Epigenetics has captured the attention of scientists in the past decades, yet its scope has been continuously changing. In this paper, we give an overview on how and why its definition has evolved and suggest several clarification on the concepts use
d in this field, in particular, on the notions of epigenetic information, epigenetic stability and epigenetic templating. Another issue that we address is the role of epigenetic information. Not only it is important in allowing alternative interpretations of genetic information, but it appears to be important in protecting the genetic information, moreover, we suggest that this function appeared first in evolution and only later on the epigenetic mechanisms were recruited to play a role in cell differentiation.
The comment mostly concerns mis-representation of my position on Quantum Biology, by stating that I am reducing cells behavior to quantum particles inside the cell. I contrast my position with that of McFadden-Al-Khalili, as well as with the position
of Asano et al. I also advertise an idea, described in our latest paper (Bordonaro, Ogryzko. Quantum Biology at the Cellular level - elements of the research program, BioSystems, 2013), for the need of synthetic biology in testing some predictions that follow from our approach.
Quantum Biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (Quantum Biology at Cellular Level),
a research program designed to extend the reach of quantum concepts to higher than molecular levels of biological organization. Key words. decoherence, macroscopic superpositions, basis-dependence, formal superposition, non-classical correlations, Basis-Dependent Selection (BDS), synthetic biology, evolvability mechanism loophole.
The common techniques to study protein-protein proximity in vivo are not well-adapted to the capabilities and the expertise of a standard proteomics laboratory, typically based on the use of mass spectrometry. With the aim of closing this gap, we hav
e developed PUB-MS (for Proximity Utilizing Biotinylation and Mass Spectrometry), an approach to monitor protein-protein proximity, based on biotinylation of a protein fused to a biotin-acceptor peptide (BAP) by a biotin-ligase, BirA, fused to its interaction partner. The biotinylation status of the BAP can be further detected by either Western analysis or mass spectrometry. The BAP sequence was redesigned for easy monitoring of the biotinylation status by LC-MS/MS. In several experimental models, we demonstrate that the biotinylation in vivo is specifically enhanced when the BAP- and BirA- fused proteins are in proximity to each other. The advantage of mass spectrometry is demonstrated by using BAPs with different sequences in a single experiment (allowing multiplex analysis) and by the use of stable isotopes. Finally, we show that our methodology can be also used to study a specific subfraction of a protein of interest that was in proximity with another protein at a predefined time before the analysis.
Protein footprinting is a new methodology that is based on probing, typically with the use of mass spectrometry, of reactivity of different aminoacid residues to a modifying reagent. Data thus obtained allow one to make inferences about protein confo
rmations and their intermolecular interactions. Most of the protein footprinting studies so far have been performed on individual proteins in vitro. We explore whether a similar approach is possible with the proteins inside of living cells, employing dimethylsulfate (DMS), a reagent widely used for the in vivo footprinting of nucleic acids. DMS can induce methylation of the lysine, histidine and glutamate residues on proteins. Using models of the histone H2B/H2AZ heterodimer assembled in vitro and from chromatin treated in vivo, we show that the methylation by deuterated DMS allows one to distinguish the accessibility of a particular residue in and out of the proteins environmental/structural context. The detection of changes in protein conformations or their interactions in vivo can provide a new approach to the identification of proteins involved in various intracellular pathways and help in the search for perspective drug targets and biomarkers of diseases.
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions. Here, we seque
nced several genomes of Escherichia coli from colonies obtained after chemical mutagenesis and observed a strikingly nonrandom distribution of the induced mutations. These include long stretches of exclusively G to A or C to T transitions along the genome and orders of magnitude intra- and inter-genomic differences in mutation density. Whereas most of these observations can be explained by the known features of enzymatic processes, the others could reflect stochasticity in the molecular processes at the single-cell level. Our results demonstrate how analysis of the molecular records left in the genomes of the descendants of an individual mutagenized cell allows for genome-scale observations of fixation and segregation of mutations, as well as recombination events, in the single genome of their progenitor.
We describe a modification of the TAP method for purification and analysis of multiprotein complexes, termed here DEF-TAP (for Differential Elution Fractionation after Tandem Affinity Purification). Its essential new feature is the use for last purif
ication step of 6XHis-Ni++ interaction, which is resistant to a variety of harsh washing conditions, including high ionic strength and presence of organic solvents. This allows us to use various fractionation schemes before the protease digestion, which is expected to improve the coverage of the analysed protein mixture and also to provide an additional insight into the structure of the purified macromolecular complex and the nature of protein-protein interactions involved. We illustrate our new approach by analysis of soluble nuclear complexes containing histone H4 purified from HeLa cells. In particular, we observed different fractionation patterns of HAT1 and RbAp46 proteins as compared to RbAp48 protein, all identified as interaction partners of H4 histone. In addition, we report all components of the licensing MCM2-7 complex and the apoptosis-related DAXX protein among the interaction partners of the soluble H4. Finally, we show that HAT1 requires N-terminal tail of H4 for its stable association with this histone.
I compare two quantum-theoretical approaches to the phenomenon of adaptive mutations, termed here Q-cell and Q-genome. I use fluctuation trapping model as a general framework. I introduce notions of R-error and D-error and argue that the fluctuation
trapping model has to employ a correlation between the R- and D- errors. Further, I compare how the two approaches can justify the R-D-error correlation, focusing on the advantages of the Q-cell approach. The positive role of environmentally induced decoherence (EID) on both steps of the adaptation process is emphasized. A starving bacterial cell is proposed to be in an einselected state. The intracellular dynamics in this state has a unitary character and I propose to interpret it as exponential growth in imaginary time, analogously to the commonly considered diffusion interpretation of the Schroedinger equation. Addition of a substrate leads to Wick rotation and a switch from imaginary time reproduction to a real time reproduction regime. Due to the variations at the genomic level (such as base tautomery), the starving cell has to be represented as a superposition of different components, all reproducing in imaginary time. Adidtion of a selective substrate, allowing only one of these components to amplify, will cause Wick rotation and amplification of this component, thus justifying the occurence of the R-D-error correlation. Further ramifications of the proposed ideas for evolutionary theory are discussed.
Application of quantum principles to living cells requires a new approximation of the full quantum mechanical description of intracellular dynamics. We discuss what principal elements any such good approximation should contain. As one such element, t
he notion of Catalytic force Cf is introduced. Cf is the effect of the molecular target of catalysis on the catalytic microenvironment that adjusts the microenvironment towards a state that facilitates the catalytic act. This phenomenon is experimentally testable and has an intriguing implication for biological organization and evolution, as it amounts to optimization without natural selection of replicators. Unlike the statistical-mechanical approaches to self-organization, the Cf principle does not encounter the problem of tradeoff between stability and complexity at the level of individual cell. Physically, the Cf is considered as a harmonic-like force of reaction, which keeps the state of the cell close to the ground state, defined here as a state where enzymatic acts work most efficiently. Ground state is subject to unitary evolution, and serves as a starting point in a general strategy of quantum description of intracellular processes, termed here Euclidean approach. The next step of this strategy is transition from the description of ground state to that one of growing state, and we suggest how it can be accomplished using arguments from the fluctuation-dissipation theorem. Finally, given that the most reliable and informative observable of an individual cell is the sequence of its genome, we propose that the non-classical correlations between individual molecular events at the single cell level could be easiest to detect using high throughput DNA sequencing.
Schroedingers book What is Life? is widely credited for having played a crucial role in development of molecular and cellular biology. My essay revisits the issues raised by this book from the modern perspective of epigenetics and systems biology. I
contrast two classes of potential mechanisms of epigenetic stability: epigenetic templating and systems biology approaches, and consider them from the point of view expressed by Schroedinger. I also discuss how quantum entanglement, a nonclassical feature of quantum mechanics, can help to address the problem of small numbers that lead Schroedinger to promote the idea of molecular code-script for explanation of stability of biological order.
