoter and ribosome-binding site are present in the region upstream from the speA gene, and a transcriptional terminator is located 69 bases downstream from the translational termination codon. The amino acid sequence of the carboxy-terminal portion of the type A streptococcal exotoxin exhibits extensive homology with the carboxy terminus of Staphylococcus aureus enterotoxins B and C1.

Identification of the pleiotropic sacQ gene of Bacillus subtilis

The sacQ gene of Bacillus subtilis, a pleiotropic gene affecting the expression of a number of secreted gene products, has been identified as a small 46-amino-acid polypeptide. The increased expression of this polypeptide in strains carrying the sacQ36 allele, or in strains carrying the sacQ gene on a high copy plasmid, appears to be responsible for the phenotype of higher levels of proteases seen in these strains. A deletion of the sacQ gene had no apparent phenotype, indicating that it is not an essential gene.

Expression of the streptokinase gene from Streptococcus equisimilis in Bacillus subtilis

The previously cloned and sequenced streptokinase gene (skc) from Streptococcus equisimilis H46A was inserted into plasmid vectors capable of replication in Bacillus subtilis. The skc gene was expressed by use of its own transcription and translation signals which appeared to meet the stringent requirements of B. subtilis for efficient foreign gene expression. The secreted streptokinase activity began to decline toward the end of the exponential growth phase suggesting that B. subtilis exoproteases hydrolyzed and inactivated the foreign protein.

Nucleotide sequence of the late region of Bacillus subtilis phage PZA, a close relative of phi 29

The 12,200-bp sequence of the late region of bacteriophage PZA was determined. Open reading frames (ORFs) and potential ribosome-binding sites were found in this region and the ORFs were assigned to eleven late genes. A potential bidirectional transcriptional terminator was found and its possible function is discussed.

Expression of the Proteus mirabilis recA gene in Bacillus subtilis is directed by its own promoter

The recA gene of Proteus mirabilis (recApm) has been cloned into the PstI site of the Bacillus promoter-probe plasmid pPL603. When present on this plasmid, the recApm1) gene is expressed in B. subtilis under the control of its own transcriptional and translational signals. It is concluded that the high AT-content of the DNA sequence upstream of the -35 region is of decisive importance for the usage of the recApm promoter by the B. subtilis RNA polymerase. The results are discussed in relation to the expression barriers found to exist for genes from gram-negative bacteria in the gram-positive B. subtilis.

Structure of the gene encoding the exoglucanase of Cellulomonas fimi

In Cellulomonas fimi the cex gene encodes an exoglucanase (Exg) involved in the degradation of cellulose. The gene now has been sequenced as part of a 2.58-kb fragment of C. fimi DNA. The cex coding region of 1452 bp (484 codons) was identified by comparison of the DNA sequence to the N-terminal amino acid (aa) sequence of the Exg purified from C. fimi. The Exg sequence is preceded by a putative signal peptide of 41 aa, a translational initiation codon, and a sequence resembling a ribosome-binding site five nucleotides (nt) before the initiation codon. The nt sequence immediately following the translational stop codon contains four inverted repeats, two of which overlap, and which can be arranged in stable secondary structures. The codon usage in C. fimi appears to be quite different from that of Escherichia coli. A dramatic (98.5%) bias occurs for G or C in the third position for the 35 codons utilized in the cex gene.

Nucleotide sequence of the late region of Bacillus phage phi 29 completes the 19,285-bp sequence of phi 29 genome. Comparison with the homologous sequence of phage PZA

The 12,177-bp nucleotide (nt) sequence of the late region of Bacillus phage luminal diameter 29 genome was determined. This sequence completes the entire 19,285-bp sequence of phage luminal diameter 29 DNA. Eleven open reading frames were found in this region, and these were assigned to eleven late genes. Ribosome-binding sites and a potential transcriptional promoter and terminator are considered. The nt sequence was compared to the homologous region of the closely related phage PZA and tolerated variations at the nt and amino acid (aa) level were evaluated. The most frequent changes are silent nt substitutions in the third position of codons, but aa substitutions are also found.

Nucleotide sequence of the right early region of Bacillus subtilis phage PZA completes the 19366-bp sequence of PZA genome. Comparison with the homologous sequence of phage phi 29

We have sequenced the rightmost 2079 bp of the Bacillus subtilis phage PZA genome. This region encompasses the right early region. We compared it with the homologous region of phage phi 29. Six open reading frames (ORFs) were found in this region of PZA and one of them was assigned to gene 17. Analysis of putative ribosome-binding sites and comparison with phi 29 ORFs indicate that at least some of the remaining ORFs could encode proteins. Corresponding genes were not identified so far by genetic methods. Promoter candidates in the right early region of PZA were found and compared to phi 29 promoters. The sequenced region together with previously determined sequences [Paces et al., Gene 38 (1985) 45-56 and 44 (1986) 107-114] completes the entire 19,366-bp sequence of phage PZA genome.

The beta-glucanase gene from Bacillus amyloliquefaciens shows extensive homology with that of Bacillus subtilis

The nucleotide sequence of a 1583-bp DNA fragment containing gene bg1A for endo-beta-1,3-1,4-glucanase (EC 3.2.1.73) of Bacillus amyloliquefaciens strain BE20/78, a high producer of secreted enzymes, has been determined. The gene bg1A comprises an open reading frame (ORF) of 717 bp (= 239 codons) starting with ATG at 469 up to the translation stop codon TAA at 1188. Upstream from the translation initiation codon ATG, the ribosome-binding sequence 5'-AAAAAAGGGGG-3' and two putative bglA promoters have been identified. A box of eleven AT out of twelve base pairs (bp) precedes the -35 region of promoter P1. Beyond the translation stop codon UAA, a sequence of 69 bp can be folded into a hook-like stem-loop structure which probably functions as a transcriptional terminator. The ORF region of the gene bglA reveals about 90% homology with another beta-glucanase gene, bglS of Bacillus subtilis C120 sequenced by Murphy et al. (1984). Three regions of frequent amino acid (aa) changes are indicated. However, the major difference between these is a set of deletions within the non-coding region separating the bglA gene from an unknown preceding ORF and by one deletion shortening the proposed signal peptide by three aa (Pro-Tyr-Leu-). The putative transcription terminator of gene bglA completely lacks homology with a B. subtilis bglS gene. The signification of deletions erasing the 'sacR-homology region' in B. amyloliquefaciens, which have been detected in proximity of the beta-glucanase gene of B. subtilis by Steinmetz and Aymerich (1986), is discussed.

Comparative studies on the structural gene for the ribosomal protein S1 in ten bacterial species

By applying the Southern blot technique we compared the structural gene rpsA for ribosomal protein S1 and its preceding sequence from Escherichia coli with nine other bacterial species. We found high homology among the structural genes of E. coli and other gram-negative but not gram-positive bacteria. In contrast, the regulatory sequence preceding the structural gene was not highly conserved among the organisms studied. Cloning and DNA sequence analysis of a 1.2 kb fragment coding for most of the structural gene for S1 from Providencia localized some strongly conserved parts of the DNA sequence, despite the fact that the codon usage showed considerable divergence from that of E. coli.

Nucleotide sequence of ermA, a macrolide-lincosamide-streptogramin B determinant in Staphylococcus aureus

The complete nucleotide sequence of ermA, the prototype macrolide-lincosamide-streptogramin B resistance gene from Staphylococcus aureus, has been determined. The sequence predicts a 243-amino-acid protein that is homologous to those specified by ermC, ermAM, and ermD, resistance determinants from Staphylococcus aureus, Streptococcus sanguis, and Bacillus licheniformis, respectively. The ermA transcript, identified by Northern analysis and S1 mapping, contains a 5' leader sequence of 211 bases which has the potential to encode two short peptides of 15 and 19 amino acids; the second, longer peptide has 13 amino acids in common with the putative regulatory leader peptide of ermC. The coding sequence for this peptide is deleted in several mutants in which macrolide-lincosamide-streptogramin B resistance is constitutively expressed. Potential secondary structures available to the leader sequence of the wild-type (inducible) transcript and to constitutive deletion, insertion, and point mutations provide additional support for the translational attenuation model for induction of macrolide-lincosamide-streptogramin B resistance.

DNA sequences specifying the transcription of the streptococcal kanamycin resistance gene in Escherichia coli and Bacillus subtilis

The gene conferring resistance to kanamycin, aphA, and originating from the streptococcal plasmid pJH1 was inserted into a shuttle vector. Full expression of aphA was obtained in Escherichia coli and Bacillus subtilis. The starting point for aphA transcription, determined by S1 nuclease mapping, was located 340 base pairs upstream from the ATG translational initiator codon. The sequence of the promoter consists of the hexanucleotides TTGACA and TATCTT, with a spacing of 17 base pairs. The stability profile of a 600 base-pair-long DNA fragment containing the aphA promoter and the translational initiation site indicated that, as already reported for Escherichia coli, both structures are located in domains of weak stability.

Nucleotide sequence of the thymidylate synthetase gene (thyP3) from the Bacillus subtilis phage phi 3T

The thyP3 gene, encoding thymidylate synthetase, from the Bacillus subtilis phage phi 3T has been cloned and the nucleotide sequence determined. The derived amino acid sequence indicates a subunit Mr of 32 748. The primary amino acid sequence is compared with the sequences of the analogous proteins specified by Escherichia coli (thyA), Lactobacillus casei, (thyA) and phage T4 (td). Extensive conservation exists in all four sequences implying a shared tertiary structure.

Nucleotide sequence analysis of DNA replication origins of the small Bacillus bacteriophages: evolutionary relationships

The ends of the small Bacillus phage genomes serve as origins and termini of their DNA replication. We have determined nucleotide sequences at the termini of four different phage DNAs and compared them with those of phi 29 DNA which has been described previously. A high degree of homology was found at the extreme ends of DNAs from phi 29, phi 15 (group A), M2Y and Nf (group B). 17 bp at the far left of the DNAs are identical. A highly conserved dodecanucleotide sequence, CCATTTCCCCAT, was also found in the righthand terminus of all these phage DNAs, at positions 27-38 from the end. Nucleotide sequences of phage GA-1 are not very similar to those of the other phages. Examination of the 5'-terminal and 3'-terminal sequences of all the phages suggests that stable 'panhandle' structures are unlikely to be formed via base pairing of both ends. However, thermodynamically more stable panhandle structures might be formed by displaced single-stranded DNA, although this requires rather large loops.

Nucleotide sequence of the Bacillus subtilis tryptophan operon

In Bacillus subtilis, tryptophan biosynthesis is one of the most thoroughly characterized biosynthetic pathways. Recombinant DNA methodology has permitted a rapid characterization of the tryptophan (trp) gene cluster at the molecular level. In this report the nucleotide sequence of the six structural genes together with the intercistronic regions and flanking regulatory regions are presented.

Nucleotide sequence of the major early region of Bacillus subtilis phage PZA, a close relative of phi 29

The 5200-bp nucleotide sequence of the major early region of bacteriophage PZA has been determined. Open reading frames (ORFs) and potential transcriptional and translational regulatory signals were found in this region. The sequence was compared with the known sequence of the homologous region of the closely related phage phi 29 (Yoshikawa and Ito, 1982). This comparison permitted a more accurate assignment of several ORFs and regulatory signals.

The complete sequence of Bacillus phage phi 29 gene 16: a protein required for the genome encapsidation reaction

We have sequenced the region of the Bacillus phage phi 29 genome that encodes gene 16, the gene product of which catalyzes the in vivo and in vitro genome-encapsidation reaction. The identity of the coding frame was confirmed by sequencing a sus mutant, sus16(300). It is concluded that gene 16 encodes a 39-kDal protein and is comprised of 331 amino acids. Only 30 bp separates gene 16 from the last open reading frame of the right early region. Analysis of potential secondary structures in this region suggests that the same sequences may be involved in the termination of both the late and early transcripts.

The complete sequence of the Bacillus phage phi 29 right early region

We have sequenced the rightmost 2216 bp of the Bacillus phage phi 29 genome. This region encompasses the right early region and completes the sequence of the phi 29 early functions. The sequence of gene 17, an early gene implicated in the replication process, is presented. From these results we predict that gene 17 encodes a 19.1-kDal protein. Further analysis of the sequence revealed five previously undetected potential genes, encoding 12.6-, 12.4-, 15.2-, 6.2- and 4.6-kDal proteins. The biological efficacies of some of these putative genes were demonstrated using an Escherichia coli in vitro transcription-translation system. We also examined the transcriptional and translational signals present on this region of the genome.

Bacteriophage SPO1 genes 33 and 34. Location and primary structure of genes encoding regulatory subunits of Bacillus subtilis RNA polymerase

Bacteriophage SPO1 gene 33 and 34 products are required for SPO1 late gene transcription. Both proteins bind to the core RNA polymerase of the Bacillus subtilis host to direct the recognition of SPO1 late gene promoters, whose sequences differ from those of SPO1 early and middle gene promoters. We have located and cloned the genes for these two regulatory proteins, and have engineered their expression in Escherichia coli by placing them under the control of the bacteriophage lambda PL promoter. Nucleotide sequence analysis indicated that genes 33 and 34 overlap by 4 base-pairs and encode highly charged, slightly basic proteins of molecular weight 11,902 and 23,677, respectively.

Cloning, nucleotide sequence and high level expression of the gene coding for the connector protein of Bacillus subtilis phage phi 29

The phi 29 DNA restriction fragment HindIII-D, shown to contain gene 10 coding for the connector protein, has been cloned in plasmid pPLc28 under the control of the pL promoter of phage lambda. After heat induction to inactivate the lambda repressor, a protein with the electrophoretic mobility of the connector protein p10 was synthesized, accounting for about 30% of the total Escherichia coli protein after 3 h of induction. The 2205 nucleotide-long sequence of the cloned HindIII-D fragment has been determined. The sequenced region has an ORF coding for a protein of Mr 35881 that was shown to correspond to the connector protein by determination of the amino-terminal sequence of purified protein p10. Features of the nucleotide sequence and the amino acid sequence of protein p10 are discussed.

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.

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.

Induction of macrolide-lincosamide-streptogramin B resistance requires ribosomes able to bind inducer

Plasmids were constructed containing the regulatory regions and N-terminal portions of ermC and of ermD , fused in phase with the coding sequence of the Escherichia coli lacZ gene. ermC and ermD are erythromycin (Em) inducible macrolide-lincosamide-streptogramin B resistance elements derived from Staphylococcus aureus and Bacillus licheniformis, respectively. The fusion plasmids were introduced into B. subtilis and used to study ermC and ermD regulation. In both cases, beta-galactosidase synthesis could be induced by low levels of Em. Induction was prevented by introduction of ole-2, a chromosomal mutation which decreases ribosomal affinity for Em. Induction also did not occur in the presence of intact copies of ermC , suggesting that prior or concomitant methylation of 23S rRNA, a treatment known to decrease ribosomal affinity for Em, was capable of interfering with ermC and ermD induction. These experiments are consistent with the translational attenuation model of ermC regulation, and together with other evidence, suggest that ermD is regulated by a similar mechanism.

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.

Replacement of the Bacillus subtilis subtilisin structural gene with an In vitro-derived deletion mutation

The entire subtilisin structural gene from Bacillus subtilis I168 has been cloned, and its nucleotide sequence has been determined. When expressed on a high-copy-number shuttle vector, a fivefold increase in serine protease activity was observed. The DNA sequence of the gene is 80% homologous to the Bacillus amyloliquefaciens subtilisin structural gene, and the translated mature coding sequence is 85% homologous to the published protein sequence of subtilisin BPN'. The chloramphenicol resistance determinant of a plasmid integrated at the subtilisin locus was mapped by PBS1 transduction and was found to be linked to glyB (83%) and argC (60%), but not with metC or purB . The chromosomal locus containing the wild-type subtilisin allele was replaced with an in vitro-derived allele of the gene (delta apr-684) that contained a 684-base-pair deletion. The technique used for introducing the deletion is a variation of the gene replacement methods used in Saccharomyces cerevisiae and Escherichia coli. When used in B. subtilis, deletion mutants could be directly screened among the transformants. Physiological characterization of the delta apr-684 mutation revealed no discernable effect on the formation of heat-resistant endospores, but strains carrying the mutation produced only 10% of wild-type serine protease activity. A model is presented that outlines the pathway for plasmid integration and deletion formation in B. subtilis.

Methylation of ribosomal proteins in bacteria: evidence of conserved modification of the eubacterial 50S subunit

Methylation of the 50S ribosomal proteins from Bacillus stearothermophilus, Bacillus subtilis, Alteromonas espejiana, and Halobacterium cutirubrum was measured after the cells were grown in the presence of [1-14C]methionine or [methyl-3H]methionine or both. Two-dimensional polyacrylamide gel electrophoretic analysis revealed, in general, similar relative electrophoretic mobilities of the methylated proteins from each eubacterium studied. Proteins known to be structurally and functionally homologous in several microorganisms were all methylated. Thus, the following group of proteins, which appear to be involved in peptidyltransferase or in polyphenylalanine-synthesizing activity in B. stearothermophilus (P.E. Auron and S. R. Fahnestock, J. Biol. Chem. 256:10105-10110, 1981), were methylated (possible Escherichia coli methylated homologs are indicated in parentheses): BTL5(EL5), BTL6(EL3), BTL8(EL10), BTL11(EL11), BTL13(EL7L12) and BTL20b(EL16). In addition, the pentameric ribosomal complex BTL13 X BTL8, analogous to the complex EL7L12 X EL10 of E. coli, contained methylated proteins. Analysis of the methylated amino acids in the most heavily methylated proteins, BSL11 from B. subtilis and BTL11 from B. stearothermophilus, showed the presence of epsilon-N-trimethyllysine as the major methylated amino acid in both proteins, in agreement with known data for E. coli. In addition, BSL11 appeared to contain trimethylalanine, a characteristic, modified amino acid previously described only in EL11 from E. coli. These results and those previously obtained from other bacteria indicate a high degree of conservation for ribosomal protein methylation and suggest an important, albeit unknown, role for the modification of these components in eubacterial ribosomes.

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.

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.

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.

A temporally regulated promoter from Bacillus subtilis is transcribed only by an RNA polymerase with a 37,000 dalton sigma factor

A 1,250 base pair Bacillus subtilis chromosomal HindIII restriction fragment (S fragment) has been cloned into the B. subtilis expression-probe plasmid pGR71. The S fragment induces the expression of the pGR71 chloramphenicol resistance gene shortly after the initiation of sporulation. The transcriptional promoter responsible for the expression of this temporally regulated genetic element has been identified and mapped in vitro. This promoter is recognized exclusively by the minor B. subtilis RNA polymerase that contains the 37,000 dalton sigma factor.

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.

Cloning and expression in Escherichia coli of the gene coding for the protein linked to the ends of Bacillus subtilis phage phi 29 DNA

A phi 29 DNA fragment containing gene 3, coding for the 5'-terminal protein, and several other early genes has been cloned in a pBR322 derivative plasmid (pKC30) under the control of the pL promoter of bacteriophage lambda. Four polypeptides of Mr 27000, 18500, 17500 and 12500 were labelled with [35S]methionine after heat induction, accounting for about 15% of the de novo synthesized protein. The Mr 27000 and 12500 proteins were characterized as p3, the 5'-terminal protein, and p4, involved in the control of late transcription, respectively. Protein p3 synthesized in Escherichia coli was active in the in vitro formation of the initiation complex p3-dAMP when supplemented with extracts from Bacillus subtilis infected with a sus3 mutant.