An ATP/ADP-dependent molecular switch regulates the stability of p53-DNA complexes.

Interaction with DNA is essential for the tumor suppressor functions of p53. We now show, for the first time, that the interaction of p53 with DNA can be stabilized by small molecules, such as ADP and dADP. Our results also indicate an ATP/ADP molecular switch mechanism which determines the off-on states for p53-DNA binding. This ATP/ADP molecular switch requires dimer-dimer interaction of the p53 tetramer. Dissociation of p53-DNA complexes by ATP is independent of ATP hydrolysis. Low-level ATPase activity is nonetheless associated with ATP-p53 interaction and may serve to regenerate ADP-p53, thus recycling the high-affinity DNA binding form of p53. The ATP/ADP regulatory mechanism applies to two distinct types of p53 interaction with DNA, namely, sequence-specific DNA binding (via the core domain of the p53 protein) and binding to sites of DNA damage (via the C-terminal domain). Further studies indicate that ADP not only stabilizes p53-DNA complexes but also renders the complexes susceptible to dissociation by specific p53 binding proteins. We propose a model in which the DNA binding functions of p53 are regulated by an ATP/ADP molecular switch, and we suggest that this mechanism may function during the cellular response to DNA damage.

Interaction with damaged DNA induces selective proteolytic cleavage of p53 to yield 40 kDa and 35 kDa fragments competent for sequence-specific DNA binding.

The p53 protein binds sites of primary DNA damage via its C-terminus. This interaction in some way activates sequence-specific binding (via the central core domain) and transactivation of p53 target genes. We now show that interaction with non-specific DNA, but not specific DNA targets, induces selective proteolysis of p53 to give a 40 kDa fragment, comprising the core plus C-terminus, and a 35 kDa conformationally intact core domain. Proteolytic cleavage was limited and yielded roughly equivalent proportions of full length p53 and the 40 kDa and 35 kDa fragments. Significantly, both 40 kDa and 35 kDa products were activated for sequence-specific DNA binding. Similar p53-related products were induced by exposure of cells to DNA damage. We propose that some functions of p53 can be activated by proteolytic processing and that this may be important in the cellular response to DNA damage.

RNA synthesis block by 5, 6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) triggers p53-dependent apoptosis in human colon carcinoma cells.

Most modern chemo- and radiotherapy treatments of human cancers use the DNA damage pathway, which induces a p53 response leading to either G1 arrest or apoptosis. However, such treatments can induce mutations and translocations leading to secondary malignancies or recurrent disease, which often have a poor prognosis because of resistance to therapy. Here we report that 5, 6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB), an inhibitor of CDK7 TFIIH-associated kinase, CKI and CKII kinases, blocking RNA polymerase II in the early elongation stage, triggers p53-dependent apoptosis in human colon adenocarcinoma cells in a transcription independent manner. The fact that DRB kills tumour-derived cells without employment of DNA damage gives rise to the possibility of the development of a new alternative chemotherapeutic treatment of tumours expressing wild type p53, with a decreased risk of therapy-related, secondary malignancies.

Wild-type p53 protein shows calcium-dependent binding to F-actin.

Nuclear localization of p53 is required for p53 to detect and respond to DNA strand abnormalities and breaks following DNA damage. This leads to activation of the tumour suppressive functions of p53 resulting in either cell cycle arrest and DNA repair; or apoptosis. Critical functional changes in DNA which require strand breaks, including gene rearrangement, may transiently mimic DNA damage: here it is important not to trigger a p53 response. The fine control of p53 in these different circumstances is unknown but may include transient sequestering of p53 in the cytoplasm. Reversible nuclear-cytoplasmic shuttling is an intrinsic property of p53 (Middeler et al., 1997) associated with cell cycle-related changes in p53's subcellular distribution. Takahashi and Suzuki (1994) described p53 inactivation by shuttling to the cytoplasm and Katsumoto et al. (1995) found wild-type p53 to be closely associated with cytoplasmic actin filaments during DNA synthesis. Here we show that, in the presence of free calcium ions, p53 binds directly to F-actin with a dissocation constant of about 10 microM. Thus, part of the regulatory machinery in normal cell cycling may involve p53-actin interactions regulated by calcium fluxes and the dynamic turnover of F-actin.

p53 binds the nuclear matrix in normal cells: binding involves the proline-rich domain of p53 and increases following genotoxic stress.

The tumour suppressor p53 is a multifunctional protein important for the maintenance of genomic integrity. It is able to form molecular complexes with different DNA targets and also with cellular proteins involved in DNA transcription and DNA repair. In mammalian cells the biochemical processing of DNA occurs on a nuclear sub-structure termed the nuclear matrix. Previously Deppert and co-workers have identified p53 in association with the nuclear matrix in viral- and non-viral transformed cell lines. In the present study we demonstrate, for the first time, that p53 is bound to the nuclear matrix in primary cultures of normal mammalian cells and that this binding increases following DNA damage. Analysis of cell lines expressing structural mutants of p53 revealed that association with the nuclear matrix is independent of the tertiary and quaternary structure of p53. However, the proline-rich domain towards the N-terminus of p53 (residues 67 to 98) appeared important for binding to the nuclear matrix. This was demonstrated by TET-ON regulated expression of p53-derived constructs in p53(-/-) murine embryonic fibroblasts (MEF p53(-/-)). The proline-rich domain of p53 has potential for SH3 protein-protein interaction, and has a role in p53-mediated apoptosis and possibly base excision repair of DNA damage. We discuss our observations in relation to the ability of p53 to facilitate DNA repair and also review evidence indicating that matrix-bound p53 in SV40-transformed cells may facilitate the transforming potential of SV40 large T antigen.

Discovery of Novel Isatin-Based p53 Inducers.

A series of isatin Schiff base derivatives were identified during in silico screening of the small molecule library for novel activators of p53. The compounds selected based on molecular docking results were further validated by a high-content screening assay using U2OS human osteosarcoma cells with an integrated EGFP-expressing p53-dependent reporter. The hit compounds activated and stabilized p53, as shown by Western blotting, at higher rates than the well-known positive control Nutlin-3. Thus, the p53-activating compounds identified by this approach represent useful molecular probes for various cancer studies.

Site-directed mutagenesis of the base recognition loop of ribonuclease from Bacillus intermedius (binase).

Members of the microbial guanyl-specific ribonuclease family show a high level of structural homology. The structural basis for guanyl base binding by microbial ribonucleases has been established for all members of the family and the existence of a guanine recognition loop was shown. However, bacillar RNases such as binase and barnase show far less specificity towards the guanyl base in hydrolysing oligonucleotides composed of more than 4 or 5 nucleotides. Using site-directed mutagenesis we introduced a number of amino acid substitutions into the base recognition loop of binase. The donor sequence originated from the guanyl specific ribonuclease Sa. Two single, two double and one triple (entire loop substitution) mutants were constructed and overproduced in E. coli. The kinetic properties of the mutant variants are different from the wild-type protein. Amino acid substitutions R61V, G60S, S56Q/R61V, G60S/R61V show 3-fold, 7-fold, 4-fold and 12-fold increased guanyl specificity respectively. However, all mutants retain the ability to catalyse the hydrolysis of a poly(A) substrate.

Ribonuclease A mutant His119 Asn: the role of histidine in catalysis.

Bovine pancreatic ribonuclease A (RNase A) has been widely used as a convenient model for structural and functional studies. The enzyme catalyzes cleavage of phosphodiester bonds in RNA and related substrates. Three amino acid residues located at the active site of RNase A (His12, His119, and Lys41) are known to be involved in catalysis. Mutation of His119 to asparagine was generated to study the role of His119 in RNase A catalysis. The mutant enzyme has been isolated and characterized. The mutation significantly decreases the rate of the transesterification reaction and has no effect on substrate affinity of the enzyme. An analysis of the enzymatic properties of H119N RNase A suggests that the imidazole ring of His119 of the wild-type enzyme must be protonated in an enzyme-substrate productive complex. Thus our results indicate that a contribution of protonated His119 into the catalysis is not restricted to protonation of oxygen atom of the substrate leaving group and that His119 participates directly in a transition state stabilization via hydrogen bonding.

Proteolytic cleavage of p53: a model for the activation of p53 in response to DNA damage.

p53 is a multifunctional protein that reacts to DNA damage within the cell and regulates the cell growth arrest and/ or apoptotic pathways. However, the mechanism of p53 activation in response to DNA damage is unknown. Recently we have shown that interaction of p53 with sites of DNA damage induces selective proteolytic cleavage of p53, resulting in fragments of 40 and 35 kDa molecular weight. We have also shown that interaction of p53 with single-stranded (ss)DNAs results in a different pattern of selective proteolysis. This interaction gives a novel of 50-kDa protein generated by C-terminal cleavage of the full length protein and released from the p53-ssDNA complexes. Here we discuss a model where p53 responds to the DNA damage by generating different sets of the proteolytic fragments according to the type of the damage.

[Superproduction of Bacillus intermedius 7P ribonuclease (binase) in Escherichia coli]. / Superproduktsiia ribonukleazy Bacillus intermedius 7P (binzay) v Escherichia coli.

We have reported previously about the cloning of the binase gene in E. coli. In this work, using an original approach named "homolog gene recombination" method (HGR), vectors for binase expression in E. coli have been constructed. Transcription of the binase gene have been directed through either tac-promoter or PR-promoter of bacteriophage lambda under the control of temperature-sensitive CI857 repressor. The last promoter gave the maximum yield of binase, up to 100 mg of protein per litre of heat-induced bacterial culture. The location of the transcription terminator at the 3' terminus of the binase gene raised the expression approximately two times more. A chromatographic method have been developed and applied for the control of binase accumulation in growth medium without measuring the ribonuclease activity.

[Barnase mutant Ser57Ala: preparation and properties]. / Mutant barnazy Ser57Ala: poluchenie i svoistva.

Barnase, an extracellular ribonuclease produced by Bacillus amyloliquefaciens, belongs to a family of small microbial ribonucleases with similar structure and properties. These enzymes hydrolyze phosphodiester bonds on the 3' side of guanosine nucleotides in RNA. The guanylic specificity of barnase is more pronounced in the hydrolysis of dinucleotides or cyclonucleotide phosphates as substrates than in the hydrolysis of RNA or polynucleotides. To have an insight into the molecular basis of this phenomenon, we mutated amino acid residue Ser-57 in the "base recognition loop" of RNase Ba. The mutant protein was expressed in Escherichia coli producing system and purified for the study of the kinetic properties in the cleavage polynucleotide reactions. It was shown that the mutation of amino acid residue Ser-57 for Ala in the "recognition loop" of RNase Ba does not significantly influence the kinetic parametres of hydrolysis of polynucleotide substrates.

[Cloning the asd and lysC genes from Cornyebacterium glutamicum]. / Klonirovanie genov asd i LysC Corynebacterium glutamicum.

Plasmids carrying an asd gene from a mutant. S-(2-aminoaethyl)-L-cysteine resistant strain of Corynebacterium glutamicum were selected from a clonoteque constructed on a plasmid cloning vector pSL5 by complementation of asd mutation in Escherichia coli. Evidence has been obtained that the cloned chromosomal DNA fragment contains also a complete sequence for feed-back-resistant aspartokinase lysC gene.

[Cloning and study of Corynebacterium glutamicum genes complementing ilvA and thrA2 mutations in Escherichia coli]. / Klonirovanie i izuchenie genov Corynebacterium glutamicum, komplementiruiushchikh mutatsii ilvA i thrA2 Escherichia coli.

Molecular cloning and expression of Corynebacterium glutamicum genes complementing Escherichia coli mutations thrA2 and ilvA was performed. It was demonstrated that the thrA2 gene of C. glutamicum is located close to thrB on EcoRI DNA fragment 4.1 kb long. The fragment was cloned in pUC18 vector. The thrA2 gene is expressed in the recombinant plasmid pOBT3 under control of the vector pUC18 Plac promoter. In E. coli minicells, the genes thrA2 and thrB determined synthesis of proteins of Mr 43kD and 25 kD, respectively. A gene complementing ilvA mutation of E. coli was identified in a library of EcoRI C. glutamicum DNA fragments. This library was constructed using plasmid vector. It was shown that the ilvA gene of C. glutamicum is located inside the 3.6 kb EcoRI fragment and is expressed using its own promoter.

[Cloning and structural-functional analysis in Escherichia coli of genes of glutamate-producing corynebacteria controlling biosynthesis of amino acids of aspartic acid series]. / Klonirovanie i strukturno-funktsional'nyi analiz v kletkakh Escherichia coli genov glutamatprodutsiruiushchikh korinebakterii, kontroliruiushchikh biosintez aminokislot asparaginovogo semeistva.

A library of EcoRI DNA fragments from Brevibacterium flavum was constructed using plasmid vector. The genes complementing ThrA2 and ThrB mutations in Escherichia coli were identified in the library. The gene thrA2 of B. flavum codes for mutant enzyme homoserine dehydrogenase insensitive to inhibition by threonine. The genes thrA2 and thrB are localized wihtin the EcoRI fragment 4.1 kb long and are expressed under the control of their own promoters in E. coli cells. Structural and functional analysis of cloned C. glutamicum gene ilvA was performed. The gene of C. glutamicum complemented ilvA mutation in E. coli and appeared to be localized within the EcoRI--SacI DNA fragment 1.6 kb in size. Using E. coli minicells we have demonstrated that the gene ilvA of C. glutamicum controls the synthesis of polypeptide of relative molecular mass 50 kD.

[Development of the vector-host system in Corynebacterium. Cloning and expression of homoserine dehydrogenase and homoserine kinase genes in Corynebacterium cells]. / Razrabotka sistemy vektor-khoziain u korinebakterii. Klonirovanie i izuchenie ékspressii genov gomoserindegidrogenazy i gomoserinkinazy v kletkakh korinebakterii.

Novel cloning vectors for glutamic acid producing bacteria have been constructed. The cryptic plasmid pBO1 (4.4 kb) from Brevibacterium sp. recombined with the plasmid pACYC184 (4.0 kb) from Escherichia coli was used to produce composite plasmid named pKA1. The plasmid could propagate and express the Cm-r phenotype in E. coli and coryneform glutamic acid producing bacteria Br. flavum, C. glutamicum, Br. lactofermentum. The pKA1 plasmid and its variants deleted within non-essential plasmid regions with unique restriction sites HindIII, SalGI, SphI were used in cloning experiments. The genes coding for threonine biosynthesis of C. glutamicum and Br. flavum were subcloned into shuttle vectors in C. glutamicum cells. Recombinant plasmids were introduced into protoplasts by polyethylenglycol-mediated transformation of plasmid DNAs. It was shown that the presence of plasmids containing the Br. flavum thrA2 gene in C. glutamicum (thrB) caused 10-fold increase in homoserine dehydrogenase activity, as compared to that of wild type strain, and in homoserine production.

An improved system for ribonuclease Ba expression.

The extracellular ribonuclease from Bacillus amyloliquefaciens (barnase, RNase Ba) is a well-characterized enzyme extensively used in structure-function studies. A new system for efficient expression and purification of barnase has been developed. The strong regulated expression cassette with the Pr promoter of lambda phage and the cooperative expression of barnase and barstar under its control have been applied to expression of these proteins in Escherichia coli. The expression cassette containing the Pr promoter of E. coli lambda phage under cI repressor regulation and the nucleotide sequence coding for barnase and barstar structural genes were merged into the plasmid pTN441, which was used for large-scale barnase production. The phoA signal peptide was used to express the target protein into cell periplasm. The purification of RNase Ba was carried out in two steps: the initial sample was concentrated followed by RP-HPLC. The system provides a stable yield of homogeneous protein of about 100-150 mg per liter of culture medium.

Proteolytic cleavage of p53 mutants in response to mismatched DNA.

Interaction of p53 with mismatched DNA induces proteolytic cleavage with release of a 35-kDa protein fragment from the p53-DNA complexes. The 35-kDa cleavage product is activated for specific biochemical function(s) and may play a role in the cellular response to DNA damage (Molinari et al (1996) Oncogene 13: 2077-2086; Okorokov et al (1997) EMBO J 16: 6008-6017). In the present study we have asked if mutants of p53 retain the ability to undergo similar proteolytic cleavage, and compared sequence-specific 'DNA contact' with 'structural' mutants commonly found in human cancer. In addition, a series of phosphorylation site mutants were generated to investigate the possible effects of phosphorylation/dephosphorylation on the proteolytic cleavage of p53. All mutants tested bound to a mismatched DNA target in vitro. Moreover, studies in vitro and in vivo indicate that p53 mutants with intact conformational structure (as determined by immunoreactivity with PAb246 and PAb1620) retain the ability to undergo proteolytic cleavage similar, if not identical, to the wild-type p53 protein. Our results suggest that the capacity for p53 to bind mismatched DNA is independent of structural conformation of the central core domain. Proteolytic cleavage, however, is crucially dependent upon a wild-type conformation of the protein.

Induced N- and C-terminal cleavage of p53: a core fragment of p53, generated by interaction with damaged DNA, promotes cleavage of the N-terminus of full-length p53, whereas ssDNA induces C-terminal cleavage of p53.

p53 is able to recognize and bind sites of DNA damage and, in some way, damage to cellular DNA activates a p53 response leading to G1 arrest or apoptosis. We have previously shown that 'damaged DNA' induces N-terminal cleavage of p53 to generate p40(DeltaN) and p35 (core) protein products. We now show that the p35 product has protease activity and is able to cleave between residues 23 and 24 of full-length p53 to generate a novel product, p50(DeltaN23). This activity was inhibited by bestatin, an aminopeptidase inhibitor. Residues 23 and 24 lie within the mdm-2 binding domain of p53 and the possibility that p50(DeltaN23) may be resistant to feedback regulation by mdm-2 is discussed. Unexpectedly, interaction with ssDNA induced two further cleavage products of p53, generated by C-terminal cleavage and designated p50(DeltaC) and p40(DeltaC). In vivo generation of a C-terminal cleavage product of endogenous p53 similar in size to p50(DeltaC) correlated with up-regulation of p21 expression in ML-1 cells exposed to either adriamycin or cisplatin. The possible significance of the various p53 cleavage products in relation to the cellular response to DNA damage is discussed.