Conserved nucleotide sequences in temporally controlled bacteriophage promoters

Construction of a High-Expression System in Bacillus through Transcriptomic Profiling and Promoter Engineering

Bacillus subtilis is an ideal host for secretion and expression of foreign proteins. The promoter is one of the most important elements to facilitate the high-level production of recombinant protein. To expand the repertoire of strong promoters for biotechnological applications in Bacillus species, 14 highly transcribed genes based on transcriptome profiling of B. pumilus BA06 were selected and evaluated for their promoter strength in B. subtilis. Consequently, a strong promoter P₂₀₆₉ was obtained, which could drive the genes encoding alkaline protease (aprE) and green fluorescent protein (GFP) to express more efficiency by an increase of 3.65-fold and 18.40-fold in comparison with the control promoter (P_aprE), respectively. Further, promoter engineering was applied to P₂₀₆₉, leading to a mutation promoter (P_2069M) that could increase GFP expression by 3.67-fold over the wild-type promoter (P₂₀₆₉). Moreover, the IPTG-inducible expression systems were constructed using the lac operon based on the strong promoters of P₂₀₆₉ and P_2069M, which could work well both in B. subtilis and B. pumilus. In this study, highly efficient expression system for Bacillus was constructed based on transcriptome data and promoter engineering, which provide not only a new option for recombinant expression in B. subtilis, but also novel genetic tool for B. pumilus.

Where to begin? Sigma factors and the selectivity of transcription initiation in bacteria

Transcription is the fundamental process that enables the expression of genetic information. DNA-directed RNA polymerase (RNAP) uses one strand of the DNA duplex as template to produce complementary RNA molecules that serve in translation (rRNA, tRNA), protein synthesis (mRNA) and regulation (sRNA). Although the RNAP core is catalytically competent for RNA synthesis, the selectivity of transcription initiation requires a sigma (σ) factor for promoter recognition and opening. Expression of alternative σ factors provides a powerful mechanism to control the expression of discrete sets of genes (a σ regulon) in response to specific nutritional, developmental or stress-related signals. Here, I review the key insights that led to the original discovery of σ factor 50 years ago and the subsequent discovery of alternative σ factors as a ubiquitous mechanism of bacterial gene regulation. These studies form a prelude to the more recent, genomics-enabled insights into the vast diversity of σ factors in bacteria.

The genome of Bacillus subtilis bacteriophage SPO1

We report the genome sequence of Bacillus subtilis phage SPO1. The unique genome sequence is 132,562 bp long, and DNA packaged in the virion (the chromosome) has a 13,185-bp terminal redundancy, giving a total of 145,747 bp. We predict 204 protein-coding genes and 5 tRNA genes, and we correlate these findings with the extensive body of investigations of SPO1, including studies of the functions of the 61 previously defined genes and studies of the virion structure. Sixty-nine percent of the encoded proteins show no similarity to any previously known protein. We identify 107 probable transcription promoters; most are members of the promoter classes identified in earlier studies, but we also see a new class that has the same sequence as the host sigma K promoters. We find three genes encoding potential new transcription factors, one of which is a distant homologue of the host sigma factor K. We also identify 75 probable transcription terminator structures. Promoters and terminators are generally located between genes and together with earlier data give what appears to be a rather complete picture of how phage transcription is regulated. There are complete genome sequences available for five additional phages of Gram-positive hosts that are similar to SPO1 in genome size and in composition and organization of genes. Comparative analysis of SPO1 in the context of these other phages yields insights about SPO1 and the other phages that would not be apparent from the analysis of any one phage alone. These include assigning identities as well as probable functions for several specific genes and inferring evolutionary events in the phages' histories. The comparative analysis also allows us to put SPO1 into a phylogenetic context. We see a pattern similar to what has been noted in phage T4 and its relatives, in which there is minimal successful horizontal exchange of genes among a "core" set of genes that includes most of the virion structural genes and some genes of DNA metabolism, but there is extensive horizontal transfer of genes over the remainder of the genome. There is a correlation between genes in rapid evolutionary flux through these genomes and genes that are small.

Removing a bottleneck in the Bacillus subtilis biotin pathway: bioA utilizes lysine rather than S-adenosylmethionine as the amino donor in the KAPA-to-DAPA reaction

In biotin biosynthesis, DAPA aminotransferase encoded by the bioA gene catalyzes the formation of the intermediate 7,8-diaminopelargonic acid (DAPA) from 7-keto-8-aminopelargonic acid (KAPA). DAPA aminotransferases from Escherichia coli, Serratia marcescens, and Bacillus sphaericus use S-adenosylmethionine (SAM) as the amino donor. Our observation that SAM is not an amino donor for B. subtilis DAPA aminotransferase led to a search for an alternative amino donor for this enzyme. Testing of 26 possible amino acids in a cell-free extract assay revealed that only l-lysine was able to dramatically stimulate the in vitro conversion of KAPA to DAPA by the B. subtilis DAPA aminotransferase. The K(m) for lysine and KAPA was estimated to be between 2 and 25 mM, which is significantly higher than the K(m) of purified E. coli BioA for SAM (0.15 mM). This higher requirement for lysine resulted in accumulation of KAPA during fermentation of B. subtilis biotin producing strains. However, this pathway bottleneck could be relieved by either addition of exogenous lysine to the medium or by introduction of lysine deregulated mutations into the production strains.

Genes and regulatory sites of the "host-takeover module" in the terminal redundancy of Bacillus subtilis bacteriophage SPO1

Early in infection of Bacillus subtilis by bacteriophage SPO1, the synthesis of most host-specific macromolecules is replaced by the corresponding phage-specific biosyntheses. It is believed that this subversion of the host biosynthetic machinery is accomplished primarily by a cluster of early genes in the SPO1 terminal redundancy. Here we analyze the nucleotide sequence of this 11.5-kb "host-takeover module," which appears to be designed for particularly efficient expression. Promoters, ribosome-binding sites, and codon usage statistics all show characteristics known to be associated with efficient function in B. subtilis. The promoters and ribosome-binding sites have additional conserved features which are not characteristic of their host counterparts and which may be important for competition with host genes for the cellular biosynthetic machinery. The module includes 24 genes, tightly packed into 12 operons driven by the previously identified early promoters PE1 to PE12. The genes are smaller than average, with half of them having fewer than 100 codons. Most of their inferred products show little similarity to known proteins, although zinc finger, trans-membrane, and RNA polymerase-binding domains were identified. Transcription-termination and RNase III cleavage sites were found at appropriate locations.

A triggered-suicide system designed as a defense against bacteriophages

A novel bacteriophage protection system for Lactococcus lactis based on a genetic trap, in which a strictly phage-inducible promoter isolated from the lytic phage phi31 is used to activate a bacterial suicide system after infection, was developed. The lethal gene of the suicide system consists of the three-gene restriction cassette LlaIR+, which is lethal across a wide range of gram-positive bacteria. The phage-inducible trigger promoter (phi31P) and the LlaIR+ restriction cassette were cloned in Escherichia coli on a high-copy-number replicon to generate pTRK414H. Restriction activity was not apparent in E. coli or L. lactis prior to phage infection. In phage challenges of L. lactis(pTRK414H) with phi31, the efficiency of plaquing was lowered to 10(-4) and accompanied by a fourfold reduction in burst size. Center-of-infection assays revealed that only 15% of infected cells released progeny phage. In addition to phage phi31, the phi31P/LlaIR+ suicide cassette also inhibited four phi31-derived recombinant phages at levels at least 10-fold greater than that of phi31. The phi31P/LlaIR+-based suicide system is a genetically engineered form of abortive infection that traps and eliminates phages potentially evolving in fermentation environments by destroying the phage genome and killing the propagation host. This type of phage-triggered suicide system could be designed for any bacterium-phage combination, given a universal lethal gene and an inducible promoter which is triggered by the infecting bacteriophage.

Identification and characterization of transcripts from the biotin biosynthetic operon of Bacillus subtilis

Northern (RNA) blot analysis of the Bacillus subtilis biotin operon, bioWAFDBIorf2, detected at least two steady-state polycistronic transcripts initiated from a putative vegetative (Pbio) promoter that precedes the operon, i.e., a full-length 7.2-kb transcript covering the entire operon and a more abundant 5.1-kb transcript covering just the first five genes of the operon. Biotin and the B. subtilis birA gene product regulated synthesis of the transcripts. Moreover, replacing the putative Pbio promoter and regulatory sequence with a constitutive SP01 phage promoter resulted in higher-level constitutive synthesis. Removal of a rho-independent terminator-like sequence located between the fifth (bioB) and sixth (bioI) genes prevented accumulation of the 5.1-kb transcript, suggesting that the putative terminator functions to limit expression of bioI, which is thought to be involved in an early step in biotin synthesis.

Compilation and analysis of Bacillus subtilis sigma A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA

Sequence analysis of 236 promoters recognized by the Bacillus subtilis sigma A-RNA polymerase reveals an extended promoter structure. The most highly conserved bases include the -35 and -10 hexanucleotide core elements and a TG dinucleotide at position -15, -14. In addition, several weakly conserved A and T residues are present upstream of the -35 region. Analysis of dinucleotide composition reveals A2- and T2-rich sequences in the upstream promoter region (-36 to -70) which are phased with the DNA helix: An tracts are common near -43, -54 and -65; Tn tracts predominate at the intervening positions. When compared with larger regions of the genome, upstream promoter regions have an excess of An and Tn sequences for n > 4. These data indicate that an RNA polymerase binding site affects DNA sequence as far upstream as -70. This sequence conservation is discussed in light of recent evidence that the alpha subunits of the polymerase core bind DNA and that the promoter may wrap around RNA polymerase.

A cytotoxic early gene of Bacillus subtilis bacteriophage SPO1

Some of the early genes of Bacillus subtilis bacteriophage SPO1 were hypothesized to function in the shutoff of host biosyntheses. Two of these genes, e3 and e22, were cloned and sequenced. E22 showed no similarity to any known protein, while E3, a highly acidic protein, showed significant similarity only to other similarly acidic proteins. Each gene was immediately downstream of a very active early promoter. Each was expressed actively during the first few minutes of infection and was then rapidly shut off and its RNA rapidly degraded. An e3 nonsense mutation severely retarded the degradation of e3 RNA. Expression of a plasmid-borne e3 gene, in either B. subtilis or Escherichia coli, resulted in the inhibition of host DNA, RNA, and protein syntheses and prevented colony formation. However, the e3 nonsense mutation caused no measurable decrease in either burst size or host shutoff during infection and, in fact, caused an increased burst size at high multiplicities of infection. We suggest that e3 is one of several genes involved in host shutoff, that its function is dispensable both for host shutoff and for phage multiplication, and that its shutoff function is not entirely specific to host activities.

Sequence and properties of mecA, a negative regulator of genetic competence in Bacillus subtilis

The development of competence in Bacillus subtilis is regulated by growth conditions and several regulatory genes. In complex media competence development is poor, and there is little or no expression of late competence genes. mec mutations permit competence development and late competence gene expression in complex media, and bypass the requirements for many of the competence regulatory genes. In this paper we describe the cloning and characterization of mecA. The mecA gene product acts negatively in the development of competence. Null mutations in mecA allowed expression of a late competence gene comG, under conditions where it is not normally expressed, including in complex media and in cells mutant for several competence regulatory genes. Overexpression of MecA from a multicopy plasmid resulted in inhibition of comG transcription. The DNA sequence of mecA was determined and the predicted gene product showed no significant similarity to any protein in the database. Expression of a mecA-lacZ translational fusion was constitutive during growth and did not vary significantly in the different media tested. The role of mecA in competence development and other stationary phase phenomena is discussed.

Bacteriophage SPO1 middle transcripts

Phage SPO1 middle transcripts are known to fall into two classes, m and m1l. Class m1l transcripts continue to be made late in the viral infection, while the synthesis of class m transcripts ceases soon after the onset of replication and late transcription. The experiments that are reported here deal with the regulatory nature of this diversity. The accumulation of transcripts associated with eight middle promoters was analyzed by S1 nuclease mapping. DNA sequence surrounding these middle promoters was determined or redetermined, and the stability of RNA associated with most of these promoters was also analyzed. Class m1l transcription was shown to be associated with SPO1 middle promoters that remain active at late stages of viral development, when middle promoters of class m are repressed. The consensus sequences of class m and m1l middle promoters were found to be indistinguishable and the search for sequences consensual with late promoters yielded only divergent candidates. No other consensus sequence that is specific and exclusive to either class of middle promoters was detected within a hundred base pairs upstream or downstream of these promoters. Considerable variations in the stabilities of SPO1 middle transcripts were found. Two promoters that are only 71 base pairs apart yielded transcripts that had substantially different stabilities. The 5'-flanking segment of the transcript associated with the upstream promoter apparently conferred a high degree of stability on this RNA.

Two amino acids in an RNA polymerase sigma factor involved in the recognition of adjacent base pairs in the -10 region of a cognate promoter

The recognition of promoter region -10 nucleotide sequences in prokaryotes is believed to be mediated by a segment of alpha-helix in a region of RNA polymerase sigma factors called 2.4. Earlier genetic studies implicated Thr-100 in region 2.4 of the Bacillus subtilis sigma factor sigma H in the recognition of the G.C base pair at position -13 in the -10 region (GAAT) of a cognate promoter. In confirmation of this assignment, we now show that a change-of-specificity mutant of sigma H in which Thr-100 was replaced with isoleucine suppresses a G.C----A.T nucleotide substitution at position -13 but not other "promoter down mutations" (causing impaired promoter activity) at positions -13, -12, and -11. We also show that a loss-of-contact mutant created by the replacement of Thr-100 with alanine (having a short side chain) enables sigma H to tolerate three different promoter down mutations at position -13 but not down mutations at other positions. Finally, we suggest the identification of an additional amino acid involved in base-pair recognition by the demonstration that the replacement of Arg-96 with alanine specifically suppresses an A.T----G.C promoter down mutation at position -12. The identification of amino acids that are four residues apart that are involved in the recognition of adjacent base pairs may fix the orientation of region 2.4 (its NH2 terminus being proximal to the promoter transcription start site) and is consistent with a model in which the recognition of promoter region -10 nucleotide sequences is mediated by an alpha-helix in which residues involved in base-pair contact are separated by one turn and clustered on one face of the helix.

Interaction of Escherichia coli RNA polymerase holoenzyme containing sigma 32 with heat shock promoters. DNase I footprinting and methylation protection

The DNase I protection pattern of E sigma 32 was assayed on three heat shock promoters, the E sigma 32 promoter for the groESL operon, P2 of the dnaKJ operon, and rpoD PHS, the E sigma 32 promoter upstream from rpoD. E sigma 32 protected each of these promoters from DNase I digestion from around -60 to around +20. Protection from dimethyl sulfate methylation was assayed at the groE promoter. E sigma 32 binding altered the sensitivity to methylation of bases in the vicinity of both the -10 and -35 regions. The DNase I footprints for the E sigma 32 promoters were very similar to the DNase I footprint of E sigma 70 on the lacUV5 promoter. After analyzing the DNase I footprints by taking into account the contacts predicted to be made by DNase I, it appeared that E sigma 32, like E sigma 70, contacts the DNA primarily on one face of the helix in the -35 region and on both faces in the -10 region.

Mutation changing the specificity of an RNA polymerase sigma factor

We describe a mutation that changes the fine specificity of promoter selection by a secondary form of RNA polymerase holoenzyme in Bacillus subtilis. The product of regulatory gene spo0H is an RNA polymerase sigma factor called sigma H, which directs transcription of a sporulation gene known as spoVG. We show that the spo0H mutation spo0H81, which blocks transcription from the wild-type spoVG promoter, enhances transcription from a mutant form of the spoVG promoter (spoVG249) bearing a severe down-mutation (a G.C to A.T transition) at position -13 in the "-10 region." Suppression of the spoVG249 mutation is specific in the sense that the transcription from several other spoVG mutant promoters was not restored by the mutant sigma. Evidently, spo0H81 is a change-of-specificity mutation that alters sigma H-RNA polymerase in a way that decreases its capacity to use the wild-type spoVG promoter, while increasing its capacity to use the mutant promoter. Transcription experiments in vitro using RNA polymerase containing the wild-type or mutant sigma support this interpretation. The spo0H81 mutation causes a threonine (Thr100) to isoleucine substitution in a region of sigma H that is highly homologous among sigma factors of diverse origins. We discuss the possibility that Thr100 is an amino acid-base-pair contact site and that sigma factors contact the -10 region of their cognate promoters by means of amino acid residues in this highly conserved region.

Activity of a phage-modified RNA polymerase at hybrid promoters. Effects of substituting thymine for hydroxymethyluracil in a phage SP01 middle promoter

Transcription of bacteriophage SP01 middle promoters is specifically initiated by a complex of the Bacillus subtilis host's RNA polymerase core (E) with the SP01 gene 28 transcription-regulating protein, gp28. Normal SP01 DNA contains hydroxymethyluracil (hmUra) in place of thymine and E . gp28 preferentially transcribes hmUra-containing DNA. Hybrid DNA molecules containing an SP01 middle promoter, PM25 . 1, have been constructed in which one DNA strand contains T and the other hmUra. The major feature of these reciprocal hybrid promoters is that one has, predominantly, T substituted for hmUra in the central -35 recognition sequence in the transcribed strand, while the other has, predominantly, T substituted for hmUra in the -10 recognition sequence in the non-transcribed strand. Binding by the E . gp28 RNA polymerase and transcription of these hybrid promoters and of the normal, all-hmUra, promoter have been compared. Both hybrid promoters are weaker than the normal PM25 . 1 promoter, but the hybrid promoter with T substituted in the -10 sequence is the weakest of the set. The DNase I footprint of the normal PM25 . 1 promoter shows temperature-dependent protection of a relatively long stretch of DNA downstream from the transcriptional start site, correlating with a thermal transition of transcriptional activity of promoter complexes. The stronger of the hybrid promoters also undergoes this transition, but the weaker does not. We discuss these findings in terms of protein-DNA interactions determining specificity for a modified nucleotide at this promoter.

The phage SPO1-specific RNA polymerase, E.gp28, recognizes its cognate promoters in thymine-containing DNA

The bacteriophage SPO1 gene 28-encoded protein, gp28, directs specific recognition of viral middle promoters in hydroxymethyluracil-containing DNA by the Bacillus subtilis host's RNA polymerase core. Using appropriately sensitive methods of detection, we have shown that discrimination against thymine-containing DNA is not absolute and that the gp28-containing RNA polymerase precisely initiates transcription at two thymine-containing SPO1 middle promoters.

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.

Nucleotide sequence and promoter region for the neutral protease gene from Bacillus stearothermophilus

The thermostable neutral protease gene nprT of Bacillus stearothermophilus was sequenced. The DNA sequence revealed only one large open reading frame, composed of 1,644 bases and 548 amino acid residues. A Shine-Dalgarno sequence was found 9 bases upstream from the translation start site (ATG), and the deduced amino acid sequence contained a signal sequence in its amino-terminal region. The sequence of the first 14 amino acids of purified extracellular protease completely matched that deduced from the DNA sequence starting at GTC (Val), 687 bases (229 amino acids) downstream from ATG. This suggests that the protease is translated as a longer polypeptide. The amino acid sequence of the extracellular form of this protease (319 amino acids) was highly homologous to that of the thermostable neutral protease from Bacillus thermoproteolyticus but less homologous to the thermolabile neutral protease from Bacillus subtilis. A promoter region determined by S1 nuclease mapping (TTTTCC for the -35 region and TATTTT for the -10 region) was different from the conserved promoter sequences recognized by the known or factors in bacilli. However, it was very homologous to the promoter sequence of the spo0B gene from B. subtilis. The guanine-plus-cytosine content of the coding region of the nprT gene was 58 mol%, while that of the third letter of the codons was much higher (72 mol%).

Consensus sequence for Escherichia coli heat shock gene promoters

We have identified promoters for the Escherichia coli heat shock operons dnaK and groE and the gene encoding heat shock protein C62.5. Transcription from each promoter is heat-inducible in vivo, and each is recognized in vitro by RNA polymerase containing sigma 32, the sigma factor encoded by rpoH (htpR) but not by RNA polymerase containing sigma 70. We compared the sequences of the heat shock promoters and propose a consensus promoter sequence, having T-N-t-C-N-C-c-C-T-T-G-A-A in the -35 region and C-C-C-C-A-T-t-T-a in the -10 region. These sequences differ from the consensus sequence recognized by holoenzyme containing sigma 70, the major sigma in E. coli. We suggest that the accumulated consensus sequences of promoters recognized by alternate forms of holoenzyme are compatible with a model in which sigma recognizes only the -10 region of the promoter.

Transcription of Bacillis subtilis plasmid pBD64 and expression of bacteriophage SPO1 genes cloned therein

Plasmid pBD64, a vector which is useful for cloning in Bacillis subtilis (T. J. Gryczan, A. G. Shivakumar, and D. Dubnau (1980), J. Bacteriol. 141, 246-253), has at least three substantial transcription units. Two of these include the single EcoRI, XbaI, and BamHI sites, while the other includes the single BglII site. Each of these transcripts was synthesized in the counterclockwise direction, relative to the pBD64 restriction map. No transcripts were detected in the opposite direction. Infection by bacteriophage SPO1 caused a substantial decrease in each of these transcripts. No new pBD64 transcripts were detected during SPO1 infection. Various SPO1 genes, cloned at several of these pBD64 sites, were tested for expression by observing their capacity to complement SPO1 mutants. Several middle and late genes were expressed substantially, regardless of the orientation in which the fragments were inserted. Since transcription from the vector could cause expression only in one orientation, this argues that the necessary transcription originated at SPO1 promoters, and, thus, that SPO1 middle and late promoters can be active in thymine-containing DNA.

Cloning and mapping of the SPO1 genome

Many of the XbaI, EcoRI, KpnI, and BglII fragments of bacteriophage SPO1, accounting for about 65% of the genomic sequences, were cloned in Bacillus subtilis. Four of the EcoRI fragments were specifically refractory to cloning in both Escherichia coli and B. subtilis, probably because of expression of deleterious genes carried on the SPO1 fragments. To permit complete identification of the regions cloned, the SPO1 restriction map has been extended to include the XbaI fragments and the previously unmapped KpnI fragments. Markers for 26 of the 39 known genes have been located on specific cloned fragments, permitting more precise determination of the positions of most of the genes. One cloned SPO1 fragment was inhibitory to SPO1 development.

Bacteriophage P2 late promoters. II. Comparison of the four late promoter sequences

The late genes of bacteriophage P2 are clustered into four transcription units. We have reported the transcription initiation sites for two of the late messenger RNAs, encoding genes QP and ONMLKRS. We have now located the 5' ends of the two remaining late mRNAs. The first gene in the VJHG transcription unit has been located by DNA sequence determination of the single nucleotide change in a V amber mutant. Location of the first gene in the FETUD transcription unit has been inferred from the DNA sequence. The 5' ends of the mRNAs for these two transcription units were located by protection of end-labeled restriction fragments in RNA-DNA hybrids from digestion with nuclease S1. Similar protection of hybrids using RNA that had been 5' end-labeled with [alpha-32P]GTP and guanylyl transferase confirmed that these 5' termini resulted from initiation of transcription. The DNA sequences preceding the P2 late transcription starts are different from the Escherichia coli promoter consensus sequences at -10 and -35, consistent with the apparent requirement for phage-encoded proteins in the regulation of P2 late gene expression. The four P2 late promoters do share sequence homologies in the -10 and -35 regions, however, and several additional homologies further upstream. P2 late gene expression also appears to involve negative regulation by a product of the ONMLKRS gene cluster. When cells are infected with P2 polar O amber mutants, a marked increase in the levels of proteins encoded by the other three gene clusters is observed. This increase is reflected in the amounts of late mRNAs, suggesting that RNA synthesis is normally repressed or that late mRNAs are more labile in the presence of a gene product from the ONMLKRS transcription unit. Satellite phage P4 induced P2 late gene expression without the usual requirement for P2 DNA replication. The 5' ends of the P2 late mRNAs are the same during P4 transactivation as during normal P2 late gene expression. Thus, the regulation of P2 late gene expression by P4 does not involve altered promoter selection.

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.

Isolation of sigma-28-specific promoters from Bacillus subtilis DNA

Sigma-28-RNA polymerase is a minor form of RNA polymerase found in vegetative cells of Bacillus subtilis which utilizes promoter sites distinct from those recognized by the major RNA polymerase. We have isolated a collection of cloned B. subtilis DNA segments that contain in vitro promoter sites for sigma 28-RNA polymerase by screening a bacteriophage lambda library of B. subtilis genomic fragments. At least nine new sigma 28-specific promoter sites have been identified in this collection, and four have been partially mapped for further study. Our strategy employed a mix of RNA probes prepared by in vitro transcription with sigma 28-RNA polymerase of total B. subtilis DNA EcoRI and HindIII fragments. Over 70% of the unique clones identified contain sigma 28-specific promoter sites, suggesting that the method may have general application for identification of promoter-containing sequences. The efficiency with which sigma 28-specific promoters are detected is consistent with there being a relatively small number of such sites in the B. subtilis genome of which twelve have been cloned.

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.

Convergent transcription of the Escherichia coli hisG gene cloned in Bacillus subtilis stops in the vicinity of the attenuator

A 5300-bp DNA segment containing the promoter, the attenuator and the first gene (hisG) of the Escherichia coli his operon has been inserted into an interspecific E. coli-Bacillus subtilis plasmid vector, pHV14. The resulting plasmid pPV48 restores the His+ phenotype to an E. coli hisG mutant, but fails to do so to a corresponding B. subtilis mutant. Experiments aimed at localizing the block to this heterologous expression in B. subtilis have shown that the enzymatic activity of the hisG+ gene product is neither detectable nor inhibited in crude extracts of B. subtilis cells harboring pPV48. Furthermore, electron microscopic, Southern blot and S1 mapping analysis of the transcripts produced in vitro and in vivo by B. subtilis RNA polymerase indicate that the hisG+ region is transcribed, but that the transcripts initiate at sites different from the his promoter, converge towards, and terminate in the vicinity of the attenuator.

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.

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.

Bacteriophage P2 late promoters. Transcription initiation sites for two late mRNAs

Divergent transcription of two of the bacteriophage P2 late mRNAs, encoding genes QP and ONMLKRS, is initiated from opposite strands of the DNA in a region near the left end of the P2 genome. The first gene in each of these transcription units (P and O) has been located in the nucleotide sequence by amino-terminal sequence analysis of the P gene product and by DNA sequence determination of the single nucleotide changes in two O amber mutants. The 5' ends of the P and O gene mRNAs are separated by 109 nucleotide pairs in the DNA template. The locations of these 5' termini were determined by protection of end-labeled restriction fragments in RNA-DNA hybrids from digestion with nuclease S1. Sequence analysis of mRNA that had been labeled at the 5' end with [alpha-32P]GTP and guanylyl transferase confirmed that these termini resulted from initiation of transcription. The DNA sequences preceding the O and P transcription starts have poor homologies to the bacterial promoter consensus sequences at -10 and -35, consistent with the apparent requirement for phage-encoded proteins in the regulation of P2 late gene expression. The O and P promoter regions also have no detectable homology to each other in the -10 or -35 regions, and are unusually G + C-rich. There are, however, blocks of sequence homology within the transcribed region of each of these two late operons near the 5' end. Satellite phage P4 induces P2 late gene expression without the usual requirement for P2 DNA replication. The 5' ends of the P2 P and O gene transcripts are the same during P4 "transactivation" as during normal P2 late gene expression. Thus the regulation of P2 late gene expression by P4 does not involve a change in the site for initiation of transcription.

Regions specifying transcriptional termination and pausing in the bacteriophage SP01 terminal repeat

We have determined the nucleotide sequences of four termination sites recognized by Bacillus subtilis RNA polymerase. These sites are located in the terminally repeated segment of the bacteriophage SP01 genome, where most early phage transcription occurs. The SP01 terminators have structures that are similar to those recognized by Escherichia coli RNA polymerase, containing a region of dyad symmetry followed by a stretch of HMU residues in the noncoding DNA strand (HMU is substituted for T in SP01 DNA). We note that in a terminator that is only 60% efficient in vitro, there is a greater distance between these two conserved elements that exists in more efficient terminators. We also find that RNA polymerase molecules which elongate a transcript through a partial terminator often pause at this site.

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.

Two RNA polymerase sigma factors from Bacillus subtilis discriminate between overlapping promoters for a developmentally regulated gene

A developmentally regulated gene (spoVG) from the spore-forming bacterium Bacillus subtilis is expressed from two overlapping promoters, which direct transcription initiating from sites separated by 10 base pairs. Utilization of the upstream promoter is determined by an RNA polymerase sigma factor of molecular weight 37,000 (sigma 37). We report the isolation of a 32,000-molecular weight species of sigma factor (sigma 32), which exclusively dictates transcription initiation from the downstream promoter, and suggest a model for the way in which sigma-specific recognition sequences are intermeshed within the spoVG transcription initiation region.

Structure of a Bacillus subtilis bacteriophage SPO1 gene encoding RNA polymerase sigma factor

Gene 28 of Bacillus subtilis bacteriophage SPO1 codes for a regulatory protein, a sigma factor known as sigma gp28, that binds to the bacterial core RNA polymerase to direct the recognition of phage middle gene promoters. middle promoters exhibit distinctive and conserved nucleotide sequences in two regions centered about 10 and 35 base pairs upstream from the start point of mRNA synthesis. Here we report the cloning of gene 28 and its complete nucleotide sequence. We infer that sigma gp28 is a 25,707-dalton protein of 220 amino acids. Neither the nucleotide sequence of gene 28 nor the inferred amino acid sequence of sigma gp28 exhibits extensive homology to the gene or protein sequence of Escherichia coli sigma factor.

T4 late transcripts are initiated near a conserved DNA sequence

Bacteriophage T4 late transcription is unusual, among prokaryotes, in its complexity. Late transcription requires the host RNA polymerase, the products of T4 genes, 33, 45 and 55, and other small polypeptides, the genes of which have not been identified. In addition the DNA template must be "competent' for late transcription. First the DNA must contain the substituted base 5-hydroxymethyl cytosine in place of cytosine (this requirement is eliminated by a mutation in the T4 alc gene). Second, the DNA must be replicating, although late transcription can be uncoupled from DNA replication by mutations in the T4 genes coding for DNA ligase (gene 30) and DNA exonuclease (gene 46). We report here the location of the initiation sites of the messenger RNAs (mRNAs) synthesized in vivo from four late genes (genes 21, 22, 23 and 36) by S1 nuclease mapping and we have determined the DNA sequences at these sites. We have found strong homology to the sequence TATAAATACTATT immediately upstream from the 5' ends of the late messages and we suggest that this sequence is specifically recognized by the complex responsible for late transcription. Also, we have examine gene 23 mRNA synthetized in the absence of DNA replication using the 30- 46- mutant described above and find that it is identical to the true late transcript synthesized in normal infections.

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

We have determined the nucleotide sequence of two Bacillus subtilis promoters (veg and tms) that are utilized by the principal form of B. subtilis RNA polymerase found in vegetative cells (sigma 55-RNA polymerase) and have compared our sequences to those of several previously reported Bacillus promoters. Hexanucleotide sequences centered approximately 35 (the "--35" region) and 10 (the "--10" region) base pairs upstream from the veg and tms transcription starting points (and separated by 17 base pairs) corresponded closely to the consensus hexanucleotides (TTGACA and TATAAT) attributed to Escherichia coli promoters. Conformity to the preferred --35 and --10 sequences may not be sufficient to promote efficient utilization by B. subtilis RNA polymerase, however, since three promoters (veg, tms and E. coli tac) that conform to these sequences and that are utilized efficiently by E. coli RNA polymerase were used with highly varied efficiencies by B. subtilis RNA polymerase. We have also analyzed mRNA sequences in DNA located downstream from eight B. subtilis chromosomal and phage promoters for nucleotide sequences that might signal the initiation of translation. In accordance with the rules of McLaughlin, Murray and Rabinowitz (1981), we observe mRNA nucleotide sequences with extensive complementarity to the 3' terminal region of B. subtilis 16S rRNA, followed by an initiation codon and an open reading frame.