Orienting rigid and flexible biological assemblies in ferrofluids for small-angle neutron scattering studies

Small-angle scattering from macromolecules in solution is widely used to study their structures, but the information content is limited because the molecules are generally randomly oriented and hence the data are spherically averaged. The use of oriented rodlike structures for scattering, as in fiber diffraction, greatly increases the amount of structural detail that can be obtained. A new technique using a ferromagnetic fluid has been developed to align elongated structures independent of their intrinsic magnetic properties. This technique is ideal for small-angle neutron scattering because the scattering from the ferrofluid particles can be reduced significantly by matching the neutron scattering length density of the particles to a D(2)O solvent ("contrast matching"). The net result is scattering primarily from the ordered biological assembly in a solution environment that can be adjusted to physiological pH and ionic strength. Scattering results from ordered tobacco mosaic virus, tobacco rattle virus, and chromain fibers are presented.

The influence of esophageal length on outcomes after laparoscopic fundoplication

BACKGROUND

It has been suggested that laparoscopic antireflux surgery has been associated with an increased incidence of postoperative paraesophageal hiatus herniation, and that this comes (at least in part) from not performing an esophageal lengthening procedure in patients with preoperative esophageal shortening. This study was undertaken to determine whether patients with esophageal shortening have an increased risk of reoperation after laparoscopic antireflux surgery.

STUDY DESIGN

All patients who underwent a laparoscopic fundoplication between December 1991 and March 1999, and who had undergone preoperative esophageal manometry in our department were included in this study. Preoperative, operative, and followup data were collected prospectively, and original manometry recordings were reviewed to determine the length of the esophagus (the distance between the midpoints of the upper and lower esophageal sphincters). An index of esophageal length versus height was also calculated by dividing esophageal length by height. Esophageal length and the index were then compared with clinical outcomes. In addition, outcomes for the 50 patients with the shortest index was compared with outcomes of the 50 patients with the longest index.

RESULTS

This study included 484 patients from an overall experience of 774 laparoscopic antireflux procedures. Postoperative followup ranged from 3 months to 5 years (median 2 years). Mean esophageal length was 23 cm (range 14 to 30 cm). There was a significant correlation between height and esophageal length (r = 0.44, p < 0.0001). Although patients with large hiatus hernias tended to have a shorter esophagus, preoperative endoscopic esophagitis grading did not influence length. Esophageal length did not influence the overall requirement for further surgical reintervention, although an analysis of esophageal length in patients who developed specific complications demonstrated that postoperative paraesophageal herniation was more likely in patients with a shorter esophagus, and reoperation for a tight esophageal hiatus was less likely in patients with a short esophagus. The incidence of paraesophageal hernia in the 50 patients with the shortest index was 8% versus 2% in the 50 patients with the longest index (p = 0.36).

CONCLUSIONS

Although the overall reoperation rate after laparoscopic fundoplication was not influenced by esophageal length, this study did demonstrate an association between esophageal shortening and postoperative paraesophageal herniation. But the increased risk of this problem is small, and for this reason a case cannot be made for patients with a manometrically short esophagus to routinely undergo an esophageal lengthening procedure.

Efficacy of a 90 degree anterior fundoplication vs a total fundoplication in an experimental model

BACKGROUND

The surgical treatment of gastroesophageal reflux disease (GERD) has improved greatly, so that excellent long-term control of symptoms can now be achieved. At present, the gold standard for treatment is the Nissen fundoplication. However, this procedure produces side effects in some patients, including persistent dysphagia, epigastric bloating, and excessive flatulence. As a result, some surgeons who have recommended the use of a partial fundoplication to lessen the occurrence of these side effects. The aim of this study was to determine the efficacy of a laparoscopically constructed 90 degree anterior fundoplication and to compare this method with the Nissen fundoplication.

METHODS

Twelve domestic white pigs underwent initial esophageal myotomy to ensure an incompetent lower esophageal sphincter. These animals were then randomized to undergo either a total fundoplication or a 90 degree wrap. All procedures were completed laparoscopically. Resting lower esophageal sphincter pressures were measured immediately and at 2 weeks postoperatively with a water-perfused esophageal manometry catheter incorporating a Dent sleeve. The efficacy of the antireflux barrier was determined at 2 weeks after surgery by fundoplication yield studies.

RESULTS

Both the total fundoplication and the 90 degree wrap produced an increase in resting lower esophageal sphincter pressure and restored adequate competence to the gastroesophageal junction in the early postoperative period.

CONCLUSION

A laparoscopically completed 90 degree anterior fundoplication restores lower esophageal sphincter competence in the early postoperative period. Clinical studies examining the long-term results and significant side effects of this procedure are required to establish the place for this procedure in the antireflux surgery armamentarium.

Experimental study of effect of embolism of different laparoscopy insufflation gases

BACKGROUND AND PURPOSE

Whilst carbon dioxide is the gas generally used for insufflation during laparoscopy, several studies have reported adverse effects specifically associated with its use. These effects may be attributable to chemical, metabolic, or immunologic effects specific to CO2. Because helium is chemically, physiologically, and pharmacologically inert, it has been suggested as a possible substitute insufflation gas. However, there has been concern about the potential implications of venous gas embolism during helium insufflation. The aim of this study was to examine the physiological effect of the intravenous injection of He and CO2 in an experimental model.

MATERIALS AND METHODS

Eleven domestic white pigs were randomly allocated to receive multiple intravenous injections of increasing volumes of either CO2 or He gas. Cardiorespiratory function was measured, and the intravenous volumes of gas that resulted in cardiac arrest were determined.

RESULT

Cardiorespiratory functional measures returned to normal quicker after CO2 than after He injection. Helium injection quickly overwhelmed the animal's ability to compensate and resulted in death at a lower volume than did CO2 injection.

CONCLUSIONS

Gas embolism during He insufflation is more likely to be lethal than is CO2 embolism. This scenario is most likely following Veress needle insertion into a large vein. Therefore, if He is to be used for insufflation during clinical laparoscopy, the possibility of venous injection should be minimized by avoiding Veress needle use. Further investigation of the safety of He insufflation is warranted before a role during clinical laparoscopy can be recommended.

Laparoscopic antireflux surgery in the treatment of gastroesophageal reflux in patients with Barrett esophagus

BACKGROUND

Patients with gastroesophageal reflux and Barrett esophagus may represent a group of patients with poorer postoperative outcomes. It has been suggested that such patients should undergo open rather than laparoscopic antireflux surgery.

HYPOTHESIS

The laparoscopic approach to antireflux surgery is appropriate treatment for patients with Barrett esophagus who have symptomatic gastroesophageal reflux disease.

METHODS

The outcome of 757 patients undergoing laparoscopic surgery for gastroesophageal reflux disease from January 1, 1992, through December 31, 1998, was prospectively examined. Barrett esophagus was present in 81 (10.7%) of these patients (58 men and 23 women). The outcome for this group of patients was compared with that of patients undergoing surgery who did not have Barrett esophagus.

RESULTS

The types of operation performed were similar for the 2 patient groups. The mean +/- SD length of columnar mucosa was 47.4 +/- 43.6 mm. The average +/- SD operation time was 79.0 +/- 33.4 minutes. Conversion to open surgery occurred in 6 patients. Postoperative outcomes were as follows. Esophageal manometry and 24-hour pH studies before and after laparoscopic fundoplication demonstrated a significant increase in lower esophageal sphincter resting and residual relaxation pressures and a significant decrease in distal esophageal acid exposure. Four patients have developed high-grade dysplasia or invasive cancer within 4 years of their antireflux surgery, and all of these have subsequently undergone esophageal resection.

CONCLUSIONS

The outcome of laparoscopic antireflux surgery is similar for patients with Barrett esophagus compared with other patients with gastroesophageal reflux disease. This suggests that laparoscopic surgery is appropriate treatment for this patient group.

Early reoperation following laparoscopic antireflux surgery

PURPOSE

To assess the outcome for patients undergoing early reoperation following laparoscopic antireflux surgery.

METHODS

The outcome was prospectively determined for 28 patients who underwent 30 reoperative procedures within 4 weeks of their initial laparoscopic fundoplication between 1992 and 1998. Follow-up ranged from 3 months to 4 years (median 2 years). Before mid 1994, patients were assessed and managed based on clinical findings (first 192 patients in overall series), whereas subsequently (for the most recent 530 patients) all patients underwent routine early postoperative barium swallow radiography, and laparoscopic exploration during the first postoperative week if problems were suspected.

RESULTS

The reoperations were performed for acute paraoesophageal hiatus hernia (8 patients), tight oesophageal hiatus (7), postoperative haemorrhage (3), tight Nissen fundoplication (8), early recurrent reflux (1), and coeliac/superior mesenteric artery thrombosis (1). Two patients required a second operation for persistent dysphagia due to a tight hiatus. Both patients initially underwent loosening of their fundoplication. Before mid 1994, reoperations were usually undertaken by an open approach, whereas subsequently a laparoscopic approach has usually been successful. Laparoscopic reintervention was easily achieved within 7 days of the first procedure whereas subsequent surgery was more difficult and often required open surgery. The change in protocol was associated with an improvement in overall patient satisfaction and dysphagia in the latter part of this experience.

CONCLUSIONS

Routine early contrast radiology following laparoscopic fundoplication and a low threshold for laparoscopic reexploration facilitates early identification of postoperative problems at a time when laparoscopic correction is easily achieved. This may result in an improved overall outcome for patients requiring early reintervention following laparoscopic antireflux surgery.

[Nonhistone chromosome proteins HMG1 and HMG2 stabilize one of the sequence-specific complexes, formed on the promotor of human retroposons of the ALU-family of other nuclear proteins]

Human retroposons of the Alu family have an internal promoter for RNA polymerase III also present in tRNA genes, but Alu are poorly transcribed by this polymerase in somatic cells in vivo, which is probably due to an efficient system of repression of the Alu transcription. The key control promoter element of the tRNA genes, known as B-box, binds basal transcription factor TFIIIC2, which initiates assembly of the full transcription complex. Previously we identified several human nuclear factors which bind to Alu Subregion covering B-box and the adjacent sequences, which can be involved in repression of Alu transcription. In this study we identified one factor, F1, as HMF1/2 and another factor, F2, as TFIIIC2-like protein reacting with B-box. Both the factors are not alu-specific, whereas the third identified Alu-binding factor, F3, seems to be specific for the Alu-specific subsequence located just downstream from B-box and can discriminate evolutionary "young" and "old" Alu subfamilies producing different numbers of transcripts in vivo. Although HMG1/2 binds to Alu in a sequence-unspecific manner, the proteins are capable of stabilizing the sequence-specific complex F3 which can be functionally significant. We believe that the factors binding to Alu B-box subregion interfere somehow with the functions of the basal factor TFIIIC2 and, hence, can be co-repressors of Alu transcription by RNA polymerase III.

The chlamydial EUO gene encodes a histone H1-specific protease

Chlamydia trachomatis is an obligate intracellular pathogen, long recognized as an agent of blinding eye disease and more recently as a common sexually transmitted infection. Recently, two eukaryotic histone H1-like proteins, designated Hc1 and Hc2, have been identified in Chlamydia. Expression of Hc1 in recombinant Escherichia coli produces chromatin condensation similar to nucleoid condensation observed late in the parasite's own life cycle. In contrast, chromatin decondensation, observed during the early life cycle, accompanies down-regulation and nondetection of Hc1 and Hc2 among internalized organisms. We reasoned that the early upstream open reading frame (EUO) gene product might play a role in Hc1 degradation and nucleoid decondensation since it is expressed very early in the chlamydial life cycle. To explore this possibility, we fused the EUO coding region between amino acids 4 and 177 from C. trachomatis serovar Lz with glutathione S-transferase (GST) and examined the effects of fusion protein on Hc1 in vitro. The purified fusion protein was able to digest Hc1 completely within 1 h at 37 degrees C. However, GST alone exhibited no Hc1-specific proteolytic activity. The chlamydial EUO-GST gene product also cleaves very-lysine-rich calf thymus histone H1 and chicken erythrocyte histone H5 but displays no measurable activity towards core histones H2A, H2B, H3, and H4 or chlamydial RNA polymerase alpha-subunit. This proteolytic activity appears sensitive to the serine protease inhibitor 4-(2-aminoethyl)-benzenesulfonyl fluoride hydrochloride (AEBSF) and aspartic protease inhibitor pepstatin but resistant to high temperature and other broad-spectrum protease inhibitors. The proteolytic activity specified by the EUO-GST fusion product selectively digested the C-terminal portion of chlamydial Hc1, the domain involved in DNA binding, while leaving the N terminus intact. At a molar equivalent ratio of 1:1 between Hc1 and DNA, the EUO gene product cleaves Hc1 complexed to DNA and this cleavage appears sufficient to initiate dissociation of DNA-Hc1 complexes. However, at a higher molar equivalent ratio of Hc1/DNA (10:1), there is partial protection conferred upon Hc1 to an extent that prevents dissociation of DNA-Hc1 complexes.

Pathological correlates of extrapyramidal signs in Alzheimer's disease

Extrapyramidal signs frequently accompany Alzheimer's disease (AD), but the pathological substrate remains unknown. Clinical and postmortem information from patients with AD, Parkinson's disease, or progressive supranuclear palsy and control subjects seen at a large tertiary medical center between 1989 and 1994 was examined. AD patients who had taken neuroleptics and AD brains that also contained Lewy bodies were excluded. The presence of extrapyramidal signs was determined using the Unified Parkinson's Disease Rating Scale. Sections of basal ganglia, subthalamic nucleus, and substantia nigra were examined for neurofibrillary tangles and neuropil threads and the nigra for neuronal numbers. Patients with AD (with or without extrapyramidal signs) did not show neuronal loss in the nigra compared to control subjects, while both Parkinson's disease and progressive supranuclear palsy brains showed marked depletion. The number of neurofibrillary tangles and neuropil threads was increased in AD (with or without extrapyramidal signs) nigra compared to control tissue, and also in progressive supranuclear palsy nigra, but not Parkinson's disease nigra. The numbers of nigral neurofibrillary tangles and neuropil threads were positively related to extrapyramidal signs in AD. There were no correlations between tangles and threads in the basal ganglia or subthalamic nucleus and extrapyramidal signs in AD. Thus, extrapyramidal signs in AD correlate best with tangle pathology in the nigra and do not require the concomitant presence of Lewy bodies.

Solution structure of the epithelial cadherin domain responsible for selective cell adhesion

Cadherins are calcium-dependent cell adhesion molecules containing extracellular repeats of approximately 110 amino acids. The three-dimensional structure of the amino-terminal repeat of mouse epithelial cadherin was determined by multidimensional heteronuclear magnetic resonance spectroscopy. The calcium ion was bound by a short alpha helix and by loops at one end of the seven-stranded beta-barrel structure. An exposed concave face is in a position to provide homophilic binding specificity and was also sensitive to calcium ligation. Unexpected structural similarities with the immunoglobulin fold suggest an evolutionary relation between calcium-dependent and calcium-independent cell adhesion molecules.

Solution structure of the tetrameric minimum transforming domain of p53

We report the solution structure of the minimum transforming domain (residues 303-366) of human p53 (p53tet) determined by multidimensional NMR spectroscopy. This domain contains a number of important functions associated with p53 activity including transformation, oligomerization, nuclear localization and a phosphorylation site for p34/cdc2 kinase. p53tet forms a symmetric dimer of dimers that is significantly different from a recent structure reported for a shorter construct of this domain. Phosphorylation of Ser 315 has only minor structural consequences, as this region of the protein is unstructured. Modelling based on the p53tet structure suggests possible modes of interaction between adjacent domains in full-length p53 as well as modes of interaction with DNA.

Purification and spectroscopic characterization of a recombinant amino-terminal polypeptide fragment of mouse epithelial cadherin

Cadherins are a family of Ca(2+)-dependent cell adhesion molecules containing four extracellular tandem repeats each of 110 amino acids. The most amino-terminal repeat is believed to confer the specificity of cell adhesion. A polypeptide containing the amino-terminal repeat of mouse epithelial cadherin has been over-expressed in E. coli and purified to homogeneity. This polypeptide binds Ca2+ with a dissociation constant of 1.6 x 10(-4) M. CD and NMR experiments indicate that the polypeptide adopts a predominantly beta-sheet conformation and that binding of Ca2+ induces only small conformational changes.

Unusual structures of the tandem repetitive DNA sequences located at human centromeres

The presence of the highly conserved repetitive DNA sequence d(AATGG)n.d(CCATT)n in human centromeres argues for a special role for this sequence in recognition, most probably through the formation of an unusual structure during mitosis. Quantitative one- and two-dimensional nuclear magnetic resonance (1D/2D NMR) spectroscopic studies reveal that the Watson-Crick duplex d(AATGG)n.d(CCATT)n adopts the usual B-DNA conformation as illustrated by taking d(AATGG)3.d(CCATT)3 as an example, whereas the d(CCATT)n strand is essentially a random coil. In contrast, the d(AATGG)n strand adopts an unusual stem-loop motif for repeat lengths n = 2, 3, 4, and 6. In addition to normal Watson-Crick A.T pairs, the stem-loop structures are stabilized by mismatched A.G and G.G pairs in the stem and G-G-A stacking in the loop. Stem-loop structures of d(AATGG)n are independently verified by gel electrophoresis and nuclease digestion studies and were also previously shown to be as stable as the corresponding Watson-Crick duplex d(AATGG)n.d(CCATT)n [Grady et al. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 1695-1699]. Therefore, the sequence d(AATGG)n can, indeed, nucleate a stem-loop structure at little free energy cost, and if, during mitosis, it is located on the chromosome surface, it can provide specific recognition sites for kinetochore function.

A calmodulin-target peptide hybrid molecule with unique calcium-binding properties

This paper describes the production and properties of a hybrid protein comprising the full length of the Xenopus laevis calmodulin (CaM) sequence, followed, through a glycylglycine linker, by the 26-residue CaM-binding region of myosin light-chain kinase (M13). This hybrid molecule appears to have high thermal stability (Tm > 75 degrees C in the presence of Ca2+) as well as unusual Ca(2+)-binding properties: (i) a wide-range biphasic Ca(2+)-binding response (extending over pCa 4.8-7.4) and (ii) a high apparent binding constant (pCa50% = 6.3, a 10-fold increase from that of wild-type CaM). NMR and CD data indicate that the CaM-M13 hybrid molecule exists in equilibrium in an approximate 1:1 ratio between two major conformations, one of which is similar to the compact globular structure of the CaM-M13 complex [M.Ikura, G.M. Clore, A.M. Gronenborn, G. Zhu, C.B. Klee and A. Bax (1992) Science, 256, 632-638] and the other to the dumb-bell-like structure of the wild type CaM [Y.S. Babu, C.E. Bugg and W.J. Cook (1988) J. Mol. Biol., 204, 191-204]. The biphasic Ca(2+)-binding curve can be interpreted using a linear combination of two Hill binding curves with significantly different dissociation constants (2 x 10(-9) M and 8 x 10(-8) M), which can be attributed to the two conformations in equilibrium. The present study has opened an avenue to engineer proteins with higher Ca(2+)-binding affinities using the known CaM structures as a template.

The abundant 19-kilodalton protein associated with human sperm nuclei that is related to seminal plasma alpha-inhibins

A basic protein with a relative molecular mass of 19 kDa has been identified and isolated to purity from sonication-resistant, partially demembranized human sperm nuclei. Several criteria prove that this is the unique sperm-specific protein, which was previously thought to be a sperm/testis histone. Partial primary structure sequencing demonstrates homologies with human seminal alpha-inhibins and semenogelin. From the sequence and Western-blotting data with antibodies against basic seminal inhibin-like peptide, we propose that this 19-kD protein is a product of 52-kDa semenogelin processing. The 19-kDa protein was not found among seminal plasma proteins and may be protected from further cleavage into inhibin-like peptides by its association with the sperm head. Immunofluorescence data indicate its localization in the nuclear periphery, with preferential concentration at the acrosome calyx boundary.

Atomic force microscope measurements of nucleosome cores assembled along defined DNA sequences

We have found that the atomic force microscope (AFM) can be used to image the "beads-on-a-string" chromatin structure in a normal air environment following adsorption onto a cover glass substrate. Individual nucleosome cores and linker DNA could be resolved clearly along chromatin fibers that were reconstituted using histone octamers and a tandemly repeated 208-bp nucleosome positioning DNA sequence (208-18). AFM measurements showed that the compaction of the 3780-bp DNA by different loadings of histone octamers was consistent with 146 bp of DNA wrapped 1.75 turns about the histone octamer to form the 11-nm nucleosome core. Precise internucleosome core spacing measurements could be performed along the chromatin fiber axis. In other experiments, AFM images of chromatin reconstituted using closed circular DNA showed highly tangled beaded fibers, as expected. These images and measurements demonstrate that AFM can provide useful high-resolution structural information about chromatin that can be used to complement other more established techniques such as electron microscopy.

DNA internal motions within nucleosomes during the cell cycle and as a function of ionic strength

We have used 31P NMR spectra to show that DNA internal motions are greatly hindered within oligonucleosomes. The fluctuations seem to be a function of both the cell cycle and the number of nucleosomes interlinked. Namely, the resonance areas, directly related to unbound phosphate, are consistently smaller in M-phase than in S-phase; at the same time, the resonance line width, inversely related to base plane, deoxyribose, and phosphate internal motions, is consistently larger in mononucleosomes than in oligonucleosomes. In all cases, the removal of chromosomal proteins, by a progressive increase of ionic strength up to 2 M NaCl, increases the internal motion, as monitored by a decrease in line width toward that of free DNA. While for both oligo- and mononucleosomes in S-phase the decrease in line width is strictly correlated to a sharp increase in resonance area, in M-phase it is not, with the 31P resonance area rather low even at 2.0 M NaCl extraction. Similarly, while S-phase 31P line widths steadily grow from mono- to oligonucleosomes, in M-phase they do not. Moreover, the increase of the ionic strength to 0.6 M NaCl, as compared to 0.35, 1.2, and 2 M NaCl, displays significant variations on 31P line width and resonance area, independent of the cell cycle phase and the number of nucleosomes interlinked. These observations agree with earlier suggestions on the differential role of the various chromosomal protein subfractions, known to preferentially dissociate at the different ionic strengths in question, in the sealing of mononucleosomes and in the overall stability of polynucleosomes.

A light microscope study of linker histone distribution in rat metaphase chromosomes and interphase nuclei

Several subtypes of the linker histone H1 are present in normal rat kidney epithelial cells (NRK-52E). Although H1 is essential in nucleosome and chromatin packaging or condensation, the unique functions of these very basic proteins are largely unknown. There has been much speculation on the role of each H1 variant on developmentally regulated or tissue specific gene expression. We have examined the global distribution of several H1 subtypes on metaphase chromosomes in an attempt to uncover large-scale differences in chromatin condensation. Polyclonal antibodies raised against HPLC-purified rat H1 subtypes revealed a pattern much like G or Q bands for all H1 variants tested on chromosomes harvested with either aqueous or organic spreading methods. H1(0), a less abundant form of H1, may be associated with terminally differentiated or senescent cells. In cultures treated to induce higher levels of H1(0) there were no visible differences at the light microscope level in the antibody banding pattern between induced and noninduced cells. The distributions of H1 subtypes on chromosomes may be visible in different tissues when viewed at higher magnifications. While chromosome patterns were consistent with the antibodies tested, the interphase nuclei displayed clear differences. An epitope specific for anti-H1A antibody is present in the nuclear envelope and is possibly used for chromosomal location or anchorage. Anti-H1B antibody did not specifically label the nuclear envelope, nor did anti-H1(0) antibody. Highly concentrated regions of H1(0) surround the nucleoli, possibly indicating a cluster of genes that are poised for transcription.

Studies of the DNA binding properties of histone H4 amino terminus. Thermal denaturation studies reveal that acetylation markedly reduces the binding constant of the H4 "tail" to DNA

The effect of acetylation on the DNA binding properties of the rigidly conserved histone H4 amino-terminal tail has been studied in detail using the technique of thermal denaturation. The quantitative DNA-binding parameters for both the non- and fully acetylated H4 amino terminus have been determined from thermal denaturation data for complexes of the peptides bound to mixed sequence 146-base pair DNA. We find that under dilute buffer conditions (5 mM Tris-HCl) the binding constant for the non-acetylated peptide to double-stranded DNA is 5 x 10(11) M-1 and that acetylation of lysine residues in the peptide reduces the binding constant to 1 x 10(5) M-1. The dramatic differences observed in the binding constants for the non- and fully acetylated peptides are probably due to the effect of acetylation on the even distribution of positively charged residues in the H4 amino terminus. In other experiments, the binding of both peptides to a 30-base pair oligonucleotide has been studied in solution with varying concentrations of sodium, magnesium, and phosphate ions. These experiments demonstrate that both magnesium and phosphate ions have strong effects on the binding of the H4 tail to DNA, especially weakening the binding of the acetylated peptide. For instance, the dissociation of the non-acetylated peptide from DNA requires 6 mM magnesium, yet the binding of the acetylated peptide is abolished in only 30 microM magnesium. The modulation of the DNA binding interactions of the H4 amino terminus by physiologically relevant ionic conditions, in addition to the effect of acetylation, can be important in the regulation of chromatin structure and function.

The purification and properties of the scaffolding protein of bacteriophage lambda

The Nu3 gene of bacteriophage lambda resides within a cluster of genes that specify structural components of the bacteriophage head. Previous experiments indicate that the Nu3 gene product (gpNu3) is associated with immature proheads but is not detectable in mature proheads or bacteriophage particles, hence its classification as a scaffolding protein. The Nu3 gene has been cloned and overexpressed, and its protein product has been purified. The purified protein is biologically active, as demonstrated by its ability to complement a gpNu3-deficient extract in an in vitro assembly reaction. The sequence of the amino terminus of the protein indicates that translation of Nu3 starts at nucleotide position 5,342 on the standard lambda DNA sequence, yielding a protein with a calculated Mr of 13,396. A combination of gel exclusion chromatography and velocity sedimentation gradient data indicates that gpNu3 possesses an unusually elongated shape.

Isolation and characterization of mutations in the bacteriophage lambda terminase genes

The terminase enzyme of bacteriophage lambda is a hetero-oligomeric protein which catalyzes the site-specific endonucleolytic cleavage of lambda DNA and its packaging into phage proheads; it is composed of the products of the lambda Nul and A genes. We have developed a simple method to select mutations in the terminase genes carried on a high-copy-number plasmid, based on the ability of wild-type terminase to kill recA strains of Escherichia coli. Sixty-three different spontaneous mutations and 13 linker insertion mutations were isolated by this method and analyzed. Extracts of cells transformed by mutant plasmids displayed variable degrees of reduction in the activity of one or both terminase subunits as assayed by in vitro lambda DNA packaging. A method of genetically mapping plasmid-borne mutations in the A gene by measuring their ability to rescue various lambda Aam phages showed that the A mutations were fairly evenly distributed across the gene. Mutant A genes were also subcloned into overproducing plasmid constructs, and it was determined that more than half of them directed the synthesis of normal amounts of full-length A protein. Three of the A gene mutants displayed dramatically reduced in vitro packaging activity only when immature (uncut) lambda DNA was used as the substrate; therefore, these mutations may lie in the endonuclease domain of terminase. Interestingly, the putative endonuclease mutations mapped in two distinct locations in the A gene separated by a least 400 bp.

Neutron and x-ray scatter studies of the histone octamer and amino and carboxyl domain trimmed octamers

The structure of the nucleosome has been under intense investigation using neutron crystallography, x-ray crystallography, and neutron solution scattering. However the dimension of the histone octamer inside the nucleosome is still a subject of controversy. The radius of gyration (Rg) of the octamer obtained from solution neutron scattering of core particles at 63% 2H2O, 37% 1H2O is 33 A, and x-ray crystallography study of isolated histone octamer gives a Rg of 32.5 A, while the reported values using x-ray crystallography of core particles from two individual studies are 29.7 and 30.4 A, respectively. We report here studies of isolated histone octamer and trypsin-limited digested octamer using both neutron solution scattering and small angle x-ray scattering. The Rg of the octamer obtained is 33 A, whereas that of the trimmed octamer is 29.8 A, similar to the structure obtained from the crystals of the core particles. The N-terminal domains of the core histones in the octamer have been shown by high resolution nuclear magnetic resonance (Schroth, G.P., Yau, P., Imai, B.S., Gatewood, J.M., and Bradbury, E.M. (1990) FEBS Lett. 268, 117-120) to be mobile and flexible; it is likely that these regions are disordered and "not seen" by x-ray crystallography.

Nucleosome linking number change controlled by acetylation of histones H3 and H4

High levels of acetylation of lysines in the amino-terminal domains of all four core histones, H2A, H2B, H3, and H4, have been shown to reduce the linking number change per nucleosome core particle in reconstituted minichromosomes (Norton, V. G., Imai, B. S., Yau, P., and Bradbury, E. M. (1989) Cell 57, 449-457). Because there is evidence to suggest that the acetylations of H3 and H4 have functions that are distinct from those of H2A and H2B, we have determined the nucleosome core particle linking number change in minichromosomes containing fully acetylated H3 and H4 and very low levels of acetylation in H2A and H2B. This linking number change was -0.81 +/- 0.05, in close agreement with the linking number change for hyperacetylated nucleosome core particles which contain high levels of acetylation in all four core histones (approximately 70% of full acetylation in H3 and H4). Therefore, high levels of acetylation of H3 and H4 alone are responsible for the reduction in the linking number change per nucleosome core particle.

Isolation and characterization of acetylated histones H3 and H4 and their assembly into nucleosomes

Nucleosome and chromatin structure/function relationships of histone acetylations are not understood. To address these questions we have developed chromatographic procedures that separate subtypes of H3 and the acetylated states of histone H3 and H4 in exceptionally pure forms. The sites of acetylation of the intermediately acetylated states of H3 have been determined and show a specific pattern of acetylation. An unexpected finding was the identification of a fifth site of acetylation in H3 at lysine 27. Nucleosome particles with fully acetylated H3 and H4 have been assembled on the Lytechinus variegatus 5 S rRNA DNA phasing sequence and characterized. These defined acetylated H3 and H4 particles migrate more slowly in polyacrylamide nucleoprotein particle gels than the control particles indicating a subtle effect of acetylation in nucleosome structure. However, DNA footprinting of these particles using DNase I show only small changes when compared to control particles over the core particle DNA length. It is shown further that H3 cysteines in the particle containing fully acetylated H3 and H4 were not accessible to iodoacetamide indicating that protein factors additional to H3 and H4 acetylation are required to make H3 cysteines accessible to the label. These findings are consistent with the proposal that histones H3, H4 acetylations exert their major effects outside of the core particle 146-base pair DNA, either on the DNA segment entering and leaving the nucleosome or possibly on the internucleosome interactions that involve the amino-terminal domains of the core histones in organization and stability of higher order chromatin structures.

A NMR study of mobility in the histone octamer

The histone octamer from chicken erythrocytes was studied in 2 M NaCl using 500 mHz 1H NMR spectroscopy. We compared the spectrum of control octamers with that of octamers isolated from trypsinized nucleosome core particles. We observe that the sharp resonances found in the spectrum of the native octamer disappear completely after trypsinization. Therefore, within the time frame of the NMR experiment, all of the mobile amino acid residues in the histone octamer are found in the well defined trypsin sensitive domains. These results indicate that there is a very clear structural demarcation between the random coil N- and C-terminal tails and the globular domains of the histones.

Histone acetylation reduces nucleosome core particle linking number change

Nucleosome core particles differing in their levels of histone acetylation have been formed on a closed circular DNA that contains a tandemly repeated 207 bp nucleosome positioning sequence. The effect of acetylation on the linking number per nucleosome particle has been determined. With increasing levels of acetylation, the negative linking number change per nucleosome decreases from -1.04 +/- 0.08 for control to -0.82 +/- 0.05 for highly acetylated nucleosomes. These results indicate that histone acetylation has the ability to release negative supercoils previously constrained by nucleosomes into a closed chromatin loop and in effect function as a eukaryotic gyrase.

Protein kinase C phosphorylates leukemia RNA polymerase II

Purified RNA polymerase II from chicken leukemia cells was found to be an effective substrate for protein kinase C but not cAMP-dependent protein kinase. Protein kinase C catalyzed the incorporation of 1-2 mol of phosphate per mol of polymerase II and the reaction was totally calcium and lipid dependent. Electrophoresis studies revealed a time-dependent increase of phosphate incorporation into RNA polymerase II subunits of 220 KDa, 180 KDa and 150 KDa, with a preferential phosphorylation of the 180 KDa polypeptide. The phosphorylated enzyme has a preference for using single-stranded DNA as the template for transcription, including transcription of the single-stranded myb oncogene sequence. Phosphoamino acid analysis indicated that both serine and threonine residues were phosphorylated at equal amounts. Phosphorylation by protein kinase C increased the affinity of substrate-polymerase binding and the initial rate of RNA synthesis, suggesting a mechanism by which gene expression can be activated by protein kinase C.

High mobility group protein 17 cross-links primarily to histone H2A in the reconstituted HMG 17-nucleosome core particle complex

The "neighbor relationship" of lamb thymus high mobility group (HMG) protein 17 to native HeLa nucleosome core particle histones in the reconstituted complex has been studied. 125I-Labeled HMG 17 was cross-linked to core histones using the protein-protein cross-linking reagent 2-iminothiolane. Specific cross-linked products were separated on a two-dimensional Triton-acid-urea/sodium dodecyl sulfate-gel system, located by autoradiography, excised, and quantified. Disulfide bonds in the cross-links were then cleaved, and the protein constituents were identified by sodium dodecyl sulfate-gel electrophoresis. HMG 17 cross-linked primarily to histone H2A while lower levels of cross-linking occurred between HMG 17 and the other histones. In contrast, cross-linking between 2 HMG 17 molecules bound on the same nucleosome core particle was relatively rare. We have concluded that H2A comprises part of the HMG 17 binding site. Less contact occurs between HMG 17 and the other core histones, and there is little contact possible between the 2 bound HMG 17 molecules. These results are in agreement with the current model for the structure of the nucleosome and the proposed binding sites for HMG 17.

Hyperacetylation of core histones does not cause unfolding of nucleosomes. Neutron scatter data accords with disc shape of the nucleosome

Recent studies report that the frictional resistance of partially acetylated core particles increases when the number of acetyl groups/particle exceeds 10 (Bode, J., Gomez-Lira, M. M. & Schröter, H. (1983) Eur. J. Biochem. 130, 437-445). This was attributed to an opening of the core particle though other explanations, e.g. unwinding of the DNA ends were also suggested. Another possible explanation is that release of the core histone N-terminal domains by acetylation increased the frictional resistance of the particle. Neutron scatter studies have been performed on core particles acetylated to different levels up to 2.4 acetates/H4 molecule. Up to this level of acetylation the neutron scatter data show no evidence for unfolding of the core particle. The fundamental scatter functions for the envelope shape and internal structure are identical to those obtained previously for bulk core particles. The structure that gave the best fit to these fundamental scatter functions was a flat disc of diameter 11-11.5 nm and of thickness 5.5-6 nm with 1.7 +/- 0.2 turns of DNA coiled with a pitch of 3.0 nm around a core of the histone octamer. The data analysis emphasizes the changes in pair distance distribution functions at relatively low contrasts, particularly when the protein is contrast matched and DNA dominates the scatter. Under these conditions there is no evidence for the unwinding of long DNA ends in the hyperacetylated core particles. The distance distribution functions go to zero between 11.5 and 12 nm which gives the maximum chord length in a particle of dimension, 11 nm X 5.5 nm. The distance distribution function for the histone octamer contains 85% of the vectors within the 7.0-nm diameter of the histone core. 15% of the histone vectors lie between 7.0 and 12.0 nm, and these are attributed to the N-terminal domains of the core histones which extend out from the central histone core. Histone vectors extending beyond 7.0 nm are necessary to account for the measured radius of gyration of the histone core of 3.3 nm. A similar value of 3.2 nm is calculated for the recent ellipsoidal shape of 11.0 X 6.5 X 6.5 nm from the crystal structure of the octamer. However, the nucleosome model based on this structure is globular, roughly 11 nm in diameter, which does not accord with the flat disc shape core particle obtained from detailed neutron scatter data nor with the cross-section radii of gyration of the histone and DNA found previously for extended chromatin in solution.

Phosphorylation of high-mobility-group proteins by the calcium-phospholipid-dependent protein kinase and the cyclic AMP-dependent protein kinase

Purified lamb thymus high-mobility-group (HMG) proteins 1, 2, and 17 have been investigated as potential substrates for the Ca2+-phospholipid-dependent protein kinase and the cAMP-dependent protein kinase. HMG proteins 1, 2, and 17 are phosphorylated by the Ca2+-phospholipid-dependent protein kinase; the reactions are totally Ca2+ and lipid dependent and are not inhibited by the inhibitor protein of the cAMP-dependent protein kinase. HMG 17 is phosphorylated predominantly in a single seryl residue, Ser 24 in the sequence Gln-Arg-Arg-Ser 24-Ala-Arg-Leu-Ser 28-Ala-Lys, with the second seryl moiety, Ser 28, modified to a markedly lesser degree. HMGs 1 and 2 are also phosphorylated in only seryl residues but with each there are multiple phosphorylation sites. HMG 17, but not HMG 1 or 2, is also phosphorylated by the cAMP-dependent protein kinase with the site phosphorylated being the minor of the two phosphorylated by the Ca2+-phospholipid-dependent protein kinase; the Km for phosphorylation by the cAMP-dependent enzyme is 50-fold higher than that by the Ca2+-phospholipid-dependent enzyme. HMG 17 is an equally effective substrate for the Ca2+-phospholipid-dependent protein kinase either as the pure protein or bound to nucleosomes. Preliminary evidence has indicated that lamb thymus HMG 14 is also a substrate for the Ca2+-phospholipid-dependent enzyme. It is phosphorylated with a Km similar to that of HMG 17 (4-6 microM), and a comparison of tryptic peptides suggests that it is phosphorylated in a site that is homologous with Ser 24 of HMG 17 and distinct from the sites phosphorylated by the cAMP-dependent protein kinase.

Effect of HMG protein 17 on the thermal stability of control and acetylated HeLa oligonucleosomes

Many studies have implicated histone acetylation and HMG proteins 14 and 17 in the structure of active chromatin. Studies of the binding of HMG 14 and 17 to chromatin core particles have shown that there are two binding sites for HMG 14 or 17 located within 20-25 bp of the DNA ends of the core particles [13-15]. Such binding sites may result from the free DNA ends in the core particle being available for the binding of HMG 14 and 17. We have studied the effects of the binding of HMG 17 on the thermal denaturation of DNA in mono, di and trinucleosomes. In each case the binding of 1 HMG 17 molecule per nucleosome reduces the DNA premelt region by 50%, while the binding of 2 HMG 17 molecules per nucleosome abolishes the premelt region. From this it is concluded that there are two HMG 17 binding sites per nucleosome which are located between the entry and exit points to the nucleosome and the strongly complexed central DNA region. Highly acetylated mono, di and trinucleosomes have been isolated from butyrate treated HeLa S3 cells. For this series of acetylated oligonucleosomes, it has been found that there are also two HMG 17 binding sites per acetylated nucleosome.

Thermal denaturation studies of acetylated nucleosomes and oligonucleosomes

The thermal melting behaviors of control and acetylated mononucleosomes, dinucleosomes and trinucleosomes have been studied. Along each series of oligonucleosomes, the melting profiles change in a manner consistent with the increasing number of nucleosomes. For the control mononucleosome, the melting profile exhibits a premelting region at about 61-64 degrees C and a major cooperative transition at 75-77 degrees C. The melting profiles of the control dinucleosomes and trinucleosomes show a premelt at 61-62 degrees C (similar to that of the nucleosome core); an intermediate transition at 73-74 degrees C for the dinucleosome and at 76-77 degrees C for the trinucleosome and a major cooperative transition at 79-80 degrees C for the dinucleosome and at 81-82 degrees C for the trinucleosome. The major cooperative transition at the highest melting temperatures in the melting profiles of the mononucleosome, dinucleosome and trinucleosome comes from the melting of the central region of DNA in the nucleosome which complexed with the core histones; the premelt region is attributed to two DNA segments per nucleosome which flank this central DNA region and are free or weakly complexed with histones. The origin of the intermediate transition found for the dinucleosomes and trinucleosomes is not fully understood but probably results from the melting of DNA at the entry to and exit from the nucleosome and the linker DNA which are complexed with histones. A very similar pattern of behavior is observed for the acetylated oligonucleosomes. Direct comparison of the melting profiles of acetylated and control mononucleosomes, dinucleosomes and trinucleosomes show that the premelt region is unaffected by histone acetylation whereas the intermediate and major cooperative transitions for the acetylated oligonucleosomes are broader and occur consistently at lower temperatures than for the controls. These differences support proposals that the N-terminal regions of core histones interact within the nucleosome and on linker DNA.

Relationships between intracisternal type A and extracellular oncornavirus-like particles produced in murine MOPC-460 myeloma cells

Oncornavirus-like particles of the "A" (both intracisternal and intracytoplasmic) and "B" or "C" (extracellular) types are produced by murine MOPC-460 myeloma cells. This communication describes a comparative study on tracisternal A and extracellular particles. Both types of particles contain an RNA-dependent DNA polymerase activity, traces of 35S and 70 S RNA in addition to larger amounts of degraded RNA, and proteins of approximately 76,000 and 45, 000 daltons. The 76,000-dalton proteins from intracisternal A and extracellular particles have the same cyanogen bromide peptides. Hybridization kinetic analysis indicates that the RNAs in the two particles are identical or very closely related and share partial homology with Moloney leukemia virus RNA. In contrast, the particles appear to have little or no relationship to murine mammary tumor virus as judged by several different criteria. Electron microscope studies indicate that the extracellular particles arise from the budding of core components through the plasma membrane. These results suggest that the intracisternal A and extracellular oncornavirus-like particles produced by MOPC-460 cells are closely related.