Isolation and characterization of the nuclear matrix in Friend erythroleukemia cells: chromatin and hnRNA interactions with the nuclear matrix.

Nuclear matrices from undifferentiated and differentiated Friend erythroleukemia cells have been obtained by a method which removes DNA in a physiological buffer. These matrices preserved the characteristic topographical distribution of condensed and diffuse "chromatin" regions, as do nuclei in situ or isolated nuclei. Histone H1 was released from the nuclear matrix of undifferentiated cells by 0.3 M KCl; inner core histones were released by 1 M KCl. Nuclear matrix from differentiated cells did not maintain H1, and histone cores were fully released in 0.7 M KCl. KCl removed the core histones as an octameric structure with no evidence of preferential release of any single histone. Electron microscopy of KCl-treated matrix revealed no condensed regions but rather a network of fibrils in the whole DNA-depleted nuclei. When nuclear matrices from both types of cell were exposed to conditions of very low ionic strength, inner core histones and condensed regions remained. These observations support the contention that inner core histones are bound to matrix through natural ionic bonds or saline-labile elements, and that these interactions are implicated in chromatin condensation. hnRNA remained undegraded and tenaciously associated to the matrix fibrils, and was released only by chemical means which, by breaking hydrophobic and hydrogen bonds, produced matrix lysis. Very few nonhistone proteins were released upon complete digestion of DNA from either type of nuclei. The remaining nonhistone proteins represent a large number of species of which the majority may be matrix components. The molecular architecture in both condensed and diffuse regions of interphase nuclei appears to be constructed of two distinct kinds of fibers; the thicker chromatin fibers are interwoven with the thinner matrix fibers. The latter are formed by a heteropolymer of many different proteins.     

Atomic force microscopy of pea starch: origins of image contrast

Atomic force microscopy (AFM) has been used to image the internal structure of pea starch granules. Starch granules were encased in a nonpenetrating matrix of rapid-set Araldite. Images were obtained of the internal structure of starch exposed by cutting the face of the block and of starch in sections collected on water. These images have been obtained without staining, or either chemical or enzymatic treatment of the granule. It has been demonstrated that contrast in the AFM images is due to localized absorption of water within specific regions of the exposed fragments of the starch granules. These regions swell, becoming "softer" and higher than surrounding regions. The images obtained confirm the "blocklet model" of starch granule architecture. By using topographic, error signal and force modulation imaging modes on samples of the wild-type pea starch and the high amylose r near-isogenic mutant, it has been possible to demonstrate differing structures within granules of different origin. These architectural changes provide a basis for explaining the changed appearance and functionality of the r mutant. The growth-ring structure of the granule is suggested to arise from localized "defects" in blocklet distribution within the granule. It is proposed that these defects are partially crystalline regions devoid of amylose.     

Structural characterization of the N-terminal mineral modification domains from the molluscan crystal-modulating biomineralization proteins, AP7 and AP24

The AP7 and AP24 proteins represent a class of mineral-interaction polypeptides that are found in the aragonite-containing nacre layer of mollusk shell (H. rufescens). These proteins have been shown to preferentially interfere with calcium carbonate mineral growth in vitro. It is believed that both proteins play an important role in aragonite polymorph selection in the mollusk shell. Previously, we demonstrated the 1-30 amino acid (AA) N-terminal sequences of AP7 and AP24 represent mineral interaction/modification domains in both proteins, as evidenced by their ability to frustrate calcium carbonate crystal growth at step edge regions. In this present report, using free N-terminal, C(alpha)-amide "capped" synthetic polypeptides representing the 1-30 AA regions of AP7 (AP7-1 polypeptide) and AP24 (AP24-1 polypeptide) and NMR spectroscopy, we confirm that both N-terminal sequences possess putative Ca (II) interaction polyanionic sequence regions (2 x -DD- in AP7-1, -DDDED- in AP24-1) that are random coil-like in structure. However, with regard to the remaining sequences regions, each polypeptide features unique structural differences. AP7-1 possesses an extended beta-strand or polyproline type II-like structure within the A11-M10, S12-V13, and S28-I27 sequence regions, with the remaining sequence regions adopting a random-coil-like structure, a trait common to other polyelectrolyte mineral-associated polypeptide sequences. Conversely, AP24-1 possesses random coil-like structure within A1-S9 and Q14-N16 sequence regions, and evidence for turn-like, bend, or loop conformation within the G10-N13, Q17-N24, and M29-F30 sequence regions, similar to the structures identified within the putative elastomeric proteins Lustrin A and sea urchin spicule matrix proteins. The similarities and differences in AP7 and AP24 N-terminal domain structure are discussed with regard to joint AP7-AP24 protein modification of calcium carbonate growth.     

The basement-membrane-like matrix of the mouse EHS tumor: I. Ultrastructure

The fine structure of the extracellular matrix was examined in the Engelbreth-Holm-Swarm (EHS) tumor of the mouse. The matrix is composed of layers parallel to the surface of the associated cells; the layers are poorly defined close to the cells (proximal region) but quite distinct at a distance from the cells (distal region). In the proximal region of the matrix, the indistinct layers are composed of three types of structures: 1) a network of 3- to 8-nm-thick "cords" makes up the bulk of the tissue. 2) Within the network are scattered few 7- to 10-nm-wide, hollow rods of indefinite length, referred to as "basotubules"; their cross section has a dense, more-or-less-circular or -pentagonal wall and a light lumen containing a spherule. In addition, many pale profiles similar to these cross sections are present; they are interpreted as small, independent structures. 3) Minute structures composed of two parallel, 3.5-nm rodlets are referred to as "double pegs." In the distal region of the matrix, the distinct layers include the same three types of structures, but basotubules are numerous and prominent; in each layer, they are arranged in picket-fence fashion along two parallel planes. Cords are packed between them. Double pegs are scattered throughout the clear interlayer spaces. Inasmuch as cord network, basotubules, and double pegs are present in the two regions of the tumor matrix, both regions resemble basement membrane. To explain the contrast between the paucity of basotubules in the proximal region and their abundance in the distal region, it is proposed that, as the production of newer matrix by the cells causes the older matrix to be displaced distally, the independent structures seen as pale profiles in the proximal region gradually assemble into basotubules.     

A freeze-etch study of angular marginal-plate-containing peroxisomes in the proximal tubules of bovine kidney

Summary The ultrastructure of peroxisomes in the proximal nephron tubules of bovine kidney cortex was studied using ultrathin-sectioning, diaminobenzidine cytochemistry for the visualization of catalase, and by freeze-fracture. Peroxisomes in this nephron segment are up to 1.5 m in diameter and exhibit a peculiar angular shape, which is probably related to the occurrence of multiple straight plate-like inclusions (marginal plates) in the matrix of peroxisomes; they lie directly underneath the peroxisomal membranes. The peroxisomal membrane in such regions follows the outline of the marginal plate. The peculiar shape of peroxisomes allows their unequivocal identification in freeze-fracture preparations. Peroxisomal membranes are recognized by their flat, often rectangular appearance. Intramembrane particles are much more numerous on P-fracture faces than on E-fracture faces. A crystalline lattice-structure with a periodicity of approximately 10 nm can be observed on the flat rectangular areas of E-fracture faces. This lattice structure is intensified after prolonged freeze-etching. Intramembranous particles seem to be superimposed over this pattern. The crystalline pattern on the E-fracture faces of peroxisomal membranes is probably not a membrane structure but it reveals the structure of the membrane-associated marginal plates. A cast of the marginal-plate surface may be generated by a collapse of the peroxisomal membrane half onto the immediately underlying matrix inclusion.     

Membrane sorting via the extracellular matrix

We consider the coupling between a membrane and the extracellular matrix. Computer simulations demonstrate that the latter coupling is able to sort lipids. It is assumed that membranes are elastic manifolds, and that this manifold is disrupted by the extracellular matrix. For a solid-supported membrane with an actin network on top, regions of positive curvature are induced below the actin fibers. A similar mechanism is conceivable by assuming that the proteins which connect the cytoskeleton to the membrane induce local membrane curvature. The regions of non-zero curvature exist irrespective of any phase transition the lipids themselves may undergo. For lipids that prefer certain curvature, the extracellular matrix thus provides a spatial template for the resulting lateral domain structure of the membrane.     

Heterochromatin regions of the chromosomes of the hen and Japanese quail in mitosis and at the lampbrush stage

The mitotic and lampbrush chromosomes of the domestic fowl and Japanese quail were analysed by fluorochrome staining technique. The lampbrush chromosomes of both the subjects displayed a typical "loop-chromomere" structure. Three distinct kinds of loops were distinguished in Gallus g. domesticus--normal, telomeric bows, and lumps. The former are distributed along the whole chromosome length. The latter and the bows were observed in subtelomeric and telomeric regions. By DNA/RNA specific acridine orange staining it was shown that each loop (especially, "lumpy" loops) contained a rich RNP matrix. A comparative analysis of the chromomycin A3/distamycin A banding pattern of mitotic and lampbrush chromosomes shows that the telomeric "bows" and "lumps" are special loops developed in telomeric heterochromatic bands. In Coturnix c. japonica, the CMA/DA-positive bands were not observed in telomeres of mitotic macrochromosomes, except a smallest band in the 2p-arm telomere. The absence of telomeric heterochromatic bands which can be visualized in the quail mitotic chromosomes coincides with the absence of "bow"-like loops. Only small lump-like structures were seen in some telomeres of macroautosomes. The biological significance of loop formation and RNA synthesis in heterochromatic band loops in growing oocytes is briefly discussed.     

A new chromosome model

We present a new model of the three-dimensional structure of chromosomes. With DNA and protein staining it could be shown by high-resolution scanning electron microscopy that metaphase chromosomes are mainly composed of DNA packed in "chromomeres" (coiled solenoides) and a dynamic matrix formed of parallel protein fibers. In the centromeric region, the chromomeres are less densely packed, giving insight into the matrix fibers. We postulate that chromosome condensation is achieved by the binding of solenoids to matrix fibers which have contact sites to one another and move antiparallel to each other. As condensation progresses, loops of solenoids accumulate to form additional chromomeres, causing chromosomes to become successively shorter and thicker as more chromomeres are formed. For sterical reasons, a tension vertical to the axial direction forces the chromatids apart. The model can simply explain the enormous variety of chromosome morphology in plant and animal systems by varying only a few cytological parameters. Primary and secondary constrictions and deletions are defined as regions devoid of chromomeres. Even in the highly condensed metaphase, all genes would be easily accessible.     

Dynamics of mitochondrial ultrastructure in small pieces of cardiac tissue under long-term anoxic incubation

Anoxic incubation of isolated small pieces of cardiac tissue for 72 h caused emergence of an unusual population of mitochondria, referred to as "mitochondrion inside mitochondrion". We studied dynamics of the origin of this event. In the most part of a mitochondrial population after a 6 h anoxic incubation of myocardial tissue, a local increase in some region of the intermembrane space was observed. Some regions of matrix with adjoined inner membrane move into these regions of intermembrane space, to be constricted eventually. After 12 h of incubation densely neighbouring layers of membrane are observed in these structures. By 24 h of incubation, inside new-formed structures well-distinguished concentric layers of membrane appear. Between these layers some electron-dense material ultrastructurally identical to mitochondrial matrix is seen. By 72 h of anoxic incubation, in cardiomyocytes of the experimental tissue structures with well-marked morphological features of mitochondria appear, which we called "mitochondrion inside mitochondrion". Results of our study are discussed in terms of a conception of changes that occur in the structure of mitochondrial reticulum during apoptosis.     

AT-rich islands in genomic DNA as a novel target for AT-specific DNA-reactive antitumor drugs

Interstrand cross-links at T(A/T)4A sites in cellular DNA are associated with hypercytotoxicity of an anticancer drug, bizelesin. Here we evaluated whether these lethal effects reflect targeting critical genomic regions. An in silico analysis of human sequences showed that T(A/T)4A motifs are on average scarce and scattered. However, significantly higher local motif densities were identified in distinct minisatellite regions (200-1000 base pairs of approximately 85-100% AT), herein referred to as "AT islands." Experimentally detected bizelesin lesions agree with these in silico predictions. Actual bizelesin adducts clustered within the model AT island naked DNA, whereas motif-poor sequences were only sparsely adducted. In cancer cells, bizelesin produced high levels of lesions (approximately 4.7-7.1 lesions/kilobase pair/microM drug) in several prominent AT islands, compared with markedly lower lesion levels in several motif-poor loci and in bulk cellular DNA (approximately 0.8-1.3 and approximately 0.9 lesions/kilobase pair/microM drug, respectively). The identified AT islands exhibit sequence attributes of matrix attachment regions (MARs), domains that organize DNA loops on the nuclear matrix. The computed "MAR potential" and propensity for supercoiling-induced duplex destabilization (both predictive of strong MARs) correlate with the total number of bizelesin binding sites. Hence, MAR-like AT-rich non-coding domains can be regarded as a novel class of critical targets for anticancer drugs.     

2 types of molecular structure (composition) of a genome in one species of transposable bacteriophages of Pseudomonas aeruginosa

Comparison of heteroduplexes (HD) between DNAs of different transposable phages of Pseudomonas aeruginosa belonging to two previously described subgroups (D3112 and B3) revealed two types of structure (composition) of the bacteriophages, designated "type A" and "type B". The properties of genome structure of type A (phages of D3112 subgroup) are as follows: high level of conservation (up to 70% of genomes of different phages are represented as blocks of homologous DNA sequences); substitutions in genomes revealed as nonhomology regions in HD are, as a rule, small and located in certain sites; the distribution of the nonhomologous regions in HD of these phages is highly reproducible in independent experiments. Bacteriophages of subgroup B3 have genomes of type B: only a small part (approx. 30%) of genomes retain homology general for all of the phages; the nonhomologous regions are distributed in a large number of sites in HD; the sizes of nonhomologous regions are substantially larger than for the phages of subgroup D3112; distribution of the regions in HD is highly variable, which is characteristic of DNAs with partial homology. There is no difference between genomes of types A and B in G + C content (approx. 61-63%). Viable recombinants can be formed in crosses between phages of different genome types not only in regions with earlier revealed large DNA/DNA homology (right ends of genomes), but also in central portions of the genomes. Nevertheless, functional incompatibility of some regions of phage genomes of types A and B was demonstrated.     

Studies on fish scale formation and resorption

Summary Electron microscopic investigation of scales of the goldfish Carassius auratus revealed that the lamellae of fibrillary plates contain sheet-like structures composed of vertically oriented collagen fibers embedded in an organic matrix. The fibers (TC fibers) are smaller in diameter (35–45 nm) than those of the lamellae and the matrix is stained intensely with lead citrate.The sheet-like structures as well as the lamellae are formed by fibroblasts located beneath the lamellae. The orientation of the collagen fibers of the sheets and the lamellae seems to be controlled by the orientation of the ridges and invaginations of the surface of the fibroblasts.The fibrillary plate of C. auratus was found to be partially calcified. Calcification was initiated by the deposition of needle-like or flaky crystals of hydroxyapatite in the organic matrix of the sheet-like structure and proceeded into the TC fibers and the matrix region of the lamellae. The potassium pyroantimonate-osmium tetroxide method showed a heavy concentration of calcium in the osteoblasts, fibroblasts, and in the matrix regions of the fibrillary plate. Calcium-containing precipitates were also present in the hole zone of the collagen fibers in the lamellae, but the significance of this location in calcification remains to be elucidated.Contribution No. 285, Belle W. Baruch Institute for Marine Biology and Coastal Research, University of South Carolina, Columbia, South Carolina, 29208, USA     

Sequence studies on the soybean chloroplast 16S–23S rDNA spacer region

The sequence of the ribosomal spacer region of soybean chloroplast DNA including the 3 end of the 16S rRNA gene, the tRNA^Ala and tRNA^Ile genes (but not their introns), the three intergenic regions and the 5 end of the 23S rRNA gene, has been determined. This sequence has been compared to corresponding regions of other angiosperm chloroplast DNAs. Secondary structure models are proposed for the entirety of the intergenic regions a, b and c and for the flanking rRNA regions. A model for a common secondary structure of the ribosomal spacer intergenic regions from chloroplasts of higher plants is proposed, which is supported by comparative evidence.     

Sequence alignment approach to pick up conformationally similar protein fragments.

Crystal structure data of globular proteins were used to prepare (phi, psi) probability maps of 20 proteinous amino acids. These maps were compared grid-wise with each other and a conformational similarity index was calculated for each pair of amino acids. A weight matrix, called Conformational Similarity Weight (CSW) matrix, was prepared using the conformational similarity index. This weight matrix was used to align sequences of 21 pairs of proteins whose crystal structures are known. The aligned regions with more than seven contiguous amino acids were further analysed by plotting average weight (W) values of overlapping hepatapeptides in these regions and carrying out curve fitting by Fourier series having TEN harmonics. The protein fragments corresponding to the half-linewidth of peaks were predicted as fragments having similar conformation in the protein pair under consideration. Such an approach allows us to pick up conformationally similar protein fragments with more than 67% accuracy.     

Discovering simple regions in biological sequences associated with scoring schemes.

Let A denote an alphabet consisting of n types of letters. Given a sequence S of length L with v(i) letters of type i on A, to describe the compositional properties and combinatorial structure of S, we propose a new complexity function of S, called the reciprocal complexity of S, as C(S) = (i=1) product operator (n) (L/nv(i))(vi) Based on this complexity measure, an efficient algorithm is developed for classifying and analyzing simple segments of protein and nucleotide sequence databases associated with scoring schemes. The running time of the algorithm is nearly proportional to the sequence length. The program DSR corresponding to the algorithm was written in C++, associated with two parameters (window length and cutoff value) and a scoring matrix. Some examples regarding protein sequences illustrate how the method can be used to find regions. The first application of DSR is the masking of simple sequences for searching databases. Queries masked by DSR returned a manageable set of hits below the E-value cutoff score, which contained all true positive homologues. The second application is to study simple regions detected by the DSR program corresponding to known structural features of proteins. An extensive computational analysis has been made of protein sequences with known, physicochemically defined nonglobular segments. For the SWISS-PROT amino acid sequence database (Release 40.2 of 02-Nov-2001), we determine that the best parameters and the best BLOSUM matrix are, respectively, for automatic segmentation of amino acid sequences into nonglobular and globular regions by the DSR program: Window length k = 35, cutoff value b = 0.46, and the BLOSUM 62.5 matrix. The average "agreement accuracy (sensitivity)" of DSR segmentation for the SWISS-PROT database is 97.3%.     

Trypanosoma congolense: structure and molecular organization of the surface glycoproteins of two early bloodstream variants

The complete primary structures of two variant specific glycoproteins (VSGs) of the nannomonad Trypanosoma (N.) congolense are presented. These coat proteins subserve the function of antigenic variation. The secondary structure potentials of both VSGs have been calculated. The amino acid sequences and secondary structure potentials of these VSGs have been compared with the primary structures and secondary structure potentials of several Trypanosoma brucei complex VSGs. In homologous regions, the T. brucei complex VSGs show a pattern of sharply contrasting secondary structure potentials. It has been suggested previously that this pattern gives rise to different folding structures in different members of this polygene protein family. Thus, different short regions of the polypeptide sequence are exposed as antigenic "caps" on the solvent-exposed surface of intact trypanosomes. A sharply contrasting secondary structure potential pattern is also found in regions of the two T. congolense VSGs. However, there is little homology of primary structure between each of the two T. congolense VSGs and any member of the T. brucei complex VSG polygene family whose primary structure has been determined.     

Isolation of matrices from maize leaf nuclei: identification of a matrix-binding site adjacent to theAdh1 gene

Nuclear matrices were isolated from maize leaves by the two conventional methods usually employed for the preparation of the corresponding structures of animal origin. It is demonstrated that functionally competent matrices, recognizing and specifically binding the MAR-containing DNA of the mousek-immunoglobulin gene may be prepared by both 2 M NaCl and LIS extractions of maize nuclei.A DNA region with a high affinity for the nuclear matrix was identified at the 5 end of the maizeAdh1-S gene, distal to the promoter region. The presence of sites of reported altered chromatin structure in this particular region is discussed. While the proximity and the cohabitation of MARs with different regulatory elements is a common feature of matrix association regions in animal systems, this is the first plant MAR identified in a region of known significance for gene regulation.     

Predictions of the secondary structure and antigenicity of human and bovine tropoelastins

Secondary structure and antigenicity predictive methods have been applied to the sequences of human and bovine tropoelastins in order to have some insight into the molecular structure of its insoluble counterpart, i.e., elastin. For both tropoelastins, all the predictions yielded 11 major regions, in which the pleated conformation was predominant, separated by 10 strong helical segments of various lengths located within alanyl rich regions of the chains. The overall conformations of human and bovine tropoelastins were estimated to contain 18 ± 5% -helices, 63 ± 17% -sheets, 13 ± 13% -turns and 6 ± 6% random coil. For both tropoelastins, antigenicity predictions indicated the presence of seven synthetic decapeptides corresponding to continuous linear epitopes of the molecule. Some of the predicted epitopes are located in the same regions in both species while others are not. These predictions have allowed us to propose an / conformation for tropoelastin. Therefore this extracellular matrix macromolecule might be more structured (10 helical segments for about 18% of the overall structure) than previously suggested.Abbreviations HTPE human tropoelastin - BTPE bovine tropoelastin - AG antigenic index - CF Chou and Fasman algorithm - GOR method of Garnier Osguthorpe and Robson - DC decision constant - CD circular dichroism - NMR nuclear magnetic resonance     

Candidates of trichocyst matrix proteins of the dinoflagellate <Emphasis Type="Italic">Oxyrrhis marina</Emphasis>

Trichocysts are a common cell organelle of ciliates and dinoflagellates. They are composed of trichocyst matrix proteins and have been intensely investigated and characterized in ciliates. Here, for the first time, data have been obtained for trichocyst matrix proteins of a dinoflagellate. A DELTA-BLAST search using 14 available and complete amino acid sequences of mature trichocyst matrix proteins of the ciliate Paramecium tetraurelia resulted in 16 hits for the dinoflagellate Oxyrrhis marina when the E values and bit values to be scored were <10^?4 and >40. They code for proteins with acidic pI values and exceeded the precursors of the trichocyst matrix proteins of the ciliate approximately twofold in length. The values calculated for coverage, identity, and positives ranged from 76 to 100, 21.5 to 28.3, and 44.9 to 53.9%, respectively. Protein conformation predictions indicate coiled-coil domains which are a common feature of mature ciliate trichocyst matrix proteins. As often several EST sequences of O. marina matched with a queried mature trichocyst matrix protein of P. tetraurelia, a multigene family can be assumed for trichocyst proteins in this dinophyte, too. Trichocyst-enriched fractions of O. marina were isolated and subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis. When samples were incubated with loading buffer without a reducing agent, the banding pattern was mainly composed of three regions in the range of >90, 75–60, and 50–35 kDa, with each region consisting of four to five bands. Tryptic in gel digestion of proteins excised from these three gel regions followed by mass spectrometry confirmed that up to 14 of the 16 predicted proteins were present within the trichocyst-enriched fractions. When the samples were reduced with either ß-mercaptoethanol or dithiothreitol, the proteins of the three regions disappeared almost completely and proteins in the range of 27 to 15 kDa became the dominating bands. Up to 12 of the predicted proteins were detected within these bands.