Congruent transcriptional controls and heterology of base sequences in coliphages lambda and phi-80

Genome of Enterobacteriophage Lula/phi80 and insights into its ability to spread in the laboratory environment

The novel temperate bacteriophage Lula, contaminating laboratory Escherichia coli strains, turned out to be the well-known lambdoid phage phi80. Our previous studies revealed that two characteristics of Lula/phi80 facilitate its spread in the laboratory environment: cryptic lysogen productivity and stealthy infectivity. To understand the genetics/genomics behind these traits, we sequenced and annotated the Lula/phi80 genome, encountering an E. coli-toxic gene revealed as a gap in the sequencing contig and analyzing a few genes in more detail. Lula/phi80's genome layout copies that of lambda, yet homology with other lambdoid phages is mostly limited to the capsid genes. Lula/phi80's DNA is resistant to cutting with several restriction enzymes, suggesting DNA modification, but deletion of the phage's damL gene, coding for DNA adenine methylase, did not make DNA cuttable. The damL mutation of Lula/phi80 also did not change the phage titer in lysogen cultures, whereas the host dam mutation did increase it almost 100-fold. Since the high phage titer in cultures of Lula/phi80 lysogens is apparently in response to endogenous DNA damage, we deleted the only Lula/phi80 SOS-controlled gene, dinL. We found that dinL mutant lysogens release fewer phage in response to endogenous DNA damage but are unchanged in their response to external DNA damage. The toxic gene of Lula/phi80, gamL, encodes an inhibitor of the host ATP-dependent exonucleases, RecBCD and SbcCD. Its own antidote, agt, apparently encoding a modifier protein, was found nearby. Interestingly, Lula/phi80 lysogens are recD and sbcCD phenocopies, so GamL and Agt are part of lysogenic conversion.

Complementary Strands of Bacteriophage phi29 Deoxyribonucleic Acid: Preparative Separation and Transcription Studies

Bacillus subtilis phage phi29 has a nonpermuted, duplex deoxyribonucleic acid (DNA) with cohesive ends and a molecular weight of 11 x 10(6). Denaturation of this DNA yielded two intact polynucleotide chains. Preferential binding of the polyribonucleotide polyuridylic-guanylic acid (poly UG) to the complementary strands of denatured phi29 DNA permitted separation of the strands in neutral CsCl gradients. In analytical CsCl density gradient centrifugation, the separated strands with poly UG appeared as two symmetrical bands, both heavier than the normal denatured DNA band. The strands differed in density by 11 mg/cc. Preparative separation of the phi29 DNA strands resulted in two fractions, heavy (H) and light (L). The H fraction was essentially free from L contamination, whereas L contained up to 25% of H, as determined both by rebanding the separated fractions in CsCl and by electron microscopic examination of self- and mixed-annealed fractions. Pulse-labeled ribonucleic acid (RNA) prepared at intervals after infection was hybridized with the self-annealed DNA strands. Preliminary experiments indicated that both strands of phi29 DNA are transcribed during the development of the virus. Early transcribed phi29-specific RNA hybridizes only with the L strand; at later times, transcription occurs from both the L and H strands.

Organization of the early region of bacteriophage phi 80. Genes and proteins

An EcoRI segment containing the early region of bacteriophage phi 80 DNA that controls immunity and lytic growth was identified as a segment whose presence on a plasmid prevented growth of infecting phi 80cI phage. The nucleotide sequence of the segment (EcoRI-F) and adjacent regions was determined. Based on the positions of amber mutations and the sizes of some gene products, the reading frames for five genes were identified. From the relative locations of these genes in the genome, the properties of some isolated gene products, and the analysis of the structures of predicted proteins, the following phi 80 to lambda analogies are deduced: genes cI and cII to their lambda namesakes; gene 30 to cro; gene 15 to O; and gene 14 to P. An amber mutation by which gene 16 was defined is a nonsense mutation in the frame for gene 15 protein, excluding the presence of gene 16. An amber mutation in gene 14 or 15 inhibits phage DNA synthesis, as is the case with their lambda analogues, gene O or P. Some characteristics of proteins from the early region predicted from their primary structures and their possible functions are discussed.

Transcriptional regulation of early functions of bacteriophage phi 80

To study the expression of early functions of phi 80 phage, various segments from the early region were transcribed with RNA polymerase. Two major transcripts (from promoters PL and PR) whose synthesis was inhibited by the CI protein were identified. Synthesis of the third major transcript (from promoter PRM) was induced by the CI protein. These studies define two operator-promoter regions, OLPL and ORPRPRM. This mode of transcription from the early region is similar to that of phage lambda. However, there are the following major differences. One is the presence of a p-independent terminator of transcription from promoter PL located immediately after gene N and the absence of a p-dependent terminator that corresponds to tR1 of lambda. The other is the uniqueness of the structure and function of the operators. Both OL and OR operator regions consist of three sites, each containing a highly homologous 19 base-pair sequence. In each site, consensus octanucleotide sequences (half-sites) exhibit dyad symmetry, except in one of the sites where the sequences are arranged tandemly. In addition, each operator region also contains a single half-site. The modes of binding of the CI protein and gene 30 protein to these operator sites are quite different from those of the lambda proteins to the lambda operators. For example, binding of the phi 80 CI protein to the OR1 site is less tight than its binding to the OR2 or OR3 site. The gene 30 protein binds to the OR1 site as tightly as to the OR3 site.

Identification and purification of the N gene product of bacteriophage phi 80

To confirm the in vivo observation that the N gene product of phi 80, phi 80-pN, prevents termination of transcription at the tL1 region and is therefore a transcription antitermination factor (Tanaka and Matsushiro 1985), we demonstrated that phi 80-tL1 is a rho-dependent terminator, similar to lambda-tL1, and that phi 80-pN has a transcription antitermination function at this site in an in vitro transcription system using a nucleic acid-free S-100 extract. In the presence of rho-protein, transcription termination at tL1 was suppressed completely with an S-100 extract prepared from Escherichia coli strain NT525 containing the pBN1-N+ plasmid. Starting from this pN-overproducing cell extract, we purified phi 80-pN to homogeneity by chromatography on DEAE-Sephacel, Sephadex G-150 and CM-Sephadex C-50. The molecular weight of purified pN was about 12,000 and the NH2-terminal sequence was NH2-Met-Ile-Asp-Asp-Ile-Lys, which was consistent with the sequence deduced from the DNA sequence.

A phi 80 function inhibitory for growth of lambdoid phage in him mutants of Escherichia coli deficient in integration host factor. I. Genetic analysis of the Rha phenotype

Bacteriophage phi 80 and lambda-phi 80 hybrid phage of the type lambda (QSR)80, in which the rightmost 10% of the lambda genome is replaced by corresponding phi 80 material, are unable to grow lytically in himA and hip/himD mutants of Escherichia coli K12 at 32 degrees. The genetic element responsible for the growth defect, rha, has been mapped to the (QSR)80 region and was located more precisely by restriction enzyme and DNA heteroduplex analysis of mutations that result in loss of the Rha phenotype. Such an Rha mutant carrying a 1.5-kb deletion beginning 0.58 kb from the right end of the chromosome and extending leftward locates the rha locus at least in part within this region of (QSR)80. In addition, a substitution derivative of lambda (QSR)80 was isolated which does not exhibit the Rha phenotype. In this phage, lambda-80hy95, the right half of the (QSR)80 region is replaced by DNA homologous to the 95-100% segment of lambda. In mixed infections in the himA42 host at 32 degrees, lambda + does not complement lambda (QSR)80 for growth and the burst size of the coinfecting lambda + is reduced in comparison to that in a single infection. Deletion mutants of lambda (QSR)80 that grow normally in himA42 at 32 degrees in single infections are inhibited for growth in mixed infections with lambda (QSR)80. These results suggest the existence of a trans-acting function which inhibits phage growth in the absence of HimA or Hip/HimD function. It is likely that the rha gene either encodes that function or indirectly controls its action.

Integration of bacteriophages lambda and phi 80 in wild-type Escherichia coli at secondary attachment sites. I. Formation of secondary lysogens

The family of lambdoid phages displays a varying specificity of integration into the host chromosome. The lambda phage DNA failed to get inserted at the secondary site(s) of the gal operon (frequency less than 2.6 X 10(-8) in the presence of the primary (normal) att site. By contrast, phi 80 and the lambda att80 hybrid (lambda X phi 80) became integrated into wild-type Escherichia coli at at least two secondary att sites of the btuB locus, and the latter near purE and purC as well (frequency 2 X 10(-3)-10(-4). The integration of phi 80 and lambda att80 into btuB occurred with about the same frequency as in cells in which the normal insertion site had been deleted (0.7-4.0 X 10(-6). An analysis of the secondary lysogens with the prophage in btuB showed them to be polylysogens; the additional prophage(s) was found at the primary att site. We also failed to observe the integration into other loci of phi 80 and lambda att80 with the formation of secondary monolysogens (frequency less than 0.0035 at MOI = 10(-3) or 10). It is presumed that these prophages become integrated at secondary att sites only if the primary site is occupied.

Genetics of bacteriophage phi 80--a review

The genetic maps of bacteriophage lambda and lambdoid phage phi 80 are compared. The gene organization of phi 80 is very similar to that of lambda, as shown by isolation and characterization of many am, ts and c (clear) mutants of the phage. In general, the essential genes located in the same position on the genetic map of the phages lambda and phi 80 fulfill the same functions. These include the gene clusters coding for the head and tail proteins, genes for DNA synthesis, and the genes controlling lysogeny and late gene expression. The specific regulatory features of phi 80 in relation to the N function of lambda are discussed, but they require further clarification. The two phages differ in immunity specificity, host range, conversion property and temperature sensitivity.

Regulation of transcription and DNA replication of bacteriophage phi 80

Transcriptional mapping and DNA replication measurements have been used to characterize a series of phi 80 suppressor-sensitive mutants which are defective in genes 15, 14, 16, and 17. These genes are localized within the inner right arm of the vegetative phi 80 DNA genome. The sus326 mutation in gene 15 leads to a decrease in major leftward (pL-att80) RNA levels and to a marked pleiotropic reduction in major rightward RNA synthesis; however, phi 80 DNA synthesis is reduced only moderately (about two-fold). These findings are consistent with the gene 15 product being a positive control regulator that is essential for normal transcriptional development, in particular, beyond a termination signal(s) (tR) located between genes 16 and 17. The sus8 and sus258 mutations (in genes 14 and 16, respectively) lead to severe blockage of both major rightward RNA transcription and phi 80 DNA synthesis. The products of genes 14 and 16 appear to be required for both autonomous phi 80 DNA replication and the "late" transcriptional development. The sus121 mutation in gene 17 reduces the level of "late" major rightward transcription (gene 17-1-13-att'80 segment) by about 10-fold but does not have any apparent effect on the levels of phi 80 DNA synthesis. These profiles identify the product of gene 17 as a "Q-type" positive control regulator for the "late" major rightward RNA. These studies reveal the functional characterization of four genes, the products of which are necessary for the efficient expression of the "early" RNA transcribed segments, autonomous DNA replication, and the production of normal levels of "late" (17-1-13-att'80) RNA synthesis.

Regulation of early gene expression of bacteriophage phi 80: transcriptional regulation by phi 80 gene 30

The gene30sus620 mutation of bacteriophage phi 80 was mapped close to the left of the cI gene on the standard genetic map. The distance between the mutation (gene30sus620) and the cI gene was about 0.01%, as judged by recombination frequencies. The transcriptional pattern of the mutant showed two distinct differences from that of the wild type; late mRNAs were not synthesized, and early genes were preferentially transcribed rightward in contrast with the predominantly leftward transcription in the wild type. The synthesis of early proteins was also affected. Wild-type phi 80 permits synthesis of five major proteins (pE, pB, pA, pC, and pD) and two minor proteins (pU and pV) upon infection of ultraviolet-irradiated cells. Synthesis of the major proteins was significantly reduced in the mutant, while synthesis of the two minor proteins was enhanced several-fold in this mutant. These results indicate that the gene 30 product regulates the transcription of the two operons in the early region of phi 80, i.e., operon 1, which is transcribed to the left and codes for the five major proteins, and operon 2, which seems to be transcribed to the right and codes for the two minor proteins.

New genes in the left arm of the bacteriophage phi 80 chromosome

We describe the isolation and partial genetic characterization of 247 amber (suppressor-sensitive) mutants of temperate bacteriophage phi 80 of Escherichia coli. Of these 247 mutants, the mutations of 201 mapped to the left arm of the phi 809 chromosome and the mutations of 39 mapped to the right arm of the genome. Complementation tests among these and previously described left arm mutants defined five additional genes in the left arm of the chromosome. The positions of these genes are consistent with the hypothesis that four of them represent functions essential for phi 80 tail assembly and one represents a capsid assembly function, probably the major coat protein. The identification of these genes brings the phi 80 genome into closer correspondence with the organization of the phage lambda genome. Two- and three-factor crosses performed between mutants with defects in each of the previously identified genes and mutants with defects in the five new genes allowed us to construct a consistent, roughly additive recombination map of the left arm of the bacteriophage phi 80 genome.

Metabolism of arginine-specific messenger ribonucleic acid in Escherichia coli K-12

Ribonucleic acid-deoxyribonucleic acid (RNA-DNA) hybridization was employed for the determination of the level of messenger RNA (mRNA) transcribed from seven of the nine genes of the arginine regulon of Escherichia coli K-12. The quantity of RNA complexing with each of the separated DNA strands of the argA, argF, argE, and argCBH operons carried on specialized transducing phages was measured. The derepressed:repressed ratio of mRNA formed in vivo was found to vary between about 3 and 4 when measured by hybridization to DNA isolated from specialized transducing phages carrying the argA, argE, argCBH, argF, and argI operons.

Dual transcription of the tryptophan operon translocated into the early region of gamma

The mode of transcription of the trp operon translocated into the early region of bacteriophage lambda was studied. Synthesis of trp mRNA specific for the translocated trp operon in lambdatrp phage was assayed after infecting a bacteria carrying a deletion mutant (trpAE1), which lacks the whole trp operon but retains a trp regulator gene (trpR). To determine trp mRNA from lambdatrp, phage phi80trp was employed as a source of DNA in hybridization assays. trp mRNA synthesis by lambdatrpE-A, which possesses the intact trp operon, was found to be only partially repressed by fully activated trp repressor in strain trpAE1. On the other hand, trp mRNA synthesis by lambdatrpE-A in strain trpAE1 (lambda), lysogenic for lambda and therefore possessing lambda repressor, was completely repressed when the trp repressor was fully activated by the addition of excess tryptophan. trp mRNA synthesis from the trp operon segment in lambdatrpBA, which carries the trpA and trpB genes but does not possess the trp promoter and operator, was not affected at all by trp repressor but was regulated completely by lambda repressor. The possibility was excluded that the trp mRNA whose synthesis is insensitive to trp repressor is anti-messenger originating from the nonsense(r)-strand of the translocated trp operon of lambdatrp. These observations led to the conclusion that transcription of the translocated trp operon in lambdatrpE-A consists of two types; one is initiated at the trp promoter and is controlled by the trp repressor, another is initiated by a lambda promoter (PL of gene N) and is controlled by the lambda repressor.

Isolation of DNA Strand-specific early messenger RNA species in cells infected by human adenovirus 2

Hybridization to the separated light (L) and heavy (H) strands of adenovirus 2 DNA in 50% formamide at 37 degrees was used to isolate undegraded virus-specific RNA molecules from the polyribosomes of cycloheximide-treated human KB cells early after infection with adenovirus 2. About 20% of polyribosomal RNA labeled with [(3)H]uridine from 4 to 7 hr after infection was virus-specific. Twice as much labeled RNA was homologous to the L strand as to the H strand. Polyacrylamide gel electrophoresis of RNA selected with unfractionated adenovirus DNA resolved a major component of virus-specific RNA in the 19-20 S region of the gel and smaller amounts of viral RNA in two heterogeneous fractions migrating at 15-18 S and 21-26 S. Selection with individual DNA strands showed that the 19-20 S main size class of early mRNA consists of two homogeneous RNA species with slightly different mobilities, the transcripts from the L and H strand having molecular weights of 7.4 x 10(5) and 7.7 x 10(5), respectively. The 15-18 S RNA hybridized with the L strand and the 21-26 S RNA with the H strand.

Size distribution and molecular polarity of newly replicated DNA in Escherichia coli

Newly synthesized DNA, in E. coli lysogenic for the phage lambda, was labeled by short pulses of [(3)H]-thymidine, isolated, and separated on the basis of size by alkaline sucrose density gradient centrifugation. The molecular polarity of this DNA was determined by hybridization with each of the separated strands of lambda DNA. The results show that, in the 3' to 5' direction, replication proceeds by synthesis of short chains that are subsequently joined to long DNA. This is true for both a polA(+) and a polA(-) strain. (The polA locus codes for DNA polymerase I.) In the 5' to 3' direction, replication proceeds continuously, by addition of nucleotides to long DNA, for the polA(+) strain. In the polA(-) strain, however, replication in the 5' to 3' direction is also discontinuous, but the discontinuities are 1-40 times less frequent than in the other direction.