Does the Semiconservative Nature of DNA Replication Facilitate Coherent Phenotypic Diversity?

Abstract

It has been clear for over sixty years that the principal method whereby cells replicate and segregate their DNA is semiconservative. It is much less clear why it should be like this rather than, say, conservative. Recently, evidence has accumulated that supports the hypothesis that one of the functions of the cell cycle is to generate phenotypically different daughter cells, even in nondifferentiating bacteria such as Escherichia coli. Evidence has also accumulated that the bacterial phenotype is determined by the functioning of extended assemblies of macromolecules termed hyperstructures. One class of these hyperstructures is attached dynamically to a DNA strand by the coupling of transcription and translation. Previously, we proposed in the strand segregation model that one set of hyperstructures accompanies one parental strand into one daughter cell while another set of hyperstructures accompanies the other parental strand into the other daughter cell. This epigenetic mechanism results in daughter cells having different phenotypes. Here, I propose that one of the reasons why semiconservative replication has been selected is because it allows the generation of a population containing cells with very different growth rates even in steady-state conditions.

Hypothesis: bacteria live on the edge of phase transitions with a cell cycle regulated by a water-clock

“…8. underpins differentiation. My collaborators and I have argued that the 'natural' result of the processes involved in cell division, which often entail locally positive and globally negative circuits, should be to generate phenotypically different daughter cells (Norris, 1995)(Norris & Amar, 2012a) (Norris, 2019a). This scenario at its most basic level would yield one daughter with mainly equilibrium hyperstructures and the other with non-equilibrium hyperstructures appropriate for survival and growth, respectively (Norris, 2015).…”

A deep learning framework combined with word embedding to identify DNA replication origins

“…Embedding layer can realize the conversions from trinucleotides to corresponding pre-training feature vectors. In convolution blocks with an activation function of ReLu, convolutional kernels are set as [2,3,4] respectively, and the number of kernels for each size is set to be 128. L2 regularization is adopted to avoid over-fitting, which can ensure the availability of the proposed architecture.…”

“…Since the theory of DNA replication was proposed, the bioscience has been undergoing profound changes, which greatly motivates various studies based on the DNA replication, including cell growth and cell division. As a rigorous biological process starting at 'ORI' (origin of replication), DNA replication can generate two identical daughter strands by unwinding the parental template strands with the semiconservative replication strategy [1][2][3][4] . To keep normal cell functions and inherit a complete set of genomic information, DNA replication is activated only once per cell cycle 5 .…”