Does the eclipse limit bacterial nucleoid complexity and cell width?

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.

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.

Extending Validity of the Bacterial Cell Cycle Model through Thymine Limitation: A Personal View

The contemporary view of bacterial physiology was established in 1958 at the "Copenhagen School", culminating a decade later in a detailed description of the cell cycle based on four parameters. This model has been subsequently supported by numerous studies, nicknamed BCD (The Bacterial Cell-Cycle Dogma). It readily explains, quantitatively, the coupling between chromosome replication and cell division, size and DNA content. An important derivative is the number of replication positions n, the ratio between the time C to complete a round of replication and the cell mass doubling time τ; the former is constant at any temperature and the latter is determined by the medium composition. Changes in cell width W are highly correlated to n through the equation for so-called nucleoid complexity NC (=(2ⁿ - 1)/(ln2 × n)), the amount of DNA per terC (i.e., chromosome) in genome equivalents. The narrow range of potential n can be dramatically extended using the method of thymine limitation of thymine-requiring mutants, which allows a more rigorous testing of the hypothesis that the nucleoid structure is the primary source of the signal that determines W during cell division. How this putative signal is relayed from the nucleoid to the divisome is still highly enigmatic. The aim of this Opinion article is to suggest the possibility of a new signaling function for nucleoid DNA.

Artificial modulation of cell width significantly affects the division time of Escherichia coli

Bacterial cells have characteristic spatial and temporal scales. For instance, Escherichia coli, the typical rod-shaped bacteria, always maintains a relatively constant cell width and cell division time. However, whether the external physical perturbation of cell width has an impact on cell division time remains largely unexplored. In this work, we developed two microchannel chips, namely straight channels and ‘necked’ channels, to precisely regulate the width of E. coli cells and to investigate the correlation between cell width and division time of the cells. Our results show that, in the straight channels, the wide cells divide much slower than narrow cells. In the ‘necked’ channels, the cell division is remarkably promoted compared to that in straight channels with the same width. Besides, fluorescence time-lapse microscopy imaging of FtsZ dynamics shows that the cell pre-constriction time is more sensitive to cell width perturbation than cell constriction time. Finally, we revealed a significant anticorrelation between the death rate and the division rate of cell populations with different widths. Our work provides new insights into the correlation between the geometrical property and division time of E. coli cells and sheds new light on the future study of spatial–temporal correlation in cell physiology.

Does the Nucleoid Determine Cell Dimensions in Escherichia coli?

Bacillary, Gram-negative bacteria grow by elongation with no discernible change in width, but during faster growth in richer media the cells are also wider. The mechanism regulating the change in cell width W during transitions from slow to fast growth is a fundamental, unanswered question in molecular biology. The value of W that changes in the divisome and during the division process only, is related to the nucleoid complexity, determined by the rates of growth and of chromosome replication; the former is manipulated by nutritional conditions and the latter-by thymine limitation of thyA mutants. Such spatio-temporal regulation is supported by existence of a minimal possible distance between successive replisomes, so-called eclipse that limits the number of replisomes to a maximum. Breaching this limit by slowing replication in fast growing cells results in maximal nucleoid complexity that is associated with maximum cell width, supporting the notion of Nucleoid-to-Divisome signal transmission. Physical signal(s) may be delivered from the nucleoid to assemble the divisome and to fix the value of W in the nascent cell pole.

Upconversion of Cellulosic Waste Into a Potential "Drop in Fuel" via Novel Catalyst Generated Using Desulfovibrio desulfuricans and a Consortium of Acidophilic Sulfidogens

Biogas-energy is marginally profitable against the "parasitic" energy demands of processing biomass. Biogas involves microbial fermentation of feedstock hydrolyzate generated enzymatically or thermochemically. The latter also produces 5-hydroxymethyl furfural (5-HMF) which can be catalytically upgraded to 2, 5-dimethyl furan (DMF), a "drop in fuel." An integrated process is proposed with side-stream upgrading into DMF to mitigate the "parasitic" energy demand. 5-HMF was upgraded using bacterially-supported Pd/Ru catalysts. Purpose-growth of bacteria adds additional process costs; Pd/Ru catalysts biofabricated using the sulfate-reducing bacterium (SRB) Desulfovibrio desulfuricans were compared to those generated from a waste consortium of acidophilic sulfidogens (CAS). Methyl tetrahydrofuran (MTHF) was used as the extraction-reaction solvent to compare the use of bio-metallic Pd/Ru catalysts to upgrade 5-HMF to DMF from starch and cellulose hydrolyzates. MTHF extracted up to 65% of the 5-HMF, delivering solutions, respectively, containing 8.8 and 2.2 g 5-HMF/L MTHF. Commercial 5% (wt/wt) Ru-carbon catalyst upgraded 5-HMF from pure solution but it was ineffective against the hydrolyzates. Both types of bacterial catalyst (5wt%Pd/3-5wt% Ru) achieved this, bio-Pd/Ru on the CAS delivering the highest conversion yields. The yield of 5-HMF from starch-cellulose thermal treatment to 2,5 DMF was 224 and 127 g DMF/kg extracted 5-HMF, respectively, for CAS and D. desulfuricans catalysts, which would provide additional energy of 2.1 and 1.2 kWh/kg extracted 5-HMF. The CAS comprised a mixed population with three patterns of metallic nanoparticle (NP) deposition. Types I and II showed cell surface-localization of the Pd/Ru while type III localized NPs throughout the cell surface and cytoplasm. No metallic patterning in the NPs was shown via elemental mapping using energy dispersive X-ray microanalysis but co-localization with sulfur was observed. Analysis of the cell surfaces of the bulk populations by X-ray photoelectron spectroscopy confirmed the higher S content of the CAS bacteria as compared to D. desulfuricans and also the presence of Pd-S as well as Ru-S compounds and hence a mixed deposit of PdS, Pd(0), and Ru in the form of various +3, +4, and +6 oxidation states. The results are discussed in the context of recently-reported controlled palladium sulfide ensembles for an improved hydrogenation catalyst.