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

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Algorithm for the Reconstruction of Mathematical Frame Models of Bacterial Transcription Regulation. / Lakhova, Tatiana N.; Kazantsev, Fedor V.; Mukhin, Aleksey M. et al.

In: Mathematics, Vol. 10, No. 23, 4480, 12.2022.

Research output: Contribution to journal › Article › peer-review

BibTeX

@article{f2e394e4ec73493482fabf322cf52a02,

title = "Algorithm for the Reconstruction of Mathematical Frame Models of Bacterial Transcription Regulation",

abstract = "Transcription regulation plays an important role in bacterial activity. The operon concept coined by Fran{\c c}ois 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{\textquoteright}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 = "bacterial transcription regulation, Hill{\textquoteright}s generalized functions, mathematical frame model",

author = "Lakhova, {Tatiana N.} and Kazantsev, {Fedor V.} and Mukhin, {Aleksey M.} and Kolchanov, {Nikolay A.} and Matushkin, {Yury G.} and Lashin, {Sergey A.}",

note = "Funding Information: The study was supported by the Kurchatov Genomic Centre of the Institute of Cytology and Genetics SB RAS No. 075-15-2019-1662 and the Ministry of Science and Higher Education budget project No. FWNR-2022-0006. Publisher Copyright: {\textcopyright} 2022 by the authors.",

year = "2022",

month = dec,

doi = "10.3390/math10234480",

language = "English",

volume = "10",

journal = "Mathematics",

issn = "2227-7390",

publisher = "MDPI AG",

number = "23",

}

RIS

TY - JOUR

T1 - Algorithm for the Reconstruction of Mathematical Frame Models of Bacterial Transcription Regulation

AU - Lakhova, Tatiana N.

AU - Kazantsev, Fedor V.

AU - Mukhin, Aleksey M.

AU - Kolchanov, Nikolay A.

AU - Matushkin, Yury G.

AU - Lashin, Sergey A.

N1 - Funding Information: The study was supported by the Kurchatov Genomic Centre of the Institute of Cytology and Genetics SB RAS No. 075-15-2019-1662 and the Ministry of Science and Higher Education budget project No. FWNR-2022-0006. Publisher Copyright: © 2022 by the authors.

PY - 2022/12

Y1 - 2022/12

N2 - 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.

AB - 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.

KW - bacterial transcription regulation

KW - Hill’s generalized functions

KW - mathematical frame model

UR - http://www.scopus.com/inward/record.url?scp=85143585232&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/d675e2b6-0e7a-303a-80cc-2823ae5e13ff/

U2 - 10.3390/math10234480

DO - 10.3390/math10234480

M3 - Article

AN - SCOPUS:85143585232

VL - 10

JO - Mathematics

JF - Mathematics

SN - 2227-7390

IS - 23

M1 - 4480

ER -

ID: 40800139