Organization,replication and modification of the human genome: Differential methylation of two classes of HeLa nuclear DNA separated on Ag+−Cs2SO4 gradients

HeLa nuclear DNA sediments as a single peak, in neutral CsCl, while it is separated in a heavier and a lighter components, in alkaline Ag⁺–Cs₂SO₄. The heavy fraction, on the average, represents about 20% of the total DNA. CsCl analytical ultracentrifugation shows that heavy DNA bands at 1.715 g/cm³ and contains 53% GC (10% of the total GC), whereas light DNA bands at 1.703 g/cm³ and contains 40% GC (32% of the total GC). Coherently, Tm values in 0.1 x SSC are 82.5°C, for heavy DNA, and 72.5°C, for light DNA. After treatment with [³H-methyl-S-adenosyl-L-methionine in isolated nuclei, the concentration of labelled 5-methylcytosine was found to be highest in the more dense regions of the heavy peak and in the less dense regions of the light peak. Exposure to ultrasound modifies the quantitative relationship of the two peaks and improves the separation of supermethylated AT- and GC-rich DNAs. Four possible triplets as sites for DNA-methylase recognition are discussed.     

Differences in the products of mitochondrial protein synthesis in vivo in human and mouse cells and their potential use as markers for the mitochondrial genome in human–mouse cell hybrids

The proteins synthesized in the mitochondria of mouse and human cells grown in tissue culture were examined by electrophoresis in polyacrylamide gels. The proteins were labelled by incubating the cells in the presence of [(35)S]methionine and an inhibitor of cytoplasmic protein synthesis (emetine or cycloheximide). A detailed comparison between the labelled products of mouse and human mitochondrial protein synthesis was made possible by developing radioautograms after exposure to slab-electrophoresis gels. Patterns obtained for different cell types of the same species were extremely similar, whereas reproducible differences were observed on comparison of the profiles obtained for mouse and human cells. Four human-mouse somatic cell hybrids were examined, and in each one only components corresponding to mouse mitochondrially synthesized proteins were detected.     

Cloning of the human α2-macroglobulin gene and detection of mutations in two functional domains: the bait region and the thiolester site

Summary Overlapping genomic clones of the human ₂-macroglobulin (2M) gene were isolated from a cosmid library and were used to map 80 kb of the chromosomal region of this gene. Fragments carrying the two exons encoding the bait region and the exon encoding the thiolester site were partially sequenced and PCR primers were designed for the amplification of both functional domains. By direct genomic sequencing of these domains in 30 healthy individuals and in 30 patients with chronic lung disease three mutations were detected. The first was a sequence polymorphism occurring near the thiolester site of the gene, changing Val¹⁰⁰⁰(GTC) to Ile¹⁰⁰⁰(ATC), with allele frequencies of 0.30 (GTC) and 0.70 (ATC), respectively. No difference of 2M serum levels was observed for these two alleles. The second mutation occured within the thiolester site of one patient, changing Cys⁹⁷²(TGT) to Tyr⁹⁷²(TAT). Since activation of the internal thiolester formed between Cys⁹⁷² and Gln⁹⁷⁵ in each of the subunits of the tetrameric 2M is involved in the covalent cross-linking of the activating proteinase, this mutation is predicted to interfere with 2M function. The 2M serum level was within the normal range in this patient. In one healthy individual we detected an alteration of the bait region sequence, which is usually encoded by two different exons separated by an intron of size 1.6kb. In this individual, PCR amplification of genomic DNA using the bait region primers produced the common fragment of size 1.8 kb and an additional variant fragment of size 0.23kb. This finding, and the genomic sequencing data of this individual, indicate that he carries two different alleles of the 2M gene: one with the regular structure (bait exon I-intron-bait exon II), the other with the two bait exons fused into one. Direct genomic sequencing of the two 2M functional domains is a useful tool for the detection of the genetic, and possibly the functional, heterogeneity of 2M. This, in turn, may provide some insight into the hitherto unknown physiological role(s) of 2M, by studying in vivo effects of naturally ocurring mutations of the gene.     

Biosynthesis of the human milk oligosaccharide 3-fucosyllactose in metabolically engineered Escherichia coli via the salvage pathway through increasing GTP synthesis and β-galactosidase modification

3-Fucosyllactose (3-FL) is one of the major fucosylated oligosaccharides in human milk. Along with 2′-fucosyllactose (2′-FL), it is known for its prebiotic, immunomodulator, neonatal brain development, and antimicrobial function. Whereas the biological production of 2′-FL has been widely studied and made significant progress over the years, the biological production of 3-FL has been hampered by the low activity and insoluble expression of α-1,3-fucosyltransferase (FutA), relatively low abundance in human milk oligosaccharides compared with 2′-FL, and lower digestibility of 3-FL than 2′-FL by bifidobacteria. In this study, we report the gram-scale production of 3-FL using E. coli BL21(DE3). We previously generated the FutA quadruple mutant (mFutA) with four site mutations at S46F, A128N, H129E, Y132I, and its specific activity was increased by nearly 15 times compared with that of wild-type FutA owing to the increase in k_cat and the decrease in K_m. We overexpressed mFutA in its maximum expression level, which was achieved by the optimization of yeast extract concentration in culture media. We also overexpressed L-fucokinase/GDP- L -fucose pyrophosphorylase to increase the supply of GDP-fucose in the cytoplasm. To increase the mass of recombinant whole-cell catalysts, the host E. coli BW25113 was switched to E. coli BL21(DE3) because of the lower acetate accumulation of E. coli BL21(DE3) than that of E. coli BW25113. Finally, the lactose operon was modified by partially deleting the sequence of LacZ (lacZΔm15) for better utilization of D -lactose. Production using the lacZΔm15 mutant yielded 3-FL concentration of 4.6 g/L with the productivity of 0.076 g·L⁻¹·hr⁻¹ and the specific 3-FL yield of 0.5 g/g dry cell weight.     

Involvements of the ABC protein ABCF2 and α-actinin-4 in regulation of cell volume and anion channels in human epithelial cells

After osmotic swelling, cell volume is regulated by a process called regulatory volume decrease (RVD). Although actin cytoskeletons are known to play a regulatory role in RVD, it is not clear how actin‐binding proteins are involved in the RVD process. In the present study, an involvement of an actin‐binding protein, α‐actinin‐4 (ACTN4), in RVD was examined in human epithelial HEK293T cells. Overexpression of ACTN4 significantly facilitated RVD, whereas siRNA‐mediated downregulation of endogenous ACTN4 suppressed RVD. When the cells were subjected to hypotonic stress, the content of ACTN4 increased in a 100,000 × g pellet, which was sensitive to cytochalasin D pretreatment. Protein overlay assays revealed that ABCF2, a cytosolic member of the ABC transporter superfamily, is a binding partner of ACTN4. The ACTN4‐ABCF2 interaction was markedly enhanced by hypotonic stimulation and required the NH₂‐terminal region of ABCF2. Overexpression of ABCF2 suppressed RVD, whereas downregulation of ABCF2 facilitated RVD. We then tested whether ABCF2 has a suppressive effect on the activity of volume‐sensitive outwardly rectifying anion channel (VSOR), which is known to mediate Cl^? efflux involved in RVD, because another ABC transporter member, CFTR, was shown to suppress VSOR activity. Whole‐cell VSOR currents were largely reduced by overexpression of ABCF2 and markedly enhanced by siRNA‐mediated depletion of ABCF2. Thus, the present study indicates that ACTN4 acts as an enhancer of RVD, whereas ABCF2 acts as a suppressor of VSOR and RVD, and suggests that a swelling‐induced interaction between ACTN4 and ABCF2 prevents ABCF2 from suppressing VSOR activity in the human epithelial cells. J. Cell. Physiol. 227: 3498–3510, 2012. © 2012 Wiley Periodicals, Inc.     

Mimosine arrests the cell cycle prior to the onset of DNA replication by preventing the binding of human Ctf4/And-1 to chromatin via Hif-1α activation in HeLa cells

Though the G₁ checkpoint in mammalian cells has been known for decades, the molecular targets that prevent S-phase entry remain unknown. Mimosine is a rare plant amino acid that arrests the cell cycle in the G₁ phase before entry into S phase. Here, we show that mimosine interrupts the binding of Ctf4 to chromatin, which is essential for the initiation of DNA replication in HeLa cells, and this effect is mediated by the Hif-1α-dependent increase in the level of p27. Depletion of Hif-1α results in an increased binding of Ctf4 to chromatin and the entry of cells into S phase even in the presence of mimosine. These results suggest that the binding of Ctf4 to chromatin is the target of the Hif-1α-dependent checkpoint pathway for cell cycle arrest in G₁ phase. Although we observed Hif-1α-dependent arrest in mimosine-treated cells, it is possible that Ctf4 may act as a common target for G₁ arrest in various other checkpoint pathways.     

How relevant are S=O and P=O Double Bonds for the Description of the Acid Molecules H2SO3, H2SO4, and H3PO4, respectively?

The acid molecules H₂SO₃, H₂SO₄, and H₃PO₄ are usually drawn using "Lewis structures" which exhibit the octet extension by 3d-orbitals on sulfur and phosphorus, respectively. Thus, S=O and P=O double bonds are assumed to be formed. The natural d-orbital occupancies on S and P, however, were calculated to be as low as 0.1 e, and therefore, an octet extension can hardly be expected. After the natural bond orbitals (NBO) search procedure was forced to attempt to form different Lewis structures of bonds and lone pairs, we defined the optimal Lewis structure, if a dominant structure exists at all, by the maximum electronic charge in Lewis orbitals. Indeed, sulfur obeys the octet rule in the optimal zwitterionic Lewis structures and does not form S=O double bonds. No dominant resonance structure could be found for H₃PO₄ where polarized PO ?-bond and zwitterionic PO bond structures exhibit similar weights.     

Unexpectedly convenient and stereoselective synthesis of 4α-acyloxy-2-chloropodophyllotoxins in the presence of BF₃ ·Et₂O

Twenty-one 4α-acyloxy-2-chloropodophyllotoxin derivatives (5a-u), whose C-4 spatial configuration was mainly stereocontrolled by the configuration of C-2 chlorine atom, were unexpectedly prepared by the reaction of 2-chloropodophyllotoxin with carboxylic acids in the presence of BF₃·Et₂O. Compared with ordinary esterifications of carboxylic acids mediated by the condensation agent, for example, N,N’-diisopropylcarbodiimide (DIC), the present method made the procedure for the preparation of 4α-acyloxy-2-chloropodophyllotoxins more convenient, practical and easy. Meanwhile, the insecticidal activity of compounds 5a-u was preliminarily evaluated against the pre-third-instar larvae of Mythimna separata Walker in vivo at the concentration of 1 mg/mL.     

Biological characteristics of two lysines on human serum albumin in the high-affinity binding of 4Z,15Z-bilirubin-IXα revealed by phage display

4Z,15Z-bilirubin-IXα (4Z,15Z-BR), an endogenous compound that is sparingly soluble in water, binds human serum albumin (HSA) with high affinity in a flexible manner. A phage library displaying recombinant HSA domain II was constructed, after three rounds of panning against immobilized 4Z,15Z-BR, and eight clones with high affinity for the pigment were found to contain conserved basic residues, such as lysine or arginine, at positions 195 and 199. The wild type and two mutants, K195A and K199A, of whole HSA as well as stand-alone domain II were expressed in Pichia pastoris for ligand-binding studies. The binding of 4Z,15Z-BR to the K195A and K199A mutants was decreased in both whole HSA and the domain II proteins. The P-helicity conformer (P-form) of 4Z,15Z-BR was found to preferentially bind to the wild types and the K195A mutants, whereas the M-form bound to the K199A mutants. Photoconversion experiments showed that the P-form of 4Z,15Z-BR was transformed into highly water-soluble isomers at a much faster rate than the M-form. In addition, the M-form of 4Z,15Z-BR showed higher affinity for domain I than for domain II. The present findings suggest that, whereas both Lys195 and Lys199 in subdomain IIA are important for the high-affinity binding of 4Z,15Z-BR, Lys199 plays a more prominent role in the elimination of 4Z,15Z-BR.     

DNA polymerases κ and ζ cooperatively perform mutagenic translesion synthesis of the C8–2′-deoxyguanosine adduct of the dietary mutagen IQ in human cells

The roles of translesion synthesis (TLS) DNA polymerases in bypassing the C8–2′-deoxyguanosine adduct (dG-C8-IQ) formed by 2-amino-3-methylimidazo[4,5-f]quinoline (IQ), a highly mutagenic and carcinogenic heterocyclic amine found in cooked meats, were investigated. Three plasmid vectors containing the dG-C8-IQ adduct at the G₁-, G₂- or G₃-positions of the NarI site (5′-G₁G₂CG₃CC-3′) were replicated in HEK293T cells. Fifty percent of the progeny from the G₃ construct were mutants, largely G→T, compared to 18% and 24% from the G₁ and G₂ constructs, respectively. Mutation frequency (MF) of dG-C8-IQ was reduced by 38–67% upon siRNA knockdown of pol κ, whereas it was increased by 10–24% in pol η knockdown cells. When pol κ and pol ζ were simultaneously knocked down, MF of the G₁ and G₃ constructs was reduced from 18% and 50%, respectively, to <3%, whereas it was reduced from 24% to <1% in the G₂ construct. In vitro TLS using yeast pol ζ showed that it can extend G₃*:A pair more efficiently than G₃*:C pair, but it is inefficient at nucleotide incorporation opposite dG-C8-IQ. We conclude that pol κ and pol ζ cooperatively carry out the majority of the error-prone TLS of dG-C8-IQ, whereas pol η is involved primarily in its error-free bypass.     

Neuron-associated class III β-tubulin, tau, and MAP2 in the D-283 Med cell line and in primary explants of human medulloblastoma

Summary The D283 Med human medulloblastoma cell line and primary explants of five surgically excised medulloblastomas were cultured using a three-dimensional Gelfoam matrix system. The cultures were evaluated immunohistochemically for a series of antigenic determinants associated with neuronal or glial differentiation. Focal immunolocalization of class III -tubulin, microtubule-associated protein 2 (MAP2), and to a lesser degree tau, was demonstrated in all cultures. Class III -tubulin isotype, MAP2, and tau protein were also detected by immunoblot in Gelfoam matrix cultures, monolayer cultures, and suspension cultures of D283 Med cells. Staining for neurofilament protein epitopes was highly variable, even among different cultures derived from the same original tumour, but time-dependent changes in neurofilament protein, which may have reflected neuronal differentiation, were not consistently shown. Widespread -enolase and focal synaptophysin reactivities were visualized in all cultures, but no S-antigen staining was detected. Leu 7 labelling was variably present in half of the cultures of D283 Med cells, but was more abundant in explants derived from four of the five original tumours. Vimentin was consistently found in D283 Med cultures at all time points. No immunoreactivity for glial fibrillary acidic protein was detected in the D283 Med cell line. Conversely, staining for this protein was demonstrated in scattered astrocytic cells in the surgical specimens of all five medulloblastomas. Concomitant with increased time in culture, three of the primary tumours displayed increased numbers of glial fibrillary acidic protein-positive cells when cultured in the Gelfoam system, but the other two tumours had a minimal astrocytic component. Collectively, our findings indicate that the D283 Med cell line and explants of five primary medulloblastomas exhibit a chiefly neuroblastic phenotype.     

Osteopontin increases the expression of β1, 4-Galactosyltransferase-I and promotes adhesion in human RL95-2 cells

Beta1, 4-Galactosyltransferase-I (β1, 4-GalT-I), which transfers galactose from UDP-Gal to N-acetylglucosamine and N-acetylglucosamine-terminated oligosaccharides of N- and O-linked glycans in a β(1-4) linkage, plays a critical role in cell adhesion, sperm-egg recognition, neurite growth, and tumor cell migration and invasion. Our previously experiments also show that β1, 4-GalT-I was up-regulated by estrogens and some important cytokines of embryo implantation especially Interleukin-1 (IL-1), TGF-α and Leukemia Inhibitory Factor (LIF) in endometrial cells. In the receptive phase human uterus, osteopontin (OPN) is the most highly up-regulated extracellular matrix/adhesion molecule/cytokine. In this study, we demonstrated the correlated expression of OPN and β1, 4-GalT-I in endometrium during early pregnancy, and recombinant human OPN (rhOPN) protein induced the β1, 4-GalT-I up-regulation in RL95-2 cells. Inhibition of MEK/ERK, PI3K/AKT and NF-κB suppressed rhOPN-induced β1, 4-GalT-I expression. In addition, rhOPN promoted the adhesion of blastocysts cells in vitro in β1, 4-GalT-I-dependent manner. Moreover, the adhesion is greatly inhibited when β1, 4-GalT-I was blocked with the specific antibody. Taken together, our data suggest that β1, 4-GalT-I provides a mechanism to bridge embryo to endometrium during implantation.     

Functional expression of human prostaglandin E2 receptor 4 (EP4) in E. coli and characterization of the binding property of EP4 with Gα proteins

Human prostaglandin E2 receptor 4 (EP4) is one of the four subtypes of prostaglandin E₂ (PGE₂) receptors and belongs to the rhodopsin-type G protein-coupled receptor (GPCR) family. Particularly, EP4 is expressed in various cancer cells and is involved in cancer-cell proliferation by a G protein signaling cascade. To prepare an active form of EP4 for biochemical characterization and pharmaceutical application, this study designed a recombinant protein comprising human EP4 fused to the P9 protein (a major envelope protein of phi6 phage) and overexpressed the P9-EP4 fusion protein in the membrane fraction of E. coli. The solubilized P9-EP4 with sarkosyl (a strong anionic detergent) was purified by affinity chromatography. The purified protein was stabilized with amphiphilic polymers derived from poly-γ-glutamate. The polymer-stabilized P9-EP4 showed specific interaction with the alpha subunits of G_s or G_i proteins, and a high content of α-helical structure by a circular dichroism spectroscopy. Furthermore, the polymer-stabilized P9-EP4 showed strong heat resistance compared with P9-EP4 in detergents. The functional preparation of EP4 and its stabilization with amphiphilic polymers could facilitate both the biochemical characterization and pharmacological applications targeting EP4.     

Characterization of Cav1.4 Complexes (α11.4, β2, and α2δ4) in HEK293T Cells and in the Retina

In photoreceptor synaptic terminals, voltage-gated Ca_v1.4 channels mediate Ca²⁺ signals required for transmission of visual stimuli. Like other high voltage-activated Ca_v channels, Ca_v1.4 channels are composed of a main pore-forming Ca_v1.4 α₁ subunit and auxiliary β and α₂δ subunits. Of the four distinct classes of β and α₂δ, β₂ and α₂δ₄ are thought to co-assemble with Ca_v1.4 α₁ subunits in photoreceptors. However, an understanding of the functional properties of this combination of Ca_v subunits is lacking. Here, we provide evidence that Ca_v1.4 α₁, β₂, and α₂δ₄ contribute to Ca_v1.4 channel complexes in the retina and describe their properties in electrophysiological recordings. In addition, we identified a variant of β₂, named here β_2X13, which, along with β_2a, is present in photoreceptor terminals. Ca_v1.4 α_1, β₂, and α₂δ₄ were coimmunoprecipitated from lysates of transfected HEK293 cells and mouse retina and were found to interact in the outer plexiform layer of the retina containing the photoreceptor synaptic terminals, by proximity ligation assays. In whole-cell patch clamp recordings of transfected HEK293T cells, channels (Ca_v1.4 α₁ + β_2X13) containing α₂δ₄ exhibited weaker voltage-dependent activation than those with α₂δ₁. Moreover, compared with channels (Ca_v1.4 α₁ + α₂δ₄) with β_2a, β_2X13-containing channels exhibited greater voltage-dependent inactivation. The latter effect was specific to Ca_v1.4 because it was not seen for Ca_v1.2 channels. Our results provide the first detailed functional analysis of the Ca_v1.4 subunits that form native photoreceptor Ca_v1.4 channels and indicate potential heterogeneity in these channels conferred by β_2a and β_2X13 variants.     

Localization of fibroblast growth factor 2 (FGF-2) protein and the receptors FGFR 1–4 in normal human seminiferous epithelium

 Fibroblast growth factor 2 (FGF-2), which occurs in various isoforms both species and tissue specifically, regulates cell proliferation and differentiation via a dual receptor system consisting of heparan sulphate proteoglycans and receptor tyrosine kinases (FGFRs). This study demonstrates for the first time the distribution pattern of FGF-2 and the receptors FGFR 1–4 in the normal seminiferous epithelium of adult men. In western blot analyses, the polyclonal antibody, anti-FGF-2, shows two immunoreactive bands at 18 and 24 kDa. On paraffin sections, positive immunoreaction occurs within the cytoplasm of spermatogonia. The distribution pattern of the polyclonal anti-FGFR 1–4 antibodies is as follows: anti-FGFR-1 (one 68-kDa band) stains nuclei and cytoplasm of spermatogonia; anti-FGFR-3 (five bands at 68, 78, 105, 125 and 145 kDa) stains the nuclei of all germ cells except those of elongated spermatids; and anti-FGFR-4 (one 48-kDa band) stains the cytoplasm of primary pachytene spermatocytes. We were unable to demonstrate FGFR-2 immunoreactivity either in western blot analysis or on paraffin sections. This distribution pattern suggests that FGF-2 in spermatogonia is involved in the autocrine and paracrine regulation of the proliferation and differentiation of spermatogonia and spermatocytes via the receptors FGFR-1, FGFR-3 and FGFR-4. Accepted: 23 December 1997     

Influence of diverse gene 43 DNA polymerases on the incorporation and replication in vivo of 2-aminopurine at A · T base-pairs in bacteriophage T4

The relative rates at which A · T → AP · T² base-pairs are formed in DNA during 2-aminopurine mutagenesis, and the relative rates at which AP · T → AP · C base-pairs are formed during the in vivo replication of templates containing 2-aminopurine, were measured for a mutator, a wild type, and two antimutator bacteriophage T4 DNA polymerases. These measurements did not require quantitation of the 2-aminopurine in the T4 DNA. The mutator polymerase had no discernible effect upon the rate of A · T → AP · T, but increased the rate of AP · T → AP · C twofold over that of the wild-type enzyme. The two antimutator polymerases decreased the rate of formation of both AP · T and AP · C base-pairs compared to the wild-type enzyme. The relative antimutator effect is asymmetrically divided between the two mutation steps producing a very large decrease in the AP · T → AP · C step but a much smaller decrease in the A · T → AP · T step. This and additional observations suggest that the fidelity-enhancing components of T4 DNA polymerases distinguish between 2-aminopurine in template DNA and 2-aminopurine at the primer terminus.