Histone Protease Research Articles

5-Substituted Pyridine-2,4-dicarboxylate Derivatives Have Potential for Selective Inhibition of Human Jumonji-C Domain-Containing Protein 5.

Jumonji-C domain-containing protein 5 (JMJD5) is a 2-oxoglutarate (2OG)-dependent oxygenase that plays important roles in development, circadian rhythm, and cancer through unclear mechanisms. JMJD5 has been reported to have activity as a histone protease, as an Nε-methyl lysine demethylase, and as an arginine residue hydroxylase. Small-molecule JMJD5-selective inhibitors will be useful for investigating its (patho)physiological roles. Following the observation that the broad-spectrum 2OG oxygenase inhibitor pyridine-2,4-dicarboxylic acid (2,4-PDCA) is a 2OG-competing JMJD5 inhibitor, we report that 5-aminoalkyl-substituted 2,4-PDCA derivatives are potent JMJD5 inhibitors manifesting selectivity for JMJD5 over other human 2OG oxygenases. Crystallographic analyses with five inhibitors imply induced fit binding and reveal that the 2,4-PDCA C5 substituent orients into the JMJD5 substrate-binding pocket. Cellular studies indicate that the lead compounds display similar phenotypes as reported for clinically observed JMJD5 variants, which have a reduced catalytic activity compared to wild-type JMJD5.

Discovery of novel antibody-drug conjugates bearing tissue protease specific linker with both anti-angiogenic and strong cytotoxic effects

Bevacizumab is an FDA-approved class of monoclonal antibodies used to inhibit angiogenesis and promote normalization of blood vessels. It is usually combined with chemotherapeutic agents to treat a variety of solid tumors. However, the whole-body toxicities and toxicity associated with chemotherapy greatly limit the clinical use of this combination therapy. Antibody-drug conjugates (ADCs) couple monoclonal antibodies to cytotoxic molecules via a linker, utilizing the high specificity of monoclonal antibodies to tumor surface antigens to act as a “biological missile” to deliver chemotherapeutic drugs to the tumor site. Herein, we designed a bevacizumab-based ADC, Bevacizumab Vedotin, conjugating bevacizumab to the microtubulin inhibitor MMAE via a tissue protease-specific linker. Biological studies showed strong stability and good tumor cell targeting of our constructed ADCs; rapid drug release was achieved in the presence of exogenous histone protease B. In addition, Bevacizumab Vedotin exhibited good anti-proliferative, apoptosis-promoting and cell cycle-stalling effects on glioma (U87), hepatocellular carcinoma (HepG2), and breast cancer (MCF-7) cell lines. Further in vitro assays demonstrated the enhanced anti-migration activity against MCF-7, potent anti-angiogenic effects, and blockade of the VEGF/VEGFR pathway of Bevacizumab Vedotin.

Partial purification of histone H3 proteolytic activity from the budding yeast Saccharomyces cerevisiae.

The proteolytic clipping of histone tails has recently emerged as a novel form of irreversible post-translational modification (PTM) of histones. Histone clipping has been implicated as a regulatory process leading to the permanent removal of PTMs from histone proteins. However, there is scarcity of literature that describes the identification and characterization of histone-specific proteases. Here, we employed various biochemical methods to report histone H3-specific proteolytic activity from budding yeast. Our results demonstrate that H3 proteolytic activity was associated with sepharose bead matrices and activity was not affected by a variety of stress conditions. We have also identified the existence of an unknown protein that acts as a physiological inhibitor of the H3-clipping activity of yeast H3 protease. Moreover, through protease inhibition assays, we have also characterized yeast H3 protease as a serine protease. Interestingly, unlike glutamate dehydrogenase (GDH), yeast H3 proteolytic activity was not inhibited by Stefin B. Together, our findings suggest the existence of a novel H3 protease in yeast that is different from other reported histone H3 proteases. The presence of histone H3 proteolytic activity, along with the physiological inhibitor in yeast, suggests an interesting molecular mechanism that regulates the activity of histone proteases. Copyright © 2016 John Wiley & Sons, Ltd.

Proteolytic clipping of histone tails: the emerging role of histone proteases in regulation of various biological processes

Chromatin is a dynamic DNA scaffold structure that responds to a variety of external and internal stimuli to regulate the fundamental biological processes. Majority of the cases chromatin dynamicity is exhibited through chemical modifications and physical changes between DNA and histones. These modifications are reversible and complex signaling pathways involving chromatin-modifying enzymes regulate the fluidity of chromatin. Fluidity of chromatin can also be impacted through irreversible change, proteolytic processing of histones which is a poorly understood phenomenon. In recent studies, histone proteolysis has been implicated as a regulatory process involved in the permanent removal of epigenetic marks from histones. Activities responsible for clipping of histone tails and their significance in various biological processes have been observed in several organisms. Here, we have reviewed the properties of some of the known histone proteases, analyzed their significance in biological processes and have provided future directions.

The Protease Degrading Sperm Histones Post-Fertilization in Sea Urchin Eggs Is a Nuclear Cathepsin L That Is Further Required for Embryo Development

Proteolysis of sperm histones in the sea urchin male pronucleus is the consequence of the activation at fertilization of a maternal cysteine protease. We previously showed that this protein is required for male chromatin remodelling and for cell-cycle progression in the newly formed embryos. This enzyme is present in the nucleus of unfertilized eggs and is rapidly recruited to the male pronucleus after insemination. Interestingly, this cysteine-protease remains co-localized with chromatin during S phase of the first cell cycle, migrates to the mitotic spindle in M-phase and is re-located to the nuclei of daughter cells after cytokinesis. Here we identified the protease encoding cDNA and found a high sequence identity to cathepsin proteases of various organisms. A phylogenetical analysis clearly demonstrates that this sperm histone protease (SpHp) belongs to the cathepsin L sub-type. After an initial phase of ubiquitous expression throughout cleavage stages, SpHp gene transcripts become restricted to endomesodermic territories during the blastula stage. The transcripts are localized in the invaginating endoderm during gastrulation and a gut specific pattern continues through the prism and early pluteus stages. In addition, a concomitant expression of SpHp transcripts is detected in cells of the skeletogenic lineage and in accordance a pharmacological disruption of SpHp activity prevents growth of skeletal rods. These results further document the role of this nuclear cathepsin L during development.

Autodigestion of chromatin in some radiosensitive and radioresistant mouse cells. Role of proteolysis and endonucleolysis.

Evidence is presented indicating that mouse thymus, spleen, kidney, lung and heart contain a protease activity with relatively high specificity for histones. It is suggested that degradation of chromatin occurring in irradiated lymphoid tissues is produced by the action of alkaline endonuclease in association with this histone protease. The autodigestion of chromatin was assessed by determining the release of soluble chromatin from cells suspended in sucrose media of low ionic strength. It was found that the protease inhibitors, phenylmethylsulphonyl fluoride and especially NaHSO3, were also capable of depressing the activity of alkaline endonuclease, the fragmentation of chromatin, and the release of soluble chromatin. The results suggest that the release of histones from irradiated lymphoid tissues cannot be considered as a determinant step in the fragmentation of DNA in chromatin.

Histone Kinase from Soybean Hypocotyls

A histone-type protein kinase (EC 2.7.1.37) has been partially purified (320-fold) from the crude extracts of soybean hypocotyls by means of a combination of gel filtration and anion exchange procedures. The purified enzyme fraction is devoid of the activities of phosphoprotein phosphatase (EC 3.1.3.16), histone protease, and casein (or phosvitin)-type kinase. The soybean histone kinase uses ATP to phosphorylate specifically lysine-rich histone H1 from either pea seedlings or calf thymus.The histone kinase requires free sulfhydryl group(s) for activity, but not stability. The pH optimum is around 9 to 10. The apparent K(m) values for histone H1 of pea seedlings and calf thymus are 0.4 and 0.9 micromolar, respectively. The K(m) values for ATP are 40 nanomolar with the optimal concentration of Mn(2+) (50 nanomolar) and 0.4 micromolar with that of Mg(2+) (5 millimolar). The estimated molecular weight of the kinase is 52,000 by gel filtration or 48,600 by sedimentation constant (3.2 S). cAMP does not alter the sedimentation velocity of the kinase. The enzyme activity is unaffected by cyclic nucleoside monophosphates and plant growth substances. Like arginine-rich histones, a variety of divalent cations and polycations (polyamines) are inhibitory.This cAMP-independent soybean histone kinase is not associated with the isolated ribosomes but shows highest specific activity in the nuclearchromatin fraction, suggesting that it may function in the regulation of histone H1 phosphorylation in the soybean hypocotyl.

Phosphoprotein Phosphatase of Soybean Hypocotyls

A soybean histone-type protein kinase was used to prepare (32)P-labeled histone H1 as substrate for purification and characterization of a phosphoprotein phosphatase (EC 3.1.3.16) from soybean hypocotyls. The phosphatase has been purified 169-fold by ammonium sulfate fractionation, ethanol precipitation, and chromatography on Sephadex G-150, DEAE-Sephadex A-25 and Sephadex G-100. The activity of the phosphoprotein phosphatase is distinct from that of acid and alkaline phosphatases (EC 3.1.3.1) as well as from that of nucleotidases. The final enzyme preparation does not contain histone protease activity, although it can be detected during the early stages of purification. The protease(s) apparently can attack phosphorylated histone H1, indicating that phosphorylation does not protect the protein against proteolytic degradation.The amounts of (32)P released from [(32)P]histone H1 are proportionally recovered as [(32)P]Pi, indicating that the dephosphorylation is due to the action of phosphoprotein phosphatase. The enzyme shows maximal activity at pH 7 to 8 and has a specific activity of 19 nanomoles of [(32)P]Pi released from [(32)P]histone H1 per minute per milligram of protein. The apparent K(m) for phosphohistone H1 is 4.0 +/- 0.4 micromolar. The estimated molecular weight of the enzyme is approximately 30,000 by gel filtration. The enzyme activity does not depend upon the addition of reducing agent and metal ion. Zn(2+), Co(2+), NaF, pyrophosphate, or ATP at 1 millimolar, however, inhibits the enzyme activity by about 70%. The enzyme activity is unaffected by cyclic nucleotides and plant growth substances but is inhibited by polyamines. All the phosphorylated histone species and protamine, not low molecular weight phosphoesters, act as competitive inhibitors for the dephosphorylation of [(32)P]histone H1.Besides its action on phosphohistone H1, the soybean enzyme also catalyzes the dephosphorylation of other phosphohistone species (H2A, H2B, H3, and H4), degraded phosphohistone H1, and possibly phosphorylated casein and phosvitin. All these results indicate that the enzyme is a nonspecific phosphoprotein phosphatase.

The histone content of chromatin preparations from leukaemic cells.

The histone compositions of chromatin preparations obtained from different adult laukaemias were compared and showed differences between myeloid, monoblastic and lymphoblastic types. The differences were observed whether or not the myeloid precursors were mature or blast forms. Mixing experiments revealed that a potent histone protease was present in the myelocyte chromatin fraction which, unlike most histone proteases, appeared not to be inhibited by serine esterase inhibitors. It is concluded that the differences observed in the histone patterns do not reflect the histon composition present in the cell but are created by proteolytic degradation during the isolation procedures. However, these may still provide some help in identifying myeloblasts in undifferentiated leukaemias.

Histone proteases and the distribution of retained histones in nuclei from rat ventral prostate cells undergoing hypertrophy or hyperplasia

1. 1. The distribution of histones retained by ventral prostate nuclei from normal rats, short (3 day) or long-term castrates (7 day), or short-term castrates treated with testosterone propionate for 3 days to induce cellular hypertrophy (growth) did not differ. 2. 2. Long-term castrates treated with androgen to induce cell division (hyperplasia) contained less histone F2a2, particularly if minced prostate was first incubated at 37°C before isolation of nuclei. 3. 3. When prostate nuclear proteins were dissociated in high ionic strength at alkaline pH, marked proteolysis of histones occurred in the five groups of animals examined. 4. 4. The distribution of partially degraded histones in nuclear extracts from growing or dividing ventral prostate cells differed from each other and from their castrated controls. 5. 5. Limited selective proteolysis of histones in nuclei from regressing, hypertrophie or hyperplastic prostate cells may be necessary to prepare chromatin for the subsequent molecular events required for these processes.

Histone proteases of avian erythroid cells

Protease activity associated with avian erythroid chromatin has been studied by gel electrophoresis of histones. Histone degradation is minimal at neutral pH, but is readily detected when chromatin is incubated at pH 3, and is evident to a lesser extent at pH 9. As a result of the pH 3 activity, the f1 and f2 chistones are preferentially degraded when the histone complement is DNA-bound, but these histones are relatively resistant to attack when present as free histone. The pH 3 activity reported here has properties similar to those of neutral histone proteases from other tissues, except that it is not inhibited by bisulphite. Added exogenous proteins are not degraded. The activity of avian erythroid histone protease decreases as maturation of the cells proceeds. Since we have previously shown that turnover of DNA-bound f2c histone occurs in reticulocytes and histone synthesis is absent in erythrocytes, it is possible that the histone protease described here may be involved in f2c histone turnover.

Cytoplasmic origin of the so-called nuclear neutral histone protease

1. We have investigated the origin of proteolytic activity which causes degradation of histones in chromatin isolated from Xenopus liver and rat liver at neutral pH. Polyacrylamide disc gel electrophoresis was used for detection of proteolytic products of histones. 2. No proteolytic degradation of histones occurs in chromatin isolated from Xenopus erythrocytes and rat liver according to our procedure even after prolonged incubation at pH 8.0 and pH 5.0. However with chromatin isolated from Xenopus liver a high level of histone degradation is observed under similar conditions. 3. Mixing isolated nuclei from Xenopus erythrocytes with a crude cytoplasmic fraction from Xenopus liver causes histone proteolysis in isolated chromatin at pH 8.0. In similar experiments with corresponding fractions from rat liver histone proteolysis can be introduced only after repeated freezing and thawing of the cytoplasmic fraction. 4. A purified lysosomal preparation from rat liver causes a similar type of histone degradation upon incubation with chromatin from Xenopus erythrocytes and rat liver. 5. The neutral proteolytic activity that can be introduced in isolated chromatin by a crude cytoplasmic fraction and by a purified lysosomal fraction from rat liver is inhibited by sodium bisulphite. 6. We conclude that the neutral proteolytic activity which causes degradation of histones in isolated chromatin is due to a contamination with neutral protease(s) originating from cytoplasmic organelles.

A histone protease of rat liver chromatin

Normal rat liver chromatin contains a protease activity with a marked preference for histone or deoxyribonucleohistone as substrate. This histone protease has been purified 20 to 30 fold from chromatin and has been analyzed for salt and pH dependence as well as for substrate specificity. The isolated enzyme appears to be similar to that responsible for the endogenous degradation of histones in calf thymus chromatin as reported by Bartley and Chalkley (1); however, its presence in adult rat liver, a tissue with very low cell turnover (and therefore low histone turnover), argues against the enzyme having only an autolytic function and suggests that it may play a role in gene derepression, etc.