The DOI matches its Crossref record; 59 of the 59 references it cites were found in a registry or an index.
Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source,l-1,2-Propanediol
Open accessAbstract
Laboratory adaptive evolution studies can provide key information to address a wide range of issues in evolutionary biology. Such studies have been limited thus far by the inability of workers to readily detect mutations in evolved microbial strains on a genome scale. This limitation has now been overcome by recently developed genome sequencing technology that allows workers to identify all accumulated mutations that appear during laboratory adaptive evolution. In this study, we evolved Escherichia coli K-12 MG1655 with a nonnative carbon source,l-1,2-propanediol (l-1,2-PDO), for ∼700 generations. We found that (i) experimental evolution of E. coli for ∼700 generations in 1,2-PDO-supplemented minimal medium resulted in acquisition of the ability to use l-1,2-PDO as a sole carbon and energy source so that the organism changed from an organism that did not grow at all initially to an organism that had a growth rate of 0.35 h−1; (ii) six mutations detected by whole-genome resequencing accumulated in the evolved E. coli mutant over the course of adaptive evolution on l-1,2-PDO; (iii) five of the six mutations were within coding regions, and IS 5 was inserted between two fuc regulons; (iv) two major mutations (mutations in fucO and its promoter) involved in l-1,2-PDO catabolism appeared early during adaptive evolution; and (v) multiple defined knock-in mutant strains with all of the mutations had growth rates essentially matching that of the evolved strain. These results provide insight into the genetic basis underlying microbial evolution for growth on a nonnative substrate.
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“Whereas certain environments can lead to fast selection of improved phenotypes, others, including the long-term adaptation to environmental pH [59,63], represent complex environments where microbial cells show low adaptive potential in terms of absolute fitness gain.”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [63]
In the citing paper
“In several recent studies, gene amplifications were identified to contribute to increased gene dosage [63,116,128] and subsequently increased fitness.”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [63]
In the citing paper
“Frequent rpoB mutations were also found during batch evolution on glucose in a more recent study [63]”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [63]
In the citing paper
“Increased growth during osmotic stress was linked to mutations that led to increased expression of enterobactin biosynthesis genes (fepA and entD among others) [63].”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [63]
In the citing paper
“but most importantly the rpoS mutation alone did not positively influence the growth rate in the ancestral ∆pgi strain; rpoS mutations were epistatically linked to additional mutations.”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [63]
In the citing paper
“Mutations in acrAB and marC were found independently in these studies; further changes were linked to carbon and nitrogen metabolism via gatY and tnaA[86], enterobactin synthesis [63] or attenuated rpoS activity via hfq mutations [87].”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [63]
In the citing paper
“and n-butanol tolerance is weakly compatible with oxidative stress [63] and leads to trade-offs in hexane and chloramphenicol resistance [86].”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [63]
In the citing paper
“Similarly, n-butanol tolerance was reported to be highly compatible with osmotic stress [63].”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [63]
In the citing paper
“Furthermore, increased oxidative stress resistance in E. coli may be linked to mutations in the soxR reducing system and increased levels of cellular catalase/peroxidase (katG) [63].”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [63]
Citations
Cites
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products.
Datsenko, K., & Wanner, B. (2000) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.120163297 · Cited by 15,902
Escherichia coli and Salmonella :cellular and molecular biology
Neidhardt, F. C. (1996) · ASM Press eBooks · Cited by 8,197
The Neutral Theory of Molecular Evolution
Kimura, M. (1979) · Scientific American · doi:10.1038/scientificamerican1179-98 · Cited by 7,687
A constant rate of spontaneous mutation in DNA-based microbes.
Drake, J. W. (1991) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.88.16.7160 · Cited by 1,199
Genome evolution and adaptation in a long-term experiment with Escherichia coli
Barrick, J. E., Yu, D. S., Yoon, S. H., Jeong, H., Oh, T. K., Schneider, D., Lenski, R. E., & Kim, J. F. (2009) · Nature · doi:10.1038/nature08480 · Cited by 1,184
Characterization of the 1918 influenza virus polymerase genes
Taubenberger, J. K., Reid, A. H., Lourens, R. M., Wang, R., Jin, G., & Fanning, T. G. (2005) · Nature · doi:10.1038/nature04230 · Cited by 1,054
Integrating high-throughput and computational data elucidates bacterial networks
Covert, M. W., Knight, E. M., Reed, J. L., Herrgard, M. J., & Palsson, B. O. (2004) · Nature · doi:10.1038/nature02456 · Cited by 792
Self-citationThe mechanisms of carbon catabolite repression in bacteria
Deutscher, J. (2008) · Current Opinion in Microbiology · doi:10.1016/j.mib.2008.02.007 · Cited by 676
The origin of the naked grains of maize
Wang, H., Wagler, T. N., Li, B., Zhao, Q., Vigouroux, Y., Faller, M., Bomblies, K., LUKENS, L. N., & Doebley, J. (2005) · Nature · doi:10.1038/nature03863 · Cited by 603
Systematic changes in gene expression patterns following adaptive evolution in yeast
Ferea, T., Botstein, D., Brown, P. O., & Rosenzweig, R. F. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.17.9721 · Cited by 479
Cited by
Sorted by citations
Adaptive laboratory evolution—Principles and applications for biotechnology
Dragosits, M., & Mattanovich, D. (2013) · Microbial Cell Factories · doi:10.1186/1475-2859-12-64 · Cited by 827
“coli culture could evolve the ability to aerobically utilize citrate [37], or the ability to use the non-natural carbon source 1,2-propanediol [71]; also, a strain deficient in glutathione biosynthesis was able to develop compensatory mutations to restore this function [147].”
BackgroundKawecki, T. J., Lenski, R. E., Ebert, D., Hollis, B., Olivieri, I., & Whitlock, M. C. (2012) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2012.06.001 · Cited by 807
Sandberg, T. E., Salazar, M. J., Weng, L. L., Palsson, B. Ø., & Feist, A. M. (2019) · Metabolic Engineering · doi:10.1016/j.ymben.2019.08.004 · Cited by 585
Self-citationBasic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli
McCloskey, D., Palsson, B. Ø., & Feist, A. M. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.18 · Cited by 327
“These changes can then be reintroduced and their effect on the organism’s fitness studied (Herring et al , 2006; Conrad et al , 2009; Lee and Palsson, 2010; Applebee et al , 2011).”
BackgroundSelf-citationAdaptive laboratory evolution — harnessing the power of biology for metabolic engineering
Portnoy, V. A., Bezdan, D., & Zengler, K. (2011) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2011.03.007 · Cited by 309
“(d) and (e) Activation of ‘latent’ pathways by forcing the microorganism to utilize or produce nonnative substrates leads to valuable biological discoveries [3,32].”
BackgroundMethod
Metadata
- Authors
- Lee, D.-H., & Palsson, B. Ø.
- Affiliations
- University of California San Diego (US)
- Venue
- Applied and Environmental Microbiology
- Publisher
- American Society for Microbiology
- Published
- 2010-07
- Volume
- 76
- Issue
- 13
- Pages
- 4158-4168
- ISSN
- 0099-2240 (ISSN-L)
- 1098-5336
- PMC
- PMC2897412
- OpenAlex
- W2135829725
- Cited by
- 160
- References
- 59
- Citations by year
- 2026: 6 · 2025: 7 · 2024: 6 · 2023: 4 · 2022: 8 · 2021: 15 · 2020: 13 · 2019: 7 · 2018: 8 · 2017: 7 · 2016: 9 · 2015: 16 · 2014: 9 · 2013: 13 · 2012: 14
- FWCI
- 8.10
- Type
- journal article
- Language
- en
- Update notices
- correction (2010-09-15)
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Applied and Environmental Microbiology (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- U.S. Department of Energy (FC02-02ER63446)
- National Institutes of Health
- Office of Science
- University of California, San Diego
- National Institute of General Medical Sciences (R01GM062791, GM 062791)
- Topics
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- Escherichia coli MG1655, adaptive evolution, whole-genome resequencing, growth rate, microbial evolution
- MeSH terms
- Adaptation, Physiological, Culture Media, DNA, Bacterial, Mutation, Polymerase Chain Reaction, Genome, Bacterial, Sequence Analysis, DNA, Directed Molecular Evolution, Propylene Glycol, Escherichia coli K12
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