Identification of a gene in Bacillus subtilis bacteriophage SPP1 determining the amount of packaged DNA

The virulent Bacillus subtilis bacteriophage SPP1 encapsidates its DNA by a headful mechanism. Analyzing phage missense mutants, which package less DNA than SPP1 wild-type but show no other affected properties, we have identified a gene whose product is involved in the sizing of phage DNA during maturation. Characterization of this gene and its product provides an experimental access to the poorly understood mechanism of DNA sizing in packaging. The gene (gene 6 or siz) was cloned and sequenced. An open reading frame (ORF) coding for a 57.3 kDa polypeptide was identified. All the single nucleotide substitutions present in different siz mutants affect the net charge of that protein. The gene was further characterized by assignment of several nonsense mutations (sus) to the ORF. Phages carrying the latter type of mutations could be complemented in trans when gene 6 is provided by a plasmid.

Molecular analysis of the Bacillus subtilis bacteriophage SPP1 region encompassing genes 1 to 6. The products of gene 1 and gene 2 are required for pac cleavage

Packaging of Bacillus subtilis phage SPP1 DNA into viral capsids is initiated at a specific DNA site termed pac. Using an in vivo assay for pac cleavage, we show that initiation of DNA synthesis and DNA packaging are uncoupled. When the DNA products of pac cleavage were analyzed, we could detect the pac end that was destined to be packaged, but we failed to detect the other end of the cleavage reaction. SPP1 conditional lethal mutants, which map adjacent to pac, were analyzed with our assay. This revealed that the products of gene 1 and gene 2 are essential for pac cleavage. SPP1 mutants that are affected in the genes necessary for viral capsid formation (gene 41) or involved in headful cleavage (gene 6) remain proficient in pac site cleavage. Analysis of the nucleotide sequence (2.769 x 10(3) base-pairs) of the region of the genes required for pac cleavage revealed five presumptive genes. We have assigned gene 1 and gene 2 to two of these open reading frames (orf), giving the gene order gene 1-gene 2-orf 3-orf 4-orf 5. The direction of transcription of the gene 1 to orf 5 operon and the length of the mRNAs was determined. We have identified, upstream from gene 1, the major transcriptional start point (P1). Transcription originating from P1 requires a phage-encoded factor for activity. The organization of gene 1 and gene 2 of SPP1 resembles the organization of genes in the pac/cos region of different Escherichia coli double-stranded DNA phages. We propose that the conserved gene organization is representative of the packaging machinery of a primordial packaging system.

Cloning, characterization and evolution of the BsuFI restriction endonuclease gene of Bacillus subtilis and purification of the enzyme

The restriction endonuclease (R.BsuFI) of Bacillus subtilis recognizes the target DNA sequence 5' CCGG. The R.BsuFI gene was found in close proximity to the cognate M.BsuFI gene, which had previously been characterized (1). Cloning of the R.BsuFI gene in E.coli was only possible with the M.BsuFI Mtase gene present on a compatible plasmid. The cloned R.BsuFI gene was expressed in E. coli and restriction activity was observed in vivo and in vitro. The R.BsuFI gene consists of 1185 bp, coding for a protein of 395 amino acids with a calculated molecular weight of 45.6 kD. The R.BsuFI enzyme was purified to homogeneity following overexpression. It presumably works as a dimer and cleaves the 5' CCGG target sequence between the two cytosines to produce sticky ends with 5' CG overhangs, like the isoschizomers R.MspI and R.HpaII. The relatedness between R.BsuFI and R.MspI is reflected by significant similarities of the amino acid sequences of both enzymes. This is the first case where such similarities have been observed between isoschizomeric restriction endonucleases which belong to 5mC specific R/M systems. This observation suggests that R.BsuFI and R.MspI genes derive from a common ancestor. In spite of such functional and evolutionary relatedness, the R/M systems differ in the arrangement of their R and M genes. In the BsuFI system transcription of the two genes is convergent, whereas divergent transcription occurs in the MspI system.

'Pseudo' domains in phage-encoded DNA methyltransferases

5-Cytosine-DNA-methyltransferases, which are found in many organisms ranging from bacteriophages to mammals, transfer a methyl group from S-adenosylmethionine to the carbon-5 of a cytosine residue in specific DNA target sequences. Some phage-encoded methyltransferases methylate more than one sequence: these enzymes contain several independent target-recognizing domains each responsible for recognizing a different site. The amino-acid sequences of these multispecific methyltransferases reveal that some enzymes in addition carry domains that do not contribute to the enzymes' methylation potential, but strongly resemble previously identified target-recognizing domains. Here we show that introducing defined amino-acid alterations into these inactive domains endows these enzymes with additional methylation specificities. Gel retardation analysis demonstrates that these novel methylation specificities correlate with the acquisition of additional DNA-binding potential of the proteins.

M.H2I, a multispecific 5C-DNA methyltransferase encoded by Bacillus amyloliquefaciens phage H2

Bacillus amyloliquefaciens phage H2 codes for a multispecific cytosine-5-DNA- methyltransferase (MTase), M.H2I, which methylates GGCC, GCNGC and [sequence: see text] target sequences. The gene coding for M.H2I was cloned in Escherichia coli and its nucleotide (nt) sequence was determined. It consists of 1509 bp, corresponding to a protein of 503 amino acids (aa) with a calculated Mr of 57,166. A comparison of the aa sequence of M.H2I with those of the multispecific MTases encoded by Bacillus subtilis phages SPR, phi 3T and rho 11S, revealed that M.H2I is closely related to these enzymes. A very high degree of homology was observed between M.H2I and M.rho 11SI, with 96.2% aa identity and 97.8% nt identity of the corresponding genes.

Functional analysis of the Bacillus subtilis bacteriophage SPP1 pac site

Encapsidation of the DNA of the virulent Bacillus subtilis phage SPP1 follows a processive unidirectional headful-mechanism and initiates at a unique genomic location (pac). We have cloned a fragment of SPP1 DNA containing the pac site flanked by reporter genes into the chromosome of B. subtilis. Infection of such cells with SPP1 led to highly efficient packaging, initiated at the inserted pac site, of chromosomal DNA. The directionality in the packaging of this DNA was the same as observed with vegetative phage DNA. Mutagenizing the chromosomal pac insert defined an 83 base pair segment containing the pac cleavage site which is sufficient to direct phage specific DNA encapsidation. The packaging recognition signal as defined can also be utilized by the SPP1 related phages 41c, SF6 and rho 15.

The amino acid sequence of the CCGG recognizing DNA methyltransferase M.BsuFI: implications for the analysis of sequence recognition by cytosine DNA methyltransferases

The Bacillus subtilis FI DNA methyltransferase (M.BsuFI) modifies the outer cytosine of the DNA sequence CCGG, causing resistance against R.BsuFI and R.MspI restriction. The M.BsuFI gene was cloned and expressed in B.subtilis and Escherichia coli. As derived from the nucleotide sequence, the M.BsuFI protein has 409 amino acids, corresponding to a molecular mass of 46,918 daltons. Including these data we have compared the nucleotide and amino acid sequences of different CCGG recognizing enzymes. These analyses showed that M.BsuFI is highly related to two other CCGG specific methyltransferases, M.MspI and M.HpaII, which were isolated from Gram-negative bacteria. Between M.BsuFI and M.MspI the sequence similarity is particularly significant in a region, which has been postulated to contain the target recognition domains (TRDs) of cytosine-specific DNA methyltransferases. Apparently M.BsuFI and M.MspI, derived from phylogenetic distant organisms, use highly conserved structural elements for the recognition of the CCGG target sequence. In contrast the very same region of M.HpaII is quite different from those of M.BsuFI and M.MspI. We attribute this difference to the different targeting of methylation within the sequence CCGG, where M.HpaII methylates the inner, M.BsuFI/M.MspI the outer cytosine. Also the CCGG recognizing TRD of the multispecific B.subtilis phage SPR Mtase is distinct from that of the host enzyme, possibly indicating different requirements for TRDs operative in mono- and multispecific enzymes.

Analysis of structural and biological parameters affecting plasmid deletion formation in Bacillus subtilis

Deletions generated following stimulation by the deletion hot spot of plasmid pHV15-1 were studied in Bacillus subtilis. Nucleotide sequencing showed that deletions extend between short direct repeat sequences. Such direct repeat sequences may have homology to the sequence of the hot spot. Deletion formation is recE-independent, but requires an active exonuclease V (AddAB) enzyme. Other structural parameters like plasmid size and structure influence deletion formation.

Cytosine-specific type II DNA methyltransferases. A conserved enzyme core with variable target-recognizing domains

Comparisons of the amino acid sequences of m5C DNA methyltransferases (Mtases) from 11 prokaryotes and one eukaryote reveal a very similar organization. Among all the enzymes one can distinguish highly conserved "core" sequences and "variable" regions. The core sequences apparently mediate steps of the methylation reaction that are common to all the enzymes. The major variable region has been shown in our previous studies on multispecific phage Mtases to contain the target-recognizing domains (TRDs) of these enzymes. Here we have compared the amino acid sequences of various TRDs from phage Mtases. This has revealed the presence of both highly conserved and variable amino acids. We postulate that the conserved residues represent a "consensus" sequence defining a TRD, whereas the specificity of the TRD is determined by the variable residues. We have observed similarity between this consensus sequence and sequences in the variable region of the monospecific Mtases. We predict that the regions thus identified represent part of the TRDs of monospecific Mtases.

Sequential order of target-recognizing domains in multispecific DNA-methyltransferases

In the multispecific DNA(cytosine-5)-methyltransferases (Mtases) of Bacillus subtilis phages SPR and phi 3T the domains responsible for recognition of DNA methylation targets CCA/TGG, CCGG, GGCC (SPR) and GCNGC, GGCC (phi 3T) represent contiguous sequences of approximately 50 amino acids each. These domains are tandemly arranged and do not overlap. They are part of a 'variable' segment within the enzymes which is flanked by 'conserved' amino acids, which are very similar amongst bacterial monospecific and the multispecific Mtases studied here. These results follow from a mutational analysis of the SPR and phi 3T Mtase genes. They further support our concept of a modular enzyme organization, according to which variability of type II Mtases with respect to target recognition is achieved by a combination of the same enzyme core with a variety of target-recognizing domains.

Chimeric multispecific DNA methyltransferases with novel combinations of target recognition

DNA target recognizing domains of different multispecific DNA-cytosine-methyltransferases can be rearranged through engineering of the corresponding genes to generate enzymes with novel combinations of target recognition.

Construction and use of chimeric SPR/phi 3T DNA methyltransferases in the definition of sequence recognizing enzyme regions

Multispecific DNA methyltransferases (Mtases) of temperate Bacillus subtilis phages SPR and phi 3T methylate the internal cytosine of the sequence GGCC. They differ in their capacity to methylate additional sequences. These are CCGG and CC(A/T)GG in SPR and GCNGC in phi 3T. Introducing unique restriction sites at equivalent locations within the two genes facilitated the construction of chimeric genes. These expressed Mtase activity at a level comparable to that of the parental genes. The methylation specificity of chimeric enzymes was correlated with the location of chimeric fusions. This analysis, which also included the use of mutant genes, showed that domains involved in the recognition of target sequences unique to each enzyme [CCGG, CC(A/T)GG or GCNGC] are represented by the central non-conserved parts of the proteins, whilst recognition of the sequence (GGCC), which is a target for both enzymes, is determined by an adjacent conserved region.

Organization of multispecific DNA methyltransferases encoded by temperate Bacillus subtilis phages

B. subtilis phage rho 11s codes for a multispecific DNA methyltransferase (Mtase) which methylates cytosine within the sequences GGCC and GAGCTC. The Mtase gene of rho 11s was isolated and sequenced. It has 1509 bp, corresponding to 503 amino acids (aa). The enzyme's Mr of 57.2 kd predicted from the nucleotide sequence was verified by direct Mr determinations of the Mtase. A comparison of the aa sequence of the rho 11s Mtase with those of related phages SPR and phi 3%, which differ in their methylation potential, revealed generalities in the building plan of such enzymes. At least 70% of the aa of each enzyme are contained in two regions of 243 and 109 aa at the N and C termini respectively, which are highly conserved among the three enzymes. In each enzyme, variable sequences separate the conserved regions. Variability is generated through the single or multiple use of related and unrelated sequence motifs. We propose that the recognition of those DNA target sequences, which are unique for each of the three enzymes, is determined by these variable regions. Evolutionary relationships between the three enzymes are discussed.

Recombinant derivatives of Bacillus subtilis phage Z containing the DNA methyltransferase genes of related methylation-proficient phages

The DNA methyltransferase (Mtase) genes of temperate Bacillus subtilis phages SPR, phi 3T, SP beta and rho 11 can be transferred by transfection and recombination to the genome of the related non-modifying phage Z. Integration of the Mtase genes occurs in phage Z DNA at a unique location which is homologous with the flanking regions of the Mtase genes of the related phages. In lysogenic cells carrying recombinant phages, expression of the Mtase genes is repressed, irrespective of whether the Mtase genes were derived from phage donors which were homo- or heteroimmune to phage Z.

Requirements for the formation of plasmid-transducing particles of Bacillus subtilis bacteriophage SPP1

We had previously proposed that the production of concatemeric plasmid DNA in plasmid-transducing SPP1 particles is a consequence of phage-directed rolling-circle-type replication of plasmid DNA. The production of such DNA was greatly enhanced when DNA/DNA homology was provided between phage and plasmid DNAs (facilitation of transduction). Here we present evidence that synthesis of concatemeric plasmid DNA can proceed after phage infection under conditions non-permissive for plasmid replication. We also propose that the naturally occurring homology between plasmid and phage is sufficient to account for the frequency of transduction observed in the absence of facilitating homology. Homology of greater than 47 bp gives the maximal facilitation of plasmid transduction. Recombination is not an essential part in the synthesis of concatemeric plasmid DNA.

Genomic organization of the related Bacillus subtilis bacteriophages SPP1, 41c, rho 15, and SF6

The genomes of the related virulent Bacillus subtilis bacteriophages SPP1, 41c, rho 15, and SF6 are partially circularly permuted and terminally redundant. Heteroduplex molecules were produced with various combinations of these DNAs. Their electron-microscopic analyses showed a consistent pattern of homologous and heterologous regions of DNA. Restriction maps of the phage DNAs were established. A comparison of these maps showed a pattern of conserved and variable DNAs compatible with the electron-microscopic analyses. In all phage genomes, regions specifying early and late functions were conserved. In each phage genome, such regions were separated by short segments of heterologous DNA characteristic for each phage.

DNA methyltransferase genes of Bacillus subtilis phages: comparison of their nucleotide sequences

The phi 3T DNA methyltransferase (Mtase) and most of the SP beta Mtase genes have been sequenced. With the exception of their promoters, no difference was found between the phi 3T and SP beta Mtase genes which code for an enzyme with a Mr of 50 507, consisting of 443 amino acids (aa). Comparison of the deduced aa sequence of the phi 3T/SP beta type Mtase (target specificity: GGCC and GCNGC) with that of the previously established sequence of the SPR Mtase (Buhk et al., 1984) which has the target specificity GGCC and CCGG, reveals strong similarities between these two types of enzymes. There is, however, one striking difference: both the phi 3T/SP beta and the SPR enzymes contain at different positions inserts of 33 aa, which have no homology to each other. We suggest that the methylation specificity unique to each of the two types of Mtases (GCNGC in phi 3T/SP beta; CCGG in SPR) depends on these inserts, while the GGCC-specific modification potential common to all Mtases is determined by structures conserved in both types of enzymes. A DNA fragment of non-modifying phage Z, which shows homology to both flanks of the SPR Mtase gene, was also sequenced. This segment can be described as a derivative of SPR DNA, in which the Mtase gene and sequences at its 5' end have been deleted, with the deletion extending between two direct repeats of 25 bp.

Plasmid transduction by Bacillus subtilis bacteriophage SPP1: effects of DNA homology between plasmid and bacteriophage

Any SPP1 DNA restriction fragment cloned into Bacillus subtilis plasmid pC194 or pUB110 increased the transduction frequency of the plasmid by SPP1 100- to 1,000-fold over the transduction level of the plasmid alone. This increment was observed irrespective of whether a fragment contained the SPP1 packaging origin (pac). Furthermore, an SPP1 derivative into whose genome pC194 DNA had been integrated transduced pC194 DNA with a greatly enhanced frequency. Transduction enhancement mediated by DNA-DNA homology between plasmid and SPP1 was independent of the extent of homology (size range analyzed, 0.5 to 3.9 kilobases) and the recombination proficiency of donor or recipient.

The genome of Bacillus subtilis phage SPP1: structure of an early promoter

The strongest of five 'early' promoters of Bacillus subtilis phage SPP1 was localized in a DNA restriction fragment by analysis of RNA polymerase binding and R-loop formation. The nucleotide sequence of the promoter region was established. The signal structures identified were similar to those recognized by the sigma 55 RNA polymerase of B. subtilis. The promoter precedes an open reading frame with 51 codons. A protein with the Mr predicted from the nucleotide sequence was identified in minicells.

Cold sensitivity in the transfer of a plasmid with a deletion hot spot into recombination deficient B. subtilis cells

Various recombination-deficient mutants of B. subtilis, which are readily transformable by plasmid DNA at 42 degrees C cannot be transformed at 30 degrees C with chimeric plasmid derivatives that contain the deletion hot spot defined previously (Alonso and Trautner 1985a, b). Such interference was also observed in protoplast transformation and SPP1 transduction.

Generation of deletions through a cis-acting mutation in plasmid pC194

When plasmid pC194-1 is ligated to pBR322 to generate plasmid pHV15-1, deletions occur with high frequency within the joined pBR322 DNA. Generation of deletions is recE4 independent, and occurs in B. subtilis with a 1,000-fold higher frequency than in Escherichia coli. In the hybrid plasmid pVH15-1, deletion end-points are not at random, but at defined locations within pBR322. We propose that the base alteration, characterizing pC194-1, has stabilized within the plasmid a stem/loop structure, which acts as a deletion generator.

Inversion and deletion mutants in Bacillus subtilis bacteriophage SPP1 as a consequence of cloning

Properties of an inversion and a deletion mutant of B. subtilis phage SPP1 which arose during cloning are described. The results are related to the biology of this bacteriophage. In preceding communications from our laboratories (Heilmann and Reeve 1982, Behrens et al. 1983) we reported the properties of genetically engineered SPP1 bacteriophages, which could be used as cloning vehicles in B. subtilis. These phages contain a unique restriction site within a dispensable region of their genomes. In the course of cloning experiments using these phage vectors, we have occasionally observed the appearance of not only the original vector and desired hybrid phages, but also of SPP1 phages which had undergone extensive genomic rearrangements. Properties of two such phages, SPP1 inv1, which was found to contain a large inversion and of SPP1 delV, a deletion mutant, which defines an additional dispensable region of the SPP1 genome, are described in this communication.

A gene controlling segregation of the Bacillus subtilis plasmid pC194

Plasmid pC194-1, a mutant of pC194, and chimeric derivatives of pC194-1 are segregationally unstable in B. subtilis. Such instability could be enhanced by exposure of pC194-1-carrying cells to methyl methanesulfonate. pC194-1 is distinct from pC194 in the addition of two A:T base pairs within the previously defined D region of pC194. Complementation experiments between pC194-1 and other plasmids suggest that the mutation of pC194-1 interferes with the production of a diffusible gene product required for plasmid maintenance.

DNA methyltransferase genes of Bacillus subtilis phages: structural relatedness and gene expression

The DNA methyltransferase (Mtase) genes of temperate Bacillus subtilis phages phi 3T, rho 11 and SP beta were cloned and expressed in Escherichia coli. Each gene specifies a 47-kDa1 protein, which modifies BsuR (GGCC) and Fnu4HI (GCNGC) target sequences. Transcription is controlled by phage promoters located on the cloned fragments. The direction of transcription and the approximate position of the Mtase genes were determined. DNA/DNA hybridization experiments revealed close structural relatedness of the phi 3T, rho 11 and SP beta genes. A significant degree of homology was also found among these genes and the Mtase gene of related phage SPR, which codes for an enzyme with different modification specificity. These results suggest a common ancestor of the different phage Mtase genes. Phage Z, the only BsuR-sensitive member of this phage group, lacks a modification gene, but contains regions homologous to sequences flanking the SPR, phi 3T, rho 11 and SP beta Mtase genes.