The catalytic mechanism for aerobic formation of methane by bacteria

Abstract

Methane is a potent greenhouse gas that is produced in significant quantities by aerobic marine organisms. These bacteria apparently catalyse the formation of methane through the cleavage of the highly unreactive carbon-phosphorus bond in methyl phosphonate (MPn), but the biological or terrestrial source of this compound is unclear. However, the ocean-dwelling bacterium Nitrosopumilus maritimus catalyses the biosynthesis of MPn from 2-hydroxyethyl phosphonate and the bacterial C-P lyase complex is known to convert MPn to methane. In addition to MPn, the bacterial C-P lyase complex catalyses C-P bond cleavage of many alkyl phosphonates when the environmental concentration of phosphate is low. PhnJ from the C-P lyase complex catalyses an unprecedented C-P bond cleavage reaction of ribose-1-phosphonate-5-phosphate to methane and ribose-1,2-cyclic-phosphate-5-phosphate. This reaction requires a redox-active [4Fe-4S]-cluster and S-adenosyl-L-methionine, which is reductively cleaved to L-methionine and 5'-deoxyadenosine. Here we show that PhnJ is a novel radical S-adenosyl-L-methionine enzyme that catalyses C-P bond cleavage through the initial formation of a 5'-deoxyadenosyl radical and two protein-based radicals localized at Gly 32 and Cys 272. During this transformation, the pro-R hydrogen from Gly 32 is transferred to the 5'-deoxyadenosyl radical to form 5'-deoxyadenosine and the pro-S hydrogen is transferred to the radical intermediate that ultimately generates methane. A comprehensive reaction mechanism is proposed for cleavage of the C-P bond by the C-P lyase complex that uses a covalent thiophosphate intermediate for methane and phosphate formation.

Utilization of Glyphosate as Phosphate Source: Biochemistry and Genetics of Bacterial Carbon-Phosphorus Lyase

“…Spectroscopy revealed the possibility of a 4Fe-4S cluster, and with the observation of the presence of four cysteine residues within PhnJ, the data are consistent with a radical reaction mechanism typical of the radical S-adenosylmethionine/4Fe-4S enzyme superfamily. Three cysteine residues (Cys241, Cys244, and Cys266) are involved in the formation of the 4Fe-4S cluster, whereas Cys272 is believed to take part in the catalytic cycle as a thiyl radical (41,43). Additionally, these data are consistent with results obtained Ͼ2 decades ago by Frost and coworkers, who demonstrated that C-P bond cleavage by C-P lyase occurs by a radical reaction mechanism (44)(45)(46).…”

A novel pathway of direct methane production and emission by eukaryotes including plants, animals and fungi: An overview

“…Metcalf et al (2012) provided an explanation that methylphosphonate is encoded by the marine archaeon Nitrosopumilus maritimus as a possible source of methylphosphonate that is common in marine environments. Subsequent research revealed the catalytic mechanism of the breakage of the highly unreactive CeP bond in methylphosphonate by marine bacteria (Kamat et al, 2013).…”

Organic phosphorus in the aquatic environment

“…[121] Interestingly, the hydrolysis of phosphonates has been implicated in the production of methane in aerobic oceanic waters. [123,124] …”