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

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.

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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

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Acknowledgements

We thank Rainer Machne and the anonymous reviewers for helpful comments. This work was in part supported by the research grant of the Deutsche Forschungsgemeinschaft (InKoMBio) to G.M.

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Correspondence to Georgi Muskhelishvili.

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Muskhelishvili, G., Travers, A. Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information. Cell. Mol. Life Sci. 70, 4555–4567 (2013). https://doi.org/10.1007/s00018-013-1394-1

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Keywords

  • Holistic methodology
  • DNA supercoiling
  • Chromosome structure
  • Gene order
  • Transcriptional regulation
  • Nucleoid-associated proteins