ArticleMolecular biology and evolution2013
Substrate ambiguous enzymes within the Escherichia coli proteome offer different evolutionary solutions to the same problem.
Article in Molecular biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 31 citations in OpenAlex.
- The Evolutionary Maintenance of Amino Acid Prototrophy in Escherichia coli.Genome biology and evolution · 2026Article
- A Pair of Promiscuous Surrogates forBiochemistry · 2025Article
- Rescue ofeLife · 2023Article
- How to Recruit a Promiscuous Enzyme to Serve a New Function.Biochemistry · 2023Article
- Coevolution of Metabolic Pathways in Blattodea and TheirMicrobiology spectrum · 2022Article
- Low protein expression enhances phenotypic evolvability by intensifying selection on folding stability.Nature ecology & evolution · 2022Article
- Bacterial rhomboid proteases mediate quality control of orphan membrane proteins.The EMBO journal · 2020Article
- Review
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- Reframing gene essentiality in terms of adaptive flexibility.BMC systems biology · 2018Article
- Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates.The ISME journal · 2017Article
- A protein constructed de novo enables cell growth by altering gene regulation.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Rapid bursts and slow declines: on the possible evolutionary trajectories of enzymes.Journal of the Royal Society, Interface · 2015Review
- Evolution of new functions de novo and from preexisting genes.Cold Spring Harbor perspectives in biology · 2015Review
- An evolutionary biochemist's perspective on promiscuity.Trends in biochemical sciences · 2015Article
- A substrate ambiguous enzyme facilitates genome reduction in an intracellular symbiont.BMC biology · 2014Article
- Escherichia coli D-malate dehydrogenase, a generalist enzyme active in the leucine biosynthesis pathway.The Journal of biological chemistry · 2014Article
- Enzyme recruitment and its role in metabolic expansion.Biochemistry · 2014Review
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2 authors at 1 institution in 1 country.
Funding
Abstract
Many enzymes exhibit some catalytic promiscuity or substrate ambiguity. These weak activities do not affect the fitness of the organism under ordinary circumstances, but can serve as potential evolutionary precursors of new catalytic functions. We wondered whether different proteins with the same substrate ambiguous activity evolve differently under identical selection conditions. Patrick et al. (Patrick WM, Quandt EM, Swartzlander DB, Matsumura I. 2007. Multicopy suppression underpins metabolic evolvability. Mol Biol Evol. 24:2716-2722.) previously showed that three multicopy suppressors, gph, hisB, and ytjC, rescue ΔserB Escherichia coli cells from starvation on minimal media. We directed the evolution of variants of Gph, histidinol phosphatase (HisB), and YtjC that complemented ΔserB more efficiently, and characterized the effects of the amino acid changes, alone and in combination, upon the evolved phosphoserine phosphatase (PSP) activity. Gph and HisB are members of the HAD superfamily of hydrolases, but they adapted through different, kinetically distinguishable, biochemical mechanisms. All of the selected mutations, except N102T in YtjC, proved to be beneficial in isolation. They exhibited a pattern of antagonistic epistasis, as their effects in combination upon the kinetic parameters of the three proteins in reactions with phosphoserine were nonmultiplicative. The N102T mutation exhibited sign epistasis, as it was deleterious in isolation but beneficial in the context of other mutations. We also showed that the D57N mutation in the chromosomal copy of hisB is sufficient to suppress the ΔserB deletion. These results in combination show that proteomes can offer multiple mechanistic solutions to a molecular recognition problem.
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