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PreprintCited by 7Microbial Metabolic Engineering and BioproductionGene Regulatory Network AnalysisBacterial Genetics and Biotechnology

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Minimization of proteome reallocation explains metabolic transition in hierarchical utilization of carbon sources

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Liu, Zhihao, Chen, Minghao, Hu, Jingmin, Wang, Yonghong, Chen, Yu·2024·mSystems
DOI 10.1101/2024.01.23.576957PMC PMC12282068

Preprint — published as 10.1128/msystems.00690-25

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Abstract

Cells choose between alternative pathways in metabolic networks under diverse environmental conditions, but the principles governing the choice are insufficiently understood, especially in response to dynamically changing conditions. Here we observed that a lactic acid bacterium Bacillus coagulans displayed homolactic fermentation on glucose or trehalose as the sole carbon source, but transitioned from homolactic to heterolactic fermentation during the hierarchical utilization of glucose and trehalose when growing on the mixture. We simulated the observation by dynamic minimization of reallocation of proteome (dMORP) using an enzyme-constrained genome-scale metabolic model of B. coagulans , which coincided with our omics data. Moreover, we evolved strains to co-utilize mixed carbon sources and repress the choice of heterolactic fermentation, and the dynamics after co-utilization of carbon sources could also be captured by dMORP. Altogether, the findings suggest that upon rapid environmental changes bacteria tend to minimize proteome reallocation and accordingly adjust metabolism, and dMORP would be useful in simulating and understanding cellular dynamics.

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Metadata

Authors
Liu, Z., Chen, M., Hu, J., Wang, Y., & Chen, Y.
Affiliations
  • East China University of Science and Technology (CN)
  • Chinese Academy of Sciences (CN)
Corresponding author
  • Wang, Yonghong
  • Chen, Yu
ORCID
Venue
mSystems
Publisher
openRxiv
Published
2024-01-25
Volume
10
Issue
7
Pages
e0069025-e0069025
ISSN
2379-5077 (ISSN-L)
DOI
10.1101/2024.01.23.576957
PMC
PMC12282068
OpenAlex
W4411784373
Cited by
7
References
1
Citations by year
2026: 5 · 2025: 2
FWCI
2.10
Type
journal article
Language
en
Open access
Licence
Locations
  • mSystems (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • National Natural Science Foundation of China (21878084)
  • National Key Research and Development Program of China (2023YFA0913900, 2024YFA0920300)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Keywords
metabolic transition, Bacillus coagulans, homolactic fermentation, heterolactic fermentation, trehalose, glucose, mixed carbon sources, genome-scale metabolic models, lactic acid bacteria
MeSH terms
Bacillus coagulans, Bacterial Proteins, Carbon, Fermentation, Glucose, Models, Biological, Trehalose, Proteome, Metabolic Networks and Pathways

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