Unique features in the ribosome binding site sequence of the gram-positive Staphylococcus aureus beta-lactamase gene

An erythromycin-resistance gene from an erythromycin-producing strain of Arthrobacter sp

A gene (ermA) coding for a presumed erythromycin-resistance (ErR) determinant from an Er-producing Arthrobacter sp. strain (NRRLB3381) was isolated from a gene bank in phage vector lambda 2001 by probing with a Streptomyces ErR gene. Strongly hybridizing fragments were subcloned and the appropriate segments sequenced. The ermA gene is 76 mol% G + C in content and specifies a protein of 340 aa with an Mr of 37454. S1 nuclease mapping and primer extension identified the putative promoter, which resembles the consensus sequence of Escherichia coli promoters particularly in the -10 region. A potential ribosome-binding site (RBS) (AGGAG) was also located. Unexpectedly, the majority of in vivo ermA transcripts detected were only 245 nt long, suggesting that expression of ErR may be regulated post-transcriptionally. Substantial homology is observed between the predicted aa sequences of the ermA-coded protein and the products of three other ErR determinants, from organisms that do not produce Er.

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.

Regulation of antibiotic resistance in bacteria: the chloramphenicol acetyltransferase system

The evaluations of antibiotic resistance has been a subject of interest to workers in several disciplines. Our current understanding of the molecular biology of plasmids, phages, and transposable elements provides a basis for appreciating the range of mechanisms likely to be involved in the horizontal spread of resistance determinants through microbial ecosystems. Rather less can be imagined with confidence about the origins of the genes or the constraints and selection pressures operating at the level of protein structure. The CAT system illustrates the extent of variation possible for an accessory gene product which is required infrequently and which is encoded by multicopy and promiscuous vectors which can cross taxonomic boundaries. Still less is known with certainty about the evolution of genetic control of the expression of antibiotic resistance. While there are sound reasons for looking in detail at prokaryotic antibiotic-producing organisms such as Streptomyces to find the progenitors of present resistance mechanisms (44, 45), it seems likely that controls of expression have been acquired during the "passage" of selectable markers through more distant bacterial genera. The CAT system is illustrative of the variety we may expect to find in control strategies used by microbial systems generally. It might indeed be a surprise to find an expression mechanism operating in the CAT system (or for any other family of resistance genes) which was not illustrative of a general strategy exploited by essential genes specifying biosynthetic or degradative functions. There may be some truth in referring to the cat structural gene as a "cartridge" for the isolation and manipulation of promoter functions. It would seem that nature has been at it for some time.

Isolation and expression of a constitutive variant of the chloramphenicol-inducible plasmid gene cat-86 under control of the Bacillus subtilis 168 amylase promoter

The amyR1 region controls the regulated expression of the Bacillus subtilis 168 amylase gene amyE. When cloned into the B. subtilis promoter-cloning plasmid pPL603, amyR1 has been shown to activate expression of the promoter-indicator gene cat-86. In this chimeric plasmid, p5' alpha B10, cat-86 expression was maximal in stationary phase B. subtilis cells and cat-86 expression was repressible by glucose. Both these properties are similar to the regulated expression of the B. subtilis amyE gene. In addition, cat-86 expression in p5' alpha B10 was inducible with chloramphenicol (Cm). The inducibility phenotype of cat-86 has been shown to be independent of the promoter that is used to activate the gene, and inducibility has been suggested to result from the presence of a pair of inverted-repeat sequences that span the ribosome-binding site (RBS) for cat-86. A spontaneous deletion mutant of p5' alpha B10 was isolated, p5' alpha B10 delta 1, in which cat-86 expression was constitutive with respect to Cm, but the basic pattern of amyR1-directed regulation of cat-86 was intact. The rightward deletion endpoint was within the upstream member of the pair of inverted repeats that immediately precede cat-86. This result is therefore consistent with the role proposed for the inverted repeats in Cm inducibility. The leftward endpoint of the deletion is within the amyR1 region and thus allows a more precise determination of the functional domain of amyR1.

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.

A developmental gene product of Bacillus subtilis homologous to the sigma factor of Escherichia coli

Sporulation of Bacillus subtilis involves sequential morphological and biochemical changes and is regulated by specific genes (spo genes) estimated to occupy more than 30 loci. A mutation in any one of these genes blocks the sporulation process at the corresponding developmental stage. Despite intensive genetic studies, the nature and function of the spo gene products remain unknown. Vegetative B. subtilis RNA polymerase core enzyme may interact with several sigma factors and discriminate among different classes of promoters. During sporulation, new polypeptides are associated with the core enzyme which may have a central role in modifying its promoter recognition specificity. As a first step to understanding their function in the switch from vegetative to sporulation mode, several early sporulation genes have been cloned and analysed. Here we report the cloning and nucleotide sequence of the spoIIG gene of B. subtilis. This gene encodes a polypeptide with a predicted relative molecular mass of 27,652 which contains a 65-amino acid region highly homologous to an internal part of the Escherichia coli sigma factor.

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.

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.

A physical and functional analysis of Tn917, a Streptococcus transposon in the Tn3 family that functions in Bacillus

The erythromycin-resistance (Emr)-conferring transposon Tn917, first isolated in the genus Streptococcus, has in previous work been shown to function efficiently in the spore-forming species Bacillus subtilis, where it has been developed as a tool for identifying and studying sporulation genes. In the present work, a physical analysis of Tn917 was undertaken, including detailed restriction mapping, chemical DNA sequencing, heteroduplex studies, and Southern hybridization analysis, as a first step in understanding the genetic organization of this useful insertion element. The location and transcriptional orientation of the transposon-borne erm gene (the gene responsible for the Emr phenotype) have been determined, and a partial sequence of DNA 5' to the coding sequence of this gene indicates that its inducibility is probably the result of "translational attenuation," a mechanism known to be responsible for the regulation of at least two other gram-positive erm genes. Restriction mapping and heteroduplex analysis have revealed extensive homology between Tn917 and the Staphylococcus transposon Tn551, throughout virtually their entire lengths, and DNA sequencing studies have revealed a remarkably high degree of sequence correspondence within the terminal inverted repeats of Tn917, Tn551 and the gram-negative transposon Tn3. Tn917 was also shown to generate a 5-bp duplication upon insertion, as do Tn3 and Tn551 (and all of the other Tn3-related elements studied thus far), strengthening the conclusion that these three transposons are members of a highly dispersed family of related insertion elements which populate both gram-positive and gram-negative genera.

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.

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.

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.

Expression in Bacillus subtilis of the gene for human urogastrone using synthetic ribosome binding sites

A chemically synthesised gene coding for human urogastrone which was earlier cloned in E. coli (Smith et al. 1982) has now been cloned into expression vectors for Bacillus subtilis. Two types of constructs have been made, one giving production of methionyl-urogastrone and the other giving rise to a methionyl-urogastrone-beta galactosidase fusion polypeptide facilitating quantification of expression levels. The ribosome binding sites used in the expression plasmids are synthetically made oligonucleotides residing on short restriction fragments to allow easy replacement by other ribosome binding sites. Using "shuttle" vectors and constitutive promoters from Bacillus phages phi 105 and SPP1, we were able to detect levels of expression amounting to a few thousand molecules per cell during logarithmic growth in both E. coli and B. subtilis.

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.

Prolipoprotein modification and processing in Escherichia coli. A unique secondary structure in prolipoprotein signal sequence for the recognition by glyceryl transferase

An Escherichia coli mutant (lpp-14-1), with an alteration of glycine to aspartic acid at the 14th amino acid residue of the prolipoprotein signal sequence, has previously been shown to contain unmodified and unprocessed prolipoprotein in its cell envelope. Both the wild-type and the lpp-14-1 alleles of the lpp gene have been cloned onto a phage lambda vector. Two pseudorevertant alleles of lpp-14-1 (14R21 and 6a) have been isolated, cloned and sequenced. Amino acid sequences, deduced from the DNA sequences of the two revertant lipoprotein alleles, and biochemical characterization of the revertant lipoproteins, show that a conversion of the aspartic acid (residue 14) to asparagine completely restores the modification and processing of the 14R21 revertant prolipoprotein, while a change of the threonine-16 to isoleucine-16 partially enhances the modification and processing of the 6a prolipoprotein, which retains the aspartate-14 substitution. Secondary structure analysis of the revertant prolipoprotein signal sequences according to the Chou and Fasman rules revealed that the specific coil region in residues 14 and 15, and the beta-sheet structure in residues 16-18 of signal sequence may be important for prolipoprotein modification. These results suggest essential roles of both a unique secondary structure and hydrophobicity in residues 14-18 of prolipoprotein signal sequence for the proper recognition by the glyceryl transferase.

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.

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.

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.

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.

Nucleotide sequence of the Bacillus subtilis trpE and trpD genes

Several overlapping portions of the tryptophan (trp) operon of Bacillus subtilis have been cloned into plasmid pBR322. The nucleotide sequence of the region comprising the trpE and trpD genes and a portion of the trpC gene has been determined. When the deduced amino acid sequences of these genes are compared with their counterparts in Escherichia coli, several regions of striking homology are seen. The probable initiation codons for the trpE, D and C genes are each preceded by a recognizable Shine-Dalgarno sequence. The coding sequences for the trpE and trpD genes and for the trpD and trpC genes overlap slightly, leaving no intercistronic regions between the genes.

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.

Expression in Streptomyces ambofaciens of an Escherichia coli K-12 gene which confers resistance to hygromycin B

We have constructed two plasmid vectors (pKC293 and pKC305) that can replicate in Escherichia coli K-12 and Streptomyces ambofaciens. These shuttle vectors were used to demonstrate the expression of two E. coli genes, hygromycin B (Hm) resistance and Tn5 neomycin (Nm) resistance, in S. ambofaciens.

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.

Complete nucleotide sequence of pT181, a tetracycline-resistance plasmid from Staphylococcus aureus

pT181 is a naturally occurring Staphylococcus aureus plasmid, encoding inducible resistance to tetracycline. The plasmid has a copy number of about 20 per cell, and belongs to the incompatibility group inc3. The complete nucleotide sequence of pT181 has been determined and consists of 4437 bp. The nucleotide sequence contains 69.8% A-T and 30.2% G-C pairs. pT181 was found to contain four open reading frames capable of coding for polypeptides containing more than 50 amino acids. All the putative polypeptides are coded by one strand. The molecular weights of the four putative polypeptides are (in daltons): A, 37,500; B, 35,000; C, 23,000, and D, 18,000. Polypeptide A corresponds to the repC protein, earlier shown to be specifically required for pT181 replication. Polypeptide B (and possibly polypeptide D) are involved in tetracycline resistance. No role has yet been established for polypeptide C; deletion of the coding sequence for the C polypeptide has no detectable effect on any property of the pT181 plasmid. A region consisting of about 1200 bp contains information for the replication and copy number control of this plasmid. The sequencing results are discussed in relation to the replication properties and tetracycline resistance associated with the pT181 plasmid.

Bacteriophage SPO1 gene 27: location and nucleotide sequence

Bacteriophage SPO1 gene 27, whose product is required for late gene transcription and DNA replication, has been cloned in Escherichia coli, and its complete nucleotide sequence has been determined. We infer that the product of gene 27 is a highly basic 17,518-dalton protein of 155 amino acids. The gene for this regulatory protein is transcribed from two promoters: an early promoter situated before the adjacent upstream gene 28 and a middle promoter located between genes 28 and 27.

Chloramphenicol-inducible gene expression in Bacillus subtilis

A cloned Bacillus pumilus cat gene expresses chloramphenicol-inducible chloramphenicol acetyltransferase activity in Bacillus subtilis. The chloramphenicol inducibility trait was shown to be determined by a 234-bp region of the cloned DNA. Nucleotide sequence analysis of this 234-bp segment indicated that the cat ribosome-binding site occurs within a 40-bp region containing 14-bp terminal inverted repeat sequences. Transcription of this region into RNA should sequester the cat ribosome-binding site in a stable stem-loop conformation. Chloramphenicol-mediated destabilization of the stem-loop is suggested as the basis for the chloramphenicol inducibility phenotype.

Nucleotide sequence of a Bacillus pumilus gene specifying chloramphenicol acetyltransferase

Gene cat-86 of Bacillus pumilus, specifying chloramphenicol-inducible chloramphenicol acetyltransferase, was previously cloned in Bacillus subtilis on plasmid pUB110. The nucleotide sequence of cat-86 indicates that the gene encodes a protein of 220 amino acids and contains TTG as the translations-initiation codon. The proteins specified by cat-86 and the cat genes present on pC194, pC221 and Tn9 appear to share regions of amino acid sequence similarity. cat-86 is a structural gene on the B. subtilis expression plasmid pPL608. Restriction sites exist within the gene that should permit the product of inserted heterologous coding sequences to be synthesized in B. subtilis as fusion proteins.

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.

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.

A complex attenuator regulates inducible resistance to macrolides, lincosamides, and streptogramin type B antibiotics in Streptococcus sanguis

Macrolide-lincosamide-streptogramin B resistance specified by Streptococcus sanguis plasmid pAM77 involves an adenine methylase, whose synthesis, demonstrable both phenotypically and by analysis of methionine-labeled proteins made in Bacillus subtilis minicells, is inducible by erythromycin, lincomycin, and streptogramin type B antibiotics. Localization of the methylase structural gene, including its control region in DNA fragments obtained with restriction endonucleases, has been deduced from DNA blot experiments with characterized target and probe DNAs from other streptococci, combined with DNA sequence analysis and comparison of the putative streptococcal methylase sequence with that of a cognate methylase in staphylococcal plasmid pE194. The streptococcal methylase migrates electrophoretically in polyacrylamide gels with the mobility of a 29,000-dalton protein. The sequence organization of the putative streptococcal methylase mRNA leader sequence partially resembles its staphylococcal counterpart and can support a similar mechanism of secondary structure rearrangement leading to methylase synthesis. The deduced 5' leader sequence preceding the pAM77 methylase structural gene sequence comprises approximately 155 nucleotides within which one can identify a putative control peptide 36 amino acid residues in length (in contrast to 19 in the pE194 peptide) and at least 14 possible classes of overlapping inverted complementary repeat sequences (in contrast to 3 in the pE194 control region), one of which can sequester the sequence AGGAG 7 nucleotides upstream from the putative (methionine) start codon of the streptococcal methylase. Comparison of the pAM77 and pE194 methylase amino acid sequences and their respective nucleotide sequences shows 51% conservation of amino acid residues (124 of 244) and 59% conservation of nucleotide residues (433 of 738), which suggests a common origin for the two methylase structural gene sequences. Differences in mRNA base composition associated with conserved amino acid residues occur mostly in the third nucleotide ("wobble") position of codons and may reflect adaptation of methylase genes to optimal expression in host cells with differing codon use patterns.

Enhanced expression of mouse dihydrofolate reductase in Bacillus subtilis

pPL608-TR1 is a high-copy plasmid that permits phenotypic expression of the mouse dihydrofolate reductase (DHFR) gene in Bacillus subtilis. A plasmid mutation has been identified that increases expression of mouse DHFR more than ten-fold. The mutation is located in a 0.2-kb segment that intervenes between the DHFR gene and the 0.3-kb promoter fragment needed for transcriptional activation of DHFR. Nucleotide sequence analysis suggests that the effect of the mutation is to facilitate translation, initiated within the promoter fragment, through the 0.2-kb segment to the site of insertion of the DHFR-containing fragment. Additional promoter-containing fragments selected by their ability to promote expression of a plasmid gene located downstream from DHFR, the CAT gene, promote either high, intermediate or no phenotypic expression of DHFR. The results indicate that promoter fragments that allow phenotypic expression of the mouse DHFR gene contain two regulatory signals. One signal is essential to transcription of both DHFR and CAT and therefore functions as a promoter. The second signal may be necessary for translation of that portion of the mRNA specifying mouse DHFR.