DNA condensation by high-affinity interaction with avidin

Avidin, the basic biotin-binding glycoprotein from chicken egg white, is known to interact with DNA, whereas streptavidin, its neutral non-glycosylated bacterial analog, does not. In the present study we investigated the DNA-binding properties of avidin. Its affinity for DNA in the presence and absence of biotin was compared with that of other positively charged molecules, namely the protein lysozyme, the cationic polymers polylysine and polyarginine and an avidin derivative with higher isoelectric point (pI approximately 11) in which most of the lysine residues were converted to homoarginines. Gel-shift assays, transmission electron microscopy and dynamic light scattering experiments demonstrated an unexpectedly strong interaction between avidin and DNA. The most pronounced gel-shift retardation occurred with the avidin-biotin complex, followed by avidin alone and then guanidylated avidin. Furthermore, ultrastructural and light-scattering studies showed that avidin assembles on the DNA molecule in an organized manner. The assembly leads to the formation of nanoparticles that are about 50-100 nm in size (DNA approximately 5 kb) and have a rod-like or toroidal shape. In these particles the DNA is highly condensed and one avidin is bound to each 18 +/- 4 DNA base pairs. The complexes are very stable even at high dilution ([DNA] =10 pM) and are not disrupted in the presence of buffers or salt (up to 200 mM NaCl). The other positively charged molecules also condense DNA and form particles with a globular shape. However, in this case, these particles disassemble by dilution or in the presence of low salt concentration. The results indicate that the interaction of avidin with DNA may also occur under physiological conditions, further enhanced by the presence of biotin. This DNA-binding property of avidin may thus shed light on a potentially new physiological role for the protein in its natural environment.     

Suppression of the alpha-isoform of class II phosphoinositide 3-kinase gene expression leads to apoptotic cell death

Phosphoinositide 3-kinases (PI3Ks) have known to be key enzymes activating intracellular signaling molecules when a number of growth factors bind to their cell surface receptors. PI3Ks are divided into three classes (I, II, and III) and enzymes of each class have different tissue-specificities and physiological functions. Class II PI3Ks consist of three isoforms (alpha,beta,gamma). Although the alpha-isoform (PI3K-C2alpha) is considered ubiquitous and preferentially activated by insulin rather than the beta-isoform, the physiological significance of PI3K-C2alpha is poorly understood. The present study aimed to determine whether PI3K-C2alpha is associated with the suppression of apoptotic cell death. Different sense- and antisense oligonucleotides (ODNs) were synthesized based on the sequence of C2 domain of PI3K-C2alpha gene. Transfection of CHO-IR cells with two different antisense ODNs clearly reduced the protein content as well as mRNA levels of PI3K-C2alpha whereas neither the nonspecific mock- nor sense ODNs affected. The decrease of PI3K-C2alpha gene expression was paralleled by cellular changes indicating apoptotic cell death such as nuclear condensation, formation of apoptotic bodies, and DNA fragmentation. PI3K-C2alpha mRNA levels were also reduced when cells were incubated in growth factor-deficient medium. Supplementing growth factors (serum or insulin) into medium lead to an increase of PI3K-C2alpha mRNA levels. This finding strongly suggests that PI3K-C2alpha is a crucial survival factor.     

Toroid formation in charge neutralized flexible or semi-flexible biopolymers: potential pathway for assembly of DNA carriers

BACKGROUND: The theoretical state diagram for semi-flexible macromolecules such as DNA predicts that a tightly wound toroid can be a stable structure. Experimentally, toroids roughly 100 nm in diameter are routinely observed for DNA in the presence of multivalent cations at low DNA concentration. Theory also predicts toroids can form between non-DNA semi-flexible polymers and multivalent counterions. This phenomenon provides a means to co-package DNA with functionalized anionic polymers to create gene delivery systems. METHODS AND RESULTS: We show using electron microscopy that non-DNA polymers (polylysine, polyglutamic acid, and dextran sulfate) form toroids when mixed with multi- or polyvalent ions of opposite charge. The non-DNA toroids are similar in diameter to ones made with DNA. The results using dextran sulfate, a semi-flexible polymer, are explained by current theory. However, theory predicts that high flexibility in polypeptides should discourage their incorporation into stable toroids. To explain these latter observations we propose that charge neutralization facilitates secondary structure formation, which confers stiffness, thereby allowing stable toroids for the polypeptides studied. We measured the secondary structure of the toroid-forming polypeptides using circular dichroism (CD). The CD spectrum indicates the polypeptides undergo transitions from non-ordered structures (random coil) to ordered secondary structures (either alpha-helix or beta-sheet) upon charge neutralization which supports the hypothesis. The type of secondary structure is dependent on the type of multivalent counterion used to form the toroids. Formation of the polypeptide toroids confers resistance to heat denaturation of the resulting polypeptide secondary structure. The CD spectrum of DNA in a toroid also is changed from that of uncomplexed DNA, but all of the counterions used to form DNA toroids created structures with similar CD spectra in the DNA region (250-290 nm). CONCLUSIONS: The toroid structure obtained using DNA is observed in other semi-flexible non-DNA polymers such as dextran sulfate, and also in flexible polymers such as polylysine and polyglutamic acid upon charge neutralization with multivalent counterions. In the flexible polymers we propose that this phenomenon is due to induction of secondary structure upon charge neutralization, which decreases polymer flexibility, i.e. increases polymer stiffness, to enable toroid formation. These results have significant implications for the co-assembly of non-DNA anionic polymers with DNA to create nanoscopic gene carriers.     

Cadmium induced apoptotic changes in chromatin structure and subphases of nuclear growth during the cell cycle in CHO cells

CHO cells were grown in the presence of 1 M CdCl₂ and subjected to ATP-dependent replicative DNA synthesis after permeabilization. By decreasing the density of the cell culture replicative DNA synthesis was diminishing. At higher than 2 × 10⁶ cell/ml concentration Cd had virtually no effect on the rate of DNA replication. Growth at higher cell concentrations could be supressed by increasing Cd concentration. After Cd treatment cells were synchronized by counterflow centrifugal elutriation. Cadmium toxicity on cell growth in early and mid S phase led to the accumulation of enlarged cells in late S phase. Flow cytometry showed increased cellular and nuclear sizes after Cd treatment. As the cells progressed through the S phase, 11 subpopulations of nuclear sizes were distinguished. Apoptotic chromatin changes were visualized by fluorescent microscopy in a cell cycle dependent manner. In the control untreated cells the main transitory forms of chromatin corresponded to those we have published earlier (veil-like, supercoiled chromatin, fibrous, ribboned structures, chromatin strings, elongated prechromosomes, precondensed chromosomes). Cadmium treatment caused: (a) the absence of decondensed veil-like structures and premature chromatin condensation in the form of apoptotic bodies in early S phase (2.2–2.4 average C-value), (b) the absence of fibrous structures, the lack of supercoiled chromatin, the appearance of uncoiled ribboned chromatin and perichromatin semicircles, in early mid S phase (2.5–2.9 C), (c) the presence of perichromatin fibrils and chromatin bodies in mid S phase (2.9–3.2 C), (d) early intra-nuclear inclusions, elongated forms of premature chromosomes, the extrusion and rupture of nuclear membrane later in mid S phase (3.3–3.4 C), (e) the exclusion of chromatin bodies and the formation of clusters of large-sized perichromatin granules in late S phase (3.5–3.8 C) and (f) large extensive disruptions and holes in the nuclear membrane and the clumping of incompletely folded chromosomes (3.8–4. C).     

Allocation and specification of the genital disc precursor cells in Drosophila

The adult structures of Drosophila melanogaster are derived from larval imaginal discs, which originate as clusters of cells within the embryonic ectoderm. The genital imaginal disc is composed of three primordia (female genital, male genital, and anal primordia) that originate from the embryonic tail segments A8, A9, and A10, respectively, and produce the sexually dimorphic genitalia and analia. We show that the genital disc precursor cells (GDPCs) are first detectable during mid-embryogenesis as a 22-cell cluster in the ventral epidermis. Analysis of mutant and double mutant phenotypes of embryonic patterning genes in the GDPCs, together with their expression patterns in these cells, revealed the following with respect to the origins and specification of the GDPCs. The allocation of the GDPCs from the ventral epidermis requires the function of ventral patterning genes, including the EGF receptor and the spitz group of genes. The ventral localization of the GDPCs is further restricted by the action of dorsal patterning genes. Along the anterior-posterior axis, several segment polarity genes (wingless, engrailed, hedgehog, and patched) are required for the proper allocation of the GDPCs. These segment polarity genes are expressed in some, but not all of the GDPCs, indicating that anterior and posterior compartments are not fully established in the GDPCs. In addition, we found that the three primordia of the larval genital disc have already been specified in the GDPCs by the coordinated actions of the homeotic (Hox) genes, abdominal-A, Abdominal-B, and caudal. By identifying how these different patterning networks regulate the allocation and primordial organization of the 22 embryonic precursors of the compound genital disc, we demonstrate that at least some of the organization of the larval disc originates as positional information in the embryo, thus providing a context for further studies on the development of the genital disc.     

Serrate-Notch signaling defines the scope of the initial denticle field by modulating EGFR activation

The Drosophila embryonic epidermis has been a key model for understanding the establishment of cell type diversity across a cellular field. During segmental patterning, distinct signaling territories are established that employ either the Hedgehog, Spitz, Serrate or Wingless ligands. How these pathways control segmental pattern is not completely clear. One major decision occurs as cells are allocated to differentiate either smooth cuticle or denticle type cuticle. This allocation is based on competition between Wingless signaling and Spitz, which activates the Epidermal Growth Factor Receptor (EGFR). Here we show that a main role for Serrate-Notch signaling is to adjust the Spitz signaling domain. Serrate accomplishes this task by activating Notch in a discrete domain, the main purpose of which is to broaden the spatially regulated expression of Rhomboid. This adjusts the breadth of the source for Spitz, since Rhomboid is necessary for the production of active Spitz. We also show that the Serrate antagonist, fringe, must temper Notch activity to insure that the activation of the EGFR is not too robust. Together, Serrate and Fringe modulate Notch activation to generate the proper level of EGFR activation. If Serrate-Notch signaling is absent, the denticle field narrows while the smooth cell field expands, as judged by the expression of the denticle field determinant Ovo/Shaven baby. This establishes one important role for the Serrate signaling territory, which is to define the extent of denticle field specification.     

Gamma irradiation-induced apoptosis in murine pre-B cells prevents the condensation of fibrillar chromatin in early S phase

Local changes in chromatin structure leading to temporally distinct geometric forms were characterized in nuclei of reversibly permeabilized cells. Reversal of permeabilization was tested by 3H-thymidine incorporation and trypan blue dye exclusion. Apoptotic changes were visualized in a cell cycle dependent manner at the chromatin level by fluorescent microscopy in non-irradiated cells and after 400 rad Co60 irradiation. Fluorescent microscopy of chromatin structures belonging mainly to the interphase of the cell cycle confirmed the existence of specific geometric forms in nuclei of non-irradiated cells. In this control population, the following main transitory forms of condensing chromatin were distinguished: decondensed veil-like structures and fibrous structures in early and mid S phase (2.0-2.5 average C-value), chromatin bodies, semicircles later in mid S phase (3.0-3.5 C), precondensed chromosomes in late S (3.5-3.7 C) and metaphase chromosomes at the end and after S phase (3.7-4.0 C). Our results show that upon gamma-irradiation (a) the cellular and nuclear sizes were increased, (b) the DNA content was lower in each elutriated subpopulation of cells, (c) the progression of the cell cycle was arrested in the early S phase at 2.4 C value, (d) the chromatin condensation was blocked between the fibrillar chromatin and precondensed elongated chromosomal forms, and (e) the number and size of apoptotic bodies were inversely correlated with the progression of the cell cycle, with many small apoptotic bodies in early S phase and less and larger apoptotic bodies in late S phase.     

Discrimination of the roles of MPF and MAP kinase in morphological changes that occur during oocyte maturation

Maturing amphibian oocytes undergo drastic morphological changes, including germinal vesicle breakdown (GVBD), chromosome condensation, and spindle formation in response to progesterone. Two kinases, maturation-promoting factor (MPF) and mitogen-activated protein kinase (MAPK), are involved in these changes, but their precise roles are unknown. Unlike in Xenopus oocytes, discrimination of the functions of MAPK and MPF in Rana oocytes is easy owing to the lack of pre-MPF. We investigated the roles of these kinases by careful observations of chromosomes and microtubules in Rana oocytes. MPF and MAPK activities were manipulated by treatment with progesterone, c-mos mRNA, or cyclin B mRNA in combination with MAPK kinase inhibitors. Activation of one kinase without activation of the other induced only limited events; GVBD was induced by MPF without MAPK, and reorganization of microtubules at GVBD was induced by MAPK without MPF, but other events were not induced. In contrast, coactivation of MPF and MAPK by injection of c-mos and cyclin B mRNA promoted almost all of the morphological changes that occur during maturation without progesterone, indicating that these are controlled by cooperation of MPF and MAPK. The results revealed the functions of MAPK and MPF in each process of sequential morphological changes during oocyte maturation.