Authors:
Paweł Błażej
;
Paweł Mackiewicz
;
Małgorzata Wańczyk
and
Stanisław Cebrat
Affiliation:
University of Wrocław, Poland
Keyword(s):
DNA Asymmetry, Genome Rearrangements, Monte Carlo Simulation, Mutational Pressure.
Related
Ontology
Subjects/Areas/Topics:
Agents
;
Artificial Intelligence
;
Bioinformatics
;
Biomedical Engineering
;
Enterprise Information Systems
;
Information Systems Analysis and Specification
;
Methodologies and Technologies
;
Operational Research
;
Sequence Analysis
;
Simulation
Abstract:
The main force shaping the structure of bacterial chromosomes is the replication-associated mutational pressure which is characterized by distinct nucleotide substitution patterns acting on differently replicated DNA strands (leading and lagging). Therefore, the composition of DNA strands is asymmetric and it is important at which strand a gene is located and into which strand it could be translocated. Thus, the mutational pressure restricts also intragenomic translocations. To analyze this effect, we have elaborated a simulation model of bacterial genome evolution assuming translocation of protein coding genes and different types of selection acting on their sequences. The ’negative’ selection eliminated individuals if the coding signal of any gene in its genome dropped below the acceptable range, whereas the ’stabilizing’ selection did not allow for the decrease in the coding signal of any gene below its original value. Under the ’negative’ selection more genes stayed or were trans
located to the lagging strand, whereas under the ’stabilizing’ selection more genes preferred the leading strand. The ’stabilizing’ selection eliminated more individuals because of the coding signal loss and slightly fewer because of the stop codon generation. The ’stabilizing’ selection allowed also for much less gene translocations between strands than the ’negative’ selection.
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