A bioactive molecule made by unusual salvage of radical SAM enzyme byproduct 5-deoxyadenosine blurs the boundary of primary and secondary metabolism

Abstract

Edited by Chris Whitfield 5-Deoxyadenosine (5dAdo) is the byproduct of many radical S-adenosyl-L-methionine enzyme reactions in all domains of life. 5dAdo is also an inhibitor of the radical S-adenosyl-Lmethionine enzymes themselves, making it necessary for cells to construct pathways to recycle or dispose of this toxic metabolite. However, the specific pathways involved have long remained unexplored. Recent research demonstrated a growth advantage in certain organisms by using 5dAdo or intermediates as a sole carbon source and elucidated the corresponding salvage pathway. We now provide evidence using supernatant analysis by GC-MS for another 5dAdo recycling route. Specifically, in the unicellular cyanobacterium Synechococcus elongatus PCC 7942 (S. elongatus), the activity of promiscuous enzymes leads to the synthesis and excretion first of 5-deoxyribose and subsequently of 7-deoxysedoheptulose. 7-Deoxysedoheptulose is an unusual deoxy-sugar, which acts as an antimetabolite of the shikimate pathway, thereby exhibiting antimicrobial and herbicidal activity. This strategy enables organisms with small genomes and lacking canonical gene clusters for the synthesis of secondary metabolites, like S. elongatus, to produce antimicrobial compounds from primary metabolism and enzymatic promiscuity. Our findings challenge the view of bioactive molecules as sole products of secondary metabolite gene clusters and expand the range of compounds that microorganisms can deploy to compete for their ecological niche.

In vivo Inhibition of the 3-Dehydroquinate Synthase by 7-Deoxysedoheptulose Depends on Promiscuous Uptake by Sugar Transporters in Cyanobacteria

“…Final concentrations are shown in the figures. 7dSh was synthesized as described in our previous publications ( Brilisauer et al, 2019 ; Rapp et al, 2021 ). Cell density of the unicellular strains was determined by the measurement of the absorbance at 750 nm (Specord, Analytik Jena).…”

“…or S. elongatus by using the natural competence of this strains. The exact procedure is described in our previous publication ( Rapp et al, 2021 ). Integration of the plasmid and segregation was confirmed by colony PCR (9+12 for Synechocystis sp., 17+18 for S. elongatus , see Table 2 ).…”

“…Synechococcus elongatus is a natural producer of 7dSh and its precursor molecule 5-deoxyribose (5dR) (Brilisauer et al, 2019;Rapp et al, 2021). In our previous work we showed that both FIGURE 5 | The putative ribokinase Synpcc7942_0116 is responsible for 5dR and 7dSh sensitivity in S. elongatus.…”

“…The compound was characterized as a rare deoxy sugar–namely 7-deoxy- D - altro -2-heptulose (7-deoxysedoheptulose, 7dSh) ( Brilisauer et al, 2019 ). Recently, we showed that 7dSh derives from 5-deoxyadenosine (5dAdo) ( Rapp et al, 2021 ), an inhibitory by-product of radical SAM enzymes, which are involved in a multitude of reactions ( Sofia et al, 2001 ), for example in the synthesis of the essential cofactors biotin and thiamine ( Choi-Rhee and Cronan, 2005 ; Challand et al, 2010 ). 5dAdo is metabolized into 5-deoxyribose (5dR) and subsequently converted to 7dSh, by the sole activity of promiscuous enzymes, without a specific gene cluster being involved ( Rapp et al, 2021 ).…”

“…Therefore, 7dSh is not a “classical” secondary metabolite as it derives from a toxic waste product of the primary metabolism. 5dAdo is only converted to 7dSh under certain environmental conditions, suggesting an unknown regulatory mechanism for the formation of the “secondary” metabolite 7dSh ( Rapp et al, 2021 ). 7dSh is most likely an antimetabolite of the shikimate pathway, as 7dSh treated cells strongly accumulate the structurally similar molecule 3-deoxy- D - arabino -heptulosonate 7-phosphate (DAHP), the substrate of the 3-dehydroquinate synthase (DHQS) (see Figure 1 ; Brilisauer et al, 2019 ).…”