Transplanting the pathway engineering toolbox to methanogens

Lyu, Zhe; Whitman, William B.

doi:10.1016/j.copbio.2019.02.009

Cited by 37 publications

(18 citation statements)

References 66 publications

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“…It can be produced through biogenic, thermogenic, and pyrogenic processes 1 . Most biogenic CH 4 is emitted by methanogenic archaea (methanogens) 2 , with minor amounts originating from cyanobacteria 3 and marine microorganisms 4 . Methanogens are a phylogenetically diverse group of microorganisms, which can be found in various anoxic environments 5 .…”

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confidence: 99%

“…Methanogens are a phylogenetically diverse group of microorganisms, which can be found in various anoxic environments 5 . Among other substrates, methanogens convert short chain organic acids and one-carbon compounds to CH 4 through their energy and carbon metabolism 2,5,6 . Their metabolic capability is important for anaerobic organic matter degradation in environments with low concentrations of sulfate, nitrate, manganese, or iron 5 .…”

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Hyperthermophilic methanogenic archaea act as high-pressure CH4 cell factories

et al. 2021

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Bioprocesses converting carbon dioxide with molecular hydrogen to methane (CH4) are currently being developed to enable a transition to a renewable energy production system. In this study, we present a comprehensive physiological and biotechnological examination of 80 methanogenic archaea (methanogens) quantifying growth and CH4 production kinetics at hyperbaric pressures up to 50 bar with regard to media, macro-, and micro-nutrient supply, specific genomic features, and cell envelope architecture. Our analysis aimed to systematically prioritize high-pressure and high-performance methanogens. We found that the hyperthermophilic methanococci Methanotorris igneus and Methanocaldococcoccus jannaschii are high-pressure CH4 cell factories. Furthermore, our analysis revealed that high-performance methanogens are covered with an S-layer, and that they harbour the amino acid motif Tyrα444 Glyα445 Tyrα446 in the alpha subunit of the methyl-coenzyme M reductase. Thus, high-pressure biological CH4 production in pure culture could provide a purposeful route for the transition to a carbon-neutral bioenergy sector.

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Hyperthermophilic methanogenic archaea act as high-pressure CH4 cell factories

et al. 2021

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“…Although the details of the pathways vary, they all possess homologs of Mcr (8). Some of these homologs are proposed to oxidize short-chain alkanes such as ethane, butane, and possibly propane (9,10), essentially expanding our knowledge from ANME to NAOA (anaerobic alkane-oxidizing Archaea) (3,(11)(12)(13)(14)(15). These novel findings not only extend the roles of Mcr in the global carbon cycle but also present exciting new opportunities for biotechnology (11).…”

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

et al. 2020

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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.

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“…During methanogenesis, methanogenic archaea use the end products of fermentation to produce methane anaerobically ( Sieber et al, 2012 ; Vanwonterghem et al, 2016 ; Lyu et al, 2018b ; Evans et al, 2019 ). There are three major pathways of methanogenesis, namely hydrogenotrophic, aceticlastic, and methylotrophic ( Lyu and Whitman, 2019 ). On the other hand, ANME treat CH 4 as a carbon source and get energy from oxidizing it into CO 2 , which is so-called anaerobic oxidation of methane (AOM; Orphan et al, 2001 ; Scheller et al, 2016 ; Timmers et al, 2017 ).…”

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Methyl-Coenzyme M Reductase and Its Post-translational Modifications

2020

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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.

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Transplanting the pathway engineering toolbox to methanogens

Cited by 37 publications

References 66 publications

Hyperthermophilic methanogenic archaea act as high-pressure CH4 cell factories

Hyperthermophilic methanogenic archaea act as high-pressure CH4 cell factories

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

Methyl-Coenzyme M Reductase and Its Post-translational Modifications

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