Participation of a DNA-RNA hybrid complex in in vivo genetic transcription

Synthetic lethal mutants in Escherichia coli define pathways necessary for survival with RNase H deficiency

Ribonucleotides frequently contaminate DNA and, if not removed, cause genomic instability. Consequently, all organisms are equipped with RNase H enzymes to remove RNA-DNA hybrids (RDHs). Escherichia coli lacking RNase HI (rnhA) and RNase HII (rnhB) enzymes, the ∆rnhA ∆rnhB double mutant, accumulates RDHs in its DNA. These RDHs can convert into RNA-containing DNA lesions (R-lesions) of unclear nature that compromise genomic stability. The ∆rnhAB double mutant has severe phenotypes, like growth inhibition, replication stress, sensitivity to ultraviolet radiation, SOS induction, increased chromosomal fragmentation, and defects in nucleoid organization. In this study, we found that RNase HI deficiency also alters wild-type levels of DNA supercoiling. Despite these severe chromosomal complications, ∆rnhAB double mutant survives, suggesting that dedicated pathways operate to avoid or repair R-lesions. To identify these pathways, we systematically searched for mutants synthetic lethal (colethal) with the rnhAB defect using an unbiased color screen and a candidate gene approach. We identified both novel and previously reported rnhAB-colethal and -coinhibited mutants, characterized them, and sorted them into avoidance or repair pathways. These mutants operate in various parts of nucleic acid metabolism, including replication fork progression, R-loop prevention and removal, nucleoid organization, tRNA modification, recombinational repair, and chromosome-dimer resolution, demonstrating the pleiotropic nature of RNase H deficiency. IMPORTANCE Ribonucleotides (rNs) are structurally very similar to deoxyribonucleotides. Consequently, rN contamination of DNA is common and pervasive across all domains of life. Failure to remove rNs from DNA has severe consequences, and all organisms are equipped with RNase H enzymes to remove RNA-DNA hybrids. RNase H deficiency leads to complications in bacteria, yeast, and mouse, and diseases like progressive external ophthalmoplegia (mitochondrial defects in RNASEH1) and Aicardi-Goutières syndrome (defects in RNASEH2) in humans. Escherichia coli ∆rnhAB mutant, deficient in RNases H, has severe chromosomal complications. Despite substantial problems, nearly half of the mutant population survives. We have identified novel and previously confirmed pathways in various parts of nucleic acid metabolism that ensure survival with RNase H deficiency.

Characterisation of a chromatin fraction bearing pulse-labelled RNA. 1. Nascent RNA, RNA polymerase B and transcribed DNA sequence content

We have further characterised a fraction of polynucleosomal chromatin from mouse cells which is enriched in transcribing regions, after separation by multistep partition in a dextran /poly(ethylene glycol) two-phase mixture [Faber, A. J. (1972) Methods Cell Biol. 16, 447--457]. This fraction contains an average of 16% of the total DNA and 63% of the 3-min pulse-labelled RNA in chromatin which, by a number of criteria, represents nascent RNA transcripts. Of the total transcribing RNA polymerase B molecules in chromatin, 52% are found in this fraction by titration with radioactive alpha-amanitin. About 28% of the single-copy DNA sequences in this fraction hybridise to nuclear polyadenylated RNA, compared with only 1.5% of the single-copy sequences in the remaining (nontranscribing) chromatin fraction.

Assembly of bacteriophage phi X174: identification of a virion capsid precursor and proposal of a model for the functions of bacteriophage gene products during morphogenesis

A capsomeric structure sedimenting with an S value of 108 in sucrose gradients was isolated from Escherichia coli infected with bacteriophage phi X174. The 108S material contained viral proteins F, G, H, and D, and the relative amounts of these proteins in the 108S material were similar to those in the infectious 132S particle, which has previously been described as a possible intermediate in the assembly of 114S phage particles. Electron micrographs indicated that the size and shape of the 108S material resemble those of the 132S particle. The 108S material contained no DNA, and its formation occurred independently of DNA synthesis. The 108S material accumulated in infected cells when viral DNA replication was prevented either by mutation in phage genes A or C or by removal of thymidine from a culture infected with wild-type phage or with a lysis gene E mutant. Upon restoration of thymidine to cells infected with the lysis gene E mutant and then starved of thymidine, the accumulated 108S material was converted to 132S particles and to 114S phage particles, implying that the 108S material is a precursor of phage particles. A model that proposes possible functions for the products of phi X174 genes A, B, C, D, F, and G during viral replication and phage maturation is described.

Characterization of a soluble simian-virus-40 transcription complex

We have previously described the isolation, from nuclei of monkey cells infected with Simian virus 40 (SV40), of a nucleoprotein complex which is able to achieve viral transcription. This complex contains SV40 DNA and RNA polymerase II molecules which have initiated transcription during the viral development. We show here, by molecular hybridization experiments, that most of the templates active in SV40 transcription can be dissociated from host DNA. In conditions where supercoiled SV40 DNA form I sediments at 21 S, the transcription complex has a sedimentation coefficient of about 25 S. Inhibition of viral DNA synthesis by cytosine arabinonucleoside or chloroquine does not affect the activity of the transcription complex, which suggests that replicating molecules are not required for viral RNA synthesis and that SV40 DNA form I could serve as template for late SV40 transcription. A large fraction of the RNA synthesized in vitro remains associated with the SV40 DNA template in cesium sulfate density gradient. The RNA chains produced by the complex are heterogeneous in size, most of them being as large or larger than the viral genome.

Functions of gene C and gene D products of bacteriophage phi X 174

Phage-related materials existing in cells infected with various mutants of bacteriophage phi chi 174 were investigated. A novel species of replicative-form (RF) DNA was found in cells infected with a phage mutant of gene B, C, D, F, or G. This species, called RFI, sedimented at a position between RFI and RFII in a neutral sucrose gradient. It was converted to RFI upon denaturation in alkali, denaturation in formamide and subsequent renaturation, or RNase treatment at low ionic strength. In cells infected with a phage mutant of gene C, RFI was derived from pulse-labeled RFII after a short chase. TLLS INFECTED WITH A MUTANT OF GENE B, D, or F. A possible function of the C gene product of phi chi 174 could be to prevent the conversion of RFII to RFI, thereby maintaining the availability of RFII to act as the template for single-stranded viral DNA synthesis. A protein complex containing no DNA, which sedimented with an S value of 108 in a sucrose gradient and contained virion proteins F, G, and H, and nonvirion protein D, was found in cells infected with the gene C mutant. A possible function of protein D was considered as a scaffolding protein for assembly of phage structural proteins.

Prokaryotic DNA in nucleoid structure

Recent studies of the structure of the bacterial nucleoid are reviewed. In the past 4 to 5 years results of electron microscopic and physical-chemical investigations of the isolated bacterial nucleoids have greatly advanced our understanding of this comparatively simple chromosome. Evidence for both long-range and short-range conformational organization of the packaged DNA has emerged, and preliminary characterization of the molecular interactions organizing this structure has been accomplished.

Studies of DNA bound RNA molecules isolated from nucleoids of Escherichia coli

Methods are developed for studying RNA molecules bound directly to DNA in bacterial nucleoids. It is found that among the 1000-3000 nascent RNA chains that normally are attached to the DNA via their associated RNA polymerase molecules, 74 +/- 14 chains per nucleoid can be bound differently. These chains unlike the other nascent RNAs remained bound to the DNA after the chromosome was deproteinized and sheared. Sensitive assays using radioactive labels detected no RNA polymerase involved in the RNA-DNA linkage. The linkage was stable at low temperatures, but the RNA separated from the DNA at high temperature. The bound RNA molecules were heterodisperse (weight average length 1200 bases). Pulse-chase experiments and studies of the fate of these RNA molecules in rifampicin treated cells demonstrated that they are nascent RNAs, degraded or released from the DNA in vivo with kinetics similar to that of the total nascent RNA. Hybridization analyses showed that the chains are composed at least in part of nascent rRNA and known mRNA molecules. Some, but not more than 5% of the bound chains, contained sequences of about 300 nucleotides in length, bound to the DNA in an RNase resistant form.

Process of infection with bacteriophage phiX174. XXXVII. RNA metabolism in phiX174-infected cells

The RNA produced in vivo from bacteriophage phiX174 DNA has been analyzed by polyacrylamide-agarose gel electrophoresis and sedimentation in dimethyl sulfoxide gradients, and the results of Hayashi and Hayashi (1970) have been confirmed and extended. An efficient procedure for recovery of RNA from gels, followed by a hybridization assay, has indicated the presence in infected cells of 18 distinct RNA species with sizes up to and greater than the unit (viral) length. The sizes of phiX mRNA's were similar irrespective of whether material was analyzed on gels or in dimethyl sulfoxide gradients. When virus-induced RNA was detected by a double-label method, seven additional low-molecular weight species were observed on gels and the resolution of dimethyl sulfoxide gradients was enhanced. The present results lend support to aspects of the model of Hayashi and Hayashi (1970) for the generation of these discrete mRNA species; an alternative model is also discussed.

Viral DNA-RNA hybrids in cells infected with simian virus: the simian virus 40 transcriptional intermediates

Brief labeling of cells infected with simian virus 40 with tritiated uridine resulted in the incorporation of part of the label into material that was soluble in 1 M NaCl and sensitive to KOH, with a buoyant density close to that of DNA. The properties of this material suggest that it represents single-stranded nascent molecules of messenger RNA of simian virus 40 hydrogen-bonded over a small portion of their length to viral DNA templates. The name "simian virus 40 transcriptional intermediate molecules" is suggested for these naturally occurring DNA.RNA hybrid molecules. The DNA in the hybrid seems to be in the form of replicative intermediate molecules.

Use of bacteriophage phi chi 174 replicative from progeny DNA as templates for transcription

The synthesis of phiX174-specific RNA has been studied in infected cells in which the thymine of the viral (+) strand of the parental RF(*), of the complementary (-) strand of the parental RF, or of both strands of the progeny RF molecules has been replaced with 5-bromouracil (5 BU). By irradiation of such cells with UV light at a wavelength of 313 nm it was possible to affect, specifically, the 5 BU-labeled strands. When the progeny RF molecules contain thymine, irradiation has no effect upon the synthesis of viral-specific RNA, regardless of 5 BU substitution in either strand of parental RF. If, however, progeny RF is labeled with 5 BU, irradiation produces a major decrease of viral RNA synthesis. It is concluded that many progeny RF molecules can serve as templates for transcription at late times of infection. Irradiation, prior to RF replication, of cells in which, particularly, the complementary strand of RF contains 5 BU, appears to decrease the ability of the parental RF to replicate.

The alkaline denaturation of DNA

A kinetic study of the alkaline transition of DNA, in clearly defined physico-chemical conditions, is presented, which allows us to identify, within the alkaline transition region, different pH ranges, corresponding to different ratelimiting factors. This analysis brings into consideration three distinct intervals of time which characterize the whole process, namely the time necessary for full hyperchromicity to be reached, the time required for strand separation in the case of a single DNA molecule, and the time for complete denaturation to be reached in the case of a DNA solution.THE RESULTS OBTAINED FROM ULTRACENTRIFUGAL, AND SPECTROPHOTOMETRIC MEASUREMENTS, INVOLVING RAPID MIXING EXPERIMENTS, SEEM TO INDICATE THE FOLLOWING CONCLUSIONS: whereas, in the lower pH ranges considered within the transition region, the denaturation process is limited by the first time constant, this same constant becomes extremely short at higher pH. On the other hand the fact that, in the higher pH range, the second and third time constants do not coincide (the time to unwind a single T2 DNA molecule being at least one order of magnitude shorter than the time required for bulk denaturation to be reached) suggests that in this pH range the overall denaturation rate is limited by a statistical process governing the initiation of unwinding.These observations are discussed in terms of a model in which the unwinding energy is given by the electrostatic repulsions which originate in the deprotonated DNA molecule. The model itself suggests some experiment which seem to confirm it.

Identification of Bacillus subtilis NRRL B-3275 as a strain of Bacillus pumilus

The physiological and biochemical properties of a species of Bacillus previously identified as B. subtilis NRRL B-3275 (B-3275) were compared with those of seven strains of B. pumilus and five strains of B. subtilis. The biotin requirement of B-3275, its inability to hydrolyze starch, and its failure to reduce nitrate indicate that the organism is more closely related to the B. pumilus strains than to those of B. subtilis. Hybridization of deoxyribonucleic acid (DNA) from B-3275 with that of the strains of B. pumilus showed a binding efficiency (compared with the homologous reaction) of 58 to 99%, depending on the strain. Hybridization with the DNA from any of the strains of B. subtilis did not exceed 24%. DNA from B-3275 was unable to transform two amino acid auxotrophic markers to prototrophy in a highly competent strain of B. subtilis 168. We conclude that B-3275 is a strain of B. pumilus which we designate as B. pumilus NRRL B-3275.

Synthesis of replicative form deoxyribonucleic acid and messenger ribonucleic acid by gene IV mutants of bacteriophage S13

Gene IV mutants of bacteriophage S13 are known to be blocked in infectious replicative form (RF) DNA synthesis, producing only a small fraction of the RF formed by wild-type phage. This investigation shows that gene IV mutants form only parental RF and are blocked in the synthesis of any progeny RF, either infectious or noninfectious. This was determined by density labeling of RF in cells treated with mitomycin C to suppress host deoxyribonucleic acid (DNA) synthesis. RF synthesis was also studied in untreated cells, using methylated albumin columns to separate RF from host DNA. In this case it was also found that synthesis of progeny RF by gene IV mutants is negligible. It has been found by DNA-ribonucleic acid (RNA) hybridization experiments that gene IV mutants form at least as much or more messenger RNA than wild-type phage. Therefore, parental RF alone can form messenger RNA in appreciable amounts.

DNA- dependent RNA-directed protein synthesis in vitro. I. Extent of genome transcription

We have described an in vitro system which couples UTP incorporation into RNA by DNA-dependent RNA polymerase with RNA-directed amino acid incorporation into polypeptides. Using the technique of DNA-RNA hybridization, we have demonstrated that the whole PhiX-174 genome is transcribed during concomitant protein synthesis.