Specific expression of nuclear proto-oncogenes before entry into meiotic prophase of spermatogenesis.

The expression of proto-oncogenes representative of several functional categories has been investigated during development of mouse male germ cells. The c-raf proto-oncogene and three members of the c-ras gene family were expressed in mitotically active stem cells, throughout the prophase of meiosis and to varying extents in post-meiotic cell types. In contrast, the nuclear proto-oncogenes c-fos, c-jun, and c-myc were specifically expressed at high levels in type B spermatogonia. High levels of c-myc and c-jun RNAs were also detected in spermatocytes early in the prophase of meiosis. The type B spermatogonia represent the last mitotic cell division before entry into meiotic prophase; therefore, these nuclear proto-oncogenes may be involved in altering programs of gene expression at this developmental transition.

Identification of the protein product of the c-mos proto-oncogene in mouse testes.

The mouse c-mos proto-oncogene RNA is expressed primarily in mouse gonadal tissues and embryos. Until now, the c-mos protein has not been identified. Utilizing two different site-directed affinity purified anti-peptide antibodies, we have identified a 43 kDa c-mos protein in mouse testes and in germ cell preparations derived from testes. This 43 kDa testicular protein was found to be structurally related to a bacterially expressed c-mos protein by peptide mapping. Immunoblots of whole mouse sections were employed to establish that the c-mos protein is expressed primarily in the testes.

Protein engineering of the restriction endonuclease EcoRV: replacement of an amino acid residue in the DNA binding site leads to an altered selectivity towards unmodified and modified substrates.

According to the crystal structure analysis of a specific EcoRV/DNA complex, the thymine residues of the recognition sequence -GATATC- are not in direct contact with any amino acid residue of the protein. However, several amino acid residues are sufficiently close that it seemed worthwhile trying to create variants of EcoRV with altered specificity by site-directed mutagenesis. Guided by molecular modelling we have replaced. Asn-188 in the catalytic center of EcoRV by Gln to produce a mutant with a relative preference (compared to wild type EcoRV) for substrates in which one thymine of the recognition sequence is replaced by uracil. We have purified and characterized the resulting N188Q mutant. The selectivity value for the engineered enzyme (the ratio of the kcat/KM values for -GATAUC- versus -GATATC-) differs from that of the wild type enzyme by a factor of more than 200.

Equine CRISP-3: primary structure and expression in the male genital tract.

Although originally described in the male rodent genital tract, cysteine-rich secretory proteins (CRISPs) are expressed in a variety of mammalian tissue and cell types. The proteins of the male genital tract have been observed associated to spermatozoa and are believed to play a role in mammalian fertilization. Here we describe the identification and primary structure of the first equine member of the CRISP family. Equine CRISP-3 is transcribed and expressed in the stallion salivary gland, in the ampulla and the seminal vesicle. It displays all 16 conserved cysteine residues and shows 82% homology to human and 78% to guinea pig CRISP-2 (AA1, TPX 1) and 77% to human CRISP-3. In contrast to other mammalia, in the horse CRISP-3 is synthesized in great amounts in the accessory sexual glands, ampulla and seminal vesicle, thus allowing the isolation of equine CRISP-3 in amounts suitable for biochemical, physiological and structural studies from stallion seminal plasma.

Mutational analysis of the function of Gln115 in the EcoRI restriction endonuclease, a critical amino acid for recognition of the inner thymidine residue in the sequence -GAATTC- and for coupling specific DNA binding to catalysis.

The Gln115 residue of the EcoRI restriction endonuclease has been proposed to form a hydrophobic contact to the methyl group of the inner thymidine of the EcoRI recognition sequence -GAATTC- and to be involved in intramolecular hydrogen bonds to the mainchain at positions 140 and 143 as well as to the side-chain of Asn173. We have exchanged Gln115 for Ala and Glu by site-directed mutagenesis and analysed the purified mutant proteins (Q115A and Q115E) biochemically and physico-chemically. Q115A and Q115E have the same secondary structure composition as wild-type EcoRI but are less stable towards thermal denaturation than the wild-type enzyme. In contrast to wild-type EcoRI the mutant proteins show a biphasic denaturation profile under alkaline pH, presumably because the amino acid exchange labilizes one part of the molecule, which unfolds before the rest of the protein is denatured. Q115A is catalytically inactive under normal buffer conditions, in part due to a diminished affinity towards DNA. At low ionic strength and alkaline pH, as well as in the presence of Mn2+, i.e. under conditions where wild-type EcoRI shows a relaxed specificity, Q115A is active, however not as much as wild-type EcoRI. Under these conditions it cleaves the canonical sequence -GAATTC- with the same kcat/Km value as the sequence -GAAUTC-, which differs from the former sequence by a single methyl group, while wild-type EcoRI shows a tenfold lower kcat/Km for cleavage of -GAAUTC- than for -GAATTC-. Binding experiments, carried out in the absence of Mg2+, demonstrate that Q115A has a similar affinity towards -GAATTC- as to -GAAUTC-, while wild-type EcoRI binds to -GAATTC- with a tenfold preference over -GAAUTC-. On the basis of these thermodynamic and kinetic results it can be concluded that the hydrophobic contact between the gamma-methylene group of Gln115 and the methyl group of the inner thymidine contributes about 3 kJ/mol (0.7 kcal/mol) to the energy of interaction, both in the ground and the transition state. Q115E is catalytically inactive under normal buffer conditions, but becomes active at low ionic strength or in the presence of Mn2+. Different from Q115A, Q115E is inactive at alkaline pH and its DNA binding affinity is highest at acidic pH.(ABSTRACT TRUNCATED AT 400 WORDS)

Site-directed mutagenesis in the catalytic center of the restriction endonuclease EcoRI.

The catalytic center of the restriction endonuclease (ENase) EcoRI is structurally homologous to that of EcoRV, BamHI and PvuII. Each of these ENases contains a short motif of three to four amino acid (aa) residues which are positioned in a similar orientation to the scissile phosphodiester bond. We have mutated these aa (Pro90, Asp91, Glu111 and Lys113) in EcoRI to determine their individual roles in catalysis. The replacement of Asp91 and Lys113, respectively, by conservative mutations (Ala91, Asn91, Ala113, Gln113, His113 and Leu113) resulted in a reduction of binding affinity and complete loss of cleavage activity. Only Lys113-->Arg substitution still allows to cleave DNA, albeit with a rate reduced by at least four orders of magnitude. Lys113 seems to stabilize the structure of the wild-type (wt) ENase since all five ENase variants with mutations at this position show a strongly enhanced tendency to aggregate. The Ala and Gln mutants of Glu111 bind the recognition sequence slightly stronger than wt EcoRI and cleave it with a low, but detectable rate. Only the Glu111-->Lys mutant, in which the charge is reversed, shows neither binding nor cleavage activity. Pro90 is not important for catalysis, because the Ala90 mutant cleaves DNA with an only slightly reduced rate. Under star conditions, however, this mutant is even more active than wt EcoRI. Therefore, the charged aa Asp91, Glu111 and Lys113 are essential for catalytic activity of the EcoRI ENase.(ABSTRACT TRUNCATED AT 250 WORDS)

Evidence for substrate-assisted catalysis in the DNA cleavage of several restriction endonucleases.

Substrate-assisted catalysis was suggested to be involved in the DNA cleavage reaction of the restriction endonucleases (ENases) EcoRI and EcoRV, because experimental evidence exists that the phosphate group 3' to the scissile bond serves to deprotonate the attacking water. Here, we have addressed the question whether this is a general mechanistic feature of the reactions catalyzed by ENases. For this purpose, the cleavage rates of modified and unmodified oligodeoxyribonucleotides (oligos), in which the phosphate group 3' to the scissile bond is substituted by a methyl phosphonate, were measured for 17 enzymes. Only five turned out not to be inhibited by this modification (BglII, BstI, BstYI, Cfr10I and MunI); all others cleave the modified substrate at a strongly reduced rate or not at all. By employing a hemisubstituted oligo substrate we were able to further investigate the mechanism of inhibition of the latter group of ENases. Some of them cleave the unmodified strand of the modified substrate with a nearly unaltered rate, whereas the modified strand is cleaved very slowly or not at all (BamHI, Bsp143I, Eco72I, MflI, NdeII, Sau3AI, XhoII). The others (AluI, Cfr9I, DpnII, MboI, PvuII) cleave the modified strand of the modified substrate with a largely reduced rate or not at all. These ENases, however, cleave the unmodified strand with a reduced rate, too. Based on these results we conclude that BamHI, Bsp143I, Cfr9I, DpnII, Eco72I, MboI, MflI, NdeII, PvuII, Sau3AI and XhoII may possibly employ substrate assistance in catalysis.

Mapping of protein-protein interactions between c-myb and its coactivator CBP by a new phage display technique.

We have developed a phage display technique for the mapping of protein-protein interaction sites and characterized the interaction between the c-myb proto-oncogene product and its co-activator CBP. Arbitrary DNA segments of the c-myb gene were cloned into a modified phagemid which allowed for expression in all possible reading frames. The mini-library encompassing all functional domains of the protein was propagated as phages and screened with different bait proteins. Alignment of the sequences revealed that the amino acids 317-342 of Myb interact with the CBP protein. Furthermore, an intramolecular interaction of the N-terminal Myb DNA binding domain with the C-terminus (amino acids 541-567) could be detected.

Does a synthetic peptide containing the leucine-zipper domain of c-myb form an alpha-helical structure in solution?

We have examined a synthetic peptide containing the putative leucine zipper domain of the chicken c-myb proto-oncogene using circular dichroism (CD) spectroscopy. The peptide adopts an alpha-helical structure only at low temperatures and in the presence 2,2,2-trifluoroethanol.

Functional diversity of recombinant human AMPA type glutamate receptors: possible implications for selective vulnerability of motor neurons.

Lower motor neurons are known to be susceptible to glutamate-mediated cell damage via overstimulation of AMPA type glutamate receptors (GluR). The molecular basis of an important hypothesis in investigating amyotrophic lateral sclerosis (ALS) is glutamate-excitotoxicity. The aim of this study was to define desensitization and deactivation kinetics of recombinant human GluR1 and GluR2 receptor channels and their splice variants by means of patch-clamp experiments employing ultrafast solution exchange techniques. By this approach, the desensitization time constants of homooligomeric channels could be measured as tau(Des)=2.95+/-0.22 ms (n=10) for GluR1flip, tau(Des)=3.17+/-0.19 ms (n=10) for GluR1flop, tau(Des)=9.86+/-0.79 ms (n=10) for GluR2flip, and tau(Des)=1.87+/-0.26 ms (n=10) for GluR2flop, respectively. In the case of GluR1flip/flop and GluR2flop, a nondesensitising steady state current of less than 1% of peak current amplitude was observed, while GluR2flip channel currents showed a marked steady state component of about 10% of the maximum current. No significant differences were detected comparing the deactivation time course of GluR1 and GluR2 splice variants. These results suggest that the human GluR subtypes tested comprise no fundamental difference to their rodent analogous. Therefore, we describe a preparation that will be useful for further investigation of motor neuron physiological properties and a methodological approach allowing to study functional recombinant human GluR channels under reliable conditions.

Interaction of androsterone and progesterone with inhibitory ligand-gated ion channels: a patch clamp study.

Gamma-aminobutyric acid receptor type A (GABA(A)) receptor channels mediate fast inhibitory neurotransmission throughout the central nervous system while the expression of ionotropic glycine receptors is mainly restricted to the spinal cord and brain stem. Neuroactive steroids are well known as positive allosteric modulators of GABA(A) receptor function. Furthermore, there have been hints for an interaction of neuroactive steroids with ionotropic glycine receptors. The aim of the study was to characterize the effect of androsterone and progesterone on alpha(1) and alpha(1)beta glycine receptor and alpha(1)beta(2)gamma(2) GABA(A) receptor channels and to examine the molecular interactions between ligands and receptors. Electrophysiological recordings were performed on HEK 293 cells using the patch clamp technique in combination with an ultrafast perfusion system. A direct activation of inhibitory ionotropic receptors was observed for androsterone at GABA(A) receptor channels. A coactivation of currents elicited by nonsaturating agonist concentrations was observed with androsterone and progesterone at glycine and GABA(A) receptor channels. We could show that association of beta subunits with alpha subunits affects the sensitivity of glycine receptors to androsterone. In contrast to previous reports in which recombinant glycine receptors were inhibited by progesterone, a potentiating effect was revealed by our experiments. At concentrations of 0.1 mM and higher, there were also hints to a channel block-like mechanism. In conclusion, different molecular mechanisms of interaction between neuroactive steroids and GABA as well as glycine receptors could be identified and quantitatively described. Our data clarify the role of steroid compounds in the modulation of inhibitory receptor channel function.

Accuracy of the EcoRV restriction endonuclease: binding and cleavage studies with oligodeoxynucleotide substrates containing degenerate recognition sequences.

In order to investigate the accuracy of the EcoRV restriction endonuclease, we have synthesized a set of double-stranded oligodeoxynucleotides comprising the canonical recognition sequence, the 9 star sequences (i.e., sequences deviating by one base pair from the canonical sequence), and the 18 mismatch sequences (i.e. sequences deviating by one base from the canonical sequence). For each individual single strand of all these 28 substrates we have measured the rate of phosphodiester bond cleavage under normal buffer conditions. Double-strand cleavage of star substrates is at least 5 orders of magnitude slower than cleavage of the canonical substrate. In contrast, most of the mismatch substrates are accepted more readily. In the absence of the essential cofactor Mg2+, EcoRV binds weakly but equally to the canonical and degenerate substrates, (i.e., KDiss is in the micromolar range). However, the inactive catalytic site mutant D90A in the presence of Mg2+ binds the canonical substrate 1-2 orders of magnitude better than degenerate substrates. Therefore, the EcoRV endonuclease needs the essential cofactor Mg2+ to create thermodynamic discrimination between degenerate and canonical sites. But the main discrimination is kinetically controlled and takes place during cleavage. While in the canonical substrate both single strands are cleaved with an equal velocity, in all other substrates one single strand is cleaved faster than the other one, resulting in a dissociation of the enzyme from the DNA between the two cuts. In vivo this may lead to a repair of the erroneous cleavage site by DNA ligases.(ABSTRACT TRUNCATED AT 250 WORDS)

A comparison of the structural requirements for DNA cleavage by the isoschizomers HaeIII, BspRI and BsuRI.

We have investigated the structural requirements for DNA cleavage by the isoschizomers HaeIII, BspRI and BsuRI which recognize the sequence -d(GGCC)-. For this purpose decadeoxynucleotides were synthesized by the solid-phase phosphotriester method and purified by high-performance liquid chromatography. The kinetics of cleavage of these oligodeoxynucleotides were determined for the three isoschizomers with the following results. The sequence adjacent to the recognition site strongly influences the rate of cleavage. The preference is qualitatively the same for all three enzymes: AGGCCT greater than TGGCCA greater than GGGCCC approximately equal to CGGCCG, and follows the thermal stability of the different decanucleotides. Substitutions within the recognition site, namely dI for dG and dU for dC, affect the rate of cleavage differently for the three enzymes. The results can be rationalized in terms of an interaction of HaeIII with the major and minor groove of the DNA, of BspRI mainly with the minor groove and of BsuRI with the major groove of DNA. It is obvious from our data that the mechanism of recognition of the same site is different for the three isoschizomers.

Analysis of the recognition mechanism involved in the EcoRV catalyzed cleavage of DNA using modified oligodeoxynucleotides.

We have prepared a series of undecadeoxynucleotides that contain changes in the functional group pattern present within the EcoRV recognition site - GATATC-. Oligonucleotides were synthesized on solid phase using normal and modified beta-cyanoethylphosphoramidites and analyzed in steady state cleavage experiments with the EcoRV restriction endonuclease. The following groups appear to interact strongly with the enzyme, since their modification or substitution renders the oligonucleotides refractory to cleavage: the exocyclic NH2-groups of both A residues, the N7 of the first A residue, the exocyclic NH2-group of the C residue and the CH3-groups of both T residues. The exocyclic NH-group of the G residue supports effective recognition, since its absence lowers the kcat of the cleavage reaction. The N7 of the second A residue and the C5 position of the C residue apparently are not recognized by EcoRV; their substitution by -CH- or modification with -Br or -CH3, resp., does not considerably change the rate of cleavage. All oligonucleotides investigated compete with the unmodified substrate for binding to the enzyme. We conclude that EcoRV recognizes its substrate presumably through hydrogen bonds to the exocyclic NH2-group and the N7 of the first A residue, the exocyclic NH2-groups of the second A and the C residue, as well as through hydrophobic interactions with both T residues.

Cross-linking of bromodeoxyuridine-substituted oligonucleotides to the EcoRI and EcoRV restriction endonucleases.

We have synthesized several self-complementary oligodeoxynucleotides which contain bromodeoxyuridine in various positions within and outside of the recognition sequence for the EcoRI and EcoRV restriction endonucleases. These oligodeoxynucleotides are cleaved in the presence of Mg2+ by their respective enzyme. Upon irradiation by long-wavelength ultraviolet light and in the absence of Mg2+ they are cross-linked in low yield to their enzymes, forming 1:1 and 1:2 (oligodeoxynucleotide:enzyme subunit) adducts. Cross-linking occurs with both specific and non-specific complexes. With EcoRI the site of cross-linking was determined to be at or close to Met-137, i.e. in a region of the molecule implicated by other studies from our laboratory [Scholtissek et al. (1986) J. Biol. Chem. 261, 2228-2234] in the binding and cleavage of the substrate.

Characterization of direct readout contacts of the Myb DNA-binding domain.

The Myb protein contacts its recognition sequence by means of direct protein-DNA interactions. We used site-directed mutagenesis in order to substitute amino acids crucial for these contacts and probed the mutant proteins for their DNA-binding and transactiving activities. We could show that amino acids involved in direct readout contacts do not contribute equivalently in the recognition process.

Quantitative polymerase chain reaction with oligodeoxynucleotide ligation assay/enzyme-linked immunosorbent assay detection.

Quantitation of nucleic acids by the polymerase chain reaction (PCR) requires coamplification of a control nucleic acid, usually a variant of the sequence to be analyzed, which is added to the sample DNA and amplified in competition. Following PCR, amplified sample and control DNAs are separated by electrophoresis and quantitated, for example by measuring the radioactivity incorporated into the products during the PCR. The need for both electrophoretic separation and radioactive labeling has considerably impeded the use of PCR for routine purposes, e.g., in the clinical laboratory, which requires automatic processing of many samples in parallel. We describe here a quantitative PCR procedure which circumvents electrophoretic separation and detection by radioactivity. It uses a point mutated version of the sample DNA as an internal control. After competitive PCR, amplified sample and control DNA are distinguished by an oligodeoxynucleotide ligation assay (OLA) (Landegren et al., Science 241, 1077-1080, 1988) using two oligodeoxynucleotides, one carrying a biotin-group at the 5'-end and another one with either a digoxigenin (specific for sample DNA) or fluorescein moiety (specific for control DNA), respectively, incorporated close to the 3'-end. Biotinylated oligodeoxynucleotides, educts as well as products of the ligation reaction, are immobilized on avidin-coated microtiter plates. Quantitation of digoxigenin and fluorescein-labeled oligodeoxynucleotide ligation products is achieved by an enzyme-linked immunosorbent assay. This method is very well suited for fast automated or semiautomated PCR.

Microinjection of antisense c-mos oligonucleotides prevents meiosis II in the maturing mouse egg.

Injection of antisense oligonucleotides was used to investigate the function of c-mos in murine oocytes. Oocytes injected with antisense c-mos oligonucleotides completed the first meiotic division but failed to initiate meiosis II. Instead, loss of c-mos function led to chromosome decondensation, reformation of a nucleus after meiosis I, and cleavage to two cells. Therefore, c-mos is required for meiosis II during murine oocyte maturation.

Mg2+ confers DNA binding specificity to the EcoRV restriction endonuclease.

The EcoRV mutant D90A which carries an amino acid substitution in its active center does not cleave DNA. Therefore, it is possible to perform DNA binding experiments with the EcoRV-D90A mutant both in the absence and in the presence of Mg2+. Like wild-type EcoRV [Taylor et al. (1991) Biochemistry 30, 8743-8753], it does not show a pronounced specificity for binding to its recognition site in the absence of Mg2+ as judged by the appearance of multiple shifted bands in an electrophoretic mobility shift assay with a 377-bp DNA fragment carrying a single EcoRV recognition sequence. In the presence of Mg2+, however, only one band corresponding to a 1:1 complex appears even with a high excess of protein over DNA. This complex most likely is the specific one, because its formation is suppressed much more effectively by a 13-bp oligodeoxynucleotide with an EcoRV site than by a corresponding oligodeoxynucleotide without an EcoRV site. The preferential interaction of the EcoRV-D90A mutant with specific DNA in the presence of Mg2+ was also demonstrated directly: a 20-bp oligodeoxynucleotide with an EcoRV site is bound with KAss = 4 x 10(8) M-1, while a corresponding oligodeoxynucleotide without an EcoRV site is bound with KAss less than or equal to 1 x 10(5) M-1. From these data it appears that Mg2+ confers DNA binding specificity to this mutant by lowering the affinity to nonspecific sites and raising the affinity to specific sites as compared to binding in the absence of Mg2+. It is concluded that this is also true for wild-type EcoRV.

A fast and accurate enzyme-linked immunosorbent assay for the determination of the DNA cleavage activity of restriction endonucleases.

We have developed an assay procedure to monitor the cleavage of DNA substrates by restriction endonucleases. This procedure uses DNA substrates that are labeled with biotin on one 5' end and with an antigenic group, e.g., fluorescein or digoxigenin, on the other 5' end. After incubation with the restriction enzyme, the reaction is stopped with EDTA and an aliquot is pipetted into the well of an avidin-coated microtiter plate. This immobilizes the unreacted substrate and the biotinylated cleavage product, whereas the other cleavage product labeled with the antigenic group is subsequently washed off. The unreacted substrate is detected by an enzyme-linked immunosorbent assay with an appropriate enzyme-linked antibody. To test our assay we have measured the steady-state rate constants for cleavage of DNA by EcoRI yielding a kcat of 8.6 min-1 and a Km of 150 nM, which are close to values measured with other assays. The advantage of this assay is that it is not only fast and accurate, but also very sensitive. It allows for many samples to be analyzed in parallel and lends itself to automation. Furthermore, this assay can be designed as a competitive assay, when two substrates carrying different antigenic groups are used. The usefulness of such competitive assay is demonstrated by determining the influence of sequence context on the rate of DNA cleavage by EcoRI.