Fluorescence microscopy of the dynamics of supercoiling, folding, and condensation of bacterial chromosomes, induced by acridine orange

The fluorescent dye, acridine orange, was used to visualize bacterial chromosomes extending from bacteria attached to a glass surface. The acridine-induced condensation of these chromosomes was followed in real-time with a low light level video camera. Acridine orange induced the packing of the bacterial chromosome into thick bundles which underwent various forms of condensation, supercoiling, folding, and rolling into a compact particle. Filaments attached to the surface at both ends were topologically constrained and supercoiled rapidly; whereas all three patterns of condensation were noted among filaments attached at only one end or free from the surface. Kinks often appeared in the filaments prior to supercoiling or folding, and the dynamic events observed often occurred around these kinks. These observations identify several mechanisms of condensation available to higher order structures of DNA, and indicate that kinks are an important intermediate step in many of the transitions.     

Filaments from Ignicoccus hospitalis Show Diversity of Packing in Proteins Containing N-Terminal Type IV Pilin Helices

Bacterial motility is driven by the rotation of flagellar filaments that supercoil. The supercoiling involves the switching of coiled-coil protofilaments between two different states. In archaea, the flagellar filaments responsible for motility are formed by proteins with distinct homology in their N-terminal portion to bacterial Type IV pilins. The bacterial pilins have a single N-terminal hydrophobic α-helix, not the coiled coil found in flagellin. We have used electron cryo-microscopy to study the adhesion filaments from the archaeon Ignicoccus hospitalis. While I. hospitalis is non-motile, these filaments make transitions between rigid stretches and curved regions and appear morphologically similar to true archaeal flagellar filaments. A resolution of ~ 7.5 Å allows us to unambiguously build a model for the packing of these N-terminal α-helices, and this packing is different from several bacterial Type IV pili whose structure has been analyzed by electron microscopy and modeling. Our results show that the mechanism responsible for the supercoiling of bacterial flagellar filaments cannot apply to archaeal filaments.     

Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling

DNA in bacterial chromosomes and bacterial plasmids is supercoiled. DNA supercoiling is essential for DNA replication and gene regulation. However, the density of supercoiling in vivo is circa twice smaller than in deproteinized DNA molecules isolated from bacteria. What are then the specific advantages of reduced supercoiling density that is maintained in vivo? Using Brownian dynamics simulations and atomic force microscopy we show here that thanks to physiological DNA–DNA crowding DNA molecules with reduced supercoiling density are still sufficiently supercoiled to stimulate interaction between cis-regulatory elements. On the other hand, weak supercoiling permits DNA molecules to modulate their overall shape in response to physiological changes in DNA crowding. This plasticity of DNA shapes may have regulatory role and be important for the postreplicative spontaneous segregation of bacterial chromosomes.     

Chromosomal domains of supercoiling in Salmonella typhimurium

The chromosomes of enteric bacteria are divided into about 50 independently supercoiled domains. It is not known whether the net level of DNA supercoiling is similar in each domain, or whether the domains are differentially supercoiled. We have addressed this question genetically, using a supercoiling-sensitive promoter to probe the relative levels of supercoiling at defined points around the Salmonella typhimurium chromosome. We conclude that, within the limits of resolution of this approach, the level of supercoiling does not differ significantly between chromosomal domains, and that each domain responds in a similar fashion to factors that perturb supercoiling. These findings have implications for the organization of the bacterial genome.     

Micro-video study of moving bacterial flagellar filaments. I. Passive rotation by hydrodynamic force in vitro.

Moving images of reconstituted single bacterial flagellar filaments in a dark-field microscope were recorded by an ultrasensitive video camera, and then transferred to 16 mm cinefilm for quantitative analysis of the dynamic properties of the filaments.Flagellar filaments are found to attach to a glass surface at only one end (the H -end). When attached helical filaments were subjected to viscous flow of methylcellulose solution, they rotated as a result of the hydrodynamic torque generated. Occasionally, two filaments associated into a bundle and rotated coordinately in the viscous flow, even though each filament was separately attached to the glass surface. In addition, we have observed partly rotating filaments which consisted of two portions, the rotating portion being connected end-to-end to the non-rotating portion.The magnitude of the hydrodynamic torque depended on the rotational friction which was determined by the manner of attachment. Based on hydrodynamic calculations, values of ?5 × 10^?12 and ?1 × 10^?13 dyne cm were obtained for the average torque for rotating filaments on glass and partly rotating filaments, respectively, in viscous fluid at a flow rate of 15 μm/s.     

Dense bodies of the contractile system of cardiac muscle in Venus mercenaria

Dense bodies in the heart muscle of Venus mercenaria exist in two forms, free and attached. Free dense bodies morphologically consist of fascicles of thin filaments in parallel array and bound together by a dense, amorphous proteinaceous material. The binding of dense bodies to the cell membrane is effected via connecting filaments of the amorphous material of the dense body which join a condensation of morphologically similar material attached to the inner osmiophilic layer of the unit membrane. This composite of dense body, connecting filaments, membrane condensation and unit cell membrane has been termed collectively the attachment plaque. The attachment plaque is part of an extensive network on the cell surface which obligates that surface to a role in the contractile process. Moreover, this set of attachment plaques imposes an organization and an orientation to most thin filaments of the cell and preserves the contractile axis of the cell.     

Novel, Attached, Sulfur-Oxidizing Bacteria at Shallow Hydrothermal Vents Possess Vacuoles Not Involved in Respiratory Nitrate Accumulation

Novel, vacuolate sulfur bacteria occur at shallow hydrothermal vents near White Point, Calif. There, these filaments are attached densely to diverse biotic and abiotic substrates and extend one to several centimeters into the surrounding environment, where they are alternately exposed to sulfidic and oxygenated seawater. Characterizations of native filaments collected from this location indicate that these filaments possess novel morphological and physiological properties compared to all other vacuolate bacteria characterized to date. Attached filaments, ranging in diameter from 4 to 100 μm or more, were composed of cylindrical cells, each containing a thin annulus of sulfur globule-filled cytoplasm surrounding a large central vacuole. A near-complete 16S rRNA gene sequence was obtained and confirmed by fluorescent in situ hybridization to be associated only with filaments having a diameter of 10 μm or more. Phylogenetic analysis indicates that these wider, attached filaments form within the gamma proteobacteria a monophyletic group that includes all previously described vacuolate sulfur bacteria (the genera Beggiatoa, Thioploca, and Thiomargarita) and no nonvacuolate genera. However, unlike for all previously described vacuolate bacteria, repeated measurements of cell lysates from samples collected over 2 years indicate that the attached White Point filaments do not store internal nitrate. It is possible that these vacuoles are involved in transient storage of oxygen or contribute to the relative buoyancy of these filaments.     

Spermiogenesis in an iceryine coccid,Steatococcus tuberculatus morrison

The spermatozoon of Steatococcus is a motile filament containing a core of two chromosomes arranged in tandem and surrounded by more than 80 microtubules in 2 1/2 concentric rings. Two sperm develop from each binucleate spermatid in the form of long papillae. From the zone corresponding to the pole of the previous division microtubules appear and lengthen, assembly apparently occurring at their proximal undifferentiated ends. As they extend, they presumably push out the cytoplasmic papilla and co-extend a nuclear papilla through bridges with the nuclear envelope. Chromatin, attached to the envelope, is thus carried into the papilla, the shorter chromosome in the lead. 100 Å chromatin filaments are reduced to 20 Å and aligned as they enter the papilla. The filaments transform into 100 Å tubular fibrils, presumably by supercoiling. These then pack hexagonally, aggregate further into packed axial filaments, and finally condense into a nearly solid core in the mature sperm. Completed papillae (sperm) detach from the spermatid leaving behind nuclei devoid of chromatin. Following cycles of spiralization and despiralization, the sperm are bundled into hexagonal packs of 32 in register by cyst wall cells. The latter form primary and secondary sheaths and lay down a matrix within the bundle. As originally reported by Hughes Schrader (1946), no evidence of centriole, acrosome, mitochondrial derivative or structure suggesting flagellar axoneme is found in either the developing papilla or the mature sperm. The microtubules determine the axis of the developing sperm; polarity is set by the direction of sperm motion and is homologous with most flagellate sperm in that the nuclear material is anterior and the microtubule initiating center is posterior. All of the functions attributed to microtubules are manifest in differentiation of this sperm: extension, support, translocation and motility.This paper is affectionately dedicated to Professor Sally Hughes-Schrader on the occasion of her seventy-fifth birthday, with warm appreciation of her friendship, her exemplary science, her keen criticism, her contagious enthusiasm, and for leading me to Steatococcus.     

New observations on the twisted arrangement of Dinoflagellate chromosomes

The Dinoflagellate Prorocentrum micans has been studied in classical and high voltage transmission electron microscopy, with the help of a goniometric stage. The general structure of the nucleus is analysed with special reference to the links observed between chromosomes and the nuclear envelope, the nucleoplasm and the nucleolus. The chromosomes present stacked series of nested arcs which are studied in detail. The sense of the arcs can be changed by a simple tilt of the section. These arcs do not correspond to DNA filaments with a genuine bend but to an illusion created by the overlap of layers of filaments whose orientation turns along the chromosome axis. — The transversal orientation of DNA and the examination of defects allow to rule out the polytenic hypothesis. It is clear that this hypothesis does not apply to bacterial nucleoids, which however can form series of nested arcs as in Dinoflagellate chromosomes. — The twisted arrangement of Dinoflagellate chromosomes is that of a liquid crystal of the cholesteric type. DNA is known to self assemble into cholesteric phases and this affords informations on the origin of the elongated shape of chromosomes and on the mechanisms of condensation and aggregation observed in this particular chromatin.     

NaCl-Induced Chromatin Condensation. Application of Static Light Scattering at 90° and Stopped Flow Technique

Abstract

We have studied the NaCl-induced condensation of calf thymus chromatin by static light scattering of 90° and shown that the increase in NaCl concentration up to 120–170 mM results in a large increase in scattering intensity of the total chromatin. Histones H1-depleted and trypsinized chromatin preparations do not reveal such a large increase in scattering intensity. The increase in the scattering intensity reflects the folding of the chromatin filaments, but not their aggregation. We have used this effect to monitor the kinetics of the chromatin condensation in response to a jump to higher NaCl concnetrations by means of a stopped-flow technique. The results show that the condensation is a fast complex process consisting of at least two steps. The first step is only partially resolved by the stopped-flow apparatus. The second step has a time constant in the range of 20–50 ms, which does not depend on chromatin concentration.     

Partitioning of the Escherichia coli chromosome: superhelicity and condensation

Segregation in Escherichia coli, the process of separating the replicated chromosomes into daughter progeny cells, seems to start long before the duplication of the genome reaches completion. Soon after initiation in mid-cell region, the daughter oriCs rapidly move apart to fixed positions inside the cell (quarter length positions from each pole) and are anchored there by yet unknown mechanism(s). As replication proceeds, the rest of the chromosome is sequentially unwound and then refolded. At termination, the two sister chromosomes are unlinked by decatenation and separated by supercoiling and/or condensation. Muk and Seq proteins are involved in different stages of this replication-cum-partition process and thus can be categorized as important partition proteins along with topoisomerases. E. coli strains, lacking mukB or seqA functions, are defective in segregation and cell division. The nucleoids in these mutant strains exhibit altered condensation and superhelicity as can be demonstrated by sedimentation analysis and by fluorescence microscopy. As the supercoiling of an extrachromosomal element (a plasmid DNA) was also influenced by the mukB and seqA mutations we concluded that the MukB and SeqA proteins are possibly involved in maintaining the general supercoiling activity in the cell. The segregation of E. coli chromosome might therefore be predominantly driven by factors that operate by affecting the superhelicity and condensation of the nucleoid (MukB, SeqA, topoisomerases and additional unknown proteins). A picture thus emerges in which replication and partition are no longer compartmentalized into separable stages with clear gaps (S and M phases in eukaryotes) but are parallel processes that proceed concomitantly through a cell cycle continuum.     

Looping Probabilities in Model Interphase Chromosomes

Fluorescence in-situ hybridization (FISH) and chromosome conformation capture (3C) are two powerful techniques for investigating the three-dimensional organization of the genome in interphase nuclei. The use of these techniques provides complementary information on average spatial distances (FISH) and contact probabilities (3C) for specific genomic sites. To infer the structure of the chromatin fiber or to distinguish functional interactions from random colocalization, it is useful to compare experimental data to predictions from statistical fiber models. The current estimates of the fiber stiffness derived from FISH and 3C differ by a factor of 5. They are based on the wormlike chain model and a heuristic modification of the Shimada-Yamakawa theory of looping for unkinkable, unconstrained, zero-diameter filaments. Here, we provide an extended theoretical and computational framework to explain the currently available experimental data for various species on the basis of a unique, minimal model of decondensing chromosomes: a kinkable, topologically constraint, semiflexible polymer with the (FISH) Kuhn length of l_K = 300 nm, 10 kinks per Mbp, and a contact distance of 45 nm. In particular: 1), we reconsider looping of finite-diameter filaments on the basis of an analytical approximation (novel, to our knowledge) of the wormlike chain radial density and show that unphysically large contact radii would be required to explain the 3C data based on the FISH estimate of the fiber stiffness; 2), we demonstrate that the observed interaction frequencies at short genomic lengths can be explained by the presence of a low concentration of curvature defects (kinks); and 3), we show that the most recent experimental 3C data for human chromosomes are in quantitative agreement with interaction frequencies extracted from our simulations of topologically confined model chromosomes.     

Helical reconstruction of Salmonella and Shigella needle filaments attached to type 3 basal bodies

Gram-negative pathogens evolved a syringe-like nanomachine, termed type 3 secretion system, to deliver protein effectors into the cytoplasm of host cells. An essential component of this system is a long helical needle filament that protrudes from the bacterial surface and connects the cytoplasms of the bacterium and the eukaryotic cell. Previous structural research was predominantly focused on reconstituted type 3 needle filaments, which lacked the biological context. In this work we introduce a facile procedure to obtain high-resolution cryo-EM structure of needle filaments attached to the basal body of type 3 secretion systems. We validate our approach by solving the structure of Salmonella PrgI filament and demonstrate its utility by obtaining the first high-resolution cryo-EM reconstruction of Shigella MxiH filament. Our work paves the way to systematic structural characterization of attached type 3 needle filaments in the context of mutagenesis studies, protein structural evolution and drug development.     

Mitotic Chromosome Structure: Reproducibility of Folding and Symmetry between Sister Chromatids

Mitotic chromosome structure and pathways of mitotic condensation remain unknown. The limited amount of structural data on mitotic chromosome structure makes it impossible to distinguish between several mutually conflicting models. Here we used a Chinese hamster ovary cell line with three different lac operator-tagged vector insertions distributed over an ∼1 μm chromosome arm region to determine positioning reproducibility, long-range correlation in large-scale chromatin folding, and sister chromatid symmetry in minimally perturbed, metaphase chromosomes. The three-dimensional positions of these lac operator-tagged spots, stained with lac repressor, were measured in isolated metaphase chromosomes relative to the central chromatid axes labeled with antibodies to topoisomerase II. Longitudinal, but not axial, positioning of spots was reproducible but showed intrinsic variability, up to ∼300 nm, between sister chromatids. Spot positions on the same chromatid were uncorrelated, and no correlation or symmetry between the positions of corresponding spots on sister chromatids was detectable, showing the absence of highly ordered, long-range chromatin folding over tens of mega-basepairs. Our observations are in agreement with the absence of any regular, reproducible helical, last level of chromosome folding, but remain consistent with any hierarchical folding model in which irregularity in folding exists at one or multiple levels.     

Effect of Organic Effectors on Chromatin Solubility,DNA-Histone H1 Interactions,DNA and Histone HI Structures

Abstract

We have extended our previous investigations on the effect of organic osmolytes (glycine, proline, taurine, mannitol, sorbitol and trimethylammonium oxide (TMAO)) on chromatin solubility, to the study of their influence on DNA stability and DNA-histone interactions. Our aim was to understand the molecular origin of the protection effects observed.

To this end, we determined the amount of histone H1 required to precipitate DNA or H1-depleted chromatin, at various salt concentrations, in the presence of the above mentioned organic compounds. We found a shift of the H1/DNA ratio required to reach 50% precipitation, towards higher values. Taurine was the most efficient compound followed by mannitol and glycine, then sorbitol and proline. On the contrary, TMAO favoured the precipitation process. We attempted to interpret these results on the basis of Manning's counterion condensation theory.

Changes in histone H1 structure folding and in DNA melting temperature T_m were also analyzed. Glycine, taurine, sorbitol and TMAO increased the degree of secondary structure folding of the protein while mannitol and sorbitol had no effect. Taurine, glycine and proline decreased the T_m of DNA TMAO largely destabilized DNA but mannitol and sorbitol had no effect

Measurements of NaC1 activity in the presence of organic osmolytes did not reveal sufficiently large changes to account for their protection effect against chromatin precipitation. The osmotic coefficient j of the organic effectors solutions increased in the order : taurine < glycine < sorbitol < mannitol < proline ? TMAO. For the two latter compounds, the j values increased above 1 at high concentration.

We consider that the organic compounds investigated maybe classified into three categories : (i) class I (zwitterionic compounds : glycine, proline, taurine) would produce sodium ions release from the DNA surface; (ii) class II (the very polar molecule TMAO) would increase sodium counterions condensation on DNA together with histone HI folding; (iii) class III compounds (mannitol and sorbitol) would possibly produce a modification of NaCl activity but no definite explanation could be found for the complex behavior of these compounds.     

Visualization of early chromosome condensation: a hierarchical folding, axial glue model of chromosome structure

Current models of mitotic chromosome structure are based largely on the examination of maximally condensed metaphase chromosomes. Here, we test these models by correlating the distribution of two scaffold components with the appearance of prophase chromosome folding intermediates. We confirm an axial distribution of topoisomerase IIalpha and the condensin subunit, structural maintenance of chromosomes 2 (SMC2), in unextracted metaphase chromosomes, with SMC2 localizing to a 150-200-nm-diameter central core. In contrast to predictions of radial loop/scaffold models, this axial distribution does not appear until late prophase, after formation of uniformly condensed middle prophase chromosomes. Instead, SMC2 associates throughout early and middle prophase chromatids, frequently forming foci over the chromosome exterior. Early prophase condensation occurs through folding of large-scale chromatin fibers into condensed masses. These resolve into linear, 200-300-nm-diameter middle prophase chromatids that double in diameter by late prophase. We propose a unified model of chromosome structure in which hierarchical levels of chromatin folding are stabilized late in mitosis by an axial "glue."     

The Role of the Central Globular Domain of Histone H5 in Chromatin Structure

Abstract

Histone H5 contains three tryosines in the central, a polar region of the molecule. All three tryosines can be spin labeled at low ionic strength. When the central globular domain is folded at high ionic strength, only one tyrosine becomes accessible to the imidazole spin label. Spin labeling the buried tyrosines prevents the folding of the globular structure, which, in turn, affects the proper binding of the H5 molecule to stripped chromatin. Chromatin complexes reconstituted from such an extensively modified H5 molecule show a weaker protection of the 168 base pair chromatosome during nuclease digestion. However, when only the surface tyrosine of the H5 molecule is labeled, such a molecule can still bind correctly to stripped chromatin, yielding a complex very similar to that of native chromatin. Our data supports the idea that not just the presence of the linker histone H5, but the presence of an intact H5 molecule with a folded, globular central domain is essential in the recognition of its specific binding sites on the nucleosomes. Our data also show that during the chromatin condensation process, the tumbling environment of the spin label attached to the surface tyrosine in the H5 molecule is not greatly hindered but remains partially mobile. This suggests that either the labeled domain of the H5 molecule is not directly involved in the condensation process or the formation of the higher-order chromatin structure does not result in a more viscous or tighter environment around the spin label. The folded globular domain of H5 molecule serves in stabilizing the nucleosome structure, as well as the higherorder chromatin structure.     

Molecular identification of bacteria associated with filaments of Nodularia spumigena and their effect on the cyanobacterial growth

Colonial and filamentous cyanobacteria frequently have bacteria associated with their extracellular mucus zone or more tightly attached to their cells surface. The toxin-producing cyanobacterium Nodularia spumigena is an important component of the Baltic Sea plankton community, and its filaments are likely to provide a microenvironment suitable for the development of a particular bacteria flora. In the present work, 13 bacterial strains associated with filaments of N. spumigena from the Baltic Sea were isolated and identified by sequencing the 16S rRNA gene. Different bacterial lineages were found associated with the cyanobacterial filaments, including the alpha, beta, and gamma subdivisions of the class Proteobacter and the division Firmicutes (Gram-positive bacteria). Several 16S rRNA gene sequences were not closely related to previously reported sequences of cultured bacteria from the Baltic Sea or to any other reported sequence. Conversely, sequences related to the gamma Proteobacter genus Shewanella, a group previously described in the Baltic Sea, were found among the isolates. The bacterial isolates were grown and added to cultures of exponentially growing N. spumigena. Five isolates, related to the alpha and gamma Proteobacter and Firmicutes, affected negatively the cyanobacterial growth, leading to a lower biomass yield up to 38% relative to controls with no bacteria addition. Five gamma Proteobacter-related strains had no effect on the cyanobacterial growth, while three strains related to Shewanella baltica had a positive effect. Although none of the bacterial isolates showed strong algicidal effect, the observed stimulatory and retarding effects on N. spumigena growth under culture conditions denotes the importance of the associated bacterial community for the dynamics of these cyanobacterial populations in nature. Moreover, several new taxa recovered in this study probably belong to species not yet described.     

Escherichia coli DNA topoisomerase I mutants: Increased supercoiling is corrected by mutations near gyrase genes

Bacterial chromosomes and plasmid (pBR322) DNA from topoisomerase I-defective Escherichia coli strains have been characterized with respect to superhelical density. The topoisomerase I defect results in increased negative superhelical density of both the bacterial chromosome and pBR322. Thus topoisomerase I is involved in determining the level of supercoiling in bacteria. Three of the topoisomerase I-defective strains we studied carry secondary mutations that decrease superhelical density; these additional mutations are closely linked to the gyrB locus in two of the strains and to the gyrA locus in the third strain.