Restriction fragment analysis of the temporal program of bacteriophage SPO1 transcription and its control by phage-modified RNA polymerases

Genomics of staphylococcal Twort-like phages--potential therapeutics of the post-antibiotic era

Polyvalent bacteriophages of the genus Twort-like that infect clinically relevant Staphylococcus strains may be among the most promising phages with potential therapeutic applications. They are obligatorily lytic, infect the majority of Staphylococcus strains in clinical strain collections, propagate efficiently and do not transfer foreign DNA by transduction. Comparative genomic analysis of 11 S. aureus/S. epidermidis Twort-like phages, as presented in this chapter, emphasizes their strikingly high similarity and clear divergence from phage Twort of the same genus, which might have evolved in hosts of a different species group. Genetically, these phages form a relatively isolated group, which minimizes the risk of acquiring potentially harmful genes. The order of genes in core parts of their 127 to 140-kb genomes is conserved and resembles that found in related representatives of the Spounavirinae subfamily of myoviruses. Functions of certain conserved genes can be predicted based on their homology to prototypical genes of model spounavirus SPO1. Deletions in the genomes of certain phages mark genes that are dispensable for phage development. Nearly half of the genes of these phages have no known homologues. Unique genes are mostly located near termini of the virion DNA molecule and are expressed early in phage development as implied by analysis of their potential transcriptional signals. Thus, many of them are likely to play a role in host takeover. Single genes encode homologues of bacterial virulence-associated proteins. They were apparently acquired by a common ancestor of these phages by horizontal gene transfer but presumably evolved towards gaining functions that increase phage infectivity for bacteria or facilitate mature phage release. Major differences between the genomes of S. aureus/S. epidermidis Twort-like phages consist of single nucleotide polymorphisms and insertions/deletions of short stretches of nucleotides, single genes, or introns of group I. Although the number and location of introns may vary between particular phages, intron shuffling is unlikely to be a major factor responsible for specificity differences.

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.

Roles of genes 44, 50, and 51 in regulating gene expression and host takeover during infection of Bacillus subtilis by bacteriophage SPO1

We show that the products of SPO1 genes 44, 50, and 51 are required for the normal transition from early to middle gene expression during infection of Bacillus subtilis by bacteriophage SPO1; that they are also required for control of the shutoff of host DNA, RNA, and protein synthesis; and that their effects on host shutoff could be accounted for by their effects on the regulation of gene expression. These three gene products had four distinguishable effects in regulating SPO1 gene expression: (i) gp44-50-51 acted to restrain expression of all SPO1 genes tested, (ii) gp44 and/or gp50-51 caused additional specific repression of immediate-early genes, (iii) gp44 and/or gp50-51 stimulated expression of middle genes, and (iv) gp44 and/or gp50-51 stimulated expression of some delayed-early genes. Shutoff of immediate-early gene expression also required the activity of gp28, the middle-gene-specific sigma factor. Shutoff of host RNA and protein synthesis was accelerated by either the 44- single mutant or the 50(-)51(-) double mutant and more so by the 44(-)50(-)51(-) triple mutant. Shutoff of host DNA synthesis was accelerated by the mutants early in infection but delayed by the 44(-)50(-)51(-) triple mutant at later times. Although gp50 is a very small protein, consisting almost entirely of an apparent membrane-spanning domain, it contributed significantly to each activity tested. We identify SPO1 genes 41 to 51 and 53 to 60 as immediate-early genes; genes 27, 28, and 37 to 40 as delayed-early genes; and gene 52 as a middle gene.

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 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.

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.

Mapping the genes in the terminal redundancy of bacteriophage SPO1 with restriction endonucleases

Although most early transcription from SPO1, a lytic DNA bacteriophage of Bacillus subtilis, is specified by the 12.6-kilobase region of the terminal redundancy, early genes from this region have not been identified by standard genetic means. We mapped genes to DNA regions of the SPO1 terminal redundancy by analyzing in vitro protein synthesis from isolated SPO1 restriction fragments in an Escherichia coli-coupled transcription-translation cell-free system. DNA from the terminal redundancy directs the synthesis in vitro of eleven proteins, e3, e4, e6, e7, e9, e12, e15, e16, e18, e20, and e21, which correspond in mobility on sodium dodecyl sulfate-polyacrylamide gels with authentic SPO1 early proteins. From their mapped positions on the DNA, genes were positioned downstream from most, but not all, of the twelve early promoter regions identified in vitro in the terminal redundancy. The temporal patterns of early protein synthesis in vivo suggest a differential turning on and off of early promoters in the terminal redundancy. Both in vivo and in vitro evidence suggests the existence of previously unidentified early promoter regions upstream from the genes for e6 and e4 as well as a middle promoter region upstream from the gene for e16.

New Ways to Study Developmental Genes in Spore-Forming Bacteria

The regulated activation of numerous sets of genes in multiple chromosomal locations is a hallmark of cellular differentiation in both eukaryotes and prokaryotes. Certain species of bacteria that experience complex developmental cycles are especially attractive as systems in which to study the mechanisms of this kind of gene regulation because they are highly amenable to both biochemical and genetic approaches. Bacillus subtilis, which undergoes extensive cellular differentiation when it sporulates, is one such system. Many new methods are now available in this Gram-positive species for identifying, manipulating, and studying the regulation of genes involved in spore formation, including the use of transposable genetic elements that create gene fusions in vivo as an automatic consequence of insertions into genes.

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.

Ribonucleoside triphosphate concentration-dependent termination of bacteriophage SP01 transcription in vitro by Bacillus subtilis RNA polymerase

Several sites specifying transcription termination in the bacteriophage SP01 terminal repeat have recently been located and characterized. Some of these were identified as partial terminators. Further characterization of three of the partial terminators leads to the conclusion that they are not sites of inefficient transcriptional termination by Bacillus subtilis RNA polymerase. Rather, these are sites where termination is either completely efficient or fails to occur at all, depending upon the ribonucleoside triphosphate (rNTP) concentration in the reaction mixture. The threshold rNTP concentration, above which termination will not occur, is the same for two of the terminators studied here and different for the third.

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.

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.

SP01 gene 27 is required for viral late transcription

The SP01 mutant sus HA20 (gene 27) was found to be defective for synthesis of viral late RNA. It is known that gene 27 is also required for viral DNA replication. The SP01 gene 27 product resembles the T4 gene 45 product, which also has a dual role in viral DNA replication and late transcription.

Developmentally regulated transcription in a cloned segment of the Bacillus subtilis chromosome

We describe a model system for studying developmentally regulated transcription during spore formation in Bacillus subtilis. This model system is a cloned cluster of genes known as 0.4 kb, ctc, and veg from the purA-cysA region of the B. subtilis chromosome. Each gene exhibited a distinct pattern of transcription in cells growing in glucose medium and in cells deprived of nutrients in sporulation medium. The 0.4 kb gene was transcribed at a low level in growing cells but was actively transcribed during nutrient deprivation in sporulation medium. This ribonucleic acid (RNA) synthesis was dependent upon the products of five B. subtilis genes that are involved in the initiation of spore formation:spo0A, spo0A, spo0E, spo0F, and spo0H. A mutation in any one of these regulatory genes severely restricted transcription of the 0.4 kb sequence. Transcription of the ctc gene was also turned on by nutrient deprivation, but this RNA synthesis was not impaired in spo0 mutants. Although not under spo0 control, the ctc gene probably corresponds to a locus, spoVC, whose product is required at a late stage of sporulation. Finally, the veg gene was actively transcribed both in growing cells and in nutrient-deprived cells. Like ctc RNA synthesis, transcription of the veg gene was not dependent upon the spo0 gene products. We propose that the spo0A, spo0B, spo0E, spo0F, and spo0H gene products are components of a pathway(s) that senses nutrient deprivation in B. subtilis and translates this environmental signal into the transcriptional activation of a subset of developmental genes.

In vivo transcription of Bacillus subtilis bacteriophage SPP1

The temporal program of SPP1 transcription was examined by hybridizing RNA extracted from infected B. subtilis cells, pulse-labelled at various times after infection, to restriction fragments of SPP1 DNA. RNA made early after infection hybridises to contiguous fragments in the left part of the SPP1 molecule, whereas hybridization to fragments in the right part of the chromosome is found late in infection. Viral gene transcription proceeds from right to left on the H-strand throughout the lytic cycle. At late times transcription occurs also from left to right using the L-strand as template. These assignments follow from the established 5'--3' polarity of the complementary (H- and L-) strains of SPP1 DNA and the determination of strand specificity in SPP1 transcription. Early and late transcriptions are also defined physiologically: protein synthesis and phage DNA replication must precede late transcription.

Early RNAs in SP82- and SP01-infected Bacillus subtilis may be processed

Transcription of SP82 and SP01 DNAs in vitro by Bacillus subtilis RNA polymerase yielded mostly large RNA species, with many in excess of 1,500 bases in length, whereas most of the RNAs synthesized in vivo early in infection were much smaller. Addition of an extract from uninfected B. subtilis to reaction mixtures containing RNAs synthesized in vitro generated additional discrete RNAs whose mobilities on polyacrylamide gels matched the mobilities of some of the smaller RNAs synthesized in vivo.

A sporulation-induced sigma-like regulatory protein from B. subtilis

We have isolated a sigma-like regulatory protein termed sigma 29 whose synthesis or association with Bacillus subtilis RNA polymerase was induced during spore formation. sigma 29 is a sporulation-specific component of RNA polymerase as it was absent in enzyme from an early-blocked sporulation mutant (SpoOA). We have demonstrated specific RNA synthesis by sigma 29-RNA polymerase using as a DNA template a cloned cluster of vegetative and sporulation genes from the purA-cysA region of the B. subtilis chromosome. The pattern of gene recognition by sigma 29-RNA polymerase was distinct from that observed for RNA polymerases containing sigma 55 or sigma 37, species of sigma factor that are present in vegetative cells of B. subtilis. A reconstitution experiment in which purified sigma 29 was added to core RNA polymerase demonstrates that sigma 29 was directly responsible for the altered transcriptional specificity of sporulation RNA polymerase. We propose that sigma 29 is a regulatory protein that controls developmental gene transcription at an early stage of spore formation.

Nucleotide sequence of a promoter recognized by Bacillus subtilis RNA polymerase

We report the nucleotide sequence of a promoter recognized by RNA polymerase from the gram-positive bacterium Bacillus subtilis. This promoter, which was isolated from B. subtilis phage SP01 DNA, is homologous to promoters for Escherichia coli RNA polymerase; the sequences of the "-35 region" and the "Pribnow box" were 5'TTGACT and 5'CATAAT, respectively (T is the thymine analog 5-hydroxymethyluracil in SP01 DNA). These sequences each differed by only a single base pair from the preferred sequences for E. coli promoters. Not surprisingly, the SP01 promoter was actively transcribed in vitro by E. coli RNA Polymerase as well as by B. subtilis RNA polymerase.

Exclusion of bacteriophage T1 by bacteriophage lambda. II. Synthesis of T1-specific macromolecules under N-mediated excluding conditions

The results of experiments investigating T1 macromolecular synthesis under N-mediated excluding conditions failed to demonstrate a substantial alteration in the T1 mRNA production in excluding cultures at any stage in the T1 infectious cycle. The number of T1 DNA sequences in the excluding culture was found to be one-third to one-half that found in T1-infected cultures. The most severe reduction in T1-specific macromolecules was seen in protein synthesis. Total incorporation of labeled amino acids was reduced sixfold, and gel experiments confirmed that the T1-specific proteins capable of detection are reduced in excluding cells.

Inhibition by lipiarmycin of bacteriophage growth in Bacillus subtilis

We have used lipiarmycin, a specific inhibitor of initiation of transcription, to study the role of host RNA polymerase in the transcription programs of various phages of Bacillus subtilis. Unlike rifampin, lipiarmycin preferentially inhibits transcription dependent on the sigma subunit of RNA polymerase because it inactivates holoenzyme at a much greater rate than it does core enzyme. With phage SP01, addition of lipiarmycin at a middle-to-late time of infection did not inhibit phage production even though phage production was sensitive to addition of rifampin at that time. This result is consistent with the notion that unmodified host RNA polymerase holoenzyme becomes dispensable after transcription of early classes of SP01 genes, even though host core enzyme is required for synthesis of all classes of phage RNA. SP01-modified forms of RNA polymerase, which lack sigma subunit but contain phage-coded polypeptides and are able to transcribe middle and late genes, were resistant to lipiarmycin in vitro. For phage phi 105, phage development was sensitive to both lipiarmycin and rifampin in wild-type cells and resistant to both drugs in resistant mutant cells, leading to the conclusion that the activity of host holoenzyme was required for phage RNA synthesis. Growth of phage PBS2, which was resistant to rifampin, was sensitive to the addition of lipiarmycin at early times of infection of a wild-type host strain. In a lipiarmycin-resistant mutant host, PBS2 growth was resistant to lipiarmycin. This result suggests that host holoenzyme plays a previously unanticipated role in transcription of PBS2 genes.