DNA Reorganization Research Articles

Patent Evaluation: A Two-Phase System for the Production of Antigens

SummaryNovelty: A hybrid live vaccine is disclosed. The vaccine comprizes a recombinant DNA producing subpopulations A and B. Subpopulation A is claimed to infect and act immunologically per se, whilst subpopulation B is claimed to be regenerated from subpopulation A, producing additional antigen and then acting immunologically with respect to this additional antigen. A process for the preparation of this live vaccine is also claimed. The vaccine has the potential for immunization of mammals.Biology: Biological data include the results of oral immunizations of BALB/c mice with hybrid Salmonella typhimurium SL3235 strains and measuring hormonal immune response. The recombinant DNA is contained in a viral live vaccine, the chromosome of a cellular live vaccine or in a plasmid. The cellular live vaccine is a bacterium or a eukaryotic cell. The division of the live vaccine into the two subpopulations occurs by spontaneous DNA reorganization, based on a specific DNA inversion, deletion or replication process. The reorganization initiates a cascade reaction leading indirectly to the formation of additional antigen in subpopulation B.Chemistry: Construction of an invertable DNA element for the production of Vibrio cholerae toxin 8-subunit antigen in Salmonella is described.

Mutations at the Arabidopsis CHM locus promote rearrangements of the mitochondrial genome.

Nuclear recessive mutations at the chloroplast mutator (CHM) locus of Arabidopsis produce a variegated phenotype that is inherited in a non-Mendelian fashion. Molecular analysis of the cytoplasmic genomes of variegated plants from two independent chm mutant lines, using specific chloroplast and mitochondrial probes, showed that the chm mutations reproducibly induce the appearance of specific new restriction fragments in the mitochondrial genome. The presence of these restriction fragments cosegregated with the variegated phenotype in the progeny of crosses between mutant and wild-type plants. Sequence analysis of one of the new restriction fragments found in the variegated plants suggested that it was the product of a rearrangement event involving regions of the mitochondrial genome. Thus, it appears that the CHM locus may encode a protein involved in the control of specific mitochondrial DNA reorganization events.

Molecular genetics ofStreptococcus thermophilus

The metabolism and genetics of Streptococcus thermophilus (presently Streptococcus salivarius ssp. thermophilus) have only been investigated recently despite its widespread use in milk fermentation processes. The development of recombinant DNA technology has allowed impressive progress to be made in the knowledge of thermophilic dairy streptococci. In particular, it has permitted a careful analysis of phenotypically altered variants which were derived from a mother strain by plasmid or chromosomal DNA reorganization. While natural phage defense mechanisms of S. thermophilus remain poorly documented, information on the bacteriophages responsible for fermentation failures has accumulated. The lysogenic state of two S. thermophilus strains has also been demonstrated for the first time. Gene transfer techniques for this species have been established and improved to the point that targeted manipulation of their chromosomal determinants is now feasible. Cloning and expression vectors have been constructed, and a few heterologous genes were successfully expressed in S. thermophilus. The first homologous genes, involved in carbohydrate utilization, have been cloned and sequenced, shedding some light on the molecular organization of key metabolic steps.

Molecular genetics of Streptococcus thermophilus

The metabolism and genetics of Streptococcus thermophilus (presently Streptococcus salivarius ssp. thermophilus) have only been investigated recently despite its widespread use in milk fermentation processes. The development of recombinant DNA technology has allowed impressive progress to be made in the knowledge of thermophilic dairy streptococci. In particular, it has permitted a careful analysis of phenotypically altered variants which were derived from a mother strain by plasmid or chromosomal DNA reorganization. While natural phage defense mechanisms of S. thermophilus remain poorly documented, information on the bacteriophages responsible for fermentation failures has accumulated. The lysogenic state of two S. thermophilus strains has also been demonstrated for the first time. Gene transfer techniques for this species have been established and improved to the point that targeted manipulation of their chromosomal determinants is now feasible. Cloning and expression vectors have been constructed, and a few heterologous genes were successfully expressed in S. thermophilus. The first homologous genes, involved in carbohydrate utilization, have been cloned and sequenced, shedding some light on the molecular organization of key metabolic steps.

Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows.

A new procedure for the analysis of the structure and molecular dynamics of duplex DNA is introduced, in which comprehensive visualization of results and pattern recognition is greatly facilitated. The method involves determining the values of the conformational and helicoidal parameters for each structure entering the analysis using the method "Curves" developed by Lavery and Sklenar, J. Biomol. Str. Dyn. 6, 63 (1988), followed by a novel computer graphic display of the results. The graphic display is organized systematically using conformation wheels, or "dials", for each IUPAC torsional parameter and "windows" on the range of values assumed by the linear and angular helicoidal parameters, and is presented in a form isomorphous with the structure per se. The complete time evolution of the conformational and helicoidal parameters of a DNA double helix can then be depicted in a set of six composite figures. Dynamical aspects of helix bending are also subsumed in this analysis. The procedure is illustrated with an analysis of the structures of canonical A and B forms of DNA and the 300 degrees K native dodecamer duplex d(CGCGAATTCGCG). The "dials and windows" are then used for a comprehensive analysis of 30 psec of molecular dynamics on the dodecamer in the vicinity of a canonical B-DNA energy minimum. This involves presentation of the time evolution of 206 conformational and 230 helicoidal parameters for the dodecamer. A number of interesting structural features can be recognized in the analysis, including crankshaft motions, BI - BII transitions, sugar repuckerings, and a description of spontaneous helix bending at what corresponds to the 1 degrees and 2 degrees "hinge points" indicated in the crystal structure. Our approach is expected to be directly useful for critical analysis of the effects of various assumptions about force field parameters, hydration and electrostatic effects and thus contribute to the development of reliable simulation protocols for nucleic acid systems. Extension of the method to present differential changes in conformational and helicoidal parameters is expected to be valuable for the analysis of structural and molecular dynamics studies of the reorganization and adaptation of DNA on complexation with various drugs and regulatory proteins.

A comparison of cytoplasmic revertants to fertility from different CMS-S maize sources

The mitochondrial genome organizations of a number of independent culture-derived fertile CMS-S revertants with the nuclear genotype W182BN were compared to spontaneous field revertants with the genotypes WF9, M825/Oh07 and 38-11. Regions of the genome around sequences homologous to the terminal repeats of the linear S1 and S2 episomes characteristic of CMS-S mitochondria were used as hybridization probes on Southern blots of BamHI and SalI digested mitochondrial DNA. The results obtained suggest that the nuclear, not the cytoplasmic, genotype of the parent plant affects the type of novel mitochondrial DNA organization found in the revertant. The DNA reorganization during reversion from CMS-S in tissue culture appears to be similar to that observed in spontaneous revertants obtained during the normal plant life-cycle. Unlike the situation for reversion from CMS-T, no common DNA sequence or reading frame appeared to be lost or disrupted in revertants.

Reorganization of mitochondrial genomes of cytoplasmic revertants in cms-S inbred line WF9 in maize

Cytoplasmic reversion to fertility in cms-S maize has been previously correlated with changes in mitochondrial genome organization, specifically with loss of the autonomously replicating linear plasmid-like DNAs, S1 and S2, and with accompanying alterations in the high molecular weight mtDNA (main genome) that specifically involved S1 and S2 sequences. These studies, however, dealt with cytoplasmic revertants occurring in the cms-VG M825 inbred line and in the cms-VG M825/Oh07 F1 hybrid. This paper deals principally with patterns of mitochondrial DNA reorganization accompanying cytoplasmic reversion to fertility in the WF9 inbred line nuclear background. Here the free S1 and S2 plasmid-like DNAs are retained in the revertants. Mitochondrial DNA analysis by Southern hybridization using cloned fragments of S1 and S2 shows altered organization around S-homologous regions in the main mitochondrial genome of revertants as compared with that of the male-sterile parental controls, but the pattern of main genome changes involving these regions differs from that of the cytoplasmic revertants that occurred in M825 and M825/Oh07 backgrounds. Similar experiments using a clone of the cytochrome oxidase I (COX I) gene of maize as a probe indicate that reorganization in this region is also involved in the changes in mtDNA that accompany cytoplasmic reversion to male fertility in cms-S WF9. The heterogeneity in patterns of reorganization of the main mtDNA genome that accompany cytoplasmic reversion in the same and different nuclear backgrounds are discussed in relation to cytoplasmic male sterility (CMS).

Large scale synchronous mating and the study of macronuclear development in Euplotes crassus.

After conjugation in hypotrichous ciliates, a new macronucleus is produced from a copy of the micronucleus. This transformation involves large-scale reorganization of DNA, with conversion of the chromosomal micronuclear genome into short, gene-sized DNA molecules in the macronucleus. To study directly the changes that occur during this process, we have developed techniques for synchronous mating of large populations of the hypotrichous ciliate Euplotes crassus. Electron microscope studies show that the micronuclear chromosomes are polytenized during the first 20 h of macronuclear development. The polytene chromosomes lack the band-interband organization observed in other hypotrichs and in the Diptera. Polytenization is followed by transectioning of the chromosomes. We isolated DNA at various times of macronuclear development and found that the average molecular weight of the DNA decreases at the time of chromosome transectioning. In addition, we have shown that a small size group of macronuclear DNA molecules (450-550 base pairs) is excised from the chromosomal DNA approximately 10 h later in macronuclear development.

Mechanisms of DNA Reorganization in Bacteria

Publisher Summary This chapter discusses the mechanisms of DNA reorganization in bacteria. Many biochemical systems exist precisely for creating new DNA structures. Nucleotide sequences in DNA molecules constitute one of the main systems for information storage in living cells. As organisms encounter varying external environments and create new internal environments for their cells, they often need to change the stored information. Biochemical components involved in the genetic change include all the activities involved in the creation of a transposable resistance determinant and its transposition to a transmissible plasmid, the activities required for plasmid replication and segregation, and the activities required for conjugal plasmid transfer of specific proteins and cell structural components. Many proteins active on DNA either do not catalyze specific chemical reactions or do not show turnover but rather function in a stoichiometric manner. The absence of turnover facilitates the control of DNA reorganizations because they can be restricted to a few reactions by limiting the amount of the proteins involved. Proteins, which act enzymatically might carry on repeated DNA reorganizations.

Programming of DNA rearrangements involving mu prophages.

Most of the papers in this Symposium provide abundant evidence that changes in DNA sequence organization — and, consequently, changes in the information content of DNA molecules — result from the action of specific biochemical systems. Over the past three decades, detailed in vivo and in vitro studies of how genetic changes occur have radically altered our ideas about the mutational process. Instead of invoking nonspecific chemical events, such as keto-enol tautomerism in purine and pyrimidine bases, we now see specific enzymatic activities as the agents of genetic change. Systems like the SOS response of enteric bacteria (Witkin 1976) show that genetic change is a biochemical process even when there has been direct physicochemical damage to DNA molecules. Some kinds of DNA reorganization, such as homology-dependent general recombination and replicative recombination, involve multiple biochemical steps and the activities of many proteins. There is, therefore, prima facie evidence for regulatory processes...