Search PubMed⌕ Search

Biomedical subjects

J Zlatanova

Publications and source records attributed to J Zlatanova.

At least 37 records · Page 2Linked to original sources
PubMed1998

Proteins that specifically recognize cisplatin-damaged DNA: a clue to anticancer activity of cisplatin.

Cisplatin, but not its trans geometric isomer, is a potent anticancer drug whose biological activity is a consequence of the formation of covalent adducts between the platinum compound and certain bases in DNA. Two classes of proteins have recently been identified that bind preferentially to damaged sites: proteins that specifically recognize those sites as a first step in their repair, and those that bind to such sites by virtue of structural similarity between the modified DNA and their own natural binding sites. Both classes of proteins may be involved, perhaps in opposing ways, in the cytotoxic effect of the drug.

Antineoplastic Agents↗
PubMed1998

Binding to four-way junction DNA: a common property of architectural proteins?

Proteins that can be shown to strongly bind in vitro to the four-way (Holliday) junction DNA include not only the obvious candidates such as enzymes involved in recombination, but also a remarkably diverse group of seemingly unrelated proteins. These include the HMG1 box proteins, members of the HMGI-Y family, winged helix proteins (including linker histones), the SWI/SNF complex, and some totally unrelated prokaryotic proteins. What these proteins seem to share is a propensity to bind to bent DNA, to bend DNA upon binding, and/or to preferentially interact with DNA crossings. Thus, they appear to be, in the main, architectural proteins, although some (like the SWI/SNF complex) have very specific functional roles as well. Perhaps because they bind to or promote the formation of particular DNA structures, the four-way junction binding proteins are frequently interchangeable in cellular function. Furthermore, since a given kind of structure can be recognized by many different protein motifs, it is not surprising that apparently unrelated proteins can fall into such a single functional class.

Chromatin↗
PubMed1997

The major chromatin protein histone H1 binds preferentially to cis-platinum-damaged DNA.

Both cis-diamminedichloroplatinum(II) (cisplatin or cis-DDP) and trans-diamminedichloroplatinum(II) form covalent adducts with DNA. However, only the cis isomer is a potent anticancer agent. It has been postulated that the selective action of cis-DDP occurs through specific binding of nuclear proteins to cis-DDP-damaged DNA sites and that binding blocks DNA repair. We find that a very abundant nuclear protein, the linker histone H1, binds much more strongly to cis-platinated DNA than to trans-platinated or unmodified DNA. In competition experiments, H1 is shown to bind much more strongly than HMG1, which had been previously considered a major candidate for such binding in vivo.

Animals↗
PubMed1997

Deoxyribonuclease I-facilitated electrotransfer of protein-DNA complexes from electrophoretic gels to nitrocellulose membranes.

A simple and reproducible technique for efficient transfer of protein-DNA complexes from electrophoretic gels to nitrocellulose membranes is described. Transfer of DNA-protein complexes may be difficult, especially when the DNA is of high molecular mass. A considerable improvement in the efficiency of transfer can be achieved by directly digesting the DNA in the gel by DNase I. The method is illustrated in the example of the preferential binding of histone H1 to superhelical plasmid DNA.

Animals↗
PubMed1997

Histone H1 preferentially binds to superhelical DNA molecules of higher compaction.

In chromatin, the physiological amount of H1 is one molecule per nucleosome or, roughly, one molecule per 200 bp of DNA. We observed that at such a stoichiometry, H1 selectively binds to supercoiled DNA with magnitude of sigma > or = 0.012 (both negative and positive), leaving relaxed, linear, or nicked DNA molecules unbound. When negative and positive DNA topoisomers of varying superhelicity are simultaneously present in the binding mixture, H1 selectively binds to the molecules with highest superhelicity; less supercoiled forms are gradually involved in binding upon increasing the amount of input protein. We explain this topological preference of H1 as the consequence of an increased probability for more than one H1-DNA contact provided by the supercoiling. The existence of simultaneous contacts of H1 with both intertwined DNA strands in the supercoiled DNA molecules is also inferred by topoisomerase relaxation of H1-DNA complexes that had been prefixed with glutaraldehyde.

Animals↗
PubMed1996

H1 binding unwinds DNA. Evidence from topological assays.

The preference of the linker histones to bind to superhelical DNA in comparison with linear or relaxed molecules suggests that these proteins might, in turn, change the twist and/or writhe of DNA molecules upon binding. In order to explore such a possibility, we looked for changes in the linking number of plasmid pBR322 caused by H1 binding, using assays that involve nicking and resealing of DNA strands. Two types of enzymes were used, eukaryotic topoisomerase I and prokaryotic DNA ligase. The results revealed that H1 binding causes unwinding of the DNA, with the unwinding angle being approximately 10 degrees . The globular domain of histone H1 is also capable of unwinding DNA, but to a lesser degree.

Animals↗
PubMed1996

What determines the folding of the chromatin fiber?

In this review, we attempt to summarize, in a critical manner, what is currently known about the processes of condensation and decondensation of chromatin fibers. We begin with a critical analysis of the possible mechanisms for condensation, considering both old and new evidence as to whether the linker DNA between nucleosomes bends or remains straight in the condensed structure. Concluding that the preponderance of evidence is for straight linkers, we ask what other fundamental process might allow condensation, and argue that there is evidence for linker histone-induced contraction of the internucleosome angle, as salt concentration is raised toward physiological levels. We also ask how certain specific regions of chromatin can become decondensed, even at physiological salt concentration, to allow transcription. We consider linker histone depletion and acetylation of the core histone tails, as possible mechanisms. On the basis of recent evidence, we suggest a unified model linking targeted acetylation of specific genomic regions to linker histone depletion, with unfolding of the condensed fiber as a consequence.

Acetylation↗
PubMed1996

Prokaryotic DNA ligases unwind superhelical DNA.

We have studied the effect on DNA topology of binding of prokaryotic DNA ligases (T4 and E. coli) to superhelical or nicked circular DNA. Performing topoisomerase I-mediated relaxation in the presence of increasing amounts of T4 ligase led to a shift in the topoisomer distribution to increasingly more negative values. This result suggested that T4 ligase unwound the DNA and was further substantiated by ligation of nicked circular molecules by E. coli DNA ligase in the presence of increasing amounts of T4 ligase. Such an experiment was possible since the two DNA ligases require different cofactors for enzymatic activity. Performing a similar experiment with reverse partners, using E. coli DNA ligase as ligand, and T4 ligase as sealing agent, we observed that the E. coli enzyme also unwound the DNA. Thus, prokaryotic DNA ligases can be added to an ever-growing list of DNA-binding proteins that unwind the DNA upon binding.

Bacteriophage T4↗
PubMed1996

Linker histones affect patterns of digestion of supercoiled plasmids by single-strand-specific nucleases.

The effect of histone H1 binding on the cleavage of superhelical plasmids by single-strand-specific nucleases was investigated. Mapping of P1 cleavage sites in pBR322, achieved by EcoRI digestion after the original P1 attack, showed an intriguing phenomenon: preexisting susceptible sites became "protected," whereas some new sites appeared at high levels of H1. Similar results were obtained with another single-strand-specific nuclease, S1. Disappearance of cutting at preexisting sites and appearance of new sites was also observed in a derivative plasmid that contains a 36-bp stretch of alternating d(AT) sequence that is known to adopt an altered P1-sensitive conformation. On the other hand, H1 titration of a dimerized version of the d(AT)18-containing plasmid led to protection of all preexisting sites except the d(AT)18 inserts, which were still cut even at high H1 levels; in this plasmid no new sites appeared. The protection of preexisting sites is best explained by long-range effects of histone H1 binding on the superhelical torsion of the plasmid. The appearance of new sites, on the other hand, probably also involves a local effect of stabilization of specific sequences in Pl-sensitive conformation, due to direct H1 binding to such sequences. That such binding involves linker histone N- and/or C-terminal tails is indicated by the fact that titration with the globular domain of H5, while causing disappearance of preexisting sites, does not lead to the appearance of any new sites.

Binding Sites↗
PubMed1996

Linker histones inhibit T4 and Escherichia coli DNA ligases.

Based on some preliminary observations that linker histones strongly inhibit the activity of prokaryotic DNA ligases, we studied the effect of these histones on the ligation of short restriction DNA fragments by either T4 or E. coli DNA ligases. The inhibitory effect was strong, but it appeared only after two molecules of H1 bound to a approximately 200 bp-long DNA fragment. A similar pattern of inhibition (but at much higher concentration) was observed with the isolated globular domain of histone H5. That the inhibition was specific to the linker histones became clear when other basic proteins, such as the core histone octamer or cytochrome C, were tested. They did not inhibit the ligases but rather significantly stimulated them. The other major linker DNA-binding protein in chromatin, the non-histone protein HMG1, showed no significant effect on the ligase activity.

Animals↗
PubMed1996

Chromatin architectural proteins and transcription factors: a structural connection.

It has long been assumed that the architectural proteins of chromatin (the histones, for example) are unrelated to their functional proteins (transcription factors, polymerases, etc). New studies drastically change this perspective. It appears that a portion of the general transcription initiation complex TFIID is made up of proteins that not only carry marked sequence and structural resemblances to the core histones of the nucleosome, but also form an octameric complex similar to the histone octamer. This can now be seen as part of a general pattern of continuity among structural and functional chromatin proteins.

Animals↗
PubMed1995

High-affinity binding sites for histone H1 in plasmid DNA.

The interaction of histone H1 isolated from chicken erythrocytes with restriction fragments from plasmids pBR322 and pUC19 was studied by gel electrophoresis. Certain restriction fragments exhibited unusually high affinity for the histone, forming high molecular mass complexes at protein to DNA ratios at which the other fragments did not show evidence for binding. The highly preferred fragments are intrinsically curved, as judged by their electrophoretic mobility in polyacrylamide gels, by computer modeling, and by imaging with scanning force microscopy. However, control experiments with either curved portions of the same fragments or highly curved kinetoplast DNA fragments showed that the presence of curvature alone was not sufficient for preferential binding. By using various restriction fragments centered around the highly preferred sequence, it was found that the high-affinity binding required in addition the presence of specific sequences on both sides of the region of curvature. Thus, both curvature and the presence of specific sites seem to be required to generate high affinity.

Animals↗
PubMed1995

Transcriptional regulation in the yeast GAL gene family: a complex genetic network.

Regulation of the GAL structural genes in the yeast Saccharomyces cerevisiae is implemented by the products of GAL-specific (GAL4, GAL80, GAL3) and general (GAL11, SWI1, 2, 3, SNF5, 6, numerous glucose repression) genes. Recent work has 1) yielded significant new insights on the DNA binding and transcription activation/Gal80 protein binding functions of the Gal4 activator protein, 2) described the characterization of purified Gal4 protein-Gal80 protein complexes, 3) deconvoluted the multiple and complex glucose repression pathways acting on GAL genes, 4) suggested a new mechanism for the Gal3 protein-mediated induction of GAL structural gene expression, 5) introduced Gal1 protein, a structural gene product, into the regulation scheme, and 6) extended our already substantial understanding of GAL regulatory gene control. The mechanisms which control structural and regulatory gene expression in the GAL family are compared and GAL structural/regulatory gene chromatin structure is discussed.

Chromatin↗
PubMed1994

Low levels of exogenous histone H1 in yeast cause cell death.

To elucidate the function of lysine-rich histone, yeast cells, which are believed to lack this histone, were transformed with an expression vector carrying the sea urchin histone H1 gene under control of an inducible promoter. Expression of full-length protein was tested by immunoblotting and the intracellular distribution was monitored by immunoelectron microscopy. Even low amounts of exogenous H1 led to dramatic changes in intracellular morphology and cell death. The cells that survived had lost either the plasmid or the ability to express the exogenous protein. Thus, even low amounts of canonical histone H1 are lethal to yeast cells.

Animals↗