Symmetry in protein-nucleic acid interaction and its genetic implications

Genetic analysis of recombination at the g locus in Sordaria fimicola

Interallelie crosses of mutants at the grey (g) spore colour locus in Sordaria fimicola, heterozygous for flanking markers, give rise to a large number of aberrant ascus genotypes, 45 of which can arise through relatively simple events and have been chosen for study. These genotypes comprise 50–75% of the aberrant asci, depending on the mutants crossed.

Comparison of the results from 10 pairwise crosses involving 7 alleles reveals that linked postmeiotic segregation and co-conversion decrease rapidly in frequency with increasing separation of the mutant sites.

The data from reciprocally recombinant asci, from asci with normal segregation at one of the two mutant sites, and from flanking marker behaviour in one- and two-point crosses, agree with the Holliday-Sobell formulation, with the following additional features:

(1) The nuclease, which nicks homologous polynucleotides and then degrades one of the two nicked chains when a mutant enters the hybrid DNA structure, can show preferential degradation of the mutant (or the wild-type) chain. In addition, a second nuclease is involved in the excision-repair process that introduces an additional preferential (marker specific) bias in the degradation of the mutant (or the wild-type) chain. This could explain why asci with odd-ratio conversion (5:3 and 3:5 ratios) sometimes show a different bias, as first reported by Emerson for Ascobolus, from those with even-ratio conversion (6:2 and 2:6 ratios), since the latter but not the former require, in addition, the action of a mismatch correction enzyme to account for them.

(2) The migratory hybrid DNA structure which enters the gene at one end may be of a different size from that which enters from the other end.

(3) Mismatch correction at the end of the hybrid DNA structure leads to a non-recombinant outside marker genotype and modifies the 1:1 ratio of parental:recombinant flanking markers that is otherwise found.

Novel dimeric configurations from bacteriophage G4 replicative form DNA

The oligomeric fraction of the replicative form of phage G4 was prepared by sedimentation on three successive CsCl velocity gradients followed by resolution on CsCl-propidium diiodide equilibrium gradients and subfractions through the equilibrium gradients were examined by electron microscopy. The most frequent dimer species were the circular dimer, the singly linked catenane and the figure 8; these occurred in a ratio of 10:3:1. The high enrichment for dimers and other oligomers made possible the observation and the determination of the frequency of occurrence of a number of minor species, some of them of novel configuration. These are (a) dimers similar to figure 8s except containing long, apparently four-stranded junctions common to the two halves (theta forms); (2) dimers similar to those in (1) except that the long junctions separate the two halves (dumbbell forms); (3) multiply catenated dimers with apparent right-handed intertwines; and (4) dimers containing a knot. Theta forms cleaved by EcoRI were shown to be stable under conditions in which EcoRI-treated figure 8s were resolved by branch migration.

Structure and distribution of inverted repeats (palindromes). II. Analysis of DNA of the mouse

The size and distribution of renatured inverted repeats (palindromes) in Mus musculus DNA were examined by electron microscopy (EM). The majority (85%) of the palindromes were found to be clustered in about one half of the DNA strands. The rest of the DNA strands were seen with a solitary looped structure - The unlooped palindromes constituted 53% of all palindromes and were always clustered. There was a significant reduction in the number of unlooped palindromes in comparison to D. melanogaster DNA (Biezunski, 1981) and as a result the palindrome clusters were smaller and contained 2-8 palindromes [4-16 inverted repeats (ir)] per DNA strand. The looped palindromes had a wide and regular distribution with spacing lengths similar to those found in D. melanogaster DNA, and showed some periodicity. The average spacing between centers of all palindromes (inside a cluster) was 4.325 kb, and between centers of looped palindromes 8.544 kb. - The lengths of the ir of unlooped and looped palindromes were grouped (similar to D. melanogaster DNA) in one size-class with a range of 30-240 bp and an average length of 130 bp. Longer ir were also observed and the average length of ir in unlooped palindromes was 186 bp, in looped 588 bp, and the total average length was 375 bp. - It was calculated that there are about 224,000-320,000 palindromes (ir pairs) in the mouse genome, with the spacing between centers of all palindromes about 13-9 kb in length. - In high molecular weight mouse DNA, complex looped structures composed of rows of 5-8 looped palindromes one on "top" the other, formed by renaturation of multiple ir, were observed. It is suggested, that clustered repetitive sequences, in direct and inverted orientation, might be of one family and homologous to one another, and be able to reassociate, in vitro and in vivo, into structures of different forms, which could function as binding sites for various regulatory proteins during mouse development.

Protein-depleted chromosomes. I. Structure of isolated protein-depleted chromosomes

Protein-depleted isolated Chinese hamster chromosomes have been obtained by different protein extraction procedures and examined by electron microscopy and SDS-polyacrylamide gel electrophoresis. Salt-resistant centromeric and telomeric structures are visible in protein-depleted chromosomes and the protein-depleted chromosomes appear to have a regular, longitudinal pattern in critical point dried preparations. The scaffold-like structure of protein-depleted chromosomes is highly affected by the ionic strength and composition of the extraction medium and by the spreading conditions. Nucleosomal histones of isolated chromosomes proved to be more sensitive to the sodium chloride treatment than histones of isolated chromatin. A small, but constant quantity of core histones was detected in 2 M salt extracted chromosomes and H3 and H4 histones of isolated chromosomes appeared to be resistant to the sodium deoxycholate treatment.

Nucleotide sequence of the simian virus 40 Hind-K restriction fragment

The restriction fragment Hind-K represents 4.2% of the genome of Simian virus 40 (SV40) and is located near the middle of the late region. Its nucleotide sequence is reported here. It was mainly established by analysis of transcription products, synthesized by means of Escherichia coli RNA polymerase and nucleoside triphosphates, one of which was (alpha-32P)-labeled. Strand assignment was possible by hybridization of asymmetric, labeled transcripts of total SV40 DNA to filter-bound Hind-K fragment. Further information and unambiguous confirmation of the sequence was obtained by the use of direct DNA-sequencing methods. For this purpose the fragment was labeled at the 5' ends by means of polynucleotide kinase and [gamma-32P]ATP and redigested with a suitable restriction enzyme. The separated products were then either partially digested with snake venom diesterase for analysis by the 'wandering spot' method or partially degraded with the base-specific reagents dimethylsulphate or hydrazine for direct sequence analysis on gel. The Hind-K sequence is 219 base pairs long. The message strand is particularly rich in adenosine (39%) and purines. The nucleotide sequence cna unambiguously be translated into an amino acid sequence and the N-terminal codon of the viral protein VP1 gene could be identified. The amino-terminal part of VP1 is rich in proline and lysine. The nucleotide sequence of Hind-K codes also for the carboxyl-terminal part of the viral protein VP2 and VP3 genes, which partly overlap the VP1 gene.

DETECTION OF ABERRANT 4:4 ASCI IN ASCOBOLUS IMMERSUS

Ascopore and mycelium markers were used to detect the aberrant 4:4 asci of the mutation b2A4 of the b2 locus of Ascobolus immersus. Previous studies have shown that this mutation produces gene conversion events with many postmeiotic (30+:5 m and 5+:3 m) in addition to meiotic (2+:6 m and 6+:2 m) segregations. But the aberrant 4:4 asci could not be scored because the octads of this fungus are unordered. The asci were screened using round-spored and granular-spored mutants and confirmed with two mycelium markers, a brown mutant and a wave mutant. Very high frequencies of aberrant 4:4 asci were observed in each cross performed (more than 40% of the postmeiotic segregations). This suggested that both chromatids are very often implicated in the process of hybrid DNA formation at this site of the locus.

Biochemical analysis of genetic recombination in eukaryotes

Recent studies concerning molecular mechanisms of genetic recombination in eukaryotes are reviewed. Since many of these studies have focused on the testable predictions arising from the hybrid DNA theory of genetic recombination, this theory is summarised. Experiments to determine the time of meiotic crossing-over and the structure of the synaptonemal complex which facilitates meiotic crossing-over are described. Investigations of DNA nicking and repair events implicated in recombination are discussed. Properties of proteins which may facilitate hybrid DNA formation, and biochemical evidence for hybrid DNA formation are presented. Finally, a nuclease which has been implicated in gene conversion is described.

Elements of a DNA-polypeptide recognition code: electrostatic potential around the double helix, and a stereospecific model for purine recognition

A model for stereospecific complex between a polynucleotide double helix and a twisted beta-ribbon type polypeptide is described. The beta ribbon lies in the major groove with alternate side chains pointing toward the interior of the groove. The base-amino acid complementarities are: Arg, G and Asn or Gln, A. It is shown that this complex can: (a) distinguish between G and A in homopolar sequences; (b) the complex is stabilized by approx. 6 Kcal/mole per hydrogen bond per base pair; (c) the required backbone conformation is in the permitted range of Ramachandran plots.

A model for the specific pairing of homologous double-stranded nucleic acid molecules during genetic recombination

A model involving a specific pairing of homologous double-stranded nucleic acid molecules is applied to some parts of genetic recombination. The most original features of this application of the model relate to the initiation process, a part of which can be described by a highly compact and symmetrical structure. The model also provides a simple view of the formation of hybrid nucleic acid. The possibilities of detecting four-strand structures are briefly discussed.

Mechanisms for sister chromatid exchanges and their relation to the production of chromosomal aberrations

By taking advantage of the fact that fluorescent light (FL) induces strand breaks only in bromodeoxyuridine(BrdUy-substituted DNA, and that those breaks eventually lead to the formation of sister chromatid exchanges (SCEs), the response of SCEs to FL was studied carefully in Chinese hamster chromosomes in which, out of four DNA strands, BrdU-substitution had occurred either in one or three strands. The FL-induced SCE frequency did not differ greatly between these two types of chromosomes. However, when they were submitted to caffeine treatment, a drastic increase in the frequency was detected in the trifilarly-substituted chromosomes while a significant decrease occurred in the unifilarly-substituted chromosomes. Based on these results, a working hypothesis was developed that the SCE can arise by at least two different mechanisms, one operating at replicating points probably utilizing the machinery of DNA replication, and the other acting only in the post-replicational DNA portion, probably in a similar fashion as assumed in a general model of crossing over in the eukaryote. These dual mechansims may account for the discrepancy encountered in the explanations of the induction of SCEs by various exogenous agents as well as spontaneous SCEs. The present study also showed that some, but clearly not all, of chromatid deletions are the outcome of the failure to complete SCEs arising through these mechanisms.

Organization and evolution of the mitochondrial genome of yeast

The mitochondrial genome of yeast (S. cerevisiae or S. carlsbergensis) appears to be formed by 60-70 genetic units, each one of which is formed by (1) a GC-rich sequence, possibly having a regulatory role; (2) a gene, and (3) an AT-rich spacer, which probably is not transcribed. Recombination in this genome appears to underlie a number of important phenomena. The organization of the mitochondrial genome of yeast and these recombinational events are discussed in relationship with the organization and evolution of the nuclear genome of eukaryotes.

Kinetics of branch migration in double-stranded DNA

The rate of branch migration in double stranded DNA has been measured by the use of a unique substrate formed by the action of the EcoRI restriction endonuclease on the dimeric figure-8 configuration of the replicative form DNA of phage G4. The figure-8 and the X-form derived from it contain a junction of the kind postulated to occur in the Holliday structure and to be an essential feature of a number of models of recombination. In the X-form this junction can branch migrate to an irreversible terminal configuration consisting of two linear monomers. The disappearance of X-forms was measured by electron microscopy. A treatment of branch migration as a random walk process was developed to permit the determination of the rate of the intrinsic process, a step movement of the junction by a distance of one base pair. A value of about 6 kilobase pairs per sec at 37 degrees was obtained.

Differences in the genetic structure of Bacillus subitilis strains carrying the trpE26 mutation and strain 168

It was previously shown that in strains of Bacillus subtilis bearing the trpE26 mutation a chromosome segment (from trpD to ilvA) is translocated to a position near the thr region. Further PBS1-mediated transduction data have now revealed that these strains also possess an inversion of part of the chromosome from the origin of replication, down to the tre locus on one side and the cysB locus on the other. These data concern evidence of linkage of tre-12- to markers in the translocation (hisH2, tyrA1, and metB3) as well as linkage of the cysB3 marker to thi-86, gly-133, and catA. They explain the previously observed absence of linkage of markers in the translocated segment to cysB3. The model proposed for the formation of merodiploids in trpE26 strains, which calls for the fusion of two genetic elements, is not incompatible with this new finding.

Cryptic mutations: their predicted biochemical basis, frequencies and effects on gene conversion

Cryptic mutations are undetected base changes in genetic DNA (or hereditary RNA). Some kinds of base change are normally undetected; others may or may not be detected, depending on experimental conditions, procedures and genotypes. Cryptic mutations could affect gene conversion results because when heterozygous they cause mismatched base pairs in hybrid DNA in the same way as known mutations, but the experimenter is unaware of them. Cryptic heterozygosity will usually be much more frequent in heterothallic than homothallic organisms. The effects of cryptic mutation heterozygosity on recombination and conversion of known mutations are predicted with reference to co-conversion, map expansion and polarity. Relevant evidence is considered.

Studies on the induction of mitotic gene conversion by ultraviolet irradiation. I. Analysis of dose-frequency relationship

The UV (270-nm) dose-frequency relationship for the induction of intragenic mitotic recombination at trp 5 locus in Saccharomyces cerevisiae was non-linear. Two parameters, alpha and a, in the proposed equation for the non-linear relationship f = (at)alpha were determined so as to fit the experimental data by the method of least squares. The analysis was extended over 5 cell stages during synchronous growth. It was found that (1) parameter alpha changed from 2.02 for unbudded small cells to 1.09 for the stage where the cell had finished the division of the nucleus, and (2) parameter a changed correspondingly from 7.25-10(-4) to 0.180-10(-4) sec-1 during the same period. One interesting outcome in this analysis was the deduction of a dose-dependent nature of relative sensitivity with respect to the stage. The determination of these two parameters enabled us to calculate dose-effect relationships beyond the limits of experimental restrictions. Such an "imaginary" relationship, calculated at an extremely low dose, revealed the existence of maximal sensitivity around the DNA synthesis period. It was further shown that this maximum would easily be masked even in the moderate dose range. Thus, we conclude that the validity of single dose comparisons is diminished unless alpha is constant regardless of the cell stage. Some considerations on the proposed parameters have been made in relation to the mechanisms of the induction of gene conversion by UV.

Antimutator activity during mitosis by a meiotic mutant of yeast

Diploids homozygous for the mutation spo7-1 do not exhibit net premeiotic DNA synthesis at 34 degrees C and are defective in commitment to recombination following exposure to sporulation medium. The spo7-1 mutation confers antimutator activity during mitosis at 34 degrees C, indicating that the SPO7 gene product is involved in both mitotic and premeiotic DNA metabolism. Strains bearing spo7-1 are slightly more sensitive to killing by ultraviolet light than the wild type but are proficient in UV induced mutation and mitotic intragenic recombination. The mitotic antimutator activity of spo7-1 is directed against a class of forward mutations known to occur more frequently during mitosis than meiosis.

Visualization of a novel junction in bacteriophage lambda DNA

At early times after infection of a recA derivative of Escherichia coli with lambdab221c126red270a42 phage, a low but significant proportion of intracellular lambda molecules show a novel junction. These junctions are also present, although in reduced numbers, in a lysate obtained at late times after infection of a recA+ host with lambdacIIcIII phage. Fine structure and denaturation mapping analyses showed that these junctions occur at homologous positions and that they are compatible with the occurrence of a cross-strand exchange between lambda DNA duplexes similar to the type proposed in most molecular models for genetic recombination. However, the results are also consistent with the structures expected if a replicating growing point undergoes branch migration.

An acridine probe into the physiological state of the cell

Acridine orange was used as a probe to look into the physiological state of the yeast cell, particularly as regards the change in the properties of the membrane (which acts as a barrier against the incoming acridine orange) and the availability of binding sites for acridine orange in chromosomal DNA during growth. After acridine orange had been introduced into the cell, the genetic change at a specific locus with incubation time was measured photodynamically. A three-fold increase in the rate of penetration of acridine orange into the cell was observed, for instance, in going from the resting phase to the dividing phase. A five-fold increase was observed in the number of binding sites in chromosomal DNA under the same transition of the cell. These two parameters may be useful as a measure of the physiological changes in the cell. Some environmental factors such as pH and temperature were also demonstrated to affect the parameters.

The repair of DNA double-strand breaks in mammalian cells and the organization of the DNA in their chromosomes

The molecular weight of native DNA has been accurately determined by the use of a semiautomated sucrose gradient system. A mondisperse size distribution (speed dependence free) of eighth-of-a-chromatid pieces [1.7 S 10(10) daltons, with 95% confidence (fiducial) limits of +/- 48%] was found. This size has been confirmed by viscoelastometry. Ionizing radiation rapidly breaks each of these pieces into about 21 subunits (again monodisperse) of 8 X 10(8) daltons each. With increaseing dose (greater than 2 krad) the subunits are themselves randomly broken down into even smaller pieces. Postirradiation incubation at 37 degrees C permits the cells to repair both DNA double-strand breaks and intersubunit linkages at the same dose-independent rate (T37) of about 55 min, the same rate as found in Micrococcus radiodurans. The repair data are compatible with a first-order-kinetics repair system, analogous to the post-UV excision-repair system, which becomes saturated at high doses (greater than 60 krad). Specially constructed "enzyme" gradients show that the linkages contain at least two protein molecules each covalently bound to the end of a subunit and linking the subunits together by a disulfide bond(s). Correlation of cell survival and DNA break kinetics yields two possible models. These are that the two-thirds of the lethal events which are due to improperly or unrepaired double-strand breaks result from either (1) a misrepair frequency of 3.5 X 10(-3) (rather high for a mutation frequency) or (2) the induction of a double-strand break in a single eighth-of-a-chromatid unit which is essential for survival but which cannot be repaired, possibly because the unit contains the double-strand break repair system gene(s).

A mechanism to activate branch migration between homologous DNA molecules in genetic recombination

A mechanism to activate branch migration between homologous DNA molecules is described that leads to synapsis in genetic recombination. The model involves a restriction-like endonucleolytic enzyme that first nicks DNA (to produce single-strand breaks) on strands of opposite polarity at symmetrically arranged nucleotide sequences (located at ends of genes or operons). This is followed by local denaturation of the region, promoted by a single-strand-specific DNA binding protein (i.e., an unwinding protein). Hydrogen-bounding between homologous DNA molecules can then be initiated and this allows for subsequent propagation of hybrid DNA in the pathway to formation of the synapton structure.