Salvage of the 5-deoxyribose byproduct of radical SAM enzymes

Abstract

5-Deoxyribose is formed from 5′-deoxyadenosine, a toxic byproduct of radical S-adenosylmethionine (SAM) enzymes. The degradative fate of 5-deoxyribose is unknown. Here, we define a salvage pathway for 5-deoxyribose in bacteria, consisting of phosphorylation, isomerization, and aldol cleavage steps. Analysis of bacterial genomes uncovers widespread, unassigned three-gene clusters specifying a putative kinase, isomerase, and sugar phosphate aldolase. We show that the enzymes encoded by the Bacillus thuringiensis cluster, acting together in vitro, convert 5-deoxyribose successively to 5-deoxyribose 1-phosphate, 5-deoxyribulose 1-phosphate, and dihydroxyacetone phosphate plus acetaldehyde. Deleting the isomerase decreases the 5-deoxyribulose 1-phosphate pool size, and deleting either the isomerase or the aldolase increases susceptibility to 5-deoxyribose. The substrate preference of the aldolase is unique among family members, and the X-ray structure reveals an unusual manganese-dependent enzyme. This work defines a salvage pathway for 5-deoxyribose, a near-universal metabolite.

Revisiting the methionine salvage pathway and its paralogues

“…The fluorinated phosphodeoxyribose is then submitted to the action of a 5‐fluoro‐5‐deoxyribose‐1‐phosphate isomerase (Onega et al ., ) and a 4‐fluorothreonine acetaldehyde transaldolase allows the bacterium to generate fluoroacetate in a mimic of the standard metabolism of acetaldehyde (Zhao et al ., ). This pathway was indeed experimentally validated in Bacillus thuringiensis after submission for publication of the present review (Beaudoin et al ., ). Another pathway would, in the presence of dioxygen, follow the route of the standard MSP, but the MtnD dioxygenase would now yield 2‐ketobutyrate instead of KMBA.…”

A bifunctional salvage pathway for two distinct S‐adenosylmethionine by‐products that is widespread in bacteria, including pathogenic Escherichia coli

“…This also enabled accurate measurement of the intrinsic ATPase activity in the absence of any cosubstrate (0.04 s –1 for both the E. coli and B. subtilis kinase). This was significantly lower than previous reports with the B. thuringiensis enzyme, which included glycerol in the reaction mixture, likely overestimating the intrinsic ATPase activity (Beaudoin et al, ). The ExPEC (ATCC 25922) isomerase equally preferred 5‐deoxyribose‐1‐phosphate and 5‐methylthioribose‐1‐phosphate (Table ; Ec MtnA).…”

“…Moreover, inactivation of the aldolase (ATCC 25922 Δ ald2 ) lowered acetaldehyde (and DHAP) formation 10‐fold (Figure c,d). The small amount of pathway activity in the aldolase deletion strain can be attributed to E. coli L‐fuculose‐1‐phosphate aldolase, which has modest activity with 5‐deoxyribulose‐1‐phosphate as a substrate (Table ; Ec FucA) (Beaudoin et al, ; Erb et al, ). Inactivation of the MTA/SAH/5ʹdAdo nucleosidase gene ( pfs ) common to all E. coli resulted in >10‐fold slower metabolism of 5ʹdAdo to 5‐deoxyribose (Figure e).…”

“…Currently, the protein residues coordinating the cobalt and its oxidation state are unknown. Recent characterization of an orthologous B. thuringiensis DHAP shunt aldolase revealed manganese(II) as the native cofactor, which conferred maximal activity (Beaudoin et al, ). However, the alternate metal cofactor preference by the R. rubrum and E. coli aldolases (Figure e) indicates metal cofactor preference varies among the orthologous DHAP shunt aldolases, likely resulting from the specific MTA and 5ʹdAdo abundance levels encountered by each organism.…”

An unusual metal-bound 4-fluorothreonine transaldolase from Streptomyces sp. MA37 catalyses promiscuous transaldol reactions

“…The L-threonine derivatives generated from the assay were confirmed by ESI-HRMS fashion. DrdA is one of the key enzymes in the salvage pathway of 5-deoxyribose, a toxic by-product of the radical Sadenosyl-L-methionine (SAM) enzyme (Beaudoin et al 2018), and MtnB is involved in the methionine pathway (Kang et al 2014). These class II aldolases normally contain an active site divalent metal acting as the Lewis acid type catalyst, coordinated by three conserved histidine residues (His95-His97-His157 in DrdA).…”