From Water and Ions to Crowded Biomacromolecules:In VivoStructuring of a Prokaryotic Cell

Abstract

SUMMARY The interactions and processes which structure prokaryotic cytoplasm (water, ions, metabolites, and biomacromolecules) and ensure the fidelity of the cell cycle are reviewed from a physicochemical perspective. Recent spectroscopic and biological evidence shows that water has no active structuring role in the cytoplasm, an unnecessary notion still entertained in the literature; water acts only as a normal solvent and biochemical reactant. Subcellular structuring arises from localizations and interactions of biomacromolecules and from the growth and modifications of their surfaces by catalytic reactions. Biomacromolecular crowding is a fundamental physicochemical characteristic of cells in vivo . Though some biochemical and physiological effects of crowding (excluded volume effect) have been documented, crowding assays with polyglycols, dextrans, etc., do not properly mimic the compositional variety of biomacromolecules in vivo . In vitro crowding assays are now being designed with proteins, which better reflect biomacromolecular environments in vivo , allowing for hydrophobic bonding and screened electrostatic interactions. I elaborate further the concept of complex vectorial biochemistry, where crowded biomacromolecules structure the cytosol into electrolyte pathways and nanopools that electrochemically “wire” the cell. Noncovalent attractions between biomacromolecules transiently supercrowd biomacromolecules into vectorial, semiconducting multiplexes with a high (35 to 95%)-volume fraction of biomacromolecules; consequently, reservoirs of less crowded cytosol appear in order to maintain the experimental average crowding of ∼25% volume fraction. This nonuniform crowding model allows for fast diffusion of biomacromolecules in the uncrowded cytosolic reservoirs, while the supercrowded vectorial multiplexes conserve the remarkable repeatability of the cell cycle by preventing confusing cross talk of concurrent biochemical reactions.

The General Phosphotransferase System Proteins Localize to Sites of Strong Negative Curvature in Bacterial Cells

“…What are these factors? The gap between the growing knowledge on bacterial macromolecular assemblies and the limited knowledge on the mechanisms that underlie their association led to the suggestion that bacterial cells have various kinds of structuring proteins, often associated with or penetrating into the cytoplasmic membrane (62). We speculate that this group includes proteins that sense membrane curvature and provide the bacterial cells with means to sort and position soluble proteins in highly curved regions.…”

Physicochemical Properties of Cells and Their Effects on Intrinsically Disordered Proteins (IDPs)

“…190,191 This organization may ensure that biomolecules, such as newly synthesized proteins are abundantly available in certain intracellular areas to enable fast interactions en route to supramolecular complex formation. In turn, such spatial restrictions may promote the establishment of functional compartments in the absence of organelles.…”

Emergence of Life from Multicomponent Mixtures of Chemicals: The Case for Experiments with Cycling Physicochemical Gradients

“…From a chemical engineering standpoint, polymeric reaction mixtures (in general, not only in biochemical situations) become vectorially complex at high levels of crowding, meaning that there is not enough free space for low-molecular-weight reactants and products (in between the surfaces of crowded macromolecules) to assume bulk concentrations independent of position Poolman, 2005, 2009;Spitzer, 2011). Such concentrations are normally expressed in terms of bulk chemical potentials of chemical thermodynamics, the formalisms of which thus cannot be exploited.…”

“…That unknown laws of ''biological complexity'' are yet to be discovered is unlikely (Goldenfeld and Kadanoff, 1999); rather, the complex (crowded, multicomponent, and multiphase) nature of progenotes and LUCAs, driven by cycling physicochemical gradients over the last 4 billion years (Rothschild, 2008), has now reached a level of a unique and very complicated ''chemical micro-reactor'' that contains its own ''distributed control system'': the nucleoid (chromosome) representing the ''software'' that defines bacterial species, which is connected to the cell envelope representing (compatible) ''hardware'' of interconnected sensors and transducers (Spitzer and Poolman, 2005;Bray, 2009;Spitzer, 2011;Lewitzky et al, 2012). There is little doubt that bottomup and top-down approaches to the phenomenon of life's emergence will eventually merge in revealing simple engineering principles governing the self-construction (Harold, 2005) and chemical operation of biological cells (Alberts, 1998;Bassler, 2010); the same or similar engineering principles will then explain how life can emerge on habitable planets anywhere in the Universe.…”