Cellular and Molecular Life Sciences

, Volume 70, Issue 23, pp 4555–4567

Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information

Authors

    • School of Engineering and ScienceJacobs University Bremen
  • Andrew Travers
    • MRC Laboratory of Molecular Biology
Review

DOI: 10.1007/s00018-013-1394-1

Cite this article as:
Muskhelishvili, G. & Travers, A. Cell. Mol. Life Sci. (2013) 70: 4555. doi:10.1007/s00018-013-1394-1

Abstract

Understanding genetic regulation is a problem of fundamental importance. Recent studies have made it increasingly evident that, whereas the cellular genetic regulation system embodies multiple disparate elements engaged in numerous interactions, the central issue is the genuine function of the DNA molecule as information carrier. Compelling evidence suggests that the DNA, in addition to the digital information of the linear genetic code (the semantics), encodes equally important continuous, or analog, information that specifies the structural dynamics and configuration (the syntax) of the polymer. These two DNA information types are intrinsically coupled in the primary sequence organisation, and this coupling is directly relevant to regulation of the genetic function. In this review, we emphasise the critical need of holistic integration of the DNA information as a prerequisite for understanding the organisational complexity of the genetic regulation system.

Keywords

Holistic methodologyDNA supercoilingChromosome structureGene orderTranscriptional regulationNucleoid-associated proteins

Abbreviations

Dps

DNA protection during starvation protein

FD

Functional domain

FIS

Factor for inversion stimulation

H-NS

Histone-like nucleoid-structuring protein

HU

Heat-stable protein from the strain U13

IHF

Integration host factor

Lrp

Leucine responsive protein

NAP

Nucleoid-associated protein

OriC

Origin of chromosomal replication

RNAP

RNA polymerase

RpoD

RNAP vegetative sigma factor (σ70)

RpoS

RNAP stationary phase sigma factor (σS)

Ter

Chromosomal replication terminus

TF

Transcription factor

TG

Target gene

Transcripton

Transcription unit

TRN

Transcriptional regulatory network

tyrT

Tyrosyl transfer RNA gene

UAS

Upstream activating sequence

Copyright information

© Springer Basel 2013