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Algorithm for the Reconstruction of Mathematical Frame Models of Bacterial Transcription Regulation

Author

Listed:
  • Tatiana N. Lakhova

    (Kurchatov Genomic Centre of Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
    Department of Mathematics and Mechanics, Mathematical Center, Novosibirsk State University, 630090 Novosibirsk, Russia)

  • Fedor V. Kazantsev

    (Kurchatov Genomic Centre of Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
    Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia)

  • Aleksey M. Mukhin

    (Kurchatov Genomic Centre of Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia)

  • Nikolay A. Kolchanov

    (Kurchatov Genomic Centre of Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
    Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia)

  • Yury G. Matushkin

    (Kurchatov Genomic Centre of Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
    Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia)

  • Sergey A. Lashin

    (Kurchatov Genomic Centre of Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
    Department of Mathematics and Mechanics, Mathematical Center, Novosibirsk State University, 630090 Novosibirsk, Russia
    Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia)

Abstract

Transcription regulation plays an important role in bacterial activity. The operon concept coined by François Jacob and Jacques Monod has had a considerable effect on investigations into gene expression regulation, including modeling. However, most such studies have considered the regulation models devised manually for one or several operons. For that reason, the objective of the present study was automated genome model reconstruction for different bacteria. The suggested algorithm accounted for all possible interactions of transcription factors and their binding sites in an operon’s promoter region. Transcription factor enumeration was performed using the deep-first search technique. The obtained models are of interest for those involved in the research of transcription factor regulatory effects on bacterial gene expression in microbiology and biotechnology.

Suggested Citation

  • Tatiana N. Lakhova & Fedor V. Kazantsev & Aleksey M. Mukhin & Nikolay A. Kolchanov & Yury G. Matushkin & Sergey A. Lashin, 2022. "Algorithm for the Reconstruction of Mathematical Frame Models of Bacterial Transcription Regulation," Mathematics, MDPI, vol. 10(23), pages 1-9, November.
    • Handle: RePEc:gam:jmathe:v:10:y:2022:i:23:p:4480-:d:985964
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    References listed on IDEAS

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    1. Zhao, Na & Liu, Haihong & Yan, Fang, 2020. "Oscillation dynamics of MeKS core module containing positive and negative feedback loops with time delay," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 538(C).
    2. Muir Morrison & Manuel Razo-Mejia & Rob Phillips, 2021. "Reconciling kinetic and thermodynamic models of bacterial transcription," PLOS Computational Biology, Public Library of Science, vol. 17(1), pages 1-30, January.
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