Abstract
The general aim of the project was to investigate and understand the coding structure in the DNA by using information theoretic, coding, and communication tools along with molecular genetics approaches. The codon encoding structure and possible mutations are modeled as a communication channel to investigate and obtain a clearer view on the codon to amino acid mappings. In addition, principles observed in the DNA are transferred into technical source coding methods. The universal source coding algorithms proposed by Lemple and Ziv in 1977 and 1978 and by Welch in 1984 actually show some similarity to alternative splicing known from eukaryotes which further increases the variability in protein encoding. Thus, the algorithms are modified by employing bi-directional reading procedures. The other main focus is on the comprehensive description of DNA as a dual coding device carrying two (digital and analog) types of information and on the biological meaning of this capacity. In particular, the interdependence of digital and analog coding properties of the DNA is studied with regard to regulation of genetic function. To this end, the role of the spatial order of genes and the genomic gradients of DNA thermodynamic stability and superhelical density in the bacterial chromosome is investigated. The analysis is performed with regard to alterations of spatiotemporal gene expression patterns and entropy (Shannon and Gibbs) profiles. Furthermore, the role of the DNA configuration and the organization of transient chromosomal structural-functional domains (TSFDs) in coordinating genomic expression with environmental changes is explored in wild type E. coli cells and in mutants lacking the chromosome-shaping factors, as well as in the plant pathogenic bacterium D. dadantii.
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Publications within the Project
Jiang X et al (2015) Chromosomal “Stress-Response” domains govern the spatiotemporal expression of the bacterial virulence program. In: mBio 6.3, e00353–15
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Henkel, W., Muskhelishvili, G., Nigatu, D., Sobetzko, P. (2018). The DNA from a Coding Perspective. In: Bossert, M. (eds) Information- and Communication Theory in Molecular Biology. Lecture Notes in Bioengineering. Springer, Cham. https://doi.org/10.1007/978-3-319-54729-9_12
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