Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 550228
Title Enzyme promiscuity shapes adaptation to novel growth substrates
Author(s) Guzmán, Gabriela I.; Sandberg, Troy E.; LaCroix, Ryan A.; Nyerges, Ákos; Papp, Henrietta; Raad, Markus de; King, Zachary A.; Hefner, Ying; Northen, Trent R.; Notebaart, Richard A.; Pál, Csaba; Palsson, Bernhard O.; Papp, Balázs; Feist, Adam M.
Source Molecular Systems Biology 15 (2019)4. - ISSN 1744-4292 - p. e8462 - e8462.
DOI https://doi.org/10.15252/msb.20188462
Department(s) Food Microbiology
Publication type Refereed Article in a scientific journal
Publication year 2019
Keyword(s) adaptive evolution - enzyme promiscuity - genome‐scale modeling - systems biology
Abstract

Evidence suggests that novel enzyme functions evolved from low-level promiscuous activities in ancestral enzymes. Yet, the evolutionary dynamics and physiological mechanisms of how such side activities contribute to systems-level adaptations are not well characterized. Furthermore, it remains untested whether knowledge of an organism's promiscuous reaction set, or underground metabolism, can aid in forecasting the genetic basis of metabolic adaptations. Here, we employ a computational model of underground metabolism and laboratory evolution experiments to examine the role of enzyme promiscuity in the acquisition and optimization of growth on predicted non-native substrates in Escherichia coli K-12 MG1655. After as few as approximately 20 generations, evolved populations repeatedly acquired the capacity to grow on five predicted non-native substrates-D-lyxose, D-2-deoxyribose, D-arabinose, m-tartrate, and monomethyl succinate. Altered promiscuous activities were shown to be directly involved in establishing high-efficiency pathways. Structural mutations shifted enzyme substrate turnover rates toward the new substrate while retaining a preference for the primary substrate. Finally, genes underlying the phenotypic innovations were accurately predicted by genome-scale model simulations of metabolism with enzyme promiscuity.

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