Active protection by bacteriophages T3 and T7 againstE. coli B-and K-specific restriction of their DNA

Summary The bacteriophages T3 and T7 are not modified and restricted byE. coli strains with different host specificity (E. coli B, K, O) in vivo. The phages code for a gene product with the ability toovercomeclassicalrestriction (ocr):ocr ^– mutants are subject to modification and restriction via DNA methylation vs cleavage. The T3 genome possesses recognition sites for the restriction endonuclease R.EcoB which, unless the DNA is B-specifically modified, trigger 5–7 DNA cleavages. Theocr gene function of T3 and T7 is located within the gene 0.3 region of these phages and is not identical with thesam (SAMase) function of T3. The mechanisms ofocr protection remains unclear, while it is certain that this protection by the gene 0.3 protein is exerted in the infected cell and not through over-all modification in the preceding growth cycle of the phage.     

Marker rescue of the adsorption properties of bacteriophage T 4 by bacteriophage T 2

Rescue of adsorption properties from UV-irradiated T4 by T2 as a helper phage, revealed progeny phage with intermediate properties. Fourteen independent progeny phages, plating onE. coli B/2, were plated on several indicator strains and their adsorption properties were also studied with specific T4 antibodies. Two of these, plating onE. coli KS/4, were not inactivated by the T4 antiserum, and were T2h without apparent T4 properties. The other 12 progeny phages did not plate on KS/4, and were inactivated, but at a slower rate than the parental T4. Their mean efficiency of plating onE. coli B/2 (0.83) was significantly lower than that of the parental T4. The efficiency of plating was positively correlated with the velocity of inactivation by T4 antiserum. The observations were explained by assuming that the progeny phages were recombinants of T4 and T2 loci for adsorption sites. Plating of these 12 progeny phages on several indicator strains showed that they were allrII mutants and all, except one, wererI mutants too. In addition, two weretu andh ⁴, respectively. The condition for the appearance of multiple mutants might be a complementation by T2 of UV-damaged functions, which otherwise fail to induce the completion of the lytic cycle in monocomplexes of extracellularly irradiated T4.     

Chromosomal evidence of hemiclonal and all-paternal offspring production in Bacillus rossius-grandii benazzii (Insecta Phasmatodea)

The stick insects Bacillus rossius-grandii benazzii and B. rossius-grandii grandii naturally reproduce by hybridogenesis and androgenesis. The hybrid karyotype of the former (2n=35, XX female; 34, X0 male) clearly sums up a B. rossius haploset (r) with n=18 and a B. grandii benazzii one (gb) with n=17. The two sets keep the parental features for C-heterochromatin amount (much larger in the gb complement) and satellites/NORs (nuclear organizer regions) (more numerous and variably located in the r set); hybridogenetically produced males always show severely impaired gametogenesis and are therefore sterile, whereas hybridogenetic females are fertile. Reproductive, karyological and cytogenetical properties of the hybridogenetic system have been exploited to obtain the chromosomal evidence of whole haploset exchanges. In progenies obtained by crossing B. rossiusgrandii benazzii females to B. rossius males with either standard or repatterned (with Robertsonian fusions) karyotypes, there has always been complete agreement between electrophoretically genotyped and karyologically analyzed hybridogenetic offspring: the unassorted maternal r haploset (r ^m) is transmitted and the gb ^m haploset replaced by that of the fathering male (r ^p), thus evidencing the hemiclonal reproduction and the new r ^m-r ^p chromosomal constitution. New karyotype traits of the offspring relate to chromosome number (2n=36, female; 35, male), C-heterochromatin pattern (the heterochromatin-rich gb haploset completely disappears) and satellite/NOR features (corresponding to r ^m plus r ^p locations). The same crosses also produce genetically and chromosomally all-paternal descendants (androgenetics), of both sexes and fully fertile, with an r ^p r ^p structure. These androgenetic progeny show segregation for alleles and chromosomes at which fathering males are heterozygous: it was therefore possible to demonstrate that androgenetics can derive from syngamy of two sperm nuclei, of the several present in the polyspermic hybridogenetic egg. The production of androgenetics from field fertilized females of B. rossius-grandii benazzii, B. rossius-grandii grandii and parthenogenetic Bacillus whitei (=B. rossius/grandii grandii) suggests the occurrence of unsuspected relationships between hybrids and their parental species, so that the hybrids cannot be simply considered as sexual parasites. Furthermore, there is a suggestion of evolution of parthenogenetic clonal species from selection of initially hybridogenetic strains. The ability to produce uniparental progeny naturally from the spermatic genome may open a new field of investigation on genomic imprinting.     

DNA-replication of spi - mutants of bacteriophage lambda in recombination-deficient bacteria

Summary Phage imm ²¹ c spi ^– infecting recA ^– cells gives a burst of 6 progeny phages compared to 120 in rec ⁺ cells. Parental spi ^– DNA is not degraded in recA ^– cells. The synthesis of early replication products is enhanced by a factor of 2 yielding 30 closed circular progeny DNA molecules per cell compared to 15 in the control. These DNA supercoils include 9% of dimer molecules under red ^– recA ^– and red ^– rec ⁺ conditions. On the other hand, the formation of linear phage DNA molecules in recA ^– cells is reduced by a factor of 5 to 6, if compared to spi ^– DNA in rec ⁺ and spi ⁺ DNA in recA ^– cells, respectively. The specific biological activity of these linear molecules in the helper phage assay system is unimpaired. Intermediates of late spi ^– replication under recA ^– conditions are supposed to be the unprotected targets of the action of the recB ⁺ recC ⁺ nuclease.     

Parent-to-Progeny Transfer and Recombination of T4rII Bacteriophage

Transfer of parental, light (not substituted with 5-bromodeoxyuridine) (32)P-deoxyribonucleic acid (DNA) from rII(-) mutants of T4 bacteriophage to heavy (5-bromodeoxyuridine-substituted) progeny in Escherichia coli B was less homogeneous than in wild phages. The net transfer was 5 to 20% of the value for wild T4 phage, and the parental contribution per progeny DNA molecule amounted to 7 to 100% of the genome. Three classes could be distinguished, based on the density distribution of parental label in CsCl analysis of the progeny phages. "Far recombined" phages contain parental material only in semiconservatively replicated subunits covalently attached to progeny DNA, amounting to 5 to 10% parental contribution per genome. "Intermediate recombinants" contain, aside from conventional recombinant DNA, parental DNA banding at the original, light density. This DNA may be unattached to heavy progeny DNA or attached by weak bonds which are very sensitive to shearing during the extraction procedure. The parental contribution is 10 to 50% per progeny DNA molecule in this class. "Conservative" phages band close to the parental, light density in CsCl; their DNA is purely light. When the parental phage is labeled with both (3)H-leucine (capsid) and (32)P (DNA), the specific activity of (3)H/(32)P in the "conservative progeny" is 10 to 40% of that in the parental, showing that at least some of the (32)P in this area belongs to phages with parental DNA as the sole DNA component inside an unlabeled capsid, i.e., parental DNA which has been injected into the host and matured in a new capsid without replication or recombination. This phenomenon occurs to about the same extent in both single and multiple infection.     

Ultraviolet inactivation and photoreactivation of the cholera phage ‘Kappa’

Summary The lysogenic cholera phage, Kappa is some ten to twenty folds more resistant to UV (254 nm) than are most of the T. phages ofE. coli, or the cholera phage PL 163/10, or the hostV. cholerae strain H218 Sm^r, the 37% (D ₃₇) and 10% (D ₁₀) survival doses being 255.8 J/m² and 633.6 J/m² respectively. The UV-irradiated Kappa phages could be photoreactivated in the hostV. cholerae strain H218 Sm^r to a maximum extent of 40%. The removal of the number of lethal hits per phage by the survival-enhancement treatment (photoreactivation) with time followed an exponential relation, the constant probability of removal of lethal hit per unit time being 2.8 × 10^–2 min^–1. The UV-irradiated phages could also be Weigle reactivated in the host strain H218 Sm^r by a small degree, the maximum reactivation factor (ratio of survivals in UV-irradiated and non-irradiated hosts) being 1.50.     

Diversity of structure and function of DNA polymerase (gp43) of T4-related bacteriophages

The replication DNA polymerase (gp43) of the bacteriophage T4 is a member of the pol B family of DNA polymerases, which are found in all divisions of life in the biosphere. The enzyme is a modularly organized protein that has several activities in one polypeptide chain (900 amino acid residues). These include two catalytic functions, POL (polymerase) and EXO (3-exonuclease), and specific binding activities to DNA, the mRNA for gp43, deoxyribonucleotides (dNTPs), and other T4 replication proteins. The gene for this multifunctional enzyme (gene 43) has been preserved in evolution of the diverse group of T4-like phages in nature, but has diverged in sequence, organization, and specificity of the binding functions of the gene product. We describe here examples of T4-like phages where DNA rearrangements have created split forms of gene 43 consisting of two cistrons instead of one. These gene 43 variants specify separate gp43A (N-terminal) and gp43B (C-terminal) subunits of a split form of gp43. Compared to the monocistronic form, the interruption in contiguity of the gene 43 reading frame maps in a highly diverged sequence separating the code for essential components of two major modules of this pol B enzyme, the FINGERS and PALM domains, which contain the dNTP binding pocket and POL catalytic residues of the enzyme. We discuss the biological implications of these gp43 splits and compare them to other types of pol B splits in nature. Our studies suggest that DNA mobile elements may allow genetic information for pol B modules to be exchanged between organisms.Translated from Biokhimiya, Vol. 69, No. 11, 2004, pp. 1489–1496.Original Russian Text Copyright © 2004 by Petrov, Karam.     

The host specificity system inEscherichia coli SK

E. coli SK has its own enzyme system providing DNA host specificity which differs from the known types of specificity inE. coli K12 andE. coli B. Modification and restriction are observed when the PBVI or PBV3 phages are transferred fromE. coli SK toE. coli B or K12 (and back).A methylase has been isolated fromE. coli SK cells and partly purified. This methylase catalyzesin vitro transfer of the labelled methyl groups from S-adenosylmethionine (SAM) to DNA of both phage and tissue origin which gives rise to 5-methylcytosine (5MC) and 6-methylaminopurine (6MAP). The methylase preparations isolated from the cells at the stationary growth have proved to be 1.5–1.7 times as active as the enzyme from the cells at the logarithmic growth stage. The extract ofE. coli SK cells infected with the phage S_D cannot methylate DNAin vitro. This fact is due tode novo synthesis of the enzyme which disintegrates SAM down to 5-methylthioadenosine (5MTA) and homoserine (HS). This enzyme is not found in the cells infected with the S_D phage in the presence of chloroamphenicole. The activity of the enzyme which disintegrates SAM is the highest between the 4th and the 5th minutes of infection. Thus it may be assumed that this enzyme, most probably, is an early virus specific protein and preventsin vivo methylation of the phage DNA.     

Gene function of heterozygotes in phage T4

Summary Gene function of various T4-heterozygotes was tested. About half of the HETs containing wild type and anam-mutation disappeared under non-permissive conditions, if theam-defect concerned early functions. The same was found when phages, heterozygous forr ⁺ and anrII-point-mutation, were adsorbed to K12 (). A much more extensive loss of HETs in K could be observed if anrIIA- and anrIIB-point-mutation (block-mutations showed different results) occurred together in a non-recombinant heterozygote. The findings provide evidence that one class of T4-heterozygotes has a heteroduplex DNA-structure.With 3 Figures in the Text     

DNA relatedness among bacteriophages of the morphological group C3

Six bacteriophages with an elongated head and a short, noncontractile tail were compared by DNA-DNA hybridization, seroneutralization kinetics, mol% G+C and molecular weight of DNA, and host range. Three phage species could be identified. Phage species 1 containedEnterobacter sakazakii phage C2,Erwinia herbicola phages E3 and E16P, andSalmonella newport phage 7–11. These phages had a rather wide host range (4 to 13 bacterial species). DNA relatedness among species 1 phages was above 75% relative binding ratio (S1 nuclease method, 60°C) when labeled DNA from phage C2 was used, and above 41% when labeled DNA from phage E3 was used. Molecular weight of DNA was about 58×10⁶ (C2) to 67 ×10⁶ (E3). The mol% G+C of DNA was 43–45. Anti-C2 serum that neutralizes all phages of species 1 does not neutralize phages of the other two species. Species 2 contains only coliphage Esc-7-11, whose host range was only oneEscherichia coli strain out of 188 strains of Enterobacteriaceae studied; it was unrelated to the other two species by seroneutralization and DNA hybridization. DNA from phage Esc-7-11 had a base composition of 43 mol% G+C and a molecular weight of about 45×10⁶. Species 3 contains onlyProteus mirabilis phage 13/3a. Its host range was limited to swarmingProteus species. Species 3 was unrelated to the other two species by seroneutralization and DNA hybridization. DNA from phage 13/3a had a base composition of 35 mol% G+C and molecular weight of about 53×10⁶. It is proposed that phage species be defined as phage nucleic acid hybridization groups.     

One way to do experiments on gene conversion?

Summary Competent cells of B. subtilis were transfected with heteroduplex SPP1 DNA, made by annealing complementary strands of wild type and 21 plaque type mutant DNAs. The frequencies of cells yielding mutant and wild type, only wild type, and only mutant phages were determined by single burst analyses of transfected cells. The data obtained reveal that an effective mechanism is operating in B. subtilis, which converts heterozygous to homozygous molecules prior to their replication. This correction mechanism is asymmetric with regard to the strand which is preferentially corrected in a given heteroduplex pair. The direction of asymmetry thus defined depends on the marker introduced into a particular heteroduplex. The efficiency of correction varies with the markers used and is correlated to the position of markers in the genetic map. From this correlation, the direction of replication of the SPP1 genome is deduced. The frequency distribution of wild type and mutant phages in cells yielding both genotypes indicates that both strands of the input DNA contribute equally to the production of progeny, i.e. DNA replication is symmetric.     

Reactivation of photodynamically inactivated lambda phages

Summary UV-irradiated c phages show a lower survival when plated on rec ^–-cells as compared to rec ⁺-cells. Photodynamically inactivated c phages show the lowest survival on hcr ^–; rec ^–-cells. The rec-functions do not influence the repair of UV- or photodynamically induced lesions in T1 phages.     

The use of specialised transducing phages in the amplification of enzyme production

Two types of trp phages have been used as model systems to investigate ways of optimising the expression of bacterial genes from transducing phage genomes.Excellent yields of trp enzymes were achieved by infecting a trpR^– host with Q ^– or Q ^– Q ^– S ^– derivatives of trpAM1, which expresses its trp genese exclusively from the trp promoter. The five trp geneproducts constituted more than 50% of the total soluble protein of infected cells under these conditions, and an even higher proportion of the protein synthesized after infection. In a trpR ⁺ host, phage DNA replication was easily able to override tryptophan-mediated repression by titration of the trp repressor protein. N ^– derivatives of trp phages carrying the trp promoter were equally productive, while having the advantage of being much simpler to construct and propagate.     

Isolation and characterization of a recombination defective-dependent bacteriophage ofRhodobacter sphaeroides

A new virulent bacteriophage, designated RZ1, was isolated from a local pond on the facultative phototrophic bacteriumRhodobacter sphaeroides ZZ101. Electron microscopic studies revealed that, in general morphology, phage RZ1 resembles the bacteriophage ofEscherichia coli. The host range of phage RZ1 is limited to some strains ofR. sphaeroides. The phage genome consists of double-stranded DNA of about 44 kb lacking cohesive ends and seems to present terminal redundancy and cyclic permutation. RZ1 phage may carry out a lytic cycle only in recombination-defective mutants ofR. sphaeroides. Nevertheless, a derivative of the RZ1 phage, termed RW1, able to grow in recombination-proficient strains ofR. sphaeroides, has also been obtained. In vitro restriction analysis of both RZ1 and RW1 phages shows the presence of a rearrangement in their DNA. Generalized transduction of Str^r and Rif^r chromosomal markers has not been detected with either RZ1 or RW1 phages.     

Genetic studies of the ribosomal proteins in Escherichia coli. XI. Mapping of the genes for L21, L27, S15 and S21 by using hybrid bacteria and over-production of these proteins in the merodiploid strains.

Summary Host capacity for growth of single-stranded DNA phages was investigated with several replication mutants of E. coli. In dnaL708, dnaM709 and dnaS707 mutants, multiplication of K was not restricted even at 42°C. In dnaM710 cells, however, growth of K was severely affected at 42°C but not at 33°C. Upon infection of K, parental replicative form was synthesized at the restrictive temperature, whereas subsequent step (replication of progeny replicative form) was blocked in the dnaZ strain. Growth of X174 and 3, as tested by transfection, was also thermosensitive in the dnaM710 mutant but not in the dnaL708, dnaM709 and dnaS707 strains. In contrast with , microvirid phages could grow in E. coli cells bearing the groPC259, groPC756 or seg-2 mutation.This paper is number 15 in the series entitled Sensivity of Escherichia coli to Viral Nucleic Acid     

Evidence for multiple carboxymethylcellulase genes in Pseudomonas fluorescens subsp. cellulosa

Summary A genomic library of Pseudomonas fluorescens subsp. cellulosa DNA was constructed in bacteriophage 47.1 and recombinants expressing carboxymethylcellulase (CMCase) activity isolated. A 7.3 kb partial EcoRI fragment, a 9.4 kb EcoRI fragment and a 5.8 kb HindIII fragment were subcloned from three different phages into pUC18 to yield recombinant plasmids pJHH1, pJHH3 and pGJH2 respectively. Cells of Escherichia coli harbouring these plasmids expressed CMCase activity. The positions of the CMCase genes in the three plasmids were determined by subcloning and transposon mutagenesis. pJHH1 contained two distinct DNA regions encoding CMCases, which were controlled by the same promoter. All four cloned enzymes cleaved p-nitrophenyl--D-glucopyranoside, although at a very low rate, but none exhibited exoglucanase activity. In common with other extracellular enzymes cloned in E. coli, all the CMCases were exported to the periplasmic space in the enteric bacterium. The carboxymethylcellulase genes encoded by pJHH1 and pJHH3, were subject to glucose repression in E. coli.Abbreviations SSC 0.15 M NaCl, 0.015 M sodium citrate - Sm^r resistance to streptomycin - Km^r resistance to kanamycin - Ap^r resistance to ampicillin - Tc^r resistance to tetracycline - Cm^r resistance to chloramphenicol - CMCase carboxymethylcellulase     

Size distribution and molecular polarity of nascent DNA in a temperature-sensitive dna G mutant of Escherichia coli

Summary In the dna G t.s. strain BT 308, made lysogenic for the phage , nascent DNA was labelled by short pulses of ³H-thymidine, isolated and separated as a function of size by alkaline sucrose gradient sedimentation. The molecular polarity of the labelled DNA was then determined by hybridization to the separated strands of DNA.At 30° C, strand r DNA, made in the direction opposite that of fork movement, is synthesized in the form of short pieces. The first observable consequences of a shift to 42° C are the preferential inhibition of strand r synthesis and the small amount of strand r DNA which is made is recovered in long pieces of DNA rather than in short fragments. This indicates that the t.s. product, in strain BT 308, may be involved in the synthesis of the strand growing in the direction opposite that of replication fork movement.Newly synthesized strand l DNA, made in the same direction as replication fork movement, is found in long pieces in wild-type bacteria; it is found in pieces of intermediate size in strain BT 308 at 30° C as well as at 42° C. This indicates additional differences in the replication machinery between strain BT 308 and wild-type bacteria.     

Host specificity of DNA produced by Escherichia coli. XII. The two restriction and modification systems of strain 15T-

Summary E. coli 15T^- carries two distinct sets of DNA restriction and modification activities. The genetic information for system A is contained in the bacterial chromosome and linked to the thr region. This fact suggests host specificity A to be related to those of strains K and B. The genes controlling system 15 are on a plasmid which is related to phage Pl: it competes with Pl for stable inheritance in the carried state and it genetically recombines with Pl. This recombination may produce plasmid genomes with newly assorted characters (see Table 3). One of them is an active, Pl-like prophage with the 15-specific instead of the parental Pl-specific restriction and modification characters. Superinfection of 15T^- with Pl may also result in curing of the bacteria from the restriction plasmid.Bot A- and 15-specific restrictions and modifications act on bacterial DNA, on the DNA of various sex factors and on the DNA of certain bacteriophages, e.g. of phage . Phage 82 DNA is sensitive only to 15-specific restriction, but not to A-specific restriction.Independently of the A- and 15-specific restrictions, the growth of phage in E. coli 15T^- encounters another limitation of yet unknown nature. No such limitation is observed either with phage 82 or with mutants of occurring at a frequency of about 10^-5.     

Host-dependent modification of bacteriophage T7 and SAMase-negative T3 derivatives affecting their adsorption ability

Summary When passaging phage T7 and SAMase-negative T3 mutants betweenE. coli strains with identical (EcoB) or without (EcoO) DNA host specificity, phenotypically a host-controlled modification and restriction is observed. This phenomenon is not due to classical modification and restriction of the bacteriophage DNA but depends on the reversibly altered adsorption capacity of the phages on the different host strains.