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

Tatiana N. Lakhova (), Fedor V. Kazantsev, Aleksey M. Mukhin, Nikolay A. Kolchanov, Yury G. Matushkin and Sergey A. Lashin ()
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Tatiana N. Lakhova: Kurchatov Genomic Centre of Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
Fedor V. Kazantsev: Kurchatov Genomic Centre of Institute of Cytology and Genetics SB RAS, 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
Yury G. Matushkin: Kurchatov Genomic Centre of Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
Sergey A. Lashin: Kurchatov Genomic Centre of Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia

Mathematics, 2022, vol. 10, issue 23, 1-9

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.

Keywords: mathematical frame model; Hill’s generalized functions; bacterial transcription regulation (search for similar items in EconPapers)
JEL-codes: C (search for similar items in EconPapers)
Date: 2022
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