Order from the Order: How a Spatiotemporal Genetic Program Is Encoded in a 2-D Genetic Map of the Bacterial Chromosome

Abstract

In this article, we sketch out a holistic methodology used for exploring how the genetic program is encoded in a 2-D genetic map of a bacterial chromosome. We argue that the major problem resides in the conceptual integration of the two logically distinct types of information encoded in the chiral double-helical DNA polymer. This integration is accomplished by mapping the genetic function on the genomic sequence organisation and therefore is potentially applicable to any chromosome. The vast generalisation achieved by this approach necessarily ignores exquisite details, yet it is fundamental in providing comprehensive methodology for exploring the role of the DNA sequence organisation in harnessing genetic information and sustaining biological order.

The Proximity of Ribosomal Protein Genes to oriC Enhances Vibrio cholerae Fitness in the Absence of Multifork Replication

“…Meanwhile, the genetic material still needs to be replicated, transcribed, and segregated along the cell cycle. In this context, a body of evidence indicates that gene order within the bacterial chromosome contributes to genome organization and to coordinated cellular homeostasis with the cell cycle (11, 12, 14). Recent research describes several examples in which the genomic position of genes is essential to achieve their cellular functions (reviewed in reference 1).…”

DNA Information: Laws of Perception

“…The gray horizontal arrows indicate the flow of time from the "initial distinction" of high oxygen pressure and nutrients in the medium and initiation of exponential growth (Exp), until the "final distinction" of their exhaustion and growth cessation in stationary phase (Stat). Adapted from Muskhelishvili and Travers (2014) Two consequences of the dual informational capacity of the DNA are of note. First, it is in keeping with the definition of an autopoietic system as an operationally closed circuit producing the tools required for its own operation and reveals this operating principle at the molecular level of genetic organization, that is, at its very roots.…”

“…Highly flexible (isotropic) and less flexible (anisotropically bendable) DNA sequences (left and right panels, respectively) occupy different volumes of configurational space. Adapted fromMuskhelishvili and Travers 2014 …”

Function of Nucleoid-Associated Proteins in Chromosome Structuring and Transcriptional Regulation

“…There is a marked association between genes that have been acquired via HGT and genes that express transfer RNA (tRNA), with many pathogenicity islands being found adjacent to tRNA genes or operons [Dobrindt et al, 2002;Guo et al, 2014]. Recent discoveries concerning barriers to the free diffusion of proteins in the cytoplasm [Montero Llopis et al, 2010;Parry et al, 2014] and the finding that folding of the nucleoid brings together in space many genes that interact suggest that inserting new genes into the genome in a completely random fashion may not produce optimal gene-gene communication and regulatory integration [Berlatzky et al, 2008;Dorman, 2013;Janga et al, 2009;Jeong et al, 2004;Junier et al, 2012;Képès, 2004;Mathelier and Carbonne, 2010;Muskhelishvili, 2014;Wright et al, 2007;Xiao et al, 2011].…”