Relationship between digital information and thermodynamic stability in bacterial genomes.

Dawit Nigatu,Werner Henkel,Patrick Sobetzko,Georgi Muskhelishvili

doi:10.1186/s13637-016-0037-x

Abstract

Ever since the introduction of the Watson-Crick model, numerous efforts have been made to fully characterize the digital information content of the DNA. However, it became increasingly evident that variations of DNA configuration also provide an “analog” type of information related to the physicochemical properties of the DNA, such as thermodynamic stability and supercoiling. Hence, the parallel investigation of the digital information contained in the base sequence with associated analog parameters is very important for understanding the coding capacity of the DNA. In this paper, we represented analog information by its thermodynamic stability and compare it with digital information using Shannon and Gibbs entropy measures on the complete genome sequences of several bacteria, including Escherichia coli (E. coli), Bacillus subtilis (B. subtilis), Streptomyces coelicolor (S. coelicolor), and Salmonella typhimurium (S. typhimurium). Furthermore, the link to the broader classes of functional gene groups (anabolic and catabolic) is examined. Obtained results demonstrate the couplings between thermodynamic stability and digital sequence organization in the bacterial genomes. In addition, our data suggest a determinative role of the genome-wide distribution of DNA thermodynamic stability in the spatial organization of functional gene groups.

Highlights

The double-helical DNA polymer is the carrier of the genetic information required for the reproduction of any organism
This is visible from the shape of Gibbs entropy curve in which the lowest point is around the terminus, attributed to the ATrichness
4 Conclusions In addition to the digital type of linear genetic code encoding the proteins, DNA contains a continuous analog type of information resulting from the physicochemical properties of the DNA polymer

Summary

Introduction

The double-helical DNA polymer is the carrier of the genetic information required for the reproduction of any organism. This information is inscribed by the sequence of the four bases adenine (A), thymine (T), cytosine (C), and guanine (G) paired in a complementary fashion (A with T and G with C). The digital nature of the genetic code can be seen in the correspondence of the “on-or-off ” type digital logic with the feature that the genes can be expressed or not [1] There is another type of information, dubbed “analog code”, that coexists with the digital code and is related to physicochemical properties of the DNA [1, 2].

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Results

Conclusion