Radiation damage to nucleoprotein complexes in macromolecular crystallography.

Significant progress has been made in macromolecular crystallography over recent years in both the understanding and mitigation of X-ray induced radiation damage when collecting diffraction data from crystalline proteins. In contrast, despite the large field that is productively engaged in the study of radiation chemistry of nucleic acids, particularly of DNA, there are currently very few X-ray crystallographic studies on radiation damage mechanisms in nucleic acids. Quantitative comparison of damage to protein and DNA crystals separately is challenging, but many of the issues are circumvented by studying pre-formed biological nucleoprotein complexes where direct comparison of each component can be made under the same controlled conditions. Here a model protein-DNA complex C.Esp1396I is employed to investigate specific damage mechanisms for protein and DNA in a biologically relevant complex over a large dose range (2.07-44.63 MGy). In order to allow a quantitative analysis of radiation damage sites from a complex series of macromolecular diffraction data, a computational method has been developed that is generally applicable to the field. Typical specific damage was observed for both the protein on particular amino acids and for the DNA on, for example, the cleavage of base-sugar N1-C and sugar-phosphate C-O bonds. Strikingly the DNA component was determined to be far more resistant to specific damage than the protein for the investigated dose range. At low doses the protein was observed to be susceptible to radiation damage while the DNA was far more resistant, damage only being observed at significantly higher doses.

Photoreactivation of DNA by an archaeal nucleoprotein Sso7d.

Sso7d is a chromosomal protein of hyperthermophilic Archaea. The crystal structure of Sso7d-d(GTAAT(I)UAC)(2) has been clarified at high resolution, showing that the protein binds in the minor groove of DNA, causing a sharp kink of approximately 60 degrees. Recently, we found that photoirradiation of Sso7d and 5-iodouracil-((I)U)-containing 5'-d(GTAAT(I)UAC)-3' efficiently induced the abstraction of hydrogen from the methyl group of T(5) at the kink. In the present study, we found that the photoreactivity of 5-bromouracil ((Br)U)-containing 5'-d(GTAAT(Br)UAC)-3' was enhanced in the presence of Sso7d. Using hypoxanthine (I)-containing 5'-d(ITAAT(Br)UAC)-3', we demonstrated that electron transfer occurs efficiently from Sso7d to DNA. Product analysis showed that Trp-24 of Sso7d, located at the surface of the DNA, is consumed to produce N'-formylkynurenine during photoirradiation, indicating that Trp-24 acts as an electron source. To explore the possibility of electron transfer between Sso7d and other DNA substrates, we examined the photochemical repair of the thymine dimer 5'-d(GTAAT<>TAC)-3' by Sso7d. Sso7d effectively repaired 5'-d(GTAAT<>TAC)-3' to 5'-d(GTAATTAC)-3' under irradiation conditions. During this reaction, Trp-24 was not oxidized significantly, indicating that the anion radical of the repaired TT sequence is oxidized by the cation radical of Trp-24, and that a so-called "circular electron transfer" mechanism is operating in this system.

Cell proteins bind to sites within the 3' noncoding region and the positive-strand leader sequence of measles virus RNA.

The genomic 3' noncoding region (NCR) of nonsegmented negative-strand RNA viruses contains recognition site(s) for the polymerase complex, while the RNA plus-strand leader sequence (LS) is probably involved in RNA encapsidation. It is known that host-encoded factors play a role in transcription and replication of some of this group of viruses. Here we report that cellular proteins interact with the genomic 3' NCR and with the plus-strand LS RNA of an important human pathogen, measles virus (MV), a member of the family Paramyxoviridae. Using gel retardation assay and RNA footprinting analysis, we demonstrated that in Vero cells, host-encoded proteins bind specifically to domains within these two sequences. A polypeptide of about 20 kDa binding to the 3' NCR and two polypeptides of about 22 and 30 kDa interacting with plus-strand LS were detected by RNA-protein UV cross-linking. Different RNA-binding activities were found in cells differing in permissiveness to MV replication. The results suggest a role for host-encoded proteins in MV replication.

Phage nucleoprotein-psoralen interaction: quantitative characterization of dark and photoreactions.

The irradiation of the phage T7 system containing psoralen as photosensitizer causes many processes, each of them leading to phage inactivation. These processes include the UV-induced photoreactions in the phage nucleic acid, and photoreactions in the nucleic acid sensitized by either psoralen or psoralen photobreakdown products. In addition the intercalation of the psoralen molecule itself in the phage nucleic acid as well as the psoralen photobreakdown products cause phage inactivation. Under appropriate experimental conditions these reactions can be studied and characterized separately. The quantitative characteristics (e.g. inactivation cross-section, action spectra and index for dark genotoxicity) are demonstrated for different linear and angular psoralens. Some theoretical and practical consequences of the results obtained are discussed.

Analysis of DNA-protein complexes induced by chemical carcinogens.

DNA-protein complexes induced in intact cells by chromate have been isolated and compared with those formed by other agents such as cis-platinum. Actin has been identified as one of the major proteins that is complexed to the DNA by chromate based upon a number of criteria including, a molecular weight and isoelectric point identical to actin, positive reaction with actin polyclonal antibody, and proteolytic mapping. Chromate and cis-platinum both complex proteins of very similar molecular weight and isoelectric points and these complexes can be disrupted by exposure to chelating or reducing agents. These results suggest that the metal itself is participating in rather than catalyzing the formation of a DNA-protein complex. An antiserum which was raised to chromate-induced DNA-protein complexes reacted primarily with a 97,000 protein that could not be detected by silver staining. Western blots and slot blots were utilized to detect p97 DNA-protein complexes formed by cis-platinum, UV, formaldehyde, and chromate. Other work in this area, involving studying whether DNA-protein complexes are formed in actively transcribed DNA compared with genetically inactive DNA, is discussed. Methods to detect DNA-protein complexes, the stability and repair of these lesions, and characterization of DNA-protein complexes are reviewed. Nuclear matrix proteins have been identified as a major substrate for the formation of DNA-protein complexes and these findings are also reviewed.

Laser (two-quantum) photolysis of polynucleotides and nucleoproteins: quantitative processing of results.

The paper offers and substantiates a technique for quantitative processing of the photochemical reactions in polynucleotides, nucleoproteins and their components caused by the action of powerful ultraviolet laser pulse radiation.

[Biological consequences of the decay of 3H and 14C incorporated into the influenza virus]. / Nekotorye biologicheskie posledstviia raspada 3H i 14C, inkorporirovannykh v virus grippa.

An influenza virus labeled with 3H-uridine loses its infectiousness when stored for a long time. It is suggested that disintegration of tritium incorporated into virus RNA causes lethal intramolecular modifications therein. At the same time, the antigenic activity of virus nucleoprotein decreases perhaps due to the direct effect of tritium. The comparison of the degree of inactivation of various antigenic sites of the nucleoprotein within a virus labeled with 3H-uridine, suggests that they are located at different distances from RNA. A long-term action of 3H disintegration on RNA of a maturing virus decreases the yield probably due to the injury of the intracellular virus RNA during the infections process. Upon storage of the influenza virus labelled with 14C-amino acids the antigenic properties are reduced by the nucleoprotein while the infectiousness remains unaffected. The long-term effect of 14C disintegration on proteins of the maturing virus does not lead to fatal outcome.

Crosslinking of DNA to nuclear lamina proteins by UV irradiation in vivo.

We have been able to demonstrate that a fraction of DNA becomes crosslinked to nuclear lamina shells isolated from Ehrlich ascites tumour cells irradiated with UV light. Terminal labeling of short DNA fragments covalently attached to proteins reveals that DNA has become crosslinked to all three lamins and to a protein comigrating with vimentin.

[Biosynthesis of nuclear sap proteins in the thymocytes of irradiated rats]. / Biosintez belkov iadernogo soka v timotsitakh obluchennykh krys.

A study was made of biosynthesis of nuclear sap proteins in rat thymus cells exposed to 8 Gy gamma-radiation. Four hours following irradiation, changes were observed in the nuclear sap protein spectrum which were not associated with proteolysis.

Effect of beta-decay of radionuclides incorporated into influenza virus RNA and proteins on the infectivity of the virus and antigenicity of its nucleoprotein.

The effect of beta-decay of radionuclides incorporated into influenza virus on the properties of the two closely adjacent structures--RNA and nucleoprotein (NP)--was studied. The long-term storage of 3H-uridine labelled influenza virus was shown to lead to the loss of infectivity. This effect may be explained by lethal intra-molecular modifications of viral RNA, caused by beta-decay of 3H incorporated into the molecule. There was an accompanying decrease of monoclonal antibody (MAB) binding activity, this also being a plausible result of beta-decay. The different rates of inactivation of MAB binding activity of different epitopes of NP of the 3H-labelled virus shown in our studies suggest that there are different types of structural organization or different location of these epitopes in the NP. The effect of 3H-decay on the intracellular RNA of reproducing virus lead to a decrease in virus yield; this may be due to radiation- and transmutation-induced damage of messenger and progeny RNA populations synthesized during the infection. The storage of influenza virus labelled with 14C-aminoacids lead to a decrease in MAB binding activity of the NP that was unaccompanied by a decrease in infectivity. Furthermore, 14C-decay in proteins of reproducing virus had no adverse effect.

Induction of polynucleotide-protein cross-linkages by ultraviolet irradiation. Peculiarities of the high-intensity laser pulse irradiation.

The efficiency and specificity of RNA-protein cross-linking in the 30S subunit of Escherichia coli ribosomes, induced by low-intensity (10(15) photons cm-2 s-1, 254 nm) and high-intensity [(1.6-6.8) X 10(24) photons cm-2 s-1, 266 nm, pulse duration 10(-8) s] ultraviolet radiation, are studied. Under the former conditions proteins S4, S7 and S9/S11, and under the latter conditions these proteins together with S3, S18 and S20, are cross-linked to 16S RNA. Biphotonic processes operate in the latter case. In the presence of 2-mercaptoethanol cross-linking occurs either directly, via a higher excited state or via activated intermediates with life-times less than 25 ns. Cross-links thus formed are specific, i.e. they are formed between regions of macromolecules which are in contact in the native (non-disturbed) complex prior to excitation. The efficiency of cross-linking (per photon absorbed) is 20-100 times higher upon two-step excitation as compared with single-step excitation and an analysable number of cross-links are produced in a single pulse. Only base U-1239 of 16S RNA is cross-linked to protein S7 by low-intensity radiation, whereas the adjacent base, G-1240 is also involved in laser-induced cross-linking. A transition from the former to the latter conditions allows one to reduce the duration of irradiation from several minutes to several nanoseconds.

Nuclear matrix proteins are crosslinked to transcriptionally active gene sequences by ionizing radiation.

Unirradiated, exponentially growing Chinese hamster cells contain a low level (less than 5%) of their DNA firmly bound to protein, as measured by a filter-binding assay. That fraction of DNA is highly enriched in sequences which hybridize to poly(A+)RNA or ribosomal RNA. After 60 Gy gamma irradiation, the additional crosslinked DNA is also enriched in transcriptionally active sequences compared to bulk DNA, while DNA crosslinked by uv radiation has a frequency of active sequences which is no higher than the bulk DNA. DNA crosslinked to protein by gamma radiation but not by uv is largely released during a 4-h postirradiation incubation. The DNA which remains bound to protein during that period becomes depleted in active sequences; this is followed by an apparent restoration of the active gene-enriched protein complex found in unirradiated cells. When nuclear matrix-associated DNA was isolated free of the majority ("loop") DNA, an enrichment for active DNA sequences was found in the matrix-associated DNA, and the frequency of DNA-protein crosslinks was found to be 10- to 16-fold greater in the matrix fraction. Gel electrophoretic analysis of the crosslinking proteins identifies them as subset of proteins of the nuclear matrix. These data are consistent with known properties of the nuclear matrix and suggest that chromatin structure plays an important role in the formation and repair of gamma-radiation-induced DNA lesions.

Protein-protein and protein-DNA interactions in calf thymus nuclear matrix using cross-linking by ultraviolet irradiation.

Nuclear matrices from calf thymus contained 30-50 protein species with one prominent band at 70 kilodaltons tentatively identified by its isoelectric point, apparent molecular weight, charge modification, and abundance as bovine lamin. The amount of DNA present in the matrix fraction was strongly dependent on the extent of digestion of the nuclei by micrococcal nuclease. The size of the DNA was higher than two kilobase pairs, although the chromatin DNA had been digested down to short oligonucleosomes. The lamin band was preferentially dissociated from isolated matrices during repeated treatment by 2 M NaCl or 5 M urea. Irradiation of calf thymus nuclear matrices at 313 nm induced protein-protein and protein-DNA cross-linking, as well as double-strand breaking of DNA, presumably at unprotected, protein-free regions. Lamin protein was more dramatically affected than other protein species by ultraviolet (UV) irradiation. In situ DNA hydrolysis, after the separation of the cross-linked matrix components on polyacrylamide-sodium dodecyl sulfate gels, followed by two-dimensional electrophoresis, showed lamin to be the major protein that was cross-linked to the DNA. Lamin molecules were also cross-linked by UV light to each other to form lamin homo-oligomers. A discrete size DNA fragment of approximately 450 base pairs is protected by lamin homo-oligomers from breakdown during UV irradiation. It is proposed that the direct contact between lamin and DNA found in this study is responsible for anchoring chromatin loops (domains) to a stable, immobile matrix structure.

Photochemical crosslinking of protein and DNA in chromatin. II. Synthesis and application of psoralen-cystamine-arylazido photocrosslinking reagents.

The synthesis and testing of a new type of nucleic acid-protein photocrosslinking reagent is described. The reagents are composed of a psoralen ligand for nucleic acid photoattachment, which is linked to an azidobenzoyl group, for protein photoattachment. The linker contains a disulfide bridge which can be opened by reduction with mercaptans. The reagents were tested in a chromatin system, where it was found that they induced cleavable crosslinks between the histones and the DNA upon irradiation with long-wavelength ultraviolet light (lambda greater than 300 nm).

Ultraviolet light induces binding of antibodies to selected nuclear antigens on cultured human keratinocytes.

Antibodies which bind to different nuclear antigens in tissue sections or in permeabilized cell cultures are useful markers of subsets of connective tissue disease, especially of lupus erythematosus (LE), but whether these antibodies are able to react with these intracellular sequestered antigens in vivo and cause immunologic tissue damage has been a matter of much debate. We report experiments which show that ultraviolet light-irradiated, cultured human keratinocytes bind IgG antibodies from the sera of LE patients with either monospecific anti-SSA/Ro, anti-RNP, or anti-Sm activity, which implies that these antigens have been made accessible on the cell surface by ultraviolet irradiation. Normal human sera or LE patient's sera with anti-double-stranded DNA, anti-single-stranded DNA, or antihistone activity do not bind to the surface of irradiated human keratinocytes. In control experiments, all antisera produced the expected patterns of nuclear and cytoplasmic staining of fixed permeabilized, unirradiated keratinocytes. Careful study of the viability and permeability of irradiated keratinocytes by several techniques showed that this apparent cell membrane expression of extractable nuclear antigens (SSA/Ro, RNP, and Sm) following irradiation was seen on injured keratinocytes whose cell membranes were intact, but not on dead cells. It is particularly significant that all six monospecific anti-SSA/Ro sera bound to irradiated keratinocytes, since this antibody antigen system is highly associated with photosensitive cutaneous LE.

Protein-RNA interaction in encephalomyocarditis virus as revealed by UV light-induced covalent linkages.

UV irradiation of encephalomyocarditis virus led to an increase in the buoyant density of the virus in CsCl gradients from 1.34 to 1.46 g/cm3. Heat treatment of the irradiated virus (20 min at 54 degrees C) reduced the density to 1.40 g/cm3 and led to the loss of approximately 55% of the labeled RNA from the virions. The non-irradiated virions were converted by such heating into empty capsids. Irradiation also resulted in an increase in the accessibility of RNA inside the virions to the action of pancreatic RNase. An increase in the UV dose did not enlarge the fraction of RNA molecules covalently linked to protein; this was revealed by the lack of any secondary increase in the apparent RNase resistance of the labeled RNA in the irradiated virions. Destruction of the irradiated virus with sodium dodecyl sulfate and 2-mercaptoethanol allowed the isolation of a 40S structure containing viral RNA and RNA-linked proteins. The latter comprised no more than 2.5% of the whole protein content of the virion. Polyacrylamide gel electrophoretic analysis of the RNase-treated 40S structure revealed at least three viral structural proteins in the same ratio as was present in the intact virions.