The helix clock: a potential biomechanical cell cycle timer

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.

Science and prizes : A case for rethinking the criteria for prizes in science (and for rewarding important discoveries in bacterial physiology)

Scientific prizes award those making important discoveries, define a field, further the public understanding of science, or support young and upcoming researchers. But they should also encourage scientists to take risks and venture into the unknown.

Successive Paradigm Shifts in the Bacterial Cell Cycle and Related Subjects

A paradigm shift in one field can trigger paradigm shifts in other fields. This is illustrated by the paradigm shifts that have occurred in bacterial physiology following the discoveries that bacteria are not unstructured, that the bacterial cell cycle is not controlled by the dynamics of peptidoglycan, and that the growth rates of bacteria in the same steady-state population are not at all the same. These paradigm shifts are having an effect on longstanding hypotheses about the regulation of the bacterial cell cycle, which appear increasingly to be inadequate. I argue that, just as one earthquake can trigger others, an imminent paradigm shift in the regulation of the bacterial cell cycle will have repercussions or "paradigm quakes" on hypotheses about the origins of life and about the regulation of the eukaryotic cell cycle.

The mechanisms responsible for 2-dimensional pattern formation in bacterial macrofiber populations grown on solid surfaces: fiber joining and the creation of exclusion zones

BACKGROUND

When Bacillus subtilis is cultured in a complex fluid medium under conditions where cell separation is suppressed, populations of multicellular macrofibers arise that mature into ball-like structures. The final sedentary forms are found distributed in patterns on the floor of the growth chamber although individual cells have no flagellar-driven motility. The nature of the patterns and their mode of formation are described in this communication.

RESULTS

Time-lapse video films reveal that fiber-fiber contact in high density populations of macrofibers resulted in their joining either by entwining or supercoiling. Joining led to the production of aggregate structures that eventually contained all of the fibers located in an initial area. Fibers were brought into contact by convection currents and motions associated with macrofiber self-assembly such as walking, pivoting and supercoiling. Large sedentary aggregate structures cleared surrounding areas of other structures by dragging them into the aggregate using supercoiling of extended fibers to power dragging. The spatial distribution of aggregate structures in 6 mature patterns containing a total of 637 structures was compared to that expected in random theoretical populations of the same size distributed in the same surface area. Observed and expected patterns differ significantly. The distances separating all nearest neighbors from one another in observed populations were also measured. The average distance obtained from 1451 measurements involving 519 structures was 0.73 cm. These spacings were achieved without the use of flagella or other conventional bacterial motility mechanisms. A simple mathematical model based upon joining of all structures within an area defined by the minimum observed distance between structures in populations explains the observed distributions very well.

CONCLUSIONS

Bacterial macrofibers are capable of colonizing a solid surface by forming large multicellular aggregate structures that are distributed in unique two-dimensional patterns. Cell growth geometry governs in an hierarchical way the formation of these patterns using forces associated with twisting and supercoiling to drive motions and the joining of structures together. Joining by entwining, supercoiling or dragging all require cell growth in a multicellular form, and all result in tightly fused aggregate structures.

Relationship between size of parent at cell division and relative size of its progeny in Escherichia coli

This article examines the empirical basis for the assumption of independence between the relative size (length or surface area) of a newborn cell w and the absolute size of its mother at cell division. Random samples from two strains of Escherichia coli B/r cells in steady-state exponential growth, covering a range of doubling times, were fixed in osmium tetroxide and prepared for electron microscopy by agar filtration. Length and diameter of over 3000 constricted cells were measured from the electron micrographs and cell surface area computed by assuming an idealized geometry of right circular cylinders with hemispherical polar caps. In general, these strains were found to divide into two daughter cells with a precision that is independent of the size of the mother. In addition, both a normal and a symmetrical beta-distribution were shown to fit the observed size distributions of w rather well; theoretical grounds for preferring the latter are discussed.

A model of bacterial DNA segregation based upon helical geometry

A new mechanism to segregate daughter genomes in bacterial cells is suggested that is based upon the rules of geometry governing the helix clock (Mendelson, 1982a). The reorientation of cell surface string arrays used as a timing reference in the helix clock is capable of drawing apart the initial products of DNA replication. Physically linking the sister DNA replication origins to the ends of the initial cell surface string inserted into the cell surface at the start of a helix clock cycle, and linking the DNA terminus to a point along the length of the same string provides a means to mark the locations to which the genomes will segregate as well as the place where cell division will occur. The parallel packing of additional cell surface strings into an array which includes the string to which DNA is attached provides the necessary spatial rearrangements. The helical segregation model can account for the precise registration of cell divisions with the completion of replication forks in a multifork replication system, provides a basis for determining the relationship of sister cell sizes at division, and can also accommodate the asymmetrical divisions associated with minicell production and sporulation. Examination of the helical segregation theory under multifork DNA replication conditions moreover reveals that adjacent helical clocks are physically linked to one another although totally independent in terms of their progression through the clock cycle. A relationship between the initiation of DNA replication forks and the insertion of the first cell surface string associated with the start of a helix clock cycle is predicted by the model.

Helical macrofiber formation in Bacillus subtilis: inhibition by penicillin G

The folding process required for helical macrofiber formation after the outgrowth of Bacillus subtilis spores was found to be blocked by very low concentrations of penicillin G (1 to 3 ng/ml). Under such conditions, growth and septation without cell separation resulted in characteristic disorganized multicellular structures. Higher concentrations (4 and 10 ng/ml) were needed to inhibit spore outgrowth and vegetative growth, respectively.

Bacterial growth and division: genes, structures, forces, and clocks

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Dynamics of Bacillus subtilis helical macrofiber morphogenesis: writhing, folding, close packing, and contraction

Helical Bacillus subtilis macrofibers are highly ordered structures consisting of individual cells packed in a geometry remarkably similar to that found in helically twisted yarns (G. A. Carnaby, in J. W. S. Hearle et al., ed., The Mechanics of Flexible Fibre Assemblies, p. 99-112, 1980; N. H. Mendelson, Proc. Natl. Acad. Sci. U.S.A. 75:2478-2482, 1978). The growth and formation of macrofibers were studied with time-lapse microscopy methods. The basic growth mode consisted of fiber elongation, folding, and the helical wrapping together of the folded portion into a tight helical fiber. This sequence was reiterated at both ends of the structure, resulting in terminal loops. Macrofiber growth was accompanied by the helical turning of the structure along its long axis. Right-handed structures turned clockwise and left-handed ones turned counterclockwise when viewed along the length of a fiber looking toward a loop end. Helical turning forced the individual cellular filaments into a close-packing arrangement during growth. Tension was evident within the structures and they writhed as they elongated. Tension was relieved by folding, which occurred when writhing became so violent that the structure touched itself, forming a loop. When the multistranded structure produced by repeated folding cycles became too rigid for additional folding, the morphogenesis of a ball-like structure began. The dynamics of helical macrofiber formation was interpreted in terms of stress-strain deformations. In view of the similarities between macrofiber structures and those found in multifilament yarns and cables, the physics of helical macrofiber structure and also growth may be suitable for analysis developed in these fields concerning the mechanics of flexible fiber assemblies (C. P. Buckley; J. W. S. Hearle; and J. J. Thwaites, in J. W. S. Hearle et al., ed., The Mechanics of Flexible Fibre Assemblies, p. 1-97, 1980).

Clockwise and counterclockwise pinwheel colony morphologies of Bacillus subtilis are correlated with the helix hand of the strain

Helical macrofiber-producing strains of Bacillus subtilis grown on fresh complex medium semisolid surfaces formed "pinwheel"-shaped colonies. Clockwise pinwheel projections arose from colonies of strains that produce right-handed helical macrofibers in fluid cultures. Most strains able to make left-handed helical macrofibers in fluid grew as disorganized wavy colonies without directed projections. A phage-resistant left-handed mutant was found that produces very tight colonies with pinwheel projections that lie counterclockwise relative to the colony. The pinwheel colony morphology is interpreted therefore in terms of the cell surface organization and helical growth.