Genetic population structure, clonal phylogeny, and pathogenicity of Salmonella paratyphi B.

Genetic diversity and relationships among 123 strains of Salmonella paratyphi B (serotype 1,4,[5],12:b:[1,2]) were estimated from an assessment of electrophoretically demonstrable allelic variation at 24 chromosomal enzyme gene loci. Fourteen electrophoretic types, marking clones, were distinguished, the phylogeny of the clonal lineages was reconstructed, and biotype and other phenotypic characters were mapped onto this structure. Most d-tartrate-negative strains are members of an abundant, globally distributed clone (Pb 1) that is polymorphic for many biotype characters (including d-tartrate utilization), bacteriophage type, rRNA pattern, and colicin M and phage ES18 sensitivity. This clone is largely responsible for S. paratyphi B enteric fever in humans. In contrast, d-tartrate-positive strains (formerly known as S. java) occurred in all seven of the clonal lineages identified by population genetic analysis, although most d-tartrate-positive isolates belong to only two clones (Pb 3 and Pb 4), which vary in frequency geographically. Monophasic strains represent four closely related clones forming a distinctive phylogenetic lineage. The Kauffmann hypothesis of convergence in serotype among distantly related cell lineages through recombination (via phage transduction or other means) may account for the considerable genotypic diversity among clones of S. paratyphi B. Pb 4, Pb 6, and Pb 7 are more closely allied with clones of S. typhimurium and S. saintpaul than with other clones of S. paratyphi B. Sensitivity or resistance to colicin M and phage ES18 and the electrophoretic pattern of the rRNA, which were incorporated into a recently proposed scheme for the identification of types of S. paratyphi B, individually or in combination fail to mark clones or other meaningful phylogenetic subdivisions.

Secondary structure and thermostability of the phage P22 tailspike. XX. Analysis by Raman spectroscopy of the wild-type protein and a temperature-sensitive folding mutant.

The thermostable tailspike endorhamnosidase of bacteriophage P22 has been investigated by laser Raman spectroscopy to determine the protein's secondary structure and the basis of its thermostability. The conformation of the native tailspike, determined by Raman amide I and amide III band analyses, is 52 to 61% beta-sheet, 24 to 27% alpha-helix, 15 to 21% beta-turn and 0 to 10% other structure types. The secondary structure of the wild-type tailspike, as monitored by the conformation-sensitive Raman amide bands, was stable to 80 degrees C, denatured reversibly between 80 and 90 degrees C, and irreversibly above 90 degrees C. The purified native form of a temperature-sensitive folding mutant (tsU38) contains secondary structures virtually identical to those in the wild-type in aqueous solution at physiological conditions (0.05 M-Na+ (pH 7.5], at both permissive (20 degrees C) and restrictive (40 degrees C) temperatures. This supports previous results showing that the mutational defect at 40 degrees C affects intermediates in the folding pathway rather than the native structure. At temperatures above 60 degrees C the wild-type and mutant forms were distinguishable: the reversible and irreversible denaturation thresholds were approximately 15 to 20 degrees C lower in the mutant than in the wild-type protein. The irreversible denaturation of the mutant tailspikes led to different aggregation/polymerization products from the wild-type, indicating that the mutation altered the unfolding pathway. In both cases only a small percentage of the native secondary structure was altered by irreversible thermal denaturation, indicating that the aggregated states retain considerable native structure.

In vitro assay of packaging protein gp3 of Salmonella phage P22.

The packaging proteins, gp2 and gp3, of Salmonella phage P22 were separated by DEAE-sephacel column chromatography. The activity of both proteins was measured by complementation in an in vitro phage packaging assay. For the first time gp3 activity was demonstrated in vitro. The majority of the gp3 activity could be separated from gp2. While gp2 was stable during chromatography and storage, gp3 was very unstable. However, it was stable when stored as a crude extract. The ratio and interaction of these two proteins critical for phage maturation are still uncertain.

[DNA structure in the particles of 5 bacteriophages from the data of circular dichroism]. / Struktura DNK v chastitsakh piati bakteriofagov po dannym krugovogo dikhroizma.

DNA optical activities in situ were studied in the particles of five medium sized bacteriophages (SB1, F15; IRA, SD and T7). Delta epsilon in the CD spectrum of intraphage DNA is not shown to correlate with the sizes of phage heads or with the light scattering characteristics of phage suspension. Bacteriophage SB1, studied for the first time, has the amplitude of CD spectrum in the 260-300 nm region higher, than the CD spectrum of its free phage DNA. CD magnitude in the 260-300 nm region is different for varying phages while the red shift of the positive band in the CD spectrum takes place for all phages studied. The dense packing of DNA is suggested to be a common factor for the red shift being observed for all phages. The different delta epsilon in the 260-300 nm region might reflect the different nature in changes of helical DNA geometry inside phage particles as compared with the changes in solutions. The increase in melting temperatures for intraphage DNA as compared with the temperature for free DNA was not shown to correlate with the CD spectrum difference of intraphage DNAs. This property of intraphage DNAs is supposed to be connected with the dense packing of DNA in bacteriophage deoxyribonucleoprotein.

Domain structure and quaternary organization of the bacteriophage P22 Erf protein.

The structure and activities of the recombination-promoting P22 Erf protein were examined in vitro. Treatment of the protein with elastase produces a stable amino-terminal fragment, consisting of amino acid residues 1 to (approximately) 136. We have purified this fragment, designated fragment B, to apparent homogeneity by gel filtration chromatography. Fragment B retains the oligomeric structure and single-stranded DNA binding specificity of intact Erf. It differs, however, in lacking the ability of intact Erf to bind single-stranded DNA into large aggregates following mild heat treatment of the protein. In addition, its binding to DNA may be weaker than that of intact Erf. Intact Erf sediments through a sucrose gradient as a discrete species with an apparent S20,w of approximately 11 X 7 S. Its sedimentation behavior is affected little, if at all, by concentration. Fragment B also sediments as a discrete species at approximately 10 X 4 S. In the electron microscope, intact Erf appears as rings, with 10 to 14 small projecting structures resembling the teeth of a gear. Fragment B is similar, except that it appears to lack the peripheral structures. From these observations, we conclude that Erf consists of at least two structurally and functionally distinct domains, and that it has a discrete ring-like oligomeric structure.

P22 c2 repressor. Domain structure and function.

The c2 repressor of bacteriophage P22 can be digested with trypsin, chymotrypsin, or elastase to yield stable fragments. Purified NH2-terminal fragments, like intact repressor, bind specifically to P22 operator DNA and also mediate positive and negative control of transcription. COOH-terminal fragments of repressor do not bind operator DNA but do undergo a concentration-dependent oligomerization similar to that observed with intact repressor. These results suggest that P22 repressor, like the related cI repressor of phage lambda, contains two structural domains which mediate different functions of the intact molecule.

Primary structure of the immI immunity region of bacteriophage P22.

The DNA sequence of the immI immunity region of bacteriophage P22 has been determined. This region includes the ant gene, which encodes the P22 antirepressor protein, and the mnt and arc genes, which encode proteins that negatively regulate antirepressor synthesis. We have purified antirepressor protein and selected tryptic peptides of antirepressor, and have determined the amino terminal sequences and amino acid composition of these molecules. These data, in combination with the DNA sequence, locate the ant gene and define the complete amino acid sequence of antirepressor (300 residues). The mnt and arc genes have been located by sequencing the mnt-am343 and arc-amH1605 mutations. The Mnt and Arc proteins are predicted to be small, basic polypeptides that are homologous in amino acid sequence. The Mnt protein also shows significant sequence homology with the lambda Cro protein. The arc and ant genes are transcribed rightward from the Pant promoter, while mnt is transcribed leftward from a promotor that may overlap Pant. The Mnt protein apparently acts by binding to an operator site located immediately adjacent to the startpoint of Pant transcription.

Evaluation of isolated cases of salmonellosis by plasmid profile analysis: introduction and transmission of a bacterial clone by precooked roast beef.

In July-August 1981, the number of isolated cases of salmonellosis in New Jersey and Pennsylvania markedly increased. Concurrently, two outbreaks in these states caused by the same Salmonella serotypes were traced to a single brand of precooked roast beef. Plasmid profiles of outbreak and isolated strains were examined, and Salmonella newport isolates from the implicated meat and from cases in the two outbreaks were identified with a unique profile, present in 45% of reported strains from isolated cases in this area during the same period. Review of the food exposure histories in isolated cases demonstrated association between this plasmid profile and consumption of precooked roast beef (P = 0.003). Examination of S newport strains from other regions and intervals indicated that this strain was introduced into these two states sometime after March 1981. Thus, plasmid profile analysis was useful in studying the epidemiology of isolated cases of salmonellosis due to a sensitive common serotype.

Phage P22 tail protein: gene and amino acid sequence.

The tail structure of the Salmonella phage P22 mediates both adsorption of the phage to its host and enzymatic hydrolysis of the bacterial O-antigen. The tail is an oligomeric structure, which is assembled from a single polypeptide species. We report here the amino- and carboxyl-terminal sequences of the P22 tail protein and the nucleotide sequence of its gene (gene 9). These data specify the complete amino acid sequence of the tail protein. The tail protein is a slightly acidic protein containing 666 amino acids. Comparison of the gene and protein sequences indicates that mature tail protein arises by cleavage of the initiator N-formyl-methionine from the nascent chain.

Structural studies of P22 phage, precursor particles, and proteins by laser Raman spectroscopy.

For the study of the protein--protein and protein--nucleic acid interactions in the assembly of virus particles, laser Raman spectra have been obtained in H2O and D2O solutions and as a function of temperature for the following Salmonella phage P22 components: mature phage particles, isolated mature phage DNA, mature protein shells empty of DNA, precursor protein shells (procapsids), and purified coat, scaffolding and tail-spike proteins. The spectra confirm that the condensed DNA within the phage capsid assumes the B-form secondary structure similar to aqueous DNA and reveal no evidence of specific molecular interactions between subgroups of DNA and protein subunits of the phage capsid. No differences were detected in the highly irregular secondary structure of the major capsid protein in mature capsids, empty capsids (lacking DNA), procapsids, and empty procapsids (lacking scaffolding protein). Features of both primary and secondary structures of the viral scaffolding and tail-spike proteins are also revealed by the spectra. Differences in thermal stability of tyrosyl side-chain interactions were observed between scaffolding protein extracted from the procapsid and within the procapsid. These differences correspond to different hydrogen bonding configurations of p-hydroxyphenyl groups and provide indirect evidence for the participation of the scaffolding proteins in specific macromolecular interactions within the procapsid.

[Bacteriophage P22 DNA structure in situ]. / Issledovanie struktury DNK in situ Bakteriofaga.

The structure of phage P22 DNA in situ was investigated by optical methods and by chemical modification with sodium bisulfite. On disruption of the phage particles by heating at 45 degrees a drop in absorbance at the 250 nm to 290 nm region was observed. At 260 nm this hypochromism was about 12%. CD spectra of intraphage DNA differed from that of free P22 DNA in the intensity as well as in the position of the positive band (lambda max 280 nm, delta epsilon max=1.3). In the intraphage DNA 21 per cent of cytosines reacted with sodium bisulfite. Cytosyl-amino acid products were found in the HClO4 and HCl hydrolysates of the modified phage. The main amino acid component of the product was identified as lysine. It was shown by means of gradient centrifugation and electron microscopy that the cytosyl-amino acid products result in the crosslinking of DNA to protein in the phage particles.

Structure and functions of the bacteriophage P22 tail protein.

The product of gene 9 (gp9) of Salmonella typhimurium bacteriophage P22 is a multifunctional structural protein. This protein is both a specific glycosidase which imparts the adsorption characteristics of the phage for its host and a protein which participates in a specific assembly reaction during phage morphogenesis. We have begun a detailed biochemical and genetic analysis of this gene product. A relatively straightforward purification of this protein has been devised, and various physical parameters of the protein have been determined. The protein has an s(20,w) of 9.3S, a D(20,w) of 4.3 x 10(-7) cm(2)/s, and a molecular weight, as determined by sedimentation equilibrium, of 173,000. The purified protein appears as a prolate ellipsoid upon electron microscopic examination, with an axial ratio of 4:1, which is similar to the observed shape when it is attached to the phage particle. The molecular weight is consistent with the tail protein being a dimer of gp9 and each phage containing six of these dimers. An altered form of the tail protein has been purified from supF cells infected with a phage strain carrying an amber mutation in gene 9. Phage "tailed" with this altered form of gp9 adsorb to susceptible cells but form infectious centers with a severely reduced efficiency (ca. 1%). Biochemical analysis of the purified wild-type and genetically altered tail proteins suggests that loss of infectivity correlates with a loss in the glycosidase activity of the protein (2.5% residual activity). From these results we propose that the glycosidic activity of the P22 tail protein is not essential for phage assembly or adsorption of the phage to its host but is required for subsequent steps in the process of infection.

Bacteriophage P22 is not a likely probe for zones of adhesion between the inner and outer membranes of Salmonella typhimurium.

Thin-section electron micrographs of plasmolyzed Salmonella typhimurium infected with bacteriophage P22 demonstrated that phage adsorbed to cells over sites of inner- and outer-membrane contact. Efforts were made to isolate such adsorption sites by infection of cells with 35S- and 32P-labeled phage and by separation of the membranes on sucrose gradients. At 37 degrees C, about 75% of the 35S radioactivity could be recovered in a region of intermediate density between the inner and outer membranes. This region (phi band) did not contain 32P. The gradient profile was independent of the multiplicity of infection (between 0.2 and 50) and of the presence or absence of chloramphenicol, dinitrophenol, or cyanide. However, ethylenediaminetetraacetate, when present during the infection step, prevented the formation of phi band. The density of phi band was at least 1.30 g/cm3, as demonstrated by prolonged centrifugation on a D2O-sucrose gradient. phi Band was shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and electron microscopy to contain empty phage heads and contaminating cellular debris. In purified preparations, phage heads were the only structures, visible by negative staining, and very little cellular phospholipid or protein was associated with the phage proteins (less than 2% and 30% by weight, respectively, as determined by using [3H]glycerol or [3H]leucine). The residual cellular protein included all of the major outer-membrane proteins rather than any one specific protein. These results are interpreted as indicating that phi band probably does not contain adhesion site material stably associated with phage heads.

E proteins of bacteriophage P22. I. Identification and ejection from wild-type and defective particles.

Of the nine proteins found in the virion of phage P22, four are ejected into the cell after adsorption. The four ejected proteins, termed E proteins, are gp16, gp20, gp26, and gp7. This was determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of radioactively labeled phage that had been adsorbed to cells and then eluted off the surface with distilled water. Phage particles that lack gp7 (7- particles) or gp20 (20- particles) successfully eject all their E proteins. The 16- particles do not eject gp7. Analysis of phage ghosts showed that they lack gp16, gp20, and gp7, but they have gp26 in close to normal quantities. Our results suggest roles for gp16 and gp26 in DNA and E protein ejection. All four E proteins are possible candidates for roles in helping the phage DNA cross the plasma membrane.