Isolation and characterization of deletion mutants affected in early genes of bacteriophage 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.

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.

Cloning and characterization of the immunity region of phage phi 80

The immunity region of phage phi 80 has been localized. It codes for at least three proteins: a protein of 34 kDa which has the biological properties of the phage repressor, and two other proteins of 9 kDa and 18 kDa which are the first proteins on the rightward operon. These two proteins are negatively regulated by the 34 kDa protein at a divergent promoter site. By position analogy with phage lambda, but not by its biological activity, the 9 kDa protein could be the cro product. The 18 kDa protein is able to block totally UV induction of phage phi 80.

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.

Virulent mutants of bacteriophage phi80

We have characterized a collection of 11 phi80 mutants that develop in wild-type lysogenic hosts ("virulent" phenotype). All these carry gross DNA rearrangements affecting the right arm of the phi80 chromosome. Our results are consistent with the notion that phi80 development is negatively controlled by the ineA gene product, encoded by one of a cluster of genes (phi80 immunity) located between the phi80 replication and recombination genes. We describe and assign positions for ineA and other genes within the immunity region.

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.