Evidence for message reading from a unique strand of pneumococcal DNA

Transforming Activity in Both Complementary Strands of Bacillus subtilis DNA

Under conditions favoring single-strand transformation, the two complementary strands of Bacillus subtilis DNA, separated by differential complexing with polyriboguanylic acid, have identical transforming activity. Moreover separated single strands, upon renaturation with unmarked (recipient) DNA, form heteroduplex molecules with similar double-strand transformin activity. These findings bear upon the mechanism of DNA integration.

Effect of mismatched base pairs on the fate of donor DNA in transformation of Streptococcus pneumoniae

Investigation of the mechanism that discriminates against mismatched base pairs in transformation of Streptococcus pneumoniae of genotype hex+ was based on the use of a radioactively labeled cloned fragment of pneumococcal DNA as donor in transformation. The fate of the donor label was followed by lysis of the transformed cells and separation by agarose gel electrophoresis of DNA fragments generated by restriction endonucleases. As a result of Hex action, most of the donor DNA fragment, which was a few kilobases in length, was lost when a mismatched base pair occurred between donor and recipient DNA. This was not observed in hex- recipient cells. Kinetic studies of mismatch-induced donor DNA loss showed that the process is faster in strain 800, an R6 derivative, than in DP1601, a strain of different origin. In the latter strain, the amount of donor label that becomes double stranded rises substantially, indicating extensive formation of donor-recipient heteroduplex structures, before falling to the expected level. At 30 degrees C the process is essentially completed 15 min after entry.

Use of a cloned DNA fragment to analyze the fate of donor DNA in transformation of Streptococcus pneumoniae

The integration of donor label into the recipient fragment is followed during transformation of Streptococcus pneumoniae. The method used involves gel analysis of restriction endonuclease-treated recipient DNA after recombination with a radioactively labeled homologous cloned fragment.

Mismatch repair in Streptococcus pneumoniae: relationship between base mismatches and transformation efficiencies

Genetic transformation in Streptococcus pneumoniae involves the insertion of single-stranded pieces of donor DNA into a recipient genome. Efficiencies of transformation strongly depend on the mutations (markers) carried by donor DNA. Markers are classified according to their transforming efficiencies into very high, high, intermediate, and low efficiency. The last is approximately 1/20th as efficient as the first. This marker effect is under the control of the Hex system, which is thought to correct mismatches at the donor-recipient heteroduplex stage in transformation. To investigate this effect, wild type, mutant, and revertant DNA sequences at five genetic sites within the amiA locus were determined. The results show that low-efficiency markers arise from transitional changes A . T to G . C. The transversion A . T to T . A corresponds to an intermediate-efficiency marker. Transversions G . C to T . A and G . C to C . G lead to high-efficiency markers. Among the eight possible mismatches that could exist transiently at the heteroduplex stage in transformation, only two--namely, A/G and C/C--are not corrected by the Hex system. It is noteworthy that the four possible base pairs (A . T, T . A, G . C, and C . G) have been encountered at the very same site (amiA6 site), which constitutes a good illustration of the marker effect. DNA sequence analysis also reveals that short deletions (33 or 34 bases long) are integrated with very high efficiencies. These results confirm that the Hex system corrects point mismatches harbored in donor-recipient heteroduplexes thousands of bases long. The correction pattern of the Hex system toward multiple-base mismatches has also been investigated. Its behavior toward double-base mismatches is complex, suggesting that neighboring sequences may affect the detection of mispaired bases.

Transformation in pneumococcus: existence and properties of a complex involving donor deoxyribonucleate single strands in eclipse

Donor deoxyribonucleic acid (DNA) single strands exist in a complex during the eclipse phase in pneumococcal transformation. This eclipse complex exhibited specific physical properties distinct from those of both pure DNA single strands and native DNA. These included a lower affinity for diethylaminoethyl-cellulose and hydroxylapatite than that of single-strand DNA, faster sedimentation than the DNA chains that it contains, and a buoyant density in Cs2SO4 lower than that of native DNA. The complex was dissociated by treatments with sodium dodecyl sulfate, NaOH, guanidine-hydrochloride, chloroform, and proteinase K but was insensitive to ribonuclease.

Mismatch correction in pneumococcal transformation: donor length and hex-dependent marker efficiency

A hypothesis that preferential rejection of donor markers by the hex system of pneumococcus is due to lethal double-strand breaks has been examined in terms of its implications for the extent of the excision required. Experiments reported here were directed at asking whether hex-dependent marker efficiency depends on the length of the donor deoxyribonucleic acid (DNA). In the absence of intracellular competition for hex function, there was no detectable effect of DNA size on hex-dependent marker efficiency as donor DNA was sheared from greater than 1 x 107 daltons to 3.6 x 105 daltons. The latter DNA was purified by two successive velocity fractionations to ensure that the activity seen was representative of DNA of that size. Quantitative examination of the system shows that, for the lethal event hypothesis to be true, the excision step has to remove an average of 7,000 to 10,000 nucleotides. This figure is so much greater than that seen in other excision processes that alternate hypotheses should be considered. The presently known properties of the hex system can be accounted for by a model invoking the migratory features of type I restriction enzymes.

Physicochemical properties of kinetoplast DNA from Crithidia acanthocephali. Crithidia luciliae, and Trypanosoma lewisi

The protozoa Crithidia and Trypanosoma contain within a mitochondrion a mass of DNA known as kinetoplast DNA (kDNA) which consists mainly of an association of thousands of small circular molecules of similar size held together by topological interlocking. Using kDNA from Crithidia acanthocephali, Crithidia luciliae, and Trypanosoma lewisi, physicochemical studies have been carried out with intact associations and with fractions of covalently closed single circular molecules, and of open single circular and unit length linear molecules obtained from kDNA associations by sonication, sucrose sedimentation, and cesium chloride-ethidium bromide equilibrium centrifugation. Buoyant density analyses failed to provide evidence for base composition heterogeneity among kDNA molecules within a species. The complementary nucleotide strands of kDNA molecules of all three species had distinct buoyant densities in both alkaline and neutral cesium chloride. For C. acanthocephali kDNA, these buoyant density differences were shown to be a reflection of differences in base composition between the complementary nucleotide strands. The molar ratios of adenine: thymine:guanine:cytosine, obtained from deoxyribonucleotide analyses were 16.8:41.0:28.1:14.1 for the heavy strand and 41.6:16.6:12.8:29.0 for the light strand. Covalently closed single circular molecules of C. acanthocephali (as well as intact kDNA associations of C. acanthocephali and T. lewisi) formed a single band in alkaline cesium chloride gradients, indicating their component nucleotide strands to be alkaline insensitive. Data from buoyant density, base composition, and thermal melting analyses suggested that minor bases are either rare or absent in Crithidia kDNA. The kinetics of renaturation of 32P labeled C. acanthocephali kDNA measured using hydroxyapatite chromatography were consistent with at least 70% of the circular molecules of this DNA having the same nucleotide sequence. Evidence for sequence homologies among the kDNAs of all three species was obtained from buoyant density analyses of DNA in annealed mixtures containing one component kDNA strand from each of two species.

Chromatographically fractionated complementary strands of Bacillus subtilis deoxyribonucleic acid: transformation of hybrids

The annealing properties as measured by the restoration of transforming activity and hypochromicity of methylated albumin-kieselguhr (MAK)-fractionated complementary strands of Bacillus subtilis deoxyribonucleic acid (DNA) are presented. Temperature-absorbance measurements performed on annealed mixtures of various L and H strand fractions indicated the existence of a complementarity gradient between the two MAK peaks. The markers purA16, leu-8, metB(5), thr-5, and the linked marker hisB(2)-try-2 exhibited different bimodal distributions on MAK columns. The transforming efficiency of heteroduplex mixtures, prepared by cross-annealing resolved complementary strands of wild-type and recipient DNA, was compared. The transforming efficiency of the wild-type L and H strands was equal in one preparation and unequal in a second preparation. It was found that in the second strand preparation the heteroduplex DNA containing the H strand from wild type was more efficient for all of the markers tested. The variations in transforming efficiencies of the complementary strands in heteroduplex molecules reported here and by others are due in part to strands of unequal length and probably to the self-annealing property of the H strands. At present, no conclusion could be made regarding the existence of strand selection bias during integration of donor DNA in competent B. subtilis cells.

Kinetics of integration of transforming DNA in pneumococcus

Integration of donor genes, as measured by recovery of their transforming activity from eclipse in lysates of newly transformed cells of pneumococcus, has been followed at temperatures from 0 to 40 degrees . There is a lag in the recovery curve that is marker-dependent and increases as temperature falls. An Arrhenius plot of the rates shows a sharp break between 15 and 20 degrees . Brief exposure of the system to 37 degrees before incubation at 10 or 15 degrees removes the lag and raises the subsequent rate of recovery. This activation is unstable, however, and disappears when the cells are held at 0 degrees after the exposure at 37 degrees and before incubation at 15 degrees . The results are interpreted in terms of a reaction sequence A right harpoon over left harpoon B --> C, with activation energies for the first forward rate-constant of the order of 50 Cal/mol, for the second, 20-21 Cal/mol, and for the reverse reaction, less than 20 Cal/mol. The properties of the first step, including its marker dependence, are the same as those observed earlier for stabilization of donor markers against intracellular inactivation, and it is suggested they may reflect an activation of the recipient chromosome prerequisite to synapsis.

Events occurring near the time of synapsis during transformation in Diplococcus pneumoniae

A marker-specific and strongly temperature-dependent reaction was observed to occur at a time during transformation in Diplococcus pneumoniae after the donor deoxyribonucleic acid (DNA) had acquired single-strand properties and immediately preceding the integration of these strands into the recipient chromosome. Operationally, it was observed as the prevention of an intracellular inactivation process, also described in this paper, which is specific for low molecular weight or for damaged DNA, and which occurs if the recipient cells are held at suboptimal temperatures after the DNA has entered. Brief exposure of the cells to a higher temperature stabilized the DNA against this inactivation, in a two step process. It is the first step which has a strong temperature dependence (DeltaHdouble dagger = 70 kcal/mole, DeltaSdouble dagger = 160 entropy units), is marker specific, and which appears to be reversible. The second step is much less temperature-dependent and overlaps in time the start of integration. The enthalpy and entropy of activation are both consistent with those needed to open a loop of six to eight base pairs in a DNA duplex. It is suggested that these observations may reflect, and provide an assay for, the kinetics of synapsis, which on this model is limited in rate by the appearance of unpaired regions on the recipient duplex.

Competent Diplococcus pneumoniae accept both single- and double-stranded deoxyribonucleic acid

The transforming activity of fractionated complementary strands of Diplococcus pneumoniae deoxyribonucleic acid (DNA) bands at the position of fully denatured DNA in CsCl at pH 11.0, and is completely (> 99.8%) destroyed by digestion with exonuclease-I. These results prove that pure single strands transform the normally prepared competent cells of this species. Their efficiency is about 0.5% that of native DNA of comparable size.

Number of transformable units per cell in Diplococcus pneumoniae

Analysis of frequencies of single and random multiple transformations in Diplococcus pneumoniae showed that there are at least two transformable units per cell of the total population in highly competent cultures. If 100% of the cells are competent in these cases, the units may be interpreted as the strands of one duplex deoxyribonucleic acid recipient chromosome. The theory is developed to allow for extension to more complex situations.

Fractionated strands of bacterial deoxyribonucleic acid. 3. Transformation efficiencies and rates of phenotypic expression

Preferential binding of guanine-rich ribopolymers to one of the complementary strands of denatured deoxyribonucleic acid (DNA) of Diplococcus pneumoniae permitted the fractionation of the complements in CsCl density gradients. Phenotypic expression of the newly acquired genes for four drug resistances was more rapid in cells transformed by the heavy fractions than in those transformed either by light fractions or by unfractionated DNA. The efficiencies of transformation with the two complements were nearly equal for the four markers tested. Both efficiency and expression results were the same whether we assayed the residual activity or the activity obtained by annealing the fractions with excess recipient DNA.

Reovirus-directed ribonucleic acid synthesis in infected L cells

Reovirus replication in L-929 mouse fibroblasts was unaffected by 0.5 mug of actinomycin per ml, a concentration which inhibited cell ribonucleic acid (RNA) synthesis by more than 90%. Under these conditions of selective inhibition, the formation of both single-stranded and double-stranded virus-specific RNA was detected beginning at 6 hr after infection. The purified double-stranded RNA was similar in size and base composition to virus RNA and presumably was incorporated into mature virus. The single-stranded RNA formed ribonuclease-resistant duplexes when annealed with denatured virus RNA but did not self-anneal, thus indicating that it includes copies of only one strand of the duplex. The single-stranded RNA was polyribosome-associated and may function as the virus messenger RNA. Production of both types of virus-induced RNA required protein synthesis 6 to 9 hr after infection. At later times in the infectious cycle, only double-stranded RNA synthesis was dependent on continued protein formation.

On the mechanism of integration of transforming deoxyribonucleate

The characteristics of the intermediates in the reaction, between DNA and pneumococcus, that results in genetic transformation are described in so far as they have been characterized. Transformation with DNA isolated from bacteria carrying in addition to genetic markers (32)P as a radioactive label and (2)H and (15)N as density labels has permitted the characterization of the product of recombination between the newly introduced DNA and the DNA of a recipient bacterium. The evidence for a single strand displacement mechanism producing a hybrid structure in the DNA of the recipient bacteria is presented. Progeny of single transformants have been examined. The results of these segregation studies permit the further characterization of this hybrid product of transformation as a genetically heterozygous structure.

Nitrous Acid Mutation of Transforming DNA: Consideration of Mode of Action

Apparently nitrous acid produces genetic alterations, expressed as antibiotic-resistant markers, directly on heat-denatured transforming DNA of Haemophilus influenzae, rather than producing DNA which acts as a non-specific mutagen. The markers which arise as a result of treatment with nitrous acid behave similarly to naturally occurring antibiotic markers. In addition, data comparing the expression and replication of induced markers to natural markers suggest that the nitrous acid-induced markers express and multiply in the same fashion as do "normal" markers. Therefore, mutations which require additional time to produce a functional DNA by a base-pair substitution, or by replication of the introduced DNA, are not responsible for the mutants observed.

Residual Activity of Thermally Denatured Transforming Deoxyribonucleic Acid from Haemophilus influenzae

Barnhart, Benjamin J. (Johns Hopkins University School of Hygiene and Public Health, Baltimore, Md.). Residual activity of thermally denatured transforming deoxyribonucleic acid from Haemophilus influenzae . J. Bacteriol. 89: 1271–1279. 1965.—The level of residual transforming activity of heated deoxyribonucleic acid (DNA) (i.e., 1 to a few per cent of native DNA-transforming activity) was found to be independent of the heating and quenching temperatures and less susceptible than native or renatured DNA to heat inactivation upon prolonged heating above or below the critical melting temperature. Similar dose-response curves were obtained for inactivation by formamide of native and renatured DNA, but the residual-active material was much more resistant. Heating DNA above the T m in the presence of 1% formaldehyde resulted in a level of residual activity 4 logs lower than that obtained without formaldehyde. Residual-active material was not inactivated by Escherichia coli phosphodiesterase, but it was susceptible to snake venom phosphodiesterase. A new genetic marker was induced in heated-quenched DNA but not in purified residual-active material following nitrous acid treatment. Residual activity was found to be less susceptible to ultraviolet inactivation and to band at a higher density region in CsCl than native DNA. In conclusion, it is suggested that the residual-active material is a structure formed by intrastrand hydrogen bonding of the separated units of heated-quenched DNA. Such a configuration would result in at least a partially double-stranded structure, which is probably the essential characteristic of the residual-active material endowing it with biological activity.