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Green R, Wang H, Botchey C, Zhang SNN, Wadsworth C, Tyrrell F, Letton J, McBain AJ, Paszek P, Krašovec R, Knight CG. Collective peroxide detoxification determines microbial mutation rate plasticity in E. coli. PLoS Biol 2024; 22:e3002711. [PMID: 39008532 PMCID: PMC11272383 DOI: 10.1371/journal.pbio.3002711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 07/25/2024] [Accepted: 06/13/2024] [Indexed: 07/17/2024] Open
Abstract
Mutagenesis is responsive to many environmental factors. Evolution therefore depends on the environment not only for selection but also in determining the variation available in a population. One such environmental dependency is the inverse relationship between mutation rates and population density in many microbial species. Here, we determine the mechanism responsible for this mutation rate plasticity. Using dynamical computational modelling and in culture mutation rate estimation, we show that the negative relationship between mutation rate and population density arises from the collective ability of microbial populations to control concentrations of hydrogen peroxide. We demonstrate a loss of this density-associated mutation rate plasticity (DAMP) when Escherichia coli populations are deficient in the degradation of hydrogen peroxide. We further show that the reduction in mutation rate in denser populations is restored in peroxide degradation-deficient cells by the presence of wild-type cells in a mixed population. Together, these model-guided experiments provide a mechanistic explanation for DAMP, applicable across all domains of life, and frames mutation rate as a dynamic trait shaped by microbial community composition.
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Affiliation(s)
- Rowan Green
- School of Natural Sciences, Faculty of Science & Engineering, University of Manchester, United Kingdom
| | - Hejie Wang
- School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, United Kingdom
| | - Carol Botchey
- School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, United Kingdom
| | - Siu Nam Nancy Zhang
- School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, United Kingdom
| | - Charles Wadsworth
- School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, United Kingdom
| | - Francesca Tyrrell
- School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, United Kingdom
| | - James Letton
- School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, United Kingdom
| | - Andrew J. McBain
- School of Health Sciences, Faculty of Biology Medicine & Health, University of Manchester, United Kingdom
| | - Pawel Paszek
- School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, United Kingdom
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Rok Krašovec
- School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, United Kingdom
| | - Christopher G. Knight
- School of Natural Sciences, Faculty of Science & Engineering, University of Manchester, United Kingdom
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2
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Sitompul SN, Diaz Garcia LA, Price J, Tee KL, Wong TS. Fast-track adaptive laboratory evolution of Cupriavidus necator H16 with divalent metal cations. Biotechnol J 2024; 19:e2300577. [PMID: 38987216 DOI: 10.1002/biot.202300577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 06/05/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024]
Abstract
Microbial strain improvement through adaptive laboratory evolution (ALE) has been a key strategy in biotechnology for enhancing desired phenotypic traits. In this Biotech Method paper, we present an accelerated ALE (aALE) workflow and its successful implementation in evolving Cupriavidus necator H16 for enhanced tolerance toward elevated glycerol concentrations. The method involves the deliberate induction of genetic diversity through controlled exposure to divalent metal cations, enabling the rapid identification of improved variants. Through this approach, we observed the emergence of robust variants capable of growing in high glycerol concentration environments, demonstrating the efficacy of our aALE workflow. When cultivated in 10% v/v glycerol, the adapted variant Mn-C2-B11, selected through aALE, achieved a final OD600 value of 56.0 and a dry cell weight of 15.2 g L-1, compared to the wild type (WT) strain's final OD600 of 39.1 and dry cell weight of 8.4 g L-1. At an even higher glycerol concentration of 15% v/v, Mn-C2-B11 reached a final OD600 of 48.9 and a dry cell weight of 12.7 g L-1, in contrast to the WT strain's final OD600 of 9.0 and dry cell weight of 3.1 g L-1. Higher glycerol consumption by Mn-C2-B11 was also confirmed by high-performance liquid chromatography (HPLC) analysis. This adapted variant consumed 34.5 times more glycerol compared to the WT strain at 10% v/v glycerol. Our method offers several advantages over other reported ALE approaches, including its independence from genetically modified strains, specialized genetic tools, and potentially carcinogenic DNA-modifying agents. By utilizing divalent metal cations as mutagens, we offer a safer, more efficient, and cost-effective alternative for expansion of genetic diversity. With its ability to foster rapid microbial evolution, aALE serves as a valuable addition to the ALE toolbox, holding significant promise for the advancement of microbial strain engineering and bioprocess optimization.
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Affiliation(s)
| | | | - Joseph Price
- Evolutor Ltd, The Innovation Centre, Sheffield, UK
| | - Kang Lan Tee
- Department of Chemical & Biological Engineering, University of Sheffield, Sheffield, UK
- Evolutor Ltd, The Innovation Centre, Sheffield, UK
| | - Tuck Seng Wong
- Department of Chemical & Biological Engineering, University of Sheffield, Sheffield, UK
- Evolutor Ltd, The Innovation Centre, Sheffield, UK
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science & Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
- School of Pharmacy, Bandung Institute of Technology, Bandung, West Java, Indonesia
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3
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Kim K, Choe D, Kang M, Cho SH, Cho S, Jeong KJ, Palsson B, Cho BK. Serial adaptive laboratory evolution enhances mixed carbon metabolic capacity of Escherichia coli. Metab Eng 2024; 83:160-171. [PMID: 38636729 DOI: 10.1016/j.ymben.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/31/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024]
Abstract
Microbes have inherent capacities for utilizing various carbon sources, however they often exhibit sub-par fitness due to low metabolic efficiency. To test whether a bacterial strain can optimally utilize multiple carbon sources, Escherichia coli was serially evolved in L-lactate and glycerol. This yielded two end-point strains that evolved first in L-lactate then in glycerol, and vice versa. The end-point strains displayed a universal growth advantage on single and a mixture of adaptive carbon sources, enabled by a concerted action of carbon source-specialists and generalist mutants. The combination of just four variants of glpK, ppsA, ydcI, and rph-pyrE, accounted for more than 80% of end-point strain fitness. In addition, machine learning analysis revealed a coordinated activity of transcriptional regulators imparting condition-specific regulation of gene expression. The effectiveness of the serial adaptive laboratory evolution (ALE) scheme in bioproduction applications was assessed under single and mixed-carbon culture conditions, in which serial ALE strain exhibited superior productivity of acetoin compared to ancestral strains. Together, systems-level analysis elucidated the molecular basis of serial evolution, which hold potential utility in bioproduction applications.
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Affiliation(s)
- Kangsan Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea; KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Donghui Choe
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Minjeong Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea; KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Sang-Hyeok Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea; KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Suhyung Cho
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Ki Jun Jeong
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea; Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea; KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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Tsukimi T, Obana N, Shigemori S, Arakawa K, Miyauchi E, Yang J, Song I, Ashino Y, Wakayama M, Soga T, Tomita M, Ohno H, Mori H, Fukuda S. Genetic mutation in Escherichia coli genome during adaptation to the murine intestine is optimized for the host diet. mSystems 2024; 9:e0112323. [PMID: 38205998 PMCID: PMC10878103 DOI: 10.1128/msystems.01123-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 11/15/2023] [Indexed: 01/12/2024] Open
Abstract
Mammalian gut microbes colonize the intestinal tract of their host and adapt to establish a microbial ecosystem. The host diet changes the nutrient profile of the intestine and has a high impact on microbiota composition. Genetic mutations in Escherichia coli, a prevalent species in the human gut, allow for adaptation to the mammalian intestine, as reported in previous studies. However, the extent of colonization fitness in the intestine elevated by genetic mutation and the effects of diet change on these mutations in E. coli are still poorly known. Here, we show that notable mutations in sugar metabolism-related genes (gatC, araC, and malI) were detected in the E. coli K-12 genome just 2 weeks after colonization in the germ-free mouse intestine. In addition to elevated fitness by deletion of gatC, as previously reported, deletion of araC and malI also elevated E. coli fitness in the murine intestine in a host diet-dependent manner. In vitro cultures of medium containing nutrients abundant in the intestine (e.g., galactose, N-acetylglucosamine, and asparagine) also showed increased E. coli fitness after deletion of the genes-of-interest associated with their metabolism. Furthermore, the host diet was found to influence the developmental trajectory of gene mutations in E. coli. Taken together, we suggest that genetic mutations in E. coli are selected in response to the intestinal environment, which facilitates efficient utilization of nutrients abundant in the intestine under laboratory conditions. Our study offers some insight into the possible adaptation mechanisms of gut microbes.IMPORTANCEThe gut microbiota is closely associated with human health and is greatly impacted by the host diet. Bacteria such as Escherichia coli live in the gut all throughout the life of a human host and adapt to the intestinal environment. Adaptive mutations in E. coli are reported to enhance fitness in the mammalian intestine, but to what extent is still poorly known. It is also unknown whether the host diet affects what genes are mutated and to what extent fitness is affected. This study suggests that genetic mutations in the E. coli K-12 strain are selected in response to the intestinal environment and facilitate efficient utilization of abundant nutrients in the germ-free mouse intestine. Our study provides a better understanding of these intestinal adaptation mechanisms of gut microbes.
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Affiliation(s)
- Tomoya Tsukimi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Nozomu Obana
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Suguru Shigemori
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Eiji Miyauchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Jiayue Yang
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Isaiah Song
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Yujin Ashino
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masataka Wakayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hirotada Mori
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
- Institute of Animal Sciences, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
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5
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Lei H, Li J, Zhao B, Kou SH, Xiao F, Chen T, Wang SM. Evolutionary origin of germline pathogenic variants in human DNA mismatch repair genes. Hum Genomics 2024; 18:5. [PMID: 38287404 PMCID: PMC10823654 DOI: 10.1186/s40246-024-00573-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 01/17/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Mismatch repair (MMR) system is evolutionarily conserved for genome stability maintenance. Germline pathogenic variants (PVs) in MMR genes that lead to MMR functional deficiency are associated with high cancer risk. Knowing the evolutionary origin of germline PVs in human MMR genes will facilitate understanding the biological base of MMR deficiency in cancer. However, systematic knowledge is lacking to address the issue. In this study, we performed a comprehensive analysis to know the evolutionary origin of human MMR PVs. METHODS We retrieved MMR gene variants from the ClinVar database. The genomes of 100 vertebrates were collected from the UCSC genome browser and ancient human sequencing data were obtained through comprehensive data mining. Cross-species conservation analysis was performed based on the phylogenetic relationship among 100 vertebrates. Rescaled ancient sequencing data were used to perform variant calling for archeological analysis. RESULTS Using the phylogenetic approach, we traced the 3369 MMR PVs identified in modern humans in 99 non-human vertebrate genomes but found no evidence for cross-species conservation as the source for human MMR PVs. Using the archeological approach, we searched the human MMR PVs in over 5000 ancient human genomes dated from 45,045 to 100 years before present and identified a group of MMR PVs shared between modern and ancient humans mostly within 10,000 years with similar quantitative patterns. CONCLUSION Our study reveals that MMR PVs in modern humans were arisen within the recent human evolutionary history.
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Affiliation(s)
- Huijun Lei
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China
| | - Jiaheng Li
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Si Hoi Kou
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Fengxia Xiao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Tianhui Chen
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China.
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China.
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China.
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6
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Choi JW, Song NE, Hong SP, Rhee YK, Hong HD, Cho CW. Engineering Bacillus subtilis J46 for efficient utilization of galactose through adaptive laboratory evolution. AMB Express 2024; 14:14. [PMID: 38282124 PMCID: PMC10822834 DOI: 10.1186/s13568-024-01666-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/08/2024] [Indexed: 01/30/2024] Open
Abstract
Efficient utilization of galactose by microorganisms can lead to the production of valuable bio-products and improved metabolic processes. While Bacillus subtilis has inherent pathways for galactose metabolism, there is potential for enhancement via evolutionary strategies. This study aimed to boost galactose utilization in B. subtilis using adaptive laboratory evolution (ALE) and to elucidate the genetic and metabolic changes underlying the observed enhancements. The strains of B. subtilis underwent multiple rounds of adaptive laboratory evolution (approximately 5000 generations) in an environment that favored the use of galactose. This process resulted in an enhanced specific growth rate of 0.319 ± 0.005 h-1, a significant increase from the 0.03 ± 0.008 h-1 observed in the wild-type strains. Upon selecting the evolved strain BSGA14, a comprehensive whole-genome sequencing revealed the presence of 63 single nucleotide polymorphisms (SNPs). Two of them, located in the coding sequences of the genes araR and glcR, were found to be the advantageous mutations after reverse engineering. The strain with these two accumulated mutations, BSGALE4, exhibited similar specific growth rate on galactose to the evolved strain BSGA14 (0.296 ± 0.01 h-1). Furthermore, evolved strain showed higher productivity of protease and β-galactosidase in mock soybean biomass medium. ALE proved to be a potent tool for enhancing galactose metabolism in B. subtilis. The findings offer valuable insights into the potential of evolutionary strategies in microbial engineering and pave the way for industrial applications harnessing enhanced galactose conversion.
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Affiliation(s)
- Jae Woong Choi
- Research Group of Traditional Food, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, 55365, Republic of Korea
| | - Nho-Eul Song
- Research Group of Traditional Food, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, 55365, Republic of Korea
| | - Sang-Pil Hong
- Research Group of Traditional Food, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, 55365, Republic of Korea
| | - Young Kyoung Rhee
- Research Group of Traditional Food, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, 55365, Republic of Korea
| | - Hee-Do Hong
- Research Group of Traditional Food, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, 55365, Republic of Korea
| | - Chang-Won Cho
- Research Group of Traditional Food, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, 55365, Republic of Korea.
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Lehmann M, Prohaska C, Zeldes B, Poehlein A, Daniel R, Basen M. Adaptive laboratory evolution of a thermophile toward a reduced growth temperature optimum. Front Microbiol 2023; 14:1265216. [PMID: 37901835 PMCID: PMC10601643 DOI: 10.3389/fmicb.2023.1265216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/14/2023] [Indexed: 10/31/2023] Open
Abstract
Thermophily is an ancient trait among microorganisms. The molecular principles to sustain high temperatures, however, are often described as adaptations, somewhat implying that they evolved from a non-thermophilic background and that thermophiles, i.e., organisms with growth temperature optima (TOPT) above 45°C, evolved from mesophilic organisms (TOPT 25-45°C). On the contrary, it has also been argued that LUCA, the last universal common ancestor of Bacteria and Archaea, may have been a thermophile, and mesophily is the derived trait. In this study, we took an experimental approach toward the evolution of a mesophile from a thermophile. We selected the acetogenic bacterium T. kivui (TOPT 66°C) since acetogenesis is considered ancient physiology and cultivated it at suboptimal low temperatures. We found that the lowest possible growth temperature (TMIN) under the chosen conditions was 39°C. The bacterium was subsequently subjected to adaptive laboratory evolution (ALE) by serial transfer at 45°C. Interestingly, after 67 transfers (approximately 180 generations), the adapted strain Adpt45_67 did not grow better at 45°C, but a shift in the TOPT to 60°C was observed. Growth at 45°C was accompanied by a change in the morphology as shorter, thicker cells were observed that partially occurred in chains. While the proportion of short-chain fatty acids increased at 50°C vs. 66°C in both strains, Adpt45_67 also showed a significantly increased proportion of plasmalogens. The genome analysis revealed 67 SNPs compared to the type strain, among these mutations in transcriptional regulators and in the cAMP binding protein. Ultimately, the molecular basis of the adaptation of T. kivui to a lower TOPT remains to be elucidated. The observed change in phenotype is the first experimental step toward the evolution of thermophiles growing at colder temperatures and toward a better understanding of the cold adaptation of thermophiles on early Earth.
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Affiliation(s)
- Maria Lehmann
- Department of Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Christoph Prohaska
- Department of Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Benjamin Zeldes
- Department of Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Mirko Basen
- Department of Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
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8
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Zeng Z, Gu J, Lin S, Li Q, Wang W, Guo Y. Molecular basis of the phenotypic variants arising from a Pseudoalteromonas lipolytica mutator. Microb Genom 2023; 9:001118. [PMID: 37850970 PMCID: PMC10634453 DOI: 10.1099/mgen.0.001118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/04/2023] [Indexed: 10/19/2023] Open
Abstract
Bacterial deficiencies in the DNA repair system can produce mutator strains that promote adaptive microevolution. However, the role of mutator strains in marine Pseudoalteromonas, capable of generating various gain-of-function genetic variants within biofilms, remains largely unknown. In this study, inactivation of mutS in Pseudoalteromonas lipolytica conferred an approximately 100-fold increased resistance to various antibiotics, including ciprofloxacin, rifampicin and aminoglycoside. Furthermore, the mutator of P. lipolytica generated variants that displayed enhanced biofilm formation but reduced swimming motility, indicating a high phenotypic diversity within the ΔmutS population. Additionally, we observed a significant production rate of approximately 50 % for the translucent variants, which play important roles in biofilm formation, when the ΔmutS strain was cultured on agar plates or under shaking conditions. Using whole-genome deep-sequencing combined with genetic manipulation, we demonstrated that point mutations in AT00_17115 within the capsular biosynthesis cluster were responsible for the generation of translucent variants in the ΔmutS subpopulation, while mutations in flagellar genes fliI and flgP led to a decrease in swimming motility. Collectively, this study reveals a specific mutator-driven evolution in P. lipolytica, characterized by substantial genetic and phenotypic diversification, thereby offering a reservoir of genetic attributes associated with microbial fitness.
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Affiliation(s)
- Zhenshun Zeng
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, PR China
| | - Jiayu Gu
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Shituan Lin
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Qian Li
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, PR China
| | - Weiquan Wang
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Yuexue Guo
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
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9
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Lobinska G, Pilpel Y, Ram Y. Phenotype switching of the mutation rate facilitates adaptive evolution. Genetics 2023; 225:iyad111. [PMID: 37293818 PMCID: PMC10471227 DOI: 10.1093/genetics/iyad111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 02/05/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
The mutation rate plays an important role in adaptive evolution. It can be modified by mutator and anti-mutator alleles. Recent empirical evidence hints that the mutation rate may vary among genetically identical individuals: evidence from bacteria suggests that the mutation rate can be affected by expression noise of a DNA repair protein and potentially also by translation errors in various proteins. Importantly, this non-genetic variation may be heritable via a transgenerational epigenetic mode of inheritance, giving rise to a mutator phenotype that is independent from mutator alleles. Here, we investigate mathematically how the rate of adaptive evolution is affected by the rate of mutation rate phenotype switching. We model an asexual population with two mutation rate phenotypes, non-mutator and mutator. An offspring may switch from its parental phenotype to the other phenotype. We find that switching rates that correspond to so-far empirically described non-genetic systems of inheritance of the mutation rate lead to higher rates of adaptation on both artificial and natural fitness landscapes. These switching rates can maintain within the same individuals both a mutator phenotype and intermediary mutations, a combination that facilitates adaptation. Moreover, non-genetic inheritance increases the proportion of mutators in the population, which in turn increases the probability of hitchhiking of the mutator phenotype with adaptive mutations. This in turns facilitates the acquisition of additional adaptive mutations. Our results rationalize recently observed noise in the expression of proteins that affect the mutation rate and suggest that non-genetic inheritance of this phenotype may facilitate evolutionary adaptive processes.
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Affiliation(s)
- Gabriela Lobinska
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yoav Ram
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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10
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Worthan SB, McCarthy RDP, Behringer MG. Case Studies in the Assessment of Microbial Fitness: Seemingly Subtle Changes Can Have Major Effects on Phenotypic Outcomes. J Mol Evol 2023; 91:311-324. [PMID: 36752825 PMCID: PMC10276084 DOI: 10.1007/s00239-022-10087-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/21/2022] [Indexed: 02/09/2023]
Abstract
Following the completion of an adaptive evolution experiment, fitness evaluations are routinely conducted to assess the magnitude of adaptation. In doing so, proper consideration should be given when determining the appropriate methods as trade-offs may exist between accuracy and throughput. Here, we present three instances in which small changes in the framework or execution of fitness evaluations significantly impacted the outcomes. The first case illustrates that discrepancies in fitness conclusions can arise depending on the approach to evaluating fitness, the culture vessel used, and the sampling method. The second case reveals that variations in environmental conditions can occur associated with culture vessel material. Specifically, these subtle changes can greatly affect microbial physiology leading to changes in the culture pH and distorting fitness measurements. Finally, the last case reports that heterogeneity in CFU formation time can result in inaccurate fitness conclusions. Based on each case, considerations and recommendations are presented for future adaptive evolution experiments.
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Affiliation(s)
- Sarah B Worthan
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Robert D P McCarthy
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Megan G Behringer
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA.
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
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11
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Abbate E, Andrion J, Apel A, Biggs M, Chaves J, Cheung K, Ciesla A, Clark-ElSayed A, Clay M, Contridas R, Fox R, Hein G, Held D, Horwitz A, Jenkins S, Kalbarczyk K, Krishnamurthy N, Mirsiaghi M, Noon K, Rowe M, Shepherd T, Tarasava K, Tarasow TM, Thacker D, Villa G, Yerramsetty K. Optimizing the strain engineering process for industrial-scale production of bio-based molecules. J Ind Microbiol Biotechnol 2023; 50:kuad025. [PMID: 37656881 PMCID: PMC10548853 DOI: 10.1093/jimb/kuad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
Biomanufacturing could contribute as much as ${\$}$30 trillion to the global economy by 2030. However, the success of the growing bioeconomy depends on our ability to manufacture high-performing strains in a time- and cost-effective manner. The Design-Build-Test-Learn (DBTL) framework has proven to be an effective strain engineering approach. Significant improvements have been made in genome engineering, genotyping, and phenotyping throughput over the last couple of decades that have greatly accelerated the DBTL cycles. However, to achieve a radical reduction in strain development time and cost, we need to look at the strain engineering process through a lens of optimizing the whole cycle, as opposed to simply increasing throughput at each stage. We propose an approach that integrates all 4 stages of the DBTL cycle and takes advantage of the advances in computational design, high-throughput genome engineering, and phenotyping methods, as well as machine learning tools for making predictions about strain scale-up performance. In this perspective, we discuss the challenges of industrial strain engineering, outline the best approaches to overcoming these challenges, and showcase examples of successful strain engineering projects for production of heterologous proteins, amino acids, and small molecules, as well as improving tolerance, fitness, and de-risking the scale-up of industrial strains.
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Affiliation(s)
- Eric Abbate
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Jennifer Andrion
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Amanda Apel
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Matthew Biggs
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Julie Chaves
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Kristi Cheung
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Anthony Ciesla
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Alia Clark-ElSayed
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Michael Clay
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Riarose Contridas
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Richard Fox
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Glenn Hein
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Dan Held
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Andrew Horwitz
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Stefan Jenkins
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | | | | | - Mona Mirsiaghi
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Katherine Noon
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Mike Rowe
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Tyson Shepherd
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Katia Tarasava
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Theodore M Tarasow
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Drew Thacker
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Gladys Villa
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
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12
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Minireview: Engineering evolution to reconfigure phenotypic traits in microbes for biotechnological applications. Comput Struct Biotechnol J 2022; 21:563-573. [PMID: 36659921 PMCID: PMC9816911 DOI: 10.1016/j.csbj.2022.12.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 12/25/2022] Open
Abstract
Adaptive laboratory evolution (ALE) has long been used as the tool of choice for microbial engineering applications, ranging from the production of commodity chemicals to the innovation of complex phenotypes. With the advent of systems and synthetic biology, the ALE experimental design has become increasingly sophisticated. For instance, implementation of in silico metabolic model reconstruction and advanced synthetic biology tools have facilitated the effective coupling of desired traits to adaptive phenotypes. Furthermore, various multi-omic tools now enable in-depth analysis of cellular states, providing a comprehensive understanding of the biology of even the most genomically perturbed systems. Emerging machine learning approaches would assist in streamlining the interpretation of massive and multiplexed datasets and promoting our understanding of complexity in biology. This review covers some of the representative case studies among the 700 independent ALE studies reported to date, outlining key ideas, principles, and important mechanisms underlying ALE designs in bioproduction and synthetic cell engineering, with evidence from literatures to aid comprehension.
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13
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Lao Z, Matsui Y, Ijichi S, Ying BW. Global coordination of the mutation and growth rates across the genetic and nutritional variety in Escherichia coli. Front Microbiol 2022; 13:990969. [PMID: 36204613 PMCID: PMC9530902 DOI: 10.3389/fmicb.2022.990969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022] Open
Abstract
Fitness and mutability are the primary traits of living organisms for adaptation and evolution. However, their quantitative linkage remained largely deficient. Whether there is any general relationship between the two features and how genetic and environmental variables influence them remained unclear and were addressed here. The mutation and growth rates of an assortment of Escherichia coli strain collections, including the wild-type strains and the genetically disturbed strains of either reduced genomes or deletion of the genes involved in the DNA replication fidelity, were evaluated in various media. The contribution of media to the mutation and growth rates was differentiated depending on the types of genetic disturbance. Nevertheless, the negative correlation between the mutation and growth rates was observed across the genotypes and was common in all media. It indicated the comprehensive association of the correlated mutation and growth rates with the genetic and medium variation. Multiple linear regression and support vector machine successfully predicted the mutation and growth rates and the categories of genotypes and media, respectively. Taken together, the study provided a quantitative dataset linking the mutation and growth rates, genotype, and medium and presented a simple and successful example of predicting bacterial growth and mutability by data-driven approaches.
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14
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Sharaev N, Chacon-Machado L, Musharova O, Savitskaya E, Severinov K. Repair of Double-Stranded DNA Breaks Generated by CRISPR–Cas9 in Pseudomonas putida KT2440. Mol Biol 2022. [DOI: 10.1134/s0026893322060152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Pseudomonas putida KT2440 is a metabolically versatile bacterium with considerable promise as a chassis strain for production and degradation of complex organic compounds. Unlike most bacteria, P. putida KT2440 encodes the Ku and LigD proteins involved in Non-Homologous End Joining (NHEJ). This pathway of repair of double-strand breaks (DSBs) in DNA has an intrinsic mutagenic potential that could be exploited in combination with currently available genome editing tools that generate programmable DSBs. Here, we investigated the effect of removal or overproduction of NHEJ-associated P. putida KT2440 enzymes on mutations generated upon repair of Cas9-mediated DSBs with the double purpose of characterizing the NHEJ pathway and investigating how it functionally interacts with the current gold standard tool for gene editing. The results of our work shed light on non-templated mechanisms of DSB repair in P. putida KT2440, an information that will serve as foundation to expand the gene engineering toolbox for this important microorganism.
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15
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Mutators Enhance Adaptive Micro-Evolution in Pathogenic Microbes. Microorganisms 2022; 10:microorganisms10020442. [PMID: 35208897 PMCID: PMC8875331 DOI: 10.3390/microorganisms10020442] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/07/2022] [Accepted: 02/10/2022] [Indexed: 02/04/2023] Open
Abstract
Adaptation to the changing environmental conditions experienced within a host requires genetic diversity within a microbial population. Genetic diversity arises from mutations which occur due to DNA damage from exposure to exogenous environmental stresses or generated endogenously through respiration or DNA replication errors. As mutations can be deleterious, a delicate balance must be obtained between generating enough mutations for micro-evolution to occur while maintaining fitness and genomic integrity. Pathogenic microorganisms can actively modify their mutation rate to enhance adaptive micro-evolution by increasing expression of error-prone DNA polymerases or by mutating or decreasing expression of genes required for DNA repair. Strains which exhibit an elevated mutation rate are termed mutators. Mutators are found in varying prevalence in clinical populations where large-effect beneficial mutations enhance survival and are predominately caused by defects in the DNA mismatch repair (MMR) pathway. Mutators can facilitate the emergence of antibiotic resistance, allow phenotypic modifications to prevent recognition and destruction by the host immune system and enable switching to metabolic and cellular morphologies better able to survive in the given environment. This review will focus on recent advances in understanding the phenotypic and genotypic changes occurring in MMR mutators in both prokaryotic and eukaryotic pathogens.
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16
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Kim K, Hou CY, Choe D, Kang M, Cho S, Sung BH, Lee DH, Lee SG, Kang TJ, Cho BK. Adaptive laboratory evolution of Escherichia coli W enhances gamma-aminobutyric acid production using glycerol as the carbon source. Metab Eng 2021; 69:59-72. [PMID: 34775076 DOI: 10.1016/j.ymben.2021.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/19/2021] [Accepted: 11/06/2021] [Indexed: 11/25/2022]
Abstract
The microbial conversion of glycerol into value-added commodity products has emerged as an attractive means to meet the demands of biosustainability. However, glycerol is a non-preferential carbon source for productive fermentation because of its low energy density. We employed evolutionary and metabolic engineering in tandem to construct an Escherichia coli strain with improved GABA production using glycerol as the feedstock carbon. Adaptive evolution of E. coli W under glycerol-limited conditions for 1300 generations harnessed an adapted strain with a metabolic system optimized for glycerol utilization. Mutation profiling, enzyme kinetic assays, and transcriptome analysis of the adapted strain allowed us to decipher the basis of glycerol adaptation at the molecular level. Importantly, increased substrate influx mediated by the mutant glpK and modulation of intracellular cAMP levels were the key drivers of improved fitness in the glycerol-limited condition. Leveraging the enhanced capability of glycerol utilization in the strain, we constructed a GABA-producing E. coli W-derivative with superior GABA production compared to the wild-type. Furthermore, rationally designed inactivation of the non-essential metabolic genes, including ackA, mgsA, and gabT, in the glycerol-adapted strain improved the final GABA titer and specific productivity by 3.9- and 4.3-fold, respectively, compared with the wild-type.
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Affiliation(s)
- Kangsan Kim
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Chen Yuan Hou
- Department of Chemical and Biochemical Engineering, Dongguk University-Seoul, Seoul, 04620, Republic of Korea
| | - Donghui Choe
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Minjeong Kang
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Bong Hyun Sung
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Dae-Hee Lee
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology & Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Taek Jin Kang
- Department of Chemical and Biochemical Engineering, Dongguk University-Seoul, Seoul, 04620, Republic of Korea.
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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17
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Fernández-Cabezón L, Cros A, Nikel PI. Spatiotemporal Manipulation of the Mismatch Repair System of Pseudomonas putida Accelerates Phenotype Emergence. ACS Synth Biol 2021; 10:1214-1226. [PMID: 33843192 DOI: 10.1021/acssynbio.1c00031] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The development of complex phenotypes in industrially relevant bacteria is a major goal of metabolic engineering, which encompasses the implementation of both rational and random approaches. In the latter case, several tools have been developed toward increasing mutation frequencies, yet the precise control of mutagenesis processes in cell factories continues to represent a significant technical challenge. Pseudomonas species are endowed with one of the most efficient DNA mismatch repair (MMR) systems found in the bacterial domain. Here, we investigated if the endogenous MMR system could be manipulated as a general strategy to artificially alter mutation rates in Pseudomonas species. To bestow a conditional mutator phenotype in the platform bacterium Pseudomonas putida, we constructed inducible mutator devices to modulate the expression of the dominant-negative mutLE36K allele. Regulatable overexpression of mutLE36K in a broad-host-range, easy-to-cure plasmid format resulted in a transitory inhibition of the MMR machinery, leading to a significant increase (up to 438-fold) in DNA mutation frequencies and a heritable fixation of mutations in the genome. Following such an accelerated mutagenesis-followed by selection approach, three phenotypes were successfully evolved: resistance to antibiotics streptomycin and rifampicin (either individually or combined) and reversion of a synthetic uracil auxotrophy. Thus, these mutator devices could be applied to accelerate the evolution of metabolic pathways in long-term evolutionary experiments, alternating cycles of (inducible) mutagenesis coupled to selection schemes toward the desired phenotype(s).
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Affiliation(s)
- Lorena Fernández-Cabezón
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Antonin Cros
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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18
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Mitigation of host cell mutations and regime shift during microbial fermentation: a perspective from flux memory. Curr Opin Biotechnol 2020; 66:227-235. [DOI: 10.1016/j.copbio.2020.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/01/2020] [Accepted: 08/12/2020] [Indexed: 12/19/2022]
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19
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Developing rapid growing Bacillus subtilis for improved biochemical and recombinant protein production. Metab Eng Commun 2020; 11:e00141. [PMID: 32874915 PMCID: PMC7452210 DOI: 10.1016/j.mec.2020.e00141] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/05/2020] [Accepted: 08/10/2020] [Indexed: 12/28/2022] Open
Abstract
Bacillus subtilis is a model Gram-positive bacterium, which has been widely used as industrially important chassis in synthetic biology and metabolic engineering. Rapid growth of chassis is beneficial for shortening the fermentation period and enhancing production of target product. However, engineered B. subtilis with faster growth phenotype is lacking. Here, fast-growing B. subtilis were constructed through rational gene knockout and adaptive laboratory evolution using wild type strain B. subtilis 168 (BS168) as starting strain. Specifically, strains BS01, BS02, and BS03 were obtained through gene knockout of oppD, hag, and flgD genes, respectively, resulting 15.37%, 24.18% and 36.46% increases of specific growth rate compared with BS168. Next, strains A28 and A40 were obtained through adaptive laboratory evolution, whose specific growth rates increased by 39.88% and 43.53% compared to BS168, respectively. Then these two methods were combined via deleting oppD, hag, and flgD genes respectively on the basis of evolved strain A40, yielding strain A4003 with further 7.76% increase of specific growth rate, reaching 0.75 h-1 in chemical defined M9 medium. Finally, bioproduction efficiency of intracellular product (ribonucleic acid, RNA), extracellular product (acetoin), and recombinant proteins (green fluorescent protein (GFP) and ovalbumin) by fast-growing strain A4003 was tested. And the production of RNA, acetoin, GFP, and ovalbumin increased 38.09%, 5.40%, 9.47% and 19.79% using fast-growing strain A4003 as chassis compared with BS168, respectively. The developed fast-growing B. subtilis strains and strategies used for developing these strains should be useful for improving bioproduction efficiency and constructing other industrially important bacterium with faster growth phenotype. Fast-growing Bacillus subtilis were constructed through rational gene knockout and adaptive laboratory evolution. Specific growth rate of engineered B. subtilis increased 53.06% compared with B. subtilis 168, reaching 0.75 h-1 in M9 medium. Production of RNA, acetoin, and ovalbumin increased 38.09%, 5.40%, and 19.79% using fast-growing strain as chassis.
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