Steric interactions and out-of-equilibrium processes control the internal organization of bacteria

Despite the absence of a membrane-enclosed nucleus, the bacterial DNA is typically condensed into a compact body—the nucleoid. This compaction influences the localization and dynamics of many cellular processes including transcription, translation, and cell division. Here, we develop a model that takes into account steric interactions among the components of the Escherichia coli transcriptional–translational machinery (TTM) and out-of-equilibrium effects of messenger RNA (mRNA) transcription, translation, and degradation, to explain many observed features of the nucleoid. We show that steric effects, due to the different molecular shapes of the TTM components, are sufficient to drive equilibrium phase separation of the DNA, explaining the formation and size of the nucleoid. In addition, we show that the observed positioning of the nucleoid at midcell is due to the out-of-equilibrium process of mRNA synthesis and degradation: mRNAs apply a pressure on both sides of the nucleoid, localizing it to midcell. We demonstrate that, as the cell grows, the production of these mRNAs is responsible for the nucleoid splitting into two lobes and for their well-known positioning to 1/4 and 3/4 positions on the long cell axis. Finally, our model quantitatively accounts for the observed expansion of the nucleoid when the pool of cytoplasmic mRNAs is depleted. Overall, our study suggests that steric interactions and out-of-equilibrium effects of the TTM are key drivers of the internal spatial organization of bacterial cells.

Challenges in Studying Steric Interactions in Highly Strained Perhalogenated Alkanes and Silanes.

The decomposition of the molecular total energy in their hyperconjugative, steric and electrostatic effects can lead to interesting interpretations about the stereoelectronic effects that govern their geometry and properties. In this work, we have studied homologous series of perfluoroalkanes, perchloroalkanes, perfluorosilanes and perchlorosilanes, and all molecules have preference for helical geometries. According to Natural Bond Orbitals (NBO) calculations, the silanes have their helical geometry stabilised by hyperconjugative interactions, as well as the perfluoroalkanes. However, it was surprisingly difficult to disclose that steric interactions are ruling the helical geometry preference in perchloroalkanes by comparing the NBO analysis and the Quantum Theory of Atoms ins Molecules (QTAIM). Although perchloroalkanes have extremely intense steric interactions between Cl lone pairs, some of them were underestimated by the NBO analysis, which showed the opposite behaviour compared with QTAIM that indicates steric effects as the leading forces to helical geometry preference.

Patterns of bacterial motility in microfluidics-confining environments

Understanding the motility behavior of bacteria in confining microenvironments, in which they search for available physical space and move in response to stimuli, is important for environmental, food industry, and biomedical applications. We studied the motility of five bacterial species with various sizes and flagellar architectures (Vibrio natriegens, Magnetococcus marinus, Pseudomonas putida, Vibrio fischeri, and Escherichia coli) in microfluidic environments presenting various levels of confinement and geometrical complexity, in the absence of external flow and concentration gradients. When the confinement is moderate, such as in quasi-open spaces with only one limiting wall, and in wide channels, the motility behavior of bacteria with complex flagellar architectures approximately follows the hydrodynamics-based predictions developed for simple monotrichous bacteria. Specifically, V. natriegens and V. fischeri moved parallel to the wall and P. putida and E. coli presented a stable movement parallel to the wall but with incidental wall escape events, while M. marinus exhibited frequent flipping between wall accumulator and wall escaper regimes. Conversely, in tighter confining environments, the motility is governed by the steric interactions between bacteria and the surrounding walls. In mesoscale regions, where the impacts of hydrodynamics and steric interactions overlap, these mechanisms can either push bacteria in the same directions in linear channels, leading to smooth bacterial movement, or they could be oppositional (e.g., in mesoscale-sized meandered channels), leading to chaotic movement and subsequent bacterial trapping. The study provides a methodological template for the design of microfluidic devices for single-cell genomic screening, bacterial entrapment for diagnostics, or biocomputation.

Chemical pumps and flexible sheets spontaneously form self-regulating oscillators in solution

The synchronization of self-oscillating systems is vital to various biological functions, from the coordinated contraction of heart muscle to the self-organization of slime molds. Through modeling, we design bioinspired materials systems that spontaneously form shape-changing self-oscillators, which communicate to synchronize both their temporal and spatial behavior. Here, catalytic reactions at the bottom of a fluid-filled chamber and on mobile, flexible sheets generate the energy to “pump” the surrounding fluid, which also transports the immersed sheets. The sheets exert a force on the fluid that modifies the flow, which in turn affects the shape and movement of the flexible sheets. This feedback enables a single coated (active) and even an uncoated (passive) sheet to undergo self-oscillation, displaying different oscillatory modes with increases in the catalytic reaction rate. Two sheets (active or passive) introduce excluded volume, steric interactions. This distinctive combination of the hydrodynamic, fluid–structure, and steric interactions causes the sheets to form coupled oscillators, whose motion is synchronized in time and space. We develop a heuristic model that rationalizes this behavior. These coupled self-oscillators exhibit rich and tunable phase dynamics, which depends on the sheets’ initial placement, coverage by catalyst and relative size. Moreover, through variations in the reactant concentration, the system can switch between the different oscillatory modes. This breadth of dynamic behavior expands the functionality of the coupled oscillators, enabling soft robots to display a variety of self-sustained, self-regulating moves.

Metal-Binding Q-Proline Macrocycles

Herein, we introduce the efficient synthesis of Q-proline (Q-Pro) based, metal-binding macrocycles (QPM), which can display up to nine functional groups. Synthesis of eight QPM was achieved through standard Fmoc-SPPS and peptoid chemistry. QPM are disordered in the absence of a metal cation, as evidenced by NMR and a crystal structure of <b>QPM-3</b> obtained through racemic crystallization. Addition of metal cations cause these macrocycles to adopt ordered, uniform core structures regardless of the functional groups. Alkylation of QPM allows for addition of reactive functional groups as the final step in a synthesis. Interestingly, the addition of secondary functional groups to the hydantoin amide position (R₂) converts the proline ring from Cg-endo to Cg-exo, due to steric interactions.

Metal-Binding Q-Proline Macrocycles

Herein, we introduce the efficient synthesis of Q-proline (Q-Pro) based, metal-binding macrocycles (QPM), which can display up to nine functional groups. Synthesis of eight QPM was achieved through standard Fmoc-SPPS and peptoid chemistry. QPM are disordered in the absence of a metal cation, as evidenced by NMR and a crystal structure of <b>QPM-3</b> obtained through racemic crystallization. Addition of metal cations cause these macrocycles to adopt ordered, uniform core structures regardless of the functional groups. Alkylation of QPM allows for addition of reactive functional groups as the final step in a synthesis. Interestingly, the addition of secondary functional groups to the hydantoin amide position (R₂) converts the proline ring from Cg-endo to Cg-exo, due to steric interactions.

Steric Control of Sorting Regimes in Self-Assembled Cages

Control of self-sorting regimes is achieved through adjustment of steric interactions in self-assembled coordination cages. The self-assembly regime of dynamic mixtures of heteroleptic cages is followed by HPLC to show...