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At least 649 records · Page 36Linked to original sources
PubMed1989

Visualization of centromere proteins CENP-B and CENP-C on a stable dicentric chromosome in cytological spreads.

We have screened for the presence of two centromere autoantigens, CENP-B (80 kDa) and CENP-C (140 kDa) at the inactive centromere of a naturally occurring stable dicentric chromosome using specific antibodies that do not cross-react with any other chromosomal proteins. In order to discriminate between the active and inactive centromeres on this chromosome we have developed a modification of the standard methanol/acetic acid fixation procedure that allows us to obtain high-quality cytological spreads that retain antigenicity with the anti-centromere antibodies. We have noted three differences in the immunostaining patterns with specific anti-CENP-B and CENP-C antibodies. (1) The amount of detectable CENP-B varies from chromosome to chromosome. The amount of CENP-C appears to be more or less the same on all chromosomes. (2) CENP-B is present at both active and inactive centromeres of stable dicentric autosomes. CENP-C is not detectable at the inactive centromeres. (3) While immunofluorescence with anti-CENP-C antibodies typically gives two discrete spots, staining with anti-CENP-B often appears as a single bright bar connecting both sister centromeres. This suggests that while CENP-C may be confined to the outer centromere in the kinetochore region, CENP-B may be distributed throughout the entire centromere. Our data suggest that CENP-C is likely to be a component of some invariant chromosomal substructure, such as the kinetochore. CENP-B may be involved in some other aspect of centromere function, such as chromosome movement or DNA packaging.

Autoantigens↗
PubMed1989

Membrane-associated assembly of a phage T4 DNA entrance vertex structure studied with expression vectors.

The DNA entrance vertex of the phage head is critical for prohead assembly and DNA packaging. A single structural protein comprises this dodecameric ring substructure of the prohead. Assembly of the phage T4 prohead occurs on the cytoplasmic membrane through a specific attachment at or near the gp20 DNA entrance vertex. An auxiliary head assembly gene product, gp40, was hypothesized to be involved in assembling the gp20 substructure. T4 genes 20, 40 and 20 + 40 were cloned into expression vectors under lambda pL promoter control. The corresponding T4 gene products were synthesized in high yield and were active as judged by their ability to complement the corresponding infecting T4 mutants in vivo. The cloned T4 gene 20 and gene 40 products were inserted into the cytoplasmic membrane as integral membrane proteins; however, gp20 was inserted into the membrane only when gp40 was also synthesized, whereas gp40 was inserted in the presence or absence of gp20. The gp20 insertion required a membrane potential, was not dependent upon the Escherichia coli groE gene, and assumed a defined membrane-spanning conformation, as judged by specific protease fragments protected by the membrane. The inserted gp20 structure could be probed by antibody binding and protein A-gold immunoelectron microscopy. The data suggest that a specific gp20-gp40-membrane insertion structure constitutes the T4 prohead assembly initiation complex.

Cell Membrane↗
PubMed1982

Orientation of cohesive end site cos determines the active orientation of chi sequence in stimulating recA . recBC-mediated recombination in phage lambda lytic infections.

Sequence chi, 5'G-C-T-G-G-T-G-G, locally enhances homologous recombination by recA and recBC proteins of Escherichia coli. Previous work showed that, in phage lambda, chi is more active in one orientation (leftward) than in the other (rightward). Inverting cos, the sequence for the mature DNA ends of lambda, reverses this orientation dependence: the rightward chi becomes fully active, and the leftward chi becomes relatively inactive. We surmise that chi action in phage lambda is coupled with DNA packaging or injection.

Bacterial Proteins↗
PubMed1980

HMG proteins (1 + 2) form beaded structures when complexed with closed circular DNA.

Structures bearing a resemblance to nucleosomes can be assembled by incubating calf thymus High Mobility Group proteins (1 + 2) with closed circular DNA. These HMG proteins are capable of forming beads and inducing superhelicity when bound to DNA. However, they do not protect from nuclease digestion the discrete DNA fragments characteristic of nucleosomes. The relationship between HMGs (1 + 2) and the "primitive" histone-like DNA-packaging proteins from prokaryotes and mitochondria is discussed.

Animals↗
PubMed1976

Properties of condensed bacteriophage T4 DNA isolated from Escherichia coli infected with bacteriophage T4.

Methods developed for isolating bacterial nucleoids were applied to bacteria infected with phage T4. The replicating pool of T4 DNA was isolated as a particle composed of condensed T4 DNA and certain RNA and protein components of the cell. The particles have a narrow sedimentation profile (weight-average s=2,500S) and have, on average, a T4 DNA content similar to that of the infected cell. Their dimensions observed via electron and fluorescence microscopy are similar to the dimensions of the intracellular DNA pool. The DNA packaging density is less than that of the isolated bacterial nucleoid but appears to be roughly similar to its state in vivo. Host-cell proteins and T4-specific proteins bound to the DNA were characterized by electrophoresis on polyacrylamide gels. The major host proteins are the RNA polymerase subunits and two envelope proteins (molecular weights, 36,000 and 31,000). Other major proteins of the host cell were absent or barely detectable. Single-strand breaks can be introduced into the DNA with gamma radiation or DNase without affecting its sedimentation rate. This and other studies of the effects of intercalated ethidium molecules have suggested that the average superhelical density of the condensed DNA is small. However, these studies also indicated that there may be a few domains in the DNA that become positively supercoiled in the presence of high concentrations of ethidium bromide. In contrast to the Escherichia coli nucleoid, the T4 DNA structure remains condensed after the RNA and protein components have been removed (although there may be slight relaxation in the state of condensation under these conditions).

Bacterial Proteins↗
PubMed2004

Information content and complexity in the high-order organization of DNA.

Nucleic acids are characterized by a vast structural variability. Secondary structural conformations include the main polymorphs A, B, and Z, cruciforms, intrinsic curvature, and multistranded motifs. DNA secondary motifs are stabilized and regulated by the primary base sequence, contextual effects, environmental factors, as well as by high-order DNA packaging modes. The high-order modes are, in turn, affected by secondary structures and by the environment. This review is concerned with the flow of structural information among the hierarchical structural levels of DNA molecules, the intricate interplay between the various factors that affect these levels, and the regulation and physiological significance of DNA high-order structures.

Binding Sites↗
PubMed1979

In vitro association of empty adenovirus capsids with double-stranded DNA.

Several lines of evidence suggest that empty adenovirus capsids are preassembled intermediates in the pathway of virion assembly. We have observed that purified empty capsids of subgroup B adenoviruses have a remarkable affinity for DNA in vitro. The products of capsid-DNA association are sufficiently stable, once formed in low-salt solution, to permit purification and characterization in CsCl density gradients. Neither virions nor the DNA-containing incomplete particles of subgroup B adenoviruses can give rise to such in vitro reaction products. The average molecular weight of the empty adenovirus capsids is about 123 X 10(6), consistent with the absence of viral core peptides and a small deficiency of exterior shell polypeptides. Electron microscopy of negatively stained capsids and the capsids bound to DNA reveals a typical adenovirus size and architecture. The particles appear with a surface discontinuity that is presumed to expose the DNA binding site(s). The DNA molecules associated with the empty capsids are susceptible to the actions of DNase and restriction endonucleases. The dependence of rate of capsid-DNA association on DNA length suggests randomly distributed binding sites on the DNA molecules. Although the DNA molecules can successively acquire additional empty capsids, the empty particles themselves are restricted to interactionwith only one DNA molecule. Electron microscopy of the capsid-DNA complexes spread in cytochrome c films shows that the particles are bo-nd along the contour of extended duplex DNA. The amount of DNA within each bound particle appears to be less than 300 base pairs, as estimated by the length of the DNA molecules visible outside of the bound particle. The empty capsid-DNA association product described in this report provides an interesting substrate for further investigation of the DNA packaging process in a defined in vitro system, with extracts or purified components from infected cells.

Adenoviridae↗
PubMed2002

A complex rearrangement involving simultaneous translocation and inversion is associated with a change in chromatin compaction.

Detailed fluorescence in situ hybridisation analysis of a previously described translocation revealed it to be a more complex rearrangement consisting of both a translocation and a paracentric inversion with an apparent coincident breakpoint at 16p13.3, t(14;16)(p32;p13.3) inv16(p13.3p12.1). This unusual three-breakpoint rearrangement was not obvious from examination of G-banding. Such rearrangements may be undiagnosed in cytogenetic studies. The presence of an interstitial deletion of 16p was unlikely as the rearranged chromosome contained probes distributed along the short arm of chromosome 16. Fluorescence in situ hybridisation studies suggested that the inverted segment was smaller in size than that on the normal chromosome. Measurements of distances between probes on metaphase chromosomes confirmed that there was differential compaction of the inverted portion on 16p. The inverted region was significantly reduced in size by 21% compared with the same region on the normal chromosome 16. The size reduction across the region was non-uniform, with one region showing a 55% increase in compaction. The change in compaction was also associated with a change in the lateral position of a probe on the chromatids. The finding that a single chromosome breakpoint can change the compaction of chromatin over an extensive region has implications for models of the structure of metaphase chromosomes. Possible explanations are either a localized severe disruption of DNA packaging over relatively short distances (hundreds of kilobases) or a more generalized change that extends over many megabases. These results raise the important possibility that chromosome breaks may result in a more global change in DNA compaction across large segments of a chromosome.

Chromatin↗
PubMed1985

Bacteriophage L: chromosome physical map and structural proteins.

Restriction endonuclease cleavage site mapping was used to locate the regions of highest sequence homology in the chromosomes of Salmonella typhimurium bacteriophages L and P22. These lie in the DNA packaging, tail, early transcription antitermination, and perhaps integration "gene modules." Other regions of the two genomes are substantially less closely related. Phage L, which has no functional immunity I region, lacks approximately 1300 bp of DNA when compared to P22 in this section of the chromosome. At least some of the virion structural proteins are interchangeable between the two phages, which suggests that the two phage structural protein genes are very closely related. In addition, the apparent molecular weights of most P22 and L phage structural proteins are very similar. However, the phage L virion contains about 140 molecules of a 15K capsid protein which apparently has no P22 analog.

Chromosome Mapping↗
PubMed1981

Knotted DNA from bacteriophage capsids.

The majority of the DNA prepared from tailless capsids of bacteriophage P2 by the phenol extraction procedure consists of monomeric rings that have their cohesive ends joined. Electron microscopic and ultracentrifugal studies indicate that these molecules have a complex structure that is topologically knotted; they have a more compact appearance and a higher sedimentation coefficient when compared with regular nicked P2 DNA rings. Linearization of these rings by thermal dissociation or repair of the cohesive ends by DNA polymerase I in the presence of all four deoxynucleoside triphosphates gives molecules that are indistinguishable from normal P2 DNA that has been similarly treated. The knotted nature of the majority of P2 head DNA is further supported by analyzing the products when these molecules are treated with ligase and the ligase-treated molecules are subsequently nicked randomly with DNase I. The data are consistent with the notion that, if such a molecule is first converted to a form that contains only one single-chain scission per molecule, strand separation gives a linear strand and a highly knotted single-stranded ring. The results suggest that the DNA packaged in tailless P2 capsids is arranged in a way that leads to the formation of a complex knot when the ends join. In an intact phage particle, the anchoring of one terminus of the DNA to the head-proximal end of the tail [Chattoraj, D. K. & Inman, R. B. (1974) J. Mol. Biol. 87, 11-22] presumably diminishes or prevents this kind of joining. The novel knotted DNA can be used to assay type II DNA topoisomerases that break and rejoin DNA in a double-stranded fashion.

Capsid↗
PubMed2005

Lonidamine transiently affects spermatogenesis in pubertal CD1 mice.

Lonidamine (LND) [1-(2,4-dichlorobenzyl)-1H-indazole-3-carboxylic acid], a well-known antispermatogenic drug, was studied for the first time in pubertal mice to assess its possible effects on spermatogenesis. Male CD1 mice were orally treated on Postnatal Day (PND) 28 with a single dose of LND (100 mg/kg body weight) and sacrificed on PND30, PND42, PND74 and PND123. On PND30 (48 h after dosing), severe testicular effects were evidenced in the treated animals: (a) reduction of the testicular sperm head concentration (approximately 50% of the control value); (b) changes in the spermatogenic cell type distribution (mild decrease of the elongated spermatids and S-phase cells fractions); and (c) morphological alterations of the Sertoli cell cytoplasm and germ cell exfoliation. These changes were recovered in adulthood, on PND74 and PND123. However, no effect on sperm chromatin structure was detected on the epididymal sperm of mature mice by sperm chromatin structure assay, suggesting that LND did not interfere with the process of chromatin reorganization and DNA packaging.

Animals↗
PubMed2005

Functional relevance of amino acid residues involved in interactions with ordered nucleic acid in a spherical virus.

In the spherical virion of the parvovirus minute virus of mice, several amino acid side chains of the capsid were previously found to be involved in interactions with the viral single-stranded DNA molecule. We have individually truncated by mutation to alanine many (ten) of these side chains and analyzed the effects on capsid assembly, stability and conformation, viral DNA encapsidation, and virion infectivity. Mutation of residues Tyr-270, Asp-273, or Asp-474 led to a drastic reduction in infectivity. Mutant Y270A was defective in capsid assembly; mutant D273A formed stable capsids, but it was essentially unable to encapsidate the viral DNA or to externalize the N terminus of the capsid protein VP2, a connected conformational event. Mutation of residues Asp-58, Trp-60, Asn-183, Thr-267, or Lys-471 led to a moderate reduction in infectivity. None of these mutations had an effect on capsid assembly or stability, or on the DNA encapsidation process. However, those five mutant virions were substantially less stable than the parental virion in thermal inactivation assays. The results with this model spherical virus indicate that several capsid residues that are found to be involved in polar interactions or multiple hydrophobic contacts with the viral DNA molecule contribute to preserving the active conformation of the infectious viral particle. Their effect appears to be mediated by the non-covalent interactions they establish with the viral DNA. In addition, at least one acidic residue at each DNA-binding region is needed for DNA packaging.

Amino Acids↗
PubMed2004

In vivo gene delivery and visualization of corneal stromal cells using an adenoviral vector and keratocyte-specific promoter.

PURPOSE: This study was conducted to determine whether intrastromal injection of adenoviral construct could be used to transfect corneal stroma cells effectively in vivo and to determine whether a tissue-specific promoter could be used to express exogenous genes in keratocytes. METHODS: An adenoviral construct with a cytomegalovirus (pCMV)-driven enhanced green fluorescent protein (EGFP) reporter gene was injected into the stroma of murine corneas. In vivo expression was quantitated and samples were analyzed by in vivo stereomicroscopy, and ex vivo expression was determined by confocal three dimensional (3-D) reconstruction. The 3.2-kb keratocan promoter was used to drive tissue-specific reporter gene expression in vivo. RESULTS: EGFP expression was first detected in vivo 11 hours after injection of adeno-EGFP in the corneal stroma, with a duration of approximately 3 weeks. Ex vivo wholemount cornea confocal analysis with 3-D reconstruction allowed visualization of EGFP expression in corneal stroma cells, to accurately assess cellular architecture and distribution in the corneal stroma. Naked pCMV-EGFP plasmid DNA did not express the reporter gene to the levels of the adeno-EGFP. The 3.2-kb keratocan promoter was capable of driving EGFP tissue-specific expression in the cornea. CONCLUSIONS: Intrastromal injection of adenovirus packaged DNA constructs is a rapid and efficient way to deliver and express genes in the corneal stroma. Intrastromal injection is also capable of delivering tissue-specific promoter constructs to the corneal stroma for gene expression. Furthermore, 3-D reconstruction provides a powerful tool for enhanced visualization of the corneal stroma environment and cellular biology.

Adenoviridae↗
PubMed1990

Role of the major capsid protein in herpes simplex virus type-1 capsid assembly.

Two herpes simplex virus type 1 (HSV-1) temperature-sensitive (ts) mutants with defects in the gene for the major capsid protein, ICP5, were examined for their effects on virion capsid assembly. Polyacrylamide gel electrophoresis revealed that both mutants were able to synthesize wild-type (WT) levels of ICP5 at the nonpermissive temperature. However, the 53 kD capsid protein disappeared concomitant with the appearance of a new, 51 kD species. These results, taken together with ultrastructural and immunological analyses indicate that the processing and assembly of capsid proteins, DNA packaging and thermal stability of HSV-1 virions are dependent upon functional ICP5.

Animals↗
PubMed2005

Nucleotides regulate the conformational state of the small terminase subunit from bacteriophage lambda: implications for the assembly of a viral genome-packaging motor.

Terminase enzymes are responsible for "packaging" of viral DNA into a preformed procapsid. Bacteriophage lambda terminase is composed of two subunits, gpA and gpNu1, in a gpA(1).gpNu1(2) holoenzyme complex. The larger gpA subunit is responsible for preparation of viral DNA for packaging, and is central to the packaging motor complex. The smaller gpNu1 subunit is required for site-specific assembly of the packaging motor on viral DNA. Terminase assembly at the packaging initiation site is regulated by ATP binding and hydrolysis at the gpNu1 subunit. Characterization of the catalytic and structural interactions between the DNA and nucleotide binding sites of gpNu1 is thus central to our understanding of the packaging motor at the molecular level. The high-resolution structure of the DNA binding domain of gpNu1 (gpNu1-DBD) was recently determined in our lab [de Beer, T., et al. (2002) Mol. Cell 9, 981-991]. The structure reveals the presence of a winged-helix-turn-helix DNA binding motif, but the location of the ATPase catalytic site in gpNu1 remains unknown. In this work, nucleotide binding to the gpNu1-DBD was probed using acrylamide fluorescence quenching and fluorescence-monitored ligand binding studies. The data indicate that the minimal DBD dimer binds both ATP and ADP at two equivalent but highly cooperative binding sites. The data further suggest that ATP and ADP induce distinct conformations of the dimer but do not affect DNA binding affinity. The implications of these results with respect to the assembly and function of a terminase DNA-packaging motor are discussed.

Acrylamide↗
PubMed1994

Binding of scaffolding subunits within the P22 procapsid lattice.

The capsid assembly pathways of the dsDNA bacteriophages, herpesviruses, and adenoviruses all proceed through a precursor shell lacking DNA. These procapsids contain scaffolding proteins required for assembly but absent from mature virions. The bacteriophage P22 procapsid contains approximately 300 molecules of the 33-kDa gene 8 scaffolding protein, in addition to the 420 molecules of gene 5 coat protein. During the process of DNA packaging and phage maturation, all 300 scaffolding molecules are released intact to participate in subsequent rounds of procapsid assembly. Low concentrations of guanidine hydrochloride (GuHCl) reproduce the release of scaffolding from procapsids in vitro, in the absence of DNA. The release was reversible; when the GuHCl was removed by dialysis, the scaffolding subunits reentered the extracted capsids to regenerate morphologically normal procapsids. The subunits presumably exited and reentered through the channels recently observed at the centers of the pentamers and hexamers (Prasad, B. V. V., Prevelige, P. E., Marietta, E., Chen, R. O., Thomas, D., King, J., and Chiu, W. (1993). J. Mol. Biol. 231 65-74). We have utilized this reaction to investigate the binding of scaffolding within normal procapsids and to other large structures of coat protein. Procapsids contained two classes of scaffolding subunits, which may represent binding of scaffolding to different specific positions within the T = 7 procapsid lattice. These sites became lost or inaccessible upon phage maturation.

Bacteriophage P22↗
PubMed1998

Characterization of bacteriophage lambda Q- mutant for stable and efficient production of recombinant protein in Escherichia coli system.

We previously demonstrated that the lambda system integrated into the host chromosome can overcome the instability encountered in continuous operations of unstable plasmid-based expression vectors. High stability of a cloned gene in a lysogenic state and a high copy number in a lytic state provide cloned-gene stability and overexpression in a two-stage continuous operation. But the expression by the commonly used S- mutant lambda was only twice as high as that of the single copy. To increase the expression in the lambda system, we constructed a Q- mutant lambda vector that can be used in long-term operations such as a two-stage continuous operation. The Q- mutant phage lambda is deficient in the synthesis of proteins involved in cell lysis and lambda DNA packaging, while the S- mutant is deficient in the synthesis of one of two phage proteins required for lysis of the host cell and liberation of the progeny phage. Therefore, it is expected that the replicated Q- lambda DNA containing a cloned gene would not be coated by a phage head and would remain naked for ample expression of the cloned gene and host cells would not lyse easily and consequently would produce larger amounts of cloned-gene products. The beta-galactosidase expression per unit cell by the Q- mutant in a lytic state was about 30 times higher than that in a lysogenic state, while the expression by the commonly used S- mutant in a lytic state was twice as high as that in a lysogenic state. The optimal switching time of the Q- mutant from the lysogenic state to the lytic state for the maximum production of beta-galactosidase was 5.3 h, which corresponds to an early log phase in the batch operation.

Bacteriophage lambda↗
PubMed1987

Initiation events in in-vitro packaging of bacteriophage phi 29 DNA-gp3.

Initiation events in the packaging of bacteriophage phi 29 DNA-gp3 (DNA-gene product 3 complex) were studied in a completely defined in-vitro system that included purified proheads, DNA-gp3 and the DNA packaging protein gp16. In the sequential interactions, gp16 first bound to, and was modified by, the prohead. The prohead-gp16 complex then bound to DNA-gp3, resulting in a second modification of gp16 that permitted binding of ATP. DNA-gp3 aggregates were produced, and the hydrolysis of ATP accompanied DNA-gp3 packaging. Binding and hydrolysis of ATP by gp16 was both prohead- and DNA-gp3-dependent. Interruption of packaging by DNase I addition revealed filled heads but few particles containing partial lengths of DNA, suggesting that following a rate-limiting initiation, the translocation of DNA-gp3 into the prohead was much faster in the defined in-vitro system than in extracts.

Adenosine Triphosphate↗