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Substrate ambiguous enzymes within the Escherichia coli proteome offer different evolutionary solutions to the same problem.

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 ?serB Escherichia coli cells from starvation on minimal media. We directed the evolution of variants of Gph, histidinol phosphatase (HisB), and YtjC that complemented ?serB 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 ?serB deletion. These results in combination show that proteomes can offer multiple mechanistic solutions to a molecular recognition problem.

SUBMITTER: Yip SH

PROVIDER: S-EPMC3842161 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature

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Substrate ambiguous enzymes within the Escherichia coli proteome offer different evolutionary solutions to the same problem.

Yip Sylvia Hsu-Chen SH Matsumura Ichiro I

Molecular biology and evolution 20130531 9

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 ...[more]

PMID: 23728795

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Project description:The Taitung region is one of Taiwan's main sites for ginger agriculture. Due to issues with disease and nutrients, farmers cannot use continuous cropping techniques on ginger, meaning that the ginger industry is constantly searching for new land. Continuous cropping increases the risk of infection by Pythium myriotylum and Ralstonia solanacearum, which cause soft rot disease and bacterial wilt, respectively. In addition, fertilizer additives, which are commonly used to increase trace elements in the soil, cannot restore the soil when it is undergoing continuous cropping on ginger, even when there has been no observable decrease in trace elements in the soil. Recent studies about soil microbiome manipulation and the application of microorganisms have shown that plant-associated microbes have the ability to improve plant growth and facilitate sustainable agriculture, but studies of this kind still need to be carried out on ginger cultivation. Therefore, in this study, we used the bacterial 16S V3-V4 hypervariable region of the 16S rRNA region to investigate microbe compositions in ginger soil to identify the difference between ginger soil with and without disease. Later, to investigate the influence of the well-known biocontrol agent B. velezensis and the fungicide Etridiazole on soil microbes and ginger productivity, we designed an experiment that collected the soil samples according to the different periods of ginger cultivation to examine the microbial community dynamics in the rhizome and bulk soil. We demonstrated that B. velezensis is beneficial to ginger reproduction. In accordance with our results, we suggest that B. velezensis may influence the plant's growth by adjusting its soil microbial composition. Etridiazole, on the other hand, may have some side effects on the ginger or beneficial bacteria in the soils that inhibit ginger reproduction. IMPORTANCE Pythium myriotylum and Ralstonia solanacearum cause soft rot disease and bacterial wilt, respectively. In this study, we used the bacterial 16S V3-V4 hypervariable region of the 16S rRNA region to investigate microbe compositions in healthy and diseased ginger soil and find out the influence of the well-known biocontrol agent B. velezensis and the fungicide Etridiazole on soil microbes and ginger productivity. These results demonstrated that B. velezensis benefits ginger reproduction and may influence the soil bacterial composition, while Etridiazole may have some side effects on the ginger or beneficial bacteria in the soils. The interactions among ginger, biocontrol agents, and fungicides need to be further investigated.

Project description:BackgroundGenome evolution in intracellular microbial symbionts is characterized by gene loss, generating some of the smallest and most gene-poor genomes known. As a result of gene loss these genomes commonly contain metabolic pathways that are fragmented relative to their free-living relatives. The evolutionary retention of fragmented metabolic pathways in the gene-poor genomes of endosymbionts suggests that they are functional. However, it is not always clear how they maintain functionality. To date, the fragmented metabolic pathways of endosymbionts have been shown to maintain functionality through complementation by host genes, complementation by genes of another endosymbiont and complementation by genes in host genomes that have been horizontally acquired from a microbial source that is not the endosymbiont. Here, we demonstrate a fourth mechanism.ResultsWe investigate the evolutionary retention of a fragmented pathway for the essential nutrient pantothenate (vitamin B5) in the pea aphid, Acyrthosiphon pisum endosymbiosis with Buchnera aphidicola. Using quantitative analysis of gene expression we present evidence for complementation of the Buchnera pantothenate biosynthesis pathway by host genes. Further, using complementation assays in an Escherichia coli mutant we demonstrate functional replacement of a pantothenate biosynthesis enzyme, 2-dehydropantoate 2-reductase (E.C. 1.1.1.169), by an endosymbiont gene, ilvC, encoding a substrate ambiguous enzyme.ConclusionsEarlier studies have speculated that missing enzyme steps in fragmented endosymbiont metabolic pathways are completed by adaptable endosymbiont enzymes from other pathways. Here, we experimentally demonstrate completion of a fragmented endosymbiont vitamin biosynthesis pathway by recruitment of a substrate ambiguous enzyme from another pathway. In addition, this work extends host/symbiont metabolic collaboration in the aphid/Buchnera symbiosis from amino acid metabolism to include vitamin biosynthesis.

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Substrate ambiguous enzymes within the Escherichia coli proteome offer different evolutionary solutions to the same problem.

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Substrate ambiguous enzymes within the Escherichia coli proteome offer different evolutionary solutions to the same problem.

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