Metabolic Regulation as a Consequence of Anaerobic 5-Methylthioadenosine Recycling in Rhodospirillum rubrum

Abstract

Rhodospirillum rubrum possesses a novel oxygen-independent, aerobic methionine salvage pathway (MSP) for recycling methionine from 5-methylthioadenosine (MTA), the MTA-isoprenoid shunt. This organism can also metabolize MTA as a sulfur source under anaerobic conditions, suggesting that the MTA-isoprenoid shunt may also function anaerobically as well. In this study, deep proteomics profiling, directed metabolite analysis, and reverse transcriptase quantitative PCR (RT-qPCR) revealed metabolic changes in response to anaerobic growth on MTA versus sulfate as sole sulfur source. The abundance of protein levels associated with methionine transport, cell motility, and chemotaxis increased in the presence of MTA over that in the presence of sulfate. Purine salvage from MTA resulted primarily in hypoxanthine accumulation and a decrease in protein levels involved in GMP-to-AMP conversion to balance purine pools. Acyl coenzyme A (acyl-CoA) metabolic protein levels for lipid metabolism were lower in abundance, whereas poly-β-hydroxybutyrate synthesis and storage were increased nearly 10-fold. The known R. rubrum aerobic MSP was also shown to be upregulated, to function anaerobically, and to recycle MTA. This suggested that other organisms with gene homologues for the MTA-isoprenoid shunt may also possess a functioning anaerobic MSP. In support of our previous findings that ribulose-1,5-carboxylase/oxygenase (RubisCO) is required for an apparently purely anaerobic MSP, RubisCO transcript and protein levels both increased in abundance by over 10-fold in cells grown anaerobically on MTA over those in cells grown on sulfate, resulting in increased intracellular RubisCO activity. These results reveal for the first time global metabolic responses as a consequence of anaerobic MTA metabolism compared to using sulfate as the sulfur source.

Revisiting the methionine salvage pathway and its paralogues

“…They further showed that in R. rubrum , the enzyme converts 5‐methylthio‐ d ‐ribulose‐1‐phosphate (MTRu‐1‐P) into a 3:1 mixture of 1‐methylthioxylulose‐5‐phosphate and 1‐methylthioribulose‐5‐phosphate (Imker et al ., ). From this point onward, many studies explored the biochemistry of the enzymes of the MSP, while also uncovering many variants of the pathway and its evolution (North et al ., ). Here, we summarize the present status of this complex metabolic cycle resulting in methionine salvage, following pathways that have been repeatedly rediscovered and combined together via convergent evolution, with many activities still of unknown nature.…”

“…In other pathways, it produces methanethiol and a precursor of isoprenoids (green) or 2-methylthioethanol (dark blue). This metabolite results in ethylene production under anaerobic conditions (light green uncovering many variants of the pathway and its evolution (North et al, 2016). Here, we summarize the present status of this complex metabolic cycle resulting in methionine salvage, following pathways that have been repeatedly rediscovered and combined together via convergent evolution, with many activities still of unknown nature.…”

Mechanisms of subzero growth in the cryophile Planococcus halocryophilus determined through proteomic analysis

“…This approach also assures that a rare or abundant peptide gets an equal chance at being detected (Hettich et al, 2013). Use of this technique is well established and widely accepted to study proteomes, especially for deep proteome measurements (Hettich et al, 2013;Bagnoud et al, 2016;North et al, 2016).…”

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

“…Like the methionine cycle, the DHAP shunt is oxygen independent for functionality in both oxic and anoxic environments (Figure a). Previous R. rubrum transcriptomic and proteomic analyses demonstrate that the DHAP shunt genes appear to be constitutively expressed and gene products produced during both aerobic and anaerobic growth, irrespective of extracellular MTA and 5ʹdAdo concentration, for continual salvage of MTA and 5ʹdAdo (Cho et al, ; Erb et al, ; North et al, ). Given the propensity of 5′dAdo formation by Radical SAM enzymes during anaerobic metabolism (Figures a and ) (Broderick et al, ), this underpins the utility of the DHAP shunt in anoxic environments, and likely explains the observation that the DHAP shunt genes are enriched in facultative and obligate anaerobic bacteria (Beaudoin et al, ; North et al, ).…”

“…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, ).…”