The biological effect of polyamines on heart RNA and histone metabolism

Summary We have observed a close relationship between polyamines (spermine and spermidine) and nucleic acids in connection with myocardial hypertrophy obtained by aortic constriction or by physical exercise. The role of spermine in RNA synthesis has been investigated on perfused heart, and we have observed a rapid increase of ribose-5-³H incorporation into RNA subcellular fractions. With the same experimental conditions we have considered the action of spermine on histone acetylation. The arginine-rich fractions are more acetylated under the action of spermine. This finding indicates a positive action of spermine on gene derepression mechanism.An invited article.     

The influence of polyamine-nucleic acid complexes on Fe2+ autoxidation

Summary Polyamines are able to affect Fe²⁺ autoxidation in the presence of suitable low molecular weight phosphorus-containing compounds; the inhibitory effect exerted by polyamines is directly related to their ability to bind phosphorus-containing compounds [1].It is well known that polyamines, as polycations at physiological pH, bind strongly to nucleic acids. In this paper it is shown that polyamines, also in the presence of nucleic acids, inhibit Fe²⁺ autoxidation and thus depress the generation of free oxygen radicals. Most of the nucleic acids tested inhibited Fe²⁺ autoxidation although the concentration which causes half maximal effect differs. Polyamine effect on Fe²⁺ autoxidation varies greatly depending on the single or double stranded nature of the nucleic acid. In the present of single stranded nucleic acids, spermine and spermidine potentiate the inhibition of Fez+ autoxidation by these nucleic acids. A relationship exists between the ability of spermine to interact with single stranded nucleic acids and to inhibit Fe²⁺ autoxidation in their presence. When double stranded nucleic acids are present, polyamines reverse the inhibition of Fee+ autoxidation exerted by these nucleic acids. Molecular mechanisms are proposed to explain these experimental results. The hypothesis that polyamines may inhibit oxidative damage caused to nucleic acids by Fe²⁺ autoxidation, is also discussed.Abbreviations poly [A] polyadenylic acid (5) - poly [C] polycytidylic acid (5) - poly [1] polyinosinic acid (5) - poly [G] polyguanylic acid (5) - poly [A. U] polyadenylic-uridylic acid - poly [A] poly [U] polyadenylic-polyuridylic acid     

Polyamines and nucleic acids during development of the chick embryo

1. A higher concentration of polyamines (spermine, spermidine, putrescine and cadaverine) during development of the chick embryo was observed between the fifth and tenth day of incubation; the concentrations of nucleic acids showed a parallel increase. 2. When spermine (5mumoles) was injected into the yolk sac of embryos at the tenth day of incubation, a high amine-oxidase activity was noted and the spermine and spermidine concentrations were decreased; also, there was a remarkable decrease in RNA and DNA concentrations and a parallel increase in that of total free nucleotides. 3. On the other hand, when iproniazid (16mumoles) was injected there was an inhibition of amine-oxidase activity and a similar increase in the concentrations of spermine and spermidine and of nucleic acids, whereas that of total free nucleotides decreased. 4. Another group of embryos injected with spermine and iproniazid together showed a remarkable increase in spermine and spermidine concentrations and a parallel increase in those of RNA and DNA, and a decrease in that of total free nucleotides.     

Polyamine stress at high pH in <Emphasis Type="Italic">Escherichia coli</Emphasis> K-12

Background  

Polyamines such as spermine and spermidine are required for growth ofEscherichia coli; they interact with nucleic acids, and they bind to ribosomes. Polyamines block porins and decrease membrane permeability, activities that may protect cells in acid. At high concentrations, however, polyamines impair growth. They impair growth more severely at high pH, probably due to their increased uptake as membrane-permeant weak bases. The role of pH is critical in understanding polyamine stress.     

Polyamine oxidase from barley and oats

The pH optimum for the stability of the barley leaf polyamine oxidase is 4.8, which is also the pH optimum for its activity with spermine as substrate. Zonal centrifugation indicates that the enzyme is associated with a particle which is slightly more dense than chloroplasts, and the peak of activity corresponds with the peak of nucleic acid. Neither DNase nor RNase released the enzyme from the particles, despite the hydrolysis of more than 50% of the nucleic acid. The enzyme from the leaves of oat seedlings grown in the dark was purified 900-fold. Mg²⁺ and Ca²⁺ inhibited both barley and oat enzymes by ca 50% at 50 mM. The optimum pH for both spermine and spermidine oxidation by the oat enzyme was 6.5. The MW of the enzyme from both sources determined by gel chromatography was ca 85 000.     

Fourier transform Raman study of the structural specificities on the interaction between DNA and biogenic polyamines

Biogenic polyamines putrescine, spermidine, and spermine are essential molecules for proliferation in all living organisms. Direct interaction of polyamines with nucleic acids has been proposed in the past based on a series of experimental evidences, such as precipitation, thermal denaturation, or protection. However, binding between polyamines and nucleic acids is not clearly explained. Several interaction models have also been proposed, although they do not always agree with one another. In the present work, we make use of the Raman spectroscopy to extend our knowledge about polyamine-DNA interaction. Raman spectra of highly polymerized calf-thymus DNA at different polyamine concentrations, ranging from 1 to 50 mM, have been studied for putrescine, spermidine, and spermine. Both natural and heavy water were used as solvents. Difference Raman spectra have been computed by subtracting the sum of the separated component spectra from the experimental spectra of the complexes. The analysis of the Raman data has supported the existence of structural specificities in the interactions, at least under our experimental conditions. These specificities lead to preferential bindings through the DNA minor groove for putrescine and spermidine, whereas spermine binds by the major groove. On the other hand, spermine and spermidine present interstrand interactions, whereas putrescine presents intrastrand interactions in addition to exo-groove interactions by phosphate moieties.     

Cations as Mediators of the Adsorption of Nucleic Acids on Clay Surfaces in Prebiotic Environments

Monovalent ([Na⁺] > 10 mM) and divalent ([Ca²⁺], [Mg²⁺] > 1.0 mM) cations induced the precipitationof nucleic acid molecules. In the presence of clay minerals (montmorillonite and kaolinite), there was adsorption instead of precipitation. The cation concentration needed for adsorption depended on both the valence of the cations and the chemical nature of the nucleic acid molecules. Double-stranded nucleic acids needed higher cation concentrations than single-stranded ones to be adsorbed to the same extent on clay. Divalent cations were more efficient than monovalent ones in mediating adsorption. Adsorption to the clay occurred only when both nucleic acids and cations were present. However, once the complexes were formed, the cations could not be removed from the system by washing, indicating that they are directly involved in the association between nucleic acids and mineral surfaces.These observations indicate that cations take part directly in the formation of nucleic acid-clay complexes, acting as a `bridge' between the negative charges on the mineral surface and those of the phosphate groups of the genetic polymer. The relatively low cation concentrations needed for adsorption and the ubiquitous presence of clay minerals in the environment suggest that the adsorption of nucleic acids on mineral surfaces could have taken place in prebiotic habitats. This may have played an important role in the formation and preservation of nucleic acids and/or their precursor polymers.     

Polyamines bound to nucleic acids during dormancy and activation of tuber cells of Helianthus tuberosus

Tuber tissue of Helianthus tuberosus L. (cv. OB1) contains a low amount of polyamines during dormancy but they are rapidly synthesized when tuber cells are activated in a growth medium and enter a new cell cycle. It was assumed that one of the reasons for this synthesis is that polyamines are necessary for the active conformation and correct functioning of nucleic acids. Complexes were found between spermine, spermidine and putrescine and rRNA, tRNA and an RNA fraction which contains poly(A) RNA and proteins. The amount of RNA-bound polyamines in the parenchyma cells of dormant tubers is dependent on the stage of dormancy and clearly increases (especially putrescine) when cells are activated. There are both tightly-bound and non-tightlybound polyamines. The significance of these bound polyamines is discussed in relation to their stabilizing role on nucleic acids.     

Polyamines and plant disease

The diamine putrescine and the polyamines spermidine and spermine are found in a wide range of organisms from bacteria to plants and animals. They are basic, small molecules implicated in the promotion of plant growth and development by activating the synthesis of nucleic acids. Polyamine metabolism has long been known to be altered in plants responding to abiotic environmental stress and to undergo profound changes in plants interacting with fungal and viral pathogens. Polyamines conjugated to phenolic compounds, hydroxycinnamic acid amides (HCAAs), have been shown to accumulate in incompatible interactions between plants and a variety of pathogens, while changes in the diamine catabolic enzyme diamine oxidase suggest a role for this enzyme in the production of hydrogen peroxide during plant defence responses. More recent work has suggested a role for the free polyamine spermine in the hypersensitive response of barley to powdery mildew and particularly in tobacco to TMV. The prospects for the genetic manipulation of HCAA levels in plants as a means of both defining their role in plant defence and in the generation of disease resistant plants is discussed briefly.     

Regulation der Nucleinsäuren-Synthese durch Polyamine in keimendem Pollen vonPetunia

Summary Putrescine, spermine, spermidine, and agmatine in concentrations between 5–15 g/ml inhibit pollen germination. Whereas spermine reduces pollen tube length, putrecine and agmatine do not affect pollen tube growth. Spermidine effects a small increase (about 5%) of pollen tube elongation. Spermine and spermidine can be found in pollen. Addition of spermine (7 or 10 g/ml) depresses protein synthesis, whilst spermidine does not affect protein synthesis. On the basis of uridine-5-T incorporation it could be shown that both spermine and spermidine increase RNA synthesis. On tho basis of thymidine-T incorporation in the first hpurs of germination it seems that DNA synthesis is also stimulated by spermine and spermidine present in the medium. A net increase of nucleic acids was found when spermidine was added to the germination substrate.These results are interpreted as suggesting that, in the pollen tubes investigated, polyamine concentration may be a factor in the regulation of nucleic acid synthesis, resulting in a prolonged synthesis of specific proteins and in this way influencing growth and the developmental pattern of pollen tubes.     

The effects of chlorphentermine and phentermine on certain metabolic parameters associated with development of rat kidney and liver.

Daily oral administration of the anorexigenic agents chlorphentermine or phentermine (60 mg/kg) to rats for either 1, 3, 5 or 7 days resulted in a significant fall in the incorporation of [¹⁴C]thymidine into renal and hepatic DNA throughout the course of the experiment. Although 24 h after treatment with either drug there was no dramatic change in the incorporation of [¹⁴C]orotic acid into liver RNA, a statistically significant reduction was noted after 3, 5 and 7 days. In rat kidney, the incorporation of [¹⁴C]orotic acid into RNA was only significantly depressed by chlorphentermine at 5 days and by phentermine at 3 days. In general, treatment with either anorexigenic agent tended to significantly lower or not affect the endogenous concentrations of renal and hepatic putrescine, spermidine and spermine. The chlorphentermine-induced decrease in liver and kidney nucleic acid synthesis was accompanied by depression in the levels of cyclic AMP in both tissues as well as a reduction in the activity of adenylate cyclase in renal tissue. In contrast, chlorphentermine produced a rise in hepatic adenylate cyclase at 5 days followed by a return to control values after 7 days. The phentermine-induced alterations in nucleic acid metabolism appeared generally to occur independent of any changes in the adenylate cyclase-cyclic AMP system of renal and hepatic tissues. In view of the fact that nucleic acids, polyamines and cyclic AMP constitute integral components of the growth process, our data suggest that chlorphentermine and phentermine interfere with certain biochemical parameters associated with the development of kidney and liver.     

Theoretical studies on protein-nucleic acid interactions. I. Interaction of positively charged amino acids with nucleic acid fragments

Coulombic interactions between the side chains of charged amino acids (Arg⁺, Lys⁺, and His⁺) and negatively charged phosphate groups of nucleic acid fragments have been studied theoretically. Diribose monophosphate and dideoxyribose monophosphate are chosen as model systems for single-stranded RNA and DNA, respectively. The interaction energies have been calculated by second-order perturbation theory using simplified formulas for individual terms. The interaction energy in this formalism is a sum of electrostatic, polarization, dispersion, and repulsive energies. Our results show that about 90% of the total interaction energy is contributed by the electrostatic term alone. Contribution from the repulsive term exceeds that from the dispersion term. Calculated interaction energies suggest that Lys⁺ and His⁺ form more stable complexes with RNA than with single-stranded DNA. On the other hand, Arg⁺ has a higher affinity for DNA than for RNA. The affinity of nucleic acids for the three amino acids is in the order Lys⁺ > His⁺ > Arg⁺. Further, the basic amino acid residues form more stable complexes with A-DNA than with B-DNA. The role of the Coulombic interactions in the specific recognition of nucleic acids by proteins is discussed.     

Theoretical studies on protein-nucleic acid interactions. II. Hydrogen bonding of amino acid side chains with bases and base pairs of nucleic acids

With a view to understanding the role of hydrogen bonds in the recognition of nucleic acids by proteins, hydrogen bonding between the bases and base pairs of nucleic acids and the amino acids (Asn, Gln, Asp and Glu, and charged residues Arg⁺, Glu^?, and Asp^?) has been studied by a second-order perturbation theory. Binding energies have been calculated for all possible configurations involving a pair of hydrogen bonds between the base (or base pair) and the amino acid residue. Our results show that the hydrogen bonding in these cases has a large contribution from electrostatic interaction. In general, the charged amino acids, compared to the uncharged ones, form more stable complexes with bases or base pairs. The hydrogen-bond energies are an order of magnitude smaller than the Coulombic interaction energies between basic amino acids (Lys⁺, Arg⁺, and His⁺) and the phosphate groups of nucleic acids. The stabilities of the complexes of amino acids Asn, Gln, Asp, and Glu with bases are in the order: G–X > C–X > A–X U–X or T–X, and G · C–X > A · T(U)–X, where X is one of these amino acid residues. It has been shown that Glu^? and Asp^? can recognize guanine in single-stranded nucleic acids; Arg⁺ can recognize G · C base pairs from A · T base pairs in double-stranded structures.     

Competitive Binding of Mg2+ and Na+ Ions to Nucleic Acids: From Helices to Tertiary Structures

Nucleic acids generally reside in cellular aqueous solutions with mixed divalent/monovalent ions, and the competitive binding of divalent and monovalent ions is critical to the structures of nucleic acids because of their polyanionic nature. In this work, we first proposed a general and effective method for simulating a nucleic acid in mixed divalent/monovalent ion solutions with desired bulk ion concentrations via molecular dynamics (MD) simulations and investigated the competitive binding of Mg²⁺/Na⁺ ions to various nucleic acids by all-atom MD simulations. The extensive MD-based examinations show that single MD simulations conducted using the proposed method can yield desired bulk divalent/monovalent ion concentrations for various nucleic acids, including RNA tertiary structures. Our comprehensive analyses show that the global binding of Mg²⁺/Na⁺ to a nucleic acid is mainly dependent on its structure compactness, as well as Mg²⁺/Na⁺ concentrations, rather than the specific structure of the nucleic acid. Specifically, the relative global binding of Mg²⁺ over Na⁺ is stronger for a nucleic acid with higher effective surface charge density and higher relative Mg²⁺/Na⁺ concentrations. Furthermore, the local binding of Mg²⁺/Na⁺ to a phosphate of a nucleic acid mainly depends on the local phosphate density in addition to Mg²⁺/Na⁺ concentrations.     

Polyamine metabolism of filaria and allied parasites

Putrescine and the polyamines spermidine and spermine occur both in prokaroytes and in eukaryotes where they seem intimately involved in regulatory processes of cellular growth and differentiation. They seem to play an important role related to the biosynthesis of nucleic acids and proteins, although at the molecular level their precise function remains unclear. In general, prokaryotes utilize putrescine and spermidine while eukaryotes tend to have higher concentrations of spermidine and spermine compared to putrescine(1-3.) Differences in polyamine metabolism between parasites and their hosts suggest several potential targets for chemotherapeutic attack As Rolf Walter discusses here, such approaches have already been exploited for African trypanosomes and also offer some leads for the chemotherapy of helminth infections.     

Spermine Condenses DNA,but Not RNA Duplexes

Interactions between the polyamine spermine and nucleic acids drive important cellular processes. Spermine condenses DNA and some RNAs, such as poly(rA):poly(rU). A large fraction of the spermine present in cells is bound to RNA but apparently does not condense it. Here, we study the effect of spermine binding to short duplex RNA and DNA, and compare our findings with predictions of molecular-dynamics simulations. When small numbers of spermine are introduced, RNA with a designed sequence containing a mixture of 14 GC pairs and 11 AU pairs resists condensation relative to DNA of an equivalent sequence or to 25 bp poly(rA):poly(rU) RNA. A comparison of wide-angle x-ray scattering profiles with simulation results suggests that spermine is sequestered deep within the major groove of mixed-sequence RNA. This prevents condensation by limiting opportunities to bridge to other molecules and stabilizes the RNA by locking it into a particular conformation. In contrast, for DNA, simulations suggest that spermine binds externally to the duplex, offering opportunities for intermolecular interaction. The goal of this study is to explain how RNA can remain soluble and available for interaction with other molecules in the cell despite the presence of spermine at concentrations high enough to precipitate DNA.     

Synthesis and Content of Polyamines in Bloodstream Trypanosoma brucei*

SYNOPSIS. The sensitive dansyl procedure was used to detect putrescine and spermidine, but not spermine and cadaverine, in pleomorphic Trypanosoma brucei. The polyamines were synthesized in vitro from [³H]ornithine, [¹⁴C]arginine and [¹⁴C]methionine. Proline, agmatine, and citrulline, but not glutamine, glutamic or pyroglutamic acids, stimulated spermidine formation from [¹⁴C]methionine. Putrescine and spermidine synthesis occurred rapidly from ornithine: putrescine synthesis peaked in 0.5 h, spermidine in 1 h. Trypanosoma brucei assimilated exogenous ¹⁴C-labeled putrescine, spermidine, and spermine; spermidine and spermine were taken up 5 times as rapidly as putrescine. Polyamine syntheses may therefore be a practical target for novel trypanocies.     

Polyaminooligonucleotide: NMR structure of duplex DNA containing a nucleoside with spermine residue,N-[4,9,13-triazatridecan-1-yl]-2′-deoxycytidine

Background

The nature of the polyamine–DNA interactions at a molecular level is not clearly understood.

Methods

In order to shed light on the binding preferences of polyamine with nucleic acids, the NMR solution structure of the DNA duplex containing covalently bound spermine was determined.

Results

The structure of 4-N-[4,9,13-triazatridecan-1-yl]-2′-deoxycytidine (dCSp) modified duplex was compared to the structure of the reference duplex. Both duplexes are regular right-handed helices with all attributes of the B-DNA form. The spermine chain which is located in a major groove and points toward the 3′ end of the modified strand does not perturb the DNA structure.

Conclusion

In our study the charged polyamine alkyl chain was found to interact with the DNA surface. In the majority of converged structures we identified the presumed hydrogen bonding interactions between O6 and N7 atoms of G4 and the first internal –NH2⁺− amino group. Additional interaction was found between the second internal –NH2⁺− amino group and the oxygen atom of the phosphate of C3 residue.

General significance

The knowledge of the location and nature of a structure-specific binding site for spermine in DNA should be valuable in understanding gene expression and in the design of new therapeutic drugs.