title: Relationship between digital information and thermodynamic stability in bacterial genomes.
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, includingEscherichia coli(E. coli),Bacillus subtilis(B. subtilis),Streptomyces coelicolor(S. coelicolor), andSalmonella 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.
authors.affiliation: Transmission Systems Group, School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, Bremen, 28759 Germany.
authors.forename: Dawit
authors.initials: D
authors.lastname: Nigatu
authors.affiliation: Transmission Systems Group, School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, Bremen, 28759 Germany.
authors.forename: Werner
authors.initials: W
authors.lastname: Henkel
authors.affiliation: Philipps-Universität Marburg, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße, Mehrzweckgebäude, Marburg, 35043 Germany.
authors.forename: Patrick
authors.initials: P
authors.lastname: Sobetzko
authors.affiliation: Microbiologie, Adaptation, Pathogénie, UMR5240 CNRS-UCBL-INSA-BayerCropScience, Lyon, France ; Jacobs University Bremen, Campus Ring 1, Bremen, 28759 Germany.
authors.forename: Georgi
authors.initials: G
authors.lastname: Muskhelishvili
keywords: Gibbs entropy; Sequence analysis; Shannon entropy; Thermodynamic stability