1-Methylthio-<scp>d</scp>-xylulose 5-Phosphate Methylsulfurylase: A Novel Route to 1-Deoxy-<scp>d</scp>-xylulose 5-Phosphate in <i>Rhodospirillum rubrum</i>

Warlick, Benjamin P.; Evans, Bradley S.; Erb, Tobias J.; Ramagopal, U.A.; Sriram, Jaya; Imker, H.J.; Sauder, J.M.; Bonanno, J.B.; Burley, S.K.; Tabita, F. Robert; Almo, Steven C.; Sweedler, Jonathan V.; Gerlt, J.A.

doi:10.1021/bi301215g

Cited by 17 publications

(20 citation statements)

References 6 publications

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“…In turn, this mixture entered a reductive pathway, the details of which are still being explored (Erb et al, 2012;North et al, 2017), involving a MTXu-5-P methylsulphurylase, a member of the cupin superfamily (Uberto and Moomaw, 2013). This enzyme produced methanethiol and 1-deoxy-D-xylulose-5-P (DXP, Warlick et al, 2012b), the key precursor of isoprenoids in bacteria (Dickschat, 2011). Subsequently, a similar pathway was identified in Rhodopseudomonas palustris (Miller et al, 2018a).…”

Section: Arrows)mentioning

confidence: 99%

Revisiting the methionine salvage pathway and its paralogues

Sekowska

Ashida

Danchin

2018

Microbial Biotechnology

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SummaryMethionine is essential for life. Its chemistry makes it fragile in the presence of oxygen. Aerobic living organisms have selected a salvage pathway (the MSP) that uses dioxygen to regenerate methionine, associated to a ratchet‐like step that prevents methionine back degradation. Here, we describe the variation on this theme, developed across the tree of life. Oxygen appeared long after life had developed on Earth. The canonical MSP evolved from ancestors that used both predecessors of ribulose bisphosphate carboxylase oxygenase (RuBisCO) and methanethiol in intermediate steps. We document how these likely promiscuous pathways were also used to metabolize the omnipresent by‐products of S‐adenosylmethionine radical enzymes as well as the aromatic and isoprene skeleton of quinone electron acceptors.

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Section: Arrows)mentioning

confidence: 99%

Revisiting the methionine salvage pathway and its paralogues

Sekowska

Ashida

Danchin

2018

Microbial Biotechnology

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“…For MTA metabolism, the DHAP shunt constitutes one of several recently discovered anaerobic salvage pathways. The MTA‐isoprenoid shunt (Figure a) converts MTA to 1‐deoxyxylulose‐5‐P (isoprenoid precursor) and methanethiol (methionine precursor) under both aerobic and anaerobic growth conditions (Cho et al, ; Erb et al, ; North et al, , ; Warlick et al, ). In R. rubrum , RuBisCO itself appears to be involved in a distinct, albeit unresolved, anaerobic MTA metabolism pathway (Figure c) (Dey et al, ; Singh & Tabita, ).…”

Section: Discussionmentioning

confidence: 99%

“…Some organisms such as P. aeruginosa and M. jannaschii employ an MTA deaminase (MtaD) and 5ʹ‐methylthioinsoine phosphorylase (MtiP) (Guan et al, , ; Miller et al, ; Miller, Rauch, et al, 2018). (a) MTA‐isoprenoid shunt from R. rubrum in which a methylthio‐glutathione intermediate is reduced to release methanethiol (CH 3 SH) by the proposed gamma‐glutamyl cycle as the immediate precursor to methionine (Cho et al, ; Erb et al, ; North et al, ; Warlick et al, ). (b) Universal methionine salvage pathway and variations thereof (Albers, ; Sekowska et al, ).…”

Section: Introductionmentioning

confidence: 99%

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

North

Wildenthal

Erb

et al. 2020

Molecular Microbiology

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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.

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“…Panel A, the classical methionine salvage pathway in which methionine is quantitatively recovered from MTA (10). Panel B, the recently discovered pathway in which MTA is ribose moiety of MTA is converted to DXP and the 5′-methylthio group is released as methanethiol that can be captured, in part, to form methionine (12). …”

Section: Figurementioning

confidence: 99%

“…The members of the first family (red nodes in Figure 2) catalyze the 2,3-diketo-5-methylthiopentane 1-phosphate (DK-MTP 1-P) “enolase” 2 reaction (Figure 1, panel B) in the well-known “methionine salvage” pathway in species of Bacilli in which the 5′-methylthioribose moiety of MTA is converted to methionine (Figure 3, panel A; in other organisms, the “enolase” reaction is catalyzed by an analogous enzyme); the product of the “enolase” reaction is 2-hydroxy-3-keto-5-methylthiopent-1-ene 1-phosphate (HK-MTP 1-P) (10). The members of the second family (blue nodes in Figure 2) catalyze the 5-methylthio-D-ribulose 1-phosphate (MTRu 1-P) 1,3-isomerase reaction (Figure 1, panel C) in a recently discovered nonmevalonate isoprene synthesis pathway (“MTA-isoprenoid shunt”) in Rhodospirillum rubrum (Figure 3, panel B) (11); the 1,3-isomerase converts MTRu 1-P to 1-methylthioxylulose 5-phosphate (MTXu 5-P) that is the immediate precursor to 1-deoxy-D-xylulose 5-phosphate (DXP) in the isoprene pathway and methanethiol that is captured, in part, for methionine synthesis (12). …”

Section: Introductionmentioning

confidence: 99%

Mechanistic Diversity in the RuBisCO Superfamily: RuBisCO from Rhodospirillum rubrum Is Not Promiscuous for Reactions Catalyzed by RuBisCO-like Proteins

Warlick¹,

Imker²,

Sriram

et al. 2012

Biochemistry

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D-Ribulose 1,5-bisphosphate carboxylase/oxygenases (RuBisCOs) are promiscuous, catalyzing not only carboxylation and oxygenation of D-ribulose 1,5-bisphosphate but also other promiscuous, presumably nonphysiological, reactions initiated by abstraction of the 3-proton of D-ribulose 1,5-bisphosphate. Also, RuBisCO has homologues that do not catalyze carboxylation; these are designated RuBisCO-like proteins or RLPs. Members of the two families of RLPs catalyze reactions in the recycling of 5′-methylthioadenosine (MTA) generated by polyamine synthesis: 1) the 2,3-diketo-5-methylthiopentane 1-phosphate (DK-MTP 1-P) “enolase” reaction in the well-known “methionine salvage” pathway in species of Bacilli; and 2) the 5-methylthio-D-ribulose 1-phosphate (MTRu 1-P) 1,3-isomerase reaction in the recently discovered “MTA-isoprenoid shunt” that generates 1-deoxy-D-xylulose 5-phosphate (DXP) for nonmevalonate isoprene synthesis in Rhodospirillum rubrum. We first studied the structure and reactivity of DK-MTP 1-P which was reported to decompose rapidly [Ashida, H., Saito, Y., Kojima, C., and Yokota, A. (2008) Biosci Biotechnol Biochem 72, 959–67]. The 2-carbonyl group of DK-MTP 1-P is rapidly hydrated in solution and can undergo enolization both nonenzymatically and enzymatically via the small amount of unhydrated material that is present. We then examined the ability of RuBisCO from R. rubrum to catalyze both of the RLP-catalyzed reactions. Contrary to a previous report [Ashida, H., Saito, Y., Kojima, C., Kobayashi, K., Ogasawara, N., and Yokota, A. (2003) Science 302, 286–290], we were unable to confirm that this RuBisCO catalyzes the DK-MTP 1-P “enolase” reaction either in vitro or in vivo. We also determined that this RuBisCO does not catalyze the MTRu 1-P 1,3-isomerase reaction in vitro. Thus, although RuBisCOs can be functionally promiscuous, RuBisCO from R. rubrum is not promiscuous for either of the known RLP-catalyzed reactions.

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1-Methylthio-d-xylulose 5-Phosphate Methylsulfurylase: A Novel Route to 1-Deoxy-d-xylulose 5-Phosphate in Rhodospirillum rubrum

Cited by 17 publications

References 6 publications

Revisiting the methionine salvage pathway and its paralogues

Revisiting the methionine salvage pathway and its paralogues

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

Mechanistic Diversity in the RuBisCO Superfamily: RuBisCO from Rhodospirillum rubrum Is Not Promiscuous for Reactions Catalyzed by RuBisCO-like Proteins

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