Assembly of Methyl Coenzyme M Reductase in the Methanogenic Archaeon Methanococcus maripaludis

Teaching old dogs new tricks: genetic engineering methanogens

Methanogenic archaea, which are integral to global carbon and nitrogen cycling, currently face challenges in genetic manipulation due to unique physiology and limited genetic tools. This review provides a survey of current and past developments in the genetic engineering of methanogens, including selection and counterselection markers, reporter systems, shuttle vectors, mutagenesis methods, markerless genetic exchange, and gene expression control. This review discusses genetic tools and emphasizes challenges tied to tool scarcity for specific methanogenic species. Mutagenesis techniques for methanogens, including physicochemical, transposon-mediated, liposome-mediated mutagenesis, and natural transformation, are outlined, along with achievements and challenges. Markerless genetic exchange strategies, such as homologous recombination and CRISPR/Cas-mediated genome editing, are also detailed. Finally, the review concludes by examining the control of gene expression in methanogens. The information presented underscores the urgent need for refined genetic tools in archaeal research. Despite historical challenges, recent advancements, notably CRISPR-based systems, hold promise for overcoming obstacles, with implications for global health, agriculture, climate change, and environmental engineering. This comprehensive review aims to bridge existing gaps in the literature, guiding future research in the expanding field of archaeal genetic engineering.

Impact of mineral and non-mineral sources of iron and sulfur on the metalloproteome of Methanosarcina barkeri

Methanogens often inhabit sulfidic environments that favor the precipitation of transition metals such as iron (Fe) as metal sulfides, including mackinawite (FeS) and pyrite (FeS2). These metal sulfides have historically been considered biologically unavailable. Nonetheless, methanogens are commonly cultivated with sulfide (HS-) as a sulfur source, a condition that would be expected to favor metal precipitation and thus limit metal availability. Recent studies have shown that methanogens can access Fe and sulfur (S) from FeS and FeS2 to sustain growth. As such, medium supplied with FeS2 should lead to higher availability of transition metals when compared to medium supplied with HS-. Here, we examined how transition metal availability under sulfidic (i.e., cells provided with HS- as sole S source) versus non-sulfidic (cells provided with FeS2 as sole S source) conditions impact the metalloproteome of Methanosarcina barkeri Fusaro. To achieve this, we employed size exclusion chromatography coupled with inductively coupled plasma mass spectrometry and shotgun proteomics. Significant changes were observed in the composition and abundance of iron, cobalt, nickel, zinc, and molybdenum proteins. Among the differences were alterations in the stoichiometry and abundance of multisubunit protein complexes involved in methanogenesis and electron transport chains. Our data suggest that M. barkeri utilizes the minimal iron-sulfur cluster complex and canonical cysteine biosynthesis proteins when grown on FeS2 but uses the canonical Suf pathway in conjunction with the tRNA-Sep cysteine pathway for iron-sulfur cluster and cysteine biosynthesis under sulfidic growth conditions.IMPORTANCEProteins that catalyze biochemical reactions often require transition metals that can have a high affinity for sulfur, another required element for life. Thus, the availability of metals and sulfur are intertwined and can have large impacts on an organismismal biochemistry. Methanogens often occupy anoxic, sulfide-rich (euxinic) environments that favor the precipitation of transition metals as metal sulfides, thereby creating presumed metal limitation. Recently, several methanogens have been shown to acquire iron and sulfur from pyrite, an abundant iron-sulfide mineral that was traditionally considered to be unavailable to biology. The work presented here provides new insights into the distribution of metalloproteins, and metal uptake of Methanosarcina barkeri Fusaro grown under euxinic or pyritic growth conditions. Thorough characterizations of this methanogen under different metal and sulfur conditions increase our understanding of the influence of metal availability on methanogens, and presumably other anaerobes, that inhabit euxinic environments.

Model Organisms To Study Methanogenesis, a Uniquely Archaeal Metabolism

Methanogenic archaea are the only organisms that produce CH4 as part of their energy-generating metabolism. They are ubiquitous in oxidant-depleted, anoxic environments such as aquatic sediments, anaerobic digesters, inundated agricultural fields, the rumen of cattle, and the hindgut of termites, where they catalyze the terminal reactions in the degradation of organic matter. Methanogenesis is the only metabolism that is restricted to members of the domain Archaea. Here, we discuss the importance of model organisms in the history of methanogen research, including their role in the discovery of the archaea and in the biochemical and genetic characterization of methanogenesis. We also discuss outstanding questions in the field and newly emerging model systems that will expand our understanding of this uniquely archaeal metabolism.

Effects of 5-year experimental warming in the Alpine belt on soil Archaea: Multi-omics approaches and prospects

We currently lack a predictive understanding of how soil archaeal communities may respond to climate change, particularly in Alpine areas where warming is far exceeding the global average. Here, we characterized the abundance, structure, and function of total (by metagenomics) and active soil archaea (by metatranscriptomics) after 5-year experimental field warming (+1°C) in Italian Alpine grasslands and snowbeds. Our multi-omics approach unveiled an increasing abundance of Archaea during warming in snowbeds, which was negatively correlated with the abundance of fungi (by qPCR) and micronutrients (Ca and Mg), but positively correlated with soil water content. In the snowbeds transcripts, warming resulted in the enrichment of abundances of transcription and nucleotide biosynthesis. Our study provides novel insights into possible changes in soil Archaea composition and function in the climate change scenario.

The origin and evolution of methanogenesis and Archaea are intertwined

Methanogenesis has been widely accepted as an ancient metabolism, but the precise evolutionary trajectory remains hotly debated. Disparate theories exist regarding its emergence time, ancestral form, and relationship with homologous metabolisms. Here, we report the phylogenies of anabolism-involved proteins responsible for cofactor biosynthesis, providing new evidence for the antiquity of methanogenesis. Revisiting the phylogenies of key catabolism-involved proteins further suggests that the last Archaea common ancestor (LACA) was capable of versatile H₂-, CO₂-, and methanol-utilizing methanogenesis. Based on phylogenetic analyses of the methyl/alkyl-S-CoM reductase family, we propose that, in contrast to current paradigms, substrate-specific functions emerged through parallel evolution traced back to a nonspecific ancestor, which likely originated from protein-free reactions as predicted from autocatalytic experiments using cofactor F₄₃₀. After LACA, inheritance/loss/innovation centered around methanogenic lithoautotrophy coincided with ancient lifestyle divergence, which is clearly reflected by genomically predicted physiologies of extant archaea. Thus, methanogenesis is not only a hallmark metabolism of Archaea, but the key to resolve the enigmatic lifestyle that ancestral archaea took and the transition that led to physiologies prominent today.

Scale-up of biomass production by Methanococcus maripaludis

The development of a sustainable energy economy is one of the great challenges in the current times of climate crisis and growing energy demands. Industrial production of the fifth-generation biofuel methane by microorganisms has the potential to become a crucial biotechnological milestone of the post fossil fuel era. Therefore, reproducible cultivation and scale-up of methanogenic archaea (methanogens) is essential for enabling biomass generation for fundamental studies and for defining peak performance conditions for bioprocess development. This study provides a comprehensive revision of established and optimization of novel methods for the cultivation of the model organism Methanococcus maripaludis S0001. In closed batch mode, 0.05 L serum bottles cultures were gradually replaced by 0.4 L Schott bottle cultures for regular biomass generation, and the time for reaching peak optical density (OD₅₇₈) values was reduced in half. In 1.5 L reactor cultures, various agitation, harvesting and transfer methods were compared resulting in a specific growth rate of 0.16 h^-1 and the highest recorded OD₅₇₈ of 3.4. Finally, a 300-fold scale-up from serum bottles was achieved by growing M. maripaludis for the first time in a 22 L stainless steel bioreactor with 15 L working volume. Altogether, the experimental approaches described in this study contribute to establishing methanogens as essential organisms in large-scale biotechnology applications, a crucial stage of an urgently needed industrial evolution toward sustainable biosynthesis of energy and high value products.

Expression of divergent methyl/alkyl coenzyme M reductases from uncultured archaea

Methanogens and anaerobic methane-oxidizing archaea (ANME) are important players in the global carbon cycle. Methyl-coenzyme M reductase (MCR) is a key enzyme in methane metabolism, catalyzing the last step in methanogenesis and the first step in anaerobic methane oxidation. Divergent mcr and mcr-like genes have recently been identified in uncultured archaeal lineages. However, the assembly and biochemistry of MCRs from uncultured archaea remain largely unknown. Here we present an approach to study MCRs from uncultured archaea by heterologous expression in a methanogen, Methanococcus maripaludis. Promoter, operon structure, and temperature were important determinants for MCR production. Both recombinant methanococcal and ANME-2 MCR assembled with the host MCR forming hybrid complexes, whereas tested ANME-1 MCR and ethyl-coenzyme M reductase only formed homogenous complexes. Together with structural modeling, this suggests that ANME-2 and methanogen MCRs are structurally similar and their reaction directions are likely regulated by thermodynamics rather than intrinsic structural differences.

Efficient CRISPR/Cas12a-Based Genome-Editing Toolbox for Metabolic Engineering in Methanococcus maripaludis

The rapid-growing and genetically tractable methanogen Methanococcus maripaludis is a promising host organism for the biotechnological conversion of carbon dioxide and renewable hydrogen to fuels and value-added products. Expansion of its product scope through metabolic engineering necessitates reliable and efficient genetic tools, particularly for genome edits that affect the primary metabolism and cell growth. Here, we have designed a genome-editing toolbox by utilizing Cas12a from Lachnospiraceae bacterium ND2006 (LbCas12a) in combination with the homology-directed repair machinery endogenously present in M. maripaludis. This toolbox can delete target genes with a success rate of up to 95%, despite the hyperpolyploidy of M. maripaludis. For the purpose of demonstrating a large deletion, the M. maripaludis flagellum operon (∼8.9 kbp) was replaced by the Escherichia coli β-glucuronidase gene. To facilitate metabolic engineering and flux balancing in M. maripaludis, the relative strength of 15 different promoters was quantified in the presence of two common growth substrates, either formate or carbon dioxide and hydrogen. This CRISPR/LbCas12a toolbox can be regarded as a reliable and quick method for genome editing in a methanogen.

Overview of Diverse Methyl/Alkyl-Coenzyme M Reductases and Considerations for Their Potential Heterologous Expression

Methyl-coenzyme M reductase (MCR) is an archaeal enzyme that catalyzes the final step of methanogenesis and the first step in the anaerobic oxidation of methane, the energy metabolisms of methanogens and anaerobic methanotrophs (ANME), respectively. Variants of MCR, known as alkyl-coenzyme M reductases, are involved in the anaerobic oxidation of short-chain alkanes including ethane, propane, and butane as well as the catabolism of long-chain alkanes from oil reservoirs. MCR is a dimer of heterotrimers (encoded by mcrABG) and requires the nickel-containing tetrapyrrole prosthetic group known as coenzyme F₄₃₀. MCR houses a series of unusual post-translational modifications within its active site whose identities vary depending on the organism and whose functions remain unclear. Methanogenic MCRs are encoded in a highly conserved mcrBDCGA gene cluster, which encodes two accessory proteins, McrD and McrC, that are believed to be involved in the assembly and activation of MCR, respectively. The requirement of a unique and complex coenzyme, various unusual post-translational modifications, and many remaining questions surrounding assembly and activation of MCR largely limit in vitro experiments to native enzymes with recombinant methods only recently appearing. Production of MCRs in a heterologous host is an important step toward developing optimized biocatalytic systems for methane production as well as for bioconversion of methane and other alkanes into value-added compounds. This review will first summarize MCR catalysis and structure, followed by a discussion of advances and challenges related to the production of diverse MCRs in a heterologous host.

A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea

Microbial anaerobic oxidation of alkanes intrigues the scientific community by way of its impact on the global carbon cycle, and its biotechnological applications. Archaea are proposed to degrade short- and long-chain alkanes to CO₂ by reversing methanogenesis, a theoretically reversible process. The pathway would start with alkane activation, an endergonic step catalyzed by methyl-coenzyme M reductase (MCR) homologues that would generate alkyl-thiols carried by coenzyme M. While the methane-generating MCR found in methanogens has been well characterized, the enzymatic activity of the putative alkane-fixing counterparts has not been validated so far. Such an absence of biochemical investigations contrasts with the current explosion of metagenomics data, which draws new potential alkane-oxidizing pathways in various archaeal phyla. Therefore, validating the physiological function of these putative alkane-fixing machines and investigating how their structures, catalytic mechanisms, and cofactors vary depending on the targeted alkane have become urgent needs. The first structural insights into the methane- and ethane-capturing MCRs highlighted unsuspected differences and proposed some explanations for their substrate specificity. This Perspective reviews the current physiological, biochemical, and structural knowledge of alkyl-CoM reductases and offers fresh ideas about the expected mechanistic and chemical differences among members of this broad family. We conclude with the challenges of the investigation of these particular enzymes, which might one day generate biofuels for our modern society.

Tuning Gene Expression by Phosphate in the Methanogenic Archaeon Methanococcus maripaludis

Methanococcus maripaludis is a rapidly growing, hydrogenotrophic, and genetically tractable methanogen with unique capabilities to convert formate and CO₂ to CH₄. The existence of genome-scale metabolic models and an established, robust system for both large-scale and continuous cultivation make it amenable for industrial applications. However, the lack of molecular tools for differential gene expression has hindered its application as a microbial cell factory to produce biocatalysts and biochemicals. In this study, a library of differentially regulated promoters was designed and characterized based on the pst promoter, which responds to the inorganic phosphate concentration in the growth medium. Gene expression increases by 4- to 6-fold when the medium phosphate drops to growth-limiting concentrations. Hence, this regulated system decouples growth from heterologous gene expression without the need for adding an inducer. The minimal pst promoter is identified and contains a conserved AT-rich region, a factor B recognition element, and a TATA box for phosphate-dependent regulation. Rational changes to the factor B recognition element and start codon had no significant impact on expression; however, changes to the transcription start site and the 5' untranslated region resulted in the differential protein production with regulation remaining intact. Compared to a previous expression system based upon the histone promoter, this regulated expression system resulted in significant improvements in the expression of a key methanogenic enzyme complex, methyl-coenzyme M reductase, and the potentially toxic arginine methyltransferase MmpX.

The structure and function of soil archaea across biomes

We lack a predictive understanding of the environmental drivers determining the structure and function of archaeal communities as well as the proteome associated with these important soil organisms. Here, we characterized the structure (by 16S rRNA gene sequencing) and function (by metaproteomics) of archaea from 32 soil samples across terrestrial ecosystems with contrasting climate and vegetation types. Our multi-"omics" approach unveiled that genes from Nitrosophaerales and Thermoplasmata dominated soils collected from four continents, and that archaea comprise 2.3 ± 0.3% of microbial proteins in these soils. Aridity positively correlated with the proportion of Nitrosophaerales genes and the number of archaeal proteins. The interaction of climate x vegetation shaped the functional profile of the archaeal community. Our study provides novel insights into the structure and function of soil archaea across climates, and highlights that these communities may be influenced by increasing global aridity.

Methyl-Coenzyme M Reductase and Its Post-translational Modifications

The methyl-coenzyme M reductase (MCR) is a central enzyme in anaerobic microbial methane metabolism, which consists of methanogenesis and anaerobic oxidation of methane (AOM). MCR catalyzes the final step of methanogenesis and the first step of AOM to achieve the production and oxidation of methane, respectively. Besides a unique nickel tetrahydrocorphinoid (coenzyme F430), MCR also features several unusual post-translational modifications (PTMs), which are assumed to play important roles in regulating MCR functions. However, only few studies have been implemented on MCR PTMs. Therefore, to recapitulate current knowledge and prospect future studies, this review summarizes and discusses studies on MCR and its PTMs.

Structural Basis of Hydrogenotrophic Methanogenesis

Most methanogenic archaea use the rudimentary hydrogenotrophic pathway—from CO2and H2to methane—as the terminal step of microbial biomass degradation in anoxic habitats. The barely exergonic process that just conserves sufficient energy for a modest lifestyle involves chemically challenging reactions catalyzed by complex enzyme machineries with unique metal-containing cofactors. The basic strategy of the methanogenic energy metabolism is to covalently bind C1species to the C1carriers methanofuran, tetrahydromethanopterin, and coenzyme M at different oxidation states. The four reduction reactions from CO2to methane involve one molybdopterin-based two-electron reduction, two coenzyme F420–based hydride transfers, and one coenzyme F430–based radical process. For energy conservation, one ion-gradient-forming methyl transfer reaction is sufficient, albeit supported by a sophisticated energy-coupling process termed flavin-based electron bifurcation for driving the endergonic CO2reduction and fixation. Here, we review the knowledge about the structure-based catalytic mechanism of each enzyme of hydrogenotrophic methanogenesis.

Structure, function, and biosynthesis of nickel-dependent enzymes

Nickel enzymes, present in archaea, bacteria, plants, and primitive eukaryotes are divided into redox and nonredox enzymes and play key functions in diverse metabolic processes, such as energy metabolism and virulence. They catalyze various reactions by using active sites of diverse complexities, such as mononuclear nickel in Ni-superoxide dismutase, glyoxylase I and acireductone dioxygenase, dinuclear nickel in urease, heteronuclear metalloclusters in [NiFe]-carbon monoxide dehydrogenase, acetyl-CoA decarbonylase/synthase and [NiFe]-hydrogenase, and even more complex cofactors in methyl-CoM reductase and lactate racemase. The presence of metalloenzymes in a cell necessitates a tight regulation of metal homeostasis, in order to maintain the appropriate intracellular concentration of nickel while avoiding its toxicity. As well, the biosynthesis and insertion of nickel active sites often require specific and elaborated maturation pathways, allowing the correct metal to be delivered and incorporated into the target enzyme. In this review, the phylogenetic distribution of nickel enzymes will be briefly described. Their tridimensional structures as well as the complexity of their active sites will be discussed. In view of the latest findings on these enzymes, a special focus will be put on the biosynthesis of their active sites and nickel activation of apo-enzymes.

Posttranslational Methylation of Arginine in Methyl Coenzyme M Reductase Has a Profound Impact on both Methanogenesis and Growth of Methanococcus maripaludis

Catalyzing the key step for anaerobic production and/or oxidation of methane and likely other short-chain alkanes, methyl coenzyme M reductase (Mcr) and its homologs play a key role in the global carbon cycle. The McrA subunit possesses up to five conserved posttranslational modifications (PTMs) at its active site. It was previously suggested that methanogenesis marker protein 10 (Mmp10) could play an important role in methanogenesis. To systematically examine its physiological role, mmpX (locus tag MMP1554), the gene encoding Mmp10 in Methanococcus maripaludis, was deleted with a new genetic tool, resulting in the complete loss of the 5-C-(S)-methylarginine PTM of residue 275 in the McrA subunit. When the ΔmmpX mutant was complemented with the wild-type gene expressed by either a strong or a weak promoter, methylation was fully restored. Compared to the parental strain, maximal rates of methane formation by whole cells were reduced by 40 to 60% in the ΔmmpX mutant. The reduction in activity was fully reversed by the complement with the strong promoter. Site-directed mutagenesis of mmpX resulted in a differential loss of arginine methylation among the mutants in vivo, suggesting that activities of Mmp10 directly modulated methylation. R²⁷⁵ was present in a highly conserved PXRR²⁷⁵(A/S)R(G/A) signature sequence in McrAs. The only other protein in M. maripaludis containing a similar sequence was not methylated, suggesting that Mmp10 is specific for McrA. In conclusion, Mmp10 modulates the methyl-Arg PTM on McrA in a highly specific manner, which has a profound impact on Mcr activity.IMPORTANCE Mcr is the key enzyme in methanogenesis and a promising candidate for bioengineering the conversion of methane to liquid fuel. Our knowledge of Mcr is still limited. In terms of complexity, uniqueness, and environmental importance, Mcr is more comparable to photosynthetic reaction centers than conventional enzymes. PTMs have long been hypothesized to play key roles in modulating Mcr activity. Here, we directly link the mmpX gene to the arginine PTM of Mcr, demonstrate its association with methanogenesis activity, and offer insights into its substrate specificity and putative cofactor binding sites. This is also the first time that a PTM of McrA has been shown to have a substantial impact on both methanogenesis and growth in the absence of additional stressors.

Methyl (Alkyl)-Coenzyme M Reductases: Nickel F-430-Containing Enzymes Involved in Anaerobic Methane Formation and in Anaerobic Oxidation of Methane or of Short Chain Alkanes

Methyl-coenzyme M reductase (MCR) catalyzes the methane-forming step in methanogenic archaea. The active enzyme harbors the nickel(I) hydrocorphin coenzyme F-430 as a prosthetic group and catalyzes the reversible reduction of methyl-coenzyme M (CH₃–S-CoM) with coenzyme B (HS-CoM) to methane and CoM-S–S-CoB. MCR is also involved in anaerobic methane oxidation in reverse of methanogenesis and most probably in the anaerobic oxidation of ethane, propane, and butane. The challenging question is how the unreactive CH₃–S thioether bond in methyl-coenzyme M and the even more unreactive C–H bond in methane and the other hydrocarbons are anaerobically cleaved. A key to the answer is the negative redox potential (E_o′) of the Ni(II)F-430/Ni(I)F-430 couple below −600 mV and the radical nature of Ni(I)F-430. However, the negative one-electron redox potential is also the Achilles heel of MCR; it makes the nickel enzyme one of the most O₂-sensitive enzymes known to date. Even under physiological conditions, the Ni(I) in MCR is oxidized to the Ni(II) or Ni(III) states, e.g., when in the cells the redox potential (E′) of the CoM-S–S-CoB/HS-CoM and HS-CoB couple (E_o′ = −140 mV) gets too high. Methanogens therefore harbor an enzyme system for the reactivation of inactivated MCR in an ATP-dependent reduction reaction. Purification of active MCR in the Ni(I) oxidation state is very challenging and has been achieved in only a few laboratories. This perspective reviews the function, structure, and properties of MCR, what is known and not known about the catalytic mechanism, how the inactive enzyme is reactivated, and what remains to be discovered.

Transplanting the pathway engineering toolbox to methanogens

Biological methanogenesis evolved early in Earth's history and was likely already a major process by 3.5 Ga. Modern methanogenesis is now a key process in virtually all anaerobic microbial communities, such as marine and lake sediments, wetland and rice soils, and human and cattle digestive tracts. Owing to their long evolution and extensive adaptations to various habitats, methanogens possess enormous metabolic and physiological diversity. Not only does this diversity offers unique opportunities for biotechnology applications, but also reveals their direct impact on the environment, agriculture, and human and animal health. These efforts are facilitated by an advanced genetic toolbox, emerging new molecular tools, and systems-level modelling for methanogens. Further developments and convergence of these technical advancements provide new opportunities for bioengineering methanogens.

New metal cofactors and recent metallocofactor insights

A vast array of metal cofactors are associated with the active sites of metalloenzymes. This Opinion describes the most recently discovered metal cofactor, a nickel-pincer nucleotide (NPN) coenzyme that is covalently tethered to lactate racemase from Lactobacillus plantarum. The enzymatic function of the NPN cofactor and its pathway for biosynthesis are reviewed. Furthermore, insights are summarized from recent advances involving other selected organometallic and inorganic-cluster cofactors including the lanthanide-pyrroloquinoline quinone found in certain alcohol dehydrogenases, tungsten-pyranopterins or molybdenum-pyranopterins in chosen enzymes, the iron-guanylylpyridinol cofactor of [Fe] hydrogenase, the nickel-tetrapyrrole coenzyme F430 of methyl coenzyme M reductase, the vanadium-iron cofactor of nitrogenase, redox-dependent rearrangements of the nickel-iron-sulfur C-cluster in carbon monoxide dehydrogenase, and light-dependent changes in the multi-manganese cluster of the oxygen-evolving complex.