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For: Patrick WM, Quandt EM, Swartzlander DB, Matsumura I. Multicopy suppression underpins metabolic evolvability. Mol Biol Evol 2007;24:2716-22. [PMID: 17884825 PMCID: PMC2678898 DOI: 10.1093/molbev/msm204] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
101
Baier F, Tokuriki N. Connectivity between catalytic landscapes of the metallo-β-lactamase superfamily. J Mol Biol 2014;426:2442-56. [PMID: 24769192 DOI: 10.1016/j.jmb.2014.04.013] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 10/25/2022]
102
k-OptForce: integrating kinetics with flux balance analysis for strain design. PLoS Comput Biol 2014;10:e1003487. [PMID: 24586136 PMCID: PMC3930495 DOI: 10.1371/journal.pcbi.1003487] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 01/10/2014] [Indexed: 11/19/2022]  Open
103
Schulenburg C, Miller BG. Enzyme recruitment and its role in metabolic expansion. Biochemistry 2014;53:836-45. [PMID: 24483367 PMCID: PMC3985712 DOI: 10.1021/bi401667f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
104
Elliott KT, Cuff LE, Neidle EL. Copy number change: evolving views on gene amplification. Future Microbiol 2014;8:887-99. [PMID: 23841635 DOI: 10.2217/fmb.13.53] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
105
Addition of Escherichia coli K-12 growth observation and gene essentiality data to the EcoCyc database. J Bacteriol 2013;196:982-8. [PMID: 24363340 DOI: 10.1128/jb.01209-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
106
Katju V, Bergthorsson U. Copy-number changes in evolution: rates, fitness effects and adaptive significance. Front Genet 2013;4:273. [PMID: 24368910 PMCID: PMC3857721 DOI: 10.3389/fgene.2013.00273] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 11/18/2013] [Indexed: 11/13/2022]  Open
107
Takemoto K, Yoshitake I. Limited influence of oxygen on the evolution of chemical diversity in metabolic networks. Metabolites 2013;3:979-92. [PMID: 24958261 PMCID: PMC3937826 DOI: 10.3390/metabo3040979] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/09/2013] [Accepted: 10/11/2013] [Indexed: 12/04/2022]  Open
108
Hamilton J, Dwivedi V, Reed J. Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models. Biophys J 2013;105:512-22. [PMID: 23870272 PMCID: PMC3714879 DOI: 10.1016/j.bpj.2013.06.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 05/18/2013] [Accepted: 06/05/2013] [Indexed: 11/24/2022]  Open
109
Yip SHC, Matsumura I. Substrate ambiguous enzymes within the Escherichia coli proteome offer different evolutionary solutions to the same problem. Mol Biol Evol 2013;30:2001-12. [PMID: 23728795 DOI: 10.1093/molbev/mst105] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
110
Does habitat variability really promote metabolic network modularity? PLoS One 2013;8:e61348. [PMID: 23593470 PMCID: PMC3625173 DOI: 10.1371/journal.pone.0061348] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/06/2013] [Indexed: 11/19/2022]  Open
111
Tervo CJ, Reed JL. FOCAL: an experimental design tool for systematizing metabolic discoveries and model development. Genome Biol 2012;13:R116. [PMID: 23236964 PMCID: PMC4056367 DOI: 10.1186/gb-2012-13-12-r116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 12/13/2012] [Indexed: 01/05/2023]  Open
112
Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martínez C, Fulcher C, Huerta AM, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Schröder I, Shearer AG, Subhraveti P, Travers M, Weerasinghe D, Weiss V, Collado-Vides J, Gunsalus RP, Paulsen I, Karp PD. EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res 2012;41:D605-12. [PMID: 23143106 PMCID: PMC3531154 DOI: 10.1093/nar/gks1027] [Citation(s) in RCA: 428] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]  Open
113
Steffen-Munsberg F, Vickers C, Thontowi A, Schätzle S, Meinhardt T, Svedendahl Humble M, Land H, Berglund P, Bornscheuer UT, Höhne M. Revealing the Structural Basis of Promiscuous Amine Transaminase Activity. ChemCatChem 2012. [DOI: 10.1002/cctc.201200545] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
114
Takemoto K. Metabolic network modularity arising from simple growth processes. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012;86:036107. [PMID: 23030980 DOI: 10.1103/physreve.86.036107] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Indexed: 06/01/2023]
115
Current understanding of the formation and adaptation of metabolic systems based on network theory. Metabolites 2012;2:429-57. [PMID: 24957641 PMCID: PMC3901219 DOI: 10.3390/metabo2030429] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 06/26/2012] [Accepted: 07/09/2012] [Indexed: 11/17/2022]  Open
116
Flores H, Lin S, Contreras-Ferrat G, Cronan JE, Morett E. Evolution of a new function in an esterase: simple amino acid substitutions enable the activity present in the larger paralog, BioH. Protein Eng Des Sel 2012;25:387-95. [PMID: 22691705 DOI: 10.1093/protein/gzs035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
117
Peretó J. Out of fuzzy chemistry: from prebiotic chemistry to metabolic networks. Chem Soc Rev 2012;41:5394-403. [PMID: 22508108 DOI: 10.1039/c2cs35054h] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
118
Copley SD. Toward a systems biology perspective on enzyme evolution. J Biol Chem 2012;287:3-10. [PMID: 22069330 PMCID: PMC3249082 DOI: 10.1074/jbc.r111.254714] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
119
Brown AM, Hoopes SL, White RH, Sarisky CA. Purine biosynthesis in archaea: variations on a theme. Biol Direct 2011;6:63. [PMID: 22168471 PMCID: PMC3261824 DOI: 10.1186/1745-6150-6-63] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Accepted: 12/14/2011] [Indexed: 11/10/2022]  Open
120
Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5'-phosphate synthesis. Mol Syst Biol 2011;6:436. [PMID: 21119630 PMCID: PMC3010111 DOI: 10.1038/msb.2010.88] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 09/30/2010] [Indexed: 11/28/2022]  Open
121
Behe MJ. Experimental evolution, loss-of-function mutations, and "the first rule of adaptive evolution". QUARTERLY REVIEW OF BIOLOGY 2011;85:419-45. [PMID: 21243963 DOI: 10.1086/656902] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
122
Soo VWC, Hanson-Manful P, Patrick WM. Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli. Proc Natl Acad Sci U S A 2011;108:1484-9. [PMID: 21173244 PMCID: PMC3029738 DOI: 10.1073/pnas.1012108108] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
123
Erijman A, Aizner Y, Shifman JM. Multispecific Recognition: Mechanism, Evolution, and Design. Biochemistry 2011;50:602-11. [DOI: 10.1021/bi101563v] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
124
Evolving promiscuously. Proc Natl Acad Sci U S A 2011;108:1199-200. [PMID: 21224414 DOI: 10.1073/pnas.1018588108] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
125
De novo designed proteins from a library of artificial sequences function in Escherichia coli and enable cell growth. PLoS One 2011;6:e15364. [PMID: 21245923 PMCID: PMC3014984 DOI: 10.1371/journal.pone.0015364] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 11/11/2010] [Indexed: 11/20/2022]  Open
126
Khersonsky O, Tawfik DS. Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu Rev Biochem 2010;79:471-505. [PMID: 20235827 DOI: 10.1146/annurev-biochem-030409-143718] [Citation(s) in RCA: 979] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
127
Hwang GH, Cho JY. Identification of a suppressor gene for the arginine-auxotrophic argJ mutation in Corynebacterium glutamicum. J Ind Microbiol Biotechnol 2010;37:1131-6. [PMID: 20544254 DOI: 10.1007/s10295-010-0760-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2010] [Accepted: 05/25/2010] [Indexed: 10/19/2022]
128
Chemoenzymatic and Bioenzymatic Synthesis of Carbohydrate Containing Natural Products. NATURAL PRODUCTS VIA ENZYMATIC REACTIONS 2010;297:105-48. [DOI: 10.1007/128_2010_78] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
129
Andersson DI, Hughes D. Gene amplification and adaptive evolution in bacteria. Annu Rev Genet 2009;43:167-95. [PMID: 19686082 DOI: 10.1146/annurev-genet-102108-134805] [Citation(s) in RCA: 205] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
130
Bacterial gene amplification: implications for the evolution of antibiotic resistance. Nat Rev Microbiol 2009;7:578-88. [PMID: 19609259 DOI: 10.1038/nrmicro2174] [Citation(s) in RCA: 248] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
131
Wackett LP. Questioning our perceptions about evolution of biodegradative enzymes. Curr Opin Microbiol 2009;12:244-51. [DOI: 10.1016/j.mib.2009.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 05/02/2009] [Accepted: 05/05/2009] [Indexed: 10/20/2022]
132
Treangen TJ, Abraham AL, Touchon M, Rocha EPC. Genesis, effects and fates of repeats in prokaryotic genomes. FEMS Microbiol Rev 2009;33:539-71. [PMID: 19396957 DOI: 10.1111/j.1574-6976.2009.00169.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
133
Mapping catalytic promiscuity in the alkaline phosphatase superfamily. PURE APPL CHEM 2009. [DOI: 10.1351/pac-con-08-10-20] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
134
Bershtein S, Tawfik DS. Ohno's Model Revisited: Measuring the Frequency of Potentially Adaptive Mutations under Various Mutational Drifts. Mol Biol Evol 2008;25:2311-8. [DOI: 10.1093/molbev/msn174] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
135
Patrick WM, Matsumura I. A study in molecular contingency: glutamine phosphoribosylpyrophosphate amidotransferase is a promiscuous and evolvable phosphoribosylanthranilate isomerase. J Mol Biol 2008;377:323-36. [PMID: 18272177 DOI: 10.1016/j.jmb.2008.01.043] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Revised: 01/14/2008] [Accepted: 01/16/2008] [Indexed: 10/22/2022]
136
Morett E, Saab-Rincón G, Olvera L, Olvera M, Flores H, Grande R. Sensitive genome-wide screen for low secondary enzymatic activities: the YjbQ family shows thiamin phosphate synthase activity. J Mol Biol 2007;376:839-53. [PMID: 18178222 DOI: 10.1016/j.jmb.2007.12.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Revised: 12/06/2007] [Accepted: 12/07/2007] [Indexed: 11/28/2022]
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