Specificity determinants for bacteriophage lambda DNA replication. II. Structure of O proteins of lambda-phi80 and lambda-82 hybrid phages and of a lambda mutant defective in the origin of replication

Characterization of a newly discovered putative DNA replication initiator from Paenibacillus polymyxa phage phiBP

The bacteriophage phiBP contains a newly discovered putative replisome organizer, a helicase loader, and a beta clamp, which together may serve to replicate its DNA. Bioinformatics analysis of the phiBP replisome organizer sequence showed that it belongs to a recently identified family of putative initiator proteins. We prepared and isolated a wild type-like recombinant protein, gpRO-HC, and a mutant protein gpRO-HCK8A, containing a lysine to alanine substitution at position 8. gpRO-HC had low ATPase activity regardless of the presence of DNA, while the ATPase activity of the mutant was significantly higher. gpRO-HC bound to both single- and double-stranded DNA substrates. Different methods showed that gpRO-HC forms higher oligomers containing about 12 subunits. This work provides the first information about another group of phage initiator proteins, which trigger DNA replication in phages infecting low GC Gram-positive bacteria.

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.

Complementation Studies of Bacteriophage λ O Amber Mutants by Allelic Forms of O Expressed from Plasmid, and O-P Interaction Phenotypes

λ genes O and P are required for replication initiation from the bacteriophage λ origin site, oriλ, located within gene O. Questions have persisted for years about whether O-defects can indeed be complemented in trans. We show the effect of original null mutations in O and the influence of four origin mutations (three are in-frame deletions and one is a point mutation) on complementation. This is the first demonstration that O proteins with internal deletions can complement for O activity, and that expression of the N-terminal portion of gene P can completely prevent O complementation. We show that O-P co-expression can limit the lethal effect of P on cell growth. We explore the influence of the contiguous small RNA OOP on O complementation and P-lethality.

Arrest of Viral Proliferation by Ectopic Copies of Its Cognate Replication Origin

The initiation step of DNA replication is the crucial determinant of proliferation in all organisms. This step depends on the specific interaction of DNA sequences present at origins of DNA replication and their cognate activators. We wished to explore the hypothesis that the presence of ectopic origin copies may interfere with proper genome duplication. Bacteriophage λ was used as a model system. To this end, the outcome of an infection of an E. coli strain harboring ectopic copies of the λ origin region was analyzed. By measuring the effect on the host growth, viral production, and electro-microscopic visualization of the resulting λ replicative intermediates, we concluded that the ectopic copies had prevented the normal initiation step of λ DNA replication. These results suggest that DNA decoys encoding viral origins could constitute effective tools to specifically arrest viral proliferation.

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.

Molecular clocks and evolutionary relationships: possible distortions due to horizontal gene flow

This paper discusses recent evidence suggesting that genetic information from one species occasionally transfers to another remotely related species. Besides addressing the issue of whether or not the molecular data are consistent with a wide-spread influence of horizontal gene transfer, the paper shows that horizontal gene flow would not necessarily preclude a linear molecular clock or change the rate of molecular evolution (assuming the neutral allele theory). A pervasive influence of horizontal gene transfer is more than just consistent with the data of molecular evolution, it also provides a unique explanation for a number of possibly conflicting phylogenies and contradictory clocks. This phenomenon might explain why some protein clocks are linear while the superoxide dismutase clock is not, how the molecular data on the phylogeny of apes and Australian song birds are not necessarily in conflict with those based on morphology, and, finally, why the mycoplasmas have an accelerated molecular clock.

Specialized nucleoprotein structures at the origin of replication of bacteriophage lambda: complexes with lambda O protein and with lambda O, lambda P, and Escherichia coli DnaB proteins

The O protein of bacteriophage lambda is required for initiation of DNA replication at the lambda replicative origin designated ori lambda. The binding sites for O protein are four direct repeats, each of which is an inverted repeat. By means of electron microscopy, we have found that phage lambda O protein utilizes these multiple binding sites to form a specific nucleoprotein structure in which the origin DNA is inferred to be folded or wound. The phage lambda O and P proteins and host DnaB protein interact at ori lambda to generate a larger structure than that formed by O protein alone; P and DnaB proteins fail to form any observable complex when O protein is excluded from the reaction mixture. We conclude that the specialized nucleoprotein structure formed by phage lambda O protein and ori lambda provides for localized initiation of DNA replication by serving as the foundation for the assembly of the initial priming structure. Specialized nucleoprotein structures may be a general means to confer exceptional accuracy on DNA transactions requiring extraordinary precision.

Comparative sequence and functional analysis of pT181 and pC221, cognate plasmid replicons from Staphylococcus aureus

The nucleotide sequence of pC221, a 4.6 kb Staphylococcus aureus plasmid is presented. The replication region of the plasmid is identified and compared with the corresponding region of pT181, a compatible but related plasmid. Both plasmids encode trans-active replicon-specific initiator proteins, RepC for pT181 and RepD for pC221. Plasmid replication rate is controlled by regulation of the rate of synthesis of the initiator protein by means of inhibitory 5' countertranscripts. Key elements of the control system are closely conserved between the two plasmids whereas less critical elements show extensive divergence. Overall architecture is also conserved, suggesting functional parallelism. The replication origin for both plasmids is contained within the N-terminal region of the initiator protein coding sequence; the two coding sequences are highly homologous but have two important areas of divergence, one within the origin region, the other near the C-terminus. In vivo recombinants between the two plasmids isolated previously (Iordanescu 1979) have crossover points within the initiator gene, between the two divergent regions. The recombinant plasmids have hybrid initiator proteins and are defective for replication, requiring the simultaneous presence of the parental plasmid from which their origin is derived. They are able to complement replication-defective mutants of the other parental plasmid, suggesting that the recognition specificity of the hybrid initiator protein resides in its C-terminal end and that the specific recognition site for the protein corresponds to the divergent region within the origin.

The terminase of bacteriophage lambda. Functional domains for cosB binding and multimer assembly

Terminase is a protein complex involved in lambda DNA packaging. The subunits of terminase, gpNul and gpA, are the products of genes Nul and A. The actions of terminase include DNA binding, prohead binding and DNA nicking. Phage 21 is a lambdoid phage that also makes a terminase, encoded by genes 1 and 2. The terminases of 21 and lambda are not interchangeable. This specificity involves two actions of terminase; DNA binding and prohead binding. In addition, the subunits of lambda terminase will not form functional multimers with the subunits of 21 terminase. lambda-21 hybrid phages can be produced as a result of recombination. We describe here lambda-21 hybrid phages that have hybrid terminase genes. The packaging specificities of the hybrids and the structure of their genes were compared in order to identify functional domains of terminase. The packaging specificities were determined in vivo by complementation tests and helper packaging experiments. Restriction enzyme site mapping and sequencing located the sites at which recombination occurred to produce the hybrid phages. lambda-21 hybrid 51 carries the lambda A gene, and a hybrid 1/Nul gene. The crossover that produced this phage occurred near the middle of the 1 and Nul genes. The amino-terminal portion of the hybrid protein is homologous to gp1 and the carboxy-terminal portion is homologous to gpNul. It binds to 21 DNA and forms functional multimers with gpA, providing evidence that the amino-terminal portion of gpNul is involved in DNA binding and the carboxy-terminal portion of gpNul is involved in the interaction with gpA. lambda-21 hybrid 54 has a hybrid 2/A gene. The amino terminus of the hybrid protein of lambda-21 hybrid 54 is homologous with gp2. This protein forms functional multimers only with gp1, providing evidence that the amino terminus of gpA is involved in the interaction with gpNul. These studies identify three functional domains of terminase.

Sequence analysis of a region from the early right operon in phage P22 including the replication genes 18 and 12

A comparison of a 3000-bp sequence of Salmonella phage P22, coding for gene c1 and the replication genes 18 and 12, with the analogous cII-O-P region of coliphage lambda permits the localization of transcriptional signals, an oop RNA species, and the origin of replication (ori) within gene 18. Gene c1 and the amino terminal region of gene 18 show homology to the respective lambda genes. In the ori domain of the replicator proteins the homology to phi 82 is most pronounced. Of two lambda:repP22 hybrids (lambda with replication genes of P22) analysed, one codes for a hybrid O/18 protein with 30 N-terminal amino acids coded for by lambda. Gene 12 is nonhomologous to its lambda counterpart (gene P), but closely related to dnaB of Escherichia coli. A ren gene is missing, whereas two open reading frames (ORFs) distal to gene 12 are almost identical to those in the lambda nin region. We try to account for the occurrence and location of highly conserved sequences among the lambdoid phages by assigning them a role in recombinational reassortment of functional units during the evolution of this phage family.

Conserved regions in mammalian beta-globins: could they arise by cross-species gene exchange?

Comparison of the nucleotide sequences from the coding regions of the four mammalian beta-globin genes shows that different parts of these genes have evolved at two different rates. Those codons designating amino acids 1-20, 41-91 and 109-146 have accumulated substitutions in a random fashion as the molecular clock hypothesis would predict. The codons at positions 21-40 and 91 to 108 behave as if they evolved at a much slower rate. Each of the slowly evolved regions contains an intron. Conservation of the coding sequences flanking the introns are hypothesized to be the result of corss-species gene exchange.

Structure and function of mutants in the P gene of bacteriophage lambda leading to the pi phenotype

The location of 14 independently isolated spontaneous pi A and pi B point mutants in the lambda P gene and their base exchanges were determined. It was found that the pi B mutation is one unique type mapping close to other pi A mutants. The number of possible pi A mutation sites could be estimated. The mutation sites are distributed asymmetrically in the gene. The N-terminal half of the protein is unchanged. It is assumed to be required for the interaction with the lambda O protein. The P protein can be changed by substitution of a limited number of amino acids at the C-terminus. All functional proteins of this type have pi character. pi proteins do not appear to have altered intracellular levels or stabilities as compared to wild-type P protein. The plating characteristics of our mutants on two groP- mutants located in the dnaJ and dnaK genes, respectively, are strikingly different.

Bacteriophage lambda initiators: preparation from a strain that overproduces the O and P proteins

A recombinant plasmid was constructed which carries bacteriophage lambda initiator genes O and P under control of tandemly arranged PL and PR promoters. These promoters were repressed by a thermosensitive repressor, cI857, at low temperature, but became active when the culture was incubated at 42 degrees C. Upon elevation of the temperature, the O and P proteins were overproduced to the extent that they constituted several per cent of the total E. coli cellular proteins. Both the O and P proteins have been purified to apparent homogeneity, and were shown to consist of 298 and 233 amino acid residues, respectively. The amino acid composition and the terminal partial amino acid sequence of each protein were determined. Through these analyses, the locations of the O and P genes in the known lambda DNA sequence were determined. The termination codon for the O gene overlaps with the initiation codon for the P gene. The purified O protein binds specifically to the replication origin of lambda (lambda ori) in accordance with our previous observations. The purified P protein inhibits an ATPase activity of dnaB protein.

Primary structure of the replication initiation protein of plasmid R6K

The cistron of the replication initiation protein of plasmid R6K has been cloned into the single-strand DNA vectors M13mp8 and M13mp9 and its complete nucleotide sequence has been determined. The amino acid sequence of the initiator protein as predicted from its nucleotide sequence shows that the protein is lysine rich and weakly basic and has a molecular weight of 35,000, which is in close agreement with that estimated from the mobility in NaDodSO4/acrylamide gels. The secondary structure of the protein, approximately by the probabilistic methods of Chou and Fasman [Chou, P. & Fasman, G. (1978) Adv. Enzymol. 47, 45-148], suggests an NH2-terminal domain of primarily positively charged alpha-helical structure, a core region of interspersed short stretches of random coils and beta-sheets and -turns, and a COOH-terminal domain of alpha-helix.

Purification of bacteriophage lambda O protein that specifically binds to the origin of replication

By means of a nitrocellulose filter binding assay, DNA binding activities among proteins fractionated from extracts of Escherichia coli carrying lambda dv have been surveyed. An activity was found that binds specifically to a fragment of 164 base pairs that specifies the lambda replication origin (lambda ori). This activity was not detected in an extract of cells not carrying the lambda dv plasmid. The activity was detected in extracts of cells carrying a hybrid plasmid in which the entire lambda O gene had been cloned and placed under the control of the lac promoter. Deletion of a 60 base pair segment in the 'amino-terminal region' of the O gene abolished this activity, indicating that the lambda ori binding protein is coded for by the lambda O gene. The ori-specific binding protein was purified by five fractionation steps. The most purified preparation consists of a major polypepide that migrates with a molecular weight of 32,000 in SDS-polyacrylamide gel electrophoresis. Binding of O protein to ori occurs in the absence of other protein aceous components.

Identification of the E. coli dnaJ gene product

We have previously shown that a mutation (groPC259) in the E. coli dnaJ gene renders the cell inviable at high temperatures and arrests bacteriophage lambda DNA replication at all temperatures (Sunshine et al., 1977). We have isolated lambda dnaJ+ transducing phages both by in vitro cloning and by abnormal excision of a lambda dnaK transducing phage integrated near the dnaJ locus. The dnaJ gene product has been identified on SDS polyacrylamide gels after infection of UV-irradiated E. coli cells by lambda dnaJ+ derivative phages. It is a polypeptide chain with an apparent molecular weight of 37,000-daltons. This has been verified by the fact that a transducing phage carrying an amber mutation in the dnaJ gene fails to induce the synthesis of the 37,000-dalton polypeptide chain upon infection of sup+ bacteria, but does so upon infection of supF or supD bacteria.

Inceptor and origin of DNA replication in lambdoid coliphages. II. The lambda DNA maximal replication system

In pBR313-lambda dv hydrid plasmids a second system for initiation of DNA replication has been detected in lambdoid replicator DNAs (in the absence of the p0 promoter). The "maximal" (or "maxi") initiation system depends on the origin of replication (ori) sequence, in conjuction with the "inceptor" (ice) element located in the lambdoid cII genes. Only leftward, but not bidirectional, primer RNA synthesis seems to be initiated at ori in its newly defined boundaries, and it appears to be catalysed by dnaG-coded primase. Only if transcriptionally activated, will ori effectively initiate lambda specific, O and P-dependent "maximal" hybrid-plasmid replication. In addition, it will repress a complete lambda "minimal" initiation system in cis, i.e., if present on the same plasmid molecule. This newly discovered repressive activity of the ori system depends on only three factors: an intact left section of ori, the O product, and transcriptional activation of ori (rightward or leftward). A repressed minimal initiation system will regain its activity as soon as a segment carrying either part of the O gene or a promoter for transcriptional activation is delected from such a plasmid which was combining both the "mini" and "maxi" systems of lambda replication.