Analysis of bacteriophage phi 29 gene function: protein synthesis in suppressor-sensitive mutant infection of Bacillus subtilis

Origin, Evolution and Diversity of φ29-like Phages-Review and Bioinformatic Analysis

Phage φ29 and related bacteriophages are currently the smallest known tailed viruses infecting various representatives of both Gram-positive and Gram-negative bacteria. They are characterised by genomic content features and distinctive properties that are unique among known tailed phages; their characteristics include protein primer-driven replication and a packaging process characteristic of this group. Searches conducted using public genomic databases revealed in excess of 2000 entries, including bacteriophages, phage plasmids and sequences identified as being archaeal that share the characteristic features of phage φ29. An analysis of predicted proteins, however, indicated that the metagenomic sequences attributed as archaeal appear to be misclassified and belong to bacteriophages. An analysis of the translated polypeptides of major capsid proteins (MCPs) of φ29-related phages indicated the dissimilarity of MCP sequences to those of almost all other known Caudoviricetes groups and a possible distant relationship to MCPs of T7-like (Autographiviridae) phages. Sequence searches conducted using HMM revealed the relatedness between the main structural proteins of φ29-like phages and an unusual lactococcal phage, KSY1 (Chopinvirus KSY1), whose genome contains two genes of RNA polymerase that are similar to the RNA polymerases of phages of the Autographiviridae and Schitoviridae (N4-like) families. An analysis of the tail tube proteins of φ29-like phages indicated their dissimilarity of the lower collar protein to tail proteins of all other viral groups, but revealed its possible distant relatedness with proteins of toxin translocation complexes. The combination of the unique features and distinctive origin of φ29-related phages suggests the categorisation of this vast group in a new order or as a new taxon of a higher rank.

Phi29 family of phages

Continuous research spanning more than three decades has made the Bacillus bacteriophage phi29 a paradigm for several molecular mechanisms of general biological processes, such as DNA replication, regulation of transcription, phage morphogenesis, and phage DNA packaging. The genome of bacteriophage phi29 consists of a linear double-stranded DNA (dsDNA), which has a terminal protein (TP) covalently linked to its 5' ends. Initiation of DNA replication, carried out by a protein-primed mechanism, has been studied in detail and is considered to be a model system for the protein-primed DNA replication that is also used by most other linear genomes with a TP linked to their DNA ends, such as other phages, linear plasmids, and adenoviruses. In addition to a continuing progress in unraveling the initiation of DNA replication mechanism and the role of various proteins involved in this process, major advances have been made during the last few years, especially in our understanding of transcription regulation, the head-tail connector protein, and DNA packaging. Recent progress in all these topics is reviewed. In addition to phi29, the genomes of several other Bacillus phages consist of a linear dsDNA with a TP molecule attached to their 5' ends. These phi29-like phages can be divided into three groups. The first group includes, in addition to phi29, phages PZA, phi15, and BS32. The second group comprises B103, Nf, and M2Y, and the third group contains GA-1 as its sole member. Whereas the DNA sequences of the complete genomes of phi29 (group I) and B103 (group II) are known, only parts of the genome of GA-1 (group III) were sequenced. We have determined the complete DNA sequence of the GA-1 genome, which allowed analysis of differences and homologies between the three groups of phi29-like phages, which is included in this review.

Phi29 family of phages

Continuous research spanning more than three decades has made the Bacillus bacteriophage phi29 a paradigm for several molecular mechanisms of general biological processes, such as DNA replication, regulation of transcription, phage morphogenesis, and phage DNA packaging. The genome of bacteriophage phi29 consists of a linear double-stranded DNA (dsDNA), which has a terminal protein (TP) covalently linked to its 5' ends. Initiation of DNA replication, carried out by a protein-primed mechanism, has been studied in detail and is considered to be a model system for the protein-primed DNA replication that is also used by most other linear genomes with a TP linked to their DNA ends, such as other phages, linear plasmids, and adenoviruses. In addition to a continuing progress in unraveling the initiation of DNA replication mechanism and the role of various proteins involved in this process, major advances have been made during the last few years, especially in our understanding of transcription regulation, the head-tail connector protein, and DNA packaging. Recent progress in all these topics is reviewed. In addition to phi29, the genomes of several other Bacillus phages consist of a linear dsDNA with a TP molecule attached to their 5' ends. These phi29-like phages can be divided into three groups. The first group includes, in addition to phi29, phages PZA, phi15, and BS32. The second group comprises B103, Nf, and M2Y, and the third group contains GA-1 as its sole member. Whereas the DNA sequences of the complete genomes of phi29 (group I) and B103 (group II) are known, only parts of the genome of GA-1 (group III) were sequenced. We have determined the complete DNA sequence of the GA-1 genome, which allowed analysis of differences and homologies between the three groups of phi29-like phages, which is included in this review.

Characterization, overproduction and purification of the product of gene 1 of Bacillus subtilis phage phi 29

Unit-length phi 29 DNA was not synthesized after restrictive infection of Bacillus subtilis with the phi 29 mutant sus1(629) indicating that the phage phi 29 protein p1 is needed for the viral DNA replication. Sequencing of the ORF-6 of mutant sus1(629) showed that a C in the wild-type (wt) phage had been changed to a T at nt position 19 of the ORF-6, giving rise to a TAA ochre codon, indicating that this ORF corresponds to gene 1. ORF-6 was cloned in plasmid pPLc28 under the control of the pL promoter of phage lambda and, after induction, a protein of about 10 kDa was overproduced, which was absent in the corresponding cells harbouring a recombinant plasmid with the sus1(629) mutation, indicating that the 10-kDa protein is the product of gene 1. In addition, a protein of lower Mr was synthesized after induction of the cells harbouring recombinant plasmids with the wt or the sus1(629) DNA. Both proteins were purified and characterized by N-terminal sequence determination and amino acid analysis. The low-Mr protein, named delta 1, has a size of 6 kDa and corresponds to an internal in-phase initiation event in ORF-6.

Nucleotide sequence of the right early region of Bacillus phage phi 15 and comparison with related phages: reorganization of gene 17 during evolution

The rightmost 2016 bp of the Bacillus subtilis phage phi 15 genome were sequenced. The nucleotide sequence was compared with the homologous regions of the related phages PZA and phi 29. There are six open reading frames (ORFs) in this region of the phi 15 genome; all of them are present in the PZA and phi 29 genomes. One of the ORFs was assigned to gene 17, which is involved in the replication of the phage DNA. Gene 17 has undergone reorganization during the evolution of this phage family. Comparison of the nucleotide sequence of its mRNA-like strand in phi 15, PZA and phi 29 showed that deletions in its central and 3'-end-proximal parts are tolerated and do not interfere with the gene 17 product function. It seems that the only portion of gene 17 that has to be conserved to encode the functional product is its 5'-end-proximal part.

Characterization of a deletion mutant of bacteriophage phi 29

A spontaneous deletion mutant of bacteriophage phi 29 (phi 29 delta 1) has been characterized. This mutant has a 1112-bp deletion, which covers almost the entire sequence of genes 14 and 15, including an early promoter (B2). While lysis is very delayed, the phage DNA synthesis and internal phage development appear to be normal in the cells infected with this deletion mutant. These results indicate that the early functions are intact in phi 29 delta 1. Our results also suggest that genes 14 and 15 are dispensable for bacteriophage phi 29 growth and that the B2 promoter may also be dispensable for early functions in phi 29.

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

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

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

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

Morphogenesis of bacteriophage phi 29 of Bacillus subtilis: prohead restoration for DNA-gp3 packaging and assembly

The DNA-protein complex DNA-gp3 of phi 29 is efficiently packaged into purified proheads with the aid of plasmid-derived gp16. The filled heads can be assembled to phage by addition of an extract providing the products for neck-tail assembly (Bjornsti et al., J. Virol. 50:766-772, 1984). However, purified proheads lost their competence to package DNA-gp3 upon storage for 2 months at 4 degrees C. Competence was restored by complementation with extracts of certain mutant-infected cells, and these experiments demonstrated that late proteins were not involved; restoration obtained with 4-8-14--infected cells was indistinguishable from that obtained with 7-8-14--infected cells. 2-8-14- and 3-8-14- extracts restored about one-third of the capacity to package exogenous DNA-gp3. A 1-8-14- extracts restored activity to package 20.6% of the DNA-gp3 added, but phage were not produced.

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.

Cloning and expression of gene 2, required for the protein-primed initiation of the Bacillus subtilis phage phi 29 DNA replication

A phi 29 DNA fragment containing gene 2, coding for a phi 29-specific DNA polymerase required for the formation of the terminal protein p3-dAMP initiation complex, the first step in phi 29 DNA replication, has been cloned in plasmid pPLc28 under the control of the pL promoter of bacteriophage lambda. Four polypeptides of Mr 68 000, 5800 and 3400 and less than 2000 were labelled with [35S]methionine after heat induction. The protein of Mr 68 000 had the size expected for protein p2 and it accounted for about 2% of the de novo synthesized protein. Protein p2 synthesized in Escherichia coli was shown to be stable and biologically active. Its enzymatic activity could be assayed by the in vitro formation of the protein p3-dAMP initiation complex when complemented with extracts from Bacillus subtilis infected with a phi 29sus2 mutant or with extracts from E. coli harbouring gene 3-containing recombinant plasmids. Moreover, protein p2-containing E. coli extracts could catalyze the initiation reaction in vitro when complemented with highly purified protein p3.

Bacteriophage phi 29 proteins required for in vitro DNA-gp3 packaging

In vitro assembly of bacteriophage phi 29 in crude extracts involves efficient packaging of a DNA-protein complex (DNA- gp3 ) into a prohead with the aid of the gene 16 product ( gp16 ) and subsequent assembly of neck and tail proteins ( Bjornsti et al., J. Virol. 41:508-517, 1982; Bjornsti et al., J. Virol. 45:383-396, 1983; Bjornsti et al., Proc. Natl. Acad. Sci. U.S.A. 78:5861-5865, 1981). To define the viral proteins required for the DNA- gp3 encapsidation phase, we purified biologically active proheads and DNA- gp3 and constructed a chimeric plasmid, pUM101 , which contained and expressed gene 16 of phi 29 and no other viral genes. The plasmid-specified gp16 was both necessary and sufficient to package 24% of the DNA- gp3 added to the purified proheads , and the DNA-filled heads so produced were efficiently complemented to infectious phage by the addition of neck and tail proteins. Purified proheads and DNA- gp3 gave linear dose-response curves with slopes of approximately 1; in contrast, a 4-fold dilution of gp16 resulted in a 1,000-fold reduction of phi 29, suggesting a requirement for multiple copies of this protein.

Characterization of the DNA-protein complex at the termini of the bacteriophage PRD1 genome

DNA of bacteriophage PRD1 has protein P8 at its termini. Extracts of infected cells are able to derivatize P8 in vitro with labeled dGTP. Two early proteins, P1 and P8, products of genes I and VIII, respectively, are the only phage proteins necessary for the formation of the protein P8-dGMP complex. This was shown by complementation of extracts from cells infected with mutants and by use of extracts from cells carrying cloned genes I and VIII. With Escherichia coli mutants that are temperature sensitive for DNA synthesis, it was possible to show that the formation of the protein P8-dGMP complex was dependent upon the host replication apparatus. The analysis of the purified protein P8-dGMP complex by hydrolysis and enzymatic digestion showed that there is a covalent phosphodiester bond between tyrosine and 5'-dGMP.

Antibodies specific for the phi 29 terminal protein inhibit the initiation of DNA replication in vitro

The phi 29 DNA-terminal protein serves as a primer for the initiation of DNA replication by covalently binding the first nucleotide in the DNA chain. Two distinct antibodies were used for functional analysis of this protein. One antibody was raised against sonicated phi 29 DNA-protein complex isolated from phage virions (anti-TP). The other antibody was raised against a conjugate of bovine serum albumin and a synthetic peptide corresponding to the carboxy-terminal of the phi 29 terminal protein (anti-gp3C), which was predicted from the nucleotide sequence of phi 29 DNA. Both antibodies react with native phi 29 terminal protein as determined by immunoprecipitation and enzyme-linked immunosorbent assay. Both antibodies specifically inhibit the complex-forming reaction between the phi 29 terminal protein and dAMP, the first nucleotide of phi 29 DNA.

In vitro initiation of bacteriophage phi 29 and M2 DNA replication: genes required for formation of a complex between the terminal protein and 5'dAMP

Cell-free extracts prepared from phi 29 and M2-infected Bacillus subtilis cells catalyse the formation of complexes between terminal protein and [alpha-32P]-dAMP in the presence of [alpha-32P]-dATP, MgCl2, ATP, and phage DNA with terminal protein covalently linked at both the 5'ends. The complex formation does not take place when proteinase K-treated DNA is added or when uninfected extract is used. The phi 29 complex thus formed is smaller than the M2 complex, primarily due to the different molecular weights of the respective terminal proteins. Extracts prepared from cells infected with suppressor-sensitive mutants of genes 2 or 3 of phi 29 or genes G or E of M2 do not support complex formation. When the pair of extracts of phi 29 or M2-infected cells are mixed, however, formation of the complex takes place as a result of in vitro complementation. These results indicate that the complex formation observed in vitro reflects in vivo initiation of phage DNA replication. The product of gene 2 of phi 29 may be the enzyme that catalyses formation of the complex.

In vitro synthesis of late bacteriophage phi 29 RNA

A crude P-100 fraction prepared from Bacillus subtilis 21 min after infection with wild-type phage phi 29 supported the in vitro synthesis of late phi 29 RNA by added RNA polymerase. Synthesis of late RNA was also detected when purified phi 29 DNA was transcribed by RNA polymerase in the presence of an S-150 fraction obtained by lysis of phi 29-infected cells in the presence of 1 M NaCl. Late phi 29 RNA was not synthesized when either the P-100 or the S-150 fraction was prepared from cultures infected with phi 29 having a mutation in gene 4.

Assembly of the tail protein of the Bacillus subtilis phage phi 29

By in vitro complementation we have determined that gene 13 product functions during phi 29 morphogenesis after the formation of 11- particles, specifically in the functional assembly of the tail protein, p9. Protein p9 from 8- but not from 8-13- extracts assembles in vitro into either 11-13- or 12-13- particles. The action of gene 13 product on p9 for its correct assembly has to take place in vivo; no complementation of 12-13- and 9- lysates occurs in vitro. Protein p9, isolated from phi 29-infected cells, copurifies with the 13+ activity and it is present both in 13+ and 13- extracts as an aggregate with dimensions similar to those of the tail assembled in mature phage.

Morphogenesis of bacteriophage phi 29 of Bacillus subtilis: oriented and quantized in vitro packaging of DNA protein gp3

The assembly of phage phi 29 occurs by a single pathway, and the DNA protein (DNA-gp3) of "packaging intermediates" can be obtained after DNase I interruption of in vitro complementation. A broad spectrum of DNA molecules of variable length was isolated from DNase I-treated proheads. Restriction endonuclease EcoRI digestion and electrophoretic analysis of these DNA molecules suggested that DNA-gp3 packaging was oriented with respect to the physical map and was a complex process. Proteinase K-treated exogenous DNA was not packaged. When exogenous DNA-gp3 was predigested with the restriction endonucleases BstEII. EcoRI, HpaI, and HpaII, the left-end fragments, ranging in size from 8 to 0.9 megadaltons, were selectively and efficiently packaged. During in vivo and in vitro assembly, DNA-gp3 is packaged into proheads, the "core-scaffolding" protein gp7 exits from the particles, and the DNA-filled heads assume the angular morphology of phage phi 29. The packaging of a 4.1-megadalton DNA-gp3 left-end fragment (one third of the genome) resulted in the exit of gp7 and the transition to angularity.

Nucleotide sequence of the major early region of bacteriophage phi 29

The nucleotide sequence of the left end of bacteriophage phi 29 DNA has been determined. Together with data reported earlier (Yoshikawa et al., 1981), this sequencing comprises the major early genetic region of this viral genome (5708 bp). Computer analysis of the DNA sequences revealed that there are up to fifteen open reading frames which could encode polypeptides containing more than thirty amino acids. The DNA sequence also revealed a number of potential regulatory signals, promoters and ribosome binding sites. The initiation and the termination of transcription and probable early gene products are discussed.

Morphogenesis of bacteriophage phi 29 of Bacillus subtilis: DNA-gp3 intermediate in in vivo and in vitro assembly

The assembly of phage phi 29 occurs by a single pathway, and DNA-protein (DNA-gp3) has been shown to be an intermediate on the assembly pathway by a highly efficient in vitro complementation. At 30 degrees C, about one-half of the viral DNA synthesized was assembled into mature phage, and the absolute plating efficiency of phi 29 approached unity. DNA packaging at 45 degrees C was comparable to that at 30 degrees C, but the burst size was reduced by one-third. When cells infected with mutant ts3(132) at 30 degrees C to permit DNA synthesis were shifted to 45 degrees C before phage assembly, DNA synthesis ceased and no phage were produced. However, a variable amount of DNA packaging occurred. Superinfection by wild-type phage reinitiated ts3(132) DNA synthesis at 45 degrees C, and if native gp3 was covalently linked to this DNA during superinfection replication, it was effectively packaged and assembled. Treatment of the DNA-gp3 complex with trypsin prevented in vitro maturation of phi 29, although substantial DNA packaging occurred. A functional gp3 linked to the 5' termini of phi 29 DNA is a requirement for effective phage assembly in vivo and in vitro.

Terminal proteins and short inverted terminal repeats of the small Bacillus bacteriophage genomes

The genome of Bacillus phage phi 29 contains covalently linked protein at both ends. These DNA terminal proteins are essential for phi 29 DNA replication. We have isolated phi 29 terminal protein from each end separately and compared their two-dimensional peptide maps. Our results showed the two proteins to be identical. The DNAs of four phages examined (phi 15, Nf, M2Y, and GA-1) also contain protein at both ends of the DNA molecules. The chymotryptic peptide maps of these DNA terminal proteins have been compared with the map of the phi 29 terminal protein. Despite the similarities in molecular size, peptide maps of the terminal proteins show clear differences among the unrelated phages. These results are consistent with the idea that the terminal proteins are encoded by viral DNA rather than by the host chromosome. We have also determined the nucleotide sequences of the termini of four phage DNAs and compared them with the sequence of phi 29 DNA. The sequence data indicate that all of these phages DNA contain short inverted terminal repeats: 5'A-A-A-G-T-A for phi 29 and phi 15, 5' A-A-A-G-T-A-A-G for Nf and M2Y, and 5' A-A-A-T-A-G-A for GA-1.

Bacteriophage phi 29 infection of Bacillus subtilis minicells

Bacteriophage phi 29 can infect B. subtilis minicells and synthesize all the phage-coded proteins detected in ultraviolet irradiated-infected B. subtilis cells. Synthesis of phage unit-length DNA has been obtained after infection of minicells with phi 29. The DNA can be encapsulated in particles with a sedimentation rate similar to that of phage phi 29 produced in B. subtilis cells. The particles produced in minicells can be adsorbed to B. subtilis cells, but infectivity has not been demonstrated because of the very low burst-size obtained.

SPP1 DNA replicative forms: growth of phage SPP1 in Bacillus subtilis mutants temperature-sensitive in DNA synthesis

The development of bacteriophages SPP1 and phi 29 has been studied in several B. sutilis mutants defective in host DNA replication, under non permissive conditions. Several gene products, involved in the synthesis of host DNA, are required for phi 29 replication, while SPP1 seems to require only the host DNA polymerase III. In addition both phages are unable to grow in a dna A mutant (ribonucleotide reductase). Taking advantage of the fact that SPP1 DNA is actively replicated in several dna mutants at non-permissive temperature, we have studied the structure of the replicative intermediates of this phage in the absence of interfering host DNA synthesis. Fast sedimenting forms of SPP1 DNA can be isolated from phage infected cells and evidence of covalently joined concatemers has been obtained, suggesting the presence of terminally repeated sequences.

Genome-linked protein associated with the 5' termini of bacteriophage phi29 DNA

A DNA-protein complex was isolated from Bacillus subtilis bacteriophage phi29 by sucrose gradient sedimentation or gel filtration in the presence of agents known to break noncovalent bonds. A 28,000-dalton protein was released from this complex by subsequent hydrolysis of the DNA. The DNA-protein complex was examined for its susceptibility to enzymes which act upon the 5' and 3' termini of DNA molecules. It was susceptible to exonucleolytic degradation from the 3' termini by exonuclease III but not from the 5' termini by lambda exonuclease. Attempts to label radioactively the 5' termini by phosphorylation with T4 polynucleotide kinase were unsuccessful despite prior treatment with alkaline phosphatase or phosphatase treatment of denatured DNA. Removal of the majority of the bound protein by proteolytic digestion did not increase susceptibility. These results suggest that the linked protein is covalently attached to the 5' termini of phi29 DNA.

Evidence that the neck appendages are adsorption organelles in Bacillus subtilis bacteriophage phi29

A mutant of Bacillus subtilis unable to adsorb phage phi29 efficiently has been isolated. This mutant can be infected by host range mutants of the phage. Since the host range mutations map in cistron 12, which codes for neck appendage protein, this would tend to confirm that these organelles are involved in viral adsorption.

Order of the two major head protein genes of bacteriophage phi 29 of Bacillus subtilis

Bacteriophage phi 29 mutation sus8(22) has been mapped by two-factor crosses between markers sus8(769) and ts8(93). Whe sus8(22) infects Bacillus subtilis su- proteins, HP1 (major head protein) and HP3 (fiber protein) are not synthesized; instead, a fragment with a molecular weight of 25,000 is produced. The tryptic peptides of the fragments overlap with corresponding peptides in protein HP1, but not with the peptides of protein HP3, showing that cistron 8 codes for the major head protein HP1.

Morphogenesis of bacteriophage phi 29 of Bacillus subtilis: mapping and functional analysis of the head fiber gene

A set of mutants of Bacillus subtilis bacteriophage phi29 unable to synthesize the head fiber protein has been identified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography. Infectious phage are produced during restrictive infection. We have focused on mutant sus 8.5(900) because the mutation is suppressible by both the su(+3) and su(+44) hosts, and it can be mapped by three- and four-factor crosses. After restrictive infection with mutant sus 8.5(900), a fragment about 70% of the size of the normal fiber is produced as well as particles that are fast-sedimenting in sucrose gradients relative to phi29(+). These particles have the buoyant density of particles with the fibers removed and have the absolute plating efficiency of phi29(+). Fiber protein is absent from prohead as well as virion. A second set of mutants produces fiber protein with a slightly altered electrophoretic mobility. This type of fiber protein is either present or absent on both prohead and virion. A third class of mutants, typified by 914, produces a "normal" fiber, but a major head protein of altered electrophoretic mobility. After infection by this mutant, the fiber is absent from both prohead and virion, and the biological and physical properties of the 914(-) particle are similar to those of particles produced after infection of the su(-) host by sus8.5(900). These observations suggest that the head fiber is not an essential component of the prohead or virion and that the assembly process is efficient in the absence of fiber protein. Three- and four-factor genetic crosses have established the order sus8(769)-8(914)-sus8.5(900)-sus9(756) and indicate that cistrons 8 and 8.5 code for the major head protein and head fiber protein, respectively.

Transcription of the genome of bacteriophage phi 29: isolation and mapping of the major early mRNA synthesized in vivo and in vitro

The phi29 early mRNA's synthesized in infected Bacillus subtilis were studied by using sedimentation velocity analysis, polyacrylamide gel electrophoresis, and hybridization of phi29 DNA fragments generated by the restriction endonuclease Eco RI. Viral RNAs synthesized in vivo in the resence of chloramphenicol were found to hybridize to Eco RI-A, -C, and -D fragments, but not to Eco RI-B and -E fragments, of the viral genome. Major early mRNA sedimenting as 16S material in neutral sucrose gradients was examined in detail. Radioactive phi29 RNA, purified by sucrose gradient centrifugation, was hybridized to either the Eco RI-A or Eco RI-C DNA fragment. The RNA was eluted from the hybrids and then tested for complementary hybrid formation with Eco RI-A and -C fragments. RNA eluted from the Eco RI-A fragment annealed only to the Eco RI-A fragment and not to the Eco RI-C fragment. Similarly, RNA eluted from the Eco RI-C fragment hybridized to the Eco RI-C and -D fragments. Viral RNAs synthesized in vitro using B. subtilis RNA polymerase hybridized to both Eco RI-A and -C DNA fragments. Furthermore, RNA initiated with [gamma-(32)P]GTP also hybridized to both Eco RI-A and -C fragments. These results indicate that there are at least two efficient promotors for early transcription on the phi29 chromosome. In addition, a low-molecular-weight RNA initiated with [gamma-(32)P]ATP was found to hybridize exclusively with the Eco RI-A fragment. Kinetic studies of phi29 mRNA synthesis during the lytic cycle have shown that viral RNAs hybridizable to the Eco RI-A and -C fragments are synthesized immediately after phage infection. On the other hand, mRNA specific for the Eco RI-B fragment was not synthesized for several minutes after phage infection. Based on the results of the in vivo and in vitro transcription studies, a transcription map of the phi29 chromosome is proposed.

DNA replication of bacteriophage phi29. Effect of two viral genes on the association of phage chromosomes with the host cell membrane

The kinetics of DNA arrest and the maintenance of the association of viral chromosomes with the cell membrane were examined by temperature-shift experiments using temperature-sensitive mutants in two early bacteriophage phi29 genes required for phage DNA replication. phi29 ts2(35), a mutant in cistron 2 whose product (protein P2) is continuously required for associating phage DNA with the Bacillus subtilis membrane, does not stop phage DNA synthesis immediately after a shift to the nonpermissive temperature. In contrast, bacteria infected with phi29 ts3(28), a mutant in cistron 3 (which codes for protein P3), stop synthesizing phage DNA immediately after transfer to the nonpermissive temperature. Parental phage DNA in phi29 ts2(35) infections rapidly dissociates from the cell membrane after a shift to 45 degrees, whereas phi29 ts3(28) DNA remains associated with the membrane after the shift to the nonpermissive temperature and then slowly dissociates. Thus the rapid dissociation of parental phage phi29 chromosomes from the membrane is dependent on a functional protein P3. These findings are discussed in terms of possible modes of action of these two proteins and suggest that protein P2 operates as a linker of phage chromosomes to the membrane, whereas protein P3 participates directly in the initiation or in the polymerization of viral DNA molecules.

Assembly of Bacillus subtilis phage phe29. 2. Mutants in the cistrons coding for the non-structural proteins

The effect on phage morphogenesis of sus mutations in the cistrons coding for nonstructural proteins has been studied. Mutants in three cistrons analyzed that are involved in phage DNA synthesis, as well as in cistron 16 which codes for a late nonstructural protein, produce prolate capsids which are more rounded at the corners than complete phage heads and have an internal core; they contain the head proteins, the upper collar protein and protein p7, not present in mature phage particles. Mutants in cistron 7 do not produce capsids nor other phage-related structures; this result and the presence of p7 in phage capsids suggest an essential role in capsid assembly for this protein. The protein product of cistron 13 is probably needed for a stable DNA encapsulation since mutants in this cistron produce mainly DNA-free complete phage particles and only about 10% of uninfective DNA-containing complete phage. Cistron 15 codes for a late, partially dispensable, nonstructural protein which is present in the DNA-free capsids produced after infection with the delayed-lysis mutant sus14(1242), used as the wild-type control, or with mutants in cistrons 9, 11,12 and 13. Proteins p15 and p16 are probably involved in the encapsulation of viral DNA in a prohead.

Assembly of Bacillus subtilis phage phi29. 1. Mutants in the cistrons coding for the structural proteins

The effect of mutations in the cistrons coding for the phage structural proteins has been studied by analyzing the phage-related structures accumulated after restrictive infection. Infection with susmutants in cistron 8, lacking both the major head and the fiber protein, does not produce any phage-related structure, suggesting a single route for the assembly of phage phi29; infection with ts mutants in this cistron produces isometric particles. Mutants is cistron 9, coding for the tail protein, TP1, produce DNA-free prolate heads with an internal core; these particles are abortive and contain the head proteins HPO, HP1 and HP3, the upper collar protein NP2 and the nonstructural proteins p7, p15 and p16. Mutants in cistron 10, coding for the upper collar protein, NP2, produce DNA-free isometric heads also with an internal core; they contain the head proteins and the nonstructural protein p7, suggesting that this protein forms the internal core. Mutants in cistrons 11 and 12, coding for the lower collar protein, NP3, and the neck appendages, NP1, respectively, give rise to the formation of DNA-containing normal capsids and DNA-free prolate particles, more rounded at the corners than the normal capsids and with an internal core; the DNA-containing 11-particles are formed by the head proteins and the upper collar protein; the DNA-free 11-particles contain, besides these proteins, the nonstructural protein p7 and a small amount of proteins p15 and 16. The DNA-containing 12-particles have all the normal phage structural proteins except the neck appendages, formed by protein NP1; the DNA-free particles are similar to the DNA-free 11-particles. After restricitive infection mutant sus14(1241) has a delayed lysis phenotype and produces a phage burst higher than normal, after artificial lysis. It produces DNA-containing particles, identical to wild-type phage, which have all the normal phage structural proteins, and DNA-free prolate particles, more rounded at the corners than the final phage particles and with an internal core; the last particles contain the same proteins as the DNA-free 11 or 12-particles. These particles could represent a prohead state, ready for DNA encapsulation. None of the DNA-containing particles have the nonstructural proteins p7, p15 or p16, suggesting that these proteins are released from the proheads upon DNA encapsulation.

Transcription in vitro of phi29 DNA and EcoRI fragments by Bacillus subtilis RNA polymerase

EcoRI fragments A, B and C produced from linear phi29 DNA, but not D or E fragments, are transcribed by purified Bacillus subtilis RNA polymerase. The transcription of fragments A and C is initiated preferentially with GTP and to a lesser extent with ATP; the reverse happens in the case of fragment B. The dinucleotides GpU and GpA respectively, compete specifically with the incorporation of [gamma-32P]GTP directed by fragments A and C. The RNA synthesized in vitro by purified B. subtilis RNA polymerase is highly asymmetric. Most of the RNA synthesis directed by fragments A and C is early RNA. However, most of the RNA produced by fragment B is anti-late-RNA. Addition of crude extracts inhibit the transcription of fragment B but not that of fragments A and C.

Morphogenesis of bacteriophage phi 29 of Bacillus subtilis: preliminary isolation and characterization of intermediate particles of the assembly pathway

Three classes of particles have been identified in restrictive phi 29 suppressor-sensitive (sus) mutant infections of Bacillus subtilis, including DNA-containing heads or phage, prohead, and empty heads. Pulse-chase labeling experiments indicate that the prohead, the first particle assembled in 14-infected cells, is converted to DNA-filled heads and phi 29. In addition to the proteins Hd, P10, and F found in mature phi 29, the prohead contains a "core" protein P7 that exits as the prohead matures and appears to recycle during subsequent rounds of prohead assembly. Prohead-like structures accumulate in UV-irradiated cells and are present in restrictive infections with sus mutants of cistrons 9 and 16. Empty heads are observed only when infection results in the formation of DNA-containing particles; this and other evidence indicates that the empty heads are probably not true intermediates. Phage phi 29 assembly apparently occurs by a single pathway in which neck and tail components interact to stabilize the completed DNA-containing head.

Analysis of gene function of bacteriophage phi 29 of Bacillus subtilis: identification of cistrons essential for viral assembly

Restrictive infection of Bacillus subtilis by suppressor-sensitive (sus) mutants of phi 29 has been used to search for cistrons that function in viral assembly. The products of cistrons 7, 9, 10, and 16 are necessary for head morphogenesis. The neck upper collar protein P10 and the tail protein P9 must be present for DNA packaging to occur. The protein P7 must be present for phage-related particles to form. A prohead-like particle has been isolated during 16-restrictive infection. The particle is composed of the proteins Hd, P10, F, and P7. P16 must function for DNA-filled particles to accumulate. A DNA-containing particle produced in the absence of the cistron 11 product may be an intermediate in the phi 29 assembly pathway. The protein P13 interacts with P9 and P11 to form a stable DNA-filled particle. The products of cistrons 2 and 3 are essential for viral DNA synthesis, and in their absence virus-related particles are not detected.

Genetic analysis of bacteriophage phi 29 of Bacillus subtilis: integration and mapping of reference mutants of two collections

Reference mutants of Bacillus subtilis phage phi 29 of the Madrid and Minneapolis collections were employed to construct a genetic map. Suppressor-sensitive and temperature-sensitive mutants were assigned to 17 cistrons by quantitative complementation. Three-factor crosses were used to assign an unambiguous order for the 17 cistrons. Recombination frequencies determined by two-factor crosses were used to construct a linear genetic map of 24.4 recombination units. The genes were numbered sequentially from left to right (1 to 17) according to their relative map position.

Bacillus subtilis phage phi29. Characterization of gene products and functions

A total of 22 phi29-induced proteins have been resolved by slab gel electrophoresis; two of these proteins are the precursor and product fragment, respectively, in the synthesis of the neck appendage protein of the phage. The protein products of 10 out of the 17 cistrons detected in the genome of phage phi29 have been identified. Mutants in two other cistrons fail to synthesize two proteins. Mutants in six genes do not synthesize phage DNA. A cistron, probably involved in the final lysis of the infected bacteria, has been found. Mutants in this gene give place, under restrictive conditions, to delayed lysis and produce, after artificial lysis, a burst size similar or higher than that obtained after wild-type phage infection.

Isolation of a strong suppressor of nonsense mutations in Bacillus subtilis

By treatment of Bacillus subtilis MO-101-P spoA- met thr- su- with ethyl methanesulfonate, a strong suppressor strain of nonsense mutations, B. subtilis MO-101-P spoA- [met-]+thr- su+44, was isolated. This strain does not suppress phage phi 29 mutant susB47, selected on a B. subtilis strain containing the su+3 suppressor isolated by Georgopoulos. A revertant from this mutant, susB610, was isolated, being suppressed by both the su+3 and su+44 suppressor strains. The efficiency of suppression by strain su+44 is about 50%. The experiments shown in this paper suggest that strain su+44 contains an amber and strain su+3 an ochre suppressor.

Morphogenesis of bacteriophage phi29 of Bacillus subtilis: cleavage and assembly of the neck appendage protein

Each of the 12 neck appendages of the Bacillus subtilis bacteriophage phi29 consists of a single protein molecule with a molecular weight of about 75,000, and on the mature virion the appendages are assembled to the lower of two collars. The appendage protein is cleaved from a precursor protein, P(J), with a molecular weight of about 88,000. This cleavage is independent of neck assembly, occurring during infection by mutants that cannot synthesize the proteins of the upper and lower collars of the neck. The cleaved form of the appendage protein is efficiently complemented in vitro to particles lacking appendages. Thus, cleavage of the appendage precursor protein apparently does not occur in situ on the maturing virus.

Genetic analysis of bacteriophage phi29 of Bacillus subtilis: mapping of the cistrons coding for structural proteins

Four phage phi29 suppressor-sensitive mutants of cistron O have been examined for production of 14C-labeled viral-specific proteins in restrictive infections of Bacillus subtilis and fail to produce the protein of the viral neck lower collar. Cistrons O and F have been placed on the genetic map, containing 12 cistrons, by three-factor crosses. The phenotypes of five cistron J mutants have been analyzed by sodium dodecyl sulfate gel electrophoresis and autoradiography, and in three instances fragments of the normal polypeptide were detected. Three factor crosses with these mutants and a virus with a clear plaque phenotype were used to initiate the mapping of cistron J and the determination of the orientation of transcription in this map region.

Bacteriophages of Bacillus subtilis

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