Laboratory Evolution and Multi-platform Genome Re-sequencing of the Cellulolytic Actinobacterium Thermobifida fusca
Open accessAbstract
Biological utilization of cellulose is a complex process involving the coordinated expression of different cellulases, often in a synergistic manner. One possible means of inducing an organism-level change in cellulase activity is to use laboratory adaptive evolution. In this study, evolved strains of the cellulolytic actinobacterium, Thermobifida fusca, were generated for two different scenarios: continuous exposure to cellobiose (strain muC) or alternating exposure to cellobiose and glucose (strain muS). These environmental conditions produced a phenotype specialized for growth on cellobiose (muC) and an adaptable, generalist phenotype (muS). Characterization of cellular phenotypes and whole genome re-sequencing were conducted for both the muC and muS strains. Phenotypically, the muC strain showed decreased cell yield over the course of evolution concurrent with decreased cellulase activity, increased intracellular ATP concentrations, and higher end-product secretions. The muS strain increased its cell yield for growth on glucose and exhibited a more generalist phenotype with higher cellulase activity and growth capabilities on different substrates. Whole genome re-sequencing identified 48 errors in the reference genome and 18 and 14 point mutations in the muC and muS strains, respectively. Among these mutations, the site mutation of Tfu_1867 was found to contribute the specialist phenotype and the site mutation of Tfu_0423 was found to contribute the generalist phenotype. By conducting and characterizing evolution experiments on Thermobifida fusca, we were able to show that evolutionary changes balance ATP energetic considerations with cellulase activity. Increased cellulase activity is achieved in stress environments (switching carbon sources), otherwise cellulase activity is minimized to conserve ATP.
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Parallel glucose-evolved E. coli cultures showed significant parallelism in the change of gene expression profiles.
“Also, a significant parallelism in the change of the gene expression profiles was noticed in these parallel cultures [64]”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [64]
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Adaptive laboratory evolution—Principles and applications for biotechnology
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- Authors
- Deng, Y., & Fong, S. S.
- Affiliations
- Dartmouth College (US)
- Virginia Commonwealth University (US)
- Corresponding author
- Fong, Stephen S.
- Venue
- Journal of Biological Chemistry
- Publisher
- Elsevier BV
- Published
- 2011-11
- Volume
- 286
- Issue
- 46
- Pages
- 39958-39966
- ISSN
- 0021-9258 (ISSN-L)
- PMC
- PMC3220580
- OpenAlex
- W1987305766
- Cited by
- 33
- References
- 48
- Citations by year
- 2025: 1 · 2024: 1 · 2023: 1 · 2022: 5 · 2021: 1 · 2020: 1 · 2019: 1 · 2018: 2 · 2017: 3 · 2016: 1 · 2015: 6 · 2014: 3 · 2013: 3 · 2012: 4
- FWCI
- 1.89
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Biological Chemistry (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Physical Sciences › Engineering › Biomedical Engineering › Biofuel production and bioconversion
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Keywords
- Thermobifida fusca, cellulase activity, cellulose degradation, adaptive laboratory evolution, cellobiose, glucose, point mutations, whole-genome resequencing
- MeSH terms
- Adenosine Triphosphate, Cellobiose, Cellulase, DNA Mutational Analysis, Energy Metabolism, Glucose, Sweetening Agents, Genome, Bacterial, Point Mutation, Evolution, Molecular, Actinobacteria
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