Hidden resources in the Escherichia coli genome restore PLP synthesis and robust growth after deletion of the essential gene pdxB

Abstract

SignificanceThe evolution of new metabolic pathways has been a driver of diversification from the last universal common ancestor 3.8 billion y ago to the present. Bioinformatic evidence suggests that many pathways were assembled by recruiting promiscuous enzymes to serve new functions. However, the processes by which new pathways have emerged are lost in time. We have little information about the environmental conditions that fostered emergence of new pathways, the genome context in which new pathways emerged, and the types of mutations that elevated flux through inefficient new pathways. Experimental laboratory evolution has allowed us to evolve a new pathway and identify mechanisms by which mutations increase fitness when an inefficient new pathway becomes important for survival.

Evolution of new enzymes by gene duplication and divergence

“…An example is the recruitment of a promiscuous activity of 3‐phosphoglycerate dehydrogenase (SerA) to catalyze dehydrogenation of erythronate in a novel pathway assembled from promiscuous enzymes that restores PLP synthesis in a laboratory‐evolved strain of E. coli lacking PdxB (4‐phospherythronate dehydrogenase) (Fig. 6) [35]. The level of 3‐phosphoglycerate, the native substrate for SerA, is diminished in this strain due to a deletion in pgl that results in diversion of glyceraldehyde 3‐phosphate from glycolysis toward the pentose phosphate pathway and a point mutation in gapA that decreases the activity of glyceraldehyde 3‐phosphate dehydrogenase in the glycolytic pathway by fivefold.…”

Evolutionary Repair Experiments as a Window to the Molecular Diversity of Life

“…Evolutionary repair experiments have been performed since the beginning of microbial experimental evolution. These original studies, like many current studies (e.g., [15]), focused on the evolution of novel metabolic and protein functions (e.g., [16][17][18]). Evolutionary repair experiments can provide insight into the mechanistic aspects of evolutionary biology and illuminate novel cell-biological phenomena.…”

Underground metabolism facilitates the evolution of novel pathways for vitamin B6 biosynthesis

“…It is tempting to speculate that RsgA is also capable of dephosphorylating 4-phosphoerythronate The four-step serendipitous pathway feeds downstream of PdxB into the disrupted pathway and enable the bacteria to produce wild type levels of PLP (Fig. 2) (Kim et al 2019). The detailed characterisation of the suppressor mutants revealed that some strains mutations improved the oxidation of erythronate to 3,4-dihydroxy-2-oxobutyrate by the 3PG dehydrogenase SerA, which is usually active in serine biosynthesis (Fig.…”

“…Recently, parallel lineages of the E. coli pdxB mutant strain have been evolved for up to 150 generations (Kim et al 2019 ). This adaptive laboratory evolution experiment led to the identification of a novel serendipitous pathway, which consist of the three promiscuous enzymes, an unknown phosphatase required for dephosphorylating 4PE, the 3-phospho-glycerate (3PG) dehydrogenase SerA and the homoserine kinase ThrB.…”

“…Another mutation decreased the cellular levels of serine, thereby preventing feedback inhibition of SerA by serine. Furthermore, several evolved pdxB suppressor carried mutations in the ybhA gene encoding a PLP phosphatase, an enzyme destroying PLP (Kuznetsova et al 2006 ; Sugimoto et al 2018 ; Kim et al 2019 ). Thus, the so-called underground metabolism caused by promiscuous enzymes allows E. coli can assemble a new pathway for synthesising an essential cofactor by patching together native promiscuous enzymes (D'Ari and Casadesus 1998 ; Notebaart et al 2014 , 2018 ; Rosenberg and Commichau 2019 ; Copley 2020 ).…”