Characterization of glycine-extracted calf thymus deoxyribonucleoproteins

• 1.1. Calf (Bos bovinus) thymus deoxyribonucleoproteins are isolated by a glycine extraction procedure, and characterized in terms of homogeneity, conformation and composition.
• 2.2. The results show that the extracted deoxyribonucleoprotein is a homogeneous, high molecular weight complex of basic protein and deoxyribonucleic acid.

     

Characterization of DNA kinase from calf thymus

DNA kinase has been purified to homogeneity from calf thymus. The purified enzyme, with a specific activity of 16.7 units/mg protein at 25 degrees C, exhibited a sharp pH/activity curve with a pH optimum at 5.5 and low activity at alkaline pH. The molecular weight of the enzyme was estimated by dodecylsulfate/polyacrylamide gel electrophoresis to be 5.4 X 10(4). The enzyme has a sedimentation coefficient of 4.0 S. An apparent molecular weight of 5.6 X 10(4) and a Stokes' radius of 3.3 nm were estimated by gel-filtration on Sephadex G-100. The enzyme phosphorylates neither yeast RNA nor poly(A) instead of DNA. Compared with rat liver DNA kinase, calf thymus DNA kinase is relatively resistant to the inhibition by sulfate (Ki = 7 mM) and pyrophosphate (Ki = 5 mM). The enzyme activity is markedly stimulated by polyamines at the sub-optimal concentration of Mg2+ but not by monovalent cations.     

Characterization of zonal fractions of calf thymus DNA

DNA isolated from calf thymus nuclei is fractionated by zonal centrifugation into 40 sedimentation-rate classes and the reduced viscosity profile determined. This profile is divided into four fractions, I–IV, IV being the fastest sedimenting. The relative concentrations of repetitive DNA sequences in these is determined by hybridization on membrane filters and also hypochromicity by reannealing at 60 °. Repetitive sequences are found in all fractions, although they are slightly more abundant in the order III > II > I. Moreover, fractions I, II, III, act as good competitors in hybridization experiments with each other, implying that a high degree of complementarity exists between repetitive sequences in each of the fractions. Fraction IV had peculiar hydrodynamic properties which have provoked observations on DNA purification.     

Characterization of ellipticine binding to native calf thymus DNA

The binding of [14C]ellipticine to native calf thymus DNA was studied using equilibrium dialysis. A Scatchard polt revealed the presence of high-and low-affinity binding sites in DNA, the former having a K of 4.0 X 10(7) M(-1) and an n (saturation limiting of binding) of 0.078 (1mol ellipticine/13 mol of DNA nucleotides). The forces involved in stabilizing the high-affinity binding, which has been equated with intercalative binding, were due to a combination of hydrophobic interactions and hydrogen bonding. Difference spectra of ellipticine in the presence of the polydeoxynucleotides, poly d(A-T) or poly d(G-C), showed that there was no base specificity involved in the high-affinity binding. Ellipticine binding to the low-affinity sites, which has been equated with surface binding, was due primarily to the participation of electrostatic interactions of ellipticine with the anionic phosphate groups on the double helical surface of DNA.     

Properties and subcellular localization of CMP-N-acetylneuraminic acid hydrolase of calf kidney.

The properties and subcellular distribution of CMP-N-acetylneuraminic acid (CMP-NAcNeu) hydrolase were studied in the cortex of calf kidney. The pH optimum was 9.0 in both Tris - HCl and glycine/NaOH buffer. The apparent Km was 0.47 mM and the apparent V 15.3 mumol/h/g wet wt of calf kidney cortex. A stimulation by divalent metal ions (Ca2+ and Mg2+) was demonstrated for the hydrolase. In the presence of Triton X-100 an increase in enzyme activity was observed. CMP-NAcNeu hydrolase was inhibited by EDTA, beta-mercaptoethanol, nucleoside phosphates and nucleotide-sugars. The inhibition was more pronounced when a sub-optimal CMP-NAcNeu concentration was used. The enzyme appeared to be localized in the plasma membranes. In the plasma membrane preparation of calf kidney cortex, which was derived mainly from the proximal tubule cells, the yield of CMP-NAcNeu hydrolase (13%) and its increase in specific activity (9-fold) was as high as for the plasma membrane marker enzymes. From subcellular distribution studies it appeared that the enzyme was localized mainly at the bursh border side of the plasma membrane of the proximal tubule cell.     

Characterization and subcellular localization of Tektin 3 in rat spermatozoa

Mammalian sperm flagella have filament‐forming Tektin proteins (Tektin 1–5) reported to be involved in the stability and structural complexity of flagella. Male mice null for Tektin3 produce spermatozoa with reduced forward progression and increased flagellar structural bending defects. The subcellular localization of Tektin3 (TEKT3) in spermatozoa, however, has not been clarified at the ultrastructural level. To elucidate the molecular localization of TEKT3 in flagella of rat spermatozoa, we performed extraction studies followed by immunoblot analysis, immunofluorescence microscopy, and immunogold electron microscopy. Extraction of sperm flagella from the cauda epididymis resulted in complete removal of axonemal tubulins, while TEKT3 was resistant to extraction with the same S‐EDTA (1% SDS, 75 mM NaCl, 24 mM EDTA, pH 7.6) solution, suggesting that TEKT3 might be present in the peri‐axonemal component and not directly associated with axonemal tubulins. Resistance to S‐EDTA extraction might be due to disulfide bond formation during epididymal maturation since concentrations of DTT greater than 5 mM drastically promoted release of TEKT3 from flagella. Immunofluorescence microscopy and pre‐embedding immunoelectron microscopy revealed that TEKT3 was predominantly associated with the surface of mitochondria and outer dense fibers in the middle piece. In addition, TEKT3 was found to be present at the equatorial segment region of the acrosome membrane in sperm heads. TEKT3 might not only work as a flagellar constituent required for flagellar stability and sperm motility but also may be involved in acrosome‐related events, such as the acrosome reaction or sperm–egg fusion. Mol. Reprod. Dev. 78:611–620, 2011. © 2011 Wiley‐Liss, Inc.     

Properties and subcellular localization of CMP-N-acetylneuraminic acid hydrolase of calf kidney

The properties and subcellular distribution of CMP-N-acetylneuraminic acid (CMP-NAcNeu) hydrolase were studied in the cortex of calf kidney. The pH optimum was 9.0 in both Tris · HCl and glycine/NaOH buffer. The apparent K_m was 0.47 mM and the apparent V 15.3 μmol/h/g wet wt of calf kidney cortex. A stimulation by divalent metal ions (Ca²⁺ and Mg²⁺) was demonstrated for the hydrolase. In the presence of Triton X-100 an increase in enzyme activity was observed. CMP-NAcNeu hydrolase was inhibited by EDTA, β-mercaptoethanol, nucleoside phosphates and nucleotide-sugars. The inhibition was more pronounced when a sub-optimal CMP-NAcNeu concentration was used, The enzyme appeared to be localized in the plasma membranes. In the plasma membrane preparation of calf kidney cortex, which was derived mainly from the proximal tubule cells, the yield of CMP-NAcNeu hydrolase (13%) and its increase in specific activity (9-fold) was as high as for the plasma membrane marker enzymes. From subcellular distribution studies it appeared that the enzyme was localized mainly at the brush border side of the plasma membrane of the proximal tubule cell.     

Characterization and subcellular localization of chlorophyllase from Ginkgo biloba

Chlorophyllase (Chlase) catalyzes the initial step of chlorophyll (Chl)-degradation, but the physiological significance of this reaction is still ambiguous. Common understanding of its role is that Chlase is involved in de-greening processes such as fruit ripening, leaf senescence, and flowering. But there is a possibility that Chlase is also involved in turnover and homeostasis of Chls. Among the de-greening processes, autumnal coloration is one of the most striking natural phenomena, but the involvement of Chlase during autumnal coloration is not clear. Previously, it was shown that Chlase activity and expression level of the Chlase gene were not increased during autumnal coloration in Ginkgo biloba, indicating that Chlase does not work specially in the de-greening processes in G. biloba. In this study, we characterized the recombinant Chlase and analyzed its subcellular localization to understand the role of the cloned Chlase of G. biloba (GbCLH). GbCLH exhibited its highest activity at pH 7.5, 40 degrees C. Kinetic analysis revealed that GbCLH hydrolyzes pheophytin (Pheo) a and Chl a more rapidly than Pheo b and Chl b. Transient expression analysis of 40 N-terminus amino acids of GbCLH fused with GFP (green fluorescent protein) and subcellular fractionation showed that GbCLH localizes within chloroplasts. Together with our previous results, property of GbCLH and its location within the chloroplasts suggest that GbCLH plays a role in the turnover and homeostasis of Chls in green leaves of G. biloba.     

Characterization and subcellular localization of GnRH analog binding in rat brain

The binding of a degradation-resistant analog of gonadotropin-releasing hormone, [D-Phe6]GnRH, to rat brain crude particulate preparation was studied. The binding of this analog at 0 degrees C was saturable and Scatchard analysis revealed the presence of 2 binding sites: one with KD = 1.39 x 10(-7) M and Bmax = 265 pmole/mg protein, and another of lower affinity but higher capacity with KD = 5.58 X 10(-6) M and Bmax = 1734 pmoles/mg protein. The binding at 0 degrees C was substantially higher than that obtained at 37 degrees C, due to binding site-inactivation processes occurring at 37 degrees C. The binding sites exhibited a considerable degree of specificity for GnRH as unrelated peptides (with the exception of ACTH) display a much weaker affinity than GnRH and GnRH analogs. Subcellular fractionation demonstrated that most of the binding was associated with the mitochondrial fraction.     

Characterization of the multisubunit cleavage-polyadenylation specificity factor from calf thymus.

Cleavage-polyadenylation specificity factor (CPSF) is one of five separable factors known to be required for 3' cleavage and polyadenylation of mRNA precursors in vitro. Previous studies have shown that the cleavage and poly(A) addition reactions can be uncoupled in vitro and have suggested that CPSF may be the only factor essential for both of these subreactions. Here we report the purification of CPSF to near homogeneity from calf thymus and show that the purified factor contains three polypeptides of 165, 105, and 70 kDa. These polypeptides cosediment precisely with CPSF activity, which has a sedimentation coefficient of 11.5 S. Consistent with previous reports from our laboratory, purified CPSF does not contain a detectable RNA component, indicating that it is a multisubunit protein and not a small nuclear ribonucleoprotein. Extensively purified bovine CPSF can function with human poly(A) polymerase to bring about AAUAAA-dependent poly(A) addition or with human cleavage factors to catalyze accurate 3' cleavage of a pre-mRNA substrate. UV cross-linking and gel retention analyses demonstrate that highly purified CPSF interacts with one of these cleavage factors, the multisubunit cleavage-stimulation factor, to facilitate stable binding of both to an AAUAAA-containing pre-mRNA. Likewise, evidence is presented indicating that poly(A) polymerase and CPSF can interact directly.     

Class III nucleotide cyclases in bacteria and archaebacteria: lineage-specific expansion of adenylyl cyclases and a dearth of guanylyl cyclases

The Class III nucleotide cyclases are found in bacteria, eukaryotes and archaebacteria. Our survey of the bacterial and archaebacterial genome and plasmid sequences identified 193 Class III cyclase genes in only 29 species, of which we predict the majority to be adenylyl cyclases. Interestingly, several putative cyclase genes were found to have non-conserved substrate specifying residues. Ancestors of the eukaryotic C1-C2 domain containing soluble adenylyl cyclases as well as the protist guanylyl cyclases were found in bacteria. Diverse domains were fused to the cyclase domain and phylogenetic analysis indicated that most proteins within a single cluster have similar domain compositions, emphasising the ancient evolutionary origin and versatility of the cyclase domain.     

Characterization of adducts formed in reactions of acrolein with thymidine and calf thymus DNA

Acrolein, an important industrial chemical and environmental contaminant, has been shown to interact with nucleic acids in vitro and in vivo. In this study, we examined the reactivity of acrolein towards thymidine and calf-thymus double- and single-stranded DNA in aqueous buffered solutions. LC-MS Analyses of the reaction mixture of acrolein with thymidine showed the formation of five structurally different adducts. The structures of the products were determined on the basis of mass spectrometry, UV absorbance, and (1)H- and (13)C-NMR spectroscopy. The adducts were identified as 3-(3-oxopropyl)thymidine (dT1), 3-[(tetrahydro-2,4-dihydroxypyran-3-yl)methyl]thymidine (dT2), 2-(hydroxymethyl)-5-(thymidin-3-yl)pent-2-enal (dT3), 3-hydroxy-2-methylidene-5-(thymidin-3-yl)pentanal (dT4), and 2-[(thymidin-3-yl)methyl]penta-2,4-dienal (dT5). The adducts dT2-dT5 were formed in reaction of dT1 with acrolein. In the reaction of acrolein with calf-thymus DNA, dT1 was the only adduct detected in the DNA hydrolysate.     

Cellular and subcellular localization of progastricsin in calf fundic mucosa: colocalization with pepsinogen and prochymosin

The presence of gastricsin in bovine abomasal juice has been reported previously, but its exact site of origin has not yet been established. Specific polyclonal antibodies were used in the peroxidase-antiperoxidase method or the protein A/gold technique to label cells producing progastricsin. This immunocytolocalization was correlated with that of pepsinogen and prochymosin using specific polyclonal antibodies against those zymogens. The present study clearly established that progastricsin was located exclusively in chief, mucous neck, transitional mucous neck/chief, foveolar epithelial and surface epithelial cells of the calf fundic mucosa. Furthermore, progastricsin was found to be colocalized with pepsinogen and prochymosin in the same secretory granules of these cells. Progastricsin was not observed in parietal, gastric endocrine and undifferentiated neck cells.