Liquid-crystalline mesophases of plasmid DNA in bacteria

Hypothesis: bacteria live on the edge of phase transitions with a cell cycle regulated by a water-clock

A fundamental problem in biology is how cells obtain the reproducible, coherent phenotypes needed for natural selection to act or, put differently, how cells manage to limit their exploration of the vastness of phenotype space. A subset of this problem is how they regulate their cell cycle. Bacteria, like eukaryotic cells, are highly structured and contain scores of hyperstructures or assemblies of molecules and macromolecules. The existence and functioning of certain of these hyperstructures depend on phase transitions. Here, I propose a conceptual framework to facilitate the development of water-clock hypotheses in which cells use water to generate phenotypes by living 'on the edge of phase transitions'. I give an example of such a hypothesis in the case of the bacterial cell cycle and show how it offers a relatively novel 'view from here' that brings together a range of different findings about hyperstructures, phase transitions and water and that can be integrated with other hypotheses about differentiation, metabolism and the origins of life.

Hunting the Cell Cycle Snark

In this very personal hunt for the meaning of the bacterial cell cycle, the snark, I briefly revisit and update some of the mechanisms we and many others have proposed to regulate the bacterial cell cycle. These mechanisms, which include the dynamics of calcium, membranes, hyperstructures, and networks, are based on physical and physico-chemical concepts such as ion condensation, phase transition, crowding, liquid crystal immiscibility, collective vibrational modes, reptation, and water availability. I draw on ideas from subjects such as the 'prebiotic ecology' and phenotypic diversity to help with the hunt. Given the fundamental nature of the snark, I would expect that its capture would make sense of other parts of biology. The route, therefore, followed by the hunt has involved trying to answer questions like "why do cells replicate their DNA?", "why is DNA replication semi-conservative?", "why is DNA a double helix?", "why do cells divide?", "is cell division a spandrel?", and "how are catabolism and anabolism balanced?". Here, I propose some relatively unexplored, experimental approaches to testing snark-related hypotheses and, finally, I propose some possibly original ideas about DNA packing, about phase separations, and about computing with populations of virtual bacteria.

Determination of DNA architecture of bacteria under various types of stress, methodological approaches, problems, and solutions

Actively growing cells maintain a dynamic, far from equilibrium order through metabolism. Under starvation stress or under stress of exposure to the analog of the anabiosis autoinducer (4-hexylresorcinol), cells go into a dormant state (almost complete lack of metabolism) or even into a mummified state. In a dormant state, cells are forced to use the physical mechanisms of DNA protection. The architecture of DNA in the dormant and mummified state of cells was studied by x-ray diffraction of synchrotron radiation and transmission electron microscopy (TEM). Diffraction experiments indicate the appearance of an ordered organization of DNA. TEM made it possible to visualize the type of DNA ordering. Intracellular nanocrystalline, liquid-crystalline, and folded nucleosome-like structures of DNA have been found. The structure of DNA within a cell in an anabiotic dormant state and dormant state (starvation stress) coincides (forms nanocrystalline structures). Data suggest the universality of DNA condensation by a protein Dps for a dormant state, regardless of the type of stress. The mummified state is very different in structure from the dormant state (has no ordering within a cell). It turned out that it is possible to visualize DNA conformation in toroidal and liquid crystal structures in which there is either no or a very small amount of the Dps protein. Observation of the DNA conformation in nanocrystals and folded nucleosome-like structures so far has been inconclusive. The methodological advances described will facilitate high-resolution visualization of the DNA conformation in the near future.

Morphological Diversity of Dps Complex with Genomic DNA

In response to adverse environmental factors, Escherichia coli cells actively produce Dps proteins which form ordered complexes (biocrystals) with bacterial DNA to protect the genome. The effect of biocrystallization has been described extensively in the scientific literature; furthermore, to date, the structure of the Dps-DNA complex has been established in detail in vitro using plasmid DNA. In the present work, for the first time, Dps complexes with E. coli genomic DNA were studied in vitro using cryo-electron tomography. We demonstrate that genomic DNA forms one-dimensional crystals or filament-like assemblies which transform into weakly ordered complexes with triclinic unit cells, similar to what is observed for plasmid DNA. Changing such environmental factors as pH and KCl and MgCl₂ concentrations leads to the formation of cylindrical structures.

Nucleoid-Associated Proteins HU and IHF: Oligomerization in Solution and Hydrodynamic Properties

Structure and function of bacterial nucleoid is controlled by the nucleoid-associated proteins (NAP). In any phase of growth, various NAPs, acting sequentially, condense nucleoid and facilitate formation of its transcriptionally active structure. However, in the late stationary phase, only one of the NAPs, Dps protein, is strongly expressed, and DNA-protein crystals are formed that transform nucleoid into a static, transcriptionally inactive structure, effectively protected from the external influences. Discovery of crystal structures in living cells and association of this phenomenon with the bacterial resistance to antibiotics has aroused great interest in studying this phenomenon. The aim of this work is to obtain and compare structures of two related NAPs (HU and IHF), since they are the ones that accumulate in the cell at the late stationary stage of growth, which precedes formation of the protective DNA-Dps crystalline complex. For structural studies, two complementary methods were used in the work: small-angle X-ray scattering (SAXS) as the main method for studying structure of proteins in solution, and dynamic light scattering as a complementary one. To interpret the SAXS data, various approaches and computer programs were used (in particular, the evaluation of structural invariants, rigid body modeling and equilibrium mixture analysis in terms of the volume fractions of its components were applied), which made it possible to determine macromolecular characteristics and obtain reliable 3D structural models of various oligomeric forms of HU and IHF proteins with ~2 nm resolution typical for SAXS. It was shown that these proteins oligomerize in solution to varying degrees, and IHF is characterized by the presence of large oligomers consisting of initial dimers arranged in a chain. An analysis of the experimental and published data made it possible to hypothesize that just before the Dps expression, it is IHF that forms toroidal structures previously observed in vivo and prepares the platform for formation of DNA-Dps crystals. The results obtained are necessary for further investigation of the phenomenon of biocrystal formation in bacterial cells and finding ways to overcome resistance of various pathogens to external conditions.

A liquid crystal world for the origins of life

Nucleic acids (NAs) in modern biology accomplish a variety of tasks, and the emergence of primitive nucleic acids is broadly recognized as a crucial step for the emergence of life. While modern NAs have been optimized by evolution to accomplish various biological functions, such as catalysis or transmission of genetic information, primitive NAs could have emerged and been selected based on more rudimental chemical-physical properties, such as their propensity to self-assemble into supramolecular structures. One such supramolecular structure available to primitive NAs are liquid crystal (LC) phases, which are the outcome of the collective behavior of short DNA or RNA oligomers or monomers that self-assemble into linear aggregates by combinations of pairing and stacking. Formation of NA LCs could have provided many essential advantages for a primitive evolving system, including the selection of potential genetic polymers based on structure, protection by compartmentalization, elongation, and recombination by enhanced abiotic ligation. Here, we review recent studies on NA LC assembly, structure, and functions with potential prebiotic relevance. Finally, we discuss environmental or geological conditions on early Earth that could have promoted (or inhibited) primitive NA LC formation and highlight future investigation axes essential to further understanding of how LCs could have contributed to the emergence of life.

Formation of Iron Oxide Nanoparticles in the Internal Cavity of Ferritin-Like Dps Protein: Studies by Anomalous X-Ray Scattering

DNA-binding protein from starved cells (Dps) takes a special place among dodecamer mini-ferritins. Its most important function is protection of bacterial genome from various types of destructive external factors via in cellulo Dps-DNA co-crystallization. This protective response results in the emergence of bacterial resistance to antibiotics and other drugs. The protective properties of Dps have attracted a significant attention of researchers. However, Dps has another equally important functional role. Being a ferritin-like protein, Dps acts as an iron depot and protects bacterial cells from the oxidative damage initiated by the excess of iron. Here we investigated formation of iron oxide nanoparticles in the internal cavity of the Dps dodecamer. We used anomalous small-angle X-ray scattering as the main research technique, which allows to examine the structure of metal-containing biological macromolecules and to analyze the size distribution of metal nanoparticles formed in them. The contributions of protein and metal components to total scattering were distinguished by varying the energy of the incident X-ray radiation near the edge of the metal atom absorption band (the K-band for iron). We examined Dps specimens containing 50, 500, and 2000 iron atoms per protein dodecamer. Analysis of the particle size distribution showed that, depending on the iron content in the solution, the size of the nanoparticles formed inside the protein molecule was 2 to 4 nm and the growth of metal nanoparticles was limited by the size of the protein inner cavity. We also found some amount of iron ions in the Dps surface layer. This layer is very important for the protein to perform its protective functions, since the surface-located N-terminal domains determine the nature of interactions between Dps and DNA. In general, the results obtained in this work can be useful for the next step in studying the Dps phenomenon, as well as in creating biocompatible and solution-stabilized metal nanoparticles.

Topological fine structure of smectic grain boundaries and tetratic disclination lines within three-dimensional smectic liquid crystals

Observing and characterizing the complex ordering phenomena of liquid crystals subjected to external constraints constitutes an ongoing challenge for chemists and physicists alike. To elucidate the delicate balance appearing when the intrinsic positional order of smectic liquid crystals comes into play, we perform Monte-Carlo simulations of rod-like particles in a range of cavities with a cylindrical symmetry. Based on recent insights into the topology of smectic orientational grain boundaries in two dimensions, we analyze the emerging three-dimensional defect structures from the perspective of tetratic symmetry. Using an appropriate three-dimensional tetratic order parameter constructed from the Steinhardt order parameters, we show that those grain boundaries can be interpreted as a pair of tetratic disclination lines that are located on the edges of the nematic domain boundary. Thereby, we shed light on the fine structure of grain boundaries in three-dimensional confined smectics.

Spatial organization of Dps and DNA-Dps complexes

DNA co-crystallization with Dps family proteins is a fundamental mechanism, which preserves DNA in bacteria from harsh conditions. Though many aspects of this phenomenon are well characterized, the spatial organization of DNA in DNA-Dps co-crystals is not completely understood, and existing models need further clarification. To advance in this problem we have utilized atomic force microscopy (AFM) as the main structural tool, and small-angle X-scattering (SAXS) to characterize Dps as a key component of the DNA-protein complex. SAXS analysis in the presence of EDTA indicates a significantly larger radius of gyration for Dps than would be expected for the core of the dodecamer, consistent with the N-terminal regions extending out into solution and being accessible for interaction with DNA. In AFM experiments, both Dps protein molecules and DNA-Dps complexes adsorbed on mica or highly oriented pyrolytic graphite (HOPG) surfaces form densely packed hexagonal structures with a characteristic size of about 9 nm. To shed light on the peculiarities of DNA interaction with Dps molecules, we have characterized individual DNA-Dps complexes. Contour length evaluation has confirmed the non-specific character of Dps binding with DNA and revealed that DNA does not wrap Dps molecules in DNA-Dps complexes. Angle analysis has demonstrated that in DNA-Dps complexes a Dps molecule contacts with a DNA segment of ~6 nm in length. Consideration of DNA condensation upon complex formation with small Dps quasi-crystals indicates that DNA may be arranged along the rows of ordered protein molecules on a Dps sheet.

Chromosomal Organization and Regulation of Genetic Function in Escherichia coli Integrates the DNA Analog and Digital Information

In this article, we summarize our current understanding of the bacterial genetic regulation brought about by decades of studies using the Escherichia coli model. It became increasingly evident that the cellular genetic regulation system is organizationally closed, and a major challenge is to describe its circular operation in quantitative terms. We argue that integration of the DNA analog information (i.e., the probability distribution of the thermodynamic stability of base steps) and digital information (i.e., the probability distribution of unique triplets) in the genome provides a key to understanding the organizational logic of genetic control. During bacterial growth and adaptation, this integration is mediated by changes of DNA supercoiling contingent on environmentally induced shifts in intracellular ionic strength and energy charge. More specifically, coupling of dynamic alterations of the local intrinsic helical repeat in the structurally heterogeneous DNA polymer with structural-compositional changes of RNA polymerase holoenzyme emerges as a fundamental organizational principle of the genetic regulation system. We present a model of genetic regulation integrating the genomic pattern of DNA thermodynamic stability with the gene order and function along the chromosomal OriC-Ter axis, which acts as a principal coordinate system organizing the regulatory interactions in the genome.

Polymorphic Protective Dps-DNA Co-Crystals by Cryo Electron Tomography and Small Angle X-Ray Scattering

Rapid increase of intracellular synthesis of specific histone-like Dps protein that binds DNA to protect the genome against deleterious factors leads to in cellulo crystallization—one of the most curious processes in the area of life science at the moment. However, the actual structure of the Dps–DNA co-crystals remained uncertain in the details for more than two decades. Cryo-electron tomography and small-angle X-ray scattering revealed polymorphous modifications of the co-crystals depending on the buffer parameters. Two different types of the Dps–DNA co-crystals are formed in vitro: triclinic and cubic. Three-dimensional reconstruction revealed DNA and Dps molecules in cubic co-crystals, and the unit cell parameters of cubic lattice were determined consistently by both methods.

Architectural Organization of Dinoflagellate Liquid Crystalline Chromosomes

Dinoflagellates have some of the largest genome sizes, but lack architectural nucleosomes. Their liquid crystalline chromosomes (LCCs) are the only non-architectural protein-mediated chromosome packaging systems, having high degrees of DNA superhelicity, liquid crystalline condensation and high levels of chromosomal divalent cations. Recent observations on the reversible decompaction–recompaction of higher-order structures implicated that LCCs are composed of superhelical modules (SPMs) comprising highly supercoiled DNA. Orientated polarizing light photomicrography suggested the presence of three compartments with different packaging DNA density in LCCs. Recent and previous biophysical data suggest that LCCs are composed of: (a) the highly birefringent inner core compartment (i) with a high-density columnar-hexagonal mesophase (CH-m); (b) the lower-density core surface compartment (ii.1) consisting of a spiraling chromonema; (c) the birefringent-negative periphery compartment (ii.2) comprising peripheral chromosomal loops. C(ii.1) and C(ii.2) are in dynamic equilibrium, and can merge into a single compartment during dinomitosis, regulated through multiphasic reversible soft-matter phase transitions.

Distinctive Nuclear Features of Dinoflagellates with A Particular Focus on Histone and Histone-Replacement Proteins

Dinoflagellates are important eukaryotic microorganisms that play critical roles as producers and grazers, and cause harmful algal blooms. The unusual nuclei of dinoflagellates "dinokaryon" have led researchers to investigate their enigmatic nuclear features. Their nuclei are unusual in terms of their permanently condensed nucleosome-less chromatin, immense genome, low protein to DNA ratio, guanine-cytosine rich methylated DNA, and unique mitosis process. Furthermore, dinoflagellates are the only known group of eukaryotes that apparently lack histone proteins. Over the course of evolution, dinoflagellates have recruited other proteins, e.g., histone-like proteins (HLPs), from bacteria and dinoflagellates/viral nucleoproteins (DVNPs) from viruses as histone substitutes. Expression diversity of these nucleoproteins has greatly influenced the chromatin structure and gene expression regulation in dinoflagellates. Histone replacement proteins (HLPs and DVNPs) are hypothesized to perform a few similar roles as histone proteins do in other eukaryotes, i.e., gene expression regulation and repairing DNA. However, their role in bulk packaging of DNA is not significant as low amounts of proteins are associated with the gigantic genome. This review intends to summarize the discoveries encompassing unique nuclear features of dinoflagellates, particularly focusing on histone and histone replacement proteins. In addition, a comprehensive view of the evolution of dinoflagellate nuclei is presented.

Hierarchical Biomineralization: from Nature's Designs to Synthetic Materials for Regenerative Medicine and Dentistry

Biomineralization is a highly dynamic, yet controlled, process that many living creatures employ to develop functional tissues such as tooth enamel, bone, and others. A major goal in materials science is to create bioinspired functional structures based on the precise organization of building blocks across multiple length scales. Therefore, learning how nature has evolved to use biomineralization could inspire new ways to design and develop synthetic hierarchical materials with enhanced functionality. Toward this goal, this review dissects the current understanding of structure-function relationships of dental enamel and bone using a materials science perspective and discusses a wide range of synthetic technologies that aim to recreate their hierarchical organization and functionality. Insights into how these strategies could be applied for regenerative medicine and dentistry are also provided.

Photochemical analysis of structural transitions in DNA liquid crystals reveals differences in spatial structure of DNA molecules organized in liquid crystalline form

The anisotropic shape of DNA molecules allows them to form lyotropic liquid crystals (LCs) at high concentrations. This liquid crystalline arrangement is also found in vivo (e.g., in bacteriophage capsids, bacteria or human sperm nuclei). However, the role of DNA liquid crystalline organization in living organisms still remains an open question. Here we show that in vitro, the DNA spatial structure is significantly changed in mesophases compared to non-organized DNA molecules. DNA LCs were prepared from pBluescript SK (pBSK) plasmid DNA and investigated by photochemical analysis of structural transitions (PhAST). We reveal significant differences in the probability of UV-induced pyrimidine dimer photoproduct formation at multiple loci on the DNA indicative of changes in major groove architecture.

The dependency of twist-bend nematic liquid crystals on molecular structure: a progression from dimers to trimers, oligomers and polymers

This article gives an overview on recent developments concerning the twist-bend nematic phase. The twist-bend nematic phase has been discussed as the missing link between the uniaxial nematic mesophase (N) and the helical chiral nematic phase (N*). After an introduction discussing the key physical properties of the N_TB phase and the methods used to identify the twist-bend nematic mesophase this review focuses on structure property relationships and molecular features that govern the incidence of this phase.

A review of immune amplification via ligand clustering by self-assembled liquid-crystalline DNA complexes

We examine how the interferon production of plasmacytoid dendritic cells is amplified by the self-assembly of liquid-crystalline antimicrobial peptide/DNA complexes. These specialized dendritic cells are important for host defense because they quickly release large quantities of type I interferons in response to infection. However, their aberrant activation is also correlated with autoimmune diseases such as psoriasis and lupus. In this review, we will describe how polyelectrolyte self-assembly and the statistical mechanics of multivalent interactions contribute to this process. In a more general compass, we provide an interesting conceptual corrective to the common notion in molecular biology of a dichotomy between specific interactions and non-specific interactions, and show examples where one can construct exquisitely specific interactions using non-specific interactions.

Milliscale Self-Integration of Megamolecule Biopolymers on a Drying Gas-Aqueous Liquid Crystalline Interface

A drying environment is always a proposition faced by dynamic living organisms using water, which are driven by biopolymer-based micro- and macrostructures. Here, we introduce a drying process for aqueous liquid crystalline (LC) solutions composed of biopolymer with extremely high molecular weight components such as polysaccharides, cytoskeletal proteins, and DNA. On controlling the mobility of the LC microdomain, the solutions showed milliscale self-integration starting from the unstable gas-LC interface during drying. In particular, we first identified giant rod-like microdomains (∼1 μm diameter and more than 20 μm length) of the mega-molecular polysaccharide, sacran, which is remarkably larger than other polysaccharides. These microdomains led to the formation of a single milliscale macrodomain on the interface. In addition, the dried polymer films on a solid substrate also revealed that such integration depends on the size of the microdomain. We envision that this simple drying method will be useful not only for understanding the biopolymer hierarchization at the macroscale level but also for preparation of surfaces with direction controllability, as seen in living organisms, for use in various fields such as diffusion, mechanics, and photonics.

Silica biomineralization via the self-assembly of helical biomolecules

The biomimetic synthesis of relevant silica materials using biological macromolecules as templates via silica biomineralization processes attract rapidly rising attention toward natural and artificial materials. Biomimetic synthesis studies are useful for improving the understanding of the formation mechanism of the hierarchical structures found in living organisms (such as diatoms and sponges) and for promoting significant developments in the biotechnology, nanotechnology and materials chemistry fields. Chirality is a ubiquitous phenomenon in nature and is an inherent feature of biomolecular components in organisms. Helical biomolecules, one of the most important types of chiral macromolecules, can self-assemble into multiple liquid-crystal structures and be used as biotemplates for silica biomineralization, which renders them particularly useful for fabricating complex silica materials under ambient conditions. Over the past two decades, many new silica materials with hierarchical structures and complex morphologies have been created using helical biomolecules. In this review, the developments in this field are described and the recent progress in silica biomineralization templating using several classes of helical biomolecules, including DNA, polypeptides, cellulose and rod-like viruses is summarized. Particular focus is placed on the formation mechanism of biomolecule-silica materials (BSMs) with hierarchical structures. Finally, current research challenges and future developments are discussed in the conclusion.

Formation and Direct Repair of UV-induced Dimeric DNA Pyrimidine Lesions

Direct repair of UV-induced DNA lesions represents an elegant method for many organisms to deal with these highly mutagenic and cytotoxic compounds. Although the participating proteins are structurally well investigated, the exact repair mechanism of the photolyase enzymes remains a vivid subject of current research. In this review, we summarize and highlight the recent contributions to this exciting field.

Applications of biomaterials to liquid crystals

Nowadays, chemically synthesized proteins and peptides are attractive building blocks and have potential in many important applications as biomaterials. In this review, applications of biomaterials to thermotropic liquid crystals are discussed. The review covers the improvement of the performance of liquid crystal displays using liquid crystal physical gels consisting of a liquid crystal and amino acid-based gelators, and also new functionalization of liquid crystals. Moreover, the influence of DNA, which is one of the more attractive biomaterials, dispersed in thermotropic liquid crystals and its potential use in the liquid crystal industry is described. In addition, we found interesting results during electrooptical measurements of liquid crystals doped with DNA, and explain them from the point of view of biological applications. These recent approaches suggest that these biomaterials may be applicable in the electronic device industry and should be considered as an interesting material with their physical properties having the potential to create or refine an industrial product.

Plasmids as scribbling pads for operon formation and propagation

Many bacterial genes are in operons and the process whereby operons are formed is therefore fundamental. To help elucidate this process, we propose in the Scribbling Pad hypothesis that bacteria have been constantly using plasmids for genetic experimentation and, in particular, for the construction of operons. This hypothesis simultaneously solves the problems of the creation of operons and the way operons are propagated. We cite results in the literature to support the hypothesis and make experimental predictions to test it.

Hyperstructure interactions influence the virulence of the type 3 secretion system in yersiniae and other bacteria

A paradigm shift in our thinking about the intricacies of the host-parasite interaction is required that considers bacterial structures and their relationship to bacterial pathogenesis. It has been proposed that interactions between extended macromolecular assemblies, termed hyperstructures (which include multiprotein complexes), determine bacterial phenotypes. In particular, it has been proposed that hyperstructures can alter virulence. Two such hyperstructures have been characterized in both pathogenic and nonpathogenic bacteria. Present within a number of both human and plant Gram-negative pathogens is the type 3 secretion system (T3SS) injectisome which in some bacteria serves to inject toxic effector proteins directly into targeted host cells resulting in their paralysis and eventual death (but which in other bacteria prevents the death of the host). The injectisome itself comprises multiple protein subunits, which are all essential for its function. The degradosome is another multiprotein complex thought to be involved in cooperative RNA decay and processing of mRNA transcripts and has been very well characterized in nonpathogenic Escherichia coli. Recently, experimental evidence has suggested that a degradosome exists in the yersiniae as well and that its interactions within the pathogens modulate their virulence. Here, we explore the possibility that certain interactions between hyperstructures, like the T3SS and the degradosome, can ultimately influence the virulence potential of the pathogen based upon the physical locations of hyperstructures within the cell.

Formation of impeller-like helical DNA-silica complexes by polyamines induced chiral packing

The helicity of DNA and its long-range chiral packing are widespread phenomena; however, the packing mechanism remains poorly understood both in vivo and in vitro. Here, we report the extraordinary DNA chiral self-assembly by silica mineralization, together with circular dichroism measurements and electron microscopy studies on the structure and morphology of the products. Mg(2+) ion and diethylenetriamine were found to induce right- and left-handed chiral DNA packing with two-dimensional-square p4mm mesostructures, respectively, to give corresponding enantiomeric impeller-like helical DNA-silica complexes. Moreover, formation of macroscopic impeller-like helical architectures depends on the types of polyamines and co-structure-directing agents and pH values of reaction solution. It has been suggested that interaction strength between negatively charged DNA phosphate strands and positively charged counterions may be the key factor for the induction of DNA packing handedness.

Three-dimensional structures of pathogenic and saprophytic Leptospira species revealed by cryo-electron tomography

Leptospira interrogans is the primary causative agent of the most widespread zoonotic disease, leptospirosis. An in-depth structural characterization of L. interrogans is needed to understand its biology and pathogenesis. In this study, cryo-electron tomography (cryo-ET) was used to compare pathogenic and saprophytic species and examine the unique morphological features of this group of bacteria. Specifically, our study revealed a structural difference between the cell envelopes of L. interrogans and Leptospira biflexa involving variations in the lipopolysaccharide (LPS) layer. Through cryo-ET and subvolume averaging, we determined the first three-dimensional (3-D) structure of the flagellar motor of leptospira, with novel features in the flagellar C ring, export apparatus, and stator. Together with direct visualization of chemoreceptor arrays, DNA packing, periplasmic filaments, spherical cytoplasmic bodies, and a unique "cap" at the cell end, this report provides structural insights into these fascinating Leptospira species.

Speculations on the initiation of chromosome replication in Escherichia coli: the dualism hypothesis

The exact nature of the mechanism that triggers initiation of chromosome replication in the best understood of all organisms, Escherichia coli, remains mysterious. Here, I suggest that this mechanism evolved in response to the problems that arise if chromosome replication does not occur. E. coli is now known to be highly structured. This leads me to propose a mechanism for initiation of replication based on the dynamics of large assemblies of molecules and macromolecules termed hyperstructures. In this proposal, hyperstructures and their constituents are put into two classes, non-equilibrium and equilibrium, that spontaneously separate and that are appropriate for life in either good or bad conditions. Maintaining the right ratio(s) of non-equilibrium to equilibrium hyperstructures is therefore a major challenge for cells. I propose that this maintenance entails a major transfer of material from equilibrium to non-equilibrium hyperstructures once per cell and I further propose that this transfer times the cell cycle. More specifically, I speculate that the dialogue between hyperstructures involves the structuring of water and the condensation of cations and that one of the outcomes of ion condensation on ribosomal hyperstructures and decondensation from the origin hyperstructure is the separation of strands at oriC responsible for triggering initiation of replication. The dualism hypothesis that comes out of these speculations may help integrate models for initiation of replication, chromosome segregation and cell division with the 'prebiotic ecology' scenario of the origins of life.

Electrostatics of strongly charged biological polymers: ion-mediated interactions and self-organization in nucleic acids and proteins

Charges on biological polymers in physiologically relevant solution conditions are strongly screened by water and salt solutions containing counter-ions. However, the entropy of these counterions can result in surprisingly strong interactions between charged objects in water despite short screening lengths, via coupling between osmotic and electrostatic interactions. Widespread work in theory, experiment, and computation has been carried out to gain a fundamental understanding of the rich, yet sometimes counterintuitive, behavior of these polyelectrolyte systems. Examples of polyelectrolyte association in biology include DNA packaging and RNA folding, as well as aggregation and self-organization phenomena in different disease states.

Effect of crowding on the conformation of interwound DNA strands from neutron scattering measurements and Monte Carlo simulations

With a view to determining the distance between the two opposing duplexes in supercoiled DNA, we have measured small angle neutron scattering from pHSG298 plasmid (2675 base pairs) dispersed in saline solutions. Experiments were carried out under full and zero average DNA neutron scattering contrast using hydrogenated plasmid and a 1:1 mixture of hydrogenated and perdeuterated plasmid, respectively. In the condition of zero average contrast, the scattering intensity is directly proportional to the single DNA molecule scattering function (form factor), irrespective of the DNA concentration and without complications from intermolecular interference. The form factors are interpreted with Monte Carlo computer simulation. For this purpose, the many body problem of a dense DNA solution was reduced to the one of a single DNA molecule in a congested state by confinement in a cylindrical potential. It was observed that the interduplex distance decreases with increasing concentration of salt as well as plasmid. Therefore, besides ionic strength, DNA crowding is shown to be important in controlling the interwound structure and site juxtaposition of distal segments of supercoiled DNA. This first study exploiting zero average DNA contrast has been made possible by the availability of perdeuterated plasmid.

Polarization-sensitive two-photon microscopy study of the organization of liquid-crystalline DNA

Highly concentrated DNA solutions exhibit self-ordering properties such as the generation of liquid-crystalline phases. Such organized domains may play an important role in the global chromatin topology but can also be used as a simple model for the study of more complex 3D DNA structures. In this work, using polarized two-photon fluorescence microscopy, we report on the orientation of DNA molecules in liquid-crystalline phases. For this purpose, we analyze the signal emitted by fluorophores that are noncovalently bound to DNA strands. In nonlinear processes, excitation occurs exclusively in the focal volume, which offers advantages such as the reduction of photobleaching of out-of-focus molecules and intrinsic 3D sectioning capability. Propidium iodide and Hoechst, two fluorophores with different DNA binding modes, have been considered. Polarimetric measurements show that the dyes follow the alignment with respect to the DNA strands and allow the determination of the angles between the emission dipoles and the longitudinal axis of the DNA double strand. These results provide a useful starting point toward the application of two-photon polarimetry techniques to determine the local orientation of condensed DNA in physiological conditions.