Cooperative binding of polyamines induces the Escherichia coli single-strand binding protein-DNA binding mode transitions.

The Escherichia coli single-strand binding (SSB) protein is an essential protein involved in DNA replication, recombination, and repair processes. The tetrameric protein binds to ss nucleic acids in a number of different binding modes in vitro. These modes differ in the number of nucleotides occluded per SSB tetramer and in the type and degree of cooperative complexes that are formed with ss DNA. Although it is not yet known whether only one or all of these modes function in vivo, based on the dramatically different properties of the SSB tetramer in these different ss DNA binding modes, it has been suggested that the different modes may function selectively in replication, recombination, and/or repair. The transitions between these different modes are very sensitive to solution conditions, including salt (concentration, as well as cation and anion type), pH, and temperature. We have examined the effects of multivalent cations, principally the polyamine spermine, on the SSB-ss poly(dT) binding mode transitions and find that the transition from the (SSB)35 to the (SSB)56 binding mode can be induced by micromolar concentrations of polyamines as well as the inorganic cation Co(NH3)6(3+). Furthermore, these multivalent cations, as well as Mg2+, induce the binding mode transition by binding cooperatively to the SSB-poly(dT) complexes. These observations are interesting in light of the fact that polyamines, such as spermidine, are part of the ionic environment in E. coli and hence these cations are likely to affect the distribution of SSB-ss DNA binding modes in vivo.(ABSTRACT TRUNCATED AT 250 WORDS)     

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.     

Lysis of Vibrio succinogenes by ethylenediamine-tetraacetic acid or lysozyme

Wolin, M. J. (University of Illinois, Urbana). Lysis of Vibrio succinogenes by ethylenediaminetetraacetic acid or lysozyme. J. Bacteriol. 91:1781-1786. 1966.-Cell suspensions of Vibrio succinogenes are lysed by ethylenediaminetetraacetic acid (EDTA) or lysozyme. Lysis occurs at alkaline pH and is prevented by 0.15 m NaCl or KCl or 0.3 m sucrose. The addition of 10(-3)m Mg(++), 10(-3)m spermine, or 10(-2)m Ca(++) prevents lysozyme lysis, and 10(-4)m spermine prevents EDTA lysis. EDTA lysis leads to the formation of a cell ghost, and lysozyme lysis leads to the formation of an empty round body. Freezing and thawing of cells permits lysozyme attack which is not prevented by the protective agents mentioned above. Much of the cell protein, and almost all of the nucleic acids, are released from the cells during EDTA lysis. Treatment of frozen-thawed cells with lysozyme at neutral pH does not cause release of more than 50% of the cell protein and 60% of the nucleic acids of the cells.     

Spermine-nucleic acid interactions: a theoretical study

The interaction of spermine with nucleic acids is simulated theoretically using refined semi-empirical energy formulae and an advanced minimization procedure. Various nucleic acids are considered: model homopolymeric DNA's, a dodecamer (CGCGAATTCGCG) of type B-DNA, as well as a transfer RNA, tRNA^Phe. The dominant role of electrostatic potential in determining the preferential binding sites of spermine is demonstrated in each of these cases and the role of counterions, nucleic acid structure, and base-pair sequence is analyzed.     

Electricity-free, sequential nucleic acid and protein isolation

Traditional and emerging pathogens such as Enterohemorrhagic Escherichia coli (EHEC), Yersinia pestis, or prion-based diseases are of significant concern for governments, industries and medical professionals worldwide. For example, EHECs, combined with Shigella, are responsible for the deaths of approximately 325,000 children each year and are particularly prevalent in the developing world where laboratory-based identification, common in the United States, is unavailable (1). The development and distribution of low cost, field-based, point-of-care tools to aid in the rapid identification and/or diagnosis of pathogens or disease markers could dramatically alter disease progression and patient prognosis. We have developed a tool to isolate nucleic acids and proteins from a sample by solid-phase extraction (SPE) without electricity or associated laboratory equipment (2). The isolated macromolecules can be used for diagnosis either in a forward lab or using field-based point-of-care platforms. Importantly, this method provides for the direct comparison of nucleic acid and protein data from an un-split sample, offering a confidence through corroboration of genomic and proteomic analysis. Our isolation tool utilizes the industry standard for solid-phase nucleic acid isolation, the BOOM technology, which isolates nucleic acids from a chaotropic salt solution, usually guanidine isothiocyanate, through binding to silica-based particles or filters (3). CUBRC's proprietary solid-phase extraction chemistry is used to purify protein from chaotropic salt solutions, in this case, from the waste or flow-thru following nucleic acid isolation(4). By packaging well-characterized chemistries into a small, inexpensive and simple platform, we have generated a portable system for nucleic acid and protein extraction that can be performed under a variety of conditions. The isolated nucleic acids are stable and can be transported to a position where power is available for PCR amplification while the protein content can immediately be analyzed by hand held or other immunological-based assays. The rapid identification of disease markers in the field could significantly alter the patient's outcome by directing the proper course of treatment at an earlier stage of disease progression. The tool and method described are suitable for use with virtually any infectious agent and offer the user the redundancy of multi-macromolecule type analyses while simultaneously reducing their logistical burden.     

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.     

Modeling protein–nucleic acid complexes with extremely large conformational changes using Flex-LZerD

Proteins and nucleic acids are key components in many processes in living cells, and interactions between proteins and nucleic acids are often crucial pathway components. In many cases, large flexibility of proteins as they interact with nucleic acids is key to their function. To understand the mechanisms of these processes, it is necessary to consider the 3D atomic structures of such protein–nucleic acid complexes. When such structures are not yet experimentally determined, protein docking can be used to computationally generate useful structure models. However, such docking has long had the limitation that the consideration of flexibility is usually limited to small movements or to small structures. We previously developed a method of flexible protein docking which could model ordered proteins which undergo large-scale conformational changes, which we also showed was compatible with nucleic acids. Here, we elaborate on the ability of that pipeline, Flex-LZerD, to model specifically interactions between proteins and nucleic acids, and demonstrate that Flex-LZerD can model more interactions and types of conformational change than previously shown.     

Rapid preparation of total nucleic acids from E. coli for multi-purpose applications

Separate protocols are commonly used to prepare plasmid DNA, chromosomal DNA, or total RNA from E. coli cells. Various methods for the rapid preparation of plasmid DNA have been developed previously, but the preparation of the chromosomal DNA and total RNA are usually laborious. We report here a simple, fast, reliable, and cost-effective method to extract total nucleic acids from E. coli by direct lysis of the cells with phenol. Five distinct and sharp bands, which correspond to chromosomal DNA, plasmid DNA, 23S rRNA, 16S rRNA, and a mixture of small RNA, were observed when analyzing the prepared total nucleic acids on a regular 1-2% agarose gel. The simple and high-quality preparation of the total nucleic acids in a single tube allowed us to rapidly screen the recombinant plasmid, as well as to simultaneously monitor the change of the plasmid copy number and rRNA levels during the growth of E. coli in the liquid medium.     

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.     

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.     

A method for differentiating proteins from nucleic acids in intermediate-resolution density maps: cryo-electron microscopy defines the quaternary structure of the Escherichia coli 70S ribosome

BACKGROUND: This study addresses the general problem of dividing a density map of a nucleic-acid-protein complex obtained by cryo-electron microscopy (cryo-EM) or X-ray crystallography into its two components. When the resolution of the density map approaches approximately 3 A it is generally possible to interpret its shape (i. e., the envelope obtained for a standard choice of threshold) in terms of molecular structure, and assign protein and nucleic acid elements on the basis of their known sequences. The interpretation of low-resolution maps in terms of proteins and nucleic acid elements of known structure is of increasing importance in the study of large macromolecular complexes, but such analyses are difficult. RESULTS: Here we show that it is possible to separate proteins from nucleic acids in a cryo-EM density map, even at 11.5 A resolution. This is achieved by analysing the (continuous-valued) densities using the difference in scattering density between protein and nucleic acids, the contiguity constraints that the image of any nucleic acid molecule must obey, and the knowledge of the molecular volumes of all proteins. CONCLUSIONS: The new method, when applied to an 11.5 A cryo-EM map of the Escherichia coli 70S ribosome, reproduces boundary assignments between rRNA and proteins made from higher-resolution X-ray maps of the ribosomal subunits with a high degree of accuracy. Plausible predictions for the positions of as yet unassigned proteins and RNA components are also possible. One of the conclusions derived from this separation is that 23S rRNA is solely responsible for the catalysis of peptide bond formation. Application of the separation method to any nucleoprotein complex appears feasible.     

Cartilage response to thyroid hormones in the sex-linked dwarf chicken

1. Trachea cartilages were dissected from normal and dwarf chickens which had been injected with thyroxine (T4, 200 micrograms/kg) or triiodothyronine (T3, 200 micrograms/kg) for seven consecutive days, and were analysed for nucleic acids, proteins and polyamines. 2. In saline-injected control chickens, RNA, but not DNA and protein, concentration of the cartilage was higher in dwarfs than in normals. The concentration of putrescine was lower in dwarfs than in normals, while that of spermine was the reverse. 3. Thyroid hormones, especially T3, tended to increase concentrations of RNA, spermidine and spermine, and to decrease that of putrescine. However, there were no clear differences in the response to hormones between breeds.     

Generate Western blot protein marker from a single construct

An expression construct, consisting of a tandem arrangement of nucleic acids coding for the constant fragments (Fc) receptor of protein G combined with nucleic acids for the Fc receptor of protein A, was constructed. When the construct was expressed in Escherichia coli, proteins of estimated molecular weights of 25, 30, 50, 58, 80, and 85 kDa were consistently obtained from this expression construct due to possible proteolytic degradation during the cultivation and purification steps. The purified proteins from this single expression construct were used as Western blot protein marker.     

A general method of analysis of ligand-macromolecule equilibria using a spectroscopic signal from the ligand to monitor binding. Application to Escherichia coli single-strand binding protein-nucleic acid interactions

We describe a general method for the analysis of ligand-macromolecule binding equilibria for cases in which the interaction is monitored by a change in a signal originating from the ligand. This method allows the absolute determination of the average degree of ligand binding per macromolecule without any assumptions concerning the number of modes or states for ligand binding or the relationship between the fractional signal change and the fraction of bound ligand. Although this method is generally applicable to any type of signal, we discuss the details of the method as it applies to the analysis of binding data monitored by a change in fluorescence of a ligand upon binding to a nucleic acid. We apply the analysis to the equilibrium binding of Escherichia coli single-strand binding (SSB) protein to single-stranded nucleic acids, which is monitored by the quenching of the intrinsic tryptophan fluorescence of the SSB protein. With this method, one can quantitatively determine the relationship between the fractional signal change of the ligand and the fraction of bound ligand, LB/LT, and rigorously test whether the signal change is directly proportional to LB/LT. For E. coli SSB protein binding to single-stranded nucleic acids in its (SSB)65 binding mode [Lohman, T. M., & Overman, L. B. (1985) J. Biol. Chem. 260, 3594; Chrysogelos, S., & Griffith, J. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 5803], we show that the fractional quenching of the SSB fluorescence is equal to the fraction of bound SSB.     

Identification of stimulators and inhibitors of Cdc7 kinase in vitro

Cdc7 is a serine-threonine kinase that regulates initiation and progression of DNA replication. The activity of purified Cdc7 kinase is significantly stimulated by polyamines such as spermine or spermidine. Positively charged polymers of lysine or arginine also stimulate its kinase activity, whereas the negatively charged substances such as polyglutamate or nucleic acids significantly inhibit the kinase activity. Spermine affects both the K(m) and V(max) of Cdc7 kinase for a minichromosome maintenance (MCM) substrate. We also found that histones, lysine- and arginine-rich basic proteins, can stimulate Cdc7 kinase activity, and a MCM complex in association with histone is a more efficient substrate of Cdc7 than the free MCM complex. These results identify potential cellular inhibitors and stimulators of Cdc7 kinase and suggest that Cdc7 may be another target of cellular polyamines and that histones may stimulate Cdc7-mediated phosphorylation of chromatin-bound substrates. Ectopic expression of an antizyme, known to reduce the cellular polyamine levels, resulted in reduction of Cdc7-mediated phosphorylation of MCM4 protein, suggesting physiological roles of polyamines in regulation of Cdc7 kinase activity in the cells.     

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.     

A rapid assay for affinity and kinetics of molecular interactions with nucleic acids

The Differential Radial Capillary Action of Ligand Assay (DRaCALA) allows detection of protein interactions with low-molecular weight ligands based on separation of the protein-ligand complex by differential capillary action. Here, we present an application of DRaCALA to the study of nucleic acid-protein interactions using the Escherichia coli cyclic AMP receptor protein (CRP). CRP bound in DRaCALA specifically to (32)P-labeled oligonucleotides containing the consensus CRP binding site, but not to oligonucleotides with point mutations known to abrogate binding. Affinity and kinetic studies using DRaCALA yielded a dissociation constant and dissociation rate similar to previously reported values. Because DRaCALA is not subject to ligand size restrictions, whole plasmids with a single CRP-binding site were used as probes, yielding similar results. DNA can also function as an easily labeled carrier molecule for a conjugated ligand. Sequestration of biotinylated nucleic acids by streptavidin allowed nucleic acids to take the place of the protein as the immobile binding partner. Therefore, any molecular interactions involving nucleic acids can be tested. We demonstrate this principle utilizing a bacterial riboswitch that binds cyclic-di-guanosine monophosphate. DRaCALA is a flexible and complementary approach to other biochemical methods for rapid and accurate measurements of affinity and kinetics at near-equilibrium conditions.     

Convenient and efficient in vitro folding of disulfide-containing globular protein from crude bacterial inclusion bodies

We investigated how the folding yield of disulfide-containing globular proteins having positive net charges from crude bacterial inclusion bodies was affected by additives in the folding buffer. In screening folding conditions for human ribonucleases and its derivative, we found that addition of salt (about 0.4 M) to a folding buffer increased the folding yield. This suggested that electrostatic interaction between polyanionic impurities such as nucleic acids and cationic unfolded protein led to the formation of aggregates under the low-salt conditions. Since inclusion bodies were found to contain nucleic acids regardless of the electrostatic nature of the expressed protein, the electrostatic interaction between phosphate moieties of nucleic acids and basic amino acid residues of a denatured protein may be large enough to cause aggregation, and therefore the addition of salt in a folding buffer may generally be useful for promotion of protein folding from crude inclusion bodies. We further systematically investigated additives such as glycerol, guanidium chloride, and urea that are known to act as chemical chaperons, and found that these additives, together with salt, synergistically improved folding yield. This study, suggesting that the addition of salt into the folding buffer is one of the crucial points to be considered, may pave the way for a systematic investigation of the folding conditions of disulfide-containing foreign proteins from crude bacterial inclusion bodies.