TY - JOUR

T1 - A software module to assess the metabolic potential of mutant strains of the bacterium Corynebacterium glutamicum

AU - Kazantsev, F. V.

AU - Trofimova, M. F.

AU - Khlebodarova, T. M.

AU - Matushkin, Yu G.

AU - Lashin, S. A.

N1 - This work was supported by the projects of the Kurchatov Genomic Centre of ICG SB RAS No. 075-15-2019-1662.

PY - 2024/12

Y1 - 2024/12

N2 - Technologies for the production of a range of compounds using microorganisms are becoming increasingly popular in industry. The creation of highly productive strains whose metabolism is aimed to the synthesis of a specific desired product is impossible without complex directed modifications of the genome using mathematical and computer modeling methods. One of the bacterial species actively used in biotechnological production is Corynebacterium glutamicum. There are already 5 whole-genome flux balance models for it, which can be used for metabolism research and optimization tasks. The paper presents fluxMicrobiotech, a software module developed at the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, which implements a series of computational protocols designed for high-performance computer analysis of C. glutamicum whole-genome flux balance models. The tool is based on libraries from the opencobra community (https://opencobra.github.io) within the Python programming language (https://www.python.org), using the Pandas (https://pandas.pydata.org) and Escher (https://escher.readthedocs.io) libraries . It is configured to operate on a 'file-in/file-out' basis. The model, environmental conditions, and model constraints are specified as separate text table files, which allows one to prepare a series of files for each section, creating databases of available test scenarios for variations of the model. Or vice versa, allowing a single model to be tested under a series of different cultivation conditions. Post-processing tools for modeling data are set up, providing visualization of summary charts and metabolic maps.

AB - Technologies for the production of a range of compounds using microorganisms are becoming increasingly popular in industry. The creation of highly productive strains whose metabolism is aimed to the synthesis of a specific desired product is impossible without complex directed modifications of the genome using mathematical and computer modeling methods. One of the bacterial species actively used in biotechnological production is Corynebacterium glutamicum. There are already 5 whole-genome flux balance models for it, which can be used for metabolism research and optimization tasks. The paper presents fluxMicrobiotech, a software module developed at the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, which implements a series of computational protocols designed for high-performance computer analysis of C. glutamicum whole-genome flux balance models. The tool is based on libraries from the opencobra community (https://opencobra.github.io) within the Python programming language (https://www.python.org), using the Pandas (https://pandas.pydata.org) and Escher (https://escher.readthedocs.io) libraries . It is configured to operate on a 'file-in/file-out' basis. The model, environmental conditions, and model constraints are specified as separate text table files, which allows one to prepare a series of files for each section, creating databases of available test scenarios for variations of the model. Or vice versa, allowing a single model to be tested under a series of different cultivation conditions. Post-processing tools for modeling data are set up, providing visualization of summary charts and metabolic maps.

KW - bacterial metabolism

KW - flux models

KW - metabolic optimization

KW - rational metabolic engineering

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85217115181&origin=inward&txGid=dd6d227d4257c8ff2492aa1fc6cfd49e

UR - https://www.mendeley.com/catalogue/cb3e4a7b-fce2-3b33-b76b-09292b97dc03/

U2 - 10.18699/vjgb-24-97

DO - 10.18699/vjgb-24-97

M3 - Article

C2 - 39944802

VL - 28

SP - 897

EP - 903

JO - Вавиловский журнал генетики и селекции

JF - Вавиловский журнал генетики и селекции

SN - 2500-0462

IS - 8

ER -