Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea.

Dipti D Nayak,Douglas A Mitchell,Nilkamal Mahanta,William W Metcalf

doi:10.7554/elife.29218

Dipti D Nayak, Douglas A Mitchell + Show 2 more

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https://doi.org/10.7554/elife.29218

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Journal: eLife	Publication Date: Sep 7, 2017
Citations: 88	License type: CC BY 4.0

Affiliation: University of Illinois Urbana-Champaign

Abstract

Methyl-coenzyme M reductase (MCR), found in strictly anaerobic methanogenic and methanotrophic archaea, catalyzes the reversible production and consumption of the potent greenhouse gas methane. The α subunit of MCR (McrA) contains several unusual post-translational modifications, including a rare thioamidation of glycine. Based on the presumed function of homologous genes involved in the biosynthesis of thioviridamide, a thioamide-containing natural product, we hypothesized that the archaeal tfuA and ycaO genes would be responsible for post-translational installation of thioglycine into McrA. Mass spectrometric characterization of McrA from the methanogenic archaeon Methanosarcina acetivorans lacking tfuA and/or ycaO revealed the presence of glycine, rather than thioglycine, supporting this hypothesis. Phenotypic characterization of the ∆ycaO-tfuA mutant revealed a severe growth rate defect on substrates with low free energy yields and at elevated temperatures (39°C - 45°C). Our analyses support a role for thioglycine in stabilizing the protein secondary structure near the active site.

Highlights

Methyl-coenzyme M reductase (MCR) is a unique enzyme found exclusively in anaerobic archaea, where it catalyzes the reversible conversion of methyl-coenzyme M (CoM, 2-methylmercaptoethanesulfonate) and coenzyme B (CoB, 7-thioheptanoylthreoninephosphate) to methane and a CoB-CoM heterodisulfide [1, 2]: CH! − S − CoM + high salt (HS) − CoB ↔ CH! + CoM − S − S − CoBThis enzymatic reaction, which is believed to proceed via an unprecedented methyl radical intermediate [3], plays a critical role in the global carbon cycle [4]
To examine the possibility that YcaO and TfuA are involved in McrA thioamidation, we reassessed the distribution, diversity, and phylogeny of genes encoding these proteins in sequenced microbial genomes, which today comprise a much larger dataset than when
It is likely that YcaO was acquired early in the evolution of methanogens and maintained largely through vertical inheritance, as expected for a trait that coevolved with MCR [35, 36]

Summary

Introduction

Methyl-coenzyme M reductase (MCR) is a unique enzyme found exclusively in anaerobic archaea, where it catalyzes the reversible conversion of methyl-coenzyme M (CoM, 2-methylmercaptoethanesulfonate) and coenzyme B (CoB, 7-thioheptanoylthreoninephosphate) to methane and a CoB-CoM heterodisulfide [1, 2]: CH! − S − CoM + HS − CoB ↔ CH! + CoM − S − S − CoBThis enzymatic reaction, which is believed to proceed via an unprecedented methyl radical intermediate [3], plays a critical role in the global carbon cycle [4]. Methyl-coenzyme M reductase (MCR) is a unique enzyme found exclusively in anaerobic archaea, where it catalyzes the reversible conversion of methyl-coenzyme M In the forward direction MCR catalyzes the formation of methane in methane-producing archaea (methanogens), whereas the enzyme initiates methane consumption in methanotrophic archaea (known as ANMEs for anaerobic oxidation of methane) in the reverse direction. Together, these processes produce and consume gigatons of methane each year, helping to establish the steadystate atmospheric levels of an important greenhouse gas. MCR displays an α2β2γ2 protein domain architecture and contains two molecules of a nickel-containing porphinoid cofactor, F430 [1, 5, 6].

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