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

A pool of peptides extracted from wheat bud chromatin inhibits tumor cell growth by causing defective DNA synthesis

Background

We previously reported that a pool of low molecular weight peptides can be extracted by alkali treatment of DNA preparations obtained from prokaryotic and eukaryotic cells after intensive deproteinization. This class of peptides, isolated from wheat bud chromatin, induces growth inhibition, DNA damage, G2 checkpoint activation and apoptosis in HeLa cells. In this work we studied their mechanism of action by investigating their ability to interfere with DNA synthesis.

Methods

BrdUrd comet assays were used to detect DNA replication defects during S phase. DNA synthesis, cell proliferation, cell cycle progression and DNA damage response pathway activation were assessed using 3H-thymidine incorporation, DNA flow cytometry and Western blotting, respectively.

Results

BrdUrd labelling close to DNA strand discontinuities (comet tails) detects the number of active replicons. This number was significantly higher in treated cells (compared to controls) from entry until mid S phase, but markedly lower in late S phase, indicating the occurrence of defective DNA synthesis. In mid S phase the treated cells showed less 3H-thymidine incorporation with respect to the controls, which supports an early arrest of DNA synthesis. DNA damage response activation was also shown in both p53-defective HeLa cells and p53-proficient U2OS cells by the detection of the phosphorylated form of H2AX after peptide treatment. These events were accompanied in both cell lines by an increase in p21 levels and, in U2OS cells, of phospho-p53 (Ser15) levels. At 24 h of recovery after peptide treatment the cell cycle phase distribution was similar to that seen in controls and CDK1 kinase accumulation was not detected.

Conclusion

The data reported here show that the antiproliferative effect exhibited by these chromatin peptides results from their ability to induce genomic stress during DNA synthesis. This effect seems to be S-phase specific since surviving cells are able to progress through their normal cell cycle when the peptide fraction is removed from the culture medium. It is likely that the subsequent apoptosis is a consequence of the failed attempt of the tumour cells to repair the DNA damage induced by the peptides.

Is there a final common path in malignancies?

We found that malignant cells and tumors contain very little low molecular weight (MW) peptides and amino acids compared to normal cells and tissues. However, the low molecular weight (MW) peptides that inhibit mitosis, cell growth and cause differentiation were recovered from cell growth medium or ascites. We therefore hypothesize that out transport and, or diffusion of the low MW compounds is possibly central to carcinogenesis, since the controlling low MW signals are lost from the cell. Without inhibitors mitosis should not or would not stop.

HYPOTHESIS

Loss of low MW peptides and amino acids may be a common trait in carcinogenesis. It would entail that normal cell regulation such as growth, mitosis inhibition and differentiation would probably be lost, especially as we recover the missing compounds (chalones) from the incubation fluid or ascites. The chalones and deprimerones seem to induce differentiation of cells when inhibiting mitosis, and when lost from the cells may explain the de-differentiation typical of malignant cells. Such a mechanism would make room for membrane damaging mechanical, inflammatory and chemical as well as viral aetiologies in carcinogenesis. Faster than normal growth also increases the probability of geneic malfunction.

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.

DNA-Bound peptides control the mRNA transcription through CDK7

The degradation of intracytosolic proteins has been well described. However, the degradation pathway and physiological functions of the DNA-Bound peptides, which are free of degradation by peptidase of the post-ubiquitin-proteasome pathway, are still unclear. In this study, the DNA-Bound peptides were isolated from barley germ and two main fractions of about 25 different peptides were obtained. The DNA-Bound peptides were found to inhibit the proliferation of HeLa cells in a series of experiments. The DNA-Bound peptides also significantly inhibited in vitro and in vivo DNA transcription activity by regulating the expression and the corresponding functions of CDK7. Furthermore, signaling issues involving NFkappaB and ERK1/2 were observed. Such data suggests that DNA transcription could be inhibited by the DNA-Bound peptides via the CDK7 pathway. Thus we concluded that some of the post-proteasomal peptides were involved in the regulation of eukaryotic mRNA transcription.

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.

Short acidic peptides isolated from wheat sprout chromatin and involved in the control of cell proliferation. Characterization by infrared spectroscopy and mass spectrometry

Low molecular weight peptides were isolated from the chromatin of wheat sprouts. Following gel filtration the peptide fraction shows a sharp inhibiting activity on the growth of HeLa cancer cells. Infrared (IR) spectroscopy and mass spectrometry have been utilized to characterize the wheat sprout peptides in an attempt to recognize the peptide sequence involved in the control of cell growth. The quantitative presence of a peptide with MH+=572 appears proportional to the cell growth inhibition activity. This compound has been subjected to extensive mass spectrometry analysis. The automatic computational analysis of the ions of second, third and fourth generations indicate a peptide sequence, AcHis-Asp-Ser-Glu-, that binds at the C-terminal a molecule of ethanolamine. Moreover, the results show that some sequences of the wheat sprout peptide family are present in the peptide fractions isolated from several other tissues, thus supporting the hypothesis of ubiquitous regulatory peptides.

Identification of peptides mimicking the ligands of proteins phosphorylated by protein kinase CK2

Synthetic peptides containing a phosphorylation site for protein kinase CK2 were used to investigate their binding properties to other peptides/proteins. The aim of this work was to find an efficient procedure to search for these peptide/protein ligands. The goal was successfully achieved through screening of random peptide libraries displayed on phage. Peptides corresponding to the amino terminal region of topoisomerase I were synthesized in both phosphorylated and unphosphorylated form and used to screen the libraries. Four of the selected sequences were also tested for their reactivity with synthetic peptides corresponding to the carboxy terminal region of the largest subunit of RNA polymerase II. The positive reaction detected supports the hypothesis that the isolated sequences may represent mimics of ligands of proteins phosphorylated by protein kinase CK2.

N-CAM expression and localization in PC12 cells modulated by extracellular peptides

The neural cell adhesion molecules (N-CAMs) play an important role in mediating cell-cell interactions in the nervous system. Different isoforms of these membrane proteins are involved in the formation of the neuronal network and in the dynamic phases of neuronal plasticity. We studied the early stages of the pseudo neuronal differentiation of PC12 cells induced by a class of small acidic peptides capable of modulating gene expression in these cells. The data presented here indicate that peptides with specific sequences induce an increase in N-CAM mRNA expression and protein translocation to the plasma membrane to a comparable degree as NGF.

Competition between citrate and heptapeptide DDSDEEN binding to DNA in presence of divalent cations

The binding of citrate and acidic peptide DDSDEEN with DNA in the presence of divalent cations is compared. Citric acid shows a higher number of binding sites on the DNA compared to the peptide; this is probably due to the bigger sitric hindrance of the peptide compared to the citric acid for the binding in the DNA grooves. Moreover. DNA preincubated with saturating amounts of citric acid is not available for the binding with successively added peptide. Therefore the peptide and citrate binding sites to some extent overlap.

Novel lymphocyte growth-inhibiting tripeptide: N-acetyl-glu-ser-GlyNH(2)

The limited and predetermined number of cells that constitutes an organ or specialized cell population is to all appearances regulated according to a negative feedback principle involving growth inhibitors with sufficient tissue specificity. To find growth-inhibiting factors in lymphoid cells, we followed established purification procedures and assays. We found a single-peak fraction in water extracts of dog spleen homogenates that inhibited proliferation of Molt (T cell) lymphoma cells at low concentrations in vitro, with no significant effect on a B cell lymphoma cell line (Ramos). C-terminal amino acid sequencing and MS analysis showed the factor to be a tripeptide: N-acetyl-Glu-Ser-GlyNH(2). Treatment with a synthetic tripeptide with the structure N-acetyl-Glu-Ser-GlyNH(2) decreased the number of cell doublings of Molt cells. The peptide also delayed cell flux at the G(2)-M transition of the cell cycle, while incorporation of tritiated thymidine was not altered at the examined time points in this cell line. However, DNA synthesis in PPD-stimulated normal human lymphocytes was significantly inhibited and with a bell-shaped dose-response curve.

Phosphorylation of the synthetic octapeptide pyroGlu-ASP-ASP-SER-ASP-GLU-GLU-ASN and binding to DNA in presence of divalent cations

Small acidic peptides involved in gene expression have been isolated from prokaryotic and eukaryotic cells. Synthetic peptides, designed on the basis of native peptides characteristics, show a biological activity similar to that of native peptides in in vitro reconstituted systems. These synthetic peptides are able to bind to DNA in presence of divalent cations (Cu2+, Fe2+, Mg2+) and salt/ethanol.

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.

Molecular models of acidic peptides from pea bud chromatin and seminal plasma. Divalent cations-mediated interaction with DNA

Small acidic peptides have been isolated from biological fluids (blood and seminal plasma) and from chromatin of several tissues. Their biological activity is related to the control of cell growth and gene expression. This work is an approach to the study of peptide structure-function relationship. Purified fractions from seminal plasma and pea bud chromatin were subjected to fast ion bombardment mass spectrometry. The results obtained were analyzed according to biochemical characteristics of the peptides studied and some possible molecular models have been designed. Two of the proposed sequences were synthesized and their biological activity assayed in cells and cell-free systems. The results demonstrate that the synthetic peptides are able to bind to DNA in the presence of divalent cations (Mg2+, Fe2+, Cu2+) with consequent inhibition of DNA transcription.

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.

Identification of a melanocyte growth-inhibiting tripeptide and determination of its structure

The function and proliferation of melanocyte cell populations are influenced by a wide range of hormones and growth factors. Local cell renewal after sudden melanocyte loss appears to be regulated according to a negative feedback principle, however. In accordance with this assumption, we have examined growth-inhibitory activity in water extracts of cultured non-transformed melanocytes and melanoma cells (B16 cells). The extracts were fractionated by gel filtration on Sephadex G-25 and Fractogel MG 2000, by ion-exchange chromatography on DEAE-cellulose and Dowex 50 and by reverse-phase high-performance liquid chromatography on Bondesil and Partisil columns. Two peptides were isolated with the structures pyroGlu-Phe-GlyNH2 and pyroGlu-Cys-GlyNH2 as revealed by mass spectrometry, peptide sequencing and amino acid analysis. The two peptides were synthesized and tested for the ability to inhibit the growth of melanocyte cultures. Only pyroGlu-Phe-GlyNH2 was inhibitory. The dose-response curve was bell-shaped with maximum inhibition around 10(-15) M. The melanocyte tripeptide thus appears to be a new member of a group of N-substituted growth-regulating oligopeptides found in other tissues.