Microbial pathway for anaerobic PNAS PLUS 5′-methylthioadenosine metabolism coupled to ethylene formation Justin A. Northa, Anthony R. Millera, John A. Wildenthala, Sarah J. Younga, and F. Robert Tabitaa,1 aDepartment of Microbiology, The Ohio State University, Columbus, OH 43210 Edited by Bob B. Buchanan, University of California, Berkeley, CA, and approved October 20, 2017 (received for review June 29, 2017) Numerous cellular processes involving S-adenosyl-L-methionine re- pathway (MSP), also known as the MTA cycle or Yang cycle, to sult in the formation of the toxic by-product, 5′-methylthioadeno- regenerate L-methionine from MTA (6–10)(Fig.1,black,blue,and sine (MTA). To prevent inhibitory MTA accumulation and retain purple arrows). biologically available sulfur, most organisms possess the “univer- A defining feature of the universal MSP is the requirement of sal” methionine salvage pathway (MSP). However, the universal molecular oxygen by a bifunctional dioxygenase (MtnD or MSP is inherently aerobic due to a requirement of molecular oxygen MtnBD; Fig. 1, enzymes J and L) to generate the L-methionine for one of the key enzymes. Here, we report the presence of an precursor 2-keto-4-(methylthio)butyric acid (Fig. 1, compound exclusively anaerobic MSP that couples MTA metabolism to ethylene 10). As such, the universal MSP is incapable of functioning under formation in the phototrophic bacteria Rhodospirillum rubrum and anoxic conditions. Indeed, the facultatively anaerobic bacterium, Rhodopseudomonas palustris. In vivo metabolite analysis of gene Bacillus subtilis, is capable of aerobic growth but incapable of deletion strains demonstrated that this anaerobic MSP functions via anaerobic growth using MTA derivatives as sole sulfur sources sequential action of MTA phosphorylase (MtnP), 5-(methylthio)ribose- (8), and the dioxygenase from Klebsiella pneumoniae is inactive 1-phosphate isomerase (MtnA), and an annotated class II aldolase-like in the absence of dioxygen (11). Consequently, unless an or- protein (Ald2) to form 2-(methylthio)acetaldehyde as an intermedi- ganism has developed some means for anaerobic L-methionine ate. 2-(Methylthio)acetaldehyde is reduced to 2-(methylthio)ethanol, salvage, MTA must be eliminated from the cell at the expense of which is further metabolized as a usable organic sulfur source, gen- biological sulfur and carbon. For example, Escherichia coli ex- erating stoichiometric amounts of ethylene in the process. Ethylene cretes 5-(methylthio)ribose (Fig. 1, compound 4), suggesting a lack of induction experiments using 2-(methylthio)ethanol versus sulfate as a functioning MSP beyond MTA hydrolysis for adenine salvage (12). sulfur sources further indicate anaerobic ethylene production from Approximately 50% of all sequenced bacteria possess a gene ho- 2-(methylthio)ethanol requires protein synthesis and that this process molog of mtnN that encodes for MTA/SAH nucleosidase (MtnN; is regulated. Finally, phylogenetic analysis reveals that the genes cor- Fig. 1, enzyme B), which catalyzes the hydrolysis of MTA to responding to these enzymes, and presumably the pathway, are 5-(methylthio)ribose and adenine (13). Alternately, eukaryotes, some widespread among anaerobic and facultatively anaerobic bacteria archaea, and ∼30% of bacteria possess a gene homolog of mtnP that from soil and freshwater environments. These results not only estab- encodes for MTA phosphorylase (MtnP) (Fig. 1, enzyme D), which lish the existence of a functional, exclusively anaerobic MSP, but they catalyzes phosphorolysis of MTA to 5-(methylthio)ribose-1-P [phos- also suggest a possible route by which ethylene is produced by mi- phate (P)] and adenine (9) (Fig. 1, compound 5). In the archaeon crobes in anoxic environments. Significance methionine salvage | 5′-methylthioadenosine | ethylene | Rhodospirillum rubrum | Rhodopseudomonas palustris Sulfur is an essential element required by all organisms. There- fore, salvage of wasteful, sulfur-containing cellular by-products iologically available sulfur is essential for the synthesis of can be critical. Methionine salvage pathways for organisms liv- BL-cysteine, L-methionine, and its derivative, S-adenosyl-L- ing in oxic environments are well established. However, if and methionine (SAM) (Fig. 1, compound 2). SAM is used for diverse by what mechanisms organisms living in anoxic environments metabolic purposes, serving primarily as a methyl donor for DNA ′ can regenerate methionine from such by-products remain and protein methylation, as a 5 -deoxyadenosyl radical donor for largely unknown. This work identifies a strictly anaerobic me- radical-SAM reactions, and as a 1-aminopropyl donor for poly- thionine salvage pathway, the key genes for which appear to be amine synthesis after decarboxylation by SAM decarboxylase to widespread among obligate and facultatively anaerobic bacte- S-adenosyl-methioninamine (1). SAM also functions as a 2-amino- ria. Strikingly, this pathway also results in the formation of butyryl donor in a wide variety of additional metabolic pathways, ethylene gas, a key plant hormone and signaling molecule. including the synthesis of acyl- and aryl-homoserine lactone Anoxic environments routinely accumulate biologically pro- quorum-sensing molecules, and synthesis of 1-aminocyclopropane- duced ethylene at significant levels, but the organisms and 1-carboxylate (ACC), an ethylene precursor in plants. SAM also is mechanisms responsible have been slow to emerge. This study used for the synthesis of the plant siderophore precursors nic- provides one possible route. otianamine and mugineic acid (2–4). As a consequence of amino- butyryl transfer from SAM or aminopropyl transfer from Author contributions: J.A.N. and F.R.T. designed research; J.A.N., A.R.M., J.A.W., and S.J.Y. MICROBIOLOGY decarboxylated SAM, a dead-end, sulfur-containing by-product, performed research; J.A.N., A.R.M., and J.A.W. contributed new reagents/analytic tools; 5′-methylthioadenosine (MTA), is formed (Fig. 1, compound 3). J.A.N., A.R.M., J.A.W., S.J.Y., and F.R.T. analyzed data; and J.A.N. and F.R.T. wrote MTA is a product inhibitor of polyamine and ACC synthases, and the paper. MTA accumulation can become toxic (1, 4). Since the assimilation The authors declare no conflict of interest. of inorganic sulfur is energetically costly and many organisms en- This article is a PNAS Direct Submission. counter sulfur-poor environments (5, 6), maintaining appropriate This is an open access article distributed under the PNAS license. levels of cellular organic sulfur pools can be critical. This is 1To whom correspondence should be addressed. Email: [email protected]. underscored by the fact that nearly all eukaryotes and many pro- This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. karyotes employ a variation of the universal methionine salvage 1073/pnas.1711625114/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1711625114 PNAS | Published online November 13, 2017 | E10455–E10464 Downloaded by guest on October 1, 2021 Fig. 1. Overview of MSPs. (Black) Universal MSP (also referred to as MTA cycle or Yang cycle) in bacteria like Klebsiella pneumoniae and eukaryotes, in- cluding plants, animals, and fungi. (Blue) Bacterial MSP variations: in Bacillus subtilis MTA phosphorylase (mtnP) is replaced by a separate MTA nucleosidase (mtnN) and MTR kinase (mtnK); the bifunctional enolase-phosphatase (mtnC) is replaced by a separate DK-MTP-1P enolase (mtnW) from the RLP Ykr clade and a HK-MTPene-1P phosphatase (mtnX) (9). (Purple) Fusion enzyme from Tetrahymena catalyzing dehydratase, enolase, and dioxygenase steps (10). (Green) MTA-isoprenoid shunt from R. rubrum, which functions both aerobically and anaerobically (16, 17, 21). (Brown) Anaerobic ethylene-forming MSP in R. rubrum and R. palustris (this study). Gene names are given in italics by each catalyzed reaction. Letters correspond to enzyme name, and numbers correspond to compound name. Methanocaldococcus jannaschii and bacteria such as Pseudomonas methanethiol release from 1-(methylthio)xylulose-5-P (16, 22). While aeruginosa, this process is performed by a separate MTA deaminase and discovery of the MTA-isoprenoid shunt clearly established the exis- 5′-methylthioinosine phosphorylase, resulting in 5-(methylthio)ribose- tence of an anaerobic MSP in bacteria, it was nevertheless dispens- 1-P and hypoxanthine (14, 15). However, the ability to further me- able under anaerobic growth conditions in R. rubrum. Indeed, there tabolize 5-(methylthio)ribose or 5-(methylthio)ribose-1-P in anoxic were strong indications of an additional, exclusively anaerobic MSP, environments is largely unknown (7, 9). as strains containing knockouts of the MTA-isoprenoid shunt genes Recently, the first oxygen-independent MSP, the “MTA- were still viable for anaerobic growth with MTA as the sole sulfur isoprenoid shunt,” was fully characterized, which functions both source (17, 23, 24). Here, we describe an exclusively anaerobic MSP aerobically (16) and anaerobically (17) in the facultative anaerobe that couples MTA metabolism to ethylene production in the purple Rhodospirillum rubrum (Fig. 1, green arrows). As with the universal nonsulfur α-proteobacteria Rhodospirillum rubrum and Rhodop- MSP, MtnP and MtnA first sequentially catalyze the conversion of seudomonas palustris (Fig. 1, brown arrows). Genes for this anaerobic MTA to 5-(methylthio)ribulose-1-P. However, then a RubisCO-like MSP appear to be widely distributed among bacteria as opposed to