Structural Insights into the Methane-Generating Enzyme from a Methoxydotrophic Methanogen Reveal a Restrained Gallery of Post-Translational Modifications

Methanogenic archaea operate an ancient, if not primordial, metabolic pathway that releases methane as an end-product. This last step is orchestrated by the methyl-coenzyme M reductase (MCR), which uses a nickel-containing F430-cofactor as the catalyst. MCR astounds the scientific world by its unique reaction chemistry, its numerous post-translational modifications, and its importance in biotechnology not only for production but also for capturing the greenhouse gas methane. In this report, we investigated MCR natively isolated from Methermicoccus shengliensis. This methanogen was isolated from a high-temperature oil reservoir and has recently been shown to convert lignin and coal derivatives into methane through a process called methoxydotrophic methanogenesis. A methoxydotrophic culture was obtained by growing M. shengliensis with 3,4,5-trimethoxybenzoate as the main carbon and energy source. Under these conditions, MCR represents more than 12% of the total protein content. The native MCR structure refined at a resolution of 1.6-Å precisely depicts the organization of a dimer of heterotrimers. Despite subtle surface remodeling and complete conservation of its active site with other homologues, MCR from the thermophile M. shengliensis contains the most limited number of post-translational modifications reported so far, questioning their physiological relevance in other relatives.

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Beyond the usual suspects: methanogenic communities in eastern North American peatlands are also influenced by nickel and copper concentrations

FEMS Microbiology Letters ◽

10.1093/femsle/fnab151 ◽

2021 ◽

Author(s):

Sydney E Bear ◽

James D Seward ◽

Louis Jamie Lamit ◽

Nathan Basiliko ◽

Tim Moore ◽

...

Keyword(s):

Strong Predictor ◽

Methanogenic Archaea ◽

Community Analysis ◽

Amplicon Sequencing ◽

Contaminated Sites ◽

Methanogenic Community ◽

Primary Driver ◽

High Concentrations ◽

Methyl Coenzyme M Reductase ◽

Eastern Half

Abstract Peatlands both accumulate carbon and release methane, but their broad range in environmental conditions means that the diversity of microorganisms responsible for carbon cycling is still uncertain. Here we describe a community analysis of methanogenic archaea responsible for methane production in 17 peatlands from 36 to 53 N latitude across the eastern half of North America, including three metal-contaminated sites. Methanogenic community structure was analyzed through Illumina amplicon sequencing of the mcrA gene. Whether metal-contaminated sites were included or not, metal concentrations in peat were a primary driver of methanogenic community composition, particularly nickel, a trace element required in the F430 cofactor in methyl-coenzyme M reductase that is also toxic at high concentrations. Copper was also a strong predictor, likely due to inhibition at toxic levels and/or to cooccurrence with nickel, since copper enzymes are not known to be present in anaerobic archaea. The methanogenic groups Methanocellales and Methanosarcinales were prevalent in peatlands with low nickel concentrations, while Methanomicrobiales and Methanomassiliicoccales were abundant in peatlands with higher nickel concentrations. Results suggest that peat-associated trace metals are predictors of methanogenic communities in peatlands.

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Methyl-Coenzyme M Reductase from Methanogenic Archaea: Isotope Effects on the Formation and Anaerobic Oxidation of Methane

Journal of the American Chemical Society ◽

10.1021/ja406485z ◽

2013 ◽

Vol 135 (40) ◽

pp. 14975-14984 ◽

Cited By ~ 42

Author(s):

Silvan Scheller ◽

Meike Goenrich ◽

Rudolf K. Thauer ◽

Bernhard Jaun

Keyword(s):

Isotope Effects ◽

Methanogenic Archaea ◽

Anaerobic Oxidation Of Methane ◽

Anaerobic Oxidation ◽

Coenzyme M ◽

Oxidation Of Methane ◽

Methyl Coenzyme M Reductase

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Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1815631116 ◽

2019 ◽

Vol 116 (11) ◽

pp. 5037-5044 ◽

Cited By ~ 66

Author(s):

Bojk A. Berghuis ◽

Feiqiao Brian Yu ◽

Frederik Schulz ◽

Paul C. Blainey ◽

Tanja Woyke ◽

...

Keyword(s):

Paradigm Shift ◽

Carbon Fixation ◽

Methanogenic Archaea ◽

Global Carbon Cycle ◽

Hydrogenotrophic Methanogenesis ◽

Shared Ancestry ◽

Hydrogenotrophic Methanogens ◽

Methyl Coenzyme M Reductase ◽

Global Carbon ◽

Insight Into

Methanogenic archaea are major contributors to the global carbon cycle and were long thought to belong exclusively to the euryarchaeal phylum. Discovery of the methanogenesis gene cluster methyl-coenzyme M reductase (Mcr) in the Bathyarchaeota, and thereafter the Verstraetearchaeota, led to a paradigm shift, pushing back the evolutionary origin of methanogenesis to predate that of the Euryarchaeota. The methylotrophic methanogenesis found in the non-Euryarchaota distinguished itself from the predominantly hydrogenotrophic methanogens found in euryarchaeal orders as the former do not couple methanogenesis to carbon fixation through the reductive acetyl-CoA [Wood–Ljungdahl pathway (WLP)], which was interpreted as evidence for independent evolution of the two methanogenesis pathways. Here, we report the discovery of a complete and divergent hydrogenotrophic methanogenesis pathway in a thermophilic order of the Verstraetearchaeota, which we have named Candidatus Methanohydrogenales, as well as the presence of the WLP in the crenarchaeal order Desulfurococcales. Our findings support the ancient origin of hydrogenotrophic methanogenesis, suggest that methylotrophic methanogenesis might be a later adaptation of specific orders, and provide insight into how the transition from hydrogenotrophic to methylotrophic methanogenesis might have occurred.

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Phylogenetic and Structural Comparisons of the Three Types of Methyl Coenzyme M Reductase from Methanococcales and Methanobacteriales

Journal of Bacteriology ◽

10.1128/jb.00197-17 ◽

2017 ◽

Vol 199 (16) ◽

Cited By ~ 17

Author(s):

Tristan Wagner ◽

Carl-Eric Wegner ◽

Jörg Kahnt ◽

Ulrich Ermler ◽

Seigo Shima

Keyword(s):

Active Site ◽

Phylogenetic Analyses ◽

Methanogenic Archaea ◽

Methane Formation ◽

Type I ◽

Type Ii ◽

Coenzyme M ◽

Content Type ◽

Type Iii ◽

Methyl Coenzyme M Reductase

ABSTRACT The phylogenetically diverse family of methanogenic archaea universally use methyl coenzyme M reductase (MCR) for catalyzing the final methane-forming reaction step of the methanogenic energy metabolism. Some methanogens of the orders Methanobacteriales and Methanococcales contain two isoenzymes. Comprehensive phylogenetic analyses on the basis of all three subunits grouped MCRs from Methanobacteriales and Methanococcales into three distinct types: (i) MCRs from Methanobacteriales, (ii) MCRs from Methanobacteriales and Methanococcales, and (iii) MCRs from Methanococcales. The first and second types contain MCR isoenzymes I and II from Methanothermobacter marburgensis, respectively; therefore, they were designated MCR type I and type II and accordingly; the third one was designated MCR type III. For comparison with the known MCR type I and type II structures, we determined the structure of MCR type III from Methanotorris formicicus and Methanothermococcus thermolithotrophicus. As predicted, the three MCR types revealed highly similar overall structures and virtually identical active site architectures reflecting the chemically challenging mechanism of methane formation. Pronounced differences were found at the protein surface with respect to loop geometries and electrostatic properties, which also involve the entrance of the active-site funnel. In addition, the C-terminal end of the γ-subunit is prolonged by an extra helix after helix γ8 in MCR type II and type III, which is, however, differently arranged in the two MCR types. MCR types I, II, and III share most of the posttranslational modifications which appear to fine-tune the enzymatic catalysis. Interestingly, MCR type III lacks the methyl-cysteine but possesses in subunit α of M. formicicus a 6-hydroxy-tryptophan, which thus far has been found only in the α-amanitin toxin peptide but not in proteins. IMPORTANCE Methyl coenzyme M reductase (MCR) represents a prime target for the mitigation of methane releases. Phylogenetic analyses of MCRs suggested several distinct sequence clusters; those from Methanobacteriales and Methanococcales were subdivided into three types: MCR type I from Methanobacteriales, MCR type II from Methanobacteriales and Methanococcales, and the newly designated MCR type III exclusively from Methanococcales. We determined the first X-ray structures for an MCR type III. Detailed analyses revealed substantial differences between the three types only in the peripheral region. The subtle modifications identified and electrostatic profiles suggested enhanced substrate binding for MCR type III. In addition, MCR type III from Methanotorris formicicus contains 6-hydroxy-tryptophan, a new posttranslational modification that thus far has been found only in the α-amanitin toxin.

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Mmp10 is required for post-translational methylation of arginine at the active site of methyl-coenzyme M reductase

10.1101/211441 ◽

2017 ◽

Cited By ~ 3

Author(s):

Zhe Lyu ◽

Chau-wen Chou ◽

Hao Shi ◽

Ricky Patel ◽

Evert C. Duin ◽

...

Keyword(s):

Active Site ◽

Methane Formation ◽

Wild Type ◽

Coenzyme M ◽

Methane Cycle ◽

Gene Encoding ◽

Post Translational Modifications ◽

Whole Cells ◽

Type Gene ◽

Methyl Coenzyme M Reductase

AbstractCatalyzing the key step for anaerobic methane production and oxidation, methyl-coenzyme M reductase or Mcr plays a key role in the global methane cycle. The McrA subunit possesses up to five post-translational modifications (PTM) at its active site. Bioinformatic analyses had previously suggested that methanogenesis marker protein 10 (Mmp10) could play an important role in methanogenesis. To examine its role, MMP1554, the gene encoding Mmp10 inMethanococcus maripaludis, was deleted with a new genetic tool, resulting in the specific loss of the 5-(S)-methylarginine PTM of residue 275 in the McrA subunit and a 40~60 % reduction in the maximal rates of methane formation by whole cells. Methylation was restored by complementations with the wild-type gene. However, the rates of methane formation of the complemented strains were not always restored to the wild type level. This study demonstrates the importance of Mmp10 and the methyl-Arg PTM on Mcr activity.

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

10.1101/121111 ◽

2017 ◽

Author(s):

Dipti D. Nayak ◽

Nilkamal Mahanta ◽

Douglas A. Mitchell ◽

William W. Metcalf

Keyword(s):

Strictly Anaerobic ◽

Methanosarcina Acetivorans ◽

Coenzyme M ◽

Α Subunit ◽

Post Translational Modifications ◽

Physiological Characterization ◽

Key Enzyme ◽

Catalytic Role ◽

Methyl Coenzyme M Reductase

AbstractThe enzyme methyl-coenzyme M reductase (MCR), found in strictly anaerobic methanogenic and methanotrophic archaea, catalyzes a reversible reaction involved in the production and consumption of the potent greenhouse gas methane. The α subunit of this enzyme (McrA) contains several unusual post-translational modifications, including an exceptionally rare thioamidation of glycine. Based on the presumed function of homologous genes involved in the biosynthesis of thioamide-containing natural products, we hypothesized that the archaealtfuAandycaOgenes would be responsible for post-translational installation of thioglycine into McrA. Mass spectrometric characterization of McrA in a ΔycaO-tfuAmutant of the methanogenic archaeonMethanosarcina acetivoransrevealed the presence of glycine, rather than thioglycine, supporting this hypothesis. Physiological characterization of this mutant suggested a new role for the thioglycine modification in enhancing protein stability, as opposed to playing a direct catalytic role. The universal conservation of this modification suggests that MCR arose in a thermophilic ancestor.

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Structural Insights Into TDP-43 and Effects of Post-translational Modifications

Frontiers in Molecular Neuroscience ◽

10.3389/fnmol.2019.00301 ◽

2019 ◽

Vol 12 ◽

Cited By ~ 3

Author(s):

Liberty François-Moutal ◽

Samantha Perez-Miller ◽

David D. Scott ◽

Victor G. Miranda ◽

Niloufar Mollasalehi ◽

...

Keyword(s):

Post Translational Modifications ◽

Structural Insights

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Genetic diversity of 16S rRNA and mcrA genes from methanogenic archaeas

Acta Scientiarum Biological Sciences ◽

10.4025/actascibiolsci.v42i1.49877 ◽

2020 ◽

Vol 42 ◽

pp. e49877

Author(s):

Keyla Vitoria Marques Xavier ◽

Eden Silva e Souza ◽

Erick de Aquino Santos ◽

Michely Correia Diniz

Keyword(s):

Genetic Diversity ◽

16S Rrna ◽

Descriptive Analysis ◽

Methanogenic Archaea ◽

Ribosomal Gene ◽

16S Rrna Genes ◽

Rrna Genes ◽

Terrestrial Environments ◽

Methyl Coenzyme M Reductase ◽

Potential Use

Methanogenic archaeas are found in aquatic and terrestrial environments and are fundamental in the conversion of organic matter into methane, a gas that has a potential use as renewable source of energy, which is also considered as one of the main agents of the greenhouse effect. The vast majority of microbial genomes can be identified by a conservative molecular marker, the 16S ribosomal gene. However, the mcrA gene have been using in studies of methanogenic archaea diversity as an alternative marker, highly conserved and present only in methanogens. This gene allows the expression of the enzyme Methyl-coenzyme M reductase, the main agent in converting by-products of anaerobic digestion into methane. In this context, we aimed to study the genetic diversity of mcrA and 16S rRNA genes sequences available in databases. The nucleotide sequences were selected from the NCBI. The heterozygosity and molecular diversity indexes were calculated using the Arlequin 3.5 software, with plots generated by package R v3.0. The diversity and heterozygosity indices for both genes may have been influenced by the number and size of the sequences. Descriptive analysis of genetic diversity generated by sequences deposited in databases allowed a detailed study of these molecules. It is known that the organisms in a population are genetically distinct, and that, despite having similarities in their gene composition, the differences are essential for their adaptation to different environments.

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Targeting Histone Onco- Modifications Using Plant- Derived Products

Current Drug Targets ◽

10.2174/1389450122666210118150716 ◽

2021 ◽

Vol 22 ◽

Author(s):

Soorya Illam ◽

Sruthi Kandiyil ◽

Achuthan C. Raghavamenon

Keyword(s):

Dna Methylation ◽

Histone Modifications ◽

Antioxidant Properties ◽

Normal Growth ◽

Epigenetic Modifications ◽

Post Translational Modifications ◽

Expression Of Genes ◽

Scientific World ◽

Adaptive Mechanisms ◽

Differential Expression Of Genes

: The regulatory mechanisms laying over the genome that determines the differential expression of genes are termed as epigenetic mechanisms. DNA methylation, acetylation, methylation and phosphorylation of histone proteins and RNAi are typical examples. These epigenetic modifications are important determinants of normal growth and metabolism at the same time aberrant histone modifications play a major role in pathological conditions and are emerging as a new area of research for the last decades. Histone onco-modification is a term introduced by scientific world to denote histone post translational modifications that are associated with cancer development and progression. These modifications are likely to act in certain conditions as adaptive mechanisms to environmental and social factors. The enzymes that regulate DNA methylation as well as histone modifications are thus become a target for cancer therapy and, chemoprevention. Since oxidative stress has been shown to modulate epigenetic changes, phytocompounds with powerful antioxidant properties assume significant place in disease pathology. Nowadays “nutri- epigenetics” is becoming an emerging area of research which deals with the influence of dietary compounds in epigenetics. This review aims to discuss the biological efficacy of promising phytocompounds that are able to counteract deleterious epigenetic modifications especially histone onco- modifications.

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