Biological Complexity and Radiosensitivity: Radiation lethality in cells and viruses is correlated with nucleic acid content, structure, and ploidy

Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site

RAD51 is the central eukaryotic recombinase required for meiotic recombination and mitotic repair of double-strand DNA breaks (DSBs)1,2. However, the mechanism by which RAD51 functions at DSB sites in chromatin has remained elusive. Here we report the cryo-electron microscopy structures of human RAD51-nucleosome complexes, in which RAD51 forms ring and filament conformations. In the ring forms, the N-terminal lobe domains (NLDs) of RAD51 protomers are aligned on the outside of the RAD51 ring, and directly bind to the nucleosomal DNA. The nucleosomal linker DNA that contains the DSB site is recognized by the L1 and L2 loops-active centres that face the central hole of the RAD51 ring. In the filament form, the nucleosomal DNA is peeled by the RAD51 filament extension, and the NLDs of RAD51 protomers proximal to the nucleosome bind to the remaining nucleosomal DNA and histones. Mutations that affect nucleosome-binding residues of the RAD51 NLD decrease nucleosome binding, but barely affect DNA binding in vitro. Consistently, yeast Rad51 mutants with the corresponding mutations are substantially defective in DNA repair in vivo. These results reveal an unexpected function of the RAD51 NLD, and explain the mechanism by which RAD51 associates with nucleosomes, recognizes DSBs and forms the active filament in chromatin.

Track to the future: historical perspective on the importance of radiation track structure and DNA as a radiobiological target

PURPOSE

Understanding the mechanisms behind induced biological response following exposure to ionizing radiation is not only important in assessing the risk associated with human exposure, but potentially can help identify ways of improving the efficacy of radiotherapy. Over the decades, there has been much discussion on what is the key biological target for radiation action and its associated size. It was already known in the 1930s that microscopic features of radiation significantly influenced biological outcomes. This resulted in the development of classic target theory, leading to field of microdosimetry and subsequently nanodosimetry, studying the inhomogeneity and stochastics of interactions, along with the identification of DNA as a key target.

CONCLUSIONS

Ultimately, the biological response has been found to be dependent on the radiation track structure (spatial and temporal distribution of ionization and excitation events). Clustering of energy deposition on the nanometer scale has been shown to play a critical role in determining biological response, producing not just simple isolated DNA lesions but also complex clustered lesions that are more difficult to repair. The frequency and complexity of these clustered damage sites are typically found to increase with increasing LET. However in order to fully understand the consequences, it is important to look at the relative distribution of these lesions over larger dimensions along the radiation track, up to the micrometer scale. Correlation of energy deposition events and resulting sites of DNA damage can ultimately result in complex gene mutations and complex chromosome rearrangements following repair, with the frequency and spectrum of the resulting rearrangements critically dependent on the spatial and temporal distribution of these sites and therefore the radiation track. Due to limitations in the techniques used to identify these rearrangements it is likely that the full complexity of the genetic rearrangements that occur has yet to be revealed. This paper discusses these issues from a historical perspective, with many of these historical studies still having relevance today. These can not only cast light on current studies but guide future studies, especially with the increasing range of biological techniques available. So, let us build on past knowledge to effectively explore the future.

Early Days of Food and Environmental Virology

In July 1962, the author joined the Food Research Institute (FRI), then at the University of Chicago, to become its food virologist. There was a limited record of waterborne viral disease outbreaks at the time; recorded data on foodborne outbreaks were fewer still. Laboratory environmental (water and wastewater) virology was in its infancy, and food virology was in gestation. Detection of viruses was most often attempted by inoculation of primary primate cell cultures, with observation for plaque formation or cytopathic effects. Focus was initially on enteroviruses and reoviruses. Environmental and food samples had to be liquefied if not already in liquid form; clarified to remove solids, bacteria, and fungi; and concentrated to a volume that could be tested in cell culture. Cytotoxicity was also a concern. Studies at the FRI and some other laboratories addressed all of these challenges. The FRI group was the World Health Organization's Collaborating Center for Food Virology for many years. Other topics studied were virus inactivation as functions of temperature, time, matrix, disinfectants, and microbial action; peroral and ex-vivo infectivity; and the suitability of various virus surrogates for environmental monitoring and inactivation experiments. Detection of noroviruses and hepatitis A virus required molecular methods, most often RT-PCR. When it was found that inactivated virus often gave the same RT-PCR signal as that of infectious virus, sample treatments were sought, which would prevent false-positive test results. Many laboratories around the world have taken up food and environmental virology since 1962, with the result that a dedicated journal has been launched.

A Caenorhabditis elegans tissue model of radiation-induced reproductive cell death

We have developed a tissue model of radiation-induced reproductive cell death in the nematode Caenorhabditis elegans. Reproductive cell death is the primary mode of death in tissue multipotential precursor cells, or "clonogens," the targets of cytotoxic therapy, whose elimination results in normal tissue damage as well as solid-tumor eradication. Through extensive morphologic and genetic analysis, we have confirmed that cell death in this model represents reproductive cell death in isolation from apoptotic cell death, affording the opportunity to define the genetic pathways required for protection from reproductive cell death. We have additionally found that the DNA damage response pathway is necessary for protection from reproductive cell death, supporting the long-held tenet that DNA damage is the cause of reproductive cell death and further validating this model. This genetic tissue model provides a valuable tool for oncology-based research and affords a platform to broaden our insight into responses to cytotoxic therapy in tissues.

Survival of life on asteroids, comets and other small bodies

The ability of living organisms to survive on the smaller bodies in our solar system is examined. The three most significant sterilizing effects include ionizing radiation, prolonged extreme vacuum, and relentless thermal inactivation. Each could be effectively lethal, and even more so in combination, if organisms at some time resided in the surfaces of airless small bodies located near or in the inner solar system. Deep within volatile-rich bodies, certain environments theoretically might provide protection of dormant organisms against these sterilizing factors. Sterility of surface materials to tens or hundreds of centimeters of depth appears inevitable, and to greater depths for bodies which have resided for long periods sunward of about 2 A.U.

Cosmic radiation and evolution of life on earth: roles of environment, adaptation and selection

The role of ionizing radiation in general, and cosmic radiation in particular, in the evolution of organisms on the earth by adaptation and natural selection is considered in a series of questions: (1) Are there times during the evolution of the earth and of life when genetic material could be exposed to heavy ion radiation? (2) Throughout the course of chemical and biological evolution on the earth, what fraction of environmental mutagenesis could be attributable to cosmic and/or solar ionizing radiation? (3) Is ionizing radiation an agent of adaptation or selection, or both? (4) What can the cladistics of the evolution of genetic repair tell us about the global history of genotoxic selection pressures? (5) How much genetic diversity can be attributed to the selection of radiation-damage repair processes?

The DNA content of some mammalian cells measured by flow cytometry and its influence on radiation sensitivity

The DNA content of nine mammalian cell lines was determined by flow cytometry. Using radiobiological data from this and other laboratories a correlation between DNA mass and 1/D0 for X-rays, alpha-particles, and heavy ions could be established when the quantities were plotted on a log-log scale. The slopes of the regression lines amounted to 0.65 (X-rays), 0.64 (alpha-particles) and 0.74 (heavy ions). A similar correlation was found between DNA content and mean inactivation dose. The rather uniform slopes close to 2/3 suggest that radiosensitivity may depend on the surface area of the sensitive target, (cell nucleus) indicating a possible non-uniform distribution of radiosensitive sites within the nucleus.

Nuclear volume and chromatin organization in some radiosensitive and radioresistant mammalian cells

Nuclear dimensions in mammalian cells appear as a determining factor of chromatin organization and cellular radiosensitivity. Most radioresistant interphase cells have a nuclear volume (Vn) of 75 to 2700 micron 3, that could allow both the topological organization of chromatin as loops attached to the inner surface of the nuclear envelope and the unfolding of condensed chromatin within the topological constraints existing along the DNA molecule. In contrast, the radiosensitive small lymphocytes, with Vn values of 20 to 65 micron 3, seem to comprise significant amounts of highly condensed chromatin and dispose of an uncompleted topological organization of DNA, which may cause their incapacity to perform replication and transcription of DNA as well as the repair of radiation damage at a cell level. The indications are that radiosensitivity (1/D37) of animal cells, containing a similar quantity of DNA, should be directly proportional to 1/nuclear volume (1/Vn). However, DNA is unevenly distributed within the nuclear space, according to a partial ordering of interphase chromosomes; and it appears that radiosensitivity increases in zones of high DNA or chromatin density.

Scrapie infectious agent is virus-like in size and susceptibility to inactivation

The virions of all known viruses are composed of small amounts of genomic nucleic acid enveloped by proteins and other macromolecules. The aetiological agents of scrapie disease and the other subacute spongiform virus encephalopathies (SSVE), a group of slow, fatal degenerative diseases of the central nervous system, are, based on their resistance to sterilization and on indirect measurements suggesting subviral size, thought to have non-viral structures (see refs 1-3 for reviews). The kinetic studies reported here demonstrate that scrapie's resistance to many inactivants is limited to small subpopulations of the total infectivity, the majority population being highly sensitive to inactivation. Moreover, control inactivations of conventional viruses provide examples of both scrapie-like resistant subpopulations and complete insensitivity to virucidal agents, especially when those viruses, like scrapie, are suspended in hamster brain homogenate. Virus controls further establish that the ability of the scrapie agent to penetrate dilute agarose-acrylamide electrophoretic gels is shared by conventional viruses. Direct comparison of scrapie's resistance to ionizing radiation with the resistances of other viruses places scrapie with the smaller viruses, as opposed to requiring a subviral size as claimed.

Biological and Clinical Approach to the Problem of Tumor Radiosensitization

The aim of every form of radiotherapy has always been the selective elimination of tumor cells from the cancerous body. Unfortunately over 70 years’ experience has shown that this goal is not usually feasible even at the local site. In attempting to explain the «failure» of traditional radiotherapy account must be taken of recent discoveries in cellular radiobiology, especially: a) the roughly equal «intrinsic radiosensitivity» of the various mammalian cells, whether normal or neoplastic; b) the relative radioprotection enjoyed by some normal and cancer cells in the cancerous organism. The two main problems facing radiotherapy at present are: 1) how to interfere with the cell's intrinsic radiosensitivity from the outside by physical, chemical and biological means; 2) how to interfere selectively with neoplastic cells. It is thus clear that modern radiotherapy calls for appropriate preparation of the substrate: the cancerous organism. The recent successful application of chemical substances tried in other fields of human pathology to attempts at radiosensitizing tumors is a promising approach to this research of new paths with old tools.

Target volume analysis of vaccinia virus: influence of virus dispersion and noninfectious particles

These data indicate that 90% of monodisperse vaccinia virus (VV) has a D(37) dose of 1.0 x 10(4) +/- 0.2 x 10(4) rad when exposed to the direct effect of gamma radiation from (137)Cs and (60)Co sources. This D(37) dose yielded a targt size of approximately 10(8) daltons, close to the molecular weight of VV deoxyribonucleic acid. This target corresponds to the first component of the survival curve of VV. Noninfectious virus seemed to play a role on the slope and the proportion of the survival curve second component, suggesting that multiplicity reactivation takes place.

Effects of ionizing radiation on synchronous cultures of Escherichia coli B-r

The sensitivity of Escherichia coli B/r to X-irradiation is correlated with the replication cycle of deoxyribonucleic acid (DNA). The sensitivity to X-irradiation in the wild type can be attributed to the presence of nuclear targets plus DNA repair mechanisms. The effects of nuclear targets are observed in the recombination-deficient (rec-) mutant B/r, but the sensitivity reflected by changes in the slope of killing curves is absent. A study of different growth conditions indicates that maximal resistance to X rays occurs toward the middle of the division cycle. Evidence is offered that branched chromosomes respond as one-hit targets to X-irradiation. The killing effects of heavy-ion bombardment on E. coli are due primarily to ionizing radiation.

Cellular changes accompanying the swarming of Proteus mirabilis. II. Observations of stained organisms

This paper describes the changes in nuclear complement, cytoplasm, and cell wall which take place when short rods of Proteus mirabilis differentiate into long swarmers. In the swarmers themselves, definite cellular units are mapped out at intervals of 1.2 to 1.8 μ. These units consist of a nucleus (or paired nuclei) and the adjacent cytoplasm, there being apparently no cross septa between successive units. The cytology of the swarmers has been compared with that of long forms of P. mirabilis induced by penicillin, lithium chloride, ultraviolet light, and gamma radiation. Depending on the inducing agent and dosage, such long forms frequently have abnormal-looking nuclei and malformed cell walls, and thus contrast strikingly with the spontaneously arising swarmers.

Radiation Resistance in Lipovirus-Altered Human Cells

Human cells altered by infection with the "lipovirus," a transmissible cytopathic agent, are highly resistant to ionizing radiation. Whereas about 500 roentgens will inhibit cell multiplication in normal cells, more than 500,000 roentgens are required to produce a similar effect in the altered cells. This gross change in cellular radiosensitivity may provide a useful system for studying in vitro the mechanisms of inhibition of cell division by radiation.