Chromosome Replication in Escherichia coli: Life on the Scales

Open Questions about the Roles of DnaA, Related Proteins, and Hyperstructure Dynamics in the Cell Cycle

The DnaA protein has long been considered to play the key role in the initiation of chromosome replication in modern bacteria. Many questions about this role, however, remain unanswered. Here, we raise these questions within a framework based on the dynamics of hyperstructures, alias large assemblies of molecules and macromolecules that perform a function. In these dynamics, hyperstructures can (1) emit and receive signals or (2) fuse and separate from one another. We ask whether the DnaA-based initiation hyperstructure acts as a logic gate receiving information from the membrane, the chromosome, and metabolism to trigger replication; we try to phrase some of these questions in terms of DNA supercoiling, strand opening, glycolytic enzymes, SeqA, ribonucleotide reductase, the macromolecular synthesis operon, post-translational modifications, and metabolic pools. Finally, we ask whether, underpinning the regulation of the cell cycle, there is a physico-chemical clock inherited from the first protocells, and whether this clock emits a single signal that triggers both chromosome replication and cell division.

Generation of Bacterial Diversity by Segregation of DNA Strands

The generation in a bacterial population of a diversity that is coherent with present and future environments is a fundamental problem. Here, we use modeling to investigate growth rate diversity. We show that the combination of (1) association of extended assemblies of macromolecules with the DNA strands and (2) the segregation of DNA strands during cell division allows cells to generate different patterns of growth rate diversity with little effect on the overall growth rate of the population and thereby constitutes an example of “order for free” on which evolution can act.

Does the Semiconservative Nature of DNA Replication Facilitate Coherent Phenotypic Diversity?

It has been clear for over sixty years that the principal method whereby cells replicate and segregate their DNA is semiconservative. It is much less clear why it should be like this rather than, say, conservative. Recently, evidence has accumulated that supports the hypothesis that one of the functions of the cell cycle is to generate phenotypically different daughter cells, even in nondifferentiating bacteria such as Escherichia coli Evidence has also accumulated that the bacterial phenotype is determined by the functioning of extended assemblies of macromolecules termed hyperstructures. One class of these hyperstructures is attached dynamically to a DNA strand by the coupling of transcription and translation. Previously, we proposed in the strand segregation model that one set of hyperstructures accompanies one parental strand into one daughter cell while another set of hyperstructures accompanies the other parental strand into the other daughter cell. This epigenetic mechanism results in daughter cells having different phenotypes. Here, I propose that one of the reasons why semiconservative replication has been selected is because it allows the generation of a population containing cells with very different growth rates even in steady-state conditions.

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.

Division-Based, Growth Rate Diversity in Bacteria

To investigate the nature and origins of growth rate diversity in bacteria, we grew Escherichia coli and Bacillus subtilis in liquid minimal media and, after different periods of ¹⁵N-labeling, analyzed and imaged isotope distributions in individual cells with Secondary Ion Mass Spectrometry. We find a striking inter- and intra-cellular diversity, even in steady state growth. This is consistent with the strand-dependent, hyperstructure-based hypothesis that a major function of the cell cycle is to generate coherent, growth rate diversity via the semi-conservative pattern of inheritance of strands of DNA and associated macromolecular assemblies. We also propose quantitative, general, measures of growth rate diversity for studies of cell physiology that include antibiotic resistance.

Combining combing and secondary ion mass spectrometry to study DNA on chips using (13)C and (15)N labeling

Dynamic secondary ion mass spectrometry ( D-SIMS) imaging of combed DNA - the combing, imaging by SIMS or CIS method - has been developed previously using a standard NanoSIMS 50 to reveal, on the 50 nm scale, individual DNA fibers labeled with different, non-radioactive isotopes in vivo and to quantify these isotopes. This makes CIS especially suitable for determining the times, places and rates of DNA synthesis as well as the detection of the fine-scale re-arrangements of DNA and of molecules associated with combed DNA fibers. Here, we show how CIS may be extended to (13)C-labeling via the detection and quantification of the (13)C (14)N (-) recombinant ion and the use of the (13)C: (12)C ratio, we discuss how CIS might permit three successive labels, and we suggest ideas that might be explored using CIS.

The membrane: transertion as an organizing principle in membrane heterogeneity

The bacterial membrane exhibits a significantly heterogeneous distribution of lipids and proteins. This heterogeneity results mainly from lipid-lipid, protein-protein, and lipid-protein associations which are orchestrated by the coupled transcription, translation and insertion of nascent proteins into and through membrane (transertion). Transertion is central not only to the individual assembly and disassembly of large physically linked groups of macromolecules (alias hyperstructures) but also to the interactions between these hyperstructures. We review here these interactions in the context of the processes in Bacillus subtilis and Escherichia coli of nutrient sensing, membrane synthesis, cytoskeletal dynamics, DNA replication, chromosome segregation, and cell division.

Why do bacteria divide?

The problem of not only how but also why cells divide can be tackled using recent ideas. One idea from the origins of life – Life as independent of its constituents – is that a living entity like a cell is a particular pattern of connectivity between its constituents. This means that if the growing cell were just to get bigger the average connectivity between its constituents per unit mass – its cellular connectivity – would decrease and the cell would lose its identity. The solution is division which restores connectivity. The corollary is that the cell senses decreasing cellular connectivity and uses this information to trigger division. A second idea from phenotypic diversity – Life on the Scales of Equilibria – is that a bacterium must find strategies that allow it to both survive and grow. This means that it has learnt to reconcile the opposing constraints that these strategies impose. The solution is that the cell cycle generates daughter cells with different phenotypes based on sufficiently complex equilibrium (E) and non-equilibrium (NE) cellular compounds and structures appropriate for survival and growth, respectively, alias ‘hyperstructures.’ The corollary is that the cell senses both the quantity of E material and the intensity of use of NE material and then uses this information to trigger the cell cycle. A third idea from artificial intelligence – Competitive Coherence – is that a cell selects the active subset of elements that actively determine its phenotype from a much larger set of available elements. This means that the selection of an active subset of a specific size and composition must be done so as to generate both a coherent cell state, in which the cell’s contents work together harmoniously, and a coherent sequence of cell states, each coherent with respect to itself and to an unpredictable environment. The solution is the use of a range of mechanisms ranging from hyperstructure dynamics to the cell cycle itself.

Molecular complementarity between simple, universal molecules and ions limited phenotype space in the precursors of cells

Background

Fundamental problems faced by the protocells and their modern descendants include how to go from one phenotypic state to another; escape from a basin of attraction in the space of phenotypes; reconcile conflicting growth and survival strategies (and thereby live on ‘the scales of equilibria’); and create a coherent, reproducible phenotype from a multitude of constituents.

Presentation of the hypothesis

The solutions to these problems are likely to be found with the organic and inorganic molecules and inorganic ions that constituted protocells, which we term SUMIs for Simple Universal Molecules and Ions. These SUMIs probably included polyphosphate (PolyP) as a source of energy and of phosphate; poly-(R)-3-hydroxybutyrate (PHB) as a source of carbon and as a transporter in association with PolyP; polyamines as a source of nitrogen; lipids as precursors of membranes; as well as peptides, nucleic acids, and calcium. Here, we explore the hypothesis that the direct interactions between PHB, PolyP, polyamines and lipids – modulated by calcium – played a central role in solving the fundamental problems faced by early and modern cells.

Testing the hypothesis

We review evidence that SUMIs (1) were abundant and available to protocells; (2) are widespread in modern cells; (3) interact with one another and other cellular constituents to create structures with new functions surprisingly similar to those of proteins and RNA; (4) are essential to creating coherent phenotypes in modern bacteria. SUMIs are therefore natural candidates for reducing the immensity of phenotype space and making the transition from a “primordial soup” to living cells.

Implications of the hypothesis

We discuss the relevance of the SUMIs and their interactions to the ideas of molecular complementarity, composomes (molecular aggregates with hereditary properties based on molecular complementarity), and a prebiotic ecology of co-evolving populations of composomes. In particular, we propose that SUMIs might limit the initial phenotype space of composomes in a coherent way. As examples, we propose that acidocalcisomes arose from interactions and self-selection among SUMIs and that the phosphorylation of proteins in modern cells had its origin in the covalent modification of proteins by PHB.

Reviewers

This article was reviewed by Doron Lancet and Kepa Ruiz-Mirazo.

What properties of life are universal? Substance-free, scale-free life

One approach to answering the question of what properties of life are universal is to try to answer the question of what are the essential properties of biology's best understood model organism, Escherichia coli. One of these properties is competitive coherence whereby E. coli reconciles the generation of a coherent cell state with the generation of a coherent sequence of cell states. The second property is differentiation which occurs ineluctably when E. coli divides. The third property is dualism which is how E. coli navigates between the two main attractors of phenotypes - survival and growth - which are based on quasi-equilibrium and non-equilibrium structures, respectively. The fourth property is complementarity: the interactions between the molecules and macromolecules that constitute E. coli protect them from degradation and confer new properties. The fifth property is multi-scale existence: E. coli exists at levels extending from the bacterium to the global super-organism. The sixth property is maintenance of connectivity; growth alters connectivity and, in the case of E. coli, alters the phenotype. The seventh property is the combination of intensity sensing (the constituents can work no harder) and quantity sensing (too much unused material has been made); this combination is used by E. coli to drive its cell cycle and thereby generate an environmentally adapted population of cells. The eighth property is subjective experience which exists even at the level of a single E. coli but which only becomes important at higher levels of organisation. I propose that the search for life at other times and in other places be based on the above eight universal properties and be independent of both particular substances and spatio-temporal scales.

New approaches to the problem of generating coherent, reproducible phenotypes

Fundamental, unresolved questions in biology include how a bacterium generates coherent phenotypes, how a population of bacteria generates a coherent set of such phenotypes, how the cell cycle is regulated and how life arose. To try to help answer these questions, we have developed the concepts of hyperstructures, competitive coherence and life on the scales of equilibria. Hyperstructures are large assemblies of macromolecules that perform functions. Competitive coherence describes the way in which organisations such as cells select a subset of their constituents to be active in determining their behaviour; this selection results from a competition between a process that is responsible for a historical coherence and another process responsible for coherence with the current environment. Life on the scales of equilibria describes how bacteria depend on the cell cycle to negotiate phenotype space and, in particular, to satisfy the conflicting constraints of having to grow in favourable conditions so as to reproduce yet not grow in hostile conditions so as to survive. Both competitive coherence and life on the scales deal with the problem of reconciling conflicting constraints. Here, we bring together these concepts in the common framework of hyperstructures and make predictions that may be tested using a learning program, Coco, and secondary ion mass spectrometry.

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.