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For: Kishimoto T, Iijima L, Tatsumi M, Ono N, Oyake A, Hashimoto T, Matsuo M, Okubo M, Suzuki S, Mori K, Kashiwagi A, Furusawa C, Ying BW, Yomo T. Transition from positive to neutral in mutation fixation along with continuing rising fitness in thermal adaptive evolution. PLoS Genet 2010;6:e1001164. [PMID: 20975944 PMCID: PMC2958811 DOI: 10.1371/journal.pgen.1001164] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 09/17/2010] [Indexed: 02/05/2023]  Open
Number Cited by Other Article(s)
1
Pérez-Morales G, Martínez-Conde KV, Caspeta L, Merino E, Cevallos MA, Gosset G, Martinez A. Thermally adapted Escherichia coli keeps transcriptomic response during temperature upshift exposure. Appl Microbiol Biotechnol 2025;109:120. [PMID: 40360840 PMCID: PMC12075407 DOI: 10.1007/s00253-025-13495-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2025] [Revised: 04/16/2025] [Accepted: 04/23/2025] [Indexed: 05/15/2025]
2
Pattanakittivorakul S, Kato S, Kuga T, Kosaka T, Matsutani M, Murata M, Ishikawa M, Charoenpunthuwong K, Thanonkeo P, Yamada M. Limited Diversity of Thermal Adaptation to a Critical Temperature in Zymomonas mobilis: Evidence from Multiple-Parallel Laboratory Evolution Experiments. Int J Mol Sci 2025;26:3052. [PMID: 40243698 PMCID: PMC11989028 DOI: 10.3390/ijms26073052] [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: 02/08/2025] [Revised: 03/07/2025] [Accepted: 03/24/2025] [Indexed: 04/18/2025]  Open
3
Worthan SB, Grant MI, Behringer MG. Rho-dependent termination: a bacterial evolutionary capacitor for stress resistance. Transcription 2025:1-14. [PMID: 40044630 DOI: 10.1080/21541264.2025.2474367] [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: 01/15/2025] [Revised: 02/25/2025] [Accepted: 02/26/2025] [Indexed: 03/28/2025]  Open
4
Pérez-Morales G, Caspeta L, Merino E, Cevallos MA, Gosset G, Martinez A. Simultaneous saccharification and fermentation for D-lactic acid production using a metabolically engineered Escherichia coli adapted to high temperature. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024;17:132. [PMID: 39488702 PMCID: PMC11531696 DOI: 10.1186/s13068-024-02579-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Accepted: 10/18/2024] [Indexed: 11/04/2024]
5
Marin J, Walewski V, Braun T, Dziri S, Magnan M, Denamur E, Carbonnelle E, Bridier-Nahmias A. Genomic evidence of Escherichia coli gut population diversity translocation in leukemia patients. mSphere 2024;9:e0053024. [PMID: 39365076 PMCID: PMC11520291 DOI: 10.1128/msphere.00530-24] [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: 06/24/2024] [Accepted: 09/09/2024] [Indexed: 10/05/2024]  Open
6
Worthan SB, McCarthy RDP, Delaleau M, Stikeleather R, Bratton BP, Boudvillain M, Behringer MG. Evolution of pH-sensitive transcription termination in Escherichia coli during adaptation to repeated long-term starvation. Proc Natl Acad Sci U S A 2024;121:e2405546121. [PMID: 39298488 PMCID: PMC11441560 DOI: 10.1073/pnas.2405546121] [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: 03/17/2024] [Accepted: 08/19/2024] [Indexed: 09/21/2024]  Open
7
Shibai A, Furusawa C. Development of specialized devices for microbial experimental evolution. Dev Growth Differ 2024;66:372-380. [PMID: 39187274 PMCID: PMC11482599 DOI: 10.1111/dgd.12940] [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: 11/30/2022] [Revised: 08/06/2024] [Accepted: 08/11/2024] [Indexed: 08/28/2024]
8
Worthan SB, McCarthy RDP, Delaleau M, Stikeleather R, Bratton BP, Boudvillain M, Behringer MG. Evolution of pH-sensitive transcription termination during adaptation to repeated long-term starvation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582989. [PMID: 38464051 PMCID: PMC10925284 DOI: 10.1101/2024.03.01.582989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
9
Wang L, Li A, Fang J, Wang Y, Chen L, Qiao L, Wang W. Enhanced Cell Wall and Cell Membrane Activity Promotes Heat Adaptation of Enterococcus faecium. Int J Mol Sci 2023;24:11822. [PMID: 37511581 PMCID: PMC10380804 DOI: 10.3390/ijms241411822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/09/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023]  Open
10
Rasmussen T. The Potassium Efflux System Kef: Bacterial Protection against Toxic Electrophilic Compounds. MEMBRANES 2023;13:465. [PMID: 37233526 PMCID: PMC10224563 DOI: 10.3390/membranes13050465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023]
11
McGuire BE, Nano FE. Whole-genome sequencing analysis of two heat-evolved Escherichia coli strains. BMC Genomics 2023;24:154. [PMID: 36973666 PMCID: PMC10044804 DOI: 10.1186/s12864-023-09266-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/21/2023] [Indexed: 03/29/2023]  Open
12
Smith TP, Mombrikotb S, Ransome E, Kontopoulos DG, Pawar S, Bell T. Latent functional diversity may accelerate microbial community responses to temperature fluctuations. eLife 2022;11:e80867. [PMID: 36444646 PMCID: PMC9708066 DOI: 10.7554/elife.80867] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/26/2022] [Indexed: 11/30/2022]  Open
13
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
14
Shibai A, Kotani H, Kawada M, Yokoi N, Furusawa C. Development of a device that generates a temperature gradient in a microtiter plate for microbial culture. SLAS Technol 2022;27:279-283. [DOI: 10.1016/j.slast.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/23/2022] [Accepted: 07/24/2022] [Indexed: 11/24/2022]
15
Nagy K, Dukic B, Hodula O, Ábrahám Á, Csákvári E, Dér L, Wetherington MT, Noorlag J, Keymer JE, Galajda P. Emergence of Resistant Escherichia coli Mutants in Microfluidic On-Chip Antibiotic Gradients. Front Microbiol 2022;13:820738. [PMID: 35391738 PMCID: PMC8981919 DOI: 10.3389/fmicb.2022.820738] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/23/2022] [Indexed: 11/13/2022]  Open
16
Kurokawa M, Nishimura I, Ying BW. Experimental Evolution Expands the Breadth of Adaptation to an Environmental Gradient Correlated With Genome Reduction. Front Microbiol 2022;13:826894. [PMID: 35154062 PMCID: PMC8826082 DOI: 10.3389/fmicb.2022.826894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/06/2022] [Indexed: 11/28/2022]  Open
17
Lu H, Aida H, Kurokawa M, Chen F, Xia Y, Xu J, Li K, Ying BW, Yomo T. Primordial mimicry induces morphological change in Escherichia coli. Commun Biol 2022;5:24. [PMID: 35017623 PMCID: PMC8752768 DOI: 10.1038/s42003-021-02954-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 12/07/2021] [Indexed: 11/09/2022]  Open
18
Lambros M, Pechuan-Jorge X, Biro D, Ye K, Bergman A. Emerging Adaptive Strategies Under Temperature Fluctuations in a Laboratory Evolution Experiment of Escherichia Coli. Front Microbiol 2021;12:724982. [PMID: 34745030 PMCID: PMC8569431 DOI: 10.3389/fmicb.2021.724982] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/27/2021] [Indexed: 11/22/2022]  Open
19
Lin Y, Alstrup M, Pang JKY, Maróti G, Er-Rafik M, Tourasse N, Økstad OA, Kovács ÁT. Adaptation of Bacillus thuringiensis to Plant Colonization Affects Differentiation and Toxicity. mSystems 2021;6:e0086421. [PMID: 34636664 PMCID: PMC8510532 DOI: 10.1128/msystems.00864-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/27/2021] [Indexed: 01/11/2023]  Open
20
Maire J, van Oppen MJH. A role for bacterial experimental evolution in coral bleaching mitigation? Trends Microbiol 2021;30:217-228. [PMID: 34429226 DOI: 10.1016/j.tim.2021.07.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 12/13/2022]
21
Matsumoto N, Osumi N, Matsutani M, Phathanathavorn T, Kataoka N, Theeragool G, Yakushi T, Shiraishi Y, Matsushita K. Thermal adaptation of acetic acid bacteria for practical high-temperature vinegar fermentation. Biosci Biotechnol Biochem 2021;85:1243-1251. [PMID: 33686416 DOI: 10.1093/bbb/zbab009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/11/2021] [Indexed: 12/30/2022]
22
Wang G, Fu L, Xiong J, Mochizuki K, Fu Y, Miao W. Identification and Characterization of Base-Substitution Mutations in the Macronuclear Genome of the Ciliate Tetrahymena thermophila. Genome Biol Evol 2021;13:evaa232. [PMID: 33146387 PMCID: PMC7788487 DOI: 10.1093/gbe/evaa232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2020] [Indexed: 02/06/2023]  Open
23
Wang G, Chen K, Zhang J, Deng S, Xiong J, He X, Fu Y, Miao W. Drivers of Mating Type Composition in Tetrahymena thermophila. Genome Biol Evol 2020;12:2328-2343. [PMID: 32946549 PMCID: PMC7846192 DOI: 10.1093/gbe/evaa197] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2020] [Indexed: 11/23/2022]  Open
24
Phillips MA, Kutch IC, Long AD, Burke MK. Increased time sampling in an evolve-and-resequence experiment with outcrossing Saccharomyces cerevisiae reveals multiple paths of adaptive change. Mol Ecol 2020;29:4898-4912. [PMID: 33135198 DOI: 10.1111/mec.15687] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 11/28/2022]
25
Spira B, Ospino K. Diversity in E. coli (p)ppGpp Levels and Its Consequences. Front Microbiol 2020;11:1759. [PMID: 32903406 PMCID: PMC7434938 DOI: 10.3389/fmicb.2020.01759] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/06/2020] [Indexed: 12/21/2022]  Open
26
Hossain MT, Yokono T, Kashiwagi A. The Single-Stranded RNA Bacteriophage Qβ Adapts Rapidly to High Temperatures: An Evolution Experiment. Viruses 2020;12:v12060638. [PMID: 32545482 PMCID: PMC7354602 DOI: 10.3390/v12060638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/05/2020] [Accepted: 06/10/2020] [Indexed: 11/22/2022]  Open
27
Min B, Kim K, Li V, Cho S, Kim H. Changes in Cell Membrane Fatty Acid Composition of Streptococcus thermophilus in Response to Gradually Increasing Heat Temperature. J Microbiol Biotechnol 2020;30:739-748. [PMID: 32482940 PMCID: PMC9745660 DOI: 10.4014/jmb.1912.12053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/28/2020] [Indexed: 12/15/2022]
28
Understanding metabolic adaptation by using bacterial laboratory evolution and trans-omics analysis. Biophys Rev 2020;12:677-682. [PMID: 32394353 DOI: 10.1007/s12551-020-00695-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/28/2020] [Indexed: 12/16/2022]  Open
29
Kurokawa M, Ying BW. Experimental Challenges for Reduced Genomes: The Cell Model Escherichia coli. Microorganisms 2019;8:E3. [PMID: 31861355 PMCID: PMC7022904 DOI: 10.3390/microorganisms8010003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/11/2019] [Accepted: 12/17/2019] [Indexed: 12/13/2022]  Open
30
Smith TP, Thomas TJH, García-Carreras B, Sal S, Yvon-Durocher G, Bell T, Pawar S. Community-level respiration of prokaryotic microbes may rise with global warming. Nat Commun 2019;10:5124. [PMID: 31719536 PMCID: PMC6851113 DOI: 10.1038/s41467-019-13109-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 10/18/2019] [Indexed: 11/22/2022]  Open
31
Kosaka T, Nakajima Y, Ishii A, Yamashita M, Yoshida S, Murata M, Kato K, Shiromaru Y, Kato S, Kanasaki Y, Yoshikawa H, Matsutani M, Thanonkeo P, Yamada M. Capacity for survival in global warming: Adaptation of mesophiles to the temperature upper limit. PLoS One 2019;14:e0215614. [PMID: 31063502 PMCID: PMC6504187 DOI: 10.1371/journal.pone.0215614] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/04/2019] [Indexed: 11/23/2022]  Open
32
Van den Bergh B, Swings T, Fauvart M, Michiels J. Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution. Microbiol Mol Biol Rev 2018;82:e00008-18. [PMID: 30045954 PMCID: PMC6094045 DOI: 10.1128/mmbr.00008-18] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
33
Wytock TP, Fiebig A, Willett JW, Herrou J, Fergin A, Motter AE, Crosson S. Experimental evolution of diverse Escherichia coli metabolic mutants identifies genetic loci for convergent adaptation of growth rate. PLoS Genet 2018;14:e1007284. [PMID: 29584733 PMCID: PMC5892946 DOI: 10.1371/journal.pgen.1007284] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 04/10/2018] [Accepted: 03/02/2018] [Indexed: 01/08/2023]  Open
34
Bidnenko E, Bidnenko V. Transcription termination factor Rho and microbial phenotypic heterogeneity. Curr Genet 2017;64:541-546. [PMID: 29094196 DOI: 10.1007/s00294-017-0775-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 10/27/2017] [Accepted: 10/28/2017] [Indexed: 12/21/2022]
35
Coordinated Changes in Mutation and Growth Rates Induced by Genome Reduction. mBio 2017;8:mBio.00676-17. [PMID: 28679744 PMCID: PMC5573674 DOI: 10.1128/mbio.00676-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]  Open
36
Horinouchi T, Sakai A, Kotani H, Tanabe K, Furusawa C. Improvement of isopropanol tolerance of Escherichia coli using adaptive laboratory evolution and omics technologies. J Biotechnol 2017. [PMID: 28645581 DOI: 10.1016/j.jbiotec.2017.06.408] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
37
Furusawa C, Kaneko K. Global relationships in fluctuation and response in adaptive evolution. J R Soc Interface 2016. [PMID: 26202686 DOI: 10.1098/rsif.2015.0482] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
38
Rodríguez-Verdugo A, Tenaillon O, Gaut BS. First-Step Mutations during Adaptation Restore the Expression of Hundreds of Genes. Mol Biol Evol 2015;33:25-39. [PMID: 26500250 PMCID: PMC4693981 DOI: 10.1093/molbev/msv228] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
39
Ying BW, Matsumoto Y, Kitahara K, Suzuki S, Ono N, Furusawa C, Kishimoto T, Yomo T. Bacterial transcriptome reorganization in thermal adaptive evolution. BMC Genomics 2015;16:802. [PMID: 26474851 PMCID: PMC4609109 DOI: 10.1186/s12864-015-1999-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 10/03/2015] [Indexed: 11/30/2022]  Open
40
Yama K, Matsumoto Y, Murakami Y, Seno S, Matsuda H, Gotoh K, Motooka D, Nakamura S, Ying BW, Yomo T. Functional specialization in regulation and quality control in thermal adaptive evolution. Genes Cells 2015;20:943-55. [PMID: 26373241 DOI: 10.1111/gtc.12298] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 08/04/2015] [Indexed: 01/22/2023]
41
Horinouchi T, Suzuki S, Hirasawa T, Ono N, Yomo T, Shimizu H, Furusawa C. Phenotypic convergence in bacterial adaptive evolution to ethanol stress. BMC Evol Biol 2015;15:180. [PMID: 26334309 PMCID: PMC4559166 DOI: 10.1186/s12862-015-0454-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 08/12/2015] [Indexed: 11/10/2022]  Open
42
Ying BW, Honda T, Tsuru S, Seno S, Matsuda H, Kazuta Y, Yomo T. Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages. PLoS One 2015;10:e0135639. [PMID: 26292224 PMCID: PMC4546238 DOI: 10.1371/journal.pone.0135639] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 07/24/2015] [Indexed: 12/15/2022]  Open
43
Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process. PLoS Genet 2015;11:e1005392. [PMID: 26177190 PMCID: PMC4503671 DOI: 10.1371/journal.pgen.1005392] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/25/2015] [Indexed: 11/21/2022]  Open
44
Oide S, Gunji W, Moteki Y, Yamamoto S, Suda M, Jojima T, Yukawa H, Inui M. Thermal and solvent stress cross-tolerance conferred to Corynebacterium glutamicum by adaptive laboratory evolution. Appl Environ Microbiol 2015;81:2284-98. [PMID: 25595768 PMCID: PMC4357955 DOI: 10.1128/aem.03973-14] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 01/12/2015] [Indexed: 11/20/2022]  Open
45
Kashiwagi A, Kitamura H, Sano Tsushima F. Characterization of a single mutation in TraQ in a strain of Escherichia coli partially resistant to Qβ infection. Front Microbiol 2015;6:124. [PMID: 25750639 PMCID: PMC4335273 DOI: 10.3389/fmicb.2015.00124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 02/02/2015] [Indexed: 01/21/2023]  Open
46
Yoshida M, Tsuru S, Hirata N, Seno S, Matsuda H, Ying BW, Yomo T. Directed evolution of cell size in Escherichia coli. BMC Evol Biol 2014;14:257. [PMID: 25514845 PMCID: PMC4279887 DOI: 10.1186/s12862-014-0257-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 11/27/2014] [Indexed: 11/16/2022]  Open
47
Ishizawa Y, Ying BW, Tsuru S, Yomo T. Nutrient-dependent growth defects and mutability of mutators in Escherichia coli. Genes Cells 2014;20:68-76. [PMID: 25378049 DOI: 10.1111/gtc.12199] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 10/04/2014] [Indexed: 11/28/2022]
48
Contribution of silent mutations to thermal adaptation of RNA bacteriophage Qβ. J Virol 2014;88:11459-68. [PMID: 25056887 DOI: 10.1128/jvi.01127-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]  Open
49
Sandberg TE, Pedersen M, LaCroix RA, Ebrahim A, Bonde M, Herrgard MJ, Palsson BO, Sommer M, Feist AM. Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations. Mol Biol Evol 2014;31:2647-62. [PMID: 25015645 PMCID: PMC4166923 DOI: 10.1093/molbev/msu209] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
50
Baldwin-Brown JG, Long AD, Thornton KR. The power to detect quantitative trait loci using resequenced, experimentally evolved populations of diploid, sexual organisms. Mol Biol Evol 2014;31:1040-55. [PMID: 24441104 PMCID: PMC3969567 DOI: 10.1093/molbev/msu048] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]  Open
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