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Authors: Paweł Błażej ; Paweł Mackiewicz and Stanisław Cebrat

Affiliation: University of Wrocław, Poland

Keyword(s): DNA asymmetry, Mutational pressure, Genome evolution, Monte Carlo simulation.

Related Ontology Subjects/Areas/Topics: Agents ; Artificial Intelligence ; Bioinformatics ; Biomedical Engineering ; Enterprise Information Systems ; Information Systems Analysis and Specification ; Methodologies and Technologies ; Operational Research ; Simulation

Abstract: Directional mutational pressure associated with DNA replication is one of the most significant forces shaping nucleotide composition and structure of bacterial chromosomes as well as influencing the evolution of their genes. Here we introduced the model of bacterial genome evolution including two mutational pressures acting in differently replicated DNA strands (called leading and lagging). The simulations were performed on the population of protein coding genes from the Borrelia burgdorferi genome which shows a very strong compositional bias between the DNA strands. The simulated genomes were eliminated by selection because of: (i) stop translation codon occurrence in their gene sequences and (ii) the loss of their coding signal which was calculated according to the algorithm for recognition of protein coding sequences. This algorithm considers three independent homogeneous Markov chains to describe transition between nucleotides separately for each of three codon positions in a giv en DNA sequence. The negative selection for stop codons appeared much stronger than the one based on the coding signal and led to elimination of more genomes from the population. The genes were subjected both to the direct mutational pressure, characteristic of the strand on which they are located and to the reverse pressure, characteristic of the opposite strand. Generally, the elimination of genomes because of stop codons occurrence was the most frequent for the reverse pressure whereas the coding signal selection eliminated the genome most often for the direct pressure. The leading strand mutational pressure was more destructive for coding signal whereas the the lagging strand pressure generated more stop codons in the gene sequences. (More)

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Paper citation in several formats:
Błażej, P.; Mackiewicz, P. and Cebrat, S. (2012). SIMULATION OF BACTERIAL GENOME EVOLUTION UNDER REPLICATIONAL MUTATIONAL PRESSURES. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2012) - BIOINFORMATICS; ISBN 978-989-8425-90-4; ISSN 2184-4305, SciTePress, pages 51-57. DOI: 10.5220/0003755900510057

@conference{bioinformatics12,
author={Paweł Błażej. and Paweł Mackiewicz. and Stanisław Cebrat.},
title={SIMULATION OF BACTERIAL GENOME EVOLUTION UNDER REPLICATIONAL MUTATIONAL PRESSURES},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2012) - BIOINFORMATICS},
year={2012},
pages={51-57},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003755900510057},
isbn={978-989-8425-90-4},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2012) - BIOINFORMATICS
TI - SIMULATION OF BACTERIAL GENOME EVOLUTION UNDER REPLICATIONAL MUTATIONAL PRESSURES
SN - 978-989-8425-90-4
IS - 2184-4305
AU - Błażej, P.
AU - Mackiewicz, P.
AU - Cebrat, S.
PY - 2012
SP - 51
EP - 57
DO - 10.5220/0003755900510057
PB - SciTePress

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