DNA sequence of the att region of coliphage 434

Hybrid Vigor: Importance of Hybrid λ Phages in Early Insights in Molecular Biology

Laboratory-generated hybrids between phage λ and related phages played a seminal role in establishment of the λ model system, which, in turn, served to develop many of the foundational concepts of molecular biology, including gene structure and control. Important λ hybrids with phages 21 and 434 were the earliest of such phages. To understand the biology of these hybrids in full detail, we determined the complete genome sequences of phages 21 and 434. Although both genomes are canonical members of the λ-like phage family, they both carry unsuspected bacterial virulence gene types not previously described in this group of phages. In addition, we determined the sequences of the hybrid phages λ imm21, λ imm434, and λ h434 imm21. These sequences show that the replacements of λ DNA by nonhomologous segments of 21 or 434 DNA occurred through homologous recombination in adjacent sequences that are nearly identical in the parental phages. These five genome sequences correct a number of errors in published sequence fragments of the 21 and 434 genomes, and they point out nine nucleotide differences from Sanger's original λ sequence that are likely present in most extant λ strains in laboratory use today. We discuss the historical importance of these hybrid phages in the development of fundamental tenets of molecular biology and in some of the earliest gene cloning vectors. The 434 and 21 genomes reinforce the conclusion that the genomes of essentially all natural λ-like phages are mosaics of sequence modules from a pool of exchangeable segments.

A genetic analysis of Xis and FIS interactions with their binding sites in bacteriophage lambda

The bacteriophage P22-based challenge-phage system was used to study the binding of Xis and FIS to their sites in attP of bacteriophage lambda. Challenge phages were constructed that contained the X1, X2, and F sites within the P22 Pant promoter, which is required for expression of antirepressor. If Xis and FIS bind to these sites in vivo, they repress transcription from Pant, allowing lysogenization to occur. Challenge phages carrying the XIX2F region in either orientation exhibited lysogenization dependent on both Xis and FIS. Neither Xis nor FIS was capable of functioning by itself as an efficient repressor in this system. This was the first time challenge phages have been constructed that require two different proteins bound simultaneously to act as a repressor. Mutations in the X1, X2, and F sites that inhibit Xis and FIS from binding were isolated by selecting mutant phages that still expressed antirepressor synthesis in the presence of Xis and FIS. DNA sequence analysis of the mutants revealed 38 unique mutations, including single-base-pair substitutions, multiple-base-pair changes, deletions, and insertions throughout the entire X1, X2, and F regions. Some of the mutations verified the importance of certain bases within the proposed consensus sequences for Xis and FIS, while others provided evidence that the DNA sequence outside of the proposed binding sites may affect the binding of the individual proteins or the cooperativity between them.

Determinants of site-specific recombination in the lambdoid coliphage HK022. An evolutionary change in specificity

The temperate bacteriophage HK022, like its relative lambda, inserts its chromosome into a specific site in the bacterial chromosome during lysogenization and excises it after induction. However, we find that the recombinational specificities of the two phages differ: they use different bacterial sites, and neither promotes efficient insertion or excision of the other phage chromosome. In order to determine the basis for this difference in specificity, we sequenced the HK022 elements that are involved in insertion and excision, and compared them to the corresponding lambda elements. The location, orientation, size and overall arrangement of the int and xis genes and the phage attachment sites are nearly identical in the two genomes, as is common for other functionally related elements in lambdoid phages. The Xis proteins of the two phages are functionally interchangeable, and their predicted amino acid sequences differ by but one residue. In contrast, the two Int proteins are not functionally interchangeable, and their sequences, although similar, differ at many positions. These sequence differences are not uniformly distributed: the amino-terminal 55 residues are completely conserved, but the remaining 302 show a pattern of differences interspersed with identities and conservative changes. These findings imply that the specificity difference between HK022 and lambda site-specific recombination is a consequence of the inability of the respective Int proteins to recognize pairs of heterologous attachment sites. The two phage attachment sites are remarkably similar, especially the two "arm" segments, which in lambda contain binding sites for Int, Xis and integration host factor. They are less similar in the segment between the two arms, which in lambda contains the points of recombinational strand exchange and a second class of binding site for Int protein (the "core-type" sites). The two bacterial attachment sites are quite different, although both have a short stretch of perfect homology with their respective phage partners at the points of strand exchange. We propose that the two Int proteins recognize similar or identical sites in the arms of their cognate attachment sites, and that differences in binding or action at the core-type sites is responsible for the divergent specificities. Genetic experiments and sequence comparisons suggest that both proteins recognize different but overlapping families of core-type sites, and that divergence in specificity has been achieved by an alternating succession of small, mutually compatible changes in protein and site.

Functional elements of DNA upstream from the integrase operon that are conserved in bacteriophages 434 and lambda

A 1488-bp restriction fragment of bacteriophage 434 DNA contains the integrase promoter and an adjacent nucleotide sequence (t'I) resembling a Rho-independent terminator. To identify and quantitate transcription termination, DNA segments were cloned into a plasmid between the galactose promoter and assayable galactokinase gene and tested for termination. Whereas the entire fragment effectively terminated transcription, a 331-bp restriction fragment containing the t'I terminator had only weak terminator activity. Random sequential deletions of the 434 DNA segment defined a strong terminator 650-bp upstream from t'I. This proposed Rho-independent terminator called tL4 consists of a 7-bp stem and 6-nt loop followed by a uridine-rich region in the RNA. Phage lambda contains an even stronger tL4 terminator that differs in 4 nt from 434 tL4. Thus, despite some sequence divergence, terminator activity has been conserved in these phages. The 434 DNA segment was also tested for promoter activity. Rightward promoter activity (opposite to pL in the phage) was located about 200 bp to the right of tL4 and was followed by an open reading frame (ORF) capable of encoding a 91 amino acid protein. Promoter activity in the same approximate location was also found in phage lambda. Thus the rightward promoter, the tL4 and t'I terminators, and ORF-55 all are elements in this segment of the genome that are conserved for function despite sequence divergence.

Structural and regulatory divergence among site-specific recombination genes of lambdoid phage

The lambdoid bacteriophage phi 80 and P22 have site-specific recombination systems similar to that of lambda. Each of the three phage has a different insertion specificity, but structural analysis of their attachment sites suggests that the three recombination pathways share similar features. In this study, we have identified and sequenced the int and xis genes of phi 80 and P22. phi 80 int and xis were identified using a plasmid recombination assay in vivo, and the P22 genes were mapped using Tn1 insertion mutations. In all three phage, the site-specific recombination genes are located directly adjacent to the phage attachment site. Interestingly, the transcriptional orientation of the phi 80 int gene is opposite to that of lambda and P22 int, resulting in convergent transcription of phi 80 int and xis. Because of its transcriptional orientation, phi 80 int cannot be expressed by the major leftward promoter, PL, and the regulatory strategy of phi 80 integration and excision must differ significantly from that of lambda. The deduced amino acid sequences of the recombination proteins of the three systems show surprisingly little homology. Sequences homologous to the lambda PI promoter are more conserved than the protein-coding sequences. Nevertheless, the Int proteins are locally related in the C-terminal sequences, particularly for a stretch of some 25 amino acid residues that lie approximately 50 residues from the C terminus. The Xis proteins can be aligned at their N termini.

Interaction of the lambda site-specific recombination protein Xis with attachment site DNA

Nuclease protection experiments show that Xis protein of bacteriophage lambda specifically binds attachment (att) site DNA. The region of Xis binding, present in both the phage att site and the right prophage att site, extends from position -102 to position -62 in the P arm. The sequence of this region, the positions of purines protected by Xis against methylation, and the binding of Xis to a resected att site indicate the presence of two binding sites. The postulated recognition elements, contained in 13-base-pair direct repeats separated by 7 base pairs, are situated on the same face of the DNA helix. Protection experiments performed with DNase I suggest that the DNA wraps around (or along the surface of) the bound Xis protein. The Xis binding data presented here establishes that Xis, like the other two proteins involved in lambda site-specific recombination, interacts specifically with att DNA. This rules out that class of models in which the profound effects of Xis on the directionality of site-specific recombination are mediated solely through protein-protein interactions or modification of another protein. In addition, nuclease protection experiments with pairwise combinations of the proteins show that Xis and integration host factor (IHF), or Xis and Int, can bind simultaneously to either the phage or right prophage att sites, and the DNA sequences protected are the sum of those protected with each protein alone. It is therefore unlikely that the effect of Xis on the direction of recombination is exerted by directly blocking the binding of Int or IHF to one or more of their respective binding sites.

Removal of a terminator structure by RNA processing regulates int gene expression

The int gene of phage lambda encodes a protein involved in site-specific recombination. Its expression is regulated differentially during successive phases of the lambda infective cycle. The gene is transcribed early after infection from one promoter, pL, and later from a second promoter pI. Each transcription event requires different positive activation factors, lambda N and cII proteins, respectively. Transcription from the pI promoter, located adjacent to int, passes through int and terminates 277 nucleotides beyond int at tI. Polymerases initiating at pL transcribe through tI and into the b segment of lambda DNA. The read-through pL transcript is sensitive to cleavage by the endonuclease, RNase III, both in vivo and in vitro. Two specific cuts are made by RNase III in a double-stranded structure about 260 nucleotides beyond int in the location of the tI terminator. Functionally, the processed pL transcript is unable to synthesize the int gene product, whereas the terminated and unprocessed pI transcript expresses int. Interestingly, unprocessed pL transcripts made in hosts defective in RNase III (rnc-) can express int. Thus a correlation exists between processing and negative control of int expression. The place where processing occurs, some 260 nucleotides beyond int, is called sib, and the control of int expression from this site is called retroregulation. Retroregulation by sib is not restricted just to the int gene; we show that if the sib site is cloned beyond a bacterial gene, the gene is controlled by sib and RNase III. Specific models are discussed with respect to control of gene expression by RNase III from a site beyond the controlled gene.

Deletion analysis of the retroregulatory site for the lambda int gene

The lambda int gene product, integrase, recombines phage and bacterial DNA at a specific site during the integration step of lysogeny. Regulation of integrase synthesis is complex. (1) Transcription of the gene can occur from either of two promoters. lambda cII protein activates transcription initiation near int at pI. The lambda N protein allows transcription of int from pL. N protein acts by preventing transcription termination at several terminators between pL and int. (2) The expression of integrase is also subject to post-transcriptional regulation by a site, sib, which is located beyond int in the b region of lambda. Expression of int from pL is inhibited by sib, whereas that from pI is not. The negative control of int expression by sib is termed retroregulation. Retroregulation of int is caused, in part, by processing of the pL transcript at the sib site by RNase III of Escherichia coli. The exonuclease, Bal31, was used to generate a set of deletions to define the sib regulatory site. Both sib+ and sib- deletions were sequenced, and it was concluded from this and other work that a dyad symmetry present in the b region, 270 base-pairs from int, was necessary for retroregulation. The RNA structure of this segment is similar to other RNase III-sensitive sites found in E. coli and phage RNAs.

The integrase promoter and T'I terminator in bacteriophages lambda and 434

The lambda integrase promoter PI lies immediately downstream from a terminator T'I. The PI promoter is activated by cII protein during lysogenization. The function of T'I is unknown. A deletion (trp-lambda 29), whose fusion point lies within one stem of T'1 retains cII-activable promoter function but shows little if any transcription termination in vivo. The nucleotide sequence of PI is identical in lambda and the related phage 434. However, the T'I sequences of the two phages, though located in the same position, are not detectably homologous. When restriction fragments carrying the promoter-terminator segments from each of these phages were inserted into the trp operon, both responded identically to cII activation, and both caused termination.

Retroregulation: control of integrase expression by the b2 region of bacteriophages lambda and 434

Genetic fusions constructed by a combination of in vivo and in vitro techniques have been used to investigate the cis-regulatory role of a 250-base-pair segment of b2 DNA in the expression of int transcripts originating from three different promoters PI, PL, and PTRP. It has been established that (a) the PI and PTRP transcripts, which produce functional int protein, are efficiently terminated by the b2 segment, (b) in the same test system, the PL transcript, which does not result in functional integrase, is not terminated by the b2 segment, (c) this b2 (sib) effect does not depend on genes lying between int and N on the phage genome, (d) the sib effect is also observed with the b2 DNA of phage 434, which resembles that of lambda between -197 and att but diverges radically from it to the left of base -197.