Small peptides controlling transcription in vitro are bound to chromatin DNA

A class of DNA-binding peptides from wheat bud causes growth inhibition, G2 cell cycle arrest and apoptosis induction in HeLa cells

Background

Deproteinized DNA from eukaryotic and prokaryotic cells still contains a low-molecular weight peptidic fraction which can be dissociated by alkalinization of the medium. This fraction inhibits RNA transcription and tumor cell growth. Removal from DNA of normal cells causes amplification of DNA template activity. This effect is lower or absent in several cancer cell lines. Likewise, the amount of active peptides in cancer cell DNA extracts is lower than in DNA preparation of the corresponding normal cells. Such evidence, and their ubiquitous presence, suggests that they are a regulatory, conserved factor involved in the control of normal cell growth and gene expression.

Results

We report that peptides extracted from wheat bud chromatin induce growth inhibition, G₂ arrest and caspase-dependent apoptosis in HeLa cells. The growth rate is decreased in cells treated during the S phase only and it is accompanied by DNA damage and DNA synthesis inhibition. In G₂ cells, this treatment induces inactivation of the CDK1-cyclin B1 complex and an increase of active chk1 kinase expression.

Conclusion

The data indicate that the chromatin peptidic pool inhibits HeLa cell growth by causing defective DNA replication which, in turn, arrests cell cycle progression to mitosis via G₂ checkpoint pathway activation.

Interaction of DDSDEEN peptide with N-CAM protein. Possible mechanism enhancing neuronal differentiation

DDSDEEN chromatin peptide, after dansylation, was studied for its ability to bind N-CAM protein. The binding causes a quenching of the Dns-peptide fluorescence emission. Dose- and time-dependent binding of Dns-peptide with N-CAM has been shown. Fluorescence quenching is completely lost if the Dns-peptide is subjected to carboxypeptidase digestion. Moreover the undansylated peptide pEDDSDEEN competes with the DnsDDSDEEN peptide for the binding with the N-CAM protein. The Dns-peptide-N-CAM bond has been related to the peptide biological activity probably involved in the promotion of neuronal differentiation. An attempt to recognize a possible N-CAM binding site for Dns-peptide was performed by alignment of N-CAM from various sources with some sequences that have been previously reported as binding sites for the pEDDSDEEN and DDSDEEN peptides. Interestingly, the alignment of N-CAM from various sources with the peptides WHPREGWAL and WFPRWAGQA recognizes on rat and human N-CAM a unique sequence that could be the specific binding site for chromatin peptide: WHSKWYDAK. This sequence is present in fibronectin type-III domain of N-CAM. In addition molecular modeling studies indicate the N-CAM sequence WHSKWYDAK as, probably, the main active site for DnsDDSDEEN (or pEDDSDEEN) peptide ligand. Accordingly the binding experiments show a high affinity between WHSKWYDAK and DnsDDSDEEN peptides.

Synthetic seminal plasma peptide inhibits testosterone production in frog testis in vitro

The role of synthetic seminal plasma peptide, designed using biochemical and mass spectroscopy analyses of native peptides extracted from seminal plasma, was studied in amphibian (Rana esculenta) testicular steroidogenesis. Production of testosterone and prostaglandin F(2alpha) was determined by incubating frog testes with synthetic peptide in vitro. Analysis of the data showed a dose-dependent inhibition of testosterone production (43% at 10(-5) M concentration) without prostaglandin F(2alpha) synthesis being affected. Determination of the peptide activity during the annual R. esculenta reproductive cycle showed inhibition of testosterone production in post-reproductive and recovery periods, suggesting a possible involvement of peptide in gonad steroidogenesis.

Desialylated N-CAM and chromatin-derived acidic peptide effects in the hypothalamus

Chromatin-derived acidic peptides (ACPs) have been shown to acutely modulate hypothalamic catecholamine release. To investigate whether this effect is mediated through membrane polysialylated neural-cell adhesion molecule (PSA-N-CAM), we pretreated rat hypothalamic synaptosomes with neuraminidase enzyme, which partially cleaves sialic acid residues from N-CAM, and perfused them with ACP-1 (Asp-Asp-Ser-Asp-Glu-Glu-Asn) or a more lipophilic derivative, ACP-2 ([Ala-Ile-Ser-Pro]-Asp-Asp-Ser-Asp-Glu-Glu-Asn). We have found that neuraminidase completely abolish the inhibitory effect of ACP-1 on dopamine release, while the inhibitory activity of ACP-1 on norepinephrine release is partially lost. On the other hand, ACP-2 inhibition of dopamine release is not modified by neuraminidase pretreatment.

Chromatin-derived acidic peptides modulate catecholamine release in the hypothalamus

We have studied the neuromodulatory effects of three synthetic peptides, structurally related to chromatin-derived acidic peptides (ACPs): ACP-1 (Asp-Asp-Ser-Asp-Glu-Glu-Asn), corresponding to the C-terminal fragment of the largest subunit of eukaryotic RNA polymerase II; a more lipophilic derivative, ACP-2 (Ala-Ile-Ser-Pro-Asp-Asp-Ser-Asp-Glu-Glu-Asn); and its phosphorylated form ACP-3 (Ala-Ile-Ser-Pro-Asp-Asp-Ser(P)-Asp-Glu-Glu-Asn). Rat hypothalamic synaptosomes, loaded with [(3)H]norepinephrine or [(3)H]dopamine, were perfused with the above peptides, both basally and during a depolarizing stimulus. We have found: ACP-1 inhibited both dopamine and norepinephrine release; ACP-2 inhibited dopamine release, without affecting norepinephrine release; ACP-3 was almost ineffective, except for a weak dopamine inhibiting effect only at a higher concentration.

Binding citrate/DNA in presence of divalent cations. Potential mimicry of acidic peptides/DNA interactions

Citric acid whose structure is comparable to that of small acidic peptides, can bind to DNA in the presence of divalent cations (Cu2+, Fe2+, Zn2+, Mg2+). Citrate-DNA interaction occurs also in a cell homogenate and in this experimental model too requires the presence of natural divalent cations. In fact the addition of 2 mM EDTA to cell homogenate strongly decreases the DNA-citrate binding. The results demonstrate that divalent cations can act as bridges between two acidic molecules and that citric acid can mimic the structure of acidic peptides.

Differential scanning calorimetry of chromatin at different levels of condensation

The thermal denaturation of calf thymus total chromatin and of fractions enriched in heterochromatin or euchromatin, has been investigated by differential scanning calorimetry and compared to that of calf thymus DNA and DNA-histone complexes. In our experimental conditions, chromatin melts in three thermal transitions: the main one, assigned to separation of the DNA double helix, occurs at 83 degrees C, while the other two occur at 63 degrees C and 74 degrees C. The data show that: (a) the transition enthalpy for denaturation of DNA in the total chromatin and in DNA-histone complexes is nearly the same as that of DNA in solution; (b) the transition at 63 degrees C is present in the thermogram of the heterocromatin enriched fraction, while it is completely absent in that of the euchromatin enriched one. The results suggest that this transition can be attributed to the higher order structures of heterochromatin.

Binding of small phosphorylated chromatin peptides to DNA

Low-molecular-weight peptides involved in gene expression and cell growth have been isolated from DNA preparation from eukaryotic cells. After phosphorylation with protein kinase CKII (pCKII) these peptides are able to bind to DNA in presence of divalent cations and salt/ethanol. This finding may explain the mechanism by which the peptides exert their activity.

Mass spectral and electrophoretic characterization of acidic peptides bound to chromatin of pea bud

Structural features of a class of chromatin peptides are studied in the aim of understanding their mechanism of action. They have been reported as a family of small acidic peptides that can affect cell proliferation and RNA transcription. Mass spectrometry analysis has suggested some molecular models of possible sequences that might be present in this group of peptides. These sequences have been synthesised and their chromatographic and electrophoretic behaviour is compared with that obtained from peptides extracted from pea bud chromatin. In this way electric charge and hydrophilic properties of the native peptides are evaluated. On the basis of these data and those obtained from further mass spectrum analysis new models for native peptides are proposed.

Purification, sequence determination and synthesis of seminal plasma peptides and synthesis of some of their analogues

Three peptides were isolated from bovine seminal plasma and purified to homogeneity. The amino acid sequences, as determined by FAB mass spectrometry, are the following: pGlu-Ala-Glu-Ser-Asn-OH, pGlu-Ala-Glu-Ser(PO3H2-Asn-OH and pGlu-Val-Gly-Glu-Ser-Glu-Asn-OH. These three peptides and some of their analogues were synthesized using liquid- and solid-phase techniques. The pentapeptide pGlu-Ala-Glu- Ser-Asn-OH showed a remarkable affinity for kinase NII and a strong inhibiting activity in DNA transcription. These findings support the hypothesis that phosphorylated acidic domains of nuclear non-histone proteins could bind to DNA, thereby controlling transcription.

Molecular models of small phosphorylated chromatin peptides. Structure-function relationship and regulatory activity on in vitro transcription and on cell growth and differentiation

We previously reported the isolation of low molecular weight phosphorylated peptides from the chromatin of several tissues. The chromatin peptides show a regulatory activity on DNA in vitro transcription and on cell growth and differentiation. In this paper, we report a molecular model of the native peptides designed according to the structural information obtained by means of biochemical and mass spectrometry analysis: pyroGlu-Ala-Gly-Glu-Asp-Ser(P)-Asp-Glu-Glu-Asn. This or very similar sequences are present in many transcription factors; on the basis of the structural model we presented and of related protein sequences, we have synthesized the peptide pyroGlu-Asp-Asp-Ser-Asp-Glu-Glu-Asn. This peptide affects transcription rate in reconstituted systems in vitro and in isolated nuclei; moreover, it inhibits the growth of HL60 cells with a parallel stimulus of differentiation.

Possible specific activation of RNA synthesis in PC-12 cell isolated nuclei by small acidic peptides

Three synthetic peptides, pyro-Glu-Ala-Gly-Glu-Ser-Glu-Asp (Pep A), pyro-Glu-Ala-Gly-Glu-Glu-Glu-Ser-Asn (Pep B), and pyro-Glu-Asp-Asp-Ser-Asp-Glu-Glu-Asn (Pep C), bear sequences possibly belonging to components of a naturally occurring family of strongly related small acidic chromatin peptides involved in regulation of gene expression. In a crude nuclear fraction and in purified nuclei from PC-12 cells, Pep A and Pep B activate RNA synthesis, specifically acting on the RNA polymerase II transcription system. On the other hand, Pep C shows an inhibitory effect on RNA synthesis in purified nuclei but an activation in the crude nuclear fraction. Control experiments show that the serum thymic factor does not affect RNA synthesis in the crude nuclear fraction or in purified nuclei. A possible regulation by peptide phosphorylation via casein kinase II (more active in purified nuclei than in the crude nuclear fraction) is discussed.

Synthetic octapeptide pyroGLU-ASP-ASP-SER-ASP-GLU-GLU-ASN controls DNA transcription in vitro by RNA polymerase II

The effect of the synthetic octapeptide pyroGLU-ASP-ASP-SER-ASP-GLU-GLU-ASN (phosphorylated by casein kinase II, CKII) on DNA transcription by RNA polymerase II has been studied. The peptide contains the acidic carboxy-terminus heptapeptide of the largest subunit of RNA polymerase II, which has been demonstrated to be a phosphorylation site for CKII. The aim of this work is to obtain some insights about the possible role of this domain in RNA polymerase II activity and DNA binding. Results demonstrated that the phosphorylated octapeptide causes strong inhibition of transcription of calf thymus DNA or pSVL SV40 plasmid DNA by RNA polymerase II, when used at concentrations between 0.4-4 micrograms/ml.

Phosphorylation of synthetic acidic peptides by casein kinase II: evidence for competition with phosphorylation of proteins involved in transcription

Phosphorylation of several synthetic acidic peptides by biochemically isolated casein kinase II (CKII) and by cellular and nuclear extracts containing CKII-like activity has been investigated. Especially the synthetic peptide pyroGlu-Asp-Asp-Ser-Asp-Glu-Glu-Asn comprising the carboxy-terminal acidic hepta-peptide of the largest subunit of RNA polymerase II was found to serve as an excellent substrate for purified CKII. Moreover, this peptide reduces the rate of 'in vitro' ATP-dependent stimulation of DNA transcription induced by the proteins in the extracts. Since the peptide itself is also significantly phosphorylated in such assays, it is supposed that it serves as a competitive substrate for the phosphorylation of proteins in the extracts whose phosphorylation seems to be a prerequisite for their activity in the transcription process. This points to the involvement of CKII and substrate(s) of CKII in the process of transcription.

Protein kinase NII from calf thymus chromatin. Isolation, characterization and some functional properties

1. A protein kinase type II was purified from calf thymus chromatin using ammonium sulphate fractionation, ion exchange chromatography on DEAE and phosphocellulose and affinity chromatography on phosvitin- and casein-sepharose columns. 2. The enzyme moves as a single band in non-denaturing gel electrophoresis at pH 8.3, which coincides with the enzyme activity assayed on gel slices. 3. Sodium dodecyl sulphate gel electrophoresis shows three separate polypeptide chains having M(r) of 40,000, 38,000 and 25,000, respectively. The native M(r) was about 130,000, as measured by HPLC on Superose 12 column, suggesting a subunit structure of alpha, alpha', beta 2 type. The enzyme incubated with [gamma 32P]ATP or [gamma 32P]GTP as phosphoryl donors undergoes autophosphorylation in the M(r) = 25,000 subunit. 4. The enzyme phosphorylates casein (Km = 7 microM) and phosvitin (Km = 5 microM) but not histones and was strongly deactivated by Zn2+ ions (I50 = 0.05 mM) and heparin (I50 = 0.1 micrograms/ml). 5. The enzyme seems to be the major phosphorylating system present in the 0.35 M NaCl chromatin extract of calf thymus. The RNA polymerase II from calf thymus and RNA polymerase from E. coli are both phosphorylated by protein kinase NII. The effect of phosphorylation, which causes a remarkable increase of DNA transcription rate, was studied in vitro and extensively discussed.

Epidermal inhibitory pentapeptide phosphorylated in vitro by calf thymus protein kinase NII is protected from serum enzyme hydrolysis

In this paper, we demonstrate that synthetic epidermal mitosis inhibiting pentapeptide (pyroGlu-Glu-Asp-Ser-Gly) is phosphorylated in vitro at serine level by protein kinase NII isolated from calf thymus chromatin. A serum enzyme, which rapidly cleaves the synthetic epidermal mitosis inhibiting pentapeptide, also hydrolyses the synthetic transcription inhibiting pentapeptide (pyroGlu-Ala-Glu-Ser-Asn). The phosphorylated forms of both pentapeptides are protected from the serum enzyme activity.

Chemical and enzymatic analysis of covalent bonds between peptides and chromosomal DNA

DNA from Ehrlich ascites tumor (EAT) cells and from human placenta was examined for covalent bonds between hydroxy amino acid residues in peptides and nucleotide phosphate groups. The residual proteinaceous material in highly purified DNA was radiolabelled with 125Iodine and the linking-groups between peptides and nucleotides released by combined protease and nuclease treatment were investigated with respect to their chemical and enzymatic stabilities. The residual nucleotide(s)-peptide(s) fraction from DNA isolated after prolonged alkaline cell lysis and phenol extraction contains mainly alkali and acid-stable but phosphodiesterase-sensitive peptide-nucleotide complexes which indicates phosphodiesters between tyrosyl residues in peptides and nucleotide phosphates. In contrast, the linking-group fraction from DNA isolated under native conditions contains additional peptide components. (a) Phospho-peptides that co-purify with DNA but that are not covalently bound to nucleotides. (b) A fraction of peptides that is released from nucleotides by alkali in a time and concentration-dependent reaction. Evidence is presented indicating that the latter fraction involves phospho-triesters between hydroxy amino acid residues in peptides and internucleotide phosphates. The phosphodiesters between hydroxy amino acids and nucleotide phosphates representing the predominant class of peptide-nucleotide complexes in alkali-denatured DNA are most likely side products of peptide-nucleotide phospho-triester hydrolysis.

Acidic pentapeptide phosphorylated in vitro by calf thymus protein kinase NII binds to DNA in the presence of Mg2+ cations

The pentapeptide pyroGlu-Ala-Glu-Ser-Asn has been synthetized and phosphorylated in vitro at level of serine by protein kinase NII isolated from calf thymus chromatin. It is noteworthy that the calf thymus kinase NII shows a remarkable affinity for this peptide. The [32P]peptide is able to bind to several DNAs in the presence of Mg2+ (lambda phage, calf thymus, pBR540 plasmid). This binding appears not specific with regard to the type of DNA and its base sequence. These data support the hypothesis that phosphorylated acidic domains of nuclear nonhistone proteins could bind directly to DNA in the presence of Mg2+ cations.

Small acidic peptides are bound to E. coli DNA

Low molecular weight peptides have been isolated by alkali extraction from deproteinized DNA of E. coli cells grown in the presence of radioactive glutamic acid or orthophosphate. The labeled peptides, purified by gel filtration chromatography on Sephadex G25 and G10, contain prevailingly glutamic acid, aspartic acid, glycine, serine and alanine. Electrophoretic studies at different pH show that some peptide fractions contain a phosphoric residue. The N-terminus of the phosphorylated peptides is apparently blocked and they were able to bind to DNA in the presence of Mg2+ ions. Moreover the acidic peptides extracted from E. coli DNA show a sharp activity in the control of lambda phage DNA transcription 'in vitro'.

Characterization of phosphopeptides released during dialysis of EDTA-reacted highly purified DNA prepared from calf thymus nuclei

The treatment of highly purified DNA obtained from calf thymus nuclei (N-DNA) with a chelating agent and subsequent repeated dialyses led to release of phosphopeptides (PPs) into the dialysates. By means of anion exchange column chromatography, the PPs were separated into 9 main fractions. Two of them (P1 and P5) contained the amino acids phosphoserine, asp, thr, ser, glu, gly, ala, val, ile, leu, and arg, as well as metal ion complexes of phosphoserine. The complexes were dissociated by deionization with nitrilotriacetate + Chelex. The proportion of phosphoserine was about twice as great in P5 as in P1. Whereas P1 and P5 contained essentially no nucleotide material, the other fractions contained ribonucleotides and deoxynucleotides. The deoxynucleotide content was less than 10% of that of total nucleotides. After a deionizing treatment, the amounts of nucleotides in these fractions were reduced to a level corresponding to 1 nucleotide per peptide of 5-15 amino acids.

Inhibition of DNA polymerization and DNA transcription to RNA by seminal plasma peptides

An oligopeptide fraction purified from the extracellular compartment of bull semen and strongly interacting with DNA was shown to hinder mononucleotide polymerizations to DNA and RNA in vitro. The fraction, collectively called seminal plasma inhibitor, was active in the endogenous DNA and RNA polymerase reactions of the nuclei from rat hepatocytes and in the analogous nucleotide polymerizations catalyzed by purified enzymes of bacterial origin. The type of the induced inhibition was studied using the RNA polymerase from Escherichia coli as a representative nucleotidyl transferase. In the enzymatic polycondensation of mononucleotides, the seminal plasma inhibitor appeared to exert its effect mainly by a competitive inhibition for the utilization of DNA templates without specificity with respect to the source and the base sequence of DNA. Concavities of the plots of V0/Vi versus the amounts of inhibitor in the nucleotide polymerizing reactions and of the Dixon plots in the assays of RNA polymerase from E. coli suggested that the isolated oligopeptide fraction contained more than one active molecular species with differential effects at low and high doses. Preliminary results on the microheterogeneity of the seminal plasma inhibitor supported this contention.

Chicken liver non-histone protein fraction repressing DNA transcription in vitro

A chicken liver non-histone protein fraction repressing DNA transcription in vitro was isolated using ultrasound shearing followed by precipitation with divalent cations. It was characterized by SDS-polyacrylamide electrophoresis and isoelectric focusing. This inhibitory protein fraction showed strong affinity to DNA and represented non-histone proteins with main bands of mol. wt about 35000 and 56000 and isoelectric points about 5.7 and 6.2. The inhibitory non-histone protein fraction seems to repress DNA transcription by interacting with DNA template rather than with RNA polymerase.

Bovine seminal plasma contains a low-molecular-weight factor that inhibits RNA synthesis

A low-MW factor (800-1000 daltons) extracted from bovine seminal plasma (bSP) and partially purified by a five-step fractionation is very active in inhibiting RNA synthesis by E. coli RNA polymerase with calf thymus DNA as template (70% inhibition at factor:DNA ratio of about 1:100). The same factor also inhibits RNA synthesis in isolated liver nuclei but to a lesser extent. The bSP factor probably exerts its inhibitory activity on initiation rather than on the elongation processes. DNA heat denaturation experiments indicate that the factor stabilizes double-stranded DNA. The activity of bSP factor is almost destroyed by protease (pronase) digestion. Trypsin digestion is ineffective. Consequently, peptide integrity seems to be important for the biological activity. The factor is heat stable and does not contain nucleic acid components. Preliminary analysis indicates the presence of acidic amino acids with no basic or aromatic ones and that the active factor is not a product of histone or protamine degradation. When injected i.p. into 25-day-old female rats, the bSP factor has an inhibinlike activity.

Regulatory activity of DNA-binding peptides on some metabolic pathways altered in aging

The Smith theory, which describes aging as a consequence of damage at DNA transcription level, suggested to us the opportunity of studying the possible action of DNA-binding peptides from calf thymus on old rats. We previously demonstrated that this peptidic fraction exerts a regulative control on transcriptional activities of DNA in cell and cell-free systems. In order to verify the possible action of these low molecular weight peptides we chose a large range of metabolic and structural parameters which are altered in aging. The results obtained indicate the following conclusions. Lipids. The lipid levels of old rat liver and serum are altered compared with those of young rats; the administration of peptidic fraction to old rats reverses the lipid alterations observed. Glucides. In old rat liver the presence of glycogen is very scanty or completely absent; the animals treated with the peptides show an amount and distribution of glycogen similar to that of adult normal rats. ATP. The peptidic fraction causes in the old rats a marked increase of blood ATP, bringing the level in the range of values determined in young rats. DNA, RNA, proteins. The total synthesis rate of DNA, RNA and proteins in old rat liver is not influenced by the DNA-binding peptides. Vice versa the nucleic acids from liver nuclei of old rats given peptidic fraction contain a greater RNA component compared to control old rats. This result is confirmed by the strong increase of transcriptional activity of DNA for RNA polymerase caused by administration of peptidic fraction to old rats. This increased DNA transcription can be interpreted as a partial recovery of DNA transcriptional capacity which evidently might imply a restoration of impaired metabolic systems. The histochemical and stereological analyses of liver cell compartments confirm the biochemical data.