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

Abstract

S‐adenosyl‐l‐methionine (SAM) is a necessary cosubstrate for numerous essential enzymatic reactions including protein and nucleotide methylations, secondary metabolite synthesis and radical‐mediated processes. Radical SAM enzymes produce 5ʹ‐deoxyadenosine, and SAM‐dependent enzymes for polyamine, neurotransmitter and quorum sensing compound synthesis produce 5ʹ‐methylthioadenosine as by‐products. Both are inhibitory and must be addressed by all cells. This work establishes a bifunctional oxygen‐independent salvage pathway for 5ʹ‐deoxyadenosine and 5ʹ‐methylthioadenosine in both Rhodospirillum rubrum and Extraintestinal Pathogenic Escherichia coli. Homologous genes for this pathway are widespread in bacteria, notably pathogenic strains within several families. A phosphorylase (Rhodospirillum rubrum) or separate nucleoside and kinase (Escherichia coli) followed by an isomerase and aldolase sequentially function to salvage these two wasteful and inhibitory compounds into adenine, dihydroxyacetone phosphate and acetaldehyde or (2‐methylthio)acetaldehyde during both aerobic and anaerobic growth. Both SAM by‐products are metabolized with equal affinity during aerobic and anaerobic growth conditions, suggesting that the dual‐purpose salvage pathway plays a central role in numerous environments, notably the human body during infection. Our newly discovered bifunctional oxygen‐independent pathway, widespread in bacteria, salvages at least two by‐products of SAM‐dependent enzymes for carbon and sulfur salvage, contributing to cell growth.

5-Deoxyadenosine Salvage by Promiscuous Enzyme Activity leads to Bioactive Deoxy-Sugar Synthesis inSynechococcus elongatus

“…The phenotype of the insertion mutant (mtnP::specR), which excretes 5dAdo instead of 5dR/7dSh, demonstrates that 5dR and 7dSh are products of 5dAdo salvage ( Figure 6). The 5dAdo salvage routes previously reported suggest that the phosphorylation of 5dR or the 5dR moiety of 5dAdo is essential to further metabolise the molecules via specific enzymes or by promiscuous activity of the enzymes of the MSP (Beaudoin et al, 2018;North et al, 2020;Sekowska et al, 2018). In S. elongatus however, 5dR-1P is subsequently dephosphorylated to 5dR for excretion or for further processing to 7dSh.…”

“…As 5dR-1P is metabolically stable we assumed the involvement of a specific phosphatase in 5dR-1P dephosphorylation. The dephosphorylation of 5dR-1P in 5dAdo salvage is surprising as in the literature it is suggested that the phosphorylation of 5dR is essential for its further metabolization (Beaudoin et al, 2018;North et al, 2020;Sekowska et al, 2018). To identify the responsible phosphatase, we analysed the genome of S. elongatus regarding the presence of phosphoric monoester hydrolases (see Table S3, Supporting information).…”

“…MtnP or MtnN/MtnK and MtnA in R. rubrum) or with a specific phosphorylase and isomerase as shown for B. thuringiensis. In vitro data suggest that the MTRu-1P-dehydratase (MtnB) from the MSP can also act as a promiscuous aldolase thereby completing the 5dAdo salvage via the DHAP shunt (Beaudoin et al, 2018;North et al, 2020). Since none of the analysed strains possesses such an Ald2 homolog, we assume that 5dR/7dSh producing strains might use the DHAP shunt by using MtnB under certain conditions.…”

“…Therefore, and because of the high bioenergetic costs of these compounds, salvage pathways are necessary. SAH is rescued via the methionine cycle (North et al, 2020). MTA salvage via the methionine salvage pathway (MSP) is also well characterised (Sekowska and Danchin, 2002;Wray and Abeles, 1995) (see Figure 1 B).…”

“…Methylthioribose 1-phosphate isomerase (MTRI) was shown to use the substrates MTR-1P, 5dR-1P and 5dR. And only recently, it was demonstrated that 5dAdo is processed to DHAP and acetaldehyde by the first enzymes of the MSP and a clustered class II aldolase in Rhodospirillum rubrum and pathogenic Escherichia coli strains, in a process they called the "DHAP shunt" (North et al, 2020)…”