Spontaneous symmetry breaking in genome evolution

The quest for evolutionary mechanisms providing separation between the coding (exons) and noncoding (introns) parts of genomic DNA remains an important focus of genetics. This work combines an analysis of the most recent achievements of genomics and fundamental concepts of random processes to provide a novel point of view on genome evolution. Exon sizes in sequenced genomes show a lognormal distribution typical of a random Kolmogoroff fractioning process. This implies that the process of intron incretion may be independent of exon size, and therefore could be dependent on intron-exon boundaries. All genomes examined have two distinctive classes of exons, each with different evolutionary histories. In the framework proposed in this article, these two classes of exons can be derived from a hypothetical ancestral genome by (spontaneous) symmetry breaking. We note that one of these exon classes comprises mostly alternatively spliced exons.     

Entropy production in chiral symmetry breaking transitions

It is now well known that nonequilibrium chemical systems may reach conditions that spontaneously generate chiral asymmetry. One can find a host of model reactions that exhibit such behavior in the literature. Among these, models based on one originally devised by Frank have been studied extensively. Though the kinetic aspects of such model reactions have been discussed in great detail, the behavior of entropy in such systems is rarely discussed. In this article, the rate of entropy production per unit volume, sigma, in a modified Frank model is discussed. It is shown that the slope of sigma changes at the point at which the asymmetric states appear, behavior similar to that observed in second-order phase transitions.     

Morphological and chiral symmetry breaking in reaction-diffusion systems

Morphological and chiral symmetry breaking in reaction-diffusion systems is considered on the basis of the theory of imperfect codimension-two bifurcations. A new type of pattern selection with two triggers is elucidated: (1) morphologically asymmetric structures displaying optical activity can probably be originated from initially racemic and homogeneous conditions when chiral interaction, having the characteristic strength delta (such as electroweak interaction and circularly polarized light) as well as external field, having the characteristic strength eta (such as gravitational field and electrostatic field) are considered; (2) the selective sensitivity of molecular chirality and morphological asymmetry is omicron(delta 1/3) and omicron(eta 1/3), respectively; the sensitivity of mode-mode interaction between chiral polarization and concentration vector is omicron(delta 2/3) or omicron(eta 2/3), respectively. The relation of these conclusions to the life problem is discussed briefly.     

Parity violation and chiral symmetry breaking of a racemic mixture

The chiral symmetry breaking of a racemic mixture by the parity violating weak interaction is considered. Particular attention is given to a mechanism recently proposed by Mason and Tranter whereby the weak neutral current interaction in chiral molecules leads to the differential absorption of unpolarized light by D vs. L enantiomers. After extending the usual theory of optical activity to include weak neutral currents, it is found that for spin-allowed transitions in typical organic molecules the weak photoabsorption asymmetry is much smaller than the value obtained using the reasoning of Mason and Tranter. Upon making a comparison with other mechanisms, it is concluded that differential radiolysis by beta electrons is likely to produce the largest symmetry breaking effect by the weak interaction.     

Demonstration of spontaneous chiral symmetry breaking in asymmetric Mannich and Aldol reactions

Spontaneous symmetry breaking in reactive systems, known as a rare physical phenomenon and for the Soai autocatalytic irreversible reaction, might in principle also occur in other, more common asymmetric reactions when the chiral product is capable to promote its formation and an element of "nonlinearity" is involved in the reaction scheme. Such phenomena are long sought after in chemistry as a possible explanation for the biological homochirality of biomolecules. We have investigated homogeneous organic stereoselective Mannich and Aldol reactions, in which the product is capable to form H-bridged complexes with the prochiral educt, and found by applying NMR spectroscopy, HPLC analysis, and optical rotation measurements 0.3-50.8% of random product enantiomeric excess under essentially achiral reaction conditions. These findings imply a hitherto overlooked mechanism for spontaneous symmetry breaking and, hence, a novel approach to the problem of absolute asymmetric synthesis and could have also potential significance for the conundrum of homochirality.     

Spontaneous symmetry breaking in a non-rigid molecule approach to intrinsically disordered proteins

An analog to Longuet-Higgins' non-rigid molecular group theory arguments can be applied to the structure and reaction dynamics of intrinsically disordered proteins via a somewhat counterintuitive Morse Function treatment inspired by statistical mechanics, providing possible symmetry classifications of the molecular 'fuzzy lock-and-key'.     

Spontaneous chiral separation in noncovalent molecular clusters.

A new method is introduced to determine the extent to which spontaneous chiral separation occurs in small noncovalently bound clusters. Soft-sampling electrospray ionization was used to transfer noncovalent complexes from solution to the gas phase. Mixing D and L enantiomers with one of the pair isotopically labeled reveals the effect of chirality on cluster stability. The observed cluster distribution is compared to the predicted statistical distribution to determine any preference for homo- or heterochirality. Arginine, for example, forms a stable trimer with no preference for the chirality of the individual amino acids. Serine, however, forms a protonated octamer with a pronounced preference for homochirality. The implications of these results for the structures of the complexes are discussed along with the broader implications for the origins of homochirality in living systems (homochirogenesis).     

Role of latent heat in chiral symmetry breaking transition in the crystallization of 1,1'-binaphthyl

The influence of latent heat dissipated by the crystallization of 1,1'-binaphthyl in its supercooled molten state on the chiral symmetry breaking transition was investigated. Temperature change in the crystallization system was monitored by infrared thermocamera. Temperature rise due to the dissipation of latent heat in the growing front of polycrystalline aggregate was about 2 degrees C in an unstirred crystallization system. The melting point of racemic mixture and racemic compound of 1,1'-binaphthyl is 145 degrees C and 158 degrees C, respectively. The latent heat generated by the crystallization could thus change the crystallization behavior when the initial temperature of the melt was slightly lower than 145 degrees C. The temperature change in both unstirred and stirred crystallization systems was monitored. In the stirred crystallization system, even in the case when the initial temperature of the melt was about 2 degrees C lower than 145 degrees C, the temperature rose by about 4 degrees C immediately after the onset of crystallization. This indicates that the role of stirring as the critical parameter for the chiral symmetry breaking transition is not only to clone the chiral crystals but also to enhance the dissipation of latent heat due to secondary nucleation.     

Studies in chiral symmetry breaking crystallization I: The effects of stirring and evaporation rates

Chiral symmetry breaking can be realized in stirred crystallization of Na-ClO₃. We present experimental and theoretical studies of the random distribution of crystal enantiomeric excess (cee) for various stirring and solvent evaporation rates. For a fixed solvent evaporation rate, as the stirring RPM is increased, the probability distribution of cee initially broadens and subsequently develops a sharp peak close to cee = 1. On further increase of stirring rate, the probability distribution once again broadens. This broad probability distribution becomes narrow, with a sharp peak near cee = 1, if the solvent evaporation rate is decreased. Thus we show some ways in which the probability distribution of cee can be controlled in stirred crystallization. In particular, our study shows that the stirring rate and the solvent evaporation rate can be adjusted to maximize crystal enantiomeric excess. © 1995 Wiley-Liss, Inc.     

Cytoskeletal symmetry breaking in animal cells

Symmetry breaking is a crucial step in structure formation and function of all cells, necessary for cell movement, cell division, and polarity establishment. Although the mechanisms of symmetry breaking are diverse, they often share common characteristics. Here we review examples of nematic, polar, and chiral cytoskeletal symmetry breaking in animal cells, and analogous processes in simplified reconstituted systems. We discuss the origins of symmetry breaking, which can arise spontaneously, or involve amplification of a pre-existing external or internal bias to the whole cell level. The underlying mechanisms often involve both chemical and mechanical processes that cooperate to break symmetry in a robust manner, and typically depend on the shape, size, or properties of the cell’s boundary.     

Mirror symmetry breaking in biochemical evolution

The problem of origination of molecular asymmetry in biochemical evolution is discussed. The theoretical analysis shows that chiral purity of biomolecules has the biological significance for self-reproduction of organisms. The models of spontaneous symmetry-breaking in molecular systems are given. The aspects of various stages of biochemical evolution associated with the development of chiral polarization are analysed.     

Spontaneous breaking of the L,D symmetry in photolytic production and degradation of amino acids

The radiolysis experiments of amino acids have revealed the presence of bimolecular interaction between like enantiomers which suppress their photodegradation and between opposite enantiomers that enhance the photodegradation. Based on a mathematical model, it is suggested that this phenomenon could have given rise to chiral stereoselection in biochemical evolution.Sumanasekara Chair in Natural science.     

Visualizing the breaking of symmetry

Axon specification is a hallmark of neuron polarization. Although several models have been proposed, few studies have provided clues about polarization events in real time. Using time-lapse imaging, a recent study described visualizing symmetry-breaking events during this process.     

Emergence of symmetry breaking in fucoid zygotes

Fucoid zygotes are model cells for the study of symmetry breaking in plants. After fertilization, their initial spherical symmetry reduces to an axial symmetry, even in the absence of any external cue. This indicates that zygotes have an intrinsic ability to break symmetry in a way that is solely dependent on their internal biochemical and/or biophysical state. In our opinion, symmetry breaking is a self-organized process. It arises around the fucoid zygotes from the ion dynamics through channels (voltage-dependent calcium channels and a potassium leak) and outside the membrane (electrodiffusion owing to slower calcium diffusion compared with potassium). The robustness of this self-organized process and its lability ensure its relevance in plants where symmetry breaking is correlated with transcellular ion currents.     

Mirror symmetry breaking in biochemical evolution.

The problem of origination of molecular asymmetry in biochemical evolution is discussed. The theoretical analysis shows that chiral purity of biomolecules has the biological significance for self-reproduction of organisms. The models of spontaneous symmetry-breaking in molecular systems are given. The aspects of various stages of biochemical evolution associated with the development of chiral polarization are analysed.     

Cracking up: symmetry breaking in cellular systems

The shape of animal cells is, to a large extent, determined by the cortical actin network that underlies the cell membrane. Because of the presence of myosin motors, the actin cortex is under tension, and local relaxation of this tension can result in cortical flows that lead to deformation and polarization of the cell. Cortex relaxation is often regulated by polarizing signals, but the cortex can also rupture and relax spontaneously. A similar tension-induced polarization is observed in actin gels growing around beads, and we propose that a common mechanism governs actin gel rupture in both systems.